Miracle-dz/UniFAR-FTUs huggingface dataset:
Low educational level: a risk factor for sexually transmitted infections among commercial sex workers in Quito, Ecuador

Few studies have assessed the effect of educational level on sexually transmitted infections (STIs) and risk-taking behaviours among commercial sex workers (CSWs). This study analysed this association among female CSWs in Quito, Ecuador. Eighty-five CSWs were given a Spanish-language questionnaire on behaviours, socioeconomics and demographics. The correlation between years of education and number of prior STIs was calculated. Three groups of varying education level were formed and risk factors were analysed by Chi-square tests and analysis of variances. Lower educational level was associated with more STIs (r = –0.36; F = 4.2; P = 0.04), poorer knowledge of HIV/AIDS (P = 0.03), earlier first prostitution (P = 0.05) and first sex (P = 0.00), willingness to engage in group sex (P = 0.05) and work on the street (P = 0.02), and presence of non-paying sexual partners (P = 0.05). CSWs with lower educational levels were disproportionately afflicted with STIs and participated in more high-risk behaviours. Low educational level may predispose CSWs to STIs and associated risk factors.
Influence of the lateral friction on the surface flow: a 3D numerical approach

To understand the complexity of dense granular ﬂows, we used three-dimensional (3D) numerical simulations which appears as complementary approaches to the experimental ones. Numerical simulations allow (i) to in-vestigate the inﬂuence of parameters difﬁcult to control experimentally and (ii) to measure quantities inacessible to experiments. In this paper we focus on numerical 3D rotating drums and shed light on the role of lateral friction on the rheology of dense granular systems. Our framework is the Non Smooth Contact Dynamics approach, powerful to perform accurate simulations of large systems of particles, essential to deal with simultaneous con-tacts. We point out the inﬂuence of lateral friction coefﬁcient on the granular ﬂow and compare the results to previous 2D simulations.
Asymptotic Analysis of a Buckling Problem for an Embedded Spherical Shell

The axisymmetric buckling of a spherical shell embedded in an elastic medium with uniaxial compression at infinity is examined in the limit of small shell thickness ratio. An asymptotic method is developed by considering the paradigm problem of a beam attached to a Winkler substrate of variable stiffness, which in the small aspect ratio limit displays the same behavior as the shell. The asymptotic method is then applied to the Euler–Lagrange equations corresponding to shell buckling. The system is analyzed in two distinguished limits, displaying good agreement with the full numerical results.
Training-Load Distribution in Endurance Runners: Objective Versus Subjective Assessment.

PURPOSE To assess the distribution of exercise intensity in long-distance recreational athletes (LDRs) preparing for a marathon and to test the hypothesis that individual perception of effort could provide training responses similar to those provided by standardized training methodologies. METHODS Seven LDRs (age 36.5 ± 3.8 y) were followed during a 5-mo training period culminating with a city marathon. Heart rate at 2.0 and 4.0 mmol/L and maximal heart rate were used to establish 3 intensity training zones. Internal training load (TL) was assessed by training zones and TRIMPi methods. These were compared with the session-rating-of-perceived-exertion (RPE) method. RESULTS Total time spent in zone 1 was higher than in zones 2 and 3 (76.3% ± 6.4%, 17.3% ± 5.8%, and 6.3% ± 0.9%, respectively; P = .000 for both, ES = 0.98, ES = 0.99). TL quantified by session-RPE provided the same result. The comparison between session-RPE and training-zones-based methods showed no significant difference at the lowest intensity (P = .07, ES = 0.25). A significant correlation was observed between TL RPE and TL TRIMPi at both individual and group levels (r = .79, P < .001). There was a significant correlation between total time spent in zone 1 and the improvement at the running speed of 2 mmol/L (r = .88, P < .001). A negative correlation was found between running speed at 2 mmol/L and the time needed to complete the marathon (r = -.83, P < .001). CONCLUSIONS These findings suggest that in recreational LDRs most of the training time is spent at low intensity and that this is associated with improved performances. Session-RPE is an easy-to-use training method that provides responses similar to those obtained with standardized training methodologies.
Design and Analysis of Bar-seq Experiments

High-throughput quantitative DNA sequencing enables the parallel phenotyping of pools of thousands of mutants. However, the appropriate analytical methods and experimental design that maximize the efficiency of these methods while maintaining statistical power are currently unknown. Here, we have used Bar-seq analysis of the Saccharomyces cerevisiae yeast deletion library to systematically test the effect of experimental design parameters and sequence read depth on experimental results. We present computational methods that efficiently and accurately estimate effect sizes and their statistical significance by adapting existing methods for RNA-seq analysis. Using simulated variation of experimental designs, we found that biological replicates are critical for statistical analysis of Bar-seq data, whereas technical replicates are of less value. By subsampling sequence reads, we found that when using four-fold biological replication, 6 million reads per condition achieved 96% power to detect a two-fold change (or more) at a 5% false discovery rate. Our guidelines for experimental design and computational analysis enables the study of the yeast deletion collection in up to 30 different conditions in a single sequencing lane. These findings are relevant to a variety of pooled genetic screening methods that use high-throughput quantitative DNA sequencing, including Tn-seq.
An Investigation of Perinatal Hepatitis B Virus Infections Among a High Risk Population: The Delivery Hospital as a Safety Net

Background: There was an increase in perinatal hepatitis B virus (HBV) infections in one Arkansas county that disproportionately affected Marshallese infants. Methods: An estimated 6000 to 10,000 Marshallese, from the Pacific island nation of the Marshall Islands where HBV is highly endemic, live in one Arkansas county. We conducted a retrospective review of hospital and health department records from 2003 to 2005 in that county. We compared maternal screening for hepatitis B surface antigen (HBsAg) between Marshallese and non-Marshallese. We also reviewed birth and immunization records for infants born to HBsAg-positive mothers to evaluate postexposure prophylaxis (PEP). Results: Ten percent (n = 41) of Marshallese births and 0.1% (n = 15) of non-Marshallese births were to HBsAg-positive women. Among those born to HBsAg-positive women, Marshallese and non-Marshallese infants were equally likely to receive PEP with hepatitis B vaccine (98% vs. 100%; P[r] = 0.98) and hepatitis B immune globulin (HBIG) ≤12 hours after birth (88% vs. 87%; P = 0.91). Approximately 57% (n = 32) of all infants born to HBsAg-positive women were tested for perinatal HBV infection. The proportion of Marshallese (17%) and non-Marshallese (13%) infants who tested positive for HBsAg at ages 9 to 25 months was similar (P = 0.78). Receiving HBIG >12 hours after birth was the only factor significantly associated with infection. Conclusions: Although HBV infection was more prevalent among Marshallese compared with non-Marshallese women, there were no differences in infant receipt of PEP and perinatal HBV infection. Delivery hospitals in this county had standing orders to administer hepatitis B vaccine to all newborns, which likely provided a safety net to prevent perinatal HBV transmission in this high-risk population.
Deletion of IκBα activates RelA to reduce acute pancreatitis in mice through up-regulation of Spi2A.

BACKGROUND & AIMS The transcription factor nuclear factor-κB (NF-κB) (a heterodimer of NF-κB1p50 and RelA) is activated rapidly in acute pancreatitis (AP). However, it is not clear whether NF-κB promotes or protects against AP. We used the NF-κB inhibitor protein, inhibitor of κB (IκB)α, to study the roles of NF-κB in the development of AP in mice. METHODS IκBα or the combination of IκBα and RelA selectively were deleted from pancreas of mice using the Cre/locus of cross-over P strategy; cerulein or L-arginine were used to induce AP. We performed microarray analyses of the IκBα- and RelA-deficient pancreata. DNA from healthy individuals and patients with acute or chronic pancreatitis were analyzed for variants in coding regions of alpha-1-antichymotrypsin. RESULTS Mice with pancreas-specific deletion of IκBα had constitutive activation of RelA and a gene expression profile consistent with NF-κB activation; development of AP in these mice was attenuated and trypsin activation was impaired. However, AP was fully induced in mice with pancreas-specific deletion of IκBα and RelA. By using genome-wide expression analysis, we identified a cluster of NF-κB-regulated genes that might protect against the development of AP. The serine protease inhibitor 2A (Spi2a) was highly up-regulated in IκBα-deficient mice. Lentiviral-mediated expression of Spi2A reduced the development of AP in C57BL/6 and RelA-deficient mice. However, we did not correlate any variants of alpha-1-antichymotrypsin, the human homologue of Spi2a, with acute or chronic pancreatitis. CONCLUSIONS Pancreas-specific deletion of IκBα results in nuclear translocation of RelA and reduces AP induction and trypsin activation in mice after administration of cerulein or L-arginine. Constitutive activation of RelA up-regulates Spi2A, which protects mice against the development of AP.
Prevalence of Molar-Incisor-Hypomineralisation among school children in four German cities.

