bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher genetic risk of schizophrenia is associated with lower cognitive performance in healthy individuals
Authors: Shafee Rebecca , Nanda Pranav , Padmanabhan Jaya L. , Tandon Neeraj , Alliey-Rodriguez Ney , Keefe Richard S. E. , Hill Scot K. , Bishop Jeffrey R. , Clementz Brett A. , Tamminga Carol A. , Gershon Elliot S. , Pearlson Godfrey D. , Keshavan Matcheri S. , Sweeney John A. , Robinson Elise B. , McCarroll Steven A. 
Published: January 2017

AbstractPsychotic disorders including schizophrenia are commonly accompanied by cognitive deficits. Recent studies have reported negative genetic correlations between schizophrenia and indicators of cognitive ability such as general intelligence and processing speed. Here we compare the effect of the genetic risk of schizophrenia (PRSSCZ) on measures that differ in their relationships with psychosis onset: a measure of current cognitive abilities (the Brief Assessment of Cognition in Schizophrenia, BACS) that is greatly reduced in psychosis patients; a measure of premorbid intelligence that is minimally affected by psychosis (the Wide-Range Achievement Test, WRAT); and educational attainment (EY), which covaries with both BACS and WRAT. Using genome-wide SNP data from 314 psychotic and 423 healthy research participants in the Bipolar-Schizophrenia Network for Intermediate Phenotypes (B-SNIP) Consortium, we investigated the association of PRSSCZwith BACS, WRAT and EY. Among apparently healthy individuals, greater genetic risk for schizophrenia (PRSSCZ) was associated with lower BACS scores (r = −0.19, p = 1 × 10−4at PT= 1 × 10−4) but did not associate with WRAT or EY, suggesting that these areas of cognition vary in their etiologic relationships with schizophrenia. Among individuals with psychosis, PRSSCZdid not associate with variation in cognitive performance. These findings suggest that the same cognitive abilities that are disrupted in psychotic disorders are also associated with schizophrenia genetic risk in the general population. Specific cognitive phenotypes, independent of education or general intelligence, could be more deeply studied for insight into the specific processes affected by the genetic influences on psychosis.SignificancePsychotic disorders such as schizophrenia often involve profound cognitive deficits, the genetic underpinnings of which remain to be elucidated. Poor educational performance early in life is a well-known risk factor for future psychotic illness, potentially reflecting either shared genetic influences or other risk factors that are epidemiologically correlated. Here we show that, in apparently healthy individuals, common genetic risk factors for schizophrenia associate with lower performance in areas of cognition that are impaired in psychotic disorders but do not associate independently with educational attainment or more general measures of intelligence. These results suggest that specific cognitive phenotypes – independent of education or general intelligence – could be more deeply studied for insight into the processes affected by the genetic influences on psychosis.
Revealing the causative variant in Mendelian patient genomes without revealing patient genomes
Authors: Jagadeesh Karthik A. , Wu David J. , Birgmeier Johannes A. , Boneh Dan , Bejerano Gill 
Published: January 2017

AbstractGiven the rapidly growing utility of critical health information revealed in the human genome, secure genomic computation is essential to moving forward, especially as genome sequencing becomes commonplace. We devise and implement proof-of-principle computational operations for precisely identifying causal variants in Mendelian patients using secure multiparty computation methods based on Yao’s protocol. We show multiple real scenarios (small patient cohorts, trio analysis, two hospital collaboration) where the causal variant is discovered jointly, while keeping up to 99.7% of all participants’ most sensitive genomic information private. All similar operations performed today to diagnose such cases are done openly, keeping 0% of participants’ genomic information private. Our work will help usher in an era where genomes can be both utilized and truly protected.
Colour Preferences of UK Garden Birds at Supplementary Seed Feeders
Authors: Rothery Luke , Scott Graham W. , Morrell Lesley J. 
Published: January 2017

AbstractSupplementary feeding of garden birds has benefits for both bird populations and human wellbeing. Birds have excellent colour vision, and show preferences for food items of particular colours, but research into colour preferences associated with artificial feeders is limited to hummingbirds. Here, we investigated the colour preferences of common UK garden birds foraging at seed-dispensing artificial feeders containing identical food. We presented birds simultaneously with an array of eight differently coloured feeders, and recorded the number of visits made to each colour over 370 30-minute observation periods in the winter of 2014/15. In addition, we surveyed visitors to a garden centre and science festival to determine the colour preferences of likely purchasers of seed feeders. Our results suggest that silver and green feeders were visited by higher numbers of individuals of several common garden bird species, while red and yellow feeders received fewer visits. In contrast, people preferred red, yellow, blue and green feeders.
Ribosome reinitiation can explain length-dependent translation of messenger RNA
Authors: Rogers David W. , Böettcher Marvin A. , Traulsen Arne , Greig Duncan 
Published: January 2017

