Miracle-dz/UniFAR-FTUs huggingface dataset:
MgrA Negatively Regulates Biofilm Formation and Detachment by Repressing the Expression of psm Operons in Staphylococcus aureus

Staphylococcus aureus is a human and animal pathogen that can cause biofilm-associated infections. PSMs have multiple functions in biofilm development and virulence in staphylococcal pathogenesis. This study has revealed that MgrA can negatively regulate psm expression by binding directly to the promoter regions of psm operons. Furthermore, our results show that MgrA can modulate biofilm structuring and development by repressing the production of PSMs in S. aureus. Our findings provide novel insights into the regulatory mechanisms of S. aureus psm gene expression, biofilm development, and pathogenesis. ABSTRACT Phenol-soluble modulins (PSMs) are amphipathic peptides that are produced by staphylococci and play important roles in Staphylococcus aureus biofilm formation and dissemination. Although the multiple functions of PSMs have been recognized, the regulatory mechanisms controlling the expression of psm operons remain largely unknown. In this study, we identified MgrA in a DNA pulldown assay and further demonstrated, by electrophoretic mobility shift assays and DNase I footprinting assays, that MgrA could bind specifically to the promoter regions of psm operons. We then constructed an isogenic mgrA deletion strain and compared biofilm formation and detachment in the wild-type and isogenic mgrA deletion strains. Our results indicated that biofilm formation and detachment were significantly increased in the mgrA mutant strain. Real-time quantitative reverse transcription-PCR data indicated that MgrA repressed the transcription of psm operons in cultures and biofilms, suggesting that MgrA is a negative regulator of psm expression. Furthermore, we analyzed biofilm formation by the psm mutant strains, and we found that PSMs promoted biofilm structuring and development in the mgrA mutant strain. These findings reveal that MgrA negatively regulates biofilm formation and detachment by repressing the expression of psm operons through direct binding to the psm promoter regions. IMPORTANCE Staphylococcus aureus is a human and animal pathogen that can cause biofilm-associated infections. PSMs have multiple functions in biofilm development and virulence in staphylococcal pathogenesis. This study has revealed that MgrA can negatively regulate psm expression by binding directly to the promoter regions of psm operons. Furthermore, our results show that MgrA can modulate biofilm structuring and development by repressing the production of PSMs in S. aureus. Our findings provide novel insights into the regulatory mechanisms of S. aureus psm gene expression, biofilm development, and pathogenesis.
Reliability of Ankle–Foot Complex Isokinetic Strength Assessment Using the Isomed 2000 Dynamometer

For quantifying muscle strength in clinical and research practice, establishing the reliability of measurements, specifically to the procedures used, is essential for credible findings. The objective was to establish the reliability of isokinetic measurement of ankle plantar and dorsal flexors (PF/DF) and invertors and evertors (INV/EV) on an IsoMed 2000 dynamometer. Twenty healthy subjects (10 males, 10 females, mean age: 23.1 ± 3.1 years) completed an isokinetic measurement session. The intraclass correlation coefficient (ICC) and standard error of measurement were assessed for peak torque and work of ankle PF/DF (concentric and eccentric) and INV/EV (concentric) for the preferred and nonpreferred limb. Standardized isokinetic measurements of reciprocal PF/DF and INV/EV muscle actions were associated with ICC ranging from 0.77 to 0.98 for the majority of observed parameters. The exception was work in the eccentric mode in the ankle DF and peak torque in the concentric mode in the ankle INV on the preferred limb, where ICC ranged from 0.64 to 0.71. The IsoMed 2000 isokinetic dynamometer can be reliably employed in future studies for reciprocal ankle PF/DF and INV/EV assessment in healthy adult subjects after implementation of a familiarization session.
Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates

The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.
Asteroids in the 2 : 1 resonance with Jupiter: dynamics and size distribution

