bluuebunny/crossref_metadata_2025_split huggingface dataset:
Down Feather Structure Varies Between Low- and High-Altitude Torrent Ducks (MerganettaArmata) in the Andes
Authors: Cheek Rebecca G. , Alza Luis , McCracken Kevin G. 
Published: October 2017

AbstractFeathers are one of the defining characteristics of birds and serve a critical role in thermal insulation and physical protection against the environment. Feather structure is known to vary among individuals, and it has been suggested that populations exposed to different environmental conditions may exhibit different patterns in feather structure. We examined both down and contour feathers from two populations of male Torrent Ducks (Merganetta armata) from Lima, Peru, including one high-altitude population from the Chancay-Huaral River at approximately 3500 meters (m) elevation and one low-altitude population from the Chillón River at approximately 1500 m. Down feather structure differed significantly between the two populations. Ducks from the high-altitude population had longer, denser down compared with low-altitude individuals. Contour feather structure varied greatly among individuals but showed no significant difference between populations. These results suggest that the innermost, insulative layer of plumage (the down), may have developed in response to lower ambient temperatures at high elevations. The lack of observable differences in the contour feathers may be due to the general constraints of the waterproofing capability of this outer plumage layer.ResumenEl plumaje es una característica que define a las aves y cumple roles críticos en el aislamiento térmico y protección física del ambiente. Se sabe que la estructura de las plumas varía ente individuos, y se ha sugerido que poblaciones expuestas a diferentes condiciones ambientales pueden exhibir diferentes patrones en la estructura de las plumas. En este estudio se examinaron tanto el plumón como las plumas de contorno de machos adultos del Pato de los Torrentes (Merganetta armata) de dos poblaciones, una en el río Chancay-Huaral a 3,500 msnm y otra en el río Chillón a 1,500 msnm, ubicadas en Lima, Perú. La estructura de los plumones difiere significativamente entre las dos poblaciones. Los patos de la población a grandes elevaciones tienen plumones largos, y densos comparados con los individuos de las partes bajas. La estructura de las plumas de contorno varía ampliamente entre individuos pero no muestra diferencias significativas entre poblaciones. Estos resultados sugieren que las diferencias entre las capas interiores de aislamiento del plumaje (plumón), haberse desarrollado como respuesta en ambientes de bajas temperaturas a grandes elevaciones. En cambio la falta de detectables diferencias en las plumas de contorno puede ser debido a la constante selección en la capacidad impermeable de la capa de plumas exteriores.
A multi-state model of chemoresistance to characterize phenotypic dynamics in breast cancer
Authors: Howard Grant R. , Johnson Kaitlyn E. , Rodriguez Ayala Areli , Yankeelov Thomas E. , Brock Amy 
Published: October 2017

AbstractThe development of resistance to chemotherapy is a major cause of treatment failure in breast cancer. Although several molecular mechanisms of chemotherapeutic resistance are well studied, a quantitative understanding of the dynamics of resistant subpopulations within a heterogeneous tumor cell population remains elusive. While mathematical models describing the dynamics of heterogeneous cancer cell populations have been proposed, few have been experimentally validated due to the complex nature of resistance that limits the ability of a single phenotypic marker to sufficiently isolate drug resistant subpopulations. In this work, we address this problem with a combined experimental and modeling system that uses drug sensitivity data to reveal the composition of multiple subpopulations differing in their level of drug resistance. We calibrate time-resolved dose-response data to three mathematical models to interrogate the models’ ability to capture the dynamics of drug. All three models demonstrated an increase in population level resistance following drug exposure. The candidate models were compared by Akaike information criterion and the model selection criteria identified a multi-state model incorporating the role of population heterogeneity and cellular plasticity. To validate the ability of this model to identify the composition of subpopulations, we mixed wild-type MCF-7 and MCF-7/ADR resistant cells at various proportions and evaluated the corresponding model output. Our blinded two-state model was able to estimate the proportions of cell subtypes, with the measured proportions falling within the 95 percent confidence intervals on the parameter estimations and at an R-squared value of 0.986. To the best of our knowledge, this contribution represents the first work to combine experimental time-resolved drug sensitivity data with a mathematical model of resistance development.
Calling song maturity in two-spotted cricket,Gryllus bimaculatus: its patterns and a possible physical explanation
Authors: Miyashita Atsushi 
Published: October 2017

