Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fight Against Severe COVID-19: Can Parasitic Worms Contribute?

As of 31 December 2021, COVID-19, caused by infection with SARS-CoV-2, had been confirmed in more than 285 million people worldwide, with more than 5.4 million dead resulting in a case fatality ratio of 1.89%. This figure is likely to be vastly underestimated, as a proportion was not registered officially as COVID-19-related/excess deaths. The United States recorded the highest number (54,656,866) of confirmed cases. In Africa, there are 47 countries affected, with 7,065,972 cumulative cases and 155,081 deaths were recorded by 31 Dec 2021 (WHO African Region numbers at a glance). To date, the currently approved vaccines have been effective in preventing COVID-19, particularly in regards to severe symptoms (1). However, several immune escape mechanisms of SARS-CoV-2 and the rapid emergence of mutated variants (2) pose a great challenge to the efficacy of these vaccines. Patients with severe COVID-19 tend to have a high concentration of pro-inflammatory cytokines (IL-2, IL-7, IL-10, G-CSF, TNF-a, CXCL10, MCP1, and MIP1a) (3), suggesting that a cytokine release syndrome (CRS) (4) (also loosely referred to as a cytokine storm), which is a form of life-threatening systemic inflammatory response syndrome (SIRS), can often feature in severe COVID-19 infections. Among the increased levels of inflammatory mediators in COVID-19 patients, the plasma levels of IL-6, an amplifier in the cytokine storm, are significantly elevated in non-survivors compared with survivors (5). The main cause of death of COVID-19 is due to severe acute respiratory distress syndrome (ARDS) with this high severity being dependent on the cytokine storm. Sepsis has been defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection (6). Endothelium damage, vascular permeability, microvascular dysfunction, coagulation pathway activation, and impaired tissue oxygenation occur during sepsis and can lead to multisystem organ dysfunction (MODS), organ failure and consequently a potentially lethal outcome. As many patients with severe COVID-19 show typical clinical manifestations of septic shock, with other symptoms meeting the diagnostic criteria for sepsis and septic shock according to the Sepsis-3 International Consensus (6), Li et al. hypothesized that viral sepsis is a crucial process in severe COVID-19 cases (7). Accumulating evidence further links the pathology of severe COVID19, such as acute kidney injury, to sepsis (8).
Constraining Arctic Climate Projections of Wintertime Warming With Surface Turbulent Flux Observations and Representation of Surface-Atmosphere Coupling

The drivers of rapid Arctic climate change—record sea ice loss, warming SSTs, and a lengthening of the sea ice melt season—compel us to understand how this complex system operates and use this knowledge to enhance Arctic predictability. Changing energy flows sparked by sea ice decline, spotlight atmosphere-surface coupling processes as central to Arctic system function and its climate change response. Despite this, the representation of surface turbulent flux parameterizations in models has not kept pace with our understanding. The large uncertainty in Arctic climate change projections, the central role of atmosphere-surface coupling, and the large discrepancy in model representation of surface turbulent fluxes indicates that these processes may serve as useful observational constraints on projected Arctic climate change. This possibility requires an evaluation of surface turbulent fluxes and their sensitivity to controlling factors (surface-air temperature and moisture differences, sea ice, and winds) within contemporary climate models (here Coupled Model Intercomparison Project 6). The influence of individual controlling factors and their interactions is diagnosed using a multi-linear regression approach. This evaluation is done for four sea ice loss regimes, determined from observational sea ice loss trends, to control for the confounding effects of natural variability between models and observations. The comparisons between satellite- and model-derived surface turbulent fluxes illustrate that while models capture the general sensitivity of surface turbulent fluxes to declining sea ice and to surface-air gradients of temperature and moisture, substantial mean state biases exist. Specifically, the central Arctic is too weak of a heat sink to the winter atmosphere compared to observations, with implications to the simulated atmospheric circulation variability and thermodynamic profiles. Models were found to be about 50% more efficient at turning an air-sea temperature gradient anomaly into a sensible heat flux anomaly relative to observations. Further, the influence of sea ice concentration on the sensible heat flux is underestimated in models compared to observations. The opposite is found for the latent heat flux variability in models; where the latent heat flux is too sensitive to a sea ice concentration anomaly. Lastly, the results suggest that present-day trends in sea ice retreat regions may serve as suitable observational constraints of projected Arctic warming.
A Burst of Numt Insertion in the Dasyuridae Family During Marsupial Evolution

