bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and predictors of giving birth in health facilities in Bugesera District, Rwanda
Authors: Joharifard Shahrzad , Rulisa Stephen , Niyonkuru Francine , Weinhold Andrew , Sayinzoga Felix , Wilkinson Jeffrey , Ostermann Jan , Thielman Nathan M 
Published: December 2012

Abstract

Background
The proportion of births attended by skilled health personnel is one of two indicators used to measure progress towards Millennium Development Goal 5, which aims for a 75% reduction in global maternal mortality ratios by 2015. Rwanda has one of the highest maternal mortality ratios in the world, estimated between 249–584 maternal deaths per 100,000 live births. The objectives of this study were to quantify secular trends in health facility delivery and to identify factors that affect the uptake of intrapartum healthcare services among women living in rural villages in Bugesera District, Eastern Province, Rwanda.

Methods
Using census data and probability proportional to size cluster sampling methodology, 30 villages were selected for community-based, cross-sectional surveys of women aged 18–50 who had given birth in the previous three years. Complete obstetric histories and detailed demographic data were elicited from respondents using iPad technology. Geospatial coordinates were used to calculate the path distances between each village and its designated health center and district hospital. Bivariate and multivariate logistic regressions were used to identify factors associated with delivery in health facilities.

Results
Analysis of 3106 lifetime deliveries from 859 respondents shows a sharp increase in the percentage of health facility deliveries in recent years. Delivering a penultimate baby at a health facility (OR = 4.681 [3.204 - 6.839]), possessing health insurance (OR = 3.812 [1.795 - 8.097]), managing household finances (OR = 1.897 [1.046 - 3.439]), attending more antenatal care visits (OR = 1.567 [1.163 - 2.112]), delivering more recently (OR = 1.438 [1.120 - 1.847] annually), and living closer to a health center (OR = 0.909 [0.846 - 0.976] per km) were independently associated with facility delivery.

Conclusions
The strongest correlates of facility-based delivery in Bugesera District include previous delivery at a health facility, possession of health insurance, greater financial autonomy, more recent interactions with the health system, and proximity to a health center. Recent structural interventions in Rwanda, including the rapid scale-up of community-financed health insurance, likely contributed to the dramatic improvement in the health facility delivery rate observed in our study.
Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling
Authors: Smith Nicholas , Campbell Brandon , Li Lin , Li Chuan , Alexov Emil 
Published: December 2012

Abstract

Background
With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results
Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand.

Conclusions
The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano shapes in conjunction with biological macromolecule(s). Charges and radii on the macromolecule atoms and the atoms in the shapes are assigned according to the user’s preferences allowing various scenarios of modeling. The default output file is in PQR (PQRE) format which is readable by almost any software available in biophysical field. It can be downloaded from: http://compbio.clemson.edu/downloadDir/ProNO_integrator.tar.gz
Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13 C metabolic flux analysis
Authors: Usui Yuki , Hirasawa Takashi , Furusawa Chikara , Shirai Tomokazu , Yamamoto Natsuko , Mori Hirotada , Shimizu Hiroshi 
Published: December 2012

