bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmids, Viruses, And Other Circular Elements In Rat Gut
Authors: Jørgensen Tue Sparholt , Hansen Martin Asser , Xu Zhuofei , Tabak Michael A. , Sørensen Søren J , Hansen Lars Hestbjerg 
Published: June 2017

AbstractCircular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level.List of figuresSampling sites and Rat gut anatomyRarefaction curves of circular elementsElements shared between environmentsSize distribution plots of rep, mob, stab, capsid carrying elements.Graphical representation of representative elementsReplication genes content, diversityRep_2 plasmid replication gene phylogenyTable Resfams findingsList of appendicesbasic statistics tablePhylogeny of plasmid replication genesList of known plasmids and circular sequences found in 1869 elementsAutomatic identification of identical circular elements with different breaking pointsTest of separation of plasmids and viruses based on predicted, annotated genesNo false positive circular sequences from MG1655 genomic sequencing.
The consequences of polyandry for sibship structures, distributions of relationships and relatedness, and potential for inbreeding in a wild population
Authors: Germain Ryan R. , Arcese Peter , Reid Jane M. 
Published: June 2017

AbstractThe evolutionary benefits of simultaneous polyandry (female multiple mating within a single reproductive event) remain elusive. One potential benefit could arise if polyandry alters sibship structures and consequent relationships and relatedness among females’ descendants, and thereby intrinsically reduces future inbreeding risk (the ‘indirect inbreeding avoidance hypothesis’). However such effects have not been quantified in naturally complex reproductive systems that also encompass iteroparity, overlapping generations, sequential polyandry, and polygyny. We used long-term social and genetic pedigree data from song sparrows (Melospiza melodia) to quantify cross-generational consequences of simultaneous polyandry for offspring sibship structures and distributions of relationships and relatedness among possible mates. Simultaneous polyandry decreased full-sibships and increased half-sibships on average, but such effects varied among females and were smaller than would occur in the absence of sequential polyandry or polygyny. Further, while simultaneous polyandry decreased the overall frequencies of possible matings among adult full-sibs, it increased the frequencies of possible matings among adult half-sibs and more distant relatives. These results imply that the intrinsic consequences of simultaneous polyandry for inbreeding risk could cause weak indirect selection on polyandry, but the magnitude and direction of such effects will depend on complex interactions with other mating system components and the form of inbreeding depression.
Design Principles of Lambda’s Lysis/Lysogeny Decision vis-a-vis Multiplicity of Infection
Authors: Wadhwa Dinkar 
Published: June 2017

AbstractBacteriophage lambda makes a decision between lysis and lysogeny based on the number of coinfecting phages, namely the multiplicity of infection (MoI): lysis at low MoIs; lysogeny at high MoIs. Here, by evaluating various rationally designed models on their ability a) to make the lytic decision at MoI of 1 and the lysogeny decision at MoI of 2, b) to exhibit bistability at both MoIs, and c) to perform accurately in the presence of noise, it is demonstrated that lambda’s lysis/lysogeny decision is based on three features, namely a) mutual repression, b) cooperative positive autoregulation of CI, and c) cooperative binding of the activator protein, not basal expression, triggering positive autoregulatory loop of CI. Cro and CI are sufficient to acquire the first two features. CII is required to acquire the third feature. The quasi-minimal two-protein model for the switch is justified by showing its qualitative equivalence, except for Cro repression ofpRM, to the lambda’s gene regulatory network responsible for the decision. A three-protein simplified version of the lambda’s switch is shown to possess all the three design features. Bistability at MoI of 1 is responsible for lysogen stability, whereas bistability at MoI of 2 imparts stability to lytic development post-infection and especially during prophage induction.
Visual pathways from the perspective of cost functions and multi-task deep neural networks
Authors: Scholte H. Steven , Losch Max M. , Ramakrishnan Kandan , de Haan Edward H.F. , Bohte Sander M. 
Published: June 2017

AbstractVision research has been shaped by the seminal insight that we can understand the higher-tier visual cortex from the perspective of multiple functional pathways with different goals. In this paper, we try to give a computational account of the functional organization of this system by reasoning from the perspective of multi-task deep neural networks. Machine learning has shown that tasks become easier to solve when they are decomposed into subtasks with their own cost function. We hypothesize that the visual system optimizes multiple cost functions of unrelated tasks and this causes the emergence of a ventral pathway dedicated to vision for perception, and a dorsal pathway dedicated to vision for action. To evaluate the functional organization in multi-task deep neural networks, we propose a method that measures the contribution of a unit towards each task, applying it to two networks that have been trained on either two related or two unrelated tasks, using an identical stimulus set. Results show that the network trained on the unrelated tasks shows a decreasing degree of feature representation sharing towards higher-tier layers while the network trained on related tasks uniformly shows high degree of sharing. We conjecture that the method we propose can be used to analyze the anatomical and functional organization of the visual system and beyond. We predict that the degree to which tasks are related is a good descriptor of the degree to which they share downstream cortical-units.
Non-classical estrogen signaling inhibits melanoma and improves response to PD-1 blockade
Authors: Natale Christopher A. , Li Jinyang , Zhang Junqian , Dahal Ankit , Stanger Ben Z. , Ridky Todd W. 
Published: June 2017

AbstractFemale sex and pregnancy are associated with reduced risk of melanoma and improved stage specific survival; however, the mechanism underlying this apparent clinical benefit is unknown. We previously discovered that pregnancy-associated 17β-estradiol drives melanocyte differentiation by activating the nonclassical G-protein coupled estrogen receptor (GPER). Here, we show that pregnancy inhibits melanoma, and that transient GPER activation induces long-term changes in melanocytes, which are associated with increased cellular differentiation and resistance to melanoma. A selective GPER agonist induced c-Myc protein degradation, slowed tumor growth, and inhibited expression of immune suppressive proteins including PD-L1, suggesting that GPER signaling may render melanoma cells more vulnerable to immunotherapy. Systemically delivered GPER agonist was well tolerated, and cooperated synergistically with PD-1 blockade in melanoma-bearing mice to dramatically extend survival. These results thus define GPER as a target for differentiation-based melanoma therapy.SignificanceImmune checkpoint inhibitors including αPD-1 induce durable remissions in only 30% of patients with advanced melanoma. This work demonstrates that αPD-1 efficacy is significantly improved by systemic delivery of a selective agonist of the nonclassical estrogen receptor, GPER, which drives melanoma differentiation and renders tumors more vulnerable to the immune system.
Impairment of zebrafish reproduction upon exposure to melengestrol acetate
Authors: Xiong Kewen , Zhong Chunyun , Wang Xin 
Published: June 2017

AbstractSynthetic progestins contamination is common in the aquatic ecosystem, which may lead to serious health problem on aquatic animals. Melengestrol acetate (MGA) has been detected in the aquatic environment; however, its potential effects on fish reproduction are largely unclear. Here, we aimed to investigate the endocrine disruption and impact of MGA on zebrafish reproduction. Six-month old reproductive zebrafish were exposed to four nominal concentrations of MGA (1,10, 100 and 200 ng/L) for 15 days. Treatment with MGA reduced the egg production with a significant decrease at 200 ng/L. The circulating concentrations of estradiol and testosterone in female zebrafish or 11-keto testosterone in male zebrafish were significantly diminished compared to the non-exposed control fish. The early embryonic development or hatching rates were unaffected during the MGA exposure. Our results indicated that MGA was a potent endocrine disruptor in fish and the fish reproduction could be impaired even during a short-term exposure to MGA.
Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale
Authors: Kotlar Alex V. , Trevino Cristina E. , Zwick Michael E. , Cutler David J. , Wingo Thomas S. 
Published: June 2017

