bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting dispersed duplications in high-throughput sequencing data using a database-free approach
Authors: Kroon M. , Lameijer E.W. , Lakenberg N. , Hehir-Kwa J.Y. , Thung D.T. , Slagboom P.E. , Kok J.N. , Ye K. 
Published: October 2015

Abstract
Motivation: Dispersed duplications (DDs) such as transposon element insertions and copy number variations are ubiquitous in the human genome. They have attracted the interest of biologists as well as medical researchers due to their role in both evolution and disease. The efforts of discovering DDs in high-throughput sequencing data are currently dominated by database-oriented approaches that require pre-existing knowledge of the DD elements to be detected.
Results: We present dd_detection, a database-free approach to finding DD events in high-throughput sequencing data. dd_detection is able to detect DDs purely from paired-end read alignments. We show in a comparative study that this method is able to compete with database-oriented approaches in recovering validated transposon insertion events. We also experimentally validate the predictions of dd_detection on a human DNA sample, showing that it can find not only duplicated elements present in common databases but also DDs of novel type.
Availability and implementation: The software presented in this article is open source and available from https://bitbucket.org/mkroon/dd_detection
Contact: kye@genome.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts
Authors: Capitani Guido , Duarte Jose M. , Baskaran Kumaran , Bliven Spencer , Somody Joseph C. 
Published: October 2015

Abstract
Modern structural biology still draws the vast majority of information from crystallography, a technique where the objects being investigated are embedded in a crystal lattice. Given the complexity and variety of those objects, it becomes fundamental to computationally assess which of the interfaces in the lattice are biologically relevant and which are simply crystal contacts. Since the mid-1990s, several approaches have been applied to obtain high-accuracy classification of crystal contacts and biological protein–protein interfaces. This review provides an overview of the concepts and main approaches to protein interface classification: thermodynamic estimation of interface stability, evolutionary approaches based on conservation of interface residues, and co-occurrence of the interface across different crystal forms. Among the three categories, evolutionary approaches offer the strongest promise for improvement, thanks to the incessant growth in sequence knowledge. Importantly, protein interface classification algorithms can also be used on multimeric structures obtained using other high-resolution techniques or for protein assembly design or validation purposes. A key issue linked to protein interface classification is the identification of the biological assembly of a crystal structure and the analysis of its symmetry. Here, we highlight the most important concepts and problems to be overcome in assembly prediction. Over the next few years, tools and concepts of interface classification will probably become more frequently used and integrated in several areas of structural biology and structural bioinformatics. Among the main challenges for the future are better addressing of weak interfaces and the application of interface classification concepts to prediction problems like protein–protein docking.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: guido.capitani@psi.ch
Vitamin A deficient mice exhibit increased viral antigens and enhanced cytokine/chemokine production in nasal tissues following respiratory virus infection despite the presence of FoxP3 + T cells
Authors: Penkert Rhiannon R. , Surman Sherri L. , Jones Bart G. , Sealy Robert E. , Vogel Peter , Neale Geoffrey , Hurwitz Julia L. 
Published: October 2015

AbstractThe World Health Organization (WHO) estimates that 250 million children under the age of five suffer from vitamin A deficiencies (VAD). Individuals with VAD experience higher rates of mortality and increased morbidity during enteric and respiratory infections compared with those who are vitamin A sufficient. Previously, our laboratory has demonstrated that VAD mice have significantly impaired virus-specific IgA and CD8 + T-cell responses in the airways. Here, we demonstrate that VAD mice experience enhanced cytokine/chemokine gene expression and release in the respiratory tract 10 days following virus infection compared with control vitamin A sufficient animals. Cytokines/chemokines that are reproducibly up-regulated at the gene expression and protein levels include IFNγ and IL-6. Despite previous indications that cytokine dysregulation in VAD animals might reflect low forkhead box P3 (FoxP3)-positive regulatory T-cell frequencies, we found no reduction in FoxP3 + T cells in VAD respiratory tissues. As an alternative explanation for the high cytokine levels, we found that the extent of virus infection and the persistence of viral antigens were increased on day 10 post-infection in VAD animals compared with controls, and consequently that respiratory tract tissues had an increased potential to activate virus-specific T cells. Results encourage cautious management of viral infections in patients with VAD, as efforts to enhance FoxP3 + T cell frequencies and quell immune effectors could potentially exacerbate disease if the virus has not been cleared.
Chemical profile of the cutaneous gland secretions from male pampas deer (
Ozotoceros bezoarticus
)
Authors: Rossini Carmen , Ungerfeld Rodolfo 
Published: October 2015

Abstract
Various cutaneous glands have been identified as sources of chemical signals that mediate many social interactions in deer. The pampas deer, a species considered near threatened, inhabits grasslands of South America. In this work, the chemical compositions from preorbital, tarsal, and digital gland secretions of semi-captive males were characterized by gas chromatography–mass spectrometry. The composition of these secretions showed a great complexity, with 143 compounds detected. Hierarchical cluster and principal component analyses show no relation to age or secretion type. Five compound classes (esters, fatty alcohols, lactones, sterols, and sulphuretted) differed with glands. The chemical complexity of the secretions, the individual differences in the whole compounds composition, and the absence of clustering by age lead to the hypothesis that these secretions may encode at once for individual information and for social status information.
Varias glándulas cutáneas han sido identificadas como productoras de señales químicas que median interacciones sociales en losciervos. El venado de las pampas es una especie considerada casi amenazada que habita los pastizales de Sudamérica. En este trabajo se caracterizó la composición química de las secreciones de las glándulas preorbital, tarsal e interdigital de machos por cromatografía de gases-espectrometría de masas. Estas secreciones mostraron una gran complejidad en su composición, con 143 compuestos detectados. No se observó ninguna agrupación de compuestos relacionada con la edad o el tipo de secreción. Cinco clases de compuestos (ésteres, alcoholes grasos, lactonas, esteroles, y compuestos azufrados) difirieron de acuerdo al origen glandular. La complejidad química de las secreciones, las diferencias individuales en dicha composición, y la ausencia de agrupamiento por edad, llevan a postular la hipótesis de que estas secreciones pueden codificar a la vez tanto información individual como del estado social.
Kozai–Lidov cycles towards the limit of circumbinary planets
Authors: Martin David V. , Triaud Amaury H. M. J. 
Published: October 2015

Abstract
In this Letter, we answer a simple question: Can a misaligned circumbinary planet induce Kozai–Lidov cycles on an inner stellar binary? We use known analytic equations to analyse the behaviour of the Kozai–Lidov effect as the outer mass is made small. We demonstrate a significant departure from the traditional symmetry, critical angles and amplitude of the effect. Aside from massive planets on near-polar orbits, circumbinary planetary systems are devoid of Kozai–Lidov cycles. This has positive implications for the existence of highly misaligned circumbinary planets: an observationally unexplored and theoretically important parameter space.
Paleoaltimetry reconstructions of the Tibetan Plateau: progress and contradictions
Authors: Deng Tao , Ding Lin 
Published: October 2015

AbstractOver the last two decades, many quantitative paleoaltimetry reconstructions of the Tibetan Plateau have been published, but they are still preliminary and controversial, although several approaches have been combined paleontology and geochemistry, including vertebrate, plant, and pollen fossils as well as oxygen, carbon, and hydrogen isotopes. The Tibetan Plateau is the youngest and highest plateau on Earth, and its paleoaltimetry reconstructions are crucial to interpret its geodynamic evolution and to understand the climatic changes in Asia. Uplift histories of the Tibetan Plateau based on different proxies differ considerably, and two viewpoints are pointedly opposing on the paleoaltimetry estimations of the Tibetan Plateau. One viewpoint is that the Tibetan Plateau did not strongly uplift to reach its modern elevation until the Late Miocene, but another one, mainly based on stable isotopes, argues that the Tibetan Plateau formed early during the Indo-Asian collision and reached its modern elevation in the Paleogene or by the Middle Miocene. With either a geochemical or paleontological approach, the present is used as the key to the past. However, there are great difficulties because modern processes of isotopic fractionation and species for creature distribution are not easily precisely determined. In addition, the climatic and environmental backgrounds of past geological times have massive differences from the present, and associated adjustments are influenced by many human factors. In the future work, the applications of multidisciplinary comprehensive methods and cross-checks of their results will be productive, and we look forward to achieving more reliable estimates for paleoelevations of the Tibetan Plateau.
Bargaining, Sorting, and the Gender Wage Gap: Quantifying the Impact of Firms on the Relative Pay of Women *
Authors: Card David , Cardoso Ana Rute , Kline Patrick 
Published: October 2015