BACKGROUND A wide range for the prevalence of Molar-Incisor-Hypomineralisation (MIH) has been found in regional studies. AIM The aim of this study was to determine the prevalence of MIH in Germany and to compare the findings with other studies. DESIGN In the compulsory dental school examination, the first permanent molars, permanent incisors, and second primary molars were examined according to EAPD criteria in 2395 children (8.1 ± 0.8 years) in four regions in Germany for the presence of MIH. Examinations were performed by five calibrated examiners (κ = 0.9) on clean teeth after toothbrushing. RESULTS The prevalence of MIH at the four regions differed considerably (4.3-14.6%) with a mean prevalence of 10.1%. The DMFT/dmft was generally low, but children with MIH exhibited statistically significant higher caries values. A total of 12.0% of the children with MIH also had at least one affected primary molar, which resulted in a statistically significant correlation between primary and permanent teeth. Most of the affected teeth had demarcated opacities, but more than half of the affected children showed at least one tooth with severe MIH. CONCLUSIONS Molar-Incisor-Hypomineralisation is a prevalent finding in German school children. The prevalence varies highly in different regions, and the high rate of severe forms has clinically relevant implications.
Seventy years after the siege of Leningrad: does early life famine still affect cardiovascular risk and aging?

Objective: To assess the cardiovascular health, markers of cardiovascular aging and telomere length in survivors of the siege of Leningrad, who were either born during the siege or lived in the besieged city in their early childhood. Methods: Survivors of the Leningrad siege (n = 305, 64–81 years) and a control group of age and sex-matched individuals (n = 51, 67–82 years) were examined in terms of a observational retrospective cohort study. All participants were interviewed regarding risk factors, cardiovascular diseases, and therapy. Blood pressure measurement, anthropometry, echocardiography, and electrocardiography were performed according to standard guidelines. Fasting lipids and glucose were measured. Relative telomere length was measured by quantitative PCR, and the ratio of telomere repeat copy number to single gene copy number (T/S) was calculated for each DNA sample. Results: Survivors had lower anthropometric parameters (height, weight, and BMI) and higher high-density lipoprotein level. There were no significant differences in the prevalence of cardiovascular diseases and target organ damage between groups. However, survivors had shorter telomere length: T/S ratio 0.44 (0.25; 0.64) vs. controls 0.91 (0.47; 1.13) (P < 0.0001), both in men and women, with clear association with the period of famine in early life. Exposure to famine in childhood and intrauterine period of life was associated with a higher prevalence of hypertension and shorter telomere length. Conclusion: Early-life famine, especially started in the intrauterine period and late childhood, may contribute to accelerated aging with telomere shortening in both sexes, but has no direct effect on the prevalence of cardiovascular diseases and risk factors after seven decades since exposure.
SSFP signal with finite RF pulses

The theoretical description of steady state free precession (SSFP) sequences is generally well accepted and unquestioned, although it is based on instantaneously acting radiofrequency (RF) pulses. In practice, however, all excitation processes are finite, thereby questioning the overall validity of the common SSFP signal description for use with finite RF pulses. In this paper, finite RF pulse effects on balanced SSFP signal formation are analyzed as a function of the RF time, the pulse repetition time, the flip angle (α) and relaxation times (T1,2). The observed signal modulations from finite RF pulses (compared to infinitesimal ones) can range from only a few percent (for RF time/pulse repetition time ≪ 1, α ≪ 90°, T2/T1 ∼ 1) to over 10% (for RF time/pulse repetition time ≪ 1, α ∼ 90°, T2/T1 ≪ 1) and may even exceed 100% in the limit of RF time/pulse repetition time → 1 (for α ∼ 90°, T2/T1 ≪ 1). As a result, a revision of SSFP signal theory is indicated not only for reasons of completeness but also seems advisable, e.g., for all quantitative SSFP methods. A simple modification for the common balanced SSFP equation is derived that provides an accurate framework for SSFP signal description over a wide variety of practical and physiologic parameters. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
The bZIP Protein MeaB Mediates Virulence Attributes in Aspergillus flavus

LaeA is a fungal specific virulence factor of both plant and human pathogenic fungi. Transcriptional profiles of laeA mutants have been successfully exploited to identify regulatory mechanisms of secondary metabolism in fungi; here we use laeA mutants as tools to elucidate virulence attributes in Aspergillus flavus. Microarray expression profiles of ΔlaeA and over-expression laeA (OE::laeA) were compared to wild type A. flavus. Strikingly, several nitrogen metabolism genes are oppositely mis-regulated in the ΔlaeA and OE::laeA mutants. One of the nitrogen regulatory genes, the bZIP encoding meaB, is up-regulated in ΔlaeA. Significantly, over-expression of meaB (OE::meaB) phenocopies the decreased virulence attributes of a ΔlaeA phenotype including decreased colonization of host seed, reduced lipase activity and loss of aflatoxin B1 production in seed. However, a double knock-down of laeA and meaB (KD::laeA,meaB) demonstrated that KD::laeA,meaB closely resembled ΔlaeA rather than wild type or ΔmeaB in growth, aflatoxin biosynthesis and sclerotia production thus suggesting that meaB does not contribute to the ΔlaeA phenotype. MeaB and LaeA appear to be part of regulatory networks that allow them to have both shared and distinct roles in fungal biology.
Effect of high-pressure/temperature (HP/T) treatments of in-package food on additive migration from conventional and bio-sourced materials

Migration was assessed during and after two high-pressure/temperature (HP/T) treatments intended for a pasteurization (800 MPa for 5 min, from 20 to 40°C) and a sterilization treatment (800 MPa for 5 min, from 90 to 115°C) and were compared with conventional pasteurization and sterilization, respectively. The specific migration of actual packaging additives used as antioxidants and ultraviolet light absorbers (Irganox 1076, Uvitex OB) was investigated in a number of food-packaging systems combining one synthetic common packaging (LLDPE) and a bio-sourced one (PLA) in contact with the four food-simulating liquids defined by European Commission regulations. After standard HP/T processing, migration kinetics was followed during the service life of the packaging material using Fourier transform infrared spectrometer (FTIR) spectroscopy. LLDPE withstood the high-pressure sterilization, whereas it melted during the conventional sterilization. No difference was observed on migration from LLDPE for both treatments. In the case of PLA, migration of Uvitex OB was very low or not detectable for all the cases studied.
Support Vector Machines with a Reject Option

We consider the problem of binary classification where the classifier may abstain instead of classifying each observation. The Bayes decision rule for this setup, known as Chow's rule, is defined by two thresholds on posterior probabilities. From simple desiderata, namely the consistency and the sparsity of the classifier, we derive the double hinge loss function that focuses on estimating conditional probabilities only in the vicinity of the threshold points of the optimal decision rule. We show that, for suitable kernel machines, our approach is universally consistent. We cast the problem of minimizing the double hinge loss as a quadratic program akin to the standard SVM optimization problem and propose an active set method to solve it efficiently. We finally provide preliminary experimental results illustrating the interest of our constructive approach to devising loss functions.
Bootstrap Restricted Likelihood Ratio Test for the Detection of Rare Variants

In this paper the detection of rare variants association with continuous phenotypes of interest is investigated via the likelihood-ratio based variance component test under the framework of linear mixed models. The hypothesis testing is challenging and nonstandard, since under the null the variance component is located on the boundary of its parameter space. In this situation the usual asymptotic chisquare distribution of the likelihood ratio statistic does not necessarily hold. To circumvent the derivation of the null distribution we resort to the bootstrap method due to its generic applicability and being easy to implement. Both parametric and nonparametric bootstrap likelihood ratio tests are studied. Numerical studies are implemented to evaluate the performance of the proposed bootstrap likelihood ratio test and compare to some existing methods for the identification of rare variants. To reduce the computational time of the bootstrap likelihood ratio test we propose an effective approximation mixture for the bootstrap null distribution. The GAW17 data is used to illustrate the proposed test.
Characterization of Arsenate Reductase in the Extract of Roots and Fronds of Chinese Brake Fern, an Arsenic Hyperaccumulator1

