Miracle-dz/UniFAR-FTUs huggingface dataset:
Serial Detection of Circulating Mucorales DNA in Invasive Mucormycosis: A Retrospective Multicenter Evaluation

Invasive mucormycosis is a fungal infection with high mortality. Early diagnosis and initiation of appropriate treatment is essential to improve survival. However, current diagnostic tools suffer from low sensitivity, leading to delayed or missed diagnoses. Recently, several PCR assays for the detection of Mucorales DNA have been developed. We retrospectively assessed the diagnostic and kinetic properties of a commercial Mucorales PCR assay (MucorGenius®, PathoNostics) on serial blood samples from patients with culture-positive invasive mucormycosis and found an overall sensitivity of 75%. Importantly, a positive test preceded a positive culture result by up to 81 days (median eight days, inter-quartile range 1.75–16.25). After initiation of appropriate therapy, the average levels of circulating DNA decreased after one week and stabilized after two weeks. In conclusion, detection of circulating Mucorales DNA appears to be a good, fast diagnostic test that often precedes the final diagnosis by several days to weeks. This test could be especially useful in cases in which sampling for culture or histopathology is not feasible.
Association between Ready-to-Eat Cereal Consumption and Nutrient Intake, Nutritional Adequacy, and Diet Quality in Adults in the National Health and Nutrition Examination Survey 2015–2016

This study examined differences in dietary intake between ready-to-eat cereal eaters and non-eaters in adults from the United States. Participants (n = 5163) from the National Health and Nutrition Examination Survey 2015–2016 were included. One-day dietary recall was used to define ready-to-eat cereal consumption status and estimate dietary intake in eaters and non-eaters. Data from Food Patterns Equivalent Database 2015–2016 were used to compare intakes of food groups by consumption status. Diet quality was assessed by Healthy Eating Index 2015. Nineteen percent of US adults were ready-to-eat cereal eaters; they had a similar level of energy intake as non-eaters, but they had significantly higher intake of dietary fiber, and several vitamins and minerals, such as calcium, iron, magnesium, potassium, zinc, vitamin A, thiamin, riboflavin, niacin, vitamin B6, folate, vitamin B12, and vitamin D. They were also more likely to meet nutrient recommendations. Compared to non-eaters, ready-to-eat cereal eaters had the same level of added sugar intake but they had significantly higher intake of whole grains, total fruits, and dairy products. The diet quality of ready-to-eat cereal eaters was significantly higher than that of non-eaters. The study supports that ready-to-eat cereal eaters have better dietary intake with a healthier dietary pattern than non-eaters in the United States.
Risk of infection in the first year of life in preterm children: An Austrian observational study

Newborns, especially preterm infants, have an immature immune system, which, in combination with the required medical interventions necessary for keeping the neonate alive may lead to an increased risk of infection. Even after reaching stability and adapting to the environment, preterm infants have adverse prognoses regarding infections and long-term outcomes compared to their full-term counterparts. The objective of this study was to research differences in the number and severity of infections between preterm and full-term infants during their first year of life. To answer this question, a monocentric prospective study was conducted in a pediatric practice in Vienna, including 71 full-term infants and 72 preterm infants who were observed during their first year of life regarding occurring infections. In respective samples, there was a significantly higher total number of infections in preterm (mean 6.01 ± 3.90) compared to full-term infants (3.85 ± 1.72) during the observation period of one year. Particularly the count of respiratory and severe infections was considerably higher in preterm infants. Otorhinolaryngeal infections were the most frequent of all types of infections in both groups. The pregnancy period, number of siblings, and length of the postnatal hospital stay, were observed as significantly influencing factors which affected the total number of infections. The group of early term infants (37+0 weeks to 38+6) was not significantly different to late term babies (>39+0). The acquired knowledge about the increased risk of infections should lead to a more extensive care for preterm infants, with the objective of reducing the rates of complications, morbidity and mortality in this vulnerable age group in the future.
Composition and processing activity of a semi-recombinant holo U7 snRNP

Abstract In animal cells, replication-dependent histone pre-mRNAs are cleaved at the 3′ end by U7 snRNP consisting of two core components: a ∼60-nucleotide U7 snRNA and a ring of seven proteins, with Lsm10 and Lsm11 replacing the spliceosomal SmD1 and SmD2. Lsm11 interacts with FLASH and together they recruit the endonuclease CPSF73 and other polyadenylation factors, forming catalytically active holo U7 snRNP. Here, we assembled core U7 snRNP bound to FLASH from recombinant components and analyzed its appearance by electron microscopy and ability to support histone pre-mRNA processing in the presence of polyadenylation factors from nuclear extracts. We demonstrate that semi-recombinant holo U7 snRNP reconstituted in this manner has the same composition and functional properties as endogenous U7 snRNP, and accurately cleaves histone pre-mRNAs in a reconstituted in vitro processing reaction. We also demonstrate that the U7-specific Sm ring assembles efficiently in vitro on a spliceosomal Sm site but the engineered U7 snRNP is functionally impaired. This approach offers a unique opportunity to study the importance of various regions in the Sm proteins and U7 snRNA in 3′ end processing of histone pre-mRNAs.
Coronary artery plaque growth: A two‐way coupled shear stress–driven model

