Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking French regions according to their prevalence of healthcare-associated infections.

OBJECTIVE To propose an original method of benchmarking regions based on their prevalence of healthcare-associated infections (HAIs) and to identify regions with unusual results. DESIGN To study between-region variability with a three-level hierarchical logistic regression model and a Bayesian non-parametric method. SETTING French 2006 national HAIs point prevalence survey. PARTICIPANTS A total of 336 858 patients from 2289 healthcare facilities in 27 regions. Patients with an imported HAI (1% of the data, 20.7% of infected patients), facilities with <5 patients and patients who had at least one missing value for the variables taken into account were excluded (5.0% of patients). MAIN OUTCOME MEASURE Binary outcome variable indicates whether a given patient was infected. RESULTS Two clusters of regions were identified: one cluster of five regions had a lower adjusted prevalence than the other one of 22 regions, while no region with unusually high prevalence could be identified. Nevertheless, the degree of heterogeneity of odds ratios between facilities for facility-specific effects of use of invasive devices was more important in some regions than in others. CONCLUSIONS The adjusted regional prevalence of HAIs can serve as an adequate benchmark to identify regions with concerning results. Although no outlier regions were identified, the proposed approach could be applied to the data of the 2012 national survey to benchmark regional healthcare policies. The estimation of facility-specific effects of use of invasive devices may orient future regional action plans.
Protective effect against brain tissues oxidative damage as a possible mechanism for beneficial effects of L-arginine on lipopolysaccharide induced memory impairment in rats

Abstract L-Arginine (LA) and nitric oxide (NO) have been suggested to have some effects on learning, memory, brain tissues oxidative damage, and neuroinflammation. In this study, protective effect against brain tissues oxidative damage as a possible mechanism for beneficial effects of LA on lipopolysaccharide (LPS) induced memory impairment was investigated. The rats were grouped into and treated by (1) control (saline), (2) LPS (1 mg/kg, IP), (3) LA (200 mg/kg) – LPS (4) LA. In passive avoidance (PA) test, LPS administration shortened the latency to enter the dark compartment in LPS group compared to control (p < .001) which was accompanied with a high level of malondialdehyde (MDA) and NO metabolite concentrations in the hippocampal tissues (p < .001and p < .05, respectively). Pretreatment with LA prolonged the latency in LA-LPS group compared with LPS group (p < .01–.001) and re-stored MDA and NO metabolites in the hippocampal tissues (p < .05). LPS also reduced superoxide dismutase (SOD) and catalase (CAT) activities and thiol content in the hippocampal tissues in LPS group compared to control (p < .05 and p < .001, respectively) which improved by LA when it was administered before LPS in LA-LPS group (p < .05 and p < .001). Finally, the serum TNFα level of LPS group was higher than the control (p < .01) while, in LA-LPS group it was lower than LPS group (p < .01). It seems that the beneficial effects of LA on memory impairment of LPS-treated rats may be due to its protective effects against brain tissues oxidative damage.
Modeling the relationship between physical activity and quality of life in menopausal-aged women: a cross-sectional study.

BACKGROUND The purpose of the present study was (a) to assess the relationship between physical activity and the intensity and duration of menopausal symptoms, (b) to investigate the relationship between physical activity and the four domains of health-related quality of life (HRQOL) and (c) to assess the relationship between physical activity and chronic diseases. METHODS This descriptive-analytical study that was conducted in Tabriz City, Iran. Data were collected in 2012 by personal home-based interviews, using structured questionnaires. All participants (n= 273), who were middle-aged (age range of 40-60 yr) were recruited from two of the 25 urban health service centers' clients, by clustered random sampling allocation. RESULTS There was a positive significant relationship between Psychological, Social, and Environmental domains of HRQOL with physical activity (P<0.001). In addition, a negative significant relation was found between somatic complaints including sexual problems (P< 0.017) and vaginal dryness (P<0.030) as well as joint-muscular discomfort (P<0.018), and the level of physical activity. Diabetic (P<0.047) and women with history of heart disease (P<0.040) performed 2.670 and 3.548 hours more than who were not. CONCLUSIONS Regular physical activity would be effective in decreasing menopausal symptoms as well as improving healthy aging and also physical activity promotion as a part of healthy life style promotion programs needs to be improved in communities where women are physically inactive. In addition, women need to be informed about importance of physical activity on their life which it leads to feel healthy aging and pre and post- menopausal stages.
Dermal bioavailability of benzo[a]pyrene on lampblack: Implications for risk assessment

Lampblack is the principal source of contamination in soils at manufactured gas plant (MGP) sites where oil was used as the feedstock. Risks and cleanup criteria at these sites are determined primarily by the total carcinogenic polynuclear aromatic hydrocarbon (PAH) content, particularly the concentration of benzo[a]pyrene (BaP). Dermal contact with soils at oil‐gas MGP sites is a significant component of the overall risks. Seven samples were collected from oil‐gas MGP sites and the steady‐state dermal fluxes were measured over 96 h in vitro. The standard dermal bioassay technique (in which 3H‐BaP is added to the soil matrix) was modified to allow direct measurement of the dermal absorption of the native BaP in the samples. The experimentally derived dermal absorption factors for BaP were 14 to 107 times lower than the default assumption of 15% over 24 h (55‐fold lower on average). The dermal fluxes were correlated positively to the total BaP and total carbon concentrations. The measured dermal absorption factors were compared to the default risk‐assessment calculations for all seven samples. The calculated excess cancer risk was reduced as a result of using the measured absorption factors by 97% on average (with reductions ranging from 93 to 99%). This work indicates the risks at oil‐gas MGP sites currently are overestimated by one to two orders of magnitude, and provides a protocol for the testing and data analysis needed to generate site‐specific cleanup levels.
A focused monopolar radiofrequency causes apoptosis: a porcine model.

BACKGROUND The purpose of this study was to demonstrate the effect of monopolar, focused radiofrequency (RF) with embedded cooling on subcutaneous skin structures. Specifically, the study was to prove that the monopolar RF with cooling can selectively heat fat, causing disintegration of adipocytes and programmed cell death (apoptosis) of the subcutaneous fat cells. METHODS A non-invasive monopolar RF device with cooling (Exilis Elite, BTL Industries, Framingham, MA) was used to reduce abdominal fat in a porcine model. The study was done on 3 Vietnamese pigs in a certified veterinary facility. The treatment was delivered to an area the size of 20 x 10cm. The treatment duration was 11 minutes, 30 seconds. Biopsy samples were taken before the first treatment, 1 hour post each treatment, as well as 8 and 20 hours post each treatment. Programmed cell death (apoptosis) was monitored using the TUNEL method. The temperature was measured on the skin surface by an infrared thermal imager and built-in IR thermometer, and by an internal probe inserted into various depths of the subcutaneous layer. The internal probe placement was monitored by diagnostic ultrasound examination. RESULTS The temperature in the treated adipose tissue was higher compared to the skin surface temperature. The average temperature gradient observed was 3.1°C. Due to the temperature gradient the skin surface remained intact, while subcutaneous layers showed significant changes. The TUNEL method proved large-scale apoptosis of fat cells after each treatment. The apoptotic index increased from 7% before the first treatment to an average of 53.4%, 39.6%, 40.2%, and 44.7% respectively for each treatment. In the three-month follow up the apoptotic index dropped back to 11.7%. Histology, blood biochemistry and hematology samples showed mild to no signs of inflammation in the treated area. CONCLUSION The study has shown that use of monopolar, focused radiofrequency can induce substantial apoptotic process in a porcine model. The data suggests that the monopolar, focused radiofrequency device can be used for reduction of fat and body shaping.
Bayesian Tree Substitution Grammars as a Usage-based Approach

