Miracle-dz/UniFAR-FTUs huggingface dataset:
A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.
Efficacy and safety of cerebral embolic protection systems during transcatheter aortic valve replacement: a review of current clinical findings

ABSTRACT Introduction Cerebrovascular events are one of the most serious consequences after transcatheter aortic valve replacement (TAVR). More than half of the cerebrovascular events following TAVR are due to procedure-related emboli. Embolic protection devices (EPDs) have the potential to decrease cerebrovascular events during TAVR procedure. However, randomized controlled trials (RCTs) have not conclusively determined if EPDs are effective, likely because of small number of patients enrolled. However, meta-analyses and propensity-matched analyses from large registries have shown efficacy and suggest the importance of EPDs in prevention of stroke during TAVR and perhaps other structural heart procedures. Areas covered This review will focus on clinical and histopathologic studies examining the efficacy, safety, and histopathologic device capture findings in the presence and absence of EPDs during TAVR procedures. Expert opinion Clinical studies have not conclusively determined the efficacy of EPDs. Current ongoing large-scale RCT (PROTECTED TAVR [NCT04149535]) has the potential to prove their efficacy. Histopathological evaluation of debris captured by EPDs contributes to our understanding of the mechanisms of TAVR procedure-related embolic events and suggests the importance of preventing cerebral embolization of debris released during this and other structural heart procedures.
Parasitoid Communities in the Variable Agricultural Environments of Blueberry Production in the Southeastern United States

Abstract In blueberry crops, there are multiple pest species, and some of those can be suppressed by natural enemies including parasitoid wasps and predators. Parasitoid wasps occur within the environment often tracking pest species for food resources to complete their lifecycle.These small wasps are also sensitive to agricultural environments including agrichemicals, habitat availability, and climate. We investigated how the structure of parasitoid communities varied between organic and conventional blueberry systems, and how the communities of these parasitoids varied within field spatial scales (forested border vs edge vs interior). With the lower intensity of agricultural interventions occurring in organic systems and forested borders, we predicted more stable parasitoid numbers that would be insulated from predicted climate variability. In our study, parasitoids were observed in low abundance in each cropping system, with community structure dependent on both management practice and field position. Unmanaged blueberry fields and forested field borders contained more parasitoid families, and in conventional systems, we saw fewer families present in the field interior as compared to field borders. In this first study to characterize Southern parasitoid communities in blueberry production systems, we observed over 50 genera of parasitoids, with a few dominant families (Braconidae and Ichneumonidae) that would contribute to biological control in blueberry systems. Overall, we captured few parasitoids, which indicates a potential vulnerability in biological control, and the need for further research using other sampling techniques to better understand these parasitoid communities.
Neuroprotective action of Cortexin, Cerebrolysin and Actovegin in acute or chronic brain ischemia in rats

This study was the first to compare the neuroprotective activity of Cerebrolysin®, Actovegin® and Cortexin® in rodent models of acute and chronic brain ischemia. The neuroprotective action was evaluated in animals with acute (middle cerebral artery occlusion) or chronic (common carotid artery stenosis) brain ischemia models in male rats. Cortexin® (1 or 3 mg/kg/day), Cerebrolysin® (538 or 1614 mg/kg/day) and Actovegin® (200 mg/kg/day) were administered for 10 days. To assess the neurological and motor impairments, open field test, adhesive removal test, rotarod performance test and Morris water maze test were performed. Brain damage was assessed macro- and microscopically, and antioxidant system activity was measured in brain homogenates. In separate experiments in vitro binding of Cortexin® to a wide panel of receptors was assessed, and blood-brain barrier permeability of Cortexin® was assessed in mice in vivo. Cortexin® or Cerebrolysin® and, to a lesser extent, Actovegin® improved the recovery of neurological functions, reduced the severity of sensorimotor and cognitive impairments in rats. Cortexin® reduced the size of necrosis of brain tissue in acute ischemia, improved functioning of the antioxidant system and prevented the development of severe neurodegenerative changes in chronic ischemia model. Radioactively labeled Cortexin® crossed the blood-brain barrier in mice in vivo with concentrations equal to 6–8% of concentrations found in whole blood. During in vitro binding assay Cortexin® (10 μg/ml) demonstrated high or moderate binding to AMPA-receptors (80.1%), kainate receptors (73.5%), mGluR1 (49.0%), GABAA1 (44.0%) and mGluR5 (39.7%), which means that effects observed in vivo could be related on the glutamatergic and GABAergic actions of Cortexin®. Thus, Cortexin, 1 or 3 mg/kg, or Cerebrolysin®, 538 or 1614 mg/kg, were effective in models acute and chronic brain ischemia in rats. Cortexin® contains compounds acting on AMPA, kainate, mGluR1, GABAA1 and mGluR5 receptors in vitro, and readily crosses the blood-brain barrier in mice.
Use of cleaved wedge geometry for plan‐view transmission electron microscopy sample preparation

A fast, convenient, and easy to perform method for preparing plan‐view transmission electron microscopy (TEM) specimens of brittle materials is proposed. The method is ideal for thin films/coatings and based on obtaining wedge‐shape geometries of the samples via conventional cutting and cleaving followed by gentle focused ion beam (FIB) milling to electron transparency. It enables multiple parallel windows for depth sectioning of the samples and facilitates FIB lift‐out procedure. The method has been successfully applied for preparing high‐quality plan‐view TEM samples for a range of films deposited on Si, SiC, and Al2O3 which significantly enhances throughput and reduces time at the FIB. The method further offers high success rate even for the novice, stable handling and reproducibility, which greatly widens the application of advanced plan‐view TEM studies in material science.
High Aspect-Ratio, Fully Conducting Gold Micropillar Array Electrodes: Silicon Micromachining and Electrochemical Characterization

In this paper we describe the design, fabrication, and characterization of cylindrical gold micropillar array electrodes. Micropillar array electrodes bring about several advantages compared to planar electrodes and microelectrode arrays, as they provide a much larger surface area than the latter devices. Micropillar array electrodes are closely related to porous electrodes, as suggested by the recent literature and as our experimental results show. We fabricated a number of different gold micropillar array structures using standard microfabrication techniques, particularly DRIE plasma etching, thermal oxidations, and gold metallization by dc sputtering. Experimental results were compared with simulations, and very good agreement was found. This served both to validate the diffusion domain approximation for these particular devices and also to deepen our understanding on the modes of mass transport controlling the current response of these devices. We found that planar diffusion dominates the response of .
Block Copolymerization of Carbon Dioxide with Butylene Oxide, Propylene Oxide and 4-Vinyl-1-Cyclohexene-1,2-Epoxide in Based Poly(Cyclohexene Carbonate)

Poly(cyclohexene carbonate) (PCHC) resulting from the copolymerization of CO2 with cyclohexene oxide (CHO) could be effectively synthesized using the coordination system Y(CF3CO2)3 (l) - diethyl zinc (II) - glycerine (Ill) and 1 ,3-dioxolane as the catalyst and solvent. t therefore was used as the base to synthesize block copolymers. Block copolymerization in the based PCHC was carried out by introducing an epoxide other than CHO right after the copolymerization of CO2 with CHO. The IR and IH-NMR spectra as well as the glass transition temperatures indicated that the resultant copolymers from the block copolymerization of CO2 with butylene oxide (BO), propylene oxide (PO), and 4-vinyl-l-cyclohexene-1,2-epoxide (VCHO) in PCHC were indeed block copolymers. The epoxide activity followed the sequence VCHO＞ PO ＞ 80 at 353 K. While the most appropriate temperature regarding yield, molecular weight and the 353 K in the block copolymerization. The most appropriate temperatures for the block copolymerization of CO2 with BO as well as CO2 with VCHO in the based PCHC were 343 K and 353 K, respectively. he molecular weights of the resulting block copolymers were found to exceed 2x \05, and the polydispersity indexes were in a range of 6.2 to 9.9. The carbonate Contents (fCO2) were observed to be in the range of 86% to 100%. The thermal and mechanical properties of the resulting block copolymers lay between those of the copolymers resulting from CO2 with an individual epoxide, such as BO, PO, CHO and VCHO. These results indicated that block copolymerization was an effective means of generating a polymer with the desired thermal and mechanical properties.
Draft Genome Sequences of Seven Cronobacter sakazakii Strains Carrying the mcr 9.1 Gene Isolated in Chile

Cronobacter sakazakii is a pathogen that causes severe diseases such as meningitis and necrotizing enterocolitis in infants under 12 months, associated with the consumption of contaminated rehydrated powdered infant formula (PIF). We present seven C. sakazakii genome sequences isolated from PIF and dairy products in Chile in 2017. ABSTRACT Cronobacter sakazakii is a pathogen that causes severe diseases such as meningitis and necrotizing enterocolitis in infants under 12 months, associated with the consumption of contaminated rehydrated powdered infant formula (PIF). We present seven C. sakazakii genome sequences isolated from PIF and dairy products in Chile in 2017.
Efficient and Outlier-Robust Simultaneous Pose and Correspondence Determination by Branch-and-Bound and Transformation Decomposition

