Miracle-dz/UniFAR-FTUs huggingface dataset:
An observational study on the association between major dietary patterns and non-alcoholic fatty liver disease in Chinese adolescents

Abstract Data on the association of dietary patterns with non-alcoholic fatty liver disease (NAFLD) among adolescents are scarce. Hence, the purpose of this study was to ascertain the influence of dietary patterns and key foods on NAFLD among adolescents in Shandong, China. Data were extracted from Linyi Nutrition and Health study during 2015 to 2016. This cross-sectional study population comprised 1639 participants aged between 16 and 23 years. Dietary intake was assessed by the use of a semiquantitative food frequency questionnaire (FFQ), containing 85 food items. NAFLD diagnosis was defined as individuals whose ultrasound examination disclosed hepatic steatosis at any stage, in the absence of excess intake of alcoholic beverages. The odds ratio (OR) and 95% confidence interval (CI) were estimated for each quartile of the dietary pattern adherence scores using logistic regression analysis. Of 1639 participants, 221 (13.5%) were classified as having NAFLD. Three major dietary patterns were derived from factor analysis: traditional Chinese, Western, and high-energy dietary patterns. There were significant differences in the intake of whole grains, tuber, and vegetable across quartiles of the traditional Chinese and Western pattern (P < .05). Besides, compared with adolescents in the lowest quartile, those in the highest quartile for whole grains intake had a lower OR for NAFLD (OR = 0.72; 95%CI: 0.61–0.98; P < .05), and for red meat and soft drink consumption had greater OR for NAFLD (OR = 1.34; 95% CI: 1.06–1.72; OR = 1.69; 95% CI: 1.34–2.56; respectively, P < .05). After adjustment for several potential confounders, participants in the highest quartile of the traditional Chinese pattern scores had lower OR for NAFLD (OR = 0.726; 95% CI: 0.383–0.960, P < .05) than did those in the lowest quartile, whereas those in the highest quartile of the Western pattern score had greater OR for NAFLD (OR = 1.197; 95% CI: 1.013–1.736, P < .01) than did those in the lowest quartile. No statistically significant association was found between the high-energy pattern and the risk of NAFLD. Our findings demonstrated that the traditional Chinese dietary pattern was associated with a lower risk, whereas the Western dietary pattern was associated with a higher risk of NAFLD.
VizAssert Visual Logic Assertion HTML + CSS Assertion QFLRA ( SMT ) 3 § 4 Accessibility Guidelines

Usability and accessibility guidelines aim to make graphical user interfaces accessible to all users, by, say, requiring that text is sufficiently large, interactive controls are visible, and heading size corresponds to importance. These guidelines must hold on the infinitely many possible renderings of a web page generated by differing screen sizes, fonts, and other user preferences. Today, these guidelines are tested by manual inspection of a few renderings, because 1) the guidelines are not expressed in a formal language, 2) the semantics of browser rendering are not well understood, and 3) no tools exist to check all possible renderings of a web page. VizAssert solves these problems. First, it introduces visual logic to precisely specify accessibility properties. Second, it formalizes a large fragment of the browser rendering algorithm using novel finitization reductions. Third, it provides a sound, automated tool for verifying assertions in visual logic. We encoded 14 assertions drawn from best-practice accessibility and mobile-usability guidelines in visual logic. VizAssert checked them on on 62 professionally designed web pages. It found 64 distinct errors in the web pages, while reporting only 13 false positive warnings. CCSConcepts • Software and its engineering→Graphical UI languages; Software maintenance tools;
Progression of regional grey matter atrophy in multiple sclerosis