Tree substitution grammar (TSG) is a generalization of context-free grammar (CFG) that permits non-terminals to rewrite as fragments of arbitrary size, instead of just depth-one productions. We discuss connections between the TSG framework and the larger family of usage-based approaches to language, showing how TSG allows us to make some of the claims of these approaches sufficiently concrete for computational modeling. A fundamental difficulty in defining a TSG is to determine the set of fragments for the grammar, because the set of possible fragments is exponential in the size of the parse trees from which TSGs are typically learned. We describe a model-based approach that learns a TSG using Gibbs sampling with a non-parametric prior to control fragment size, yielding grammars that contain mostly small fragments but that include larger ones as the data permits. We evaluate these grammars on two tasks (parsing accuracy and grammaticality classification), and find that these Bayesian TSGs achieve excellent performance on two tasks relative to a set of heuristically extracted TSGs spanning the spectrum of representations, from a standard depth-one context-free Treebank grammar to explicit approximations of the Data-Oriented Parsing model.
A Prospective Comparison of Spectrophotometric Intracutaneous Analysis to Clinical Judgment in the Diagnosis of Nonmelanoma Skin Cancer

Introduction:Research indicates that spectrophotometric intracutaneous analysis (SIAscopy) may be a useful adjunct in nonmelanoma skin cancer (NMSC) diagnosis. A study was performed to prospectively assess the accuracy of NMSC diagnosis by the SIAscope as compared with a clinician. Methods:Prior to excision, 323 consecutive lesions were examined and diagnosed by a clinician. SIAgraphs were then taken of the lesions and examined blindly at a later date. Diagnostic accuracy for the clinician and SIAscope was compared between the clinician and SIAscope and to histology. Results:Sensitivity, specificity, positive and negative predictive values for clinical diagnoses were 95.6%, 75.8%, 0.79, and 0.95, respectively. Results for SIA diagnoses were 97.5%, 86.7%, 0.88, and 0.97. Statistical comparison revealed comparable sensitivities for the 2 groups but significantly better specificity for the SIAscope at the 95% confidence level. Conclusion:This study indicates that the SIAscope may be useful in NMSC diagnosis, with accuracies comparable to a clinician.
Corticosteroid-dependent eosinophilic oesophagitis: azathioprine and 6-mercaptopurine can induce and maintain long-term remission

Background Eosinophilic oesophagitis (EO) is a chronic inflammatory disorder of the oesophagus that is rapidly increasing in prevalence. Although systemic and topical corticosteroids are effective in treating EO, some patients develop corticosteroid dependency. Alternative therapeutic approaches that avoid corticosteroids are scarce. Aim To analyse our experience at inducing and maintaining remission with an immunomodulatory therapy in steroid-dependent EO patients. Methods We analysed the clinical and histological response to azathioprine (AZA) and 6-mercaptopurine in three patients with EO (one also with eosinophilic gastroenteritis) and corticosteroid dependency. Results In all three patients, AZA or 6-mercaptopurine-induced clinical and histological remission that was maintained during the follow-up period (range 3–8 years). Two patients experienced relapses after ceasing AZA therapy. Remission, however, resumed when short-term corticosteroid treatment was followed by AZA. In all the patients, blood eosinophilia disappeared under AZA treatment. Only jumbo biopsies confirmed suspected EO with predominant muscle-layer involvement in one patient. Conclusion In adult patients with corticosteroid-dependent EO, immunomodulatory treatment with purine analogues is a promising therapeutic approach for inducing and maintaining long-term remission without the need for further corticosteroids. Jumbo forcep biopsies might be needed to confirm a diagnosis of muscle-layer predominant EO.
Evaluating the clinical appropriateness of nurses’ prescribing practice: method development and findings from an expert panel analysis

