Miracle-dz/UniFAR-FTUs huggingface dataset:
Hospital Urinary Tract Infections in Healthcare Units on the Example of Mazovian Specialist Hospital Ltd

Microbiological diagnostics is of great importance in limiting the spread of nosocomial infections. The information on etiological agents of infections and their susceptibility to antibiotics enables a quick response in the case of a suspected epidemic outbreak. The aim of this study is to analyze the incidence of nosocomial urinary tract infections among patients hospitalized in hospital wards over a period of 2 years and to determine the predominant etiological agent depending on the method of clinical specimen collection. Data from the Mazovian Specialist Hospital (MSH) in Radom constitute the material for the preparation of this study. Urine was collected using two methods. The first one was the method of collecting urine from the central stream, while the second method was urine collected from patients with a urinary catheter in place. The statistical calculations were conducted using the statistical software. Based on hospital data, it was shown that 5,870 urine tests were performed during the period under review, of which 2,070 were positive. The number of positive results in 2021 decreased by 2.84% compared to that in 2020. On the basis of the statistical analysis, differences in the occurrence of multiple strains were observed between catheter-based and midstream urine collection. Differences were observed especially for Acinetobacter baumannii, Candida albicans, Escherichia coli, and Pseudomonas aeruginosa. A. baumannii, C. albicans, and P. aeruginosa were significantly more frequently found in urine samples collected through the catheter than from the midstream. Furthermore, E. coli (51.56%) and Enterococcus species (25.46%) were more frequent when collected from the middle stream than when urine was collected through a catheter. However, for the strain K. pneumoniae, the results were comparable when urine was collected from catheterized patients (13.83%) and from midstream (13.35%). Urinary tract infection among hospitalized patients of the Mazovian Specialist Hospital in Radom was diagnosed quite frequently. In 2021, 32 more urine cultures were performed than in 2020. In the analyzed period, among all ordered urine cultures, 35.27% of samples were positive.
Robust Assessment of EEG Connectivity Patterns in Mild Cognitive Impairment and Alzheimer's Disease

The prevalence of dementia, including Alzheimer's disease (AD), is on the rise globally with screening and intervention of particular importance and benefit to those with limited access to healthcare. Electroencephalogram (EEG) is an inexpensive, scalable, and portable brain imaging technology that could deliver AD screening to those without local tertiary healthcare infrastructure. We study EEG recordings of subjects with sporadic mild cognitive impairment (MCI) and prodromal familial, early-onset, AD for the same working memory tasks using high- and low-density EEG, respectively. A challenge in detecting electrophysiological changes from EEG recordings is that noise and volume conduction effects are common and disruptive. It is known that the imaginary part of coherency (iCOH) can generate functional connectivity networks that mitigate against volume conduction, while also erasing true instantaneous activity (zero or π-phase). We aim to expose topological differences in these iCOH connectivity networks using a global network measure, eigenvector alignment (EA), shown to be robust to network alterations that emulate the erasure of connectivities by iCOH. Alignments assessed by EA capture the relationship between a pair of EEG channels from the similarity of their connectivity patterns. Significant alignments—from comparison with random null models—are seen to be consistent across frequency ranges (delta, theta, alpha, and beta) for the working memory tasks, where consistency of iCOH connectivities is also noted. For high-density EEG recordings, stark differences in the control and sporadic MCI results are observed with the control group demonstrating far more consistent alignments. Differences between the control and pre-dementia groupings are detected for significant correlation and iCOH connectivities, but only EA suggests a notable difference in network topology when comparing between subjects with sporadic MCI and prodromal familial AD. The consistency of alignments, across frequency ranges, provides a measure of confidence in EA's detection of topological structure, an important aspect that marks this approach as a promising direction for developing a reliable test for early onset AD.
Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel

Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100–4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.
Remote Patient Management May Reduce All-Cause Mortality in Patients With Heart-Failure and Renal Impairment

Background Remote patient management (RPM) in heart failure (HF) patients has been investigated in several prospective randomized trials. The Telemedical Interventional Management in Heart Failure II (TIM-HF2)-trial showed reduced all-cause mortality and hospitalizations in heart failure (HF) patients using remote patient management (RPM) vs. usual care (UC). We report the trial's results for prespecified eGFR-subgroups. Methods TIM-HF2 was a prospective, randomized, controlled, parallel-group, unmasked (with randomization concealment), multicenter trial. A total of 1,538 patients with stable HF were enrolled in Germany from 2013 to 2017 and randomized to RPM (+UC) or UC. Using CKD-EPI-formula at baseline, prespecified subgroups were defined. In RPM, patients transmitted their vital parameters daily. The telemedical center reviewed and co-operated with the patient's General Practitioner (GP) and cardiologist. In UC, patients were treated by their GPs or cardiologist applying the current guidelines for HF management and treatment. The primary endpoint was the percentage of days lost due to unplanned cardiovascular hospitalizations or death, secondary outcomes included hospitalizations, all-cause, and cardiovascular mortality. Results Our sub analysis showed no difference between RPM and UC in both eGFR-subgroups for the primary endpoint (<60 ml/min/1.73 m2: 40.9% vs. 43.6%, p = 0.1, ≥60 ml/min/1.73 m2 26.5 vs. 29.3%, p = 0.36). In patients with eGFR < 60 ml/min/1.73 m2, 1-year-survival was higher in RPM than UC (89.4 vs. 84.6%, p = 0.02) with an incident rate ratio (IRR) 0.67 (p = 0.03). In the recurrent event analysis, HF hospitalizations and all-cause death were lower in RPM than UC in both eGFR-subgroups (<60 ml/min/1.73 m2: IRR 0.70, p = 0.02; ≥60 ml/min/1.73 m2: IRR 0.64, p = 0.04). In a cox regression analysis, age, NT-pro BNP, eGFR, and BMI were associated with all-cause mortality. Conclusion RPM may reduce all-cause mortality and HF hospitalizations in patients with HF and eGFR < 60 ml/min/1.73 m2. HF hospitalizations and all-cause death were lower in RPM in both eGFR-subgroups in the recurrent event analysis. Further studies are needed to investigate and confirm this finding.
Effects of Different Roughages on Growth Performance, Nutrient Digestibility, Ruminal Fermentation, and Microbial Community in Weaned Holstein Calves

This study aimed to assess the effects of feeding with different forage sources and starter concentrations on growth performance, nutrient digestibility, ruminal fermentation, and the microbial community in weaned Holstein calves. A total of 54 Holstein calves (body weight (BW) = 77.50 ± 5.07 kg; age = 70 ± 2.54 days) were assigned to 1 of 3 treatment groups (n = 18/group) that were offered diets with different forages: (1) peanut vine (PV), (2) oat hay (OH), or (3) an alfalfa hay + oat hay combination (alfalfa hay:oat hay =1:1, AO). Starter and forage intakes were recorded daily, while BW and growth parameters were assessed at 15-day intervals. The apparent digestibility of nutrients was determined. Ruminal fluid samples were collected and used to detect relevant indicators. A difference was observed for the forage × age interaction for all feed, nutrient intake, BW, ADG, and body structure parameters (P < 0.05). The final BW, average daily feed intake (ADFI), and average daily gain of the PV calves were higher than those of calves from the other groups (P < 0.05). The ruminal propionate concentration evidently increased in calves of the AO group (P < 0.05). The abundances of Rikenellaceae_RC9_gut_group and Shuttleworthia showed distinct responses to feeding with different forages (P < 0.05) at the genus level. The relative abundance of Shuttleworthia was negatively related to rumen pH and acid detergent fiber digestibility (P < 0.05) and strongly positively related to propionate concentration (P < 0.01). A positive correlation was found between Ruminococcus_1 abundance and butyrate concentration and neutral detergent fiber digestibility (P < 0.05). The relative abundances of Succiniclasticum and Prevotella_7 were negatively related to butyrate concentration (P < 0.05). In conclusion, there was an interaction between the factors (forage × age). The peanut vine used as a forage source promoted a higher starter concentrate intake compared to other diets and increased with the calves' age. The growth performance and rumen bacterial community of the calves were further improved. These results indicate that peanut vine can be used as the main source of forage in the diets of weaned calves.
Sphingomyelin Depletion Inhibits CXCR4 Dynamics and CXCL12-Mediated Directed Cell Migration in Human T Cells

Sphingolipids, ceramides and cholesterol are integral components of cellular membranes, and they also play important roles in signal transduction by regulating the dynamics of membrane receptors through their effects on membrane fluidity. Here, we combined biochemical and functional assays with single-particle tracking analysis of diffusion in the plasma membrane to demonstrate that the local lipid environment regulates CXCR4 organization and function and modulates chemokine-triggered directed cell migration. Prolonged treatment of T cells with bacterial sphingomyelinase promoted the complete and sustained breakdown of sphingomyelins and the accumulation of the corresponding ceramides, which altered both membrane fluidity and CXCR4 nanoclustering and dynamics. Under these conditions CXCR4 retained some CXCL12-mediated signaling activity but failed to promote efficient directed cell migration. Our data underscore a critical role for the local lipid composition at the cell membrane in regulating the lateral mobility of chemokine receptors, and their ability to dynamically increase receptor density at the leading edge to promote efficient cell migration.
Bad for Girls and Boys: Gender Does Not Modify the Negative Effect of Physical Inactivity on Life Satisfaction in Adolescents

