Serum protein risk stratification score for diagnostic evaluation of metabolic dysfunction-associated steatohepatitis.

Background: Reliable, noninvasive tools to diagnose at-risk metabolic dysfunction-associated steatohepatitis (MASH) are urgently needed to improve management. We developed a risk stratification score incorporating proteomics-derived serum markers with clinical variables to identify high-risk patients with MASH (NAFLD activity score >4 and fibrosis score >2).

Methods: In this 3-phase proteomic study of biopsy-proven metabolic dysfunction-associated steatotic fatty liver disease, we first developed a multi-protein predictor for discriminating NAFLD activity score >4 based on SOMAscan proteomics quantifying 1305 serum proteins from 57 US patients.

Impact of EUCAST Rapid Antimicrobial Susceptibility Testing (RAST) on optimal antimicrobial therapy in gram-negative bloodstream infections.

Objectives: To evaluate the possible impact of RAST on optimal antimicrobial therapy via de-escalation or escalation, and to determine the reduction in antibiotic susceptibility reporting time with RAST.

Methods: In this single-center, prospective descriptive study, RAST was performed on clinical blood cultures containing E. coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii isolates.

Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge.

Multi-omics has the promise to provide a detailed molecular picture of biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimal structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community.

Differentiation of memory processing stages and effect of demographic variables with alternative scoring approaches to the Rey auditory verbal learning test.

Background: The Rey Auditory Verbal Learning Test (RAVLT) is the third most popular verbal memory test and the tenth most frequently used neuropsychological test. The original scoring system of RAVLT does not differentiate stages of memory processing, but a recently developed composite scoring system has this potential. The objectives were to compare the two systems in terms of their capacity to differentiate the stages of memory processing and to study the effect of demographic variables on the learning trials (T) of the Turkish form of RAVLT (T-RAVLT).

KEGG2Net: Deducing gene interaction networks and acyclic graphs from KEGG pathways.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database provides a manual curation of biological pathways that involve genes (or gene products), metabolites, chemical compounds, maps, and other entries. However, most applications and datasets involved in omics are gene or protein-centric requiring pathway representations that include direct and indirect interactions only between genes. Furthermore, special methodologies, such as Bayesian networks require acyclic representations of graphs.

Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes.

Background: Zebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte.

Construct Validity of Auditory Verbal Learning Test.

Objective: Auditory Verbal Learning Test (AVLT) is frequently used in neuropsychology literature to comprehensively assess the memory. The test measures verbal learning as immediate and delayed free recall, recognition, and retroactive and proactive interference. Adaptation of AVLT to the Turkish society has been completed, whereas research and development studies are still underway.

[A Study to Determine the Norms for the Trail Making Test For the Age Range of 20-49 in Turkey].

Objective: The main goal of the study is to determine the normative values of Trail Making Test (TMT) for people between 20-49 years of age; to examine the effect of age, education and sex variables over TMT scores and identify the reliability coefficient of the test.

Method: The sample of the study consisted of 133 women and 130 men, 261 voluntary and healthy participants in total. The data of the research was collected according to 3 x 2 x 2 factorial experimental design; and the participants were distributed to experimental conditions well balanced in terms of the levels of age, education and sex.

Whole genome sequence of a Turkish individual.

Although whole human genome sequencing can be done with readily available technical and financial resources, the need for detailed analyses of genomes of certain populations still exists. Here we present, for the first time, sequencing and analysis of a Turkish human genome. We have performed 35x coverage using paired-end sequencing, where over 95% of sequencing reads are mapped to the reference genome covering more than 99% of the bases.

[Evaluation of visual-motor integration functions in children between 6-15 years of age].

Objective: Visual-motor integration skills are considered an essential domain of clinical and psycho-educational assessment. The goal of the present investigation is to provide the Turkish norms for the Beery-Buktenica Developmental Visual-Motor Integration Test (VMI-4th) for children and adolescents between the ages of 6-15 years as part of a comprehensive neuropsychological test battery.

Method: A total of 1887 children from elementary and high schools in the city of Bursa were recruited for this study.

Proteomic identification of interleukin-2 therapy response in metastatic renal cell cancer.

Purpose: To detect a predictive protein profile that distinguishes interleukin-2 therapy responders and nonresponders among patients with metastatic renal cell carcinoma we used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry.

Materials And Methods: Protein extracts from 56 patients with metastatic clear cell patients renal cell carcinoma obtained from radical nephrectomy specimens before interleukin-2 therapy were applied to protein chip arrays of different chromatographic properties and analyzed using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry. A class prediction algorithm was applied to identify a subset of protein peaks with expression values associated with interleukin-2 response status.

Genomic expression pathways associated with brain injury after cardiopulmonary bypass.

Objectives: Neurologic injury after cardiac surgery, often manifested as neurocognitive decline, is a common postoperative complication without clear cause. We studied acute variations in gene-expression profiles of patients with neurocognitive decline (NCD group) compared with those without neurocognitive decline (NORM group) after cardiopulmonary bypass.

Methods: Forty-two patients undergoing coronary artery bypass grafting, valve procedures, or both by using cardiopulmonary bypass were administered a validated neurocognitive battery preoperatively and postoperatively at day 4.

Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy.

Objective: We examined whether proteomic technologies identify novel urine proteins associated with subsequent development of diabetic nephropathy in subjects with type 2 diabetes before evidence of microalbuminuria.

Research Design And Methods: In a nested case-control study of Pima Indians with type 2 diabetes, baseline (serum creatinine <1.2 mg/dl and urine albumin excretion <30 mg/g) and 10-year urine samples were examined.

Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns.

Normal adult liver is uniquely capable of renewal and repair after injury. Whether this response represents simple hyperplasia of various liver elements or requires recapitulation of the genetic program of the developing liver is not known. To study these possibilities, we examined transcriptional programs of adult liver after partial hepatectomy and contrasted these with developing embryonic liver.

The transcriptome of human oocytes.

The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol.