Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut–Brain Axis and Mood Disorder

Humans have over 100 trillion bacteria, highly abundant in the intestinal tract. Evidence suggests that intestinal microbiota is associated with the neuro-endocrine-immune pathways and can be associated with various mood disorders. This review summarizes findings from studies looking into neurobiochemical, neuroendocrine, and neuroimmune system mechanisms of the gut–brain axis to determine the relationship between intestinal microbiota and mood disorders. The effect of prebiotics, probiotics and antibiotics on mood disorders are also discussed, with the aim to propose some new therapeutic strategies for mood disorders.
Spatial relationship between climatic diversity and biodiversity conservation value

Capturing the full range of climatic diversity in a reserve network is expected to improve the resilience of biodiversity to climate change. Therefore, a study on systematic conservation planning for climatic diversity that explicitly or implicitly hypothesizes that regions with higher climatic diversity support greater biodiversity is needed. However, little is known about the extent and generality of this hypothesis. We used the case of Yunnan, southwest China, to quantitatively classify climatic units and modeled 4 climatic diversity indicators, including the variety (VCU), rarity (RCU), endemism (ECU) of climatic units, and a composite index of climatic diversity (CICD). We used 5 schemes that reliably identify priority conservation areas (PCAs) to identify areas with high biodiversity conservation value. We then investigated the spatial relationships between the 4 climatic diversity indicators and the results of the 5 PCA schemes and assessed the representation of climatic diversity within the existing nature reserves. The CICD was the best indicator of areas with high conservation value, followed by ECU and RCU. Contrary to conventional knowledge, VCU was not positively associated with biodiversity conservation value. The rarer or more endemic climatic units tended to have higher reserve coverage than the more common units. However, only 28 units, covering 10.5% of the land in Yunnan, had >17% of their areas protected. In addition to climatic factors, topography and human disturbances also significantly affected the relationship between climatic diversity and biodiversity conservation value. Our results suggest that climatic diversity can be an effective surrogate for establishing a more robust reserve network under climate change in Yunnan. Our study improves understanding of the relationship between climatic diversity and biodiversity and helps build an evidence‐based foundation for systematic conservation planning that targets climatic diversity in response to climate change.
Association of Cardiovascular Outcomes With Masked Hypertension Defined by Home Blood Pressure Monitoring in a Japanese General Practice Population

Importance The clinical outcomes associated with masked hypertension defined by home blood pressure monitoring (HBPM) in clinical settings remain uncertain. Objective To assess the association between masked hypertension and cardiovascular disease events in clinical settings. Design, Setting, and Participants This observational cohort study used data from 4261 outpatients treated at 71 primary practices or university hospitals throughout Japan who were enrolled in the Japan Morning Surge–Home Blood Pressure study between January 1, 2005, and December 31, 2012. Participants had a history of or risk factors for cardiovascular disease and were followed up through March 31, 2015. Participants underwent clinic blood pressure (BP) measurements on 2 occasions as well as HBPM measurements in the morning and evening for a 14-day period. Urine albumin to creatinine ratio and circulating brain (or B-type) natriuretic peptide levels were quantified at baseline as a marker of cardiovascular end-organ damage. Data were analyzed from July 1, 2017, to October 31, 2017. Exposures Participants were categorized into 4 BP groups: (1) masked hypertension—hypertensive home BP levels (systolic, ≥135 mm Hg; diastolic, ≥85 mm Hg) and nonhypertensive clinic BP levels (systolic, <140 mm Hg; diastolic, <90 mm Hg); (2) white-coat hypertension—nonhypertensive home BP levels (systolic, <135 mm Hg; diastolic, <85 mm Hg) and hypertensive clinic BP levels (systolic, ≥140 mm Hg; diastolic, ≥90 mm Hg); (3) sustained hypertension—hypertensive home and clinic BP levels; and (4) controlled BP—nonhypertensive home and clinic BP levels. Main Outcomes and Measures Incident stroke and coronary heart disease. Results Of the 4261 participants, 2266 (53.2%) were women, 3374 (79.2%) were taking antihypertensive medication, and the mean (SD) age was 64.9 (10.9) years. During a median (interquartile range) follow-up of 3.9 (2.4-4.6) years, 74 stroke (4.4 per 1000 person-years) and 77 coronary heart disease (4.6 per 1000 person-years) events occurred. The masked hypertension group had a greater risk for stroke compared with the controlled BP group (hazard ratio, 2.77; 95% CI, 1.20-6.37), independent of traditional cardiovascular risk factors, urine albumin to creatinine ratio, and circulating B-type natriuretic peptide levels. Conversely, masked hypertension yielded no association with coronary heart disease risk. Conclusions and Relevance In the Japanese general practice population, masked hypertension defined by HBPM may be associated with an increased risk for stroke events. Use of HBPM may improve the assessment of BP-related risks and identify new therapeutic interventions aimed at preventing cardiovascular disease events.
Compact and Computationally Efficient Representation of Deep Neural Networks

