Miracle-dz/UniFAR-FTUs huggingface dataset:
PD-1 Expression on Mycobacterium tuberculosis-Specific CD4 T Cells Is Associated With Bacterial Load in Human Tuberculosis

Persistent antigen stimulation in chronic infections has been associated with antigen-specific T cell dysfunction and upregulation of inhibitory receptors, including programmed cell death protein 1 (PD-1). Pulmonary tuberculosis (TB) disease is characterized by high levels of Mycobacterium tuberculosis (Mtb), yet the relationship between bacterial load, PD-1 expression, and Mtb-specific T cell function in human TB has not been well-defined. Using peripheral blood samples from adults with LTBI and with pulmonary TB disease, we tested the hypothesis that PD-1 expression is associated with bacterial load and functional capacity of Mtb-specific T cell responses. We found that PD-1 was expressed at significantly higher levels on Th1 cytokine-producing Mtb-specific CD4 T cells from patients with smear-positive TB, compared with smear-negative TB and LTBI, which decreased after completion of anti-TB treatment. By contrast, expression of PD-1 on Mtb-specific CD8 T cells was significantly lower than on Mtb-specific CD4 T cells and did not differ by Mtb infection and disease status. In vitro stimulation of PBMC with Mtb antigens demonstrated that PD-1 is induced on proliferating Mtb-specific CD4 T cells and that Th1 cytokine production capacity is preferentially maintained within PD-1+ proliferating CD4 T cells, compared with proliferating Mtb-specific CD4 T cells that lack PD-1 expression. Together, these data indicate that expression of PD-1 on Mtb-specific CD4 T cells is indicative of mycobacterial antigen exposure and identifies a population of effector cells with Th1 cytokine production capacity. These studies provide novel insights into the role of the PD-1 pathway in regulating CD4 and CD8 T cell responses in Mtb infection and provide rationale for future studies to evaluate PD-1 expression on antigen-specific CD4 T cells as a potential biomarker for bacterial load and treatment response in human TB.
Can the Dispersal Behavior of Halyomorpha halys (Hemiptera: Pentatomidae) Inform the Use of Insecticide-Treated Netting to Mitigate Homeowner Issues From its Fall Invasion?

Abstract Brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), is a serious agricultural pest and can be a significant nuisance when it invades human dwellings during its fall dispersal to overwintering sites. Methods informed by behavioral data to exclude or reduce its entry into buildings are needed. The temporal and spatial distribution of adults on an invaded building was assessed over multiple years, revealing its seasonal dispersal pattern and that its numbers varied by wall aspect. Moreover, its density was higher in recessed doorways than on associated walls, raising questions about its behavioral response to dark, contrasting surfaces. This response was evaluated using black, framed panels of deltamethrin-incorporated netting, non-treated netting, and an open frame with no netting, deployed in pairs on the wall of a private residence. More dispersing adults landed on panels of non-treated netting than on open panels, but there was no difference between panels with treated and non-treated netting. Adults remained on treated panels for less time than on non-treated panels, and most walked rather than flew from both. Adult male and female H. halys collected during the dispersal period were exposed to panels of treated and non-treated netting in a laboratory, using durations derived from field recordings. Exposures to treated panels intoxicated but did not kill them over a 7-d assessment period. The deployment of insecticidetreated netting, guided by the behavior of adult H. halys alighting on buildings, is discussed in relation to potential options to mitigate homeowner issues from this serious annual problem.
The adverse effect of low levels of ambient air pollutants on lung function growth in preadolescent children.

