Miracle-dz/UniFAR-FTUs huggingface dataset:
Trends in Drug Resistance Prevalence in HIV-1–infected Children in Madrid: 1993 to 2010 Analysis

Background: Drug resistance mutations compromise antiretroviral treatment (ART) effectiveness in HIV-1–infected children. Trends in drug resistance prevalence have not been previously evaluated in HIV-infected children in Spain. Methods: HIV-1 variants, drug resistance prevalence dynamics and drug susceptibility were analyzed from 1993 to 2010 in HIV-infected children with available pol sequence, sample or drug resistance profile. HIV-1 variants were characterized by phylogenetic analysis. Resistance mutations in pretreated and naive patients were identified according to International AIDS Society-2010 and the World Health Organization list, respectively. Results: In 232 patients, genotypic resistance profiles (n = 11) or pol sequences (n = 128) were recovered or newly generated from infected samples (n = 93). Patients were mainly in care at pediatric units (63%), were mostly Europeans (84%), with moderate AIDS symptoms (65%), on ART (91%) and infected by HIV-1 subtype B (89%). Transmitted major drug resistance mutations were selected in 6 (13.6%) of the 44 ART-naive children: 4.8%, 9.3% and 11.6%, for protease inhibitors, nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors, respectively. Overall resistance prevalence was higher (71.8%) among ART-exposed children: 39.9%, 66.5% and 35.3% for protease inhibitors, nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors, respectively. Resistance prevalence among ART-exposed children was higher in 2009 to 2010 relative to 1993 to1999 for nonnucleoside reverse transcriptase inhibitors (42% versus 6%; P = 0.006), protease inhibitors (39% versus 13%; P = 0.004) and nucleoside reverse transcriptase inhibitors (63% versus 44%; P = NS). Susceptibility to each drug in resistant viruses was predicted. The rate of non-B infections increased in the last years, mainly caused by recombinant viruses. Conclusions: The increasing resistance prevalence among the HIV-infected pediatric population in Spain highlights the importance of specific drug resistance and drug susceptibility surveillance in long-term pretreated children to optimize treatment regimens.
The daily variation of the concentration of suspended particles in the surface layer of the atmosphere of the village Berezovka (Krasnoyarsk region)

PM10 concentrations in the surface layer of the atmosphere of Berezovka are 2-3 times higher in winter than in summer. The daily variation of suspended particle concentrations is characterized by two maxima and two minima. It is more pronounced in January and February than in June and July. Winter maxima are mainly due to the time intervals of 9-11 and 19-21 hours, and summer-on 9-11 and 22-23 h. Minima are due to 4-5 and 15-17 h in winter, and in summer - 4-6 and 14-18 h. The daily variation of PM2.5 is similar to the daily variation of PM10 in winter. The difference is that the concentration of PM2,5 increases to values that are significantly higher in the evening than in the afternoon. Air pollution is associated with coal heating of individual houses in the village and the daily variation of the concentration of PM is determined by the heating regime of dwellings.
Through the patients' eyes - Psychometric evaluation of the 64-item version of the Experienced Patient-Centeredness Questionnaire (EPAT-64)

