bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate change will drive novel cross-species viral transmission
Authors: Carlson Colin J. , Albery Gregory F. , Merow Cory , Trisos Christopher H. , Zipfel Casey M. , Eskew Evan A. , Olival Kevin J. , Ross Noam , Bansal Shweta 
Published: January 2020

AbstractAt least 10,000 species of mammal virus are estimated to have the potential to spread in human populations, but the vast majority are currently circulating in wildlife, largely undescribed and undetected by disease outbreak surveillance1–3. In addition, changing climate and land use are already driving geographic range shifts in wildlife, producing novel species assemblages and opportunities for viral sharing between previously isolated species4, 5. In some cases, this will inevitably facilitate spillover into humans6, 7—a possible mechanistic link between global environmental change and emerging zoonotic disease8. Here, we map potential hotspots of viral sharing, using a phylogeographic model of the mammal-virus network, and projections of potential geographic range shifts for 3,139 mammal species under climate change and land use scenarios for the year 2070. Range-shifting mammal species are predicted to aggregate at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the novel cross-species transmission of their viruses an estimated 4,000 times. Counter to expectations, holding warming under 2°C within the century does not reduce new viral sharing, due to greater potential range expansions— highlighting the need to invest in surveillance even in a low-warming future. Most projected viral sharing is driven by diverse hyperreservoirs (rodents and bats) and large-bodied predators (carnivores). Because of their unique dispersal capacity, bats account for the majority of novel viral sharing, and are likely to share viruses along evolutionary pathways that could facilitate future emergence in humans. Our findings highlight the urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking species’ range shifts, especially in tropical countries that harbor the most emerging zoonoses.
Local stabilization of subunit-subunit contacts causes global destabilization of Hepatitis B virus capsids
Authors: Schlicksup Christopher John , Laughlin Patrick , Dunkelbarger Steven , Wang Joseph Che-Yen , Zlotnick Adam 
Published: January 2020

AbstractDevelopment of antiviral molecules that bind virion is a strategy that remains in its infancy and the details of their mechanisms are poorly understood. Here we investigate the behavior of DBT1, a dibenzothiazapine, which specifically interacts with the capsid protein of Hepatitis B Virus (HBV). We found that DBT1 stabilizes protein-protein interaction, accelerates capsid assembly, and can induce formation of aberrant particles. Paradoxically, DBT1 can cause pre-formed capsids to dissociate. These activities may lead to (i) assembly of empty and defective capsids, inhibiting formation of new virus and (ii) disruption of mature viruses, which are metastable, to inhibit new infection. Using cryo-electron microscopy we observed that DBT1 led to asymmetric capsids where well-defined DBT1 density was bound at all inter-subunit contacts. These results suggest that DBT1 can support assembly by increasing buried surface area but induce disassembly of metastable capsids by favoring asymmetry to induce structural defects.
Tandem tension sensor reveals substrate rigidity-dependence of integrin molecular tensions in live cells
Authors: Sarkar Anwesha , LeVine Dana , Zhao Yuanchang , Mollaeian Keyvan , Ren Juan , Wang Xuefeng 
Published: January 2020

AbstractResponse of integrin tensions to substrate rigidity is important in cell rigidity sensing but has not been confirmed. Current fluorescent tension sensors produce cellular force signals collectively resulted from integrin tension magnitude, tension dwell time, integrin density and activity, ligand density and accessibility, etc., making it challenging to monitor the absolute molecular force level of integrin tensions in live cells. Here we developed a tandem tension sensor (TTS) consisting of two coupled tension sensing units which are subject to the same tension and respond with different activation probabilities to the tension. Reported by fluorescence, the activation probability ratio of these two units solely responds to the force level of local integrin tensions, excluding the bias from other non-force factors. We verified the feasibility of TTS in detecting integrin tensions and applied it to study cells on elastic substrates. TTS unambiguously reported that integrin tensions in platelets decrease monotonically with the substrate rigidity, verifying the rigidity-dependence of integrin tensions in live cells.
An atlas of cell types in the mammalian epididymis and vas deferens
Authors: Rinaldi Vera D. , Donnard Elisa , Gellatly Kyle J. , Rasmussen Morten , Kucukural Alper , Yukselen Onur , Garber Manuel , Sharma Upasna , Rando Oliver J. 
Published: January 2020