Nuclear pseudogenes of mitochondrial origin (numts) are common in all eukaryotes. Our previous scan of numts in sequenced nuclear genomes suggested that the highest numt content currently known in animals is that in the gray short-tailed opossum. The present work sought to determine numt content in marsupials and to compare it to those in placental and monothematic mammals as well as in non-mammalian vertebrates. To achieve this, 70 vertebrate species with available nuclear and mitochondrial genomes were scanned for numt content. An extreme numt content was found in the Dasyuridae, with 3,450 in Sarcophilus harrisii (1,955 kb) and 2,813 in Antechinus flavipes (847 kb). The evolutionarily closest species analyzed, the extinct Thylacinus cynocephalus belonging to the Thylacindae family, had only 435 numts (238 kb). These two Dasyuridae genomes featured the highest numt content identified in animals to date. A phylogenetic analysis of numts longer than 300 bp, using a Diprotodonita mitochondrial tree, indicated a burst of numt insertion that began before the divergence of the Dasyurini and Phascogalini, reaching a peak in the early evolution of the two tribes. No comparable increase was found in the early divergent species T. cynocephalus. Divergence of the Dasyuridae tribes has been previously dated to shortly after the Miocene climate transition, characterized by a rapid temperature decline. Interestingly, deviation from optimal growth temperature is one of the environmental factors reported to increase numt insertions in a laboratory setting.
OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block

The maintenance of genome stability requires the coordinated actions of multiple proteins and protein complexes, that are collectively known as genome guardians. Within this broadly defined family is a subset of proteins that contain oligonucleotide/oligosaccharide-binding folds (OB-fold). While OB-folds are widely associated with binding to single-stranded DNA this view is no longer an accurate depiction of how these domains are utilized. Instead, the core of the OB-fold is modified and adapted to facilitate binding to a variety of DNA substrates (both single- and double-stranded), phospholipids, and proteins, as well as enabling catalytic function to a multi-subunit complex. The flexibility accompanied by distinctive oligomerization states and quaternary structures enables OB-fold genome guardians to maintain the integrity of the genome via a myriad of complex and dynamic, protein-protein; protein-DNA, and protein-lipid interactions in both prokaryotes and eukaryotes.
Plaque Characteristics in Young Adults With Symptomatic Intracranial Atherosclerotic Stenosis: A Preliminary Study

Purpose To determine how intracranial vascular wall and atherosclerosis plaque characteristics differ between young and old adults with sICAS. Methods Eighty-four consecutive patients with sICAS who underwent high-resolution magnetic resonance imaging (HRMRI) from December 2017 to July 2020 were retrospectively collected. These participants were divided into young adult group (18–50 years, n = 28) and old adult group (>50 years, n = 56). Reviewers were blinded to any clinical information and HRMRI scans were analyzed for qualitative and quantitative indicators of vascular walls and plaque at the maximal lumen narrowing site using the independent-sample t-test, Mann–Whitney U-test, chi-square test or Fisher exact test, and logistic regression analysis. Results Young patients with sICAS had significantly smaller maximum wall thickness (1.45 ± 0.38 vs.1.75 ± 0.51 mm2, P = 0.003), higher prevalence of positive remodeling (53.57 vs. 21.43%, P = 0.003), and lower prevalence of diabetes mellitus (14.29 vs. 35.71%, P = 0.04) than old patients. Plaque burden and other plaque features were comparable between young and old patients. Conclusion Young patients with sICAS have smaller maximum wall thickness and greater ability to reconstruct, and are more likely to show positive remodeling, which may lead to some atherosclerotic lesions being missed. Young patients with evidence of vessel narrowing should be carefully examined for presence of high-risk atherosclerotic plaque.
The Effects of Rosiglitazone on Task Specific Anxiety-Like Behavior and Novelty Seeking in a Model of Chronic Adolescent Unpredictable Stress