Atherosclerosis in coronary arteries can lead to plaque growth, stenosis formation, and blockage of the blood flow supplying the heart tissue. Several studies have shown that hemodynamics play an important role in the growth of coronary artery plaques. Specifically, low wall shear stress (WSS) appears to be the leading hemodynamic parameter promoting atherosclerotic plaque growth, which in turn influences the blood flow and WSS distribution. Therefore, a two‐way coupled interaction exists between WSS and atherosclerosis growth. In this work, a computational framework was developed to study the coupling between WSS and plaque growth in coronary arteries. Computational fluid dynamics (CFD) was used to quantify WSS distribution. Surface mesh nodes were moved in the inward normal direction according to a growth model based on WSS. After each growth stage, the geometry was updated and the CFD simulation repeated to find updated WSS values for the next growth stage. One hundred twenty growth stages were simulated in an idealized tube and an image‐based left anterior descending artery. An automated framework was developed using open‐source software to couple CFD simulations with growth. Changes in plaque morphology and hemodynamic patterns during different growth stages are presented. The results show larger plaque growth towards the downstream segment of the plaque, agreeing with the reported clinical observations. The developed framework could be used to establish hemodynamic‐driven growth models and study the interaction between these processes.
GenoSurf: metadata driven semantic search system for integrated genomic datasets

Abstract Many valuable resources developed by world-wide research institutions and consortia describe genomic datasets that are both open and available for secondary research, but their metadata search interfaces are heterogeneous, not interoperable and sometimes with very limited capabilities. We implemented GenoSurf, a multi-ontology semantic search system providing access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of 10 attributes are semantically enriched by making use of the most suited available ontologies. The user of GenoSurf provides as input the search terms, sets the desired level of ontological enrichment and obtains as output the identity of matching data files at the various sources. Search is facilitated by drop-down lists of matching values; aggregate counts describing resulting files are updated in real time while the search terms are progressively added. In addition to the consolidated attributes, users can perform keyword-based searches on the original (raw) metadata, which are also imported; GenoSurf supports the interplay of attribute-based and keyword-based search through well-defined interfaces. Currently, GenoSurf integrates about 40 million metadata of several major valuable data sources, including three providers of clinical and experimental data (TCGA, ENCODE and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq); it can be used as a standalone resource for targeting the genomic datasets at their original sources (identified with their accession IDs and URLs), or as part of an integrated query answering system for performing complex queries over genomic regions and metadata.
Development and Evaluation of a Duo Zaire ebolavirus Real-Time RT-PCR Assay Targeting Two Regions within the Genome

Preparedness and response actions to mitigate Ebola virus disease (EVD) outbreaks rely on rapid diagnosis to be implemented locally to sort suspect patients attending health centers. Our aim was (i) to develop and evaluate an RT-qPCR assay combining primers and probes derived from two reference assays targeting different genomic regions; (ii) to study whether sensitivity and specificity of this dual-target assay were at least equal or better to the parental assays; (iii) to implement this dual-target assay onto the Cepheid GeneXpert open cartridge as a proof of principle for technological transfer aiming at bedsite testing locally. To do so, three home-made published RT-qPCR assays were selected to be compared with the RealStar® Filovirus Screen RT-PCR kit 1.0 (Altona Diagnostics, Hamburg, Germany), a technique that was largely deployed during the 2014–2015 West African EVD outbreak. Primers and probes sequences of the custom-made assays were analyzed in silico against a multiple sequence alignment, including >250 complete sequences corresponding to strains that have caused EVD epidemics in the past. Genomic RNA purified from the Mekambo strain of Zaire ebolavirus (EBOV) was used to study the sensitivity of the five methods. Based on these results, two in-house methods were selected and adapted to design the dual-target assay, which performances were compared to those of the parental assays using a synthetic RNA control. The dual-target assay showed better sensitivity and limit of detection (LoD95 at 0.4 copies/µL) than the parental methods (1.7 and 2.2 copies/µL). Ultimately, the dual-target assay was transferred onto the GeneXpert Flex-03 open cartridge, demonstrating a LoD95 at 0.75 copies/µL. Together these results indicate that EBOV dual-target assay has the potential to be used during EVD outbreak in the laboratory having performed molecular testing during the recent outbreaks.
Distinct cerebellar regions for body motion discrimination