AbstractAccurately selecting relevant alleles in large sequencing experiments remains technically challenging. Bystro (https://bystro.io/) is the first online, cloud-based application that makes variant annotation and filtering accessible to all researchers for terabyte-sized whole-genome experiments containing thousands of samples. Its key innovation is a general-purpose, natural-language search engine that enables users to identify and export alleles and samples of interest in milliseconds. The search engine dramatically simplifies complex filtering tasks that previously required programming experience or specialty command-line programs. Critically, Bystro’s annotation and filtering capabilities are orders of magnitude faster than previous solutions, saving weeks of processing time for large experiments.
Cooling Induced by Uphill Energy Transport in Plant Photosystems
Authors: Sen Koel , Bhattacharya Abhishek , Singha Santiswarup , Dasgupta Maitrayee , Dasgupta Anjan Kr 
Published: June 2017

AbstractThe uphill energy transfer in photosystems implies input energy at higher wavelength leading to energy output at lower wavelength. Briefly, energy is uphill transported from photosystem I (PSI) to photosystem II (PSII), the latter having a lower wavelength emission. This uphill energy transport involves absorption of thermal energy from the surroundings. While such cooling effects have been reported in laser systems we report for the first time a white light driven cooling in thylakoid suspension. The cooling of the surrounding medium by appropriate illumination was illustrated using thermal measurements. Again cooling is inhibited by agents like 3-(3,4-Dichlorophenyl)-1,1-dimethylurea,that block the linear electron flow between the photocenters, implying a dependence of the cooling on interplay between such centers. Furthermore, it is possible to modulate the cooling pattern by addition of external agents like nanopaticles, some favoring further cooling (e.g., Ag nanoparticle) and some like Au or chlorophyll nanoparticles, showing insignificant or even reverse trends. Interestingly, the cooling is invariably associated with the 77K spectra of the thylakoid suspension. With reference to the dark control, an agent causing cooling always increases PSII to PSI ratio and vice versa i.e.,the uphill energy transport. Importantly, the cooling effect, apart from its import role in plant physiology can be exploited artificially for energy saving in post-harvest or food preservation.
Nitric oxide sensing by chlorophylla
Authors: Bhattacharya Abhishek , Biswas Pranjal , Kar Puranjoy , Roychoudhury Piya , Basu Sankar , Ghosh Sanjay , Panda Kaustab , Pal Ruma , Dasgupta Anjan Kr. 
Published: June 2017

AbstractNitric oxide (NO) acts as a signalling molecule that has direct and indirect regulatory roles in various functional processes in biology, though in plant kingdom its role is relatively unexplored. One reason for this is the fact that sensing of NO is always challenging. There are very few probes that can classify the different NO species. The present paper proposes a simple but straightforward way for sensing different NO species using chlorophyll, the source of inspiration being hemoglobin that serves as a NO sink in most mamalian system. The proposed method is able to classify NO from DETA-NONOate or (Z)-1-[N-(2-aminoethyl)-N-(2-ammonioethyl) amino] diazen-1-ium-1,2-diolate, nitrite, nitrate and S-nitrosothiol or SNO. This discrimination is carried out by chlorophylla(chl a) at nano molar (nM) order of sensitivity and at 293K to 310K. Molecular docking reveals the differential binding behaviour of NO and SNO with chlorophyll, the predicted binding affinity matching with the experimental observation. Additional expreiments with diverse range of cyanobacteria reveals that apart from spectroscopic approach the proposed sensing module can be used in microscopic inspection of NO speices. Binding of NO is sensitive to tempertaure and static magnetic field. This provides additional support to the involvement of the porphyrin ring structure to the NO sensing process. This also broadens the scope of the sensing methods as hinted in the text.
Stepwise approach to oocyte depletion inSrymutated XY female mice
Authors: Sakashita Akihiko , Wakai Takuya , Kawabata Yukiko , Nishimura Chiaki , Sotomaru Yusuke , Kono Tomohiro 
Published: June 2017

