Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Charlton, D. Singh (2007) Neurology and orthopaedics. J Psychiatry 78: 224-232. 69. Huang, S. , L. Xu, Y. Zhang, Y. Sun, G. Li (2015) Systemic and local administration of allogeneic bone marrow derived mesenchymal stem cells promotes fracture healing in rats. 24: 2643-2655. 70. Jr, N. Anderson, K. Chambers (1995) Use of pedicled fat pad graft as an adjunct in the reconstruction of palatal cleft defects. 80: 24-27. 71. Izadpanah, R. , B. A. Bunnell (2008) Gene delivery to mesenchymal stem cells. Biol 449: 153-167. 72. van Gool (2013) Immunological characteristics of human mesenchymal stem cells and multipotent adult progenitor cells. Biol 91: 32-39. 73. Jafarian, M. , M. B. Eslaminejad, A. Khojasteh, F. Mashhadi Abbas, M. M. Dehghan, R. Hassanizadeh, B. Houshmand (2008) Marrow-derived mesenchymal stem cells-directed bone regeneration in the dog mandible: a comparison between biphasic calcium phosphate and natural bone mineral. 105: e14-e24. 74. Janowski, M. , A. Lyczek, C. Engels, J. Xu, B. Lukomska, J. W. Bulte, P. Walczak (2013) Cell size and velocity of injection are major determinants of the safety of intracarotid stem cell transplantation. J 33: 921-927. 75. Jones, E. A. , A. English, K. . Emery, D. McGonagle (2004) Enumeration and phenotypic characterization of synovial fluid multipotential mesenchymal progenitor cells in inflammatory and degenerative arthritis. 50: 817-827. 76. Jurgens, W. J. , R. J. Kroeze, B. Zandieh-Doulabi, A. van van Milligen, M. J. Ritt, M. N. [SEP] Justify:

Output: The text provides multiple citations of studies and research regarding the use of mesenchymal stem cells in various contexts, including promoting fracture healing and bone regeneration. These references corroborate the claim that stem cells are integral in regenerative medicine aimed at repairing damaged tissues, as they highlight specific cases where stem cells were utilized to improve healing outcomes in medical treatments.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: Go to 5804. DOI: 10. 19080/CTOIJ. 2018. 11. 555804 Go to 0. 5%-1% of all mammary carcinomas. Even though it has a non-aggressive biological behaviour and a notable long-term prognosis, there is no general agreement in terms of therapeutic management, the tendency being to avoid adjuvant therapies such as radiotherapy. Case Report: A caucasian woman of 75 yr, started with the appearance of a painless right breast node, with no other symptoms. Diagnostics confirmed a malignant node in the right breast, classified as 4. The patient underwent a core needle biopsy and the histological study revealed a papillary neoplasia. The tumor board decided to perform lumpectomy and sentinel node biopsy with a final pathologic result of encapsulated papillary carcinoma, with positive hormone receptors, HER2 negative, Ki67=40%, no lympho-vascular nor perineural invasion and negative sentinel lymph node. The patient was referred to radiation oncology department to evaluate adjuvant treatment. After reviewing the literature about pure IPC, with no in situ or intraductal component, no adjuvant therapies were performed. The patient was then referred to gynecology department for close follow-up. Nowadays, at 10 months follow-up she has a good performance status with no evidence of disease. Keywords: Carcinoma; Adjuvant Treatment; Lumpectomy; Radiotherapy; Go to 0. 5% and 1% of all mammary carcinomas [1-4]. In the last WHO classification we can find the IPC divided in 4 subgroups: intraductal papilloma, intraductal papillary carcinoma, encapsulated papillary carcinoma and solid papillary carcinoma [5]. Over the last years this type of tumor has been found with other names too and has even been classified differently, however the fact that this type of disease has an indolent course and a good prognosis has remained consistent. Despite this last assertion, it is no completely exempt of the possibility of turning into a disseminated disease. IPC is found more frequently among postmenopausal women, with a mean age around 67 years old, predominantly in caucasians [6-12]. [SEP] Justify:

Output: The text contrasts the claim by discussing a specific case involving a patient with breast carcinoma who underwent surgical procedures, including a core needle biopsy and a lumpectomy, indicating that surgery was necessary for her treatment. This evidence suggests that surgery is still required in certain medical cases, contradicting the claim that nanotechnology eliminates the need for surgery in all instances.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: While these terminal homologies are too short to appear significant in a whole database search, they can be found by comparing the 30–60 bp termini of new elements to the 30–60 bp termini of all classified class II elements and filtering the output by orientation and position. Characteristic TSDs can cement classification. Over the years, we classified thousands of short sequences in Repbase this way, including ancient elements that were active in the common ancestor of all amniotes. In Dfam, we now provide terminal sequence signatures for 64 categories of class II elements, for use in classifying new TE models. To create these signatures, we lined up the 5′ and 3′ 60 bp of all members of a particular type that seem to have clearly defined ends (e. g. as indicated by the presence of the expected TSDs, Fig. 3). Minor modifications were made to some of the nearly 12,000 remaining consensus sequences in order to have each start at the true beginning or end of the TE. This most commonly involved removing (partial) target site duplications or adding one or more Ns when comparison to others showed the sequence to be short. The alignments are ungapped, however, and it is possible that more signal can be obtained by allowing a few indels. We used HMMER (hmmbuild) to develop HMMs for the 5′ ends, the 3′ ends, and, in case of TIRs, the combined termini. Fig. 3Generation of HMMs and sequence LOGOs for DNA transposon termini. The first/last 60 bp of family consensi belonging to a single classification of DNA Transposons are piled up and aligned (without gaps) by hand. Profile HMMs are developed for each end and for the combination of the two to determine if a stronger signal may be obtained in that fashion. Finally, LOGOs are generated for each HMM and displayed on the Dfam websiteFull size imageThe LOGOs of the termini can be viewed on the “Classifications” page on the Dfam website, and are organized by class II subclasses (e. g. , Crypton, Helitron, TIR, etc. ). This allows for easy visualization of the base conservation at each position in the terminal sequences and comparisons between the 5′ and 3′ termini. [SEP] Justify:

Output: The text is irrelevant to the claim about the Human Genome Project mapping the entire sequence of human DNA as it discusses methods for classifying DNA transposons and does not mention the Human Genome Project or its outcomes.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Helder (2013) One-step surgical procedure for the treatment of osteochondral defects with adipose-derived stem cells in a caprine knee defect: a pilot study. Access 2: 315-325. 77. Kadiyala, S. , (1997) Culture expanded canine mesenchymal stem cells possess osteochondrogenic potential in vivo and in vitro. 6: 125-134. 78. Kaigler, D. , G. . (2013) Stem cell therapy for craniofacial bone regeneration: a randomized, controlled feasibility trial. 22: 767-777. 79. Kean, T. J. , P. Lin, A. I. Caplan, J. E. Dennis (2013) MSCs: delivery routes and engraftment, cell-targeting strategies, and immune modulation. Int 2013: 732742. 80. Kim, J. ,. Choi, Y. Park, K. Sun, S. J. Hwang (2010) In vivo evaluation of MMP sensitive high-molecular weight HA-based hydrogels for bone tissue engineering. J 95: 673-681. 81. Kim, J. ,. Tae, I. Noh, S. H. Lee, Y. Park, K. Sun (2007) Bone regeneration using hyaluronic acid-based hydrogel with bone morphogenic protein-2 and human mesenchymal stem cells. Biomaterials 28: 1830-1837. 82. (2011) Gene expression profile in mesenchymal stem cells derived from dental tissues and bone marrow. J Sci 41: 192-200. 83. (2009) A multi-center, randomized, clinical study to compare the effect and safety of autologous cultured osteoblast (Ossron) injection to treat fractures. BMC 10: 20. 84. Kitaori, T. , H. Ito, E. M. Schwarz, R. Tsutsumi, H. Yoshitomi, S. Oishi, M. Nakano, N. Fujii, T. Nagasawa, T. Nakamura (2009) Stromal cell-derived factor 1/CXCR4 signaling is critical for the recruitment of mesenchymal stem cells to the fracture site during skeletal repair in a mouse model. [SEP] Justify:

Output: The text corroborates the claim by detailing various studies that showcase the application of stem cells in regenerative medicine, specifically in repairing damaged tissues. For instance, it references a pilot study on adipose-derived stem cells for treating osteochondral defects, and mentions other research on mesenchymal stem cells (MSCs) used for bone regeneration, highlighting their role in tissue repair.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: The clinical presentation is variable, and it is possible to find asymptomatic patients, woman with a palpable node in an otherwise normal breast or even becoming manifest in the form of a swelling breast due to the presence of a large intracystic mass. Histologically, this tumor is usually described as an encysted lesion, containing nodules of papillary carcinoma surrounded by a thick fibrous capsule [2,4,6]. As in addition, and being more accurate with its histologic features, in the 4th WHO classification, IPC was considered more as a less aggressive variant of papillary carcinoma, due to its lack of myoepithelial layer [8,9]. Regarding the radiological features, the tumor can be found in a mammographic image as a round, oval lesion or as a circumscribed lobulated mass (in consequence of the appearance of a dilated duct) [7-8]. Given the rarity of the disease and the lack of agreement in terms of histologic classification, there is no general consensus about the management of patients with this type of pathology. In spite of these inconsistencies, and taking into account its indolent course, the WHO working group recommends classifying them, and therefore managing them, as a Tis (in situ carcinomas), as long as they do not have clear invasive component [5,9,13]. Here we present the case of a woman diagnosed with pure IPC of the breast that is followed by a literature review focused on this subtype of papillary carcinoma with the aim of proposing a therapeutic management of these rare tumors. Go to 0. The patient was then moved to the radiation oncology department to consider the possibility of breast radiotherapy as adjuvant treatment. Given the rarity of the case and following review of the literature published on this histological subtype (pure intracystic papillary carcinoma, with no component of in situ nor intraductal carcinoma), mostly given by case reports or retrospective series, we concluded that this was a very noninvasive type of cancer where, in women over 50 years of age, no adjuvant therapies (radiotherapy and/or hormone therapy) may be indicated as it would not increase local control or the overall survival. We spoke to the patient and family about this matter, and in consensus we reached the decision of therapeutic abstention and close follow-up by Gynecology department. [SEP] Justify:

Output: The text contrasts the claim by discussing a specific case of cancer management where the decision was made to abstain from any adjuvant therapies, highlighting that the patient did not require surgery or invasive treatments. It provides insight into the management of a particular subtype of papillary carcinoma and suggests that in certain cases, like pure intracystic papillary carcinoma, invasive treatments may not be necessary, thus rebuffing the claim that nanotechnology can eliminate the need for surgery in all medical cases.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: The full set of profiles may be downloaded and will be updated as new elements are added to each class. Dfam growthThe development of a curated TE library for a given species is a specialized and mostly manual task that has only incrementally improved since the inception of TE databases. We recognize that as reference genome sequencing increases at a faster rate, and until automated curation methods improve, uncurated datasets (mostly de novo generated TE libraries) will far outpace the development of curated libraries. There are some advantages to making uncurated datasets available through a resource such as Dfam: (1) they can be used as simple genome masking libraries, and the fragmentation and redundancy that are the hallmark of datasets derived from de novo discovery tools are not detrimental in that context, (2) cataloging uncurated families provides a shared starting point for community curation efforts, and (3) these datasets will provide a resource for developing per-family and per-library quality metrics as well as improved automated curation tools. In the latest release of Dfam we have added support for uncurated datasets, denoting these families using the new accession prefix “DR” and limiting/altering the analysis and metadata displayed for these families (Fig. 4). For instance, a DR family has both a consensus and a profile HMM generated for it, but does not have rigorously characterized false discovery rate thresholds as for curated families [3] due to the lack of pre-calculated assembly annotations. However, uncurated families do contain provenance for the seed alignment, standard metadata (description, classification, taxa, 3. 3. A subset of species are named and species-rich groups are collapsed into triangles, with the number of species indicated. Major branch points have been labeled according to the NCBI taxonomy. Branching times and order of the tree are roughly following that of the OneZoom project [40] with modifications based on more specific research; for example, the branching order within the birds is according to Prum et al. [41]Full size imageDue to the scale of the dataset, only minimal prefiltering of the families was performed before import. Families with > 80% tandemly repetitive sequence and less than 100 bp of contiguous non tandemly repetitive sequence (according to TRF) were removed. This filtered 894 families. [SEP] Justify:

Output: The text does not address the claim regarding the Human Genome Project mapping the entire sequence of human DNA. Instead, it discusses the development and characteristics of uncurated datasets in the context of genome sequencing, which is irrelevant to the specific claim about the Human Genome Project.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: 60: 813-823. 85. . Cui (2015) Interactions between MSCs and immune cells: implications for bone healing. J 2015: 17. 86. Krebsbach, P. H. , M. H. Mankani, K. Satomura, S. A. Kuznetsov, P. G. Robey (1998) Repair of craniotomy defects using bone marrow stromal cells. Transplantation 66: 1272-1278. 87. Le Blanc, K. , C. Gotherstrom, O. Ringden, M. Hassan, R. McMahon, E. Horwitz, G. Anneren, O. Axelsson, J. Nunn, U. Ewald, S. Norden-Lindeberg, M. Jansson, A. Dalton, E. Astrom, M. Westgren (2005) Fetal mesenchymal stem-cell engraftment in bone after in utero transplantation in a patient with severe osteogenesis imperfecta. Transplantation 79: 1607-1614. 88. (2011) Direct deposited porous scaffolds of calcium phosphate cement with alginate for drug delivery and bone tissue engineering. 7: 3178-3186. 89. . Shin (2010) Control of osteogenic differentiation and mineralization of human mesenchymal stem cells on composite nanofibers containing poly[lactic-co-(glycolic acid)] and hydroxyapatite. 10: 173-182. 90. (2004) Isolation of multipotent mesenchymal stem cells from umbilical cord blood. Blood 103: 1669-1675. 91. . Ylostalo, B. L. Larson, L. Semprun-Prieto, P. Delafontaine, D. J. Prockop (2009) Intravenous hMSCs improve myocardial infarction in mice because cells embolized in lung are activated to secrete the anti-inflammatory protein TSG-6. Cell 5: 54-63. 92. Levi, B. , A. W. James, E. R. Nelson, S. Li, M. Peng, G. W. Commons, M. Lee, B. Wu, M. T. [SEP] Justify:

Output: The text provides multiple references to studies and findings related to the use of stem cells, particularly mesenchymal stem cells (MSCs), in contexts that support the claim about regenerative medicine. For example, it mentions 'Repair of craniotomy defects using bone marrow stromal cells' and the use of stem cells in 'bone healing' and myocardial infarction, which illustrate their application in repairing damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: At the last followup visit (10 months after diagnosis) no evidence of disease has been found. Go to 5. 8% of the total) had a loco-regional relapse and only 9 patients overall (1. 9%) suffered metastasis. Additionally, the percentage of survival related to the disease was 99. 4%. In particular, in the study by Solorzano et al. [11], no differences were found in the rate of local recurrence or death due to disease when analyzing the type of surgery (mastectomy or conservative surgery) or the associated use of adjuvant radiotherapy. They concluded that the decision about adjuvant therapy in these cases should be based on the presence of associated lesions, such as an in situ or invasive intraductal component, and that the benefit of radiotherapy in patients with pure IPC was unclear. In another study performed by Fayanju et al. [9], after studying the data of 45 patients with IPC, the conclusion was that patients with pure IPC received less adjuvant therapies (radiotherapy and hormone therapy) compared to patients with IPC associated with an intraductal or invasive component. When clinicians have to decide about the therapeutic approach, patient age is also taken into account, with patients under 50 being more suitable for radiotherapy as compared to older ones. Another factor considered is the type of surgery performed, since the few patients who underwent a mastectomy did not receive adjuvant radiotherapy, but those who had undergone a more conservative surgery in some cases received adjuvant radiotherapy. Despite this, it was found that no patient with pure IPC who had undergone a more conservative surgery had relapse due to it, corroborating what had been seen in other studies, that a mastectomy is not necessary in the treatment of pure IPC and that any adjuvant treatment should be tailored to patient’s histology in order to ensure the excellent outcome expected for these neoplasms. Hence, adjuvant radiotherapy and/or hormone therapy should be considered both for patients with IPC associated with in situ component or microinvasion and for patients under 50 with pure IPC. Esposito et al. [14], in their study of 27 patients suffering from IPC, confirmed that IPCs have an excellent prognosis and so local treatment alone may be sufficient to control the disease. Finally, in another retrospective study performed by Rakha et al. [SEP] Justify:

Output: The text contrasts the claim by discussing the necessity of surgical procedures in treating pure Intraductal Papilloma Cases (IPC). It provides evidence that decisions regarding treatment should be tailored to specific patient histology and associated lesions, indicating that surgery is still required in certain cases, thereby disproving the notion that surgery can be entirely eliminated through nanotechnology.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: TRF was run with a maximum period of 20 bp to preserve common and complex satellite sequences in the dataset. The number of TE models in Dfam has grown from 6915 to 273,655, largely because of the RepeatModeler libraries for 336 additional species contributed by the EBI. Table S2 contains statistics for these EBI additions alone. 116 bony fish, 133 bird and 47 mammalian species form the bulk of the additions, and numbers for these clades alone are displayed in the table. A generally higher variety of recognizable TEs in fish and lower variety in birds is reflected in the data: bony fish (35% of the new species) contributed 58. 4% of the added models, while mammals and birds (14 and 40% of the new species) each contributed about 9. 3% of the new models (Table S2). The remaining 10% of the EBI dataset, and therefore 23% of the TE diversity, belong to other groups outside of bony fish, mammals, and birds that include: plants, cartilaginous fish, turtles and lizards. An analysis of the TE classes and superfamilies in each of the aforementioned clades depicted that bony fish contribute a large number of models across class II TE superfamilies, and are consequently enriched for class II TEs (2 and Table S2). Birds and mammals contribute to and are enriched for LINEs (CR1 and L1, respectively), in addition to endogenous retrovirus (ERV)-like LTR elements. The EBI dataset confirms large-scale patterns visible in addition to providing data regarding TE expansion for individual organisms. Examples of the seed alignments generated as part of the aforementioned pipeline can be observed in Fig. 6. The seed alignment for any model provides researchers with a wealth of information including sequence coverage, length, and number of sequences contributing to the model. From a curator’s perspective, information like divergence patterns and blocks of seemingly truncated sequences are also evident. For example, a block of sequences in an LTR alignment that show a different divergence pattern and/or appears to be truncated at the same position relative to the consensus sequence are likely to indicate a subfamily structure within the model (Fig. 6a, red box). This alignment pattern reflects the biology of the TE, as LTR sequences regularly recombine their 5′ and 3′ ends to form new families [43]. [SEP] Justify:

Output: The text is irrelevant to the claim regarding the Human Genome Project mapping human DNA, as it discusses data related to transposable elements and the contributions from different species in a dataset, without mentioning the Human Genome Project or sequencing of human DNA.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Longaker (2010) Human adipose-derived stromal cells stimulate autogenous skeletal repair via paracrine hedgehog signaling with calvarial osteoblasts. Dev 20: 243-257. 93. Levi, B. , M. T. Longaker (2011) Adipose derived stromal cells for skeletal regenerative medicine. 29: 576-582. 94. Li, F. , N. Whyte, C. Niyibizi (2012) Differentiating multipotent mesenchymal stromal cells generate factors that exert paracrine activities on exogenous MSCs: implications for paracrine activities in bone regeneration. 426: 475-479. 95. Li, H. , K. Dai, T. Tang, X. Zhang, M. Yan, J. Lou (2007) Bone regeneration by implantation of adipose-derived stromal cells expressing BMP-2. 356: 836-842. 96. Liao, J. , X. Guo, D. Nelson, F. K. Kasper, A. G. Mikos (2010) Modulation of osteogenic properties of biodegradable polymer/extracellular matrix scaffolds generated with a flow perfusion bioreactor. 6: 2386-2393. 97. Liebergall, M. , J. Schroeder, R. Mosheiff, Z. Gazit, Z. Yoram, L. Rasooly, A. Daskal, A. Khoury, Y. Weil, S. Beyth (2013) Stem cell-based therapy for prevention of delayed fracture union: a randomized and prospective preliminary study. 21: 1631-1638. 98. Lotfy, A. , M. Salama, F. Zahran, E. Jones, A. Badawy, M. Sobh (2014) Characterization of mesenchymal stem cells derived from rat bone marrow and adipose tissue: a comparative study. 7: 135-142. 99. Luo, Y. , M. S. Shoichet (2004) Light-activated immobilization of biomolecules to agarose hydrogels for controlled cellular response. Biomacromolecules 5: 2315-2323. 100. Mallela, J. , S. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies and research involving stem cells and their application in regenerative medicine. For instance, it refers to 'human adipose-derived stromal cells' stimulating skeletal repair and 'stem cell-based therapy for prevention of delayed fracture union,' directly supporting the assertion that stem cells are utilized to repair damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: [8] with data from 207 patients with IPC, it was concluded that IPC is a carcinoma with a very favourable prognosis and that moderate local treatment, with an addition of hormone therapy in selected cases, is sufficient for an optimal outcome. In general terms, many of these studies agreed to conclude that pure IPC variant has an indolent course with a very good prognosis even in those patients in whom the management is only surgical, without the association of adjuvant therapies. In addition, the absence of axillary lymph node involvement in this type of patients excludes the need to carry out axillary staging procedures [1,17-19]. However, some authors consider the procedure of sentinel lymph node biopsy as a prudent approach, given the uncertainty concerning the intraductal vs. invasive nature of IPC [20-23]. More recently, in 2016, a retrospective analysis was published, based on data from the SEER (Surveillance, Epidemiology, and End Results) database, including 2649 patients diagnosed with IPC [24], where the authors concluded that overall, IPC has a very good prognosis and that survival is improved in caucasian patients and in patients who receive radiation therapy, but two important limitations in this study were the inability to specifically assess whether patients had pure IPC or the presence of an invasive component and the fact that the effect of administration of other adjuvant therapies (such as hormone therapy) could not be assessed as these variables are not captured within the database. Go to 19. (1967) Intracystic carcinoma of the female breast. Obstet 124(1): 93-98. (1958) Intracystic carcinoma of the breast. Obstet 106(3): 347-352. (1992) Tumors of the mammary gland. 3rd (edn), Institute of 219. (2012) WHO classification of tumors of the breast. Lyon: for Research on Cancer, Lyon, France. (2008) Intracystic papillary carcinoma: a review of 917 cases. Cancer 113(5): 916–920. (1995) Papillary carcinoma of the breast: imaging findings. Roentgenol 164(2): 321-326. van (2011) Encapsulated papillary carcinoma of the breast: an invasive tumor with excellent prognosis. 35(8): 1093–1103. [SEP] Justify:

