bluuebunny/crossref_metadata_2025_split huggingface dataset:
Respiratory Viral Sequencing Panel identifies SARS-CoV-2 variants, transmission and other co-circulating viruses in Georgia, USA: A Diagnostic and Epidemiologic Tool for Mass Surveillance in COVID-19 Pandemic
Authors: Sahajpal Nikhil S , Mondal Ashis K , Njau Allan , Petty Zachary , Chen Jiani , Ananth Sudha , Ahluwalia Pankaj , Williams Colin , Ross Ted M , Chaubey Alka , DeSantis Grace , Schroth Gary P. , Bahl Justin , Kolhe Ravindra 
Published: July 2021

AbstractBackgroundIn the current phase of COVID-19 pandemic, we are facing two serious public health challenges that include deficits in SARS-CoV-2 variant monitoring, and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent and dynamics of the outbreak are required to understand the transmission of the virus amongst seemingly unrelated cases and provide critical epidemiological information. To address these challenges, we evaluated a new high-throughput next-generation sequencing (NGS), respiratory viral panel (RVP) that includes 40 viral pathogens with the aim of analyzing viral subtypes, mutational variants of SARS-CoV-2, model to understand the spread of the virus in the state of Georgia, USA, and to assess other circulating viruses in the same population.MethodsThis study evaluated a total of 522 samples that included 483 patient samples and 42 synthetic positive control material. The performance metrics were calculated for both clinical and reference control samples by comparing detection results with the RT-PCR assay. The limit of detection (LoD) studies were conducted as per the FDA guidelines. Inference and visualization of the phylogeny of the SARS-CoV-2 sequences were performed through the Nextstrain Command-Line Interface (CLI) tool, utilizing the associated augur and auspice toolkits.ResultsThe performance metrics calculated using both the clinical samples and the reference controls revealed a PPA, NPA and accuracy of 95.98%, 85.96% and 94.4%, respectively. The LoD was determined to be 10 copies/ml with all 25 replicates detected across two different runs. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF 3a and, S84L in ORF8 covarying with the D614G spike protein mutation were the most prevalent, early in the pandemic, in Georgia, USA. In our analysis, isolates from the same county formed paraphyletic groups, which indicated virus transmission between counties.ConclusionThe study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats, models that provide insights into viral transmission patterns and predict transmission/ resurgence of regional outbreaks and provide critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.
Trial-wise exposure to visual appetitive cues increases physiological arousal but not temporal discounting
Authors: Knauth Kilian , Peters Jan 
Published: July 2021

AbstractHumans and many animals devalue future rewards as a function of time (temporal discounting). Increased discounting has been linked to various psychiatric conditions, including substance-use-disorders, behavioral addictions and obesity. Despite its high intra-individual stability, temporal discounting is partly under contextual control. One prominent manipulation that has been linked to increases in discounting is the exposure to highly arousing appetitive cues. However, results from trial-wise cue exposure studies appear highly mixed, and changes in physiological arousal were not adequately controlled. Here we tested the effects of appetitive (erotic), aversive and neutral visual cues on temporal discounting in thirty-five healthy male participants. The contribution of single-trial physiological arousal was assessed using comprehensive monitoring of autonomic activity (pupil size, heart rate, electrodermal activity). Physiological arousal was elevated following aversive and in particular erotic cues. In contrast to our pre-registered hypothesis, if anything, we observed decreased temporal discounting following erotic cue exposure. Aversive cues tended to increase decision noise. Computational modeling revealed that trial-wise arousal only accounted for minor variance over and above aversive and erotic condition effects, arguing against a general effect of physiological arousal on temporal discounting.
Heat-inactivated modified vaccinia virus Ankara boosts Th1-biased cellular and humoral immune responses as a vaccine adjuvant by activating the STING-mediated cytosolic DNA-sensing pathway
Authors: Yang Ning , Garzia Aitor , Meyer Cindy , Tuschl Thomas , Merghoub Taha , Wolchok Jedd D. , Deng Liang 
Published: July 2021

AbstractBackgroundProtein or peptide-based subunit vaccines are promising platforms for combating human cancers and infectious diseases. However, one primary concern regarding subunit vaccines is the relatively weak immune responses induced by proteins or peptides. Therefore, developing novel and effective vaccine adjuvants is critical for the success of subunit vaccines. Modified vaccinia virus (MVA) is a safe and effective vaccine against smallpox and monkeypox. In this study, we explored the potential of heat-inactivated MVA (heat-iMVA) as a novel vaccine adjuvant.MethodsWe co-administered heat-iMVA with a model antigen, chicken ovalbumin (OVA), either intramuscularly or subcutaneously twice, two weeks apart, and analyzed anti-OVA specific CD8+ and CD4+ T cells in the spleens and skin draining lymph nodes (dLNs) and serum anti-OVA IgG1 and IgG2c antibodies. We also compared the adjuvanticity of heat-iMVA with several known vaccine adjuvants, including complete Freund’s adjuvant (CFA) and AddaVax, an MF59-like preclinical grade nano-emulsion. In addition, we tested whether co-administration of heat-iMVA plus tumor neoantigen peptides or irradiated tumor cells improves antitumor efficacy in a B16-F10 therapeutic vaccination model. Using Stimulator of Interferon Genes (STING) or Batf3-deficient mice, we evaluated the contribution of the STING pathway and Batf3-dependent CD103+/CD8α DCs in heat-iMVA-induced immunity.ResultsCo-administration of protein- or peptide-based immunogens with heat-iMVA dramatically enhances Th1-biased cellular and humoral immune responses. This adjuvant effect of heat-iMVA is dependent on the STING-mediated cytosolic DNA-sensing pathway, and the antigen-specific CD8+ T cell response requires Batf3-dependent CD103+/CD8α+ dendritic cells (DCs). Heat-iMVA infection of bone marrow-derived DCs (BMDCs) promoted antigen cross-presentation, whereas live MVA infection did not. RNA-seq analyses revealed that heat-iMVA is a more potent activator of the STING pathway than live MVA. Additionally, combining tumor neoantigen peptides or irradiated tumor cells with heat-iMVA delayed tumor growth and extended the median survival in B16-F10 therapeutic vaccination models.ConclusionsHeat-iMVA induces type I interferon (IFN) production and antigen cross-presentation via a STING-dependent mechanism in DCs. Co-administration of heat-iMVA with peptide antigen generates strong Th1-biased cellular and humoral immunity. Collectively, our results demonstrate that heat-iMVA is a safe and potent vaccine adjuvant.
Lateral habenula M2 muscarinic receptor control of neuronal activity and cocaine seeking behavior
Authors: Wolfe Clara I.C. , Hwang Eun-Kyung , Zapata Agustin , Hoffman Alexander F. , Lupica Carl R. 
Published: July 2021

AbstractThe lateral habenula (LHb) plays a central role in balancing reward and aversion by opposing the contributions of brain reward nuclei. Using a rat cocaine self-administration model, we previously found that LHb inhibition or non-selective blockade of LHb muscarinic acetylcholine receptors (mAChRs) led to persistent cocaine seeking despite its signaled unavailability. As understanding roles for the LHb and cholinergic signaling in behavioral control is important to psychiatric illness and addiction, we examine how mAChRs act on LHb neurons using in vitro electrophysiology. We find that different groups of LHb neurons are depolarized or hyperpolarized by the cholinergic agonist carbachol (CCh), and that CCh could inhibit GABAergic and glutamatergic synaptic inputs to these cells. Presynaptic CCh effects were reversed by the M2 mAChR (M2R) antagonist AFDX-116, but not by pirenzepine, an M1R antagonist. Contemporaneous measurement of CCh effects on synaptic inhibition and excitation in LHb neurons showed a smaller effect on inhibition, suggesting a net shift in synaptic integration toward greater inhibition by mAChRs. Synaptic currents elicited by light-activation of ventral tegmental area (VTA) axons in the LHb, following channelrhodopsin-2 transfection of VTA, were also inhibited by M2Rs, suggesting the VTA as at least one M2R-sensitive LHb afferent. Finally, Go-NoGo cocaine seeking studies showed that blockade of LHb M2Rs, and not M1Rs, triggered continued cocaine seeking. These data identify LHb M2Rs as a potential control point of LHb function that enables withholding responses for cocaine and define cellular mechanisms through which mAChRs modulate LHb activity.
The cold-drought tolerance trade-off in temperate woody plants constrains range size, but not range filling
Authors: Puglielli Giacomo , Tordoni Enrico , Humphreys Aelys M. , Kalwij Jesse M. , Hutchings Michael J. , Laanisto Lauri 
Published: July 2021

AbstractInterspecific differences in plant species’ ranges are shaped by complex mechanistic interactions, which have so far remained largely beyond the reach of comprehensive models and explanations. Previous attempts to find underlying mechanisms by examining physiological tolerances to cold and heat separately have yielded contradictory results. Here we test the hypothesis that, instead of examining single stressors, abiotic stress tolerance syndromes that involve trade-offs between multiple abiotic stressors (namely drought, cold, waterlogging and shade), will provide reliable explanations.We compiled a dataset of actual range size and range filling (the ratio between actual and potential species range) as range metrics for 331 temperate woody plants species from Europe and North America. Tolerance syndromes were expressed as two PCA axes. One axis reflects a drought-cold/waterlogging tolerance trade-off (cold/wet-drought trade-off), the second axis represents a shade tolerance spectrum. Phylogenetic generalized linear mixed models were used to model the range metric-tolerance axes relationships using latitude as an additional main effect, and phylogeny and plant functional type as random effects.Actual range scaled negatively with the cold/wet-drought tolerance trade-off axis, mostly independently of latitude and continent. Thus, cold/wet-tolerant species had the largest ranges and drought tolerant species the smallest. The sign (−) of the relationship was independent of phylogeny and plant functional type. In contrast, range filling depended on latitude. However, deciduous and evergreen species displayed different distributions of range metrics and tolerance syndromes. No significant relationships with the shade tolerance spectrum were found.Our findings demonstrate that the cold/wet-drought trade-off partly explains interspecific range size differences. However, this trade-off did not explain range filling. We also showed that fundamental adaptations of species also significantly influence range sizes – stress avoidance through the deciduous habit also explained interspecific differences in range size.
Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies
Authors: Davis Luke K. , Ford Ian J. , Hoogenboom Bart W. 
Published: July 2021

AbstractThe rapid (< 1 ms) transport of biological material to and from the cell nucleus is regulated by the nuclear pore complex (NPC). At the core of the NPC is a permeability barrier consisting of intrinsically disordered Phe-Gly (FG) nucleoporins (FG Nups). Various types of nuclear transport receptors (NTRs) facilitate transport by partitioning in the FG Nup assembly, overcoming the barrier by their affinity to the FG Nups, and comprise a significant fraction of proteins in the NPC barrier. In previous work, we revealed that the experimental binding of the NTRs NTF2 and – the larger – Impβ to different planar assemblies of FG Nups follows a universal physical law defined by negative cooperativity, which was further validated by a minimal physical model that treated the FG Nups as flexible homopolymers and the NTRs as uniformly cohesive spheres Zahn et al. (2016). Here, we build upon our original study by first parametrizing our model to experimental data, and next to predict the effects of crowding by different types of NTRs. We show how varying the amounts of one type of NTR modulates how the other NTR penetrates the FG Nup assembly. Notably, at similar and physiologically relevant NTR concentrations, our model predicts demixed phases of NTF2 and Impβ within the FG Nup assembly. The functional implication of NTR phase separation is that NPCs may sustain separate transport pathways that are determined by inter-NTR competition.
A Combined Spectroscopic and Molecular Modeling Study on Structure-Function-Dynamics under Chemical Modification: Alpha-Chymotrypsin with Formalin Preservative
Authors: Biswas Pritam , Adhikari Aniruddha , Pal Uttam , Mondal Susmita , Mukherjee Dipanjan , Ghosh Ria , Saha-Dasgupta Tanusri , Chowdhury Sudeshna Shyam , Das Ranjan , Pal Samir Kumar 
Published: July 2021

AbstractEnzyme conformations can be altered via modification of its amino acid residues, side chains and large-scale domain modifications, which are closely linked to its function. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of covalent cross-linker formalin. Optical spectroscopy studies exhibit reduced catalytic activity of the enzyme with increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-anilino-1- napthelenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on minimal local residue modifications in CHT reveals formation of a stable enzyme-substrate complex even with the serine-histidine cross-linked enzyme which prohibits product formation giving rise to reduced catalytic activity.
Epigenetic Malleability at Core Promoter Regulates Tobacco PR-1a Expression after Salicylic Acid Treatment
Authors: Lodhi Niraj , Singh Mala , Srivastava Rakesh , Sawant Samir V. , Tuli Rakesh 
Published: July 2021

ABSTRACTTobacco’s PR-1a gene is induced by pathogen attack or exogenous application of Salicylic Acid (SA). However, the epigenetic modifications of the most important inducible promoter of the PR-1a gene are not understood clearly.Nucelosome mapping and chromatin immunoprecipitation assay were used to define the histone modification on the PR-1a promoter.Here, we report the epigenetic modifications over core promoter lead to disassembly of nucleosome (spans from −102 to +55 bp,masks TATA and transcription initiation) and repressor complex in induced state. ChIP assays demonstrate repressive chromatin of dimethylation at H3K9 and H4K20 of core promoter maintain uninduced state. While, active chromatin marks di and trimethylation of H3K4, acetylation of H3K9 and H4K16 are increased and lead the induction of PR-1a following SA treatment. TSA enhances expression of PR-1a by facilitating the histone acetylation, however increased expression of negative regulator (SNI1) of AtPR1, suppresses its expression in Arabidopsis thaliana’s mutants.Constitutive expression of AtPR1 in Histone Acetyl Transferases (HATs), LSD1, and SNI1 suggests that its inactive state is indeed maintained by a repressive complex and this strict regulation of pathogenesis related genes is conserved across species.SUMMARYHistone methylation and acetylation regulation of tobacco PR-1a promoter are significant for disassembly of the nucleosome and repressor proteins during induction.
Molecular Learning of a Soft-Disks Fluid
Authors: Zammataro Luca 
Published: July 2021

AbstractThis work is based on the Equivalence between Molecular Dynamics and Neural Network. It provides learning proofs in a Lennard-Jones (LJ) fluid, presented as a network of particles having non-bonded interactions. I describe the fluid’s learning as the property of an order that emerges as an adaptation in establishing equilibrium with energy and thermal conservation. The experimental section demonstrates the fluid can be trained with logic-gates patterns. The work goes beyond Molecular Computing’s application, explaining how this model uses its intrinsic minimizing properties in learning and predicting outputs. Finally, it gives hints for a theory on real chemistry’s computational universality.
Driving Native-like Zonal Enthesis Formation in Engineered Ligaments Using Mechanical Boundary Conditions and β-Tricalcium Phosphate
Authors: Brown M. Ethan , Puetzer Jennifer L. 
Published: July 2021

AbstractFibrocartilaginous entheses are structurally complex tissues that translate load from elastic ligaments to stiff bone via complex zonal organization with gradients in organization, mineralization, and cell phenotype. Currently, these gradients, necessary for long-term mechanical function, are not recreated in soft tissue-to-bone healing or engineered replacements, leading to high failure rates. Previously, we developed a culture system which guides ligament fibroblasts to develop aligned native-sized collagen fibers using high density collagen gels and mechanical boundary conditions. These constructs hold great promise as ligament replacements, however functional ligament-to-bone attachments, or entheses, are required for long-term function in vivo. The objective of this study was to investigate the effect of compressive mechanical boundary conditions and the addition of beta tricalcium phosphate (βTCP), a known osteoconductive agent, on the development of zonal ligament-to-bone entheses. We found that compressive boundary clamps, that restrict cellular contraction and produce a zonal tensile-compressive environment, guide ligament fibroblasts to produce 3 unique zones of collagen organization, and zonal accumulation of glycosaminoglycans (GAGs), type II and type X collagen by 6 weeks of culture, ultimately resulting in similar organization and composition as immature bovine entheses. Further, βTCP under the clamp enhanced the maturation of these entheses, leading to increased GAG accumulation, sheet-like mineralization, and significantly improved tensile moduli, suggesting the initiation of endochondral ossification. This culture system produced some of the most organized entheses to date, closely mirroring early postnatal enthesis development, and provides an in vitro platform to better understand the cues that drive enthesis maturation in vivo.
How alginate lyase produces quasi-monodisperse oligosaccharides: a normal mode analysis-based docking and molecular dynamics simulation study
Authors: Xu Hengyue , Gao Qi , Ming Dengming 
Published: July 2021

