bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing a complicated problem: can COVID-19 asymptomatic cases be detected – and epidemics stopped− when testing is limited and the location of such cases unknown?
Authors: Rivas Ariel L. , Hoogesteijn Almira L. , Hittner James B. , Fasina Folorunso O. , van Regenmortel Marc H.V. 
Published: November 2020

AbstractCan the COVID-19 pandemic be stopped when the principal disseminators −asymptomatic cases− are not easily observable? This question was addressed exploring the cumulative epidemiologic data reported by 51 countries, up to October 2, 2020. In particular, the validity of test positivity and its inverse (the ratio of tests performed per case detected) to indicate whether asymptomatic cases are being detected and isolated –even when only a minor percentage of the population is tested− was evaluated. By linking test positivity data to the number of COVID-19 related deaths reported per million inhabitants, the research question was answered: countries that expressed a high percentage of test positivity (>5%) reported, on average, 15 times more deaths than countries that exhibited <1% test positivity. It is suggested that such a large difference in outcomes is due to the exponential growth that epidemics may experience when silent (asymptomatic) cases are not detected and, consequently, the disease disseminates. Because temporal and geo-referenced data on test positivity may facilitate cost-effective, site-specific testing policies, it is postulated that the risk of uncontrolled epidemics may be ameliorated when test positivity is investigated.
Effect of Lumbar Medial Branch Nerve Radiofrequency Ablation on Lumbar Spondylolisthesis
Authors: Patel Trusharth , Watterson Christopher , McKenzie-Brown Anne Marie , Spektor Boris , Egan Katherine , Boorman David 
Published: November 2020

AbstractImportanceRadiofrequency ablation (RFA) is a denervation therapy commonly performed for pain of facet etiology. Degenerative spondylolisthesis may be a co-existing condition; yet the effect of RFA on advancing listhesis is unknown.ObjectiveTo test the hypothesis that RFA of painful facets in the setting of spondylolisthesis may contribute to advancement of further degenerative spondylolisthesis.DesignRetrospective and prospective, observational study conducted at a single academic center among 15 participants with pre-existing degenerative Grade I or Grade II spondylolisthesis undergoing lumbar RFA encompassing spondylolisthesis level and followed with post-RFA imaging at 12 months and beyond to measure percent change in spondylolisthesis.Main Outcomes and MeasuresThe primary outcome was the percent advancement of spondylolisthesis per year measured on post-RFA lateral lumbar spine imaging compared to non-intervention baseline advancement of 2.6% per limited observational studies.ResultsAmong the 15 participants enrolled, 14 completed the study (median age 66; 64.3% women; median BMI 33.5; mean follow-up time 23.9 months). The mean advancement of spondylolisthesis per year after RFA was 1.30% (95% CI −0.14 to 2.78%), with 9/14 below 1.25%.Conclusion and RelevanceAmong patients with lumbar pain originating from facets in the setting of degenerative spondylolisthesis who underwent lumbar RFA, the observed advancement of spondylolisthesis is clinically similar to the baseline of 2.6% per year change. The study findings did not find a destabilizing effect of lumbar RFA in advancing spondylolisthesis in this patient population.
Do predictors of adherence to pandemic guidelines change over time? A panel study of 21,000 UK adults during the COVID-19 pandemic
Authors: Wright Liam , Fancourt Daisy 
Published: November 2020

AbstractIn the absence of a vaccine, governments have focused on behaviour change (e.g. social distancing and enhanced hygiene procedures) to tackle the COVID-19 pandemic. Existing research on the predictors of compliance with pandemic measures has often produced discrepant results. One explanation for this may be that the determinants of compliance are context specific. Understanding whether this is the case is important for designing public health messaging and for evaluating the generalisability of existing research. We used data from the UCL COVID-19 Social Study; a large weekly panel of UK adults from first five months of lockdown in the UK (n = 21,000). We tested whether the extent to which demographic, socio-economic position, personality traits, pro-social motivations, and the living environment predict compliance changed across the pandemic. Low compliance was strongly related to younger age and also to risk attitudes, empathic concern, and high income, among other factors. But the size of some of these associations was larger in later months when less stringent lockdown and household mixing measures were in place, suggesting context-specific effects. The results also showed that compliance fell faster across some groups, suggesting the importance that public health communications adopt a plurality of messages to maximize broad adherence.
Using Real World Data to Understand HIV and COVID-19 in the U.S.A. and Spain: Characterizing Co-Infected Patients Across the Care Cascade
Authors: Kohler Julianna , Kostka Kristin , Makadia Rupa , Paredes Roger , Duarte-Salles Talita , Duvall Scott , Cheng Alison , Golozar Asieh , Lane Jennifer C. E. , Sena Anthony G. , Rijnbeek Peter R. , Morales Daniel R. , Ryan Patrick B. , Reich Christian , Matheny Michael E. , Lynch Kristine E. , Siberry George K. , Prieto-Alhambra Daniel 
Published: November 2020

ABSTRACTObjectiveMost patients severely affected by COVID-19 have been elderly and patients with underlying chronic disease such as diabetes, cardiovascular disease, or respiratory disease. People living with HIV (PLHIV) may have greater risk of contracting or developing severe COVID-19 due to the underlying HIV infection or higher prevalence of comorbidities.DesignThis is a cohort study, including PLHIV diagnosed, hospitalized, or requiring intensive services for COVID-19.MethodsData sources include routine electronic medical record or claims data from the U.S. and Spain. Patient demographics, comorbidities, and medication history are described.ResultFour data sources had a population of HIV/COVID-19 coinfected patients ranging from 288 to 4606 lives. PLHIV diagnosed with COVID-19 were younger than HIV-negative patients diagnosed with COVID-19. PLHIV diagnosed with COVID-19 diagnosis had similar comorbidities as HIV-negative COVID-19 patients with higher prevalence of those comorbidities and history of severe disease. Treatment regimens were similar between PLHIV diagnosed with COVID-19 or PLHIV requiring intensive services.ConclusionsOur study uses routine practice data to explore HIV impact on COVID-19, providing insight into patient history prior to COVID-19. We found that HIV and COVID-19 coinfected patients have higher prevalence of underlying comorbidities such as cardiovascular and respiratory disease as compared to HIV-negative COVID-19 infected patients. We also found that, across the care cascade, co-infected patients who received intensive services were more likely to have more serious underlying disease or a history of more serious events as compared to PLHIV who were diagnosed with COVID-19.
Leprosy in wild chimpanzees
Authors: Hockings Kimberley J. , Mubemba Benjamin , Avanzi Charlotte , Pleh Kamilla , Düx Ariane , Bersacola Elena , Bessa Joana , Ramon Marina , Metzger Sonja , Patrono Livia V. , Jaffe Jenny E. , Benjak Andrej , Bonneaud Camille , Busso Philippe , Couacy-Hymann Emmanuel , Gado Moussa , Gagneux Sebastien , Johnson Roch C. , Kodio Mamoudou , Lynton-Jenkins Joshua , Morozova Irina , Mätz-Rensing Kerstin , Regalla Aissa , Said Abílio R. , Schuenemann Verena J. , Sow Samba O. , Spencer John S. , Ulrich Markus , Zoubi Hyacinthe , Cole Stewart T. , Wittig Roman M. , Calvignac-Spencer Sebastien , Leendertz Fabian H. 
Published: November 2020

ABSTRACTHumans are considered the main host forMycobacterium leprae, the aetiologic agent of leprosy, but spill-over to other mammals such as nine-banded armadillos and red squirrels occurs. Although naturally acquired leprosy has also been described in captive nonhuman primates, the exact origins of infection remain unclear. Here, we report on leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in the Cantanhez National Park, Guinea-Bissau, and the Taï National Park, Côte d’Ivoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence ofM. lepraeas the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). The independent evolutionary origin ofM. lepraein two geographically distant populations of wild chimpanzees, with no prolonged direct contact with humans, suggests multiple introductions ofM. lepraefrom an unknown animal or environmental source.
A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples
Authors: Liu Tiantian , Chen Zhong , Chen Wanqiu , Chen Xin , Hosseini Maryam , Yang Zhaowei , Li Jing , Ho Diana , Turay David , Gheorghe Ciprian , Jones Wendell , Wang Charles 
Published: November 2020

AbstractThe COVID-19 pandemic is a once-in-a-lifetime event, exceeding mortality rates of the flu pandemics from the 1950’s and 1960’s. Whole-genome sequencing (WGS) of SARS-CoV-2 plays a critical role in understanding the disease. Performance variation exists across SARS-CoV-2 viral WGS technologies, but there is currently no benchmarking study comparing different WGS sequencing protocols. We compared seven different SARS-CoV-2 WGS library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions. We constructed multiple WGS libraries encompassing three different viral inputs: 1,000,000, 250,000 and 1,000 copies. Libraries were sequenced using two distinct platforms with varying sequencing depths and read lengths. We found large differences in mappability and genome coverage, and variations in sensitivity, reproducibility and precision of single-nucleotide variant calling across different protocols. We ranked the performance of protocols based on six different metrics. Our results indicated that the most appropriate protocol depended on viral input amount and sequencing depth. Our findings offer guidance in choosing appropriate WGS protocols to characterize SARS-CoV-2 and its evolution.
Integrative Transcriptomic Analysis Reveals the Immune Mechanism for A CyHV-3-Resistant Common Carp Strain
Authors: Jia Zhiying , Wu Nan , Jiang Xiaona , Li Heng , Sun Jiaxin , Shi Mijuan , Li Chitao , Hu Xuesong , Ge Yanlong , Ye Weidong , Tang Ying , Shan Junwei , Cheng Yingyin , Xia Xiao-Qin , Shi Lianyu 
Published: November 2020

