bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of sex, gender, age, and ethnicity on psychosocial factors and substance use throughout phases of the COVID-19 pandemic
Authors: Brotto Lori A. , Chankasingh Kyle , Baaske Alexandra , Albert Arianne , Booth Amy , Kaida Angela , Smith Laurie W. , Racey Sarai , Gottschlich Anna , Murray Melanie C.M. , Sadarangani Manish , Ogilvie Gina S. , Galea Liisa 
Published: June 2021

AbstractThe SARS-CoV-2 (COVID-19) pandemic has had profound physical and mental health effects on populations around the world. Limited empirical research has used a gender-based lens to evaluate the mental health impacts of the pandemic, overlooking the impact of public health measures on marginalized groups, such as women, and the gender diverse community. This study used a gender-based analysis to determine the prevalence of psychosocial symptoms and substance use by age, ethnicity, income, rurality, education level, Indigenous status, and sexual orientation.Participants in the study were recruited from previously established cohorts as a part of the COVID-19 Rapid Evidence Study of a Provincial Population-Based Cohort for Gender and Sex (RESPPONSE) study. Those who agreed to participate were asked to self-report symptoms of depression, anxiety, pandemic stress, loneliness, alcohol use, and cannabis use across five phases of the pandemic as well as retrospectively before the pandemic.For all psychosocial outcomes, there was a significant effect of time with all five phases of the pandemic being associated with more psychosocial symptoms relative to pre-COVID levels (p < .0001). Gender was significantly associated with all outcomes (p < .0001) with men exhibiting lower scores (i.e., less symptoms) than women and gender diverse participants, and women exhibiting lower scores than the gender diverse group. Other significant predictors were age (younger populations experiencing more symptoms, p < .0001), ethnicity (Chinese/Taiwanese individuals experiencing less symptoms, p = .005), and Indigenous status (Indigenous individuals experiencing more symptoms, p < .0001). Alcohol use and cannabis use increased relative to pre-pandemic levels, and women reported a greater increase in cannabis use than men (p < .0001). Our findings highlight the need for policy makers and leaders to proactively consider gender when tailoring public health measures for future pandemics.
Liana optical traits increase tropical forest albedo and reduce ecosystem productivity
Authors: Meunier Félicien , Visser Marco D. , Shiklomanov Alexey , Dietze Michael C. , Guzmán Q. J. Antonio , Sanchez-Azofeifa Arturo , De Deurwaerder Hannes P. T. , Krishna Moorthy Sruthi M. , Schnitzer Stefan A. , Marvin David C. , Longo Marcos , Chang Liu , Broadbent Eben N. , Almeyda Zambrano Angelica M. , Muller-Landau Helene , Detto Matteo , Verbeeck Hans 
Published: June 2021

AbstractLianas are a key growth form in tropical forests. Their lack of self-supporting tissues and their vertical position on top of the canopy make them strong competitors of resources. A few pioneer studies have shown that liana optical traits differ on average from those of colocated tree. Those trait discrepancies were hypothesized to be responsible for the competitive advantage of lianas over trees. Yet, in the absence of reliable modelling tools, it is impossible to unravel their impact on the forest energy balance, light competition and on the liana success in Neotropical forests. To bridge this gap, we performed a meta-analysis of the literature to gather all published liana leaf optical spectra, as well as all canopy spectra measured over different levels of liana infestation. We then used a Bayesian data assimilation framework applied to two radiative transfer models (RTMs) covering the leaf and canopy scales to derive tropical tree and liana trait distributions, which finally informed a full dynamic vegetation model. According to the RTMs inversion, lianas grew thinner, more horizontal leaves with lower pigment concentrations. Those traits made the lianas particularly efficient at light interception and completely modified the forest energy balance and its carbon cycle. While forest albedo increased by 14% in the shortwave, light availability was dramatically reduced in the understory (−30% of the PAR radiation) and soil temperature decreased by 0.5°C. Those liana-specific traits were also responsible for a significant reduction of tree (−19%) and ecosystem (−7%) gross primary productivity (GPP) while lianas benefited from them (their GPP increased by +27%). This study provides a novel mechanistic explanation to the increase in liana abundance, new evidence of the impact of structural parasitism on forest functioning, and paves the way for the evaluation of the large-scale impacts of woody vines on forest biogeochemical cycles.
Population structure analysis and laboratory monitoring of Shigella with a standardised core-genome multilocus sequence typing scheme
Authors: Yassine Iman , Lefèvre Sophie , Hansen Elisabeth E. , Ruckly Corinne , Carle Isabelle , Lejay-Collin Monique , Fabre Laëtitia , Rafei Rayane , Clermont Dominique , de la Gandara Maria Pardos , Dabboussi Fouad , Thomson Nicholas R. , Weill François-Xavier 
Published: June 2021