AbstractMales ofGryllus bimaculatus(two-spotted cricket) emit acoustic signals by stridulating two forewings. One of their songs, calling song, plays a role in attracting females to mate, yet the significance of each song trait in attracting conspecific females remains unclear. Among such traits, the relevance of frequency component (i.e. song pitch) has been underestimated, as orthopterans had long been believed incapable of song pitch recognition. However, recent literatures suggested that ears of orthopteran species are capable of frequency recognition as mammalians do. My previous report demonstrated that their calling song recorded from mature adults has constant and pure peak frequency component around 5.7 kHz, further supporting a biological significance of the frequency component. In this study, I tracked its change over time in sexual maturity phase (i.e. from early adult phase). 300 calling songs were recorded over time from a pool of 122 adult crickets, as it required large number of animals because the crickets rarely sing at very early adult stage. A maturation process of calling song was observed, where the peak frequency distributed lower and more variable frequency in early adult phase (e.g. mean peak value was 4.9 kHz on day 3), then it gradually increased and converged to 5.8 kHz with two weeks. The coefficient of variance also decreased over the process, showing minimum around day 20. Also, I found that the young crickets (supposed to emit immature song), emit perfectly tuned calling song with 5.8 kHz peak in helium-substituted (80% Helium and 20% Oxygen) environment. These findings suggest that the robustly regulated frequency of the calling song is acquired during the early-to-mid adult stage, and it may be associated with sexual maturity of males. Also, the helium-substitution experiment suggests that physical resistance from surrounding gas molecules negatively impacts stability of calling songs of young males, implying that a muscle development and/or forewing hardening may help song maturation. This study highlights a biological significance of the frequency component, such that females may adaptively select sexually mature males based on the song trait.
MeShClust: an intelligent tool for clustering DNA sequences
Authors: James Benjamin T. , Luczak Brian B. , Girgis Hani Z. 
Published: October 2017

ABSTRACTSequence clustering is a fundamental step in analyzing DNA sequences. Widely-used software tools for sequence clustering utilize greedy approaches that are not guaranteed to produce the best results. These tools are sensitive to one parameter that determines the similarity among sequences in a cluster. Often times, a biologist may not know the exact sequence similarity. Therefore, clusters produced by these tools do not likely match the real clusters comprising the data if the provided parameter is inaccurate. To overcome this limitation, we adapted the mean shift algorithm, an unsupervised machine-learning algorithm, which has been used successfully thousands of times in fields such as image processing and computer vision. The theory behind the mean shift algorithm, unlike the greedy approaches, guarantees convergence to the modes, e.g. cluster centers. Here we describe the first application of the mean shift algorithm to clustering DNA sequences. MeShClust is one of few applications of the mean shift algorithm in bioinformatics. Further, we applied supervised machine learning to predict the identity score produced by global alignment using alignment-free methods. We demonstrate MeShClust’s ability to cluster DNA sequences with high accuracy even when the sequence similarity parameter provided by the user is not very accurate.
Short-term effects of sound localization training in virtual reality
Authors: Steadman Mark A. , Kim Chungeun , Lestang Jean-Hugues , Goodman Dan F. M. , Picinali Lorenzo 
Published: October 2017

ABSTRACTHead-related transfer functions (HRTFs) capture the direction-dependant way that sound interacts with the head and torso. In virtual audio systems, which aim to emulate these effects, non-individualized, generic HRTFs are typically used leading to an inaccurate perception of virtual sound location. Training has the potential to exploit the brain’s ability to adapt to these unfamiliar cues. In this study, three virtual sound localization training paradigms were evaluated; one provided simple visual positional confirmation of sound source location, a second introduced game design elements (“gamification”) and a final version additionally utilized head-tracking to provide listeners with experience of relative sound source motion (“active listening”). The results demonstrate a significant effect of training after a small number of short (12-minute) training sessions, which is retained across multiple days. Gamification alone had no significant effect on the efficacy of the training, but active listening resulted in a significantly greater improvements in localization accuracy. In general, improvements in virtual sound localization following training generalized to a second set of non-individualized HRTFs, although some HRTF-specific changes were observed in polar angle judgement for the active listening group. The implications of this on the putative mechanisms of the adaptation process are discussed.
Zebrafish yolk syncytial nuclei migrate along a dynamic microtubule network
Authors: Fei Zhonghui , Bae Koeun , Parent Serge E. , Goodwin Katharine , Tanentzapf Guy , Bruce Ashley E.E. 
Published: October 2017

