bluuebunny/crossref_metadata_2025_split huggingface dataset:
TatA complexes exhibit a marked change in organisation in response to expression of the TatBC complex
Authors: Smith Sarah M. , Yarwood Andrew , Fleck Roland A. , Robinson Colin , Smith Corinne J. 
Published: October 2016

AbstractThe twin arginine translocation (Tat) system is an integral membrane protein complex that accomplishes the remarkable feat of transporting large, fully-folded polypeptides across the inner membrane of bacteria, into the periplasm. InEscherichia coliTat is comprised of three membrane proteins: TatA, TatB and TatC. How these proteins arrange themselves in the inner membrane to permit passage of Tat substrates, whilst maintaining membrane integrity, is still poorly understood. TatA is the most abundant component of this complex and facilitates assembly of the transport mechanism. We have utilised immunogold labelling in combination with array tomography to gain insight into the localisation and distribution of the TatA protein inE. colicells. We show that TatA exhibits a uniform distribution throughout the inner membrane ofE. coliand that altering the expression of TatBC shows a previously uncharacterised distribution of TatA in the inner membrane. Array tomography was used to provide our first insight into this altered distribution of TatA in 3D space, revealing that this protein forms linear clusters in the inner membrane ofE.coli upon increased expression of TatBC. This is the first indication that TatA organisation in the inner membrane alters in response to changes in Tat subunit stoichiometry.Summary statementThe volumetric electron-microscopy technique, array tomography, revealed a novel distribution of TatA protein (from the twin arginine translocase complex), inEscherichia coli.
Comparative transcriptome analysis by deep RNA sequencing at early stage of skin pigmentation in goats (Capra hircus)
Authors: Ren Hangxing , Wang Gaofu , Jiang Jing , Liu Liangjia , Li Nianfu , Li Jie , Fu Lin , Zhang Haiyan , Na Risu , Huang Yongfu , Zhang Li , Chen Lei , Huang Yong , Zhou Peng 
Published: October 2016

ABSTRACTAlthough specific genes have been found to be associated with skin pigmentation, the global gene expression profile for the early stage of skin pigmentation and development in mammals is still not well understood. Here we reported a rare natural group of goat (Youzhou dark goat) featuring the dark skin of body including the visible mucous membranes, which may be an exclusive kind of large mammalian species with this special phenotype so far. In the present study, we characterized the 100-day-old fetal skin transcriptome in hyperpigmented (dark-skinned) and wild-type (white-skinned) goats using deep RNA-sequencing. A total of 923,013,870 raw reads from 6 libraries were obtained, and a large number of alternative splicing events were identified in the transcriptome of fetal skin, including the well-known melanogenic genesASIP,TYRP1, andDCT, which were differentially expressed in the skin between the dark-skinned and white-skinned goats. Further analysis demonstrated that differential genes includingASIP,TYRP1,DCT,WNT2,RAB27A,FZD4, andCREB3L1were significantly overrepresented in themelanogenesispathway and several biological process associated with pigmentation. On the other hand, we identified 1616 novel transcripts in goat skin based on the characteristics of their expression level and gene composition. These novel transcripts may represent two distinct groups of nucleic acid molecules. Our findings contribute to the understanding of the characteristics of global gene expression at early stages of skin pigmentation and development, as well as describe an animal model for human diseases associated with pigmentation.
Optimal foraging models reveal barriers and stepping stones to the evolution of host-range generalism in bacteriophage
Authors: Draghi Jeremy 
Published: October 2016