AbstractBackgroundIt has long been recognized that analyzing the behaviour of the complex intracellular biological networks is important for breeding industrially useful microorganisms. However, because of the complexity of these biological networks, it is currently not possible to obtain all the desired microorganisms. In this study, we constructed a system for analyzing the effect of gene expression perturbations on the behavior of biological networks inEscherichia coli. Specifically, we utilized13C metabolic flux analysis (13C-MFA) to analyze the effect of perturbations to the expression levels ofpgiandenogenes encoding phosphoglucose isomerase and enolase, respectively on metabolic fluxes.ResultsWe constructed gene expression-controllableE. colistrains using a single-copy mini F plasmid. Using thepgiexpression-controllable strain, we found that the specific growth rate correlated with thepgiexpression level.13C-MFA of this strain revealed that the fluxes for the pentose phosphate pathway and Entner-Doudoroff pathway decreased, as thepgiexpression lelvel increased. In addition, the glyoxylate shunt became active when thepgiexpression level was almost zero. Moreover, the flux for the glyoxylate shunt increased when thepgiexpression level decreased, but was significantly reduced in thepgi-knockout cells. Comparatively,enoexpression could not be decreased compared to the parent strain, but we found that increasedenoexpression resulted in a decreased specific growth rate.13C-MFA revealed that the metabolic flux distribution was not altered by an increasedenoexpression level, but the overall metabolic activity of the central metabolism decreased. Furthermore, to evaluate the impact of perturbed expression ofpgiandenogenes on changes in metabolic fluxes inE. coliquantitatively, metabolic sensitivity analysis was performed. As a result, the perturbed expression ofpgigene had a great impact to the metabolic flux changes in the branch point between the glycolysis and pentose phosphate pathway, isocitrate dehydrogenase reaction, anaplerotic pathways and Entner-Doudoroff pathway. In contrast, the impact of perturbedenoexpression to the flux changes inE. colimetabolic network was small.ConclusionsOur results indicate that the response of metabolic fluxes to perturbation topgiexpression was different from that toenoexpression; perturbations topgiexpression affect the reaction related to the Pgi protein function, the isocitrate dehydrogenase reaction, anaplerotic reactions and Entner-Doudoroff pathway. Meanwhile,enoexpression seems to affect the overall metabolic activity, and the impact of perturbedenoexpression on metabolic flux change is small. Using the gene expression control system reported here, it is expected that we can analyze the response and adaptation process of complex biological networks to gene expression perturbations.
Activation of nuclear factor kappa B in peripheral blood mononuclear cells from malaria patients
Authors: Punsawad Chuchard , Krudsood Srivicha , Maneerat Yaowapa , Chaisri Urai , Tangpukdee Noppadon , Pongponratn Emsri , Nantavisai Kwannan , Udomsangpetch Rachanee , Viriyavejakul Parnpen 
Published: December 2012

AbstractBackgroundMalaria parasites and their products can activate a specific immune response by stimulating cytokine production in the host’s immune cells. Transcription nuclear factor kappa B (NF-κB) is an important regulator for the control of many pro-inflammatory genes, such as interleukin-1 (IL-1) and tumor necrosis factor (TNF). The activation and expression of NF-κB p65 in peripheral blood mononuclear cells (PBMCs) of malaria patients were investigated and correlated with the levels of IL-10 and TNF to study the nature of NF-κB p65 and its linkage to inflammatory cytokines.MethodsThe sample group comprised 33 patients admitted with malaria caused byPlasmodium vivax(n = 11), uncomplicatedPlasmodium falciparum(n = 11), and complicatedPlasmodium falciparum(n = 11). Peripheral blood was collected at admission and on day 7 for PBMC isolation. Healthy subjects were used as a control group. The expressions of NF-κB p65 in the PBMCs from malaria patients and the plasma levels of IL-10 and TNF were measured by using enzyme-linked immunosorbent assay (ELISA). The immunofluorescence technique was used to determine NF-κB nuclear translocation.ResultsAt admission, patients withP. vivaxand uncomplicatedP. falciparumhad significantly elevated phospho-NF-κB p65 levels in the PBMCs compared with those of healthy controls. However, patients with complicatedP. falciparummalaria had decreased levels of phospho-NF-κB p65. On day 7 post-treatment, significantly increased phospho-NF-κB p65 was found in the PBMCs of patients with complicatedP. falciparum, compared with healthy controls. The plasma level of IL-10 was elevated in day 0 in patients with complicatedP. falciparummalaria and was found to be negatively correlated with phospho-NF-κB p65 level (rs = −0.630,p = 0.038). However, there was no correlation between phospho-NF-κB p65 expression and TNF level in patients with complicatedP. falciparummalaria.ConclusionsThis is the first report demonstrating alterations in NF-κB p65 activity in the PBMCs of malaria patients. The altered lower features of NF-κB p65 in the PBMCs of patients with complicatedP. falciparumat admission could be due to a suppressive effect of high IL-10 associated with complicatedP. falciparummalaria.
Comparison of the absolute and relative efficiencies of electroporation-based transfection protocols for Plasmodium falciparum
Authors: Hasenkamp Sandra , Russell Karen T , Horrocks Paul 
Published: December 2012

Abstract

Background
Several electroporation protocols exist to transfect exogenous DNA into Plasmodium falciparum. To date, however, only a subjective analysis of their relative efficiencies has been reported.

