Miracle-dz/UniFAR-FTUs huggingface dataset:
Covichem: A biochemical severity risk score of COVID-19 upon hospital admission

Clinical and laboratory predictors of COVID-19 severity are now well described and combined to propose mortality or severity scores. However, they all necessitate saturable equipment such as scanners, or procedures difficult to implement such as blood gas measures. To provide an easy and fast COVID-19 severity risk score upon hospital admission, and keeping in mind the above limits, we sought for a scoring system needing limited invasive data such as a simple blood test and co-morbidity assessment by anamnesis. A retrospective study of 303 patients (203 from Bordeaux University hospital and an external independent cohort of 100 patients from Paris Pitié-Salpêtrière hospital) collected clinical and biochemical parameters at admission. Using stepwise model selection by Akaike Information Criterion (AIC), we built the severity score Covichem. Among 26 tested variables, 7: obesity, cardiovascular conditions, plasma sodium, albumin, ferritin, LDH and CK were the independent predictors of severity used in Covichem (accuracy 0.87, AUROC 0.91). Accuracy was 0.92 in the external validation cohort (89% sensitivity and 95% specificity). Covichem score could be useful as a rapid, costless and easy to implement severity assessment tool during acute COVID-19 pandemic waves.
Plasma osteopontin versus intima media thickness of the common carotid arteries in well-characterised patients with systemic lupus erythematosus

Objective The progress of accelerated atherosclerosis in systemic lupus erythematosus (SLE) is incompletely understood. Circulating osteopontin (OPN) is increased in autoimmune conditions, e.g. SLE, and its serum concentration was recently reported to associate with subclinical atherosclerosis in SLE, as measured by carotid intima-media thickness. The aim of this study was to investigate whether OPN may be used as a surrogate biomarker of subclinical atherosclerosis in SLE patients with different disease phenotypes. Methods We recruited 60 well-characterised SLE cases and 60 age- and sex-matched healthy controls. The SLE cases were divided into three different disease phenotypes: SLE with antiphospholipid syndrome (APS), lupus nephritis, and isolated skin and joint involvement. Plasma OPN was detected by ELISA (Quantikine®, R&D Systems). Common carotid arteries intima media thickness was compared between the studied groups in relation to OPN levels and risk factors for vascular changes. Intima media thickness of common carotid arteries was measured by using a sensitive ultrasound technique (LOGIQ™ E9 ultrasound, GE Healthcare). Results OPN levels were significantly higher among the entire SLE group (n = 60) compared to the healthy controls (P = 0.03). SLE cases with concomitant APS (n = 20) showed higher OPN levels than the controls (P = 0.004), whereas none of the other two subgroups differed significantly from the healthy controls. OPN and intima media thickness were correlated to several traditional risk factors of atherosclerosis, as well as to SLE-related factors. Yet, no significant correlation was observed between OPN levels and ultrasound findings of the common carotid arteries. Conclusions In line with previous studies, we observed increased OPN levels among SLE patients as compared to matched controls. However, the OPN concentrations did not correlate with intima media thickness of the common carotid arteries. Based on our findings, the use of OPN as a surrogate biomarker of subclinical atherosclerosis in SLE subjects, regardless of clinical phenotypes, cannot be recommended.
Learning to Be Inclusive? Testing the Effects of News Media Diet on Attitudes Toward LGT Equality

ABSTRACT This study analyzed a large national survey, the 2016 version of American National Election Study (ANES), to identify the predictors of attitudes toward the equal rights of lesbians, gay men, and transgender individuals. Egalitarian attitudes are associated with being female, younger, more liberal, less Republican, having a higher income and a lower level of fundamentalist religiosity, as well as consuming a wider variety of news media. Liberals tend to consume a larger number of news sources than conservatives. Also, news media diet mediates, instead of moderates, the effects of political ideology on support for the LGT community. Overall, a healthy diet of news media is associated with support for equality rights.
Reduced neural responsiveness to looming stimuli is associated with increased aggression

