Addressing the heterogeneity in liver diseases using biological networks

The abnormalities in human metabolism have been implicated in the progression of several complex human diseases, including certain cancers. Hence, deciphering the underlying molecular mechanisms associated with metabolic reprogramming in a disease state can greatly assist in elucidating the disease aetiology. An invaluable tool for establishing connections between global metabolic reprogramming and disease development is the genome-scale metabolic model (GEM). Here, we review recent work on the reconstruction of cell/tissue-type and cancer-specific GEMs and their use in identifying metabolic changes occurring in response to liver disease development, stratification of the heterogeneous disease population and discovery of novel drug targets and biomarkers. We also discuss how GEMs can be integrated with other biological networks for generating more comprehensive cell/tissue models. In addition, we review the various biological network analyses that have been employed for the development of efficient treatment strategies. Finally, we present three case studies in which independent studies converged on conclusions underlying liver disease

A nationwide multicentre study in Turkey for establishing reference intervals of haematological parameters with novel use of a panel of whole blood

IntroductionA nationwide multicentre study was conducted to establish well-defined reference intervals (RIs) of haematological parameters for the Turkish population in consideration of sources of variation in reference values (RVs). Materials and methodsK2-EDTA whole blood samples (total of 3363) were collected from 12 laboratories. Sera were also collected for measurements of iron, UIBC, TIBC, and ferritin for use in the latent abnormal values exclusion (LAVE) method. The blood samples were analysed within 2 hours in each laboratory using Cell Dyn and Ruby (Abbott), LH780 (Beckman Coulter), or XT-2000i (Sysmex). A panel of freshly prepared blood from 40 healthy volunteers was measured in common to assess any analyser-dependent bias in the measurements. The SD ratio (SDR) based on ANOVA was used to judge the need for partitioning RVs. RIs were computed by the parametric method with/without applying the LAVE method. ResultsAnalyser-dependent bias was found for basophils (Bas), MCHC, RDW and MPV from the panel test results and thus those RIs were derived for each manufacturer. RIs were determined from all volunteers’ results for WBC, neutrophils, lymphocytes, monocytes, eosinophils, MCV, MCH and platelets. Gender-specific RIs were required for RBC, haemoglobin, haematocrit, iron, UIBC and ferritin. Region-specific RIs were required for RBC, haemoglobin, haematocrit, UIBC, and TIBC. ConclusionsWith the novel use of a freshly prepared blood panel, manufacturer-specific RIs’ were derived for Bas, Bas%, MCHC, RDW and MPV. Regional differences in RIs were observed among the 7 regions of Turkey, which may be attributed to nutritional or environmental factors, including altitude

Volume CXIV, Number 4, November 7, 1996

Objective: Turner syndrome (TS) is a chromosomal disorder caused by complete or partial X chromosome monosomy that manifests various clinical features depending on the karyotype and on the genetic background of affected girls. This study aimed to systematically investigate the key clinical features of TS in relationship to karyotype in a large pediatric Turkish patient population.Methods: Our retrospective study included 842 karyotype-proven TS patients aged 0-18 years who were evaluated in 35 different centers in Turkey in the years 2013-2014.Results: The most common karyotype was 45,X (50.7%), followed by 45,X/46,XX (10.8%), 46,X,i(Xq) (10.1%) and 45,X/46,X,i(Xq) (9.5%). Mean age at diagnosis was 10.2±4.4 years. The most common presenting complaints were short stature and delayed puberty. Among patients diagnosed before age one year, the ratio of karyotype 45,X was significantly higher than that of other karyotype groups. Cardiac defects (bicuspid aortic valve, coarctation of the aorta and aortic stenosis) were the most common congenital anomalies, occurring in 25% of the TS cases. This was followed by urinary system anomalies (horseshoe kidney, double collector duct system and renal rotation) detected in 16.3%. Hashimoto's thyroiditis was found in 11.1% of patients, gastrointestinal abnormalities in 8.9%, ear nose and throat problems in 22.6%, dermatologic problems in 21.8% and osteoporosis in 15.3%. Learning difficulties and/or psychosocial problems were encountered in 39.1%. Insulin resistance and impaired fasting glucose were detected in 3.4% and 2.2%, respectively. Dyslipidemia prevalence was 11.4%.Conclusion: This comprehensive study systematically evaluated the largest group of karyotype-proven TS girls to date. The karyotype distribution, congenital anomaly and comorbidity profile closely parallel that from other countries and support the need for close medical surveillance of these complex patients throughout their lifespa

Combining ability and heterosis for fiber quality traits in cotton.

Combining ability analysis and heterosis for cotton fiber quality traits were studied in a set of diallel crosses involving eight cotton (Gossypium sp.) genotypes. Randomized complete block design was used to test 56 F1 and 8 parents for fiber quality traits; length (Len), strength (Str), micronaire (Mic), uniformity (Unf), elongation (Elg), spinning consistency index (Sci) and short fiber index (Sfi). Analysis revealed significant general combining ability (GCA) and specific combining ability (SCA) effects for all the traits and additive gene effects were important in the inheritance of the traits. Giza-45 had the highest GCA effects for Len, Sci, Unf and Elg while Is-4 had the highest Str value. Mic and Sfi values were lowest for Askabat-100 and Giza-45, respectively. The cross Cukurova-1518 × 108-F and Nazilli-84S × Askabat-100 had the lowest SCA effects for Mic and Sfi, respectively. The highest values for Len (Askabat-100 × 108-F), for Str (Acala Prema × 108-F), for Sci (Is-4 × Giza-45), for Unf (Stoneville-453 × Askabat-100) and for Elg (108-F × Is-4) were also obtained. Hybridizations among Askabat-100 × Nazilli-84S, Is-4 × Giza-45, Askabat-100 × Stoneville-453, Askabat-100 × Giza-45, Is-4 × 108F, Giza-45 × 108F, Giza-45 × Acala Prema, Nazilli-84S × Giza-45, Is-4 × Nazilli-84S and Acala Prema × Askabat-100 crosses yielded the best heterosis and heterobeltiosis values. Aforementioned parents and crosses could be utilized for further selection of high fiber quality and applying 3-way crosses or modified backcross or recurrent selection to genotypes having good combining ability would improve fiber quality..

