Miracle-dz/UniFAR-FTUs huggingface dataset:
A clinical guideline on Dientamoeba fragilis infections

Abstract Dientamoeba fragilis (D. fragilis) is an intestinal parasite frequently detected in humans with abdominal pain and diarrhoea, but it is also commonly found in asymptomatic subjects. Hence its clinical relevance is often disputed. The introduction of polymerase chain reaction (PCR) is a versatile and sensitive diagnostic technique for the detection of intestinal parasites, and in some Western world countries PCR has almost completely replaced microscopic diagnostics. PCR has however resulted in an increase in the number of D. fragilis-positive patients. The disputed pathogenic nature of this intestinal parasite and an apparent increase in the incidence of patients with positive PCR results have renewed the discussions between clinicians and microbiologists on how to deal with an infected patient. Moreover, treatment guidelines differ throughout the world which makes it difficult for clinicians to choose an optimal therapeutic regimen. Aim To summarize and discuss the current knowledge on the pathogenicity, best diagnostic approach, treatment and follow-up of children and adults infected with D. fragilis.
Neighborhood collective efficacy and collective action: The role of civic engagement.

Theory suggests that by strengthening collective efficacy among neighbors, neighborhoods can more effectively engage in collective action. The research linking the two components of collective efficacy-social cohesion and social control-with collective action is limited. This study uses structural equation modeling with a nationally representative sample from the United States Census Bureau's American Housing Survey (N = 22,106) to analyze these relationships. This analysis finds that neither component of collective efficacy is directly associated with collective action. Instead, social cohesion is negatively, directly associated with civic engagement, social control is positively directly associated with civic engagement, and civic engagement is positively associated with collective action. Social cohesion and social control are indirectly associated with collective action when including civic engagement. Understanding the associations between collective efficacy, civic engagement, and collective action is informative for understanding effective and efficient community participation to facilitate change.
An approach to management of critical indoor air problems in school buildings.

This study was conducted in a school center that had been the focus of intense public concern over 2 years because of suspected mold and health problems. Because several attempts to find solutions to the problem within the community were not satisfactory, outside specialists were needed for support in solving the problem. The study group consisted of experts in civil engineering, indoor mycology, and epidemiology. The studies were conducted in close cooperation with the city administration. Structures at risk were opened, moisture and temperature were measured, and the causes of damage were analyzed. Microbial samples were taken from the air, surfaces, and materials. Health questionnaires were sent to the schoolchildren and personnel. Information on the measurements and their results was released regularly to school employees, students and their parents, and to the media. Repairs were designed on the basis of this information. Moisture damage was caused mainly by difficult moisture conditions at the building site, poor ventilation, and water leaks. Fungal genera (concentrations <200 colony-forming units (cfu)/m(3), <3000 cfu/cm(2)) typical to buildings with mold problems (e.g., Aspergillus versicolor, Eurotium) were collected from the indoor air and surfaces of the school buildings. Where moisture-prone structures were identified and visible signs of damage or elevated moisture content were recorded, the numbers of microbes also were high; thus microbial results from material samples supported the conclusions made in the structural studies. Several irritative and recurrent symptoms were common among the upper secondary and high school students. The prevalence of asthma was high (13%) among the upper secondary school students. During the last 4 years, the incidence of asthma was 3-fold that of the previous 4-year period. ImagesFigure 1
Grammar Induction with Neural Language Models: An Unusual Replication

A substantial thread of recent work on latent tree learning has attempted to develop neural network models with parse-valued latent variables and train them on non-parsing tasks, in the hope of having them discover interpretable tree structure. In a recent paper, Shen et al. (2018) introduce such a model and report near-state-of-the-art results on the target task of language modeling, and the first strong latent tree learning result on constituency parsing. In an attempt to reproduce these results, we discover issues that make the original results hard to trust, including tuning and even training on what is effectively the test set. Here, we attempt to reproduce these results in a fair experiment and to extend them to two new datasets. We find that the results of this work are robust: All variants of the model under study outperform all latent tree learning baselines, and perform competitively with symbolic grammar induction systems. We find that this model represents the first empirical success for latent tree learning, and that neural network language modeling warrants further study as a setting for grammar induction.
PTH assays in dialysis patients: Practical considerations

