Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: MainGiven the disappointing results obtained by the Human Genetics community through systematic linkage screenings of the genome, Risch and Merinkangas1argued that ‘the future of the genetics of complex diseases is likely to require large scale testing by association studies’. If linkage studies have low power to detect common variants with small odds ratios (OR), they are also doing a poor job at detecting very frequent variants with high genotypic or allelic ORs, a situation where association tests might perform better. A good illustration of this point is provided by the VNTR flanking the insulin gene. The association between the locus and type I diabetes is easily detected, and the risk allele is frequent (about 70% in the general population) with an allelic OR around 3. 9. 2 The distribution of alleles shared identical by descent (IBD) in sib-pairs, however, is very close to its null expectation and linkage is very difficult to detect. Even on large sib-pair samples, discordant results have been described. 3, 4 An additional interesting feature of association studies is to allow a much more precise location of risk factors. Whereas the precision of location provided by linkage studies is sized in cM, it is sized in kb or even bp for association studies. Technological developments have rapidly made large-scale association studies a reality. The HapMap project (www. hapmap. org) launched by an international consortium by the end of 2002 publicly released the first data in 2005. The first genome-wide association studies have been published recently. 5, 6, 7 Large-scale association studies using maps of anonymous and frequent SNPs are presented as the new tool that will accelerate the discovery of genes related to common diseases' (HapMap Press Release, 7 February 2005). In the present paper, we would like to debate around two questions that are central to the discussion on the power of genome-wide association studies: will most genetic variants involved in complex diseases be detectable by systematic association testing and, in the best-case scenario where a signal is observed, what will be its contribution to the understanding of the pathological process? Will most genetic variants involved in complex diseases be detectable by systematic association testing? The standard strategy for systematic association testing is to perform allelic tests using SNPs tagging common variants and/or haplotypes to limit both the multiple testing correction and the genotyping cost. [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations of current genetic studies, particularly the difficulties in detecting genetic variants associated with complex diseases. It suggests that simply altering the human genome may not lead to the eradication of diseases, as evidenced by the challenges faced in identifying risk factors through genetic studies. The text highlights that while large-scale association studies are underway, there remains uncertainty about the detectability of most genetic variants involved in complex diseases, thus challenging the assertion that altering the genome can eradicate all diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: 3. 21. Ik meen dat alleen aanwijzingen die zich voordoen vóór de peildatum en die niet bekend zijn in de markt een indicatie kunnen opleveren dat de waarde van de aandelen niet overeenkomt met de biedprijs. De systematiek van de peildatum dwingt tot uitsluiting van aanwijzingen die zich voordoen ná de peildatum. De reden daarvoor is dat de peildatum het moment is waarop het aan de aandelen verbonden risico in verband met waardeverschuivingen overgaat op de bieder. Of zich daarna nog omstandigheden voordoen die de waarde van de onderneming beïnvloeden, komt voor rekening van de bieder en is daarom niet van belang bij de vraag wat een billijke prijs voor de aandelen is. Daarnaast geldt in de bedrijfseconomie dat de waarde van een vermogensbestanddeel gelijk is aan de netto contante waarde van de op de peildatum verwachte toekomstige kasstromen die uit dat aandeel voortvloeien. Centraal staan daarom de verwachtingen over toekomstige nettokasstromen en de opportuniteitskosten van het aandeel op de peildatum en niet verwachtingen die daarna ontstaan. 61x K. W. M. Scheepers, Waarderen bij uitkoopprocedures na Unit4 en DIM Vastgoed, in: J. Huizink (red. ), Waardering van aandelen na Unit4, Deventer: 2016, p. 33-35. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses financial valuation principles and does not mention any cultures or legends related to creatures like Bigfoot or the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Natural selection drives evolution through differential survival. [SEP] Text: To control for the expression level of adjacent genes, enhancers were divided into three groups depending on the expression level of the adjacent gene, < 200, 200-400, and ≥ 400. D and D/d4 were then compared for the enhancers of the four tissues within a given group. After such controls, embryonic heart enhancers still had the highest D (Figure 5A) and D/d4 (Figure 5B) values. These results suggest that the relatively low pleiotropy of embryonic heart enhancers, and their physical proximity to highly expressed genes, only partially accounts for their high rate of evolution and biases in selection. Figure 5Pleiotropy and expression levels of adjacent genes do not explain enhancer evolutionary rate variations. Comparisons of D (A) and D/d4 (B) for mouse forebrain (FB), midbrain (MB), limb (LM), and heart (HT) enhancers after controlling for the enhancer pleiotropy and the expression level of adjacent genes. Only specific enhancers are included in the analysis. The values of upper quartile, median, and lower quartile are indicated in each box, whereas the bars outside the box indicate semi-quartile ranges. Pairwise comparisons showing significant difference in D or D/d4 are connected with gray lines (***P≦0. 001 by Mann-test). Full size imageConclusionsThe rapid evolution rates of mouse embryonic heart enhancers can potentially be explained by elevated rates of mutation and/or changes in the direction or intensity of natural selection. In the present study, neutral sites of the neighboring gene were used as 11. 5 heart enhancers cannot be explained by potential confounding factors examined in the present study, and therefore, may be directly associated with embryonic tissue factors. The identification and understanding of regulatory DNAs in the mammalian genome is a major goal in the post-genomic era. This study employed a simple, yet effective, method to explore the role of natural selection on the evolution of non-coding sequences. Although the present study indicates that the rapid evolution of heart enhancers is likely to have been the result of a selective force associated with the type of embryonic tissue involved, the underlying causes for the relaxed selective constraint, or the higher frequency/intensity of positive selection, remain to be discovered. [SEP] Justify:

Output: The text corroborates the claim by discussing how the rapid evolution rates of mouse embryonic heart enhancers can be explained by 'elevated rates of mutation and/or changes in the direction or intensity of natural selection.' This suggests that natural selection is indeed a driving force in evolution, particularly in the context of embryonic tissue factors affecting enhancer evolution.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: By construction, this approach has been recognized to have low power to detect the effects of rare variants, which are poorly tagged by common SNPs. Relatively rare variants are known to contribute to a variety of common, complex diseases. In Crohn's disease, the three risk alleles in the NOD2 gene have frequencies smaller than 5% in populations of European descent. 8, 9 Population genetics modelling of the expected genetic variation at disease susceptibility loci has also suggested that rare variants may play an important role in complex disease susceptibility. 10, 11 When selection is weak, as seems likely for many complex disease mutations, genetic drift becomes important, and the total frequency of susceptibility mutations is expected to vary widely among loci. In contrast, almost all common SNP-based variation as well as other SNP-correlated common variants (including common deletions12, 13) can be interrogated either directly or by surrogate SNPs or haplotypes. The issue is whether we will be able to design studies powerful enough to detect them. A number of variants with both high frequency and sizeable effects have been identified, including ApoE4 in Alzheimer's disease and cardio-vascular diseases or HLA factors in autoimmune diseases. Variants with similar sizeable effects may still have to be discovered. Some may have escaped identification by linkage studies because of a very high susceptibility allele frequency. Others may be located in regions already broadly detected by linkage as in the recent whole genome association successes. 6, 7Aside from these large effect variants, common susceptibility alleles or haplotypes with quite modest ORs – in the range of 1. 15–1. 5, with the majority in the range of 1. 15–1. 2514 have been shown to have reproducible effects (via meta-analysis) on various phenotypes. These variants with low marginal risks may, in fact, have strong effects on disease, but restricted to particular genetic background or environment. Indeed, complex models of interaction between genes, sex and environment have been extensively described in animal models for various complex traits. 15 Identifications of these variants – that may be far from exceptions in humans – may thus constitute important steps in the understanding of the physiopathology of the diseases, but very challenging ones. Finally, to control for the multiple testing in genome-wide context, effects of SNPs may only be tested at the allelic6, 7 or simple haplotypic level (haplotypes made of 2 or 3 markers). [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations of genome alteration in regards to complex diseases. It highlights the importance of rare variants and the challenges of detecting them, indicating that not all diseases can be fully addressed through changes in the human genome. Furthermore, it emphasizes that the effect of many genetic variants can vary based on genetic background and environmental factors, suggesting that the simplistic view of eradicating all diseases through genomic alteration is overly optimistic.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Het gebruiken van een historische peildatum en de manier waarop vermogensbestanddelen gewaardeerd worden, maken dat alleen aanwijzingen die zich voordeden vóór de datum van de betaalbaarstelling onder het bod invloed kunnen hebben op de billijke prijs. 62x (OK) 7 juli 2015, ECLI:NL:GHAMS:2015:2775, ARO 2015/178 (Unit4), r. o. 3. 17. De OK kiest in beginsel voor een historische peildatum. Dit standpunt is later bevestigd in onder meer (OK) 14 juli 2015, ECLI:NL:GHAMS:2015:2897, ARO 2015/200 (Nutreco) (voor art. 2:92a BW) en (OK) 14 juli 2015, ECLI:NL:GHAMS:2015:2914, ARO 2015/204 (Exact Holding) (voor art. 2:359c BW); en Bulten bepleitten deze systematiek al in 2014: M. W. & C. D. J. Bulten, Kroniek uitkoop en geschillenregeling 2014, in: M. Holtzer, A. F. J. A. Leijten & D. J. Oranje, Geschriften vanwege de Litigation 2014-2015 (VDHI nr. 128), Deventer: 2015, p. 148-153. In de inleiding noemde ik dat er één arrest is waarin – ambtshalve63x kan de OK ambtshalve afwijken van het prijsvermoeden en zelfstandig een uitkoopprijs vaststellen wanneer de omstandigheden daartoe nopen, zie Salemink 2014, p. 232. – is afgeweken van het billijke prijsvermoeden. In de Mediq-casus werd een openbaar bod gedaan door AI Garden B. V. [SEP] Justify:

Output: The text is irrelevant to the claim, as it discusses legal matters related to valuation and historical dates, rather than cultural legends or mythical creatures like Bigfoot and the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Natural selection drives evolution through differential survival. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Natural selection drives chemical resistance of Datura stramonium All reviews of published 2023. Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the 2016. The first revision was submitted on March 10th, 2016 and was reviewed by 2 reviewers and the Academic Editor. A further revision was submitted on March 14th, 2016 and was reviewed by the Academic Editor. The 2016. Version 0. 3 (accepted) Marion Röder · Mar 15, 2016 · to a very good manuscript. 0. 3 (PDF) Download author's response letter - submitted Mar 14, 2016 Version 0. 2 Marion Röder · Mar 13, 2016 · Both reviewers agree that the manuscript was significantly improved. There are remaining minor concerns about typos in the manuscript. Please, review your manuscript carefully for typing errors, before it can finally be accepted. Reviewer 1 · Mar 11, 2016 Basic reporting Very good. The initial version was good and this version is even better. Experimental design Good. I can see the argument for changing the statistical analyses and think that the authors did a good job on those reanalyses. Validity of the findings The results seem to be carefully interpreted. Additional comments The manuscript could use one more reading for typos, for example: line 234: length, not lenght line 578: This points that. . . " A word seems to be missing line: 705: predator, add s Cite this review as (2016) #1 of "Natural selection drives chemical resistance of Datura stramonium (v0. 2)". PeerJ · Mar 10, 2016 Basic reporting Experimental design Validity of the findings Additional comments The manuscript is greatly improved. In my opinion this 0. 2)". PeerJ 0. 2 (PDF) Download author's response letter - submitted Mar 10, 2016 Version 0. 1 (original submission) Marion Röder · Jan 22, 2016 · Both reviewers agree that the study is valuable and performed well. Both have some minor comments regarding mainly formal things, which should be easy to comply. Please, also take in consideration the attached annotated manuscript. [SEP] Justify:

Output: The text corroborates the claim by stating that 'Natural selection drives chemical resistance of Datura stramonium'. This implies that natural selection is indeed a mechanism that leads to changes in populations, hence driving evolution through differential survival based on chemical resistance.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: But interaction between alleles or between distant SNPs within a susceptibility gene may be poorly detected at the allele level even in the presence of non-negligible effects at the genotype/haplotype level. Whether we will be able to power studies to detect common risk alleles with OR<1. 25 for all diseases is a critical issue. Apart from the challenge to collect huge samples without compromising on the quality of phenotypes, the crucial issue is whether human samples of sufficient sizes with homogeneous allele frequencies and pattern of linkage disequilibrium (LD) do exist. For some diseases, the inter-population variability may be too large to allow the recruitment of samples not subject to population stratification and large enough to detect variants with small effects. Similarly, once the variant is detected in a first study, it might be difficult to obtain samples to perform replication studies. First, these samples will need to be as large or even larger16 and, second, the difference in both variant frequencies and LD pattern among populations may make the signal undetectable in other populations. The difficulty of replication is well illustrated in the recent work of Reich et al. 17 on multiple sclerosis, (MS) where an association on chromosome 1 in African-Americans is not replicated in another sample of Afro-Caribbeans. Consequently, it is not possible to decide whether the association described is driven by a causal variant or whether it is just another false positive result. Altogether, we believe that these different elements invite cautiousness regarding the ability of genome-wide association studies to detect most genetic variants involved in complex diseases. In the best-case scenario where a signal is observed, what will be its contribution to the understanding of the pathological process? The main motivation behind looking for genetic risk factors for complex diseases is to get a better insight into the pathological process of the diseases. However, to go from an association signal to a deeper knowledge on the causal variants and their effect measurements is not that simple. The study of the HLA component in auto-immune diseases well illustrates the caveats encountered. If the association between type I diabetes (IDDM) and the HLA class II regions has been known for more than 20 years, the causal variants of the region have still to be identified. [SEP] Justify:

Output: The text contrasts the claim by highlighting the complexities and challenges associated with genomic studies and the identification of genetic risk factors for diseases. It points out issues such as the difficulty of detecting genetic variants, the need for large homogenous samples, and the variability across populations. The discussion emphasizes that while associations can be found, moving from these associations to understanding the underlying causal mechanisms is not straightforward, indicating that simply altering the human genome may not lead to the eradication of all diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: op de aandelen Mediq N. V. De biedprijs bedroeg EUR 14 en er was voldaan aan het 90%-criterium. 64x (OK) 11 maart 2014, ECLI:NL:GHAMS:2014:785 (Mediq II). Ter ondersteuning van de gevorderde uitkoopprijs, die gelijk was aan de biedprijs, heeft de bieder een assurancerapport overlegd. Uit het eindarrest blijkt dat de OK op basis van een nieuwe deskundigenverklaring afwijkt van het billijke prijsvermoeden omdat de waarde van de onderneming is gestegen in het jaar nadat de uitkoopprocedure aanhangig is gemaakt. 65x (OK) 13 mei 2014, ECLI:NL:GHAMS:2014:1976 (Mediq III), r. o. 2. 4. Veranderde marktomstandigheden na afloop van het bod rechtvaardigen een hogere prijs. De waarde van de aandelen steeg in de uitkoopprocedure van EUR 14 naar EUR 17. 66x (OK) 13 mei 2014, ECLI:NL:GHAMS:2014:1976 (Mediq III), r. o. 2. 3. De oplettende lezer ziet dat de veranderende marktomstandigheden waardoor de waarde van de aandelen steeg, zich in deze casus voordeden na de datum van de betaalbaarstelling onder het bod. Doordat de OK is omgegaan in het Unit4-arrest kunnen omstandigheden die zich voordoen na de datum van betaalbaarstelling onder het bod – zoals de veranderende marktomstandigheden uit de Mediq-casus – niet meer noodzaken tot een aanpassing van de billijke prijs. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses financial transactions and market conditions related to Mediq N. V. and does not mention any legends, folklore, or mythical creatures.


Input: Task: corroborate the claim using the given text. Claim: Natural selection drives evolution through differential survival. [SEP] Text: In addition to this reviewer 2 has suggestions about alternative or additional forms of statistical analysis. I let it for the decision of the authors if they want to pick up these suggestions. If they do not want to change their analysis, please give some comments about this decision. Download annotated manuscript Reviewer 1 · Jan 16, 2016 Basic reporting This is an excellent study. The questions are clear and the analyses are appropriate. and Figures need some clarifications to help readers. Table 1: add sample sizes Table 2: In the table caption, identify T as the test statistical and expand the acronym AIC and and briefly explain how it is used here. Most readers will know, but everything in a table should be briefly identified in table captions. Figure 2: Briefly explain in the table caption the meaning of infestation intensity so that readers can understand the scale on the Y-axis without going back to the Methods. Figures 3 and 4: Give correlation values and p-values on the figures so that readers can assess the lines that are shown Figure 4: Indicate whether the error bars are standard errors, confidence limits, or something else. The manuscript should be proof-read for a few remaining typographical errors (e. g. , unknow rather than unknown in one place; a missing "to" on line 289). I do not know if "All appropriate raw data have been made available. . . " Experimental design The methods are clearly described and the statistical analyses are appropriate. There are multiple ways of analyzing results such as these, but the authors have taken a reasonable approach. Validity of the findings The results are convincing and suggest strong, geographically variable, and potentially reciprocal, selection on these interacting species. This study appears to have been carefully done, carefully interpreted, and not over-interpreted. The conclusions do not go beyond the results. This is a very good paper, requiring considerable field and laboratory work. It is among the few studies have have assessed selection differentials among potentially coevolving species in many populations. The results suggest ongoing selection on the species and potentially ongoing reciprocal selection in some localities. Additional comments This is a nicely designed and analyzed study, suggesting the potential of a geographic mosaic of coevolution between these species. Cite this review as (2016) #1 of "Natural selection drives chemical resistance of Datura stramonium (v0. 1)". [SEP] Justify:

