Miracle-dz/UniFAR-FTUs huggingface dataset:
Energetic particles and multi-scale dynamics in fusion plasmas

The role of energetic particles (EPs) in fusion plasmas is unique as they could act as mediators of cross-scale couplings. More specifically, EPs can drive instabilities on the macroand meso-scales and intermediate between the microscopic thermal ion Larmor radius and the macroscopic plasma equilibrium scale lengths. On one hand, EP driven shear Alfvén waves (SAWs) could provide a nonlinear feedback onto the macro-scale system via the interplay of plasma equilibrium and fusion reactivity profiles. On the other hand, EP-driven instabilities could also excite singular radial mode structures at SAW continuum resonances, which, by mode conversion, yield microscopic fluctuations that may propagate and be absorbed elsewhere, inducing nonlocal behaviors. The above observations thus suggest that a theoretical approach based on advanced kinetic treatment of both EPs and thermal plasma is more appropriate for burning fusion plasmas. Energetic particles, furthermore, may linearly and nonlinearly (via SAWs) excite zonal structures, acting, thereby, as generators of nonlinear equilibria that generally evolve on the same time scale of the underlying fluctuations. These issues are presented within a general theoretical framework, discussing evidence from both numerical simulation results and experimental observations. Analogies of fusion plasmas dynamics with problems in condensed matter physics, nonlinear dynamics, and accelerator physics are also emphasized.
Visual and health outcomes, measured with the activity inventory and the EQ‐5D, in visual impairment

Generic instruments to assess health utilities can be used to express the burden of health problems in widely used indexes. That is in contrast with what can be obtained with condition‐specific instruments, outcomes are very specific and difficult to compare across conditions. The purpose of this study was to assess health and visual outcomes and its determinants in patients with visual impairment (VI) using the EQ‐5D‐3L and the Activity Inventory (AI).
Targeted sequencing reveals TP53 as a potential diagnostic biomarker in the post-treatment surveillance of head and neck cancer

Head and neck squamous cell carcinomas (HNSCC) form a large heterogeneous group of tumors and have a relatively poor outcome in advanced cases. Revealing the underlying genetic mutations in HNSCC facilitates the development of diagnostic biomarkers, which might lead to improved diagnosis and post treatment surveillance. We retrospectively analyzed mutational hotspots using targeted next-generation sequencing (NGS) of 239 HNSCC tumor samples in order to examine the mutational profile of HNSCC. Furthermore, we assessed prevalence, co-occurrence, and synonymy of gene mutations in (matched) tumor samples. TP53 was found mutated the most frequent with mutation rates of up to 83% in all tumors, compared to mutation rates of between 0 and 21% of CDKN2A, PIK3CA, HRAS, CDK4, FBXW7 and RB1. Mutational co-occurrence predominantly existed between TP53 and PIK3CA, TP53 and CDKN2A, and HRAS and PIK3CA. Mutational synonymy between primary tumor and associated metastasis and recurrence was present in respectively 88% and 89%. TP53 mutations were concordantly mutated in 95% of metastases and in 91% of recurrences. This indicates TP53 mutations to be highly prevalent and concordant in primary tumors and associated locoregional metastases and recurrences. In turn, this provides ground for further investigating the use of TP53 mutations as diagnostic biomarkers in HNSCC patients.
A Clinical Practice Guideline for the Management of Patients With Acute Spinal Cord Injury: Recommendations on the Type and Timing of Rehabilitation

Introduction: The objective of this study is to develop guidelines that outline the appropriate type and timing of rehabilitation in patients with acute spinal cord injury (SCI). Methods: A systematic review of the literature was conducted to address key questions related to rehabilitation in patients with acute SCI. A multidisciplinary guideline development group used this information, and their clinical expertise, to develop recommendations for the type and timing of rehabilitation. Based on GRADE (Grading of Recommendation, Assessment, Development and Evaluation), a strong recommendation is worded as “we recommend,” whereas a weaker recommendation is indicated by “we suggest. Results: Based on the findings from the systematic review, our recommendations were: (1) We suggest rehabilitation be offered to patients with acute spinal cord injury when they are medically stable and can tolerate required rehabilitation intensity (no included studies; expert opinion); (2) We suggest body weight–supported treadmill training as an option for ambulation training in addition to conventional overground walking, dependent on resource availability, context, and local expertise (low evidence); (3) We suggest that individuals with acute and subacute cervical SCI be offered functional electrical stimulation as an option to improve hand and upper extremity function (low evidence); and (4) Based on the absence of any clear benefit, we suggest not offering additional training in unsupported sitting beyond what is currently incorporated in standard rehabilitation (low evidence). Conclusions: These guidelines should be implemented into clinical practice to improve outcomes and reduce morbidity in patients with SCI by promoting standardization of care, decreasing the heterogeneity of management strategies and encouraging clinicians to make evidence-informed decisions.
Association of hemoglobin glycation index with outcomes of acute ischemic stroke in type 2 diabetic patients