Estimating the pose of a calibrated camera relative to a 3D point set from one image is an important task in computer vision. Perspective-n-Point algorithms are often used if perfect 2D-3D correspondences are known. However, it is difficult to determine 2D-3D correspondences perfectly, and then the simultaneous pose and correspondence determination problem is needed to be solved. Early methods aimed to solve this problem by local optimization. Recently, several new methods are proposed to globally solve this problem by using branch-and-bound (BnB) method, but they tend to be slow because the time complexity of the BnB-based methods is exponential to the dimensionality of the parameter space, and they directly search the 6D parameter space. In this paper, we propose to decompose the joint searching into two separate searching processes by introducing a rotation invariant feature (RIF). Specifically, we construct RIFs from the original 3D and 2D point sets and search for the globally optimal translation to match these two RIFs first. Then, the original 3D point set is translated and matched with the 2D point set to find a globally optimal rotation. Experiments on challenging data show that the proposed method outperforms state-of-the-art methods in terms of both speed and accuracy.
Somatosensory Tinnitus Diagnosis: Diagnostic Value of Existing Criteria

Supplemental Digital Content is available in the text. Background: Tinnitus can be influenced by changes in somatosensory afference from the cervical spine or temporomandibular area, then called somatosensory or somatic tinnitus (ST). In 2018, a new set of diagnostic criteria for ST was agreed upon by a large group of ST experts. Currently, however, it still requires extensive and specific expertise to diagnose ST correctly. The next step in the development of easily applicable diagnostic criteria is to assess the diagnostic value of each individual criterion. Objectives: The aim of this study was, therefore, to further investigate the diagnostic value of these criteria, validate them empirically, and identify their sensitivity and specificity. Methods: An online survey, questioning the presence of 12 diagnostic criteria for ST in a convenience sample of participants with tinnitus, was launched on the online forum Tinnitus Talk, managed by Tinnitus Hub. Participants were divided into three groups: a group with no somatic influence, a group with some somatic influence and a group with large somatic influence on their tinnitus. Chi-square tests were used to calculate differences between these groups. Afterward, sensitivity, specificity, positive and negative likelihood ratios (LR), and pre- and posttest probabilities were calculated for each ST diagnostic criterion. For this analysis, all patients with some and large somatic influence were compared as one group to the group with no somatic influence. Results: In total, 8221 participants filled out the online survey. As expected, the diagnostic criteria for ST are more prevalent in the groups with somatic influence, but the criterium of tinnitus modulation also often occurs in the group with no somatic influence. The simultaneous onset or increase and decrease of both tinnitus and pain complaints have the highest positive LR (6.29 and 10.72, respectively), next to the influence of certain postures on the tinnitus (+LR: 6.04). To rule out ST, the absence of neck pain or tension in the neck extensor muscles are most suited, as they decrease the posttest probability to 18% and 19%, respectively. Conclusion: The simultaneous onset or increase and decrease of tinnitus and neck or jaw pain and the influence of certain postures are most suited to use as a single criterion for identifying patients with a somatic influence on their tinnitus. On the other hand, the absence of neck pain or tension in the neck extensor muscles is valid criterion to rule out a somatic influence. Additional analysis is needed to identify clusters of symptoms and criteria to further aid ST diagnosis.
Effects of respiratory muscle training in soccer players: a systematic review with a meta-analysis

Abstract Respiratory muscle training can improve strength and reduce respiratory muscle fatigue during high-intensity exercise. Little is known about the existing evidence in soccer players. A systematic review with a meta-analysis was performed to analyse the existing evidence on the effects of respiratory muscle training in soccer players. Two independent researchers reviewed 17 databases until July 2019. Inclusion criteria were controlled clinical trials (randomised or not), soccer players (professional or recreational), females and/or males, and respiratory muscle training compared with simulated or regular training groups. The methodological quality and quality of evidence were evaluated with the Cochrane Collaboration Tool and GRADE score, respectively. Statistical analysis was performed using the integral meta-analysis 3.3. 070. Nine studies met the eligibility criteria. The meta-analysis was performed for eight variables related to respiratory muscle function, lung function and sports performance. Respiratory muscle training provided a significant improvement compared with simulated or regular training in maximal inspiratory buccal pressure (6 studies, SDM = 0.89; 95 % CI = 0.42, 1.35) and maximum consumption of oxygen (3 studies, SDM = 0.92; 95 % CI = 0.24; 1.61). No significant improvements were observed for other variables. The quality of the evidence was rated as low or very low.
Three-dimensional stochastic simulation of chemoattractant-mediated excitability in cells

