julilili42/papers huggingface dataset:
De Novo and Dominantly Inherited SPTAN1 Mutations Cause Spastic Paraplegia and Cerebellar Ataxia
2022-02-12

ABSTRACT Background Pathogenic variants in SPTAN1 have been linked to a remarkably broad phenotypical spectrum. Clinical presentations include epileptic syndromes, intellectual disability, and hereditary motor neuropathy. Objectives We investigated the role of SPTAN1 variants in rare neurological disorders such as ataxia and spastic paraplegia. Methods We screened 10,000 NGS datasets across two international consortia and one local database, indicative of the level of international collaboration currently required to identify genes causative for rare disease. We performed in silico modeling of the identified SPTAN1 variants. Results We describe 22 patients from 14 families with five novel SPTAN1 variants. Of six patients with cerebellar ataxia, four carry a de novo SPTAN1 variant and two show a sporadic inheritance. In this group, one variant (p.Lys2083del) is recurrent in four patients. Two patients have novel de novo missense mutations (p.Arg1098Cys, p.Arg1624Cys) associated with cerebellar ataxia, in one patient accompanied by intellectual disability and epilepsy. We furthermore report a recurrent missense mutation (p.Arg19Trp) in 15 patients with spastic paraplegia from seven families with a dominant inheritance pattern in four and a de novo origin in one case. One further patient carrying a de novo missense mutation (p.Gln2205Pro) has a complex spastic ataxic phenotype. Through protein modeling we show that mutated amino acids are located at crucial interlinking positions, interconnecting the three‐helix bundle of a spectrin repeat. Conclusions We show that SPTAN1 is a relevant candidate gene for ataxia and spastic paraplegia. We suggest that for the mutations identified in this study, disruption of the interlinking of spectrin helices could be a key feature of the pathomechanism. © 2022 International Parkinson and Movement Disorder Society
Pre-pregnancy BMI but not mild stress directly influences Interleukin-6 levels and insulin sensitivity during late pregnancy
2022-02-12

Background: This study investigates the influence of maternal stress during pregnancy on maternal insulin sensitivity and Interleukin-6 (IL-6) levels in pregnant women (N = 277) in dependence of pre-pregnancy Body-Mass-Index (BMI). Methods: Gestational diabetes was diagnosed in 80 women. We used the Patient Health Questionnaire (PHQ-D) to investigate maternal stress during pregnancy with a higher scoring indicating higher maternal stress level. IL-6 and cortisol were measured and maternal insulin sensitivity was assessed with the non-esterified fatty acid insulin sensitivity index (NEFA-ISI). Generalized Linear Model analysis was used to analyze effects within different stress groups. Results: Maternal low stress symptoms during pregnancy showed no significant association with maternal insulin sensitivity or IL-6. Higher cortisol levels during pregnancy were associated with elevated IL-6 concentrations. Pre-pregnancy BMI had the strongest positive effect on IL-6 levels and was negatively associated with insulin sensitivity during pregnancy. Conclusions: Therefore, preconceptional interventions to reduce BMI are needed to improve maternal metabolism during pregnancy.
A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice
2022-02-12

The complex interplay of a pathogen with its virulence and fitness factors, the host’s immune response, and the endogenous microbiome determine the course and outcome of gastrointestinal infection. The expansion of a pathogen within the gastrointestinal tract implies an increased risk of developing severe systemic infections, especially in dysbiotic or immunocompromised individuals. We developed a mechanistic computational model that calculates and simulates such scenarios, based on an ordinary differential equation system, to explain the bacterial population dynamics during gastrointestinal infection. For implementing the model and estimating its parameters, oral mouse infection experiments with the enteropathogen, Yersinia enterocolitica (Ye), were carried out. Our model accounts for specific pathogen characteristics and is intended to reflect scenarios where colonization resistance, mediated by the endogenous microbiome, is lacking, or where the immune response is partially impaired. Fitting our data from experimental mouse infections, we can justify our model setup and deduce cues for further model improvement. The model is freely available, in SBML format, from the BioModels Database under the accession number MODEL2002070001.
Evaluation of the specificity and accuracy of SARS-CoV-2 rapid antigen self-tests compared to RT-PCR from 1015 asymptomatic volunteers
2022-02-13

Abstract Objective Evaluation of the specificity and accuracy of four CE-approved SARS-CoV-2 antigen rapid self-tests (AG-ST) Anbio, Clungene, Hotgene and Mexacare. Method 1015 asymptomatic volunteers were screened for SARS-CoV-2 by means of an oropharyngeal swab taken by qualified personnel and subsequent RT-PCR testing. Each participant additionally performed nasal self-swabs for two of the four rapid antigen tests at the same day according to the manufacturers’ instructions. Study participants transmitted a photo and own interpretation of their test results to the study center. The results of the two self-tests provided by the participants were correlated with the results of the SARS-CoV-2 RT-PCR and independently assessed and evaluated by the study center. Results None of the volunteers tested positive upon RT-PCR, whereas 13 AG-ST showed a false positive test result (0.7 %). The highest false positivity rate was found for the Clungene test (2.1 % compared to 0.2 % for the other tests), while the highest test failure rate (invalid) was found for the Mexacare test (3.7%). The Anbio and Hotgene tests produced the fewest false positive results when evaluated by the participants and also showed the best agreement among themselves. Conclusion SARS-CoV-2 Antigen rapid self-tests with higher false positive test rates, such as the Clungene test, or with high rates of invalid test results, such as the Mexacare test, are less suitable for screening purposes of asymptomatic study participants especially in low-prevalence settings. False positive or inadequate test results increase the burden on certified test laboratories due to verification PCR tests and cause a substantial economic loss due to unnecessary quarantine measurements and cause psychological stress in the affected study participants. In addition to earlier defined requirements for sensitivity for SARS-CoV-2 detection, a lower acceptance boundary for the false positivity rate of &lt; 0.3% should be demanded.
Underdispersion in the reported Covid-19 case and death numbers may suggest data manipulations
2022-02-13

Abstract We suggest a statistical test for underdispersion in the reported Covid-19 case and death numbers, compared to the variance expected under the Poisson distribution. Screening all countries in the World Health Organization (WHO) dataset for evidence of underdispersion yields 21 country with statistically significant underdispersion. Most of the countries in this list are known, based on the excess mortality data, to strongly undercount Covid deaths. We argue that Poisson underdispersion provides a simple and useful test to detect reporting anomalies and highlight unreliable data.
Presence of the peculiar carnivore Sivanasua in Carinthia
2022-02-13

A lophocyonid carnivore (Mammalia) is reported for the first time from Miocene (lower Badenian, ca. 16 My) deposits in Austria. A single, lower first molar from Schönweg-”Brüchl” (Lavanttal, Carinthia) is assigned to Sivanasua viverroides. The species is also recognised in Germany in few faunas of similar ages.
Pharmaceutical pollution of the world’s rivers
2022-02-14

Environmental exposure to active pharmaceutical ingredients (APIs) can have negative effects on the health of ecosystems and humans. While numerous studies have monitored APIs in rivers, these employ different analytical methods, measure different APIs, and have ignored many of the countries of the world. This makes it difficult to quantify the scale of the problem from a global perspective. Furthermore, comparison of the existing data, generated for different studies/regions/continents, is challenging due to the vast differences between the analytical methodologies employed. Here, we present a global-scale study of API pollution in 258 of the world’s rivers, representing the environmental influence of 471.4 million people across 137 geographic regions. Samples were obtained from 1,052 locations in 104 countries (representing all continents and 36 countries not previously studied for API contamination) and analyzed for 61 APIs. Highest cumulative API concentrations were observed in sub-Saharan Africa, south Asia, and South America. The most contaminated sites were in low- to middle-income countries and were associated with areas with poor wastewater and waste management infrastructure and pharmaceutical manufacturing. The most frequently detected APIs were carbamazepine, metformin, and caffeine (a compound also arising from lifestyle use), which were detected at over half of the sites monitored. Concentrations of at least one API at 25.7% of the sampling sites were greater than concentrations considered safe for aquatic organisms, or which are of concern in terms of selection for antimicrobial resistance. Therefore, pharmaceutical pollution poses a global threat to environmental and human health, as well as to delivery of the United Nations Sustainable Development Goals.
Gut Microbiota-Derived Small Extracellular Vesicles Endorse Memory-like Inflammatory Responses in Murine Neutrophils
2022-02-14