Background Patient-reported experience measures (PREMs) are valuable tools for evaluating patient-centeredness (PC) from the patients' perspective. Despite their utility, a comprehensive PREM addressing PC has been lacking. To bridge this gap, we developed the preliminary version of the Experienced Patient-Centeredness Questionnaire (EPAT), a disease-generic tool based on the integrative model of PC comprising 16 dimensions. It demonstrated content validity. The aim of this study was to test its psychometric properties and to develop a final 64-items version (EPAT-64). Methods In this cross-sectional study, we included adult patients treated for cardiovascular diseases, cancer, musculoskeletal diseases, and mental disorders in inpatient or outpatient settings in Germany. For each dimension of PC, we selected four items based on item characteristics such as item difficulty and corrected item-total correlation. We tested structural validity using confirmatory factor analysis, examined reliability by McDondald's Omega, and tested construct validity by examining correlations with general health status and satisfaction with care. Results Analysis of data from 2.024 patients showed excellent acceptance and acceptable item-total-correlations for all EPAT-64 items, with few items demonstrating ceiling effects. The confirmatory factor analysis indicated the best fit of a bifactor model, where each item loaded on both a general factor and a dimension-specific factor. Omega showed high reliability for the general factor while varying for specific dimensions. Construct validity was confirmed by absence of strong correlations with general health status and a strong correlation of the general factor with satisfaction with care. Conclusions The EPAT-64 demonstrated commendable psychometric properties. This tool allows comprehensive assessment of PC, offering flexibility to users who can measure each dimension with a 4-item module or choose modules based on their needs. The EPAT-64 serves multiple purposes, including quality improvement initiatives and evaluation of interventions aiming to enhance PC. Its versatility empowers users in diverse healthcare settings. What is already known on this topic: Patient-reported experience measures (PREMs) can be used to assess patient-centeredness (PC) from the patients' perspective. The "Experienced Patient-Centeredness Questionnaire" (EPAT) is the first PREM to comprehensively assess 16 dimensions of PC. What this study adds: In this study, we tested the psychometric properties of all items developed for the EPAT and developed the 64-item version of the EPAT (EPAT-64), which demonstrated good psychometric properties. How this study might affect research, practice or policy: The EPAT-64 can be used in research and routine care, e.g. to evaluate interventions, provide feedback to healthcare professionals, support quality improvement, set benchmarks, and, consequently improve PC.
Probabilistic Evaluation of Fault Sources Based on Paleoseismic Evidence From Mass‐Transport Deposits: The Example of Aysén Fjord, Chile

Contemporaneous mass‐transport deposits (MTDs) recorded in lake and fjord sediments provide evidence of past seismic shaking. However, because they are usually not connected to a fault rupture, assessment of the earthquake source remains difficult. Based on observed coseismic mass wasting and associated seismic shaking, previous studies assigned minimum intensities required to trigger them. Attempts to infer their earthquake source relied on methods developed to estimate the location and magnitude of historical earthquakes using intensity prediction equations, but considered these thresholds as actual intensities. Here we develop a probabilistic method to infer the most likely earthquake sources from the spatial distribution (or absence) of MTDs. This approach simultaneously allows the triggering intensity to exceed the assumed threshold and takes into account intensity prediction equation uncertainties, two shortcomings of existing methods. Additionally, we consider known active faults rather than a grid of possible epicenters. We apply this method to Aysén Fjord (southern Chile), which is intersected by the Liquiñe‐Ofqui Fault Zone. In 2007, an MW = 6.2 earthquake hit the fjord with intensities of VIII+, causing major landslides entering the fjord. Seismic‐reflection profiles show that its sedimentary fill contains nine prehistoric MTD levels. Following a sensitivity analysis, application of the method to the MTD record allows identifying the most likely fault sections and magnitude range for most events, confirming that they are mainly attributed to crustal earthquakes on the Liquiñe‐Ofqui Fault Zone. We conclude that the method has good potential to constrain the size and location of paleoearthquakes for which only shaking evidence is available.
Ballistic tongue projection in chameleons maintains high performance at low temperature

Environmental temperature impacts the physical activity and ecology of ectothermic animals through its effects on muscle contractile physiology. Sprinting, swimming, and jumping performance of ectotherms decreases by at least 33% over a 10 °C drop, accompanied by a similar decline in muscle power. We propose that ballistic movements that are powered by recoil of elastic tissues are less thermally dependent than movements that rely on direct muscular power. We found that an elastically powered movement, ballistic tongue projection in chameleons, maintains high performance over a 20 °C range. Peak velocity and power decline by only 10%–19% with a 10 °C drop, compared to >42% for nonelastic, muscle-powered tongue retraction. These results indicate that the elastic recoil mechanism circumvents the constraints that low temperature imposes on muscle rate properties and thereby reduces the thermal dependence of tongue projection. We propose that organisms that use elastic recoil mechanisms for ecologically important movements such as feeding and locomotion may benefit from an expanded thermal niche.
Sexual Behaviors Over a 3-Year Period Among Individuals With Advanced HIV/AIDS Receiving Antiretroviral Therapy in an Urban HIV Clinic in Kampala, Uganda