AbstractThere is growing evidence that firm-specific pay premiums are an important source of wage inequality. These premiums will contribute to the gender wage gap if women are less likely to work at high-paying firms or if women negotiate (or are offered) worse wage bargains with their employers than men. Using longitudinal data on the hourly wages of Portuguese workers matched with income statement information for firms, we show that the wages of both men and women contain firm-specific premiums that are strongly correlated with simple measures of the potential bargaining surplus at each firm. We then show how the impact of these firm-specific pay differentials on the gender wage gap can be decomposed into a combination of sorting and bargaining effects. We find that women are less likely to work at firms that pay higher premiums to either gender, with sorting effects being most important for low- and middle-skilled workers. We also find that women receive only 90% of the firm-specific pay premiums earned by men. Importantly, we find the same gender gap in the responses of wages to changes in potential surplus over time. Taken together, the combination of sorting and bargaining effects explain about one-fifth of the cross-sectional gender wage gap in Portugal.
Exophiala phaeomuriformis Fungal Keratitis: Case Report and In Vivo Confocal Microscopy Findings
Authors: Aggarwal Shruti , Yamaguchi Takefumi , Dana Reza , Hamrah Pedram 
Published: October 2015

Purpose:
Corneal infections, particularly fungal keratitis due to rare fungal species, pose a diagnostic and therapeutic challenge because of difficulty in identification and varying susceptibility profiles. In this study, we report the first case of fungal keratitis because of Exophiala phaeomuriformis.

Methods:
We report the clinical findings and microbial identification techniques of a case of fungal keratitis due to E. phaeomuriformis. An 84-year-old woman presented with redness, pain, and itching in the left eye for 2 weeks. Slit-lamp biomicroscopy revealed one broken suture from previous penetrating keratoplasty (PKP), black infiltrates at the 4-o'clock position, without an overlying epithelial defect and hypopyon. Microbial identification was based cultures on Sabouraud dextrose agar and DNA sequencing and correlations to laser in vivo confocal microscopy (IVCM; Heidelberg Retinal Tomograph 3/Rostock Cornea Module, Heidelberg Engineering) and multiphoton microscopy (Ultima Microscope; Prairie Technologies) images.

Results:
Slit-lamp biomicroscopy revealed one broken suture from previous PKP, black infiltrates at the 4-o'clock position, without an overlying epithelial defect and hypopyon. Based on a clinical suspicion of fungal keratitis, antifungals and fortified antibiotics were started. However, the patient did not respond to therapy and required urgent PKP. After surgery, the patient was maintained on topical and systemic voriconazole and also topical 2% cyclosporine for 5 months because of possibility of scleral involvement noticed during surgery. At the end of the treatment period, her vision improved from hand motion to 20/40, with no recurrence observed in a follow-up period of 1 year. Results of diagnostic tests were supported by fungal elements in stroma on IVCM. Culture from the infiltrate grew black yeast. DNA sequencing led to the diagnosis of E. phaeomuriformis keratitis. Antifungal susceptibility testing revealed sensitivity to voriconazole.

Conclusion:
This is, to our knowledge, the first reported case of E. phaeomuriformis fungal keratitis. Diagnostic testing included slit-lamp biomicroscopy, which revealed pigmented infiltrates, culture plates grew black yeast, microscopy showed branched fungal hyphae with budding conidia, and physiological features showed tolerance to high temperatures, nitrate assimilation, and ribosomal DNA sequencing. Collectively, these tests demonstrate unique features seen for this microorganism. High suspicion should be kept with pigmented infiltrates and with dark yeast on culture plates. Prompt and aggressive medical management with voriconazole or therapeutic PKP in nonresponsive cases is essential to prevent irreversible loss of vision.
Tear Osmolarity and Tear Film Parameters in Patients With Ocular Rosacea
Authors: Karaman Erdur Sevil , Eliacik Mustafa , Kocabora Mehmet Selim , Balevi Ali , Demirci Goktug , Ozsutcu Mustafa , Gulkilik Gokhan , Aras Cengiz 
Published: October 2015

Objectives:
The aim of this study was to evaluate tear osmolarity and tear film parameters in patients with ocular rosacea.

