Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison the diagnostic value of serological and molecular methods for screening and detecting Chlamydia trachomatis in semen of infertile men: A cross-sectional study

Background: Chlamydia trachomatis (CT) with damaging effects on sperm quality parameters can often cause infertility in men. Objective: The main objective of this study was to determine the diagnostic value of polymerase chain reaction (PCR) and enzyme linked immuno sorbent assay (ELISA) for screening and detecting CT in semen samples of infertile men. Materials and Methods: In this cross-sectional study, 465 men referring to the clinical laboratory of Royan Institute were chosen for primary screening and detection of the presence of CT. 93 samples were normozoospermia with normal sperm parameters i.e. sperm number, motility and morphology (Asymptomatic) and 372 had abnormal sperm parameters (Symptomatic) in semen analysis. ELISA test was performed as the screening test. Samples with optical density (OD) >0.200 were selected as the case and asymptomatic samples with OD <0.200 were selected as the control group for the confirmatory test. PCR assay was used to confirm the serological results. Results: In the case groups (n=62), 4 out of 32 symptomatic samples (12.5%), and 1 out of 30 asymptomatic samples (3.3%) revealed positive results in PCR. No PCR positive sample was observed in the control group (n=34). The final results revealed that considering OD >0.400 as the ELISA positive, the diagnostic value of CT-ELISA positive in symptomatic and asymptomatic infertile patients were 0.019 (7 of 372) and 0.021 (2 of 93), respectively. There was no relationship between the presence of CT infection and different sperm abnormalities. Conclusion: The anti-CT IgA ELISA test may be introduced as an appropriate tool for screening purpose in the seminal plasma to select suspicious samples for PCR confirmatory tests.
Online Compact Convexified Factorization Machine

Factorization Machine (FM) is a supervised learning approach with a powerful capability of feature engineering. It yields state-of-the-art performances in various batch learning tasks where all the training data is made available prior to the training. However, in real-world applications where the data arrives sequentially in a streaming manner, the high cost of re-training with batch learning algorithms has posed formidable challenges in the online learning scenario. The initial challenge is that no prior formulations of FM could directly fulfill the requirements in Online Convex Optimization (OCO) -- the paramount framework for online learning algorithm design. To address this aforementioned challenge, we invent a new convexification scheme leading to a Compact Convexified FM (CCFM) that seamlessly meets the requirements in OCO. However for learning Compact Convexified FM (CCFM) in the online learning settings, most existing algorithms suffer from expensive projection operations. To address this subsequent challenge, we follow the general projection-free algorithmic framework of Online Conditional Gradient and propose an Online Compact Convex Factorization Machine (OCCFM) algorithm that eschews the projection operation with efficient linear optimization steps. In support of the proposed OCCFM in terms of its theoretical foundation, we prove that the developed algorithm achieves a sub-linear regret bound. To evaluate the empirical performance of OCCFM, we conduct extensive experiments on 6 real-world datasets for online regression and online classification tasks. The experimental results show that OCCFM outperforms the state-of-art online learning methods for FM.
Maintenance of Physical Function 1 Year After Exercise Intervention in At-Risk Older Adults: Follow-up From the LIFE Study

Background Structured physical activity interventions delay the onset of disability for at-risk older adults. However, it is not known if at-risk older adults continue to participate in physical activity or maintain mobility benefits after cessation of structured intervention. Methods One thousand six hundred and thirty-five sedentary men and women aged 70-89 years with Short Physical Performance Battery (SPPB) scores of 9 or less and able to walk 400 m were randomized to a structured, moderate-intensity physical activity (PA) program consisting of center-based (twice/week) and home-based (three to four times per week) aerobic, resistance, and flexibility training or a health education (HE) program combined with upper extremity stretching. Results Most of the participants (88% of HE and 87% of PA) returned for a follow-up visit (POST) 1 year after cessation of formal intervention. The HE group reported about 1-hour less activity per week than the PA group at end of intervention (LAST TRIAL; -68.9; 95% confidence interval [CI] = -86.5 to -51.3) but similar weekly activity at POST (-13.5; 95% CI = -29.5 to 2.47). SPPB did not differ between the two groups at LAST TRIAL (-0.06; 95% CI = -0.31 to 0.19) nor POST (-0.18; 95% CI = -0.45 to 0.088). Conclusions Although sedentary at-risk older adults increased their physical activity during a structured physical activity intervention, they did not continue at this level following the cessation of intervention. Future exercise interventions need to include novel methods to support older adults in continued physical activity following structured interventions.
Salvage Surgery after Radiation Failure in T1/T2 Larynx Cancer: Outcomes following Total versus Conservation Surgery

Objective After radiation failure for early T-stage larynx cancer, national guidelines recommend salvage surgery. Total laryngectomy and conservation laryngeal surgery with an open or endoscopic approach are both used. Beyond single-institution studies, there is a lack of evidence concerning the outcomes of these procedures. We aim to study whether treatment with conservation laryngeal surgery is associated with poorer outcomes than treatment with total laryngectomy as salvage surgery after radiation failure for T1/T2 larynx cancers. Study Design A retrospective study was conducted of adult squamous cell larynx cancer cases in the National Cancer Database diagnosed from 2004 to 2012. Setting Commission on Cancer cancer programs in the United States. Methods Demographic, facility, tumor, and survival variables were included in the analyses. Multivariate survival regressions as well as univariate Kaplan-Meier analyses were conducted. Results Slightly more than 7% of patients receiving radiotherapy for T1/T2 larynx cancers later received salvage surgery. Salvage with partial laryngectomy was not associated with diminished survival as compared with total laryngectomy. However, positive surgical margins were associated with worse outcomes (hazard ratio, 1.782; P = .001), and a larger percentage of patients receiving partial laryngectomy had positive margins than those receiving total laryngectomy. Facility characteristics were not associated with differences in salvage surgery type or outcomes. Conclusion In recognition of the inherent selection bias, patients who experienced recurrences after radiation for T1/T2 larynx cancer and underwent conservation salvage laryngeal surgery demonstrated clinical outcomes similar to those of patients undergoing salvage total laryngectomy. Increased rates of positive surgical margins were observed among patients undergoing salvage conservation surgery.
Influence of gender, working field and psychosocial factors on the vulnerability for burnout in mental hospital staff: results of an Austrian cross‐sectional study

INTRODUCTION According to the European Agency for Safety and Health at Work (EU-OSHA), hospitals represent a work environment with high job strain. Prolonged perceived occupational stress may result in symptoms of burnout, such as emotional exhaustion (EE), depersonalisation (DP) and reduced personal accomplishment (PA). Understanding which factors may reduce vulnerability for burnout is an important requirement for well-targeted occupational stress prevention in mental hospital staff. OBJECTIVE To identify the influence of gender, age, working field, family structure, education, voluntarily occupational training during holidays and length of stay on job on occupational stress perception. METHODS In a cross-sectional design, 491 employees (311 female, 180 male) of an Austrian mental health centre participated in the study. The extent of perceived occupational stress was assessed by the Maslach Burnout Inventory (MBI) with the scales for emotional exhaustion, depersonalisation and personal accomplishment. Participants were divided according to their working field in those working with/without patients. FINDINGS Prevalence of emotional exhaustion was higher in women working with patients compared to men working with patients (25% vs. 18%, p = 0.003). Age above 45 years was significantly associated with decreased vulnerability for burnout in men (EE p = 0.040, DP p = 0.010, PA p = 0.007), but not in women. A lower level of education had a significant impact on depersonalisation in both sexes (p = 0.001 for men, p = 0.048 for women). Length of stay on job showed a significant influence on emotional exhaustion. No significant relationship was found between family structure and vulnerability for burnout. CONCLUSION Gender had a differential effect on perceived occupational stress indicating a need for gender-tailored preventive strategies. Age, working field, education, voluntarily occupational training during holidays and length of stay on job affect vulnerability for burnout in mental hospital staff.
Ecological consequences of forest elephant declines for Afrotropical forests