Root extracts from the arsenic (As) hyperaccumulating Chinese brake fern (Pteris vittata) were shown to be able to reduce arsenate to arsenite. An arsenate reductase (AR) in the fern showed a reaction mechanism similar to the previously reported Acr2p, an AR from yeast (Saccharomyces cerevisiae), using glutathione as the electron donor. Substrate specificity as well as sensitivity toward inhibitors for the fern AR (phosphate as a competitive inhibitor, arsenite as a noncompetitive inhibitor) was also similar to Acr2p. Kinetic analysis showed that the fern AR had a Michaelis constant value of 2.33 mm for arsenate, 15-fold lower than the purified Acr2p. The AR-specific activity of the fern roots treated with 2 mm arsenate for 9 d was at least 7 times higher than those of roots and shoots of plant species that are known not to tolerate arsenate. A T-DNA knockout mutant of Arabidopsis (Arabidopsis thaliana) with disruption in the putative Acr2 gene had no AR activity. We could not detect AR activity in shoots of the fern. These results indicate that (1) arsenite, the previously reported main storage form of As in the fern fronds, may come mainly from the reduction of arsenate in roots; and (2) AR plays an important role in the detoxification of As in the As hyperaccumulating fern.
Detection of Metastatic Cervical Lymph Nodes in Recurrent Papillary Thyroid Carcinoma: Computed Tomography Versus Positron Emission Tomography-Computed Tomography

Objective: We sought to determine whether positron emission tomography-computed tomography (PET-CT) is more accurate than CT for detecting metastatic cervical lymph nodes in recurrent papillary thyroid carcinoma (PTC) and to determine the relationship between the CT features and PET-CT findings of metastatic nodes. Methods: Eleven consecutive patients with recurrent PTC underwent contrast-enhanced CT (CECT) and PET-CT before surgery. We retrospectively evaluated CECT and PET-CT images to determine the presence of metastatic nodes by level-by-level analysis. The CT findings of the PET-CT results that were positive and negative for metastatic nodes were compared. Results: Metastatic nodes were found at 28 (78%) of 36 neck levels surgically explored. The sensitivity, specificity, and accuracy of CECT for the detection of metastatic nodes were 75.0%, 87.5%, and 77.8%, respectively, and those of PET-CT were 35.7%, 87.5%, and 48.6%, respectively, by level-by-level analysis. No significant difference in the CT features was found between the PET-CT findings positive and negative for metastatic nodes (P > 0.05). Conclusions: Computed tomography is more sensitive and accurate than PET-CT for detecting metastatic lymph nodes in recurrent PTC. No significant relationship was found between the CT features and the PET-CT findings of the metastatic nodes.
A nationwide survey of combined central and peripheral demyelination in Japan

Objectives To clarify the clinical features of combined central and peripheral demyelination (CCPD) via a nationwide survey. Methods The following characteristics were used to define CCPD: T2 high-signal intensity lesions in the brain, optic nerves or spinal cord on MRI, or abnormalities on visual-evoked potentials; conduction delay, conduction block, temporal dispersion or F-wave abnormalities suggesting demyelinating neuropathy based on nerve conduction studies; exclusion of secondary demyelination. We conducted a nationwide survey in 2012, sending questionnaires to 1332 adult and paediatric neurology institutions in Japan. Results We collated 40 CCPD cases, including 29 women. Age at onset was 31.7±14.1 years (mean±SD). Sensory disturbance (94.9%), motor weakness (92.5%) and gait disturbance (79.5%) were common. Although cerebrospinal fluid protein levels were increased in 82.5%, oligoclonal IgG bands and elevated IgG indices were detected in 7.4% and 18.5% of cases, respectively. Fifteen of 21 patients (71.4%) had abnormal visual-evoked potentials. Antineurofascin 155 antibodies were positive in 5/11 (45.5%). Corticosteroids, intravenous immunoglobulins and plasmapheresis resulted in an 83.3%, 66.7% and 87.5% improvement, respectively, whereas interferon-β was effective in only 10% of cases. CCPD cases with simultaneous onset of central nervous system (CNS) and peripheral nervous system (PNS) involvement exhibited greater disability, but less recurrence and more frequent extensive cerebral and spinal cord MRI lesions compared to those with temporarily separated onset, whereas optic nerve involvement was more common in the latter. Conclusions CCPD shows different characteristics from classical demyelinating diseases, and distinctive features exist between cases with simultaneous and temporarily separated onset of CNS and PNS involvement.