ABSTRACTThe laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance of Shigella infections has been implemented in several countries, but without the use of a standardised typing scheme. We studied over 4,000 reference strains and clinical isolates of Shigella, covering all serotypes, with both the current serotyping scheme and the standardised EnteroBase core-genome multilocus sequence typing scheme (cgMLST). The Shigella genomes were grouped into eight phylogenetically distinct clusters, within the E. coli species. The cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognised the natural groupings for Shigella. By contrast, the serotyping scheme was affected by horizontal gene transfer, leading to a conflation of genetically unrelated Shigella strains and a separation of genetically related strains. The use of this cgMLST scheme will enhance the laboratory surveillance of Shigella infections.
Simulation of foraging behavior using a decision-making agent with Bayesian and inverse Bayesian inference: Temporal correlations and power laws in displacement patterns
Authors: Shinohara Shuji , Okamoto Hiroshi , Manome Nobuhito , Gunji Pegio-Yukio , Nakajima Yoshihiro , Moriyama Toru , Chung Ung-il 
Published: June 2021

AbstractIt has been stated that in human migratory behavior, the step length series may have temporal correlation and that there is some relationship between this time dependency and the fact that the frequency distribution of step length follows a power-law distribution. Furthermore, the frequency of occurrence of the step length in some large marine organisms has been found to switch between power-law and exponential distributions, depending on the difficulty of prey acquisition. However, to date it has not been clarified how the aforementioned three phenomena arise: the positive correlation created in the step length series, the relation between the positive correlation of the step length series and the form of an individual’s step length distribution, and the switching between power-law and exponential distributions depending on the abundance of prey. This study simulated foraging behavior using the Bayesian decision-making agent simultaneously performing both knowledge learning and knowledge-based inference to analyze how the aforementioned three phenomena arise. In the agent with learning and inference, past experiences were stored as hypotheses (knowledge) and they were used in current foraging behavior; at the same time, the hypothesis continued to be updated based on new experiences. The simulation results show that the agent with both learning and inference has a mechanism that simultaneously causes all the phenomena.
TissueGrinder, a novel technology for rapid generation of patient-derived single cell suspensions from solid tumors by mechanical tissue dissociation
Authors: Scheuermann Stefan , Lehmann Jonas M. , Mohan Ramkumar Ramani , Reißfelder Christoph , Rückert Felix , Langejürgen Jens , Pallavi Prama 
Published: June 2021

AbstractIntroductionRecent advances hold promise of making personalized medicine a step closer to implementation in clinical settings. However, traditional sample preparation methods are not robust and reproducible. In this study, the TissueGrinder, a novel mechanical semi-automated benchtop device, which can isolate cells from tissue in a very fast and enzyme-free way is tested for cell isolation from surgically resected tumor tissues.Methods33 surgically resected tumor tissues from various but mainly pancreatic, liver or colorectal origins were processed by both novel TissueGrinder and explant method. An optimized processing program for tumors from pancreatic, liver or colorectal cancer was developed. The viability and morphological characteristics of the isolated cells were evaluated microscopically. Expression of pancreatic cancer markers was evaluated in cells isolated from pancreatic tumors. Finally, the effect of mechanical stress on the cells was evaluated by assessing apoptosis markers via western blotting.ResultsTissueGinder was more efficient in isolating cells from tumor tissue with a success rate of 75% when compared to explant method 45% in terms of cell outgrowth six weeks after processing. Cells isolated with TissueGinder had a higher abundance and were more heterogeneous in composition as compared to explant method. Mechanical processing of the cells with TissueGrinder does not lead to apoptosis but causes slight stress to the cells.DiscussionOur results show that TissueGrinder can process solid tumor tissues more rapidly and efficiently and with higher success rate compared to the conventionally used explant method. The results of the study suggest that the TissueGrinder might be a suitable method for obtaining cells, which is important for its application in individualized therapy. Due to the great variance in different tumor entities and the associated individual tissue characteristics, a further development of the dissociation protocol for other types of tumors and normal will be targeted.
Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro
Authors: Gauhar Aziz , Privezentzev Cyril V , Demydchuk Mykhaylo , Gerlza Tanja , Rieger Julia , Kungl Andreas J , Walsh Frank S , Lynn Rutkowski J , Stocki Pawel 
Published: June 2021