At the core of any inference procedure, deep neural networks are dot product operations, which are the component that requires the highest computational resources. For instance, deep neural networks, such as VGG-16, require up to 15-G operations in order to perform the dot products present in a single forward pass, which results in significant energy consumption and thus limits their use in resource-limited environments, e.g., on embedded devices or smartphones. One common approach to reduce the complexity of the inference is to prune and quantize the weight matrices of the neural network. Usually, this results in matrices whose entropy values are low, as measured relative to the empirical probability mass distribution of its elements. In order to efficiently exploit such matrices, one usually relies on, inter alia, sparse matrix representations. However, most of these common matrix storage formats make strong statistical assumptions about the distribution of the elements; therefore, cannot efficiently represent the entire set of matrices that exhibit low-entropy statistics (thus, the entire set of compressed neural network weight matrices). In this paper, we address this issue and present new efficient representations for matrices with low-entropy statistics. Alike sparse matrix data structures, these formats exploit the statistical properties of the data in order to reduce the size and execution complexity. Moreover, we show that the proposed data structures can not only be regarded as a generalization of sparse formats but are also more energy and time efficient under practically relevant assumptions. Finally, we test the storage requirements and execution performance of the proposed formats on compressed neural networks and compare them to dense and sparse representations. We experimentally show that we are able to attain up to $\times 42$ compression ratios, $\times 5$ speed ups, and $\times 90$ energy savings when we lossless convert the state-of-the-art networks, such as AlexNet, VGG-16, ResNet152, and DenseNet, into the new data structures and benchmark their respective dot product.
Appropriateness of antibiotic prescriptions for acute sinusitis and pharyngitis in an integrated healthcare system

Abstract We evaluated the appropriateness of antibiotic prescriptions for acute sinusitis and pharyngitis. Overall, 81% of antibiotic prescriptions for acute sinusitis were inappropriate and 48% of antibiotic prescriptions for pharyngitis were inappropriate. Types of prescribing errors differed between the 2 infections, including lack of an indication for antibiotics and excessive duration in ~50% of sinusitis cases and incorrect antibiotic dose in ~33% of pharyngitis cases. Infect Control Hosp Epidemiol 2018; 0, 1–3
Influence of Psychological Empowerment on Organizational Commitment among Medical Employees in a Hospital Setting.

INTRODUCTION People within organizations are a key factor for efficiency. Thus employee empowerment has become a popular management strategy. The study aimed to investigate the relationship between psychological empowerment and organizational commitment among medical staff of a hospital in Zahedan city. METHODS This cross sectional study was carried out in 2013. A random sample of 172 medical employees in Khatam-ol-Anbia hospital at Zahedan city was selected and responded to items of the questionnaires using a 7-point Likert scale ranging from 1 to 7. For measuring psychological empowerment and organizational commitment, Mishra & Spreitzer's scale and Meyer and Allen's questionnaire were used. A higher score means a higher degree of psychological empowerment or organizational commitment. Analysis was carried out using SPSS. RESULTS The level of organizational commitment and psychological empowerment significantly were higher than average. There was a significant positive relationship between employees' empowerment and their commitment to organization. Psychological empowerment was a significant predictor of organizational commitment (β = .524). Out of the five dimensions of empowerment three dimensions are significant predictors of commitment and explain 37.1% of the variance in commitment. CONCLUSIONS Due to The positive influence of psychological empowerment on organizational commitment, programs for in-service education should focus on facilitating psychological empowerment to improve and increase organizational commitment. Also, since impact of employees psychological empowerment on organizational commitment partially supported, there are other variables that influence the organizational commitment.
To model magnetic field of RF planar coil for portable NMR applications

In this paper, an analytical model to calculate magnetic field distribution for Planar Spiral Coil (PSC) is proposed. The magnetic field modeling plays a crucial role where magnetic field uniformity is of highest concern. PSC of three turns, inner radius (1mm), is modeled with the proposed model. Analytical results are verified with experimentally measured magnetic field results. Analytical modeling is carried out in MATLAB, whereas 3D FDTD tool Computer Simulation Technology (CST) is used for simulation.
Effect of a Patient and Clinician Communication-Priming Intervention on Patient-Reported Goals-of-Care Discussions Between Patients With Serious Illness and Clinicians: A Randomized Clinical Trial