Grey matter atrophy is present from the earliest clinical stages of multiple sclerosis (MS), but the temporal ordering is poorly understood. We aimed to determine the sequence in which grey matter regions become atrophic in MS, and its association with disability accumulation. In this longitudinal study, we included 1,417 subjects: 253 with clinically-isolated syndrome (CIS), 708 relapsing-remitting MS (RRMS), 128 secondary-progressive MS (SPMS), 125 primary-progressive MS (PPMS), and 203 healthy controls from 7 European centres. Subjects underwent repeated MRI scanning (total number of scans 3,604); the mean follow-up for patients was 2.41yrs (SD±1.97). Disability was scored using the Expanded Disability Status Scale (EDSS). We calculated the volume of brain grey matter regions and brainstem using an unbiased within-subject template. We used an established data-driven event-based model (EBM) to determine the sequence of occurrence of atrophy and its uncertainty. We assigned each subject to a specific EBM stage, based on the number of their atrophic regions. We used nested linear mixed-effects regression models to explore the associations between the rate of increase in the EBM stages over time, disease duration and annual rate of EDSS gain. The first regions to become atrophic in CIS and relapse-onset MS patients (RRMS and SPMS) were the posterior cingulate cortex and precuneus, followed by the middle cingulate cortex, brainstem and thalamus. The sequence of atrophy in PPMS showed a similar involvement of the thalamus, cuneus, precuneus, and pallidum, followed by the brainstem and posterior cingulate cortex. The cerebellum, caudate and putamen showed early atrophy in relapse-onset MS and late atrophy in PPMS. Patients with SPMS showed the highest EBM stages (highest number of atrophic regions, all p<0.001) at study entry. Rates of increase in EBM stages were significantly different from healthy controls in all MS phenotypes, except for CIS. The increase in the number of atrophic regions (EBM stage) was associated with disease duration in all patients. EBM stage was associated with disability accumulation in RRMS independent of disease duration (p<0.0001). This data-driven staging of atrophy progression in a large MS sample demonstrates that grey matter atrophy spreads to involve more regions over time. The sequence in which regions become atrophic is reasonably consistent across MS phenotypes. The spread of atrophy was associated with disease duration, and disability accumulation in RRMS. Abbreviations MS multiple sclerosis GM grey matter FLAIR Fluid Attenuated Inversion Recovery PPMS primary progressive multiple sclerosis; primary-progressive MS
Smartphone-Based in-Gel Loop-Mediated Isothermal Amplification (gLAMP) System Enables Rapid Coliphage MS2 Quantification in Environmental Waters

Model coliphages (e.g., ΦX174, MS2, and PRD1) have been widely used as surrogates to study the fate and transport of pathogenic viruses in the environment and during wastewater treatment. Two groups of coliphages (F-specific and somatic) are being explored as indicators of viral fecal pollution in ambient water. However, the detection and quantification of coliphages still largely rely on time-consuming culture-based plaque assays. In this study, we developed an in-gel loop-mediated isothermal amplification (gLAMP) system enabling coliphage MS2 quantification within 30 min using standard laboratory devices. Viral particles (MS2) were immobilized with LAMP reagents in polyethylene glycol hydrogel, and then viral RNAs were amplified through a LAMP reaction. Due to the restriction effect of the hydrogel matrix, one viral particle would only produce one amplicon dot. Therefore, the sample virus concentrations can be determined based on the number of fluorescent amplicon dots using a smartphone for imaging. The method was validated by using artificially spiked and naturally contaminated water samples. gLAMP results were shown to correlate well with plaque assay counts (R2 = 0.984, p < 0.05) and achieved similar sensitivity to quantitative reverse-transcription polymerase chain reaction (RT-qPCR; 1 plaque-forming unit per reaction). Moreover, gLAMP demonstrated a high level of tolerance against inhibitors naturally present in wastewater, in which RT-qPCR was completely inhibited. Besides MS2, gLAMP can also be used for the quantification of other microbial targets (e.g., Escherichia coli and Salmonella). Considering its simplicity, sensitivity, rapidity, and versatility, gLAMP holds great potential for microbial water-quality analysis, especially in resource-limited settings.
Large Deviations for a matching problem related to the ∞-Wasserstein distance