Background:Few studies have prospectively examined sexual behaviors of HIV-infected person on antiretroviral therapy (ART) in sub-Saharan Africa. Methods:Between 2004 and 2005, 559 HIV-infected, ART-naïve individuals initiating ART at an HIV clinic in Kampala, Uganda, were enrolled into a prospective study and followed to 2008. Clinical and sexual behavior information was assessed at enrollment and semiannually for 3 years after ART initiation. Using log-binomial regression models, we estimated prevalence ratios (PRs) to determine factors associated with being sexually active and having unprotected sex over 3 years after initiating ART. Results:Five hundred fifty-nine adults contributed 2594 person-visits of follow-up. At the time of ART initiation, 323 (57.9%) were sexually active of which 176 (54.5%) had unprotected sex at last sexual intercourse. The majority (63.4%) of married individuals were unaware of their partner's HIV status. Female gender (PR, 2.97; 95% confidence interval, 1.85-4.79), being married (PR, 1.48; 95% confidence interval, 1.06-2.06), and reporting unprotected sex before ART (PR, 1.68; 95% confidence interval, 1.16-2.42) were among the factors independently associated with unprotected sex while on ART. Overall, 7.3% of visit intervals of unprotected sex, 1.0% of intervals of sexual activity, occurred when plasma viral load greater than 1500 copies/mL, representing periods of greater HIV transmission risk. Conclusions:Although unprotected sex reduced over time, women reported unprotected sex more often than men. Disclosure of HIV status was low. Integration of comprehensive prevention programs into HIV care is needed, particularly ones specific for women.
Prognostic difference between surgery and external radiation in patients with stage I liver cancer based on competitive risk model and conditional survival rate

Purpose This study aimed to assess the difference in prognosis of patients with early-stage liver cancer after surgery or external radiation. Methods Between 2010 and 2015, 2155 patients with AJCC 7th stage I liver cancer were enrolled in the SEER database. Among these, 1972 patients had undergone surgery and 183 had undergone external beam radiation. The main research endpoints were overall survival (OS) and disease-specific survival (DSS). The competitive risk model was used to calculate the risk ratio of liver cancer-specific deaths when there was a competitive risk. Propensity Score Matching (PSM) method using a 1:1 ratio was used to match confounders such as sex, age, and treatment method. Conditional survival was dynamically assessed for patient survival after surgery or external radiation. Results Multivariate analysis of the competitive risk model showed that age, disease diagnosis time, grade, and treatment [surgery and external beam radiation therapy (EBRT)] were independent prognostic factors for patients with hepatocellular carcinoma. Surgery had a higher survival improvement rate than that of EBRT. As the survival of patients with liver cancer increased, the survival curve of surgery declined more slowly than that of radiotherapy patients and stabilized around 3 years after surgery. The survival curve of radiotherapy patients significantly dropped within 4 years and then stabilized. Conclusion Surgery was better than EBRT for patients with stage I liver cancer. Close follow-up was required for 3 years after surgery or 4 years after external radiation. This study can help clinicians make better informed clinical decisions.
Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach

MOTIVATION Peak detection is a key step in the preprocessing of untargeted metabolomics data generated from high-resolution liquid chromatography-mass spectrometry (LC/MS). The common practice is to use filters with predetermined parameters to select peaks in the LC/MS profile. This rigid approach can cause suboptimal performance when the choice of peak model and parameters do not suit the data characteristics. RESULTS Here we present a method that learns directly from various data features of the extracted ion chromatograms (EICs) to differentiate between true peak regions from noise regions in the LC/MS profile. It utilizes the knowledge of known metabolites, as well as robust machine learning approaches. Unlike currently available methods, this new approach does not assume a parametric peak shape model and allows maximum flexibility. We demonstrate the superiority of the new approach using real data. Because matching to known metabolites entails uncertainties and cannot be considered a gold standard, we also developed a probabilistic receiver-operating characteristic (pROC) approach that can incorporate uncertainties. AVAILABILITY AND IMPLEMENTATION The new peak detection approach is implemented as part of the apLCMS package available at http://web1.sph. emory.edu/apLCMS/ CONTACT: tyu8@emory.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Transfer learning from rating prediction to Top-k recommendation