The 2 : 1 mean motion resonance with Jupiter in the main asteroid belt is associated to one of the largest Kirkwood gaps: the so-called Hecuba gap. Centred at about 3.3 au, the Hecuba gap is characterized by a very small number of asteroids when compared to its neighbourhoods. Long-term instabilities caused by resonant planetary perturbations are thought to be responsible for the almost lack of bodies in the gap. However, current observations suggest a significant population of asteroids in the 2 : 1 resonance. The origin of these bodies is puzzling. Do we observe the few lucky survivors of a much larger population formed in the resonance in primordial times? Do the resonant orbits of the observed asteroids have a more recent origin? To understand these issues, we performed numerical simulations of the orbital evolution of both real and fictitious asteroids in the 2 : 1 resonance. Our models include gravitational perturbations by the major planets. Based on the dynamical lifetimes, we classify the observed resonant asteroids into three groups: (i) the Zhongguos, which seems to be stable over the age of the Solar system; (ii) the Griquas, with typical lifetimes in the resonance of the order of some 100 Myr; and (iii) the strongly unstable asteroids, which escape from the resonance in a few 10 Myr or less. Our simulations confirm that the Zhongguos may be primordial asteroids, located in the 2 : 1 resonance since the formation of the Solar system. The dynamics of the Zhongguos constitute a typical example of slow chaotic evolution confined to a small region of the resonance. On the other hand, an analysis of the size distribution of the Zhongguos reveals a rather steep distribution. Such a distribution would not be compatible with a long collisional history, rather suggesting that the Zhongguos are likely to be the outcomes of a recent breakup event. Thus, while dynamics points toward a primordial resonant origin, the size distribution rather points to a recent origin. A possible explanation is that the Zhongguos formed by the cratering/ fragmentation of a large resonant or near-resonant asteroid.
Effectiveness of amoxicillin alone in the treatment of uncomplicated acute otitis media: a systematic review protocol

Introduction Amoxicillin is the first-line antibiotic recommended by most scientific societies for the treatment of uncomplicated acute otitis media (AOM) in children and adults. In low-income and middle-income countries however, absence of setting-specific recommendations and antibiotic resistance, promoted by higher population density and over-the-counter antibiotic availability, could hamper the effectiveness of amoxicillin. We aim to provide updated information to enable evidence-based decisions for first-line therapy of uncomplicated AOM in our setting. Methods and analysis We will conduct a systematic review of all randomised controlled trials on the clinical effectiveness of amoxicillin for the treatment of uncomplicated AOM in children above 6 months and adults. The search will include studies published from the generation of the included databases to 31 December 2017. Study selection will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and study quality will be assessed by the Risk of Bias Assessment Tool from the Cochrane Handbook for randomised trials. A meta-analysis will be conducted for homogeneous studies, eventually, using the fixed-effect model. Subgroup analysis will include age groups, amoxicillin dosage, treatment duration, effectiveness criteria, time of trial realisation, study quality and region of the world involved. Ethics and dissemination Formal ethical approval is not required, as primary data will not be collected. The results will be disseminated through a peer-reviewed publication and presented at scientific meetings. PROSPERO registration number CRD42017080029.
Observations of the Effects of Angiotensin II Receptor Blocker on Angiotensin II-Induced Morphological and Mechanical Changes in Renal Tubular Epithelial Cells Using Atomic Force Microscopy

Objective Angiotensin II (Ang II) plays a profibrotic role in the kidneys. Although many pathways of Ang II have been discovered, the morphological and mechanical aspects have not been well investigated. We observed the changes in tubular epithelial cells (TECs) after Ang II treatment with or without Ang II receptor blockers (ARBs) using atomic force microscopy (AFM). Methods TECs were stimulated with Ang II with or without telmisartan, PD123319, and blebbistatin. AFM was performed to measure the cellular stiffness, cell volume, and cell surface roughness. Epithelial to mesenchymal transition markers were determined via immunocytochemistry. Results After Ang II stimulation, cells transformed to a flattened and elongated mesenchymal morphology. Cell surface roughness and volume significantly increased in Ang II treated TECs. Ang II also induced an increase in phospho-myosin light chain and F-actin and a decrease in E-cadherin. Ang II coincubation with either telmisartan or blebbistatin attenuated these Ang II-induced changes. Conclusion We report, for the first time, the use of AFM in directly observing the changes in TECs after Ang II treatment with or without ARBs. Simultaneously, we successfully measured the selective effect of PD123319 or blebbistatin. AFM could be a noninvasive evaluating strategy for cellular processes in TECs.
Validation and Assessment of Osteoporosis Self-Efficacy Among Iraqi General Population