Let (E, d) be a compact metric space, X = (X1, . . . , Xn, . . . ) and Y = (Y1, . . . , Yn, . . . ) two independent sequences of independent E-valued random variables and (Ln )n≥1 and (L Y n )n≥1 the associated sequences of empirical measures. We establish a Large Deviation Principle for (W∞(L X n , L Y n ))n≥1 where W∞ is the ∞-Wasserstein distance, W∞(L X n , L Y n ) = min σ∈Sn max 1≤i≤n d(Xi, Yσ(i)) where Sn stands for the set of permutations of {1, . , n}.
A dual-user teleoperated system with Virtual Fixtures for robotic surgical training

This paper proposes a teleoperated dual-user system incorporating Virtual Fixtures (VFs) that allows concurrent performance of a robotic surgical task by an expert and a trainee. In order to guide the trainee through the procedure, an adaptive VF is created in the trainee's workspace according to the motion generated by the expert who is performing the surgery at the same time. The VF gets adaptively adjusted based on the level of expertise the trainee shows during the surgery. In addition, the trainee's level of expertise is used to adaptively adjust the dual-user dominance factor in an online fashion, which gives the trainee some authority over the task based on his/her skill level. To quantify the trainee's expertise level, a performance measure is proposed, based on the force generated by the VF. Three performance measures from the literature are also used. To satisfy the desired objectives of the proposed system, an impedance-based control methodology is adopted. Stability of the closed-loop system is investigated using the small-gain theorem. A sufficient stability condition is derived that guarantees stability in the presence of time-varying communication delay. Experimental results are given to validate the performance of the system.
T cell immunotherapy for melanoma from bedside to bench to barn and back: how conceptual advances in experimental mouse models can be translated into clinical benefit for patients

A solid scientific basis now supports the concept that cytotoxic T lymphocytes can specifically recognize and destroy melanoma cells. Over the last decades, clinicians and basic scientists have joined forces to advance our concepts of melanoma immunobiology. This has catalyzed the rational development of therapeutic approaches to enforce melanoma‐specific T cell responses. Preclinical studies in experimental mouse models paved the way for their successful translation into clinical benefit for patients with metastatic melanoma. A more thorough understanding of how melanomas develop resistance to T cell immunotherapy is necessary to extend this success. This requires a continued interdisciplinary effort of melanoma biologists and immunologists that closely connects clinical observations with in vitro investigations and appropriate in vivo mouse models: From bedside to bench to barn and back.
Mutator Natural Escherichia coliIsolates Have an Unusual Virulence Phenotype

ABSTRACT A small percentage of natural Escherichia coli isolates (both commensal and pathogenic) have a mutator phenotype related to defects in methyl-directed mismatch repair (MR) genes. We investigated whether there was a direct link between the mutator phenotype and virulence by (i) studying the relationships between mutation rate and virulence in a mouse model of extraintestinal virulence for 88 commensal and extraintestinal pathogenic E. coli isolates and (ii) comparing the virulence in mice of MR-deficient and MR-proficient strains that were otherwise isogenic. The results provide no support for the hypothesis that the mutator phenotype has a direct role in virulence or is associated with increased virulence. Most of the natural mutator strains studied displayed an unusual virulence phenotype with (i) a lack of correspondence between the number of virulence determinants and pathogenicity in mice and (ii) an intermediate level of virulence. On a large evolutionary scale, the mutator phenotype may help parasites to achieve an intermediate rate of virulence which mathematical models predict to be selected for during long-term parasite-host interactions.
Transcriptomic profiling of human skin biopsies in the clinical trial setting: A protocol for high quality RNA extraction from skin tumours

