Miracle-dz/UniFAR-FTUs huggingface dataset:
A U-statistics for integrative analysis of multilayer omics data

MOTIVATION The emerging multi-layer omics data provide unprecedented opportunities for detecting biomarkers that are associated with complex diseases at various molecular levels. However, the high-dimensionality of multi-omics data and the complex disease etiologies have brought tremendous analytical challenges. RESULTS We developed a U-statistics-based non-parametric framework for the association analysis of multi-layer omics data, where consensus and permutation-based weighting schemes are developed to account for various types of disease models. Our proposed method is flexible for analyzing different types of outcomes as it makes no assumptions about their distributions. Moreover, it explicitly accounts for various types of underlying disease models through weighting schemes and thus provides robust performance against them. Through extensive simulations and the application to dataset obtained from the Alzheimer's Disease Neuroimaging Initiatives, we demonstrated that our method outperformed the commonly used kernel regression-based methods. AVAILABILITY The R-package is available at https://github.com/YaluWen/Uomic. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Origin of Stability and Transition from Anionic to Cationic Surface Ligand Passivation of All-Inorganic Cesium Lead Halide Perovskite Nanocrystals.

Recently, the structural stability of all-inorganic halide perovskite nanocrystals has been significantly enhanced. To understand the enhancement, we developed surface passivation models for cubic CsPbBr3 nanocrystals with anionic (oleate) and cationic (oleylammonium) organic ligands based on first-principles calculations and nuclear magnetic resonance investigations. We propose that the (100) surface is initially terminated with oleate ligand complexes on PbBr2(100) surfaces. Also, the ligand transition to oleylammonium on the Pb-rich surfaces is expected due to the addition of metal halides (ZnBr2) during colloidal synthesis. The significant improvement in the structural stability of the cationic ligand-passivated CsPbBr3 nanocrystals was attributed to the suppressed exposure of the merging-vulnerable (110) surface, caused by the large formation energy difference between the ligand-passivated (100) and Br-passivated (110) surfaces.
"Just tell me what's going on": The views of parents of children with genetic conditions regarding the research use of their child's electronic health record

OBJECTIVE The purpose of this study was to understand the ethical, legal, and social issues described by parents of children with known or suspected genetic conditions that cause intellectual and developmental disabilities regarding research use of their child's electronic health record (EHR). MATERIALS AND METHODS We conducted 4 focus groups with parents of children with a known (n = 12) or suspected (n = 11) genetic condition, as well as 2 comparison groups with parents who had a child with no known genetic condition (n = 15). Focus group transcripts were coded and analyzed using directed content analysis. RESULTS After weighing the risks and benefits, parents of children with known or suspected genetic conditions were willing to share their child's EHR for research studies under certain conditions. Preferences were for studies conducted by universities or nonprofits that might benefit their child or others with the same condition. Parents also valued return of research results. DISCUSSION Trust, transparency, altruism, and concerns about privacy emerged as factors that affect parents' willingness to allow research use of their child's EHR. CONCLUSION Researchers should consider how to build trust with parents by increasing transparency of the research process and explaining specifically how they will ensure the confidentiality of EHR data.
Universal screening versus risk‐based protocols for antibiotic prophylaxis during childbirth to prevent early‐onset group B streptococcal disease: a systematic review and meta‐analysis

Early‐onset group B streptococcal (EOGBS) disease (including sepsis, meningitis, and pneumonia) causes significant morbidity and mortality in newborn infants worldwide. Antibiotic prophylaxis can prevent vertical streptococcal transmission, yet no uniform criteria exist to identify eligible women for prophylaxis. Some guidelines recommend universal GBS screening to pregnant women in their third trimester (screening‐based protocol), whereas others employ risk‐based protocols.
Correlations between tumor-infiltrating and circulating lymphocyte subpopulations in advanced renal cancer patients treated with nivolumab

