bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Homocysteine and Related Compounds on Prostacyclin Production by Cultured Human Vascular Endothelial Cells
Authors: Wang Jian , Dudman Nicholas P B , Wilcken David E L 
Published: July 2018

SummaryElevated plasma homocysteine is associated with an increased risk of intravascular thrombosis. Platelet aggregation and thrombosis are inhibited by prostacyclin produced by the vascular endothelium. Our aim was to investigate whether homocysteine and related metabolites inhibit endothelial prostacyclin production. We used a radioimmunoassay for 6-ketoprostaglandin-F1α to assay medium which had been in contact with confluent cultured endothelial cells. In medium containing 20% human serum, endothelial prostacyclin production was not specifically inhibited by homocysteine, S-adenosylhomocysteine or protein-bound homocysteine. Further, there was no consistent difference in prostacyclin production by cells cultured in medium containing sera from homocystinuria patients, compared with medium containing normal healthy sera. We conclude that vascular disorder in homocystinuria is unlikely to result from effects of homocysteine or related metabolites on endothelial prostacyclin production. By contrast, S-adenosylhomocysteine and protein-bound homocysteine specifically inhibited prostacyclin production by cells cultured in medium containing 20% fetal calf serum.
The Influence of Insulin, ß-Estradiol, Dexamethasone and Thyroid Hormone on the Secretion of Coagulant and Anticoagulant Proteins by HepG2 Cells
Authors: Niessen René W L M , Pfaffendorf Birgit A , Sturk Augueste , Lamping Roy J , Schaap Marianne C L , Hack C Erik , Peters Marjolein 
Published: July 2018

SummaryAs a basis for regulatory studies on the influence of hormones on (anti)coagulant protein production by hepatocytes, we examined the amounts of the plasma proteins antithrombin III (AT III), protein C, protein S, factor II, factor X, fibrinogen, and prealbumin produced by the hepatoma cell line HepG2, into the culture medium, in the absence and presence of insulin, β-estradiol, dexamethasone and thyroid hormone. Without hormones these cells produced large amounts of fibrinogen (2,452 ± 501 ng/mg cell protein), AT III (447 ± 16 ng/mg cell protein) and factor II (464 ± 31 ng/mg cell protein) and only small amounts of protein C (50 ± 7 ng/mg cell protein) and factor X (55 ± 5 ng/mg cell protein). Thyroid hormone had a slight but significant effect on the enrichment in the culture medium of the anticoagulant protein AT III (1.34-fold) but not on protein C (0.96-fold) and protein S (0.91-fold). This hormone also significantly increased the amounts of the coagulant proteins factor II (1.28-fold), factor X (1.45-fold) and fibrinogen (2.17-fold). Insulin had an overall stimulating effect on the amounts of all the proteins that were investigated. Neither dexamethasone nor ß-estradiol administration did substantially change the amounts of these proteins.We conclude that the HepG2 cell is a useful tool to study the hormonal regulation of the production of (anti)coagulant proteins. We studied the overall process of protein production, i.e., the amounts of proteins produced into the culture medium. Detailed studies have to be performed to establish the specific hormonal effects on the underlying processes, e.g., transcription, translation, cellular processing and transport, and secretion.
Transcriptional Regulation of Tissue- and Urokinase-type Plasminogen Activator Genes by Thrombin in Human Fetal Lung Fibroblasts
Authors: Hayakawa Yumiko , Tazawa Shigeki , Ishikawa Tai-ichi , Niiya Kenji , Sakuragawa Nobuo 
Published: July 2018