Objectives: Physical activity (PA) has a positive effect on life satisfaction (LS) among adolescents, but the moderating effect of gender and level of PA intensity have been equivocal. Our aim was to examine the pattern of physical activity by grade in high school students, and the role of gender and grade on the association between physical activity and life satisfaction. Methods Four repeated cross-sectional online questionnaire surveys between 2011 and 2013 were carried out among all students in one Hungarian high school (N = 3,450). Health status and behavior was assessed by the Hungarian online version of the health behavior of school-aged children (HBSC) questionnaire. Regression with robust variance estimator was used to identify determinants of life satisfaction. Results Good self-reported health as opposed to bad increased life satisfaction by 0.30 standard deviation; having very well or well-off family as opposed to not well-off increased LS by 0.16 standard deviation; and being inactive compared to being vigorously active decreased LS by 0.1 standard deviation. Conclusions Physical inactivity has a negative effect on life satisfaction in boys and girls regardless of grade but compounded by low perceived family wealth.
Effects of Online Psychological Crisis Intervention for Frontline Nurses in COVID-19 Pandemic

Objective The psychological problems of frontline nurses in COVID-19 prevention and control are very prominent, and targeted intervention is needed to alleviate them. This study was to assess the impact of online intervention programs on psychological crisis of anxiety, depression levels and physical symptoms among frontline nurses fighting the COVID-19 pandemic. Methods A three-stage online psychological crisis intervention program was established. The General Anxiety 7 (GAD-7) assessment, Patient Health Questionnaire-9 (PHQ-9), and the Self-rating Somatic Symptom Scale (SSS) were used to evaluate the effect of intervention on the day before entering isolation wards (Time 1), the first day after leaving the isolation ward (Time 2), and at the end of the intervention (Time 3). Results Sixty-two nurses completed the study, including 59 female (95.2%) and three male nurses (4.8%) with an age range of 23–49 (mean 33.37 ± 6.01). A significant (P < 0.01) difference existed in the scores of GAD-7, PHQ-9, and SSS at different intervention periods. The GAD-7 score was significantly (P < 0.001) lower at the end of quarantine period (time 3) than that before entering the isolation wards (time 1) or after leaving the isolation wards (time 2), the PHQ-9 score was significantly (P = 0.016) lower at the end of quarantine period (time 3) than that after leaving the isolation wards (time 2), and the SSS score was significantly (P < 0.001) lower at the end of quarantine period (time 3) than that before entering the isolation wards (time 1) or after leaving the isolation wards (time 2). Conclusion The three-stage online intervention program based on the psychological crisis can be effective in reducing negative emotions and somatic symptoms and improving the mental health of frontline nurses in prevention and control of the COVID-19 epidemic. It may provide an empirical basis for psychological crisis intervention of frontline medical staff when facing public health emergencies.
Perioperative Inflammatory Response and Cancer Recurrence in Lung Cancer Surgery: A Narrative Review

While surgical resection is the gold standard treatment for solid tumors, cancer recurrence after surgery is common. Immunosurveillance of remnant tumor cells is an important protective mechanism. Therefore, maintenance of anti-tumor cell activity and proper levels of inflammatory mediators is crucial. An increasing body of evidence suggests that surgery itself and perioperative interventions could affect these pathophysiological responses. Various factors, such as the extent of tissue injury, perioperative medications such as anesthetics and analgesics, and perioperative management including transfusions and methods of mechanical ventilation, modulate the inflammatory response in lung cancer surgery. This narrative review summarizes the pathophysiological mechanisms involved in cancer recurrence after surgery and perioperative management related to cancer recurrence after lung cancer surgery.
Wheat Biofortification: Utilizing Natural Genetic Diversity, Genome-Wide Association Mapping, Genomic Selection, and Genome Editing Technologies