ABSTRACT Objective This study aimed to investigate the association between the hemoglobin glycation index (HGI) and the prognosis of diabetic patients with ischemic stroke. Methods Data were derived from the Abnormal Glucose Regulation in Patients with Acute Stroke across China (ACROSS-China) registry. Diabetic patients with ischemic stroke were included. HGI was calculated by subtracting the predicted HbA1c based on fasting plasma glucose from the observed HbA1c, and then classified into three groups by the tertiles: low HGI (<−0.62), moderate HGI (−0.62 to 0.35) and high HGI (≥0.36). Outcomes included stroke recurrence, all-cause death and poor outcome at 12 months. Results A total of 976 diabetic patients were included. Low HGI was associated with an increased risk of stroke recurrence and poor outcome (adj.hazard ratio 1.53, 95% confidence intervals (CIs) 1.11–2.12, p = 0.01; and adj.odds ratio 1.64, 95% CI 1.13–2.38, p = 0.01, respectively), and high HGI was associated with an increased risk of poor outcome (adj.odds ratio 1.54, 95% CI 1.06–2.24, p = 0.02), compared with moderate HGI. We found a U-shaped association between HGI and the prognosis. Conclusion Both low HGI and high HGI was associated with an increased risk of poor prognosis in diabetic patients with ischemic stroke, compared with moderate HGI.
Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis.

CONTEXT Probiotics are live microorganisms intended to confer a health benefit when consumed. One condition for which probiotics have been advocated is the diarrhea that is a common adverse effect of antibiotic use. OBJECTIVE To evaluate the evidence for probiotic use in the prevention and treatment of antibiotic-associated diarrhea (AAD). DATA SOURCES Twelve electronic databases were searched (DARE, Cochrane Library of Systematic Reviews, CENTRAL, PubMed, EMBASE, CINAHL, AMED, MANTIS, TOXLINE, ToxFILE, NTIS, and AGRICOLA) and references of included studies and reviews were screened from database inception to February 2012, without language restriction. STUDY SELECTION Two independent reviewers identified parallel randomized controlled trials (RCTs) of probiotics (Lactobacillus, Bifidobacterium, Saccharomyces, Streptococcus, Enterococcus, and/or Bacillus) for the prevention or treatment of AAD. DATA EXTRACTION Two independent reviewers extracted the data and assessed trial quality. RESULTS A total of 82 RCTs met inclusion criteria. The majority used Lactobacillus-based interventions alone or in combination with other genera; strains were poorly documented. The pooled relative risk in a DerSimonian-Laird random-effects meta-analysis of 63 RCTs, which included 11 811 participants, indicated a statistically significant association of probiotic administration with reduction in AAD (relative risk, 0.58; 95% CI, 0.50 to 0.68; P < .001; I(2), 54%; [risk difference, -0.07; 95% CI, -0.10 to -0.05], [number needed to treat, 13; 95% CI, 10.3 to 19.1]) in trials reporting on the number of patients with AAD. This result was relatively insensitive to numerous subgroup analyses. However, there exists significant heterogeneity in pooled results and the evidence is insufficient to determine whether this association varies systematically by population, antibiotic characteristic, or probiotic preparation. CONCLUSIONS The pooled evidence suggests that probiotics are associated with a reduction in AAD. More research is needed to determine which probiotics are associated with the greatest efficacy and for which patients receiving which specific antibiotics.
Disposition kinetics of omeprazole in healthy female volunteers in Pakistan

Omeprazole (OMP) a proton pump inhibitor is widely used to suppress gastric acid secretions of parietal cells of stomach and metabolized predominantly by CYP2C19. The objective of the present study was to investigate the pharmacokinetics and dosage regimen of OMP, after its single oral administration in eight healthy adult female subjects. Blood samples were collected at different time intervals after oral administration and their pH was measured. Plasma concentration of OMP was determined by high performance liquid chromatography (HPLC) system equipped with UVvisible Detector. The concentration versus time data was used to compute the pharmacokinetic parameters with the help of computer software programme MW/PHRAM APO version 3.02. Peak plasma concentration was (Cmax) 0.38±0.04 μg/ml achieved at 2.07±0.22 hrs. The elimination half-life (t1/2β) was1.82±0.42 hrs. Volume of distribution (Vd) in the present study was 0.40±0.07 l/kg with total body clearance (ClB) 0.19±0.02 l/hr/kg and area under the curve (AUC) 1.89 ±0.23 μg. hr/ml.The pharmacokinetic properties which are different from the literature after oral administration of 20 mg OMP in eight healthy female volunteers may be due to the variations of environment and genetic variation between Pakistan and drug manufacturing of foreign countries.
Nine-year study of US high school soccer injuries: data from a national sports injury surveillance programme

Background Research on high school soccer injury epidemiology is sparse. Aim To describe high school soccer injury rates, trends and patterns by type of athlete exposure (AE), position and sex. Methods This descriptive epidemiological study used data from a large national high school sports injury surveillance programme to describe rates and patterns of soccer-related injuries including concussion sustained from 2005/2006 to 2013/2014. Injury rates are calculated per 1000 AEs. Results Overall, 6154 soccer injuries occurred during 2 985 991 AEs; injury rate=2.06 per 1000 AEs. Injury rates were higher during competition (4.42) than practice (1.05; rate ratio (RR)=4.19; 95% CI 3.98 to 4.41), and in girls (2.33) than boys (1.83; RR=1.27, 95% CI 1.21 to 1.34). Boys' non-concussion injury rates decreased significantly (p=0.001) during the study period while reported concussion rates increased significantly (p=0.002). Girls' non-concussion rates were relatively stable and reported concussion rates increased significantly (p=0.004). Player–player contact was the injury mechanism that led to the most competition injuries (injury proportion ratio (IPR)=2.87; 95% CI 2.57 to 3.21), while non-contact injuries were the most common mechanisms among practice injuries (IPR=2.10; 95% CI 1.86 to 2.38). Recovery from concussion was >7 days in a third of the cases. Injury patterns were similar between sexes with respect to position played and location on the field at the time of injury. Conclusions High school soccer injury rates vary by sex and type of exposure, while injury patterns are more similar across sexes. Reported concussion rates increased significantly over the study period in male and female athletes.
Understanding the elevated suicide risk of female soldiers during deployments

Background The Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS) has found that the proportional elevation in the US Army enlisted soldier suicide rate during deployment (compared with the never-deployed or previously deployed) is significantly higher among women than men, raising the possibility of gender differences in the adverse psychological effects of deployment. Method Person-month survival models based on a consolidated administrative database for active duty enlisted Regular Army soldiers in 2004–2009 (n = 975 057) were used to characterize the gender × deployment interaction predicting suicide. Four explanatory hypotheses were explored involving the proportion of females in each soldier's occupation, the proportion of same-gender soldiers in each soldier's unit, whether the soldier reported sexual assault victimization in the previous 12 months, and the soldier's pre-deployment history of treated mental/behavioral disorders. Results The suicide rate of currently deployed women (14.0/100 000 person-years) was 3.1–3.5 times the rates of other (i.e. never-deployed/previously deployed) women. The suicide rate of currently deployed men (22.6/100 000 person-years) was 0.9–1.2 times the rates of other men. The adjusted (for time trends, sociodemographics, and Army career variables) female:male odds ratio comparing the suicide rates of currently deployed v. other women v. men was 2.8 (95% confidence interval 1.1–6.8), became 2.4 after excluding soldiers with Direct Combat Arms occupations, and remained elevated (in the range 1.9–2.8) after adjusting for the hypothesized explanatory variables. Conclusions These results are valuable in excluding otherwise plausible hypotheses for the elevated suicide rate of deployed women and point to the importance of expanding future research on the psychological challenges of deployment for women.
miR‐31 Regulates Spermatogonial Stem Cells Meiosis via Targeting Stra8

