Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of abnormal pulmonary vasculature on CT scan for COVID-19 infection with decreased diffusion capacity in follow up: A retrospective cohort study

Background Coronavirus Disease 2019 (COVID-19) is a respiratory viral illness causing pneumonia and systemic disease. Abnormalities in pulmonary function tests (PFT) after COVID-19 infection have been described. The determinants of these abnormalities are unclear. We hypothesized that inflammatory biomarkers and CT scan parameters at the time of infection would be associated with abnormal gas transfer at short term follow-up. Methods We retrospectively studied subjects who were hospitalized for COVID-19 pneumonia and discharged. Serum inflammatory biomarkers, CT scan and clinical characteristics were assessed. CT images were evaluated by Functional Respiratory Imaging with automated tissue segmentation algorithms of the lungs and pulmonary vasculature. Volumes of the pulmonary vessels that were ≤5mm (BV5), 5-10mm (BV5_10), and ≥10mm (BV10) in cross sectional area were analyzed. Also the amount of opacification on CT (ground glass opacities). PFT were performed 2–3 months after discharge. The diffusion capacity of carbon monoxide (DLCO) was obtained. We divided subjects into those with a DLCO <80% predicted (Low DLCO) and those with a DLCO ≥80% predicted (Normal DLCO). Results 38 subjects were included in our cohort. 31 out of 38 (81.6%) subjects had a DLCO<80% predicted. The groups were similar in terms of demographics, body mass index, comorbidities, and smoking status. Hemoglobin, inflammatory biomarkers, spirometry and lung volumes were similar between groups. CT opacification and BV5 were not different between groups, but both Low and Normal DLCO groups had lower BV5 measures compared to healthy controls. BV5_10 and BV10 measures were higher in the Low DLCO group compared to the normal DLCO group. Both BV5_10 and BV10 in the Low DLCO group were greater compared to healthy controls. BV5_10 was independently associated with DLCO<80% in multivariable logistic regression (OR 1.29, 95% CI 1.01, 1.64). BV10 negatively correlated with DLCO% predicted (r = -0.343, p = 0.035). Conclusions Abnormalities in pulmonary vascular volumes at the time of hospitalization are independently associated with a low DLCO at follow-up. There was no relationship between inflammatory biomarkers during hospitalization and DLCO. Pulmonary vascular abnormalities during hospitalization for COVID-19 may serve as a biomarker for abnormal gas transfer after COVID-19 pneumonia.
Comparing the controlled attenuation parameter using FibroScan and attenuation imaging with ultrasound as a novel measurement for liver steatosis

Background/Aims In a recent study, attenuation imaging (ATI) with ultrasound was used as a new approach for detecting liver steatosis. However, although there are many studies on ATI and controlled attenuation parameter (CAP) that prove their practicability, there are few studies comparing these two methods. As such, this study compared CAP and ATI for the detection and evaluation of liver steatosis. Methods A prospective analysis of 28 chronic liver disease patients who underwent liver biopsy, FibroScan® imaging, and ATI with ultrasound was conducted. The presence and degree of steatosis, as measured with the FibroScan® device and ATI, were compared with the pathological results obtained using liver biopsy. Results The areas under the receiver operating characteristic curve (AUROC) of ATI and CAP for differentiating between normal and hepatic steatosis were 0.97 (95% confidence interval [CI] 0.83–1.00) and 0.96 (95% CI 0.81–0.99), respectively. ATI has a higher AUROC than CAP does in liver steatosis, at 0.99 (95% CI, 0.86–1.00) versus 0.91 (95% CI, 0.74–0.98) in grade ≥ 2 and 0.97 (95% CI, 0.82–1.00) versus 0.88 (95% CI, 0.70–0.97) in grade = 3, respectively. Conclusion The ATI and CAP results showed good consistency and accuracy for the steatosis grading when compared with the liver biopsy results. Moreover, ATI is even better than CAP in patients with moderate or severe steatosis. Therefore, ATI represents a non-invasive and novel diagnostic tool with which to support the diagnosis of liver steatosis in clinical practice.
miR-141-3p is Poorly Expressed in Polycystic Ovary Syndrome and Correlates with Glucose and Lipid Metabolism

