Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures

The family Caryophanaceae/Planococcaceae is a taxonomically heterogeneous assemblage of >100 species classified within 13 genera, many of which are polyphyletic. Exhibiting considerable phylogenetic overlap with other families, primarily Bacillaceae, the evolutionary history of this family, containing the potent mosquitocidal species Lysinibacillus sphaericus, remains incoherent. To develop a reliable phylogenetic and taxonomic framework for the family Caryophanaceae/Planococcaceae and its genera, we report comprehensive phylogenetic and comparative genomic analyses on 124 genome sequences from all available Caryophanaceae/Planococcaceae and representative Bacillaceae species. Phylogenetic trees were constructed based on multiple datasets of proteins including 819 core proteins for this group and 87 conserved Firmicutes proteins. Using the core proteins, pairwise average amino acid identity was also determined. In parallel, comparative analyses on protein sequences from these species have identified 92 unique molecular markers (synapomorphies) consisting of conserved signature indels that are specifically shared by either the entire family Caryophanaceae/Planococcaceae or different monophyletic clades present within this family, enabling their reliable demarcation in molecular terms. Based on multiple lines of investigations, 18 monophyletic clades can be reliably distinguished within the family Caryophanaceae/Planococcaceae based on their phylogenetic affinities and identified molecular signatures. Some of these clades are comprised of species from several polyphyletic genera within this family as well as other families. Based on our results, we are proposing the creation of three novel genera within the family Caryophanaceae/Planococcaceae, namely Metalysinibacillus gen. nov., Metasolibacillus gen. nov., and Metaplanococcus gen. nov., as well as the transfer of 25 misclassified species from the families Caryophanaceae/Planococcaceae and Bacillaceae into these three genera and in Planococcus, Solibacillus, Sporosarcina, and Ureibacillus genera. These amendments establish a coherent taxonomy and evolutionary history for the family Caryophanaceae/Planococcaceae, and the described molecular markers provide novel means for diagnostic, genetic, and biochemical studies. Lastly, we are also proposing a consolidation of the family Planococcaceae within the emended family Caryophanaceae.
Exposure to 3-Nitropropionic Acid Mitochondrial Toxin Induces Tau Pathology in Tangle-Mouse Model and in Wild Type-Mice

Oxidative stress, particularly of mitochondrial origin, plays an important role in the pathogenesis of neurodegenerative disorders, including Alzheimer’s disease (AD) and other tauopathies. Controversies regarding the responses of tau phosphorylation state to various stimuli causing oxidative stress have been reported. Here we investigated the effect of 3-nitropropionic acid (3NP), a mitochondrial toxin which induces oxidative stress, on the tangle-pathology in our previously generated double mutant (E257T/P301S, DM) -Tau-tg mice and in WT-mice. We detected an increase in tangle pathology in the hippocampus and cortex of the DM-Tau-tg mice following exposure of the mice to the toxin, as well as generation of tangles in WT-mice. This increase was accompanied with alterations in the level of the glycogen synthase kinase 3β (GSK3β), the kinase which phosphorylates the tau protein, and in the phosphorylation state of this kinase. A response of microglial cells was noticed. These results point to the involvement of mitochondrial dysfunction in the development of the tangle-pathology and may suggest that interfering with mitochondrial dysfunction may have an anti-tangle therapeutic potential.
Altered Default Mode Network Dynamics in Civil Aviation Pilots

Background Airlines occupy an increasingly important place in the economy of many countries. Because air disasters may cause substantial losses, comprehensive surveys of the psychophysiological mechanism of flying are needed; however, relatively few studies have focused on pilots. The default mode network (DMN) is an important intrinsic connectivity network involved in a range of functions related to flying. This study aimed to examine functional properties of the DMN in pilots. Method Resting-state functional magnetic resonance imaging data from 26 pilots and 24 controls were collected. Independent component analysis, a data-driven approach, was combined with functional connectivity analysis to investigate functional properties of the DMN in pilots. Results The pilot group exhibited increased functional integration in the precuneus/posterior cingulate cortex (PCC) and left middle occipital gyrus. Subsequent functional connectivity analysis identified enhanced functional connection between the precuneus/PCC and medial superior frontal gyrus. Conclusion The pilot group exhibited increased functional connections within the DMN. These findings highlight the importance of the DMN in the neurophysiological mechanism of flying.
A Novel Square-Stepping Exercise Program for Older Adults (StepIt): Rationale and Implications for Falls Prevention

