bluuebunny/crossref_metadata_2025_split huggingface dataset:
A photometric and kinematic analysis of UDG1137+16 (dw1137+16): Probing ultradiffuse galaxy formation in a group environment
Authors: Gannon Jonah S , Dullo Bililign T , Forbes Duncan A , Rich R Michael , Román Javier , Couch Warrick J , Brodie Jean P , Ferré-Mateu Anna , Alabi Adebusola , Mould Jeremy 
Published: February 2021

ABSTRACT
The dominant physical formation mechanism(s) for ultradiffuse galaxies (UDGs) is still poorly understood. Here, we combine new, deep imaging from the Jeanne Rich Telescope with deep integral field spectroscopy from the Keck II telescope to investigate the formation of UDG1137+16 (dw1137+16). Our new analyses confirm both its environmental association with the low density UGC 6594 group, along with its large size of 3.3 kpc and status as a UDG. The new imaging reveals two distinct stellar components for UDG1137+16, indicating that a central stellar body is surrounded by an outer stellar envelope undergoing tidal interaction. Both the components have approximately similar stellar masses. From our integral field spectroscopy, we measure a stellar velocity dispersion within the half-light radius (15 ± 4 km s−1) and find that UDG1137+16 is similar to some other UDGs in that it is likely dark matter dominated. Incorporating literature measurements, we also examine the current state of UDG observational kinematics. Placing these data on the central stellar velocity dispersion–stellar mass relation, we suggest there is little evidence for UDG1137+16 being created through a strong tidal interaction. Finally, we investigate the constraining power current dynamical mass estimates (from stellar and globular cluster velocity dispersions) have on the total halo mass of UDGs. As most are measured within the half-light radius, they are unable to accurately constrain UDG total halo masses.
ESTIMATION OF ENTRANCE SURFACE AIR KERMA IN DIGITAL RADIOGRAPHIC EXAMINATIONS
Authors: Kaushik Chanchal , Sandhu Inderjeet Singh , Srivastava A K , Chitkara Mansi 
Published: February 2021

Abstract
Purpose: Contribution of radiation doses from medical X-ray examination to collective dose is significant. Unusually, high doses may increase the risk of stochastic effects of radiations. Therefore, radiation dose assessment was performed in 241 digital X-ray examinations in the study and was compared with published dose reference levels (DRLs). Methods: Entrance surface air kerma (ESAK) was calculated in chest PA, cervical AP/Lat, abdomen AP, lumbar AP/Lat and pelvis AP digital radiographic examinations (119 male and 122 female) following the International Atomic Energy Agency recommended protocol. Initially, 270 digital examinations were selected, reject analysis was performed and final 241 examinations were enrolled in the study for dose calculations. The exposure parameters and X-ray tube output were used for dose calculations. Effective doses were estimated with the help of conversion coefficients from ICRP 103. Results: Median ESAK (mGy) and associated effective doses obtained were cervical spine AP (1.30 mGy, 0.045 mSv), cervical spine Lat (0.25 mGy, 0.005 mSv), chest PA (0.11 mGy, 0.014 mSv), abdomen AP (0.90 mGy, 0.118 mSv), lumbar spine AP (1.52 mGy, 0.177 mSv), lumbar spine Lat (7.76 mGy, 0.209 mSv) and pelvis AP (0.82 mGy, 0.081 mSv). Results were compared with the studies of UK, Oman, India and Canada. Conclusion: The calculated ESAK and effective dose values were less than or close to previously published literature except for cervical spine AP and lumbar spine Lat. The results reinforce the need for radiation protection optimization, improving examination techniques and appropriate use of automatic exposure control in digital radiography. ESAK values reported in this study could further contribute to establishing local DRLs, regional DRLs and national DRLs.
Persistent COVID-19 symptoms minimally impact the development of SARS-CoV-2 specific cellular immunity
Authors: Fang HengSheng , Wegman Adam D. , Ripich Kianna , Friberg Heather , Currier Jeffrey R. , Thomas Stephen J. , Endy Timothy P. , Waickman Adam T. 
Published: February 2021