Methods
A time-course of luciferase reporter expression is used to provide an objective quantitative analysis of the absolute efficiency of three electroporation techniques; direct electroporation of ring stage infected erythrocytes, preloading of erythrocytes and a novel “double-tap” protocol that combines both approaches.

Results
Preloading of erythrocytes shows a mean efficiency of 9.59x10-6, some 5–180 fold more efficient than matched experiments utilizing the “double-tap” and direct electroporation of ring stage infected erythrocytes alone, respectively.

Conclusion
Evidence presented here provides the first quantitative assessment of both the absolute and relative efficiencies of a key molecular tool used to study the biology and pathogenesis of this important human pathogen.
Dihydrotestosterone regulating apolipoprotein M expression mediates via protein kinase C in HepG2 cells
Authors: Yi-zhou Ye , Bing Cao , Ming-qiu Li , Wei Wang , Ru-xing Wang , Jun Rui , Liu-yan Wei , Zhao-hui Jing , Yong Ji , Guo qing Jiao , Jian Zou 
Published: December 2012

Abstract

Background
Administration of androgens decreases plasma concentrations of high-density lipid cholesterol (HDL-C). However, the mechanisms by which androgens mediate lipid metabolism remain unknown. This present study used HepG2 cell cultures and ovariectomized C57BL/6 J mice to determine whether apolipoprotein M (ApoM), a constituent of HDL, was affected by dihydrotestosterone (DHT).

Methods
HepG2 cells were cultured in the presence of either DHT, agonist of protein kinase C (PKC), phorbol-12-myristate-13-acetate (PMA), blocker of androgen receptor flutamide together with different concentrations of DHT, or DHT together with staurosporine at different concentrations for 24 hrs. Ovariectomized C57BL/6 J mice were treated with DHT or vehicle for 7d or 14d and the levels of plasma ApoM and livers ApoM mRNA were measured. The mRNA levels of ApoM, ApoAI were determined by real-time RT-PCR. ApoM and ApoAI were determined by western blotting analysis.

Results
Addition of DHT to cell culture medium selectively down-regulated ApoM mRNA expression and ApoM secretion in a dose-dependent manner. At 10 nM DHT, the ApoM mRNA levels were about 20% lower than in untreated cells and about 40% lower at 1000 nM DHT than in the control cells. The secretion of ApoM into the medium was reduced to a similar extent. The inhibitory effect of DHT on ApoM secretion was not blocked by the classical androgen receptor blocker flutamide but by an antagonist of PKC, Staurosporine. Agonist of PKC, PMA, also reduced ApoM. At 0.5 μM PMA, the ApoM mRNA levels and the secretion of ApoM into the medium were about 30% lower than in the control cells. The mRNA expression levels and secretion of another HDL-associated apolipoprotein AI (ApoAI) were not affected by DHT. The levels of plasma ApoM and liver ApoM mRNA of DHT-treated C57BL/6 J mice were lower than those of vehicle-treated mice.

Conclusions
DHT directly and selectively down-regulated the level of ApoM mRNA and the secretion of ApoM by protein kinase C but independently of the classical androgen receptor.
Local bifurcation of limit cycles and integrability of a class of nilpotent systems
Authors: Li Hongwei , Wu Yusen , Jin Yinlai 
Published: December 2012

Abstract
In this article, center conditions and bifurcation of limit cycles at the nilpotent critical point in a class of seventh-degree systems are investigated. With the help of computer algebra system MATHEMATICA, the first 13 quasi-Lyapunov constants are deduced. As a result, sufficient and necessary conditions in order to have a center are obtained. The result that there exist 13 small amplitude limit cycles created from the three-order nilpotent critical point is also proved. Henceforth, we give a lower bound of cyclicity of three-order nilpotent critical point for seventh-degree nilpotent systems.