Polycystic ovary syndrome (PCOS) is a common endocrinopathy with high prevalence. miR-141-3p downregulation was reported in PCOS rats. This study intended to investigate miR-141-3p expression in serum of PCOS patients and its correlation with glucose and lipid metabolism. A total of 100 PCOS patients and 100 healthy controls were enrolled in this study. Clinical parameters and glucose and lipid indexes were analyzed. A 3-month fat reduction intervention was conducted to PCOS-obese patients. Expressions of miR-141-3p and PTEN were detected. WHR and levels of TG, HDL-C, FBG, FINS, HOMA-β, and HOMA-IR showed significant differences in PCOS patients. miR-141-3p was downregulated in PCOS patients. Area under ROC curve of miR-141-3p diagnosing PCOS-obese patients was 0.985 with specificity 95.35% and flexibility 93.33%. Levels of glucose and lipid metabolism indexes were increased while HDL-C level was decreased in miR-141-3p low expression group. Indexes of PCOS-obese patients were improved and miR-141-3p was upregulated after fat reduction intervention. PTEN was upregulated in PCOS patients and negatively correlated with miR-141-3p. In conclusion, miR-141-3p was downregulated in PCOS patients and had higher diagnostic value on PCOS and associated with glucose and lipid metabolism. miR-141-3p might play a role in glucose and lipid metabolism in PCOS-obese patients by targeting PTEN.
External validation of the priapism impact profile in a Jamaican cohort of patients with sickle cell disease

Background Priapism impairs quality of life and has a predilection for males with sickle cell disease (SCD). The Priapism Impact Profile (PIP) is a novel 12-item instrument designed to measure general health-related impact of priapism. The aim of the study was to evaluate the validity and reliability of the PIP in a Jamaican cohort of SCD patients experiencing priapism. Methods One hundred SCD patients with a history of priapism were recruited from a sickle cell clinic in Kingston, Jamaica and administered the PIP questionnaire. Patients rated each item of the PIP for clarity and importance. Statistical testing was employed to evaluate the psychometric performance of the PIP. Content validation was assessed based on patient descriptive rating of the items based on clarity, and importance and criterion-oriented validity were assessed by evaluating the PIP’s ability to distinguish between patient subgroups. Test-retest repeatability was assessed in 20 of the 100 patients. Results Patients were stratified into active (54) and remission (46) priapism groups based on their experience of priapism within the past year. Patients in the active priapism group were younger (p = 0.011), had a shorter duration of disease (p = 0.023), and had more frequent priapism episodes (p = 0.036) than the remission group. PIP questionnaire scores differed significantly with respect to priapism activity (p < 0.001) and prevalence of erectile dysfunction (p < 0.05) but not by priapism severity (p = 0.62). The PIP questionnaire had good content validity, with questions rated as having medium or high clarity and importance by an average of 82.8% and 69.2% of patients, respectively. Conclusion The PIP questionnaire was successfully validated in a Jamaican cohort of SCD patients and adequately discriminated patients with active priapism from those in remission. The instrument may be utilized in routine clinical management of patients with SCD-associated priapism. Further clinical investigations are warranted in other populations.
Rotational Ground-State Bands of 168 Hf Nucleus

This paper has been explained to study the rotational arrangement of even-even Hf isotope using the phenomenological fitting, Sood’s semiempirical formula. The rotational energies from the calculated values were compared to the experimental data. The result shows that in Hf, calculated energies fit the experimental values to a remarkable degree of accuracy.
Season-Long Changes in the Body Composition Profiles of Competitive Female Rugby Union Players Assessed via Dual Energy X-Ray Absorptiometry