AbstractModels of mRNA translation usually presume that transcripts are linear; upon reaching the end of a transcript each terminating ribosome returns to the cytoplasmic pool before initiating anew on a different transcript. A consequence of linear models is that faster translation of a given mRNA is unlikely to generate more of the encoded protein, particularly at low ribosome availability. Recent evidence indicates that eukaryotic mRNAs are circularized, potentially allowing terminating ribosomes to preferentially reinitiate on the same transcript. Here we model the effect of ribosome reinitiation on translation and show that, at high levels of reinitiation, protein synthesis rates are dominated by the time required to translate a given transcript. Our model provides a simple mechanistic explanation for many previously enigmatic features of eukaryotic translation, including the negative correlation of both ribosome densities and protein abundance on transcript length, the importance of codon usage in determining protein synthesis rates, and the negative correlation between transcript length and both codon adaptation and 5' mRNA folding energies. In contrast to linear models where translation is largely limited by initiation rates, our model reveals that all three stages of translation - initiation, elongation, and termination/reinitiation - determine protein synthesis rates even at low ribosome availability.
High GC Content Causes Orphan Proteins to be Intrinsically Disordered
Authors: Basile Walter , Sachenkova Oxana , Light Sara , Elofsson Arne 
Published: January 2017

AbstractDe novocreation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the populationThese orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. InDrosophilayoung proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed.To solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC) andDrosophila(high GC). GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.Author SummaryWe show that the GC content of a genome is of great importance for the properties of an orphan protein. GC content affects the frequency of the codons and this affects the probability for each amino acid to be included in ade novocreated protein. The codons encoding for Ala, Pro and Gly contain 80% GC, while codons for Lys, Phe, Asn, Tyr and Ile contain 20% or less. The three high GC amino acids are all disorder promoting, while Phe, Tyr and Ile are order promoting. Therefore, random protein sequences at a high GC will be more disordered than the ones created at a low GC. The structural properties of the youngest proteins match to a large degree the properties of random proteins when the GC content is taken into account. In contrast, structural properties of ancient proteins only show a weak correlation with GC content. This suggests that even after fixation in the population, proteins largely resemble random proteins given a certain GC content. Thereafter, during evolution the correlation between structural properties and GC weakens.
European Flint reference sequences complement the maize pan-genome
Authors: Unterseer Sandra , Seidel Michael A. , Bauer Eva , Haberer Georg , Hochholdinger Frank , Opitz Nina , Marcon Caroline , Baruch Kobi , Spannagl Manuel , Mayer Klaus F.X. , Schön Chris-Carolin 
Published: January 2017

AbstractThe genomic diversity of maize is reflected by a large number of SNPs and substantial structural variation. Here, we report thede novoassembly of two European Flint maize lines to remedy the scarcity of sequence resources for the Flint pool. EP1 and F7 are important founder lines of European hybrid breeding programs. The lines were sequenced on an Illumina platform at 320X and 225X coverage. Using NRGene´s DeNovoMAGIC 2.0 technology, pseudochromosomes were assembled encompassing a total of 2,463 Mb for EP1 and 2,405 Mb for F7. Structural and functional annotation of the two genomes is currently in progress. The two high-qualityde novoassemblies complement the existing maize pan-genome and will pave the way for future functional and comparative studies.
Colour vision models: a practical guide, some simulations, andcolourvisionR package
Authors: Gawryszewski Felipe M. 
Published: January 2017