Neutrophils are classically characterized as merely reactive innate effector cells. However, the microbiome is known to shape the education and maturation process of neutrophils, improving their function and immune-plasticity. Recent reports demonstrate that murine neutrophils possess the ability to exert adaptive responses after exposure to bacterial components such as LPS (Gram-negative bacteria) or LTA (Gram-positive bacteria). We now ask whether small extracellular vesicles (EVs) from the gut may directly mediate adaptive responses in neutrophils in vitro. Murine bone marrow-derived neutrophils were primed in vitro by small EVs of high purity collected from colon stool samples, followed by a second hit with LPS. We found that low-dose priming with gut microbiota-derived small EVs enhanced pro-inflammatory sensitivity as indicated by elevated levels of TNF-α, IL-6, ROS and MCP-1 and increased migratory and phagocytic activity. In contrast, high-dose priming resulted in a tolerant phenotype, marked by increased IL-10 and decreased transmigration and phagocytosis. Alterations in TLR2/MyD88 as well as TLR4/MyD88 signaling were correlated with the induction of adaptive cues in neutrophils in vitro. Taken together, our study shows that small EVs from stools can drive adaptive responses in neutrophils in vitro and may represent a missing link in the gut–immune axis.
Cerebrospinal Fluid Biomarkers in Cerebral Amyloid Angiopathy: New Data and Quantitative Meta-Analysis
2022-02-14

Background To evaluate the diagnostic accuracy of cerebrospinal fluid (CSF) biomarkers in patients with probable cerebral amyloid angiopathy (CAA) according to the modified Boston criteria in a retrospective multicentric cohort. Methods Beta-amyloid 1-40 (Aβ40), beta-amyloid 1-42 (Aβ42), total tau (t-tau), and phosphorylated tau 181 (p-tau 181 ) were measured in 31 patients with probable CAA, 28 patients with Alzheimer’s disease (AD), and 30 controls. Receiver-operating characteristics (ROC) analyses were performed for the measured parameters as well as the Aβ42/40 ratio to estimate diagnostic parameters. A meta-analysis of all amenable published studies was conducted. Results In our data Aβ42/40 (AUC 0.88) discriminated best between CAA and controls while Aβ40 did not perform well (AUC 0.63). Differentiating between CAA and AD, p-tau 181 (AUC 0.75) discriminated best in this study while Aβ40 (AUC 0.58) and Aβ42 (AUC 0.54) provided no discrimination. In the meta-analysis, Aβ42/40 (AUC 0.90) showed the best discrimination between CAA and controls followed by t-tau (AUC 0.79), Aβ40 (AUC 0.76), and p-tau 181 (AUC 0.71). P-tau 181 (AUC 0.76), Aβ40 (AUC 0.73), and t-tau (AUC 0.71) differentiated comparably between AD and CAA while Aβ42 (AUC 0.54) did not. In agreement with studies examining AD biomarkers, Aβ42/40 discriminated excellently between AD and controls (AUC 0.92–0.96) in this study as well as the meta-analysis. Conclusion The analyzed parameters differentiate between controls and CAA with clinically useful accuracy (AUC &amp;gt; ∼0.85) but not between CAA and AD. Since there is a neuropathological, clinical and diagnostic continuum between CAA and AD, other diagnostic markers, e.g., novel CSF biomarkers or other parameters might be more successful.
Neuronal codes for arithmetic rule processing in the human brain
2022-02-14

Arithmetic is a cornerstone of scientifically and technologically advanced human culture, but its neuronal mechanisms are poorly understood. Calculating with numbers requires temporary maintenance and manipulation of numerical information according to arithmetic rules. We explored the brain mechanisms involved in simple arithmetic operations by recording single-neuron activity from the medial temporal lobe of human subjects performing additions and subtractions. We found abstract and notation-independent codes for addition and subtraction in neuronal populations. The neuronal codes of arithmetic in different brain areas differed drastically. Decoders applied to time-resolved recordings demonstrate a static code in hippocampus based on persistently rule-selective neurons, in contrast to a dynamic code in parahippocampal cortex originating from neurons carrying rapidly changing rule information. The implementation of abstract arithmetic codes suggests different cognitive functions for medial temporal lobe regions in arithmetic.
Simultaneous Insight into Dissolution and Aggregation of Metal Sulfide Nanoparticles through Single-Particle Inductively Coupled Plasma Mass Spectrometry
2022-02-14