Importance Clinician communication about goals of care is associated with improved patient outcomes and reduced intensity of end-of-life care, but it is unclear whether interventions can improve this communication. Objective To evaluate the efficacy of a patient-specific preconversation communication-priming intervention (Jumpstart-Tips) targeting both patients and clinicians and designed to increase goals-of-care conversations compared with usual care. Design, Setting, and Participants Multicenter cluster-randomized trial in outpatient clinics with physicians or nurse practitioners and patients with serious illness. The study was conducted between 2012 and 2016. Interventions Clinicians were randomized to the bilateral, preconversation, communication-priming intervention (n = 65) or usual care (n = 67), with 249 patients assigned to the intervention and 288 to usual care. Main Outcomes and Measures The primary outcome was patient-reported occurrence of a goals-of-care conversation during a target outpatient visit. Secondary outcomes included clinician documentation of a goals-of-care conversation in the medical record and patient-reported quality of communication (Quality of Communication questionnaire [QOC]; 4-indicator latent construct) at 2 weeks, as well as patient assessments of goal-concordant care at 3 months and patient-reported symptoms of depression (8-item Patient Health Questionnaire; PHQ-8) and anxiety (7-item Generalized Anxiety Disorder survey; GAD-7) at 3 and 6 months. Analyses were clustered by clinician and adjusted for confounders. Results We enrolled 132 of 485 potentially eligible clinicians (27% participation; 71 women [53.8%]; mean [SD] age, 47.1 [9.6] years) and 537 of 917 eligible patients (59% participation; 256 women [47.7%]; mean [SD] age, 73.4 [12.7] years). The intervention was associated with a significant increase in a goals-of-care discussion at the target visit (74% vs 31%; P < .001) and increased medical record documentation (62% vs 17%; P < .001), as well as increased patient-rated quality of communication (4.6 vs 2.1; P = .01). Patient-assessed goal-concordant care did not increase significantly overall (70% vs 57%; P = .08) but did increase for patients with stable goals between 3-month follow-up and last prior assessment (73% vs 57%; P = .03). Symptoms of depression or anxiety were not different between groups at 3 or 6 months. Conclusions and Relevance This intervention increased the occurrence, documentation, and quality of goals-of-care communication during routine outpatient visits and increased goal-concordant care at 3 months among patients with stable goals, with no change in symptoms of anxiety or depression. Understanding the effect on subsequent health care delivery will require additional study. Trial Registration ClinicalTrials.gov identifier: NCT01933789
A cerebellar adaptation to uncertain inputs

Under uncertain conditions, the cerebellum keeps responses adaptive by scaling the probability, but not the size of response. Noise and variability are inherent and unavoidable features of neural processing. Despite this physiological challenge, brain systems function well, suggesting the existence of adaptations that cope with noise. We report a novel adaptation that the cerebellum implements to maintain correct responses in the face of ambiguous inputs. We found that under these conditions, the cerebellum used a probabilistic binary choice: Although the probability of behavioral response gradually increased or decreased depending on the degree of similarity between current and trained inputs, the size of response remained constant. That way the cerebellum kept responses adaptive to trained input corrupted by noise while minimizing false responses to novel stimuli. Recordings and analysis of Purkinje cells activity showed that the binary choice is made in the cerebellar cortex. Results from large-scale simulation suggest that internal feedback from cerebellar nucleus back to cerebellar cortex plays a critical role in implementation of binary choice.
Lung cancer in never smokers from the Princess Margaret Cancer Centre

Introduction Lung cancer in never smokers represents a distinct epidemiological, clinical, and molecular entity. Results Most 712 never smoking lung cancer patients were female (72%) with a median age at diagnosis of 62.2 years (18–94). Caucasians (46%), East Asians (42%), adenocarcinoma histology (87%) and presentation with metastatic disease at diagnosis (59%) were common. Of 515 patients with available archival tissue, the most common identified single mutations were EGFR (52.2%), followed by ALK (7.5%), KRAS (2.3%), TP53 (1.3%), ERBB2 (1%), BRAF (0.4%), PIK3CA (0.4%), SMAD4 (0.4%), CTNNB1 (0.2%), AKT1 (0.2%), and NRAS (0.2%); 8% tumors had multiple mutations, while 25.8% had none identified. Median overall survival (mOS) was 42.2 months (mo) for the entire cohort. Patients with mutations in their tumors had significantly better mOS (69.5 mo) when compared to those without (31.0 mo) (HR = 0.59; 95% CI: 0.44–0.79; p < 0.001). Earlier stage (p < 0.001), adenocarcinoma histology (p = 0.012), good performance status (p < 0.001) and use of targeted therapy (p < 0.001) were each independently associated with longer survival. Patients with ALK-translocation-positive tumours have significantly longer OS compared to those without any mutations (p = 0.0029) and to those with other and null mutations (p = 0.022). Conclusions Lung cancer in never smokers represents a distinct clinical and molecular entity characterized by a high incidence of targetable mutations and long survival. Methods We analyzed retrospectively the data from electronic patient records of never smokers diagnosed with lung cancer treated at the Princess Margaret Cancer Centre (Toronto) between 1988–2015 to characterize demographic and clinical features, pathology, molecular profile (using hotspot or targeted sequencing panels), treatment and survival.
Understanding Performance Decrements in a Letter-Canceling Task: Overcoming Habits or Inhibition of Reading