AbstractSingle domain shark VNAR antibodies can offer a viable alternative to conventional Ig-based monoclonal antibodies in treating COVID-19 disease during the current pandemic. Here we report the identification of neutralizing single domain VNAR antibodies selected against the SARS-CoV-2 spike protein derived from the Wuhan variant using phage display. We identified 56 unique binding clones that exhibited high affinity and specificity to the spike protein. Of those, 10 showed an ability to block both the spike protein receptor binding domain from the Wuhan variant and the N501Y mutant from interacting with recombinant ACE2 receptor in vitro. In addition, 3 antibody clones retained in vitro blocking activity when the E484K spike protein mutant was used. The inhibitory property of the VNAR antibodies was further confirmed for all 10 antibody clones using ACE2 expressing cells with spike protein from the Wuhan variant. The viral neutralizing potential of the VNAR clones was also confirmed for the 10 antibodies tested using live Wuhan variant virus in in vitro cell infectivity assays. Single domain VNAR antibodies due to their low complexity, small size, unique epitope recognition and formatting flexibility should be a useful adjunct to existing antibody approaches to treat COVID-19.
It happened again: convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato
Authors: Lou Yann-Ru , Anthony Thilani M. , Fiesel Paul D. , Arking Rachel E. , Christensen Elizabeth M. , Jones A. Daniel , Last Robert L. 
Published: June 2021

AbstractPlants synthesize myriad phylogenetically-restricted specialized (aka ‘secondary’) metabolites with diverse structures. Metabolism of acylated sugar esters in epidermal glandular secreting trichomes across the Solanaceae (nightshade) family are ideal for investigating the mechanisms of evolutionary metabolic diversification. We developed methods to structurally analyze acylhexose mixtures by 2D NMR, which led to the insight that the Old World species black nightshade (Solanum nigrum) accumulates acylglucoses and acylinositols in the same tissue. Detailed in vitro biochemistry – cross validated by in vivo virus induced gene silencing – revealed two unique features of the four-step acylglucose biosynthetic pathway: a trichome-expressed, neofunctionalized invertase-like enzyme, SnASFF1, converts BAHD-produced acylsucroses to acylglucoses, which in turn are substrates for the first-reported acylglucose acyltransferase, SnAGAT1. This biosynthetic pathway evolved independently from that recently described in the wild tomato S. pennellii, reinforcing that acylsugar biosynthesis is evolutionarily dynamic with independent examples of primary metabolic enzyme cooption and additional variation in BAHD acyltransferases.TeaserAnalysis of plant protective surface hair chemistry revealed evolutionary mechanisms leading to metabolic innovation.
Vitamin D modulation of mitochondrial oxidative metabolism and mTOR enforces stress tolerance and anti-cancer responses
Authors: Quigley Mikayla , Rieger Sandra , Capobianco Enrico , Wang Zheng , Zhao Hengguang , Hewison Martin , Lisse Thomas S. 
Published: June 2021

