Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV, multimorbidity, and health-related quality of life in rural KwaZulu-Natal, South Africa: A population-based study

Health-related quality of life (HRQoL) assesses the perceived impact of health status across life domains. Although research has explored the relationship between specific conditions, including HIV, and HRQoL in low-resource settings, less attention has been paid to the association between multimorbidity and HRQoL. In a secondary analysis of cross-sectional data from the Vukuzazi (“Wake up and know ourselves” in isiZulu) study, which identified the prevalence and overlap of non-communicable and infectious diseases in the uMkhanyakunde district of KwaZulu-Natal, we (1) evaluated the impact of multimorbidity on HRQoL; (2) determined the relative associations among infectious diseases, non-communicable diseases (NCDs), and HRQoL; and (3) examined the effects of controlled versus non-controlled disease on HRQoL. HRQoL was measured using the EQ-5D-3L, which assesses overall perceived health, five specific domains (mobility, self-care, usual activities, pain/discomfort, and anxiety/depression), and three levels of problems (no problems, some problems, and extreme problems). Six diseases and disease states were included in this analysis: HIV, diabetes, stroke, heart attack, high blood pressure, and TB. After examining the degree to which number of conditions affects HRQoL, we estimated the effect of joint associations among combinations of diseases, each HRQoL domain, and overall health. Then, in one set of ridge regression models, we assessed the relative impact of HIV, diabetes, stroke, heart attack, high blood pressure, and tuberculosis on the HRQoL domains; in a second set of models, the contribution of treatment (controlled vs. uncontrolled disease) was added. A total of 14,008 individuals were included in this analysis. Having more conditions adversely affected perceived health (r = -0.060, p<0.001, 95% CI: -0.073 to -0.046) and all HRQoL domains. Infectious conditions were related to better perceived health (r = 0.051, p<0.001, 95% CI: 0.037 to 0.064) and better HRQoL, whereas non-communicable diseases (NCDs) were associated with worse perceived health (r = -0.124, p<0.001, -95% CI: 0.137 to -0.110) and lower HRQoL. Particular combinations of NCDs were detrimental to perceived health, whereas HIV, which was characterized by access to care and suppressed viral load in the large majority of those affected, was counterintuitively associated with better perceived health. With respect to disease control, unique combinations of uncontrolled NCDs were significantly related to worse perceived health, and controlled HIV was associated with better perceived health. The presence of controlled and uncontrolled NCDs was associated with poor perceived health and worse HRQoL, whereas the presence of controlled HIV was associated with improved HRQoL. HIV disease control may be critical for HRQoL among people with HIV, and incorporating NCD prevention and attention to multimorbidity into healthcare strategies may improve HRQoL.
Associations of thyroid feedback quantile-based index with diabetes in euthyroid adults in the United States and China

Abstract Background We aimed to investigate the associations between thyroid hormone sensitivity indices and diabetes in euthyroid adults in the United States and China. Methods 2296 euthyroid adults from the NHANES in the United States and 8319 euthyroid adults from the SPEED-Shunde in China were involved. The thyroid sensitivity indices, namely TFQIFT4 and TFQIFT3, were calculated. Multivariable logistic regression, restricted cubic spline analysis, and general ordinal logit regression were utilized. Results In the NHANES, compared with participants in quartile 1st (Q1), those in Q4 of TFQIFT3 (OR 2.12, 95% CI (1.18, 3.81)) and those in Q3 of TFQIFT4 (OR 2.31, 95% CI (1.18, 4.53)) (both P for trend < 0.05) were associated with a greater prevalence of diabetes. In the SPEED-Shunde, compared with participants in Q1, those in Q4 of TFQIFT3 had a greater prevalence of diabetes (OR 1.36, 95% CI (1.11, 1.66) (P for trend < 0.05), while no significant associations between TFQIFT4 and diabetes were found. Conclusions TFQIFT3 was associated with a higher prevalence of diabetes both in the United States and China. However, TFQIFT4 was only associated with a higher prevalence of diabetes in the United States, not in China. Further prospective cohort studies are necessary to validate these findings.
ADH-Enhancer: an attention-based deep hybrid framework for enhancer identification and strength prediction