The ability to effectively execute compensatory steps is critical for preventing accidental falls, and consequently stepping training is an essential ingredient of fall prevention programs. In this paper, we propose a concept for stepping training that aims to maximize training effects by taking into account recent research evidence and a precise dosing of training ingredients. The concept addresses motor as well as cognitive falls-related aspects, it is suitable for individual as well as group based training, and it does not require costly equipment. Theory and evidence behind all of the training principles is reviewed, and an example of an exercise protocol is described in detail. Participants are presented with stepping patterns which they have to memorize and implement on a mat. In order to enable investigation of dose-response effects, the difficulty level systematically and gradually increases session by session based on four principles: execution speed, pattern complexity, pattern length and execution in dual-/multi-tasking conditions. The presented concept can be used as a framework for the development of further prevention and/or rehabilitation stepping exercise programs. Further studies using this exercise regimen or modified versions of it are encouraged.
Narrelations — Visualizing Narrative Levels and their Correlations with Temporal Phenomena

We present findings from interdisciplinary research at the intersection between literary studies, information visualization, and interface design. Despite a growing interest in text visualization among literary scholars, so far, narrative visualizations are not designed to support the particular tasks involved in narratological analysis and often fail to reveal nuanced narratological features. One major outcome of our iterative research and design process is Narrelations , a novel visualization technique specifically suited for analyzing and interpreting narrative levels of a story and temporal aspects of its narrative representation. The visualization provides an overview of the nesting and distribution of narrative levels, integrates the representation of temporal phenomena, and facilitates the examination of correlations between these aspects. With this research we explore how collaboratively designed visual encodings and interaction techniques may allow for an insightful analysis at a high level coupled with a close inspection of text passages. We discuss prior work relevant to our research objectives and explain the specific characteristics of narrative levels and temporal aspects of narrative representation. After describing the research process and design principles, we apply the visualization on a test corpus of eight annotated German short stories and demonstrate its heuristic value for literary analyses and interpretations. In particular, we explore the intricate connections between the literary content of the novellas and their narrative form.
Fibrilación auricular en pacientes con ataque cerebrovascular: experiencia en un centro de referencia del suroccidente colombiano

Introduction: Atrial fibrillation is presented as one of the main risk factors for the presence of stroke of cardioembolic origin. Its increasing prevalence is particularly caused by the aging population growth. This type of arrhythmia requires secondary prevention compared to the treatment of other illnesses. Objective: To describe the characteristics of ischemic stroke patients and its relationship with atrial fibrillation. Materials and methods: Retrospective descriptive study of individuals admitted with ischemic stroke. Information of risk factors for cerebrovascular disease, presence or abscense of atrial fibrillation and treatment received was collected. Comparative tables according to the presence or absence of atrial fibrillation were performed. Values less than 0.05 were considered significant. Results: There were 246 patients with ischemic stroke. The median of age was 71 years and half were male. The prevalence of risk factors for ischemic stroke were 73.9% for arterial hypertension (HT), 23.9% previous stroke, 20.7% for smoking. The prevalence of atrial fibrillation was 24.3%, being higher in patients with concomitant heart failure (OR 3.5 95% CI 1.6 to 7.75 p = 0.000). There were lower probability of atrial fibrillation among men (OR 0.49 95% CI 0.26-0.92 p = 0.018). Dilatation of the left atrium was present in 43.1% ischemic stroke patients. 57% of the individuals who were taking oral anticoagulants had atrial fibrillation Only 15% met criteria for thrombolysis. The all-cause mortality in patients with ischemic stroke was 13.8% and in the atrial fibrillation group was 16%. Conclusion: Ischemic stroke is a prevalent disease in our population and nearly one in five patients with ischemic stroke have previous atrial fibrillation or de novo diagnosed during the event. The mortality in this subgroup of patients is 16%.
CCL14 is a prognostic biomarker and correlates with immune infiltrates in hepatocellular carcinoma

