bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of 12 weeks of aerobic, resistance or combination exercise training on cardiovascular risk factors in the overweight and obese in a randomized trial
Authors: Ho Suleen S , Dhaliwal Satvinder S , Hills Andrew P , Pal Sebely
Published: August 2012

Background

Evidence suggests that exercise training improves CVD risk factors. However, it is unclear whether health benefits are limited to aerobic training or if other exercise modalities such as resistance training or a combination are as effective or more effective in the overweight and obese. The aim of this study is to investigate whether 12 weeks of moderate-intensity aerobic, resistance, or combined exercise training would induce and sustain improvements in cardiovascular risk profile, weight and fat loss in overweight and obese adults compared to no exercise.

Methods

Twelve-week randomized parallel design examining the effects of different exercise regimes on fasting measures of lipids, glucose and insulin and changes in body weight, fat mass and dietary intake. Participants were randomized to either: Group 1 (Control, n = 16); Group 2 (Aerobic, n = 15); Group 3 (Resistance, n = 16); Group 4 (Combination, n = 17). Data was analysed using General Linear Model to assess the effects of the groups after adjusting for baseline values. Within-group data was analyzed with the paired t-test and between-group effects using post hoc comparisons.

Results

Significant improvements in body weight (−1.6%, p = 0.044) for the Combination group compared to Control and Resistance groups and total body fat compared to Control (−4.4%, p = 0.003) and Resistance (−3%, p = 0.041). Significant improvements in body fat percentage (−2.6%, p = 0.008), abdominal fat percentage (−2.8%, p = 0.034) and cardio-respiratory fitness (13.3%, p = 0.006) were seen in the Combination group compared to Control. Levels of ApoB48 were 32% lower in the Resistance group compared to Control (p = 0.04).

Conclusion

A 12-week training program comprising of resistance or combination exercise, at moderate-intensity for 30 min, five days/week resulted in improvements in the cardiovascular risk profile in overweight and obese participants compared to no exercise. From our observations, combination exercise gave greater benefits for weight loss, fat loss and cardio-respiratory fitness than aerobic and resistance training modalities. Therefore, combination exercise training should be recommended for overweight and obese adults in National Physical Activity Guidelines.

This clinical trial was registered with the Australian New Zealand Clinical Trials Registry (ANZCTR), registration number: ACTRN12609000684224.
Researcher-decision-maker partnerships in health services research: Practical challenges, guiding principles
Authors: Hofmeyer Anne , Scott Catherine , Lagendyk Laura
Published: August 2012

Background

In health services research, there is a growing view that partnerships between researchers and decision-makers (i.e., collaborative research teams) will enhance the effective translation and use of research results into policy and practice. For this reason, there is an increasing expectation by health research funding agencies that health system managers, policy-makers, practitioners and clinicians will be members of funded research teams. While this view has merit to improve the uptake of research findings, the practical challenges of building and sustaining collaborative research teams with members from both inside and outside the research setting requires consideration. A small body of literature has discussed issues that may arise when conducting research in one’s own setting; however, there is a lack of clear guidance to deal with practical challenges that may arise in research teams that include team members who have links with the organization/community being studied (i.e., are “insiders”).

Discussion

In this article, we discuss a researcher-decision-maker partnership that investigated practice in primary care networks in Alberta. Specifically, we report on processes to guide the role clarification of insider team members where research activities may pose potential risk to participants or the team members (e.g., access to raw data).

These guiding principles could provide a useful discussion point for researchers and decision-makers engaged in health services research.
Patient-centered, comparative effectiveness of esophageal cancer screening: protocol for a comparative effectiveness research study to inform guidelines for evidence-based approach to screening and surveillance endoscopy
Authors: Kramer Jennifer R , Arney Jennifer , Chen John , Richardson Peter , Duan Zhigang , Street Richard L , Hinojosa-Lindsey Marilyn , Naik Aanand D , El-Serag Hashem B
Published: August 2012

Background

The comparative effectiveness (CE) of endoscopic screening (versus no screening) for Barrett’s esophagus (BE) in patients with GERD symptoms, or among different endoscopic surveillance strategies in patients with BE, for the early detection of esophageal adenocarcinoma (EA) is unknown. Furthermore, it is unclear if patients or providers have or will adopt any of these strategies (screening only, screening and surveillance, vs. none), irrespective of their effectiveness. Endoscopic screening and surveillance is expensive and can be risky. Therefore, it is imperative to establish the CE and acceptability about the risks and outcomes related to these practices to better inform expert recommendations and provider-patient decisions.

