Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach

Background Metagenomic shotgun sequencing has the potential to change how many infections, particularly those caused by difficult-to-culture organisms, are diagnosed. Metagenomics was used to investigate prosthetic joint infections (PJIs), where pathogen detection can be challenging. Methods Four hundred eight sonicate fluid samples generated from resected hip and knee arthroplasties were tested, including 213 from subjects with infections and 195 from subjects without infection. Samples were enriched for microbial DNA using the MolYsis basic kit, whole-genome amplified, and sequenced using Illumina HiSeq 2500 instruments. A pipeline was designed to screen out human reads and analyze remaining sequences for microbial content using the Livermore Metagenomics Analysis Toolkit and MetaPhlAn2 tools. Results When compared to sonicate fluid culture, metagenomics was able to identify known pathogens in 94.8% (109/115) of culture-positive PJIs, with additional potential pathogens detected in 9.6% (11/115). New potential pathogens were detected in 43.9% (43/98) of culture-negative PJIs, 21 of which had no other positive culture sources from which these microorganisms had been detected. Detection of microorganisms in samples from uninfected aseptic failure cases was conversely rare (7/195 [3.6%] cases). The presence of human and contaminant microbial DNA from reagents was a challenge, as previously reported. Conclusions Metagenomic shotgun sequencing is a powerful tool to identify a wide range of PJI pathogens, including difficult-to-detect pathogens in culture-negative infections.
Herbicide Exposure, Vietnam Service, and Hypertension Risk in Army Chemical Corps Veterans

Objective: We examined hypertension risk in Army Chemical Corps (ACC) veterans who sprayed defoliant in Vietnam. Methods: We analyzed data from the 2013 health survey of 3086 ACC veterans and investigated the association between self-reported physician-diagnosed-hypertension (SRH) and herbicide-spray-history adjusting for Vietnam-service-status, rank, age, tobacco/alcohol use, race, and body mass index (BMI). Spray-history was verified against serum 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (n = 636). SRH was confirmed by blood pressure (BP) measurement by trained medical technicians and medical record reviews. Results: Herbicide-spray-history (ORadjusted[95%confidence interval {CI}] = 1.74[1.44,2.11]) and Vietnam-service-status (ORadjusted = 1.26[1.05,1.53]) were significantly associated with SRH. The association was highest when comparing Vietnam-service-sprayers to non-Vietnam-service-nonsprayers (ORadjusted = 2.21[1.76,2.77]). Serum TCDD was highest for Vietnam-service-sprayers. Mean systolic BPs were significantly higher among veterans with SRH than those without (P ⩽ 0.001). Medical records and SRH overall agreement was 89%. Conclusion: Occupational herbicide exposure history and Vietnam-service-status were significantly associated with hypertension risk.
Arterial blood gases during diving in elite apnea divers.

Elite apnea divers have considerably extended the limits of dive depth and duration but the mechanisms allowing humans to tolerate the compression- and decompression-induced changes in alveolar gas partial pressures are still not fully understood. Therefore we measured arterial blood gas tensions and acid-base-status in two elite apnea divers during simulated wet dives lasting 3 : 55 and 5 : 05 minutes, respectively. Arterial pO2 followed the compression-(from 13.8/16.9 kPa before the dive to 30 kPa at the start of the bottom time) and decompression-induced (from 13.7/21.0 kPa to 3.3/4.9 kPa immediately after surfacing) variations of ambient pressure, while the arterial pCO2 remained within the physiologic range (3.0/3.9 kPa before diving vs. 5.7/5.9 kPa at the end of the bottom time), probably due to the CO2 storage capacity of the blood. These findings may help to explain why humans can sustain deep and long apnea dives without major increases in respiratory drive.
Methadone Maintenance Treatment: A 15-year Retrospective Study in Split-Dalmatia County, Croatia