During the last decade, a consensus has emerged that the stochastic triggering of an excitable system drives pseudopod formation and subsequent migration of amoeboid cells. The presence of chemoattractant stimuli alters the threshold for triggering this activity and can bias the direction of migration. Though noise plays an important role in these behaviors, mathematical models have typically ignored its origin and merely introduced it as an external signal into a series of reaction-diffusion equations. Here we consider a more realistic description based on a reaction-diffusion master equation formalism to implement these networks. In this scheme, noise arises naturally from a stochastic description of the various reaction and diffusion terms. Working on a three-dimensional geometry in which separate compartments are divided into a tetrahedral mesh, we implement a modular description of the system, consisting of G-protein coupled receptor signaling (GPCR), a local excitation-global inhibition mechanism (LEGI), and signal transduction excitable network (STEN). Our models implement detailed biochemical descriptions whenever this information is available, such as in the GPCR and G-protein interactions. In contrast, where the biochemical entities are less certain, such as the LEGI mechanism, we consider various possible schemes and highlight the differences between them. Our simulations show that even when the LEGI mechanism displays perfect adaptation in terms of the mean level of proteins, the variance shows a dose-dependence. This differs between the various models considered, suggesting a possible means for determining experimentally among the various potential networks. Overall, our simulations recreate temporal and spatial patterns observed experimentally in both wild-type and perturbed cells, providing further evidence for the excitable system paradigm. Moreover, because of the overall importance and ubiquity of the modules we consider, including GPCR signaling and adaptation, our results will be of interest beyond the field of directed migration.
Complete Genome Sequence of a Third- and Fourth-Generation Cephalosporin-Resistant Comamonas kerstersii Isolate

Here, we report the complete genome sequence of Comamonas kerstersii 3132976, a strain isolated from a human rectal swab sample in Switzerland. The isolate was resistant to third- and fourth-generation cephalosporins and possessed a novel class A β-lactamase gene. The complete genome is 3,693,404 bp long with a GC content of 59.4%. ABSTRACT Here, we report the complete genome sequence of Comamonas kerstersii 3132976, a strain isolated from a human rectal swab sample in Switzerland. The isolate was resistant to third- and fourth-generation cephalosporins and possessed a novel class A β-lactamase gene. The complete genome is 3,693,404 bp long with a GC content of 59.4%.
Correction for Zhou et al., Scaffold association factor B (SAFB) is required for expression of prenyltransferases and RAS membrane association

, Inhibiting membrane association of RAS has long been considered a rational approach to anticancer therapy, which led to the development of farnesyltransferase inhibitors (FTIs). However, FTIs proved ineffective against KRAS -driven tumors. To reveal alternative therapeutic strategies, we carried out a genome-wide CRISPR-Cas9 screen designed to identify genes required for KRAS4B membrane association. We identified five enzymes in the prenylation pathway and SAFB, a nuclear protein with both DNA and RNA binding domains. Silencing SAFB led to marked mislocalization of all RAS isoforms as well as RAP1A but not RAB7A, a pattern that phenocopied silencing FNTA , the prenyltransferase α subunit shared by farnesyltransferase and geranylgeranyltransferase type I. We found that SAFB promoted RAS membrane association by controlling FNTA expression. SAFB knockdown decreased GTP loading of RAS, abrogated alternative prenylation, and sensitized RAS -mutant cells to growth inhibition by FTI. Our work establishes the prenylation pathway as para- mount in KRAS membrane association, reveals a regulator of prenyltransferase expression, and suggests that reduction in FNTA expression may enhance the efficacy of FTIs.
Efficient interspecies transmission of synthetic prions

Prions are comprised solely of PrPSc, the misfolded self-propagating conformation of the cellular protein, PrPC. Synthetic prions are generated in vitro from minimal components and cause bona fide prion disease in animals. It is unknown, however, if synthetic prions can cross the species barrier following interspecies transmission. To investigate this, we inoculated Syrian hamsters with murine synthetic prions. We found that all the animals inoculated with murine synthetic prions developed prion disease characterized by a striking uniformity of clinical onset and signs of disease. Serial intraspecies transmission resulted in a rapid adaptation to hamsters. During the adaptation process, PrPSc electrophoretic migration, glycoform ratios, conformational stability and biological activity as measured by protein misfolding cyclic amplification remained constant. Interestingly, the strain that emerged shares a strikingly similar transmission history, incubation period, clinical course of disease, pathology and biochemical and biological features of PrPSc with 139H, a hamster adapted form of the murine strain 139A. Combined, these data suggest that murine synthetic prions are comprised of bona fide PrPSc with 139A-like strain properties that efficiently crosses the species barrier and rapidly adapts to hamsters resulting in the emergence of a single strain. The efficiency and specificity of interspecies transmission of murine synthetic prions to hamsters, with relevance to brain derived prions, could be a useful model for identification of structure function relationships between PrPSc and PrPC from different species.
Response to Vaccination in Infants Exposed to Antitumor Necrosis Factor Alpha In Utero

Supplemental Digital Content is available in the text. In this retrospective cohort study, the response to routinely administered Haemophilus influenzae type B vaccine, pneumococcal and pertussis vaccinations in 27 children exposed to antitumor necrosis factor alpha (anti-TNFα) during pregnancy was measured. The overall vaccination response seems comparable for children exposed to anti-TNFα and healthy infants. After primary vaccination series, inadequate response was present in some patients and might be related to exposure to anti-TNFα.