MSC: 34C05; 34C07.
A comparative review of cell culture systems for the study of microglial biology in Alzheimer’s disease
Authors: Stansley Branden , Post Jan , Hensley Kenneth 
Published: December 2012

AbstractOver the past two decades, it has become increasingly apparent that Alzheimer’s disease neuropathology is characterized by activated microglia (brain resident macrophages) as well as the classic features of amyloid plaques and neurofibrillary tangles. The intricacy of microglial biology has also become apparent, leading to a heightened research interest in this particular cell type. Over the years a number of different microglial cell culturing techniques have been developed to study either primary mammalian microglia, or immortalized cell lines. Each microglial system has advantages and disadvantages and should be selected for its appropriateness in a particular research context. This review summarizes several of the most common microglial cell culture systems currently being employed in Alzheimer’s research including primary microglia; BV2 and N9 retroviral immortalized microglia; human immortalized microglia (HMO6); and spontaneously immortalized rodent microglial lines (EOC lines and HAPI cells). Particularities of cell culture requirements and characteristics of microglial behavior, especially in response to applied inflammogen stimuli, are compared and discussed across these cell types.
DHEA administration and exercise training improves insulin resistance in obese rats
Authors: Sato Koji , Iemitsu Motoyuki , Aizawa Katsuji , Mesaki Noboru , Ajisaka Ryuichi , Fujita Satoshi 
Published: December 2012

Abstract

Background
Dehydroepiandrosterone (DHEA) is precursor of sex steroid hormone. We demonstrated that acute DHEA injection to type 1 diabetes model rats induced improvement of hyperglycemia. However, the effect of the combination of DHEA administration and exercise training on insulin resistance is still unclear. This study was undertaken to determine whether 6-weeks of DHEA administration and/or exercise training improve insulin resistance in obese male rats.

Methods
After 14 weeks of a high-sucrose diet, obese male Wistar rats were assigned randomly to one of four groups: control, DHEA administration, exercise training, and a combination of DHEA administration and exercise training (n = 10 each group).

Results
After 6-weeks of DHEA administration and/or exercise training, rats in the combination group weighed significantly less and had lower serum insulin levels than rats in the other groups. Moreover, the rats treated with DHEA alone or DHEA and exercise had significantly lower fasting glucose levels (combination, 84 ± 6.5 mg/dL; DHEA, 102 ± 9.5 mg/dL; control, 148 ± 10.5 mg/dL). In addition, insulin sensitivity check index showed significant improvements in the combination group (combination, 0.347 ± 0.11; exercise, 0.337 ± 0.16%; DHEA, 0.331 ± 0.14; control, 0.308 ± 0.12). Muscular DHEA and 5α-dihydrotestosterone (DHT) concentrations were significantly higher in the combination group, and closely correlated with the quantitative insulin-sensitivity check index (DHEA: r = 0.71, p < 0.01; DHT: r = 0.69, p < 0.01).

Conclusion
These results showed that a combination of DHEA administration and exercise training effectively improved fasting blood glucose and insulin levels, and insulin sensitivity, which may reflect increased muscular DHEA and DHT concentrations.
Mucinous adenocarcinoma of the intestinal type arising from mature cystic teratoma of the ovary: a rare case report and review of the literature
Authors: Takai Masaaki , Kanemura Masanori , Kawaguchi Hiroshi , Fujiwara Satoe , Yoo Saha , Tanaka Yoshimichi , Tsunetoh Satoshi , Terai Yoshito , Yamada Takashi , Ohmichi Masahide 
Published: December 2012

Abstract

Background
Mature cystic teratomas (MCTs) are the most common germ cell tumors of the ovary. Malignant tranformation occurs in 1-2% of these neoplasms. Although most of the malignancies arising from MCTs are squamous cell carcinomas, adenocarcinoma of the gastrointestinal type is extremery rare. We herein present a case of adenocarcinoma of the intestinal type arising from a MCT.

