Miracle-dz/UniFAR-FTUs huggingface dataset:
Home Dialysis Is Associated with Lower Costs and Better Survival than Other Modalities: A Population-Based Study in Ontario, Canada

Background: How and where to initiate dialysis are policy challenges with enormous economic and health consequences. Initiating with home hemodialysis (HD) or peritoneal dialysis (PD) may reduce costs and improve outcomes but evidence is conflicting. Methods: We conducted a population-based study in patients aged ≥ 18 years who initiated chronic dialysis in the province of Ontario, Canada from 2006 to 2014 (N = 12,691) using linked administrative data. Patients were grouped by initial modality: facility HD, facility short daily or slow nocturnal (SD/SN) HD, PD, home HD. We estimated publicly-paid healthcare costs (2015 Canadian dollars; 1 = 0.947 US dollar) and survival, from dialysis initiation to March 2015. Results: By 5 years after dialysis initiation, mean 30-day costs (as-treated) for patients receiving PD and home HD were 50% and 64% lower, respectively, than for facility HD patients ($11,011). Approximately 50% of costs were unrelated to dialysis, reflecting high comorbidity in these patients. With covariate adjustment, mean 5-year cumulative costs were similar for initiators of home HD and PD ($304,178 and $349,338) and higher for facility HD initiators ($410,981). The highest 5-year unadjusted survival was for home HD patients (80%), followed by PD (52%), SD/SN HD (50%), and facility HD (42%). Conclusions: This study in a large cohort over 9 years provides new population-based evidence suggesting that initiating dialysis at home is cost-effective, with lower costs and better survival, than starting with facility HD. Survival differences persisted after adjustment for baseline characteristics but we could not adjust for functional status or severity of comorbidities.
Teaching Big Data Management – An Active Learning Approach for Higher Education

Since big data analytics has become an imperative for business success in the digital economy, universities face the challenge to train data scientists and data engineers on various technological and managerial skills. In addition to traditional lectures, active learning formats ensure a practice oriented education enabling students to handle novel big data technologies. In this paper, we present a big data management syllabus for master students in the field of big data analytics, which includes various hands-on and action learning elements. The course encompasses seven lectures and nine tutorials and takes place at Chemnitz University of Technology. It covers a broad range of big data applications and facilitates knowledge on various cognitive levels. The paper gives an overview of the course content and assigns learning objectives to lectures and tutorials using Krathwohl’s revised taxonomy. Finally, we present the feedback, which we have received by the students over the years.
Relapse of Atypical Hemolytic Uremic Syndrome During Pregnancy in a Patient on Eculizumab Maintenance Treatment: A Case Report

Patient: Female, 28 Final Diagnosis: Relapse of atypical hemolytic uremic syndrome during pregnancy Symptoms: Anemia • edema • hemolysis • oliguria Medication: — Clinical Procedure: — Specialty: Nephrology Objective: Rare disease Background: Atypical hemolytic uremic syndrome (aHUS) is a genetic disorder with uncontrolled complement activation leading to systemic thrombotic microangiopathy; kidneys are almost invariably involved. Eculizumab has dramatically improved the prognosis of aHUS and affected women in the childbearing age are more likely to consider pregnancy, even if this could represent a risk for disease reactivation. Pregnancies in women with aHUS during Eculizumab treatment have been reported, with no cases of aHUS relapse. Case Report: We report the case of a female patient affected by aHUS with no specific gene mutations who had a pregnancy-associated aHUS relapse at 26-weeks of gestation during maintenance Eculizumab treatment. The patient developed stage II acute kidney injury and microangiopathic hemolytic anemia. Delivery by cesarean section at week 27, plasma exchange sessions and several supplemental Eculizumab administrations were required. After appropriate treatment, the patient partially recovered kidney function; the baby had a prolonged stay in the intensive care unit and showed no signs of neurologic damage. Conclusions: Previous reports indicated that pregnancy-related aHUS relapses were unlikely in women undergoing Eculizumab treatment. Based on our case, we suggest caution in counselling pregnancy in women with aHUS treated with Eculizumab, especially in the absence of pathogenic mutations in complement-regulating genes. Clinicians should be aware of possible aHUS relapse in pregnancy during Eculizumab treatment.
Working hours and nonalcoholic fatty liver disease according to sleep duration

ABSTRACT There is no study on the relationship between working hours and nonalcoholic fatty liver disease (NAFLD). The objective of the present study was to determine the relationship between working hours and NAFLD by sleep duration using a large set of abdominal ultrasonography examination data. Data from 194,625 patients who underwent health examinations from 2015 to 2017 were analyzed. Chi-square tests, linear-by-linear association and ANOVA were performed to compare general characteristics according to working hours. Multivariate logistic regression analysis was performed to determine the relationship between working hours and NAFLD by sleep duration. There was no significant relationship between working hours and NAFLD prevalence in the group of short sleep duration of ≤5 hours or the group of long sleep duration of ≥7 hours. The risk of NAFLD in the >52 working hour group was significantly higher (aOR, 1.09; 95% CI, 1.04–1.14) than that in the 40- to 52-hour working hour group after adjusting for confounding factors in the 5- to 6-hour sleep duration group. There was no significant difference between ≤40 working hours and 40 ~ 52 working hours in the 5 ~ 6 hours sleep duration group (aOR, 1.02; 95% CI, 0.97–1.06). In general, working hours were significantly related to NAFLD. There was a difference in the relationship between working hours and NAFLD according to sleep duration.
Recognition and processing of branched DNA substrates by Slx1–Slx4 nuclease

Abstract Structure-selective endonucleases cleave branched DNA substrates. Slx1 is unique among structure-selective nucleases because it can cleave all branched DNA structures at multiple sites near the branch point. The mechanism behind this broad range of activity is unknown. The present study structurally and biochemically investigated fungal Slx1 to define a new protein interface that binds the non-cleaved arm of branched DNAs. The DNA arm bound at this new site was positioned at a sharp angle relative to the arm that was modeled to interact with the active site, implying that Slx1 uses DNA bending to localize the branch point as a flexible discontinuity in DNA. DNA binding at the new interface promoted a disorder-order transition in a region of the protein that was located in the vicinity of the active site, potentially participating in its formation. This appears to be a safety mechanism that ensures that DNA cleavage occurs only when the new interface is occupied by the non-cleaved DNA arm. Models of Slx1 that interacted with various branched DNA substrates were prepared. These models explain the way in which Slx1 cuts DNA toward the 3′ end away from the branch point and elucidate the unique ability of Slx1 to cleave various DNA structures.
Draft Genome Sequence of Microbacterium sp. Gd 4-13, Isolated from Gydanskiy Peninsula Permafrost Sediments of Marine Origin

Here, we report the draft genome sequence of Microbacterium sp. strain Gd 4-13, isolated from late Pleistocene permafrost of marine origin located on the Gydanskiy Peninsula. Genome sequence analysis was performed to understand strain survivability mechanisms under permafrost conditions and to expand biotechnology applications. ABSTRACT Here, we report the draft genome sequence of Microbacterium sp. strain Gd 4-13, isolated from late Pleistocene permafrost of marine origin located on the Gydanskiy Peninsula. Genome sequence analysis was performed to understand strain survivability mechanisms under permafrost conditions and to expand biotechnology applications.
Xylanase and xylo- oligosaccharide prebiotic improve the growth performance and concentration of potentially prebiotic oligosaccharides in the ileum of broiler chickens

ABSTRACT 1. The objective of this study was to investigate the effect of supplementing broiler diets with xylanase or xylo- oligosaccharide (XOS) on growth performance, the concentration of non-starch polysaccharide (NSP) hydrolysis products in the ileum and concentration of short chain fatty acids (SCFA) in the caeca of broiler chickens. 2. In total, 500 male Ross 308 broilers were used in this 29-day (d) study. The treatments were organised into a 2 × 2 plus 1 factorial arrangement consisting of two additives (xylanase or XOS) at two levels (low or high) plus a control treatment with no additives. This gave five treatments with 100 birds in each treatment group. The diets were slightly deficient in protein by 20 g/kg and energy by 1 MJ/kg. 3. On d 14 and 28, two birds per pen were euthanised, the caeca content collected and analysed for short chain fatty acid (SCFA) concentration. On d 29, six birds per pen were euthanised and ileal digesta were collected and analysed for the concentration of NSP fractions. 4. On d 14, caecal acetic acid, iso-butyric acid, iso-valeric acid, n-valeric acid and total SCFA concentrations were significantly greater (P ≤ 0.05) when diets were supplemented with XOS compared with xylanase. 5. Ileal concentration of arabinose, galactose and glucuronic acid (GlucA2) were significantly greater (P ≤ 0.05) in the insoluble NSP fraction when diets were supplemented with a high level of xylanase, compared with the control treatment. Ileal concentration of fructose was significantly greater (P ≤ 0.05) in the water soluble NSP when a high level of xylanase or low level of XOS were included in the diet compared with the control. 6. It was concluded that xylanase and XOS had similar effects on NSP concentration and SCFA in the caeca, although there was little effect on performance. This observation demonstrated further benefits of xylanase supplementation in wheat-based broiler diets beyond digesta viscosity reduction and the release of extra nutrients.
Xq26 duplications lead to undergrowth or overgrowth via competing pathways including GPC3/GPC4

The Xq26 locus has importance in human growth with multiple genes and regions playing important roles, which potentially leads to macrosomia or microsomia if disrupted. One region of Xq26.2 comprises the genes GPC3 and GPC4; deletion or duplication of this region has been recently been shown to result in overgrowth, specifically Simpson–Golabi–Behmel syndrome. We describe a male patient with two maternally inherited Xq26 microduplications; the first was 0.8 Mb at Xq26.2 affecting only GPC3 and GPC4, and the second, a distal 0.6 Mb duplication at Xq26.3 affecting seven genes. Rather than having Simpson–Golabi–Behmel syndrome, our patient had microcephaly and undergrowth, with development that was within normal limits at 25 months of age. This finding suggests that the molecular pathway leading to overgrowth secondary to GPC3/GPC4 haploinsufficiency can be overpowered by a disruption to the distal Xq26.3 region. Of the genes in that region, we propose that SLC9A6 is the most likely to play an important role as mutations in this gene lead to Christianson syndrome, in which patients may have microcephaly and weight loss.
Complete Chloroplast Genome Sequence of the Medicinal Plant Arctium lappa (Burdock).

Arctium lappa, also named burdock, has a long medicinal and edible history. It has recently gained increasing attention because of its economic value. In this study, we obtained the complete chloroplast genome of A. lappa by Illumina Hiseq. The complete chloroplast genome of A. lappa is a typical circular structure with 152,708 bp in length. The GC content in the whole chloroplast genome of A. lappa is 37.7%. A total of 37 tRNA genes, 8 rRNA genes and 87 protein-coding genes were successfully annotated. And the chloroplast genome contains 113 unique genes, 19 of which are duplicated in the inverted repeat. The distribution of 39 simple sequence repeats was analysed, and most of them are located in the large single-copy (LSC) sequence. An inversion comprising 16 genes was found in the LSC region, which is 26,283 bp long. We performed multiple sequence alignments using 72 common protein-coding genes of 29 species and constructed the Maximum Parsimony (MP) tree. The MP phylogenetic result shows that A. lappa grouped together with Carthamus tinctorius, Centaurea diffusa and Saussurea involucrate. The chloroplast genome of A. lappa is valuable resource for further studies of Asteraceae species.
Improving pneumovirus isolation using a centrifugation and AZD1480 combined method.

The isolation of respiratory viruses, especially from clinical specimens, often shows poor efficiency with classical cell culture methods. The lack of suitable methods to generate virus particles inhibits the development of diagnostic assays, treatments, and vaccines. We compared three inoculation methods, classical cell culture, the addition of a JAK2 inhibitor AZD1480, and centrifugation-enhanced inoculation (CEI), to replicate human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV). In addition, a combined method using AZD1480 treatment and CEI was used on throat swabs to verify that this method could increase virus isolation efficiency from human clinical specimens. Both CEI and AZD1480 treatment increased HRSV and HMPV genome replication. Also, the combined method using CEI and AZD1480 treatment enhanced virus proliferation synergistically. The combined method is particularly suited for the isolation of interferon-sensitive or slowly growing viruses from human clinical specimens.
Fermentation for tailoring the technological and health related functionality of food products

Abstract Fermented foods are experiencing a resurgence due to the consumers’ growing interest in foods that are natural and health promoting. Microbial fermentation is a biotechnological process which transforms food raw materials into palatable, nutritious and healthy food products. Fermentation imparts unique aroma, flavor and texture to food, improves digestibility, degrades anti-nutritional factors, toxins and allergens, converts phytochemicals such as polyphenols into more bioactive and bioavailable forms, and enriches the nutritional quality of food. Fermentation also modifies the physical functional properties of food materials, rendering them differentiated ingredients for use in formulated foods. The science of fermentation and the technological and health functionality of fermented foods is reviewed considering the growing interest worldwide in fermented foods and beverages and the huge potential of the technology for reducing food loss and improving nutritional food security.
The Cumulative Risk of Chemical and Nonchemical Exposures on Birth Outcomes in Healthy Women: The Fetal Growth Study

Metals, stress, and sociodemographics are commonly studied separately for their effects on birth outcomes, yet often jointly contribute to adverse outcomes. This study analyzes two methods for measuring cumulative risk to understand how maternal chemical and nonchemical stressors may contribute to small for gestational age (SGA). SGA was calculated using sex-specific fetal growth curves for infants of pregnant mothers (n = 2562) enrolled in the National Institute of Child Health and Human Development (NICHD) Fetal Growth Study. The exposures (maternal lead, mercury, cadmium, Cohen’s perceived stress, Edinburgh depression scores, race/ethnicity, income, and education) were grouped into three domains: metals, psychosocial stress, and sociodemographics. In Method 1 we created cumulative risk scores using tertiles. Method 2 employed weighted quantile sum (WQS) regression. For each method, logistic models were built with three exposure domains individually and race/ethnicity, adjusting for age, parity, pregnancy weight gain, and marital status. The adjusted effect of overall cumulative risk with three domains, was also modeled using each method. Sociodemographics was the only exposure associated with SGA in unadjusted models ((odds ratio) OR: 1.35, 95% (confidence interval) CI: 1.08, 1.68). The three cumulative variables in adjusted models were not significant individually, but the overall index was associated with SGA (OR: 1.17, 95% CI: 1.02, 1.35). In the WQS model, only the sociodemographics domain was significantly associated with SGA. Sociodemographics tended to be the strongest risk factor for SGA in both risk score and WQS models.
Experimental and Computational Approaches to Direct Cell Reprogramming: Recent Advancement and Future Challenges

The process of direct cell reprogramming, also named transdifferentiation, permits for the conversion of one mature cell type directly into another, without returning to a dedifferentiated state. This makes direct reprogramming a promising approach for the development of several cellular and tissue engineering therapies. To achieve the change in the cell identity, direct reprogramming requires an arsenal of tools that combine experimental and computational techniques. In the recent years, several methods of transdifferentiation have been developed. In this review, we will introduce the concept of direct cell reprogramming and its background, and cover the recent developments in the experimental and computational prediction techniques with their applications. We also discuss the challenges of translating this technology to clinical setting, accompanied with potential solutions.
Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.
Inhalable Dry Powder of Bedaquiline for Pulmonary Tuberculosis: In Vitro Physicochemical Characterization, Antimicrobial Activity and Safety Studies

Bedaquiline is a newly developed anti-tuberculosis drug, conditionally approved by the United States Food and Drug Administration (USFDA) for treating drug-resistant tuberculosis in adults. Oral delivery of bedaquiline causes severe side effects such as increased hepatic aminotransferase levels and cardiac arrhythmias (prolongation of QT-interval). This study aimed to develop inhalable dry powder particles of bedaquiline with high aerosolization efficiency to reduce the side-effects of oral bedaquiline. Bedaquiline (with or without l-leucine) powders were prepared using a Buchi Mini Spray-dryer. The powders were characterized for physicochemical properties and for their in vitro aerosolization efficiency using a next-generation impactor (NGI). The formulation with maximum aerosolization efficiency was investigated for physicochemical and aerosolization stability after one-month storage at 20 ± 2 °C/30 ± 2% relative humidity (RH) and 25 ± 2 °C/75% RH in an open Petri dish. The cytotoxicity of the powders on A549 and Calu-3 cell-lines was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The powders were also evaluated for antimicrobial activity against Mycobacterium tuberculosis. The aerodynamic diameter of the l-leucine-containing powder was 2.4 µm, and the powder was amorphous in nature. The aerosolization efficiency (fine-particle fraction) of l-leucine-containing powder (fine-particle fraction (FPF): 74.4%) was higher than the bedaquiline-only powder (FPF: 31.3%). l-leucine containing powder particles were plate-shaped with rough surfaces, but the bedaquiline-only powder was spherical and smooth. The optimized powder was stable at both storage conditions during one-month storage and non-toxic (up to 50 µg/mL) to the respiratory cell-lines. Bedaquiline powders were effective against Mycobacterium tuberculosis and had a minimal inhibitory concentration (MIC) value of 0.1 µg/mL. Improved aerosolization may help to combat pulmonary tuberculosis by potentially reducing the side-effects of oral bedaquiline. Further research is required to understand the safety of the optimized inhalable powder in animal models.
Embracing study heterogeneity for finding genetic interactions in large‐scale research consortia

Genetic interactions have been recognized as a potentially important contributor to the heritability of complex diseases. Nevertheless, due to small effect sizes and stringent multiple‐testing correction, identifying genetic interactions in complex diseases is particularly challenging. To address the above challenges, many genomic research initiatives collaborate to form large‐scale consortia and develop open access to enable sharing of genome‐wide association study (GWAS) data. Despite the perceived benefits of data sharing from large consortia, a number of practical issues have arisen, such as privacy concerns on individual genomic information and heterogeneous data sources from distributed GWAS databases. In the context of large consortia, we demonstrate that the heterogeneously appearing marginal effects over distributed GWAS databases can offer new insights into genetic interactions for which conventional methods have had limited success. In this paper, we develop a novel two‐stage testing procedure, named phylogenY‐based effect‐size tests for interactions using first 2 moments (YETI2), to detect genetic interactions through both pooled marginal effects, in terms of averaging site‐specific marginal effects, and heterogeneity in marginal effects across sites, using a meta‐analytic framework. YETI2 can not only be applied to large consortia without shared personal information but also can be used to leverage underlying heterogeneity in marginal effects to prioritize potential genetic interactions. We investigate the performance of YETI2 through simulation studies and apply YETI2 to bladder cancer data from dbGaP.