AbstractHuman colour vision differs from the vision of other animals. The most obvious differences are the number and type of photoreceptors in the retina. E.g., while humans are insensitive to ultraviolet (UV) light, most non-mammal vertebrates and insects have a colour vision that spans into the UV. The development of colour vision models allowed appraisals of colour vision independent of the human experience. These models are now widespread in ecology and evolution fields. Here I present a guide to colour vision modelling, run a series of simulations, and provide a R package –colourvision– to facilitate the use of colour vision models.I present the mathematical steps for calculation of the most commonly used colour vision models: Chittka (1992) colour hexagon, Endler & Mielke (2005) model, and Vorobyev & Osorio (1998) linear and log-linear receptor noise limited models (RNL). These models are then tested using identical simulated and real data. These comprise of reflectance spectra generated by a logistic function against an achromatic background, achromatic reflectance against an achromatic background, achromatic reflectance against a chromatic background, and real flower reflectance data against a natural background reflectance.When the specific requirements of each model are met, between model results are, overall, qualitatively and quantitatively similar. However, under many common scenarios of colour measurements, models may generate spurious values and/or considerably different predictions. Models that log-transform data and use relative photoreceptor outputs are prone to generate unrealistic results when the stimulus photon catch is smaller than the background photon catch. Moreover, models may generate unrealistic results when the background is chromatic (e.g. leaf reflectance) and the stimulus is an achromatic low reflectance spectrum.Colour vision models are a valuable tool in several ecology and evolution subfields. Nonetheless, knowledge of model assumptions, careful analysis of model outputs, and basic knowledge of calculation behind each model are crucial for appropriate model application, and generation of meaningful and reproducible results. Other aspects of vision not incorporated into these models should be considered when drawing conclusion from model results.
The Negev hospital-university-based (HUB) autism database
Authors: Meiri Gal , Dinstein Ilan , Michaelowski Analya , Flusser Hagit , Ilan Michal , Faroy Michal , Bar-Sinai Asif , Manelis Liora , Stolowicz Dana , Yosef Lili Lea , Davidovitch Nadav , Golan Hava , Arbelle Shosh , Menashe Idan 
Published: January 2017

AbstractElucidating the heterogeneous etiologies of autism will require investment in comprehensive longitudinal data acquisition from large community based cohorts. With this in mind, we have established a hospital-university-based (HUB) database of autism which incorporates prospective and retrospective data from a large and ethnically diverse population. Here we present initial findings from 188 children who were diagnosed with autism during the first eighteen months of the study. The unique characteristics of this cohort included: significant differences between Bedouin and Jewish children in different risk factors and clinical characteristics; complete birth records for >90% of the children; and a high frequency of consanguineous marriages. Thus, the Negev HUB autism database comprises a remarkably unique resource to study different aspects of autism.
No evidence of early head circumference enlargements in children later diagnosed with autism in Israel
Authors: Dinstein Ilan , Haar Shlomi , Atsmon Shir , Schtaerman Hen 
Published: January 2017

AbstractBackgroundLarge controversy exists regarding the potential existence and clinical significance of larger brain volumes in toddlers who later develop autism. Assessing this relationship is important for determining the clinical utility of early head circumference (HC) measures and for assessing the validity of the early overgrowth hypothesis of autism, which suggests that early accelerated brain development may be a hallmark of the disorderMethodWe performed a retrospective comparison of HC, height, and weight measurements between 66 toddlers who were later diagnosed with autism and 66 matched controls. These toddlers represent an unbiased regional sample from a single health service provider in the southern district of Israel. Using 4-12 measurements between birth and the age of two, we were able to characterize individual HC, height, and weight development with high precision and fit a negative exponential growth model to the data of each toddler with exceptional accuracyResultsThe analyses revealed that HC sizes and growth rates were not significantly larger in toddlers with autism even when stratifying the autism group based on verbal capabilities at the time of diagnosis. In addition, there were no significant correlations between ADOS scores at the time of diagnosis and HC at any time-point during the first two years of lifeConclusionsThese negative results add to accumulating evidence, which suggest that brain volume is not necessarily larger in toddlers who develop autism. While early brain overgrowth may characterize specific individuals with autism, it is not likely to represent a common etiology of the entire autism population
Spontaneous mutations and transmission distortions of genic copy number variants shape the standing genetic variation inPicea glauca
Authors: Sahli Atef , Giguére Isabelle , Bousquet Jean , MacKay John 
Published: January 2017