Background: Poor quality of life, fractures and disability are the consequences of preventable osteoporosis. Objectives: The aims of this study were to validate and assess Osteoporosis Self-efficacy Scale (OSES-A) Arabic version among Iraqi general population. Methods: A cross-sectional study with a random cluster sampling method from the community was used. Forward–backward-forward translation method was used to translate the questionnaire from English to Arabic. Beside OSES-A, Osteoporosis Knowledge Tool (OKT) and Osteoporosis Health Belief Scale (OHBS) Arabic versions were used to assess osteoporosis preventive behaviours. Results: The results showed good face validity and reliability. The construct validity showed two factors which explain 80.86% of the variance. In addition, the result showed low self-efficacy score (658.43±222.014) with 83.33% were found to have low OSES-A level. There were significant associations between age, gender, and self-reported osteoporosis with OSES-A levels. In addition, there were significant differences between age, gender, marital status, family history of osteoporosis, self-reported osteoporosis and osteoporosis diagnosis or screening in relation to total OSES-A scores. Moreover, there were positive correlations between the OSES-A total score with total knowledge and health belief. Multivariate analysis revealed that OKT levels, OHBS levels, age and gender were predictors for OSES-A levels. Conclusion: This study showed good cultural adaptation and psychometric properties of OSES-A tool and could be used in any osteoprotective educational program.
Multilocus Sequence Analysis of Root Nodule Bacteria Associated with Lupinus spp. and Glycine max

Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule bacteria associated with Lupinus and soybean. Out of 17 bacterial strains analyzed, 13 strains isolated from root nodules of Lupinus spp. were obtained from the National Rhizobium Germplasm Resource Collection, USDA. Additionally, two strains of root-nodule bacteria isolated each from native lupinus and domestic soybean were examined. Sequences of the 16S rRNA gene and three house-keeping genes (atpD, dnaK and glnII) were used. All the reference genes were retrieved from the existing complete genome sequences only. The clustering of 12 of the strains was consistent among single and concatenated gene trees, but not USDA strains 3044, 3048, 3504, 3715, and 3060. According to the concatenated phylogeny, we suggest that USDA 3040, 3042, 3044, 3048, 3051, 3060, 3504, 3709 and 3715 are Bradyrhizobium, USDA 3063 and 3717 are Mesorhizobium, USDA 3043 is Burkholderia and USDA 3057a is Microvirga. The two strains isolated from native lupines in this study are Burkholderia and Rhizobium, whereas the two from domestic soybean are Bradyrhizobium. This study emphasizes the robustness of MLSA, the diversity of bacterial species that are capable of nodulating lupine and the substantial capability of Burkholderia spp. to colonize lupine root nodules.
Awareness and current knowledge of Parkinson’s disease: a neurodegenerative disorder

Abstract Context: Parkinson’s disease (PD) is the second common progressive neurodegenerative disease, distressing older men and is prevalent Worldwide. Objectives: This article is aimed to review the epidemiology, etiology, pathogenesis, clinical manifestation, diagnosis and management of PD. Methods: A google search was performed to recognise studies that review the characteristics of PD. Search terms included ‘Parkinson’s disease’, ‘epidemiology’, ‘etiology’, ‘pathogenesis’, ‘clinical manifestations’, ‘diagnosis’ and ‘management of Parkinson disease’. Results: PD is linked to factors such as environmental chemicals, aging, family history and pesticide exposure such as the use of synthetic heroin. PD is characterised clinically by tremors at rest, postural instability, expressionless countenance, lead pipe rigidity and less commonly cognitive impairment. After 60 years of age, PD is commonly prevalent in 1–% of the population, no racial differences are apparent, but the prevalence of PD is more common in men than women. There has also been a better understanding that the disorder may be linked with major non-motor trouble in addition to the additional generally recognised motor complications. There are various management options for the timely management of PD. As the ailment advances, further management strategies are existing; however, the management of non-motor manifestations and late stage motor complications remains mainly testing and will advantage from additional clinical studies. Conclusions: In this article, we have discussed current progress in the understanding of the epidemiology, clinical manifestations, pathogenesis and management strategies of the disease.
The Patello-Femoral Joint Degeneration and the Shape of the Patella in the Population Needing an Arthroscopic Procedure

Background: the main goal of the study was to investigate the prevalence of the articular cartilage defects (ACD) in the patellofemoral (PF) region of the knee joint based on the anatomical shapes of patella and its impact on the level of physical activity in the population needing arthroscopic procedures for all types of pathologies in the knee. Methods: The articular cartilage status of the PF region was obtained from 1098 arthroscopic procedures of the knee joint. The ACD were correlated to Wiberg’s shape of the patella and classified according to the degree, size and depth of the ACD in the PF region using the ICRS (International Cartilage Repair Society) system: group I consisting of patients with Wiberg type I shape (W1), group II—patients with Wiberg type II shape (W2) and group III—patients with Wiberg type III shape (W3). The Tegner physical activity scale was used to evaluate the physical activity of the patients. Results: The mean of ACD size (PF region) in the W3 group was 3.10 ± 0.99 cm2, which was a statistically significantly larger area in comparison with the W1 (1.90 ± 0.63 cm2; p < 0.0000) and W2 (1.95 ± 0.71 cm2; p < 0.0000). The patients from the W3 group (mean 3.10 ± 0.99) were less physically active (<4 Tegner) compared to the W2 group (mean of 4.48 ± 0.88; p = 0.004) and W1 group (mean of 4.55 ± 0.72; p = 0.002). Conclusions: The patients with the Wiberg type III patella shape had a higher incidence and larger size of ACD in the PF of the knee compared to the groups of Wiberg type I and II. Wiberg III patients with a lower level of physical activity had a larger size of ACD in the PF joint.
Influencers identification in complex networks through reaction-diffusion dynamics