Abstract Enhancers play an important role in the process of gene expression regulation. In DNA sequence abundance or absence of enhancers and irregularities in the strength of enhancers affects gene expression process that leads to the initiation and propagation of diverse types of genetic diseases such as hemophilia, bladder cancer, diabetes and congenital disorders. Enhancer identification and strength prediction through experimental approaches is expensive, time-consuming and error-prone. To accelerate and expedite the research related to enhancers identification and strength prediction, around 19 computational frameworks have been proposed. These frameworks used machine and deep learning methods that take raw DNA sequences and predict enhancer’s presence and strength. However, these frameworks still lack in performance and are not useful in real time analysis. This paper presents a novel deep learning framework that uses language modeling strategies for transforming DNA sequences into statistical feature space. It applies transfer learning by training a language model in an unsupervised fashion by predicting a group of nucleotides also known as k-mers based on the context of existing k-mers in a sequence. At the classification stage, it presents a novel classifier that reaps the benefits of two different architectures: convolutional neural network and attention mechanism. The proposed framework is evaluated over the enhancer identification benchmark dataset where it outperforms the existing best-performing framework by 5%, and 9% in terms of accuracy and MCC. Similarly, when evaluated over the enhancer strength prediction benchmark dataset, it outperforms the existing best-performing framework by 4%, and 7% in terms of accuracy and MCC.
Optimum rotation for harvesting of cajuput leave at KPH Yogyakarta

The productivity of cajuput plantation has improved through tree breeding, while manipulation of site and management engineering of timber plantations have been less attention. Management engineering can be obtained by determining the optimum cycle of cajuput leaves harvesting. This study aims to determine the optimum cycling of cajuput leaves harvesting at KPH Yogyakarta by considering the biological cycles of cajuput leaves, chemical physical properties, and the yield of cajuput oil. The tools used in the research were digital scales, distillation devices, and testing tools of physical-chemical properties of cajuput oil. The material for research was the cajuput plants at KPH Yogyakarta. Data of cajuput leave-twig biomass were obtained for 9 months from 9 plots which were well distributed on various ages. Biological cycle analysis uses curent monthly increment (CMI) and mean monthly increment (MMI) intersection approach. Analysis of the physical-chemical properties on cajuput oil refers to SNI 3954:2014 on cajuput oil. The results showed that the biological cycles of cajuput leaves were obtained 5 months after leaves harvesting. The chemical physical properties of cajuput oil that meet the requirements of SNI were achieved after the leaves are 7 months after harvested. The yield of cajuput oil which is above 0.7% was obtained after the leaves are 8 months after harvested. Thus, the optimum cycle for harvesting of cajuput leaves in KPH Yogyakarta is after 8 months.
Molecular Biomonitoring of Microbial Communities in Tannery Wastewater Treatment Plant for the Removal of Retanning Chemicals

This chapter focuses on culture-independent characterization and monitoring of microbial communities in tannery wastewater treatment system, with special reference to the degradation of two xenobiotic chemicals used in retanning processes. Molecular survey of a tannery wastewater treatment system through metagenomic and metatranscriptomic approaches revealed a diverse microbial community in each component of the treatment system with high gene copies for enzymes involved in the degradation of cyclic aromatic compounds such as nitrotoluene. A combination of flow cytometry and molecular fingerprinting methods was used in a lab-scale reactor to monitor the dynamics of the microbes in the sludge and the fate of two retanning chemicals. The identified key microbial communities for the removal of the two xenobiotic chemicals belong to members of the group Proteobacteria and the phylum Bacteroidetes.
Effect of a smart temperature logger on correctly storing biological disease-modifying antirheumatic drugs at home: a pre-post study.

