Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small RNA Profiling: A Multiple Protocol Study Across Multiple Laboratories [preprint]

Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation with randomized end-nucleotides, and computational correction factors. Despite this technical bias, relative quantification using small RNA-seq was remarkably accurate and reproducible, even across multiple laboratories using different methods. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols

Spectroscopic Survey of {\gamma} Doradus Stars I. Comprehensive atmospheric parameters and abundance analysis of {\gamma} Doradus stars

We present a spectroscopic survey of known and candidate $\gamma$\,Doradus stars. The high-resolution, high signal-to-noise spectra of 52 objects were collected by five different spectrographs. The spectral classification, atmospheric parameters (\teff, $\log g$, $\xi$), $v\sin i$ and chemical composition of the stars were derived. The stellar spectral and luminosity classes were found between G0-A7 and IV-V, respectively. The initial values for \teff\ and \logg\ were determined from the photometric indices and spectral energy distribution. Those parameters were improved by the analysis of hydrogen lines. The final values of \teff, \logg\ and $\xi$ were derived from the iron lines analysis. The \teff\ values were found between 6000\,K and 7900\,K, while \logg\,values range from 3.8 to 4.5\,dex. Chemical abundances and $v\sin i$ values were derived by the spectrum synthesis method. The $v\sin i$ values were found between 5 and 240\,km\,s$^{-1}$. The chemical abundance pattern of $\gamma$\,Doradus stars were compared with the pattern of non-pulsating stars. It turned out that there is no significant difference in abundance patterns between these two groups. Additionally, the relations between the atmospheric parameters and the pulsation quantities were checked. A strong correlation between the $v\sin i$ and the pulsation periods of $\gamma$\,Doradus variables was obtained. The accurate positions of the analysed stars in the H-R diagram have been shown. Most of our objects are located inside or close to the blue edge of the theoretical instability strip of $\gamma$\,Doradus.Comment: 18 pages, 13 figure

A New Record for Occurrence of Symphodus bailloni (Osteichthyes: Perciformes: Labridae) in the Western Black Sea Coast of Turkey

The fish species Symphodus bailloni (Valenciennes, 1839) reported in the present study were collected between June 2010 and June 2011 from the western Black Sea coasts which were previously not recorded from the Black Sea coast of Turkey. A total of 717 specimens of S. bailloni were measured, ranging between 8.9 and 15.4 cm TL. Morphometrics, meristics, and diagnostic characteristics of the species are presented

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies

BACKGROUND: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2. RESULTS: We detected over 19,000 independent lead cis-eQTLs and over 6000 independent lead trans-eQTLs, targeting over 10,000 gene targets (eGenes), with a false discovery rate (FDR) \u3c 5%. Of previously published significant GWAS SNPs, 48% are identified to be significant eQTLs in our study. Some trans-eQTLs point toward novel mechanistic explanations for the association of the SNP with the GWAS-related phenotype. We also identify 59 distinct blocks or clusters of trans-eQTLs, each targeting the expression of sets of six to 229 distinct trans-eGenes. Ten of these sets of target genes are significantly enriched for microRNA targets (FDR \u3c 5%). Many of these clusters are associated in GWAS with multiple phenotypes. CONCLUSIONS: These findings provide insights into the molecular regulatory patterns involved in human physiology and pathophysiology. We illustrate the value of our eQTL database in the context of a recent GWAS meta-analysis of coronary artery disease and provide a list of targeted eGenes for 21 of 58 GWAS loci

The Influence of Hydrogen Addition to Argon as a Shielding Gas on the Fatigue Performance of TIG Welded AISI 304 Stainless Steel

In this study, AISI 304 austenitic stainless steel sheets are joined through TIG welding under various shielding media. Bending fatigue, notch impact and bending tests are performed on the joined materials. Hardness of the joined materials is also determined. The welding processes are carried using pure argon, argon + 1.5% H₂ and argon + 5% H₂ as shielding media at three different welding currents. Both butt and overlap welding processes are carried out at the same welding parameters. The ER 308 L type wire is used as the filler material for all the joints. The highest fatigue and impact strengths are obtained for both types of joints for argon shielding media. The bending test is applied up to 180°, and no tearing, crack or any other bending defects after visual examination of the bended samples are observed. The welding metal gives the highest hardness values, and they are followed by HAZ and base material.У даному дослідженні листи неіржавійної аустенітної сталі AISI 304 з’єднувалися газовольфрамовим дуговим зварюванням у середовищі різних захисних газів. З’єднані матеріали були піддані тестам на вигин, утомним випробуванням на вигин та випробуванням на ударний вигин із розрізом. Визначалася також твердість з’єднаних матеріалів. Процеси зварювання виконувалися з використанням чистого арґону, арґону + 1,5% H₂ та арґону + 5% H₂ як захисних середовищ при трьох різних струмах зварювання. Виконувалося як зварювання зі стиком упритул, так і внапусток при однакових параметрах зварювання. Для всіх зварних швів як присаджувальний матеріал використовувався дріт типу ER 308 L. Для обох типів швів найбільша утомна і ударна міцності були одержані при використанні арґонового захисного середовища. Випробування на вигин виконувалися до значень кута вигину у 180°; при цьому на зігнутих зразках візуально не спостерігалося жодних розривів, тріщин та будь-яких інших дефектів вигину. Зварюваний метал мав найвищу твердість як у пришовній зоні, так і в основному матеріалі.В данном исследовании листы нержавеющей аустенитной стали AISI 304 соединялись газовольфрамовой дуговой сваркой в среде различных защитных газов. Соединённые материалы были подвергнуты тестам на изгиб, усталостным испытаниям на изгиб и испытаниям на ударный изгиб с разрезом. Определялась также твёрдость соединённых материалов. Процессы сварки производились с использованием чистого аргона, аргона + 1,5% H₂ и аргона + 5% H₂ в качестве защитных сред при трёх разных токах сварки. Выполнялась как сварка встык, так и внахлёст при одинаковых параметрах сварки. Для всех сварных швов в качестве присадочного материала использовалась проволока типа ER 308 L. Для обоих типов швов наибольшая усталостная и ударная прочности были получены при использовании аргоновой защитной среды. Испытания на изгиб проводились до значений угла изгиба в 180°; при этом на согнутых образцах визуально не наблюдалось никаких разрывов, трещин и любых других дефектов изгиба. Свариваемый металл обладал наивысшей твёрдостью как в околошовной зоне, так и в основном материале

Impurity-free quantum well intermixing for large optical cavity high-power laser diode structures

We report on the correlation of atomic concentration profiles of diffusing species with the blueshift of the quantum well luminescence from both as-grown and impurity free quantum wells intermixed on actual large optical cavity high power laser diode structures. Because it is critical to suppress catastrophic optical mirror damage, sputtered SiO2 and thermally evaporated SrF2 were used both to enhance and suppress quantum well intermixing, respectively, in these (Al)GaAs large optical cavity structures. A luminescence blueshift of 55 nm (130 meV) was obtained for samples with 400 nm thick sputtered SiO2These layers were used to generate point defects by annealing the samples at 950 °C for 3 min. The ensuing Ga diffusion observed as a shifting front towards the surface at the interface of the GaAs cap and AlGaAs cladding, as well as Al diffusion into the GaAs cap layer, correlates well with the observed luminescence blue shift, as determined by x-ray photoelectron spectroscopy. Although this technique is well-known, the correlation between the photoluminescence peak blue shift and diffusion of Ga and Al during impurity free quantum well intermixing on actual large optical cavity laser diode structures was demonstrated with both x ray photoelectron and photoluminescence spectroscopy, for the first time. © 2016 IOP Publishing Ltd

Diverse human extracellular RNAs are widely detected in human plasma

There is growing appreciation for the importance of non-protein-coding genes in development and disease. Although much is known about microRNAs, limitations in bioinformatic analyses of RNA sequencing have precluded broad assessment of other forms of small-RNAs in humans. By analysing sequencing data from plasma-derived RNA from 40 individuals, here we identified over a thousand human extracellular RNAs including microRNAs, piwi-interacting RNA (piRNA), and small nucleolar RNAs. Using a targeted quantitative PCR with reverse transcription approach in an additional 2,763 individuals, we characterized almost 500 of the most abundant extracellular transcripts including microRNAs, piRNAs and small nucleolar RNAs. The presence in plasma of many non-microRNA small-RNAs was confirmed in an independent cohort. We present comprehensive data to demonstrate the broad and consistent detection of diverse classes of circulating non-cellular small-RNAs from a large population