Transcriptomic profiling of skin disease using next generation sequencing allows for detailed information on aspects of RNA biology including gene expression, non-coding regulatory elements and gene splicing. The application of RNA sequencing to human skin disease and cancer is often hampered by degraded RNA. Here we describe a protocol that allows for consistently intact RNA to be extracted from snap frozen skin biopsy samples, which has been validated in a clinical trial setting. Human skin tumour punch biopsies (n=28) ranging from 4-6mm in diameter were obtained from 14 patients with an inherited skin tumour syndrome (CYLD cutaneous syndrome) and frozen in liquid nitrogen prior to being stored at -80°C. These samples were then subject to cyrostat sectioning, allowing for histological assessment, and were homogenised using a bead-based lysis platform. RNA extraction was performed using a silica column-based system. RNA concentration was measured using fluorescent quantitation and RNA integrity assessed using microfluidic gel electrophoresis. We also processed normal skin biopsies using the same protocol (n=10). The mean RNA integrity score of the tumour and normal samples was 9.5, and the quantity of RNA obtained from the small amounts of tissue used exceeded requirements for RNA-seq library generation. We propose that the method of RNA extraction suggested here allows for transcriptomic profiling from small pieces of human tissue without the need for PCR amplification during library preparation. This protocol could be utilised in healthy and diseased skin to improve mechanistic understanding in a range of human skin diseases.
Oncolytic Viral Therapy and the Immune System: A Double-Edged Sword Against Cancer

Oncolytic viral therapy is a new promising strategy against cancer. Oncolytic viruses (OVs) can replicate in cancer cells but not in normal cells, leading to lysis of the tumor mass. Beside this primary effect, OVs can also stimulate the immune system. Tumors are an immuno-suppressive environment in which the immune system is silenced in order to avoid the immune response against cancer cells. The delivery of OVs into the tumor wakes up the immune system so that it can facilitate a strong and durable response against the tumor itself. Both innate and adaptive immune responses contribute to this process, producing an immune response against tumor antigens and facilitating immunological memory. However, viruses are recognized by the immune system as pathogens and the consequent anti-viral response could represent a big hurdle for OVs. Finding a balance between anti-tumor and anti-viral immunity is, under this new light, a priority for researchers. In this review, we provide an overview of the various ways in which different components of the immune system can be allied with OVs. We have analyzed the different immune responses in order to highlight the new and promising perspectives leading to increased anti-tumor response and decreased immune reaction to the OVs.
A computer model to dynamically simulate protein folding: Studies with crambin

The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximately the effect of each side chains. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealinghas been used to dynamically sample the conformations available to this sample model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence‐dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide, suggestion the model may accurately simulate the folding process.
Flexible Signaling of Myeloid C-Type Lectin Receptors in Immunity and Inflammation

Myeloid C-type lectin receptors (CLRs) are important sensors of self and non-self that work in concert with other pattern recognition receptors (PRRs). CLRs have been previously classified based on their signaling motifs as activating or inhibitory receptors. However, specific features of the ligand binding process may result in distinct signaling through a single motif, resulting in the triggering of non-canonical pathways. In addition, CLR ligands are frequently exposed in complex structures that simultaneously bind different CLRs and other PRRs, which lead to integration of heterologous signaling among diverse receptors. Herein, we will review how sensing by myeloid CLRs and crosstalk with heterologous receptors is modulated by many factors affecting their signaling and resulting in differential outcomes for immunity and inflammation. Finding common features among those flexible responses initiated by diverse CLR-ligand partners will help to harness CLR function in immunity and inflammation.
Low Dose Influenza Virus Challenge in the Ferret Leads to Increased Virus Shedding and Greater Sensitivity to Oseltamivir

Ferrets are widely used to study human influenza virus infection. Their airway physiology and cell receptor distribution makes them ideal for the analysis of pathogenesis and virus transmission, and for testing the efficacy of anti-influenza interventions and vaccines. The 2009 pandemic influenza virus (H1N1pdm09) induces mild to moderate respiratory disease in infected ferrets, following inoculation with 106 plaque-forming units (pfu) of virus. We have demonstrated that reducing the challenge dose to 102 pfu delays the onset of clinical signs by 1 day, and results in a modest reduction in clinical signs, and a less rapid nasal cavity innate immune response. There was also a delay in virus production in the upper respiratory tract, this was up to 9-fold greater and virus shedding was prolonged. Progression of infection to the lower respiratory tract was not noticeably delayed by the reduction in virus challenge. A dose of 104 pfu gave an infection that was intermediate between those of the 106 pfu and 102 pfu doses. To address the hypothesis that using a more authentic low challenge dose would facilitate a more sensitive model for antiviral efficacy, we used the well-known neuraminidase inhibitor, oseltamivir. Oseltamivir-treated and untreated ferrets were challenged with high (106 pfu) and low (102 pfu) doses of influenza H1N1pdm09 virus. The low dose treated ferrets showed significant delays in innate immune response and virus shedding, delayed onset of pathological changes in the nasal cavity, and reduced pathological changes and viral RNA load in the lung, relative to untreated ferrets. Importantly, these observations were not seen in treated animals when the high dose challenge was used. In summary, low dose challenge gives a disease that more closely parallels the disease parameters of human influenza infection, and provides an improved pre-clinical model for the assessment of influenza therapeutics, and potentially, influenza vaccines.
Secondary peak in the Nusselt number distribution of impinging jet flows: A phenomenological analysis