The main purpose of our study was to assess the effect of low concentrations of ambient air pollution on lung function growth in preadolescent children. We accounted for height velocity over the follow-up period and also for other possible confounders such as baseline anthropometric and physiologic characteristics of children. In addition to outdoor air pollution, we considered the possible effects of social class and exposure to indoor pollutants such as gas stove fumes or environmental tobacco smoke. The cohort prospective study was carried out in 1,001 preadolescent children from two areas of Krakow, Poland, that differed in ambient air pollutants. In the city center (higher pollution area), the mean annual level [+/- standard deviation (SD)] of suspended particulate matter was 52.6 +/- 53.98 microg/m(3) and that of SO(2) was 43.87 +/- 32.69 microg/m(3); the corresponding values in the control area were 33.23 +/- 35.99 microg/m(3) and 31.77 +/- 21.93 microg/m(3). Mean lung function growth rate adjusted to height velocity and lung function level at the study entry was significantly lower in boys and girls living in the more polluted areas. Also, the proportion of children with the slower lung function growth (SLFG) was higher in the children from the more polluted area of the city. The analysis completed in the group of children after the exclusion of asthmatic subjects and those with asthmalike symptoms confirmed that, in boys, odds ratios (ORs) for SLFG [forced vital capacity (FVC)] and air pollution after adjustment to baseline FVC, height, and growth rate was significant [OR = 2.15; 95% confidence interval (CI), 1.25-3. 69)]. The analysis also confirmed that for SLFG(FEV(1)) the OR was 1. 90 (CI, 1.12-3.25). The corresponding OR values in girls were insignificant (OR = 1.50; CI, 0.84-2.68 and OR = 1.39; CI, 0.78-2. 44). The association between ambient pollutants and poorer gain of pulmonary volumes in children living in more polluted areas suggests that air pollution in the residence area may be a part of the causal chain of reactions leading to retardation in pulmonary function growth during the preadolescent years. ImagesFigure 1Figure 2
Evaluation of Sex, Ethnic, and Racial Diversity Across US ACGME-Accredited Orthopedic Subspecialty Fellowship Programs.

In recent years, there has been an increasing trend toward subspecialization in orthopedic surgery via fellowships. This study sought to characterize sex, ethnic, and racial representation within each fellowship program and to examine their changes over time to identify trends and/or gaps. Demographic data were obtained from the National Graduate Medical Education Census. Diversity was assessed using proportions of minority and female trainees. The trends in racial, ethnic, and sex diversity from 2006 to 2015 for orthopedics as a whole and within each subspecialty were analyzed. Of 3722 orthopedic fellows, 2551 identified as white (68.5%), 648 as Asian (17.4%), 175 as Hispanic (4.7%), 161 as black (4.3%), 8 as Native Hawaiian/Pacific Islander (0.21%), and 3 as American Indian/Alaskan Native (0.08%). Further, 479 identified as female (12.9%). Racial and ethnic minority representation among orthopedic fellows did not increase over time. Female representation did increase proportionally with female residents. Asian fellows preferred reconstructive adult and spine, whereas white fellows preferred sports medicine, hand surgery, and trauma. Female fellows preferred pediatrics, hand surgery, and musculoskeletal oncology. Although sex diversity among orthopedic fellows has increased in the past 10 years, racial and ethnic minority representation lacked similar growth. Asian and female fellows preferred specific subspecialties over others. These data are presented as an initial step in determining factors that attract minority groups to different orthopedic subspecialties. Further research should define specific factors and identify ways to increase minority distribution among fellowship programs. [Orthopedics. 2018; 41(5):282-288. ].
Turn Back the TIMe: Targeting Tumor Infiltrating Myeloid Cells to Revert Cancer Progression

Tumor cells frequently produce soluble factors that favor myelopoiesis and recruitment of myeloid cells to the tumor microenvironment (TME). Consequently, the TME of many cancer types is characterized by high infiltration of monocytes, macrophages, dendritic cells and granulocytes. Experimental and clinical studies show that most myeloid cells are kept in an immature state in the TME. These studies further show that tumor-derived factors mold these myeloid cells into cells that support cancer initiation and progression, amongst others by enabling immune evasion, tumor cell survival, proliferation, migration and metastasis. The key role of myeloid cells in cancer is further evidenced by the fact that they negatively impact on virtually all types of cancer therapy. Therefore, tumor-associated myeloid cells have been designated as the culprits in cancer. We review myeloid cells in the TME with a focus on the mechanisms they exploit to support cancer cells. In addition, we provide an overview of approaches that are under investigation to deplete myeloid cells or redirect their function, as these hold promise to overcome resistance to current cancer therapies.
A Variational Feature Encoding Method of 3D Object for Probabilistic Semantic SLAM

This paper presents a feature encoding method of complex 3D objects for high-level semantic features. Recent approaches to object recognition methods become important for semantic simultaneous localization and mapping (SLAM). However, there is a lack of consideration of the probabilistic observation model for 3D objects, as the shape of a 3D object basically follows a complex probability distribution. Furthermore, since the mobile robot equipped with a range sensor observes only a single view, much information of the object shape is discarded. These limitations are the major obstacles to semantic SLAM and view-independent loop closure using 3D object shapes as features. In order to enable the numerical analysis for the Bayesian inference, we approximate the true observation model of 3D objects to tractable distributions. Since the observation likelihood can be obtained from the generative model, we formulate the true generative model for 3D object with the Bayesian networks. To capture these complex distributions, we apply a variational auto-encoder. To analyze the approximated distributions and encoded features, we perform classification with maximum likelihood estimation and shape retrieval.
FIT & STRONG! PLUS: DESCRIPTIVE DEMOGRAPHIC AND RISK CHARACTERISTICS IN A COMPARATIVE EFFECTIVENESS TRIAL FOR OLDER AFRICAN-AMERICAN ADULTS WITH OSTEOARTHRITIS.

Objectives The prevalence of osteoarthritis (OA) has increased in the US. We report on a comparative effectiveness trial that compares Fit & Strong! , an existing evidence-based physical activity (PA) program, to Fit & Strong! Plus, which combines the Fit & Strong! intervention with a weight management intervention. Methods Participants included 413 overweight/obese (BMI 25-50 kg/m2) adults with lower extremity (LE) OA. The majority of the sample was African-American and female. Both interventions met 3 times weekly for 8 weeks. Primary measures included diet and weight. Results The baseline mean BMI for all participants was 34.8 kg/m², percentage of calories from fat was high, and self-reported PA was low. Discussion This sample of overweight/obese African-American adults had lifestyle patterns at baseline that were less than healthful, and there were differences between self-report and performance-based measures as a function of age.
Initial experience with EUS-guided microbiopsy forceps in diagnosing pancreatic cystic lesions: A multicenter feasibility study (with video)

Background and Objectives: Cystic lesions of the pancreas represent a diagnostic dilemma. Recently, a through-the-needle microbiopsy forceps has become available, enabling procurement of EUS-guided histological specimens from the pancreatic cyst wall. The aim of this study was to evaluate the use of this novel instrument in a multicenter clinical setting. Patients and Methods: Patients referred for EUS evaluation of pancreatic cysts and attempted EUS-guided microbiopsy was included retrospectively from six international tertiary centers. Patient's demographics, EUS findings, technical and clinical success, and histopathological results were recorded. Results: A total of 28 patients were identified. We report a technical success rate of 85.7% (n = 24). Biopsies were generally of good quality and contributed to the diagnosis in 20 patients (clinical success of 71.4%). Three adverse events were recorded (10.7%). Conclusions: The use of the microbiopsy forceps is feasible with acceptable rates of technical and clinical success. Prospective studies are warranted to determine the diagnostic potential compared to the other modalities. However, the results from this preliminary study are promising.
Variable selection and validation in multivariate modelling

