bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Authors: Hill Jason , Lillie Mette , Pettersson Mats E. , Rubin Carl-Johan , Grant B. Rosemary , Grant Peter R. , Andersson Leif , Jern Patric 
Published: October 2022

AbstractEndogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Measurements of metastable helium in Earth’s atmosphere by resonance lidar
Authors: Kaifler Bernd , Geach Christopher , Büdenbender Hans Christian , Mezger Andreas , Rapp Markus 
Published: October 2022

AbstractMonitoring and predicting space weather activity is increasingly important given society’s growing reliance on space-based infrastructure but is hampered by a lack of observational data. Airglow at 1083 nm from metastable helium He(23S) in the thermosphere has long been a target for remote-sensing instruments seeking to fill that gap; however, passive measurements of He(23S) fluorescence are limited by low brightness, and interpretation of these observations is complicated by the > 500 km depth of the He(23S) layer. Here, we demonstrate a lidar instrument that is able to stimulate and detect He(23S) fluorescence, and we present measured profiles of He(23S) density. These measurements provide crucial validation to space weather models, support predictions of peak number density ( ~ 1 cm−3) and the dependence of density on altitude, solar zenith angle, and season, and extend by a factor of 4 the maximum probed altitude range by an atmospheric profiling lidar. These measurements open the door for the development of more sophisticated lidars: by applying well-established spectroscopic lidar techniques, one can measure the Doppler shift and broadening of the He(23S) line, thereby retrieving profiles of neutral wind speed and temperature, opening a window for studying space weather phenomena.
A predictive computational platform for optimizing the design of bioartificial pancreas devices
Authors: Ernst Alexander U. , Wang Long-Hai , Worland Scott C. , Marfil-Garza Braulio A. , Wang Xi , Liu Wanjun , Chiu Alan , Kin Tatsuya , O’Gorman Doug , Steinschneider Scott , Datta Ashim K. , Papas Klearchos K. , James Shapiro A. M. , Ma Minglin 
Published: October 2022

AbstractThe delivery of encapsulated islets or stem cell-derived insulin-producing cells (i.e., bioartificial pancreas devices) may achieve a functional cure for type 1 diabetes, but their efficacy is limited by mass transport constraints. Modeling such constraints is thus desirable, but previous efforts invoke simplifications which limit the utility of their insights. Herein, we present a computational platform for investigating the therapeutic capacity of generic and user-programmable bioartificial pancreas devices, which accounts for highly influential stochastic properties including the size distribution and random localization of the cells. We first apply the platform in a study which finds that endogenous islet size distribution variance significantly influences device potency. Then we pursue optimizations, determining ideal device structures and estimates of the curative cell dose. Finally, we propose a new, device-specific islet equivalence conversion table, and develop a surrogate machine learning model, hosted on a web application, to rapidly produce these coefficients for user-defined devices.
TGF-β-dependent lymphoid tissue residency of stem-like T cells limits response to tumor vaccine
Authors: Li Guo , Srinivasan Saranya , Wang Liwen , Ma Chaoyu , Guo Kai , Xiao Wenhao , Liao Wei , Mishra Shruti , Zhang Xin , Qiu Yuanzheng , Lu Qianjin , Liu Yong , Zhang Nu 
Published: October 2022

AbstractTGF-β signaling is necessary for CD8+T cell differentiation into tissue resident memory T cells (TRM). Although higher frequency of CD8+TRMcells in the tumor microenvironment is associated with better prognosis, TGF-β−blockade typically improves rather than worsens outcomes. Here we show that in a mouse melanoma model, in the tumor-draining lymph nodes (TDLN) rather than in the tumors themselves, stem-like CD8+T cells differentiate into TRMs in a TGF-β and tumor antigen dependent manner. Following vaccination against a melanoma-specific epitope, most tumour-specific CD8+T cells are maintained in a stem-like state, but a proportion of cells lost TRMstatus and differentiate into CX3CR1+effector CD8+T cells in the TDLN, which are subsequently migrating into the tumours. Disruption of TGF-β signaling changes the dynamics of these developmental processes, with the net result of improving effector CD8+T cell migration into the tumours. In summary, TDLN stem-like T cells transiently switch from a TGF-β-dependent TRMdifferentiation program to an anti-tumor migratory effector development upon vaccination, which transition can be facilitated by targeted TGF-β blockade.
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Authors: Gounot Jean-Sebastien , Chia Minghao , Bertrand Denis , Saw Woei-Yuh , Ravikrishnan Aarthi , Low Adrian , Ding Yichen , Ng Amanda Hui Qi , Tan Linda Wei Lin , Teo Yik-Ying , Seedorf Henning , Nagarajan Niranjan 
Published: October 2022