Recommender system has made great strides in two major research fields, rating prediction and Top-k recommendation. In essence, rating prediction is a regression task, which aims to predict users scores on other items, while Top-k is a classification task selecting the items that users have the most potential to interact with. Both characterize users and items, but the optimization of parameters varies widely for their respective tasks. Inspired by the idea of transfer learning, we consider extracting the information learned from rating prediction models for serving for Top-k tasks. To this end, we propose a universal transfer model for recommender systems. The transfer model consists of two sub-components: quadruple-based Bayesian Converter (BC) and Prediction-based Multi-Layer Perceptron (PMLP). As the main part, BC is responsible for transforming the feature vectors extracted from the rating prediction model. Meanwhile, PMLP extracts the prediction ratings, constructs the prediction rating matrix, and uses multi-layer perceptron to enhance the final performance. On four benchmark datasets, we use the information extracted from the singular value decomposition plus plus (SVD++) model to demonstrate the effectiveness of BC-PMLP, comparing to classical and state-of-the-art baselines. We also conduct extra experiments to verify the utility of BC, and performance within different parameter values.
Neurodegeneration-related genes influence C. elegans pharyngeal activity

Pharyngeal pumping and its reduction following mechanical insult are well-studied C. elegans behaviors. Here, we assessed new applications of pharyngeal pumping assays in the study of neurodegenerative disease and psychiatric illness. We examined five genes implicated in two forms of neurodegeneration, Hereditary Spastic Paraplegia (HSPs) and Alzheimer’s Disease (AD), for both baseline pharyngeal pumping and the depressive response after touch stimulus. All five mutants showed reduced baseline pumping rate, suggesting a potential utility of this assay to study neurodegenerative disease on a broad scale. However, regarding the induced pumping response, which has been linked to schizophrenia, only specific genes, the HSP-related atln-1/ Atlastin and the AD-related ptl-1/ tau, showed defects. Together, we highlight two pharyngeal pumping behaviors as genetically distinct, potentially informative settings for understanding the functions of genes linked to neurodegeneration.
The Importance of the Volatility Risk Premium for Volatility Forecasting

In this paper, we study the role of the volatility risk premium for the forecasting performance of implied volatility. We introduce a non-parametric and parsimonious approach to adjust the model-free implied volatility for the volatility risk premium and implement this methodology using more than 20 years of options and futures data on three major energy markets. Using regression models and statistical loss functions, we find compelling evidence to suggest that the risk premium adjusted implied volatility significantly outperforms other models, including its unadjusted counterpart. Our main finding holds for different choices of volatility estimators and competing time-series models, underlying the robustness of our results.
Self-reported pain severity and use of cannabis and opioids in persons with HIV in an urban primary care setting in Northern California: A cross-sectional study

