bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of response to pegylated-interferon-α and ribavirin therapy in Chinese patients infected with different hepatitis C virus genotype
Authors: Guo Xiaoyan , Zhao Zhixin , Xie Junqiang , Cai Qingxian , Zhang Xiaohong , Peng Liang , Gao Zhiliang 
Published: June 2012

Abstract

Background
The standard treatment for patients with chronic hepatitis C (CHC), pegylated interferon-α (PEG-IFN) plus ribavirin (RBV) does not provide a sustained virological response (SVR) in all patients. Genetic variations at the interleukin 28B (IL-28B) locus are important in predicting outcome following therapy in CHC patients.

Results
We investigated the role of IL28B variations (rs8099917) in response to PEG-IFN-α/RBV treatment and evaluated its association with the risk of the null virological response (NVR) and relapse (REL) in different viral genotypes. We found that the overall distributions of the genotype among the SVR, NVR, and REL groups were significantly different (P<0.001). Patients with the TG genotype had an increased risk of NVR and REL (OR=6.45 95% CI =2.88–14.47, P<0.001 for NVR; OR=2.51, 95% CI =1.29–4.86, P=0.006 for REL, respectively), and patients with the GG genotype had a further increased risk of NVR and REL (OR=12.04, 95% CI =3.21–45.13, P<0.001 for NVR; ,OR=4.30, 95% CI =1.21–15.13, P=0.017 for REL, respectively). G variant genotypes (TG+GG) also had an increased risk of NVR and REL, and there was a significant trend for a dose-effect of G allele on the risk of NVR and REL (P<0.05). The SVR rate in TT higher than in TG+GG was more pronounced in those patients infected with non-G1 compared to the patients infected with G1. The treatment response did differ based on the rs8099917 genotype in patients with different viral genotypes, compared with patients infected with the non-G1, the G1 infected patients had an increased risk of NVR and REL (OR=2.03 95% CI =1.03–4.01, P=0.04 for NVR and OR=2.58, 95% CI =1.35–4.94, P=0.004 for REL, respectively). Moreover, multivariate regression analysis show that the rs8099917 G allele was the only independent factor significantly associated with a NVR and REL.

Conclusion
This study suggests that host genetic polymorphisms rs8099917 in the vicinity of IL-28B is the most important predictor of treatment response of PEG-IFN-α/RBV for HCV patients in China.
Stimulation of the autonomic nervous system in colorectal surgery: a study protocol for a randomized controlled trial
Authors: Berghmans Tim MP , Hulsewé Karel WE , Buurman Wim A , Luyer Misha DP 
Published: June 2012

Abstract

Background
Postoperative ileus (POI) is a well-known complication of abdominal surgery and is considered to be caused by a local inflammation in the gut. Previously it has been shown that both local and systemic inflammation can be reduced by stimulation of the autonomic nervous system via lipid rich nutrition. Stimulation of the autonomic nervous system releases acetylcholine from efferent vagal nerve endings that binds to nicotinic receptors located on the inflammatory cells leading to a decrease of pro-inflammatory mediators. Besides administration of nutrition there are other ways of stimulating the autonomic nervous system such as gum chewing.

Methods/design
This prospective, placebo-controlled randomized trial will include 120 patients undergoing colorectal surgery which are randomized for gum chewing preoperatively and in the direct postoperative phase or a placebo. Postoperative ileus will be assessed both clinically by time to first flatus and time to first defecation and by determination of gastric motility using ultrasound to measure dimensions of the antrum. Furthermore the inflammatory response is quantified by analyzing pro-inflammatory mediators. Finally, markers of gut barrier integrity will be measured as well as occurrence of postoperative complications.

Discussion
We hypothesize that chewing gum preoperatively and in the direct postoperative phase in patients undergoing colorectal surgery dampens local and systematic inflammation, via activation of the autonomic nervous system. Down-regulation of the inflammatory cascade via stimulation of the vagus nerve will ameleriote POI and enhance postoperative recovery.