ABSTRACT Background: Reference data for the body composition values of female athletes are limited to very few sports, with female Rugby Union players having mostly been omitted from such analyses.Methods: Using dual energy X-ray absorptiometry (DXA) scans, this study assessed the body composition profiles (body mass, bone mineral content; BMC, fat mass; FM, lean mass; LM, bone mineral density; BMD) of 15 competitive female Rugby Union players before and after the 2018/19 competitive season. Total competitive match-play minutes were also recorded for each player.Results: Body mass (73.7 ± 9.6 kg vs 74.9 ± 10.2 kg, p ≤ 0.05, d = 0.13) and BMC (3.2 ± 0.4 kg vs 3.3 ± 0.4 kg, p ≤ 0.05, d = 0.15) increased pre- to post-season for all players. Conversely, FM (21.0 ± 8.8 kg), LM (50.7 ± 3.9 kg), and BMD (1.31 ± 0.06 g·cm−2) were similar between time-points (all p > .05). Accounting for position, body mass (r partial(12) = 0.196), FM (r partial(12) = −0.013), LM (r partial(12) = 0.351), BMD (r partial(12) = 0.168) and BMC (r partial(12) = −0.204) showed no correlation (all p > .05) against match-play minutes.Conclusion: The demands of the competitive season influenced specific body composition indices (i.e., body mass, BMC) in female Rugby Union players; a finding which was unrelated to the number of minutes played in matches. While the causes of such differences remain unclear, practitioners should be cognizant of the body composition changes occurring throughout a female Rugby Union competitive season and, where necessary, consider modifying variables associated with adaptation and recovery accordingly.
Deep learning-based thoracic CBCT correction with histogram matching

Kilovoltage cone-beam computed tomography (CBCT)-based image-guided radiation therapy (IGRT) is used for daily delivery of radiation therapy, especially for stereotactic body radiation therapy (SBRT), which imposes particularly high demands for setup accuracy. The clinical applications of CBCTs are constrained, however, by poor soft tissue contrast, image artifacts, and instability of Hounsfield unit (HU) values. Here, we propose a new deep learning-based method to generate synthetic CTs (sCT) from thoracic CBCTs. A deep-learning model which integrates histogram matching (HM) into a cycle-consistent adversarial network (Cycle-GAN) framework, called HM-Cycle-GAN, was trained to learn mapping between thoracic CBCTs and paired planning CTs. Perceptual supervision was adopted to minimize blurring of tissue interfaces. An informative maximizing loss was calculated by feeding CBCT into the HM-Cycle-GAN to evaluate the image histogram matching between the planning CTs and the sCTs. The proposed algorithm was evaluated using data from 20 SBRT patients who each received 5 fractions and therefore 5 thoracic CBCTs. To reduce the effect of anatomy mismatch, original CBCT images were pre-processed via deformable image registrations with the planning CT before being used in model training and result assessment. We used planning CTs as ground truth for the derived sCTs from the correspondent co-registered CBCTs. The mean absolute error (MAE), peak signal-to-noise ratio (PSNR), and normalized cross-correlation (NCC) indices were adapted as evaluation metrics of the proposed algorithm. Assessments were done using Cycle-GAN as the benchmark. The average MAE, PSNR, and NCC of the sCTs generated by our method were 66.2 HU, 30.3 dB, and 0.95, respectively, over all CBCT fractions. Superior image quality and reduced noise and artifact severity were seen using the proposed method compared to the results from the standard Cycle-GAN method. Our method could therefore improve the accuracy of IGRT and corrected CBCTs could help improve online adaptive RT by offering better contouring accuracy and dose calculation.
Validity and reliability of 1-h automated office blood pressure measurement for the diagnosis of hypertension

