Miracle-dz/UniFAR-FTUs huggingface dataset:
More than Fast Food: Development of a Story Map to Compare Adolescent Perceptions and Observations of Their Food Environments and Related Food Behaviors

The purpose of this convergent, multiphase, mixed methods study was to better understand the perceptions of adolescents’ food environments and related food behaviors using grounded visualization and story mapping. Adolescents from one high school (13–16 years) in the southeastern United States were evaluated via data from health behavior surveys (n = 75), school environment maps, focus groups (n = 5 groups), and Photovoice (n = 6) from October 2016 to April 2017. Data from each phase were integrated using grounded visualization and new themes were identified (n = 7). A story map using ArcGIS Online was developed from data integration, depicting the newly identified themes. Participants failed to meet national recommendations for fruit and vegetable intake (2.71 cups). Focus group and Photovoice findings indicated the need for convenience food items in all environments. The story map is an online, interactive dissemination of information, with five maps, embedded quotes from focus groups, narrative passages with data interpretation, pictures to highlight themes, and a comparison of the participants’ food environments. Story mapping and qualitative geographic information systems (GIS) approaches may be useful when depicting adolescent food environments and related food behaviors. Further research is needed when evaluating story maps and how individuals can be trained to create their own maps.
Therapeutic uses of metronidazole and its side effects: an update.

OBJECTIVE Metronidazole is an antibiotic widely used in different medical conditions such as trichomoniasis, amoebiasis, and giardiasis among others. Its use has been associated with toxicity; however, it is not well characterized. In this review, we discuss the different therapeutic uses of metronidazole and its side effects in order to aid future investigation in this field. MATERIALS AND METHODS Relevant information, original research articles, clinical trials, and reviews were collected from PubMed to know the state of the art of the different therapeutic uses of metronidazole and the reported side effects. RESULTS Metronidazole was used by the first time in 1959, to treat an infection caused by Trichomonas vaginalis; subsequently, new therapeutic properties were discovered. Nowadays, Metronidazole is used to treat infections caused by Bacteroides, Fusobacteria and Clostridia, rosacea, oral and dental infections, bone and joint infections, gynecologic infections, endocarditis, septicemia, and respiratory tract infections. It also can be used to treat Crohn´s disease or even like prophylaxis, before surgical procedures. Metronidazole is well tolerated with mild to moderate side effects such as nausea, abdominal pain, and diarrhea. Nevertheless, serious neurotoxicity, optic neuropathy, peripheral neuropathy, and encephalopathy have been reported in rare cases. Their genotoxic effects observed in animal models are controversial in humans. CONCLUSIONS The therapeutic use of metronidazole had increased worldwide. Even though it is widely used, metronidazole has been associated with neurotoxicity and genotoxicity; however, its side effects are not well established. Conversely, its veterinary use is restricted in some countries because of its tumor association. Subsequently, further studies are needed to discover the secure use of metronidazole and describe new usages for this drug.
Effects of Consuming Calcium-Rich Foods on the Incidence of Type 2 Diabetes Mellitus

The effect of calcium consumption in the prevention of type 2 diabetes mellitus (T2DM) remains controversial, and depends on food calcium sources. This prospective study aimed to evaluate the association between calcium-rich food consumption and T2DM incidence among Korean adults. We analyzed the data of 8574 adults aged 40–69 years, without a history of T2DM, cardiovascular disease, and cancer at the baseline from the Korean Genome and Epidemiology Study. The consumption of calcium-rich foods was assessed using a validated semi-quantitative food frequency questionnaire. T2DM-related data were collected using biennial questionnaires, health examinations, and clinical tests. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using Cox proportional hazards regression models. In the multivariate-adjusted model, yogurt intake was inversely associated with T2DM risk (HR: 0.73; 95% CI: 0.61–0.88 in the fourth quartile as compared to the first quartile). However, the intakes of other calcium-rich foods, including milk and anchovies, were not significantly associated with T2DM risk. Yogurt may provide protective effects against T2DM in Korean adults, owing to the beneficial effects of probiotics. Further prospective large-scale cohort studies should be conducted to validate these findings.
Application of machine learning in rheumatic disease research