Abstract Visual processing of human movements is critical for adaptive social behavior. Cerebellar activations have been observed during biological motion discrimination in prior neuroimaging studies, and cerebellar lesions may be detrimental for this task. However, whether the cerebellum plays a causal role in biological motion discrimination has never been tested. Here, we addressed this issue in three different experiments by interfering with the posterior cerebellar lobe using transcranial magnetic stimulation (TMS) during a biological discrimination task. In Experiments 1 and 2, we found that TMS delivered at onset of the visual stimuli over the vermis (vermal lobule VI), but not over the left cerebellar hemisphere (left lobule VI/Crus I), interfered with participants’ ability to distinguish biological from scrambled motion compared to stimulation of a control site (vertex). Interestingly, when stimulation was delivered at a later time point (300 ms after stimulus onset), participants performed worse when TMS was delivered over the left cerebellar hemisphere compared to the vermis and the vertex (Experiment 3). Our data show that the posterior cerebellum is causally involved in biological motion discrimination and suggest that different sectors of the posterior cerebellar lobe may contribute to the task at different time points.
Fuzzy Logic Model for Benchmarking Knowledge Management Performance of AEC Firms

Knowledge management is rapidly becoming a key capability for creating competitive advantage in the construction industry. The emergence of knowledge management as a key capability for creating competitive advantage poses enormous challenges to executives of construction firms. This paper proposes a model for benchmarking knowledge management performance of AEC firms that can guide construction business executives to meet these challenges. The proposed model incorporates benchmarking and knowledge management concepts with fuzzy set theory to adequately handle imprecision, vagueness and uncertainty that prevail in this process. It uses the fuzzy-weighted average (FWA) algorithm to benchmark the knowledge management performance of AEC firms. It is an internal reporting model that can guide executives of AEC firms to benchmark and evaluate their firm’s ability to achieve their strategic objectives and to pinpoint their firm’s strengths and weaknesses in order to neutralize threats and to exploit opportunities presented by today’s construction business environment. A real-world case study is presented to illustrate the implementation and utility of the proposed model.
European Society of Cardiology/Heart Failure Association position paper on the role and safety of new glucose‐lowering drugs in patients with heart failure

Type 2 diabetes mellitus (T2DM) is common in patients with heart failure (HF) and associated with considerable morbidity and mortality. Significant advances have recently occurred in the treatment of T2DM, with evidence of several new glucose‐lowering medications showing either neutral or beneficial cardiovascular effects. However, some of these agents have safety characteristics with strong practical implications in HF [i.e. dipeptidyl peptidase‐4 (DPP‐4) inhibitors, glucagon‐like peptide‐1 receptor agonists (GLP‐1 RA), and sodium–glucose co‐transporter type 2 (SGLT‐2) inhibitors].
Dual RNA Sequencing of Vitis vinifera during Lasiodiplodia theobromae Infection Unveils Host–Pathogen Interactions

Lasiodiplodia theobromae is one of the most aggressive agents of the grapevine trunk disease Botryosphaeria dieback. Through a dual RNA-sequencing approach, this study aimed to give a broader perspective on the infection strategy deployed by L. theobromae, while understanding grapevine response. Approximately 0.05% and 90% of the reads were mapped to the genomes of L. theobromae and Vitis vinifera, respectively. Over 2500 genes were significantly differentially expressed in infected plants after 10 dpi, many of which are involved in the inducible defense mechanisms of grapevines. Gene expression analysis showed changes in the fungal metabolism of phenolic compounds, carbohydrate metabolism, transmembrane transport, and toxin synthesis. These functions are related to the pathogenicity mechanisms involved in plant cell wall degradation and fungal defense against antimicrobial substances produced by the host. Genes encoding for the degradation of plant phenylpropanoid precursors were up-regulated, suggesting that the fungus could evade the host defense response using the phenylpropanoid pathway. The up-regulation of many distinct components of the phenylpropanoid pathway in plants supports this hypothesis. Moreover, genes related to phytoalexin biosynthesis, hormone metabolism, cell wall modification enzymes, and pathogenesis-related proteins seem to be involved in the host responses observed. This study provides additional insights into the molecular mechanisms of L. theobromae and V. vinifera interactions.
Key Aspects of Myo-Inositol Hexaphosphate (Phytate) and Pathological Calcifications