Methods/Results

We propose a mixed methods study which will involve: (1) an analysis of secondary databases (VA and VA-Medicare linked datasets for 2004–09) to examine CE of endoscopic screening and surveillance in an observational study cohort (an estimated 680,000 patients with GERD; 25,000–30,000 with BE; and 3,000 with EA); (2) a structured electronic medical record (EMR) review on a national sample of patients using VA EMRs to verify all EA cases, identify cancer stage, cancer-targeted therapy, and validate the screening and surveillance endoscopy; and (3) qualitative in depth interviews with patients and providers to elicit preferences, norms, and behaviors to explain clinical contexts of these findings and address gaps arising from the CE study.

Conclusion

This study will compare clinical strategies for detecting and monitoring BE, a pre-cancerous lesion. Additionally, by eliciting acceptability of these strategies for patients and providers, we will be able to propose effective and feasible strategies that are likely to be implemented in routine use. Findings will inform recommendations for clinical practice guidelines. Our innovative approach is consistent with the methodological standards of patient-centered outcomes research, and our findings will offer a significant contribution to the literature on cancer surveillance.

Trial Registration

Not applicable
Variation in apoptosis mechanisms employed by malaria parasites: the roles of inducers, dose dependence and parasite stages
Authors: Matthews Holly , Ali Medhat , Carter Victoria , Underhill Ann , Hunt Jennifer , Szor Hannah , Hurd Hilary
Published: August 2012

Background

Plasmodium berghei ookinetes exhibit an apoptotic phenotype when developing within the mosquito midgut lumen or when cultured in vitro. Markers of apoptosis increase when they are exposed to nitric oxide or reactive oxygen species but high concentrations of hydrogen peroxide cause death without observable signs of apoptosis. Chloroquine and other drugs have been used to induce apoptosis in erythrocytic stages of Plasmodium falciparum and to formulate a putative pathway involving cysteine protease activation and mitochondrial membrane permeabilization; initiated, at least in the case of chloroquine, after its accumulation in the digestive vacuole causes leakage of the vacuole contents. The lack of a digestive vacuole in ookinetes prompted the investigation of the effect of chloroquine and staurosporine on this stage of the life cycle. Finally, the suggestion that apoptosis may have evolved as a strategy employed by ookinetes to increase the fitness of surviving parasites was explored by determining whether increasing the ecological triggers parasite density and nutrient depletion induced apoptosis.

Methods

Ookinetes were grown in culture then either exposed to hydrogen peroxide, chloroquine or staurosporine, or incubated at different densities and in different media. The proportion of ookinetes displaying positive markers for apoptosis in treated samples was compared with controls and results were analyzed using analysis of variance followed by a Turkey’s test, or a Kruskal-Wallis test as appropriate.

Results

Hydrogen peroxide below 50 μM triggered apoptosis but cell membranes were rapidly compromised by higher concentrations, and the mode of death could not be defined. Both chloroquine and staurosporine cause a significant increase in ookinetes with condensed chromatin, caspase-like activity and, in the case of chloroquine, phosphatidylserine translocation and DNA fragmentation (not investigated for staurosporine). However, mitochondrial membrane potential remained intact. No relationship between ookinete density and apoptosis was detected but nutrient depletion significantly increased the proportion of ookinetes with chromatin condensation in four hours.

Conclusions

It is proposed that both a mitochondrial and an amitochondrial apoptotic pathway may be involved, dependent upon the trigger that induces apoptosis, and that pathways may differ between erythrocytic stages and ookinetes, or between rodent and human malaria parasites.
High-throughput sorting of mosquito larvae for laboratory studies and for future vector control interventions
Authors: Marois Eric , Scali Christina , Soichot Julien , Kappler Christine , Levashina Elena A , Catteruccia Flaminia
Published: August 2012

Background

Mosquito transgenesis offers new promises for the genetic control of vector-borne infectious diseases such as malaria and dengue fever. Genetic control strategies require the release of large number of male mosquitoes into field populations, whether they are based on the use of sterile males (sterile insect technique, SIT) or on introducing genetic traits conferring refractoriness to disease transmission (population replacement). However, the current absence of high-throughput techniques for sorting different mosquito populations impairs the application of these control measures.

Methods

A method was developed to generate large mosquito populations of the desired sex and genotype. This method combines flow cytometry and the use of Anopheles gambiae transgenic lines that differentially express fluorescent markers in males and females.

Results

Fluorescence-assisted sorting allowed single-step isolation of homozygous transgenic mosquitoes from a mixed population. This method was also used to select wild-type males only with high efficiency and accuracy, a highly desirable tool for genetic control strategies where the release of transgenic individuals may be problematic. Importantly, sorted males showed normal mating ability compared to their unsorted brothers.

Conclusions

The developed method will greatly facilitate both laboratory studies of mosquito vectorial capacity requiring high-throughput approaches and future field interventions in the fight against infectious disease vectors.
Mathematical modelling of the action potential of human embryonic stem cell derived cardiomyocytes
Authors: Paci Michelangelo , Sartiani Laura , Del Lungo Martina , Jaconi Marisa , Mugelli Alessandro , Cerbai Elisabetta , Severi Stefano
Published: August 2012

Background

Human embryonic stem cell derived cardiomyocytes (hESC-CMs) hold high potential for basic and applied cardiovascular research. The development of a reliable simulation platform able to mimic the functional properties of hESC-CMs would be of considerable value to perform preliminary test complementing in vitro experimentations.