AbstractDespite extensive efforts to address it, the vastness of uncharacterized ‘dark matter’ microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36–88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
Optineurin links Hace1-dependent Rac ubiquitylation to integrin-mediated mechanotransduction to control bacterial invasion and cell division
Authors: Petracchini Serena , Hamaoui Daniel , Doye Anne , Asnacios Atef , Fage Florian , Vitiello Elisa , Balland Martial , Janel Sebastien , Lafont Frank , Gupta Mukund , Ladoux Benoit , Gilleron Jerôme , Maia Teresa M. , Impens Francis , Gagnoux-Palacios Laurent , Daugaard Mads , Sorensen Poul H. , Lemichez Emmanuel , Mettouchi Amel 
Published: October 2022

AbstractExtracellular matrix (ECM) elasticity is perceived by cells via focal adhesion structures, which transduce mechanical cues into chemical signalling to conform cell behavior. Although the contribution of ECM compliance to the control of cell migration or division is extensively studied, little is reported regarding infectious processes. We study this phenomenon with the extraintestinal Escherichia coli pathogen UTI89. We show that UTI89 takes advantage, via its CNF1 toxin, of integrin mechanoactivation to trigger its invasion into cells. We identify the HACE1 E3 ligase-interacting protein Optineurin (OPTN) as a protein regulated by ECM stiffness. Functional analysis establishes a role of OPTN in bacterial invasion and integrin mechanical coupling and for stimulation of HACE1 E3 ligase activity towards the Rac1 GTPase. Consistent with a role of OPTN in cell mechanics, OPTN knockdown cells display defective integrin-mediated traction force buildup, associated with limited cellular invasion by UTI89. Nevertheless, OPTN knockdown cells display strong mechanochemical adhesion signalling, enhanced Rac1 activation and increased cyclin D1 translation, together with enhanced cell proliferation independent of ECM stiffness. Together, our data ascribe a new function to OPTN in mechanobiology.
Stable isotopes of C and N differ in their ability to reconstruct diets of cattle fed C3–C4 forage diets
Authors: Jaramillo David M. , Dubeux Jose C. B. , Ruiz-Moreno Martin , DiLorenzo Nicolas , Vendramini Joao M. B. , Sollenberger Lynn , Mackowiak Cheryl , Queiroz Luana M. D. , Abreu Daciele S. , Garcia Liza , Santos Erick R. S. , Kieke Burney A. 
Published: October 2022

AbstractStable isotopes are useful for estimating livestock diet selection. The objective was to compare δ13C and δ15N to estimate diet proportion of C3–C4 forages when steers (Bos spp.) were fed quantities of rhizoma peanut (Arachisglabrata; RP; C3) and bahiagrass (Paspalumnotatum; C4).Treatments were proportions of RP with bahiagrass hay: 100% bahiagrass (0%RP); 25% RP + 75% bahiagrass (25%RP); 50% RP + 50% bahiagrass (50%RP); 75% RP + 25% bahiagrass (75%RP); and 100% RP (100% RP). Feces, plasma, red blood cell (RBC), and hair were collected at 8-days intervals, for 32 days. Two-pool mixing model was utilized to back-calculate the proportion of RP based on the sample and forage δ13C or δ15N. Feces showed changes using δ13C by 8 days, and adj. R2 between predicted and observed RP proportion was 0.81 by 8 days. Plasma, hair, and RBC required beyond 32-days to reach equilibrium, therefore were not useful predictors of diet composition during the study. Diets were best represented using fecal δ13C at both 8-days and 32-days. By 32-days, fecal δ15N showed promise (R2 = 0.71) for predicting diet composition in C3–C4 diets. Further studies are warranted to further corroborate fecal δ15N as a predictor of diet composition in cattle.
Heat Wave Resilient Systems Architecture for Underwater Data Centers
Authors: Periola A. A. , Alonge A. A. , Ogudo K. A. 
Published: October 2022

AbstractThe need to design computing platforms with low water footprint and enhanced energy efficiency makes non-terrestrial computing platforms attractive. Large scale computing platforms in non-terrestrial environments are increasingly receiving attention. In this regard, underwater data centers (UDCs) are considered to have operational benefits due to their low cooling cost. Underwater data centers experience challenges due to marine heat waves. The occurrence of marine heat waves limits the amount of ocean water available for UDC cooling. This paper proposes a mechanism to detect marine heat waves, and ensure continued UDC functioning. The proposed mechanism utilizes reservoirs to store water and ensure continued functioning of underwater data center. In addition, the proposed research presents the reservoir as a service (RaaS) for ensuring UDC cooling. Furthermore, the presented research also describes modular form factor approach for UDC development. This is being done with the aim of enhancing UDC adoption and use in capital constrained contexts. The underwater data center operational duration is investigated. Evaluation shows that the proposed solution enhances the operational duration by an average of (5.5–12.3) % and (5.2–11.5) % given that marine heat waves span 10 epochs and 15 epochs during an operational phase, respectively.
Towards bright gamma-ray flash generation from tailored target irradiated by multi-petawatt laser
Authors: Hadjisolomou Prokopis , Jeong Tae Moon , Bulanov Sergei V. 
Published: October 2022