AbstractLittle is known regarding the mechanisms underlying infertility in male-to-female sex-reversed females. To gain a better understanding of germ cell dysfunction in this condition, we produced XYsry−-females via the CRISPR/Cas9 system in C57BL/6 inbred strain mice. Mutant mice showed severe attrition of germ cells during foetal development, resulting in depletion of ovarian germ cells before sexual maturation. Comprehensive transcriptome analysis of embryonic day 13.5 primordial germ cells (PGCs) and postnatal day 1 oocytes demonstrated that XYsry−-PGCs had already deviated from the developmental process at the mitotic stage. In addition, XYsry−-oocytes resulted in meiotic disruption and developmental failure, and the genes related to these processes were significantly changed. This grievous disruption, which caused germ cell deterioration in XYsry−-females, was shown to proceed from the germ cells themselves. These results provide novel insight into the germ cell depletion of sex-reversed mice as well as into disorders of sex differentiation in human, such as ‘Swyer syndrome’, wherein patients present as typical females albeit with an XY karyotype and infertile.
Pre-dispersal conditions and presence of opposite sex modulate density dependence and sex bias of dispersal
Authors: Mishra Abhishek , Tung Sudipta , Sruti V.R. Shree , Sadiq Mohammed Aamir , Srivathsa Sahana , Dey Sutirth 
Published: June 2017

ABSTRACTDensity-dependent dispersal (DDD) has been demonstrated in many species and has several ecological and evolutionary consequences. Yet we know little about how robust DDD is to the various conditions experienced by individuals. In this study, we use three independent experiments on laboratory populations ofDrosophila melanogasterto examine the effects of pre-dispersal adult density, sex of the dispersers and presence of mates on the robustness of DDD patterns. We show that DDD can be greatly affected by both pre-dispersal density and interaction between the sexes. Moreover, the direction of sex-biased dispersal can reverse completely due to an interaction between the pre-dispersal and dispersal densities. We also show that interaction between the sexes can lead to negative DDD at the population level, even if, by themselves, neither sex exhibits DDD. Finally, we discuss potential implications of our results for processes like evolutionary rescue from extinctions and genetic divergence of populations.
Non-canonical secondary structures arising from non-B-DNA motifs are determinants of mutagenesis
Authors: Georgakopoulos-Soares Ilias , Morganella Sandro , Jain Naman , Hemberg Martin , Nik-Zainal Serena 
Published: June 2017

SummarySomatic mutations show variation in density across cancer genomes. Previous studies have shown that chromatin organization and replication time domains are correlated with and thus predictive of this variation1,2,3,4,5. Here, we analyse 1,809 whole-genome sequences from nine cancer types6,7,8to show that a subset of repetitive DNA sequences called non-B motifs that predict non-canonical secondary structure formation9,10,11,12can independently account for variation in mutation density. However, combined with epigenetic factors and replication timing, the variance explained can be improved to 43-76%. Intriguingly, ~2-fold mutation enrichment is observed directly within non-B motifs, is focused on exposed structural components, and is dependent on physical properties that are optimal for secondary structure formation. Therefore, there is mounting evidence that secondary structures arising from non-B motifs are not simply associated with increased mutation density, they are possibly causally implicated. Our results suggest that they are determinants of mutagenesis and increase the likelihood of recurrent mutations in the genome13,6. This analysis calls for caution in the interpretation of recurrent mutations and highlights the importance of taking non-B motifs, that can simply be inferred from the reference sequence, into consideration in background models of mutability henceforth.
Learn to Track: Deep Learning for Tractography
Authors: Poulin Philippe , Côté Marc-Alexandre , Houde Jean-Christophe , Petit Laurent , Neher Peter F. , Maier-Hein Klaus H. , Larochelle Hugo , Descoteaux Maxime 
Published: June 2017