Adolescence is characterized as a period of increased social behavior, risk taking, and novelty seeking, partly due to ongoing maturation in critical brain areas and the hypothalamic-pituitary-adrenal (HPA) negative-feedback system. During this period there is heightened vulnerability to stress that can drive neuro-immune-endocrine remodeling, resulting in the emergence of maladaptive behaviors that increase susceptibility to alcohol and substance abuse. Here we used a rat model to investigate the impact of chronic adolescent unpredictable stress on a battery of behavioral measures to assess anxiety, novelty seeking, risk taking, depression, and voluntary ethanol consumption while determining whether the PPARγ agonist rosiglitazone can attenuate these effects. Adolescent female rats that experienced stress showed increased risk taking behavior and novelty seeking behavior with no change in ethanol consumption. The administration of rosiglitazone during stress induction attenuated stress-induced cortisol elevation, normalized risk taking behavior in a model anxiety, and attenuated novelty seeking in a task-specific manner. Depressive-like behavior was not impacted by adolescent unpredictable stress or the administration of rosiglitazone. The results from this study demonstrate that exposure to unpredictable stress during adolescence increases the prevalence of maladaptive behaviors that are known to increase susceptibility to alcohol and substance abuse, and that rosiglitazone may be an effective therapeutic to attenuate the emergence of select risk taking and novelty seeking behaviors in females.
Network Analysis of Time Series: Novel Approaches to Network Neuroscience

In the last two decades, there has been an explosion of interest in modeling the brain as a network, where nodes correspond variously to brain regions or neurons, and edges correspond to structural or statistical dependencies between them. This kind of network construction, which preserves spatial, or structural, information while collapsing across time, has become broadly known as “network neuroscience. ” In this work, we provide an alternative application of network science to neural data: network-based analysis of non-linear time series and review applications of these methods to neural data. Instead of preserving spatial information and collapsing across time, network analysis of time series does the reverse: it collapses spatial information, instead preserving temporally extended dynamics, typically corresponding to evolution through some kind of phase/state-space. This allows researchers to infer a, possibly low-dimensional, “intrinsic manifold” from empirical brain data. We will discuss three methods of constructing networks from nonlinear time series, and how to interpret them in the context of neural data: recurrence networks, visibility networks, and ordinal partition networks. By capturing typically continuous, non-linear dynamics in the form of discrete networks, we show how techniques from network science, non-linear dynamics, and information theory can extract meaningful information distinct from what is normally accessible in standard network neuroscience approaches.
Placental Macrophage (Hofbauer Cell) Responses to Infection During Pregnancy: A Systematic Scoping Review