ABSTRACTAnti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp is resistant to this disease. This study illustrates the immune mechanisms involved in anti-CyHV-3 ability. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at day 0 (the healthy control) and day 7 after CyHV-3 infection (the survivors), and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. In order to dig out details in the immune aspect, The DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-XSexpression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops marked resistance to CyHV-3 through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition on inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3) as well as galectin 3 function by lncRNA may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.
Voltage-gated calcium channels contribute to spontaneous glutamate release directly via nanodomain coupling or indirectly via calmodulin
Authors: Lee Byoung Ju , Yang Che Ho , Lee Seung Yeon , Lee Suk-Ho , Kim Yujin , Ho Won-Kyung 
Published: November 2020

ABSTRACTNeurotransmitter release occurs either synchronously with action potentials (evoked release) or spontaneously (spontaneous release). Whether the molecular mechanisms underlying evoked and spontaneous release are identical, especially whether voltage-gated Ca2+channels (VGCCs) can trigger spontaneous events, is still a matter of debate in glutamatergic synapses. To elucidate this issue, we characterized the VGCC dependence of miniature excitatory postsynaptic currents (mEPSCs) in various synapses with different coupling distances between VGCCs and synaptic vesicles, known as a critical factor in evoked release. We found that most of the extracellular calcium-dependent mEPSCs were attributable to VGCCs in cultured autaptic hippocampal neurons and the mature calyx of Held where VGCCs and vesicles were tightly coupled. Among loosely coupled synapses, mEPSCs were not VGCC-dependent at immature calyx of Held and CA1 pyramidal neuron synapses, whereas VGCCs contribution was significant at CA3 pyramidal neuron synapses. Interestingly, the contribution of VGCCs to spontaneous glutamate release in CA3 pyramidal neurons was abolished by a calmodulin antagonist, calmidazolium. These data suggest that coupling distance between VGCCs and vesicles determines VGCC dependence of spontaneous release at tightly coupled synapses, yet VGCC contribution can be achieved indirectly at loosely coupled synapses.HighlightsExtracellular Ca2+-dependent spontaneous glutamate release is mediated by VGCCs.Ca2+cooperativity of spontaneous and evoked release is comparable.Synapses at different areas and ages show distinct VGCC dependence on mini events.Nanodomain coupling between VGCCs and Ca2+sensors determines VGCC dependence.
Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation
Authors: Frank Filipp , Liu Xu , Ortlund Eric A. 
Published: November 2020

AbstractThe glucocorticoid receptor (GR) is a ligand-regulated transcription factor (TF) that controls the tissue- and gene-specific transactivation and transrepression of thousands of target genes. Distinct GR DNA binding sequences with activating or repressive activities have been identified, but how they modulate transcription in opposite ways is not known. We show that GR forms phase-separated condensates that specifically concentrate known co-regulators via their intrinsically disordered regions (IDRs)in vitro.A combination of dynamic, multivalent (between IDRs) and specific, stable interactions (between LxxLL motifs and the GR ligand binding domain) control the degree of recruitment. Importantly, GR DNA-binding directs the selective partitioning of co-regulators within GR condensates such that activating DNAs cause enhanced recruitment of co-activators. Our work shows that condensation controls GR function by modulating co-regulator recruitment and provides a mechanism for the up- and down-regulation of GR target genes controlled by distinct DNA recognition elements.
Attention and prediction modulations in expected and unexpected visuospatial trajectories
Authors: Baker Kristen S. , Pegna Alan J. , Yamamoto Naohide , Johnston Patrick 
Published: November 2020

