Miracle-dz/UniFAR-FTUs huggingface dataset:
The ‘SELection End points in Communities of bacTeria’ (SELECT) Method: A Novel Experimental Assay to Facilitate Risk Assessment of Selection for Antimicrobial Resistance in the Environment

Background: Antimicrobial resistance (AMR) is one of the most significant health threats to society. A growing body of research demonstrates selection for AMR likely occurs at environmental concentrations of antibiotics. However, no standardized experimental approaches for determining selective concentrations of antimicrobials currently exist, preventing appropriate environmental and human health risk assessment of AMR. Objectives: We aimed to design a rapid, simple, and cost-effective novel experimental assay to determine selective effect concentrations of antibiotics and to generate the largest experimental data set of selective effect concentrations of antibiotics to date. Methods: Previously published methods and data were used to validate the assay, which determines the effect concentration based on reduction of bacterial community (wastewater) growth. Risk quotients for test antibiotics were generated to quantify risk. Results: The assay (SELection End points in Communities of bacTeria, or the SELECT method) was used to rapidly determine selective effect concentrations of antibiotics. These were in good agreement with quantitative polymerase chain reaction effect concentrations determined within the same experimental system. The SELECT method predicted no effect concentrations were minimally affected by changes in the assay temperature, growth media, or microbial community used as the inoculum. The predicted no effect concentrations for antibiotics tested ranged from 0. 05μg/L for ciprofloxacin to 1,250μg/L for erythromycin. Discussion: The lack of evidence demonstrating environmental selection for AMR, and of associated human health risks, is a primary reason for the lack of action in the mitigation of release of antibiotics into the aquatic environment. We present a novel method that can reliably and rapidly fill this data gap to enable regulation and subsequent mitigation (where required) to lower the risk of selection for, and human exposure to, AMR in aquatic environments. In particular, ciprofloxacin and, to a lesser extent, azithromycin, cefotaxime, and trimethoprim all pose a significant risk for selection of AMR in the environment. https://doi.org/10.1289/EHP6635
مطالعه وقوع گونه های ویبریو در صدف صید شده از خلیج فارس به روش Multiplex-PCR

Background & Objective: Staphylococcus aureus is one of the most frequently opportunistic pathogens isolated from nosocomial infections, responsible for severe infections such as bacteremia, endocarditis, and skin infections. Surface proteins such as fibrinogen and fibronectin-binding proteins are important factors in adhesion and invasion of S. aureus. Therefore, the objective of this study is to evaluate the presence of genes clfA, clfB, fnbA, and fnbB in isolates of S. aureus collected from clinical specimens of hospitalized patients in Hospitals of Zabol -Iran. Materials & Methods: In this cross-sectional study, 100 S. aureus isolates were collected from January to August 2013 from hospitalized patients at zabol-Iran. The isolates were confirmed by conventional biochemical tests. DNA of all isolates was extracted by boiling method. Multiplex PCR was used to identify the presence of virulence genes. The data were analyzed using Fisher's exact test. Results: The results of this study showed that 50% of isolates possess at least one of the studied genes. The frequency of genes encoding fibrinogen (clfA, clfB) and fibronectin (fnbA, fnbB) were 19%, 16% and 25%, 19% respectively. Conclusion: This study showed that the studied genes are found in small percentage of isolates. Further investigations on these genes are needed to clarify their role in the pathogenesis of S. aureus infections.
An Autopsy Case of an Elderly Patient with Classic Hodgkin Lymphoma Presenting with a Plethora of Clinical Symptoms and Signs