OBJECTIVES Biological disease-modifying antirheumatic drugs (bDMARDs) require specific storage temperatures, but are frequently stored outside the recommended range of 2-8°C. As incorrect storage may affect therapy effectiveness and consequently lead to higher disease activity, compliance with recommended storage temperatures should be improved. eHealth interventions can provide insight into storage temperatures and alerts in case of deviations from recommended temperatures. Therefore, this study aims to assess the effect of a smart temperature logger on correctly storing bDMARDs at home by patients with rheumatic diseases. METHODS A pre-post study was performed in a hospital in the Netherlands. The baseline period consisted of 12 weeks of storage temperature measurement with a passive temperature logger, and the intervention period consisted of 12 weeks of storage temperature measurement with a smart temperature logger. This smart logger included a smartphone application which provided insight into storage temperatures and real-time alerts when exceeding recommended temperatures. The main outcome measure was the difference in the number of patients who stored their bDMARDs correctly between baseline and intervention. Secondary outcomes were the difference in the proportion of measurement time within 2-8°C between baseline and intervention, the distribution of measurement time among temperature categories, and the patient's acceptance measured using a questionnaire based on the Technology Acceptance Model. RESULTS In total, 48 participants (median age 55 years (IQR 47-64), 53% male) were analysed. The proportion of participants correctly storing bDMARDs increased from 18.8% (n=9) during baseline to 39.6% (n=19) during intervention (p=0.004). The median proportion of measurement time between 2-8°C improved by 6% (IQR 0-34%) (p<0.0001). Technology acceptance was scored as moderate. CONCLUSIONS Temperature monitoring and real-time feedback with a smart temperature logger shows potential to improve at-home storage of bDMARDs, provided that continuous connection is realised to ensure real-time alerts and data collection.
Calculating high-pressure vibrational frequencies analytically with the extended hydrostatic compression force field approach.

We report the implementation of the analytical Hessian for the mechanochemical extended hydrostatic compression force field method in the Q-Chem program package. To verify the implementation, the analytical Hessian was compared with finite difference calculations. In addition, we calculated the pressure dependency of the Raman active vibrational modes of methane, ethane, and hydrogen, as well as all IR and Raman active modes of Buckminsterfullerene, and compared the results with experimental and theoretical data. Our implementation paves the way for the analysis of geometric points on a pressure-deformed potential energy surface and provides a straightforward model to calculate the vibrational properties of molecules under high pressure.
Solar cycle variations in the ionosphere of Mars

Solar cycle variations in solar radiation create notable changes in the Martian ionosphere, which have been analysed with Mars Express plasma datasets in this paper. In general, lower densities and temperatures of the ionosphere are found during the low solar activity phase, while higher densities and temperatures are found during the high solar activity phase. In this paper, we assess the degree of influence of the long term solar flux variations in the ionosphere of Mars.
Equivalent Circuit Models of Finite Slot Antennas

We present a systematic approach to describe planar slot antennas embedded in generic stratified media. An equivalent transmission line model for the slot is proposed, based on a spectral domain analysis. First, we introduce a method of moments solution to model semiinfinite or finite slots, fed by a delta-gap excitation. The solution entails only two basis functions, one located at the feed and the other at the termination. The latter basis function is chosen to properly account for the field diffractive behavior at the antenna end points. An approximate circuit model is then introduced, which describes the main mode propagating along the slot as an equivalent transmission line. Lumped impedances are extracted to accurately describe the source and the end points: the reactances account for the reactive nature of the feed and the termination, while the resistances represent the radiated space waves, emerging from both the feed and the end points. This procedure can be used to derive the input impedance of planar slot antennas with arbitrary length in generic layered media or the interaction between multiple feeds within the same slot.
Species sensitivities to artificial light at night: A phylogenetically controlled multilevel meta-analysis on melatonin suppression.

The rapid urbanization of our world has led to a surge in artificial lighting at night (ALAN), with profound effects on wildlife. Previous research on wildlife's melatonin, a crucial mechanistic indicator and mediator, has yielded inconclusive evidence due to a lack of comparative analysis. We compiled and analysed an evidence base including 127 experiments with 437 observations across 31 wild vertebrates using phylogenetically controlled multilevel meta-analytic models. The evidence comes mainly from the effects of white light on melatonin suppression in birds and mammals. We show a 36% average decrease in melatonin secretion in response to ALAN across a diverse range of species. This effect was observed for central and peripheral melatonin, diurnal and nocturnal species, and captive and free-living populations. We also reveal intensity-, wavelength-, and timing-dependent patterns of ALAN effects. Exposure to ALAN led to a 23% rise in inter-individual variability in melatonin suppression, with important implications for natural selection in wild vertebrates, as some individuals may display higher tolerance to ALAN. The cross-species evidence has strong implications for conservation of wild populations that are subject to natural selection of ALAN. We recommend measures to mitigate harmful impacts of ALAN, such as using 'smart' lighting systems to tune the spectra to less harmful compositions.
Chromosome structure modeling tools and their evaluation in bacteria

Abstract The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.
Wild fish consumption and latitude as drivers of vitamin D status among Inuit living in Nunavik, northern Québec

Objective: To measure vitamin D status and estimate factors associated with serum 25-hydroxyvitamin D (25(OH)D) in Nunavimmiut (Inuit living in Nunavik) adults in 2017. Design: Data were from Qanuilirpitaa? 2017 Nunavik Inuit Health Survey, a cross-sectional study conducted in August–October 2017. Participants underwent a questionnaire, including an FFQ, and blood samples were analysed for total serum 25(OH)D. Setting: Nunavik, northern Québec, Canada. Participants: A stratified proportional model was used to select respondents, including 1,155 who identified as Inuit and had complete data. Results: Geometric mean serum vitamin D levels were 65·2 nmol/l (95 % CI 62·9–67·6 nmol/l) among women and 65·4 nmol/l (95 % CI 62·3–68·7 nmol/l) among men. The weighted prevalence of serum 25(OH)D < 75 nmol/l, <50 nmol/l <30 nmol/l was 61·2 %, 30·3 % and 7·0 %, respectively. Individuals who were older, female, lived in smaller and/or more southerly communities and/or consumed more country (traditional) foods were at a reduced risk of low vitamin D status. Higher consumption of wild fish was specifically associated with increased serum 25(OH)D concentration. Conclusion: It is important that national, regional and local policies and programs are in place to secure harvest, sharing and consumption of nutritious and culturally important country foods like Arctic char and other wild fish species, particularly considering ongoing climate change in the Arctic which impacts the availability, access and quality of fish as food.
[Effect of Aging on the Mechanical Properties of CAD/CAM-Milled and 3D-Printed Acrylic Resins for Denture Bases].

PURPOSE The purpose of this study was to investigate the mechanical properties of acrylic resins at different aging times for denture bases manufactured using the conventional method, microwave processing, milling, and 3D printing. MATERIALS AND METHODS A total of 160 rectangular samples (64 Å~ 10 Å~ 3.3 ± 0.03 mm) were prepared, divided among the four main resin groups, and subdivided into four analysis times (T0, T1, T2, and T3), resulting in 10 samples per subgroup. The samples were stored in distilled water at 37° ± 2°C for 24 hours (T0), then subjected to thermocycling at temperatures of 5° ± 1°C and 55° ± 1°C in different numbers of cycles: 5,000 (T1); 10,000 (T2); and 20,000 (T3). The mechanical properties evaluated were surface microhardness, flexural strength, and modulus of elasticity. Statistical differences between resin groups and aging time were evaluated using two-way analysis of variance (P < .05). RESULTS The 3D-printed resin showed the significantly lowest values of microhardness, flexural strength, and modulus of elasticity compared to other resins (P < .001). CONCLUSIONS The CAD/CAM-milled denture resin showed mechanical properties similar to those of traditional resins (conventional and microwave-processed). The 3D-printing resin did not show adequate mechanical properties for long-term clinical use. Despite this, new studies are developing better properties of this resin for long-term use.
Microseismic multiplets in the northeastern Bohemian Massif

We have analysed >1800 records of very weak microearthquakes (-1.9 12 years) and time distributions of the events. The magnitude-distribution of events from individual re-activated foci obeys Gutenberg-Richter law at least in the magnitude range -1.3<=ML&<=1.3. The typical b-values are close to b=1, which also applies for the whole catalogue of events located in the region. In this respect, the investigated region is similar to other presently deformed regions where seismicity is controlled by far-field stresses. Based on the fault geometry, the evolution of sedimentary basin in the most active part of the region, and the spatial co-incidence of the earthquake epicentres with carbonated mineral springs in a rhomb-shaped domain, we suggest a preliminary model explaining the studied region as a transfer zone with releasing geometry (pull-apart mechanism), operating within the system of dextral wrench faults.
Yoga Therapy as an Intervention to Improve Patient-Reported Outcomes Among Adults After Treatment for Cancer: Preliminary Findings From a Trial Using Single-Subject Experimental Design

Background: Cancer is a chronic condition associated with a substantial symptom burden, which can impair recovery after treatment. Investigating interventions with potential to improve self-reported disease and/or treatment effects—known as patient-reported outcomes (PROs)—is paramount to inform cancer care. The objective of this study was to evaluate the effects of a yoga therapy (YT) intervention on key PROs (ie, cancer-related fatigue, anxiety, cognitive function, depression, stress, quality of life [QoL]) among adults after treatment for cancer. Methods: Data from 20 adults (Mage = 55.74 years, 85% female; Mtime since diagnosis = 2.83 years) who had completed treatment for cancer were analyzed for this study. In this single-subject exploratory experimental study, the YT intervention comprised a 1:1 YT session (ie, 1 participant with 1 yoga therapist) followed by 6 weekly small (ie, 2–3 participants) group YT sessions. Group sessions were facilitated by the same yoga therapist who delivered participants’ 1:1 session to ensure an in-depth personalized approach. PROs were assessed before (ie, pre-intervention) and after the 1:1 YT session (ie, during the intervention), as well as after the last group YT session (ie, post-intervention). Hierarchical linear modeling was used to analyze the data. Results: Participants showed improvements in cancer-related fatigue, state anxiety, trait anxiety, perceived cognitive impairments, impacts of perceived cognitive impairments on QoL, and 1 dimension of QoL (ie, functional wellbeing) over time. Notably, cancer-related fatigue and state anxiety increased immediately after the 1:1 session, but showed greater improvements over time afterward (ie, during the intervention phase). No changes were observed for the remaining PROs. Conclusion: Although results require confirmation in future trials, this study highlights the importance of continuing to investigate YT as an intervention to enhance important PROs (ie, cancer-related fatigue and state anxiety) after treatment for cancer. More research is needed to identify additional beneficial effects and factors that influence participants’ responses to 1:1 and group YT (ie, moderators and mediators). Registration number: ISRCTN64763228 Date of registration: December 12, 2021. This trial was registered retrospectively. URL of trial registry record: https://www.isrctn. com/ISRCTN64763228 Published Protocol: Brunet, J., Wurz, A. , Hussien, J., Pitman, A. , Conte, E. , Ennis, J. K. , . & Seely, D. (2022). Exploring the Effects of Yoga Therapy on Heart Rate Variability and Patient-Reported Outcomes After Cancer Treatment: A Study Protocol. Integrative Cancer Therapies, 21, 15347354221075576.