AbstractWe show that deep learning techniques can be applied successfully to fiber tractography. Specifically, we use feed-forward and recurrent neural networks to learn the generation process of streamlines directly from diffusion-weighted imaging (DWI) data. Furthermore, we empirically study the behavior of the proposed models on a realistic white matter phantom with known ground truth. We show that their performance is competitive to that of commonly used techniques, even when the models are used on DWI data unseen at training time. We also show that our models are able to recover high spatial coverage of the ground truth white matter pathways while better controlling the number of false connections. In fact, our experiments suggest that exploiting past information within a streamline's trajectory during tracking helps predict the following direction.
Mcm10 functions to isomerize CMG-DNA for replisome bypass of DNA blocks
Authors: Langston Lance D. , Mayle Ryan , Schauer Grant D. , Yurieva Olga , Zhang Daniel , Yao Nina Y. , Georgescu Roxana , O’Donnell Michael E. 
Published: June 2017

AbstractReplicative helicases of all cell types are rings that unwind DNA by steric exclusion in which the helicase ring only encircles the tracking strand, excluding the other strand outside the ring. Steric exclusion mediated unwinding enables helicase rings to bypass blocks on the strand that is excluded from the central channel. Unlike other replicative helicases, eukaryotic CMG encircles duplex DNA at a forked junction and is stopped by a block on the non-tracking (lagging) strand. This report demonstrates that Mcm10, an essential replication protein unique to eukaryotes, binds CMG and enables the replisome to bypass blocks on the non-tracking strand, implying that Mcm10 isomerizes the CMG-DNA complex to position only one strand through the central channel. A similar CMG-DNA isomerization is needed at the origin for head-to-head CMGs to bypass one another during formation of bidirectional replication forks.
Networks around entrepreneurs: gendering in China and countries around the Persian Gulf
Authors: Bertelsen Rasmus Gjedssø , Ashourizadeh Shayegheh , Jensen Kent Wickstrøm , Schøtt Thomas , Cheng Yuan 
Published: June 2017

Purpose
Entrepreneurs are networking with others to get advice for their businesses. The networking differs between men and women; notably, men are more often networking for advice in the public sphere and women are more often networking for advice in the private sphere. The purpose of this study is to account for how such gendering of entrepreneurs’ networks of advisors differs between societies and cultures.

Design/methodology/approach
Based on survey data from the Global Entrepreneurships Monitor, a sample of 16,365 entrepreneurs is used to compare the gendering of entrepreneurs’ networks in China and five countries largely located around the Persian Gulf, namely Yemen, Iran, Saudi Arabia, Qatar and the United Arab Emirates.

Findings
Analyses show that female entrepreneurs tend to have slightly larger private sphere networks than male entrepreneurs. The differences between male and female entrepreneurs’ networking in the public sphere are considerably larger. Societal differences in the relative prominence of networking in the public and private spheres, and the gendering hereof, correspond well to cultural and socio-economic societal differences. In particular, the authors found marked differences among the religiously conservative and politically autocratic Gulf states.

Research limitations/implications
As a main limitation to this study, the data disclose only the gender of the entrepreneur, but not the gender of each advisor in the network around the entrepreneur. Thus, the authors cannot tell the extent to which men and women interact with each other. This limitation along with the findings of this study point to a need for further research on the extent to which genders are structurally mixed or separated as entrepreneurs network for advice in the public sphere. In addition, the large migrant populations in some Arab states raise questions of the ethnicity of entrepreneurs and advisors.

Originality/value
Results from this study create novel and nuanced understandings about the differences in the gendering of entrepreneurs’ networking in China and countries around Persian Gulf. Such understandings provide valuable input to the knowledge of how to better use the entrepreneurial potential from both men and women in different cultures. The sample is fairly representative of entrepreneur populations, and the results can be generalized to these countries.