ABSTRACTThe nature and stability of coexistence of specialist species with more generalized competitors present theoretical questions that have been difficult to resolve. Recent surveys of bacteriophage host-ranges suggest that generalist phage often coexistent with specialists. However, previous theoretical work has explained this coexistence only in terms of strict genetic trade-offs, which are not consistently observed when phage are challenged to evolve to multiple hosts in laboratory environments. Here we use the framework of optimal foraging to identify conditions that might prevent generalists from outcompeting specialist relatives. Our analysis shows that heterogeneities in phage life-history properties make host-range specialist more viable, and that endogenous fluctuations in host density permit a narrow window of stable coexistence between specialists and generalists without the need for genetic trade-offs. These results are especially relevant for understanding the barriers to the evolution of broader host-ranges in bacteriophage and other pathogens with similar life-cycles.
GW-CALL: Accurate Genome-Wide Variant Caller
Authors: Ghareghani M. , Motahari S. A. , Khazaei S. , Tavassolipour M. 
Published: October 2016

AbstractThe main challenge in reliable variant calling using DNA reads is to extract information from reads mappable to multiple locations on the reference genome. Conventional approaches ignore these reads and rely on reads mappable uniquely to the reference genome. These approaches fail to perform satisfactorily in variant calling within repeat regions which are abundant in many species including homo sapiens. This, in turn, lowers the reliability of any downstream analysis including poor performance in genome-wide association studies. GW-CALL, a fast and accurate variant caller, is proposed. GW-CALL exploits information of all reads in a genome-wide decision making process. In particular, it partitions the genome into several independent regions called clusters and incorporates an efficient algorithm to use all reads belonging to a cluster in calling variants within that cluster.AvailabilityGW-CALL is implemented in C++ and is freely available at URL:brl.ce.sharif.edu/gwcall.
Exploratory bioinformatics analysis reveals importance of “junk” DNA in early embryo development
Authors: Ge Steven Xijin 
Published: October 2016

AbstractBackgroundInstead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to investigate how the early mouse embryos develop from fertilized eggs through a complex, poorly understood process.ResultsStarting with a single-cell RNA-seq dataset of 259 mouse embryonic cells from zygote to blastocyst stages, we reconstructed the temporal and spatial dynamics of gene expression. Our analyses revealed similarities in the expression patterns of regular genes and those of retrotransposons, and the enrichment of transposable elements in the promoters of corresponding genes. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. The presence of B1 and B2 SINEs (Short Interspersed Nuclear Elements) in promoters is highly correlated with broad upregulation of intracellular genes in a dosage-and distance-dependent manner. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. Promoters for genes specifically expressed in embryonic stem cells (ESCs) are rich in B1 and B2 SINEs, but low in CpG islands.ConclusionsOur results provide evidence that transposable elements may play a significant role in establishing the expression landscape in early embryos and stem cells. This study also demonstrates that open-ended, exploratory analysis aimed at a broad understanding of a complex process can pinpoint specific mechanisms for further study.Major findingSingle-cell RNA-seq data enables estimation of retrotransposon expression during PDSimilar expression dynamics of retrotransposons and regular genes during PDLong terminal repeats may be essential for the 1stwave of gene expressionObox homeobox factors are possible regulators of PD, upstream of Zscan4SINE repeats predict expression of nearby genes in murine, human and bovine embryosExploratory analysis of large single-cell data pinpoints developmental pathways
Research article, Biological Sciences - Anthropology, Genetics Of cats and men: the paleogenetic history of the dispersal of cats in the ancient world
Authors: Ottoni Claudio , Van Neer Wim , De Cupere Bea , Daligault Julien , Guimaraes Silvia , Peters Joris , Spassov Nikolai , Prendergast Mary E. , Boivin Nicole , Morales Arturo , Bălăşescu Adrian , Becker Cornelia , Benecke Norbert , Boronenanţ Adina , Buitenhuis Hijlke , Chahoud Jwana , Crowther Alison , Llorente Laura , Manaseryan Nina , Monchot Hervé , Onar Vedat , Osypińska Marta , Putelat Olivier , Studer Jacqueline , Wierer Ursula , Decorte Ronny , Grange Thierry , Geigl Eva-Maria 
Published: October 2016