Abstract While neuro-cognitive work examining aggression has examined patients with conditions at increased risk for aggression or individuals self-reporting past aggression, little work has attempted to identify neuro-cognitive markers associated with observed/recorded aggression. The goal of the current study was to determine the extent to which aggression by youth in the first three months of residential care was associated with atypical responsiveness to threat stimuli. This functional MRI study involved 98 (68 male; mean age = 15.96 [sd = 1.52]) adolescents in residential care performing a looming threat task involving images of threatening and neutral human faces or animals that appeared to be either loom or recede. Level of aggression was negatively associated with responding to looming stimuli (irrespective of whether these were threatening or neutral) within regions including bilateral inferior frontal gyrus, right inferior parietal lobule, right superior/middle temporal gyrus and a region of right uncus proximal to the amygdala. These data indicate that aggression level is associated with a decrease in responsiveness to a basic threat cue-looming stimuli. Reduced threat responsiveness likely results in the individual being less able to represent the negative consequences that may result from engaging in aggression, thereby increasing the risk for aggressive episodes.
Between inflammation and thrombosis: endothelial cells in COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing the current coronavirus disease (COVID-19) pandemic [1]. Over recent months, a plethora of novel research articles has been published, dealing with multiple aspects and manifestations of the disease. Increasing evidence points to a central role of endothelial cells in SARS-CoV-2 infection [2–5]. Early studies have already indicated increased expression of vascular and inflammatory factors (such as vascular cell adhesion molecule (VCAM)-1, interleukin (IL)-8 or monocyte-chemoattractant protein (MCP)-1) in COVID-19 lung tissue [2]. Such markers of endothelial dysfunction and altered endothelial cell integrity are important predictors of a poor outcome in SARS-CoV-2 infections [6], and they are associated with pulmonary oedema, intravascular thrombosis and acute respiratory distress syndrome (ARDS). The pulmonary endothelium is crucial for regulation of vascular tone, inflammatory responses, coagulation/fibrinolysis and maintenance of vascular homeostasis and permeability. Disturbances of these tightly regulated processes may directly contribute to morbidity and mortality. However, the exact mechanisms leading to pulmonary vasculopathy in COVID-19 are still unclear. Here, we provide an analysis of several important vascular markers implicated in the inflammatory response (E-selectin, intercellular cell adhesion molecule (ICAM)-1, VCAM-1), maintenance of microvascular integrity (CD31, vascular endothelial growth factor receptor (VEGFR)-2), platelet activation and coagulation (P-selectin, von Willebrand factor (vWF)) in lung tissue and plasma samples of COVID-19 patients. Elevated levels of several endothelial markers, including CD31, VEGFR-2, ICAM-1, VCAM-1, E-selectin, P-selectin and vWF, in lung tissue and circulation support an important role of the pulmonary endothelium in local and systemic COVID-19 pathology https://bit.ly/3eQObIR
On comprehensive analysis of root canal shaping ability of three endodontic files of different kinematics

Infection of the tooth’s root canal requires what is called root canal treatment (RTC). The most important part of endodontic treatment is to shape the root canal and remove its infected portion using endodontic files of various protocols, kinematics and designs that suit the particular geometry. Cleaning and Shaping the canal efficiently remove the root canal bacterial biofilms or tissue remnants while keeping its natural geometry. The result is determined by shaping the ability of the relevant endodontic file. In the available literature, no norm has been established for the measurement of various endodontic files’ ability to do effective shaping. We present in this study a method to analyse and measure the shaping ability of endodontic files of three different kinematics.
COVID‐19: vaccine’s progress

Under the pressure of the COVID‐19 pandemic, vaccines were developed and rolled out into mass vaccination campaigns at incredible speed. What normally takes a decade was worked out within a year. Vaccines were produced along many different platforms ranging from inactivated whole virus vaccines over adenovirus‐vectored vaccines, recombinant protein vaccines and nanoparticles to mRNA vaccines. Several vaccines went through preclinical testing and completed successful phase 1 to phase 3 clinical trials. The first evaluations of national vaccination campaigns document astonishing high levels of protection against disease. The present article summarizes the published reports leading to these striking achievements with vaccines based on different concepts.
Validating Pore Size Estimates in a Complex Microfibre Environment on a Human MRI System

Purpose Recent advances in diffusion-weighted MRI provide ‘restricted diffusion signal fraction’ and restricting pore size estimates. Materials based on co-electrospun oriented hollow cylinders have been introduced to provide validation for such methods. This study extends this work, exploring accuracy and repeatability using an extended acquisition on a 300 mT/m gradient human MRI scanner, in substrates closely mimicking tissue, i.e., non-circular cross-sections, intra-voxel fibre crossing, intra-voxel distributions of pore-sizes and smaller pore-sizes overall. Methods In a single-blind experiment, diffusion-weighted data were collected from a biomimetic phantom on a 3T Connectom system using multiple gradient directions/diffusion times. Repeated scans established short-term and long-term repeatability. The total scan time (54 minutes) matched similar protocols used in human studies. The number of distinct fibre populations was estimated using spherical deconvolution, and median pore size estimated through the combination of CHARMED and AxCaliber3D framework. Diffusion-based estimates were compared with measurements derived from scanning electron microscopy. Results The phantom contained substrates with different orientations, fibre configurations and pore size distributions. Irrespective of one or two populations within the voxel, the pore-size estimates (~5μm) and orientation-estimates showed excellent agreement with the median values of pore-size derived from scanning electron microscope and phantom configuration. Measurement repeatability depended on substrate complexity, with lower values seen in samples containing crossing-fibres. Sample-level repeatability was found to be good. Conclusion While no phantom mimics tissue completely, this study takes a step closer to validating diffusion microstructure measurements for use in vivo by demonstrating the ability to quantify microgeometry in relatively complex configurations.
Temporal, Sex-Specific, Social Media-Based Alcohol Influences during the Transition to College

Abstract Background The transition to college is an important developmental phase, usually met with increased social desirability, access to alcohol, and new peer groups. Recently, research has utilized social media as a predictor of events during college, but few have assessed how social media can influence alcohol use during the transition to college. Methods: Participants (N = 320) were recruited prior to entering their first year of college. Participants were 18 years old, 60.7% were women, with 46.3% identifying as White, 16.5% Hispanic, 14.9% Asian, 9.5% Black, and 7.6% other. Each participant was assessed three times: prior to matriculation, first semester, and second semester of their freshman year. We assessed the effect of exposure to alcohol content via social media on long-term trajectories of alcohol use. We also assessed self-reported sex as a moderator. Results: Exposure to alcohol content (over and above one’s own posting of alcohol content) was associated with greater frequency of drinking during the transition to college. In the multi-group model, exposure to alcohol content was associated with greater drinking prior to matriculation for men. However, for women, exposure to alcohol content was associated with greater alcohol use in the first semester of college. Conclusion: Our results indicate exposure to alcohol-related media content is a strong predictor, over and above one’s own positing, of increased drinking, and this effect varies by sex and point in time. Our results lend support for more tailored and time-specific prevention programming for incoming freshmen that should integrate social media normative feedback.
The Value of Web-Based Patient Education Materials on Transarterial Chemoembolization: Systematic Review

Background Thousands of web searches are performed related to transarterial chemoembolization (TACE), given its palliative role in the treatment of liver cancer. Objective This study aims to assess the reliability, quality, completeness, readability, understandability, and actionability of websites that provide information on TACE for patients. Methods The five most popular keywords pertaining to TACE were searched on Google, Yahoo, and Bing. General website characteristics and the presence of Health On the Net Foundation code certification were documented. Website assessment was performed using the following scores: DISCERN, Journal of the American Medical Association, Flesch-Kincaid Grade Level, Flesch Reading Ease Score, and the Patient Education Materials Assessment Tool. A novel TACE content score was generated to evaluate website completeness. Results The search yielded 3750 websites. In total, 81 website entities belonging to 78 website domains met the inclusion criteria. A medical disclaimer was not provided on 28% (22/78) of website domains. Health On the Net code certification was present on 12% (9/78) of website domains. Authorship was absent on 88% (71/81) of websites, and sources were absent on 83% (67/81) of websites. The date of publication or of the last update was not listed on 58% (47/81) of websites. The median DISCERN score was 47.0 (IQR 40.5-54.0). The median TACE content score was 35 (IQR 27-43). The median readability grade level was in the 11th grade. Overall, 61% (49/81) and 16% (13/81) of websites were deemed understandable and actionable, respectively. Not-for-profit websites fared significantly better on the Journal of the American Medical Association, DISCERN, and TACE content scores. Conclusions The content referring to TACE that is currently available on the web is unreliable, incomplete, difficult to read, understandable but not actionable, and characterized by low overall quality. Websites need to revise their content to optimally educate consumers and support shared decision-making. Trial Registration PROSPERO International Prospective Register of Systematic Reviews CRD42020202747; https://www.crd. york.ac. uk/prospero/display_record. php? ID=CRD42020202747
Effectiveness of skin cleanser and protectant regimen on incontinence‐associated dermatitis outcomes in acute care patients: A cluster randomised trial

Skin cleansers and protectants protect skin from incontinent matter to reduce the risk of incontinence‐associated dermatitis (IAD), but their effectiveness treating established IAD in the tropics is unknown. We conducted an open‐label cluster randomised trial to compare the effectiveness of a combined regimen of (1) specialised skin cleansers with disposable body wipes and (2) either an acrylic terpolymer (T1) or zinc oxide (T2) skin protectant against disposable body wipes and zinc oxide protectant (control) in promoting IAD healing and reducing the risk of deterioration. Eighty‐four patients were recruited in a tertiary hospital in Singapore between April 2019 and January 2020 (T1: n = 23; T2: n = 37; Control: n = 24). Although not statistically significant, patients treated with T1 and T2 were 1.5 times as likely to experience IAD healing within seven days compared with the control (P = .66). Healing was more pronounced in participants with skin loss treated with T1 or T2. No treatment was superior in preventing IAD deterioration, the prevalence of which remained small (8%‐14%). While skin cleaning and protectants reduced the overall risk of skin deterioration, the addition of skin cleansers enhanced IAD healing within a short period, an important consideration for future research examining IAD treatment in acute care.
Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision

Abstract RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity and lack of precision. As a result, the full potential of (sc)RNA-seq is limited. Major factors in this respect are the presence of global bias in most datasets, which affects detection and quantitation of RNA in a length-dependent fashion. In particular, scRNA-seq is affected by technical noise and a high rate of dropouts, where the vast majority of original transcripts is not converted into sequencing reads. We discuss these biases origins and implications, bioinformatics approaches to correct for them, and how biases can be exploited to infer characteristics of the sample preparation process, which in turn can be used to improve library preparation.
Managing Tumor changes during Radiotherapy using a Deep Learning Model.

