bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures
Authors: Ghosh-Harihar Mousumi , Gurung Nehal , Shukla Harsh , Sinha Ishani , Pandit Awadhesh , Prakash Vibhu , Green Rhys E. , Ramakrishnan Uma 
Published: September 2019

AbstractAn understanding of the factors affecting the diet composition of critically endangered Gyps vultures in the Indian subcontinent has important applications to the design of effective conservation strategies. After suffering a massive decline (~99%) in numbers caused by veterinary use of the nephrotoxic drug diclofenac, vultures now persist in very low numbers, mostly concentrated within or near National Parks. This spatial association might be attributed to the availability of wild ungulate carcasses free from toxic veterinary drugs. Hence, quantification of vulture diets and the factors affecting them is critical to test this hypothesis. Here, we describe and validate a robust “field-to-benchtop-to-desktop” metabarcoding workflow for assessing the species- and sex-specific diet of these obligate scavengers from non-invasively collected faecal samples. Seven metabarcodes targeting mitochondrial and nuclear genes were used to simultaneously determine the vulture species identity, sex and species consumed. The amplicons were sequenced using an Illumina Miseq platform. We included controls and three replicates per sample to establish a series of non-arbitrary thresholds to filter the sequence data and eliminate cross-contamination, PCR/sequencing errors and false positives. Using this strategy enabled identification of species and sex for all samples. Diet species-specific sequences could be identified with high taxonomic resolution for 93% of samples. Out of the seven metabarcodes, just four were sufficient to meet the objectives. From this preliminary analysis, domestic livestock seem to be the most frequently consumed diet item across samples from inside and outside protected habitats. Our method provides a rapid and reliable tool for describing large-scale variation in consumption of domestic versus wild species in the diet of these species, paving the way for a better understanding of the role protected areas play in persistence and recovery of the remaining Gyps vulture populations in the wild.
Sleep homeostasis reflects temporally integrated local cortical neuronal activity
Authors: Thomas Christopher W. , Guillaumin Mathilde C. C. , McKillop Laura E. , Achermann Peter , Vyazovskiy Vladyslav V. 
Published: September 2019

AbstractThe homeostatic regulation of sleep manifests as a relative constancy of its daily amount and intensity. Theoretical descriptions of this phenomenon define “Process S”, a variable with dynamics dependent only on sleep-wake history, whose levels are reflected in electroencephalogram (EEG) slow wave activity (0.5 – 4 Hz) during sleep. Here we developed novel mathematical models of Process S in mice, assuming that its dynamics are a function of the deviation of cortical neuronal firing rates from a locally defined set-point, crucially without explicit knowledge of sleep-wake state. Our results suggest that Process S tracks global sleep-wake history through an integration of local cortical neuronal activity levels over time. We posit that, instead of reflecting sleep-wake-dependent changes in specific variables and serving their homeostatic regulation, Process S may be a time-keeping mechanism which enables individuals to obtain a species-specific and ecologically-relevant quantity of sleep, even in the absence of external temporal information.
Connecting Histopathology Imaging and Proteomics in Kidney Cancer through Machine Learning
Authors: Azuaje Francisco , Kim Sang-Yoon , Hernandez Daniel Perez , Dittmar Gunnar 
Published: September 2019

AbstractProteomics data encode molecular features of diagnostic value and accurately reflect key underlying biological mechanisms in cancers. Histopathology imaging is a well-established clinical approach to cancer diagnosis. The predictive relationship between large-scale proteomics and H&E-stained histopathology images remains largely uncharacterized. Here we investigate such associations through the application of machine learning, including deep neural networks, to proteomics and histology imaging datasets generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) from clear cell renal cell carcinoma patients. We report robust correlations between a set of diagnostic proteins and predictions generated by an imaging-based classification model. Proteins significantly correlated with the histology-based predictions are significantly implicated in immune responses, extracellular matrix reorganization and metabolism. Moreover, we showed that the genes encoding these proteins also reliably recapitulate the biological associations with imaging-derived predictions based on strong gene-protein expression correlations. Our findings offer novel insights into the integrative modeling of histology and omics data through machine learning, as well as the methodological basis for new research opportunities in this and other cancer types.
Multiband acceleration can provide moderate improvements in single-subject voxel-wise statistics in block-design task-based fMRI
Authors: Bhandari Ritu , Gazzola Valeria , Keysers Christian 
Published: September 2019

AbstractMultiband (MB) acceleration of functional magnetic resonance imaging has become more widely available to neuroscientists. Here we compare MB factors of 1, 2 and 4 while participants view complex hand actions vs. simpler hand movements to localize the action observation network. While in a previous study, we show that MB4 shows moderate improvements in the group-level statistics, here we explore the impact it has on single subject statistics. We find that MB4 provides an increase in p values at the first level that is of medium effect size compared to MB1, providing moderate evidence across a number of voxels that MB4 indeed improves single subject statistics. This effect was localized mostly within regions that belong to the action observation network. In parallel, we find that Cohen’s d at the single subject level actually decreases using MB4 compared to MB1. Intriguingly, we find that subsampling MB4 sequences, by only considering every fourth acquired volume, also leads to increased Cohen’s d values, suggesting that the FAST algorithm we used to correct for temporal auto-correlation may over-penalize sequences with higher temporal autocorrelation, thereby underestimating the potential gains in single subject statistics offered by MB acceleration, and alternative methods should be explored. In summary, considering the moderate gains in statistical values observed both at the group level in our previous study and at the single subject level in this study, we believe that MB technology is now ripe for neuroscientists to start using MB4 acceleration for their studies, be it to accurately map activity in single subjects of interest (e.g. for presurgical planning or to explore rare patients) or for the purpose of group studies.
Urbanization and market-integration have strong, non-linear effects on cardio-metabolic health in the Turkana
Authors: Lea Amanda J. , Martins Dino , Kamau Joseph , Gurven Michael , Ayroles Julien F. 
Published: September 2019

ABSTRACTCardio-metabolic disease is a leading cause of death worldwide, with high prevalence in western, industrialized societies relative to developing nations and subsistence-level populations. This stark difference has been attributed to the dietary and lifestyle changes associated with industrialization, but current work has relied on health comparisons between separate, genetically distinct populations to draw conclusions. To more robustly determine how lifestyle impacts health, we collected interview and health biomarker data from a single population undergoing a rapid lifestyle transition. Specifically, we sampled Turkana individuals who practice subsistence-level, nomadic pastoralism (the traditional, ancestral way of life for this group), as well as individuals who no longer practice pastoralism and engage either minimally or strongly with the market economy. Comparisons across this lifestyle gradient revealed clear, non-linear effects of industrialization: only individuals with highly urban, market-integrated lifestyles experience increases in BMI, body fat, blood pressure, and other biomarkers of cardio-metabolic health. These health differences are partially mediated by increased consumption of refined carbohydrates, and more strongly by fine-scale measures of urbanicity. Finally, because many Turkana are transitioning between rural and urban areas within their lifetime, we were able to show that being born in an urban area is associated with worse adult metabolic health, independent of adult lifestyle. Together, these analyses provide comprehensive insight into the timing, magnitude, and causes of health declines in urban, industrialized groups – an area of critical study given the massive public health burden of cardio-metabolic disease and the rate at which developing nations are experiencing lifestyle transitions.SIGNIFICANCEThe “mismatch” between evolved human physiology and western, industrialized lifestyles is thought to explain to the current epidemic of cardiovascular disease (CVD). However, this hypothesis has been difficult to test in real time. To do so, we studied a traditional pastoralist group—the Turkana—that is currently transitioning from their ancestral way of life to an urban, industrialized lifestyle. We found that Turkana who move to cities exhibit poor cardio-metabolic health, partially because of a shift toward “western diets” high in carbohydrates. We also show that early life urbanicity independently predicts adult health, such that life-long city dwellers will experience the greatest CVD risk. Our work thus uncovers the timing, magnitude, and evolutionary causes of a major health gradient.
Detecting fabrication in large-scale molecular omics data
Authors: Bradshaw Michael S. , Payne Samuel H. 
Published: September 2019