AbstractThe origin and dispersal of the domestic cat remain elusive despite its importance to human societies around the world. Archaeological evidence for domestication centers in the Near East and in Egypt is contested, and genetic data on modern cats show thatFelis silvestris lybica, the subspecies of wild cat inhabiting at present the Near East and Northern Africa, is the only ancestor of the domestic cat. Here we provide the first broad geographic and chronological dataset of ancient cat mtDNA sequences, drawing on archaeological specimens from across western Eurasia and northern and eastern Africa, dating from throughout the Holocene and spanning ~9,000 years. We characterized the ancient phylogeography ofF. s. lybica,showing that it expanded up to southeastern Europe prior to the Neolithic, and reconstructed the subsequent movements that profoundly transformed its distribution and shaped its early cultural history. We found that maternal lineages from both the Near East and Egypt contributed to the gene pool of the domestic cat at different historical times, with the Near Eastern population providing the first major contribution during the Neolithic and the Egyptian cat spreading efficiently across the Old World during the Classical period. This expansion pattern and range suggest dispersal along maritime and terrestrial routes of trade and connectivity. Late trait selection is suggested by the first occurrence in our dataset of the major allele for blotched-tabby body marking not earlier than during the Late Middle Ages.SignificanceThe cat has long been important to human societies as a pest-control agent, object of symbolic value, and companion animal, but little is known about its domestication process and early anthropogenic dispersal. Our DNA analyses of geographically and temporally widespread archaeological cat remains show that while the cat’s world-wide conquest began in prehistoric times, when tamed cats accompanied humans on their journeys over land and sea, it gained momentum during the Classical period, when the Egyptian cat successfully spread throughout the ancient world. The appearance of a new coat pattern at the end of the Middle Ages suggests late breeding control that might explain the semi-domestic status of the cat. This distinguishes the domestication process of cats from that of most other domesticates.
Energy subtraction angiography is comparable to digital subtraction angiography in terms of iodine Rose SNR
Authors: Burton Christiane S. , Mayo John R. , Cunningham Ian A. 
Published: October 2016

PurposeX‐ray digital subtraction angiography (DSA) is widely used for vascular imaging. However, motion artifacts render it largely unsuccessful for some applications including cardiac imaging. Dual‐energy imaging using fast kV switching was proposed in the past to provide the benefits of DSA with fewer motion artifacts, but image quality was inferior to DSA. This study compares the iodine Rose SNR that can be achieved using dual‐energy methods, called energy‐subtraction angiography (ESA), with that of DSA and examines the technical conditions required to achieve near‐optimal SNR.MethodsA Rose SNR model is described, experimentally validated, and used to compare ESA with DSA. The model considers detector quantum efficiency, readout noise (quantum‐limit exposure), and scatter‐to‐primary ratio.ResultsThe theoretical Rose SNR showed excellent agreement with experimental results for both ESA and DSA images, and shows that near‐optimal SNR is harder to achieve with ESA than DSA. In comparison to DSA, ESA requires: (1) high detector quantum efficiency at a higher energy (120 kV); (2) lower detector readout noise by a factor of four (approximately 0.005 μGy air KERMA or lower); and (3) lower scatter‐to‐primary ratio by a factor of three (approximately 0.05 or lower). These conditions were not achievable in the past, and remain difficult but not impossible to achieve at present.ConclusionsESA and DSA can provide similar iodine Rose SNR for the same patient exposure, but only when satisfying the above conditions. This may explain why dual‐energy methods have been unsuccessful in the past and suggests ESA methods may offer a viable alternative to DSA when implemented under optimal conditions.
A scintillator‐based approach to monitor secondary neutron production during proton therapy
Authors: Clarke S. D. , Pryser E. , Wieger B. M. , Pozzi S. A. , Haelg R. A. , Bashkirov V. A. , Schulte R. W. 
Published: October 2016