SummaryThe mechanism of thrombin induction of tissue- and urokinase-type plasminogen activator (t-PA and u-PA) biosynthesis was investigated in cultured human fetal lung fibroblast cells, IMR-90. Northern blot analysis of total RNA from thrombin-treated cells showed marked accumulations of both t-PA and u-PA mRNA during 24 h. Nuclear run-on experiments showed that the transcription rates of both genes were increased in the thrombin-treated cells.These thrombin effects were inhibited by cycloheximide (CHX), an inhibitor of protein biosynthesis. Treatment of IMR-90 cells with CHX alone caused an increase in u-PA mRNA but not in t-PA mRNA. CHX, however, did not affect the transcription rates of both genes in the cells. Thus, on-going protein synthesis is required for increased accumulations of both t-PA and u-PA mRNA by thrombin but not for the constitutive expression of u-PA gene in IMR-90 cells. Therefore, we conclude that the accumulations of t-PA and u-PA mRNA due to thrombin result mainly from increased rates of their gene transcriptions, and that this influence is exerted in part by proteins synthesized by thrombin stimulation.Thrombin also increased plasminogen activator inhibitor type-1 (PAI-1) in the levels of both antigen and mRNA more rapidly than it increased t-PA in IMR-90 cells. In conditioned medium, most of the secreted PAI-1 seemed to form a complex with t-PA. Northern blot analysis using a PAI-2 cDNA probe showed that the levels of PAI-2 mRNA were markedly increased in response to thrombin. PAI-2 appeared not to have been secreted by the cells because the antigen was rarely detectable in the conditioned medium. Thus, thrombin increases not only plasminogen activators, but their inhibitors as well.
Relationship between Endothelial Tissue Factor and Thrombogenesis under Blood Flow Conditions
Authors: Diquélou Armelle , Dupouy Dominique , Gaspin Dominique , Constans Jacques , Sié Pierre , Boneu Bernard , Sakariassen Kjell S , Cadroy Yves 
Published: July 2018

SummaryWe have evaluated the relationship between the level of tissue factor (TF) expression by stimulated endothelial cells and thrombus formation under blood flow conditions. Cultures of human umbilical venous endothelial cells (HUVECs) were treated in order to express different levels of TF activity. They were stimulated for 4 h with either I) lipopolysaccharides (LPS, 10 µg/ml), II) recombinant interleukin Iß (IL1ß, 50 Ul/ml) or III) simultaneously with LPS and IL1ß (LPS + IL1ß). TF activity was low on confluent HUVECs or on the corresponding extracellular-matrix (ECM prepared by exposure of HUVECs to 0.1 N NH4OH). In contrast, it was high when HUVECs were stimulated with LPS or IL1ß, and significantly higher (p <0.05) with LPS+IL1ß. The TF activity associated with the stimulated ECM was 2-fold higher (p <0.05) than that expressed on the luminal surface of the stimulated HUVECs, irrespective of the agonist or combination of agonists used.These surfaces were exposed to non-anticoagulated human blood at a venous (50 s-1) and an arterial (650 s-1) wall shear rate in parallel-plate perfusion chambers for 5 min. Thrombus formation was morphologically quantified by measuring the deposition of platelets and fibrin. Fibrin deposition was also immunologically quantified. Fibrin deposition was related to the level of TF expression. Non-stimulated HUVECs and corresponding ECMs were not thrombogenic. The luminal surface of HUVECs stimulated with LPS or IL1ß alone expressed low levels of TF activity and was a poor inducer of platelet deposition and fibrin deposition (<15%) at 50 s-1. In contrast, fibrin deposition increased to 80% when the cells were stimulated with LPS and IL1ß simultaneously. This fibrin deposition was comparable to that found on the corresponding ECM, despite a two-fold lower TF activity. However, at 650 s-1, platelet and fibrin deposition on HUVECs stimulated with LPS + IL1ß were significantly lower than that observed on the corresponding ECM. In all circumstances, the thrombogenicity was TF-dependent, since fibrin deposition was totally blocked by anti-TF antibodies. Thus, it appears that the level of TF activity expressed on endothelial cells governs thrombus formation. However, the impact of TF expression on thrombus formation is also affected by the blood flow.
The Reproductive Health of Women with von Willebrand Disease Unresponsive to DDAVP: Results of an International Survey
Authors: Foster Paul A 
Published: July 2018