Output: The text corroborates the claim by stating that the results suggest strong, geographically variable, and potentially reciprocal selection on these interacting species. It discusses the ongoing selection on species, which aligns with the concept of natural selection influencing evolutionary processes through differential survival.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: A particular amino acid (non-‘Asp57’) of the DQβ chain was suspected for a while18 as it is strongly associated with the disease: patients with an aspartic acid at position 57 in the DQβ chain are very rare. However, this hypothesis was rejected,19 because it could neither explain the overall HLA genotype distribution nor the HLA haplotype sharing of affected sibs. 19 This example illustrates the importance of not only considering allelic association but also genotypic distributions and the importance of identifying models that can explain both the association and linkage information and not only one of them. In celiac disease, genetic susceptibility in the HLA region is mainly explained by one DQ heterodimer whose two components (DQA1 and DQB1 alleles) can either be on the same HLA haplotype (cis-position) or one on each complementary haplotype (trans-position). 20 This functionally relevant model was found using both biological elements on the structure and function of HLA molecules21 and the observed genotype distribution in patients. However, because it cannot clearly explain the HLA sharing among affected sibs and because there are geographical differences in the risks conferred by the DQ heterodimers,22 this model cannot account for the whole HLA component of the disease, which suggests that other HLA factors must be involved. In these two examples, the HLA component acts differently, through complex interactions of numerous variants. Deeper understanding could be obtained only through more detailed knowledge of gene diversity, patient genotype distributions, IBD sharing in affected siblings conditional on patient genotype, and biological understanding of the function of genes in the HLA region. Detection of an association was only the very first step. In a recent study, Lincoln et al. 23 used a large-scale SNP association strategy for studying the involvement of the MHC in MS. The strongest association is observed with haplotype blocks in the HLA class II region and, conditional on this association, there is no evidence for other HLA-region risk factors for MS. These results are an additional illustration of the limits of strategies relying on only association information. Despite the use of large numbers of simplex and multiplex families with dense SNP typing, the study just ends at a result which has been known for many years. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities of genetic associations and the limitations of current models in explaining disease susceptibility. It specifically mentions that factors beyond the DQ heterodimers must be accounted for in diseases like celiac disease and challenges the notion that merely altering the genome will lead to eradication of diseases by stating that a deeper understanding of genetic diversity and the function of genes in the HLA region is necessary.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Dit heeft tot gevolg dat deze casus zich niet meer voor kan doen na het Unit4-arrest. Deze foto van het monster van blijkt toch een drijvende boomstam te zijn. Er kunnen zich bijzondere omstandigheden voordoen die noodzaken tot afwijking van de peildatum, waardoor omstandigheden na de datum van betaalbaarstelling wel van invloed kunnen zijn op de hoogte van de billijke prijs. Afwijking is, voor zover dat in de jurisprudentie aan de orde is geweest, alleen mogelijk bij een lang tijdsverloop tussen de betaalbaarstelling onder het bod en het uitbrengen van de dagvaarding. Die situatie doet zich bij het billijke prijsvermoeden niet voor, omdat het billijke prijsvermoeden alleen gebruikt kan worden wanneer de minderheidsaandeelhouders binnen drie maanden gedagvaard worden. 67x (OK) 7 juli 2015, ECLI:NL:GHAMS:2015:2775, ARO 2015/178 (Unit4), r. o. 3. 18. Er is dan per definitie geen sprake van een lang tijdsverloop tussen de betaalbaarstelling onder het bod en de dagvaarding. Lang tijdsverloop in de procedure zelf lijkt geen reden te zijn voor een andere peildatum. 68x In Unit4 werd ondanks een vertraging in de procedure van negen maanden de datum van de betaalbaarstelling onder het bod nog steeds als peildatum toegepast. De ratio achter het prijsvermoeden verplicht tot een tweede beperking op welke aanwijzingen in acht kunnen worden genomen. [SEP] Justify:

Output: The text does not address the claim about cultural legends of creatures like Bigfoot and the Loch Ness Monster. Instead, it discusses legal proceedings and issues concerning the timing of legal claims, which is irrelevant to the topic of legends.


Input: Task: corroborate the claim using the given text. Claim: Natural selection drives evolution through differential survival. [SEP] Text: PeerJ · Jan 21, 2016 Basic reporting Experimental design This is a great dataset with a correct “experimental” design. With those data it is possible to study how T. soror affects defensive alkaloids in seeds and leaves of the plants and whether these selective pressures affect the geographic variation on plant traits –such as the variation on levels of defensive compounds. However the current treatment of data is not completely satisfactory. Important but easy-to-fix changes in the analytical approach should we made in order to make this research correct. The general approach is great but there are some mistakes regarding the types of model used, or even the response variable in the latest two models (which are the more important in this ms). Note that I took the opportunity to analyze the data myself (from the dataset in the submission) and actually found that the effect of natural selection drives among populations variation on the concentration of alkaloids, thus the main message in the manuscript is not going to change once it is properly analyzed. I think that the phenotypic trait which should be studied in the latest two models is the content on defensive compounds. It should be analyzed how quantity of atropine and scopolamine in seeds and leaves (or altogether) affect the number of seeds surviving from predation. It would be also possible to make combinations of these four traits (for example, total alkaloids in seeds or in leafs, or total atropine or scopolamine in plants). The first step (which in my opinion is optional) could be to analyze how number of seeds saved from predation depends on the population, the number of fruits per plant, the atropine in seeds, atropine in leafs, scopolamine in leafs, scopolamine in seeds (correlations between phenotypic traits should be taken into controlling for colinearity issues). In this model interaction between population and each of the phenotypic traits should be included. This would shed some light in the issue of whether defensive compounds affect the reproductive output of plants (after predation, i. e. the number of seeds saved from predation) and whether that relationship is constant or varies among populations. Second step would be what you already have correctly performed. You properly run phenotypic selection analyses at the level of population. [SEP] Justify:

Output: The text corroborates the claim by discussing how natural selection drives variation among populations in the concentration of alkaloids in plants. It indicates that selective pressures, such as predation, influence the survival of certain traits, thereby supporting the idea that natural selection plays a crucial role in evolution.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: HLA is certainly a unique region of the genome for its genetic complexity (level of polymorphism, pattern of LD and clustering of many functionally related genes). Therefore, the challenges encountered in this region are not fully representatives of the ones that we face elsewhere on the genome. Still, the HLA region is one of the most extensively studied and one exhibiting the strongest genetic factors for many complex diseases described so far. This, together with the accumulation of experiences in other regions of the genome, makes us believe that, though different, these non-HLA challenges may not be less complex. The availability of tools (e. g. high-throughput genotyping platforms) and information (e. g. a haplotype map of the human genome) are a valued and welcome addition to the armamentarium geneticists can use to identify and characterize the genetic component to common diseases with complex transmission. But we should resist the temptation to assume that the models most favourable for the utility of these new tools must be the right models for all the variants involved in complex diseases just because our studies will work better if these most favourable models are correct. We can ill afford to go from a generation of underpowered and ultimately disappointing linkage and family studies directly to a generation of underpowered and disappointing association studies. At the same time, the impressive diversity of causal variant models already identified favours continued diversification of strategies. Identification of biologically relevant novel pathways of disease susceptibility followed by candidate gene strategies allowing for the simultaneous consideration of these connected genes may be quite effective at identifying new variants affecting susceptibility. Linkage data contain considerable additional information capable of aiding the discrimination of causal variation from the nearby variation that is merely in LD. Consequently, linkage studies may still pay dividends even if the newer tools are as successful as we all hope, and we believe efforts to recruit family data should not be given up too quickly in favour of only large samples of cases and controls. Linkage and association studies should be considered as complementary strategies and not as concurrent. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities and challenges in understanding and manipulating the human genome, specifically mentioning that the HLA region's unique genetic properties complicate assumptions about genome alteration's effectiveness for disease eradication. The mention of varied causal models and the importance of diverse genetic research strategies suggests that altering the genome alone does not guarantee the eradication of diseases, as the mechanisms are more complicated than a simple alteration could resolve.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Aanwijzingen dat de biedprijs niet overeenstemt met de daadwerkelijke waarde van de aandelen moeten aanwijzingen zijn waarvan de maatman-aandeelhouder niet op de hoogte kan zijn. Het moet gaan om informatie die niet bekend is in de markt. 69x Scheepers 2016, p. 33-35. De geïnformeerde maatman-aandeelhouder heeft alle beschikbare informatie namelijk tot zich genomen en daarop de beslissing gebaseerd dat de biedprijs een billijke prijs is en om zijn aandelen aan te melden. Alleen niet-beschikbare informatie had hem tot een ander oordeel kunnen brengen. Dat bepaalde informatie niet beschikbaar is, zal zich in de praktijk niet vaak voordoen. Een openbaar bod is in de regel goed gedocumenteerd, met onder meer een biedingsbericht, fairness opinion(s) en analistenrapporten. De informatie over de waarde van de aandelen op de peildatum zal daarom zo accuraat mogelijk beschikbaar zijn. Het argument dat beursvennootschappen die lijken op de doelvennootschap een hogere beurskoers hebben en daarom de biedprijs hoger had moeten zijn,70x Dit argument werd door minderheidsaandeelhouders aangedragen in de NIBC-uitkoopprocedure. (OK) 12 april 2022, ECLI:NL:GHAMS:2022:1217, ARO 2022/107 (NIBC), r. o. 3. 27. kan dus niet opgaan. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses issues related to stock market information and shareholder decisions, with no mention of creatures like Bigfoot or the Loch Ness Monster, nor any cultural legends associated with them.