Supplemental Digital Content is available in the text Aims: The objective of this study was to examine the validity of 1 h automated office blood pressure measurement for the diagnosis of hypertension. Methods: We included patients requiring a hypertension diagnostic test. Participants underwent ambulatory blood pressure monitoring, 1 h automated office blood pressure measurement, office blood pressure measurement and home blood pressure monitoring. The prevalence of hypertension and subtypes were calculated. Mean values of ambulatory blood pressure monitoring were compared with 1 h automated office blood pressure measurement using the correlation coefficient and Bland–Altman graphs. The Kappa concordance index, sensitivity, specificity and diagnostic accuracy were calculated, and the area under the receiver operating characteristic curve was used to establish the diagnostic threshold of the 1-h measurement. Results: Of 562 participants, 438 (87.6%) completed the four diagnostic methods. The 1-h method had a sensitivity of 76.6 [95% confidence interval (95% CI): 71.1–81.5], a specificity of 64.8% (95% CI: 57–72.1) and the best diagnostic accuracy (72.1%, 95% CI: 67.7–76.3) compared with the office and home measurements. Moderate-high correlations were observed between DBP (r = 0.73) and SBP (r = 0.58) readings. The 1-h method classified more patients as normotensive (24.4%) and fewer patients with white-coat hypertension (13.3%). A diagnostic threshold of at least 133/83 mmHg for the 1-h method could improve diagnostic accuracy by 2.3%. Conclusion: One-hour automated blood pressure measurement is a valid, reliable method for the diagnosis of hypertension in undiagnosed patients. The diagnostic accuracy permits detection of white-coat and masked hypertension. To diagnose hypertension, the 1-h method or conventional home blood pressure monitoring should be used rather than office measurements. Trial registration: ClinicalTrials.gov Identifier: NCT03147573.
SMOG 2 and OpenSMOG: Extending the limits of structure-based models

Applying simulations with structure-based (Gō-like) models has proven to be an effective strategy for investigating the factors that control biomolecular dynamics. The common element of these models is that some (or all) of the intra/inter-molecular inter-actions are explicitly defined to stabilize an experimentally-determined structure. To facilitate the development and application of this broad class of models, we previously released the SMOG 2 software package. This suite allows one to easily customize and distribute structure-based (i.e. SMOG) models for any type of polymer-ligand system. Since its original release, user feedback has driven the implementation of numerous enhancements. Here, we describe recent extensions to the software and demonstrate the capabilities of the most recent version, SMOG v2.4. Changes include new tools that aid user-defined customization of force fields, as well as an interface with the OpenMM simulation libraries (OpenSMOG v1.0). To illustrate the utility of these advances, we present several applications of SMOG2 and OpenSMOG, which include systems with millions of atoms, long polymers and explicit ions. We also highlight how one can incorporate non-structure-based (e.g. AMBER-based) energetics to define a hybrid class of models. The representative applications include large-scale rearrangements of the SARS-CoV-2 Spike protein, the HIV-1 capsid in the presence of explicit ions, and crystallographic lattices of ribosomes and proteins. In summary, SMOG 2 and OpenSMOG provide robust support for researchers who seek to apply structure-based models to large and/or intricate biomolecular systems.
Adaptive asynchronous control system of robotic arm based on augmented reality-assisted brain–computer interface

Objective. Brain-controlled robotic arms have shown broad application prospects with the development of robotics, science and information decoding. However, disadvantages, such as poor flexibility restrict its wide application. Approach. In order to alleviate these drawbacks, this study proposed a robotic arm asynchronous control system based on steady-state visual evoked potential (SSVEP) in an augmented reality (AR) environment. In the AR environment, the participants were able to concurrently see the robot arm and visual stimulation interface through the AR device. Therefore, there was no need to switch attention frequently between the visual stimulation interface and the robotic arm. This study proposed a multi-template algorithm based on canonical correlation analysis and task-related component analysis to identify 12 targets. An optimization strategy based on dynamic window was adopted to adjust the duration of visual stimulation adaptively. Main results. Experimental results of this study found that the high-frequency SSVEP-based brain–computer interface (BCI) realized the switch of the system state, which controlled the robotic arm asynchronously. The average accuracy of the offline experiment was 94.97 % , whereas the average information translate rate was 67.37 ± 14.27 bits·min−1. The online results from ten healthy subjects showed that the average selection time of a single online command was 2.04 s, which effectively reduced the visual fatigue of the subjects. Each subject could quickly complete the puzzle task. Significance. The experimental results demonstrated the feasibility and potential of this human-computer interaction strategy and provided new ideas for BCI-controlled robots.
Ratio estimators of intervention effects on event rates in cluster randomized trials