ABSTRACTSARS-CoV-2 represents an unprecedented public health challenge with many unknowns remaining regarding the factors that impact viral pathogenicity and the development of immunity after infection. While the majority of SARS-CoV-2 infected individuals with mild-to-moderate COVID-19 resolve their infection with few complications, a significant number of individuals experienced prolonged symptoms lasting for weeks after initial diagnosis. Persistent viral infections are commonly accompanied by immunologic dysregulation, especially within the cellular immune compartment. However, it is unclear if persistent mild-to-moderate COVID-19 impacts the development of virus-specific cellular immunity. To this end, we analyzed the development of SARS-CoV-2 specific cellular immunity in convalescent COVID-19 patients who experienced eight days or fewer of COVID-19 symptoms, or symptoms persisting for 18 days or more. We observed that the duration of COVID-19 symptoms minimally impacts the magnitude, antigen specificity, and transcriptional profile of SARS-CoV-2 specific cellular immunity within both the CD4+ and CD8+ T cell compartments. Furthermore, we observed that reactivity against the structural N protein from SARS-CoV-2 in convalescent COVID-19 patients correlates with the amount of reactivity against the seasonal human coronaviruses 229E and NL63. These results provide additional insight into the complex processes that regulate the development of cellular immunity against SARS-CoV-2 and related human coronaviruses.
dSCOPE: a software to detect sequences critical for liquid-liquid phase separation
Authors: Li Shihua , Yu Kai , Zhang Qingfeng , Liu Zekun , Liu Jia , Ju Huai-Qiang , Zuo Zhixiang , Li Xiaoxing , Wang Zhenlong , Cheng Han , Liu Ze-Xian 
Published: February 2021

ABSTRACTMembrane based cells are the fundamental structure and function units of organisms, while evidences were increasing that liquid-liquid phase separation (LLPS) is associated with the formation of membraneless organelles, such as P-bodies, nucleoli and stress granules. Many studies have been undertaken to explore the functions of protein phase separation, but these studies lacked an effective tool to identify the sequence segments that critical for LLPS (SCOPEs). In this study, we presented a novel software called dSCOPE (http://dscope.omicsbio.info) to predict the SCOPEs. To develop the predictor, we curated experimentally identified sequence segments that can drive LLPS from published literature. Then sliding sequence window based physiological, biochemical, structural and coding features were integrated by random forest algorithm to perform prediction. Through rigorous evaluation, dSCOPE was demonstrated to achieve satisfactory performance. Furthermore, large-scale analysis of human proteome based on dSCOPE showed that the predicted SCOPEs enriched various protein post-translational modifications and cancer mutations, and the proteins which contain predicted SCOPEs enriched critical cellular signaling pathways. Taken together, dSCOPE precisely predicted the protein sequence segments critical for LLPS, with various helpful information visualized in the webserver to facilitate LLPS related research.
Identification of a conserved neutralizing epitope present on spike proteins from all highly pathogenic coronaviruses
Authors: Huang Yimin , Nguyen Annalee W. , Hsieh Ching-Lin , Silva Rui , Olaluwoye Oladimeji S. , Wilen Rebecca E. , Kaoud Tamer S. , Azouz Laura R. , Qerqez Ahlam N. , Le Kevin C. , Bohanon Amanda L. , DiVenere Andrea M. , Liu Yutong , Lee Alison G. , Amengor Dzifa , Shoemaker Sophie R. , Costello Shawn M. , Marqusee Susan , Dalby Kevin N. , D’Arcy Sheena , McLellan Jason S. , Maynard Jennifer A. 
Published: February 2021