Background Congenital infection of the fetus via trans-placental passage of pathogens can result in severe morbidity and mortality. Even without transmission to the fetus, infection of the placenta itself is associated with pregnancy complications including pregnancy loss and preterm birth. Placental macrophages, also termed Hofbauer cells (HBCs), are fetal-origin macrophages residing in the placenta that are likely involved in responding to placental infection and protection of the developing fetus. As HBCs are the only immune cell present in the villous placenta, they represent one of the final opportunities for control of infection and prevention of passage to the developing fetus. Objective and Rationale The objective of this review was to provide a systematic overview of the literature regarding HBC responses during infection in pregnancy, including responses to viral, bacterial, and parasitic pathogens. Methods PubMed and Scopus were searched on May 20th, 2021, with no limit on publication date, to identify all papers that have studied placental macrophages/Hofbauer cells in the context of infection. The following search strategy was utilized: (hofbauer* OR “hofbauer cells” OR “hofbauer cell” OR “placental macrophage” OR “placental macrophages”) AND [infect* OR virus OR viral OR bacteri* OR parasite* OR pathogen* OR LPS OR “poly(i:c)” OR toxoplasm* OR microb* OR HIV)]. Outcomes 86 studies were identified for review. This included those that investigated HBCs in placentas from pregnancies complicated by maternal infection and in vitro studies investigating HBC responses to pathogens or Pathogen-Associated Molecular Patterns (PAMPs). HBCs can be infected by a variety of pathogens, and HBC hyperplasia was a common observation. HBCs respond to pathogen infection and PAMPs by altering their transcriptional, translational and secretion profiles. Co-culture investigations demonstrate that they can replicate and transmit pathogens to other cells. In other cases, they may eliminate the pathogen through a variety of mechanisms including phagocytosis, cytokine-mediated pathogen elimination, release of macrophage extracellular traps and HBC-antibody-mediated neutralization. HBC responses differ across gestation and may be influenced by pre-existing immunity. Clinical information, including gestational age at infection, gestational age of the samples, mode of sample collection and pregnancy outcome were missing for the majority of studies.
Hypoxia Promotes Neutrophil Survival After Acute Myocardial Infarction

Phagocytosis, degranulation, and neutrophil extracellular traps (NETs) formation build the armory of neutrophils for the first line of defense against invading pathogens. All these processes are modulated by the microenvironment including tonicity, pH and oxygen levels. Here we investigated the neutrophil infiltration in cardiac tissue autopsy samples of patients with acute myocardial infarction (AMI) and compared these with tissues from patients with sepsis, endocarditis, dermal inflammation, abscesses and diseases with prominent neutrophil infiltration. We observed many neutrophils infiltrating the heart muscle after myocardial infarction. Most of these had viable morphology and only few showed signs of nuclear de-condensation, a hallmark of early NET formation. The abundance of NETs was the lowest in acute myocardial infarction when compared to other examined diseases. Since cardiac oxygen supply is abruptly abrogated in acute myocardial infarction, we hypothesized that the resulting tissue hypoxia increased the longevity of the neutrophils. Indeed, the viable cells showed increased nuclear hypoxia inducible factor-1α (HIF-1α) content, and only neutrophils with low HIF-1α started the process of NET formation (chromatin de-condensation and nuclear swelling). Prolonged neutrophil survival, increased oxidative burst and reduced NETs formation were reproduced under low oxygen tensions and by HIF-1α stabilization in vitro. We conclude that nuclear HIF-1α is associated with prolonged neutrophil survival and enhanced oxidative stress in hypoxic areas of AMI.
Effects of Arterial Carbon Dioxide Tension on Cerebral and Somatic Regional Tissue Oxygenation and Blood Flow in Neonates After the Norwood Procedure With Deep Hypothermic Cardiopulmonary Bypass

Neonates undergoing the Norwood procedure for hypoplastic left heart syndrome are at higher risk of impaired systemic oxygen delivery with resultant brain, kidney, and intestinal ischemic injury, shock, and death. Complex developmental, anatomic, and treatment-related influences on cerebral and renal-somatic circulations make individualized treatment strategies physiologically attractive. Monitoring cerebral and renal circulations with near infrared spectroscopy can help drive rational therapeutic interventions. The primary aim of this study was to describe the differential effects of carbon dioxide tension on cerebral and renal circulations in neonates after the Norwood procedure. Using a prospectively-maintained database of postoperative physiologic and hemodynamic parameters, we analyzed the relationship between postoperative arterial carbon dioxide tension and tissue oxygen saturation and arteriovenous saturation difference in cerebral and renal regions, applying univariate and multivariate multilevel mixed regression techniques. Results were available from 7,644 h of data in 178 patients. Increases in arterial carbon dioxide tension were associated with increased cerebral and decreased renal oxygen saturation. Differential changes in arteriovenous saturation difference explained these effects. The cerebral circulation showed more carbon dioxide sensitivity in the early postoperative period, while sensitivity in the renal circulation increased over time. Multivariate models supported the univariate findings and defined complex time-dependent interactions presented graphically. The cerebral and renal circulations may compete for blood flow with critical limitations of cardiac output. The cerebral and renal-somatic beds have different circulatory control mechanisms that can be manipulated to change the distribution of cardiac output by altering the arterial carbon dioxide tension. Monitoring cerebral and renal circulations with near infrared spectroscopy can provide rational physiologic targets for individualized treatment.
Epidemiology and Survival of Patients With Optic Pathway Gliomas: A Population-Based Analysis