Patient: Female, 88-year-old Final Diagnosis: Hodgkin lymphoma Symptoms: Fever • weight loss • dypnea Medication: — Clinical Procedure: — Specialty: Pathology Objective: Unusual clinical course Background: Hodgkin lymphoma (HL) is a potentially curable disease with favorable outcomes. However, elderly patients with HL usually have more adverse prognostic factors and hence a much worse prognosis than younger patients. Case Report: The patient was a woman in her 80s. She reported high fever, anorexia, and a weight loss of 8 kg within 5 months. She had been on treatment for diabetes mellitus and hypertension. She had undergone percutaneous coronary intervention and pacemaker implantation to treat acute coronary syndrome and sinus arrhythmia, respectively. Blood tests showed elevation of alkaline phosphatase, C-reactive protein, leukocyte count, CA 19-9, and carcinoembryonic antigen. Computed tomography did not show tumors in the liver, and cholangitis and sepsis were suspected. Aspartate transaminase, alanine aminotransferase, and total bilirubin gradually increased through the course of the patient’s hospital stay. Despite treatment, her condition deteriorated and she died 22 days after hospital admission. At autopsy, we found stage IV HL with lymph node swelling on both sides of the diaphragm, as well as diffusely disseminated nodules in the liver and spleen. Conclusions: Our patient had several poor prognostic factors including B symptoms, comorbidity, advanced stage, Epstein-Barr virus infection, and expression of programmed death-ligand 1 and interleukin-6, all of which were closely connected with her advanced age. Her age and comorbidities may have been the most adverse prognostic factors for her illness. An effective HL screening method for elderly individuals should be developed to ameliorate poor prognosis and adverse outcomes.
Signaling Pathways for Triacylglycerol Lipid Droplet Formation

It is well established that lipid droplets form from the endoplasmic reticulum (ER) bilayer in organisms across the phylogenetic tree. What it less understood is how gene products combine actions to make this event occur. Since lipid droplets have a neutral lipid core, much effort has gone into understanding the roles of neutral lipid synthesizing enzymes in droplet biogenesis. In yeast, these include the phosphatidic acid phosphatase (Pah1), which converts phosphatidic acid (PA) to diacylglycerol (DAG), the acyl-CoA-diacylglycerol acyltransferase (Dga1), which converts diacylglycerol (DAG) to triacylglycerol (TAG), the phospholipid:diacylglycerol acyltransferse (Lro1/Plh1), which converts DAG and phospholipids to TAG, and the acyl-CoA sterol acyltransferases (Are1 and Are2), which convert sterols to sterol esters. Here, we focus on signaling pathways for TAG synthesis.
Desain Banyumas Smart City Berbasis Internet of Things (IoT) Menggunakan Fog Computing Architecture

Internet use in Banyumas Regency is now increasingly diverse according to the demands of the needs. The development of communication technology raises various aspects that also develop. For example, the use of the internet for a traffic light control system so that it can be adjusted according to the settings and can be monitored in real time. In the development of communication technology, the term Internet of Things (IoT) emerged as the concept of extending the benefits of internet communication systems to give impulses to other systems. In other words, IoT is used as a communication for remote control and monitoring by utilizing an internet connection. The Internet of Things in the era is now being developed to create an intelligent system for the purposes of controlling various public needs until the concept of the smart city emerges. Basically, smart cities utilize internet connections for many purposes such as controlling CCTV, traffic lights, controlling arm robots in the industry and storing data in hospitals. If the system is carried out directly from the device to the central server, there will be a very long queue of data while the system created requires speed and accuracy of time so that a system is needed that allows sufficient data control and processing to be carried out on network edge users. Then fog Computing is used with the hope that the smart city system can work with small latency values ​​so that the system is more real-time in sending or receiving data
Integration of strength training into UK Defence Rehabilitation practice: current trends and future challenges

The use of strength and conditioning (S&C) in musculoskeletal rehabilitation has gained wide acceptance among the rehabilitation community. However, there is an absence of evidence demonstrating how to best integrate the principles of S&C into rehabilitation practice. This article discusses four broad themes: (1) an overview of the UK Defence Rehabilitation care pathway, (2) the historical and current approaches to physical training to support operational readiness of the British Armed Forces, (3) the current and future challenges of integrating S&C into Defence Rehabilitation practice and (4) research priorities relating to the use of S&C in Defence Rehabilitation. We detail the importance of strength/power-based physical attributes within our military population. We recommend that consideration be given to the benefits of an alternative education/coaching-based model to be used during the current 3-week residential care pathway, which aims to ensure effective implementation of therapeutic S&C over a longer period of care.
Classification of the Multiple Stages of Parkinson’s Disease by a Deep Convolution Neural Network Based on 99mTc-TRODAT-1 SPECT Images