ABSTRACTThree pathogenic human coronaviruses have emerged within the last 20 years, with SARS-CoV-2 causing a global pandemic. Although therapeutic antibodies targeting the SARS-CoV-2 spike currently focus on the poorly conserved receptor-binding domain, targeting essential neutralizing epitopes on the more conserved S2 domain may provide broader protection. We report an antibody binding an epitope conserved in the pre-fusion core of MERS-CoV, SARS-CoV and SARS-CoV-2 spike S2 domains. Antibody 3A3 binds a conformational epitope with ~2.5 nM affinity and neutralizes spike from SARS-CoV, SARS-CoV-2 and variants of concern inin vitropseudovirus assays. Hydrogen-deuterium exchange mass spectrometry identified residues 980-1006 in the flexible hinge region at the S2 apex as the 3A3 epitope, suggesting 3A3 prevents the S2 conformational rearrangements required for conversion to the spike post-fusion state and virus-host cell fusion. This work defines a conserved vulnerable site on the SARS-CoV-2 S2 domain and guides the design of pan-protective spike immunogens.
Cell-type specific expression and behavioral impact of galanin and GalR1 in the locus coeruleus during opioid withdrawal
Authors: Foster Stephanie L. , Galaj Ewa , Karne Saumya L. , Ferré Sergi , Weinshenker David 
Published: February 2021

ABSTRACTThe neuropeptide galanin is reported to attenuate opioid withdrawal symptoms, potentially by reducing neuronal hyperactivity in the noradrenergic locus coeruleus (LC) via galanin receptor 1 (GalR1). We evaluated this mechanism by using RNAscopein situhybridization to characterize GalR1 mRNA distribution in the dorsal pons and to compare galanin and GalR1 mRNA expression in tyrosine hydroxylase-positive (TH+) LC cells at baseline and following chronic morphine or precipitated withdrawal. We then used genetically altered mouse lines and pharmacology to test whether noradrenergic galanin (NE-Gal) modulates withdrawal symptoms. RNAscope revealed that, while GalR1 signal was abundant in the dorsal pons, 80.7% of the signal was attributable to TH-neurons outside the LC. Galanin and TH mRNA were abundant in LC cells at baseline and were further increased by withdrawal, whereas low basal GalR1 mRNA expression was unaltered by chronic morphine or withdrawal. Naloxone-precipitated withdrawal symptoms in mice lacking NE-Gal (GalcKO-Dbh) were largely similar to WT littermates, indicating that loss of NE-Gal does not exacerbate withdrawal. Complimentary experiments using NE-Gal overexpressor mice (NE-Gal OX) and systemic administration of the galanin receptor agonist galnon revealed that increasing galanin signaling also failed to alter behavioral withdrawal, while suppressing noradrenergic transmission with the alpha-2 adrenergic receptor agonist clonidine attenuated multiple symptoms. These results indicate that galanin does not acutely attenuate precipitated opioid withdrawal via an LC-specific mechanism, which has important implications for the general role of galanin in regulation of somatic and affective opioid responses and LC activity.
Faecal metabarcoding reveals pervasive long-distance impacts of garden bird feeding
Authors: Shutt Jack D , Trivedi Urmi H , Nicholls James A 
Published: February 2021

AbstractSupplementary feeding of wildlife is widespread, being undertaken by more than half of households in many countries. However, the impact that these supplemental resources have is unclear, with impacts assumed to be restricted to urban ecosystems. We reveal the pervasiveness of supplementary foodstuffs in the diet of a wild bird using metabarcoding of blue tit (Cyanistes caeruleus) faeces collected in early spring from a 220km transect in Scotland with a large urbanisation gradient. Supplementary foodstuffs were present in the majority of samples, with peanut (Arachis hypogaea) the single commonest (either natural or supplementary) dietary item. Consumption rates exhibited a distance decay from human habitation but remained high at several hundred metres from the nearest household and continued to our study limit of 1.4km distant. Supplementary food consumption was associated with a near quadrupling of blue tit breeding density and a five-day advancement of breeding phenology. We show that woodland bird species using supplementary food have increasing UK population trends, while species that don’t, and/or are outcompeted by blue tits, are likely to be declining. We suggest that the impacts of supplementary feeding are larger and more spatially extensive than currently appreciated and could be disrupting population and ecosystem dynamics.
Viral evolutionary dynamics predict Influenza-Like-Illnesses in patients
Authors: Wallbank Christopher D. , Aris-Brosou Stéphane 
Published: February 2021

