Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical and parasite species risk factors for pentavalent antimonial treatment failure in cutaneous leishmaniasis in Peru.

BACKGROUND Treatment for cutaneous leishmaniasis (CL) with standard pentavalent antimonial therapy is hampered by cumbersome administration, toxicity, and potential failure. Knowledge of factors influencing treatment outcome is essential for successful management. METHODS A case-control study of incident cases was performed with patients experiencing their first CL episode. The standard treatment for CL for these patients was 20 mg/kg/day of sodium stibogluconate for 20 days. Clinical and epidemiological data were recorded, and parasite isolates were species typed. Patients were followed up for 6 months to assess treatment outcome. Clinical cure was defined as complete wound closure and re-epithelization without inflammation or infiltration; new lesions, wound reopening, or signs of activity were classified as treatment failure. Descriptive, bivariate, and logistic regression analyses were performed. RESULTS One hundred twenty-seven patients were recruited; 63 (49.6%) were infected with Leishmania (Viannia) peruviana, 29 (22.8%) were infected with Leishmania (Viannia) braziliensis, 27 (21.3%) were infected with Leishmania (Viannia) guyanensis, and 8 (6.3%) were infected with other species. Only patients infected with the 3 most common species were selected for risk-factor analysis (n=119). Final failure rate at 6 months was 24.4% (95% confidence interval [CI], 16.5%-32.1%), with 96% of failures occurring within the first 3 months of follow-up assessment. Risk factors for treatment failure identified in the final multivariate model were age (per year, odds ratio [OR], 0.95; 95% CI, 0.92-0.99; P=.017), stay of <72 months in area of disease acquisition (OR, 30.45; 95% CI, 2.38-389.25; P=.009), duration of disease <5 weeks (OR, 4.39; 95% CI, 1.12-17.23; P=.034), additional lesion (per lesion, OR, 2.06; 95% CI, 1.3-3.28; P=.002), infection with L. (V.) peruviana (OR, 9.85; 95% CI, 1.01-95.65; P=.049), and infection with L. (V.) braziliensis (OR, 22.36; 95% CI, 1.89-263.96; P=.014). CONCLUSIONS The identification of parasite species and clinical risk factors for antimonial treatment failure should lead to an improved management of CL in patients in Peru.
Improved ontology ranking algorithm based on semantic web

By exploring the advantages and weaknesses of two universally-used ontology ranking algorithms in the semantic web, namely, OntoRank algorithm and AKTiveRank algorithm, this paper proposes an integration of these two algorithms, the way which is achieved by extending the semantic terms set of user's query set. Experimental results indicate that the improved algorithm can better meet the needs of users and be more effective.
Fibroblast Growth Factor Homologous Factors Modulate Cardiac Calcium Channels

Rationale: Fibroblast growth factor (FGF) homologous factors (FHFs; FGF11–14) are intracellular modulators of voltage-gated Na+ channels, but their cellular distribution in cardiomyocytes indicated that they performed other functions. Objective: We aimed to uncover novel roles for FHFs in cardiomyocytes, starting with a proteomic approach to identify novel interacting proteins. Methods and Results: Affinity purification of FGF13 from rodent ventricular lysates followed by mass spectroscopy revealed an interaction with junctophilin-2, a protein that organizes the close apposition of the L-type Ca2+ channel CaV1.2 and the ryanodine receptor 2 in the dyad. Immunocytochemical analysis revealed that overall T-tubule structure and localization of ryanodine receptor 2 were unaffected by FGF13 knockdown in adult ventricular cardiomyocytes but localization of CaV1.2 was affected. FGF13 knockdown decreased CaV1.2 current density and reduced the amount of CaV1.2 at the surface as a result of aberrant localization of the channels. CaV1.2 current density and channel localization were rescued by expression of an shRNA-insensitive FGF13, indicating a specific role for FGF13. Consistent with these newly discovered effects on CaV1.2, we demonstrated that FGF13 also regulated Ca2+-induced Ca2+ release, indicated by a smaller Ca2+ transient after FGF13 knockdown. Furthermore, FGF13 knockdown caused a profound decrease in the cardiac action potential half-width. Conclusions: This study demonstrates that FHFs not only are potent modulators of voltage-gated Na+ channels but also affect Ca2+ channels and their function. We predict that FHF loss-of-function mutations would adversely affect currents through both Na+ and Ca2+ channels, suggesting that FHFs may be arrhythmogenic loci, leading to arrhythmias through a novel, dual-ion channel mechanism.
Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution

One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral sequence reconstruction with synthetic biology allows us to resurrect the past within a modern context and has expanded our understanding of protein functionality within a historical context. Experimental evolution, on the other hand, provides us with the ability to study evolution in action, under controlled conditions in the laboratory. Here we describe a novel experimental setup that integrates two disparate fields - ancestral sequence reconstruction and experimental evolution. This allows us to rewind and replay the evolutionary history of ancient biomolecules in the laboratory. We anticipate that our combination will provide a deeper understanding of the underlying roles that contingency and determinism play in shaping evolutionary processes.
Direct comparison of the diagnostic yield of ultrasound-assisted Abrams and Tru-Cut needle biopsies for pleural tuberculosis

Background Tuberculous pleuritis remains the commonest cause of exudative effusions in areas with a high prevalence of tuberculosis and histological and/or microbiological confirmation on pleural tissue is the gold standard for its diagnosis. Uncertainty remains regarding the choice of closed pleural biopsy needles. Objectives This prospective study compared ultrasound-assisted Abrams and Tru-Cut needle biopsies with regard to their diagnostic yield for pleural tuberculosis. Methods 89 patients (54 men) of mean±SD age 38.7±16.7 years with pleural effusions and a clinical suspicion of tuberculosis were enrolled in the study. Transthoracic ultrasound was performed on all patients, who were then randomly assigned to undergo ≥4 Abrams needle biopsies followed by ≥4 Tru-Cut needle biopsies or vice versa. Medical thoracoscopy was performed on cases with non-diagnostic closed biopsies. Histological and/or microbiological proof of tuberculosis on any pleural specimen was considered the gold standard for pleural tuberculosis. Results Pleural tuberculosis was diagnosed in 66 patients, alternative diagnoses were established in 20 patients and 3 remained undiagnosed. Pleural biopsy specimens obtained with Abrams needles contained pleural tissue in 81 patients (91.0%) and were diagnostic for tuberculosis in 54 patients (sensitivity 81.8%), whereas Tru-Cut needle biopsy specimens only contained pleural tissue in 70 patients (78.7%, p=0.015) and were diagnostic in 43 patients (sensitivity 65.2%, p=0.022). Conclusions Ultrasound-assisted pleural biopsies performed with an Abrams needle are more likely to contain pleura and have a significantly higher diagnostic sensitivity for pleural tuberculosis.
The C.R.E.A.T.E. Approach to Primary Literature Shifts Undergraduates’ Self-Assessed Ability to Read and Analyze Journal Articles, Attitudes about Science, and Epistemological Beliefs

The C.R. E.A. T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method uses intensive analysis of primary literature in the undergraduate classroom to demystify and humanize science. We have reported previously that the method improves students’ critical thinking and content integration abilities, while at the same time enhancing their self-reported understanding of “who does science, and why. ” We report here the results of an assessment that addressed C.R. E.A. T.E. students’ attitudes about the nature of science, beliefs about learning, and confidence in their ability to read, analyze, and explain research articles. Using a Likert-style survey administered pre- and postcourse, we found significant changes in students’ confidence in their ability to read and analyze primary literature, self-assessed understanding of the nature of science, and epistemological beliefs (e.g., their sense of whether knowledge is certain and scientific talent innate). Thus, within a single semester, the inexpensive C.R. E.A. T.E. method can shift not just students’ analytical abilities and understanding of scientists as people, but can also positively affect students’ confidence with analysis of primary literature, their insight into the processes of science, and their beliefs about learning.
Analysis of Passive Optical Networks for Subcarrier Multiplexed Quantum Key Distribution

