Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of genes required for lipoteichoic acid glycosylation predicts two distinct mechanisms for wall teichoic acid glycosylation

The bacterial cell wall is an important and highly complex structure that is essential for bacterial growth because it protects bacteria from cell lysis and environmental insults. A typical Gram-positive bacterial cell wall is composed of peptidoglycan and the secondary cell wall polymers, wall teichoic acid (WTA) and lipoteichoic acid (LTA). In many Gram-positive bacteria, LTA is a polyglycerol-phosphate chain that is decorated with d-alanine and sugar residues. However, the function of and proteins responsible for the glycosylation of LTA are either unknown or not well-characterized. Here, using bioinformatics, genetic, and NMR spectroscopy approaches, we found that the Bacillus subtilis csbB and yfhO genes are essential for LTA glycosylation. Interestingly, the Listeria monocytogenes gene lmo1079, which encodes a YfhO homolog, was not required for LTA glycosylation, but instead was essential for WTA glycosylation. LTA is polymerized on the outside of the cell and hence can only be glycosylated extracellularly. Based on the similarity of the genes coding for YfhO homologs that are required in B. subtilis for LTA glycosylation or in L. monocytogenes for WTA glycosylation, we hypothesize that WTA glycosylation might also occur extracellularly in Listeria species. Finally, we discovered that in L. monocytogenes, lmo0626 (gtlB) was required for LTA glycosylation, indicating that the encoded protein has a function similar to that of YfhO, although the proteins are not homologous. Together, our results enable us to propose an updated model for LTA glycosylation and also indicate that glycosylation of WTA might occur through two different mechanisms in Gram-positive bacteria.
Evidence of Benefit of Telerehabitation After Orthopedic Surgery: A Systematic Review

Background In addition to traditional physiotherapy, studies based on telerehabilitation programs have published the results of effectiveness, validity, noninferiority, and important advantages in some neurological, cognitive, and musculoskeletal disorders, providing an opportunity to define new social policies and interventions. Objectives The aim of this systematic review is to investigate the effects of telerehabilitation after surgical procedures on orthopedic conditions as well as to describe how interventions are designed and to determine whether telerehabilitation is comparable with conventional methods of delivery. This systematic review summarizes the levels of evidence and grades of recommendation regarding telerehabilitation intervention (synchronous or asynchronous provided via the telerehabilitation medium, either in conjunction with, or in isolation of, other treatment interventions) after surgical procedures on orthopedic conditions. Methods Study quality was assessed using the Physiotherapy Evidence Database (PEDro) scores and grade of recommendation following the recommendation of the Oxford Centre for Evidence-Based Medicine. Results We found 3 studies with PEDro scores between 6 and 8, which is considered as level 1 evidence (good; 20% [3/15]), 4 studies with a score of 5, which is considered as level 2 evidence (acceptable; 27% [4/15]), and the remaining 8 studies had scores of 4 or less, which is considered (poor; 53% [8/15]). A total of 1316 participants received telerehabilitation intervention in the selected studies, where knee and hip replacement were 75% of all the studies. Strong and moderate grades of evidence (grade of recommendation A–B) were found in knee and hip replacement interventions. Studies on the upper limb were 25% of the studies, but only 1 study presented a moderate grade of evidence (grade of recommendation B) and the rest were of poor methodological quality with weak evidence (grade of recommendation C). Conclusions Conclusive evidence on the efficacy of telerehabilitation for treatment after an orthopedic surgery, regardless of pathology, was not obtained. We found strong evidence in favor of telerehabilitation in patients following total knee and hip arthroplasty and limited evidence in the upper limb interventions (moderate and weak evidence). Future research needs to be more extensive and conclusive. To the best of the authors’ knowledge, this is the first attempt at evaluating the quality of telerehabilitation intervention research after surgical procedures on orthopedic conditions in a systematic review. Clinical messages and future research recommendations are included in the review.
Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation

Constant optogenetic stimulation targeting both pyramidal cells and inhibitory interneurons has recently been shown to elicit propagating waves of gamma-band (40–80 Hz) oscillations in the local field potential of non-human primate motor cortex. The oscillations emerge with non-zero frequency and small amplitude—the hallmark of a type II excitable medium—yet they also propagate far beyond the stimulation site in the manner of a type I excitable medium. How can neural tissue exhibit both type I and type II excitability? We investigated the apparent contradiction by modeling the cortex as a Wilson-Cowan neural field in which optogenetic stimulation was represented by an external current source. In the absence of any external current, the model operated as a type I excitable medium that supported propagating waves of gamma oscillations similar to those observed in vivo. Applying an external current to the population of inhibitory neurons transformed the model into a type II excitable medium. The findings suggest that cortical tissue normally operates as a type I excitable medium but it is locally transformed into a type II medium by optogenetic stimulation which predominantly targets inhibitory neurons. The proposed mechanism accounts for the graded emergence of gamma oscillations at the stimulation site while retaining propagating waves of gamma oscillations in the non-stimulated tissue. It also predicts that gamma waves can be emitted on every second cycle of a 100 Hz oscillation. That prediction was subsequently confirmed by re-analysis of the neurophysiological data. The model thus offers a theoretical account of how optogenetic stimulation alters the excitability of cortical neural fields.
Identification of COL4A1 as a potential gene conferring trastuzumab resistance in gastric cancer based on bioinformatics analysis

Trastuzumab, the first targeted antibody against human epidermal growth factor receptor 2 (HER2), has been used to treat gastric cancer patients with HER2 overexpression. However, trastuzumab resistance often occurs following an initial period of benefits, and the underlying mechanisms remain largely unclear. The present study revealed that collagen type IV α1 chain (COL4A1), whose expression is upregulated in gastric cancer tissues and trastuzumab-resistant gastric cancer cells, may potentially confer trastuzumab resistance in gastric cancer. By performing bioinformatics analysis of 2 microarray datasets, the present study initially identified COL4A1, overexpressed in gastric cancer tissues and trastuzumab-resistant gastric cancer cells, as a potential candidate for inducing trastuzumab resistance. The drug resistance function of COL4A1 in gastric cancer was then validated by performing protein/gene interactions and biological process annotation analyses, and further validated by analyzing the functionality of microRNAs that target COL4A1 mRNA. Collectively, these data indicated that COL4A1 may confer trastuzumab resistance in gastric cancer.
Promoter methylation patterns of ABCB1, ABCC1 and ABCG2 in human cancer cell lines, multidrug-resistant cell models and tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients

Overexpression of ABCB1, ABCC1 and ABCG2 in tumor tissues is considered a major cause of limited efficacy of anticancer drugs. Gene expression of ABC transporters is regulated by multiple mechanisms, including changes in the DNA methylation status. Most of the studies published so far only report promoter methylation levels for either ABCB1 or ABCG2, and data on the methylation status for ABCC1 are scarce. Thus, we determined the promoter methylation patterns of ABCB1, ABCC1 and ABCG2 in 19 human cancer cell lines. In order to contribute to the elucidation of the role of DNA methylation changes in acquisition of a multidrug resistant (MDR) phenotype, we also analyzed the promoter methylation patterns in drug-resistant sublines of the cancer cell lines GLC-4, SW1573, KB-3-1 and HL-60. In addition, we investigated if aberrant promoter methylation levels of ABCB1, ABCC1 and ABCG2 occur in tumor and tumor-surrounding tissues from breast cancer patients. Our data indicates that hypomethylation of the ABCC1 promoter is not cancer type-specific but occurs in cancer cell lines of different origins. Promoter methylation was found to be an important mechanism in gene regulation of ABCB1 in parental cancer cell lines and their drug-resistant sublines. Overexpression of ABCC1 in MDR cell models turned out to be mediated by gene amplification, not by changes in the promoter methylation status of ABCC1. In contrast to the promoters of ABCC1 and ABCG2, the promoter of ABCB1 was significantly higher methylated in tumor tissues than in tumor-adjacent and tumor-distant tissues from breast cancer patients.
Desert dust suppressing precipitation: A possible desertification feedback loop

The effect of desert dust on cloud properties and precipitation has so far been studied solely by using theoretical models, which predict that rainfall would be enhanced. Here we present observations showing the contrary; the effect of dust on cloud properties is to inhibit precipitation. Using satellite and aircraft observations we show that clouds forming within desert dust contain small droplets and produce little precipitation by drop coalescence. Measurement of the size distribution and the chemical analysis of individual Saharan dust particles collected in such a dust storm suggest a possible mechanism for the diminished rainfall. The detrimental impact of dust on rainfall is smaller than that caused by smoke from biomass burning or anthropogenic air pollution, but the large abundance of desert dust in the atmosphere renders it important. The reduction of precipitation from clouds affected by desert dust can cause drier soil, which in turn raises more dust, thus providing a possible feedback loop to further decrease precipitation. Furthermore, anthropogenic changes of land use exposing the topsoil can initiate such a desertification feedback process.
Versatile modular electronics for rapid design and development of humanoid robotic subsystems

The development of humanoid robots is a highly complex process. Consisting of numerous subsystems which need to be combined for actuation such as electric motors or hydraulic valves, as well as sophisticated sensors and sensing units like skin. In this paper, we introduce our strategy to simplify the development of these complex electrical systems by using modular components. We took a generalised approach in the realisation of our design. By utilising a standard module based around a Field Programmable Gate Array (FPGA) it will be shown that our design is effective in terms of flexibility as well as scalability while at the same time ensuring compatibility over multiple generations and types of humanoid robotic systems. In this paper, we will present a few examples of humanoid subsystems showing the benefits of this approach.
Hemoglobin Glycation Index Is Associated With Cardiovascular Diseases in People With Impaired Glucose Metabolism

Context There is a substantial interindividual variation in the association between glycated hemoglobin (HbA1c) and plasma glucose concentrations. Its impact on cardiovascular disease (CVD) has not been comprehensively evaluated. Objective We examined associations between interindividual variations in HbA1c, which was estimated as the hemoglobin glycation index (HGI), and CVD. Design, Setting, and Participants We performed a cross-sectional analysis with 1248 treatment-naïve subjects with prediabetes or diabetes. The HGI was defined as the measured HbA1c minus predicted HbA1c, which was calculated from the linear relationship between HbA1c and fasting plasma glucose levels. Main Outcome Measures The prevalence of composite and individual CVDs including coronary artery disease (CAD), stroke, and peripheral artery disease (PAD). Results The overall prevalence of composite CVD was 10.3% and individual prevalences of CAD, stroke, and PAD were 5.7%, 5.1%, and 1.3%, respectively. All prevalences significantly increased from the first to third tertile of HGI. In multivariate analysis, the highest HGI tertile was independently associated with composite CVD [odds ratio (95% confidence interval): 2.81 (1.59-4.98)], and individual CAD [2.30 (1.12-4.73)], stroke [3.40 (1.50-7.73)], and PAD [6.37 (1.18-34.33)] after adjustment for other CVD risk factors including HbA1c levels. Two consecutive measurements of HGI obtained on different days showed good correlation (r = 0.651, P < 0.001) and high concordance rate in the tertile classification (69.1%). Conclusions High HGI was independently associated with overall and individual CVDs. This result suggests that discrepancy between HbA1c and fasting glucose levels can reflect vascular health in subjects with impaired glucose metabolism.
SOS-Convex Lyapunov Functions and Stability of Difference Inclusions

We introduce the concept of sos-convex Lyapunov functions for stability analysis of both linear and nonlinear difference inclusions (also known as discrete-time switched systems). These are polynomial Lyapunov functions that have an algebraic certificate of convexity and that can be efficiently found via semidefinite programming. We prove that sos-convex Lyapunov functions are universal (i.e., necessary and sufficient) for stability analysis of switched linear systems. We show via an explicit example however that the minimum degree of a convex polynomial Lyapunov function can be arbitrarily higher than a non-convex polynomial Lyapunov function. In the case of switched nonlinear systems, we prove that existence of a common non-convex Lyapunov function does not imply stability, but existence of a common convex Lyapunov function does. We then provide a semidefinite programming-based procedure for computing a full-dimensional subset of the region of attraction of equilibrium points of switched polynomial systems, under the condition that their linearization be stable. We conclude by showing that our semidefinite program can be extended to search for Lyapunov functions that are pointwise maxima of sos-convex polynomials.
Microglia–Neuron Communication in Epilepsy

Epilepsy has remained a significant social concern and financial burden globally. Current therapeutic strategies are based primarily on neurocentric mechanisms that have not proven successful in at least a third of patients, raising the need for novel alternative and complementary approaches. Recent evidence implicates glial cells and neuroinflammation in the pathogenesis of epilepsy with the promise of targeting these cells to complement existing strategies. Specifically, microglial involvement, as a major inflammatory cell in the epileptic brain, has been poorly studied. In this review, we highlight microglial reaction to experimental seizures, discuss microglial control of neuronal activities, and propose the functions of microglia during acute epileptic phenotypes, delayed neurodegeneration, and aberrant neurogenesis. Future research that would help fill in the current gaps in our knowledge includes epilepsy‐induced alterations in basic microglial functions, neuro–microglial interactions during chronic epilepsy, and microglial contribution to developmental seizures. Studying the role of microglia in epilepsy could inform therapies to better alleviate the disease. GLIA 2016;65:5–18
Fast Algorithms for Structured Sparsity (ICALP 2015 Invited Tutorial)

Sparsity has become an important tool in many mathematical sciences such as statistics, machine learning, and signal processing. While sparsity is a good model for data in many applications, data often has additional structure that goes beyond the notion of “standard” sparsity. In many cases, we can represent this additional information in a structured sparsity model. Recent research has shown that structured sparsity can improve the sample complexity in several applications such as compressive sensing and sparse linear regression. However, these improvements come at a computational cost, as the data needs to be “fitted” so it satisfies the constraints specified by the sparsity model. In this survey, we introduce the concept of structured sparsity, explain the relevant algorithmic challenges, and briefly describe the best known algorithms for two sparsity models. On the way, we demonstrate that structured sparsity models are inherently combinatorial structures, and employing structured sparsity often leads to interesting algorithmic problems with strong connections to combinatorial optimization and discrete algorithms. We also state several algorithmic open problems related to structured sparsity.
Analysis of Transient Behavior in Linear Differential Algebraic Equations Dr .

The linearized Navier-Stokes equations form a type of system called a differential algebraic equation (DAE). These equations impose both algebraic and differential constraints on the solution, and present significant challenges to solving. This paper discusses a method for solving DAEs by the Schur factorization to avoid some of the obstacles that are typically present. We also investigate the transient behavior of the solution using results from pseudospectral theory, which will help us understand whether the solution to the linearized Navier-Stokes system will become turbulent if its steady state is disturbed. If a flow does indeed grow substantially in energy, then we must be cautious about using the linearized model. Thus, having information about transient behavior is quite instructive.
The Open University ’ s repository of research publications and other research outputs Topology aware adaptive security Conference Item

Adaptive security systems aim to protect valuable assets in the face of changes in their operational environment. They do so by monitoring and analysing this environment, and deploying security functions that satisfy some protection (security, privacy, or forensic) requirements. In this paper, we suggest that a key characteristic for engineering adaptive security is the topology of the operational environment, which represents a physical and/or a digital space including its structural relationships, such as containment, proximity, and reachability. For adaptive security, topology expresses a rich representation of context that can provide a system with both structural and semantic awareness of important contextual characteristics. These include the location of assets being protected or the proximity of potentially threatening agents that might harm them. Security-related actions, such as the physical movement of an actor from a room to another in a building, may be viewed as topological changes. The detection of a possible undesired topological change (such as an actor possessing a safe’s key entering the room where the safe is located) may lead to the decision to deploy a particular security control to protect the relevant asset. This position paper advocates topology awareness for more effective engineering of adaptive security. By monitoring changes in topology at runtime one can identify new or changing threats and attacks, and deploy adequate security controls accordingly. The paper elaborates on the notion of topology and provides a vision and research agenda on its role for systematically engineering adaptive security systems.
Effects Of A Neuromuscular Dentistry-designed Mouthguard On Muscular Endurance And Anaerobic Power: 943

Athletes of various sports are required to utilize mouthguards during practice and competitions for protection against orofacial and dental injuries, regardless of the effects on performance. Recent advances in neuromuscular dentistry have led to the development of a mouthguard touted also to enhance the performance through jaw realignment. The purpose of this study was to compare the effects of a neuromuscular dentistry-based mouthguard to a standard, custom-fitted mouthguard (CFM) on muscular endurance, anaerobic power and anaerobic capacity in competitive athletes. Professional and Division I college athletes (n 1⁄4 22, Mweight 1⁄4 86.2 ^ 3.1 kg) participated in this double-blind, crossover study. Subjects were randomly assigned to order of use of either the experimental (Pure Power Mouthguard (PPM)) or the traditional CFM. Subjects completed two separate sessions in which they completed three performance tests, which included vertical jump (VJ), bench press (BP) and a 30 s Wingate anaerobic test (WAnT) þ eight 10 s intervals, while wearing the assigned mouthguard. Significantly better performance was found for PPM compared with CFM for VJ (67.6 þ 9.4 cm vs. 65.3 þ 8.6 cm; P 1⁄4 0.003), 30 s WAnT peak power (11.6 ^ 1.7 W kg vs. 11.1 ^ 1.5 W kg, P 1⁄4 0.038), average peak power for WAnT þ intervals (10.6 ^ 1.4 W kg vs. 10.1 ^ 1.2 W kg, P 1⁄4 0.025) and average mean power for WAnT þ intervals (9.0 ^ 1.1 W kg vs. 8.7 ^ 1.0 W kg, P 1⁄4 0.034). There were no significant differences for either BP or 30 s WAnT mean power (P . 0.48). Compared with a CFM, a neuromuscular dentistry-based mouthguard appears to enhance peak power output, performance and repeated maximal efforts. When required to wear a mouthguard, athletes may benefit from wearing a neuromuscular dentistry-designed mouthguard compared with a CFM.
Digital dissection of the masticatory muscles of the naked mole-rat, Heterocephalus glaber (Mammalia, Rodentia)

The naked mole-rat, Heterocephalus glaber, of the family Bathyergidae is a subterranean rodent that feeds on underground roots and tubers and digs extensive tunnel systems with its incisors. It is a highly unusual mammal with regard to its social structure, longevity, pain insensitivity and cancer resistance, all of which have made it the subject of a great deal of research in recent years. Yet, much of the basic anatomy of this species remains undocumented. In this paper, we describe the morphology of the jaw-closing musculature of the naked mole-rat, as revealed by contrast-enhanced micro-computed tomography. This technique uses an iodine stain to enable the imaging of soft tissues with microCT. The iodine-enhanced scans were used to create 3D reconstructions of the naked mole-rat masticatory muscles from which muscle masses were calculated. The jaw-closing musculature of Heterocephalus glaber is relatively very large compared to other rodents and is dominated by the superficial masseter, the deep masseter and the temporalis. The temporalis in particular is large for a rodent, covering the entirety of the braincase and much of the rear part of the orbit. The morphology of the masseter complex described here differs from two other published descriptions of bathyergid masticatory muscles, but is more similar to the arrangement seen in other rodent families. The zygomaticomandibularis (ZM) muscle does not protrude through the infraorbital foramen on to the rostrum and thus the naked mole-rat should be considered protrogomorphous rather than hystricomorphous, and the morphology is consistent with secondarily lost hystricomorphy as has been previously suggested for Bathyergidae. Overall, the morphology of the masticatory musculature indicates a species with a high bite force and a wide gape–both important adaptations for a life dominated by digging with the incisors.