AbstractViral infections such as those caused by the influenza virus can put a strain on healthcare systems. However, such a burden is typically difficult to predict. In order to improve such predictions, we hypothesize that the severity of epidemics can be linked to viral evolutionary dynamics. More specifically, we posit the existence of a negative association between patients’ health and the stability of coevolutionary networks at key viral proteins. To test this, we performed a thorough evolutionary analysis of influenza viruses circulating in continental US between 2010 and 2019, assessing how measures of the stability of these coevolutionary networks correlate with clinical data based on outpatient healthcare visits showing Influenza-Like Illness (ILI) symptoms. We first show evidence of a significant correlation between viral evolutionary dynamics and increased influenza activity during seasonal epidemics, and then show that these dynamics closely follow the progression of epidemics through each season, providing us with predictive power based on genetic data collected between week 20 and week 40/52, that is one to fifteen weeks prior to peak ILI. Viral evolutionary dynamics may hence be used by health authorities to further guide non-pharmaceutical interventions.
Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study
Authors: Han Li , Jara Carlos P , Wang Ou , Thibivilliers Sandra , Wóycicki Rafał K. , Carlson Mark A. , Velander William H. , Araújo Eliana P. , Libault Marc , Zhang Chi , Lei Yuguo 
Published: February 2021

AbstractThe Pigskin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. However, studying pigskin with scRNA-Seq is still rare. Here we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pigskin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. Also, we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.
Artificial seawater based long-term culture of colonial ascidians
Authors: Wawrzyniak M. , Matas Serrato L.A. , Blanchoud S. 
Published: February 2021

AbstractTunicates are highly diverse marine invertebrate filter-feeders that are vertebrates’ closest relatives. These organisms, despite a drastically different body plan during their adulthood, have a tissue complexity related to that of vertebrates. Ascidians, which compose most of the Tunicata, are benthic sessile hermaphrodites that reproduce sexually through a motile tadpole larval stage. Over half of the known ascidians species are able to reproduce asexually by budding, typically leading to the formation of colonies where animals, called zooids, are interconnected through an external vascular system. In addition, colonial ascidians are established models for important biological processes including allorecognition, immunobiology, aging, angiogenesis and whole-body regeneration. However, the current paucity in breeding infrastructures limits the study of these animals to coastal regions.To promote a wider scientific spreading and popularity of colonial ascidians, we have developed a flexible recirculating husbandry setup for their long-term in-lab culture. Our system is inspired both by the flow-through aquariums used by coastal ascidian labs, as well as by the recirculating in-lab systems used for zebrafish research. Our hybrid system thus combines colony breeding, water filtering and food culturing in a semi-automated system where specimens develop on hanging microscopy glass slides. Temperature, light/dark cycles, flow speed and feeding rates can be controlled independently in four different breeding environments to provide room for species-specific optimization as well as for running experiments. This setup is complemented with a quarantine for the acclimatization of wild isolates.Herein we present our success in breedingBotrylloides diegensis, a species of colonial ascidians, for more than 3 years in recirculating artificial seawater over 600 km away from their natural habitat. We show that colonies adapt well to in-lab culturing provided that a suitable marine microbiome is present, and that a specific strain can be isolated, propagated and efficiently used for research over prolonged periods of time. The flexible and modular structure of our system can be scaled and adapted to the needs of specific species, such asBotryllus schlosseri, as well as of particular laboratory spaces. Overall, we show thatBotrylloides diegensiscan be proficiently bred in-land and suggest that our results can be extended to other species of colonial ascidians to promote research on these fascinating animals.HighlightsFirst artificial seawater based recirculating aquaculture for colonial ascidiansOver 3 years of continuous breedingSemi-automated setup with minimized maintenanceGood biomass production for strain propagation4 different culture conditions for optimized breeding for species of interest
Single cell analysis of population-wide nuclear and cytosolic drug responses using high-content FRET imaging: measuring protein kinase activation in rat primary striatal neurons
Authors: Jones-Tabah Jace , Martin Ryan D. , Tanny Jason C. , Clarke Paul B.S. , Hébert Terence E. 
Published: February 2021