Stra8 (stimulated by retinoic acid gene 8) is a specific gene that is expressed in mammalian germ cells during transition from mitosis to meiosis and plays a key role in the initiation of meiosis in mammals and birds. So, the evaluation of the Stra8 pathway in cSSCs may provide a deeper insight into mammalian spermatogenesis. miRNA was also an important regulating factor for meiosis of SSCs. However, there is currently no data indicating that miRNA regulate the meiosis of SSCs via Stra8. Here, we predicted the prospective miRNA targeting to Stra8 using the online Bioinformatics database‐Targetscan, and performed an analysis of the dual‐luciferase recombinant vector, pGL3‐CMV‐LUC‐MCS‐Stra8‐3′UTR. miR‐31 mimics (miR‐31m), miR‐31 inhibitors (miR‐31i), Control (NC, scrambled oligonucleotides transfection) were transfected into cSSCs; Stra8 and miRNA were analyzed by RT‐qPCR, immunofluorescence, and Western blot. The detection of haploid was conducted by flow cytometry. The results showed that miR‐31 regulates meiosis of cSSCs via targeting Stra8 in vitro and in vivo. Our study identifies a new regulatory pathway that miR‐31 targets Stra8 and inhibits spermatogenesis. J. Cell. Biochem. 118: 4844–4853, 2017. © 2017 Wiley Periodicals, Inc.
ZRF1 mediates remodeling of E3 ligases at DNA lesion sites during nucleotide excision repair

How ubiquitylation of multiple substrates, including repair proteins and histones, is regulated during nucleotide excision repair (NER) has been unclear. Gracheva et al. show that the histone H2A-ubiquitin binding factor ZRF1 is essential in NER as it mediates remodeling of the novel ubiquitin E3 complex responsible for monoubiquitylation of histone H2A at DNA lesion sites.
Structural constraints in complex networks

We present a link rewiring mechanism to produce surrogates of a network where both the degree distribution and the rich-club connectivity are preserved. We consider three real networks, the autonomous system (AS)-Internet, protein interaction and scientific collaboration. We show that for a given degree distribution, the rich-club connectivity is sensitive to the degree–degree correlation, and on the other hand the degree–degree correlation is constrained by the rich-club connectivity. In particular, in the case of the Internet, the assortative coefficient is always negative and a minor change in its value can reverse the network's rich-club structure completely; while fixing the degree distribution and the rich-club connectivity restricts the assortative coefficient to such a narrow range, that a reasonable model of the Internet can be produced by considering mainly the degree distribution and the rich-club connectivity. We also comment on the suitability of using the maximal random network as a null model to assess the rich-club connectivity in real networks.
Cognitive and psychological flexibility after a traumatic brain injury and the implications for treatment in acceptance-based therapies: A conceptual review

This paper provides a selective review of cognitive and psychological flexibility in the context of treatment for psychological distress after traumatic brain injury, with a focus on acceptance-based therapies. Cognitive flexibility is a component of executive function that is referred to mostly in the context of neuropsychological research and practice. Psychological flexibility, from a clinical psychology perspective, is linked to health and well-being and is an identified treatment outcome for therapies such as acceptance and commitment therapy (ACT). There are a number of overlaps between the constructs. They both manifest in the ability to change behaviour (either a thought or an action) in response to environmental change, with similarities in neural substrate and mental processes. Impairments in both show a strong association with psychopathology. People with a traumatic brain injury (TBI) often suffer impairments in their cognitive flexibility as a result of damage to areas controlling executive processes but have a positive response to therapies that promote psychological flexibility. Overall, psychological flexibility appears a more overarching construct and cognitive flexibility may be a subcomponent of it but not necessarily a pre-requisite. Further research into therapies which claim to improve psychological flexibility, such as ACT, needs to be undertaken in TBI populations in order to clarify its utility in this group.
Exploring Problems in Following the Hemodialysis Diet and Their Relation to Energy and Nutrient Intakes: The BalanceWise Study.

