Parameter estimation for biochemical reaction networks using Wasserstein distances

We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a reaction network at different parameter settings and train a Gaussian process to learn the Wasserstein distance between observations and the simulator output for all parameters. We then use Bayesian optimization to find parameters minimizing this distance based on the trained Gaussian process. The effectiveness of our method is demonstrated on the three-stage model of gene expression and a genetic feedback loop for which moment-based methods are known to perform poorly. Our method is applicable to any simulator model of stochastic reaction networks, including Brownian Dynamics.Comment: 22 pages, 8 figures. Slight modifications/additions to the text; added new section (Section 4.4) and Appendi

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Crisis management in Turkish construction industry

Various economical crises have affected Turkish economy during the last decade and construction industry has always been among the hardest hit; giving the idea that a comprehensive approach to crisis management is unavoidable. However, literature showed no findings related with crisis management applications by construction companies. Thus, a questionnaire survey was undertaken by the top management of 120 construction companies to investigate the degree of crisis management applications throughout the industry, mainly focusing on the outcomes during the economical crisis in 2001. Frequency analysis, Likert scale of comparison, Thurstone's paired comparisons, Pearson's chi-square test and Fisher's exact test were used to evaluate the results. The results showed that government policies and instable market conditions were the most important causes of crisis for Turkish construction companies. Meanwhile, only a small number of the companies utilized a systematic crisis management and the extent of crisis management applications varied depending on the size and the structure of the companies. Consequently, panic and powerlessness were the common feelings shared throughout the industry during the economical crisis in 2001. Despite, it was still encouraging that the managers utilized contemporary decision-making methods to get out of the crisis and their final decisions were generally in favour of strategically repositioning themselves. © 2005 Elsevier Ltd. All rights reserved

Role of cited-1 and caspase-6 expression in HELLP syndrome

OBJECTIVE: In this study, we investigated the immunohistochemical staining of cited-1 and caspase-6 expression in the placentas of pregnant women with HELLP syndrome. PATIENTS AND METHODS: Placentas of 20 normotensive patients and 20 women with HELLP syndrome were processed for routine histological tissue processing. The biochemical and clinical parameters of patients were recorded. Placentas were stained with hematoxylin-eosin and cited-1 and caspase-6 immunostaining. RESULTS: Placentas of normotensive patients showed normal histology. Placentas of women with HELLP syndrome showed degenerated cells, hyalinization and vacuolization. Cited-1 expression was negative in normotensive group; however, it was increased in HELLP group, especially in decidual cells, endothelial cells and other placental cells. Caspase-6 expression was negative in placental structures of normotensive groups. However, it was intense in decidual cells, vacuolar and hyalinized areas, inflammatory cells and connective tissue cells in HELLP group. CONCLUSIONS: Cited-1 and caspase-6 are a marker in determining the severity of HELLP syndrome

Propensity Score Analysis of Flow Diverters Placed in Scaffolding Stents

Abstract Background and purpose: Flow-diverter deployment within a stent remains controversial, but flow-diverter deployment within a scaffolding stent has been performed occasionally. To date, an analysis of this scaffolding technique has not been reported. We aimed to evaluate whether the scaffolding technique adversely affects the outcomes of flow diversion. Materials and methods: Patients who had undergone intracranial aneurysm treatment using a Silk flow diverter with (scaffolding group) or without (bare flow-diverter group) a scaffolding stent were identified retrospectively and compared. Propensity score matching was used to match the aneurysms in both groups for variables with a significant difference between groups. Aneurysm occlusion rates and clinical outcomes were compared. Results: There were 84 patients (105 aneurysms) in the bare flow-diverter group and 21 patients (22 aneurysms) in the scaffolding group (using 20 LEO stents and 1 Enterprise stent). The aneurysms in the scaffolding group were larger (mean, 13.1 [SD, 10.7] versus 7 [SD, 4.5] mm, P = .001) and more likely to be fusiform (40.9% versus 5.7%, P .99), 3-6 months (55.5 versus 75.0%, P = .44), 7-12 months (65.0 versus 90.0%, P = .21), or beyond 1 year (73.6 versus 91.6%, P = .36). There was no difference in complication rates between the groups (P > .99). Conclusions: Placement of a scaffolding stent before flow diversion does not adversely affect aneurysm occlusion or complication rates.PubMe

Angiotensin-1 and vimentin expression and ultrastructural examination in severe preeclampsia complicated by HELLP syndrome changes in the structure of the umbilical cord