Background We aimed to analyze the epidemiology and outcomes of pediatric patients and adult patients with optic pathway gliomas in the United States using a population-based method. Methods Data for patients with optic pathway gliomas diagnosed between 2000 and 2018 were extracted from the SEER database. We divided the patients into a pediatric group and an adult group. Descriptive analyses were conducted to analyze demographic and clinical characteristics and treatment. We used the chi-square test to evaluate differences between pediatric and adult patients with optic pathway gliomas. The possible prognostic indicators were analyzed by Kaplan–Meier curves and Cox proportional hazards models. Results Optic pathway gliomas represented 86.6% of all lesions originating from the optic pathway. In total, 1257 cases of optic pathway gliomas were included in our study. Pediatric patients accounted for 83.7% in this cohort, and most of the patients were diagnosed at 1-4 years old. Chemotherapy was chosen most often for pediatric patients, but radiation therapy was chosen most often for adult patients. Pilocytic astrocytoma accounted for 59.1% of pediatric patients and 37.5% of adult patients. The overall survival (OS) rates were 94.8% 5 years after diagnosis and 93.0% 10 years after diagnosis. Survival analysis showed that surgery, radiation and chemotherapy did not help patients obtain a better prognosis. Overall, pediatric patients had a better prognosis. Conclusion Optic pathway gliomas are relatively rare lesions with good prognosis. They mostly affect children, and pilocytic astrocytoma is the most common histological diagnosis. Highly individualized treatment is essential for such patients.
Animal and Plant Protein Food Sources in Indonesia Differ Across Socio-Demographic Groups: Socio-Cultural Research in Protein Transition in Indonesia and Malaysia

Background Plant-based diets in lower-income countries are often associated with inadequate protein nutrition and adverse health outcomes. Objective To examine the diversity of protein food sources, in both animal and plant, across diverse socio-demographic groups in Indonesia as compared to Malaysia. Design The SCRiPT (Socio Cultural Research in Protein Transition) study was based on population-based samples recruited in Indonesia (N = 1665) and in Malaysia (N = 1604). Data from 24-h in-person dietary recalls in each country were used to construct the frequency counts of protein sources by food group. Protein sources were defined as fish, poultry, red meat (beef, pork, and mutton), eggs, dairy, and plants (cereals, pulses, and tubers). The percent reported frequencies for animal and plant proteins were compared across socio-demographic strata and by country. Analyses were based on one-way Anovas and general linear model regressions adjusting for covariates. Results Animal protein frequency counts were 34% of total in Indonesia, but 50% in Malaysia's. Higher reported consumption frequencies for poultry and red meat in both countries were associated with urban living, greater modernization, and higher socioeconomic status, with stronger social gradients observed in Indonesia. Reported fish consumption was higher in Indonesia than in Malaysia. Fish was more likely to be listed by rural island populations in Indonesia and was associated with lower education and incomes. Consumption frequencies for plant-based proteins were associated with lower socio-economic status in Indonesia and in Malaysia. Conclusions More affluent groups in both countries reported higher frequencies for meat, eggs, and dairy as opposed to fish. Greater economic development in Southeast (SE) Asia is associated with more animal protein, particularly from poultry, which may displace fish, the traditional source of high quality protein for the region.