AbstractGenetically-encoded biosensors are used to track biochemical activities in living cells by measuring changes in fluorescence emitted by one or more fluorescent proteins. In the present article, we describe the application of genetically-encoded FRET biosensors with high content microscopy to image the signaling responses of thousands of neurons in response to drug treatments. We applied this approach to reveal intercellular variation in signaling responses among cultured striatal neurons stimulated with multiple drugs. The striatum is largely composed of medium-spiny GABAergic neurons which are divided into two broad sub-types based in part on their expression of dopamine D1vs.D2 receptors. Using high content FRET imaging and immunofluorescence, we identified neuronal sub-populations with unique responses to pharmacological manipulation. Focusing on dopamine- and glutamate-regulated PKA and ERK1/2 signaling in both the cytoplasm and nucleus, we identified pronounced intercellular differences, in both the magnitude and kinetics of signaling responses to drug application. Importantly, we found that a conventional “bulk” analysis that included all cells in culture yielded a different rank order of drug potency than that revealed by our single-cell analysis. The high degree of heterogeneity that we observed at the single cell level would not have been detectable using common population-level analyses, derived for example from western blotting or plate reader-based measurements. In conclusion, our single-cell analytical approach highlights the limitations of population-level analyses, and provides a novel way to study signaling biology.
Consequences of the Nyquist-Shannon sampling criterion in Mesoscopic Multiphoton Microscopy to avail full-field sub-micron resolution resolvability
Authors: Borah Bhaskar Jyoti , Lee Jye-Chang , Chi Han-Hsiung , Hsiao Yang-Ting , Yen Chen-Tung , Sun Chi-Kuang 
Published: February 2021

AbstractWith a limited effective voxel rate, to date, each laser-scanning mesoscopic multiphoton microscope (MPM), despite securing an ultra-large field of view (FOV) and an ultra-high optical resolution simultaneously, experiences afundamental issue with digitization; i.e., inability to satisfy the Nyquist-Shannon sampling criterion to resolve the optics-limited sub-micron resolution over the whole FOV. Such a system either neglects the criterion degrading the digital resolution to twice the pixel size, or significantly reduces the imaging area and/or the imaging speed to respect the digitization. Here we introduce a Nyquist figure of merit parameter to assess this issue, further to comprehend a maximum aliasing-free FOV and a cross-over excitation wavelength for a laser scanning MPM system. Based on our findings we demonstrate an ultra-high voxel rate acquisition in a custom-builtmesoscopic MPM systemto exceed the Nyquist-rate for a >3800 FOV-resolution ratio while not compromising the imaging speed as well as the photon-budget.
Stimulated oxygen transport in tissue by magnetic needle acupuncture
Authors: Liu Zhu , Wen Chenyu , Zhang Shi-Li 
Published: February 2021

AbstractAimTo understand physiology of magnetic needle acupuncture by investigating O2transport in tissue during needle intervention.MethodsO2transport in tissue is modeled by utilizing COMSOL with magnetic needle inserted into muscle tissue in a 2D porous media. The damaged tissue has been mimicked by an extracted tissue block with 1storder O2consumption rate. The convection-diffusion O2transport in the damaged tissue has been further evaluated by varying magnetic flux densityB0of the needle (0-1 T), myoglobin concentration (0-1 mM), O2tension (5-100 Torr), O2consumption rates, tissue permeability (10−12-10−6m2) and porosity (0.1-0.9).Results1) Active O2transport carried by interstitial flow is enhanced with the intervention of a magnetic needle by generating a high gradient magnetic field around the tip, which exerts a strong force (104N/m3) on the diamagnetic interstitial fluid to accelerate the flow. 2) This interstitial flow can reach 30 μm/s atB0= 1T and strongly correlates to the needleB0and tissue permeability. 3) The needle stirs the interstitial flow can pump O2flux by 1-2 orders of magnitude compared to that without magnetic field. 4) The enhancement of active O2transport by magnetic needle is site-specific to the tissue in the vicinity of the tip. This enhancement is more effective in edema condition with a high tissue permeability (>10−9m2).ConclusionsThe dramatic enhancement of O2transport to restore the O2mitochondria metabolism for dysfunctional muscle tissues is the fundamental physiological mechanism of magnetic needle acupuncture.