Background: In clinical trials with immunotherapy, histological features such as tumor-infiltrating lymphocytes (TILs) are investigated as potential predictive biomarkers, with the limit of an outdated parameter for a typically dynamic element. Methods: This explorative study compared, in metastatic renal cell carcinoma (mRCC) patients, basal pathological data about TILs on diagnostic histological specimens with circulating lymphocyte subpopulations measured before and during therapy with nivolumab. Results: Of 11 mRCC patients, 5 had low presence of TILs (L-TILs), 3 moderate amount (M-TILs) and 3 high number (H-TILs). Overall, 8 patients had low intratumoral pathological CD4+/CD8+ ratio (LIPR) ≤1 and 3 cases high intratumoral pathological ratio (HIPR) ≥2. Of 8 patients with LIPR, only 2 matched with low circulating CD4+/CD8+ ratio (LCR) ≤1; 5 had high circulating ratio (HCR) ≥2. All 3 cases with HIPR (≥2) conversely had LCR (≤1). Circulating CD4+/CD8+ ratio remained unchanged during therapy (mean -0.12 in 8 weeks). The respective percentage values of CD4+ and CD8+ circulating T cells also remained stable (variation 0%); the absolute value of CD4+ was more likely to increase (mean +46.3/mm3); the level of CD8+ tended to slightly decrease (mean -6.5/mm3). No correlation of lymphocyte subpopulations with treatment outcome was found. Of note, we did not evidence correspondence between histopathological and circulating findings in terms of T-lymphocyte subpopulations, also suggesting the inconsistency of circulating data in terms of relative variations. Conclusions: Considering the likely high dynamism of TILs, rebiopsy before therapy might be proposed to assess the utility of TILs characterization for predictive purpose. (www.actabiomedica.it)
Sustainable Recovery of Gaseous Mercury by Adsorption and Electrothermal Desorption using Activated Carbon Fiber Cloth.

The presented work aims to develop a novel and sustainable approach to adsorb and recover the low-concentration Hg0 in the off-gas downstream a distillation/condensation system in the recycling processes for waste Hg-containing devices. Hg0 adsorption and regeneration efficiency of raw and HNO3-treated activated carbon fiber cloth (ACFC) were examined. The adsorption experiments were conducted with an initial Hg0 concentration of 260‒300 µg/m3 at room temperature. The regeneration of ACFC was done by an electrothermal swing process with 20, 40, and 60 W direct current. The experimental results showed that the Hg0 adsorption efficiency of raw ACFC increased to approximately 90% after 60-W electrothermal regeneration. After HNO3 treatment, the content of oxygen functional groups on HNO3-treated ACFC increased, which enhanced the Hg0 adsorption performance and resulted in over 90% of adsorption efficiency for the samples before and after electrothermal regeneration. Importantly, both raw and HNO3-treated ACFCs remained high adsorption efficiency after nine cycles of adsorption/regeneration, indicating that both raw and HNO3-treated ACFCs were effective and renewable adsorbents for low-concentration Hg0 adsorption and recovery. A Hg adsorption/regeneration mechanism was proposed to explain the increasing adsorption efficiency after electrothermal regeneration and the great adsorption efficiency of HNO3-treated ACFC.
Behavioral and neuronal interactions between exercise and alcohol: Sex and genetic differences

Alcohol use disorders (AUDs) lead to early death and many devastating consequences for individuals, families and society. Currently, few effective treatments are available, but emerging research suggests exercise might be beneficial in some individuals. To develop the most effective exercise treatment program, more research on intensity, type, timing, stage of addiction, drug involved, sex of subject and subject population is needed. This review highlights the complexity of the interaction between alcohol behaviors and exercise, with a focus on the role of sex and genetics. Moreover, we describe a variety of rodent models used to investigate the neuronal physiology changes that underlie alcohol consumption and exercise. Specifically, current data indicate that moderate exercise may ameliorate neuronal damage caused by alcohol consumption. Additionally, we describe studies of rodent models in the context of hedonic substitution to draw broad conclusions about shared underlying neurobiological mechanisms. Until recently, most studies in rodents were performed only in males, and few studies have utilized different genetic strains of mice or rats. Comparing similar behavioral paradigms across sex and strain, it has become clear that major sex and genetic differences exist for each behavioral context alone (alcohol consumption and exercise) and combined. Therefore, future research in this area should be developed with careful study design and attention to address both of these factors.
Sentinel lymph node mapping in endometrial cancer: performance of hysteroscopic injection of tracers