AbstractThe relationship between vitamin D and reactive oxygen species (ROS), two integral signaling and damaging molecules of the cell, is poorly understood. This is striking, given that both factors are involved in cancer cell regulation and metabolism. Mitochondria (mt) dysfunction is one of the main drivers of cancer, producing higher cellular energy and ROS that can enhance oxidative stress and stress tolerance responses. To study the effects of vitamin D on metabolic and mt dysfunction, we used the vitamin D receptor (VDR)-sensitive MG-63 osteosarcoma cell model. Using biochemical approaches, active vitamin D (1,25-dihydroxyvitamin D, 1,25(OH)2D3) decreased mt ROS levels, membrane potential (ΔΨmt), biogenesis, and translation, while enforcing endoplasmic reticulum/mitohormetic stress tolerance responses. Using a mitochondria-focused transcriptomic approach, gene set enrichment and pathway analyses show that 1,25(OH)2D3 lowered mt fusion/fission and oxidative phosphorylation (OXPHOS). By contrast, mitophagy, ROS defense, and epigenetic gene regulation were enhanced after 1,25(OH)2D3 treatment, as well as key metabolic enzymes that regulate fluxes of substrates for cellular architecture and a shift toward non-oxidative energy metabolism. ATACseq revealed putative oxi-sensitive and tumor-suppressing transcription factors that may regulate important mt functional genes such as the mTORC1 inhibitor, DDIT4/REDD1. DDIT4/REDD1 was predominantly localized to the outer mt membrane in untreated MG-63 cells yet sequestered in the cytoplasm after 1,25(OH)2D3 and rotenone treatments, suggesting a level of control by membrane depolarization to facilitate its cytoplasmic mTORC1 inhibitory function. The results show that vitamin D activates distinct adaptive metabolic responses involving mitochondria to regain redox balance and control the growth of cancer cells.
Lyso-Phosphatidic Acid Acyl-Transferases: a link with intracellular protein transport in Arabidopsis root cells?
Authors: Wattelet-Boyer Valérie , Guédard Marina Le , Dittrich-Domergue Franziska , Maneta-Peyret Lilly , Kriechbaumer Verena , Boutté Yohann , Bessoule Jean-Jacques , Moreau Patrick 
Published: June 2021

AbstractPhosphatidic acid (PA) and Lysophosphatidic acid acyltransferases (LPAATs) might be critical for the secretory pathway. Four extra-plastidial LPAATs (numbered 2,3,4 and 5) were identified in A. thaliana. These AtLPAATs, displaying an enzymatic activity specific for LPA to produce PA, are located in the endomembrane system. We focused on the putative role of the AtLPAATs 3, 4 and 5 in the secretory pathway of root cells through genetical (knock-out mutants), biochemical (activity inhibitor, lipid analyses) and imaging (live and immuno-confocal microscopies) approaches. Treating a lpaat4;lpaat5 double mutant with the LPAAT inhibitor CI976 showed a primary root growth decrease. The transport of the auxin transporter PIN2 was disturbed in this lpaat4;lpaat5 double mutant treated with CI976, but not that of H+-ATPases. The lpaat4;lpaat5 double mutant was sensitive to salt stress and the transport of the aquaporin PIP2;7 to the plasma membrane in the lpaat4;lpaat5 double mutant treated with CI976 was reduced. We measured the amounts of neo-synthesized PA in roots, and found a decrease in PA only in the lpaat4;lpaat5 double mutant treated with CI976, suggesting that the protein transport impairment was due to a critical PA concentration threshold.HighlightPhosphatidic acid produced by Lyso-Phosphatidic Acid Acyl-Transferases has an impact on the efficiency of the intracellular transport of some proteins in Arabidopsis thaliana root cells.
Targeting of Protein Kinase CK2 Elicits Antiviral Activity on Bovine Coronavirus Infection
Authors: Ramón Ailyn C. , Pérez George V. , Caballero Evelin , Rosales Mauro , Aguilar Daylén , Vázquez-Blomquist Dania , Ramos Yassel , Rodríguez Arielis , Falcón Viviana , Rodríguez María P. , Ke Yang , Perera Yasser , Perea Silvio E. 
Published: June 2021