C-C motif chemokine ligand 14 (CCL14) is a chemokine promoting the activation of immune cells. However, the relationship between CCL14 expression, tumor immunity, and prognosis in Hepatocellular Carcinoma (HCC) remain unclear. CCL14 expression and its influence on tumor prognosis were analyzed by the ONCOMINE, Tumor Immune Estimation Resource (TIMER) and Kaplan-Meier plotter. The relationship between CCL14 expression and tumor immunity were analyzed by TIMER and Gene Expression Profiling Interactive Analysis (GEPIA). CCL14 expression was significantly lower in several human cancers, including HCC, than in corresponding normal tissues. CCL14 expression in HCC tissues correlated with prognosis. Low CCL14 expression associated with poorer overall survival, disease-specific survival, progression-free survival, and relapse-free survival in multiple cohorts of HCC patients, particularly at early disease stages (stage 1+2 or grade 2). CCL14 showed strong correlation with tumor-infiltrating B cells, CD4+ and CD8+ T cells, macrophages, neutrophils, and dendritic cells. CCL14 expression in HCC negatively correlated with expression of several immune cell markers, including exhausted T cell markers, PD-1, TIM-3 and CTLA-4, suggesting its role in regulating tumor immunity. These findings demonstrate that CCL14 is a potential prognostic biomarker that determines cancer progression and correlated with tumor immune cells infiltration in HCC.
Is rotator cuff related shoulder pain a multidimensional disorder? An exploratory study

Abstract Background and aims Rotator cuff related shoulder pain has been associated with factors from multiple dimensions such as strength changes, psychosocial measures, comorbidities and level of education. However, to date little research has been undertaken to evaluate which factors explain the greatest variance in pain and disability levels in people with rotator cuff related shoulder pain. The objective of this study was therefore to evaluate which multidimensional examination findings were associated with higher pain and disability in a primary care cohort with rotator cuff related shoulder pain. Methods This was an exploratory cross-sectional cohort study. Sixty-seven participants with rotator cuff related shoulder pain were assessed for: pain intensity, disability; demographic, psychological, social and lifestyle characteristics, and isometric strength of shoulder internal and external rotator muscles. Univariable associations between pain intensity/disability and each variable were assessed using linear regression. Variables with univariable associations (p < 0.1) were entered into backwards stepwise multivariable regression models. Results The multivariable model for pain intensity included sleep and perceived persistence and explained 46.5% of the variance (37.6% uniquely by sleep, 5.4% uniquely by perceived persistence). The multivariable model for disability included sleep and sex and explained 26.8% of the variance (4.5% shared by predictors, 16.4% uniquely by sleep, 5.9% uniquely by sex). Conclusions Rotator cuff-related shoulder pain and disability are associated with sleep disturbance, perceived symptom persistence and sex. Rotator cuff related shoulder pain may be considered a multidimensional disorder. Implications Clinicians need to evaluate sleep and perceived symptom persistence in people with rotator cuff related shoulder pain. Future research may examine whether management strategies for RCRSP directed towards these factors afford improved treatment outcomes.
The Superiority of the Otolith System

Background: The peripheral vestibular end organ is considered to consist of semi-circular canals (SCC) for detection of angular accelerations and the otoliths for detection of linear accelerations. However, otoliths being phylogenetically the oldest part of the vestibular sensory organs are involved in detection of all motions. Summary: This study elaborates on this property of the otolith organ, as this concept can be of importance for the currently designed vestibular implant devices. Key Message: The analysis of the evolution of the inner ear and examination of clinical examples shows the robustness of the otolith system and inhibition capacity of the SCC. The otolith system must be considered superior to the SCC system as illustrated by evolution, clinical evidence, and physical principles.
Sedation Provided for Consultations in the Pediatric Emergency Department: Another Perspective.