Poaching is rapidly extirpating African forest elephants (Loxodonta cyclotis) from most of their historical range, leaving vast areas of elephant‐free tropical forest. Elephants are ecological engineers that create and maintain forest habitat; thus, their loss will have large consequences for the composition and structure of Afrotropical forests. Through a comprehensive literature review, we evaluated the roles of forest elephants in seed dispersal, nutrient recycling, and herbivory and physical damage to predict the cascading ecological effects of their population declines. Loss of seed dispersal by elephants will favor tree species dispersed abiotically and by smaller dispersal agents, and tree species composition will depend on the downstream effects of changes in elephant nutrient cycling and browsing. Loss of trampling and herbivory of seedlings and saplings will result in high tree density with release from browsing pressures. Diminished seed dispersal by elephants and high stem density are likely to reduce the recruitment of large trees and thus increase homogeneity of forest structure and decrease carbon stocks. The loss of ecological services by forest elephants likely means Central African forests will be more like Neotropical forests, from which megafauna were extirpated thousands of years ago. Without intervention, as much as 96% of Central African forests will have modified species composition and structure as elephants are compressed into remaining protected areas. Stopping elephant poaching is an urgent first step to mitigating these effects, but long‐term conservation will require land‐use planning that incorporates elephant habitat into forested landscapes that are being rapidly transformed by industrial agriculture and logging.
The SQ House Dust Mite SLIT-Tablet Is Well Tolerated in Patients with House Dust Mite Respiratory Allergic Disease

Background: The SQ house dust mite (HDM) SLIT-tablet (ALK, Denmark) addresses the underlying cause of HDM respiratory allergic disease, and a clinical effect has been demonstrated for both HDM allergic rhinitis and allergic asthma. Here, we present pooled safety data from an adult population with HDM respiratory allergy, with particular focus on the impact of asthma on the SQ HDM SLIT-tablet tolerability profile. Methods: Safety data from 2 randomised double-blind, placebo-controlled clinical trials were included: MT-04: 834 adults with HDM allergic asthma not well controlled by inhaled corticosteroids and with HDM allergic rhinitis, and MT-06: 992 adults with moderate-to-severe HDM allergic rhinitis despite the use of allergy pharmacotherapy and with or without asthma. Results: The proportion of subjects experiencing adverse events (AEs) was greater in the active treatment group (12 SQ-HDM; 73% of subjects) compared to placebo (53%). The most common treatment-related AEs were local allergic reactions. No AEs were reported as systemic allergic reactions. Regardless of asthma status, most AEs were mild or moderate (>97% of AEs) and the frequency of serious AEs was low. Subgroup analysis revealed no statistically significant difference in the risk of experiencing moderate or severe treatment-related AEs for subjects with asthma compared to subjects without asthma (p = 0.88). In addition, subjects with partly controlled or uncontrolled asthma were no more likely to experience moderate or severe treatment-related AEs than subjects with controlled asthma (p = 0.42). Conclusion: The SQ HDM SLIT-tablet is well tolerated, and the safety profile was comparable for subjects with HDM respiratory allergic disease irrespective of asthma status.
Chemical-protein relation extraction with ensembles of SVM, CNN, and RNN models

Text mining the relations between chemicals and proteins is an increasingly important task. The CHEMPROT track at BioCreative VI aims to promote the development and evaluation of systems that can automatically detect the chemical-protein relations in running text (PubMed abstracts). This manuscript describes our submission, which is an ensemble of three systems, including a Support Vector Machine, a Convolutional Neural Network, and a Recurrent Neural Network. Their output is combined using a decision based on majority voting or stacking. Our CHEMPROT system obtained 0.7266 in precision and 0.5735 in recall for an f-score of 0.6410, demonstrating the effectiveness of machine learning-based approaches for automatic relation extraction from biomedical literature. Our submission achieved the highest performance in the task during the 2017 challenge.
Tree shrew (Tupaia belangeri) as a novel laboratory disease animal model