This paper provides an analysis of the performance of different passive optical network (PON) topologies for the distribution of multiuser quantum keys using subcarrier multiplexing and the Bennet-Brassard (BB84) protocol. PON topologies are evaluated in terms of the achievable quantum bit error rate (QBER) and the useful key rate. Results show that wavelength routed (WR) networks outperform broadcast topologies as the first are not subject to division losses. Within WR architecture the star configuration is the most efficient in terms of network scalability, maximum reachable distance and maximum useful distribution rate. The effect of subcarrier modulation index on the network performance has also been considered showing a similar and non significant impact for the range considered in this paper.
New Appraisal of Atrial Fibrillation Burden and Stroke Prevention.

Atrial fibrillation (AF) quintuples the risk of stroke, and patients with stroke and AF are the most likely to be left dead or permanently disabled.1–4 More than 5 million people in the United States and >8 million people in the European Union were estimated to have AF in 2010.5–7 The lifetime risk of AF is high, with a quarter of 40-year-old patients expected to develop AF during the course of their lifetime.8 Because of aging populations, the prevalence of AF in the United Sates is expected to exceed 12 million by 2030, whereas in the European Union estimates 17.9 million cases by 2060.6,7 The risk of stroke can be stratified by various scores, including CHADS2 (congestive heart failure, hypertension, age ≥75 years, diabetes mellitus [1 point], and previous stroke or transient ischemic attack [TIA; 2 points]) and the CHA2DS2-VASc score (congestive heart failure/left ventricular dysfunction, hypertension [1 point], age ≥75 years [2 points], diabetes mellitus [1 point], previous stroke or TIA [2 points], vascular disease, age 65–75 years, and female sex [1 point]). 9,10 Multiple trials have demonstrated the efficacy of anticoagulation in reducing the risk of stroke by 65% to 80% in patients with clinically detected AF and other risk factors.10–13 AF burden can be defined as the time spent in AF per unit of time (day, week, month, etc). It is noteworthy that the burden of AF is not part of any risk stratification scoring system. In fact, current practice views AF as a dichotomous variable; one that is either present—whether paroxysmal, persistent, or permanent—or absent. Implicit in this perspective is an assumption that the burden AF is not relevant to stroke risk. This assumption is based on …
Parameter analysis of a new AFIPM for light electric vehicle application

The electrical machines are gaining more and more attentions nowadays, especially for the electric vehicle application. Compared with the radial flux machine, the axial flux machine can have higher torque density and efficiency due to its tight structure. However, most of the axial flux machines are designed with the surface mounted permanent magnets (PMs) rotor, where the reluctance torque ability is reduced. To improve the torque ability of the axial flux machine, a new axial flux interior permanent magnet machine (AFIPM) is proposed and analyzed in this paper. The rotor of the proposed AFIPM is manufactured by the rolling the electrical steels as a ring core, then the PMs are inserted in the holes of the rotor ring, the axial side of the rotor ring is designed with the several different steps to eliminate the harmonics of the back EMF as well. The static performance and electromagnetic parameters of the AFIPM is calculated and it shows that the reluctance torque ability of the AFIPM is very good, based on the 3D finite element method (FEM) and frozen magnetic permeability technology.
Phase II study of paclitaxel, ifosfamide, and carboplatin in patients with recurrent or metastatic head and neck squamous cell carcinoma