Methods

We developed the first computational model of hESC-CM action potential by integrating our original electrophysiological recordings of transient-outward, funny, and sodium-calcium exchanger currents and data derived from literature on sodium, calcium and potassium currents in hESC-CMs.

Results

The model is able to reproduce basal electrophysiological properties of hESC-CMs at 15 40 days of differentiation (Early stage). Moreover, the model reproduces the modifications occurring through the transition from Early to Late developmental stage (50-110, days of differentiation). After simulated blockade of ionic channels and pumps of the sarcoplasmic reticulum, Ca2+ transient amplitude was decreased by 12% and 33% in Early and Late stage, respectively, suggesting a growing contribution of a functional reticulum during maturation. Finally, as a proof of concept, we tested the effects induced by prototypical channel blockers, namely E4031 and nickel, and their qualitative reproduction by the model.

Conclusions

This study provides a novel modelling tool that may serve useful to investigate physiological properties of hESC-CMs.
MicroRNA expression in ovarian carcinoma and its correlation with clinicopathological features
Authors: Lee Heejeong , Park Chul Soo , Deftereos Georgios , Morihara Janice , Stern Joshua E , Hawes Stephen E , Swisher Elizabeth , Kiviat Nancy B , Feng Qinghua
Published: August 2012

Background

MicroRNA (miRNA) expression is known to be deregulated in ovarian carcinomas. However, limited data is available about the miRNA expression pattern for the benign or borderline ovarian tumors as well as differential miRNA expression pattern associated with histological types, grades or clinical stages in ovarian carcinomas. We defined patterns of microRNA expression in tissues from normal, benign, borderline, and malignant ovarian tumors and explored the relationship between frequently deregulated miRNAs and clinicopathologic findings, response to therapy, survival, and association with Her-2/neu status in ovarian carcinomas.

Methods

We measured the expression of nine miRNAs (miR-181d, miR-30a-3p, miR-30c, miR-30d, miR-30e-3p, miR-368, miR-370, miR-493-5p, miR-532-5p) in 171 formalin-fixed, paraffin-embedded ovarian tissue blocks as well as six normal human ovarian surface epithelial (HOSE) cell lines using Taqman-based real-time PCR assays. Her-2/neu overexpression was assessed in ovarian carcinomas (n = 109 cases) by immunohistochemistry analysis.

Results

Expression of four miRNAs (miR-30c, miR-30d, miR-30e-3p, miR-370) was significantly different between carcinomas and benign ovarian tissues as well as between carcinoma and borderline tissues. An additional three miRNAs (miR-181d, miR-30a-3p, miR-532-5p) were significantly different between borderline and carcinoma tissues. Expression of miR-532-5p was significantly lower in borderline than in benign tissues. Among ovarian carcinomas, expression of four miRNAs (miR-30a-3p, miR-30c, miR-30d, miR-30e-3p) was lowest in mucinous and highest in clear cell samples. Expression of miR-30a-3p was higher in well-differentiated compared to poorly differentiated tumors (P = 0.02), and expression of miR-370 was higher in stage I/II compared to stage III/IV samples (P = 0.03). In multivariate analyses, higher expression of miR-181d, miR-30c, miR-30d, and miR-30e-3p was associated with significantly better disease-free or overall survival. Finally, lower expression of miR-30c, miR-30d, miR-30e-3p and miR-532-5p was significantly associated with overexpression of Her-2/neu.

Conclusions

Aberrant expression of miRNAs is common in ovarian tumor suggesting involvement of miRNA in ovarian tumorigenesis. They are associated with histology, clinical stage, survival and oncogene expression in ovarian carcinoma.
Cytomegalovirus seropositivity is associated with glucose regulation in the oldest old. Results from the Leiden 85-plus Study
Authors: Chen Sijia , JM de Craen Anton , Raz Yotam , Derhovanessian Evelyna , Vossen CTM Ann , Westendorp GJ Rudi , Pawelec Graham , Maier Andrea B
Published: August 2012

Background

Cytomegalovirus (CMV) infection has been reported to contribute to the pathogenesis of type 1 diabetes and post-transplantation diabetes. However, CMV infection has not been evaluated as a possible risk factor for type 2 diabetes. Our aim was to investigate potential associations between CMV seropositivity, CMV IgG antibody level and glucose regulation in the oldest old.

Results

CMV seropositive subjects were more likely to have type 2 diabetes (17.2% vs 7.9%, p = 0.016), had a higher level of HbA1c (p = 0.014) and higher non-fasting glucose (p = 0.024) in the oldest olds. These associations remained significant after adjustment for possible confounders. CMV IgG antibody level was not significantly associated with glucose regulation (all p > 0.05).