Persons with HIV (PWH) experience high levels of pain. We examined the relationship of pain severity with use of cannabis and prescription opioids among PWH. This cross-sectional study evaluated associations between self-reported pain (moderate/severe vs mild/none) and cannabis and prescription opioid use in a primary care sample of PWH enrolled in an alcohol use treatment study at Kaiser Permanente, San Francisco. Prevalence ratios (PR) for moderate/severe pain associated with cannabis, opioid use, or both in the prior 30 days were obtained from Poisson regression models. Adjusted models included race/ethnicity, education, employment, HIV ribonucleic acid levels, depression, and anxiety. Overall, 614 PWH completed baseline questionnaires from May 2013 to May 2015, among whom 182/614 (29.6%) reported moderate/severe pain. The prevalence of moderate/severe pain varied by substances: 19.1% moderate/severe pain among study participants who reported neither cannabis or opioids, 30.2% for cannabis alone, 41.2% for opioids alone, and 60.9% for those reporting both substances. In adjusted models, compared with PWH who reported neither substance (reference), prevalence of moderate/severe pain was higher for those using cannabis alone (PR 1.54; 95% CI 1.13–2.09), opioids alone (PR 1.96; 95% CI 1.31–2.94), and those reporting both (PR 2.66; 95% CI 1.91–3.70). PWH who reported opioid and/or cannabis use were more likely to report moderate/severe pain compared with PWH who did not report use of these substances. To improve patient care, it is vital to assess patients’ approaches to pain management including substance use and target appropriate interventions to reduce pain in PWH.
Internalization, qualitative methods, and evaluation

Information Visualization (InfoVis) is at least in part defined by a process that occurs within the subjective internal experience of the users of visualization tools. Hence, users' interaction with these tools is seen as an 'experience'. Relying on standard quantitative usability measures evaluates the interface. Yet, there is more to users' interaction with InfoVis tools than merely the interface. Qualitative methods targets users' subjective experiences. In this paper we demonstrate the potential benefits of qualitative methods, more specifically Grounded Theory, for generating a theoretical understanding of users' InfoVis experiences through discussing the results of a qualitative study we conducted. The study was conducted in order to evaluate a visualization of the academic literature domain, which we have designed and built using a user-centered design approach. The study resulted in us identifying categories that are essential to the InfoVis experience. This paper argues that these categories can be used as a foundation for building an InfoVis theory of interaction.
Plant nutrient removal and soil residual chemical properties as impacted by maize planting date and density

This study aimed to measure maize (Zea mays) plant nutrient content and nutrient removal in grain, and to evaluate the residual soil nitrogen, phosphorus, and potassium as impacted by planting date and density. Field experiments were conducted to evaluate six plant densities and seven planting dates using a split-split plot design with three replications. Besides the crop growth and yield parameters, six plants were collected at the maturity and soil was sampled from each plot for nutrient analysis. Plant N, P, and K concentrations varied with planting date and density and within the ranges of 0.6–1.024%, 0.054–0.127%, and 0.75–1.71%, respectively. Grain N, P, and K concentrations decreased with plant density and varied from 1.059 to 1.558%, 0.20 to 0.319%, and 0.29 to 0.43%, respectively. Soil residual nutrient varied with depth, planting density and date. Residual N concentration in the topsoil varied from 0.6 to 37.2 mg kg-1 in 2019 and from 1.5 to 11.2 mg kg-1 in 2020 and was high under the last two planting dates. Soil residual N concentration was higher in the second layer than in the topsoil. The N concentration in the third layer varied from 0.1 to 33.2 mg kg-1 and was impacted by plant density. Topsoil P did not vary among planting dates and densities. The second and third soil layers P concentration was not affected. There was 83% increase in topsoil K in 2020 compared to 2019, and a decrease of 65 and 23% in soil K was observed in the second and third soil layers, respectively. For maize production system sustainability, future research should use a holistic approach investigating the impact of planting date, plant density on crop growth, yield, nutrient uptake and remobilization, and soil properties under different fertilizer rates to develop the fertilizer recommendation for maize while reducing the environmental impact of the production system.
Tuning Windowed Chi-Squared Detectors for Sensor Attacks

A model-based windowed chi-squared procedure is proposed for identifying falsified sensor measurements. We employ the widely-used static chi-squared and the dynamic cumulative sum (CUSUM) fault/attack detection procedures as benchmarks to compare the performance of the windowed chi-squared detector. In particular, we characterize the state degradation that a class of attacks can induce to the system while enforcing that the detectors do not raise alarms (zero-alarm attacks). We quantify the advantage of using dynamic detectors, which leverage the history of the state, over a static detectors which uses a single measurement at a time. Simulations using a chemical reactor are presented to illustrate the performance of our tools.