AbstractOne of the remarkable phenomena in the laser-matter interaction is the extremely efficient energy transfer to $$\gamma $$
γ
-photons, that appears as a collimated $$\gamma $$
γ
-ray beam. For interactions of realistic laser pulses with matter, existence of an amplified spontaneous emission pedestal plays a crucial role, since it hits the target prior to the main pulse arrival, leading to a cloud of preplasma and drilling a narrow channel inside the target. These effects significantly alter the process of $$\gamma $$
γ
-photon generation. Here, we study this process by importing the outcome of magnetohydrodynamic simulations of the pedestal-target interaction into particle-in-cell simulations for describing the $$\gamma $$
γ
-photon generation. It is seen that target tailoring prior the laser-target interaction plays an important positive role, enhancing the efficiency of laser pulse coupling with the target, and generating high energy electron-positron pairs. It is expected that such a $$\gamma $$
γ
-photon source will be actively used in various applications in nuclear photonics, material science and astrophysical processes modelling.
Gravity and magnetic anomalies of earthquake-prone areas in the southwestern Ulleung basin margin, East Sea (Sea of Japan)
Authors: Kim Chang Hwan , Kim Kwang-Hee , Choi Soon Young , Kim Won Hyuck , Choi Hyun Ok , Park Chan Hong 
Published: October 2022

AbstractSubmarine earthquakes have increased in the southwestern Ulleung Basin adjacent to the Korean Peninsula. This study analyzed the gravitational and magnetic properties of the three earthquake-prone areas (Hupo Bank and offshore regions near Pohang and Ulsan) in the basin. The basin was affected by tensile and compressive stresses during the formation of the East Sea. The southern Hupo Bank and the Pohang offshore exhibited high gravity anomalies and strong magnetic anomalies. Hupo Bank was separated from the peninsula and earthquakes in this region have been influenced by crustal fractures that facilitated igneous activities during the formation of the basin. Dense volcanic rocks and seaward dipping reflectors along the Pohang coast and continental slope suggest magmatic activities during the formation of the East Sea. Comparatively, the Ulsan offshore, with a thick sedimentary layer, exhibited a slightly higher gravity anomaly than the surrounding area, but no significant differences in the magnetic anomaly. Sequential tensile and compressive stresses related to the creation of the basin produced complex tectonic structures in this region. The magnetic tilt derivative results suggest that earthquakes were located near magnetic source boundaries. The results show that it is important to monitor earthquake-prone areas with gravity and magnetic anomalies.
Exposure to air pollution and its effect on ischemic strokes (EP-PARTICLES study)
Authors: Kuźma Łukasz , Roszkowska Sylwia , Święczkowski Michał , Dąbrowski Emil Julian , Kurasz Anna , Wańha Wojciech , Bachórzewska-Gajewska Hanna , Dobrzycki Sławomir 
Published: October 2022

AbstractIt is well known that exceeded levels of particulate matter in the air and other air pollutants harmfully affect the cardiovascular system. Empirical analyses of the effects of these factors on stroke incidence and mortality are still limited. The main objective of our analyses was to determine the association between short-term exposure to air pollutants and stroke incidence in non-industrial areas, more specifically in north-eastern Poland. To achieve this aim, we used data from the National Health Fund on patients hospitalized for stroke between 2011 and 2020 in the largest city of the region described as the Green Lungs of Poland. The pollution levels and atmospheric conditions data were obtained from the Provincial Inspectorate for Environmental Protection and the Institute of Meteorology and Water Management. Using daily data on hospitalizations, atmospheric conditions, and pollution, as well as ordered logistic regression models the hypotheses on the impact of weather and air pollution conditions on ischemic strokes were tested. The study group included 4838 patients, 45.6% of whom were male; the average patient age was approximately 74 years. The average concentrations of PM2.5 were 19.09 µg/m3, PM10 26.66 µg/m3 and CO 0.35 µg/m3. Analyses showed that an increase in PM2.5 and PM10 concentrations by 10 µg/m3 was associated with an increase in the incidence of stroke on the day of exposure (OR = 1.075, 95% CI 0.999–1.157, P = 0.053; OR = 1.056, 95% CI 1.004–1.110, P = 0.035) and the effect was even several times greater on the occurrence of a stroke event in general (PM2.5: OR = 1.120, 95% CI 1.013–1.237, P = 0.026; PM10: OR = 1.103, 95% CI 1.028–1.182, P = 0.006). Furthermore, a short-term (up to 3 days) effect of CO on stroke incidence was observed in the study area. An increase of 1 μg/m3 CO was associated with a lower incidence of stroke 2 days after the exposure (OR = 0.976, 95% CI 0.953–0.998, P = 0.037) and a higher incidence 3 days after the exposure (OR = 1.026, 95% CI 1.004–1.049, P = 0.022).
Immediate protein expression from exogenous mRNAs in embryonic brain
Authors: Naruse Masae , Saito Tetsuichiro 
Published: October 2022