Alleviating micronutrients associated problems in children below five years and women of childbearing age, remains a significant challenge, especially in resource-poor nations. One of the most important staple food crops, wheat attracts the highest global research priority for micronutrient (Fe, Zn, Se, and Ca) biofortification. Wild relatives and cultivated species of wheat possess significant natural genetic variability for these micronutrients, which has successfully been utilized for breeding micronutrient dense wheat varieties. This has enabled the release of 40 biofortified wheat cultivars for commercial cultivation in different countries, including India, Bangladesh, Pakistan, Bolivia, Mexico and Nepal. In this review, we have systematically analyzed the current understanding of availability and utilization of natural genetic variations for grain micronutrients among cultivated and wild relatives, QTLs/genes and different genomic regions regulating the accumulation of micronutrients, and the status of micronutrient biofortified wheat varieties released for commercial cultivation across the globe. In addition, we have also discussed the potential implications of emerging technologies such as genome editing to improve the micronutrient content and their bioavailability in wheat.
Revealing Selection in Breeding and Genetic Characteristics of Economically Important Traits of New Species of Apostichopus Japonicas Based on Genome Resequencing and GWAS Analysis

Apostichopus japonicas is an economically important species with high nutritional value. However, our knowledge of its genetic diversity and the genetic changes that occurred during its domestication or trait selection is quite limited. In this study, the whole genomes of 254 A. japonicas samples were resequenced. Analyses of the population genetic structure revealed that the genetic diversity of A. japonicas in the north of China is generally high, there was no difference in the population structure among the six cultured populations, and they were divided into two subpopulations together with AY-1 (new species). The results also showed that the genetic diversity of the AY-1 population was relatively low, the degree of linkage of alleles was high, and this population had been subjected to more positive selection. Based on Tajima’s D, FST analysis, and ROD analysis, the selected intervals and genes of the AY-1 population were identified, with some of the candidate intervals being related to an economically important trait and breeding target, namely, the number of parapodia. Gene Ontology analysis of the candidate genes revealed that the two subpopulations differed in their immune function, protein synthesis, decomposition, and transport, among others. Using GWAS, we identified 39 candidate genes for four economically important traits of A. japonicas, and we verified that those genes contained non-synonymous SNPs. Through this verification, BSL78_00022 and BSL78_00023 were found to be key genes for the number of parapodia in A. japonicas. Of these two genes, BSL78_00022 encodes a protein related to cell differentiation and proliferation, so it was assumed that three non-synonymous substitutions (Ser-Phe, Glu-Asp, and Ala-Val) in this gene are related to the changes in the number of parapodia. Meanwhile, the pleiotropic gene BSL78_04631, which is related to body weight and body wall weight, and promotes protein synthesis and cell growth, has a non-synonymous substitution (IlE-Val), which is assumed to be the reason for the difference in body weight and body wall weight of A. japonicas. These results provide a new perspective for explaining the genetic structure characteristics of A. japonicas and analyzing the selection and economically important traits in the breeding of new species.
Soft Ionics: Governing Physics and State of Technologies

Soft ionic materials combine charged mobile species and tailored polymer structures in a manner that enables a wide array of functional devices. Traditional metal and silicon electronics are limited to two charge carriers: electrons and holes. Ionic devices hold the promise of using the wide range of chemical and molecular properties of mobile ions and polymer functional groups to enable flexible conductors, chemically specific sensors, bio-compatible interfaces, and deformable digital or analog signal processors. Stand alone ionic devices would need to have five key capabilities: signal transmission, energy conversion/harvesting, sensing, actuation, and signal processing. With the great promise of ionically-conducting materials and ionic devices, there are several fields working independently on pieces of the puzzle. These fields range from waste-water treatment research to soft robotics and bio-interface research. In this review, we first present the underlying physical principles that govern the behavior of soft ionic materials and devices. We then discuss the progress that has been made on each of the potential device components, bringing together findings from a range of research fields, and conclude with discussion of opportunities for future research.
Bridging Reinforcement Learning and Iterative Learning Control: Autonomous Motion Learning for Unknown, Nonlinear Dynamics

This work addresses the problem of reference tracking in autonomously learning robots with unknown, nonlinear dynamics. Existing solutions require model information or extensive parameter tuning, and have rarely been validated in real-world experiments. We propose a learning control scheme that learns to approximate the unknown dynamics by a Gaussian Process (GP), which is used to optimize and apply a feedforward control input on each trial. Unlike existing approaches, the proposed method neither requires knowledge of the system states and their dynamics nor knowledge of an effective feedback control structure. All algorithm parameters are chosen automatically, i.e. the learning method works plug and play. The proposed method is validated in extensive simulations and real-world experiments. In contrast to most existing work, we study learning dynamics for more than one motion task as well as the robustness of performance across a large range of learning parameters. The method’s plug and play applicability is demonstrated by experiments with a balancing robot, in which the proposed method rapidly learns to track the desired output. Due to its model-agnostic and plug and play properties, the proposed method is expected to have high potential for application to a large class of reference tracking problems in systems with unknown, nonlinear dynamics.