SummaryAn international registry was established on the reproductive health of women with types of von Willebrand disease (vWd) unresponsive to DDAVP. Data was collected on 44 women from 16 treatment centers in nine countries. Severe menorrhagia requiring blood product therapy occurred at least once in 80% of the women for whom data was reported. Most of the reported episodes occurred prior to the diagnosis of vWd and/or the use of oral contraceptive (OC) therapy. OC therapy was clinically effective in the treatment of chronic menorrhagia in 22 of 25 (88%) women treated. Two of the women, however, were unable to tolerate chronic OC use and a third became refractory to treatment. Hysterectomy was performed in 10 of the 44 women (23%). The reported indication for six of the procedures was menorrhagia. Seventy percent were performed at two treatment centers, suggesting different thresholds for the performance of the procedure. There were 69 pregnancies reported in 31 of the 44 women. Fifteen of the pregnancies resulted in spontaneous abortions. The incidence of miscarriage was 22% and appeared clustered, with 10 of 15 of the miscarriages occurring in just four of the women
Score Establishment and Brazilian Portuguese version of the Pregnancy Sexual Response Inventory (PSRI)
Authors: Rudge Cibele Vieira Cunha , Calderon Iracema de Mattos Paranhos , Almeida Ana Paula Machado de , Piculo Fernanda , Rudge Marilza Vieira Cunha , Barbosa Angélica Mércia Pascon 
Published: July 2018

Objective To establish the Pregnancy Sexual Response Inventory (PSRI) scores for each domain before and during pregnancy, and to publish the Brazilian Portuguese version of the PSRI.
Methods Pregnant women were recruited during antenatal care; the PSRI was administered to 244 women prenatally at Faculdade de Medicina de Botucatu, at Universidade do Estado de São Paulo (UNESP, in the Portuguese acronym). The PSRI scores were estimated based on the Kings Health Questionnaire (KHQ) and the Medical Outcomes Study 36-item short form survey (SF-36). The raw scale type was used to standardize the minimal value and amplitude of each domain. For each domain, the score varied from 0 to 100, and the composite score was obtained as the domain average. The composite score before and during pregnancy was determined by the sum of the scores of all specific domains for each divided by the full domain number. The categorization of the scale into quartiles was established when all PSRI-specific and composite scores were combined.
Results The composite and specific scores for each domain were categorized into quartiles: 0 < 25 as “very bad;” 25 < 50 as “bad;” 50 < 75 as “good” and 75 to 100 as “excellent.” The mean scores were lower during pregnancy than before pregnancy in 8 of the 10 domains. The Brazilian Portuguese PSRI version is presented.
Conclusion This study allowed the establishment of the PSRI composite and specific scores for each domain, and the categorization of scores into quartiles: very bad, bad, good and excellent. In addition, the Brazilian Portuguese version of the PSRI is presented in full for application in the Brazilian population.
Biofilm Biology and Vaccine Strategies for Otitis Media Due to Nontypeable Haemophilus influenzae
Authors: Novotny Laura , Brockman Kenneth , Mokrzan Elaine , Jurcisek Joseph , Bakaletz Lauren 
Published: July 2018

AbstractOtitis media (OM) is one of the most common diseases of childhood, and nontypeable Haemophilus influenzae (NTHI) is the predominant causative agent of chronic and recurrent OM, as well as OM for which treatment has failed. Moreover, NTHI is now as important a causative agent of acute OM as the pneumococcus. NTHI colonizes the human nasopharynx asymptomatically. However, upon perturbation of the innate and physical defenses of the airway by upper respiratory tract viral infection, NTHI can replicate, ascend the Eustachian tube, gain access to the normally sterile middle ear space, and cause disease. Bacterial biofilms within the middle ear, including those formed by NTHI, contribute to the chronic and recurrent nature of this disease. These multicomponent structures are highly resistant to clearance by host defenses and elimination by traditional antimicrobial therapies. Herein, we review several strategies utilized by NTHI to persist within the human host and interventions currently under investigation to prevent and/or resolve NTHI-induced diseases of the middle ear and uppermost airway.
Pediatric Deep Neck Space Infections: A Medical and Surgical Perspective
Authors: Gregory Stacie , Chun Robert , Huppler Anna , Mohandas Sindhu 
Published: July 2018

AbstractPediatric deep neck space infections (DNSI) are common in children. If unrecognized, DNSIs can rapidly progress with the potential for developing serious complications. Children fair better than their adult counterparts in the face of complications such as mediastinitis, but early recognition and aggressive management is key to prevent mortality and limit morbidity. Knowledge of the anatomy related to the deep neck spaces helps in anticipating and managing the potential complications. In this article, we review the clinical presentation, complications, and management in pediatric DNSI from the point of view of the pediatric infectious disease physician and the otolaryngologist. We discuss the best management based on current available evidence and the experience of the authors.
Revascularization of AlloDerm Used during Endoscopic Skull Base Surgery
Authors: Taufique Zahrah , Bhatt Nupur , Zagzag David , Lebowitz Richard , Lieberman Seth 
Published: July 2018

Objectives AlloDerm is an acellular dermal matrix often used for reconstruction throughout the body. AlloDerm has been shown to undergo revascularization when used to reconstruct soft tissue such as in abdominal wall reconstruction. In this study, the authors review the literature on revascularization of AlloDerm and demonstrate the histologic findings of AlloDerm after implantation during skull base reconstruction.
Study Design Literature review and case reports.
Setting Tertiary Care Institution
Participants Patients from a tertiary care institution
Main Outcome Measures Histologic slides are evaluated and compared with nonimplanted AlloDerm.
Methods The authors review a case of explanted AlloDerm that had been used for skull base reconstruction after endoscopic skull base surgery.
Results Upon reviewing the histologic slides of explanted AlloDerm to nonimplanted AlloDerm, we demonstrate revascularization of AlloDerm when used in skull base reconstruction. Representative slides will be included.
Conclusions AlloDerm undergoes revascularization when used for skull base reconstruction.
Identification of flood area in the coastal region using remote sensing in Karawang Regency, West Java
Authors: Riadi Bambang , Barus Baba , Widiatmaka  , Yanuar Moh , Pramudya Bambang 
Published: July 2018

Abstract
Flooding often occurs in the lowlands, while the area is usually a rice production centres which affects the rice crop. Rice fields is generally located on fluvial plains and usually located in coastal areas, with relatively lower altitudes than roads or settlements. Physically wetland is an area flooding hazard and wetlands tend to longer floods than surrounding areas. Flood-hazard areas are formed due to sedimentation and usually at the confluence of river. This area is a fertile area for agriculture, has shallow ground water which is well suited for residential and urban areas. Karawang regency is one of the largest producers of rice commodities in West Java, therefore the Karawang regency government faces a challenge in maintaining the level of rice production due to global climate change that worsen the threat of flood hazard, in addition to land use change and increasing population. Based on the results of the spatial analysis from period of 2000 to 2006 the wetland area have been converted up to 7,493 ha. For the period of 2006 to 2015 wetland area have been converted up to 14,416 ha. Utilization of Geographic Information System with a model of Cellular Automata - Marcov Chain is an appropriate method for studying the phenomenon of expansion of build ups land in coastal region. The primary data used in the research is a land cover map of 2000, 2006 and 2015, which were the results of the multispectral classification of Landsat. The prediction of land cover change for the next fifteen years shows a continuous increase in built up area. The expansion of built up area and the possibility of widespread flood hazard areas, have inverse relationship with the decreasing of agricultural land area.
Interpretation of differential gene expression results of RNA-seq data: review and integration
Authors: McDermaid Adam , Monier Brandon , Zhao Jing , Liu Bingqiang , Ma Qin 
Published: July 2018

Abstract
Differential gene expression (DGE) analysis is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes across two or more conditions and is widely used in many applications of RNA-seq data analysis. Interpretation of the DGE results can be nonintuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we reviewed DGE results analysis from a functional point of view for various visualizations. We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich visualizations for the interpretation of DGE results from three widely used tools, Cuffdiff, DESeq2 and edgeR. The implemented functions are also tested on five real-world data sets, consisting of one human, one Malus domestica and three Vitis riparia data sets.
FLYCOP: metabolic modeling-based analysis and engineering microbial communities
Authors: García-Jiménez Beatriz , García José Luis , Nogales Juan 
Published: July 2018

Abstract

Motivation
Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account.

Results
In contrast to previous systems optimizing microbial consortia, FLYCOP has novel characteristics to face up to new problems, to represent additional features and to analyze events influencing the consortia behavior. In this manuscript, FLYCOP optimizes a Synechococcus elongatus-Pseudomonas putida consortium to produce the maximum amount of bio-plastic (PHA, polyhydroxyalkanoate), and highlights the influence of metabolites exchange dynamics in a four auxotrophic Escherichia coli consortium with parallel growth. FLYCOP can also provide an explanation about biological evolution driving evolutionary engineering endeavors by describing why and how heterogeneous populations emerge from monoclonal ones.

Availability and implementation
Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP

Supplementary information
Supplementary data are available at Bioinformatics online.
Bayesian inference on stochastic gene transcription from flow cytometry data
Authors: Tiberi Simone , Walsh Mark , Cavallaro Massimo , Hebenstreit Daniel , Finkenstädt Bärbel 
Published: July 2018

Abstract

Motivation
Transcription in single cells is an inherently stochastic process as mRNA levels vary greatly between cells, even for genetically identical cells under the same experimental and environmental conditions. We present a stochastic two-state switch model for the population of mRNA molecules in single cells where genes stochastically alternate between a more active ON state and a less active OFF state. We prove that the stationary solution of such a model can be written as a mixture of a Poisson and a Poisson-beta probability distribution. This finding facilitates inference for single cell expression data, observed at a single time point, from flow cytometry experiments such as FACS or fluorescence in situ hybridization (FISH) as it allows one to sample directly from the equilibrium distribution of the mRNA population. We hence propose a Bayesian inferential methodology using a pseudo-marginal approach and a recent approximation to integrate over unobserved states associated with measurement error.

Results
We provide a general inferential framework which can be widely used to study transcription in single cells from the kind of data arising in flow cytometry experiments. The approach allows us to separate between the intrinsic stochasticity of the molecular dynamics and the measurement noise. The methodology is tested in simulation studies and results are obtained for experimental multiple single cell expression data from FISH flow cytometry experiments.

Availability and implementation
All analyses were implemented in R. Source code and the experimental data are available at https://github.com/SimoneTiberi/Bayesian-inference-on-stochastic-gene-transcription-from-flow-cytometry-data.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Boolean network inference from time-series gene expression data using a genetic algorithm
Authors: Barman Shohag , Kwon Yung-Keun 
Published: July 2018

Abstract

Motivation
Inferring a gene regulatory network from time-series gene expression data is a fundamental problem in systems biology, and many methods have been proposed. However, most of them were not efficient in inferring regulatory relations involved by a large number of genes because they limited the number of regulatory genes or computed an approximated reliability of multivariate relations. Therefore, an improved method is needed to efficiently search more generalized and scalable regulatory relations.

Results
In this study, we propose a genetic algorithm-based Boolean network inference (GABNI) method which can search an optimal Boolean regulatory function of a large number of regulatory genes. For an efficient search, it solves the problem in two stages. GABNI first exploits an existing method, a mutual information-based Boolean network inference (MIBNI), because it can quickly find an optimal solution in a small-scale inference problem. When MIBNI fails to find an optimal solution, a genetic algorithm (GA) is applied to search an optimal set of regulatory genes in a wider solution space. In particular, we modified a typical GA framework to efficiently reduce a search space. We compared GABNI with four well-known inference methods through extensive simulations on both the artificial and the real gene expression datasets. Our results demonstrated that GABNI significantly outperformed them in both structural and dynamics accuracies.

Conclusion
The proposed method is an efficient and scalable tool to infer a Boolean network from time-series gene expression data.

Supplementary information
Supplementary data are available at Bioinformatics online.