Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis |...
Quality control (QC) analyses for 54,334 autosomal and 1,341 BTA X markers were conducted through the check.marker function of ... SNPs genotyping and quality control. Non-European taurine introgressed EASZ (n = 425), from 20 randomly selected sub-locations ... EASZ cattle show a degree of resistance to Rhipicephalus appendiculatus ticks infestation8, as well tolerance to poor quality ... These genes may be associated to superior fertility and semen quality in zebu cattle under heat stress conditions compared to ...
Polygenic risk score analysis revealed shared genetic background in attention deficit hyperactivity disorder and narcolepsy |...
Psychostimulants are effective for the symptomatic control of ADHD (primary recommended intervention) and the two sleep ... In brief, the quality controls for retaining SNPs and individuals were as follows: missing data for SNP , 0.02, Pi-hat ... Genotyping, quality control, and imputation. Genotyping was conducted using Japonica array, designed specifically for 650,000 ... and 1562 healthy controls. The discovery cohort for EHS was 125 EHS patients without HLA-DQB1*06:02 and 562 controls without ...
Human ancestry correlates with language and reveals that race is not an objective genomic classifier | Scientific Reports
We accomplished all data management and quality control using PLINK version 1.965. We generated graphics with R66. Maps were ... Data collection and quality control. In our study, statistical populations are defined as ethno-linguistic groups. Statistical ... A multicenter case-control study of the effect of e-nos VNTR polymorphism on upper gastrointestinal hemorrhage in NSAID users * ... First, controlling for population structure in genome-wide association studies is necessary to prevent spurious association. ...
A genomic data archive from the Network for Pancreatic Organ donors with Diabetes | Scientific Data
nPOD recovers, processes, analyzes, and distributes high-quality biospecimens, collected using optimized standard operating ... Quality control assessment of the UFDIchip genotype array. As of this report, 372 nPOD donors have been genotyped on the ... The software includes quality control (QC) procedures at the sample, plate, and SNP levels. These QC threshold parameters were ... 1c) using the Agilent SureSelect Human All Exon kit (Agilent Technologies, CA, USA). Procedures and quality control (QC) ...
Twelve-month specific IgG response to SARS-CoV-2 receptor-binding domain among COVID-19 convalescent plasma donors in Wuhan |...
Plasma preparation and quality control. Plasma preparation was conducted in accordance with the "Protocol of Clinical Treatment ... For preventing and controlling SARS-CoV-2, as well as the vaccine development, the duration of functional neutralizing antibody ...
Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates | Scientific Reports
... a phenomenon whereby cells are directed to migrate under control of an electrical field. We investigate two cell lines for ... qRT-PCR: RNA isolation and quality control. RNA was isolated using a RNeasy Micro Kit (Qiagen 74004). Sample purity and ... RNA-SEQ: RNA isolation, quality control and library preparation. RNA was extracted using a RNeasy Micro Plus Kit (Qiagen 74034 ... The 3 biological replicates with the best quality control results were chosen for each of the 6 conditions. Library preparation ...
Optimized metrics for orthogonal combinatorial CRISPR screens | Scientific Reports
Removing the residual template plasmid and quality control. Plasmid DNA was isolated from the overnight culture to obtain the ... High-throughput sequencing data quality control, read count table generation, and analysis. Read counts of individual gRNA ... Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014). ... The purified library quality was assessed by next-generation sequencing.. Plasmid library high-throughput sequencing. The ...
Dysregulation of brain and choroid plexus cell types in severe COVID-19 | Nature
... control individuals (including 1 patient with terminal influenza) and 8 patients with COVID-19. Although our ... Individual samples after undergoing quality control (described in snRNA-seq quality control) are integrated in a step-wise ... snRNA-seq quality control. Raw gene counts were obtained by aligning reads to the hg38 genome (refdata-gex-GRCh38-2020-A) using ... Three approaches were combined for quality control: (1) ambient cell free mRNA contamination was removed using SoupX51 for each ...
Reply to: Ptbp1 deletion does not induce astrocyte-to-neuron conversion | Nature
1 Quality control in analyzing the scRNA-seq data.. a,b,c, Violin plots of n-count_RNA, n-feature_RNA and Percent_mt ( ... The master negative regulator REST/NRSF controls adult neurogenesis by restraining the neurogenic program in quiescent stem ...
Genetic factors influencing a neurobiological substrate for psychiatric disorders | Translational Psychiatry
Genotyping, quality control, and imputation. DNA extraction and genome-wide genotyping were conducted as described before28,31, ... Quality control and imputation were conducted separately for each genotyping batch, using the same protocols, in PLINK, R, and ... 311 healthy controls29), Max Planck Institute of Psychiatry (MPIP) (n = 385 MDD patients; n = 197 healthy controls30,31), and ... controls: median = 0.18; MDD: median = −0.010, comparison to controls: p = 3.9 × 10−3; BD: median = −0.35, p = 2.8 × 10−5; ...
Economical analysis of saturation mutagenesis experiments | Scientific Reports
We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer ... purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency and ... In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various ... Table 1 Quick Quality Control and Q-values. Library specifications with resulting QQC charts and Q-values. The three pie charts ...
Neurodegenerative diseases - Latest research and news | Nature
LONRF2 exerts protein quality control in ageing neurons A new study identifies LONRF2 as a protein quality control ubiquitin ... TANGO: a placebo-controlled randomized phase 2 study of efficacy and safety of the anti-tau monoclonal antibody gosuranemab in ...
Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases |...
We sequenced 208 candidate genes from >11,730 cases and >2,867 controls. We identified 91 genes, including 38 new NDD ... Supplementary Figure 1 smMIP quality control for the Gold pool.. For 960 sibling control samples, the frequency of samples (y- ... Supplementary Figure 2 smMIP quality control for the ASD4 pool.. For 960 sibling control samples, the frequency of samples (y- ... Supplementary Figure 3 smMIP quality control for the ASD5 pool.. For 960 sibling control samples, the frequency of samples (y- ...
Volume 44 Issue 8, August 2012
Control of grain size, shape and quality by OsSPL16 in rice Xiangdong Fu and colleagues map variants in OsSPL16 that influence ... Including known covariates can reduce power to detect genetic effects in case-control studies Peter Donnelly and colleagues ... show that higher expression of OsSPL16 promotes cell division and grain filling and can lead to improvements in grain quality ...
Punctuated evolution of canonical genomic aberrations in uveal melanoma | Nature Communications
NGS data sources, quality control, and alignment. Raw data files from 80 TCGA UM samples was obtained from the Cancer Genomics ... Sequence data were quality controlled using FastQC (v0.11.3). WES and WGS reads were trimmed (if required) and aligned to the ... Raw RNA-seq FASTQ files from TCGA were obtained from CGHub and from Furney et al.20 via EGA, assessed for quality using FastQC ...
Self-cooling of a micromirror by radiation pressure | Nature
... and high mechanical quality (Q ≈ 10,000). We observe cooling of the mechanical oscillator by a factor of more than 30; that is ... Quality factor control of mechanical resonators using variable phononic bandgap on periodic microstructures *Naoki Inomata ... Quality factor control of mechanical resonators using variable phononic bandgap on periodic microstructures *Naoki Inomata ... Mertz, J. & Heidmann, A. Photon noise reduction by controlled deletion techniques. J. Opt. Soc. Am. B 10, 745-752 (1993) ...
Undisclosed, unmet and neglected challenges in multi-omics studies | Nature Computational Science
The Quartet Data Portal: integration of community-wide resources for multiomics quality control *Jingcheng Yang ... The Quartet Data Portal: integration of community-wide resources for multiomics quality control *Jingcheng Yang ... Harmonization of quality metrics and power calculation in multi-omic studies. Nat. Commun. 11, 3092 (2020). ... Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain ...
Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes | Nature Neuroscience
Supplementary Figure 1 Methodological considerations for and quality control of single-cell RNA-seq. (a) Neuron numbers per ... Pancreatic polypeptide controls energy homeostasis via Npy6r signaling in the suprachiasmatic nucleus in mice. Cell Metab. 19, ... Obesity-driven synaptic remodeling affects endocannabinoid control of orexinergic neurons. Proc. Natl. Acad. Sci. USA 110, ... Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R ...
A cryo-electron microscopic study of ribosome-bound termination factor RF2 | Nature
Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome *Fuxing Zeng ...
Structural basis for stop codon recognition in eukaryotes | Nature
Shao, S., Brown, A., Santhanam, B. & Hegde, R. S. Structure and assembly pathway of the ribosome quality control complex. Mol. ... Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control *Franziska ... Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control *Franziska ... Extended Data Figure 3 Quality of maps and models.. a, Fourier shell correlation (FSC) curves for the electron microscopy maps ...
DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells | Cell Research
1. Data quality control. Adapter or other artificial sequence polluted reads, such as the illumina sequencing adapters or reads ... The quality-ensured RNA-seq libraries were also pooled and sequenced on HiSeq 2500 platform with 100 or 150 bp paired-end mode ... as the control. Intriguingly, both chrX and chr1 clearly undergo global DNA methylation resetting during human and mouse germ ...
Reduction in local ozone levels in urban São Paulo due to a shift from ethanol to gasoline use | Nature Geoscience
Impact of emission control strategies on air quality: a case study in Piracicaba, São Paulo-Brazil *F. M. Maciel ... CETESB, Relatório Anual sobre a Qualidade do Ar no Estado de São Paulo [Annual Report on Air Quality in the State of São Paulo] ... Auffhammer, M. & Kellogg, R. Clearing the air? The effects of gasoline content regulation on air quality. Am. Econ. Rev. 101, ... Anderson, L. G. Ethanol fuel use in Brazil: Air quality impacts. Energy Environ. Sci. 2, 1015-1037 (2009). ...
Defining blood-induced microglia functions in neurodegeneration through multiomic profiling | Nature Immunology
4 Quality control for primary microglia scRNA-seq and BMDM scRNA-seq datasets.. a, b, Violin plots of number genes (a) and ... 9 Quality control for scRNA-seq data related to Fig. 7.. a, Violin plots of gene counts, UMI counts, and %mito for each ... 8 Ligand-induced profile overlays with EAE innate immune cell signatures, and quality control data related to Fig. 6.. a, Dot ... Three samples did not pass RNA and cDNA library quality control (QC) testing; another was removed owing to large deviation on ...
The Notch and Wnt pathways regulate stemness and differentiation in human fallopian tube organoids | Nature Communications
Quality control and quantification of total RNA were assessed using an Agilent 2100 Bioanalyzer with an RNA Nano 6000 ... RNA quantification and quality control. Total RNA was isolated with TRIzol (Life Technologies) according to the suppliers ... Notch and Wnt signals cooperatively control cell proliferation and tumorigenesis in the intestine. Proc. Natl Acad. Sci. USA ... Representative confocal images of control (a) and DBZ-treated (1 μM) organoids (b), showing an increase in the number of ...
Choice of Voxel-based Morphometry processing pipeline drives variability in the location of neuroanatomical brain markers |...
Data quality control. First, we inspected apparent artifacts and image quality by visual inspection, which confirmed high image ... S8). Furthermore, after controlling the template and excluding images that did not pass quality control (low spatial similarity ... 70 indicates satisfactory to excellent image quality). Thus, all data passed the quality control procedure. ... In contrast, quality control of the preprocessed images by means of excluding images with low spatial similarity reduced ...
A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit | Nature Communications
MRM2 controls mitochondrial respiration by regulating mitoribosome biogenesis. In its absence, mtLSU particles (visualized by ... Thus, the strict quality control of mtLSU assembly is fulfilled. This adds to previous evidence that the binding of assembly ... Elongational stalling activates mitoribosome-associated quality control. Science 370, 1105-1110 (2020). ... a Levels of DmMRM2 transcripts in L3 larvae ubiquitously expressing control (n = 3) or DmMRM2 (n = 4) RNAi under the da-GAL4 ...
Novel biphenylidene-thiopyrimidine derivatives as corrosion inhibitors for carbon-steel in oilfield produced water | Scientific...
Quality Control Laboratory, Operations Department, Jotun, Egypt. Ashraf S. Abousalem. Authors. *Hajar A. Ali. View author ... Also, the inhibitor controls both the dissolution of the anodic steel and the cathodic hydrogen evolution reactions by blocking ... Hussien, B. M., Al-Sabagh, A. M., Migahed, M. A., Shaban, M. M. & Moawad, Z. Corrosion control of X-60 type carbon steel in ... COMPASS force field is used in the simulation of corrosion inhibition process, as it is a high quality forcefield that enables ...
Production of full-length soluble Plasmodium falciparum RH5 protein vaccine using a Drosophila melanogaster Schneider 2 stable...
Production, quality control, stability, and potency of cGMP-produced Plasmodium falciparum RH5.1 protein vaccine expressed in ... In the final analysis, we compared the quality of the antibodies elicited by the v2.0 protein produced in Drosophila S2 cells, ... These data suggest in situ antigen production from the immunized muscle cells led to some improvement in immunogen quality, and ... The differences in GIA seen here could be due to differences in anti-PfRH5 antibody quantity and/or quality. To address this, ...
Comparison of NUCLEOCOUNTER, ANDROVISION with Leja chambers and the newly developed ANDROVISION eFlow for sperm concentration...
Christensen, P., Knudsen, D. B., Wachmann, H. & Madsen, M. T. Quality control in boar semen production by use of the FACSCount ... The determination of sperm concentration is an important part of the quality control of raw boar ejaculates during sperm ... Brito, L.F.C. et al. NAAB-CSS semen quality control program minimum guidelines. (2012). ... National Commitee for pig production guidelines for AI stations: Semen Preservation and Health Control (2005). ...
Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4...
Negative control experiments confirmed that these mechanical and physical effects were induced neither by the acidity of SC4 ... In vitro chromatin assembly - strategies and quality control. Methods Enzymol. 573, 3-41 (2016). ... As a control experiment, SC4 was injected in the channel to test the effect on DNA bundles but did not show any mechanical or ... A second negative control experiment was performed by injecting a nitric acid solution having the same pH as that of the SC4 ...