A media analysis of food crisis: from qualitative analysis to a quantitative approach

In 2007-2008, when food prices started to increase dramatically, purchasing power parity of consumers started to decrease automatically. High food prices were argued to cause poverty, hunger, and food riots among urban populations. Henceforward, ‘food crisis’ became a new story line on the current debate. This paper analyzes different media coverage of urban consumers and rural producers under changes in relative incomes for the 2000-2013 period and propounds media bias on the food crisis debate by using content analysis and OLS regression model

Rhizobacteria promoted yield of cucumber plants grown in perlite under Fusarium wilt stress

WOS: 000317445300004This study was carried out to determine the effects of plant-growth-promoting rhizobacteria (PGPR) on cucumber (Cucumis sativus L cv. Sardes F-1) production in perlite under unheated greenhouse conditions. Four native bacterial strains (18/1K: Pseudomonas putida, 62: Serratia marcescens, 66/3: Bacillus spp., 70: Pseudomonas fluorescens) and one commercial product (FZB24: Bacillus amyloliquefaciens) were tested. Rhizobacteria inoculation took place before sowing and after transplanting. Plants were affected by Fusarium oxysporum f.sp. cucumerinum occurred naturally and effects of PGPR on cucumber yield were found statistically significant. Plants inoculated with Pseudomonas putida strain 18/1K and Serratia marcescens strain 62 gave significantly higher yield compared to the control plants. (C) 2013 Elsevier B.V. All rights reserved.Turkish Scientific Research Council - TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [105 O 571]; Ege University Scientific Research FundEge University [2005 ZRF 004]This work was supported by Turkish Scientific Research Council - TUBITAK (Contract No: 105 O 571) and Ege University Scientific Research Fund (Contract No: 2005 ZRF 004)

Risk Factors For Diabetic Polyneuropathy

INTRODUCTION: The aim of this study was to investigate the risk factors for distal symmetric sensory-motor polyneuropathy (DSP) in patients with type 2 diabetes mellitus (DM). METHOD: Sixty seven patients with type 2 DM (33 males and 34 females) were included in the study. In addition to a detailed neurological examination, the Michigan Neuropathy Screening Instrument was administered to all patients and their total neuropathy scores were calculated. Nerve conduction examinations were performed for all patients. RESULTS: The mean age of the patients was 52.83±.87 years. The mean glycosylated hemoglobin (HbA1C) value was 8.56±2.07% (normal: 3–6.5%). The total neuropathy score significantly correlated with diabetes duration, hypertension, retinopathy, and HbA1C. CONCLUSION: This study confirms the previous reports regarding the association of neuropathy with poor glycaemic control and duration of the disease. The association of neuropathy with retinopathy and hypertension is important

Item analyses of Turkish Society of Cardiovascular Surgery Board 2015 written exam

WOS: 000357842000002Background: This study aims to analyze the items of the recent board written exam conducted by the Turkish Society of Cardiovascular Surgery and develop recommendations on key issues to prepare a superior exam set for future exams. Methods: In the study, items of the recent board exam, which was held in Eskisehir on April 12, 2015, were analyzed in terms of difficulty, discrimination, and validity. Results: It was detected that correct answer items were distributed equally in the exam set, the average rate of questions answered correctly was 63.79%, 59% of the questions were answered correctly above average, and range of exam scores was wide. Rate of questions with desired difficulty index level was 51% and rate of questions with desired discrimination index level was 76%. Of the questions, 9% was invalid while 66% had a high level of validity. Conclusion: Board written exam seems to be a valid test since exam questions cover all topics in the field of expertise, and the number of questions and rate of valid questions are high. The proportion of those successful in the exam was high and candidates were entitled to take the next step. It is assumed that candidates will be successful in the next phase

An experience in the COVID-19 pandemic period: Turkish Cardiovascular Surgery Online Board Exam 2020

Background: The aim of this study was to provide information about the results of the Turkish Cardiovascular Surgery Board written exam, which was held online due to the pandemic. Methods: This cross-sectional study included a total of 41 cardiovascular surgeons and residents (39 males, 2 females) in November 21st, 2020 between 10:00 A.M. and 12:00 P.M. After the online exam was completed, data on participant information and answers to exam questions were obtained from the information system. Results: Of all participants, 39% were working in university hospitals. A total of 82.9% of the participants were specialists. The total mean score of the participants was 60.3 +/- 10.2 and 53.7% of them were declared successful-passed. Aortic surgery (63%), heart failure surgery (50%), and mitral valve surgery (50%) were the most incorrectly answered questions. Conclusion: With the online exam, the Board gained different experiences regarding exam planning and implementation. The Turkish Cardiovascular Surgery Board did not give up the Board exam during the pandemic period and conducted a reliable written exam with many participants