OBJECTIVE To identify the problems experienced by hemodialysis (HD) patients in attempting to follow the HD diet and their relation to energy and nutrient intakes. DESIGN Cross-sectional analysis of baseline data from the BalanceWise Study. SUBJECTS Participants included community-dwelling adults recruited from outpatient HD centers. After excluding participants with incomplete dietary analyses (n = 50), 140 African American and white (40/60%) men and women (52/48%) on chronic intermittent HD for at least 3 months (median 3 years) were included. INTERVENTION Participant responses, on a 5-point Likert scale ranging from "not at all a problem" to "a very important problem for me," to 34 questions pertaining to potential barriers to following the HD diet in the previous 2 months were classified as either a problem (1) or not a problem (2-5). MAIN OUTCOME MEASURE Energy and nutrient intakes determined using the Nutrition Data System for Research® based on 3, non-consecutive, unscheduled, 2-pass 24-hour dietary recalls collected on 1 dialysis and 1 non-dialysis weekday, and 1 non-dialysis weekend day. RESULTS More than half of participants reported having problems related to specific behavioral factors (e.g., feeling deprived), technical difficulties (e.g., tracking nutrients), and physical condition (e.g., appetite), but issues of time and food preparation and behavioral factors tended to be most deterministic of reported dietary intakes. Longer duration of HD was associated with lower intakes of protein, potassium, and phosphorus (P < .05). CONCLUSION Registered dietitian nutritionists should consider issues of time and food preparation, and behavioral factors in their nutrition assessment of HD patients and should continually monitor HD patients for changes in protein intake that may occur over time.
Histopathological study of chronic wounds modulated by intermittent negative pressure therapy under limited access dressing

Aim: Negative pressure wound therapy (NPWT) has achieved widespread success in the treatment of chronic wounds. However, its effects have been only partially explored, and investigations have generally concentrated on the wound-dressing interface; a detailed histopathological description of the evolution of wounds under NPWT is still lacking. The present study was performed to investigate the effect of a limited access dressing (LAD) which exerts intermittent NPWT in a moist environment on chronic wounds. Methods: A total of 140 patients were randomized into 2 groups: LAD group ( n = 64) and conventional dressing group ( n = 76). By histopathological analysis of the granulation tissue, the amount of inflammatory infiltrate, necrotic tissue, angiogenesis, and extracellular matrix (ECM) deposition was studied and compared to determine healing between the 2 groups. Results: After 10 days of treatment, histopathological analysis showed a significant decrease in necrotic tissue with LAD compared to the conventional dressing group (mean ± standard error, 11.5 ± 0.48 vs . 10.1 ± 0.30, P = 0.007), the number of inflammatory cells (12.6 ± 0.60 vs . 8.63 ± 0.35, P = 0.018), a significant increase in new blood vessels (12.8 ± 0.58 vs . 9.3 ± 0.29, P = 0.005) and ECM deposit (13.3 ± 0.50 vs . 9.6 ± 0.24, P = 0.001). Conclusion: LAD exerts its beneficial effects on chronic wound healing by decreasing the amount of necrotic tissue and inflammatory cells while increasing the amount of ECM deposition and angiogenesis.
Phytochemical Screening and Antioxidant Activity of Edible Wild Fruits in Benguet, Cordillera Administrative Region, Philippines

This study identified the secondary metabolites present and determined the antioxidant activity of 31 edible wild fruits grown in Benguet province, Cordillera Administrative Region, Philippines. Total polyphenol and flavonoid content were estimated using Folin-Ciocalteu and aluminium chloride method respectively. Antioxidant activity was measured through diphenyl-1-picrylhydrazyl assay. Based on the results, the following bioactive constituents are present in the fruits: alkaloids, steroid glycosides, saponins, flavonoids, polyphenols and tannins. The fruits contain more polyphenols than flavonoids. All the fruits except Physalis peruviana (Solanaceae) exhibited higher antioxidant activity than Vitamin E (Myra E), ascorbic acid (50 ug/mL), and trolox (1000 uM). Dillenia philippinensis (Dilleniaceae) exhibited the highest antioxidant activity. The antioxidant activity of the fruits and controls is significantly different (ρ ≤ 0.05). Post-hoc Tukey analysis of data reveals that several fruits have equal activity. Finally, there is a positive moderate correlation (r=0.50) between the total polyphenol content and antioxidant activity of the fruits.