Trial registration
NTR2867
Oncogenic reg IV is a novel prognostic marker for glioma patient survival
Authors: Wang Qi , Deng Jianping , Yuan Jun , Wang Liang , Zhao Zhenwei , He Shiming , Zhang Yongsheng , Tu Yanyang 
Published: June 2012

Abstract

Aim
The aberrant expression of regenerating islet-derived family member, 4 (Reg IV) has been found in various human cancers. However, the roles of Reg IV gene and its encoding product in human glioma have not been clearly understood. Therefore, the aim of this study was to investigate the clinicopathological significance of Reg IV expression in glioma.

Methods
Reg IV mRNA and protein expression in human gliomas and non-neoplastic brain tissues were respectively detected by real-time quantitative RT-PCR assay, Western blot, and immunohistochemistry. The association of Reg IV immunostaining with clinicopathological factors and prognosis of glioma patients was also statistically analyzed.

Results
Reg IV mRNA and protein expression levels in glioma tissues were both significantly higher than those in the corresponding non-neoplastic brain tissues (both P < 0.001). Additionally, the increased Reg IV immunostaining in glioma tissues was significantly associated with advanced pathological grade (P = 0.008). Reg IV protein up-regulation was also significantly correlated with low Karnofsky performance score (KPS) (P = 0.02). Moreover, the overall survival of patients with high Reg IV protein expression was dramatically shorter than those with low Reg IV protein expression (P < 0.001). Multivariate Cox regression analysis further confirmed that Reg IV expression was an independent prognostic factor for patients with gliomas (P = 0.008).

Conclusions
These convinced evidences suggest for the first time that Reg IV might accelerate disease progression and act as a candidate prognostic marker for gliomas.

Virtual slides
The virtual slide(s) for this article can be found here:

http://www.diagnosticpathology.diagnomx.eu/vs/2145344361720706
Isolation and characterization of bovine parainfluenza virus type 3 from water buffaloes (Bubalus bubalis) in Argentina
Authors: Maidana Silvina S , Lomonaco Patricia M , Combessies Gustavo , Craig María I , Diodati Julian , Rodriguez Daniela , Parreño Viviana , Zabal Osvaldo , Konrad José L , Crudelli Gustavo , Mauroy Axel , Thiry Etienne , Romera Sonia A 
Published: June 2012

Abstract

Background
Parainfluenza virus type 3 (PIV3) was isolated from dairy buffaloes (Bubalus bubalis) naturally affected with respiratory and reproductive clinical conditions.

Results
Examination of nasal and vaginal swabs collected from 12 diseased buffaloes led to the isolation of three paramyxovirus isolates from two animals. Antigenic, morphological and biological characteristics of these three isolates were essentially similar to those of members of the Paramyxoviridae family. Antigenic analysis by direct immunofluorescence and cross neutralization test placed these isolates together with bovine parainfluenza virus type 3 (BPIV3). Nucleotide and amino acid phylogenetic analysis of partial matrix gene sequences of the buffalo isolates and six field BPIV3 isolates from bovines in Argentina were studied. Buffalo isolates were similar to genotype B (BPIV3b) while the six BPIV3 isolates were similar to genotypes A (BPIV3a) and C (BPIV3c).

Conclusions
This is the first characterization of BPIV3 in water buffalo.
According to the samples analyzed, in Argentina, the genotype B was found in buffalo and the genotypes A and C were found in cattle.
Mediastinoscope-controlled parasternal fenestration of the pericardium: definitive surgical palliation of malignant pericardial effusion
Authors: Toth Imre , Szucs Geza , Molnar Tamas F 
Published: June 2012

Abstract

Background
The tumorous infiltration or carcinosis of the pericardium could cause pericardial effusion in up to one-third of cases of malignancy, thus potentially interfere with the otherwise desirable oncological treatment. The existing surgical methods for the management of pericardial fluid are well-established but are not without limitations in the symptomatic relief of malignant pericardial effusion (MPE). The recurrence rate ranges between 43 and 69% after pericardiocentesis and 9 to 16% after pericardial drainage. The desire to overcome relative limitations of the existing methods led us to explore an alternative approach.

Methods
The standard armamentarium of the Carlens collar mediastinoscopy procedure was utilized in a Chamberlain parasternal approach of the pericardial sac. The laterality of approach was decided based upon the pleural involvement, as tumor-free pericardiopleural reflection is required. A pericardio-pleural window at least 3 cm in diameter was created. From January 2000 to December 2009, 22 cases were operated on with mediastinoscope-controlled parasternal fenestration (MCPF). Considering the type of the primary tumor, there were 11 lung cancer, 6 breast cancers, 2 haematologic malignancies and in 3 patients the origin of malignancy could not be verified.

Results
There were no operative deaths. We lost one patient (4.5%) in the postoperative hospital period. All of the surviving patients had a minimum of 2 months of symptom-free survival. We detected transient recurrence of MPE in one patient (4.5%) 14 days after the MCPF, which disappeared spontaneously after 24 hours.

Conclusion
The MCPF offers a real alternative in certain cases of pericardial effusion. We recommend this method especially for the definitive surgical palliation of MPE.
Improving metabolic flux predictions using absolute gene expression data
Authors: Lee Dave , Smallbone Kieran , Dunn Warwick B , Murabito Ettore , Winder Catherine L , Kell Douglas B , Mendes Pedro , Swainston Neil 
Published: June 2012

Abstract

Background
Constraint-based analysis of genome-scale metabolic models typically relies upon maximisation of a cellular objective function such as the rate or efficiency of biomass production. Whilst this assumption may be valid in the case of microorganisms growing under certain conditions, it is likely invalid in general, and especially for multicellular organisms, where cellular objectives differ greatly both between and within cell types. Moreover, for the purposes of biotechnological applications, it is normally the flux to a specific metabolite or product that is of interest rather than the rate of production of biomass per se.

Results
An alternative objective function is presented, that is based upon maximising the correlation between experimentally measured absolute gene expression data and predicted internal reaction fluxes. Using quantitative transcriptomics data acquired from Saccharomyces cerevisiae cultures under two growth conditions, the method outperforms traditional approaches for predicting experimentally measured exometabolic flux that are reliant upon maximisation of the rate of biomass production.

Conclusion
Due to its improved prediction of experimentally measured metabolic fluxes, and of its lack of a requirement for knowledge of the biomass composition of the organism under the conditions of interest, the approach is likely to be of rather general utility. The method has been shown to predict fluxes reliably in single cellular systems. Subsequent work will investigate the method’s ability to generate condition- and tissue-specific flux predictions in multicellular organisms.
Spinal subarachnoid hematoma in a woman with HELLP syndrome: a case report
Authors: Fujimaki Hisako , Nakazawa Toshiyuki , Ueno Masaki , Imura Takayuki , Saito Wataru , Takahira Naonobu , Takaso Masashi 
Published: June 2012

AbstractIntroductionSubarachnoid hemorrhages of spinal origin are extremely rare during pregnancy. We present the case of a patient with hemolytic anemia, elevated liver enzymes and low platelet count (the so-called HELLP syndrome), a potentially life-threatening complication associated with pre-eclampsia, who presented with an idiopathic spinal subarachnoid hematoma.Case presentationAt 29 gestational weeks, a 35-year-old Japanese woman was diagnosed with HELLP syndrome based on bilateral leg paralysis, diminished sensation and reflexes, and laboratory findings. The pregnancy was immediately brought to an end by Cesarean delivery. Post-operatively, an MRI scan revealed a space-occupying lesion in her thoracic spinal canal. Emergency decompression was followed by total laminectomy. A subarachnoid hematoma, partially extending as far as the ventral side, was removed. After thorough washing and drain placement, the operation was completed with the suturing of artificial dura mater. Eight months post-operatively, her lower extremity sensation had improved to a score of 8 out of 10, but improvements in her muscular strength were limited to slight gains in her toes. MRI scans taken two months post-operatively revealed edematous spinal cord changes within her medulla.ConclusionsA subarachnoid hematoma during pregnancy is extremely rare, possibly due to increased coagulability during pregnancy. However, this complication is potentially devastating should a clot compress the spinal cord or cauda equina. While several causes of hematoma have been proposed, we speculate that the factors underlying hemorrhagic diathesis in our case were the decreased platelet count characteristic of HELLP syndrome and vascular fragility due to elevated estrogen levels, in addition to increased abdominal pressure during pregnancy and pressure from the gravid uterus resulting in ruptured vessels around the spinal cord. In cases displaying a progressive lesion and severe neurological signs, prompt decompression is crucial.
Antibacterial and antibiotic-potentiation activities of the methanol extract of some cameroonian spices against Gram-negative multi-drug resistant phenotypes
Authors: Voukeng Igor K , Kuete Victor , Dzoyem Jean P , Fankam Aimé G , Noumedem Jaures A K , Kuiate Jules R , Pages Jean-Marie 
Published: June 2012

Abstract

Background
The present work was designed to evaluate the antibacterial properties of the methanol extracts of eleven selected Cameroonian spices on multi-drug resistant bacteria (MDR), and their ability to potentiate the effect of some common antibiotics used in therapy.

Results
The extract of Cinnamomum zeylanicum against Escherichia coli ATCC 8739 and AG100 strains showed the best activities, with the lowest minimal inhibitory concentration (MIC) of 64 μg/ml. The extract of Dorstenia psilurus was the most active when tested in the presence of an efflux pump inhibitor, phenylalanine Arginine-β- Naphtylamide (PAβN), a synergistic effect being observed in 56.25 % of the tested bacteria when it was combined with Erythromycin (ERY).

Conclusion
The present work evidently provides information on the role of some Cameroonian spices in the fight against multi-resistant bacteria.
Genotypes and drug susceptibility of Mycobacterium tuberculosis Isolates in Shihezi, Xinjiang Province, China
Authors: Zhang Juan , Mi Ligu , Wang Yuanzhi , Liu Peizhi , Liang Haiyan , Huang Yi , Lv Bing , Yuan Li 
Published: June 2012

Abstract

Background
Tuberculosis (TB) remains a major global health problem. To investigate the genotypes of Mycobacterium tuberculosis (MTB) and the distribution of Beijing family strains, molecular epidemiology technologies have been used widely.

Methods
From June 2010 to June 2011, 55 M. tuberculosis isolates from patients with pulmonary TB were studied by Beijing family-specific PCR (detection of the deletion of region of difference 105 [RD105]), and mycobacterial interspersed repetitive units variable number tandem repeat (MIRU-VNTR) analysis. Twenty-four MIRU-VNTR loci defined the genotypes and clustering characteristics of the local strains. All strains were subjected to a drug susceptibility test (DST) by the proportion method on Lowenstein-Jensen (LJ) culture media.

Results
Fifty-five clinical isolates of MTB were collected. Beijing family strains represented 85.5% of the isolates studied. Using 24 loci MIRU-VNTR typing categorized the strains into eight gene groups, 46 genotypes, and seven clusters. 83.6% (46/55) of the isolates belonged to the largest gene group. Thirty-six isolates (65.5%) were susceptible, nineteen (34.5%) were resistant to at least one drug, seven (12.8%) were Multidrug-Resistant Tuberculosis (MDR TB), and two (3.6%) were extremely drug-resistant tuberculosis (XDR-TB).

Conclusion
The results showed there were obvious polymorphisms of VNTRs of MTB clinical strains. Beijing family strains of MTB were predominant in the Shihezi region of Xinjiang province. There was no correlation between the drug-resistance and Beijing family strains of MTB. It is necessary to strengthen the monitoring, treatment, and management of drug-resistance TB in Shihezi region, Xinjiang.
Rapid genome-scale mapping of chromatin accessibility in tissue
Authors: Grøntved Lars , Bandle Russell , John Sam , Baek Songjoon , Chung Hye-Jung , Liu Ying , Aguilera Greti , Oberholtzer Carl , Hager Gordon L , Levens David 
Published: June 2012

Abstract

Background
The challenge in extracting genome-wide chromatin features from limiting clinical samples poses a significant hurdle in identification of regulatory marks that impact the physiological or pathological state. Current methods that identify nuclease accessible chromatin are reliant on large amounts of purified nuclei as starting material. This complicates analysis of trace clinical tissue samples that are often stored frozen. We have developed an alternative nuclease based procedure to bypass nuclear preparation to interrogate nuclease accessible regions in frozen tissue samples.

Results
Here we introduce a novel technique that specifically identifies Tissue Accessible Chromatin (TACh). The TACh method uses pulverized frozen tissue as starting material and employs one of the two robust endonucleases, Benzonase or Cyansase, which are fully active under a range of stringent conditions such as high levels of detergent and DTT. As a proof of principle we applied TACh to frozen mouse liver tissue. Combined with massive parallel sequencing TACh identifies accessible regions that are associated with euchromatic features and accessibility at transcriptional start sites correlates positively with levels of gene transcription. Accessible chromatin identified by TACh overlaps to a large extend with accessible chromatin identified by DNase I using nuclei purified from freshly isolated liver tissue as starting material. The similarities are most pronounced at highly accessible regions, whereas identification of less accessible regions tends to be more divergence between nucleases. Interestingly, we show that some of the differences between DNase I and Benzonase relate to their intrinsic sequence biases and accordingly accessibility of CpG islands is probed more efficiently using TACh.

Conclusion
The TACh methodology identifies accessible chromatin derived from frozen tissue samples. We propose that this simple, robust approach can be applied across a broad range of clinically relevant samples to allow demarcation of regulatory elements of considerable prognostic significance.
Ultrasound-guided oblique approach for peripheral venous access in a phantom model
Authors: Tassone Heather M , Tayal Vivek S , Weekes Anthony J , Garner Craymon L , Norton James H 
Published: June 2012

Abstract

Background
Ultrasound (US) vascular guidance is traditionally performed in transverse (T) and longitudinal (L) axes, each with drawbacks. We hypothesized that the introduction of a novel oblique (O) approach would improve the success of US-guided peripheral venous access. We examined emergency physician (EP) performance using the O approach in a gel US phantom.

Methods
In a prospective, case control study, EPs were enrolled from four levels of physician experience including postgraduate years one to three (PGY1, PGY2, PGY3) and attending physicians. After a brief training session, each participant attempted vessel aspiration using a linear probe in T, L, and O axes on a gel US phantom. Time to aspiration and number of attempts to aspiration were recorded. The approach order was randomized, and descriptive statistics were used.

Results
Twenty-four physicians participated. The first-attempt success rate was lower for O, 45.83%, versus 70.83% for T (p = 0.03) and 83.33% for L (p = 0.01). The average time to aspiration was 12.5 s (O) compared with 9.47 s (T) and 9.74 s (L), respectively. There were no significant differences between all four groups in regard to total amount of time and number of aspiration attempts; however, a trend appeared revealing that PGY3 and attending physicians tended to aspirate in less time and by fewer attempts in all three orientations when compared with the PGY2 and PGY1 physicians.

Conclusion
In this pilot study, US-guided simulated peripheral venous access using a phantom gel model in a mixed user group showed that the novel oblique approach was not initially more successful versus T and L techniques.
Satellite cell heterogeneity revealed by G-Tool, an open algorithm to quantify myogenesis through colony-forming assays
Authors: Ippolito Joseph , Arpke Robert W , Haider Kerri T , Zhang Jianyi , Kyba Michael 
Published: June 2012

Abstract

Background
Muscle growth and repair is accomplished by the satellite cell pool, a self-renewing population of myogenic progenitors. Functional heterogeneity within the satellite cell compartment and changes in potential with experimental intervention can be revealed by in vitro colony-forming cell (CFC) assays, however large numbers of colonies need to be assayed to give meaningful data, and manually quantifying nuclei and scoring markers of differentiation is experimentally limiting.

Methods
We present G-Tool, a multiplatform (Java) open-source algorithm that analyzes an ensemble of fluorescent micrographs of satellite cell-derived colonies to provide quantitative and statistically meaningful metrics of myogenic potential, including proliferation capacity and propensity to differentiate.

Results
We demonstrate the utility of G-Tool in two applications: first, we quantify the response of satellite cells to oxygen concentration. Compared to 3% oxygen which approximates tissue levels, we find that 21% oxygen, the ambient level, markedly limits the proliferative potential of transit amplifying progeny but at the same time inhibits the rate of terminal myogenic differentiation. We also test whether satellite cells from different muscles have intrinsic differences that can be read out in vitro. Compared to masseter, dorsi, forelimb and hindlimb muscles, we find that the diaphragm satellite cells have significantly increased proliferative potential and a reduced propensity to spontaneously differentiate. These features may be related to the unique always-active status of the diaphragm.

Conclusions
G-Tool facilitates consistent and reproducible CFC analysis between experiments and individuals. It is released under an open-source license that enables further development by interested members of the community.