Parathyroid hormone (PTH) 1‐84 is the main biologically active hormone produced by the parathyroid cells. Circulating PTH molecules include the whole PTH 1‐84 along with amino (N) and carboxyl (C) terminal fragments. While PTH is the best available noninvasive biomarker to assess bone turnover in dialysis patients, the biological roles of individual circulating PTH fragments are still not completely known. The understanding that there is an enormous variation in the target specificity of currently available PTH assays for different circulating forms of PTH has led to the evolution of assays from first to second then third generation. With a reduction in kidney function, there is a preferential increase in circulating C fragments and non‐PTH 1‐84 forms, resulting in a decrease in the ratio of PTH 1‐84/non‐PTH 1‐84. However, there are also substantial differences in between‐assay measurements, with several fold variations in results. Targets based on multiples of the upper limit of normal (ULN) should be used rather than PTH ranges using absolute iPTH values. To date, the second‐generation PTH remains the most widely used assay. Current guidelines recommend following iPTH trends rather than absolute values. Herein, we highlight problems and challenges in PTH assays/measurements and their interpretations in dialysis patients.
Antiphosphatidylserine Antibody as a Cause of Multiple Dural Venous Sinus Thromboses and ST-Elevation Myocardial Infarction

Patient: Male, 48 Final Diagnosis: Antiphospholipid syndrome Symptoms: Chest pain • confusion • seizure-like activity Medication: — Clinical Procedure: Endovascular venous suction thrombectomy Specialty: Hematology Objective: Rare disease Background: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by antibodies directed against phospholipids on plasma membranes. Through unclear mechanisms, APS confers hypercoagulability. APS may cause recurrent thromboses in the arterial and venous vasculature. We report a case of primary APS resulting in cerebral venous thrombosis and ST-elevation myocardial infarction (STEMI) for which only antiphosphatidylserine (aPS) IgM antibody was positive after extensive investigation. Case Report: A 48-year-old male was admitted after a witnessed generalized seizure with subsequent confusion. Imaging demonstrated thrombosis of multiple central nervous system (CNS) sinuses, including the superior sagittal sinus and bilateral transverse sinuses. The patient was heparinized with aggressive hydration, which proved inadequate, prompting endovascular thrombectomy. Three months later, despite anticoagulation therapy, the patient developed a STEMI when International Normalized Ratio (INR) was 1.8. Echocardiogram (ECHO) and PAN CT scan were normal. Initial coagulation studies demonstrated normal anticardiolipin antibody, prothrombin time, partial thromboplastin time, and platelet count. Outpatient coagulation studies revealed normal antithrombin III, protein C/S, hemoglobin electrophoresis, homocysteine, anti-β2 glycoprotein 1 antibodies, and D-Dimer. Factor V Leiden, JAK 2 mutation, prothrombin gene mutation, and tests for paroxysmal nocturnal hemoglobinuria (PNH) were negative. A positive phosphatidylserine IgM was detected. The patient was continued on warfarin (10 mg daily) with a target INR of 3.0–3.5 and clopidogrel (75 mg daily). Conclusions: Despite extensive investigation, this patient only showed evidence of elevated aPS IgM antibodies, likely contributing to his CNS venous sinus thromboses and STEMI. It is important to screen for antiphosphatidylserine antibodies in cases of unprovoked thrombosis when standard thrombophilia analysis is unrevealing. This will assist in identifying pathogenicity and help prevent recurrence of subsequent thromboses.
The detection of primary and secondary EGFR mutations using droplet digital PCR in patients with nonsmall cell lung cancer