Motivation Validation of variable selection and predictive performance is crucial in construction of robust multivariate models that generalize well, minimize overfitting and facilitate interpretation of results. Inappropriate variable selection leads instead to selection bias, thereby increasing the risk of model overfitting and false positive discoveries. Although several algorithms exist to identify a minimal set of most informative variables (i.e. the minimal‐optimal problem), few can select all variables related to the research question (i.e. the all‐relevant problem). Robust algorithms combining identification of both minimal‐optimal and all‐relevant variables with proper cross‐validation are urgently needed. Results We developed the MUVR algorithm to improve predictive performance and minimize overfitting and false positives in multivariate analysis. In the MUVR algorithm, minimal variable selection is achieved by performing recursive variable elimination in a repeated double cross‐validation (rdCV) procedure. The algorithm supports partial least squares and random forest modelling, and simultaneously identifies minimal‐optimal and all‐relevant variable sets for regression, classification and multilevel analyses. Using three authentic omics datasets, MUVR yielded parsimonious models with minimal overfitting and improved model performance compared with state‐of‐the‐art rdCV. Moreover, MUVR showed advantages over other variable selection algorithms, i.e. Boruta and VSURF, including simultaneous variable selection and validation scheme and wider applicability. Availability and implementation Algorithms, data, scripts and tutorial are open source and available as an R package (‘MUVR’) at https://gitlab.com/CarlBrunius/MUVR.git. Supplementary information Supplementary data are available at Bioinformatics online.
Comparative study between four ultrasound Shear Waves Elastographic methods for liver fibrosis assessment.

AIMS Non-invasive methods to assess the severity of chronic liver diseases have become more and more popular. The aim of our study was to evaluate the correlation of four Shear Waves Elastographic methods in a cohort of patients with chronic liver diseases of mixed etiologies and to compare their performances for liver fibrosis evaluation. MATERIAL AND METHODS A prospective study was conducted on 127 consecutive patients with chronic liver diseases of mixed etiologies. LS measurements were performed in all subjects, in one session, during the same day, by means of 4 elastographic methods: Transient Elastography (TE), Virtual Touch Quantification (VTQ), ElastPQ and 2D-SWE.SSI. The diagnosis accuracies of VTQ, ElastPQ, 2D-SWE.SSI were then compared using TE as reference method. RESULTS Valid LS measurements by all four shear waves ultrasound elastographic methods were obtained in 116/127 subjects with VTQ, in 108/127 subjects with 2D-SWE.SSI, in 111/127 with TE and in 109/127 with ElastPQ, so the final analysis included 82/127 subjects (64.5%). A good and significant correlation was found between all 4 elastographic methods. The diagnostic accuracy of VTQ, 2D-SWE.SSI and ElastPQ for the diagnosis of significant and severe fibrosis (F2/F3), and liver cirrhosis were similar for all elastographic techniques: VTQ vs 2D-SWE.SSI vs ElastPQ: 84.1% vs 85.3% vs. 84% (p>0.05); 93.9% vs 94% vs 94% (p>0.05). CONCLUSION considering TE as the reference method for liver fibrosis evaluation, VTQ, ElastPQ, and 2D-SWE.SSI obtained similar accuracies for diagnosing at least significant fibrosis (F≥2) and liver cirrhosis.
Basic characteristics and representativeness of the German Disease Analyzer database .

PURPOSE The aim of this study was to evaluate the representativeness of diagnoses in the Disease Analyzer (DA) database for major chronic diseases (cancer, dementia, diabetes). MATERIALS AND METHODS DA contains anonymized longitudinal data on drug prescriptions, diagnoses as well as medical and demographic data directly obtained from the computer system of a representative sample of practices throughout Germany. DA contains data from 2,498 practices with 7.8 million patients (2017). The distribution and sex-specific incidence of various cancer subsites among new cancer cases, the age- and sex-specific prevalence of dementia, and the prevalence of diabetes were assessed. National reference data were obtained from official sources. RESULTS Mean age (43 years) and sex distribution (47% men) of primary care patients in DA were similar to the German population. Among incident cancer cases, there was good agreement between DA data and national data with respect to the various cancer subsites (e.g., breast cancer: DA 17%; reference: 15%). Furthermore, sex distribution was largely similar. The age distribution of prevalent dementia was similar to national reference data, both in men (80 - 84 years: DA: 26.8%; reference: 27.0%) and in women (80 - 84 years: DA: 24.6%; reference: 24.1%). Diabetes prevalence in the DA (10.7%) was higher than in claims data from physicians (9.8%) or patients from statutory health insurances (9.9%). CONCLUSION There was a good agreement of the incidence or prevalence of major chronic diseases in the outpatient DA with German reference data. The higher diabetes prevalence in the DA is due to the increased number of outpatient visits of diabetes patients.
Does shared decision-making reduce antibiotic prescribing in primary care?

