Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and determinants of depressive symptoms among adults in Indonesia: A cross-sectional population-based national survey.

AIMS To analyze the association between personal health conditions (self-rated health, physical function, and chronic conditions) and symptoms of depression in Indonesia. METHODS Data were collected from the Indonesian family life survey 5. This study used a cross-sectional study design with a sample size of 17,734 respondents. We included depressive symptoms, self-rated health, physical function, chronic conditions, demographics and socioeconomic variables. The center for epidemiologic studies depression scale was used to measure symptoms of depression. Multivariate logistic regression analysis was used to analyze the data. RESULTS The results showed that 23.47% of respondents had depressive symptoms, 20.04% had poor self-rated health, 55.93% had a poor physical function, and 32.37% had at least one chronic disease. Respondents who had poor self-rated health, had poor physical function, or had a chronic condition were all had a significantly higher odds of experiencing symptoms of depression after controlling for demographic variables (age, sex, married, and education level), social-economic, and smoking status. CONCLUSION Depressive symptoms were significantly associated with personal health conditions including self-rated health, physical functioning, and chronic conditions among community residents. Strategies that can improve personal health conditions needed to be studied at the community level to improve the level of mental health.
Amidochelocardin Overcomes Resistance Mechanisms Exerted on Tetracyclines and Natural Chelocardin

The reassessment of known but neglected natural compounds is a vital strategy for providing novel lead structures urgently needed to overcome antimicrobial resistance. Scaffolds with resistance-breaking properties represent the most promising candidates for a successful translation into future therapeutics. Our study focuses on chelocardin, a member of the atypical tetracyclines, and its bioengineered derivative amidochelocardin, both showing broad-spectrum antibacterial activity within the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) panel. Further lead development of chelocardins requires extensive biological and chemical profiling to achieve favorable pharmaceutical properties and efficacy. This study shows that both molecules possess resistance-breaking properties enabling the escape from most common tetracycline resistance mechanisms. Further, we show that these compounds are potent candidates for treatment of urinary tract infections due to their in vitro activity against a large panel of multidrug-resistant uropathogenic clinical isolates. In addition, the mechanism of resistance to natural chelocardin was identified as relying on efflux processes, both in the chelocardin producer Amycolatopsis sulphurea and in the pathogen Klebsiella pneumoniae. Resistance development in Klebsiella led primarily to mutations in ramR, causing increased expression of the acrAB-tolC efflux pump. Most importantly, amidochelocardin overcomes this resistance mechanism, revealing not only the improved activity profile but also superior resistance-breaking properties of this novel antibacterial compound.
Identification and validation of a novel anti-virulent that binds to pyoverdine and inhibits its function

ABSTRACT Pseudomonas aeruginosa: causes serious infections in patients with compromised immune systems and exhibits resistance to multiple antibiotics. The rising threat of antimicrobial resistance means that new methods are necessary for treating microbial infections. We conducted a high-throughput screen for compounds that can quench the innate fluorescence of the chromophore region of the P. aeruginosa siderophore pyoverdine, a key virulence factor. Several hits were identified that effectively quench pyoverdine fluorescence, and two compounds considerably improved the survival of Caenorhabditis elegans when worms were challenged with P. aeruginosa. Commercially available analogs of the best hit, PQ3, were tested for their ability to rescue C. elegans from P. aeruginosa and to interact with pyoverdine via fluorescence and solution NMR spectroscopy. 1H-15N and 1H-13C HSQC NMR were used to identify the binding site of PQ3c. The structure model of pyoverdine in complex with PQ3c was obtained using molecular docking and molecular dynamics simulations. PQ3c occupied a shallow groove on pyoverdine formed by the chromophore and N-terminal residues of the peptide chain. Electrostatic interactions and π-orbital stacking drove stabilization of this binding. PQ3c may serve as a scaffold for the development of pyoverdine inhibitors with higher potency and specificity. The discovery of a small-molecule binding site on apo-pyoverdine with functional significance provides a new direction in the search of therapeutically effective reagent to treat P. aeruginosa infections. Abbreviations: NMR: nuclear magnetic resonance; SAR: structure–activity relationship; MD: molecular dynamics; RMSF: root-mean-square fluctuation; HSQC: heteronuclear single quantum correlation; DMSO: dimethyl sulfoxide; Δδavg: average amide chemical shift change; DSS: 2,2-dimethyl-2-silapentane-5-sulfonate; RMSD: root-mean-square deviation; LJ-SR: Lennard–Jones short-range; Coul-SR: Coulombic short-range; FRET: fluorescence resonance energy transfer
Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes

The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
Game-Based Meditation Therapy to Improve Posttraumatic Stress and Neurobiological Stress Systems in Traumatized Adolescents: Protocol for a Randomized Controlled Trial

Background Many adolescents in residential care have been exposed to prolonged traumatic experiences such as violence, neglect, or abuse. Consequently, they suffer from posttraumatic stress. This not only negatively affects psychological and behavioral outcomes (eg, increased anxiety, depression, and aggression) but also has adverse effects on physiological outcomes, in particular on their neurobiological stress systems. Although current evidence-based treatment options are effective, they have their limitations. An alternative to traditional trauma treatment is meditation-based treatment that focuses on stress regulation and relaxation. Muse is a game-based meditation intervention that makes use of adolescents’ intrinsic motivation. The neurofeedback element reinforces relaxation abilities. Objective This paper describes the protocol for a randomized controlled trial in which the goal is to examine the effectiveness of Muse (InteraXon Inc) in reducing posttraumatic stress and normalizing neurobiological stress systems in a sample of traumatized adolescents in residential care. Methods This will be a multicenter, multi-informant, and multimethod randomized controlled trial. Participants will be adolescents (N=80), aged 10 to 18 years, with clinical levels of posttraumatic symptoms, who are randomized to receive either the Muse therapy sessions and treatment as usual (intervention) or treatment as usual alone (control). Data will be collected at 3 measurement instances: pretest (T1), posttest (T2), and at 2-month follow-up. Primary outcomes will be posttraumatic symptoms (self-report and mentor report) and stress (self-report) at posttest. Secondary outcomes will be neurobiological stress parameters under both resting and acute stress conditions, and anxiety, depression, and aggression at posttest. Secondary outcomes also include all measures at 2-month follow-up: posttraumatic symptoms, stress, anxiety, depression aggression, and neurobiological resting parameters. Results The medical-ethical committee Arnhem-Nijmegen (NL58674.091.16) approved the trial on November 15, 2017. The study was registered on December 2, 2017. Participant enrollment started in January 2018, and the results of the study are expected to be published in spring or summer 2021. Conclusions Study results will demonstrate whether game-based meditation therapy improves posttraumatic stress and neurobiological stress systems, and whether it is more effective than treatment as usual alone for traumatized adolescents. Trial Registration Netherlands Trial Register NL6689 (NTR6859); https://www.trialregister. nl/trial/6689 International Registered Report Identifier (IRRID) DERR1-10.2196/19881
A Time-Lagged Examination of the Greenhaus and Allen Work-Family Balance Model

The work-family interface is a compelling topic that calls into question labor market dynamics and work processes, together with important social and family composition changes. The present study aimed at examining the antecedents of Work-Family Balance (WFB) in Italy consistent with Greenhaus and Allen’s (2011) conceptual model in which the characteristics of work and family roles have an indirect impact on work-family balance through Work-Family Conflict (WFC) and Work-Family Enrichment (WFE), and where job and family satisfaction are considered as predictors of WFB. A total of 568 workers participated in a time-lagged correlational study, filling a questionnaire. The theoretical model was tested by assessing the mediating role of job and family satisfaction as well as related antecedents, conflict, and enrichment between the family and work contexts, through Structural Equation Modeling (SEM). The results partially confirmed the theoretical model: work-to-family enrichment and work-to-family conflict predicted family satisfaction, which also mediated their association with WFB. The results in the family-to-work direction did not support the initial research hypotheses. The hypotheses about associations between demands and resources, conflict and enrichment in both directions, and of the moderating role of core self-evaluations were partially confirmed. The results highlighted that organizations need to carry out periodic assessments of WFC and WFE, in order to provide benefits and resources, to reduce conflict, and increase enrichment, through proper interventions (training activities, professional development, mentoring, and forms of flexibility).
Towards an interpretable classifier for characterization of endoscopic Mayo scores in ulcerative colitis using Raman Spectroscopy.

Ulcerative colitis (UC) is one of the main types of chronic inflammatory diseases that affect the bowel, but its pathogenesis has yet to be completely defined. Assessing the disease activity of UC is vital for developing a personalized treatment. Conventionally, the assessment of UC is performed by colonoscopy and histopathology. However, conventional methods fail to retain biomolecular information associated to the severity of UC and are solely based on morphological characteristics of the inflamed colon. Further, assessing endoscopic disease severity is limited by the requirement for experienced human reviewers. Therefore, this work presents a non-destructive bio-spectroscopic technique, e.g. Raman spectroscopy, for assessing endoscopic disease severity according to the four-level Mayo subscore. This contribution utilizes the multi-dimensional Raman spectroscopic data to generate a predictive model for identifying colonic inflammation. The predictive modelling of the Raman spectroscopic data is performed using a one-dimensional deep convolutional neural network (1D-CNN). The classification results of 1D-CNN achieved a mean sensitivity of 78% and a mean specificity of 93% for the four Mayo endoscopic scores. Furthermore, the results of the 1D-CNN are interpreted by a first-order Taylor expansion, which extracts the Raman bands important for classification. Additionally, a regression model of the 1D-CNN model is constructed to study the extent of misclassification and border-line patients. The overall results of Raman spectroscopy with 1D-CNN as classification and regression model show a good performance, and such method can serve as a complementary method for UC analysis.
NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning

The NineTeen Complex (NTC), also known as pre-mRNA-processing factor 19 (Prp19) complex, regulates distinct spliceosome conformational changes necessary for splicing. During Drosophila midblastula transition, splicing is particularly sensitive to mutations in NTC-subunit Fandango, which suggests differential requirements of NTC during development. We show that NTC-subunit Salsa, the Drosophila ortholog of human RNA helicase Aquarius, is rate-limiting for splicing of a subset of small first introns during oogenesis, including the first intron of gurken. Germline depletion of Salsa and splice site mutations within gurken first intron impair both adult female fertility and oocyte dorsal–ventral patterning, due to an abnormal expression of Gurken. Supporting causality, the fertility and dorsal–ventral patterning defects observed after Salsa depletion could be suppressed by the expression of a gurken construct without its first intron. Altogether, our results suggest that one of the key rate-limiting functions of Salsa during oogenesis is to ensure the correct expression and efficient splicing of the first intron of gurken mRNA. Retention of gurken first intron compromises the function of this gene most likely because it undermines the correct structure and function of the transcript 5′UTR.
Coupled intra- and interdomain dynamics support domain cross-talk in Pin1

The functional mechanisms of multidomain proteins often exploit interdomain interactions, or “cross-talk. ” An example is human Pin1, an essential mitotic regulator consisting of a Trp–Trp (WW) domain flexibly tethered to a peptidyl-prolyl isomerase (PPIase) domain, resulting in interdomain interactions important for Pin1 function. Substrate binding to the WW domain alters its transient contacts with the PPIase domain via means that are only partially understood. Accordingly, we have investigated Pin1 interdomain interactions using NMR paramagnetic relaxation enhancement (PRE) and molecular dynamics (MD) simulations. The PREs show that apo-Pin1 samples interdomain contacts beyond the range suggested by previous structural studies. They further show that substrate binding to the WW domain simultaneously alters interdomain separation and the internal conformation of the WW domain. A 4.5-μs all-atom MD simulation of apo-Pin1 suggests that the fluctuations of interdomain distances are correlated with fluctuations of WW domain interresidue contacts involved in substrate binding. Thus, the interdomain/WW domain conformations sampled by apo-Pin1 may already include a range of conformations appropriate for binding Pin1's numerous substrates. The proposed coupling between intra-/interdomain conformational fluctuations is a consequence of the dynamic modular architecture of Pin1. Such modular architecture is common among cell-cycle proteins; thus, the WW–PPIase domain cross-talk mechanisms of Pin1 may be relevant for their mechanisms as well.
Estimation on Fixed-Bed Column Parameters of Breakthrough Behaviors for Gold Recovery by Adsorption onto Modified/Functionalized Amberlite XAD7

The objective of this paper was to evaluate the potential of a new adsorbent material to recover Au (III) from real wastewater, in a column with a fixed bed in a dynamic regime. The material was obtained through functionalization, by impregnation of the commercial resin, Amberlite XAD 7 type, with L-glutamic acid, which has active groups –NH2 and –COOH. The goal of the experiments was to follow the correlation of fixed-bed column specific adsorption parameters (the effluent volume, the amounts of adsorbent, heights of the adsorbent layer in column) with the time necessary to cross the column. The experimental data obtained were modeled, using the Bohart–Adams, Yoon–Nelson Thomas and Clark models, to establish the mechanism of the Au (III) recovery process, in a dynamic regime. Also, we established the number of cycles for adsorption–desorption for which the new material can be used. We used 5% HNO3 (5%) as desorption agent in five adsorption–desorption cycles, until the process was no longer efficient. The degree of desorption varied between 84% and 34% from cycle 1 to cycle 5.
Ribosomal protein QM/RPL10 positively regulates defence and protein translation mechanisms during nonhost disease resistance

Abstract Ribosomes play an integral part in plant growth, development, and defence responses. We report here the role of ribosomal protein large (RPL) subunit QM/RPL10 in nonhost disease resistance. The RPL10‐silenced Nicotiana benthamiana plants showed compromised disease resistance against nonhost pathogen Pseudomonas syringae pv. tomato T1. The RNA‐sequencing analysis revealed that many genes involved in defence and protein translation mechanisms were differentially affected due to silencing of NbRPL10. Arabidopsis AtRPL10 RNAi and rpl10 mutant lines showed compromised nonhost disease resistance to P. syringae pv. tomato T1 and P. syringae pv. tabaci. Overexpression of AtRPL10A in Arabidopsis resulted in reduced susceptibility against host pathogen P. syringae pv. tomato DC3000. RPL10 interacts with the RNA recognition motif protein and ribosomal proteins RPL30, RPL23, and RPS30 in the yeast two‐hybrid assay. Silencing or mutants of genes encoding these RPL10‐interacting proteins in N. benthamiana or Arabidopsis, respectively, also showed compromised disease resistance to nonhost pathogens. These results suggest that QM/RPL10 positively regulates the defence and translation‐associated genes during nonhost pathogen infection.
Future directions for research on yoga and positive embodiment

ABSTRACT This article provides the concluding thoughts on the special issue, Yoga for Positive Embodiment in Eating Disorder Prevention and Treatment, which illustrate the progress being made on the relationship between yoga practice and the different indicators of positive embodiment that is relevant for the prevention and treatment of eating disorders. Based on the current body or work, we offer recommendations for the next steps for researchers for population-based, qualitative, and prevention and intervention research.
Capsaicin-Loaded Chitosan Nanocapsules for wtCFTR-mRNA Delivery to a Cystic Fibrosis Cell Line

Cystic fibrosis (CF), a lethal hereditary disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene coding for an epithelial chloride channel, is characterized by an imbalanced homeostasis of ion and water transports in secretory epithelia. As the disease is single-gene based, transcript therapy using therapeutic mRNA is a promising concept of treatment in order to correct many aspects of the fatal pathology on a cellular level. Hence, we developed chitosan nanocapsules surface-loaded with wtCFTR-mRNA to restore CFTR function. Furthermore, we loaded the nanocapsules with capsaicin, aiming to enhance the overall efficiency of transcript therapy by reducing sodium hyperabsorption by the epithelial sodium channel (ENaC). Dynamic light scattering with non-invasive back scattering (DLS-NIBS) revealed nanocapsules with an average hydrodynamic diameter of ~200 nm and a Zeta potential of ~+60 mV. The results of DLS-NIBS measurements were confirmed by asymmetric flow field-flow fractionation (AF4) with multidetection, while transmission electron microscopy (TEM) images confirmed the spherical morphology and size range. After stability measurements showed that the nanocapsules were highly stable in cell culture transfection medium, and cytotoxicity was ruled out, transfection experiments were performed with the CF cell line CFBE41o-. Finally, transepithelial measurements with a new state-of-the-art Ussing chamber confirmed successfully restored CFTR function in transfected cells. This study demonstrates that CS nanocapsules as a natural and non-toxic delivery system for mRNA to target cells could effectively replace risky vectors for gene delivery. The nanocapsules are not only suitable as a transcript therapy for treatment of CF, but open aspiring possibilities for safe gene delivery in general.
Assessment of Rice Developmental Stage Using Time Series UAV Imagery for Variable Irrigation Management

Rice is one of the three major crops in the world and is the major crop in Asia. Climate change and water resource shortages may result in decreases in rice yields and possible food shortage crises. In this study, water-saving farming management was tested, and IOT field water level monitoring was used to regulate water inflow automatically. Plant height (PH) is an important phenotype to be used to determine difference in rice growth periods and yields using water-saving irrigation. An unmanned aerial vehicle (UAV) with an RGB camera captured sequential images of rice fields to estimate rice PH compared with PH measured on site for estimating rice growth stages. The test results, with two crop harvests in 2019, revealed that with adequate image calibration, the correlation coefficient between UAV-PH and field-PH was higher than 0.98, indicating that UAV images can accurately determine rice PH in the field and rice growth phase. The study demonstrated that water-saving farming is effective, decreasing water usage for the first and second crops of 2019 by 53.5% and 21.7%, respectively, without influencing the growth period and final yield. Coupled with an automated irrigation system, rice farming can be adaptive to water shortage situations.
A proportional risk model for time-to-event analysis in randomized controlled trials

Regression models for continuous, binary, nominal, and ordinal outcomes almost completely rely on parametric models, whereas time-to-event outcomes are mainly analyzed by Cox’s Proportional Hazards model, an essentially non-parametric method. This is done despite a long list of disadvantages that have been reported for the hazard ratio, and also for the odds ratio, another effect measure sometimes used for time-to-event modelling. In this paper, we propose a parametric proportional risk model for time-to-event outcomes in a two-group situation. Modelling explicitly a risk instead of a hazard or an odds solves the current interpretational and technical problems of the latter two effect measures. The model further allows for computing absolute effect measures like risk differences or numbers needed to treat. As an additional benefit, results from the model can also be communicated on the original time scale, as an accelerated or a prolongated failure time thus facilitating interpretation for a non-technical audience. Parameter estimation by maximum likelihood, while properly accounting for censoring, is straightforward and can be implemented in each statistical package that allows coding and maximizing a univariate likelihood function. We illustrate the model with an example from a randomized controlled trial on efficacy of a new glucose-lowering drug for the treatment of type 2 diabetes mellitus and give the results of a small simulation study.