Background: The aim of this retrospective study is to use existing epidemiological data on patients in methadone maintenance treatment in Split-Dalmatia County from 2001 to 2015 to evaluate the substitution treatment system and policy of opiate addicts treatment, the epidemiological trend, and risk of overdose mortality. In addition, we would like to highlight the problem of poor control of methadone therapy and thus the possibility of selling methadone. The result is a greater number of deaths caused by methadone in people who were not in methadone therapy. Methods: The research included data collected from 3189 patients who had been in the drug abuse treatment program in Split-Dalmatia County during 2001–2015 and data gathered from autopsy examinations of patients in Split-Dalmatia County with emphasis on data for 186 overdosed patients during research period. Results: The total number of patients in the methadone treatment program in Split-Dalmatia County during the research period, except in 2005 and 2006, has been stable, while the number of new opiate patients, being in first-time treatment, decreased by 62.5%. The number of addicts who were in a long-term maintenance program has increased by 198%, whereas the number of addicts who were in a short-term detoxification treatment has decreased by 96.4%. According to results obtained from performed autopsies, 186 death cases were determined as overdoses. Methadone was found in 56 of those cases and was declared as the cause of death in 39 cases (70%). Of the total number of autopsied patients with diagnosed methadone overdose, only 23 (59%) had been recorded to receive methadone therapy in Public Health Institute of Split-Dalmatia County database. Conclusions: The results of this study show the favorable epidemiological trend because of the decreasing number of new opiate patients in treatment. The retention of opiate patients in substitution therapy indicates the effectiveness of methadone maintenance programs. Our research did not determine any influence of methadone substitution therapy on an increasing risk of specific (overdose) mortality.
Intra-Operative Inspired Fraction of Oxygen and the Risk of Surgical Site Infections in Patients with Type 1 Surgical Incisions.

BACKGROUND Whether the fraction of inspired oxygen (FIO2) influences the risk of surgical site infection (SSI) is controversial. The World Health Organization and the World Federation of Societies of Anesthesiologists offer conflicting recommendations. In this study, we evaluate simultaneously three different definitions of FIO2 exposure and the risk of SSI in a large surgical population. PATIENTS AND METHODS Patients with clean (type 1) surgical incisions who developed superficial and deep organ/space SSI within 30 days after surgery from January 2003 through December 2012 in five surgical specialties were matched to specialty-specific controls. Fraction of inspired oxygen exposure was defined as (1) nadir FIO2, (2) percentage of operative time with FIO2 greater than 50%, and (3) cumulative hyperoxia exposure, calculated as the area under the curve (AUC) of FIO2 by time for the duration in which FIO2 greater than 50%. Stratified univariable and multivariable logistic regression models tested associations between FIO2 and SSI. RESULTS One thousand two hundred fifty cases of SSI were matched to 3,248 controls. Increased oxygen exposure, by any of the three measures, was not associated with the outcome of any SSI in a multivariable logistic regression model. Elevated body mass index (BMI; 35+ vs. <25, odds ratio [OR] 1.78, 95% confidence interval [CI] 1.43-2.24), surgical duration (250+ min vs. <100 min, OR 1.93, 95% CI 1.48-2.52), diabetes mellitus (OR 1.37, 95% CI 1.13-1.65), peripheral vascular disease (OR 1.52, 95% CI 1.10-2.10), and liver cirrhosis (OR 2.48, 95% CI 1.53-4.02) were statistically significantly associated with greater odds of any SSI. Surgical sub-group analyses found higher intra-operative oxygen exposure was associated with higher odds of SSI in the neurosurgical and spine populations. CONCLUSION Increased intra-operative inspired fraction of oxygen was not associated with a reduction in SSI. These findings do not support the practice of increasing FIO2 for the purpose of SSI reduction in patients with clean surgical incisions.
Ropivacaine versus Bupivacaine for Inter Scalene Block Clinical and Pharmacological Comparative Study