AbstractFraud is a pervasive problem and can occur as fabrication, falsification, plagiarism or theft. The scientific community is not exempt from this universal problem and several studies have recently been caught manipulating or fabricating data. Current measures to prevent and deter scientific misconduct come in the form of the peer-review process and on-site clinical trial auditors. As recent advances in high-throughput omics technologies have moved biology into the realm of big-data, fraud detection methods must be updated for sophisticated computational fraud. In the financial sector, machine learning and digit-preference are successfully used to detect fraud. Drawing from these sources, we develop methods of fabrication detection in biomedical research and show that machine learning can be used to detect fraud in large-scale omic experiments. Using the raw data as input, the best machine learning models correctly predicted fraud with 84-95% accuracy. With digit frequency as input features, the best models detected fraud with 98%-100% accuracy. All of the data and analysis scripts used in this project are available at https://github.com/MSBradshaw/FakeData.
Use of Nanosphere Self-Assembly to Pattern Nanoporous Membranes for the Study of Extracellular Vesicles
Authors: Mireles Marcela , Soule Cody W. , Dehghani Mehdi , Gaborski Thomas R. 
Published: September 2019

AbstractNanoscale biocomponents naturally released by cells, such as extracellular vesicles (EVs), have recently gained interest due to their therapeutic and diagnostic potential. Membrane based isolation and co-culture systems have been utilized in an effort to study EVs and their effects. Nevertheless, improved platforms for the study of small EVs are still needed. Suitable membranes, for isolation and co-culture systems, require pore sizes to reach into the nanoscale. These pore sizes cannot be achieved through traditional lithographic techniques and conventional thick nanoporous membranes commonly exhibit low permeability. Here we utilized nanospheres, similar in size and shape to the targeted small EVs, as patterning features for the fabrication of freestanding SiN membranes (120 nm thick) released in minutes through a sacrificial ZnO layer. We evaluated the feasibility of separating subpopulation of EVs based on size using these membranes. The membrane used here showed an effective size cut-off of 300 nm with the majority of the EVs ≤200 nm. This work provides a convenient platform with great potential for studying subpopulations of EVs.
Development of a monkey avatar to study social perception in macaques
Authors: Wilson Vanessa A.D. , Kade Carolin , Moeller Sebastian , Treue Stefan , Kagan Igor , Fischer Julia 
Published: September 2019

AbstractFollowing the expanding use and applications of virtual reality in every-day life, dynamic virtual stimuli are of increasing interest in cognitive studies. They allow for control of features such as gaze, expression and movement, which may help to overcome limitations of using either static or poorly controlled real stimuli. In using virtual stimuli however, one must be careful to avoid the uncanny valley effect - where realistic stimuli can be perceived as eerie, and induce an aversion response. At the same time, it is important to establish whether responses to virtual stimuli mirror responses to depictions of a real conspecific. In the current study, we describe the development of a new avatar with realistic features for nonhuman primates, the ‘primatar’. As a first step towards validation, we assessed how monkeys respond to images of this avatar compared to images of real monkeys, and an unrealistic avatar. We also compared responses between original images and scrambled as well as obfuscated versions of these images. We measured looking time to images in six free moving long-tailed macaques (Macaca fascicularis) and eye movement exploration behaviour in three rhesus macaques (Macaca mulatta). Both groups showed more of such signs of overt attention to original images than scrambled or obfuscated images. In addition, we assessed whether the realistic avatar created an uncanny valley effect through decreased looking time, finding that in both groups, monkeys did not differentiate between real, realistic or unrealistic images. These results provide support for further development of our avatar for use in social cognition studies, and more generally for cognitive research with virtual stimuli in nonhuman primates. Future research needs to shed light on the source of the inconsistent findings for the uncanny valley effect in macaques, to elucidate the roots of this mechanism in humans.
Selective activation of estrogen receptors α and β: Implications for depressive-like phenotypes in female mice exposed to chronic unpredictable stress
Authors: Eid Rand S. , Lieblich Stephanie E. , Duarte-Guterman Paula , Chaiton Jessica A. , Mah Amanda G. , Wong Sarah J. , Wen Yanhua , Galea Liisa A.M. 
Published: September 2019