This paper focuses on a wall-resolved Large Eddy Simulation (LES) of an isothermal round submerged air jet impinging on a heated flat plate, at a Reynolds number of 23 000 (based on the nozzle diameter and the bulk velocity at the nozzle outlet) and for a nozzle to plate distance of two jet diameters. This specific configuration is known to lead to a non-monotonic variation of the temporal-mean Nusselt number as a function of the jet center distance, with the presence of two distinct peaks located on the jet axis and close to two nozzle diameters from the jet axis. The objectives are here twofold: first, validate the LES results against experimental data available in the literature and second to explore this validated numerical database by the use of high order statistics such as skewness and probability density functions of the temporal distribution of temperature and pressure to identify flow features at the origin of the second Nusselt peak. Skewness (Sk) of the pressure temporal distribution reveals t.
Is Passive Syntax Semantically Constrained? Evidence From Adult Grammaticality Judgment and Comprehension Studies

Abstract To explain the phenomenon that certain English verbs resist passivization (e.g., *£5 was cost by the book), Pinker (1989) proposed a semantic constraint on the passive in the adult grammar: The greater the extent to which a verb denotes an action where a patient is affected or acted upon, the greater the extent to which it is compatible with the passive. However, a number of comprehension and production priming studies have cast doubt upon this claim, finding no difference between highly affecting agent‐patient/theme‐experiencer passives (e.g., Wendy was kicked/frightened by Bob) and non‐actional experiencer theme passives (e.g., Wendy was heard by Bob). The present study provides evidence that a semantic constraint is psychologically real, and is readily observed when more fine‐grained independent and dependent measures are used (i.e., participant ratings of verb semantics, graded grammaticality judgments, and reaction time in a forced‐choice picture‐matching comprehension task). We conclude that a semantic constraint on the passive must be incorporated into accounts of the adult grammar.
Programmatic mapping to determine the size and dynamics of sex work and injecting drug use in Mauritius

HIV in Mauritius is in a concentrated phase. Most HIV infection is among key populations (KPs) including female sex workers (FSW), people who inject drugs (PWID), men who have sex with men (MSM), and transgender sex workers (TGSW). The objective of this research was to use geographical mapping to determine the precise locations, typologies and population estimates of each KP in Mauritius. From May to July 2014 a programmatic mapping approach determined national estimates and information on the specific locations, “hotspots”, frequented by KPs in Mauritius. Data were collected through multiple levels of activity. Key informants provided information about hotspots where KPs congregated and were actively engaged in risky behaviours. Validation of hotspots was done by engaging KPs. A total of 17 248 KP members were estimated spread over 1 964 hotspots in Mauritius. The largest KP was PWID with an estimate of 7 598 (range: 4 091–6 223), followed by 6 223 (range: 5 090–7 456) FSWs, spread over 694 and 731 hotspots respectively. A total of 2 020 (range: 1 595–2 446) MSM and 294 geographic MSM hotspots, and 1 407 TGSWs (range: 1 165–1 649) distributed over 245 hotspots. This research provided Mauritius with validated KPs size estimations and provided the first national data on KP hotspots and operational dynamics. The use of these data will strengthen HIV prevention, intervention, and programme planning in the country through focusing efforts to systematically target high-risk areas.