Introduction : The interscalene approach to the brachial plexus for shoulder surgeries provides excellent anaesthesia with remarkable safety and minimal or no systemic disturabances. Material and Methods : 60 abult patients ASA I-II undergoing elective shoulder surgery. Patients were randomly allocated into 3 groups. The patients recived 20ml of either ropivacaine 1% GI (20 patients), ropivacaine 0.75% GII (20 patients) and bupivacaine 0.5% GIII (20 patients). Onset time of sensory and motor block, duration of analgesia and the need for supplementary analgesics were recorded. Pain was assessed by using VAPS. Haemodynamic parameters, oxygen saturation and respiratory rate were recorded. Unwanted side effects, cardiovascular, neurological, nausea and vomiting etc were recorded. Also, patients satisfaction were noted. The pharmacological study was done on pentobarbitone cats to determine the effect of different doses of ropivacaine (0.35-2.8mg/kg) versus buipvacaine (0.5-4mg/kg) on arterial blood pressure, ECG and respiratory rate. Results: The mean onset time of analgesia was faster in ropivacaine groups than bupivacaine group (p‹0.005). The studied groups were comparable regarding the duration of analgesia, motor and sensory block, cadio vascular and respiratory effects. The incidence of paraesthesia was more frequent in bupivacaine group than both ropivacaine groups (30% vs 10%) There was more patient satisfaction in ropivacaine groups than bupivacaine groups. On the other hand the pharmacological study showed that ropivacaine had more less toxic effects on cardiovascular and respiratory systems. Conclusion : This study concluded that interscalene block performed with either 0.75% or 1% ropivacaine allows for a prolonged postoperative pain relief similar to bupivacaine 0.5% with shorter onset time, more cardiovascular Introduction : Interscalene brachial plexus block (ISB) is used to provide anaesthesia and analgesia for shoulder surgery. Single injection interscalene brachial plexus block is an effective anaesthetic; however it is limited by the duration of action of local anaesthetic. Bupivacaine and ropivacaine have been compared both at different an equal volumes and concentration for ISB. Kinnard and Lirette, (1996). Bupivacaine is a long-acting local anaesthetic which has been reported to be associated with slower onset time for nerve blockade compared with other intermediate stability and higher patient satisfaction.
Satellite Rainfall (TRMM 3B42-V7) Performance Assessment and Adjustment over Pahang River Basin, Malaysia

The Tropical Rainfall Measuring Mission (TRMM) was the first Earth Science mission dedicated to studying tropical and subtropical rainfall. Up until now, there is still limited knowledge on the accuracy of the version 7 research product TRMM 3B42-V7 despite having the advantage of a high temporal resolution and large spatial coverage over oceans and land. This is particularly the case in tropical regions in Asia. The objective of this study is therefore to analyze the performance of rainfall estimation from TRMM 3B42-V7 (henceforth TRMM) using rain gauge data in Malaysia, specifically from the Pahang river basin as a case study, and using a set of performance indicators/scores. The results suggest that the altitude of the region affects the performances of the scores. Root Mean Squared Error (RMSE) is lower mostly at a higher altitude and mid-altitude. The correlation coefficient (CC) generally shows a positive but weak relationship between the rain gauge measurements and TRMM (0 < CC < 0.4), while the Nash-Sutcliffe Efficiency (NSE) scores are low (NSE < 0.1). The Percent Bias (PBIAS) shows that TRMM tends to overestimate the rainfall measurement by 26.95% on average. The Probability of Detection (POD) and Threat Score (TS) demonstrate that more than half of the pixel-point pairs have values smaller than 0.7. However, the Probability of False Detection (POFD) and False Alarm Rate (FAR) show that most of the pixel-point gauges have values lower than 0.55. The seasonal analysis shows that TRMM overestimates during the wet season and underestimates during the dry season. The bias adjustment shows that Mean Bias Correction (MBC) improved the scores better than Double-Kernel Residual Smoothing (DS) and Residual Inverse Distance Weighting (RIDW). The large errors imply that TRMM may not be suitable for applications in environmental, water resources, and ecological studies without prior correction.
Personality traits distinguishing dementia with Lewy bodies from Alzheimer disease