Over the past decade, there has been a paradigm shift in how clinical data are collected, processed and utilized. Machine learning and artificial intelligence, fueled by breakthroughs in high-performance computing, data availability and algorithmic innovations, are paving the way to effective analyses of large, multi-dimensional collections of patient histories, laboratory results, treatments, and outcomes. In the new era of machine learning and predictive analytics, the impact on clinical decision-making in all clinical areas, including rheumatology, will be unprecedented. Here we provide a critical review of the machine-learning methods currently used in the analysis of clinical data, the advantages and limitations of these methods, and how they can be leveraged within the field of rheumatology.
Linkage Abundance and Molecular Weight Characteristics of Technical Lignins by Attenuated Total Reflection‐FTIR Spectroscopy Combined with Multivariate Analysis

Abstract Lignin is an attractive material for the production of renewable chemicals, materials and energy. However, utilization is hampered by its highly complex and variable chemical structure, which requires an extensive suite of analytical instruments to characterize. Here, we demonstrate that straightforward attenuated total reflection (ATR)‐FTIR analysis combined with principle component analysis (PCA) and partial least squares (PLS) modelling can provide remarkable insight into the structure of technical lignins, giving quantitative results that are comparable to standard gel‐permeation chromatography (GPC) and 2D heteronuclear single quantum coherence (HSQC) NMR methods. First, a calibration set of 54 different technical (fractionated) lignin samples, covering kraft, soda and organosolv processes, were prepared and analyzed using traditional GPC and NMR methods, as well as by readily accessible ATR‐FTIR spectroscopy. PLS models correlating the ATR‐FTIR spectra of the broad set of lignins with GPC and NMR measurements were found to have excellent coefficients of determination (R 2 Cal.>0.85) for molecular weight (M n, M w) and inter‐unit abundances (β‐O‐4, β‐5 and β‐β), with low relative errors (6.2–14 %) as estimated from cross‐validation results. PLS analysis of a second set of 28 samples containing exclusively (fractionated) kraft lignins showed further improved prediction ability, with relative errors of 3.8–13 %, and the resulting model could predict the structural characteristics of an independent validation set of lignins with good accuracy. The results highlight the potential utility of this methodology for streamlining and expediting the often complex and time consuming technical lignin characterization process.
Functionally oriented analysis of cardiometabolic traits in a trans-ethnic sample

Abstract Interpretation of genetic association results is difficult because signals often lack biological context. To generate hypotheses of the functional genetic etiology of complex cardiometabolic traits, we estimated the genetically determined component of gene expression from common variants using PrediXcan (1) and determined genes with differential predicted expression by trait. PrediXcan imputes tissue‐specific expression levels from genetic variation using variant‐level effect on gene expression in transcriptome data. To explore the value of imputed genetically regulated gene expression (GReX) models across different ancestral populations, we evaluated imputed expression levels for predictive accuracy genome‐wide in RNA sequence data in samples drawn from European‐ancestry and African‐ancestry populations and identified substantial predictive power using European‐derived models in a non‐European target population. We then tested the association of GReX on 15 cardiometabolic traits including blood lipid levels, body mass index, height, blood pressure, fasting glucose and insulin, RR interval, fibrinogen level, factor VII level and white blood cell and platelet counts in 15 755 individuals across three ancestry groups, resulting in 20 novel gene‐phenotype associations reaching experiment‐wide significance across ancestries. In addition, we identified 18 significant novel gene‐phenotype associations in our ancestry‐specific analyses. Top associations were assessed for additional support via query of S‐PrediXcan (2) results derived from publicly available genome‐wide association studies summary data. Collectively, these findings illustrate the utility of transcriptome‐based imputation models for discovery of cardiometabolic effect genes in a diverse dataset.
Reproducible detection of nigral iron deposition in 2 Parkinson's disease cohorts

Previous studies investigating nigral iron accumulation used T2 or T2*‐weighted contrasts to define the regions of interest (ROIs) in the substantia nigra with mixed results. Because these contrasts are not sensitive to neuromelanin, ROIs may have inadvertently missed the SNpc. An approach sensitive to neuromelanin should yield consistent results. We examine iron deposition in ROIs derived from neuromelanin‐sensitive and T2*‐weighted contrasts, respectively.
The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy

BACKGROUND In gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression. RESULTS GeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap. CONCLUSION In this study, we demonstrate the potential of implementing SINEs -notably the B1 element- as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression.
Ribosomal protein L6 (RPL6) is recruited to DNA damage sites in a poly(ADP-ribose) polymerase–dependent manner and regulates the DNA damage response

Ribosomal proteins are the building blocks of ribosome biogenesis. Beyond their known participation in ribosome assembly, the ribosome-independent functions of ribosomal proteins are largely unknown. Here, using immunoprecipitation, subcellular fractionation, His-ubiquitin pulldown, and immunofluorescence microscopy assays, along with siRNA-based knockdown approaches, we demonstrate that ribosomal protein L6 (RPL6) directly interacts with histone H2A and is involved in the DNA damage response (DDR). We found that in response to DNA damage, RPL6 is recruited to DNA damage sites in a poly(ADP-ribose) polymerase (PARP)–dependent manner, promoting its interaction with H2A. We also observed that RPL6 depletion attenuates the interaction between mediator of DNA damage checkpoint 1 (MDC1) and H2A histone family member X, phosphorylated (γH2AX), impairs the accumulation of MDC1 at DNA damage sites, and reduces both the recruitment of ring finger protein 168 (RNF168) and H2A Lys-15 ubiquitination (H2AK15ub). These RPL6 depletion–induced events subsequently inhibited the recruitment of the following downstream repair proteins: tumor protein P53-binding protein 1 (TP53BP1) and BRCA1, DNA repair-associated (BRCA1). Moreover, the RPL6 knockdown resulted in defects in the DNA damage–induced G2–M checkpoint, DNA damage repair, and cell survival. In conclusion, our study identifies RPL6 as a critical regulatory factor involved in the DDR. These findings expand our knowledge of the extraribosomal functions of ribosomal proteins in cell physiology and deepen our understanding of the molecular mechanisms underlying DDR regulation.
An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species

Abstract Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.
The effects of a randomized trial of brief forms of stress management on RAGE‐associated S100A8/A9 in patients with breast cancer undergoing primary treatment

Women with breast cancer (BCa) experience heightened distress, which is related to greater inflammation and poorer outcomes. The s100 protein family facilitates the inflammatory response by regulating myeloid cell function through the binding of Toll‐like receptor 4 and the receptor for advanced glycation end products (RAGE). The heterodimer s100A8/A9 RAGE ligand is associated with hastened tumor development and metastasis. Previously, a 10‐week stress‐management intervention using cognitive behavioral therapy (CBT) and relaxation training (RT) was associated with less leukocyte inflammatory gene expression in patients with BCa; however, its impact on s100A8/A9 was not examined. Because a 10‐week intervention may be impractical during primary treatment for BCa, the authors developed briefer forms of CBT and RT and demonstrated their efficacy in reducing distress over 12 months of primary treatment. Here, the effects of these briefer interventions were tested effects on s100A8/A9 levels over the initial 12 months of BCa treatment.
New assay method based on Raman spectroscopy for enzymes reacting with gaseous substrates

Enzyme activity is typically assayed by quantitatively measuring the initial and final concentrations of the substrates and/or products over a defined time period. For enzymatic reactions involving gaseous substrates, the substrate concentrations can be estimated either directly by gas chromatography or mass spectrometry, or indirectly by absorption spectroscopy, if the catalytic reactions involve electron transfer with electron mediators that exhibit redox‐dependent spectral changes. We have developed a new assay system for measuring the time course of enzymatic reactions involving gaseous substrates based on Raman spectroscopy. This system permits continuous monitoring of the gas composition in the reaction cuvette in a non‐invasive manner over a prolonged time period. We have applied this system to the kinetic study of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. This enzyme physiologically catalyzes the reversible oxidation of H2 and also possesses the nonphysiological functions of H/D exchange and nuclear spin isomer conversion reactions. The proposed system has the additional advantage of enabling us to measure all of the hydrogenase‐mediated reactions simultaneously. Using the proposed system, we confirmed that H2 (the fully exchanged product) is concomitantly produced alongside HD by the H/D exchange reaction in the D2/H2O system. Based on a kinetic model, the ratio of the rate constants of the H/D exchange reaction (k) at the active site and product release rate (kout) was estimated to be 1.9 ± 0.2. The proposed assay method based on Raman spectroscopy can be applied to the investigation of other enzymes involving gaseous substrates.
Transcriptome profile with 20 nm silver nanoparticles in yeast

Abstract Engineered nanomaterials are commercially used in everyday products including zinc sunscreens and water‐resistant fabrics and surfaces. Therefore, understanding the effects of engineered nanomaterials on the environment is crucial for the responsible use of these technologies. We investigated the effects of 20 nm spherical citrate‐coated silver nanoparticles (AgNPs) on the budding yeast Saccharomyces cerevisiae. Our growth assay showed that AgNPs have an inhibitory effect on yeast growth with concentrations above 5 &mgr;g/mL. Hundreds of genes in AgNP‐treated cells were differentially expressed according to our transcriptome analysis based on RNAseq, including genes implicated in rRNA processing, ribosome biogenesis, cell wall formation, cell membrane integrity and mitochondrial functions. In particular, genes whose functions are associated with processing of small and large subunits of ribosomes were upregulated, while genes for cell wall/plasma membrane/mitochondrial integrity were downregulated. Consistently, our cell wall stability assay confirmed that cells with AgNPs are more susceptible to cell wall damage than non‐treated cells. Levels of four significantly altered genes with AgNPs, including FAF1, SDA1, TIR1 and DAN1, were validated by reproducible results with RT‐qPCR assays. Our transcriptome profile leads us to conclude that the exposure of cells to sublethal amounts of AgNPs affects many cellular processes negatively.
Immunohistochemistry for aldosterone synthase CYP11B2 and matrix-assisted laser desorption ionization imaging mass spectrometry for in-situ aldosterone detection

Purpose of review Immunohistochemistry for aldosterone synthase (CYP11B2) has markedly provided a comprehensive picture of the adrenocortical diseases, particularly primary aldosteronism. The findings from CYP11B2-immunohistochemistry are consistent with the clinical courses of most patients with primary aldosteronism. We herein review the updated pathophysiology and usefulness of the method for understanding individual patients with different subtypes of primary aldosteronism. Recent findings After our discovery of aldosterone-producing cell clusters (APCCs) using the immunohistochemistry for CYP11B2, we found possible APCC-to-APA transitional lesions (pAATLs) in a few cases that had been hitherto classified as unilateral hyperplasia or multiple nodules. On the basis of morphological and functional features of pAATLs as well as distributions of somatic mutations within the lesions, we have made a hypothesis that APCC grows to APA via pAATL for one of developmental courses of APA. Recently, we successfully performed in-situ detection of aldosterone on adrenal tissue sections using a state-of-the-art technique, matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI-imaging). This method revealed in-situ synthesis of aldosterone in APCCs and APAs in addition to several other steroids. Summary CYP11B2 immunohistochemistry revealed the pathophysiology of aldosterone production in the past decade, especially formation of APCC in normal adrenals and pAATL that is a possible lesion developing from APCC to APA. The term ‘idiopathic hyperaldosteronism’ may soon become obsolete.
Reliability, validity and responsiveness of the Mandarin (Simplified) Chinese version of the EORTC QLQ‐OH45 among cancer patients

PURPOSE The goal of our study was to evaluate the reliability, validity, responsiveness and acceptability of the Mandarin (simplified) Chinese version of the EORTC QLQ-OH45. METHODS From October 2017 to February 2018, 393 cancer patients were enrolled from three different hospitals in China. A forward and backward translation was made to develop the Mandarin (simplified) Chinese version of EORTC QLQ-OH15. The QLQ-C30 and QLQ-OH15 questionnaires (which we have assembled and named QLQ-OH45 in this paper) were self-administered. Results were statistically analysed using SPSS 21.0. The reliability and validity tests of the questionnaires were assessed by Cronbach's α coefficient, Pearson correlation test and Mann-Whitney U tests. Responsiveness to change was measured in an independent sample of patients with head and neck cancer undergoing surgery or radiotherapy or chemotherapy. RESULTS An acceptable internal consistency reliability for most multiple-item scales was demonstrated, as Cronbach's α coefficients were greater than 0.7 for most multiple-item scales, excepting for cognitive functioning (0.36) and oral health-related QoL functioning (0.55). All domain's test-retest reliability coefficients (r) was higher than 0.8. Multi-trait scaling analysis showed good convergent and discriminant validity. A difference in the quality of life (QoL) between older (≥65 years) and younger (<65 years) groups of patients was showed by the known-group comparisons. Low correlations were found between the scales of the QLQ-OH15 and QLQ-C30 in all areas. CONCLUSION The Mandarin (simplified) Chinese version of QLQ-OH45 demonstrates satisfactory psychometric properties and can be used to measure the oral health-related QoL (OHRQoL) for Chinese cancer patients.