Background Increasing antibiotic resistance is recognized as a major threat to global health and is related to antibiotic prescription rates in primary care. Shared decision-making (SDM), the process in which patients and doctors participate together in making decisions, is argued to possibly promote more appropriate use of antibiotics and reduce prescribing. However, it is unknown whether in practice fewer antibiotics are prescribed where more SDM takes place. Objectives To investigate whether more SDM is related to less antibiotic prescribing and whether this relationship differs between subgroups of patients (male/female and age groups). Patients and methods A questionnaire survey was conducted among 2670 members of the Dutch Health Care Consumer Panel to measure SDM (response rate 45%). Average practice-level SDM scores were calculated for 15 general practices. Data from routine electronic health records of 8192 adult patients of these general practices participating in the Nivel Primary Care Database were used to assess relevant illness episodes (acute cough, acute rhinosinusitis and urinary tract infection), the indication for antibiotics and antibiotic prescriptions. Logistic multilevel regression analyses were performed to investigate the relationship between practice-level SDM and patient-level antibiotic prescriptions. Results In practices where more SDM takes place, general practitioners prescribed fewer antibiotics for adult patients under the age of 40 years in preference-sensitive situations (i.e. situations in which antibiotics could be considered according to clinical guidelines). Conclusions SDM can be a framework to reduce the prescribing of antibiotics and thus to control antibiotic resistance.
Clopidogrel may decrease the risk of post‐stroke infection after ischaemic stroke

The P2Y12 receptor, a well‐known factor in the platelet activation pathway, plays a role in thrombosis as well as systemic inflammation. Clopidogrel, a prototype P2Y12 receptor antagonist, reportedly decreases inflammation and systemic infection. The aim of this study was to evaluate whether clopidogrel use decreases the risk of post‐stroke infection following ischaemic stroke.
Muscle Atrophy Due to Nerve Damage Is Accompanied by Elevated Myofibrillar Protein Synthesis Rates

Muscle loss is a severe complication of many medical conditions such as cancer, cardiac failure, muscular dystrophies, and nerve damage. The contribution of myofibrillar protein synthesis (MPS) to the loss of muscle mass after nerve damage is not clear. Using deuterium oxide (D2O) labeling, we demonstrate that MPS is significantly increased in rat m. tibialis anterior (TA) compared to control (3.23 ± 0.72 [damaged] to 2.09 ± 0.26%∗day−1 [control]) after 4 weeks of nerve constriction injury. This is the case despite substantial loss of mass of the TA (350 ± 96 mg [damaged] to 946 ± 361 mg [control]). We also show that expression of regulatory proteins involved with MPS (p70s6k1: 2.4 ± 0.3 AU [damaged] to 1.8 ± 0.2 AU [control]) and muscle protein breakdown (MPB) (MAFbx: 5.3 ± 1.2 AU [damaged] to 1.4 ± 0.4 AU [control]) are increased in nerve damaged muscle. Furthermore, the expression of p70s6k1 correlates with MPS rates (r2 = 0.57). In conclusion, this study shows that severe muscle wasting following nerve damage is accompanied by increased as opposed to decreased MPS.
Exploring audio and kinetic sensing on earable devices

In this paper, we explore audio and kinetic sensing on earable devices with the commercial on-the-shelf form factor. For the study, we prototyped earbud devices with a 6-axis inertial measurement unit and a microphone. We systematically investigate the differential characteristics of the audio and inertial signals to assess their feasibility in human activity recognition. Our results demonstrate that earable devices have a superior signal-to-noise ratio under the influence of motion artefacts and are less susceptible to acoustic environment noise. We then present a set of activity primitives and corresponding signal processing pipelines to showcase the capabilities of earbud devices in converting accelerometer, gyroscope, and audio signals into the targeted human activities with a mean accuracy reaching up to 88% in varying environmental conditions.