BACKGROUND Many procedures requiring sedation in the pediatric emergency department are performed by consultants from outside the department. This team usually includes orthopedic surgeons and general surgeons. As sedation is now a standard of care in such cases, we evaluated consultants' views on sedation. OBJECTIVES To evaluate consultants' views on sedation. METHODS A questionnaire with both open-ended questions and Likert-type scores was distributed to all orthopedic surgeons and general surgeons performing procedures during the study period. The questionnaire was presented at three medical centers. RESULTS The questionnaire was completed by 31 orthopedic surgeons and 16 general surgeons. Although the vast majority (93-100%) considered sedation important, a high percentage (64-75%) would still perform such procedures without sedation if not readily available. CONCLUSIONS Sedation is very important for patients and although consultants understand its importance, the emergency department staff must be vigilant in both being available and not allowing procedures to "escape" the use of sedation.
Equity of access to post‐mastectomy breast reconstruction at a regional plastic surgery centre

The Plastic and Reconstructive Surgery Department at the Counties Manukau District Health Board provides tertiary‐level access to post‐mastectomy breast reconstruction for all women in the northern region of New Zealand. Access to breast reconstruction is not always equitable. We aim to assess equity of access to breast reconstruction in this department.
Protective Effects of Hydrogen-Rich Water Against Cartilage Damage in a Rat Model of Osteoarthritis by Inhibiting Oxidative Stress, Matrix Catabolism, and Apoptosis

Background The aim of this study was to investigate the mechanisms underlying the potential effects of hydrogen-rich water (HW) on articular cartilage in a rat osteoarthritis (OA) model. Material/Methods A rat model of OA was established using the modified Hulth method, and rats were forced to exercise for 30 min every day 1 week after surgery for 7 weeks. Mankin’s method was used to score the severity of OA. The animals were assigned into the OA group, OA+HW group, and sham operation group. After 8 weeks, the animals in the OA group had a Mankin score >8 points, and HW was administered into the knee joint. After 2 weeks of treatment, articular cartilage was obtained for pathological examination, consisting of hematoxylin and eosin, toluidine blue, and Hoechst staining, as well as quantitative real-time PCR and Western blot analyses. This combination of pharmacological and molecular biological analyses was performed to examine the mechanism underlying the protective effect of HW on articular cartilage. Results The antioxidant effects of HW suppressed oxidative damage, which may have aided the inhibition of ECM-degrading enzymes (MMP3, MMP13, ADAMT4, and ADAMT5), the upregulation of Col II and aggrecan expression, and the downregulation of COX-2, iNOS, and NO expression. The results of HE staining indicated intra-articular treatment of HW attenuated cartilage degradation. However, Hoechst staining in the OA group indicated the nuclei of the fragmented chondrocytes were condensed compared to the sham operation group, and this effect was inhibited by HW. Conclusions HW showed a protective effect against the progression of OA in an animal model, which may have been mediated by its anti-oxidant and anti-apoptotic activities.
Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction

Analyses of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) implicated in myocardial infarction (MI) have increased our understanding of gene regulatory mechanisms in MI. However, it is not known how their expression fluctuates over the different stages of MI progression. In this study, we used time-series gene expression data to examine global lncRNA and miRNA expression patterns during the acute phase of MI and at three different time points thereafter. We observed that the largest expression peak for mRNAs, lncRNAs, and miRNAs occurred during the acute phase of MI and involved mainly protein-coding, rather than non-coding RNAs. Functional analysis indicated that the lncRNAs and miRNAs most sensitive to MI and most unstable during MI progression were usually related to fewer biological functions. Additionally, we developed a novel computational method for identifying dysregulated competing endogenous lncRNA-miRNA-mRNA triplets (LmiRM-CTs) during MI onset and progression. As a result, a new panel of candidate diagnostic biomarkers defined by seven lncRNAs was suggested to have high classification performance for patients with or without MI, and a new panel of prognostic biomarkers defined by two lncRNAs evidenced high discriminatory capability for MI patients who developed heart failure from those who did not.
Low-Latency Reconfigurable Entropy Digital True Random Number Generator With Bias Detection and Correction