Single photon emission computed tomography (SPECT) has been employed to detect Parkinson’s disease (PD). However, analysis of the SPECT PD images was mostly based on the region of interest (ROI) approach. Due to limited size of the ROI, especially in the multi-stage classification of PD, this study utilizes deep learning methods to establish a multiple stages classification model of PD. In the retrospective study, the 99mTc-TRODAT-1 was used for brain SPECT imaging. A total of 202 cases were collected, and five slices were selected for analysis from each subject. The total number of images was thus 1010. According to the Hoehn and Yahr Scale standards, all the cases were divided into healthy, early, middle, late four stages, and HYS I~V six stages. Deep learning is compared with five convolutional neural networks (CNNs). The input images included grayscale and pseudo color of two types. The training and validation sets were 70% and 30%. The accuracy, recall, precision, F-score, and Kappa values were used to evaluate the models’ performance. The best accuracy of the models based on grayscale and color images in four and six stages were 0.83 (AlexNet), 0.85 (VGG), 0.78 (DenseNet) and 0.78 (DenseNet).
The Impact of Wrist Percooling on Physiological and Perceptual Responses during a Running Time Trial Performance in the Heat

Environmental heat stress poses significant physiological challenge and impairs exercise performance. We investigated the impact of wrist percooling on running performance and physiological and perceptual responses in the heat. In a counterbalanced design, 13 trained males (33 ± 9 years, 15 ± 7% body fat, and maximal oxygen consumption, VO2max 59 ± 5 mL/kg/min) completed three 10 km running time trials (27 °C, 60% relative humidity) while wearing two cooling bands: (1) both bands were off (off/off), (2) one band on (off/on), (3) both bands on (on/on). Heart rate (HR), HR variability (HRV), mean arterial pressure (MAP), core temperature (TCO), thermal sensation (TS), and fatigue (VAS) were recorded at baseline and recovery, while running speed (RS) and rating of perceived exertion (RPE) were collected during the 10 km. Wrist cooling had no effect (p > 0.05) at rest, except modestly increased HR (3–5 ∆beats/min, p < 0.05). Wrist percooling increased (p < 0.05) RS (0.25 ∆mi/h) and HR (5 ∆beats/min), but not TCO (∆ 0.3 °C), RPE, or TS. Given incomplete trials, the distance achieved at 16 min was not different between conditions (off/off 1.96 ± 0.16 vs. off/on 1.98 ± 0.19 vs. on/on 1.99 ± 0.24 miles, p = 0.490). During recovery HRV, MAP, or fatigue were unaffected (p > 0.05). We demonstrate that wrist percooling elicited a faster running speed, though this coincides with increased HR; although, interestingly, sensations of effort and thermal comfort were unaffected, despite the faster speed and higher HR.
Protein structure and function analyses to understand the implication of mutually exclusive splicing

Alternative splicing (AS) has been suggested as one of the major processes expanding the diversity of proteomes in multicellular organisms. Mutually exclusive exons (MXE) provide one form of AS that is less likely to disrupt protein structure and is over-represented in the proteome compared to other forms of AS. We used domain structure information from the CATH classification to perform a systematic structural analysis of the effects of MXE splicing in high quality animal genomes (e.g. human, fly, mouse and 2 fishes) and we were able to annotate approximately 50% of MXE events with structural information. For those MXE events which can be mapped to a structure, we found that although embedded in domains, they were strongly enriched in surface exposed residues. We also demonstrated that the variable residues between splicing events lie close to known and/or predicted functional sites. We present some examples of MXE events in proteins that have important roles in cells. This work presents the first large scale systematic study of the structural/functional effects of MXE splicing using predominantly domain based modelling and functional annotation tools. Our study supports and expands on previous work in this field and helps to build a picture of how MXE events facilitate evolution of new functions.
Mechanism of Type IA Topoisomerases

Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5′-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3′-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.
Learning quadrupedal locomotion over challenging terrain

A learning-based locomotion controller enables a quadrupedal ANYmal robot to traverse challenging natural environments. Legged locomotion can extend the operational domain of robots to some of the most challenging environments on Earth. However, conventional controllers for legged locomotion are based on elaborate state machines that explicitly trigger the execution of motion primitives and reflexes. These designs have increased in complexity but fallen short of the generality and robustness of animal locomotion. Here, we present a robust controller for blind quadrupedal locomotion in challenging natural environments. Our approach incorporates proprioceptive feedback in locomotion control and demonstrates zero-shot generalization from simulation to natural environments. The controller is trained by reinforcement learning in simulation. The controller is driven by a neural network policy that acts on a stream of proprioceptive signals. The controller retains its robustness under conditions that were never encountered during training: deformable terrains such as mud and snow, dynamic footholds such as rubble, and overground impediments such as thick vegetation and gushing water. The presented work indicates that robust locomotion in natural environments can be achieved by training in simple domains.
Ultrastructural localization of glutamate delta 1 (GluD1) receptor immunoreactivity in the mouse and monkey striatum

The glutamate receptor delta 1 (GluD1) is strongly expressed in the striatum. Knockout of GluD1 expression in striatal neurons elicits cognitive deficits and disrupts the thalamostriatal system in mice. To understand the potential role of GluD1 in the primate striatum, we compared the cellular and subcellular localization of striatal GluD1 immunoreactivity (GluD1‐IR) in mice and monkeys. In both species, striatal GluD1‐IR displayed a patchy pattern of distribution in register with the striosome/matrix compartmentation, but in an opposite fashion. While GluD1 was more heavily expressed in the striosomes than the matrix in the monkey caudate nucleus, the opposite was found in the mouse striatum. At the electron microscopic level, GluD1‐IR was preferentially expressed in dendritic shafts (47.9 ± 1.2%), followed by glia (37.7 ± 2.5%), and dendritic spines (14.3 ± 2.6%) in the matrix of the mouse striatum. This pattern was not statistically different from the labeling in the striosome and matrix compartments of the monkey caudate nucleus, with the exception of a small amount of GluD1‐positive unmyelinated axons and axon terminals in the primate striatum. Immunogold staining revealed synaptic and perisynaptic GluD1 labeling at putative axo‐dendritic and axo‐spinous glutamatergic synapses, and intracellular labeling on the surface of mitochondria. Confocal microscopy showed that GluD1 is preferentially colocalized with thalamic over cortical terminals in both the striosome and matrix compartments. These data provide the anatomical substrate for a deeper understanding of GluD1 regulation of striatal glutamatergic synapses, but also suggest possible extrasynaptic, glial, and mitochondrial GluD1 functions.
Does Functionality Condition the Population Structure and Genetic Diversity of Endangered Dog Breeds under Island Territorial Isolation?