AbstractThe estrogen receptor (ER) mechanisms by which 17β-estradiol influences depressive-like behaviour have primarily been investigated acutely and not within an animal model of depression. Therefore, the current study aimed to dissect the contribution of ERα and ERβ to the effects of 17β-estradiol under non-stress and chronic stress conditions. Ovariectomized (OVX) or sham-operated mice were treated chronically (47 days) with 17β-estradiol (E2), the ERβ agonist diarylpropionitrile (DPN), the ERα agonist propylpyrazole-triol (PPT), or vehicle. On day 15 of treatment, mice from each group were assigned to Chronic Unpredictable Stress (CUS; 28 days) or non-CUS conditions. Mice were assessed for anxiety- and depressive-like behaviour and hypothalamic-pituitary-adrenal (HPA) axis function. Cytokine and chemokine levels, and postsynaptic density protein 95 were measured in the hippocampus and frontal cortex, and adult hippocampal neurogenesis was assessed. Overall, the effects of CUS were more robust that those of estrogenic treatments, as seen by increased immobility in the tail suspension test (TST), reduced PSD-95 expression, reduced neurogenesis in the ventral hippocampus, and HPA axis negative feedback dysregulation. However, we also observe CUS-dependent and -independent effects of ovarian status and estrogenic treatments. The effects of CUS on PSD-95 expression, the cytokine milieu, and in TST were largely driven by PPT and DPN, indicating that these treatments were not protective. Independent of CUS, estradiol increased neurogenesis in the dorsal hippocampus, blunted the corticosterone response to an acute stressor, but increased anxiety-like behaviour. These findings provide insights into the complexities of estrogen signaling in modulating depressive-like phenotypes under non-stress and chronic stress conditions.
The inverse relationship between fibronectin and neuroligins in the embryonic rat colon
Authors: Gao Ni , Hou Peimin , Zhang Qiangye , Mu Weijing , Wang Jian , Wang Dongming , Li Aiwu 
Published: September 2019

AbstractOur previous study identified that the abnormal expression of fibronectin (FN), neuroligin-1 (NL1) and neuroligin-2 (NL2) in the colons of children with Hirschsprung disease (HSCR), but the correlated relationship between the three in the development of the enteric nervous system (ENS) remains unclear. Colons of Wistar rats and PC12 neurons were used to investigate the relationship between FN and the neuroligins (NLs). Colon tissues from thirty healthy embryonic rats, including fifteen at embryonic day 16 (E16), eight at E18, seven at E20, and fifteen newborn rats within 24 hours (Ep0) were analyzed to determine the correlated expression of FN and NLs using Western blot (WB) analysis and real-time fluorescence quantitative PCR (qRT-PCR) methods. Small interfering ribonucleic acid (siRNA) targeting and gene plasmids were used to explore the functional interaction between FN and NLs by using PC12 neuron cells. Furthermore, we used recombinant FN and NL proteins to confirm their interactions. Our studies showed that there were downregulatory effects between FN and the NLs in the embryonic rat colon and different cell lines, indicating that FN and NLs could directly regulate each other, and there is a negative linear correlation between them. The imbalanced interaction between extracellular matrix and synapse-related genes may provide a new perspective for the pathogenesis and treatment of HSCR and neuronal intestinal malformations (NIMs).
Ubiquitylated H2A.Z nucleosomes are associated with nuclear architectural proteins and global transcriptional silencing
Authors: Ng Marlee K. , Braunschweig Ulrich , Blencowe Benjamin J. , Cheung Peter 
Published: September 2019