Objective To report on the performance of hysteroscopic injection of tracers (indocyanine green (ICG) and technetium-99m (Tc-99m)) for sentinel lymph node (SLN) mapping in endometrial cancer. Methods Single-center retrospective evaluation of consecutive patients who underwent SLN mapping following hysteroscopic peritumoral injection of tracer. Detection rate (overall/bilateral/aortic) diagnostic accuracy, and oncologic outcomes were evaluated. Results A total of 221 procedures met the inclusion criteria. Mean patient age was 60 (range 28–84) years and mean body mass index was 26.9 (range 15–47) kg/m2 . In 164 cases (70.9%) mapping was performed laparoscopically. The overall detection rate of the technique was 94.1% (208/221 patients). Bilateral pelvic mapping was found in 62.5% of cases with at least one SLN detected and was more frequent using ICG than with Tc-99m (73.8% vs 53.3%; p<0.001). In 47.6% of cases SLNs mapped in both pelvic and aortic nodes, and in five cases (2.4%) only in the aortic area. In eight patients (3.8%) SLNs were found in aberrant (parametrial/presacral) areas. Mean number of detected SLNs was 3.7 (range 1–8). In 51.9% of cases at least one node other than SLNs was removed. Twenty-six patients (12.5%) had nodal involvement: 12 (46.2%) macrometastases, six (23.1%) micrometastases, and eight (30.7%) isolated tumor cells. In 12 cases (46.8%) the aortic area was involved. Overall, 6/221 (2.7%) patients had isolated para-aortic nodes. Three false-negative results were found, all in the Tc-99m group. All had isolated aortic metastases. Overall sensitivity was 88.5% (95% CI 71.7 to 100.0) and overall negative predictive value was 96.5% (95% CI 86.8 to 100.0). There were 10 (4.8%) recurrences: five abdominal/distant, four vaginal, and one nodal (in the aortic area following a unilateral mapping plus side-specific pelvic lymphadenectomy). Most recurrences (9/10 cases) were patients in whom a completion lymphadenectomy was performed. No deaths were reported after a mean follow-up of 47.7 months. Conclusions Hysteroscopic injection of tracers for SLN mapping in endometrial cancer is as accurate as cervical injection with a higher detection rate in the aortic area. ICG improves the bilateral detection rate. Adding lymphadenectomy to SLN mapping does not reduce the risk of relapse.
Mast Cell Infiltration Is Associated With Persistent Symptoms and Endoscopic Abnormalities Despite Resolution of Eosinophilia in Pediatric Eosinophilic Esophagitis.

OBJECTIVES Mast cells (MCs) are increased in eosinophilic esophagitis (EoE). Endoscopic abnormalities, symptoms, and epithelial changes can persist after treatment despite a reduction of esophageal eosinophilia. It is unknown whether this could be due to persistent MC infiltration. We aimed to determine whether patients with histologically inactive (HI) EoE (defined as <15 eosinophils per high-powered field) with persistent symptoms, endoscopic, or epithelial abnormalities after treatment have increased MCs. METHODS Secondary analysis of prospective data from 93 children with EoE undergoing post-treatment endoscopy between 2011 and 2015. Thirty-five non-EoE controls were included. Immunohistochemistry for tryptase, an MC marker, was performed on mid and distal esophageal biopsies. Total and degranulated intraepithelial MCs per high-powered field (MC/hpf) were quantified. Symptoms and endoscopic findings were recorded at time of endoscopy. MC/hpf were compared between HI-EoE and control, and among HI-EoE based on endoscopic and histologic findings, and symptoms. Nine clinical remission (CR) patients were identified, with absence of endoscopic abnormalities and symptoms. RESULTS MC/hpf were increased in HI-EoE compared with control (17 ± 11 vs 8 ± 6, P < 0.0). Patients with persistent endoscopic abnormalities had increased total (20 ± 12 vs 13 ± 10, P = 0.001) and degranulated (8 ± 6 vs 5 ± 4, P = 0.002) MC/hpf, with no difference in eosinophils. MC/hpf predicted furrowing (odds ratio = 1.06, P = 0.01) and rings (odds ratio = 1.05, P = 0.03) after controlling for treatment type, proton-pump inhibitor, eosinophils, and duration of therapy. Patients with persistent basal zone hyperplasia and dilated intercellular spaces had increased MC/hpf. Eosinophils were weakly correlated with MC/hpf in the mid (r = 0.30, P < 0.001) and distal (r = 0.29, P < 0.001) esophagus. Clinical remission patients had lower MC/hpf compared with patients with persistent symptoms and/or endoscopic abnormalities. DISCUSSION MC density is increased in patients with endoscopic and epithelial abnormalities, as well as a few symptoms, despite resolution of esophageal eosinophilia after treatment. This association warrants further study to ascertain whether MCs play an eosinophil independent role in EoE.
Predictors of remission from the ultra‐high risk state for psychosis