AbstractIn teleosts, the yolk syncytial layer is a multinucleate syncytium that functions as an extraembryonic signaling center to pattern the mesendoderm, coordinate morphogenesis and supply nutrients to the embryo. The zebrafish is an excellent system for studying this morphogenetically active tissue. The external yolk syncytial nuclei (e-YSN) undergo microtubule dependent epiboly movements that distribute the nuclei over the yolk. How e-YSN epiboly proceeds, and what role the yolk microtubule network plays is not understood but currently it is proposed that e-YSN are pulled vegetally as the microtubule network shortens from the vegetal pole. Data from our live imaging studies suggest that the yolk microtubule network is dismantled from the animal and vegetal regions and show that a region of stabilized microtubules forms before nuclear migration begins. e-YSN do not appear to be pulled vegetally but rather move along a dynamic microtubule network. We also show that overexpression of the KASH domain of Syne2a impairs e-YSN movement, implicating the LINC complex in e-YSN migration. This work provides new insights into the role of microtubules in morphogenesis of an extraembryonic tissue.Summary StatementAnalysis of yolk syncytial nuclear migration during zebrafish epiboly reveals that nuclei migrate along and largely beneath a dynamically yolk microtubule network.
High degree of virulence gene diversity in Streptococcus pyogenes isolated in Central Italy
Authors: Bencardino Daniela , Luca Maria Chiara Di , Petrelli Dezemona , Prenna Manuela , Vitali Luca Agostino 
Published: October 2017

AbstractGlobally, Streptococcus pyogenes poses a continuous burden on human health, causing both self-limiting and life-threatening diseases. Therefore, studying the profile of virulence genes and their combinations is essential to monitor the epidemiology and pathogenetic potential of this important species. Thus, the aim of this study was to analyze some genetic features of clinical strains collected in Italy in 2012.We conducted fibronectin-collagen-T antigen (FCT) region typing and emm typing in 122 S. pyogenes strains. Furthermore, several additional virulence genes were screened by polymerase chain reaction.We found correlations between emm types and FCT region profiles. emm1 strains were mainly associated with FCT2 and FCT6, while emm89 and emm12 strains were associated with FCT4. FCT5 was mainly represented in emm4, emm6, and emm75 strains. Noteworthy, we defined subtypes for each FCT type based on the differences in single and multiple loci compared to the reference scheme used for the classification of the FCT region. In addition, new FCT types were identified. Cluster analysis based on virulence gene profiling showed a non-random distribution within each emm type.This study showed the high variability of S. pyogenes strains and the great diversification that this pathogen has undergone during its evolution in the human host.
Mapping of the Fondaparinux Binding Site of JR-FL gp120 by High Resolution Hydroxyl Radical Protein Footprinting and Computational Docking
Authors: Misra Sandeep K. , Sood Amika , Soares Paulo A. , Pomin Vitor H. , Woods Robert J. , Sharp Joshua S. 
Published: October 2017