PurposeThe primary objective of this work is to measure the secondary neutron field produced by an uncollimated proton pencil beam impinging on different tissue‐equivalent phantom materials using organic scintillation detectors. Additionally, the Monte Carlo code mcnpx‐PoliMi was used to simulate the detector response for comparison to the measured data. Comparison of the measured and simulated data will validate this approach for monitoring secondary neutron dose during proton therapy.MethodsProton beams of 155‐ and 200‐MeV were used to irradiate a variety of phantom materials and secondary particles were detected using organic liquid scintillators. These detectors are sensitive to fast neutrons and gamma rays: pulse shape discrimination was used to classify each detected pulse as either a neutron or a gamma ray. The mcnpx‐PoliMi code was used to simulate the secondary neutron field produced during proton irradiation of the same tissue‐equivalent phantom materials.ResultsAn experiment was performed at the Loma Linda University Medical Center proton therapy research beam line and corresponding models were created using the mcnpx‐PoliMi code. The authors’ analysis showed agreement between the simulations and the measurements. The simulated detector response can be used to validate the simulations of neutron and gamma doses on a particular beam line with or without a phantom.ConclusionsThe authors have demonstrated a method of monitoring the neutron component of the secondary radiation field produced by therapeutic protons. The method relies on direct detection of secondary neutrons and gamma rays using organic scintillation detectors. These detectors are sensitive over the full range of biologically relevant neutron energies above 0.5 MeV and allow effective discrimination between neutron and photon dose. Because the detector system is portable, the described system could be used in the future to evaluate secondary neutron and gamma doses on various clinical beam lines for commissioning and prospective data collection in pediatric patients treated with proton therapy.
Mineral weathering and soil development in the earliest land plant ecosystems
Authors: Mitchell Ria L. , Cuadros Javier , Duckett Jeffrey G. , Pressel Silvia , Mavris Christian , Sykes Dan , Najorka Jens , Edgecombe Gregory D. , Kenrick Paul 
Published: October 2016

Abstract
Land colonization by plants and their fungal and bacterial symbionts during the Paleozoic was fundamental to the evolution of terrestrial ecosystems, but how these early communities influenced mineral weathering and soil development remains largely unknown. We investigated cryptogamic ground covers (CGCs) in Iceland to identify modern analogous communities and to characterize soil structure and biologically mediated weathering features. Using a novel application of X-ray microcomputed tomography, we show that moss-dominated CGCs and their soils are not adequate analogues of early communities. Comparisons with the 407 Ma Rhynie Chert (Scotland) biota indicate that modern CGCs dominated by lichens, liverworts, and their associated symbionts (fungi, cyanobacteria) are more representative of early soil-forming communities. Liverwort and lichen soils are thin, and their depth and complexity are constrained by the size and growth form of the dominant plants or lichens. They are aggregated and stabilized by cyanobacteria, mycorrhizal and lichenized fungi, rhizoids, and associated exudates. Smectite was associated with liverwort but not with moss CGC soils. Soil grain dissolution features are diverse and attributable to different organisms (e.g., bacteria, fungi) and types of interaction (e.g., symbiosis). We postulate that such features provide a novel indirect means of inferring biotic interactions in paleosols.
Impact of weekday surgery on application of enhanced recovery pathway: a retrospective cohort study
Authors: Romain Benoît , Grass Fabian , Addor Valérie , Demartines Nicolas , Hübner Martin 
Published: October 2016