Case
A 49-year-old female underwent surgery for a left ovarian tumor. The histology of the cyst walls revealed a MCT with a few hair shafts and a squamous layer, while another part of the tumor showed adenocarcinoma of the intestinal type. Five years after surgery, she is alive without disease.
Phytochemical screening and evaluation of cardioprotective activity of ethanolic extract of Ocimum basilicum L. (basil) against isoproterenol induced myocardial infarction in rats
Authors: Fathiazad Fatemeh , Matlobi Amin , Khorrami Arash , Hamedeyazdan Sanaz , Soraya Hamid , Hammami Mojtaba , Maleki-Dizaji Nasrin , Garjani Alireza 
Published: December 2012

Abstract

Background and the purpose of the study
The objectives of the present study were phytochemical screening and study of the effects of ethanolic extract of aerial parts of Ocimum basilicum (basil) on cardiac functions and histopathological changes in isoproterenol-induced myocardial infarction (MI).

Methods
The leaves of the plant were extracted with ethanol by maceration and subjected to colorimetry to determine flavonoids and phenolic compounds. High-performance TLC analysis and subsequent CAMAG's TLC scanning were performed to quantify rosmarinic acid content. Wistar rats were assigned to 6 groups of normal control, sham, isoproterenol, and treatment with 10, 20, and 40 mg/kg of the extract two times per day concurrent with MI induction. A subcutaneous injection of isoproterenol (100 mg/kg/day) for 2 consecutive days was used to induce MI.

Results
Phytochemical screening indicated the presence of phenolic compounds (5.36%) and flavonoids (1.86%). Rosmarinic acid was the principal phenolic compound with a 15.74% existence. The ST-segment elevation induced by isoproterenol was significantly suppressed by all doses of the extract. A severe myocardial necrosis and fibrosis with a sharp reduction in left ventricular contractility and a marked increase in left ventricular end-diastolic pressure were seen in the isoproterenol group, all of which were significantly improved by the extract treatment. In addition to in-vitro antioxidant activity, the extract significantly suppressed the elevation of malondialdehyde levels both in the serum and the myocardium.

Conclusion
The results of the study demonstrate that Ocimum basilicum strongly protected the myocardium against isoproterenol-induced infarction and suggest that the cardioprotective effects could be related to antioxidative activities.
Indoleamine-2,3-dioxygenase activity in experimental human endotoxemia
Authors: Padberg Jan-Sören , Van Meurs Matijs , Kielstein Jan T , Martens-Lobenhoffer Jens , Bode-Böger Stefanie M , Zijlstra Jan G , Kovesdy Csaba P , Kümpers Philipp 
Published: December 2012

Abstract

Background
Excessive tryptophan metabolism to kynurenine by the rate-limiting enzyme endothelial indoleamine 2,3-dioxygenase 1 (IDO) controls arterial vessel relaxation and causes hypotension in murine endotoxemia. However, its relevance in human endotoxemia has not been investigated so far. We thus aimed to study changes in blood pressure in parallel with tryptophan and kynurenine levels during experimental endotoxemia in humans.

Findings
Six healthy male volunteers were given E. coli lipopolysaccharide (LPS; 4 ng/kg) as a 1-min intravenous infusion. They had levels of soluble E-Selectin and soluble vascular cell adhesion molecule-1 as well as IDO activity assessed as the kynurenine-to-tryptophan plasma ratio by liquid chromatography-tandem mass spectrometry at various time points during a 24 h time course. During endotoxemia, IDO activity significantly increased, reaching peak levels at 8 h after LPS infusion (44.0 ± 15.2 vs. 29.4 ± 6.8 at baseline, P<0.0001). IDO activity correlated inversely with the development of hypotension as shown by random effects linear regression models. Finally, IDO activity exhibited a kinetic profile similar to that of soluble endothelial-specific adhesion molecules.

Conclusions
LPS is a triggering factor for the induction of IDO in men. Our findings strongly support the concept that the induction of IDO in the vascular endothelium contributes to hypotension in human sepsis.