Methods:
In a single center, 25 eyes of 25 patients with ocular rosacea (group 1), 25 eyes of 25 patients with rosacea without ocular involvement (group 2), and 20 eyes of 20 healthy individuals (group 3) were evaluated using the Ocular Surface Disease Index (OSDI) questionnaire, Schirmer I test, tear film break-up time (TBUT), scoring of ocular surface fluorescein staining using modified Oxford scale, and tear osmolarity.

Results:
Tear osmolarity values, OSDI and Oxford scale scores were significantly higher in group 1 than in groups 2 and 3 (P<0.001 for all). Schirmer I test and TBUT in group 1 were significantly lower than in groups 2 and 3 (P<0.001 for all). There were no significant differences in OSDI, Schirmer I test, TBUT, Oxford scores, or tear osmolarity between groups 2 and 3 (P=0.629, P=0.175, P=0.713, P=865, and P=0.388, respectively).

Conclusions:
This study showed that ocular rosacea is associated with tear hyperosmolarity and tear film dysfunction.
Dietary Breadth is Positively Correlated with Venom Complexity in Cone Snails
Authors: Phuong Mark A , Mahardika Gusti N , Alfaro Michael E 
Published: October 2015

AbstractAlthough diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist. We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90% of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. Our results suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. These results indicate that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.
Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic variation
Authors: Wright Kevin M. , Gaudinier Allison , Hellsten Uffe , Jeong Annie L. , Sreedasyam Avinash , Holalu Srinidhi , Vegara Miguel Flores , Carvajal Arianti Rojas , Xu Chenling , Chapman Jarrod A. , Franks Robert , Grimwood Jane , Barry Kerrie , Jenkins Jerry , Lovell John , Coop Graham , Schmutz Jeremy , Kelly John K. , Rokhsar Daniel S. , Blackman Benjamin K. , Willis John H. 
Published: October 2015

AbstractAnthropogenic environmental changes create evolutionary pressures on populations to adapt to novel stresses. It is as yet unclear, when populations respond to these selective pressures, the extent to which this results in convergent genetic evolution and whether convergence is due to independent mutations or shared ancestral variation. We address these questions using a classic example of adaptation by natural selection by investigating the rapid colonization of the plant speciesMimulus guttatusto copper contaminated soils. We use field-based reciprocal transplant experiments to demonstrate that mine alleles at a major copper tolerance locus, Tol1, are strongly selected in the mine environment. We assemble the genome of a mine adapted genotype and identify regions of this genome in tight genetic linkage to Tol1. We discover a set of a multicopper oxidase genes that are genetically linked to Tol1 and exhibit large differences in expression between tolerant and non-tolerant genotypes. We overexpressed this gene inM. guttatusandA. thalianaand found the introduced gene contributes to enhanced copper tolerance. We identify convergent adaptation loci that are additional to Tol1 by measuring genome-wide differences in allele frequency between pairs of mine and off-mine populations and narrow these regions to specific candidate genes using differences in protein sequence and gene expression. Furthermore, patterns of genetic variation at the two most differentiated candidate loci are consistent with selection acting upon alleles that predates the existence of the copper mine habitat. These results suggest that adaptation to the mine habitat occurred via selection on ancestral variation, rather than independentde novomutations or migration between populations.
Elevation of linkage disequilibrium above neutral expectations in ancestral and derived populations ofDrosophila melanogaster
Authors: Garud Nandita R. , Petrov Dmitri A. 
Published: October 2015

ABSTRACTThe extent to which selection and demography impact patterns of genetic diversity in natural populations ofDrosophila melanogasteris yet to be fully understood. We previously observed that the pattern of LD at scales of ~10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. Further, we demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which this pattern is specific to this derived and admixed population is unknown. Neither is it clear whether such a pattern may have arisen as a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze > 100 fully sequenced strains from Zambia, an ancestral population to the Raleigh population, that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. This data set allows us to determine whether patterns of elevated LD and signatures of abundant soft sweeps are generic to multiple populations ofD. melanogasteror whether they are generated either by inbreeding, bottlenecks or admixture in the DGRP dataset. We find an elevation in long-range LD and haplotype homozygosity in the Zambian dataset, confirming the result from the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for many sources of LD in the data including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic inD. melanogaster.