AbstractCoronaviruses constitute a global threat to human population since three highly pathogenic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have crossed species to cause severe human respiratory disease. Considering the worldwide emergency status due to the current COVID-19 pandemic, effective pan-coronavirus antiviral drugs are required to tackle the ongoing as well as future (re)emerging virus outbreaks. Protein kinase CK2 has been deemed a promising therapeutic target in COVID-19 supported by its in vitro pharmacologic inhibition and molecular studies on SARS-CoV-2 infected cells. CIGB-325 is a first-in-class synthetic peptide impairing the CK2-mediated signaling whose safety and clinical benefit have been evidenced in Covid-19 and cancer patients after intravenous administration. Here, we explored the putative antiviral effect of CIGB-325 over MDBK cells infected by bovine coronavirus (BCoV) Mebus. Importantly, CIGB-325 inhibited both the cytopathic effect and the number of plaques forming units with a half-inhibitory concentrations IC50 = 3.5 μM and 17.7 μM, respectively. Accordingly, viral protein accumulation at the cytoplasm was clearly reduced by treating BCoV-infected cells with CIGB-325 over time, as determined by immunocytochemistry. Of note, data from pull-down assay followed by western blot and/or mass spectrometry identification revealed physical interaction of CIGB-325 with nucleocapsid (N) protein and a bona fide cellular CK2 substrates. Functional enrichment and network analysis from the CIGB-325 interacting proteins indicated cytoskeleton reorganization and protein folding as the most represented biological processes disturbed by this anti-CK2 peptide. Altogether, our findings not only unveil the direct antiviral activity of CIGB-325 on coronavirus infection but also provide molecular clues underlying such effect. Also, our data reinforce the scientific rationality behind the pharmacologic inhibition of CK2 to treat coronavirus infections.
Multiscale mechanistic modelling of the host defense in invasive aspergillosis reveals leukocyte activation and iron acquisition as drivers of infection outcome
Authors: Ribeiro Henrique AL , Vieira Luis Sordo , Scindia Yogesh , Adhikari Bandita , Wheeler Matthew , Knapp Adam , Schroeder William , Mehrad Borna , Laubenbacher Reinhard 
Published: June 2021

AbstractAspergillus species are ubiquitous environmental molds, the spores of which are inhaled daily by most humans. Immunocompromised hosts can develop an invasive infection resulting in high mortality. There is, therefore, a pressing need for host-centric therapeutics for this infection. To address this need, we created a multi-scale computational model of the infection, focused on its interaction with the innate immune system and iron, a critical nutrient for the pathogen. The model, parameterized using published data, was found to recapitulate a wide range of biological features and was experimentally validatedin vivo. Conidial swelling was identified as critical in fungal strains with high growth, whereas the siderophore secretion rate is an essential prerequisite for establishment of the infection in low-growth strains. In immunocompetent hosts, high growth, high swelling probability, and impaired leukocyte activation lead to a high conidial germination rate. Similarly, in neutropenic mice, high fungal growth was achieved through synergy between high growth rate, high swelling probability, slow leukocyte activation, and high siderophore secretion. In summary, the model reveals a small set of parameters related to fungal growth, iron acquisition, and leukocyte activation as key determinants of the fate of the infection.
Cortical waves mediate the cellular response to electric fields
Authors: Yang Qixin , Miao Yuchuan , Campanello Leonard J. , Hourwitz Matt J. , Abubaker-Sharif Bedri , Bull Abby L. , Devreotes Peter N. , Fourkas John T. , Losert Wolfgang 
Published: June 2021

AbstractElectrotaxis, the directional migration of cells in a constant electric field, is important in regeneration, development, and wound healing. Electrotaxis has a slower response and a smaller dynamic range than guidance by other cues, suggesting that the mechanism of electrotaxis share both similarities and differences with chemical-gradient-sensing pathways. We examined a mechanism centered on the excitable system consisting of cortical waves of biochemical signals coupled to cytoskeletal reorganization, which has been implicated in random cell motility. We use electro-fused giantDictyostelium discoideumcells to decouple waves from cell motion and employ nanotopographic surfaces to limit wave dimensions and lifetimes. We demonstrate that wave propagation in these cells is guided by electric fields. The wave area and lifetime gradually increase in the first 10 minutes after an electric field is turned on, leading to more abundant and wider protrusions in the cell region nearest the cathode. The wave directions display “U-turn” behavior upon field reversal, and this switch occurs more quickly on nanotopography. Our results suggest that electric fields guide cells by controlling waves of signal transduction and cytoskeletal activity, which underlie cellular protrusions. Whereas surface receptor occupancy triggers both rapid activation and slower polarization of signaling pathways, electric fields appear to act primarily on polarization, explaining why cells respond to electric fields more slowly than to other guidance cues.