Background: The number of nurses independently prescribing medicines in England is rising steadily. There had been no attempt systematically to evaluate the clinical appropriateness of nurses’ prescribing decisions. Aims: (i) To establish a method of assessing the clinical appropriateness of nurses’ prescribing decisions; (ii) to evaluate the prescribing decisions of a sample of nurses, using this method. Method: A modified version of the Medication Appropriateness Index (MAI) was developed, piloted and subsequently used by seven medical prescribing experts to rate transcripts of 12 nurse prescriber consultations selected from a larger database of 118 audio-recorded consultations collected as part of a national evaluation. Experts were also able to give written qualitative comments on each of the MAI dimensions applied to each of the consultations. Analysis: Experts’ ratings were analysed using descriptive statistics. Qualitative comments were subjected to a process of content analysis to identify themes within and across both MAI items and consultations. Results: Experts’ application of the modified MAI to transcripts of nurse prescriber consultations demonstrated validity and feasibility as a method of assessing the clinical appropriateness of nurses’ prescribing decisions. In the majority of assessments made by the expert panel, nurses’ prescribing decisions were rated as clinically appropriate on all nine items in the MAI. Conclusion: A valid and feasible method of assessing the clinical appropriateness of nurses’ prescribing practice has been developed using a modified MAI and transcripts of audio-recorded consultations sent to a panel of prescribing experts. Prescribing nurses in this study were generally considered to be making clinically appropriate prescribing decisions. This approach to measuring prescribing appropriateness could be used as part of quality assurance in routine practice, as a method of identifying continuing professional development needs, or in future research as the expansion of non-medical prescribing continues.
Cloning and Characterization of Two NAD Kinases from Arabidopsis. Identification of a Calmodulin Binding Isoform1[w]

NAD kinase (NADK; ATP:NAD 2′-phosphotransferase, EC 2.7.1.23), an enzyme found in both prokaryotes and eukaryotes, generates the important pyridine nucleotide NADP from substrates ATP and NAD. The role of NADKs in plants is poorly understood, and cDNAs encoding plant NADKs have not previously been described to our knowledge. We have cloned two cDNAs from Arabidopsis predicted to encode NADK isoforms, designated NADK1 and NADK2, respectively. Expressed as recombinant proteins in bacteria, both NADK1 and NADK2 were catalytically active, thereby confirming their identity as NADKs. Transcripts for both isoforms were detected in all tissues examined and throughout development. Although the predicted catalytic regions for NADK1 and NADK2 show sequence similarity to NADKs from other organisms, NADK2 possesses a large N-terminal extension that appears to be unique to plants. Using recombinant glutathione-S-transferase fusion proteins and calmodulin (CaM)-affinity chromatography, we delineated a Ca2+-dependent CaM-binding domain to a 45-residue region within the N-terminal extension of NADK2. Although recombinant NADK2 was not responsive to CaM in vitro, immunoblot analysis suggests that native NADK2 is a CaM-binding protein. In Arabidopsis crude extracts, CaM-dependent NADK activity was much greater than CaM-independent activity throughout development, particularly in young seedlings. A native CaM-dependent NADK was partially purified from Arabidopsis seedlings (KmNAD=0.20 mM, KmMg2+−ATP=0.17 mM). The enzyme was fully activated by conserved CaM (S0.5 = 2.2 nm) in the presence of calcium but displayed differential responsiveness to eight CaM-like Arabidopsis proteins. Possible roles for NADKs in plants are discussed in light of our observations.
CD8+ cells suppress oil‐induced arthritis

Oil‐induced arthritis is a genetically restricted polyarthritis that develops in the DA rat after injection of the mineral oil Freund's incomplete adjuvant. Here, we investigated the role of the potentially disease‐limiting cell populations CD8+ T cells, γδ T cells, natural killer (NK) cells and NK T cells in inguinal lymph nodes for the development of this adjuvant‐induced arthritis. Flow cytometry analysis before and at disease onset revealed a higher proportion of lymph node T cells expressing NKR‐P1 in the disease‐resistant LEW.1AV1 compared with the disease‐susceptible DA strain, suggesting that NK T cells might be disease protective. However, prophylactic in vivo administration of an anti‐NKR‐P1 MoAb (clone 10/78) did not consistently affect the disease course. The proportion of CD8+ T cells and the ratio CD4+/CD8+ T cells in inguinal lymph nodes did not differ significantly between DA and LEW.1AV1 rats before or at disease onset. Nevertheless, prophylactic in vivo depletion of CD8+ cells by the OX8 MoAb in the DA strain resulted in an earlier disease onset compared with the control group, demonstrating that CD8+ cells regulate arthritis development. In vivo depletion of γδ T cells by the V65 MoAb did not alter the disease course, indicating that the disease‐suppressive CD8+ cells are αβ T cells or NK cells.
Spontaneous fetal loss rates in a non-selected population.

The objective of this work was to determine the rate of spontaneous fetal loss up to 28 weeks of gestation in uncomplicated pregnancies of a low-risk population after sonographically identified intact intrauterine pregnancy during the first trimester. Transvaginal ultrasounds were given to 2,534 women at between six and 12 weeks of gestation. Inclusion criteria were a positive fetal cardiac activity and no antecedent signs of vaginal bleeding. Gestational age was confirmed by measurement of the crown-rump length and/or biparietal diameter (BIP). Patients were followed until delivery or up to a fetal loss. The mean fetal loss rate between 12 and 28 weeks was 3.86% (n = 99). Fetal loss increased with maternal age: fetal loss rate under 20 yr: 2.94% (OR 0.75; CI 0.23-2. 46), 20-24 yr: 3.20% (OR 0.77; CI 0.48-1.23), 25-29 yr: 3.39% (OR 0.77; CI 0.50-1.19), 30-34 yr: 3.89% (OR 1.01; CI 0.59-1.71), 35-39 yr: 7.82% (OR 2.13; CI 1.04-4.32), 40-45 y: 50% (OR 13.84; CI 6.67-28.72) and > 45 yr: 50% (OR 13.05; CI 1.96-86.71) respectively. The frequency of spontaneous fetal loss before 28 weeks gestation was assessed systematically in a low-risk population. There was a very clear correlation with advancing maternal age. These data now can be used as background loss rate information for evaluating the safety of invasive prenatal diagnosis, and they will be more valid for this purpose than the available data taken from selected cohorts of women, such as those from hospital clinics or from infertility programs.
Insulin-degrading Enzyme Rapidly Removes the β-Amyloid Precursor Protein Intracellular Domain (AICD)*

The intramembranous γ-secretase cleavage of the β-amyloid precursor protein (APP) is dependent on biologically active presenilins (PS). Notch also undergoes a similar PS-dependent γ-secretase-like cleavage, resulting in the liberation of the Notch intracellular domain (NICD), which is critically required for developmental signal transduction. γ-Secretase processing of APP results in the production of a similar fragment called AICD (APPintracellular domain), which may function in nuclear signaling as well. AICD, like NICD, is rapidly removed. By using a battery of protease inhibitors we demonstrate that AICD, in contrast to NICD, is degraded by a cytoplasmic metalloprotease. In vitro degradation of AICD can be reconstituted with cytoplasmic fractions obtained from neuronal and non-neuronal cells. Taking into account the inhibition profile and the cytoplasmic localization, we identified three candidate enzymes (neurolysin, thimet oligopeptidase, and insulin-degrading enzyme (IDE), also known as insulysin), which all are involved in the degradation of bioactive peptides in the brain. When insulin, a well characterized substrate of IDE, was added to the in vitro degradation assay, removal of AICD was efficiently blocked. Moreover, overexpression of IDE resulted in enhanced degradation of AICD, whereas overexpression of the inactive IDE E111Q mutant did not affect AICD degradation. Finally, immunodepletion of IDE significantly reduced the AICD degrading activity. Therefore our data demonstrate that IDE, which is one of the proteases implicated in the removal of extracellular Aβ, also removes the cytoplasmic product of γ-secretase cleaved APP.
Got Technical Debt? Surfacing Elusive Technical Debt in Issue Trackers

Concretely communicating technical debt and its consequences is of common interest to both researchers and software engineers. In the absence of validated tools and techniques to achieve this goal with repeatable results, developers resort to ad hoc practices. Most commonly they report using issue trackers or their existing backlog management practices to capture and track technical debt. In a manual examination of 1,264 issues from four issue trackers from open source industry and government projects, we identified 109 examples of technical debt. Our study reveals that technical debt and its related concepts have entered the vernacular of developers as they discuss development tasks through issue trackers. Even when issues are not explicitly tagged as technical debt, it is possible to identify technical debt items in these issue trackers using a categorization method we developed. We use our results and data to motivate an improved definition and an approach to explicitly report technical debt in issue trackers.