Conclusions

In the oldest old, CMV seropositivity is significantly associated with various indicators of glucose regulation. This finding suggests that CMV infection might be a risk factor for the development of type 2 diabetes in the elderly.
A novel walking speed estimation scheme and its application to treadmill control for gait rehabilitation
Authors: Yoon Jungwon , Park Hyung-Soon , Damiano Diane Louise
Published: August 2012

Background

Virtual reality (VR) technology along with treadmill training (TT) can effectively provide goal-oriented practice and promote improved motor learning in patients with neurological disorders. Moreover, the VR + TT scheme may enhance cognitive engagement for more effective gait rehabilitation and greater transfer to over ground walking. For this purpose, we developed an individualized treadmill controller with a novel speed estimation scheme using swing foot velocity, which can enable user-driven treadmill walking (UDW) to more closely simulate over ground walking (OGW) during treadmill training. OGW involves a cyclic acceleration-deceleration profile of pelvic velocity that contrasts with typical treadmill-driven walking (TDW), which constrains a person to walk at a preset constant speed. In this study, we investigated the effects of the proposed speed adaptation controller by analyzing the gait kinematics of UDW and TDW, which were compared to those of OGW at three pre-determined velocities.

Methods

Ten healthy subjects were asked to walk in each mode (TDW, UDW, and OGW) at three pre-determined speeds (0.5 m/s, 1.0 m/s, and 1.5 m/s) with real time feedback provided through visual displays. Temporal-spatial gait data and 3D pelvic kinematics were analyzed and comparisons were made between UDW on a treadmill, TDW, and OGW.

Results

The observed step length, cadence, and walk ratio defined as the ratio of stride length to cadence were not significantly different between UDW and TDW. Additionally, the average magnitude of pelvic acceleration peak values along the anterior-posterior direction for each step and the associated standard deviations (variability) were not significantly different between the two modalities. The differences between OGW and UDW and TDW were mainly in swing time and cadence, as have been reported previously. Also, step lengths between OGW and TDW were different for 0.5 m/s and 1.5 m/s gait velocities, and walk ratio between OGS and UDW was different for 1.0 m/s gait velocities.

Conclusions

Our treadmill control scheme implements similar gait biomechanics of TDW, which has been used for repetitive gait training in a small and constrained space as well as controlled and safe environments. These results reveal that users can walk as stably during UDW as TDW and employ similar strategies to maintain walking speed in both UDW and TDW. Furthermore, since UDW can allow a user to actively participate in the virtual reality (VR) applications with variable walking velocity, it can induce more cognitive activities during the training with VR, which may enhance motor learning effects.
The role of crude saliva and purified salivary mucins in the inhibition of the Human Immunodeficiency Virus type 1
Authors: Peacocke Julia , Lotz Zoe , de Beer Corena , Roux Paul , Mall Anwar S
Published: August 2012

Background

Sub-Saharan Africa is the world’s worst HIV-AIDS affected region. More interventions to manage this pandemic are urgently required. Transmission of the virus through an exchange of saliva is rarely known to occur. This project sought to verify statistically previous findings in our laboratory, that crude saliva from uninfected individuals together with its purified mucin components inhibited HIV-1, whilst mucins from infected saliva did not show this inhibition, in an in vitro assay.

Methods

Saliva was extracted in 4 M guanidinium hydrochloride and proteolytic inhibitors at pH 6.5, followed by the isolation of MUC5B and MUC7 by Sepharose 4B gel filtration and further purification of these mucins by density-gradient ultra-centrifugation in caesium chloride. Agarose gel electrophoresis, Western blotting and amino acid compositional analysis determined the size, purity and identity of the mucins. The inhibitory activity of crude saliva and purified MUC5B and MUC7, from HIV negative (n=20) and HIV positive (n=20) donors, was tested by their incubation with subtype C HIV-1 and subsequent infection of peripheral blood mononuclear cells (PBMCs). PCR was done on tandem repeat regions of MUC5B and MUC7 DNA to investigate whether any association existed between gene polymorphism and susceptibility to infection.

Results

There was an inter-individual variation in the amounts of MUC5B and MUC7 in saliva. In contrast to previous studies, crude saliva and purified mucins from both HIV negative and HIV positive individuals inhibited the infection of HIV-1 in an in vitro assay. DNA analysis of the tandem repeat regions of MUC5B and MUC7 revealed no difference between groups.