AbstractThe adhesion of HIV gp120 antigen to human cells is modulated in part by interactions with heparan sulfate. The HXB2 strain of gp120 has been shown to interact with heparin primarily through the V3 loop, although other domains including the C-terminal domain were also implicated. However, the JR-FL strain (representative of CCR5-interacting strains that make up newest infections) was shown to have a drastically lowered affinity to heparin due to the loss of several basic residues in the V3 loop, and deletion of the V3 loop in JR-FL gp120 was shown to abrogate some, but not all, heparin binding. Here, we use high resolution hydroxyl radical protein footprinting to measure the changes in protein surface oxidation levels that result from the binding of a model heparin fragment (fondaparinux). Protection in both the V3 loop and the N-terminus of JR-FP gp120 is observed. The well-defined composition of fondaparinux allowed us to perform docking simulations, which showed two clusters of fondaparinux binding: the V3 loop, and a domain consisting of the N- and C-termini. Together, the experimental and theoretical results indicate the heparin/heparan sulfate binding sites on JR-FL gp120 and the efficient interaction of fondaparinux, a widely exploited therapeutic carbohydrate, on gp120.
Elucidation of dose-dependent transcriptional events immediately following ionizing radiation exposure
Authors: Rouchka Eric C. , Flight Robert M. , Fasciotto Brigitte H. , Estrada Rosendo , Eaton John W. , Patibandla Phani K. , Waigel Sabine J. , Li Dazhuo , Kirtley John K. , Sethu Palaniappan , Keynton Robert S. 
Published: October 2017

AbstractLong duration space missions expose astronauts to ionizing radiation events associated with highly energetic and charged heavy particles. Such exposure can result in chromosomal aberrations increasing the likelihood of the development of cancer. Early detection and mitigation of these events is critical in providing positive outcomes. In order to aid in the development of portable devices used to measure radiation exposure, we constructed a genome-wide screen to detect transcriptional changes in peripheral blood lymphocytes shortly after (approximately 1 hour) radiation exposure at low (0.3 Gy), medium (1.5 Gy) and high (3.0 Gy) doses compared to control (0.0 Gy) using Affymetrix®Human Gene 1.0 ST v1 microarrays. Our results indicate a number of sensitive and specific transcriptional profiles induced by radiation exposure that can potentially be implemented as biomarkers for radiation exposure as well as dose effect. For overall immediate radiation exposure,KDELC1,MRPS30,RARS, andHEXIM1were determined to be effective biomarkers whilePRDM9,CHST4, andSLC26A10were determined to be biomarkers specific to 0.3 Gy exposure;RPH,CCDC96,WDYHV1, andIFNA16were identified for 1.5 Gy exposure; andCWC15,CHCHD7, andDNAAF2were determined to be sensitive and specific to 3.0 Gy exposure. The resulting raw and analyzed data are publicly available through NCBI's Gene Expression Ominibus via accession GSE64375.
Programmable RNA recognition using a CRISPR-associated Argonaute
Authors: Lapinaite Audrone , Doudna Jennifer A. , Cate Jamie H. D. 
Published: October 2017

ABSTRACTArgonaute proteins (Agos) are present in all domains of life. While the physiological function of eukaryotic Agos in regulating gene expression is well documented, the biological roles of many of their prokaryotic counterparts remain enigmatic. In some bacteria, Agos are associated with CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci and use non-canonical 5’-hydroxyled guide RNAs (gRNAs) for nucleic acid targeting. Here we show that using 5-bromo-2′-deoxyuridine (BrdU) as the 5’ nucleotide of gRNAs stabilizes in vitro reconstituted CRISPR-associated Marinitoga piezophila Argonaute-gRNA complexes (MpAgo RNPs) and significantly improves their specificity and affinity for RNA targets. Using reconstituted MpAgo RNPs with 5’-BrdU modified gRNAs, we mapped the seed region of the gRNA, and identified the nucleotides of the gRNA that play the most significant role in targeting specificity. We also show that these MpAgo RNPs can be programmed to distinguish between substrates that differ by a single nucleotide, using permutations at the 6th and 7th positions in the gRNA. Using these specificity features, we employed MpAgo RNPs to detect specific Adenosine to Inosine edited RNAs in a complex mixture. These findings broaden our mechanistic understanding of the interactions of Argonautes with guide and substrate RNAs, and demonstrate that MpAgo RNPs with 5’-BrdU modified gRNAs can be used as a highly-specific RNA-targeting platform to probe RNA biology.SIGNIFICANCEArgonaute proteins are present in bacteria, archaea and eukaryotes. They play an important role in a wide range of biological processes, from transcriptional and translational gene expression regulation to defense against viruses and silencing of mobile genetic elements. Here we present mechanistic insights into the interactions of the CRISPR-associated Marinitoga piezophila Argonaute (MpAgo) with its guide RNA (gRNA) and RNA substrates. By modifying the 5’-nucleotide of the gRNA, we demonstrate that MpAgo-gRNA complexes (RNPs) are easily programmable, have high affinity to fully complementary RNA substrates, and can discriminate by over 300 fold between substrates that differ by only a single nucleotide. These MpAgo RNPs should be useful for probing endogenous RNAs in living cells.
geck: trio-based comparative benchmarking of variant calls
Authors: Kómár Péter , Kural Deniz 
Published: October 2017