PURPOSE We propose a treatment planning framework that accounts for weekly lung tumor shrinkage using cone beam computed tomography (CBCT) images with a deep learning-based model. METHODS Sixteen patients with non-small cell lung cancer (NSCLC) were selected with one planning CT and six weekly CBCTs each. A deep learning-based model was applied to predict the weekly deformation of the primary tumor based on the spatial and temporal features extracted from previous weekly CBCTs. Starting from Week 3, the tumor contour at Week N was predicted by the model based on the input from all the previous weeks (1,2…N-1), and was evaluated against the manually contoured tumor using Dice coefficient, precision, average surface distance and Hausdorff distance. Information about the predicted tumor was then entered into the treatment planning system and the plan was re-optimized every week. The objectives were to maximize the dose coverage in the target region while minimizing the toxicity to the surrounding healthy tissue. Dosimetric evaluation of the target and organs at risk (heart, lung, esophagus, spinal cord) was performed on four cases, comparing between a conventional plan (ignoring tumor shrinkage) and the shrinkage-based plan. RESULTS The primary tumor volumes decreased on average by 38% ± 26% during six weeks of treatment. Dice coefficients (DSC) and average surface distance (ASD) between the predicted tumor and the actual tumor for Week 3, 4, 5, 6 were (0.81, 0.82, 0.79, 0.78) and (1.49, 1.59, 1.92, 2.12) mm, respectively, which were significantly superior to the score of (0.70, 0.68, 0.66, and 0.63) and (2.81, 3.22, 3.69, and 3.63) mm between the rigidly transferred tumors ignoring shrinkage and the actual tumor. While target coverage metrics were maintained for the re-optimized plans, lung mean dose dropped by 2.85, 0.46, 2.39, and 1.48 Gy for four sample cases when compared to the original plan. Doses in other organs such as esophagus were also reduced for some cases. CONCLUSION We developed a deep learning-based model for tumor shrinkage prediction. This model used CBCTs and contours from previous weeks as input and produced reasonable tumor contours with a high prediction accuracy (DSC, precision, HD, ASD). The proposed framework maintained target coverage while reducing dose in the lungs and esophagus.
Injuries related to electric scooter and bicycle use in a Washington, DC, emergency department

Abstract Objective E-scooter use has grown rapidly in the United States. Its rise in popularity has coincided with the promotion of cycling in many cities, but more needs to be known about how these transportation modes compare to determine if cycling should serve as an appropriate benchmark for policy decisions and safety expectations regarding e-scooters. Methods We examined characteristics of adults seeking treatment in a Washington, DC, emergency department (ED) for injuries associated with riding e-scooters during 2019 (n = 99) or bicycles during 2015–2017 (n = 337). Results E-scooter incidents less frequently involved moving vehicles (13.1% vs. 37.7%) or occurred on roads (24.5% vs. 50.7%) than cycling incidents. A smaller proportion of injured e-scooter riders were ages 30–49 (32.3% vs. 48.4%) and a larger proportion were 50 and older (34.3% vs. 22.6%) or female (45.5% vs. 29.1%). Distal lower extremity injuries were more common among e-scooter riders (13.1% vs. 3.0%; RR, 2.76; 95% CI, 1.79–3.54), and injuries to the proximal upper extremity (9.1% vs. 20.5%; RR, 0.49; 95% CI, 0.24–0.92) or chest, abdomen, and spine (3.0% vs. 14.0%; RR, 0.24; 95% CI, 0.07–0.70) were less common. Head injury rates were similar, but e-scooter riders more often experienced concussion with loss of consciousness (4.0% vs. 0.6%; RR, 3.03; 95% CI, 1.20–4.09) and were far less likely to wear helmets (2.0% vs. 66.4%). Estimated ED presentation rates per million miles traveled citywide were higher among e-scooter riders than cyclists (RR, 3.76; 95% CI, 3.08–4.59). Conclusions E-scooters and bicycles are both popular forms of micromobility, but the characteristics of riders injured on them, the ways in which they become injured, and the types of injuries they sustain differ substantially. E-scooter rider injury rates, though currently high, may decrease as they gain experience; however, if the number of new users continues to climb, they will persist in using the ED more often than cyclists per mile that they travel.
Multimodal Evoked Potentials as Candidate Prognostic and Response Biomarkers in Clinical Trials of Multiple Sclerosis

Summary: Evoked potentials (EPs) measure quantitatively and objectively the alterations of central signal propagation in multiple sclerosis and have long been used for diagnosis. More recently, their utility for prognosis has been demonstrated in several studies, summarizing multiple EP modalities in a single score. In particular, visual, somatosensory, and motor EPs are useful because of their sensitivity to pathology in the frequently affected optic nerve, somatosensory tract, and pyramidal system. Quantitative EP scores show higher sensitivity to change than clinical assessment and may be used to monitor disease progression. Visual EP and the visual system have served as a model to study remyelinating therapies in the setting of acute and chronic optic neuritis. This review presents rationale and evidence for using multimodal EP as prognostic and response biomarkers in clinical trials, targeting remyelination or halting disease progression in multiple sclerosis.