OBJECTIVE: The purpose of this study was to examine the histopathologic, ultrastructural and immunohistochemical changes in the umbilical cord in women diagnosed with HELLP syndrome. MATERIALS AND METHODS: Postpartum umbilical cords of 40 patients at the 35-38th week of pregnancy were included. 20 severe preeclamptic (HELLP) and 20 normal umbilical cords were used. After the follow-up of tissue parts of 10% formaldehyde solution for histopathology and immunohistochemistry, histopathological and angiopoietin-1 and vimentin antibodies were examined as immunohistochemical after routine paraffin follow-up. For electron microscope analysis, umbilical cord samples were taken into 2.5% glutaral aldehyde solution. RESULTS: In the statistical comparison, mean difference in increased diameter and additional anomaly on the ultrasound of preeclamptic patients was statistically different compared to control patients. In the HELLP group, hyperplasia and degenerative changes, pyknosis of the endothelial cell nuclei of the vessels and apoptotic changes in some regions were observed. Immunohistochemical analysis showed that endothelial cells, basal membrane and fibroblast cells in the HELLP group expressed high levels of vimentin. Angiotensin-1 expression was increased in amniotic epithelial cells, endothelial cells and some pericyte cells. CONCLUSIONS: As a result, it was observed that the signaling that started with trophoblastic invasion with the effect of hypoxia in severe preeclampsia and continued with dysfunction in endothelial cells was parallel to the increase in angiotensin and vimentin receptors. It is thought that the ultrastructural change in endothelial cells may cause disruption of the collagenized structure in Wharton gel, which supports this, and may cause adverse effects in fetal development and nutrition

Industry financial ratios-application of factor analysis in Turkish construction industry

Turkish economy has been hit by various economical crises between the years 1998 and 2001 and the economic stagnation still continues. Past experiences in various countries show that it is vitally important to encourage construction activities in order to get out of stagnation, as construction output directly affects about 200 other sectors and industry financial ratio analysis is a means to provide a basis for the governments to undertake corrective action. However, there are over 50 financial ratios that can be used during analysis and some are more important than the others for different industries. Previous research has shown that there are about 25 factors that are important for the construction companies. This, in turn, requires elimination of unrelated data. Factor analysis is a data reduction and classification technique, which can be applied in financial analysis. Factor analysis was thus applied to the financial data collected from Turkish construction companies for a 5-year period in order to determine the financial indicators that can be used to analyse the financial trend of the industry. Five independent factors, i.e. liquidity, capital structure and profitability, activity efficiency, profit margin and growth, and assets structure were identified to be sensitive to the economical changes in the country. The results of the factor-based analysis can be used both by the government to analyse the changes in the industry with respect to time and by the construction companies to analyse their financial state with respect to their rivals. © 2005 Elsevier Ltd. All rights reserved

Determining the effect of long-term dexamethasone and prednisolone treatment on sugammadex

PubMedID: 30384570Background/aim: We aimed to investigate the effect of long-term use of dexamethasone and prednisolone on the reversal effect of sugammadex. Materials and methods: TTwenty-four male Wistar albino rats were divided into three groups. Dexamethasone (600 µg/kg) was given to group D, prednisolone (10 mg/kg) was given to group P, and an equivalent volume of saline per day was administered intraperitoneally to group S for 14 days, respectively. The left hemidiaphragm with attached phrenic nerve was maintained in Krebs solution. Sugammadex (30 µmol/L) was applied while rocuronium (10 µmol/L) was present in an organ bath and a single twitch was obtained. The right hemidiaphragm was used for both adult (?-subunit) and fetal nicotinic acetylcholine receptor (AChR) (?-subunit) determination using polymerase chain reaction. Results: All animals lost weight, except group S. The mean baseline single-twitch tension was lower in both group D (14.4 ± 1.7 g) and group P (12.68 ± 0.05 g) than group S (16.8 ± 0.5 g) (P < 0.001). When sugammadex was added to the organ bath while rocuronium was present, the single twitch was measured to be lower in both group D (11.7 ± 0.7 g) and group P (11.5 ± 0.78 g) than group S (16.5 ± 0.24 g) (P < 0.001). ?-AChR expression was higher in both dexamethasone and prednisolone than in saline. Conclusion: Long-term medication with dexamethasone and prednisolone caused muscle weakness, resistance to neuromuscular blockers, and upregulation of immature ?-AChR and reduced the neuromuscular reversal effect of sugammadex. © TÜBİTAK

Evaluation of Tetrazolium Violet and Resazurin Assays for Ciprofloxacin Susceptibility Testing of Resistant Mycobacterium tuberculosis Isolates

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Full Paper Epibatidine Alkaloid Chemistry: 5. Domino-Heck Reactions of Azabicyclic and Tricyclic

molecule