Conclusions

Crude saliva and its mucins, MUC5B and MUC7, from both uninfected controls and HIV positive individuals inhibited HIV-1 in an in vitro assay.
Using psychological theory to inform methods to optimize the implementation of a hand hygiene intervention
Authors: Boscart Veronique M , Fernie Geoff R , Lee Jae H , Jaglal Susan B
Published: August 2012

Background

Careful hand hygiene (HH) is the single most important factor in preventing the transmission of infections to patients, but compliance is difficult to achieve and maintain. A lack of understanding of the processes involved in changing staff behaviour may contribute to the failure to achieve success. The purpose of this study was to identify nurses’ and administrators’ perceived barriers and facilitators to current HH practices and the implementation of a new electronic monitoring technology for HH.

Methods

Ten key informant interviews (three administrators and seven nurses) were conducted to explore barriers and facilitators related to HH and the impact of the new technology on outcomes. The semi structured interviews were based on the Theoretical Domains Framework by Michie et al. and conducted prior to intervention implementation. Data were explored using an inductive qualitative analysis approach. Data between administrators and nurses were compared.

Results

In 9 of the 12 domains, nurses and administrators differed in their responses. Administrators believed that nurses have insufficient knowledge and skills to perform HH, whereas the nurses were confident they had the required knowledge and skills. Nurses focused on immediate consequences, whereas administrators highlighted long-term outcomes of the system. Nurses concentrated foremost on their personal safety and their families’ safety as a source of motivation to perform HH, whereas administrators identified professional commitment, incentives, and goal setting. Administrators stated that the staff do not have the decision processes in place to judge whether HH is necessary or not. They also highlighted the positive aspects of teams as a social influence, whereas nurses were not interested in group conformity or being compared to others. Nurses described the importance of individual feedback and self-monitoring in order to increase their performance, whereas administrators reported different views.

Conclusions

This study highlights the benefits of using a structured approach based on psychological theory to inform an implementation plan for a behavior change intervention. This work is an essential step towards systematically identifying factors affecting nurses’ behaviour associated with HH.
Contemporary incidence and risk factors for carotid artery disease in patients referred for coronary artery bypass surgery
Authors: Wanamaker Kelly M , Moraca Robert J , Nitzberg Diane , Magovern George J
Published: August 2012

Background

In the past decade, there has been an increase in the amount of patients with medical co-morbidities referred for coronary artery bypass surgery (CABG). Significant carotid artery disease in patients undergoing CABG procedures increases the risk of neurological complications. We review the results of routine carotid screening in patients undergoing CABG to determine the contemporary incidence and risk factors for carotid artery disease.

Methods

Between 2008 through 2010, 673 patients were referred for isolated coronary artery bypass surgery at a single institution. Patients were identified through a systematic review of The Department of Cardiothoracic Surgery Society of Thoracic Surgery Outcomes Database. A retrospective analysis of prospectively collected demographic, clinical data and outcomes were performed. All patients with screening preoperative carotid duplex were reviewed. We defined the degree of carotid disease as: none to mild stenosis (<50%), moderate stenosis (50-69%), severe stenosis (70-99%). Multivariate analysis was performed to identify risk factors.

Results

559 (83%) patients underwent screening preoperative carotid ultrasonography prior to CABG. The incidence of carotid artery disease (>50% stenosis) was 36% with 18% unilateral moderate disease, 10% bilateral moderate and 8% severe disease. Risk factors associated with carotid artery disease included: advanced age, renal failure, previous stroke, peripheral vascular disease, left main coronary artery disease, and previous myocardial infarction.

Conclusions

There is a significant incidence of carotid artery stenosis in patients referred for CABG. Routine screening will identify patients with carotid artery disease and may reduce the risk of postoperative stroke.
ROCK-phosphorylated vimentin modifies mutant huntingtin aggregation via sequestration of IRBIT
Authors: Bauer Peter O , Hudec Roman , Goswami Anand , Kurosawa Masaru , Matsumoto Gen , Mikoshiba Katsuhiko , Nukina Nobuyuki
Published: August 2012

Background

Huntington's Disease (HD) is a fatal hereditary neurodegenerative disease caused by the accumulation of mutant huntingtin protein (Htt) containing an expanded polyglutamine (polyQ) tract. Activation of the channel responsible for the inositol-induced Ca2+ release from ensoplasmic reticulum (ER), was found to contribute substantially to neurodegeneration in HD. Importantly, chemical and genetic inhibition of inositol 1,4,5-trisphosphate (IP3) receptor type 1 (IP3R1) has been shown to reduce mutant Htt aggregation.

Results

In this study, we propose a novel regulatory mechanism of IP3R1 activity by type III intermediate filament vimentin which sequesters the negative regulator of IP3R1, IRBIT, into perinuclear inclusions, and reduces its interaction with IP3R1 resulting in promotion of mutant Htt aggregation. Proteasome inhibitor MG132, which causes polyQ proteins accumulation and aggregation, enhanced the sequestration of IRBIT. Furthermore we found that IRBIT sequestration can be prevented by a rho kinase inhibitor, Y-27632.