In the current study the authors assessed the antitumor activity (including response rate, duration of response, and survival) and toxicity profile (including anorexia, fatigue, emesis, and peripheral neuropathy) of a combination of paclitaxel, ifosfamide, and carboplatin (TIC) in patients with recurrent or metastatic squamous cell carcinoma of the head and neck (SCCHN). The trial hypothesis was that the TIC therapeutic index would be as high as that of paclitaxel, ifosfamide, and cisplatin (TIP) in this setting, but with less toxicity.
Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer

Riboswitches are motifs in the untranslated regions (UTRs) of RNA transcripts that sense metabolite levels and modulate the expression of the corresponding genes for metabolite import, export, synthesis, or degradation. All riboswitches contain an aptamer: an RNA structure that, upon binding ligand, folds to expose or sequester regulatory elements in the adjacent sequence through alternative nucleotide pairing. The coupling between ligand binding and aptamer folding is central to the regulatory mechanisms of thiamine pyrophosphate (TPP) riboswitches and has not been fully characterized. Here, we show that TPP aptamer folding can be decomposed into ligand-independent and -dependent steps that correspond to the formation of secondary and tertiary structures, respectively. We reconstructed the full energy landscape for folding of the wild-type (WT) aptamer and measured perturbations of this landscape arising from mutations or ligand binding. We show that TPP binding proceeds in two steps, from a weakly to a strongly bound state. Our data imply a hierarchical folding sequence, and provide a framework for understanding molecular mechanism throughout the TPP riboswitch family.
Oropharyngeal Transition of the Bolus in Post-Stroke Patients

ObjectiveThe purposes of this study were to determine whether two bolus transition durations (oral transit time and pharyngeal transit time) were different during oropharyngeal swallowing in post-stroke patients who aspirated and who did not aspirate and to examine those differences across varying bolus viscosities. DesignMeans and standard deviations of oral transit time and pharyngeal transit time were analyzed on 5 ml of thin and nectar thick liquids and puree swallows from videofluoroscopic swallowing examinations of 30 post-stroke patients. Statistical comparisons were made by repeated measures analysis of variance, with the within-subject variable being the three consistencies and the between-subject variable being the two groups. Significance level was set at P < 0.025. ResultsOral transition of the bolus did not differ between the two patient groups. Pharyngeal transition of the bolus differentiated the patients who aspirated from the patients who did not aspirate. Both the oral and pharyngeal transitions differed significantly for the puree compared with the thin and nectar thick liquids. ConclusionsPatients who demonstrate prolonged pharyngeal transit times may be at risk for aspiration.
Auto-Regressive Modeling of the Shadowing for RSS Mobile Tracking

In this paper, we consider the tracking of mobile terminals based on the received signal strength (RSS) measured from several base stations. The spatial correlation of the random shadowing is exploited in order to improve the position tracking. We define an auto-regressive (AR) model of the temporal evolution of the shadowing. This model allows for performing a joint tracking of the position and the shadowing by applying a Rao- Blackwellized (RB) particle filter approximating the posterior probability distributions numerically. The simulation results show that the tracking can be improved by considering sufficiently high auto-regressive orders.
Shallow seismic reflection does not always work

Summary Shallow seismic reflection has seen widespread use in a variety of environmental, groundwater, and engineering applications over the last 15 years. Seismic reflection, like any other geophysical technique, has reasonably well defined limitations. Besides the well-published resolution limitation, the effectiveness of the technique is strongly dependent, and in many cases controlled, by near-surface conditions. Moisture content, sorting, grain size, organic matter, and consolidation are just a few of the key properties of the near-surface that can dramatically affect the quality of seismic reflection data. In some difficult data areas thoughtful parameter design, high-quality equipment (large dynamic range and small electronic noise), and careful processing can overcome adverse near-surface c onditions. Tendencies to suggest that data processing is the key to bringing out reflections on CMP stacks that are not identifiable on shot or CMP gathers leads to overselling the technique and inevitable skepticism by clients and potential clients as to the reliability of shallow seismic reflection. As difficult as it may be for shallow seismic reflection practitioners to admit, shallow seismic reflection simply will not work in some settings and for some targets.
Elevated resting heart rate is associated with dyslipidemia in middle-aged and elderly Chinese.