Objective: To identify personality traits that distinguish dementia with Lewy bodies (DLB) from Alzheimer disease (AD). Methods: We examined 290 participants enrolled in a longitudinal study (nondemented control = 34, DLB = 128, AD = 128) followed to autopsy. As part of the annual interview with the collateral source, the clinician asked about specific changes in personality, interests, and drives based on items from the Blessed Dementia Scale (BDS). Statistical analysis was performed using χ2 and Fisher exact tests. Factor analysis was performed to determine underlying structure and receiver operating characteristic curves assessed the ability for each of three derived factors to discriminate DLB from AD. Results: The sample was evaluated for a mean of 4.8 visits (range 1 to 14) with a mean age of 77.6 ± 9.9 years. The participants' cognitive status ranged from nondemented (Clinical Dementia Rating [CDR] 0) through all stages of dementia (CDR ≥ 0.5). Personality traits that distinguished DLB included diminished emotional responsiveness (p = 0.004), relinquishing hobbies (p = 0.01), growing apathy (p = 0.03), and purposeless hyperactivity (p = 0.003). Factor analyses of the BDS revealed a PASSIVE factor (diminished emotional responsiveness, relinquished hobbies, growing apathy, and purposeless hyperactivity) explaining 10.4% of variance and that DLB was more likely to manifest these personality traits than AD (p = 0.001). The PASSIVE factor discriminated DLB from AD (area under the curve = 0.61, 95% CI: 0.54 to 0.68, p = 0.006). Any change in personality is associated with the presence of visual hallucinations. Conclusions: Our results suggest that incorporating a brief, simple inventory of personality traits may improve the identification of individuals with dementia with Lewy bodies.
Investigation of physico-mechanical properties of flexible poly (vinyl chloride) filled with antimony trioxide using ionizing radiation

ABSTRACT Composites of polyvinyl chloride (PVC) with 2% calcium carbonate, 2% diethyl phthalate, 2% paraffin wax and 2% lead sulphate and different contents of antimony trioxide (Sb2O3) prepared by melting and irradiated with gamma ray have been considered. Assessment of the mechanical and thermal properties of the unirradiated and irradiated ﬂexible polyvinyl chloride (FPVC) were completed utilizing elasticity (TS), Elongation at break (Eb) and thermogravimetric analysis measurements. TS and thermal stability of FPVC displayed advanced improvement after addition of additives and this approach highlighted the efficiency of those ingredients on PVC. The compounding of FPVC with Sb2O3 in various extents was examined by FTIR, X-ray diffraction and scanning electron microscope methods. It is obvious that the presence of Sb2O3 begins impacting oxidative degradation, leading to a decrease in mechanical properties up to 10%. Moreover, a slight increase in the thermal stability of composites by exposure to ionizing radiation is apparently due to cross-linking of FPVC chains. GRAPHICAL ABSTRACT
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

Motivation: It is well known that microRNAs (miRNAs) and genes work cooperatively to form the key part of gene regulatory networks. However, the specific functional roles of most miRNAs and their combinatorial effects in cellular processes are still unclear. The availability of multiple types of functional genomic data provides unprecedented opportunities to study the miRNA–gene regulation. A major challenge is how to integrate the diverse genomic data to identify the regulatory modules of miRNAs and genes. Results: Here we propose an effective data integration framework to identify the miRNA–gene regulatory comodules. The miRNA and gene expression profiles are jointly analyzed in a multiple non-negative matrix factorization framework, and additional network data are simultaneously integrated in a regularized manner. Meanwhile, we employ the sparsity penalties to the variables to achieve modular solutions. The mathematical formulation can be effectively solved by an iterative multiplicative updating algorithm. We apply the proposed method to integrate a set of heterogeneous data sources including the expression profiles of miRNAs and genes on 385 human ovarian cancer samples, computationally predicted miRNA–gene interactions, and gene–gene interactions. We demonstrate that the miRNAs and genes in 69% of the regulatory comodules are significantly associated. Moreover, the comodules are significantly enriched in known functional sets such as miRNA clusters, GO biological processes and KEGG pathways, respectively. Furthermore, many miRNAs and genes in the comodules are related with various cancers including ovarian cancer. Finally, we show that comodules can stratify patients (samples) into groups with significant clinical characteristics. Availability: The program and supplementary materials are available at http://zhoulab.usc.edu/SNMNMF/. Contact: xjzhou@usc.edu; zsh@amss.ac. cn Supplementary information: Supplementary data are available at Bioinformatics online.
Bi-population CMA-ES agorithms with surrogate models and line searches