Background: We share our experience of using droplet digital polymerase chain reaction (DdPCR) in liquid biopsy specimens for detecting primary and secondary epidermal growth factor receptor (EGFR) mutations among patients with nonsmall-cell lung cancer who had tissue biopsy initially analyzed for del19, L858R and T790M. Materials and Methods: Three groups of patients were chosen: Group 1: patients positive for EGFR mutation (del 19 or L858R) by conventional tissue biopsy that were treatment naïve, Group 2: patients positive for EGFR mutation (del 19 or L858R) by conventional tissue biopsy with acquired resistance to tyrosine kinase inhibitor (TKI) therapy, documented by radiology, and Group 3: no known EGFR mutation detected on primary tissue biopsy and treatment naive. Results: One hundred and thirty-three patients were included in the study. Group 1 had 40 cases, of which 21 (52.5%) and 19 (47.5%) were positive for del19 and L858R mutations, respectively, by tissue biopsy. DdPCR detected primary mutation in all but 5 cases. DdPCR additionally found four patients to have T790M mutation. Group 2 had 73 cases and DdPCR detected T790M mutation in 39 (53.4%) cases. Liquid biopsy also picked the original primary mutation in 56/73 cases. Secondary tissue biopsy for T790M mutation status was performed in 11 patients and while it detected mutation in 2 out of 11 cases, DdPCR detected the same in 7 cases, thus providing significantly superior yield (46% difference, McNemar's test, P value 0.063). Tissue biopsy additionally detected c-MET amplification in a patient who had T790M mutation on liquid biopsy. Group 3 had 20 patients and none were falsely positive for EGFR mutation on liquid biopsy. Overall, DdPCR had a Cohen's kappa of 0.82 (standard error 0.074, 95% CI 0.68–0.97) indicating “very good agreement” with conventional tissue biopsy. Conclusion: DdPCR demonstrated 87.5% sensitivity and 100% specificity in detecting primary EGFR mutations in patients who were treatment naïve with overall positive and negative predictive value of 100% and 80%, respectively. DdPCR demonstrated T790M mutation postprogression on TKI therapy in 53.4% patients.
Linking Structural Capabilities and Workplace Climate in Community Health Centers

Many strategies to improve health care quality focus on improving the structural capabilities of primary care practices, including quality infrastructure and registry use, which are critical to managing chronic diseases. However, improving structural capabilities requires practices to expend significant resources and can be especially disruptive to community health centers (CHCs) serving high proportions of socioeconomically vulnerable patients. We explore the relationship between the structural capabilities and workplace climate in CHCs. The final sample for this analysis includes 25 CHC sites that could be matched across CHC site director surveys of structural capabilities and CHC adult primary care clinicians and staff (n = 446). To estimate the association between structural capabilities and dimensions of workplace climate, we estimated multivariate linear regression models that included the climate scales as dependent variables and the 5 structural capability scales as the main independent variables, with the 3 clinic-level and 2 staff-level covariates. More manageable clinic workload was associated with lower electronic record functionality (β = −0.47, P = .007), but positively associated with quality infrastructure (β = 0.92, P = .007). Staff relationships and quality improvement orientation were positively associated with quality infrastructure (β = 1.09, P = .006 and β = 0.87, P = .005). Manager readiness was associated with more robust quality infrastructure (β = 1.35, P = .016), but lower electronic record functionality (β = −0.48, P = .015) and less proactive patient outreach (β = −1.32, P = .025). Complex relationships between structural capabilities and workplace climate were found in CHCs. Further clarification of these complex connections may enable policy makers and practitioners to design and implement nuanced strategies to improve quality of care in CHCs.
Sex matters: exploring differences in responses to exposures.

