bluuebunny/crossref_metadata_2025_split huggingface dataset:
The epidemiology of herpes simplex virus type 2 in sub-Saharan Africa: systematic review, meta-analyses, and meta-regressions
Authors: Harfouche Manale , Abu-Hijleh Farah M. , James Charlotte , Looker Katharine J. , Abu-Raddad Laith J. 
Published: January 2021

AbstractBackgroundHerpes simplex virus type 2 (HSV-2) infection is a prevalent sexually transmitted infection with a sizable disease burden that is highest in sub-Saharan Africa. This study aimed to characterize HSV-2 epidemiology in this region.MethodsCochrane and PRISMA guidelines were followed to systematically review, synthesize, and report HSV-2 related findings. Meta-analyses and meta-regressions were conducted.FindingsFrom 218 relevant publications, 451 overall outcome measures and 869 stratified measures were extracted. Pooled incidence rates ranged between 2.4-19.4 per 100 person-years across populations. Pooled seroprevalence was lowest at 37.3% (95% confidence interval (CI): 34.9-39.7%) in general populations and high in female sex workers and HIV positive individuals at 62.5% (95% CI: 54.8-70.0%) and 71.3% (95% CI: 66.5-75.9%), respectively. In general populations, pooled seroprevalence increased steadily with age. Compared to women, men had a lower seroprevalence with an adjusted risk ratio (ARR) of 0.61 (95% CI: 0.56-0.67).Seroprevalence decreased in recent decades with an ARR of 0.98 (95% CI: 0.97-0.99) per year. Seroprevalence was highest in Eastern and Southern Africa. Pooled HSV-2 proportion in genital ulcer disease was 50.7% (95% CI: 44.7-56.8%) and in genital herpes it was 97.3% (95% CI: 84.4-100%).InterpretationSeroprevalence is declining by 2% per year, but a third of the population is infected. Age and geography play profound roles in HSV-2 epidemiology. Temporal declines and geographic distribution of HSV-2 seroprevalence mirror that of HIV prevalence, suggesting sexual risk behavior has been declining for three decades. HSV-2 is the etiological cause of half of GUD and nearly all genital herpes cases.FundingThis work was supported by pilot funding from the Biomedical Research Program at Weill Cornell Medicine in Qatar and by the Qatar National Research Fund [NPRP 9-040-3-008].
A Mathematical Model of Platelet Antiparasitic Action in Erythrocytes and Merozoites During Malaria Infection
Authors: Rubio Felipe Alves , Yang Hyun Mo 
Published: January 2021

AbstractPlatelets have been seen traditionally as fragments of blood mediating coagulation. However, evidence during malaria infection suggests that platelets also act against merozoites, an infectious form of malaria in the bloodstream, and megakaryocytes can release giant platelets with a larger volume than normal platelets. We propose a mathematical model to study the interaction between red blood cells, merozoites, and platelets during malaria infection. We analyzed two cases of the interaction of platelets with malaria infection. In the first one, we considered the isolated action of normal platelets and, in the second one, the joint antiparasitic action of both normal and giant platelets. Numerical simulations were performed to evaluate the stability of the equilibrium points of the system of equations. The model showed that the isolated antiparasitic action of normal platelets corroborates malaria infection control. However, the system can converge to a presence-merozoite equilibrium point, or an oscillatory behavior may appear. The joint antiparasitic action of both normal and giant platelets eliminated the oscillatory behavior and drove the dynamics to converge to lower parasitic concentration than the case of isolated action of normal platelets. Moreover, the joint antiparasitic action of platelets proved more easily capable of eliminating the infection.
SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface
Authors: Lu-Culligan Alice , Chavan Arun R. , Vijayakumar Pavithra , Irshaid Lina , Courchaine Edward M. , Milano Kristin M. , Tang Zhonghua , Pope Scott D. , Song Eric , Vogels Chantal B.F. , Lu-Culligan William J. , Campbell Katherine H. , Casanovas-Massana Arnau , Bermejo Santos , Toothaker Jessica M. , Lee Hannah J. , Liu Feimei , Schulz Wade , Fournier John , Muenker M. Catherine , Moore Adam J. ,   Yale IMPACT Team, Konnikova Liza , Neugebauer Karla M. , Ring Aaron , Grubaugh Nathan D. , Ko Albert I. , Morotti Raffaella , Guller Seth , Kliman Harvey J. , Iwasaki Akiko , Farhadian Shelli F. 
Published: January 2021