A significant proportion of individuals at Ultra‐High Risk (UHR) for psychosis do not transition to manifest psychosis. Many non‐transitioning UHR individuals do, however, display poor long‐term outcomes such as persistence of attenuated psychotic symptoms. Evidence is scarce on which variables may predict a better clinical and functional prognosis such as remission from the UHR state.
Investigating serotonergic contributions to cognitive effort allocation, attention, and impulsive action in female rats

Background: Individuals must frequently evaluate whether it is worth allocating cognitive effort for desired outcomes. Motivational deficits are a common feature of psychiatric illness such as major depression. Selective serotonin reuptake inhibitors are commonly used to treat this disorder, yet some data suggest these compounds are ineffective at treating amotivation, and may even exacerbate it. Aims: Here we used the rodent Cognitive Effort Task (rCET) to assess serotonergic (5-hydroxytryptamine, 5-HT) contributions to decision-making with cognitive effort costs. Methods: The rCET is a modified version of the 5-choice serial reaction time task, a well-validated test of visuospatial attention and impulse control. At the start of each rCET trial, rats chose one of two levers, which set the difficulty of an attentional challenge, namely the localization of a visual stimulus illuminated for 0.2 or 1 s on hard versus easy trials. Successful completion of hard trials was rewarded with double the sugar pellets. Twenty-four female Long–Evans rats were trained on the rCET and systemically administered the 5-HT1A agonist 8-OH-DPAT, the 5-HT2A antagonist M100907, the 5-HT2C agonist Ro-60-0175, as well as the 5-HT2C antagonist SB 242, 084. Results: 5-HT2A antagonism dose-dependently reduced premature responding, while 5-HT2C antagonism had the opposite effect. 8-OH-DPAT impaired accuracy of target detection at higher doses, while Ro-60-0175 dose-dependently improved accuracy on difficult trials. However, none of the drugs affected the rats’ choice of the harder option. Conclusion: When considered with existing work evaluating decision-making with physical effort costs, it appears that serotonergic signalling plays a minor role in guiding effort allocation.
Assessment of the effect of specimen size and confinement method on the results of simple shear test

Direct simple shear test has been widely used in geotechnical engineering due to its simplicity and reliability in evaluating soil characteristics under both monotonic and dynamic loading conditions. Different recommendations have been also provided with respect to the size and the confinement method of the tested soil specimens. However, a conclusive opinion on their effects on the shear strength, the generated pore pressure as well as the stress path of the tested soil has not yet been formed among practitioners and geotechnical engineers. Therefore, the prime objective of this paper is to assess the effect of the specimen size and the adopted confinement methods on the results of simple shear tests under both monotonic and dynamic loading. To this end, a series of monotonic and cyclic simple shear tests were performed using the recently developed combined Triaxial Simple Shear (TxSS) apparatus (Chekired et al. 2015) on two sensitive Sea Champlain clays from eastern Canada. Soil specimens with different height-to-diameter ratios were tested in the TxSS apparatus adopting different confinement methods (i.e., a reinforced and unreinforced membrane). The results of this study would be a valuable contribution to the ongoing global effort towards a more precise soil characterization at laboratory. RÉSUMÉ L'essai de cisaillement direct simple a été largement utilisé en génie géotechnique pour sa simplicité et sa fiabilité dans l'évaluation des caractéristiques du sol dans des conditions de charge monotone et dynamique. Différentes recommandations ont également été fournies en ce qui concerne la taille et la méthode de confinement des échantillons de sol testés. Cependant, une opinion concluante sur leurs effets sur la résistance au cisaillement, la pression interstitielle générée ainsi que le cheminement de contrainte du sol testé n'a pas encore été formée chez les praticiens et les ingénieurs en géotechnique. Par conséquent, l'objectif principal de cet article est d'évaluer l'effet de la taille de l'échantillon et des méthodes de confinement sur les résultats d'essais de cisaillement simples sous chargement monotone et dynamique. À cette fin, une série d'essais de cisaillement simple monotone et cyclique ont été réalisés à l'aide de l'appareil combiné Triaxial Simple Shear (TxSS) récemment développé (Chekired et al., 2015) sur deux argiles sensibles de Champlain de l'est du Canada. Des échantillons de sol ayant différents rapports hauteur sur diamètre ont été testés dans l'appareil TxSS en utilisant différentes méthodes de confinement (c'est-à-dire une membrane renforcée et non renforcée). Les résultats de cette étude constitueraient une contribution précieuse à l'effort global en cours pour une caractérisation plus précise des sols en laboratoire.
CHEF’S COMPETENCY AS A KEY ELEMENT IN FOOD TOURISM SUCCESS: A LITERATURE REVIEW

The chef expertise is considered a key to food tourism success. However, studies to identify the competencies of successful chefs are still scarce. This literature review study aims to identify the chef's skill to succeed in his career. There are 38 relevant articles reviewed using the grounded theory method. The results reveal that the chef's competencies include functional competencies, core competencies, and general competencies. The chef's functional competency is culinary expertise that provides for cooking skills, taste and food knowledge, and service tightening. Chef's core competencies include conceptual ability, cleanliness, and business sense. Meanwhile, general competence consists of interpersonal, leadership, managerial, and motivational skills. The identification of chef competencies is used as a guide for culinary educators and trainers for sustainable careers development in the culinary profession.
The Effectiveness of Metacognition on Academic Achievement among the Jordanian Universities Students

The study aimed to investigate the effect of the metacognition on academic achievement among the Jordanian universities’ student. The sample consisted of (440) first academic year students in the faculty of education. This study follows the quantitative study approach. The study employed the Stratified Random Sampling and Simple Random probability sampling techniques. The results showed a level of students was a moderate generally in their metacognition level, results also showed a significant difference between the degrees of students with high achievement on the test compared with the degrees of students with moderate and low achievement, there is a significant difference in the achievement metacognition level of male and female. The mean level of females is higher than males. Metacognition dimensions had a positive predictive effect on academic achievement among the Jordanian students in their first academic year. According to these findings, the study recommended activating the blended learning strategies in teaching at universities.
www.econstor.eu Competitive and Segmented Informal Labor Markets

It has recently been argued that the informal sector in developing countries shows a dual structure, with part of the informal sector being competitive to the formal sector and part of the informal sector being the result of market segmentation. We formulate an econometric model to test this hypothesis. The model allows for sector multiplicity with unobserved sector affiliation in the informal sector and takes into account sample selection bias induced by the employment decision of individuals. An estimation of the model for the urban labor market in Côte d’Ivoire shows that the informal labor market is indeed composed of two segments with both competitive as well as segmented employment. JEL Codes: J42, O17
Repair and Replacement Perception of Dental Restorations@@@استبدال وإصلاح حشوات الأسنان

Replacement of dental restorations still plays a major role in daily dental practice. However, replacing restorations has the disadvantages of being time consuming; can lead to unnecessary removal of tooth structure. Repair of restorations on the other hand is an alternative choice of treatment, but is not widely done as the criteria of repairing restorations are still controversial and not widely taught in dental schools. The purpose of this study is to evaluate the perception of repair and replacement of dental restorations by graduates and undergraduates at King Abdulaziz University, and what clinical criteria do they follow for either choice, if any. A survey questionnaire of 19 questions was designed and prepared in English. Two hundred questionnaires were given to the faculty, interns, fifth and sixth year dental students at the Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia. Most of them have replaced dental restorations. Only 42.7 % have actually repaired restorations as generally they had no clinical experience, and because of their supervisors recommendation. Secondary caries was the main cause of replacing dental restorations), which was significantly higher than other causes. Composite was mainly used in the replacement and repair of dental restorations.