Nanoparticles (NPs) and their colloidal aggregates are ubiquitous and play important roles in the transport and release of metals. Knowledge of their dissolution rates and aggregation behavior in solution are crucial for better prediction of their fate in biogeochemical cycling, ecotoxicity, and environmental remediation. There are however significant technical challenges to accurately obtain such information as a result of the heterogeneity and highly dynamic transformation exhibited by NPs, particularly at relatively low particle concentrations in aqueous systems. Here, we quantitatively examine the simultaneous dissolution and aggregation behavior of metal sulfide NPs using single-particle inductively coupled plasma mass spectrometry (spICP–MS). We focus on nickel sulfide (NiS), with additional data presented for copper sulfide (CuS) and cobalt sulfide (CoS). The kinetics of metal release (dissolution and disaggregation) of NiS was fastest under strongly oxidizing conditions (from 0.04 to &gt;3 min&lt;sup&gt;–1&lt;/sup&gt; with H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;) and were slower under near-neutral (HEPES buffer/H&lt;sub&gt;2&lt;/sub&gt;O) and acidic (1 mM HNO&lt;sub&gt;3&lt;/sub&gt;) conditions (≤0.006 min&lt;sup&gt;–1&lt;/sup&gt;). Metal release kinetics in HNO&lt;sub&gt;3&lt;/sub&gt; was not faster than in H&lt;sub&gt;2&lt;/sub&gt;O or HEPES, suggesting that the solution pH has an influence over both the dissolution kinetics of individual particles and the NP aggregation states, which in combination affect metal release rates over time. Between different metal sulfides, the measured metal release rates were largely consistent with predictions based on the crystallinity, solubility products, and specific surface areas of the NPs, following an order of CoS &gt; NiS &gt; CuS. Here, the spICP–MS approach described here can be easily applied to the characterization of metal release and aggregation of other NPs at low concentrations (~10&lt;sup&gt;5&lt;/sup&gt; particles/mL) typically found in natural environments.
Clonal hematopoiesis as a pitfall in germline variant interpretation in the context of Mendelian disorders
2022-02-14

Abstract Clonal hematopoiesis because of somatic mutations in hematopoietic stem/progenitor cells is an age-related phenomenon and commonly observed when sequencing blood DNA in elderly individuals. Several genes that are implicated in clonal hematopoiesis are also associated with Mendelian disorders when mutated in the germline, potentially leading to variant misinterpretation. We performed a literature search to identify genes associated with age-related clonal hematopoiesis followed by an OMIM query to identify the subset of genes in which germline variants are associated with Mendelian disorders. We retrospectively screened for diagnostic cases in which the presence of age-related clonal hematopoiesis confounded exome sequencing data interpretation. We found 58 genes in which somatic mutations are implicated in clonal hematopoiesis, while germline variants in the same genes are associated with Mendelian (mostly neurodevelopmental) disorders. Using five selected cases of individuals with suspected monogenic disorders, we illustrate how clonal hematopoiesis in either variant databases or exome sequencing datasets poses a pitfall, potentially leading to variant misclassification and erroneous conclusions regarding gene–disease associations.
In vitro and in vivo anti-inflammatory and anticoagulant activities of Myrciaria plinioides D. Legrand ethanol leaf extract
2022-02-14

Abstract Myrciaria plinioides D. Legrand (Myrtaceae) is a native plant of Southern Brazil, which have potential in the food industry due to its edible fruits. Many plants belonging to this genus have been used for a variety of illnesses, including inflammatory disorders due to antioxidant properties. However, therapeutic uses of M. plinioides have been poorly studied. The aim of study was to assess the anti-inflammatory and anticoagulant activities of the ethanol leaf extract of M. plinioides . In M. plinioides extract-treated RAW 264.7 cells, assessments of cell viability, TNF-α release and p38 MAPK pathway-dependent protein expression were detected. In addition, rat paw edema models were used to analyze the anti-inflammatory effect of the extract. Macrophages cell line treated with M. plinioides extract showed a slight decrease in cell viability. In LPS-stimulated macrophages treated with different concentrations of the extract for 24 h, TNF-α release was inhibited, while modulation of p38 signaling pathway and inhibition of NF-κB p65 protein expression were dose-dependent. In rats, the extract inhibited the formation of paw edema, while an inhibitory effect on trypsin-like enzymes derived from mast cells was seen. Furthermore, the extract presented anticoagulant activity via extrinsic pathway, being able to block specifically factor Xa and thrombin. The study suggests that extract possess potent anti-inflammatory and anticoagulant effects. M. plinioides present great biological potential as a source for the development of anti-inflammatory and anticoagulant drugs. Additional studies can be proposed to better elucidate the mechanism by which M. plinioides exerts its effects.
FiNN: A toolbox for neurophysiological network analysis
2022-02-14