ABSTRACTFollowing spermatogenesis in the testis, mammalian sperm continue to mature over the course of approximately 10 days as they transit a long epithelial tube known as the epididymis. The epididymis is comprised of multiple segments/compartments that, in addition to concentrating sperm and preventing their premature activation, play key roles in remodeling the protein, lipid, and RNA composition of maturing sperm. In order to understand the complex roles for the epididymis in reproductive biology, we generated a single cell atlas of gene expression from the murine epididymis and vas deferens. We recovered all the key cell types of the epididymal epithelium, including principal cells, clear cells, and basal cells, along with associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Moreover, our data illuminate extensive regional specialization of principal cell populations across the length of the epididymis, with a substantial fraction of segment-specific genes localized in genomic clusters of functionally-related genes. In addition to the extensive region-specific specialization of principal cells, we find evidence for functionally-specialized subpopulations of stromal cells, and, most notably, two distinct populations of clear cells. Analysis of ligand/receptor expression reveals a network of potential cellular signaling connections, with several predicted interactions between cell types that may play roles in immune cell recruitment and other aspects of epididymal function. Our dataset extends on existing knowledge of epididymal biology, and provides a wealth of information on potential regulatory and signaling factors that bear future investigation.
Assessing Goodness-of-Fit in Marked-Point Process Models of Neural Population Coding via Time and Rate Rescaling
Authors: Yousefi Ali , Amidi Yalda , Nazari Behzad , Eden Uri. T. 
Published: January 2020

AbstractMarked-point process models have recently been used to capture the coding properties of neural populations from multi-unit electrophysiological recordings without spike sorting. These ‘clusterless’ models have been shown in some instances to better describe the firing properties of neural populations than collections of receptive field models for sorted neurons and to lead to better decoding results. To assess their quality, we previously proposed a goodness-of-fit technique for marked-point process models based on time-rescaling, which for a correct model, produces a set of uniform samples over a random region of space. However, assessing uniformity over such a region can be challenging, especially in high dimensions. Here, we propose a set of new transformations both in time and in the space of spike waveform features, which generate events that are uniformly distributed in the new mark and time spaces. These transformations are scalable to multi-dimensional mark spaces and provide uniformly distributed samples in hypercubes, which are well suited for uniformity tests. We discuss properties of these transformations and demonstrate aspects of model fit captured by each transformation. We also compare multiple uniformity tests to determine their power to identify lack-of-fit in the rescaled data. We demonstrate an application of these transformations and uniformity tests in a simulation study. Proofs for each transformation are provided in the Appendix section. We have made the MATLAB code used for the analyses in this paper publicly available through our Github repository athttps://github.com/YousefiLab/Marked-PointProcess-Goodness-of-Fit
Removing mains power artefacts from EEG – a novel template-based method
Authors: Zhang Shenghuan , McCane Brendan , Neo Phoebe S-H , McNaughton Neil 
Published: January 2020

ABSTRACTEEG signals are often contaminated with artefacts, particularly with mains power from electrical equipment. Low-pass filtering and notch filtering can lose valuable data. Here we describe a novel mains power noise removal method based on the fact that mains power noise is a sine wave component with an essentially fixed frequency and the same phase across all channels. This removes the mains power component, leaving uncontaminated EEG largely unchanged. Mains removal had a success rate of >99.9% recovered variance of the original EEG when removing synthesised mains power components. We compared this method with two other popular mains power noise removal methods. Our method was better than Cleanline which is an ICA based method and multiple PLI which is an adaptive notch filter based method. With the higher recovery, our method shows clear advantages over Cleanline and multiple PLI for removing mains power noise. From the aspect of data loss, it is obviously better than low-pass filter and normal notch filter.
Morality recruits neural reward circuitry to shape economic decision making
Authors: Liu Jie , Huang Xiaoxuan , Liao Chong , Cui Fang 
Published: January 2020