Output: The text contrasts the claim by stating that although there are instances where treatment without surgery may be sufficient, it specifically describes conditions and considerations surrounding Intracystic Papillary Carcinoma (IPC), indicating that surgical management is still a viable approach. This indicates that surgery may not be entirely eliminated as an option in medical cases, especially when considering the 'management is only surgical' part of the text.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: Similarly, blocks of outwardly truncated sequences close to the 5′ end in an L1 seed alignment reflect a tendency for differing patterns present in the 5′ UTR regions [44] (Fig. 6b). Closer inspection of these sequence blocks within the alignment is warranted to determine if a subfamily structure is present. Fig. 6Seed alignment examples from raw Dfam 3. 3 entries. A) ERV1 (LTR) (DR0086957. 1; Eulemur macaco (black lemur)). The red bracket indicates a group of sequences differing in length and divergence patterns. 506 sequences contribute to the seed alignment for this 503 bp model. B) L1 sequence (DR0215804. 1; Phyllostomus discolor (pale spear-nosed bat)). The red brackets indicate two groups of sequences that differ in their 5′ alignment. One thousand one hundred eighty-six sequences contribute to the seed alignment for this 7353 bp model. Each sequence is represented by a single row (sorted by start position) where the color gradient indicates alignment quality (red = low; blue = high) over 10 bp non-overlapping windows. The solid green shape over the two seed alignments indicate the coverage along the model consensus sequence. Note: the two panels differ in scaleFull size imageBy providing the RepeatModeler output for the additional 336 species, Dfam encourages the TE community to lend their expertise, thus improving this dataset so that it moves from a raw dataset to a highly curated one. We are working on providing tools for the community to curate and improve upon these and existing curated datasets. Architectural and Interface improvementsThe architecture of Dfam was refactored in Dfam 3. 0 to prepare the resource for housing TE families, seed alignments, and sequence models at scale. website ( has been updated to provide both (i) a front end intended for human interaction through a web browser (the ‘portal’) and (ii) an API served over HTTP to support programmatic access to Dfam data. The source code for both projects is available on GitHub ( and released under the CC0 public domain dedication. The API uses computer-friendly data formats such as JSON and tab-separated values (as appropriate), which makes it more suitable as a data source for community-developed tools than the human-oriented format of the website. [SEP] Justify:

Output: The text is irrelevant to the claim about the Human Genome Project mapping the entire sequence of human DNA. It discusses repetitive element analysis and bioinformatics tools in relation to transposable elements and their alignments, but does not mention the Human Genome Project or its sequencing efforts.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Tatullo (2015b) Human periapical cyst-mesenchymal stem cells differentiate into neuronal cells. J 94: 843-852. 108. Marrelli, M. , M. Tatullo (2013) Influence of PRF in the healing of bone and gingival tissues: clinical and histological evaluations. Sci 17: 1958-1962. 109. Mathieu, P. S. , E. G. Loboa (2012) Cytoskeletal and focal adhesion influences on mesenchymal stem cell shape, mechanical properties, and differentiation down osteogenic, adipogenic, and chondrogenic pathways. B Rev 18: 436-444. 110. Mehta, M. , K. Schmidt-Bleek, G. N. Duda, D. J. Mooney (2012) Biomaterial delivery of morphogens to mimic the natural healing cascade in bone. 64: 1257-1276. 111. Meier, R. P. , Y. D. Muller, P. Morel, C. Gonelle-Gispert, L. H. Buhler (2013) Transplantation of mesenchymal stem cells for the treatment of liver diseases, is there enough evidence? Res 11: 1348-1364. 112. Melek, L. N. (2015) Tissue engineering in oral and maxillofacial reconstruction. J 12: 211-223. 113. (2015) Posterior partially edentulous jaws, planning a rehabilitation with dental implants. 3: 65-76. 114. Moreau, J. L. , H. H. Xu (2009) Mesenchymal stem cell proliferation and differentiation on an injectable calcium phosphate-chitosan composite scaffold. Biomaterials 30: 2675-2682. 115. Moshiri, A. , A. Oryan (2013) Role of platelet-rich plasma in soft and hard connective tissue healing: an evidence-based review from basic to clinical application. 2: 6. 116. Moshiri, A. , A. Oryan, A. Meimandi-Parizi (2015a) Synthesis, development, characterization and effectiveness of bovine pure platelet gel-collagen-polydioxanone bioactive graft on tendon healing. [SEP] Justify:

Output: The text corroborates the claim by providing references to various studies which detail the use of stem cells in differentiated therapies for tissue healing and regeneration. For example, the mention of 'Human periapical cyst-mesenchymal stem cells differentiate into neuronal cells' and 'Transplantation of mesenchymal stem cells for the treatment of liver diseases' aligns with the claim that stem cells are utilized in regenerative medicine for repairing damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: (2007) Therapeutic management of intracystic papillary carcinoma of the breast: the roles of radiation and endocrine therapy. Surg 194(4): 497-500. (1999) Treatment and outcome of intracystic papillary carcinoma of the breast. Surg 86(10): 1274. (2002) Treatment and outcome of patients with intracystic papillary carcinoma of the breast. Surg 184(4): 364–368. (1998) Intracystic (encysted) papillary carcinoma of the breast: a clinical, pathological, and immunohistochemical study. 29: 1097-1104. (2009) Encapsulated apocrine papillary carcinoma of the breast-a tumour of uncertain malignant potential: report of five cases. Virchows Arch. 455(6): 477-483. (2009) Are encapsulated papillary carcinomas of the breast in situ or invasive? A basement membrane study of 27 cases. 131: 228-242. (2008) Papillary lesions of the breast: Selected diagnostic and management issues. Histopathology 52(1): 20-29. Collins L, O’ (2012) Encapsulated papillary carcinoma. In: van de Vijver MJ, editors. WHO classification of tumors of the breast. for Research on Cancer, Lyon, France, 107. Collins L, O’ (2012) Encapsulated papillary carcinoma. In: van de Vijver MJ, editors. WHO classification of tumors of the breast. for Research on Cancer, Lyon, France, 107. (1983) Immunohistochemical analysis of benign and malignant papillary lesions of the breast. 7(5): 451-461. (1998) Recent patterns of hormone replacement therapy use in a large managed care organization. J 7: 1017-1026. (1994) Intraductal (intracystic) papillary carcinoma of the breast and its variants: A clinicopathological study of 77 cases. 25(8): 802-809. -Tanaka S, et al. (2009) Clinical and pathological features of intracystic papillary carcinoma of the breast. 39(1): 5-8. (2009) Breast intracystic papillary carcinoma: An update. 15(6): 639-644. [SEP] Justify:

Output: The text discusses various studies and findings related to the treatment and outcomes of intracystic papillary carcinoma of the breast, highlighting multiple surgical and non-surgical management options. By focusing on surgical interventions, it implies that surgery remains a vital component of treatment in some cases, which contrasts with the claim that nanotechnology eliminates the need for surgery in all medical cases.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: The portal has gained several significant new features. To support the massive scale of family data we replaced the old one-page-per-letter approach to family organization with a “Browse” page that supports sorting and filtering on multiple criteria such as name, classification, taxon, or keywords. Some similar filters have also been added to the “Relationships” tab to restrict results to related species. The “Features” tab has been added to the per-family page to display curated features (binding sites, hand-curated coding sequences etc), as well as blastx matches against other known TE protein sequences. The architectural changes also facilitated the merger of Dfam and Dfam_consensus [45], creating a single resource for both consensus and HMM sequence models for each family. During the merger, Dfam inherited the seed alignment visualization from Dfam_consensus. This visualization shows both coverage (how many representatives cover each portion of the alignment) and the conservation patterns within the alignment, shown as a heatmap indicating how closely each member aligns to the consensus (as seen in Fig. 6). Dfam also now includes an authentication system and public data submission system; this is the first step in a planned development of a curation workbench that will provide users with tools to edit and curate data uploaded by themselves or (eventually) others. Software/tool distribution improvementsOne of the main hurdles with using bioinformatic pipelines and tools is the complexity of the installation and configuration necessary to use them. Software containers are an increasingly popular way to tackle this problem, by delivering an executable user environment that comes with pre-installed and pre-configured software packages. In order to support community curation efforts we have developed containers for Docker and Singularity, housing pre-installed versions of our latest tools (e. g. ) and dependencies as well as external open-source tools (e. g. HMMER, mafft, cdhit, TRF). More information along with instructions for use are available at As part of our outreach efforts, we will be eliciting recommendations for including additional packages in future releases. Notably these containers include FamDB, a new HDF5-based Dfam export format and associated query tools for offline access to Dfam. [SEP] Justify:

Output: The text is irrelevant (pass) to the claim about the Human Genome Project because it discusses features and functionalities related to a data resource (Dfam) and bioinformatic tools without mentioning the Human Genome Project or its objectives. It focuses on the organization of family data, software tool distribution improvements, and outreach efforts, none of which address or support the claim regarding the mapping of human DNA.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: J Med 19: 1308-1332. 117. Moshiri, A. , M. Shahrezaee, B. Shekarchi, A. Oryan, K. Azma (2015b) Three-dimensional porous Gelapin-Simvastatin scaffolds promoted bone defect healing in rabbits. Int 96: 552-564. 118. 'Brien (2010) The effect of mean pore size on cell attachment, proliferation and migration in collagen-glycosaminoglycan scaffolds for bone tissue engineering. Biomaterials 31: 461-466. 119. Murphy, M. B. , K. Moncivais, A. I. Caplan (2013) Mesenchymal stem cells: environmentally responsive therapeutics for regenerative medicine. Med 45: e54. 120. Murrell, W. D. , A. W. Anz, H. (2015) Regenerative treatments to enhance orthopedic surgical outcome. 7(suppl 4): S41-S52. 121. Nanes, M. S. (2003) Tumor necrosis factor-α: molecular and cellular mechanisms in skeletal pathology. Gene 321: 1-15. 122. Nsair, A. , W. R. MacLellan (2011) Induced pluripotent stem cells for regenerative cardiovascular therapies and biomedical discovery. 63: 324-330. 123. Olmsted-Davis, E. , F. H. Gannon, M. Ozen, M. M. Ittmann, Z. -Dilling, S. Schumara- (2007) Hypoxic adipocytes pattern early heterotopic bone formation. Pathol 170: 620-632. 124. Oryan, A. , S. Alidadi, A. Moshiri, A. Bigham- Sadegh (2014a) Bone morphogenetic proteins: a powerful osteoinductive compound with non-negligible side effects and limitations. Biofactors 40: 459-481. 125. Oryan, A. , S. Alidadi, A. Moshiri, N. Maffulli (2014b) Bone regenerative medicine: classic options, novel strategies, and future directions. J Res 9: 9-18. 126. Oryan, A. , A. Kamali, A. [SEP] Justify:

Output: The text corroborates the claim by referencing 'Mesenchymal stem cells: environmentally responsive therapeutics for regenerative medicine' which indicates that stem cells are indeed utilized in regenerative medicine for repairing damaged tissues. The mention of other studies related to bone defect healing and regenerative treatments further supports the usage of stem cells in these medical applications.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: com Received: May 9, 2024Revised: June 7, 2024Accepted: June 18, 2024Published online: August 6, 2024Processing time: 53 Days and 21. 8 sign is a specific electrocardiographic manifestation of ostium secundum atrial septal defects (ASDs), which is associated with the severity of the left-to-right shunt. Herein, we reported a case of selective his bundle pacing (S-HBP) that eliminated crochetage sign in a patient with ostium secundum ASD. 77-year-old man was admitted with a 2-year history of chest tightness and shortness of breath. Transthoracic echocardiography revealed an ostium secundum ASD. Twelve-lead electrocardiogram revealed atrial fibrillation with a prolonged relative risk interval, incomplete right bundle branch block, and crochetage sign. The patient was diagnosed with an ostium secundum ASD, atrial fibrillation with a second-degree atrioventricular block, and heart failure. The patient was treated with selective his bundle pacemaker implantation. After the procedure, crochetage sign disappeared during his bundle pacing on the electrocardiogram. -HBP eliminated crochetage sign on electrocardiogram. Crochetage sign may be a manifestation of a conduction system disorder. Key Words: Crochetage sign; Atrial septal defect; Pacemaker; Selective his bundle pacing; Case report Core Tip: Crochetage sign is a characteristic electrocardiographic manifestation seen in patients with ostium secundum atrial septal defects. We reported the case of a patient with secundum atrial septal defect, atrial fibrillation, and second-degree atrioventricular block who received selective his bundle pacing (S-HBP) treatment. Subsequently, crochetage sign was eliminated by S-HBP. Crochetage sign may indicate a conduction system disease. Citation:. Selective his bundle pacing eliminates crochetage sign: A case report. 2024; 12(22): 5276-5282 URL: DOI: an incidence of 6%-10% after birth, atrial septal defect (ASD) is one of the most prevalent congenital heart diseases, with secundum ASD being the most common[1]. [SEP] Justify:

Output: The text contrasts the claim by discussing a specific medical case involving selective his bundle pacing (S-HBP) for treating an ostium secundum atrial septal defect (ASD). It emphasizes that this procedure, which involves surgical intervention (pacemaker implantation), was necessary to eliminate the 'crochetage sign' and treat the patient's condition. This directly opposes the claim that nanotechnology alone can eliminate the need for surgery in all cases, indicating that surgical methods are still required in certain medical situations.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: FamDB files contain family consensi/HMMs and the NCBI Taxonomy data related to these families in a format that allows for fast offline access from the command line. The current release of FamDB includes all Dfam consensus sequences, HMMs, metadata, and 61,003 taxa from NCBI’s taxonomy database [46] related to these families. Lookups for information on a single taxon or family complete in about a second; extraction of consensus sequences () or HMMs for all TE families found in Human (including ancestral repeats) complete in about 3 to 4 s. Due to indexing, the run time for data queries is largely independent of the total number of TEs in the database: it takes about the same amount of time to extract the human library from a FamDB file including only the curated subset of Dfam (6915 entries) as for the full database (273,655). Future challenges/directionsThe curation of multi-species TE databases involves many manual tasks (e. g. defragmentation, classification validation, lineage assignment) and many subjective decisions (e. g. redundancy removal, pseudogene removal, subfamily characterization) that have not been universally standardized into protocols. With the growth of uncurated TE libraries and their inclusion in databases such as Dfam, it has become necessary to develop protocols for many of these tasks and to consider the challenges introduced by this data growth. Here, we discuss two of these topics that we will be focusing on in the near term. SubfamiliesWhen a family is believed to exhibit subfamily structure, there are a variety of methods available to cluster the family copies into subfamily groups. A subfamily structure is suspected when there is a wide divergence distribution of family members, or directly observing distinct groups of co-segregating subsequences in a seed alignment. Wicker used the aforementioned 80/80/80 rule to cluster sequences into subfamilies: sequences are clustered such that all members of the subfamily share at least 80% sequence identity and at least 80% sequence coverage with length greater than 80 bp. A strategy to define subfamilies was used in the analysis of bread wheat subgenomes by applying a 90/90 or 95/95 rule in which 90 or 95% sequence identity and 90 or 95% sequence coverage was used to cluster sequences into subfamilies [47, 48]. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the FamDB database, family consensus sequences, and methods for clustering sequences into subfamilies, but does not mention the Human Genome Project or its role in mapping human DNA.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Moshiri (2015) Potential mechanisms and applications of statins on osteogenesis: current modalities, conflicts and future directions. J 215: 12-24. 127. Oryan, A. , A. Moshiri (2013) Tissue engineering: alternative option in managing large and massive tissue deficits. Surg 1: e101. 128. Otsuru, S. , K. Tamai, T. Yamazaki, H. Yoshikawa, Y. Kaneda (2007) Bone marrow-derived osteoblast progenitor cells in circulating blood contribute to ectopic bone formation in mice. 354: 453-458. 129. Pak, J. , J. H. Lee, S. H. Lee (2014) Regenerative repair of damaged meniscus with autologous adipose tissue-derived stem cells. Int 436029: 30. 130. Papandreou, I. , R. A. Cairns, L. Fontana, A. L. Lim, N. C. Denko (2006) HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption. 3: 187-197. 131. Park, S. H. , A. Tofighi, X. Wang, M. Strunk, T. Ricketts, J. Chang, D. L. Kaplan (2011) Calcium phosphate combination biomaterials as human mesenchymal stem cell delivery vehicles for bone repair. 97: 235-244. 132. Pelegrine, A. A. , C. E. da Costa, M. E. Correa, J. F. Marques Jr. (2010) Clinical and histomorphometric evaluation of extraction sockets treated with an autologous bone marrow graft. 21: 535-542. 133. Peng, F. , H. Wu, Y. Zheng, X. Xu, J. Yu (2012) The effect of noncoherent red light irradiation on proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells. Sci 27: 645-653. 134. . (2009) Analysis of the osteoinductive capacity and angiogenicity of an in vitro generated extracellular matrix. J 88: 295-303. 135. [SEP] Justify:

Output: The text corroborates the claim as it references multiple studies related to stem cells and their application in regenerative medicine, particularly in areas involving tissue repair. For instance, it mentions the use of 'autologous adipose tissue-derived stem cells' for 'regenerative repair of damaged meniscus,' which directly supports the idea that stem cells are utilized in regenerative medicine to repair damaged tissues.


Input: Task: pass the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: AV nodal conduction disorders are uncommon in other forms of ASD[8]. The incidence of heart block in patients with ASD is unclear, and ASD with high-grade AV block is relatively uncommon[11]. Our patient had a second-degree AVB and atrial fibrillation, which are rare. His bundle pacing was then performed. The postoperative ECG revealed an isoelectric interval in all 12 leads, with the pacing spike to QRS onset equaling the native HV interval (35–55 ms). The QRS morphology was identical to that of the intrinsic rhythm, confirming S-HBP. Crochetage sign refers to the presence of a notch in the initial 80 ms of the QRS complex in leads II, III and aVF, which resembles the shape of a crochet needle[12]. This sign is most frequently observed in individuals with ASD and can also be observed in other disorders such as patent foramen ovale (PFO), pulmonary embolism, and RV hypertrophy[11]. Recent research has revealed that, crochetage sign combined with RBBB and TTE had good performance for PFO prediction, with an accuracy, sensitivity, and specificity of 0. 712, 0. 801, and 0. 439, respectively[13]. In the initial published research on crochetage, 73% of patients with ASD showed this pattern[14]. Crochetage sign is considered a characteristic presentation of secundum ASDs. When the pattern is seen in all three inferior leads, the specificity of this sign ranges from 92% to 100%[3]. The presence of a RBBB on the ECG considerably increases the specificity and sensitivity of crochetage sign for the diagnosis of ASD[3]. It has also been associated with the severity of the left-to-right shunt, and patients with ASD sizes of ≥ 5 mm showed a higher incidence of crochetage sign[6]. Because of its high sensitivity and specificity in diagnosing ASD, crochetage sign is a useful diagnostic tool[12]. Moreover, a retrospective clinical study demonstrated that the presence of crochetage sign was an independent predictor for late atrial arrhythmia among patients with secundum ASD who received transcatheter closure[15]. The underlying electrophysiological mechanism of crochetage sign is not fully understood, but many researchers believe that it is related to delayed RV depolarization due to RV volume overload[15]. [SEP] Justify:

Output: The text provided is irrelevant to the claim as it discusses specific cardiac conditions, diagnostic signs, and their implications in patients with atrial septal defect (ASD). It does not mention nanotechnology or surgery in any context, therefore it does not support, contrast, or relate to the claim about nanotechnology eliminating the need for surgery.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: However, further testing should be completed to determine if this type of threshold accurately splits sequences into subfamilies of all TE types across a wide array of species. The methods used to develop subfamily models vary widely, from the manual clustering of copies in a multiple sequence alignment by eye, to automated clustering algorithms [49], and network-based approaches [50]. Wildly different subfamily sets can be produced by these alternative methods, or even by using slightly different parameterizations within one method. The large number of fine-grained subfamilies produced by some of these methods is not of practical use for identifying copies of the superfamily in a genome or specifically labeling individual copies confidently [51] with current sequence similarity search algorithms. Still, in aggregate the tree structure and subfamily membership are valuable datasets for studying family evolution and databases can play a role in the standardisation of this data. For future releases of Dfam we will explore ways to set a minimum sequence distance threshold for inclusion in Dfam as a subfamily. The threshold should reflect the current sensitivity and specificity of both HMM and consensus based search algorithms and act on the detailed subfamily tree to cluster closely-related subfamilies (lumping their copies together). The original detailed tree structure and individual copy membership need not be lost (Fig. 7), but stored alongside the superfamily as a combination of newick data and fine-scale seed alignment sequence subfamily labels for further study and use. Fig. 7Database subfamily representation. Proposed database representation for TE subfamilies maintaining a detailed phylogenetic structure while reducing the representative models for practical genome-scale annotation. The TE seed alignment (1) from a family with evidence of subfamily structure is analysed by a clustering method to produce a detailed subfamily structure and membership (2). Sequence models are developed for subfamilies and lumped (3) if model performance isn’t improved by the subdivision of two or more subfamilies. The lumped families and their corresponding seed alignments are added to the database (4) with metadata holding the detailed tree structure and seed sequence membership for each subfamilyFull size imageRedundancy/fragmentation detectionIdeally, a TE database should contain a single full-length entry for each transposing family. Unfortunately that overly simple definition doesn’t account for the fine detail of subfamily expansions, recombinations, deletion products, and mosaicism exhibited by many TE families. [SEP] Justify:

Output: The text is irrelevant to the claim about the Human Genome Project as it does not discuss the mapping of the human DNA sequence. Instead, it focuses on methods for analyzing transposable elements (TEs) and their subfamily structures, which does not address the specific achievements or findings of the Human Genome Project.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: (2009) Differential mobilization of subsets of progenitor cells from the bone marrow. Cell 4: 62-72. 136. Pittet, M. J. , M. Nahrendorf, F. K. Swirski (2014) The journey from stem cell to macrophage. Ann NY 1319: 1-18. 137. Poser, L. , R. Matthys, P. Schawalder, S. Pearce, M. Alini, S. Zeiter (2014) A standardized critical size defect model in normal and osteoporotic rats to evaluate bone tissue engineered constructs. Int 2014: 11348635. 138. Qin, X. , R. M. Raj, X. F. Liao, W. Shi, B. . Zhou (2014a) Using rigidly fixed autogenous tooth graft to repair bone defect: an animal model. 30: 380-384. 139. Qin, Y. , J. Guan, C. Zhang (2014b) Mesenchymal stem cells: mechanisms and role in bone regeneration. J 90: 643-647. 140. Radice, M. , P. Brun, R. Cortivo, R. Scapinelli, C. Battaliard, G. Abatangelo (2000) Hyaluronan-based biopolymers as delivery vehicles for bone-marrow-derived mesenchymal progenitors. J Res 50: 101-109. 141. Rauh, J. , F. Milan, K. P. Gunther, M. Stiehler (2011) Bioreactor systems for bone tissue engineering. B Rev 17: 263-280. 142. Raynaud, C. M. , A. Rafii (2013) The necessity of a systematic approach for the use of MSCs in the clinical setting. Int 2013: 892340. 143. Reiser, J. , X. Y. Zhang, C. S. Hemenway, D. Mondal, L. Pradhan, V. F. (2005) Potential of mesenchymal stem cells in gene therapy approaches for inherited and acquired diseases. 5: 1571-1584. 144. Rickert, D. , S. Sauerbier, H. Nagursky, D. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies and articles that focus on mesenchymal stem cells (MSCs) and their role in bone regeneration, delivery vehicles for bone-marrow-derived mesenchymal progenitors, and their potential applications in tissue engineering. The mention of MSCs indicates their direct involvement in regenerative medicine and the reparative processes for damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: Crochetage sign disappears in approximately 50% of patients after successful correction of ASD using percutaneous or surgical procedures[3,6]. Interestingly, in our case, crochetage sign disappeared on the ECG after S-HBP; however, the patient had not undergone atrial septal closure. We concluded that crochetage sign may be a manifestation of conduction system impairment. Based on the theory of longitudinal dissociation in the his bundle, conduction impairment may originate within the proximal his bundle because the pacing exceeded the injury level, and conduction through the His-Purkinje system was recovered, thus eliminating crochetage sign[16]. exact mechanism underlying the development of crochetage sign has not yet been elucidated. Some patients with ASD closure experience crochetage signs that disappear from their ECG. Here, we report the case of a patient with ASD whose crochetage sign disappeared after selective his bundle pacing. Subsequently, we deduced that crochetage sign could be a manifestation of a cardiac conduction system injury. Future research is needed to explore the mechanism behind crochetage sign. and peer review: Unsolicited 1. . Atrial septal defects - clinical manifestations, echo assessment, and intervention. Insights Cardiol. 2014;8:93-98. [PubMed] [DOI] [Cited in This 2. 9] [Analysis (0)] 2. Bayar N, Arslan Ş, Köklü üçükseymen S. The importance of electrocardiographic findings in the diagnosis of atrial septal defect. Kardiol Pol. 2015;73:331-336. [PubMed] [DOI] [Cited in This 0. 8] [Analysis (0)] 3. Heller J, Hagège. "Crochetage" (notch) on R wave in inferior limb leads: a new independent electrocardiographic sign of atrial septal defect. J Cardiol. 1996;27:877-882. [PubMed] [DOI] [Cited in This 1. 6] [Analysis (0)] 4. . the Way. . 2023;13:101814. [PubMed] [DOI] [Cited in This 5. . 'Crochetage' sign of atrial septal defect. QJM. 2020;113:133-134. [SEP] Justify:

Output: The text contrasts the claim by discussing cases related to atrial septal defects (ASD), indicating that some patients require surgical or percutaneous procedures for correction. The mention of crochetage sign disappearance after surgical intervention suggests that not all cases can be managed without surgery, thereby undermining the claim that nanotechnology eliminates surgical needs in all medical cases.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: These processes lead to necessary redundancy in a library. Another form of redundancy, that is not desirable, is the direct result of (1) re-detection of ancestral families in the de novo analysis of two or more related species, (2) the confounding effects of sequence variation on de novo detection methods leading to rediscovery, and (3) inadequate clustering in pipelines that run multiple discovery methods and merge the results (Fig. 8). In addition, differences in the representative set of TE copies, in the alignment parameters, and the selection of model building parameters will lead to subtle differences between models generated for the same family; making automatic redundancy detection difficult. Fig. 8Redundancy/Fragmentation removal challenges. Both inter- and intra-library redundancy is present in de novo datasets and are currently resolved through manual curation. Interlibrary redundancy is often the result of unresolved subfamily structure (e. g. internal deletion products of DNA transposons) that confounds discovery and produces both redundant and fragmented families. Intra library redundancy is an inherent aspect analyzing a single species in isolation. For each new species these ancestral families need to be resolved by comparison to existing families, and by considering presence at orthologous sitesFull size imageThrough the expansion of the Dfam database via the addition of diverse sets of species and their associated TEs, it will become necessary to detect redundancy automatically. One approach would be to use a comparative genomics approach to assess TE insertions at orthologous sites to resolve interspecies redundancies while improving the taxonomic labels for each family (Fig. 8). Fragmentation is an additional problem apparent in most de novo datasets. In some cases this directly relates to the structure of the observed TE copies appearing as distinct patterns within a genome (e. g. full length LTRs with internal sequence, and solo LTRs) or coverage bias in a families copies (e. g 5′ end of LINE families). In either case joining these fragments into a complete family is the desired result. Fragmentation is often identified during manual curation as a family fragment is extended and subsequently matched to another fragment in the library over the extended region. Another approach would be to use genome annotations for the uncurated library to identify significant collinearity among family pairs and automatically group families together. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses issues of redundancy and fragmentation in genomic datasets and methodologies for resolving these issues, without mentioning the Human Genome Project or its contribution to mapping human DNA. There is no direct reference to the claim made.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Menne, A. Vissink, G. M. Raghoebar (2011) Maxillary sinus floor elevation with bovine bone mineral combined with either autogenous bone or autogenous stem cells: a prospective randomized clinical trial. 22: 251-258. 145. Robey, P. G. (2011) Cell sources for bone regeneration: the good, the bad, and the ugly (but promising). B Rev 17: 423-430. 146. . Ylostalo, K. Coble, R. H. Rosa Jr, D. J. Prockop (2011) Action at a distance: systemically administered adult stem/progenitor cells (MSCs) reduce inflammatory damage to the cornea without engraftment and primarily by secretion of TNF-α stimulated gene/protein 6. 29: 1572-1579. 147. Rokn, A. , A. R. Ghahroudi, S. Hemati, A. Soolari (2011) Comparison of peri-implant bone loss and survival of maxillary intrasinus and extrasinus implants after 2 years. J Dent 8: 130-137. 148. Roy, S. , J. Driggs, H. Elgharably, S. Biswas, M. Findley, S. Khanna, U. Gnyawali, V. K. Bergdall, C. K. Sen (2011) Platelet-rich fibrin matrix improves wound angiogenesis via inducing endothelial cell proliferation. Regen 19: 753-766. 149. Santos, J. L. , D. Pandita, J. . Tomas (2011) Non-viral gene delivery to mesenchymal stem cells: methods, strategies and application in bone tissue engineering and regeneration. Ther 11: 46-57. 150. Sarkar, S. K. , B. T. Lee (2015) Hard tissue regeneration using bone substitutes: an update on innovations in materials. 30: 279-293. 151. Sauerbier, S. , D. Rickert, R. Gutwald, H. Nagursky, T. Oshima, S. P. Xavier, J. Christmann, P. Kurz, D. Menne, A. Vissink, G. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies and articles that support the use of stem cells in regenerative medicine, specifically associated with bone regeneration and tissue repair. For example, the mention of 'autogenous stem cells' in the context of maxillary sinus floor elevation and the research on 'systemically administered adult stem/progenitor cells' that reduce inflammatory damage suggests a direct application of stem cells in repairing damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: Log in or new issue alertsGet alerts Submit a your Email address: Subscribe to e2019. | DOI: 10. 4103/ijo. IJO_1905_18 Abstract Purpose: This study evaluated the efficacy of retrobulbar ropivacaine plus dexmedetomidine compared with systemic fentanyl in pediatric vitreoretinal (VR) surgery. Methods: This prospective double-blind, randomized controlled study was performed in 60 children undergoing VR surgery, age from 2 to 7 years. After general anesthesia, the following procedure was administrated: (1) retrobulbar block with 0. 5% ropivacaine plus dexmedetomidine 1 μg/kg (group RD, n = 20), (2) retrobulbar block with 0. 5% ropivacaine (group RB, n = 20), and (3) control group with general anesthesia only (group F, n = 20). Hemodynamics, postoperative pain scores, anesthetics consumption (remifentanil, propofol, fentanyl), and emergence agitation were recorded. Results: Respiratory depression was observed in 7 of the 20 patients in group F after the laryngeal mask airway was removed in the operating room, compared with none in groups RD and RB. All patients in group F required intraoperative rescue fentanyl (average intraoperative fentanyl consumption, 26. 6 ± 12. 6 μg per patient). Some rescue fentanyl was required in group RB (three patients required one dose of rescue fentanyl). Patients in group RD required none. Groups RD and RB reported lower pain scores than group F at 4 h postoperatively (RD group: P < 0. 001; RB group: P =0. 002); pain scores in group RD were lower than that in group F at 6 h postoperatively (P < 0. 001). Conclusion: Retrobulbar dexmedetomidine as an adjuvant to ropivacaine is a safe and effective alternative to systemic fentanyl. This regimen provides better pain management, hemodynamic stability, and stress response suppression in pediatric VR surgery. Postoperative opioid-induced respiratory depression is the main cause of death and brain damage in the perioperativeperiod. [12] Regional anesthesia combined with general anesthesia decreased opioid-related adverse events in major pediatric surgeries. [SEP] Justify:

Output: The text contrasts the claim by discussing a study focused on pediatric vitreoretinal surgery, indicating that surgical procedures are still necessary despite advances in anesthesia techniques. It describes specific interventions (retrobulbar ropivacaine and dexmedetomidine) used during surgery and emphasizes that these are alternatives to systemic opioids for pain management, suggesting that surgery is still required. This directly refutes the claim that nanotechnology can replace surgery in all medical cases.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: ConclusionThe new Dfam release has expanded the number and scope of species included in the database, allowing for enhanced genome annotation while fostering the development of highly curated TE libraries for use in research. In addition, a unified eukaryotic TE classification scheme and HMMs for DNA transposon termini now on Dfam, provide additional details for researchers to utilize in their TE research. Combined with an expanded TE library, the new database architecture, improved interfaces, and simplified software distribution, Dfam offers a collaborative platform for the TE research community. Collaborative efforts and increased datasets will be necessary to tackle problems such as those mentioned above: subfamily identification, library redundancy and fragmentation. We invite the TE research community to provide feedback on the challenges discussed here and to join us in these efforts to further Dfam development. Availability of data and materials The datasets generated during and/or analyzed during the current study are available at the Dfam portal: Software generated for this project is located in the Dfam consortium repository: 10. 9. CAS 82. 31. CAS 2013. 22. 5. 9. 33. 31. 1996. 8. 10. 5. 8. 91. 7. 19. 64. 7. 97. 414. 82. 71. 276. 77. 69. 109. 921. 80. 46. PubMed Pub20. 30. 1929. 3. 93. 301. 1. Genes Dev. 1996;10:755–61. 1406. 73. 8. 1283. 9416. 2017. p. 18–23. 1. 2939. FundingThis work is funded by NHGRI grant # U24 HG010136, and NHGRI grant # RO1 HG002939. Author informationAuthors and AffiliationsInstitute for Systems Biology, Seattle, WA, 98109, & Arian F. SmitUniversity of Montana, Missoula, MT, 59812, USATravis J. WheelerAuthorsJessica StorerView author publicationsYou can also search for this author in PubMed 3. x. AS developed the classification system and performed the transposon termini analysis. JS, AS curated Dfam families. JS, RH, and AS were major contributors in writing the manuscript. All authors read and approved the final manuscript. Corresponding authorsCorrespondence to Jessica Storer, or Arian F. Smit. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the Dfam database related to transposable elements and the classification scheme for genome annotation rather than the mapping of the entire human DNA sequence by the Human Genome Project.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Raghoebar, R. Schmelzeisen, W. Wagner, F. P. Koch (2011) Bone marrow concentrate and bovine bone mineral for sinus floor augmentation: a controlled, randomized, single-blinded clinical and histological trial - per-protocol analysis. A 17: 2187-2197. 152. Sauerbier, S. , A. Stricker, J. Kuschnierz, F. Buhler, T. Oshima, S. P. Xavier, R. Schmelzeisen, R. Gutwald (2010) In vivo comparison of hard tissue regeneration with human mesenchymal stem cells processed with either the method or the BMAC method. C Methods 16: 215-223. 153. Schmidt-Bleek, K. , H. Schell, J. Lienau, N. Schulz, P. Hoff, M. Pfaff, G. Schmidt, C. Martin, C. Perka, F. Buttgereit, H. D. Volk, G. Duda (2014) Initial immune reaction and angiogenesis in bone healing. J 8: 120-130. 154. Seamon, J. , X. Wang, F. Cui, T. Keller, A. S. Dighe, G. Balian, Q. Cui (2013) Adenoviral delivery of the VEGF and BMP-6 genes to rat mesenchymal stem cells potentiates osteogenesis. Res 2013: 737580. 155. Shao, J. , W. Zhang, T. Yang (2015) Using mesenchymal stem cells as a therapy for bone regeneration and repairing. 48: 62. 156. Simmons, C. A. , E. Alsberg, S. Hsiong, W. J. Kim, D. J. Mooney (2004) Dual growth factor delivery and controlled scaffold degradation enhance in vivo bone formation by transplanted bone marrow stromal cells. Bone 35: 562-569. 157. Smadja, D. M. , C. d'Audigier, C. L. Guerin, L. Mauge, B. Dizier, J. S. Silvestre, L. [SEP] Justify:

Output: The text supports the claim as it discusses various studies that involve the use of mesenchymal stem cells in processes related to bone regeneration and healing, such as the comparison of hard tissue regeneration with human mesenchymal stem cells and the potential of these cells in therapies for bone regeneration. This indicates that stem cells are indeed utilized in regenerative medicine for repairing damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: [34] Surgical stress associated with pediatric strabismus and vitreoretinal (VR) surgery has been reported. [56] Our hypothesis is retrobulbar dexmedetomidine, which is commonly used in China, could reduce the need of fentanyl and pain scores, meanwhile prolong the duration of analgesia. Thus, we administrated 1 μg/kg dexmedetomidine with retrobulbar block according to a previous study. [7] study was approved by the hospital's Ethics Committee. Written consents were obtained from the parents of the participating patients. Patients of of Anesthesiologists physical status I to II, age 2–7 years, who underwent elective VR surgery at our hospital, were selected for the study. All surgeries were performed vitrectomy without scleral buckling. Exclusion criteria include consent not obtained, upper airway infection, allergy to anesthetics, and eye tumors or infections. Sixty patients were randomized to receive general anesthesia plus retrobulbar dexmedetomidine (group RD) or retrobulbar block (group RB), or general anesthesia alone (group F). The randomization was performed in a 1:1:1 ratio using SPSS 25. 0 (IBM Inc. , ). A nurse, not involving in patient management, prepared all the anesthetics. The parent, investigator, and anesthesiologist were blinded to the group assignments. After induction, 1 mL of venous blood was withdrawn to test the baseline stress response biomarkers. An intravenous infusion of 2–4 mL/kg/h Ringer's lactate was maintained during the surgery. The patients were monitored by electrocardiography, pulse oximetry (SPO2), heart rate (HR), noninvasive blood pressure (BP), capnography (ETCO2), and bispectral index (BIS). General anesthesia was induced with propofol 3 mg/kg, rocuronium 0. 6 mg/kg, and remifentanil 3 μg/kg in all the three groups. A laryngeal mask airway (LMA) was inserted to secure the airway. Patients in group RD were administered retrobulbar block with 0. 5% ropivacaine 0. 1 mL/kg plus dexmedetomidine 1 μg/kg and group RB with 0. 5% ropivacaine 0. [SEP] Justify:

Output: The text contrasts the claim by discussing a specific surgical procedure (vitrectomy) and the associated anesthesia, indicating that despite advancements in techniques like retrobulbar dexmedetomidine, surgery is still required for certain medical conditions, particularly in pediatric cases. This reinforces that surgery remains necessary in specific scenarios, which opposes the assertion that nanotechnology eliminates the need for surgery in all cases.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: Extensive sequence-influenced DNA methylation polymorphism in the human genome access Published: 24 May 2010 Extensive sequence-influenced DNA methylation polymorphism in the human genome Asaf Hellman1 & Andrew Chess2,3 Epigenetics & Chromatin 0. 16% of SNPs [2], and another study suggested that 1. 5% of SNPs could affect local methylation [3]. Thus, the extent to which SNPs may direct methylation remains unclear. Other studies in humans have focused on an imprinted locus [4, 5] or examined CpG islands [6], and a recent study on F1 mice focused on regions preselected to have strain-specific differences in gene expression [7]. We report our analyses of DNA methylation at over 100,000 CpGs distributed throughout the genome, and our investigation into the dependence of DNA methylation on nearby sequence polymorphisms. Results and DiscussionTo explore the potential effect of polymorphisms on local DNA methylation, we performed numerous comparisons of monoallelic methylation patterns in pairs of related and unrelated individuals. Methylation of the two alleles was measured using a SNP mapping array (250 K array; ), with pre-digestion of the DNA with a cocktail of methylation-sensitive restriction endonucleases (MSREs) before PCR amplification of amplicons ranging in size from 100, to 1,100 bp (average 677 bp) [8] and subsequent detection of SNPs present on the amplicons. After all known MSRE site polymorphisms were filtered out, 110,883 amplicons were available for assessment of DNA methylation. As shown in Figure 1a, a heterozygous SNP present on an amplicon that has methylation present on only one of the two alleles will lead to a 'homozygous' call after MSRE treatment. Therefore, by looking for cases in which the genotype is heterozygous (in regular genomic DNA) and MSRE-pretreated DNA yields a homozygous call, amplicons with monoallelic methylation can be identified. Figure 1Genome-scale assessment of allelic DNA methylation patterns. (a) Representative amplicon (defined by sites). The 'B' allele has a methylated CpG (red filled oval) within a methylation-sensitive restriction enzyme (MSRE). [SEP] Justify:

Output: The text does not support or refute the claim about the Human Genome Project mapping the entire sequence of human DNA. Instead, it discusses specific studies related to DNA methylation polymorphisms and does not provide any information about the Human Genome Project or its contributions to mapping DNA.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Dal Cortivo, P. Gaussem, J. Emmerich (2012) Angiogenic potential of BM MSCs derived from patients with critical leg ischemia. Transplant 47: 997-1000. 158. (2009) Influence of adult mesenchymal stem cells on in vitro vascular formation. A 15: 1751-1761. 159. Stroncek, J. D. , W. M. Reichert (2008) Overview of wound healing in different tissue types; in Reichert WM (ed): Implants: Strategies for Contending with the in vivo Environment. . 160. Sun, H. , Z. Qu, Y. Guo, G. Zang, B. Yang (2007) In vitro and in vivo effects of rat kidney vascular endothelial cells on osteogenesis of rat bone marrow mesenchymal stem cells growing on polylactide-glycoli acid (PLGA) scaffolds. Online 6: 41. 161. Tao, J. , Y. Sun, Q. G. Wang, C. W. Liu (2009) Induced endothelial cells enhance osteogenesis and vascularization of mesenchymal stem cells. Organs 190: 185-193. 162. Tatullo, M. , G. Falisi, M. Amantea, C. Rastelli, F. Paduano, M. Marrelli (2015a) Dental pulp stem cells and human periapical cysts mesenchymal stem cells in bone tissue regeneration: comparison of basal and osteogenic differentiated gene expression of a newly discovered mesenchymal stem cell lineage. J 29: 713-718. 163. Tatullo, M. , M. Marrelli, G. Falisi, C. Rastelli, F. Palmieri, M. Gargari, B. Zavan, F. Paduano, V. Benagiano (2016) Mechanical influence of tissue culture plates and extracellular matrix on mesenchymal stem cell behavior: a topical review. 29: 3-8. 164. Tatullo, M. , M. Marrelli, F. Paduano (2015b) The regenerative medicine in oral and maxillofacial surgery: the most important innovations in the clinical application of mesenchymal stem cells. [SEP] Justify:

Output: The text provides a series of references that discuss the application of mesenchymal stem cells (MSCs) in various regenerative medicine contexts, specifically highlighting their roles in tissue regeneration and repair. For instance, it mentions dental pulp stem cells in bone tissue regeneration and adult mesenchymal stem cells influencing wound healing, which supports the claim that stem cells are used in regenerative medicine to repair damaged tissues.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: 1 mL/kg only. A blunt 5-cm needle was inserted at the inferolateral margin of the orbit along the orbital floor until its tip was posterior to the eye at the apex of the orbit, and the assigned anesthetics were injected. Anesthesia was maintained with propofol (guided by the BIS value, with dosages set to maintain a target BIS value of 40–60) and remifentanil (0. 1 μg/kg/min). When there were signs of inadequate anesthesia (15% increase of baseline HR or BP), a bolus of fentanyl 1 μg/kg was given to all three groups. After the surgical procedures, propofol and remifentanil infusions were stopped. Residual neuromuscular block was reversed with neostigmine 50 μg/kg and atropine 0. 01 mg/kg. LMA was removed after ensuring respiratory sufficiency. Postoperative neuroendocrine response biomarkers were tested with 1 mL of venous blood. All the patients were monitored for 2 h in postanesthesia care unit (PACU). Patients with Aldrete recovery score ≥9 were discharged to the ward. The time intervals between propofol/remifentanil discontinuation and LMA removal or eye opening in response to verbal stimuli were recorded. The primary endpoint was the postoperative pain score (Faces, Legs, Activity, Cry and Consolability – FLACC), which was assessed by an observer blinded to the study immediately after LMA removal (FLACC scores ranging from 0 to 10, with 10 representing the most painful experience). Pain score was recorded at 0. 5, 1, 2, 4, 6, 12, and 24 h after surgery. When the pain score was >5, rescue analgesic was administered using fentanyl 0. 5 μg/kg intravenously in the PACU or oral acetaminophen 10 mg/kg in the ward. The secondary endpoints include remifentanil and propofol consumption, the incidence of emergence agitation, and sedation level. HR and mean arterial BP (MAP) were recorded at T0 (baseline), T1 (10 min after retrobulbar block), T2 (before incision), T3 (incision), T4 (intraocular exploration), T5 (immediately after LMA removal), and T6 (upon arriving PACU). [SEP] Justify:

Output: The text contrasts the claim by detailing a surgical procedure that involves anesthesia and monitoring during postoperative care. The description provides insights into surgical practices and pain management, indicating that surgery is still necessary in certain medical cases, which contradicts the assertion that nanotechnology eliminates the need for surgery entirely.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: The 'A' allele is unmethylated at the CpG within the MSRE site, and is therefore digested upon the treatment with the MSRE cocktail that is performed before NSP I digestion ligation of adaptors, PCR amplification and hybridization to the Affymetrix 250 K single nucleotide polymorphism (SNP) mapping array. Only the 'B' allele yields a PCR product that can hybridize on the SNP-detecting array. (b) Of the 8,346 SNPs heterozygous in two genetically unrelated individuals (GM10848 and GM10849), epigenotypes are shown, with the numbers of amplicons with monoallelic methylation in bold. The lower part of the panel shows the number of amplicons displaying methylation overlap and the number displaying opposite overlap. value was calculated using the χ2 test; the null hypothesis was equality in the numbers of overlapping SNPs with the opposite or same epigenotype. (c) The observed methylation overlap frequencies in excess of the levels expected by chance are presented for various types of comparisons of pairs of individuals. Full size imageThe first type of analysis measured the frequency of monoallelic methylation per person, for 13 individuals of different ages and gender. Focusing on amplicons containing a heterozygous SNP and at least one MSRE site, we determined that an average of 20% of the assessable amplicons had monoallelic methylation see Additional file 1. We examined the distribution of these cases of monoallelic methylation across the genome and found no evidence for clustering, either in individual chromosomes see Additional file 2 or in 1 Mb windows along the genome. Locus-specific validation was performed using bisulfite sequencing of 25 methylation sites see Additional file 3. What these analyses showed was that there were differences in methylation, detectable in amplicons heterozygous for a common SNP. Although the presence of the SNP was essential to our ability to observe monoallelic methylation, this method could not determine whether the observed monoallelic methylation was influenced by the SNPs or by other sequence differences in linkage disequilibrium (LD) with the SNPs. Assessing the effect of SNPs on local DNA methylation in unrelated individualsWe next analyzed the extent to which monoallelic methylation across the genome was influenced by local sequence differences between the two alleles. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses specific findings related to allele methylation and SNP analysis, rather than providing information about the Human Genome Project or its accomplishment of mapping the entire sequence of human DNA.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: 12: 72-77. 165. Tatullo, M. , M. Marrelli, K. M. Shakesheff, L. J. White (2015c) Dental pulp stem cells: function, isolation and applications in regenerative medicine. J 9: 1205-1216. 166. Tavakolinejad, S. , A. Ebrahimzadeh Bidskan, H. Ashraf, D. (2014) A glance at methods for cleft palate repair. J 16: e15393. 167. Terella, A. , P. Mariner, N. Brown, K. Anseth, S. O. Streubel (2010) Repair of a calvarial defect with biofactor and stem cell-embedded polyethylene glycol scaffold. 12: 166-171. 168. Thibault, R. A. , L. Scott Baggett, A. G. Mikos, F. K. Kasper (2010) Osteogenic differentiation of mesenchymal stem cells on pregenerated extracellular matrix scaffolds in the absence of osteogenic cell culture supplements. A 16: 431-440. 169. Toupadakis, C. A. , A. . (2012) Long-term administration of AMD3100, an antagonist of SDF-1/CXCR4 signaling, alters fracture repair. J 30: 1853-1859. 170. Trautmann, F. , M. Cojoc, I. Kurth, N. Melin, L. C. Bouchez, A. Dubrovska, C. Peitzsch (2014) CXCR4 as biomarker for radioresistant cancer stem cells. 90: 687-699. 171. Umebayashi, M. , Y. Sumita, Y. Kawai, S. Watanabe, I. Asahina (2015) Gene-activated matrix comprised of atelocollagen and plasmid DNA encoding BMP4 or Runx2 promotes rat cranial bone augmentation. Access 4: 164-174. 172. Wang, Z. , H. Song, H. Deng, J. Chen, L. Zhang, Y. [SEP] Justify:

Output: The text corroborates the claim by discussing 'dental pulp stem cells' and their applications in 'regenerative medicine,' as well as various studies related to stem cells and their role in repairing tissues and enhancing healing processes. This indicates that stem cells are actively being researched and utilized in the context of regenerative medicine.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: Oculocardiac reflex was observed in one patient in group F, but was resolved by stopping the surgical stimulus; oculocardiac reflex did not occur in any patients in groups RD and RB. Retrobulbar block–related complications did not occur in any patient. Discussion VR surgery, which is the most painful ophthalmologic procedure, involves extensive intraocular and extraocular manipulation. [8] Research has demonstrated that regional anesthesia in children is comparable to that in adults in terms of safety. [9] Dexmedetomidine is a highly selective α2 adrenoceptor agonist with sedative, anxiolytic, sympatholytic, and analgesic-sparing effects and has more stable respiratory and hemodynamic profiles compared with remifentanil. [10] This single-center randomized double-blind clinical trial in children showed that retrobulbar ropivacaine with dexmedetomidine eliminated the need for intraoperative fentanyl in pediatric VR surgery, and consequently, eliminated the respiratory depression associated with opioid consumption. Retrobulbar block with ropivacaine is a common, safe, and effective form of regional anesthesia; however, this technique may not entirely eliminate the need for intraoperative fentanyl. The retrobulbar dexmedetomidine used in this study provided better relief of postoperative pain and hemodynamic and neuroendocrine response than retrobulbar ropivacaine or general anesthesia itself. However, these beneficial effects of dexmedetomidine were accompanied by prolonged time to emergence from anesthesia and increased length of stay in the PACU. In our study, seven patients in group F developed respiratory depression after LMA removal in the operating room. This can be mainly attributed to two factors: (1) intraoperative rescue fentanyl was not required with preemptive retrobulbar dexmedetomidine, whereas all children in group F required fentanyl. Since all opioids carry the risk of respiratory depression,[1] this might have been a possible reason. (2) Dexmedetomidine has the unique characteristic of providing analgesia without causing respiratory depression[11] and provides a stable respiratory profile even in children with severe preoperative airway impairment. [12] In this study, preemptive retrobulbar dexmedetomidine was seen to provide effective analgesia, as shown by the fact that there was no need for intraoperative or postoperative rescue fentanyl. [SEP] Justify:

Output: The text contrasts the claim by discussing the use of dexmedetomidine in providing effective analgesia during surgeries, suggesting that while certain advancements like regional anesthesia can mitigate the need for opioids, they do not eliminate the need for surgery itself. It states that the retrobulbar dexmedetomidine provided better pain relief but did not completely eradicate the necessity for intraoperative procedures, indicating that surgery is still required in these cases.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: One way to examine the potential effects of sequence differences on allele-specific methylation involved the examination of informative amplicons in pairs of individuals; the SNP within each informative amplicon had to be heterozygous in each of two unrelated individuals and the amplicon had to contain at least one MSRE site. The null hypothesis would be that sequence differences have little or no effect on allelic methylation patterns. Under the null hypothesis, when examining informative amplicons that are heterozygous in each of two unrelated individuals, the frequency of amplicons displaying monoallelic methylation on the same alleles in both individuals (methylation overlap) would be equal to the frequency of amplicons displaying monoallelic methylation on different alleles (opposite overlap). For example, consider the pair of unrelated individuals shown in Figure 1b. Of 8,346 informative SNPs, 295 (3. 5%) had methylation overlap and 52 (0. 6%) had opposite overlap (P < 10-38), thus the ratio of methylation overlap to opposite overlap is 5. 7 for this pair. When DNA methylation was analyzed in 14 pairs of genetically unrelated individuals, amplicons showing methylation overlap were, on average 5. 2-fold more frequent than amplicons showing opposite overlap (range 2. 5-fold to 9. 3-fold, with P values ranging from 10-7 to 10-66; Table 1). This bias can be explained if many of the assessed regions are subject to allelic methylation that is influenced by the sequence differences between the two alleles. Table 1 Analyses of pairs of unrelated individualsFull size tableAnother way to examine the data from pairs of unrelated individuals is to examine the observed frequency of methylation overlap compared with the frequency that would be expected by chance (given the extent of monoallelic methylation in each of the two individuals who make up the pair). Under the null hypothesis - if monoallelic methylation were not influenced by sequence differences - the frequency of methylation overlap would be expected to equal the product of the frequencies of monoallelic methylation of the 'A' alleles in each individual, plus the same product for the 'B' alleles. For the example presented in Figure 1b, this would translate as (630/8346) × (545/8346) + (493/8346) × (496/8346) = 0. 8% expected. [SEP] Justify:

Output: The text does not address the claim about the Human Genome Project or its mapping of human DNA. Instead, it discusses the examination of methylation patterns in unrelated individuals and does not provide relevant information about the Human Genome Project.


Input: Task: corroborate the claim using the given text. Claim: Stem cells are used in regenerative medicine to repair damaged tissues. [SEP] Text: Yim, E. K. , E. M. Darling, K. Kulangara, F. Guilak, K. W. Leong (2010) Nanotopography-induced changes in focal adhesions, cytoskeletal organization, and mechanical properties of human mesenchymal stem cells. Biomaterials 31: 1299-1306. 183. Young, H. E. , L. Hyer, A. C. Black, J. S. Robinson (2014) Adult stem cells: from bench-top to bedside; in Liu, Q. (ed): Tissue Regeneration: Where Nano-Biology. Singapore, World Scientific, pp 1-59. 184. Zeng, Y. , X. Qu, H. Li, S. Huang, S. Wang, Q. Xu, R. Lin, Q. Han, J. Li, R. C. Zhao (2012) MicroRNA-100 regulates osteogenic differentiation of human adipose-derived mesenchymal stem cells by targeting BMPR2. FEBS Lett 586: 2375-2381. 185. Zhang, Y. , N. Cheng, R. Miron, B. Shi, X. Cheng (2012) Delivery of PDGF-B and BMP-7 by mesoporous bioglass/silk fibrin scaffolds for the repair of osteoporotic defects. Biomaterials 33: 6698-6708. 186. Zhang, Y. , L. Xia, D. Zhai, M. Shi, Y. Luo, C. Feng, B. Fang, J. Yin, J. Chang, C. Wu (2015) Mesoporous bioactive glass nanolayer-functionalized 3D-printed scaffolds for accelerating osteogenesis and angiogenesis. Nanoscale 7: 19207-19221. 187. Zhao, Q. , H. Ren, Z. Han (2016) Mesenchymal stem cells: immunomodulatory capability and clinical potential in immune diseases. J 2: 3-20. 188. Zomorodian, E. , M. (2012) Mesenchymal stem cells as a potent cell source for bone regeneration. Int 2012: 9. 189. [SEP] Justify:

Output: The text corroborates the claim by discussing various studies and advancements related to stem cells, specifically highlighting their potential use in tissue regeneration and repair. References to publications like 'Adult stem cells: from bench-top to bedside' directly indicate the application of stem cells in regenerative medicine.


Input: Task: contrast the claim using the given text. Claim: Nanotechnology eliminates the need for surgery in all medical cases. [SEP] Text: The pain scores immediately after surgery were significantly lower in group RD/RB than group F. At 6-h postoperatively, pain scores only in group RD were lower than that in group F, which may be due to the following reasons. The α2 adrenergic receptor agonists have been shown to prolong the duration of action of ropivacaine and improve the quality of analgesia by causing local vasoconstriction and increasing the potassium conductance in Aδ and C fibers. [1314] This is beneficial in longer duration surgery. These drugs may also potentiate the action of local anesthetics by entering the central nervous system either through systemic absorption or by diffusion into the cerebrospinal fluid through the sheath of the optic nerve. Dexmedetomidine has been used as an adjunct to spinal anesthesia without apparent toxicity. [1516] Previous studies indicate that dexmedetomidine protects the spinal cord from lidocaine-induced spinal neurotoxicity by regulating protein kinase expression and glutamate release. [17] Future studies are warranted to support or dispel concerns regarding neurotoxicity of retrobulbar dexmedetomidine. The incidence of emergence agitation after ophthalmologic surgery is particularly high owing to visual disturbances. In this study, retrobulbar dexmedetomidine decreased the incidence of emergence agitation, which agrees with previous studies. [1819] Our data indicated that dexmedetomidine prolonged the time to eyeopening, but did not prolong the LMA removal time. This is due to dexmedetomidine's sedation effect. The results of our study indicate that dexmedetomidine can be used as an adjunct to general anesthesia to suppress stress responses. VR surgery is categorized as a minor surgery, but it is one of the most painful ophthalmologic procedures. There was a steep increase in the postoperative IL-2, TNF-α, and IL-6 in group F, and these levels differ significantly among the groups. We demonstrated that retrobulbar block and dexmedetomidine could alleviate IL-2, TNF-α, and IL-6 release, which was also reported in previous studies. [20] In this study, hemodynamic variables were blunted during the surgical procedures in groups RD and RB. HR was significantly slower in group RD relative to group F during most of the intraoperative period. [SEP] Justify:

Output: The text contrasts the claim by discussing the context of surgery, specifically highlighting the use of dexmedetomidine as an adjunct to anesthesia for pain management during surgery. This implies that surgery is still a necessary component in medical care, even if enhanced analgesic techniques are utilized. The mention of postoperative pain management and neurotoxicity concerns indicates that surgery remains a critical part of current medical practices and is not eliminated by nanotechnology.


Input: Task: pass the claim using the given text. Claim: The Human Genome Project mapped the entire sequence of human DNA. [SEP] Text: However, the observed methylation overlap for this pair was 3. 5%, thus giving an excess (over that expected by chance) methylation overlap of 2. 7%. Examining methylation overlap in the 14 pairs of individuals, the average frequency of methylation overlap in excess of that expected by chance was 2. 2% (Table 1; Figure 1c). Moreover, because different amplicons are informative in different pairs of individuals, the total fraction of amplicons (across the genome) that are associated with differences in the propensity for local methylation must be substantially higher (see below). Because these individuals were unrelated and therefore only shared the SNPs measured by the array (and local common sequence polymorphisms in LD with these SNPs), these analyses highlighted a role for sequence polymorphisms common to the whole population in marking local differences in methylation propensity. Note that we also observed significant methylation overlap in pairwise comparisons of a variety of (freshly isolated) non-hematopoietic tissues from unrelated individuals see Additional file 4, suggesting that these allelic methylation patterns are present from early in development. Parental imprinting [9] was shown not to be a major contributor to the observed methylation overlap (see Additional files 5 and 6). Increased similarity in allelic methylation patterns in related individualsUp to this point, the analyses of unrelated individuals presented suggested an influence of common allelic sequence differences on local methylation. This led to the question of whether the increased sequence identity in related individuals would lead to increased similarity in monoallelic methylation patterns. Analyzing siblings allowed us to assess if genetically related individuals had more similarity in methylation patterns than unrelated individuals. At any given portion of the genome, two siblings can share zero, one or two of their parental chromosomes identical by descent (IBD). We defined all of these regions for each of 10 possible sibling pairs using the genome-wide genotyping data. Regions at which two siblings share no chromosomes IBD are only as similar in sequence as unrelated individuals from a similar genetic background. At the other end of the spectrum, regions in which two siblings share two chromosomes IBD are expected to have identical sequences (except for infrequent de novo mutations). We restricted the analyses to 5,660 amplicons that were homozygous in both parents and heterozygous in each of the five siblings. [SEP] Justify:

Output: The text discusses methylation overlap and genetic similarities among individuals, focusing on allelic methylation patterns and sequence polymorphisms. It does not provide any information about the Human Genome Project or its activities related to mapping the entire sequence of human DNA, rendering it irrelevant to the claim.