The importance of self-regulation in human behavior is readily apparent and diverse theoretical accounts for explaining self-regulation failures have been proposed. Typically, these accounts are based on a sequential task methodology where an initial task is presented to deplete self-regulatory resources, and carryover effects are then examined on a second outcome task. In the aftermath of high profile replication failures using a popular letter-crossing task as a means of depleting self-regulatory resources and subsequent criticisms of that task, current research into self-control is currently at an impasse. This is largely due to the lack of empirical research that tests explicit assumptions regarding the initial task. One such untested assumption is that for resource depletion to occur, the initial task must first establish an habitual response and then this habitual response must be inhibited, with behavioral inhibition being the causal factor in inducing depletion. This study reports on four experiments exploring performance on a letter-canceling task, where the rules for target identification remained constant but the method of responding differed (Experiment 1) and the coherence of the text was manipulated (Experiments 1–4). Experiment 1 established that habit forming and behavioral inhibition did not produce any performance decrement when the targets were embedded in random letter strings. Experiments 2–4 established that target detection was sensitive to language characteristics and the coherence of the background text, suggesting that participants’ automatic reading processes is a key driver of performance in the letter-e task.
Effects of human relaxin-2 (serelaxin) on hypoxic pulmonary vasoconstriction during acute hypoxia in a sheep model

Purpose Hypoxia induces pulmonary vasoconstriction with a subsequent increase of pulmonary artery pressure (PAP), which can result in pulmonary hypertension. Serelaxin has shown an increase of pulmonary hemodynamic parameters after serelaxin injection. We therefore investigated the response of pulmonary hemodynamic parameters after serelaxin administration in a clinically relevant model. Methods Six controls and six sheep that received 30 μg/kg serelaxin underwent right heart catheterization during a 12-minute hypoxia period (inhalation of 5% oxygen and 95% nitrogen) and subsequent reoxygenation. Systolic, diastolic, and mean values of both PAP (respectively, PAPs, PAPd, and PAPm) and pulmonary capillary wedge pressure (respectively, PCWPs, PCWPd, and PCWPm), blood gases, heart rate (HR), and both peripheral and pulmonary arterial oxygen saturation were obtained. Cardiac output (CO), stroke volume (SV), pulmonary vascular resistance (PVR), pulmonary arterial compliance (PAcompl), and systemic vascular resistance (SVR) were calculated. Results The key findings of the current study are that serelaxin prevents the rise of PAPs (p≤0.001), PAPm, PCWPm, PCWPs (p≤0.03), and PAPd (p≤0.05) during hypoxia, while it simultaneously increases CO and SV (p≤0.001). Similar courses of decreases of PAPm, PAPd, PAPs, CO, SVR (p≤0.001), and PCWPd (p≤0.03) as compared to hypoxic values were observed during reoxygenation. In direct comparison, the experimental groups differed during hypoxia in regard to HR, PAPm, PVR, and SVR (p≤0.03), and during reoxygenation in regard to HR (p≤0.001), PAPm, PAPs, PAPd, PVR, SVR (p≤0.03), and PCWPd (p≤0.05). Conclusion The findings of this study suggest that serelaxin treatment improves pulmonary hemodynamic parameters during acute hypoxia.
Rodent Models of Experimental Endometriosis: Identifying Mechanisms of Disease and Therapeutic Targets

Background: Although it has been more than a century since endometriosis was initially described in the literature, understanding the etiology and natural history of the disease has been challenging. However, the broad utility of murine and rat models of experimental endometriosis has enabled the elucidation of a number of potentially targetable processes which may otherwise promote this disease. Objective: To review a variety of studies utilizing rodent models of endometriosis to illustrate their utility in examining mechanisms associated with development and progression of this disease. Results: Use of rodent models of endometriosis has provided a much broader understanding of the risk factors for the initial development of endometriosis, the cellular pathology of the disease and the identification of potential therapeutic targets. Conclusion: Although there are limitations with any animal model, the variety of experimental endometriosis models that have been developed has enabled investigation into numerous aspects of this disease. Thanks to these models, our under-standing of the early processes of disease development, the role of steroid responsiveness, inflammatory processes and the peritoneal environment has been advanced. More recent models have begun to shed light on how epigenetic alterations con-tribute to the molecular basis of this disease as well as the multiple comorbidities which plague many patients. Continued de-velopments of animal models which aid in unraveling the mechanisms of endometriosis development provide the best oppor-tunity to identify therapeutic strategies to prevent or regress this enigmatic disease.
The MR-Base platform supports systematic causal inference across the human phenome

Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base (http://www.mrbase.org): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies.