Takshan/R1 huggingface dataset:
Sarcopenia, obesity, and mortality in US adults with and without chronic kidney disease.

INTRODUCTION: In pre-dialysis chronic kidney disease (CKD), the association of muscle mass with mortality is poorly defined, and no study has examined outcomes related to the co-occurrence of low muscle mass and excess adiposity (sarcopenic-obesity). Methods: We examined abnormalities of muscle and fat mass in adult participants of the National Health and Nutrition Examination Survey 1999-2004. We determined whether associations of body composition with all-cause mortality differed between participants with CKD compared to those without. RESULTS: CKD modified the association of body composition with mortality (p=0.01 for interaction). In participants without CKD, both sarcopenia and sarcopenic obesity were independently associated with increased mortality compared with normal body composition (hazard ratio (HR) 1.44 (95%CI 1.07-1.93) and 1.64 (95%CI 1.26-2.13), respectively). These associations were not present among participants with CKD. Conversely, obese persons had the lowest adjusted risk of death, with an increased risk among those with sarcopenia (HR 1.43 (95%CI 1.05-1.95)) but not sarcopenic-obesity (p=0.003 for interaction by CKD status; HR 1.21 (95%CI 0.89-1.65)), compared with obesity. CONCLUSION: Sarcopenia associates with increased mortality regardless of eGFR, but excess adiposity modifies this association among people with CKD. Future studies of prognosis and weight loss and exercise interventions in CKD patients should consider muscle mass and adiposity together rather than in isolation.
Oral health-related behaviours do not mediate the effect of maternal education on adolescents' gingival bleeding: A birth cohort study.

OBJECTIVES: To test whether maternal education has a direct effect on gingival bleeding in adolescents aged 12 and to assess whether oral health behaviours over time mediate that association. METHODS: Two oral health studies nested in the 1993 Pelotas (Brazil) birth cohort study were carried out in participants aged 6 (n = 359) and 12 years (n = 339). The proportion of teeth with bleeding on probing (BOP) and the median number of teeth with gingivitis at age 12 were recorded. Maternal education at birth was the exposure. Toothbrushing frequency and dental visit at ages 6 and 12 years were investigated as mediators of the association between maternal education at birth and gingival bleeding. Time-varying family income through childhood and adolescence was included as later confounder. Paternal education was taken as baseline confounder. The controlled direct effect (CDE) of maternal education at child's birth on gingival bleeding at age 12 was estimated using marginal structural models (MSM). Additionally, path analysis was employed to estimate standardized direct, indirect and total effects of maternal education at birth on gingival bleeding. RESULTS: Adjusted analyses using MSM showed that adolescents whose mothers had <8 years of education had 3.82 higher risk of having teeth with gingival bleeding above the median (rate ratio RR 3.82; 95% CI: 1.68-8.19). Low maternal education doubled the proportion of gingival bleeding at age 12 not mediated by dental visit and toothbrushing frequency (RR 1.99; 95% CI: 1.52-2.60). Path analysis revealed that maternal education had a direct effect on gingival bleeding independently of the mediators. CONCLUSIONS: The pattern of oral health behaviours does not explain the association between mother's education and adolescent's gingival bleeding. Individual-based approaches focused on oral health-related behaviours tend to fail to prevent gingival bleeding.
Association between Growth Hormone-Insulin-Like Growth Factor-1 Axis Gene Polymorphisms and Short Stature in Chinese Children.

Objective: This study was designed to analyze the association between the growth hormone-insulin-like growth factor-1 (GH-IGF-1) axis gene polymorphisms and short stature in Chinese children. Methods: 181 growth hormone deficiency (GHD) patients and 206 normal stature controls were enrolled to attend this study. Five single-nucleotide polymorphisms in the GH receptor (GHR) and 5 SNPs within the GH-signaling pathway were genotyped by matrix-assisted laser desorption/ionization time of flight mass spectrometry. We conducted an association study between these SNPs and the risk of developing short stature. Linkage disequilibrium analysis was performed using Haploview software and the associations of the SNPs frequencies with short stature were analyzed using X2 tests. Results: No significant difference was found in gender, weight, height, and BMI between the GHD and control groups, except that the age of GHD group was older than the control one. Allele and genotype frequencies were consistent with those expected from Hardy-Weinberg equilibrium. Compared with the controls, heterozygous genotype frequencies (CT) of rs12515480 and rs6873545 of GHR gene were significantly lower. Genotype frequencies of the other 8 SNPs did not show significant difference between these two groups. Considering a dominant model, an OR < 1 was observed for genotypes rs12515480 (OR = 0.532, P = 0.019) and rs6873545 (OR = 0.587, P = 0.017). Conclusions: The heterozygous genotypes of rs12515480 and rs6873545 of GHR gene were associated with decreased risk of GHD in Chinese children.
Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of Arabidopsis Thaliana.

BACKGROUND: Recently, identification and functional studies of circular RNAs, a type of non-coding RNAs arising from a ligation of 3' and 5' ends of a linear RNA molecule, were conducted in mammalian cells with the development of RNA-seq technology. METHOD: Since compared with animals, studies on circular RNAs in plants are less thorough, a genome-wide identification of circular RNA candidates in Arabidopsis was conducted with our own developed bioinformatics tool to several existing RNA-seq datasets specifically for non-coding RNAs. RESULTS: A total of 164 circular RNA candidates were identified from RNA-seq data, and 4 circular RNA transcripts, including both exonic and intronic circular RNAs, were experimentally validated. Interestingly, our results show that circular RNA transcripts are enriched in the photosynthesis system for the leaf tissue and correlated to the higher expression levels of their parent genes. Sixteen out of all 40 genes that have circular RNA candidates are related to the photosynthesis system, and out of the total 146 exonic circular RNA candidates, 63 are found in chloroplast.
Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors.

Background: Super-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for super-resolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared with organic dyes, which are more commonly used. Publically available experimental data can facilitate development of new data analysis algorithms. Findings: Four complete, freely available single molecule super-resolution microscopy datasets on YFP-tagged growth factor receptors expressed in a human cell line are presented, including both raw and analyzed data. We report methods for sample preparation, for data acquisition, and for data analysis, as well as examples of the acquired images. We also analyzed the SMLM datasets using a different method: super-resolution optical fluctuation imaging (SOFI). The 2 modes of analysis offer complementary information about the sample. A fifth single molecule super-resolution microscopy dataset acquired with the dye Alexa 532 is included for comparison purposes. Conclusions: This dataset has potential for extensive reuse. Complete raw data from SMLM experiments have typically not been published. The YFP data exhibit low signal-to-noise ratios, making data analysis a challenge. These datasets will be useful to investigators developing their own algorithms for SMLM, SOFI, and related methods. The data will also be useful for researchers investigating growth factor receptors such as ErbB3.
Reducing unnecessary culturing: a systems approach to evaluating urine culture ordering and collection practices among nurses in two acute care settings.

Background: Inappropriate ordering and acquisition of urine cultures leads to unnecessary treatment of asymptomatic bacteriuria (ASB). Treatment of ASB contributes to antimicrobial resistance particularly among hospital-acquired organisms. Our objective was to investigate urine culture ordering and collection practices among nurses to identify key system-level and human factor barriers and facilitators that affect optimal ordering and collection practices. Methods: We conducted two focus groups, one with ED nurses and the other with ICU nurses. Questions were developed using the Systems Engineering Initiative for Patient Safety (SEIPS) framework. We used iterative categorization (directed content analysis followed by summative content analysis) to code and analyze the data both deductively (using SEIPS domains) and inductively (emerging themes). Results: Factors affecting optimal urine ordering and collection included barriers at the person, process, and task levels. For ED nurses, barriers included patient factors, physician communication, reflex culture protocols, the electronic health record, urinary symptoms, and ED throughput. For ICU nurses, barriers included physician notification of urinalysis results, personal protective equipment, collection technique, patient body habitus, and Foley catheter issues. Conclusions: We identified multiple potential process barriers to nurse adherence with evidence-based recommendations for ordering and collecting urine cultures in the ICU and ED. A systems approach to identifying barriers and facilitators can be useful to design interventions for improving urine ordering and collection practices.
Endogenous lycopene improves ethanol production under acetic acid stress in Saccharomyces cerevisiae.

Background: Acetic acid, generated from the pretreatment of lignocellulosic biomass, is a significant obstacle for lignocellulosic ethanol production. Reactive oxidative species (ROS)-mediated cell damage is one of important issues caused by acetic acid. It has been reported that decreasing ROS level can improve the acetic acid tolerance of Saccharomyces cerevisiae. Results: Lycopene is known as an antioxidant. In the study, we investigated effects of endogenous lycopene on cell growth and ethanol production of S. cerevisiae in acetic acid media. By accumulating endogenous lycopene during the aerobic fermentation of the seed stage, the intracellular ROS level of strain decreased to 1.4% of that of the control strain during ethanol fermentation. In the ethanol fermentation system containing 100 g/L glucose and 5.5 g/L acetic acid, the lag phase of strain was 24 h shorter than that of control strain. Glucose consumption rate and ethanol titer of yPS002 got to 2.08 g/L/h and 44.25 g/L, respectively, which were 2.6- and 1.3-fold of the control strain. Transcriptional changes of INO1 gene and CTT1 gene confirmed that endogenous lycopene can decrease oxidative stress and improve intracellular environment. Conclusions: Biosynthesis of endogenous lycopene is first associated with enhancing tolerance to acetic acid in S. cerevisiae. We demonstrate that endogenous lycopene can decrease intracellular ROS level caused by acetic acid, thus increasing cell growth and ethanol production. This work innovatively   puts forward a new strategy for second generation bioethanol production during lignocellulosic fermentation.
Association of tobacco use and other determinants with pregnancy outcomes: a multicentre hospital-based case-control study in Karachi, Pakistan.

OBJECTIVES: The study aimed to identify the effects of maternal tobacco consumption during pregnancy and other factors on birth outcomes and obstetric complications in Karachi, Pakistan. DESIGN: A multicentre hospital-based case-control study. SETTING: Four leading maternity hospitals of Karachi. PARTICIPANTS: A random sample of 1275 women coming to the gynaecology and obstetric department of selected hospitals for delivery was interviewed within 48 hours of delivery from wards. Cases were women with adverse birth outcomes and obstetric complications, while controls were women who had normal uncomplicated delivery. PRIMARY AND SECONDARY OUTCOME MEASURES: Adverse birth outcomes (preterm delivery, low birth weight, stillbirth, low Apgar score) and obstetric complications (antepartum haemorrhage, caesarean section, etc). RESULTS: Final multiple logistic regression analysis revealed that with every 1 year increase in age the odds of being a case was 1.03 times as compared with being a control. Tobacco use (adjusted OR (aOR): 2.24; 95% CI 1.56 to 3.23), having no slits in the kitchen (proxy indicator for indoor air pollution) (aOR=1.90; 95% CI 1.05 to 3.43), gravidity (aOR=0.83; 95% CI 0.73 to 0.93), non-booked hospital cases (aOR=1.87; 95% CI 1.38 to 2.74), history of stillbirth (aOR=4.06; 95% CI 2.36 to 6.97), miscarriages (aOR=1.91; 95% CI 1.27 to 2.85) and preterm delivery (aOR=6.04; 95% CI 2.52 to 14.48) were significantly associated with being a case as compared with control. CONCLUSIONS: This study suggests that women who had adverse pregnancy outcomes were more likely to have exposure to tobacco, previous history of adverse birth outcomes and were non-booked cases. Engagement of stakeholders in tobacco control for providing health education, incorporating tobacco use in women in the tobacco control policy and designing interventions for tobacco use cessation is warranted. Prenatal care and health education might help in preventing such adverse events.
Glycan analysis of colorectal cancer samples reveals stage-dependent changes in CEA glycosylation patterns.

Background: Carcinoembryonic antigen (CEA) is a glycoprotein associated with colorectal cancer (CRC). While the functions of its gene and protein have been fully characterized, its post-translational modifications in the context of CRC development remain undefined. Methods: To show the correlation between the different stages of CRC development and changes in the glycosylation patterns of CEA, we analyzed CEA in tumor tissues (CEA-T) and paired tumor-adjacent normal tissues (CEA-A) from 53 colorectal cancer patients using a high-density lectin microarray containing 56 plant lectins. Results: We detected higher expression levels of fucose, mannose and Thomsen-Friedenreich antigen, and lower expression levels of N-acetylgalactosamine, N-acetylglucosamine, galactose, branched and bisecting N-glycans on CEA in the tumor tissues relative to the tumor-adjacent normal tissues. Furthermore, a combinatorial assessment of 9 lectins is sufficient to distinguish CRC tumor tissues from tumor-adjacent normal tissues with 83% sensitivity and ~ 90% specificity. Moreover, the levels of N-acetylgalactosamine, mannose, galactose, N-acetylglucosamine on CEA showed a downward trend after first experiencing an increase at Stage II with the stages of CRC. Conclusions: Our insights into the changing CEA glycosylation patterns and their role in the development of CRC highlight the importance of glycan variants on CEA for early clinical detection and staging of CRC.
COL4A5 and LAMA5 variants co-inherited in familial hematuria: digenic inheritance or genetic modifier effect?

BACKGROUND: About 40-50% of patients with familial microscopic hematuria (FMH) caused by thin basement membrane nephropathy (TBMN) inherit heterozygous mutations in collagen IV genes (COL4A3, COL4A4). On long follow-up, the full phenotypic spectrum of these patients varies a lot, ranging from isolated MH or MH plus low-grade proteinuria to chronic renal failure of variable degree, including end-stage renal disease (ESRD). METHODS: Here, we performed Whole Exome Sequencing (WES) in patients of six families, presenting with autosomal dominant FMH, with or without progression to proteinuria and loss of renal function, all previously found negative for severe collagen IV mutations. Hierarchical filtering of the WES data was performed, followed by mutation prediction analysis, Sanger sequencing and genetic segregation analysis. RESULTS: In one family with four patients, we found evidence for the contribution of two co-inherited variants in two crucial genes expressed in the glomerular basement membrane (GBM); LAMA5-p. Pro1243Leu and COL4A5-p. Asp654Tyr. Mutations in COL4A5 cause classical X-linked Alport Syndrome, while rare mutations in the LAMA5 have been reported in patients with focal segmental glomerulosclerosis. The phenotypic spectrum of the patients includes hematuria, proteinuria, focal segmental glomerulosclerosis, loss of kidney function and renal cortical cysts. CONCLUSIONS: A modifier role of LAMA5 on the background of a hypomorphic Alport syndrome causing mutation is a possible explanation of our findings. Digenic inheritance is another scenario, following the concept that mutations at both loci more accurately explain the spectrum of symptoms, but further investigation is needed under this concept. This is the third report linking a LAMA5 variant with human renal disease and expanding the spectrum of genes involved in glomerular pathologies accompanied by familial hematurias. The cystic phenotype overlaps with that of a mouse model, which carried a Lama5 hypomorphic mutation that caused severely reduced Lama5 protein levels and produced kidney cysts.
Cross-cultural measurement invariance of the Revised Child Anxiety and Depression Scale across 11 world-wide societies.

BACKGROUND: In order to compare estimates by one assessment scale across various cultures/ethnic groups, an important aspect that needs to be demonstrated is that its construct across these groups is invariant when measured using a similar and simultaneous approach (i.e., demonstrated cross-cultural measurement invariance). One of the methods for evaluating measurement invariance is testing for differential item functioning (DIF), which assesses whether different groups respond differently to particular items. The aim of this study was to evaluate the cross-cultural measurement invariance of the Revised Child Anxiety and Depression Scale (RCADS) in societies with different socioeconomic, cultural, and religious backgrounds. METHODS: The study was organised by the International Child Mental Health Study Group. Self-reported data were collected from adolescents residing in 11 countries: Brazil, Bulgaria, Croatia, Indonesia, Montenegro, Nigeria, Palestinian Territories, the Philippines, Portugal, Romania and Serbia. The multiple-indicators multiple-causes model was used to test the RCADS items for DIF across the countries. RESULTS: Ten items exhibited DIF considering all cross-country comparisons. Only one or two items were flagged with DIF in the head-to-head comparisons, while there were three to five items flagged with DIF, when one country was compared with the others. Even with all cross-culturally non-invariant items removed from nine language versions tested, the original factor model representing six anxiety and depressive symptoms subscales was not significantly violated. CONCLUSIONS: There is clear evidence that relatively small number of the RCADS items is non-invariant, especially when comparing two different cultural/ethnic groups, which indicates on its sound cross-cultural validity and suitability for cross-cultural comparisons in adolescent anxiety and depressive symptoms.
Cross-Cultural Measurement Invariance of Adolescent Self-Report on the Pediatric Quality of Life Inventory(™) 4.0.

This study evaluated the cross-cultural measurement invariance of the Pediatric Quality of Life Inventory version 4.0 (PedsQL(™)) among adolescents sampled from Bulgaria, Croatia, India, Indonesia, Nigeria, Serbia, and Turkey. The multiple-indicator multiple-cause (MIMIC) model was used, which allowed controlling of demographic variables (i.e., age, gender, and socioeconomic status). Significant effects of country on scores within the PedsQL(™) domains were observed, with up to 17 items showing differential item functioning (DIF) across the countries. We did not find support for cross-cultural measurement invariance hypotheses for scores on the PedsQL(™) adolescent self-report in this study. Researchers should use caution in making cross-cultural quality of life comparisons while using the PedsQL.
Distal renal tubular acidosis in a Libyan patient: Evidence for digenic inheritance.

AIM OF THE STUDY: Recent advances in understanding the underlying molecular mechanism for distal renal tubular acidosis (dRTA), led to an increased attention towards the primary and the familial forms of the disease. Mutations in ATP6V1B1 and ATP6V0A4 are usually responsible for the recessive form of the disease. Mutations in gene AE1 encoding the Cl-/HCO3- exchanger, usually present as dominant dRTA, but a recessive pattern has been recently described. Our objective is to identify the mutational spectrum responsible of dRTA in a consanguineous Libyan family. MATERIALS AND METHODS: Both ATP6V0A4 and ATP6V1B1 genes were preferentially screened in our patient. Additional whole exome sequencing (WES) in the same patient, offered a wider view on potential chromosomal rearrangements as well as the mutational spectrum of other genes involved in this disease. RESULTS: The patient is a heterozygote for two different mutations, one in each of the genes ATP6V0A4 and ATP6V1B1, while no deleterious variation was detected in the remaining genes responsible for the recessive form of dRTA. Homozygosity mapping and WES confirmed our findings and supported the hypothesis of a digenic inheritance model existing as an explanation for dRTA. CONCLUSIONS: To our knowledge, this is the first report describing a Libyan patient with dRTA who suffered from early-onset sensorineural hearing loss, with a digenic mode of inheritance, supported by the identification of two novel mutations. This study increases the understanding of how dRTA is genetically transmitted, while offers a good outline towards the molecular diagnostics and genetic counseling for dRTA in Lybians.
Frequent COL4 mutations in familial microhematuria accompanied by later-onset Alport nephropathy due to focal segmental glomerulosclerosis.

Familial microscopic hematuria (FMH) is associated with a genetically heterogeneous group of conditions including the collagen-IV nephropathies, the heritable C3/CFHR5 nephropathy and the glomerulopathy with fibronectin deposits. The clinical course varies widely, ranging from isolated benign familial hematuria to end-stage renal disease (ESRD) later in life. We investigated 24 families using Next Generation Sequencing (NGS) for five genes: COL4A3, COL4A4, COL4A5, CFHR5 and FN1. In 17 families (71%), we found 15 pathogenic mutations in COL4A3/A4/A5, nine of them novel. In five families patients inherited classical AS with hemizygous X-linked COL4A5 mutations. Even more patients developed later-onset Alport-related nephropathy having inherited heterozygous COL4A3/A4 mutations that cause thin basement membranes. Amongst 62 heterozygous or hemizygous patients, eight (13%) reached ESRD, while 25% of patients with heterozygous COL4A3/A4 mutations, aged >50-yrs, reached ESRD. In conclusion, COL4A mutations comprise a frequent cause of FMH. Heterozygous COL4A3/A4 mutations predispose to renal function impairment, supporting that thin basement membrane nephropathy is not always benign. The molecular diagnosis is essential for differentiating the X-linked from the autosomal recessive and dominant inheritance. Finally, NGS technology is established as the gold standard for the diagnosis of FMH and associated collagen-IV glomerulopathies, frequently averting the need for invasive renal biopsies.