MotivationClassical methods of comparing the accuracies of variant calling pipelines are based on truth sets of variants whose genotypes are previously determined with high confidence. An alternative way of performing benchmarking is based on Mendelian constraints between related individuals. Statistical analysis of Mendelian violations can provide truth set-independent benchmarking information, and enable benchmarking less-studied variants and diverse populations.ResultsWe introduce a statistical mixture model forcomparing two variant calling pipelines from genotype data they produce after running on individual members of a trio. We determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our method is able to estimate differential precision and recall between the two pipelines with 10-3 uncertainty.AvailabilityThe Python library geck, and usage examples are available at the following URL: https://github.com/sbg/geckContactpeter.komar@sbgdinc.comSupplementary informationSupplementary materials are available at bioRxiv.
Improvement of individual performance in the public sector
Authors: Palma Raffaela , Hinna Alessandro , Mangia Gianluigi 
Published: October 2017

PurposeThe purpose of this paper is to explore whether a pro-social motivation called user orientation (UO), which aims at helping specific others, may affect performance of public sector employees in addition to public service motivation (PSM), and whether any personal, and/or contextual factors affect this relationship (age, tenure, role, and context).Design/methodology/approachUtilizing cross-sectional survey data obtained from 618 Italian public teachers, PLS-structural equation modeling is used to investigate the relationship between PSM, UO, and performance, along with the moderating effects of individual/contextual factors.FindingsFindings show positive relationships between the two levers (PSM/UO) and individual performance (IP), depending on job and organizational tenure, role, and the social environment of the areas the schools are located in.Research limitations/implicationsThere might be problems related to causal inference and common method variance, due to the use of the cross-sectional self-reported data.Practical implicationsManagers should be aware of the crucial role UO and PSM play in order to improve IP in contexts where there is direct contact with the service beneficiaries.Originality/valueThe paper contributes to a clearer understanding of which motives are involved in the process that leads public service employees to enhance their performance.
Facets of job satisfaction and work engagement
Authors: Yalabik Zeynep Yesim , Rayton Bruce A. , Rapti Andriana 
Published: October 2017

PurposeThe purpose of this paper is to analyze the relationship between the facets of job satisfaction and the work engagement. Previous studies that focus on the linkages between work engagement and overall job satisfaction ignore the multi-faceted nature of job satisfaction construct. In this study, how job satisfaction facets are linked to three dimensions of work engagement – i.e. vigor, dedication and absorption – is discussed by drawing on the social exchange theory.Design/methodology/approachThe cross-lagged data used in this study come from the specialist lending division of a UK bank. The linear multiple regression analyses are run to test the proposed theoretical model.FindingsThe results show that among all the job satisfaction facets, the “satisfaction with work itself” is the key driver of all dimensions of work engagement, i.e. vigor, dedication and absorption. The “satisfaction with conditions” is negatively linked to absorption of employees in their work. This means that the employees with high workload might not be absorbed in their work. Finally, it is found that employees who are satisfied with the communication in their work are also absorbed in their work.Originality/valueThis study contributes to our knowledge of the drivers of work engagement over time. The facets of job satisfaction as the drivers help us to have a comprehensive understanding of the link between the job satisfaction facets and work engagement. This study first contributes to the work engagement literature which has neglected the multi-dimensional approach of job satisfaction. This study also contributes to the limited number of work engagement studies conducted in service sector and in UK.