A pivotal idea in network science, marketing research, and innovation diffusion theories is that a small group of nodes—called influencers—have the largest impact on social contagion and epidemic processes in networks. Despite the long-standing interest in the influencers identification problem in socioeconomic and biological networks, there is not yet agreement on which is the best identification strategy. State-of-the-art strategies are typically based either on heuristic centrality measures or on analytic arguments that only hold for specific network topologies or peculiar dynamical regimes. Here, we leverage the recently introduced random-walk effective distance—a topological metric that estimates almost perfectly the arrival time of diffusive spreading processes on networks—to introduce a centrality metric which quantifies how close a node is to the other nodes. We show that the new centrality metric significantly outperforms state-of-the-art metrics in detecting the influencers for global contagion processes. Our findings reveal the essential role of the network effective distance for the influencers identification and lead us closer to the optimal solution of the problem.
A theoretical framework for retinal computations: insights from textbook knowledge

Neural circuits in the retina divide the incoming visual scene into more than a dozen distinct representations that are sent on to central brain areas, such as the lateral geniculate nucleus and the superior colliculus. The retina can be viewed as a parallel image processor made of a multitude of small computational devices. Neural circuits of the retina are constituted by various cell types that separate the incoming visual information in different channels. Visual information is processed by retinal neural circuits and several computations are performed extracting distinct features from the visual scene. The aim of this article is to understand the computational basis involved in processing visual information which finally leads to several feature detectors. Therefore, the elements that form the basis of retinal computations will be explored by explaining how oscillators can lead to a final output with computational meaning. Linear versus nonlinear systems will be presented and the retina will be placed in the context of a nonlinear system. Finally, simulations will be presented exploring the concept of the retina as a nonlinear system which can perform understandable computations converting a known input into a predictable output.
Characteristics of Text-to-Speech and Other Corpora

Extensive TTS corpora exist for commercial systems created for high-resource languages such as Mandarin, English, and Japanese. Speakers recorded for these corpora are typically instructed to maintain constant f0, energy, and speaking rate and are recorded in ideal acoustic environments, producing clean, consistent audio. We have been developing TTS systems from “found” data collected for other purposes (e.g. training ASR systems) or available on the web (e.g. news broadcasts, audiobooks) to produce TTS systems for low-resource languages (LRLs) which do not currently have expensive, commercial systems. This study investigates whether traditional TTS speakers do exhibit signiﬁcantly less variation and better speaking characteristics than speakers in found genres. By examining characteristics of f0, energy, speaking rate, articulation, NHR, jitter, and shimmer in found genres and comparing these to traditional TTS corpora, We have found that TTS recordings are indeed characterized by low mean pitch, standard deviation of energy, speaking rate, and level of articulation, and low mean and standard deviations of shimmer and NHR; in a number of respects these are quite similar to some found genres. By identifying similarities and differences, we are able to identify objective methods for selecting found data to build TTS systems for LRLs.
Risk Factors for Male Perpetration and Female Victimization of Intimate Partner Homicide: A Meta-Analysis

Intimate partner homicide (IPH) is a serious problem throughout the world. Research has identified the continued need to examine risk factors for IPH to identify individuals who may be at a greater risk of IPH perpetration or victimization. In this study, we conducted a meta-analysis on risk factors for male IPH perpetration and female IPH victimization. This meta-analysis examined results from 17 studies, which included 148 effect sizes used in the analysis. Primary findings from this research suggest the strongest risk factors for IPH were the perpetrator having direct access to a gun, perpetrator’s previous nonfatal strangulation, perpetrator’s previous rape of the victim, perpetrator’s previous threat with a weapon, the perpetrator’s demonstration of controlling behaviors, and the perpetrator’s previous threats to harm the victim. Implications for law enforcement personnel, medical professionals, victim advocates, mental health professionals, and other professionals who may be in contact with potential IPH perpetrators and victims are discussed.