Digital true-random number generators (TRNG) are increasingly employed to generate random channels in low-power resource-constrained IoT devices at the network edge. However, their susceptibility to process variations, or even intrusion attacks, degrade the generated entropy requiring an on-the-fly processor for detection of bias variations and correction. This work proposes a two-step search process to implement an optimized search that minimizes the latency (number of clock-cycles) for bias correction implemented on a FPGA platform. The first step implements a subset of NIST tests for entropy validation and an additional autocorrelator is used for entropy validation and bias detection on-the-fly in the second step. Measured results with the proposed algorithm implemented on FPGA shows significant improvement in the probability of bias correction with low number of trials. The measured power consumption of the TRNG and the bias correction is 10.22mW and 10.96mW respectively at 1.25 V with 18 kHz throughput for three random channels.
Towards Reliable Things: Formal Verification of IoT Software with Frama-C

Among distributed systems, connected devices and services, also referred to as the Internet of Things (IoT), have proliferated very quickly in the past years. There are now billions of interconnected devices, and this number is growing. It is anticipated that by 2021, about 46 billions of devices will be in use. Some of these devices are in service in safety and security critical domains, and even in domains that are not necessarily critical, privacy issues may arise with devices collecting and transmitting a lot of personal information. Moreover insufficiently secured devices may be used for example for massive distributed denial of service attacks. This raises important security challenges. Formal methods have been used successfully for years in highly critical domains, now they can help to bring security into the IoT field. While the correctness of an implementation with respect to a formal functional specification provides the strongest form of guarantee, it can be very costly to achieve. In practice it is therefore more common to rely on a combination of formal methods to achieve an appropriate degree of guarantee: static analyses to guarantee the absence of runtime errors, deductive verification of functional correctness, dynamic verification for parts that cannot be proved using deductive verification. Frama-C1 is a source code analysis platform that aims at conducting verification of industrial-size programs written in ISO C99 source code. Frama-C fully supports the combination of formal methods approach, by providing to its users with a collection of plug-ins that perform static and dynamic analysis for safety and security critical software. Moreover collaborative verification across cooperating plugins is enabled by their integration on top of a shared kernel, and their compliance to a common specification language: ACSL [1]. Recently Frama-C has been applied to the verification of software in the context of the Internet of Things, more
SMC-PBC-SVM: A Parallel Pmplementation of Support Vector Machines for Data Classification

The Support Vector Machine (SVM) is one of the most effective machine learning algorithms for data classification, which have a significant area of research. Since the training process of large datasets is computationally intensive, there is a need to improve its efficiency using high performance computing techniques. In this paper, we developed an efficient parallel algorithm, SMC-PBC-SVM, which combines a Parallel Binary Class with Serial Multi-class Support Vector Machines for classification. The SMC-PBC-SVM algorithm was implemented using the object-oriented C++ programming language and standard Message passing Interface (MPI) communication routines. The parallel code was executed on an ALBACORE Linux cluster, and then tested with four datasets with different sizes: Earthworm, Protein, Mnist, and Mnist8m. The results show that the SMC-PBC-SVM implementation can significantly improve the performance of data classification without the loss of accuracy. The results also demonstrated a form of proportionality between the size of the dataset and the SMCPBC-SVM efficiency. As the dataset becomes larger, the SMCPBC-SVM achieves a higher efficiency. KeywordsClassification; SVM; parallel computing.