Simple Summary Early references to Ca de Rater and Ca de Bestiar endangered autochthonous breeds were witnesses to their exceptional ratting/pet and shepherding/guard skills for centuries. Studbooks or associations promote an increase in the number of effectives and their genealogies. Genetic diversity parameters were evaluated along the history of definition of both dog breeds. Guard or hunting purposes condition an increased registration of genealogical information. Hunting animals have more complete genealogies and need more time to select breeding animals. Male guard dogs are preferred over females due to their suitability for guarding. Selection for performance acts as a diversity promoter and breeding policy driver. The uses or purposes for which certain breeds were selected condition the genetic diversity evolution of endangered breeds, even if these share the same geographic isolation conditions. Abstract Despite the undefinition of the origins of Ca de Rater (CR) and Ca de Bestiar (CB) dogs, references to these endangered autochthonous breeds highlighted their ratting/pet and shepherding/guard skills for centuries. Genealogical historical records were traced back to founders. Founder number in the reference population (146 and 53 for CR and CB, respectively), historical and reference maximum generations traced (eight and seven for CR and CB, respectively), and historical average number of complete generations (1.04 for both breeds) were determined. Structure assessment revealed the existence of subpopulations regarding criteria such as breeders (75 and 17), breeder location (32 and eight), owners (368 and 198), and owner location (73 and 51) for CR and CB, respectively. Average inbreeding (F) within breed subpopulations ranged from 0.27–1.20% for CB breeders and the rest of subpopulation criteria for both breeds, respectively, except for CB owners and owner location. F ranged from 0.27–1.41% for CB historical population and CR current population, respectively. The study of genetic diversity revealed a relatively similar genetic background between subpopulations. Average coancestry between and within breeds suggested a similar evolutionary process. However, Mann–Whitney U test determined significant differences for diversity parameters (F, ΔR, coancestry, nonrandom mating degree, maximum, complete, and equivalent generations, ΔF, and genetic conservation index) between breeds and their functionalities. Conclusively, functionality in dog breeds may determine the genetic diversity evolution of endangered breeds, even when these share the same geographic isolation conditions.
A protocol for systematic review and meta-analysis

Background: Rheumatoid arthritis has the characteristics of slow progression, long course, and repeated attacks. At present, western medicine commonly used in clinical practice not only reduces pain and improves symptoms, but also has more adverse reactions, affecting the health, and life of patients. In ancient China, Huangqi Guizhi Wuwu decoction was used by doctors to treat rheumatoid arthritis, with remarkable effect. In recent years, many clinical studies have also shown that Huangqi Guizhi Wuwu decoction has reliable effect in treating rheumatoid arthritis, but there is no evidence of evidence-based medicine. Therefore, this study aims to systematically evaluate the clinical efficacy and safety of Huangqi Guizhi Wuwu decoction in the treatment of rheumatoid arthritis. Methods: Using computer to retrieve PubMed, The Cochrance Library, Embase, Web of Science, CNKI, VIP and Wanfang database, in addition manually retrieve Google academic and Baidu academic to collect all randomized controlled trials for Huangqi Guizhi Wuwu decoction in the treatment of rheumatoid arthritis, including relevant academic journal and conference papers, dissertations, from the establishment of the database to July 2020. After 2 evaluators independently screened the literature, extracted the data, and evaluated the risk of bias included in the study, RevMan5.3 software was used to analyze the data. Results: This research evaluate the efficacy and safety of Huangqi Guizhi Wuwu decoction in treating Rheumatoid arthritis from the aspects of clinical efficacy rate, visual analog scale (VAS), swollen joint count (SJC), morning stiffness time, Rrythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), and adverse reaction incidence. Conclusion:This study will provide reliable evidence for the clinical application of Huangqi Guizhi Wuwu decoction in the treatment of rheumatoid arthritis. Ethics and dissemination: The private information from individuals will not publish. This systematic review also will not involve endangering participant rights. Ethical approval is not required. The results may be published in a peer-reviewed journal or disseminated in relevant conferences. OSF Registration number: DOI 10.17605/OSF.IO/RZY3V. Abbreviations: CI= confidence interval, CRP=C-reactive protein, ESR=Rrythrocyte sedimentation rate, GRADE= The Grading of Recommendations, Assessment, Development, and Evaluation, PRISMA = preferred reporting items for systematic reviews and meta-analyses, RA = rheumatoid arthritis, RCTs = randomized controlled trails, RF = rheumatoid factor, RR = relative risk, SJC = swollen joint count, SMD = standardized mean difference, TCM = traditional Chinese medicine, VAS = visual analog scale, WMD = weighted mean difference.