The tree shrew (Tupaia belangeri) is a promising laboratory animal that possesses a closer genetic relationship to primates than to rodents. In addition, advantages such as small size, easy breeding, and rapid reproduction make the tree shrew an ideal subject for the study of human disease. Numerous tree shrew disease models have been generated in biological and medical studies in recent years. Here we summarize current tree shrew disease models, including models of infectious diseases, cancers, depressive disorders, drug addiction, myopia, metabolic diseases, and immune-related diseases. With the success of tree shrew transgenic technology, this species will be increasingly used in biological and medical studies in the future.
Perceived Barriers to Physical Activity in Older and Younger Veterans With Serious Mental Illness

Objective: Individuals with serious mental illness endorse many more medical and psychosocial barriers to physical activity (PA) than the general population. However, it is unknown if older adults with serious mental illness are at greater risk of experiencing barriers to PA than their younger counterparts. Method: The present study utilized a national VA dataset to compare veterans with serious mental illness ages 55 and older (n = 9,044) to veterans with serious mental illness ages 54 and younger (n = 8,782) on their responses to a questionnaire assessment of barriers to PA. Results: Older veterans were more likely to endorse arthritis and cardiopulmonary disease, and less likely to endorse work schedule, as barriers to PA. Conclusions and Implications for Practice: Interventions designed to increase PA for young/middle-aged adults with serious mental illness may be broadly useful for older adults with serious mental illness, with some modification to address specific health concerns.
The HTM Spatial Pooler—A Neocortical Algorithm for Online Sparse Distributed Coding

Hierarchical temporal memory (HTM) provides a theoretical framework that models several key computational principles of the neocortex. In this paper we analyze an important component of HTM, the HTM spatial pooler (SP). The SP models how neurons learn feedforward connections and form efficient representations of the input. It converts arbitrary binary input patterns into sparse distributed representations (SDRs) using a combination of competitive Hebbian learning rules and homeostatic excitability control. We describe a number of key properties of the spatial pooler, including fast adaptation to changing input statistics, improved noise robustness through learning, efficient use of cells and robustness to cell death. In order to quantify these properties we develop a set of metrics that can be directly computed from the spatial pooler outputs. We show how the properties are met using these metrics and targeted artificial simulations. We then demonstrate the value of the spatial pooler in a complete end-to-end real-world HTM system. We discuss the relationship with neuroscience and previous studies of sparse coding. The HTM spatial pooler represents a neurally inspired algorithm for learning sparse representations from noisy data streams in an online fashion.
Highly-Bioreactive Silica-Based Mesoporous Bioactive Glasses Enriched with Gallium(III)

Beneficial effects in bone cell growth and antibacterial action are currently attributed to Ga3+ ions. Thus, they can be used to upgrade mesoporous bioactive glasses (MBGs), investigated for tissue engineering, whenever they released therapeutic amounts of gallium ions to the surrounding medium. Three gallium-enriched MBGs with composition (in mol %) xSiO2–yCaO–zP2O5–5Ga2O3, being x = 70, y = 15, z = 10 for Ga_1; x = 80, y = 12, z = 3 for Ga_2; and x = 80, y = 15, z = 0 for Ga_3, were investigated and compared with the gallium-free 80SiO2–15CaO–5P2O5 MBG (B). 29Si and 31P MAS NMR analyses indicated that Ga3+ acts as network modifier in the glass regions with higher polymerization degree and as network former in the zones with high concentration of classical modifiers (Ca2+ ions). Ga_1 and Ga_2 exhibited a quick in vitro bioactive response because they were coated by an apatite-like layer after 1 and 3 days in simulated body fluid. Although we have not conducted biological tests in this paper (cells or bacteria), Ga_1 released high but non-cytotoxic amounts of Ga3+ ions in Todd Hewitt Broth culture medium that were 140 times higher than the IC90 of Pseudomonas aeruginosa bacteria, demonstrating its potential for tissue engineering applications.
Unconsciously Perceived Fear in Peripheral Vision Alerts the Limbic System: A MEG Study