Background: Endothelial dysfunction (ED) is functionally characterized by decreased vasorelaxation, increased thrombosis, increased inflammation, and altered angiogenic potential, has been intimately associated with the progression and severity of cardiovascular disease. Patients with compromised cardiac function oftentimes have a state of chronic mild decreased oxygen at the level of the vasculature and organs, which has been shown to exacerbate ED. Hypoxia inducible factor (HIF) is a transcription factor complex shown to be the master regulator of the cellular response to decreased oxygen levels and many HIF target genes have been shown to be associated with ED. Methods: Human endothelial and aortic smooth muscle cells were exposed either to A) normoxia (21% O2) for three weeks, or to B) mild decreased oxygen (15% O2) for three weeks to mimic blood oxygen levels in patients with heart failure, or to C) mild decreased oxygen for two weeks followed by one week of normoxia ("memory" treatment). Levels of HIF signaling genes (HIF-1α, HIF-2α, VEGF, BNIP3, GLUT-1, PAI-1 and iNOS) were measured both at the protein and mRNA levels. Results: It was found that chronic exposure to mild decreased oxygen resulted in significantly increased HIF signaling. There was also a "memory" of HIF-1α and HIF target gene induction when oxygen levels were normalized for one week, and this "memory" could be interrupted by adding a small molecule HIF inhibitor to the last week of normalized oxygen. Finally, levels of ubiquitylated HIF-1α were reduced in response to chronic mild decreased oxygen and were not full restored after oxygen normalization. Conclusion: These data suggest that HIF signaling may be contributing to the pathogenesis of endothelial dysfunction and that normalization of oxygen levels may not be enough to reduce vascular stress. Published: 18 January 2007 BMC Cardiovascular Disorders 2007, 7:4 doi:10.1186/1471-2261-7-4 Received: 23 October 2006 Accepted: 18 January 2007 This article is available from: http://www.biomedcentral. com/1471-2261/7/4 © 2007 Kamat et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Evaluation of self-report adherence measures and their associations with detectable viral load among people living with HIV (PLHIV) in China

Objectives Self-report antiretroviral therapy (ART) adherence has been consistently associated with clinical outcomes. This study aims to compare the accuracy of self-report ART adherence measures with varying recall timeframes or item contents to predict virological response. Methods Data from a cross-sectional study among 2146 participants on ART in Guangxi, China were used. Detectable viral load was defined as viral load > 50 copies/ml. Adherence was measured using the number of days on which all doses were taken in the past month (i.e., the “one-month days taken” measure), the number of days on which any dose was missed in the past month (i.e., the “one-month days missed” measure), missed doses over the past 3 days, and missed days over the past weekend. Each adherence measure was dichotomized at an empirically determined cut-off to determine poor vs. good adherence. Accuracy of using each dichotomized adherence measure to predict detectable viral load was assessed by sensitivity, specificity, and the area under the receiver-operating characteristic (AUROC) curve. Logistic regressions were used to calculate the association between poor adherence and detectable viral load. Results All four measures had sensitivity below 10.0%, specificity above 90.0%, and AUROC slightly above 0.50. In univariate logistic regression, detectable viral load was statistically significantly associated with poor adherence determined by the one-month days taken measure (OR = 1.98, 95% CI 1.15–3.42), the 3-day measure (OR = 2.18, 95% CI 1.10–4.34), and the weekend measure (OR = 2.86, 95% CI 1. 54–5.34). After adjusting for covariates, statistically significant association persisted only for the weekend measure (OR = 2.57, 95% CI 1.33–4.99). Conclusions Adherence measures asking about days on which all doses were taken might work better than items asking about days on which respondents missed their doses, and weekend measures should be included to comprehensively capture adherence behaviors. Further studies looking at intermediate timeframes are also needed to capture patients’ dose-missing patterns that may better predict detectable viral load.
Definition and Consensus Diagnostic Criteria for Neurosarcoidosis: From the Neurosarcoidosis Consortium Consensus Group