AbstractPregnant women appear to be at increased risk for severe outcomes associated with COVID-19, but the pathophysiology underlying this increased morbidity and its potential impact on the developing fetus is not well understood. In this study of pregnant women with and without COVID-19, we assessed viral and immune dynamics at the placenta during maternal SARS-CoV-2 infection. Amongst uninfected women, ACE2 was detected by immunohistochemistry in syncytiotrophoblast cells of the normal placenta during early pregnancy but was rarely seen in healthy placentas at full term. Term placentas from women infected with SARS-CoV-2, however, displayed a significant increase in ACE2 levels. Using immortalized cell lines and primary isolated placental cells, we determined the vulnerability of various placental cell types to direct infection by SARS-CoV-2in vitro. Yet, despite the susceptibility of placental cells to SARS-CoV-2 infection, viral RNA was detected in the placentas of only a subset (∼13%) of women in this cohort. Through single cell transcriptomic analyses, we found that the maternal-fetal interface of SARS-CoV-2-infected women exhibited markers associated with pregnancy complications, such as preeclampsia, and robust immune responses, including increased activation of placental NK and T cells and increased expression of interferon-related genes. Overall, this study suggests that SARS-CoV-2 is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. While this likely represents a protective mechanism shielding the placenta from infection, inflammatory changes in the placenta may also contribute to poor pregnancy outcomes and thus warrant further investigation.
Covid-19 in end-stage renal disease patients with renal replacement therapies: a systematic review and meta-analysis
Authors: Nopsopon Tanawin , Kittrakulrat Jathurong , Takkavatakarn Kullaya , Eiamsitrakoon Thanee , Kanjanabuch Talerngsak , Pongpirul Krit 
Published: January 2021

AbstractIntroductionThe novel coronavirus (COVID-19), caused by SARS-CoV-2, showed various prevalence and case-fatality rates (CFR) among patients with different pre-existing chronic conditions. End-stage renal disease (ESRD) patients with renal replacement therapy (RRT) might have a higher prevalence and CFR due to reduced immune function from uremia and kidney tropism of SARS-CoV-2, but there was no systematic study on the infection and mortality of the SARS-CoV-2 infection in ESRD patients who are on RRT.MethodsWe searched five electronic databases and performed a systematic review and meta-analysis up to June 30, 2020, to evaluate the prevalence and case fatality rate (CFR) of the COVID-19 infection among ESRD patients with RRT. The global COVID-19 data were retrieved from the international database on June 30, 2020, for estimating the prevalence and CFR of the general population as referencing points.ResultsOf 3,272 potential studies, 34 were eligible studies consisted of 1,944 COVID-19 confirmed cases in 21,873 ESRD patients with RRT from 12 countries in four WHO regions. The overall pooled prevalence in ESRD patients with RRT was 3.10% [95% confidence interval (CI) 1.25–5.72] which was higher than referencing 0.14% global average prevalence. The overall estimated CFR of COVID-19 in ESRD patients with RRT was 18.06% (95%CI 14.09– 22.32) which was higher than the global average at 4.98%.ConclusionsThis meta-analysis suggested high COVID-19 prevalence and CFR in ESRD patients with RRT. ESRD patients with RRT should have their specific protocol of COVID-19 prevention and treatment to mitigate excess cases and deaths.Author summaryChronic kidney disease (CKD) was associated with increasing severity and mortality of COVID-19. End-stage renal disease (ESRD) patients were at the terminal stage of CKD and had reduced immune function due to uremia. Additionally, ESRD patients with kidney transplantation had a diminished immune system from immunosuppressive agents. Kidneys might be the secondary target of SARS-CoV-2 after the respiratory tract regardless of the previous history of kidney disease, preferably the glomerulus, which was associated with the richness of some specific protein-coding genes in the kidney. The overall pooled prevalence in ESRD patients with renal replacement therapy was approximately 22 times of the referencing global average prevalence. The overall estimated case fatality rate of COVID-19 in ESRD patients with renal replacement therapy was approximately 3.6 times the global average. ESRD patients with renal replacement therapy had high COVID-19 prevalence and case fatality rate. We suggested that ESRD patients with renal replacement therapy should have their specific protocol of COVID-19 prevention and treatment to mitigate excess cases and deaths.
PREVALENCE OF ABDOMINAL OBESITY AND ITS ASSOCIATION WITH CARDIOVASCULAR RISK AMONG THE ADULT POPULATION IN BURKINA FASO
Authors: Cisse Kadari , Samadoulougou Sékou , Ouedraogo Mady , Kouanda Seni , Kirakoya-Samadoulougou et Fati 
Published: January 2021

ABSTRACTObjectiveThe objective of this study is to determine the prevalence of abdominal obesity and its associated factors in Burkina Faso. We hypothesize that there is a high burden of abdominal obesity and it is significantly associated with sociodemographic and cardiovascular risk factors.DesignWe performed secondary analysis of the survey conducted in Burkina Faso using the World Health Organization (WHO) STEPwise approach.SettingThe study was conducted in Burkina Faso with all 13 regions of the country included.ParticipantsOur study involved 4308 adults of both sexes aged 25 to 64 years.Main outcomeOur primary outcome was the abdominal obesity which was could defined using a cut-off point of waist circumference (WC) of ≥94 cm for men and ≥80 cm for women.ResultsThe overall age-standardized prevalence of abdominal obesity was 22.5% (95% CI: 21.3–23.7). This age-standardized prevalence was 35.9% (95% CI: 33.9–37.9) among women and 5.2% (95% CI: 4.3–6.2) among men (p < 0.001). In urban areas, the age-standardized prevalence of abdominal obesity was 42.8% (95% CI: 39.9–45.7) and 17.0% (95%CI: 15.7–18.2) in rural areas (p < 0.001). The overall age-standardized prevalence of very high WC (WC ≥102 cm for men and ≥88 cm for women) was 10.2% (95%CI: 9.3–11.1). According to the National Institute for Health and Clinical Excellence (NICE) BMI–WC matrix, which combines the body mass index (BMI) and WC to define different levels of cardiovascular health risk, 14.6% of adult Burkinabè had an increased cardiovascular health risk.ConclusionOur study shows a high prevalence of abdominal obesity among the adult population in Burkina Faso. These findings suggest that the measurement of WC should be systematically incorporated in Burkina Faso primary healthcare centers for the early detection of high cardiovascular risk in order to reduce levels of premature death.STRENGTHS AND LIMITATIONS OF THIS STUDY➢This is the first national representative study on abdominal obesity in the context of an emerging epidemiological transition in Burkina Faso.➢A recommended cut-off point was used to define abdominal obesity among the adult population in Burkina Faso, which we found to be associated with “intermediate” cardiovascular risk factors.➢The waist circumference and risk factors used in this study were measured using the standard approach proposed by the WHO [1]. However, some risk factors such as physical inactivity, alcohol consumption, and type of fat were self-reported and may therefore be affected by information bias.➢This study was a cross-sectional study and must not be considered to make causal inference.Target journalhttps://bmjopen.bmj.com/
An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time
Authors: Barnes Allison C , Rodríguez-Zapata Fausto , Blöcher-Juárez Karla A , Gates Daniel J , Janzen Garrett M , Kur Andi , Wang Li , Jensen Sarah E , Estévez-Palmas Juan M , Crow Taylor M , Kavi Heli S , Pil Hannah D , Stokes Ruthie L , Knizner Kevan T , Aguilar-Rangel Maria R , Demesa-Arévalo Edgar , Skopelitis Tara , Pérez-Limón Sergio , Stutts Whitney L , Thompson Peter , Chiu Yu-Chun , Jackson David , Muddiman David C , Fiehn Oliver , Runcie Daniel , Buckler Edward S , Ross-Ibarra Jeffrey , Hufford Matthew B , Sawers Ruairidh JH , Rellán-Álvarez Rubén 
Published: January 2021

AbstractNative Americans domesticated maize (Zea maysssp.mays) from lowland teosinteparviglumis(Zea maysssp.parviglumis) in the warm Mexican southwest and brought it to the highlands of México and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability, and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identifyHigh PhosphatidylCholine 1(HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation atHPC1, with the highlandHPC1allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maizeHPC1variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis ofHPC1via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highlandHPC1allele entered cultivated maize by introgression from the wild highland teosinteZea maysssp.mexicanaand has been maintained in maize breeding lines from the Northern US, Canada and Europe. Thus,HPC1introgressed from teosintemexicanaunderlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
An Alternative, Cas12a-based CRISPR Interference System for Mycobacteria
Authors: Fleck Neil , Grundner Christoph 
Published: January 2021

ABSTRACTThe introduction of CRISPR interference (CRISPRi) has made gene repression in mycobacteria much more efficient, but technical challenges of the prototypical Cas9-based platform, for example in multigene regulation, remain. Here, we introduce an alternative CRSPRi platform that uses the minimal Cas12a enzyme in combination with synthetic CRISPR arrays. This system is simple, tunable, and can regulate multiple genes simultaneously, providing a new tool to probe higher-order genetic interactions in mycobacteria includingMycobacterium tuberculosis(Mtb).
Spatiotemporal Trajectories in Resting-state FMRI Revealed by Convolutional Variational Autoencoder
Authors: Zhang Xiaodi , Maltbie Eric , Keilholz Shella 
Published: January 2021

AbstractRecent resting-state fMRI studies have shown that brain activity exhibits temporal variations in functional connectivity by using various approaches including sliding window correlation, co-activation patterns, independent component analysis, quasi-periodic patterns, and hidden Markov models. These methods often model the brain activity as a discretized hopping among several brain states that are defined by the spatial configurations of network activity. However, the discretized states are merely a simplification of what is likely to be a continuous process, where each network evolves over time following its unique path. To model these characteristic spatiotemporal trajectories, we trained a variational autoencoder using rs-fMRI data and evaluated the spatiotemporal features of the latent variables obtained from the trained networks. Our results suggest that there are a relatively small number of approximately orthogonal whole-brain spatiotemporal patterns that capture the most prominent features of rs-fMRI data, which can serve as the building blocks to construct all possible spatiotemporal dynamics in resting state fMRI. These spatiotemporal patterns provide insight into how activity flows across the brain in concordance with known network structures and functional connectivity gradients.
SARS-CoV-2 receptor binding mutations and antibody mediated immunity
Authors: Mejdani Marios , Haddadi Kiana , Pham Chester , Mahadevan Radhakrishnan 
Published: January 2021

AbstractSARS-CoV-2 mutations can impact infectivity, viral load, and overall morbidity/mortality during infection. In this analysis, we look at the mutational landscape of the SARS-CoV-2 receptor binding domain, a structure that is antigenic and allows for viral binding to the host. We analyze 104193 GISAID sequences acquired on October 15th, 2020 with a majority of sequences (96%) containing point mutations. We report high frequency mutations with improved binding affinity to ACE2 including S477N, N439K, V367F, and N501Y and address the potential impact of RBD mutations on antibody binding. The high frequency S477N mutation is present in 6.7% of all SARS-CoV-2 sequences, co-occurs with D614G, and is currently present in 14 countries. To address RBD-antibody interactions we take a subset of human derived antibodies and define their interacting residues using PDBsum. Our analysis shows that adaptive immunity against SARS-CoV-2 enlists broad coverage of the RBD suggesting that antibody mediated immunity should be sufficient to resolve infection in the presence of RBD point mutations that conserve structure.
Surface-based Single-subject Morphological Brain Networks: Effects of Morphological Index, Brain Parcellation and Similarity Measure, Sample Size-varying Stability and Test-retest Reliability
Authors: Li Yinzhi , Wang Ningkai , Wang Hao , Lv Yating , Zou Qihong , Wang Jinhui 
Published: January 2021

AbstractMorphological brain networks, in particular those at the individual level, have become an important approach for studying the human brain connectome; however, relevant methodology is far from being well-established in their formation, description and reproducibility. Here, we extended our previous study by constructing and characterizing single-subject morphological similarity networks from brain volume to surface space and systematically evaluated their reproducibility with respect to effects of different choices of morphological index, brain parcellation atlas and similarity measure, sample size-varying stability and test-retest reliability. Using the Human Connectome Project dataset, we found that surface-based single-subject morphological similarity networks shared common small-world organization, high parallel efficiency, modular architecture and bilaterally distributed hubs regardless of different analytical strategies. Nevertheless, quantitative values of all interregional similarities, global network measures and nodal centralities were significantly affected by choices of morphological index, brain parcellation atlas and similarity measure. Moreover, the morphological similarity networks varied along with the number of participants and approached stability until the sample size exceeded ∼70. Using an independent test-retest dataset, we found fair to good, even excellent, reliability for most interregional similarities and network measures, which were also modulated by different analytical strategies, in particular choices of morphological index. Specifically, fractal dimension and sulcal depth outperformed gyrification index and cortical thickness, higher-resolution atlases outperformed lower-resolution atlases, and Jensen-Shannon divergence-based similarity outperformed Kullback-Leibler divergence-based similarity. Altogether, our findings propose surface-based single-subject morphological similarity networks as a reliable method to characterize the human brain connectome and provide methodological recommendations and guidance for future research.
Nigrostriatal Dopamine Signals Sequence-Specific Action-Outcome Prediction Errors
Authors: Hollon Nick G. , Williams Elora W. , Howard Christopher D. , Li Hao , Traut Tavish I. , Jin Xin 
Published: January 2021

ABSTRACTDopamine has been suggested to encode cue-reward prediction errors during Pavlovian conditioning. While this theory has been widely applied to reinforcement learning concerning instrumental actions, whether dopamine represents action-outcome prediction errors and how it controls sequential behavior remain largely unknown. Here, by training mice to perform optogenetic intracranial self-stimulation, we examined how self-initiated goal-directed behavior influences nigrostriatal dopamine transmission during single as well as sequential instrumental actions. We found that dopamine release evoked by direct optogenetic stimulation was dramatically reduced when delivered as the consequence of the animal’s own action, relative to non-contingent passive stimulation. This action-induced dopamine suppression was specific to the reinforced action, temporally restricted to counteract the expected outcome, and exhibited sequence-selectivity consistent with hierarchical control of sequential behavior. Together these findings demonstrate that nigrostriatal dopamine signals sequence-specific prediction errors in action-outcome associations, with fundamental implications for reinforcement learning and instrumental behavior in health and disease.
Global analysis of protein arginine methylation
Authors: Zhang Fangrong , Kerbl-Knapp Jakob , Rodriguez Colman Maria J. , Macher Therese , Vujić Nemanja , Fasching Sandra , Jany-Luig Evelyne , Korbelius Melanie , Kuentzel Katharina B. , Mack Maximilian , Akhmetshina Alena , Paar Margret , Rinner Beate , Hörl Gerd , Steyrer Ernst , Stelzl Ulrich , Burgering Boudewijn , Eisenberg Tobias , Pertschy Brigitte , Kratky Dagmar , Madl Tobias 
Published: January 2021

SummaryQuantitative information about the levels and dynamics of post-translational modifications (PTMs) is critical for an understanding of cellular functions. Protein arginine methylation (ArgMet) is an important subclass of PTMs and is involved in a plethora of (patho)physiological processes. However, due to the lack of methods for global analysis of ArgMet, the link between ArgMet levels, dynamics and (patho)physiology remains largely unknown. We utilized the high sensitivity and robustness of Nuclear Magnetic Resonance (NMR) spectroscopy to develop a general method for the quantification of global protein ArgMet. Our NMR-based approach enables the detection of protein ArgMet in purified proteins, cells, organoids, and mouse tissues. We demonstrate that the process of ArgMet is a highly prevalent PTM and can be modulated by small-molecule inhibitors and metabolites and changes in cancer and during ageing. Thus, our approach enables to address a wide range of biological questions related to ArgMet in health and disease.Graphical Abstract