Input: Task: corroborate the claim using the given text. Claim: Natural selection drives evolution through differential survival. [SEP] Text: By regressing each phenotypic trait (for example atropine in seeds) on the plant relative fitness (number of seed saved from predation relative to the average of the population) selective differentials are assessed (S). Also you understood, and I agree, that the important question in here is not the significance of those selective differentials within populations. The relevant question here is addressed on the next step –which is studying how the selective pressures explain variation on phenotypic traits among populations. On the third step selective pressures should be covariates explaining phenotypic traits at the population level (one model for each trait as response variable, one for average population atropine in seeds, another for average population scopolamine in seeds etc. ). This is where you performed an important conceptual mistake by running the models for the response variable “infestation” instead of the selected phenotypic traits which would be “alkaloids”. I agree with you with the importance of adding environmental covariates to control for other sources of variation in these models. If selective differentials are found to be significant in explaining the among population variation on defensive traits (and my analyses using your dataset shows they are indeed), then it would be actually possible to state that “natural selection by T. soror drives, at least in part, the variation on defensive compounds across D. stramonium populations”. Some minor considerations (Please also see notes on attached pdf) • Please use GLM instead of LMM because your response variables are not normal. It is better to analyze actual distribution of variables by means of Models which allow fitting response variables to different error distributions and link functions depending on the nature of the response variables. • Please send table 1 to supplementary materials. • Analyses in figure 3 should be done at the plant level including populations as random factor (not using population averages) and only necessary for the sound seeds, the rest (in my opinion) is redundant. You are trying to show that infestation changes fitness. If you use sound seeds as response, and infestation levels as predictors, at the same time population as random factor that would be a better approach. If you add the interaction of population with infestation level, and it proves significant, that would show how selective pressures by weevils on defenses vary among population. Another possibility is to escape this step altogether and show the analyses done only from the calculations of selection coefficients on. [SEP] Justify:

Output: The text corroborates the claim by discussing selective differentials and their role in explaining phenotypic variation among populations. It mentions that natural selection (in this case, by T. soror) drives variation in defensive traits across D. stramonium populations, directly linking natural selection to evolutionary changes. The analysis focuses on how selective pressures influence phenotype, thus supporting the assertion that natural selection is a key mechanism in evolutionary processes.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: As described above, mutations were reported, therefore, only if the disease associated protein has a close homolog that has been proven experimentally to interact with a protein that contains the same binding partner domain as seen in the PDB structure the interaction was modeled from (the 'structural template'). For example, [OMIM:+264900. 0011] is a Ser576Arg mutation of the human coagulation factor IX (PTA). The residue is part of a trypsin domain and seen to interact with Ecotin. However, the interaction between PTA and Ecotin is not yet recorded in any interaction database; therefore, the mutation cannot be included in our predictions. Using these criteria, 1,428 mutations from 264 proteins were predicted to be interaction-related (Figure 3). The full list is available in Additional data file 1. In total, we collected 25,322 mutations from OMIM and UniProt. This means that approximately 4% of all mutations could be linked to a protein interaction. Figure 3Data integration steps for interacting residue prediction. Schematic outline of data integration for the prediction of interacting residues. Mutations from OMIM and UniProt for which a residue in a homologous structure is involved in an interaction are selected. This set is restricted further by searching for homologous proteins with known interactions, taken from a range of protein interaction databases. We require that the the homologous interacting proteins contain the same pair of Pfam domains that was observed in the structural template. This results in a set of 1,428 interaction related mutations. Full size image Amongst these mutations, 454 mapped to a structure that exhibits an interaction between different proteins (hetero-interaction), while 1,094 mutations mapped to a structure with an interaction between two identical proteins (homo-interaction). This means that 120 mutations are found in structures of both homo- and hetero-interactions. The large proportion of homo-interactions can be explained by the overrepresentation of homo-interactions in the structural templates set: 70% of all distinct protein pairs in iPfam are homo-interactions, which is in accordance with recent findings that homo-interactions are more common than hetero-interactions [30]. [SEP] Justify:

Output: The text contrasts the claim by detailing the complexity of mutations and protein interactions, indicating that merely altering the human genome is not sufficient for disease eradication. It emphasizes the requirements for predicting interaction-related mutations, implying that not all mutations lead to functional changes capable of eradicating diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: We moeten ervan uitgaan dat de maatman-aandeelhouder die informatie in zijn keuze om de biedprijs te steunen heeft verwerkt. De maatman-aandeelhouder vindt de biedprijs voor deze vennootschap namelijk nog steeds een billijke prijs, ondanks een afwijkende beurskoers van soortgelijke beursvennootschappen. Uit het voorgaande volgt dat alleen aanwijzingen die zich voordeden vóór de peildatum en die niet bekend waren in de markt een indicatie kunnen zijn dat de waarde van de aandelen niet overeenkomt met de biedprijs. Die aanwijzingen zullen zich slechts in zeer uitzonderlijke situaties voordoen. 71x Duynstee & 2017, p. 177. De Xeikon-casus is hier een voorbeeld van. Voor de overname van Xeikon door XBC – dus voor de peildatum – zijn er enkele onzakelijke transacties verricht waarvan de exacte impact op Xeikon niet bekend was. Hangende de uitkoopprocedure werd de impact op Xeikon via een enquêteprocedure duidelijk. Door de onzakelijke transacties verdampte op papier minstens EUR 30 miljoen van de ondernemingswaarde. Die waarde zat echter nog steeds in de vennootschap, bestaande uit vorderingen die Xeikon had op de oud-bestuurders die aan de onzakelijke transacties hadden meegewerkt. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses financial and corporate matters, specifically about shareholder reactions and transactions related to a company, which has no connection to cultural legends like Bigfoot or the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Natural selection drives evolution through differential survival. [SEP] Text: • In the dataset and in the manuscript it is not clear when showing results on alkaloids if results are on alkaloids of seeds or leaves or a combination of both. In the next version of the paper this information should be clarified. Validity of the findings No comments Additional comments The manuscript “Natural selection drives chemical resistance of Datura stramonium to its specialized seed predator” constitutes a very interesting piece of information. The study of effects of natural selection on geographic variation of plant traits is not commonly addressed. This is a very meritorious approach which is very scarce in literature. The research aimed to find out if seed predation by T. soror on Datura stramonium caused selective pressures and if this natural selection drives differences in plant resistance among populations. It was already known that atropine in this species is a defensive compound to leaf herbivory but it was not known whether this defensive compound was also related to predation upon seeds. Besides this interesting approach I find another major strength on this manuscript. I commend the authors on the nice dataset they have collected. Ecological studies comprising a large number of populations across broad geographical scales are uncommon –despite many evolutionary questions in ecology should be addressed from this perspective. This study comprises 31 populations of D. stramonium across central Mexico in which between 21 and 30 individuals per population have been studied, although actually between 7 and 10 plants per populations were used in the main analyses. The level of infestation by T. soror and the levels of defensive alkaloids (atropine and scopolamine) both in leaves and seeds for 7-10 plants per population (278 plants) have been measured. Additionally, some environmental covariates at the level of populations (mean annual temperature and precipitation) have been collected –which is a very good idea so that some environmental variation can be controlled in analyses showing how T. soror affects defensive compounds in D. stramonium. Download annotated manuscript Cite this review as (2016) #2 of "Natural selection drives chemical resistance of Datura stramonium (v0. 1)". PeerJ Submission (PDF) - submitted Jan 7, 2016 All text and materials provided via this peer-review history page are made available under a Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. [SEP] Justify:

Output: The text aligns with the claim as it discusses a study that investigates how natural selection influences plant traits in Datura stramonium through selective pressures from seed predation. It mentions that the research aimed to determine if seed predation caused by T. soror leads to differences in plant resistance among populations, illustrating the concept of differential survival driven by natural selection.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: Properties of mutations in interaction interfacesCurated set of interaction-related mutationsIn addition to the automatically derived data, we collected 119 mutations in 65 distinct diseases from the scientific literature for which there is evidence that they change the interactions of the protein they occur in (see Materials and methods). We call this the 'curated set' of interaction-related mutations (Additional data file 2). To our knowledge, it represents the biggest collection of high confidence interaction-related mutations to date. Below, we explore differences between interaction-related mutations and non-interaction-related mutations. We focus on the mechanism of the mutation, the mode of inheritance and residue composition. For most of the 1,428 mutations from the automatically generated set, no information about their mode of inheritance or functional mechanism was instantly available. To allow a comparison with the manually curated set, we sampled 100 mutations randomly and conducted a manual search of the literature in order to annotate their properties. Classification according to functionWe suggest a classification that groups mutations according to their effects into loss of function (LOF) and gain of function (GOF). Below this broad distinction, the GOF mutations can be further divided into two groups: pathological aggregation and aberrant recognition. Similarly, LOF mutations can be split into one class that disrupts obligate interactions between protein subunits and another class that interferes with transient interactions. From the curated set of interaction-related mutations, 95 mutations result in LOF, 17 in GOF, 4 mutations were reported to change the interaction preference of the protein and 3 could not be determined. The class of GOF mutations that result in protein aggregation contains 12 cases, comprising amyloid diseases like Alzheimer's or Creutzfeldt-Jacob, but also, for example, sickle cell anemia [OMIM:+141900. 0243]. Five cases result in aberrant recognition; for example, a Gly233Val mutation in glycoprotein Ib that leads to von Willebrand disease [OMIM:*606672. 0003] by increasing the affinity for von Willebrand factor. Amongst the LOF mutations, 61 affect transient interactions and 34 affect obligate interactions. The latter usually render proteins dysfunctional, for example, in the case of lipoamide dehydrogenase deficiency caused by impaired dimerization [31]. [SEP] Justify:

Output: The text contrasts the claim by detailing various mutations related to distinct diseases and their effects on protein interactions. It highlights the complexity and variability of mutations, suggesting that not all diseases can be easily impacted by altering the human genome as different mutations have different mechanisms of action and impact on disease pathology.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Vanwege de onbekendheid met het bestaan van de vorderingen is de waarde van de vorderingen niet verdisconteerd in de biedprijs en heeft de maatman-aandeelhouder die informatie niet mee kunnen nemen in zijn beslissing om de biedprijs te steunen. 72x (OK) 18 december 2018, ECLI:NL:GHAMS:2018:4684, ARO 2019/60 (Xeikon/Recalcico), r. o. 2. 27-2. 28. Omdat de billijke prijs de prijs is die de hypothetische meest biedende koper betaalt, kan worden gezegd dat de bieder een hogere biedprijs had betaald als hij van de schadevorderingen op de bestuurders had geweten. Daarmee is de billijke prijs in de systematiek van artikel 2:359c BW in deze casuspositie een hogere prijs dan de biedprijs. De maatman-aandeelhouder is een geïnformeerde aandeelhouder die deze biedprijs niet had geaccepteerd als hij bekend was geweest met deze prijsverhogende omstandigheid. In zijn aanvaarding van het bod kan geen steun voor de biedprijs worden gelezen. Dit heeft tot gevolg dat niet aan het 90%-criterium wordt voldaan. Het prijsvermoeden verliest al zijn waarde, nu de maatman-aandeelhouder geen betrouwbare beslissing heeft kunnen nemen over de billijkheid van de biedprijs. De OK kan in dat geval niet anders dan deskundigen benoemen die in hun advies over de uitkoopprijs rekening houden met de vorderingen die de doelvennootschap heeft op haar oud-bestuurders. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses legal proceedings and shareholder decisions, with no mention of legends or cultural beliefs regarding creatures like Bigfoot or the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities. eLife digest From the depths of the ocean to the lining of the human gut, almost every environment on Earth is home to a unique community of microorganisms referred to as a microbiome. Within these communities, unrelated microorganisms can exchange genetic information through a process known as horizontal gene transfer. For example, genes linked to antibiotic resistance are often transferred between different microorganisms, which can create increasingly drug resistant microbes and has important implications for human health. Horizontal gene transfer has been studied for almost 100 years, but examining it directly is challenging because, almost by definition, it requires studying a community of microbes rather than one microbe in isolation. As such, researchers are looking for simple models of microbial communities that can be easily manipulated in experiments. Bonham et al. have now turned to the outer surface of cheese, also known as cheese rind, to better understand horizontal gene transfer. As a model system, the cheese rind microbiome is relatively simple to work with because cheese rind is easy to replicate in the laboratory, and the microbes growing on cheese can be grown on their own or in combinations with other microbes. By comparing the genetic material of 165 cheese-associated bacteria to one another, Bonham et al. identified over 4,000 genes that were shared between the bacteria, including several large clusters of genes that were shared by many species. Many of the identified genes (about 23% to be precise) appear to help the microorganisms acquire nutrients that are known to be in short supply on the surface of cheese surface, including iron. [SEP] Justify:

Output: The text corroborates the claim by explaining how horizontal gene transfer (HGT) enables microbes to rapidly gain new capabilities, allowing them to adapt to changing environments. It provides specific examples of genes acquired through HGT in a model microbiome of cheese rinds, detailing the identification of many horizontally transferred genes that play vital roles in the microbes' nutrient acquisition and adaptation. This directly supports the idea that HGT allows bacteria to acquire new traits.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: LOF mutations in transient interactions cause changes in localization or transmission of information, exemplified by a mutation in the BRCA2 gene that predisposes women to early onset breast cancer: a Tyr42Cys mutation in BRCA2 inhibits the interaction of BRCA2 with replication protein A, a protein essential for DNA repair, replication and recombination [32]. Lack of this interaction inhibits the recruitment of double stranded break repair proteins and eventually leads to an accumulation of carcinogenic DNA changes. Mode of inheritanceWe investigated the mode of inheritance for all mutations in the curated set, if information was available in the literature. All GOF mutations showed dominant inheritance (the two hemoglobin mutations exhibit incomplete dominance). Out of 61 LOF mutations for which inheritance information was available, 24 were autosomal dominant and 37 were recessive. Jimenez-Sanchez et al. [33] studied the mode of inheritance of human disease genes. According to them, mutations in enzymes are predominantly recessive, while mutations in receptors, transcription factors and structural proteins are often dominant. Overall, they find a ratio of 188:335 of dominant to recessive diseases. In our data set, the ratio of dominant to recessive mutations is 41:37 (31:29 in terms of diseases). This enrichment for dominant mutations is statistically significant, as determined by a two-sided test for equality of proportions (P-value < 0. 014). The increase was seen across functional categories, in enzymes as well as regulators and signaling proteins (data not shown). In the 100 randomly chosen mutations from the predicted set, we found a ratio of dominant to recessive mutations of 38:41, which is very similar to the ratio observed in the curated set (two-sided test for equality of proportions; P-value > 0. 68; hypothesis of difference in proportions rejected). In GOF mutations, dominant inheritance is not surprising, but the high proportion (39%) of dominant LOF mutations is noteworthy. Dominant inheritance in LOF mutations can be explained by either haploinsufficency or dominant negative effects [34]. In yeast, dosage sensitivity of members of protein complexes has been shown [35]. According to what Papp et al. call the 'balance hypothesis', stoichiometric imbalances have negative effects on the function of protein complexes. Dominance would thus be a result simply of a lack of functional protein subunits. [SEP] Justify:

Output: The text contrasts the claim by discussing specific genetic mutations and their relationship to disease, particularly that not all diseases relate directly to a singular alteration in the genome. It highlights the complexity of inheritance patterns and demonstrates that certain mutations, like those in the BRCA2 gene, predispose individuals to diseases rather than confirming that altering the genome can eradicate all diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: 5. 3 Wat zegt een geringe free float over de billijkheid van de biedprijs? De tweede situatie waarin naar huidig recht het prijsvermoeden weerlegd kan worden, is de situatie dat er sprake is van een ‘geringe free float’. De OK heeft tot op heden niet duidelijk gemaakt wanneer daar sprake van is. Ik geef eerst een definitie. De ‘free float’ is het aantal aandelen dat vrij verhandelbaar is op de beurs: de uitstaande aandelen. 73x M. J. G. C. Raaijmakers, Ondernemingsrecht (Pitlo, deel 2), Deventer: 2017, p. 369. Een geringe free float is daarom een situatie waarbij er weinig aandelen uitstaan en er daarom weinig liquiditeit is. Dat wil zeggen dat een belegger zijn positie niet snel kan op- of afbouwen. Er is economisch onderzoek dat bevestigt dat een geringe free float leidt tot een grotere kans op informatieasymmetrie en een belemmering van efficiënte prijsvorming op de aandelenmarkt, ook wel prijsvolatiliteit genoemd. 74x X. S. Ding, Y. Ni & L. Zhong, Free float and market liquidity around the world, Journal of (38) 2016, p. 236-257; H. Le & A. Gregoriou, Liquidity and asset pricing: Evidence form a new free-float-adjusted price impact ratio, Journal of (49) 2002, afl. 4, p. 751-771. Dit wordt erkend in de wetsgeschiedenis, zie Kamerstukken II 2005/06, 30419, nr. 3, p. 49. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses topics related to stock market liquidity and shareholder dynamics, with no mention of creatures like Bigfoot or the Loch Ness Monster or any cultural legends. Therefore, it does not support or refute the claim.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Bacteria typically use specialized molecules called siderophores to scavenge for iron and uptake systems to carry the iron-bound siderophore back into the cell. Notably, only the genes associated with the uptake systems were found in some of the shared gene clusters. This finding suggests that horizontal gene transfer has allowed some microbes to “cheat” and take up iron-bound siderophores without expending energy to produce the siderophores themselves. Using the cheese rind microbiome as a model system, it becomes possible to explore how horizontal gene transfer works in more detail than before. A better understanding of this process can then be applied to other important microbiomes, including those where genes conferring antibiotic resistance are commonly exchanged. strides have been made in characterizing the composition of microbiomes, and in understanding their importance in the ecology of natural systems, in agriculture and in human health. However, despite these advances, the forces that shape the diversity, structure, and function of microbiomes remain poorly understood (Widder et al. , 2016). Investigating these underlying mechanisms in situ is difficult, as observational and sequenced-based analysis rarely enables causal conclusions (Nemergut et al. , 2013). Replicating microbial communities in vitro is also an enormous challenge, because of high levels of diversity and the difficulties in establishing pure cultures of most bacterial species. These obstacles significantly hamper our ability to move from observations of microbial diversity to the molecular mechanisms shaping key processes such as species interactions and microbial evolution. Horizontal gene transfer (HGT) is a major force in microbial evolution and can lead to the wholesale acquisition of novel functions. In some cases, these novel functions can have significant adaptive consequences, such as in the transfer of antibiotic resistance genes (Ochman et al. , 2000). HGT also allows rapid adaptation to new niches (Wiedenbeck and Cohan, 2011), as ecologically relevant genes may be acquired by species not previously adapted to a particular niche (Tasse et al. , 2010; Hehemann et al. , 2010). The movement of microbes to new environments has been shown to increase both the rate and impact of HGT, and HGT is most frequent for genes under positive selection (Niehus et al. , 2015). [SEP] Justify:

Output: The text corroborates the claim by explaining that horizontal gene transfer (HGT) is a major force in microbial evolution and allows bacteria to acquire new functions. It specifically mentions that HGT can lead to the wholesale acquisition of novel functions which can have significant adaptive consequences, such as the transfer of antibiotic resistance genes. This directly supports the idea that HGT enables bacteria to gain new traits.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: Genome-wide association studies are coming for human infectious diseases : 10 February 2009 Genome-wide association studies are coming for human infectious diseases Sonia Davila1 & Hibberd1 0. 1% [1]. Is this infectious disease distribution predominantly due to widespread general resistance over multiple genes or is susceptibility due to rare mutations in a few specific genes? This question on the nature of the genetic change, rare or common, has remained, despite numerous population studies of infectious disease. Candidate gene studiesAlthough family-specific mutations have been shown to have indisputable consequences in infectious disease [2–5], their effects in the general population are thought to be small [6]. There are also some very well established population-based mutations with clear effects on disease, from sickle cell trait protection against malaria [7] to CCR5, a known receptor of HIV, defective alleles in which have been associated with resistance to HIV infection [8]. Indeed, rare mutations leading to increased susceptibility to infectious disease can be identified in the general population, when looked for carefully [9]. Interestingly, the evidence from this field of work is currently pointing towards the concept of 'one gene, one infection' [10]. The strong evidence that a mutation in a single gene frequently leads to increased susceptibility to only one infection is also supported by animal studies, which have used forward genetics to show that, although many genes may be involved in recognizing a single pathogen, mutations in only one or a few lead to increased susceptibility to disease [11]. Despite the clear evidence identifying these so called 'major genes', it is unlikely that mutations in single genes are the only causes of genetic susceptibility in a population. So far, the work done to extend this approach to a population basis has used candidate gene studies and, in general, when they harmonize with the major genes findings, significant insights can be gained from them. For example, in meningococcal disease the 'major genes' lie in the complement pathway, with mutations in many of these genes (each restricted to just a few individuals) leading to greatly increased risk of disease [12]. Using one of these genes (that encoding mannose binding lectin) as a candidate gene in a population-based study has supported and extended these findings to the general population, revealing a polymorphism that can alter the initiation of this pathway, and thus the susceptibility to disease, in a large number of individuals [13]. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexity of genetic susceptibility to diseases, indicating that while some genetic mutations do influence disease resistance or susceptibility, they do not imply that all diseases can be eradicated by altering the human genome. The mention of both single genes and population-wide genetic factors suggests that genetic alteration is not a comprehensive solution for all diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Als het bod ziet op een relatief klein aantal aandelen, is de biedprijs geen betrouwbaar referentiepunt voor de waarde van die aandelen, zo lijkt de gedachte achter deze weerleggingsgrond. 75x (OK) 4 april 2017, ECLI:NL:GHAMS:2017:1203, JOR 2017/162 m. nt. M. W. (I), r. o. 3. 21 en noot punt 9; (OK) 18 september 2012, ECLI:NL:GHAMS:2012:BX9490, ARO 2012/139 (IFCO Systems), r. o. 3. 10; in de IFCO Systems-uitkoopprocedure sluit de OK voor de waardering niet aan bij de biedprijs, onder meer omdat het bod slechts betrekking heeft op 3,33% van het geplaatste kapitaal. Er is geen overeenstemming over de vraag vanaf welk percentage vrij verhandelbare aandelen er sprake is van een ‘geringe’ free float. Ik vraag mij af of het altijd uitmaakt hoe gering de free float is. De vraag die ertoe doet is: maakt het aanwezig zijn van een geringe free float dat er geen marktappreciatie kan worden gelezen in de aanmelding van aandelen door aandeelhouders? Stel dat er een bod wordt uitgebracht op alle aandelen in een beursvennootschap met een 1%-free float. De grootaandeelhouder meldt zijn hele pakket aandelen aan en verkeert niet in een wezenlijk andere positie dan de maatman-aandeelhouder. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses financial concepts related to the valuation of stocks and the effects of free float on market appreciation, with no mention of cultural legends or creatures like Bigfoot and the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: In moving to a new environment, microbes can face novel abiotic conditions (temperature, moisture, salinity, pH, and nutrients) and novel biotic challenges and opportunities resulting from the presence of microbial neighbors. Evaluating HGT within the context of microbial communities could provide new insights concerning the extent, mechanisms, and ecological impact of this important process. Advances in genome sequencing have begun to provide a glimpse into HGT within environmentally, medically and economically important microbiomes (McDaniel et al. , 2010; Andam et al. , 2015). For example, extensive gene sharing has been observed throughout the commensal human microbiome, including sharing of genes that enable nutrient acquisition from novel food sources (Hehemann et al. , 2010; Smillie et al. , 2011), and pathogenicity islands and antibiotic resistance genes in pathogenic microbes (McCarthy et al. , 2014; Hiramatsu et al. , 2001; Forsberg et al. , 2012). There is evidence of extensive HGT in other natural habitats, such as soil (Coombs and Barkay, 2004; Heuer and Smalla, 2012) and aquatic environments (McDaniel et al. , 2010; Frischer et al. , 1994). Although these studies offer valuable insights into the frequency and potential impact of genes that can be transferred in microbial communities, the complexity of these systems makes difficult any further examination of the effects of these HGT events on their evolution and ecology. The microbial communities of fermented foods experience strong selection as a result of growing in novel, human-made environments. Previous work has demonstrated that HGT can be a major driver of adaptation in food systems and other human-managed environments (Andam et al. , 2015; Rossi et al. , 2014). Prior analysis of microbial species from cheese has revealed several instances of HGT in this environment. Lactic acid bacteria (LAB) such as Lactobacillus and Lactococcus, which are used in the initial fermentation of milk, are known to harbor antibiotic resistance genes and may be reservoirs for transfer to pathogenic enterococci (Wang et al. , 2006; Mathur and Singh, 2005) and other pathogenic microbes. Other food-associated bacteria may also contribute to antibiotic resistance gene transfer (Cocconcelli et al. , 2003; Delorme, 2008; Flórez et al. , 2005). [SEP] Justify:

Output: The text corroborates the claim by discussing how horizontal gene transfer (HGT) enables microbes to acquire new traits, such as gene sharing observed in the human microbiome that facilitates nutrient acquisition and the sharing of antibiotic resistance genes. It specifically mentions instances where HGT serves as a major driver of adaptation in various environments, including fermented foods, highlighting its ecological significance.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: However, candidate gene approaches are ultimately restricted to those few genes that can be strongly implicated by current knowledge, and there is little understanding of their overall contribution to disease in relation to other genes. Moving towards genome-wide studiesTwo of the first efforts to apply a genome-wide approach to multi-factorial infectious diseases were done in schistosomiasis and tuberculosis, carried out in Brazilian and African families, respectively [14, 15]. The tools available at the time only allowed linkage studies using a few hundred genetic markers spread across the whole genome. Nowadays, data generated after the sequencing of the human genome and the HapMap project have identified millions of single nucleotide polymorphisms facilitating the implementation of genome-wide association studies (GWASs). The GWAS approach, although new, is already well described and has significant methodological improvements compared with previous approaches; GWAS analysis has already enabled the successful identification and replication of novel genes for several complex disorders such as Crohn's disease, rheumatoid arthritis, type 1 and type 2 diabetes, macular degeneration and prostate cancer [16–18]. The first GWAS in infectious disease was done in 2007, when Fellay et al. [19] determined genetic components influencing the viral load of HIV-positive patients during the asymptomatic phase of the disease. However, this study did not investigate host genetic susceptibility. The first GWAS of infectious disease susceptibility was carried out in a group of patients affected with Kawasaki disease [20], a self-limiting acute vasculitis mostly affecting children below 5 years of age [21]. This study started by genotyping a small group of European origin patients and controls with an Affymetrix 250K Nsp chip; a follow-up group comprising affected children and parents was then used to confirm the initial findings; and finally a third stage, including fine-mapping of eight associated genes, further validated the genetic associations. Interestingly, five of the eight fine-mapped genes formed a connected network that also showed significant differences in transcript levels between acute and convalescent stages of the disease, suggesting that multiple genes in a pathway may be involved in susceptibility to disease, something that may turn out to be important for other infectious diseases. [SEP] Justify:

Output: The text contrasts the claim by discussing the limitations of current genetic approaches in understanding and combating diseases. It highlights that candidate gene approaches are limited to a few implicated genes and that there is little understanding of how these genes contribute to diseases in relation to others. Additionally, the text explains that advancements like genome-wide association studies (GWAS) have improved identification of genes related to complex disorders, but it does not support the idea that altering the human genome can eradicate all diseases, as it emphasizes the complexity and multifactorial nature of diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Waarom kan in díé aanmelding geen marktappreciatie van de biedprijs worden gelezen? De prijs lijkt mij juist meer dan redelijk als de grootaandeelhouder slechts vanwege de biedprijs zijn hele pakket aandelen aanbiedt. Het enige belang dat de grootaandeelhouder in dat geval heeft, is het krijgen van een zo hoog mogelijke prijs. Daarnaast gaat het argument dat bij een geringe free float er een te laag aantal aandelen is voor een betrouwbare prijsvorming niet altijd op. Bij een zeer klein beursfonds met een 70%-free float kan de liquiditeit kleiner zijn dan bij een zeer groot beursfonds met een 15%-free float. De overname van door 3G Capital is een voorbeeld van een geringe free float-situatie. 76x Ik ga er voor the sake of argument van uit dat de private deal tussen familie Sonnenberg en 3G Capital een openbaar bod op alle aandelen was, nu de casuspositie bekend is en zich goed leent voor mijn argumentatie. Ten tijde van het uitbrengen van het bod had het aandeel een free float van ongeveer 18%. Grootaandeelhouder familie Sonnenberg hield 82%. 77x Zie addvaluefund. nl/uploads/media/Add%20Value%20Fund%20N. V. %20Hunter%20Douglas%20d. d. %205%20juni%202020. pdf. in juni 2020 was de free float bij ongeveer 18%. De biedprijs bedroeg EUR 175 per aandeel. 78x Zie investor. hunterdouglasgroup. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses financial matters regarding market appreciation, shareholder interests, and free float situations. There is no mention of legends, creatures, or cultural stories related to Bigfoot or the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: In yogurt, another dairy ferment using of metabolic genes has been observed between protocooperative species L. bulgaricus and S. thermophilus (Li et al. , 2013; Liu et al. , 2009). Sequencing of Penicillium species isolated from the cheesemaking environment identified HGT of large genomic islands between these key fungal inhabitants of cheese (Cheeseman et al. , 2014; Ropars et al. , 2015; Gibbons and Rinker, 2015). During the aging of traditional styles of cheese in caves or aging rooms, bacteria and fungi form a multi-species biofilm called the rind (Button and Dutton, 2012). We have previously shown that these communities can be used to examine community-based processes, such as succession and interspecies interactions, within an experimentally tractable system (Wolfe et al. , 2014; Kastman et al. , 2016). Given that biofilms such as these are densely populated, and microbes in cheese rinds are under strong selection to obtain limited nutrients (e. g. free amino acids, iron) as well as tolerate cell stress (Monnet et al. , 2015), we predicted that HGT might be widespread in cheese rind microbiomes and therefore might provide a useful experimental model for HGT within microbial communities. We sought to determine the diversity, distribution, and functional content of HGT in bacterial species isolated from cheese rinds. Specifically, we predicted that (1) HGT would be widespread, (2) HGT genes would be enriched for functions related to survival in cheese environment, and (3) there would be uneven distribution of HGT events across taxa. We analyzed the genomes of newly isolated and sequenced cheese-associated bacterial species (31 genomes) and those available in public databases (134 additional genomes). We present data which suggest that there is extensive HGT in cheese-associated bacteria. The regions of DNA identified appear to encode a number of functions which would be expected to provide adaptive advantages within the cheese environment. In particular, we identified three large multi-gene islands that are shared within multiple Actinobacteria, Proteobacteria, and Firmicutes species. These genomic regions are not related, but appear to have analogous functions involving iron acquisition, and are widely distributed in geographically distant cheeses. [SEP] Justify:

Output: The text corroborates the claim by providing evidence that horizontal gene transfer (HGT) is observed in cheese-associated bacteria. It specifically mentions that HGT is widespread in cheese rind microbiomes and that there is extensive HGT in bacterial species isolated from cheese rinds, leading to adaptive advantages such as iron acquisition. The identification of multi-gene islands that provide functions beneficial for survival in the cheese environment further supports the claim that horizontal gene transfer enables bacteria to acquire new traits.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: However, in comparison with disorders such as inflammatory bowel disease or macular degeneration, for which the small number of genetic variants detected were shown to confer a highly significant disease risk to carriers [17, 22], the study on Kawasaki disease [20] has not found such a profound effect, hinting that infectious disease may not yield easily to the GWAS approach. It is also interesting to see that the HLA locus, such a clear candidate region for infectious disease because its role in discriminating self from non-self was thought to have evolved to protect from infection, did not cause the dominant association seen in many autoimmune diseases [23, 24], and this may also turn out to be true for many infectious disease studies. Facing new challengesThere are several challenges for the application of GWAS to determine genetic variants that confer susceptibility to infectious diseases. First, the current design of commercially available single nucleotide polymorphism chips is skewed towards common variants, with at least 1% presence in the population, following the 'common variant, common disease' hypothesis [25, 26]. However, if susceptibility to an infectious disease is caused by one or a combination of rare variants, as previously reported for other disorders such as autism [27], we would not be able to detect them using the current technology. In that scenario, sequencing of the candidate genes would be the most direct way to tackle the problem. Second, structural variants, such as copy number variants that were barely analyzed in the past, are currently being investigated in more detail and have been successfully linked to susceptibility to schizophrenia [28, 29]. Recent development of new technologies as well as analysis tools will facilitate the study of copy number variants, which might potentially be involved in host susceptibility to infectious diseases. Third, a landmark paper by the Consortium [16] introduced the concept of using the same set of population controls, without detailed phenotype information for different diseases, in case-control studies. Although there is the possibility of misclassification, meaning that a proportion of controls might have the disease or might develop it in the future, this could be a very useful approach for the many infectious diseases for which the incidence rates in the general population are low (less than 1%), such as meningococcal disease, severe dengue and others. [SEP] Justify:

Output: The text contrasts the claim by discussing the complexities and limitations of using genetic approaches, such as the GWAS (Genome-Wide Association Studies), to identify genetic variants that contribute to susceptibility to diseases, particularly infectious diseases. It points out that many diseases may not yield to such genetic approaches, indicating that altering the human genome might not be sufficient for eradicating all diseases. It highlights the challenges associated with current genetic research technologies and the notion that infectious diseases may be influenced by rare variants that are not captured by prevalent genome-wide techniques.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: com/news-releases/news-release-details/3g-capital-completes-acquisition-controlling-interest-hunter. In het jaar voorafgaande aan het bod schommelde de beurskoers tussen EUR 65 en EUR 100 per aandeel. 79x Zie live. euronext. com/nl/product/equities/ANN4327C1220-XAMS. Het kan zo zijn dat de beurskoers hier gedrukt wordt door een lage liquiditeit. Dat is mijns inziens niet relevant voor de vraag wat een billijke prijs is, zolang de bieder net zoveel betaalt als de hypothetische meest biedende en onafhankelijke koper en de aanmeldende aandeelhouders van mening zijn dat de biedprijs van EUR 175 een fair market value vertegenwoordigt. De vraag waarop het antwoord altijd doorslaggevend moet zijn voor de werking van het prijsvermoeden is: staat er een groot genoeg percentage maatman-aandeelhouders achter de biedprijs? Wanneer kan een geringe free float wel leiden tot een correctie in het 90%-criterium? Daarvoor is noodzakelijk dat er een aantal aandeelhouders is dat zijn aandelen niet aanmeldt vanwege de biedprijs, maar omdat het de enige optie is om uit de geringe free float en de lage liquiditeit te ontsnappen. Als voorbeeld dient opnieuw de Hunter Douglas-saga. Voor het bod door 3G Capital bracht Sonnenberg zelf een openbaar bod uit op de aandelen die in de geringe free float zitten. De biedprijs bedroeg EUR 64. 80x Zie fd. [SEP] Justify:

Output: The text does not address the claim regarding cultures and their legends about creatures like Bigfoot and the Loch Ness Monster. Instead, it discusses financial matters and stock prices which are irrelevant to the topic of folklore and cultural legends.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: This work provides foundational knowledge in an experimentally tractable system in which future work could help to provide insight into the role of HGT within microbiomes. of putative horizontally transferred regions To establish a diverse database of cheese-associated bacterial genomes, we isolated species from cheese samples collected as part of previous work (Wolfe et al. , 2014). A total of 31 isolates, representing four bacterial phyla and 11 genera, were selected for genome sequencing using Illumina and PacBio (Supplementary file 1a). Recently, a large collection of cheese-associated bacterial genomes were sequenced (Almeida et al. , 2014), allowing inclusion of additional genomes in our analysis. Our isolates were from cheeses produced in the United States, Spain, Italy, and France, while the Almeida et al. collection was almost exclusively from France. We also included genomes from the NCBI reference sequence (RefSeq) database that are associated with cheese, for a total of 165 bacterial genomes. We next developed a computational pipeline for identification of putative horizontally transferred genes, adapted from work on the human microbiome (Smillie et al. , 2011). We built a central BLAST database containing all ORFs from all cheese-associated genomes. For each gene in each genome, we performed BLAST against this database, and compiled a list of hits (Figure 1—figure supplement 1, Materials and methods). For each hit, we examined the length and percent identity of aligned regions. Closely related species will have many nearly identical genes as a result of vertical inheritance. To avoid capturing these genes in our analysis, we determined the pairwise average nucleotide identity (ANI) between species within the same genus (Chan et al. , 2012; Rodriguez-R and Konstantinidis, 2016). ANI provides a measure of the overall similarity of two genomes. We tested varying thresholds for length and ANI to examine the effects of these parameters on the results (Supplementary file 1c). Higher maximum ANI cutoffs and shorter lengths are more likely to yield false positives, as closely related species are more likely to share short stretches of high nucleotide identity. At the same time, a lower maximum ANI cutoff may exclude legitimate HGT events, especially considering that closely related species are also more likely to engage in HGT. [SEP] Justify:

Output: The text corroborates the claim by discussing the identification of putative horizontally transferred genes in cheese-associated bacterial genomes. The mention of 'putative horizontally transferred regions' and the analysis of these regions indicates that horizontal gene transfer (HGT) is being examined for its role in acquiring new traits by bacteria. Additionally, the text notes the challenges in accurately identifying HGT events, which implicitly supports the idea that HGT is a significant mechanism by which bacteria can acquire new genetic traits.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: It is worth noting, however, that for infectious disease the environmental agent (the pathogen) that triggers the disease is usually known and past exposure to the agent is often easily measured (using serology), criteria that are frequently not available in diseases such as cancer or autoimmunity. This means that it is possible in infectious disease to select controls with known (antibody detected) exposure, but without disease. Finally, another important aspect to take into account is the role of the pathogen's genetic variability and its interaction with host genetics. An interesting study by Caws et al. [30] has hinted at a relationship between host and pathogen genotypes in the development of tuberculosis. When these challenges are successfully addressed, a GWAS will offer substantial insights into the role of common variation in an infectious disease and, with its comprehensive nature, will hopefully enable us to elucidate the involvement of multiple genes or previously unsuspected pathways in disease. Clinical significanceMoving from genetic discovery to direct clinical relevance has not been as difficult for infectious disease as it has been for many other diseases, perhaps because there is a relatively detailed understanding of the immune system. For instance, patients with Mendelian diseases characterized by diminished production of interferon or interferon pathway activation could be treated with recombinant forms of interferon, helping them to mount an immune response against various pathogens. Although there is still no treatment using the CCR5 gene, it has been a tempting target for therapies in the HIV field and may yet prove to be effective. In another example, a polymorphism associated with increased serum concentrations of complement was revealed to be a susceptibility factor for meningococcal disease, as bound to and protected the causative bacteria from complement attack [31]. This is a finding with implications for the vaccine community, which showed that antibodies that prevent this binding enable complement-mediated killing of the bacteria and, when incorporated into a vaccine, has been the first successful strategy to prevent group B meningococcal disease [32]. With the arrival of the GWAS approach to infectious disease, we can expect many more genetic loci to be revealed, molecular pathways to disease described and thus therapeutic targets identified, with the hope that these can be quickly translated into treatments. In conclusion, the first GWASs of infectious diseases have been published [19, 20], and more will come in the near future, with important implications for our understanding of these diseases. [SEP] Justify:

Output: The text contrasts the claim by highlighting the complexities of infectious diseases and the interaction between host genetics and pathogens. It notes that while genome-wide association studies (GWAS) can provide insights into infectious diseases, there remain significant challenges in understanding diseases like cancer and autoimmunity, which are not straightforwardly linked to genetic manipulation. The mention of specific examples, such as the need for a detailed understanding of immune responses in treating certain diseases, further underscores that simply altering the human genome is not a blanket solution for eradicating all diseases.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: nl/bedrijfsleven/1425652/luxaflex-fabrikant-hunter-douglas-komt-in-handen-van-3g-capital#:~:text=Premie%20van%2073%25,Douglas%20op%20€101%2C40. De minderheidsaandeelhouders lijken in deze situatie vast te zitten omdat het zeer onwaarschijnlijk is dat Sonnenberg een bod van een derde zal accepteren en doordat er nauwelijks handel in het aandeel plaatsvindt, zeker niet nadat het bod is uitgebracht. Er zijn aandeelhouders die toch maar hun aandelen aanmelden onder het bod omdat ze anders nooit uit de vennootschap kunnen. Minderheidsaandeelhouders die aanmelden omdat zij klem zitten in de vennootschap, melden niet slechts aan omdat zij de biedprijs een billijke prijs vinden. Zij verkeren daarom in een wezenlijk andere positie dan de maatman-aandeelhouder. De twijfel over de zuiverheid van het billijke prijsvermoeden wordt daarmee opgelost in het 90%-criterium. Dit is zuiverder omdat het prijsvermoeden in het 90%-criterium wordt aangetast. Deze aandeelhouders hebben namelijk niet aangemeld omdat zij de biedprijs een billijke prijs vinden. De minderheidsaandeelhouder in de uitkoopprocedure moet stellen en zo nodig bewijzen dat de ‘geringe free float’-aandeelhouders in een wezenlijk andere positie verkeren dan de maatman-aandeelhouder. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a financial situation involving minority shareholders and does not mention anything related to legends of creatures like Bigfoot and the Loch Ness Monster.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer allows bacteria to acquire new traits. [SEP] Text: Based on our most conservative gene identity parameters (minimum 99% identity over 500 nucleotides), we identified at least one putative horizontally transferred gene in 130/165 (78. 8%) cheese-associated species in the analysis, for a total of 4733 genes (Figure 1A, Supplementary file 1d). Because this analysis depends on the species included for comparison, this list of HGT is almost certainly an underestimate. Figure 1 with 2 supplements see all Download asset Open asset Extensive horizontal gene transfer in the cheese microbiome. (A) All HGT events in analyzed cheese-associated bacteria. Connection thickness is scaled to number of shared protein coding sequences. Maximum likelihood tree based on 16S RNA alignment using Project (RDP). (B) HGT events clustered into 264 ‘groups’ based on genomic proximity. Groups are plotted based on total nucleotide content (x-axis, from low to high), and the mean number of genes per species (y-axis). Diameter of each circle is proportional to the total number of species in the group. Groups highlighted in red are described further in the text. (C) Quantification of KEGG modules and submodules for protein coding genes (CDS) identified as horizontally transferred. Annotations were generated by BLAST-Koala. Genes without function prediction are not depicted. As multiple genes can be transferred in a single HGT event, we next assembled the putative HGT genes into groups based on genomic proximity. Individual coding sequences (CDS) for each species were grouped into islands if they were found within 5000 nucleotides of one another on the same contig. These islands were then clustered with islands in other species that shared at least one CDS. The 4733 genes were clustered into 264 individual groups (Figure 1B, Supplementary file 1d). Mobile elements such as transposons complicate our method of group clustering, as non-contiguous islands may be grouped together if they share a common transposon. Indeed, this appears to have occurred with Group 1, which contains genes from several disparate genomic regions. In other cases, a single species may have genes in a single group spread across multiple contigs (Figure 2—figure supplement 1), but this may accurately represent a single HGT event. Most HGT groups identified (231, 87. [SEP] Justify:

Output: The text corroborates the claim by providing evidence of extensive horizontal gene transfer (HGT) in cheese-associated bacteria. It mentions that at least one putative horizontally transferred gene was identified in a significant proportion of the species analyzed, demonstrating that HGT allows these bacteria to acquire new genetic traits. The identification of 4733 genes through HGT further supports this assertion, indicating that these genetic transfers contribute to the diversity of traits among bacterial species.


Input: Task: contrast the claim using the given text. Claim: All diseases can be eradicated by altering the human genome. [SEP] Text: Although initial hints suggest that big hits will not lead the way, the unraveling of disease mechanisms through networks of genes should reveal novel ways of tackling infectious diseases in the clinic. AbbreviationsGWAS: genome-wide association study. 386. 10. 1111/j. 1365-3156. 2005. 01388. x. 1435. 10. 1126/science. 280. 5368. 1432. 2040. 10. 1172/JCI4950. 1438. 10. 1126/science. 280. 5368. 1435. 2079. 10. 1126/science. 1081902. 486. 10. 1146/annurev. genet. 40. 110405. 090546. 294. 10. 1136/bmj. 1. 4857. 290. 725. 10. 1038/382722a0. 6080. 10. 1073/pnas. 1031605100. 922. 10. 1038/sj. emboj. 7601558. 766. 10. 1038/nri2174. 240. 10. 1016/j. tim. 2007. 03. 005. 1053. 10. 1016/S0140-6736(98)08350-0. 33. Nat Genet. 1996, 14: 181-184. 10. 1038/ng1096-181. 8009. 10. 1073/pnas. 140201897. 678. 10. 1038/nature05911. 389. 10. 1126/science. 1109557. 644. 10. 1038/ng2015. 1. Science. 2007, 317: 944-947. 10. 1126/science. 1143767. 10. 1371/journal. pgen. 1000319. 544. 10. 1016/S0140-6736(04)16814-1. 1463. 10. 1126/science. 1135245. 555. 10. 1038/ng1782. 1209. 10. 1056/NEJMoa073491. 1517. 10. 1126/science. 273. 5281. 1516. 539. 10. 1126/science. 274. 5287. 536. 11. 2 and autism. N Med. 2008, 358: 667-675. 10. [SEP] Justify:

Output: The text contrasts the claim by suggesting that while understanding gene networks may help in attacking infectious diseases, it does not imply that altering the human genome alone can eradicate all diseases. The mention of unraveling disease mechanisms through networks of genes indicates that a multifaceted approach is necessary, rather than solely relying on genomic alterations.


Input: Task: pass the claim using the given text. Claim: Some cultures have legends of creatures like Bigfoot and the Loch Ness Monster. [SEP] Text: Meldt 90% van de free float zich wel aan en doen zij dat wegens hun enthousiasme voor de biedprijs, dan blijft het prijsvermoeden overeind ondanks dat er een kleine free float is, zoals hiervoor is besproken. Klaarblijkelijk vindt 90% van de aandeelhouders de prijs die de grootaandeelhouder betaalt een billijke prijs. Ook de OK lijkt in Unilever bij één soort aandeel voorbij te gaan aan het feit dat er sprake is van een geringe free float. 81x (OK) 27 maart 2018, ECLI:NL:GHAMS:2018:1029, JOR 2018/178 (Unilever). De OK lijkt dat te doen omdat de biedprijs een aanzienlijke premie op de beurskoers inhoudt. Zie ik dat goed, dan lijkt mij dat in overeenstemming met de ratio achter het prijsvermoeden. 82x G. P. Oosterhof, annotatie bij (OK) 27 maart 2018, ECLI:NL:GHAMS:2018:1029, JOR 2018/178 (Unilever), punt 3; Duynstee & Drenth 2022, p. 479. Zelfs wanneer de koers volatiel is en er een gebrek aan liquiditeit is, moet er voor de uitkoopprijs worden aangesloten bij de biedprijs wanneer voldoende aandeelhouders kwalificeren als maatman-aandeelhouder. 83x Uit het arrest zelf en het verschenen commentaar daarop wordt niet helemaal duidelijk hoe gering die free float was van het preferente aandeel met de aanduiding ‘cumpref 7%’. Volgens mijn berekeningen gaat het om een free float van 17,88%. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses financial topics related to shareholder behavior and stock prices, without mentioning any cultural legends or creatures similar to Bigfoot or the Loch Ness Monster.