SummaryH2A.Z mono-ubiquitylation has been linked to transcriptional repression, but the mechanisms involved are not well understood. To address this, we developed a biotinylation-based approach to purify ubiquitylated H2A.Z (H2A.Zub) mononucleosomes for biochemical and genome-wide analyses. We observe that H2A.Zub nucleosomes are enriched for the repressive histone post-translational modification H3K27me3, but depleted of H3K4 methylation and other modifications associated with active transcription. ChIP-Seq analyses reveal that H2A.Zub-nucleosomes are enriched over non-expressed genes, and suggest that it is the relative ratio of ubiquitylated to non-ubiquitylated H2A.Z, rather than absolute presence or absence of H2A.Z ubiquitylation, that correlates with gene silencing. Finally, we observe that H2A.Zub-eniched mononucleosomes preferentially co-purify with transcriptional silencing factors as well as proteins involved in higher order chromatin organization such as CTCF and cohesin. Collectively, these results suggest an important role for H2A.Z ubiquitylation in mediating global transcriptional repression through its recruitment of silencing factors and nuclear architectural proteins.
Odorant Receptor Inhibition is Fundamental to Odor Encoding
Authors: Pfister Patrick , Smith Benjamin C. , Evans Barry J. , Brann Jessica H. , Trimmer Casey , Sheikh Mushhood , Arroyave Randy , Reddy Gautam , Jeong Hyo-Young , Raps Daniel A. , Peterlin Zita , Vergassola Massimo , Rogers Matthew E. 
Published: September 2019

SUMMARYMost natural odors are complex mixtures of many volatile components, competing to bind odorant receptors (ORs) expressed in olfactory sensory neurons (OSNs) of the nose. To date surprisingly little is known about how OR antagonism shapes neuronal representations in the periphery of the olfactory system. Here, we investigated its prevalence, the degree to which it disrupts OR ensemble activity, and its conservation across related ORs. Calcium imaging microscopy of dissociated OSNs revealed significant inhibition, often complete attenuation, of responses to indole, a commonly occurring volatile associated with both floral and fecal odors, by a set of 36 tested odorants. To confirm an OR mechanism for the observed inhibition, we performed single-cell transcriptomics on OSNs that exhibited specific response profiles to a diagnostic panel of odorants and identified the receptor Olfr743 which, when tested in vitro, recapitulated ex vivo responses. We screened ten ORs from the Olfr743 clade with 800 perfumery-related odorants spanning a range of chemical scaffolds and functional groups, over half of which (430) antagonized at least one of the ten ORs. Furthermore, OR activity outcomes were divergent rather than redundant, even for the most closely related paralogs. OR activity fitted a mathematical model of competitive receptor binding and suggests that normalization of OSN ensemble responses to odorant mixtures is the rule rather than the exception. In summary, we observed OR antagonism, inverse agonism and partial agonism occurring frequently and in a combinatorial manner. Thus, extensive receptor-mediated computation of mixture information appears to occur in the olfactory epithelium prior to transmission of odor information to the olfactory bulb.
Employers’ attitudes to HOU postgraduates’ qualities and skills
Authors: Hoang Minh Tuyet 
Published: September 2019

Purpose
The purpose of this paper is to investigate employers’ attitudes towards qualities and skills for the twenty-first century of Hanoi Open University (HOU) postgraduates. More specifically, it is to find out employers’ assessment and satisfaction on five sets of skills: foundation skills, professional competencies, personal attributes, organizational skills and technical knowledge and skills.

Design/methodology/approach
The study used a survey questionnaire as a tool to collect data. The survey was conducted on employers of HOU postgraduates who graduated during the academic years 2015–2016 from five faculties at HOU.

Findings
The findings of the study show that employers highly appreciated HOU postgraduates in numeracy skills, ICT literacy skills and information literacy within foundation skills; critical thinking and problem solving skills, collaboration skills and conceptual skills within professional competencies; responsible, integrity and interpersonal skills within organization skills; productivity, organization and planning and time management within organizational skills; knowledge-related regulations and policies at workplace, capacity to use knowledge and skills at workplace and lifelong learning within technical knowledge and skills.

Originality/value
The values of the study are that the employer attitudes identified can be used to evaluate educational programs and can be used as a quality assurance measure. The study helps to indicate the gap between the expectation and the satisfaction of employers on HOU postgraduates. Thereby, suggestions can be given to HOU’s management to improve the services at the university in general and the services to postgraduate students in particular to upgrade their qualities and skills to meet social demands.