Importance The Neurosarcoidosis Consortium Consensus Group, an expert panel of physicians experienced in the management of patients with sarcoidosis and neurosarcoidosis, engaged in an iterative process to define neurosarcoidosis and develop a practical diagnostic approach to patients with suspected neurosarcoidosis. This panel aimed to develop a consensus clinical definition of neurosarcoidosis to enhance the clinical care of patients with suspected neurosarcoidosis and to encourage standardization of research initiatives that address this disease. Observations The work of this collaboration included a review of the manifestations of neurosarcoidosis and the establishment of an approach to the diagnosis of this disorder. The proposed consensus diagnostic criteria, which reflect current knowledge, provide definitions for possible, probable, and definite central and peripheral nervous system sarcoidosis. The definitions emphasize the need to evaluate patients with findings suggestive of neurosarcoidosis for alternate causal factors, including infection and malignant neoplasm. Also emphasized is the need for biopsy, whenever feasible and advisable according to clinical context and affected anatomy, of nonneural tissue to document the presence of systemic sarcoidosis and support a diagnosis of probable neurosarcoidosis or of neural tissue to support a diagnosis of definite neurosarcoidosis. Conclusions and Relevance Diverse disease presentations and lack of specificity of relevant diagnostic tests contribute to diagnostic uncertainty. This uncertainty is compounded by the absence of a pathognomonic histologic tissue examination. The diagnostic criteria we propose are designed to focus investigations on NS as accurately as possible, recognizing that multiple pathophysiologic pathways may lead to the clinical manifestations we currently term NS. Research recognizing the clinical heterogeneity of this diagnosis may open the door to identifying meaningful biologic factors that may ultimately contribute to better treatments.
Learning to adapt: a meta-learning approach for speaker adaptation

The performance of automatic speech recognition systems can be improved by adapting an acoustic model to compensate for the mismatch between training and testing conditions, for example by adapting to unseen speakers. The success of speaker adaptation methods relies on selecting weights that are suitable for adaptation and using good adaptation schedules to update these weights in order not to overfit to the adaptation data. In this paper we investigate a principled way of adapting all the weights of the acoustic model using a meta-learning. We show that the meta-learner can learn to perform supervised and unsupervised speaker adaptation and that it outperforms a strong baseline adapting LHUC parameters when adapting a DNN AM with 1.5M parameters. We also report initial experiments on adapting TDNN AMs, where the meta-learner achieves comparable performance with LHUC.
Robot_gym: accelerated robot training through simulation in the cloud with ROS and Gazebo

Rather than programming, training allows robots to achieve behaviors that generalize better and are capable to respond to real-world needs. However, such training requires a big amount of experimentation which is not always feasible for a physical robot. In this work, we present robot_gym, a framework to accelerate robot training through simulation in the cloud that makes use of roboticists' tools, simplifying the development and deployment processes on real robots. We unveil that, for simple tasks, simple 3DoF robots require more than 140 attempts to learn. For more complex, 6DoF robots, the number of attempts increases to more than 900 for the same task. We demonstrate that our framework, for simple tasks, accelerates the robot training time by more than 33% while maintaining similar levels of accuracy and repeatability.
Overconfidence is universal? Elicitation of Genuine Overconfidence (EGO) procedure reveals systematic differences across domain, task knowledge, and incentives in four populations

Overconfidence is sometimes assumed to be a human universal, but there remains a dearth of data systematically measuring overconfidence across populations and contexts. Moreover, cross-cultural experiments often fail to distinguish between placement and precision and worse still, often compare population-mean placement estimates rather than individual performance subtracted from placement. Here we introduce a procedure for concurrently capturing both placement and precision at an individual level based on individual performance: The Elicitation of Genuine Overconfidence (EGO) procedure. We conducted experiments using the EGO procedure, manipulating domain, task knowledge, and incentives across four populations—Japanese, Hong Kong Chinese, Euro Canadians, and East Asian Canadians. We find that previous measures of population-level overconfidence may have been misleading; rather than universal, overconfidence is highly context dependent. Our results reveal cross-cultural differences in sensitivity to incentives and differences in overconfidence strategies, with underconfidence, accuracy, and overconfidence. Comparing sexes, we find inconsistent results for overplacement, but that males are consistently more confident in their placement. These findings have implications for our understanding of the adaptive value of overconfidence and its role in explaining population-level and individual-level differences in economic and psychological behavior.