OBJECTIVE To study the relationship between resting heart rate and blood lipid level. METHODS A total of 9 415 subjects aged ⋝ 40 years were included in the present study. Their resting heart rate was monitored and their serum levels of triglyceride (TG), total cholesterol (TC), low density lipoprotein cholesterol (LDL-C) and high density lipoprotein cholesterol (HDL-C) were measured to define dyslipidemia according to the 2007 Chinese Guidelines on Prevention and Treatment of Dyslipidemia in Adults. RESULTS The subjects were divided into group A with their resting heart rate <70 beats/min, group B with their resting heart rate =70-79 beats/min, group C with their resting heart rate =80-89 beats/min, and group D with their resting heart rate ⋝ 90 beats/min. High TG, TC, and LDL-C were presented across the resting heart rate (Ptrend <0.01). Multiple logistic regression analysis revealed that the risk of high TG and TC was higher in subjects with their resting heart rate ⋝ 90 beats/min than in those with their resting heart rate <70 beats/min (OR=1.42; 95% CI: 1.16-1.74 and OR=1.33; 95% CI: 1.09-1.64, respectively). CONCLUSION Elevated resting heart rate is associated with high TG and TC in middle-aged and elderly Chinese subjects.
Performance analysis of the developed mandatory access control system in the DBMS

In this paper, the problem of performance analysis of the developed mandatory access control system (DBMS) is considered. An additional program module (access manager), which implements the principle of mandatory access instead of the existing discretionary access was developed in the DBMS. The mathematical models of DBMS have been designed with the help of the mathematical formalism of the theory of queuing networks. Important results about performance of the fixed protection systems DBMS and developed system were received by analyzing the mathematical models.
Real-time real-world analysis of seasonal influenza vaccine effectiveness: method development and assessment of a population-based cohort in Stockholm County, Sweden, seasons 2011/12 to 2014/15

Real-world estimates of seasonal influenza vaccine effectiveness (VE) are important for early detection of vaccine failure. We developed a method for evaluating real-time in-season vaccine effectiveness (IVE) and overall seasonal VE. In a retrospective, register-based, cohort study including all two million individuals in Stockholm County, Sweden, during the influenza seasons from 2011/12 to 2014/15, vaccination status was obtained from Stockholm’s vaccine register. Main outcomes were hospitalisation or primary care visits for influenza (International Classification of Disease (ICD)-10 codes J09-J11). VE was assessed using Cox multivariate stratified and non-stratified analyses adjusting for age, sex, socioeconomic status, comorbidities and previous influenza vaccinations. Stratified analyses showed moderate VE in prevention of influenza hospitalisations among chronically ill adults ≥ 65 years in two of four seasons, and lower but still significant VE in one season; 53% (95% confidence interval (CI): 33–67) in 2012/13, 55% (95% CI: 25–73) in 2013/14 and 18% (95% CI: 3–31) in 2014/15. In conclusion, seasonal influenza vaccination was associated with substantial reductions in influenza-specific hospitalisation, particularly in adults ≥ 65 years with underlying chronic conditions. With the use of population-based patient register data on influenza-specific outcomes it will be possible to obtain real-time estimates of seasonal influenza VE.
On Maximum-Likelihood SINR Estimation of MPSK in a Multiuser Fading Channel

In this paper, maximum-likelihood (ML) signal-to-interference-plus-noise ratio (SINR) estimation is derived for a multiuser fading channel with additive Gaussian noise and M-ary phase-shift keying (MPSK) signaling for the users. This problem is analyzed in light of works that consider a single-user channel in performing ML signal-to-noise ratio estimation. This work is motivated by the importance of a user's knowledge of its SINR in resource-allocation decisions, particularly power control and rate adaptation.