AbstractHumans are constantly exposed to a rich tapestry of visual information in a potentially changing environment. To cope with the computational burden this engenders, our perceptual system must use prior context to simultaneously prioritise stimuli of importance and suppress irrelevant surroundings. This study investigated the influence of prediction and attention in visual perception by investigating event-related potentials (ERPs) often associated with these processes, N170 and N2pc for prediction and attention, respectively. A contextual trajectory paradigm was used which violated visual predictions and neglected to predetermine areas of spatial interest, to account for the potentially unpredictable nature of a real-life visual scene. Participants (N=36) viewed a visual display of cued and non-cued shapes rotating in a five-step predictable trajectory, with the fifth and final position of either the cued or non-cued shape occurring in a predictable or unpredictable spatial location. To investigate the predictive coding theory of attention we used factors of attention and prediction, whereby attention was manipulated as either cued or non-cued conditions, and prediction manipulated in either predictable or unpredictable conditions. Results showed both enhanced N170 and N2pc amplitudes to unpredictable compared to predictable stimuli. Stimulus cueing status also increased N170 amplitude, but this did not interact with stimulus predictability. The N2pc amplitude was not affected by stimulus cueing status. In accordance with previous research these results suggest the N170 is in part a visual prediction error response with respect to higher-level visual processes, and furthermore the N2pc may index attention reorientation. The results demonstrate prior context influences the sensitivity of the N170 and N2pc electrophysiological responses. These findings add further support to the role of N170 as a prediction error signal and suggest that the N2pc may reflect attentional reorientation in response to unpredicted stimulus locations.
NyuWa Genome Resource: Deep Whole Genome Sequencing Based Chinese Population Variation Profile and Reference Panel
Authors: Zhang Peng , Luo Huaxia , Li Yanyan , Wang You , Wang Jiajia , Zheng Yu , Niu Yiwei , Shi Yirong , Zhou Honghong , Song Tingrui , Kang Quan ,   The Han100K Initiative, Xu Tao , He Shunmin 
Published: November 2020

AbstractThe lack of Chinese population specific haplotype reference panel and whole genome sequencing resources has greatly hindered the genetics studies in the world’s largest population. Here we presented the NyuWa genome resource based on deep (26.2X) sequencing of 2,999 Chinese individuals, and constructed NyuWa reference panel of 5,804 haplotypes and 19.3M variants, which is the first publicly available Chinese population specific reference panel with thousands of samples. Compared with other panels, NyuWa reference panel reduces the Han Chinese imputation error rate by the range of 30% to 51%. Population structure and imputation simulation tests supported the applicability of one integrated reference panel for both northern and southern Chinese. In addition, a total of 22,504 loss-of-function variants in coding and noncoding genes were identified, including 11,493 novel variants. These results highlight the value of NyuWa genome resource to facilitate genetics research in Chinese and Asian populations.
Tumor-derived extracellular vesicles regulate tumor-infiltrating regulatory T cells via the inhibitory immunoreceptor CD300a
Authors: Nakazawa Yuta , Kanemaru Kazumasa , Nakahashi-Oda Chigusa , Shibuya Akira 
Published: November 2020

AbstractAlthough tumor-infiltrating regulatory T (Treg) cells play a pivotal role in tumor immunity, how Treg cell activation are regulated in tumor microenvironments remains unclear. Here, we found that mice deficient in the inhibitory immunoreceptor CD300a on their dendritic cells (DCs) have increased numbers of Treg cells in tumors and greater tumor growth compared with wild-type mice after transplantation of B16 melanoma. Pharmacological impairment of extracellular vesicle (EV) release decreased Treg cell numbers in CD300a-deficient mice. Coculture of DCs with tumor-derived EV (TEV) induced the internalization of CD300a and the incorporation of EVs into endosomes, in which CD300a inhibited TEV-mediated TLR3-TRIF signaling for activation of the IFN-β-Treg cells axis. We also show that higher expression of CD300A was associated with decreased tumor-infiltrating Treg cells and longer survival time in patients with melanoma. Our findings reveal the role of TEV and CD300a on DCs in Treg cell activation in the tumor microenvironment.
Bioelectrical pattern discrimination ofMiconiaplants by spectral analysis and machine learning
Authors: Gimenez Valéria M M , Pauletti Patrícia M , Silva Ana Carolina Sousa , Costa Ernane José Xavier 
Published: November 2020

AbstractWe have conducted anin locoinvestigation into the speciesMiconia albicans(SW.) Triana andMiconia chamissoisNaudin (Melastomataceae), distributed in different phytophysiognomies of three Cerrado fragments in the State of São Paulo, Brazil, to characterize their oscillatory bioelectrical signals and to find out whether these signals have distinct spectral density. The experiments provided a sample bank of bioelectrical amplitudes, which were analyzed in the time and frequency domain. On the basis of the power spectral density (PSD) and machine learning techniques, analyses in the frequency domain suggested that each species has a characteristic biological pattern. Comparison between the oscillatory behavior of the species clearly showed that they have bioelectrical features, that collecting data is feasible, thatMiconiadisplay a bioelectrical pattern, and that environmental factors influence this pattern. From the point of view of experimental Botany, new questions and concepts must be formulated to advance understanding of the interactions between the communicative nature of plants and the environment. The results of this on-site technique represent a new methodology to acquire non-invasive information that might be associated with physiological, chemical, and ecological aspects of plants.HighlightIn lococharacterization of the bioelectrical signals of twoMiconiaspecies in the time and frequency domain suggests that the species have distinct biological patterns.