AbstractmRNA vaccines for SARS-CoV-2 have been widely used and saving millions of people in the world. How efficiently proteins are produced from exogenous mRNAs in the embryonic brain, however, is less known. Here we show that protein expression occurs highly efficiently in neural stem cells, in a very narrow time window after mRNA electroporation in the embryonic mouse brain, where plasmids have been successfully transfected. Protein expression is detected 1 h and 12 h after the electroporation of mRNAs and plasmids, respectively. The delivery of exogenous mRNAs may be useful for not only vaccines but also functional analysis in the brain.
Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core
Authors: Pacheco-García Juan Luis , Loginov Dmitry S. , Naganathan Athi N. , Vankova Pavla , Cano-Muñoz Mario , Man Petr , Pey Angel L. 
Published: October 2022

AbstractPhosphoglycerate kinase has been a model for the stability, folding cooperativity and catalysis of a two-domain protein. The human isoform 1 (hPGK1) is associated with cancer development and rare genetic diseases that affect several of its features. To investigate how mutations affect hPGK1 folding landscape and interaction networks, we have introduced mutations at a buried site in the N-terminal domain (F25 mutants) that either created cavities (F25L, F25V, F25A), enhanced conformational entropy (F25G) or introduced structural strain (F25W) and evaluated their effects using biophysical experimental and theoretical methods. All F25 mutants folded well, but showed reduced unfolding cooperativity, kinetic stability and altered activation energetics according to the results from thermal and chemical denaturation analyses. These alterations correlated well with the structural perturbation caused by mutations in the N-terminal domain and the destabilization caused in the interdomain interface as revealed by H/D exchange under native conditions. Importantly, experimental and theoretical analyses showed that these effects are significant even when the perturbation is mild and local. Our approach will be useful to establish the molecular basis of hPGK1 genotype–phenotype correlations due to phosphorylation events and single amino acid substitutions associated with disease.
Assessment of variability in the plasma 7k SomaScan proteomics assay
Authors: Candia Julián , Daya Gulzar N. , Tanaka Toshiko , Ferrucci Luigi , Walker Keenan A. 
Published: October 2022

AbstractSomaScan is a high-throughput, aptamer-based proteomics assay designed for the simultaneous measurement of thousands of proteins with a broad range of endogenous concentrations. In its most current version, the 7k SomaScan assay v4.1 is capable of measuring 7288 human proteins. In this work, we present an extensive technical assessment of this platform based on a study of 2050 samples across 22 plates. Included in the study design were inter-plate technical duplicates from 102 human subjects, which allowed us to characterize different normalization procedures, evaluate assay variability by multiple analytical approaches, present signal-over-background metrics, and discuss potential specificity issues. By providing detailed performance assessments on this wide range of technical aspects, we aim for this work to serve as a valuable resource for the growing community of SomaScan users.
Combining NGN2 programming and dopaminergic patterning for a rapid and efficient generation of hiPSC-derived midbrain neurons
Authors: Sheta Razan , Teixeira Maxime , Idi Walid , Pierre Marion , de Rus Jacquet Aurelie , Emond Vincent , Zorca Cornelia E. , Vanderperre Benoît , Durcan Thomas M. , Fon Edward A. , Calon Frédéric , Chahine Mohamed , Oueslati Abid 
Published: October 2022

AbstractThe use of human derived induced pluripotent stem cells (hiPSCs) differentiated to dopaminergic (DA) neurons offers a valuable experimental model to decorticate the cellular and molecular mechanisms of Parkinson’s disease (PD) pathogenesis. However, the existing approaches present with several limitations, notably the lengthy time course of the protocols and the high variability in the yield of DA neurons. Here we report on the development of an improved approach that combines neurogenin-2 programming with the use of commercially available midbrain differentiation kits for a rapid, efficient, and reproducible directed differentiation of hiPSCs to mature and functional induced DA (iDA) neurons, with minimum contamination by other brain cell types. Gene expression analysis, associated with functional characterization examining neurotransmitter release and electrical recordings, support the functional identity of the iDA neurons to A9 midbrain neurons. iDA neurons showed selective vulnerability when exposed to 6-hydroxydopamine, thus providing a viable in vitro approach for modeling PD and for the screening of small molecules with neuroprotective proprieties.