We consider five asymptotically unbiased estimators of intervention effects on event rates in non‐matched and matched‐pair cluster randomized trials, including ratio of mean counts r1 , ratio of mean cluster‐level event rates r2 , ratio of event rates r3 , double ratio of counts r4 , and double ratio of event rates r5 . In the absence of an indirect effect, they all estimate the direct effect of the intervention. Otherwise, r1 , r2, and r3 estimate the total effect, which comprises the direct and indirect effects, whereas r4 and r5 estimate the direct effect only. We derive the conditions under which each estimator is more precise or powerful than its alternatives. To control bias in studies with a small number of clusters, we propose a set of approximately unbiased estimators. We evaluate their properties by simulation and apply the methods to a trial of seasonal malaria chemoprevention. The approximately unbiased estimators are practically unbiased and their confidence intervals usually have coverage probability close to the nominal level; the asymptotically unbiased estimators perform well when the number of clusters is approximately 32 or more per trial arm. Despite its simplicity, r1 performs comparably with r2 and r3 in trials with a large but realistic number of clusters. When the variability of baseline event rate is large and there is no indirect effect, r4 and r5 tend to offer higher power than r1 , r2, and r3 . We discuss the implications of these findings to the planning and analysis of cluster randomized trials.
Vitamin E supplementation in inflammatory skin diseases

Vitamin E is a powerful lipophilic antioxidant that protects membranes from lipid peroxidation, and consequently, oxidative damage. Oxidative stress plays a role in the development of neurodegenerative diseases. Vitamin E supplementation is recommended in patients with vitamin E deficiency due to fat malabsorption. The addition of vitamin E to the diet slows Alzheimer's disease progression and protects older patients against respiratory infections. Recent studies also point to the involvement of oxidative stress in the pathology of immune‐mediated skin diseases, such as atopic dermatitis and psoriasis. We reviewed the available clinical trials that investigated the role of vitamin E supplementation in preventing and treating atopic dermatitis and psoriasis. Data from these studies point to a positive role of vitamin E supplementation in these diseases. Still, due to limitations in study design, further evidence is needed to reach a definite conclusion.
Real-Time Visualization of Large-Scale Geological Models With Nonlinear Feature-Preserving Levels of Detail

The rapidly growing size and complexity of 3D geological models has increased the need for level-of-detail techniques and compact encodings to facilitate interactive visualization. For large-scale hexahedral meshes, state-of-the-art approaches often employ wavelet schemes for level of detail as well as for data compression. Here, wavelet transforms serve two purposes: (1) they achieve substantial compression for data reduction; and (2) the multiresolution encoding provides levels of detail for visualization. However, in coarser detail levels, important geometric features, such as geological faults, often get too smoothed out or lost, due to linear translation-invariant filtering. The same is true for attribute features, such as discontinuities in porosity or permeability. We present a novel, integrated approach addressing both purposes above, while preserving critical data features of both model geometry and its attributes. Our first major contribution is that we completely decouple the computation of levels of detail from data compression, and perform nonlinear filtering in a high-dimensional data space jointly representing the geological model geometry with its attributes. Computing detail levels in this space enables us to jointly preserve features in both geometry and attributes. While designed in a general way, our framework specifically employs joint bilateral filters, computed efficiently on a high-dimensional permutohedral grid. For data compression, after the computation of all detail levels, each level is separately encoded with a standard wavelet transform. Our second major contribution is a compact GPU data structure for the encoded mesh and attributes that enables direct real-time GPU visualization without prior decoding.
Home-Based Telework and Presenteeism

Indirect work control (such as management by objectives and application of performance measures) promotes the use of telework for work intensification (i.e. teleworking after regular working hours in the main office or on weekends and times off) which is associated with enhanced sickness presenteeism. Objective: Previous research found increased sickness presenteeism (working despite sickness) associated with home-based telework. The Covid-19 pandemic offers new insights into mechanisms, as a large proportion of the workforce was forced to work from home, irrespective of organizational and individual predispositions. Methods: A path analysis based on survey data from a sample of teleworkers collected during the Covid-crisis was performed. Results: We found no general relationship between telework and sickness presenteeism. However, employees with telework experience before the pandemic use telework more often for work intensification which is associated with increased sickness presenteeism. As teleworking before the pandemic is associated with indirect work control (goal-directed management), indirect effects of such work organizations on presenteeism were confirmed. Conclusion: As hypothesized in prior research, indirect work control may increase self-endangering behavior which is amplified by telework.