AbstractPolysaccharide degradation products are widely used in medicine, health food, textile and other industries. The preparation of monosaccharides by enzymatic degradation is a key technology in bio industrial production. Unfortunately, most of the known digested products are complex oligosaccharide mixtures, which limit their industrial processing and application. In this study, we explored a docking technique based on normal mode analysis to examine the possible cleavage mechanism of an alginate lyase (AlyB) from Birio Splendidus, which contains the catalytic domain of polysaccharide lyase family 7 (PL7) and a CBM32 sugar binding module, and was observed to produce trisaccharide products with quasi-monosaccharide distribution. We compared the molecular interactions of the enzyme with the natural alginates, the polyMG whose products has the quasi-monodisperse distribution of tri-saccharide and two synthetic polysaccharides, the polyM and polyG whose products has a wider distribution of oligosaccharides. Our calculations quantitatively show that there are a series of deterministic conformational changes in the catalytic pocket, which control the specificity of the substrate; at the same time, it determines the uniformity of the final product together with the spatial position of the key catalytic sites. The dynamic simulations revealed that CBM domain plays a key role in assisting the release of tri-saccharides. Our data highlights the important role of enzyme flexibility in determining product uniformity, which may provide new insight into design of enzymes for the production of high-value mono-distributed oligosaccharides.
Bats host the most virulent—but not the most dangerous—zoonotic viruses
Authors: Guth Sarah , Mollentze Nardus , Renault Katia , Streicker Daniel G. , Visher Elisa , Boots Mike , Brook Cara E. 
Published: July 2021

AbstractIdentifying virus characteristics associated with the largest public health impacts on human populations is critical to informing zoonotic risk assessments and surveillance strategies. Efforts to assess “zoonotic risk” often use trait-based analyses to identify which viral and reservoir host groups are most likely to source zoonoses but have not fully addressed how and why the impacts of zoonotic viruses vary in terms of disease severity (‘virulence’), capacity to spread within human populations (‘transmissibility’), or total human mortality (‘death burden’). We analyzed trends in human case fatality rates, transmission capacities, and total death burdens across a comprehensive dataset of mammalian and avian zoonotic viruses. Bats harbor the most virulent zoonotic viruses even when compared to birds, which alongside bats, have been hypothesized to be “special” zoonotic reservoirs due to molecular adaptations that support the physiology of flight. Reservoir host groups more closely related to humans—in particular, Primates—harbor less virulent, but more highly transmissible viruses. Importantly, disproportionately high human death burden, arguably the most important metric of zoonotic risk, is not associated with any animal reservoir, including bats. Our data demonstrate that mechanisms driving death burdens are diverse and often contradict trait-based predictions. Ultimately, total human mortality is dependent on context-specific epidemiological dynamics, which are shaped by a combination of viral traits and conditions in the animal host population and across and beyond the human-animal interface. Understanding the conditions that predict high zoonotic burden in humans will require longitudinal studies of epidemiological dynamics in wildlife and human populations.Significance statementThe clear need to mitigate zoonotic risk has fueled increased viral discovery in specific reservoir host taxa. We show that a combination of viral and reservoir traits can predict zoonotic virus virulence and transmissibility in humans, supporting the hypothesis that bats harbor exceptionally virulent zoonoses. However, pandemic prevention requires thinking beyond zoonotic capacity, virulence, and transmissibility to consider collective ‘burden’ on human health. For this, viral discovery targeting specific reservoirs may be inefficient as death burden correlates with viral, not reservoir, traits, and depends on context-specific epidemiological dynamics across and beyond the human-animal interface. These findings suggest that longitudinal studies of viral dynamics in reservoir and spillover host populations may offer the most effective strategy for mitigating zoonotic risk.