Abstract Recently, neuroscience has seen a shift from localist approaches to network-wide investigations of brain function. Neurophysiological signals across different spatial and temporal scales provide insight into neural communication. However, additional methodological considerations arise when investigating network-wide brain dynamics rather than local effects. Specifically, larger amounts of data, investigated across a higher dimensional space, are necessary. Here, we present FiNN ( Fi nd N europhysiological N etworks), a novel toolbox for the analysis of neurophysiological data with a focus on functional and effective connectivity. FiNN provides a wide range of data processing methods, and statistical and visualization tools to facilitate inspection of connectivity estimates and the resulting metrics of brain dynamics. The Python toolbox ( https://github.com/neurophysiological-analysis/FiNN ) and its documentation ( https://neurophysiological-analysis.github.io/FiNN/ ) are freely available. We evaluated FiNN against a number of established frameworks on both a conceptual and an implementation level. We found FiNN to require much less processing time and memory than other toolboxes. In addition, FiNN adheres to a design philosophy of easy access and modifiability, while providing efficient data processing implementations. Since the investigation of network-level neural dynamics is experiencing increasing interest, we place FiNN at the disposal of the neuroscientific community as open-source software.
Getting Personal with Epigenetics: Towards Machine-Learning-Assisted Precision Epigenomics
2022-02-14

Abstract Epigenetic modifications are dynamic control mechanisms involved in the regulation of gene expression. Unlike the DNA sequence itself, they vary not only between individuals but also between different cell types of the same individual. Exposure to environmental factors, somatic mutations, and ageing contribute to epigenomic changes over time, which may constitute early hallmarks or causal factors of disease. Epigenetic changes are reversible and, therefore, promising therapeutic targets. However, mapping efforts to determine an individual’s cell-type-specific epigenome are constrained by experimental costs. We developed eDICE, an attention-based deep learning model, to impute epigenomic tracks. eDICE achieves improved overall performance compared to previous models on the reference Roadmap epigenomes. Furthermore, we present a proof of concept for the imputation of personalised epigenomic measurements on the ENTEx dataset, where eDICE correctly predicts individual- and cell-type-specific epigenetic patterns. This case study constitutes an important step towards robustly employing machine-learning-based approaches for personalised epigenomics.
Climate variables for twelve HadCM3 climate model simulations for a Glacial and Interglacial state
2022-02-14

Here we provide data of twelve climate model simulations in supplement to Ellerhoff et al., 2022. More information on the simulations can be found in the file README.txt and the preprint this upload supplements.
Cell Wall Signaling in Plant Development and Defense
2022-02-15

Plant architecture fundamentally differs from that of other multicellular organisms in that individual cells serve as osmotic bricks, defined by the equilibrium between the internal turgor pressure and the mechanical resistance of the surrounding cell wall, which constitutes the interface between plant cells and their environment. The state and integrity of the cell wall are constantly monitored by cell wall surveillance pathways, which relay information to the cell interior. A recent surge of discoveries has led to significant advances in both mechanistic and conceptual insights into a multitude of cell wall response pathways that play diverse roles in the development, defense, stress response, and maintenance of structural integrity of the cell. However, these advances have also revealed the complexity of cell wall sensing, and many more questions remain to be answered, for example, regarding the mechanisms of cell wall perception, the molecular players in this process, and how cell wall–related signals are transduced and integrated into cellular behavior. This review provides an overview of the mechanistic and conceptual insights obtained so far and highlights areas for future discoveries in this exciting area of plant biology.