Phytate (myo-inositol hexaphosphate, InsP6) is an important component of seeds, legumes, nuts, and whole cereals. Although this molecule was discovered in 1855, its biological effects as an antinutrient was first described in 1940. The antinutrient effect of phytate results because it can decrease the bioavailability of important minerals under certain circumstances. However, during the past 30 years, researchers have identified many important health benefits of phytate. Thus, 150 years have elapsed since the discovery of phytate to the first descriptions of its beneficial effects. This long delay may be due to the difficulty in determining phytate in biological media, and because phytate dephosphorylation generates many derivatives (InsPs) that also have important biological functions. This paper describes the role of InsP6 in blocking the development of pathological calcifications. Thus, in vitro studies have shown that InsP6 and its hydrolysates (InsPs), as well as pyrophosphate, bisphosphonates, and other polyphosphates, have high capacity to inhibit calcium salt crystallization. Oral or topical administration of phytate in vivo significantly decreases the development of pathological calcifications, although the details of the underlying mechanism are uncertain. Moreover, oral or topical administration of InsP6 also leads to increased urinary excretion of mixtures of different InsPs; in the absence of InsP6 administration, only InsP2 occurs at detectable levels in urine.
Effect of Two Choreographed Fitness Group-Workouts on the Body Composition, Cardiovascular and Metabolic Health of Sedentary Female Workers

Daily sedentary working hours contribute negatively to body composition, cardiovascular and metabolic health, especially in women, who are usually less active than men. The objective of this study was to analyze the effect of two trending choreographed fitness group-workouts on the body composition and cardiovascular and metabolic health of sedentary female workers. A total of 98 physically inactive and working women (38.9 ± 6.4 years of age) were randomly assigned to three study groups: Control group (CG) = 31, Zumba Fitness® with three one-hour classes per week (ZF) = 39, and Zumba Fitness with 20 min of additional Bodyweight strength training (ZF + BW) = 28. Measurements included body composition, blood pressure, cardiovascular risk by the Framingham Heart Study tools (10 yr cardiovascular risk and vascular age) and a metabolic blood panel. Post-intervention, both choreographed fitness group-workouts reached a similar significant loss of fat mass (ZF = 2.805 ± 0.48, p < 0.0001; ZF + BW = 3.540 ± 0.04, p < 0.0001), an increase in muscle mass (ZF = 1.70 ± 0.581, p = 0.005; ZF + BW = 3.237 ± 0.657, p < 0.0001) and a decrease in SBP (ZF= 6.454 ± 1.70, p < 0.0001; ZF + BW = 4.12 ± 1.95, p = 0.039). Only the ZF group significantly improved the 10 yr cardiovascular risk (p = 0.032) and metabolic age (p = 0.0025) post-intervention. No significant improvement was observed in the metabolic panel for both choreographed fitness group-workouts. In conclusion, the ZF program generated improvements in cardiovascular and metabolic risk variables compared to ZF + BW or CG. Both choreographed fitness group-workouts contributed similarly to the improvement in systolic blood pressure, fat mass, muscle mass, and also engendered a great adherence to exercise.
EV71 Infection Induces IFNβ Expression in Neural Cells

Enterovirus 71 (EV71) can invade the central nervous system (CNS) and cause neurological disease. Accumulating evidence indicates that EV71 can directly infect neurons in the CNS. Innate immune responses in the CNS have been known to play an essential role in limiting pathogen infections. Thus, investigating the effects of EV71 infection of neural cells is important for understanding disease pathogenesis. In this study, human neural cells were infected with EV71, and interferonβ (IFNβ) expression was examined. Our results show that IFNβ expression was upregulated in EV71-infected neural cells via pattern recognition receptors (PRRs) sensing of virus RNA. The PRRs Toll-like receptor 3 (TLR3), Toll-like receptor 8 (TLR8), and melanoma differentiation-associated gene-5 (MDA-5), but not retinoic acid-inducible gene-I (RIG-I) and Toll-like receptor 7 (TLR7), were found to be EV71-mediated IFNβ induction. Although viral proteins exhibited the ability to cleave mitochondrial antiviral signaling protein (MAVS) and Toll/IL-1 receptor (TIR) domain-containing adaptor-inducing IFN-β (TRIF) in neural cells, levels of viral protein expression were low in these cells. Furthermore, neural cells efficiently produced IFNβ transcripts upon EV71 vRNA stimulation. Treating infected cells with anti-IFNβ antibodies resulted in increased virus replication, indicating that IFNβ release may play a role in limiting viral growth. These results indicate that EV71 infection can induce IFNβ expression in neural cells through PRR pathways.
Understanding the Role of the Unfolded Protein Response Sensor IRE1 in the Biology of Antigen Presenting Cells

The unfolded protein response (UPR) is an adaptive response that maintains the fidelity of the cellular proteome in conditions that subvert the folding capacity of the cell, such as those noticed in infection and inflammatory contexts. In immunity, the UPR sensor IRE1 (Inositol-requiring enzyme 1-alpha) has emerged as a critical regulator of the homeostasis of antigen presenting cells (APCs). In the past few years, it has become clear that IRE1 plays canonical and non-canonical roles in APCs, many of which intersect with key features of these cells, including the initiation of inflammation, antibody production, and antigen presentation. The aims of the present review are to provide recent insights on the mechanisms by which IRE1 regulates the diversity of APC functions and to highlight its relevance in the coordination of innate and adaptive immunity.