ObjectiveTo compare the enhanced recovery after surgery (ERAS) protocol compliance and clinical outcomes depending on the weekday of surgery.SettingsCohort of consecutive non-selected patients undergoing elective colorectal surgery from January 2012 to March 2015. This retrospective analysis of our prospective database compared patients operatedearlyin the week (Monday and Tuesday) with patients operated in the second half (late: Thursday, Friday).Primary outcome measuresCompliance with the ERAS protocol, functional recovery, complications and length of stay.ResultsDemographic and surgical details were similar between the early (n=352) and late groups (n=204). Overall compliance with the ERAS protocol was 78% vs 76% for the early and late groups, respectively (p=0.009). Significant differences were notably prolonged urinary drainage and intravenous fluid infusion in the late group. Complication rates and length of stay, however, were not different between surgery on Monday or Tuesday and surgery on Thursday or Friday.ConclusionsApplication of the ERAS protocol showed only minor differences for patients operated on early or late during the week, and clinical outcomes were similar. A fully implemented ERAS programme appears to work also over the weekend.
Choosing Wisely: assessment of current US top five list recommendations’ trustworthiness using a pragmatic approach
Authors: Horvath Karl , Semlitsch Thomas , Jeitler Klaus , Abuzahra Muna E , Posch Nicole , Domke Andreas , Siebenhofer Andrea 
Published: October 2016

ObjectivesIdentification of sufficiently trustworthy top 5 list recommendations from the US Choosing Wisely campaign.SettingNot applicable.ParticipantsAll top 5 list recommendations available from the American Board of Internal Medicine Foundation website.Main outcome measures/interventionsCompilation of US top 5 lists and search for current German highly trustworthy (S3) guidelines. Extraction of guideline recommendations, including grade of recommendation (GoR), for suggestions comparable to top 5 list recommendations. For recommendations without guideline equivalents, the methodological quality of the top 5 list development process was assessed using criteria similar to that used to judge guidelines, and relevant meta-literature was identified in cited references. Judgement of sufficient trustworthiness of top 5 list recommendations was based either on an ‘A’ GoR of guideline equivalents or on high methodological quality and citation of relevant meta-literature.Results412 top 5 list recommendations were identified. For 75 (18%), equivalents were found in current German S3 guidelines. 44 of these recommendations were associated with an ‘A’ GoR, or a strong recommendation based on strong evidence, and 26 had a ‘B’ or a ‘C’ GoR. No GoR was provided for 5 recommendations. 337 recommendations had no equivalent in the German S3 guidelines. The methodological quality of the development process was high and relevant meta-literature was cited for 87 top 5 list recommendations. For a further 36, either the methodological quality was high without any meta-literature citations or meta-literature citations existed but the methodological quality was lacking. For the remaining 214 recommendations, either the methodological quality was lacking and no literature was cited or the methodological quality was generally unsatisfactory.Conclusions131 of current US top 5 list recommendations were found to be sufficiently trustworthy. For a substantial number of current US top 5 list recommendations, their trustworthiness remains unclear. Methodological requirements for developing top 5 lists are recommended.
Examination of the influence of social capital on depression in fragile families
Authors: Wilmot Neil A , Dauner Kim Nichols 
Published: October 2016

BackgroundWhile it appears that social capital has a positive effect on mental health, most studies have been cross-sectional in nature and/or employ weak measures of social capital or mental health. Even less attention has been paid to vulnerable populations, such as low-income women with children. Thus, our objective was to explore how different dimensions of social capital impact depression in this population.MethodsWe used data from the Fragile Families and Child Wellbeing Study, which has followed a cohort of children born in large US cities to mostly minority, unmarried parents for over 9 years. These families tend to be at greater risk for falling into poverty. Four separate measures of social capital were constructed, using measures that are reliable and that offer evidence of validity including social support and trust, social participation, perceptions of neighbourhood social cohesion and perceptions of neighbourhood social control. The temporal effect of social capital on mental health, as measured by a standardised screening for depression was investigated using logistic regression.ResultsAfter controlling for relevant socioeconomic and demographic factors, prior depression, and prior self-rated health, the social capital dimensions of social support and trust and perceived neighbourhood social cohesion are significant predictors of depression.ConclusionsThese results suggest that social and neighbourhood environments play an important role in mental health status. Intervention and policy initiatives that increase social capital may be viable for improving mental health among low-income urban, minority women.