AbstractCopy number variations (CNVs) are large genetic variations detected among the individuals of every multicellular organism examined so far. These variations are believed to play an important role in the evolution and adaptation of species. In plants, little is known about the characteristics of CNVs, particularly regarding the rates at which they are generated and the mechanics of their transmission from a generation to the next. Here, we used SNP-array raw intensity data for 55 two-generations families (3663 individuals) to scan the gene space of the conifer treePicea glauca(Moench) Voss for CNVs. We were particularly interested in the abundance, inheritance, spontaneous mutation rate spectrum and the evolutionary consequences they may have on the standing genetic variation of white spruce. Our findings show that CNVs affect a small proportion of the gene space and are predominantly copy number losses. CNVs were either inherited or generated throughde novoevents.De novoCNVs present high rates of spontaneous mutations that vary for different genes and alleles and are correlated with gene expression levels. Most of the inherited CNVs (70%) are transmitted from the parents in violation of Mendelian expectations. These transmission distortions can cause considerable frequency changes between generations and be dependent on whether the heterozygote parents contribute as male or female. Transmission distortions were also influenced by the partner genotype and the parents’ genetic background. This study provides new insights into the effects of different evolutionary forces on copy number variations based on the analysis of a perennial plant.
Escape Excel: a tool for preventing gene symbol and accession conversion errors
Authors: Welsh Eric A. , Stewart Paul A. , Kuenzi Brent M. 
Published: January 2017

AbstractBackgroundMicrosoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text and numbers into dates, scientific notation, and other numerical representations, which may lead to subsequent, irreversible corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary data containing gene lists in Excel format suffer from this issue.ResultsHere, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is available in the Galaxy web environment and can be installed through the Galaxy ToolShed. Escape Excel is also available as a stand-alone, command line Perl script on GitHub (http://www.github.com/pstew/escape_excel). A Galaxy test server implementation is accessible athttp://apostl.moffitt.org.ConclusionsEscape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alpha-numeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data-corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications.
Polymorphism‐aware protein databases – a prerequisite for an unbiased proteomic analysis of natural populations
Authors: Otte Kathrin A. , Schlötterer Christian 
Published: January 2017

AbstractRecent technological advances have increased the throughput of proteomics, facilitating the characterization of molecular phenotypes on the population level, thus bearing the potential to complement transcriptomic analyses. Reference protein databases are crucial for the analysis and quantification, because only peptides in the protein database can be identified. Any peptide carrying an amino acid variant cannot be identified. Because most proteomic studies, even of natural populations, do not account for polymorphisms, we analysed the influence of variant peptides on quantitative proteomic analyses. We used transcriptomic and proteomic data of two Drosophila melanogaster genotypes and identified genotype‐specific variants from RNA‐seq data. We introduce a simple pipeline to include these variants in a polymorphism‐aware protein database and compared the results to an unmodified reference database. The polymorphism‐aware database not only identifies more peptides, but the quantitative values also changed when peptide variants were included. We conclude that proteomic quantification is likely to be biased, in particular for small genes, when polymorphisms are being ignored. Polymorphism‐aware databases may be therefore a key step towards improved proteomic data analyses, especially for the analysis of pooled individuals and the comparison of population samples.
Haplostrips: revealing population structure through haplotype visualization
Authors: Marnetto Davide , Huerta‐Sánchez Emilia 
Published: January 2017

Summary

Population genetic analyses often identify polymorphic variants in regions of the genome that indicate the effect of non‐neutral evolutionary processes. However, in order to obtain deeper insights into the evolutionary processes at play, we often resort to summary statistics, sacrificing the information encoded in the complexity of the original data.

Here, we present haplostrips, a tool to visualize polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command‐line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.

Haplostrips is available at: https://bitbucket.org/dmarnetto/haplostrips. It can be applied in several fields and in all living systems for which a phased haplotype is available to visualize complex effects of, among others: introgression, domestication, selection, demographic events.

Haplostrips can reveal hidden patterns of genetic variation without losing the basic information encoded in variant sequences.
Neil Smith's Long Revolutionary Imperative
Authors: Heynen Nik , Kent Andrew , McKittrick Katherine , Gidwani Vinay , Larner Wendy 
Published: January 2017

AbstractWhether writing about gentrification or nature, the production of space or the politics of scale, uneven development or public space, globalization or revolution, the geographer Neil Smith was nothing if not provocative. Neither Festschrift nor hagiography, this special issue of Antipode critically engages Smith's work—not to unpick the rich tapestry, but to draw the threads out and spin them on in new directions. Consisting of newly commissioned essays by comrades from across the human sciences, it considers the entire range of Smith's oeuvre. This paper introduces the essays by offering not only some thoughts about Smith's intellectual contributions generally, but also new insight into the role he played in Antipode.