Background In ecological situations, threatening stimuli often come out from the peripheral vision. Such aggressive messages must trigger rapid attention to the periphery to allow a fast and adapted motor reaction. Several clues converge to hypothesize that peripheral danger presentation can trigger off a fast arousal network potentially independent of the consciousness spot. Methodology/Principal Findings In the present MEG study, spatio-temporal dynamics of the neural processing of danger related stimuli were explored as a function of the stimuli position in the visual field. Fearful and neutral faces were briefly presented in the central or peripheral visual field, and were followed by target faces stimuli. An event-related beamformer source analysis model was applied in three time windows following the first face presentations: 80 to 130 ms, 140 to 190 ms, and 210 to 260 ms. The frontal lobe and the right internal temporal lobe part, including the amygdala, reacted as soon as 80 ms of latency to fear occurring in the peripheral vision. For central presentation, fearful faces evoked the classical neuronal activity along the occipito-temporal visual pathway between 140 and 190 ms. Conclusions Thus, the high spatio-temporal resolution of MEG allowed disclosing a fast response of a network involving medial temporal and frontal structures in the processing of fear related stimuli occurring unconsciously in the peripheral visual field. Whereas centrally presented stimuli are precisely processed by the ventral occipito-temporal cortex, the related-to-danger stimuli appearing in the peripheral visual field are more efficient to produce a fast automatic alert response possibly conveyed by subcortical structures.
Residual and Systemic Efficacy of Chlorantraniliprole and Flubendiamide Against Corn Earworm (Lepidoptera: Noctuidae) in Soybean

Experiments were conducted in Mississippi from 2013 to 2015 to determine the systemic and residual efficacy of chlorantraniliprole and flubendiamide against corn earworm, Helicoverpa zea (Boddie), in soybean. Both insecticides were applied at V4 and R3. Ten leaves that were present at the time of application and 10 newly emerged leaves that were not present at the time of application were collected to measure residual and systemic efficacy, respectively. Ten pods were removed from each plot at R5.5. For all assays, corn earworm larvae were placed on plant material. Chlorantraniliprole appeared to provide systemic control of H. zea, but was dependent on soybean growth stage at the time of application. In the V4 experiment, chlorantraniliprole resulted in greater mortality than the control on new leaves at 7 d after treatment, but not at 14 d. In the R3 experiment, chlorantraniliprole resulted in greater than 90% mortality on new leaves at all evaluation intervals. Mortality of H. zea on new leaves was <17% for flubendiamide and was not different than the control. Both insecticides resulted in significant mortality of H. zea on leaves that were present at the time of application for at least 31 d after application. Chlorantraniliprole resulted in greater mortality than flubendiamide at 24 and 31 d. Neither insecticide resulted in mortality of H. zea feeding on reproductive structures. These results suggest that chlorantraniliprole moves to new vegetative structures but not to reproductive structures of soybean, and that flubendiamide does not move systemically.
Functional Amyloid Protection in the Eye Lens: Retention of α-Crystallin Molecular Chaperone Activity after Modification into Amyloid Fibrils

Amyloid fibril formation occurs from a wide range of peptides and proteins and is typically associated with a loss of protein function and/or a gain of toxic function, as the native structure of the protein undergoes major alteration to form a cross β-sheet array. It is now well recognised that some amyloid fibrils have a biological function, which has led to increased interest in the potential that these so-called functional amyloids may either retain the function of the native protein, or gain function upon adopting a fibrillar structure. Herein, we investigate the molecular chaperone ability of α-crystallin, the predominant eye lens protein which is composed of two related subunits αA- and αB-crystallin, and its capacity to retain and even enhance its chaperone activity after forming aggregate structures under conditions of thermal and chemical stress. We demonstrate that both eye lens α-crystallin and αB-crystallin (which is also found extensively outside the lens) retain, to a significant degree, their molecular chaperone activity under conditions of structural change, including after formation into amyloid fibrils and amorphous aggregates. The results can be related directly to the effects of aging on the structure and chaperone function of α-crystallin in the eye lens, particularly its ability to prevent crystallin protein aggregation and hence lens opacification associated with cataract formation.