Miracle-dz/UniFAR-FTUs huggingface dataset:
An Adaptive Median Filter Based on Sampling Rate for R-Peak Detection and Major-Arrhythmia Analysis

With the advancement of the Internet of Medical Things technology, many vital sign-sensing devices are being developed. Among the diverse healthcare devices, portable electrocardiogram (ECG) measuring devices are being developed most actively with the recent development of sensor technology. These ECG measuring devices use different sampling rates according to the hardware conditions, which is the first variable to consider in the development of ECG analysis technology. Herein, we propose an R-point detection method using an adaptive median filter based on the sampling rate and analyze major arrhythmias using the signal characteristics. First, the sliding window and median filter size are determined according to the set sampling rate, and a wider median filter is applied to the QRS section with high variance within the sliding window. Then, the R point is detected by subtracting the filtered signal from the original signal. Methods for detecting major arrhythmias using the detected R point are proposed. Different types of ECG signals were used for a simulation, including ECG signals from the MIT-BIH arrhythmia database and MIT-BIH atrial fibrillation database, signals generated by a simulator, and actual measured signals with different sampling rates. The experimental results indicated the effectiveness of the proposed R-point detection method and arrhythmia analysis technique.
Social Determinants of Health and Diabetes: A Scientific Review

Decades of research have demonstrated that diabetes affects racial and ethnic minority and low-income adult populations in the U.S. disproportionately, with relatively intractable patterns seen in these populations’ higher risk of diabetes and rates of diabetes complications and mortality (1). With a health care shift toward greater emphasis on population health outcomes and value-based care, social determinants of health (SDOH) have risen to the forefront as essential intervention targets to achieve health equity (2–4). Most recently, the COVID-19 pandemic has highlighted unequal vulnerabilities borne by racial and ethnic minority groups and by disadvantaged communities. In the wake of concurrent pandemic and racial injustice events in the U.S., the American College of Physicians, American Academy of Pediatrics, Society of General Internal Medicine, National Academy of Medicine, and other professional organizations have published statements on SDOH (5–8), and calls to action focus on amelioration of these determinants at individual, organizational, and policy levels (9–11). In diabetes, understanding andmitigating the impact of SDOH are priorities due to disease prevalence, economic costs, and disproportionate population burden (12–14). In 2013, the American Diabetes Association (ADA) published a scientific statement on socioecological determinants of prediabetes and type 2 diabetes (15). Toward the goal of understanding and advancing opportunities for health improvement among the population with diabetes through addressing SDOH, ADA convened the current SDOH and diabetes writing committee, prepandemic, to review the literature on 1) associations of SDOH withdiabetes risk andoutcomes and2) impact of interventions targeting amelioration of SDOHon diabetes outcomes. This article begins with an overview of key definitions and SDOH frameworks. The literature review focuses primarily on U.S.-based studies of adults with diabetes and on five SDOH: socioeconomic status (education, income, occupation); neighborhood and physical environment (housing, built environment, toxic environmental exposures); food environment (food insecurity, food access); health care (access, affordability, quality); and social context (social cohesion, social capital, social support). This review concludes with recommendations for linkages across health care and community sectors from national advisory committees, recommendations for diabetes research, and recommendations for research to inform practice.
Stem growth characteristics of high yielding Miscanthus correlate with yield, development and intraspecific competition within plots

High yielding perennial grasses are utilized as biomass for the bioeconomy and to displace fossil fuels. Many such grasses, including Miscanthus, are largely undomesticated. The main Miscanthus crop is a naturally occurring hydrid M. × giganteus (Mxg). All above ground biomass from Miscanthus is harvested. Stem traits correlate strongly with yield and therefore understanding the seasonal progression of stem growth should identify routes for improved yield. If such studies utilized high yielding commercial genotypes growing in plots the conclusions are likely to be more commercially relevant. Stem elongation was measured from five high yielding genotypes, 10 plants per plot from 20 plots in a replicated field trial over 4 years. Richards growth function produced an accurate fit to stem elongation. Differentials, double differentials and integrals of the parameterized function produced six growth characteristics, describing growth rate, timing and duration of the logarithmic growth phase and area under the growth curve. Maximum growth rate was correlated with yield and compensatory interactions were identified, for example plants with higher maximal growth rates had shorter durations of logarithmic growth. Plant position within plots of lower yielding genotypes did not affect growth characteristics but had a significant effect on late season growth characteristics in higher yielding genotypes. Two high yielding genotypes were compared over 3 years and growth parameterized using four different factors. The inverse correlation between maximum growth rate and duration of logarithmic growth was consistent across years and factors in both genotypes except when parameterized using temperature and only in Mxg. This suggested that different limitations to growth were exerted on the two genotypes which may help explain the exceptional performance of the Mxg genotype. We discuss the implications of the identified complex interactions in growth characteristics for approaches to maximize seasonal yield in perennial biomass crops.
Protein crowding mediates membrane remodeling in upstream ESCRT-induced formation of intraluminal vesicles

Significance Intraluminal vesicle (ILV) formation plays a crucial role in the attenuation of growth factor receptor signaling. The endosomal sorting complex required for transport (ESCRT-0 to -III/VPS4) mediates this process. The general dogma has been that upstream ESCRTs (0 to II) sequester receptors at the surface of endosomes and the downstream ESCRTs (III/VPS4) remodel the endosome membrane leading to the abscission and formation of receptor-containing ILVs. We now show that upstream ESCRTs not only sequester cargo, but in addition play a crucial role for the initiation of membrane shape remodeling in ILV budding. Through a combination of mathematical modeling and experimental measurements we show that upstream ESCRTs facilitate ILV budding by crowding with a high density in the membrane neck region. As part of the lysosomal degradation pathway, the endosomal sorting complexes required for transport (ESCRT-0 to -III/VPS4) sequester receptors at the endosome and simultaneously deform the membrane to generate intraluminal vesicles (ILVs). Whereas ESCRT-III/VPS4 have an established function in ILV formation, the role of upstream ESCRTs (0 to II) in membrane shape remodeling is not understood. Combining experimental measurements and electron microscopy analysis of ESCRT-III–depleted cells with a mathematical model, we show that upstream ESCRT-induced alteration of the Gaussian bending rigidity and their crowding in concert with the transmembrane cargo on the membrane induce membrane deformation and facilitate ILV formation: Upstream ESCRT-driven budding does not require ATP consumption as only a small energy barrier needs to be overcome. Our model predicts that ESCRTs do not become part of the ILV, but localize with a high density at the membrane neck, where the steep decline in the Gaussian curvature likely triggers ESCRT-III/VPS4 assembly to enable neck constriction and scission.
CXCL9, CXCL10, and CXCL11; biomarkers of pulmonary inflammation associated with autoimmunity in patients with collagen vascular diseases–associated interstitial lung disease and interstitial pneumonia with autoimmune features

Introduction Interstitial lung disease (ILD) is a heterogeneous group of diseases characterized by varying degrees of lung inflammation and/or fibrosis. We investigated biomarkers to infer whether patients with collagen vascular diseases associated ILD (CVD–ILD) and interstitial pneumonia with autoimmune features (IPAF) benefit from immunosuppressive therapy. Materials and methods We retrospectively investigated patients with CVD–ILD, IPAF, and idiopathic pulmonary fibrosis (IPF) between June 2013 and May 2017 at our department. First, we assessed differences in serum and bronchoalveolar lavage fluid (BALF) levels of cytokines between groups. Second, we assessed the associations of patient’s clinical variables with serum and BALF levels of those cytokines that were different between groups. Finally, we assessed the associations of diagnosis and response to immunosuppressive therapy with serum levels of those cytokines that were different between groups. Results We included 102 patients (51 with IPF, 35 with IPAF, and 16 with CVD–ILD). Serum and BALF levels of CXCL9, CXCL10, and CXCL11 were significantly elevated in patients with IPAF or CVD–ILD compared with those in patients with IPF. BALF levels of CXCL9 and CXCL10 were correlated with the percentages of lymphocytes and macrophages in BALF. Serum levels of CXCL9 and CXCL10 were correlated with BALF levels. Serum levels of CXCL9, CXCL10, and CXCL11 were correlated C-reactive protein, percent predicted forced vital capacity, alveolar-arterial oxygen difference, and the percentages of lymphocytes and macrophages in BALF. Serum levels of CXCL9, CXCL10, and CXCL11 showed moderate accuracy to distinguish patients with CVD–ILD from those with IPAF and IPF. Pre-treatment serum levels of CXCL9 and CXCL11 showed strong positive correlations with the annual forced vital capacity changes in patients with IPAF and CVD–ILD treated with immunosuppressive drugs. Conclusions Serum CXCL9, CXCL10, and CXCL11 are potential biomarkers for autoimmune inflammation and predictors of the immunosuppressive therapy responses in ILD with background autoimmunity.
Recursive Multistage Estimator for Bearings only Passive Target Tracking in ESM EW Systems

Background/Objectives: A recursive multistage estimator for underwater target applications in Electronic Support Measures (ESM)/Electronic Warfare (EW) systems in presented in this paper. Methods/Statistical Analysis: The technique of recursive multistage estimator involves Maximum Likelihood Estimator (MLE) and Pseudo Linear Estimator (PLE), which is converted to sequential processing to suit real time applications. MLE is choosen for the purpose of estimation of target motion parameters as it follows Cramer Rao lower bound. Monte Carlo simulation is carried out and the efficiency of the algorithm is tested against two typical scenarios. Findings: From the results, MLE with PLE algorithm is recommended for as it follows Cramer Rao lower bound. Application/Improvement: The algorithm is found to be accurate for passive target applications and can be used in the field of Navy.
Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast

Degradation of mitochondria through mitophagy contributes to the maintenance of mitochondrial function. In this study, we identified that Atg43, a mitochondrial outer membrane protein, serves as a mitophagy receptor in the model organism Schizosaccharomyces pombe to promote the selective degradation of mitochondria. Atg43 contains an Atg8-family-interacting motif essential for mitophagy. Forced recruitment of Atg8 to mitochondria restores mitophagy in Atg43-deficient cells, suggesting that Atg43 tethers expanding isolation membranes to mitochondria. We found that the mitochondrial import factors, including the Mim1–Mim2 complex and Tom70, are crucial for mitophagy. Artificial mitochondrial loading of Atg43 bypasses the requirement of the import factors, suggesting that they contribute to mitophagy through Atg43. Atg43 not only maintains growth ability during starvation but also facilitates vegetative growth through its mitophagy-independent function. Thus, Atg43 is a useful model to study the mechanism and physiological roles, as well as the origin and evolution, of mitophagy in eukaryotes.
Comparison of continuous versus intermittent infusion cyclosporine and impact on transplant related outcomes in allogeneic transplant recipients

Introduction Continuous infusion (CIVI) cyclosporine (CsA) is an alternative for allograft recipients intolerant of twice daily infusions (TDI). The importance of achieving therapeutic levels of CsA early after allogeneic HCT has been demonstrated in previous studies. Our study evaluated the incidence of acute graft versus host disease (GVHD) and survival among patients receiving CIVI vs. TDI CsA during their first allogeneic HCT. Methods A retrospective study of adult patients undergoing first allogeneic HCT at the University of Minnesota Medical Center between 2011 and 2017. Patients were grouped according to the administration method. The primary outcome was the occurrence of acute grade II-IV GVHD by day +180. Secondary outcomes included the 1-year incidence of chronic GVHD, relapse, and overall survival. Results 42 patients intolerant of TDI CsA received CsA via CIVI for >48 hours for a median of 9 days (range, 3–32 days). CsA concentrations were similar between groups. We found no difference between the rates of grade II–IV acute (45% vs 53%, p = 0.59) or chronic (17% vs 30%, p = 0.20) GVHD or overall survival (57% vs 67%, p = 0.10). Subgroup analysis of patients that received myeloablative conditioning or umbilical cord blood did not reveal significant differences in GVHD or overall survival. Cumulative incidence of relapse was higher among the continuous infusion group (39% vs. 23%, p < 0.01). Conclusion Due to the finding of increased risk of relapse, cyclosporine should be administered as traditional twice daily infusion unless necessary. A prospective clinical trial is needed to confirm these results.
Staphylococcus aureus biofilm eradication by the synergistic effect exerted by PEG-coated silicon dots immobilized in silica films and light irradiation

Immobilization of PEG-covered silicon dots, PEGSiDs, on glass substrates was performed following a simple strategy involving particle embedding by a sol-gel process forming a silica film on glass slides. The obtained films, denoted as fSiO x -PEGSiD, constitute a water-wettable, strongly supported, photoluminescent glass coating. The films showed high capacity for photosensitizing singlet oxygen (1O2) in the UVA when immersed in water. Staphylococcus aureus colonies formed on fSiO x -PEGSiDs modified glasses revealed the inhibition of bacterial adhesion and bacterial growth leading to the formation of loosely-packed and smaller S. aureus colonies. Upon 350 nm light irradiation of the biofilmed fSiO x -PEGSiDs -modified glasses, S. aureus growth was inhibited and bacteria killed reducing the number of living bacteria by three orders of magnitude. Eradication of attached bacteria was achieved by the synergistic effect exerted by a less adherent fSiO x -PEGSiDs surface that inhibits biofilm formation and the ability of the surface to photosensitize 1O2 to kill bacteria.
Prognostic Effect of a Novel Simply Calculated Nutritional Index in Acute Decompensated Heart Failure

The TCB index (triglycerides × total cholesterol × body weight), a novel simply calculated nutritional index based on serum triglycerides (TGs), serum total cholesterol (TC), and body weight (BW), was recently reported to be a useful prognostic indicator in patients with coronary artery disease. Thus, this study aimed to investigate the relationship between TCBI and long-term mortality in acute decompensated heart failure (ADHF) patients. Patients with a diagnosis of ADHF who were consecutively admitted to the cardiac intensive care unit in our institution from 2007 to 2011 were targeted. TCBI was calculated using the formula TG (mg/dL) × TC (mg/dL) × BW (kg)/1000. Patients were divided into two groups according to the median TCBI value. An association between admission TCBI and mortality was assessed using univariable and multivariable Cox proportional hazard analyses. Overall, 417 eligible patients were enrolled, and 94 (22.5%) patients died during a median follow-up period of 2.2 years. The cumulative survival rate with respect to all-cause, cardiovascular, and cancer-related mortalities was worse in patients with low TCBI than in those with high TCBI. In the multivariable analysis, although TCBI was not associated with cardiovascular and cancer mortalities, the association between TCBI and reduced all-cause mortality (hazard ratio: 0.64, 95% confidence interval: 0.44–0.94, p = 0.024) was observed. We computed net reclassification improvement (NRI) when TCBI or Geriatric Nutritional Risk Index (GNRI) was added on established predictors such as hemoglobin, serum sodium level, and both. TCBI improved discrimination for all-cause mortality (NRI: 0.42, p < 0.001; when added on hemoglobin and serum sodium level). GNRI can improve discrimination for cancer mortality (NRI: 0.96, p = 0.002; when added on hemoglobin and serum sodium level). TCBI, a novel and simply calculated nutritional index, can be useful to stratify patients with ADHF who were at risk for worse long-term overall mortality.
Nutrient Intake and Nutritional Status in Adult Patients with Inherited Metabolic Diseases Treated with Low-Protein Diets: A Review on Urea Cycle Disorders and Branched Chain Organic Acidemias

Low-protein diets (LPDs) are the main treatment for urea cycle disorders (UCDs) and organic acidemias (OAs). In most cases, LPDs start in childhood and must be continued into adulthood. The improved life expectancy of patients with UCDs and OAs raises the question of their consequences on nutritional status in adult subjects. As this topic has so far received little attention, we conducted a review of scientific studies that investigated the nutrient intake and nutritional status in adult patients with UCDs and branched chain organic acidemias (BCOAs) on LPD. Methods: The literature search was conducted in PubMed/MEDLINE, Scopus, EMBASE and Google Scholar from 1 January 2000 to 31 May 2020, focusing on nutrient intake and nutritional status in UCD and OA adult patients. Results: Despite protein restriction is recommended as the main treatment for UCDs and OAs, in these patients, protein intake ranges widely, with many patients who do not reach safety levels. When evaluated, micronutrient intake resulted below recommended values in some patients. Lean body mass resulted in most cases lower than normal range while fat body mass (FM) was often found normal or higher than the controls or reference values. Protein intake correlated inversely with FM both in adult and pediatric UCD patients. Conclusions: The clinical management of adult patients with UCDs and BCOAs should include an accurate assessment of the nutritional status and body composition. However, as little data is still available on this topic, further studies are needed to better clarify the effects of LPDs on nutritional status in adult UCD and BCOA patients.
Cardiotropic Isolates of Listeria monocytogenes with Enhanced Vertical Transmission Dependent upon the Bacterial Surface Protein InlB

Listeria monocytogenes is a facultative Gram-positive intracellular bacterium that is capable of causing serious invasive infections in pregnant women, resulting in abortion, still-birth, and disseminated fetal infection. Previously, a clinical L. monocytogenes isolate, 07PF0776, was identified as having an enhanced ability to target cardiac tissue. This tissue tropism appeared to correlate with amino acid variations found within internalin B (InlB), a bacterial surface protein associated with host cell invasion. ABSTRACT Listeria monocytogenes is a facultative Gram-positive intracellular bacterium that is capable of causing serious invasive infections in pregnant women, resulting in abortion, still-birth, and disseminated fetal infection. Previously, a clinical L. monocytogenes isolate, 07PF0776, was identified as having an enhanced ability to target cardiac tissue. This tissue tropism appeared to correlate with amino acid variations found within internalin B (InlB), a bacterial surface protein associated with host cell invasion. Given that the mammalian receptor bound by InlB, Met, is abundantly expressed by placental tissue, we assessed isolate 07PF0776 for its ability to be transmitted from mother to fetus. Pregnant Swiss Webster mice were infected on gestational day E13 via tail vein injection with the standard isolate 10403S, a noncardiotropic strain, or 07PF0776, the cardiac isolate. Pregnant mice infected with 07PF0776 exhibited significantly enhanced transmission of L. monocytogenes to placentas and fetuses compared to 10403S. Both bacterial burdens and the frequency of placental and fetal infection were increased in mice infected with the cardiac isolate. Strain 07PF0776 also exhibited an enhanced ability to invade Jar human trophoblast tissue culture cells in comparison to 10403S, and was found to have increased levels of InlB associated with the bacterial cell surface. Overexpression of surface InlB via genetic manipulation was sufficient to confer enhanced invasion of the placenta and fetus to both 10403S and 07PF0776. These data support a central role for surface InlB in promoting vertical transmission of L. monocytogenes.
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi. doe.gov/vr, and the underlying data are available to download at https://genome.jgi. doe.gov/portal/IMG_VR.