Severe Convective Storm Environments in Turkey

Severe convective storms occasionally result in loss of life and property in Turkey, a country not known for its severe convective weather. However, relatively little is known about the characteristics of Turkish severe weather environments. This paper documents these characteristics using European Centre for Medium-Range Weather Forecasts (ECMWF) reanalysis data on tornado and severe hail days in Turkey from 1979 to 2013. Severe storm environments are characterized by larger convective available potential energy (CAPE) in Turkey compared to the rest of Europe, but the CAPE values are less than those in typical U.S. severe storm environments. Severe hail is associated with large CAPE and vertical wind shear. Nonmesocyclonic tornadoes are associated with less CAPE compared with the other forms of severe weather. Deep-layer vertical wind shear is slightly weaker in Turkish supercell environments than in U.S. supercell environments, and Turkish tornadic supercell environments are characterized by much weaker low-level shear than in the United States and Europe, at least in the ECMWF reanalysis data. Composite parameters such as the supercell composite parameter (SCP) and energy–helicity index (EHI) can discriminate between very large hail and large hail environments.

Conforming with current regulation in Turkey regarding the freezing of oocytes: A case report of the first pregnancy in Turkey achieved through oocyte vitrification

Objectives: To present the first pregnancy achieved in Turkey with frozen–warmed oocytes in a case with previous nine unsuccessful assisted reproductive technology (ART) attempts. Methods: The clinical follow-up of a 33-year-old female applying to our ART centre after a long and complicated history of infertility is described. Results: In April 2013, the woman attempted our centre for her 10th ART trial. She informed us on oocyte pick-up (OPU) day that her husband had been hospitalized following a car crush in Albania and was unable to travel to our clinic to give a sperm sample. We were therefore placed in the position of having to make an emergency decision. OPU was done and seven oocytes were retrieved. Six metaphase II (MII) oocytes out of seven Cumulus Oocyte Complexes (COCs) were vitrified using the Kitazato Vitrification Cryotop Kit. Six months later, in November 2013, the patient applied for transfer. Two blastocysts were transferred and the ART trial resulted with a singleton pregnancy and the birth of a healthy new-born at term via cesarean section. Conclusion: Regulation Codes on Assisted Reproductive Procedures and Assisted Reproductive Technology Centres, published in the Official Gazette of the Republic of Turkey, on 6 March 2010 forbade the freezing of gonad cells and tissues except when essential for medical reasons and stated that this would be specified later. However, the Regulation Codes published in the Official Gazette of the Republic of Turkey, on 30 September 2014 provided no further clarification. Unfortunately, the wording of the regulations did not specifically address this unexpected emergency situation. However, we saw our decision to cryopreserve the oocytes as a valid interpretation of the regulations, bearing in mind also the requirement that sperm and oocyte in the IVF process must be those of a married couple. Turkish medicolegal regulations should be revised to increase the chances of more women taking advantage of the procedure to preserve their reproductive autonomy and to give guidance on what action may be taken in emergency situations

Arthroscopic treatment of osteochondral lesions of the talus: Nanofracture versus hyaluronic acid-based cell-free scaffold with concentration of autologous bone marrow aspirate

Biased IGH VDJ gene repertoire and clonal expansions in B cells of chronically hepatitis C virus–infected individuals

Key Points Chronic HCV infection leads to extensive BCR immunoglobulin gene repertoire alterations with pathological features even in absence of MC. Many large B-cell clones are consistently found, mainly among IgM+ memory B cells, showing a massive influence of HCV on this compartment.

Messenger RNA and MicroRNA transcriptomic signatures of cardiometabolic risk factors

Background Cardiometabolic (CM) risk factors are heritable and cluster in individuals. We hypothesized that CM risk factors are associated with multiple shared and unique mRNA and microRNA (miRNA) signatures. We examined associations of mRNA and miRNA levels with 6 CM traits: body mass index, HDL-cholesterol and triglycerides, fasting glucose, and systolic and diastolic blood pressures through cross-sectional analysis of 2812 Framingham Heart Study who had whole blood collection for RNA isolation for mRNA and miRNA expression studies and who consented to genetic research. We excluded participants taking medication for hypertension, dyslipidemia, or diabetes. We measured mRNA ( n  = 17,318; using the Affymetrix GeneChip Human Exon 1.0 ST Array) and miRNA ( n  = 315; using qRT-PCR) expression in whole blood. We used linear regression for mRNA analyses and a combination of linear and logistic regression for miRNA analyses. We conducted miRNA-mRNA coexpression and gene ontology enrichment analyses to explore relations between pleiotropic miRNAs, mRNA expression, and CM trait clustering. Results We identified hundreds of significant associations between mRNAs, miRNAs, and individual CM traits. Four mRNAs ( FAM13A, CSF2RB, HIST1H2AC, WNK1 ) were associated with all 6 CM traits (FDR < 0.001) and four miRNAs (miR-197-3p, miR-328, miR-505-5p, miR-145-5p) were associated with four CM traits (FDR < 0.05). Twelve mRNAs, including WNK1 , that were coexpressed with the four most pleiotropic miRNAs, were also miRNA targets. mRNAs coexpressed with pleiotropic miRNAs were enriched for RNA metabolism (miR-505-5p), ubiquitin-dependent protein catabolism (miR-197-3p, miR-328) and chromatin assembly (miR-328). Conclusions We identified mRNA and miRNA signatures of individual CM traits and their clustering. Implicated transcripts may play causal roles in CM risk or be downstream consequences of CM risk factors on the transcriptome. Studies are needed to establish whether or not pleiotropic circulating transcripts illuminate causal pathways for CM risk. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3533-9) contains supplementary material, which is available to authorized users.

Molecular and agro-morphological characterization of ancient wheat landraces of turkey

Background Turkey is one of the important gene centers for many crop species. In this research, some ancient wheats such as tetraploid and diploid hulled wheats together with hexaploid tir wheats ( Triticum aestivum ssp. leucospermum Korn.) landraces mainly adapted to harsh winter conditions of Eastern Anatolian region of Turkey were characterized at agro-morphological and molecular level. Totally 50 hulled wheat population from Kastamonu, Konya and Kayseri provinces and 15 tir wheats from Kars provinces of Turkey were in-situ collected for characterization in 2013. Some quantitative and qualitative traits of each population were determined. Results Twenty three hulled wheat population collected from Kastamonu province were distinguished into nine emmer and 14 einkorn wheats at morphological level. Additionally, Konya, Kayseri and Kars population were characterized as einkorn, emmer and tir wheat, respectively. Among the evaluated traits, protein ratios of hulled wheats were strikingly higher than registered cultivars. All the populations were also examined by molecular level by using fluorescently labelled 11 polymorphic SSRs primers. The primers exhibited 104 bands, ranging from 6 to 16 with a mean value 9.45 per loci. The clustering analysis separated the germplasm into two clusters which were also divided into two subclusters based on genetic similarity coefficient. Sixty-five population and five checks were analyzed to estimate mean number of alleles (N), expected and observed heterozygoties (He and Ho), polymorphism information content (PIC), Wright fix index (F), genetic deviation from Hardy-Weinberg expectation ( Fit - Fis ) and genetic variation ( Fst ) were determined as 9.45, 0.71, 0.07, 0.67, 0.90, 0.39, 0.87 and 0.39, respectively. A clear genetic deviation from Hardy – Weinberg expectation was observed among population in particular. These results showed considerable genetic variation among landraces rather than within population. Conclusions These molecular information has revealed genetically diverse einkorn, emmer wheat and tir wheat population could be used as parents for further breeding studies in both Turkey and abroad. Furthermore, the molecular analysis has also generally discriminated the germplasm into ploidy level.

The Turkish validation of the Brief International Cognitive Assessment for Multiple Sclerosis (BICAMS) battery

Background Cognitive impairment may be seen in as many as 43–70% of patients with multiple sclerosis (MS) and may be observed in all MS subtypes. The Brief International Cognitive Assessment in Multiple Sclerosis (BICAMS) battery may be used to evaluate cognition status. The purpose of the current study is to validate the BICAMS battery in Turkish. Methods Patients with MS attending our clinic between September 2014 and April 2015 were invited to participate. Healthy control participants were matched in terms of age, gender and years of education. Results One hundred seventy-three MS patients and 153 healthy control participants were enrolled in the study. MS patients performed significantly worse in all trials than the members of the healthy control group. In addition, cognitive dysfunction was identified in 78 of the 173 (45.1%) patients. In the MS with cognitive impairment group, 64 out of 151 (42.4%) subjects were RRMS patients, 12 out of 18 (66.7%) were secondary progressive MS patients, and 2 out of 4 (50%) were primer progressive MS patients. Conclusions The BICAMS has been proposed for assessing cognitive impairment in MS patients. This study shows that the battery is suitable for use in Turkey.

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) < 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 < 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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1142-6) contains supplementary material, which is available to authorized users.

Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?

Drug-like ligands obtained from protein–ligand complexes deposited in the Protein Databank were subjected to conformational searching using various force fields and solvation settings. For each ligand, the resulting conformer pool was examined for the presence of the bioactive (crystal pose-like) conformation. Similarity of conformers toward the crystal-pose was quantified as the best achievable root mean squared deviation (RMSD, heavy atoms only). Analyzing the conformer pools generated by various force fields revealed only small differences in the likelihood of finding a crystal pose-like conformation. However, employing different solvents in the conformational search was found to be very important for achieving RMSDs below 1.0 Å. The best statistical values of likelihood were observed with a recently released force field covering a large portion of dihedral angles occurring in drug-like compounds in combination with the water as solvent. In order to enable computational chemists and modelers to efficiently use available software tools, we have additionally performed several focused analyses on ligands, grouped according to descriptors most relevant for the rational drug design. Electronic supplementary material The online version of this article (doi:10.1186/s13321-017-0216-0) contains supplementary material, which is available to authorized users.

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets

Background Modern synchrotron light sources and detectors produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used imaging techniques that generates data at tens of gigabytes per second is computed tomography (CT). Although CT experiments result in rapid data generation, the analysis and reconstruction of the collected data may require hours or even days of computation time with a medium-sized workstation, which hinders the scientific progress that relies on the results of analysis. Methods We present Trace, a data-intensive computing engine that we have developed to enable high-performance implementation of iterative tomographic reconstruction algorithms for parallel computers. Trace provides fine-grained reconstruction of tomography datasets using both (thread-level) shared memory and (process-level) distributed memory parallelization. Trace utilizes a special data structure called replicated reconstruction object to maximize application performance. We also present the optimizations that we apply to the replicated reconstruction objects and evaluate them using tomography datasets collected at the Advanced Photon Source.Results Our experimental evaluations show that our optimizations and parallelization techniques can provide 158× speedup using 32 compute nodes (384 cores) over a single-core configuration and decrease the end-to-end processing time of a large sinogram (with 4501 × 1 × 22,400 dimensions) from 12.5 h to <5 min per iteration. Conclusion The proposed tomographic reconstruction engine can efficiently process large-scale tomographic data using many compute nodes and minimize reconstruction times.