In this paper, three extensions of the BI-population Covariance Matrix Adaptation Evolution Strategy with weighted active covariance matrix update (BIPOP-aCMA-ES) are investigated. First, to address expensive optimization, we benchmark a recently proposed extension of the self-adaptive surrogate-assisted CMA-ES which benefits from more intensive surrogate model exploitation (BIPOP-saACM-k). Second, to address separable optimization, we propose a hybrid of BIPOP-aCMA-ES and STEP algorithm with coordinate-wise line search (BIPOP-aCMA-STEP). Third, we propose HCMA, a hybrid of BIPOP-saACM-k, STEP and NEWUOA to benefit both from surrogate models and line searches. All algorithms were tested on the noiseless BBOB testbed using restarts till a total number of function evaluations of 106n was reached, where n is the dimension of the function search space. The comparison shows that BIPOP-saACM-k outperforms its predecessor BIPOP-saACM up to a factor of 2 on ill-conditioned problems, while BIPOP-aCMA-STEP outperforms the original BIPOP-based algorithms on separable functions. The hybrid HCMA algorithm demonstrates the best overall performance compared to the best algorithms of the BBOB-2009, BBOB-2010 and BBOB-2012 when running for more than 100n function evaluations.
Nutritional profiling of Eurasian woodcock meat: chemical composition and myoglobin characterization.

BACKGROUND Meat from birds is a rich source of proteins for the human diet. In this framework, Eurasian woodcock (Scolopax rusticola L.), a medium-small wading bird hunted as game in many Eurasian countries, is considered one of the best meats for culinary purposes. Since the nutritional composition of Eurasian woodcock meat has not yet been reported, we decided to determine the nutritional profile of S. rusticola meat. RESULTS Macronutrient components (proteins, lipids and fatty acids) were determined, as well as free and total amino acids, and compared with those of the common pheasant. Eurasian woodcock meat contains high levels of proteins and essential amino acids. The levels of unsaturated fatty acids represent a great contribution to the total lipid amount. Among polyunsaturated fatty acids, linoleic acid (C18:2, n-6) is the major essential fatty acid. Finally, we report the characterization of myoglobin (Mb) from Eurasian woodcock. CONCLUSION The data revealed that meat from this bird could be a good source of quality raw proteins because of its amino acid composition, and it had a low lipid content. On the other hand, Mb characterization might be of benefit to the meat industry, by providing useful information for the determination of species-specific differences in meat from birds. © 2018 Society of Chemical Industry.
The Voice Conversion Challenge 2018: Promoting Development of Parallel and Nonparallel Methods

We present the Voice Conversion Challenge 2018, designed as a follow up to the 2016 edition with the aim of providing a common framework for evaluating and comparing different state-of-the-art voice conversion (VC) systems. The objective of the challenge was to perform speaker conversion (i.e. transform the vocal identity) of a source speaker to a target speaker while maintaining linguistic information. As an update to the previous challenge, we considered both parallel and non-parallel data to form the Hub and Spoke tasks, respectively. A total of 23 teams from around the world submitted their systems, 11 of them additionally participated in the optional Spoke task. A large-scale crowdsourced perceptual evaluation was then carried out to rate the submitted converted speech in terms of naturalness and similarity to the target speaker identity. In this paper, we present a brief summary of the state-of-the-art techniques for VC, followed by a detailed explanation of the challenge tasks and the results that were obtained.
On Convergence of Population Processes in Random Environments to the Stochastic Heat Equation with Colored Noise

We consider the stochastic heat equation with a multiplicative colored noise term on the real space for dimensions greater or equal to 1. First, we prove convergence of a branching particle system in a random environment to this stochastic heat equation with linear noise coefficients. For this stochastic partial differential equation with more general non-Lipschitz noise coefficients we show convergence of associated lattice systems, which are infinite dimensional stochastic differential equations with correlated noise terms, provided that uniqueness of the limit is known. In the course of the proof, we establish existence and uniqueness of solutions to the lattice systems, as well as a new existence result for solutions to the stochastic heat equation. The latter are shown to be jointly continuous in time and space under some mild additional assumptions.