AbstractThe present study combined a novel hypothetical investment game with functional magnetic resonance imaging systemtically examined how morality modulates economic decision making in decision phase and outcome phase. We manipulated the morality of the investments by choosing each investment project based on subjective ratings on their moral valence and social benefits. There were three categories of investment morality: Green (moral), Red (immoral), and Neutral. The behavioral and neural responses during the investment decision and outcome phases were recorded and compared. Results showed that: behaviorally, people are willing to invest a larger amount of money into a moral project that may benefit society than they are into an immoral project that they think will harm society. They also rate gains in moral investments as more pleasant and losses as the most unpleasant. In the brain, we found that the reward system, especially the bilateral striatum, was involved in modulating functional connectivity during both phases, but in different ways. During decision making, the functional connectivity between fusiform gyrus and striatum might underlie the observed investing bias (Green over Red projects), while the covariation of BOLD signals in bilateral striatum with the behavioral tendency might explain the effect observed during the outcome evaluations. Our study provides evidence that morality modulates both the decision making and the outcome evaluation in economic situations.
MicroRNA-9 Mediated the Protective Effect of Ferulic Acid on Hypoxic-Ischemic Brain Injury in Neonatal Rats
Authors: Yao Keli , Yang Qin , Li Yajuan , Lan Ting , Yu Hong , Yu Yang 
Published: January 2020

AbstractNeonatal hypoxic-ischemic brain damage (NHIBD) leads to cognitive and memory impairments, and there is no effective clinical treatment. Ferulic acid (FA) is found within members of the genusAngelica, reportedly shows protective effects on neuronal damage; however, the mechanism of the protective effects of FA on rats following NHIBD remains unclear. Using the Morris water maze task, we herein found that the impairment of spatial memory formation in adult rats exposed to NHIBD was significantly reversed by FA treatment and the administration of LNA-miR-9. RT-PCR analyses revealed that miRNA-9 was significantly increased in the hippocampus of neonatal rats and neuronal PC12 cells following NHIBD and that FA and LNA-miR-9 both inhibited the expression of miRNA-9, suggesting that the therapeutic effect of FA was mainly attributed to the inhibition of miRNA-9 expression. Indeed, the silencing of miR-9 by LNA-miR-9 or FA similarly attenuated neuronal damage and cerebral atrophy in the rat hippocampus after NHIBD, which was consistent with the restored expression levels of brain-derived neurotrophic factor (BDNF). Therefore, FA treatment may protect against neuronal death through the inhibition of miRNA-9 induction in the rat hippocampus following hypoxic-ischemic damage.
Matrix Stiffness Regulates Liver Sinusoidal Endothelial Cell Function Mimicking Responses in Fatty Liver Disease
Authors: Natarajan Vaishaali , Moeller Michael , Casey Carol A. , Harris Edward N. , Kidambi Srivatsan 
Published: January 2020

AbstractLiver sinusoidal endothelial cells (LSECs) are a highly specialized endothelial cell that participates in numerous liver metabolic activities and collectively function as a scavenger system in the liver by removing waste macromolecules playing a vital role in the balance of lipids, cholesterol, and vitamins. Prior to hepatic fibrosis, independent of their etiology, LSECs become highly pro-inflammatory, capillarized (loss in fenestrations), and loss in specialized receptors (Stabilin-1, Stabilin-2, CD31 and SE-1). Liver fibrosis also leads to significant loss in the endocytosis function of LSECs. Thus understanding regulation of LSEC phenotype may be critical to understanding fibrosis. Extensive remodeling of the extracellular matrix occurs during fibrosis that leads to liver stiffening. The role of matrix stiffness as related to subtle but pivotal changes in LSECs physiology is under explored. Theoverall goalof our study is the development and implementation of a platform that enables the convergence of engineered cell microenvironments with the phenotypic and functional analysis of LSECs. Using our innovative biomimetic liver fibrosis model that allows modulation of substrate stiffness, we investigated the role of liver matrix stiffness in modulating LSECs function in fibrotic-like microenvironment. Primary LSECs were cultured on our novel polymer film coated polydimethylsiloxane (PDMS) gels with 2 kPa, 9 kPa 25 kPa and 55 kPa elastic modulus mimicking healthy, early fibrotic, fibrotic and extremely fibrotic substrates. SEM was used to image to fenestrations of LSECs and HA endocytosis assay was performed to measure the LSECs function. LSECs cultured on stiffer environment had significant remodeling of cytoskeletal proteins and morphology indicated of stress fibers. Also we observed that LSECs on fibrotic substrates resulted in loss of fenestrations (capillarization). This is critical as capillarization has been show to precede hepatic fibrosis and “capillarized” LSECs lose the ability to promote hepatic stellate cell (HSC) quiescence. LSECs on stiffer environment also had higher expression of cell adhesion molecules, VCAM-1 and ICAM-1 indicating the loss of phenotype of the cells. Fibrotic stiffness also impeded the HA endocytosis in LSECs, one of the main functions of the cells. These data suggest a plausible mechanism that increased stiffness modulates hepatocyte and LSEC function causing liver functional failure. Similar effect was observed in LSECs isolated from Non-Alcoholic Fatty Liver Disease (NAFLD) rat models indicating correlation to physiological conditions. Together, all these data demonstrates the plausible role of stiffness in regulating LSECs function and contribute to HSC activation and progression of liver fibrosis.
Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD)
Authors: Buch-Larsen Sara C. , Hendriks Ivo A. , Lodge Jean M. , Rykær Martin , Furtwängler Benjamin , Shishkova Evgenia , Westphall Michael S. , Coon Joshua J. , Nielsen Michael L. 
Published: January 2020

SUMMARYADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in a wide range of cellular processes. Mass spectrometry (MS)-based analysis of ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. Here, we describe the applicability of Activated Ion Electron Transfer Dissociation (AI-ETD) for MS-based proteomics analysis of physiological ADPr using our unbiased Af1521 enrichment strategy. To benchmark AI-ETD, we profiled 9,000 ADPr peptides mapping to >5,000 unique ADPr sites from a limited number of cells exposed to oxidative stress, corresponding to 120% and 28% more ADPr peptides compared to contemporary strategies using ETD and EThcD, respectively. Under physiological conditions AI-ETD identified 450 ADPr sites on low-abundant proteins, includingin vivocysteine auto-modifications on PARP8 and tyrosine auto-modifications on PARP14, hinting at specialist enzymatic functions for these enzymes. Collectively, our data provides new insights into the physiological regulation of ADP-ribosylation.
Architecture of the AP2:clathrin coat on the membranes of clathrin-coated vesicles
Authors: Kovtun Oleksiy , Kane Dickson Veronica , Kelly Bernard T. , Owen David. J. , Briggs John A. G. 
Published: January 2020

AbstractClathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell’s plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which cargo-selecting clathrin adaptors are attached. AP2 is the key adaptor in CME. Crystallography has shown AP2 to adopt a range of conformations. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures, interactions and arrangements of clathrin and AP2 at the key steps of coat assembly, from AP2 in solution to membrane-assembled clathrin-coated vesicles (CCVs). AP2 binds cargo and PtdIns(4,5)P2-containing membranes via multiple interfaces, undergoing conformational rearrangement from its cytosolic state. The binding mode of AP2 β2-appendage into the clathrin lattice in CCVs and buds implies how the adaptor structurally modulates coat curvature and coat disassembly.
Assortative mating, sexual selection and their consequences for gene flow inLittorina
Authors: Perini Samuel , Rafajlović Marina , Westram Anja M. , Johannesson Kerstin , Butlin Roger K. 
Published: January 2020

AbstractWhen divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail,Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern inL. saxatiliswith respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.
Measuring ‘Islamic accountability’ in Islamic social enterprise (ISE)
Authors: Kamaruddin Muhammad Iqmal Hisham , Auzair Sofiah Md 
Published: January 2020

Purpose
This study aims to present an effort to construct a measurement instrument to capture Islamic accountability from “accountability for what” aspect. These measurement instruments are developed by considering both social and economic natures in Islamic organisations.

Design/methodology/approach
This study defined the concept of Islamic accountability from the perspective of “accountability for what”. It is decomposed into specific items that suit an Islamic social enterprise (ISE). Next, these items are operationalised into scale items and re-composed empirically through factor analysis on data obtained from ISE stakeholders in Malaysia.

Findings
This study successfully developed an Islamic accountability measurement instruments from the “accountability for what” perspective for ISE. A total of 25 items are recognised and validated under four accountability dimensions, namely, accountability for input, accountability for output, accountability for procedural and accountability for Islamic principles and values.

Research limitations/implications
Not all measurement instruments are fit for every Islamic organisation type because of the different characteristics of Islamic organisations.

Practical implications
Developed items can be used as part of Islamic accountability index, especially by ISE and other similar organisations to measure their accountability practices. Besides, these developed items can also be adopted for reporting purposes. In the case of Malaysia, respective government agencies, such as the Companies Commission of Malaysia , the Registry of Society, the Ministry of Entrepreneur Development as well as the Malaysia Institute of Accountant, should have a look at the developed items to be considered into their respective guidelines or standards.

Originality/value
This study is believed to be a pioneering study in developing measurement instruments of Islamic accountability specific for ISE. It proposes measurement instruments of Islamic accountability that can be re-used for future research and is among the few studies of ISE.