Conclusions

Our results suggest that vimentin represents a novel and additional target for the therapy of polyQ diseases.
Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile
Authors: Tang Weihua , Morgan Douglas R , Meyers Michael O , Dominguez Ricardo L , Martinez Enrique , Kakudo Kennichi , Kuan Pei Fen , Banet Natalie , Muallem Hind , Woodward Kimberly , Speck Olga , Gulley Margaret L
Published: August 2012

Background

EBV DNA is found within the malignant cells of 10% of gastric cancers. Modern molecular technology facilitates identification of virus-related biochemical effects that could assist in early diagnosis and disease management.

Methods

In this study, RNA expression profiling was performed on 326 macrodissected paraffin-embedded tissues including 204 cancers and, when available, adjacent non-malignant mucosa. Nanostring nCounter probes targeted 96 RNAs (20 viral, 73 human, and 3 spiked RNAs).

Results

In 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infectedversusuninfected cancers, and in malignantversusadjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels ofEBER1andEBER2RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs,EBNA1from the Q promoter andBRLF1were highly expressed whileEBNA2levels were low positive in only 6/14 infected cancers. Concomitant upregulation of cellular factors implies that virus is not an innocent bystander but rather is linked to NFKB signaling (FCER2, TRAF1) and immune response(TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC), withPPARGexpression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressedINHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS, three collagens, the cell proliferation markersMYCandPCNA, and EBVBLLF1while they lackedCDH1 (E-cadherin), CLDN18,PTEN, SDC1(CD138),GAST(gastrin) and its downstream effectorCHGA(chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressedCLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG, andCDH17while they had diminished levels ofIFITM1andHIF1A. The druggable targets ERBB2 (Her2), MET, and the HIF pathway, as well as several other potential pharmacogenetic indicators (including EBV infection itself, as well asSPARC, TYMS, FCGR2BandREG4) were identified in some tumor specimens.

Conclusion

This study shows how modern molecular technology applied to archival fixed tissues yields novel insights into viral oncogenesis that could be useful in managing affected patients.
CADLIVE optimizer: web-based parameter estimation for dynamic models
Authors: Inoue Kentaro , Maeda Kazuhiro , Kato Yuki , Tonami Shinpei , Takagi Shogo , Kurata Hiroyuki
Published: August 2012

Computer simulation has been an important technique to capture the dynamics of biochemical networks. In most networks, however, few kinetic parameters have been measured in vivo because of experimental complexity. We develop a kinetic parameter estimation system, named the CADLIVE Optimizer, which comprises genetic algorithms-based solvers with a graphical user interface. This optimizer is integrated into the CADLIVE Dynamic Simulator to attain efficient simulation for dynamic models.
New bactericide derived from Isatin for treating oilfield reinjection water
Authors: Chen Gang , Su Hui-jun , Zhang Min , Huo Fang , Zhang Jie , Hao Xiao-jiang , Zhao Jing-rui
Published: August 2012

Isatin, an extract from Strobilanthes cusia (Nees) Kuntze, was the base for synthesizing derivatives that were screened for antibacterial activity against oilfield water-borne bacteria. The bacterial groups are sulfate reducing, iron and total. The derivatives were characterized by spectrums and they showed good to moderate activity against sulfate reducing bacteria.
Portable bacterial identification system based on elastic light scatter patterns
Authors: Bae Euiwon , Ying Dawei , Kramer Donald , Patsekin Valery , Rajwa Bartek , Holdman Cheryl , Sturgis Jennifer , Davisson V Jo , Robinson J Paul
Published: August 2012

Background

Conventional diagnosis and identification of bacteria requires shipment of samples to a laboratory for genetic and biochemical analysis. This process can take days and imposes significant delay to action in situations where timely intervention can save lives and reduce associated costs. To enable faster response to an outbreak, a low-cost, small-footprint, portable microbial-identification instrument using forward scatterometry has been developed.

Results

This device, weighing 9 lb and measuring 12 × 6 × 10.5 in., utilizes elastic light scatter (ELS) patterns to accurately capture bacterial colony characteristics and delivers the classification results via wireless access. The overall system consists of two CCD cameras, one rotational and one translational stage, and a 635-nm laser diode. Various software algorithms such as Hough transform, 2-D geometric moments, and the traveling salesman problem (TSP) have been implemented to provide colony count and circularity, centering process, and minimized travel time among colonies.

Conclusions

Experiments were conducted with four bacteria genera using pure and mixed plate and as proof of principle a field test was conducted in four different locations where the average classification rate ranged between 95 and 100%.
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides
Authors: Berendzen Joel , Bruno William J , Cohn Judith D , Hengartner Nicolas W , Kuske Cheryl R , McMahon Benjamin H , Wolinsky Murray A , Xie Gary
Published: August 2012

Background

Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers.

Results

At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database.

Conclusions

Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions.
Epidemiology of anti-tuberculosis drug resistance patterns and trends in tuberculosis referral hospital in Addis Ababa, Ethiopia
Authors: Abate Dereje , Taye Bineyam , Abseno Mohammed , Biadgilign Sibhatu
Published: August 2012

Background

Drug-resistant TB has emerged as a major challenge facing TB prevention and control efforts. In Ethiopia, the extent/trend of drug resistance TB is not well known. The aim of this study was to determine the pattern and trend of resistance to first line anti-TB drugs among culture positive retreatment cases at St.Peter’s TB Specialized Hospital.

Findings

A hospital based retrospective study was used to assess the pattern of anti-TB drug resistance among previously treated TB patients referred to St.Peter’s TB Specialized Hospital from January 2004-December 2008 Gregorian calendar(GC) for better diagnosis and treatment.

Among 376 culture positive for M. tuberculosis one hundred and two (27.1%) were susceptible to all of the four first line anti-TB drugs -Isoniazid (INH), Rifampicin (RIF), Ethambutol (ETB) & Streptomycin (STM). While 274 (72.9%) were resistant to at least one drug. Any resistance to STM (67.3%) was found to be the most common and the prevalence of MDR-TB was 174 (46.3%). Trend in resistance rate among re-treatment cases from 2004 to 2008 showed a significant increase for any drug as well as for INH, RIF, and MDR resistance (P <0.05 for trend).

Conclusions

There has been an increasing trend in drug resistance in recent years, particularly in retreatment cases. Therefore, establishing advanced diagnostic facilities for early detection of MDR-TB and expanding second line treatment center to treat MDR-TB patients and to prevent its transmission is recommended.
Specific-mutational patterns of p53 gene in bladder transitional cell carcinoma among a group of Iraqi patients exposed to war environmental hazards
Authors: Al-Kashwan Thekra A , Houshmand Massoud , Al-Janabi Asaad , Melconian Alice K , Al-Abbasi Dhafir , Al-Musawi Muhammad N , Rostami Maryam , Yasseen Akeel A
Published: August 2012

Background

To unfold specific-mutational patterns in TP53 gene due to exposures to war environmental hazards and to detect the association of TP53 gene alteration with the depth of bladder cancer.

Methods

Twenty-nine bladder carcinomas were analyzed for TP53 alterations. PCR-single strand conformational polymorphism analysis, DNA sequencing and immunohistochemical analysis using monoclonal mouse anti-human p53 antibody (Clone DO-7) were employed.

Results

TP53 gene mutations occurred in 37.9% of the cases while TP53 overexpression occurred in 58.6%. Both of them were associated with deep invasive-tumors. Single mutations were seen in 63.6%, whereas only 27.3% have shown double mutations. Four mutations were frameshifted (30.8%); two of them showed insertion A after codon 244. There was no significant association between TP53 mutations and protein overexpression (P>0.05), while a significant association was observed between TP53 alterations and tumors progression (P ≤ 0.01).

Conclusion

The infrequent TP53mutations, especially insertion A and 196 hotspot codon, may represent the specific-mutational patterns in bladder carcinoma among the Iraqi patients who were exposed to war environmental hazards. TP53 alteration associated with bladder cancer progression should be analyzed by both mutational and protein expression analysis.
Selected imprinting of INS in the marsupial
Authors: Stringer Jessica M , Suzuki Shunsuke , Pask Andrew J , Shaw Geoff , Renfree Marilyn B
Published: August 2012

Background

In marsupials, growth and development of the young occur postnatally, regulated by milk that changes in composition throughout the long lactation. To initiate lactation in mammals, there is an absolute requirement for insulin (INS), a gene known to be imprinted in the placenta. We therefore examined whether INS is imprinted in the mammary gland of the marsupial tammar wallaby (Macropus eugenii) and compared its expression with that of insulin-like growth factor 2 (IGF2).

Results

INS was expressed in the mammary gland and significantly increased, while IGF2 decreased, during established milk production. Insulin and IGF2 were both detected in the mammary gland macrophage cells during early lactation and in the alveolar cells later in lactation. Surprisingly, INS, which was thought only to be imprinted in the therian yolk sac, was imprinted and paternally expressed in the liver of the developing young, monoallelically expressed in the tammar mammary gland and biallelic in the stomach and intestine. The INS transcription start site used in the liver and mammary gland was differentially methylated.

Conclusions

This is the first study to identify tissue-specific INS imprinting outside the yolk sac. These data suggest that there may be an advantage of selective monoallelic expression in the mammary gland and that this may influence the growth of the postnatal young. These results are not consistent with the parental conflict hypothesis, but instead provide support for the maternal–infant co-adaptation hypothesis. Thus, imprinting in the mammary gland maybe as critical for postnatal growth and development in mammals as genomic imprinting in the placenta is prenatally.
GC-MS analysis of insecticidal essential oil of flowering aerial parts of Saussurea nivea Turcz
Authors: Chu Sha Sha , Jiang Guo Hua , Liu Zhi Long
Published: August 2012

Background

Several species from Saussurea have been used in the traditional medicine, such as S. lappa, S. involucrate, and S. obvallata. There is no report on medicinal use of S. nivea. The aim of this research was to determine chemical composition and insecticidal activity of the essential oil of S. nivea Turcz (Asteraceae) aerial parts against maize weevils (Sitophilus zeamais Motschulsky) for the first time.

Results

Essential oil of S. nivea flowering aerial parts was obtained by hydrodistillation and analyzed by gas chromatography–mass spectrometry (GC-MS). A total of 43 components of the essential oil of S. nivea were identified. The principal compounds in the essential oil were (+)-limonene (15.46%), caryophyllene oxide (7.62%), linalool (7.20%), α-pinene (6.43%), β-pinene (5.66%) and spathulenol (5.02%) followed by β-eudesmoll (4.64%) and eudesma-4,11-dien-2-ol (3.76%). The essential oil of S. nivea exhibited strong contact toxicity against S. zeamais with an LD50 value of 10.56 μg/adult. The essential oil also possessed fumigant toxicity against S. zeamais with an LC50 value of 8.89 mg/L.

Conclusion

The study indicates that the essential oil of S. nivea flowering aerial parts has a potential for development into a natural insecticide/fumigant for control of insects in stored grains.
Concomitant production of lipase, protease and enterocin by Enterococcus faecium NCIM5363 and Enterococcus durans NCIM5427 isolated from fish processing waste
Authors: Ramakrishnan Vrinda , Balakrishnan Bijinu , Rai Amit Kumar , Narayan Bhaskar , Halami Prakash M
Published: August 2012

Enterococci are widely distributed in the environment ranging from foods to humans and are gaining industrial importance due to their technological traits. In the present study, enterococci (Enterococcus faecium NCIM5363 (EF-63) and Enterococcus durans NCIM5427 (ED-27)) which are native to fish processing waste with an ability to produce lipase, protease and enterocin concomitantly were characterised. Lipase assay was performed by titrimetry and protease activity and was estimated using haemoglobin and casein as substrates in the presence of buffers at acidic, basic and neutral pH. Furthermore, enterocin produced by the isolates was characterised. Enterocin was also checked for its stability at different pH, temperature and proteolytic enzymes. Lipase production was found to be 22 and 10 U/ml in the absence of tributryin and increased to 40 and 24 U/ml in its presence for EF-63 and ED-27, respectively, indicating that the lipase produced is substrate dependent. Protease production was confirmed by protease assay, and the protease produced showed more affinity towards the acidic substrate. Enterocin produced was stable at low pH (2 to 3) and high temperature (121°C, 15 min) and had a molecular weight of approximately 6 kDa. It exhibited antibacterial activity against both Gram-positive and Gram-negative food-borne pathogens. Proteinase K inactivated enterocin completely, whereas trypsin did not. Novelty of this work lies in the immense industrial importance these cultures hold as they are capable of producing lipase, protease and enterocin apart from being useful in recovering proteins and lipids from fish processing wastes.
Tumor Stage Affects Risk and Prognosis of Contralateral Breast Cancer: Results From a Large Swedish-Population–Based Study
Authors: Vichapat Voralak , Garmo Hans , Holmqvist Marit , Liljegren Göran , Wärnberg Fredrik , Lambe Mats , Fornander Tommy , Adolfsson Jan , Lüchtenborg Margreet , Holmberg Lars
Published: August 2012

Purpose

The number of breast cancer survivors at risk of developing contralateral breast cancer (CBC) is increasing. However, ambiguity remains regarding risk factors and prognosis for women with CBC.

Patients and Methods

In a cohort of 42,670 women with breast cancer in the Uppsala/Örebro and Stockholm regions in Sweden in 1992 to 2008, we assessed risk factors for and prognosis of metachronous CBC by using survival analysis. Breast cancer–specific survival for women with CBC was evaluated and compared with results for women with unilateral breast cancer (UBC) by using time-dependent Cox-regression modeling.

Results

An increased risk for CBC was observed among women who had primary breast cancer with ≥ 10 involved lymph nodes compared with node-negative women (adjusted hazard ratio [HR], 1.8; 95% CI, 1.2 to 2.7). The prognosis was poorer in women with CBC than with UBC. The hazard of dying from breast cancer was especially high for women with a short interval time to CBC (adjusted HR, 2.3; 95% CI, 1.8 to 2.8 for CBC diagnosed ≤ 5 years v UBC) and gradually decreased with longer follow-up time but remained higher than the hazard originating from the primary tumor for ≥ 10 years.

Conclusion

Women with advanced-stage primary breast cancer had an increased risk of developing CBC. CBC is associated with an increased risk of dying from breast cancer throughout a long period of follow-up after the primary tumor. Our findings suggest that the event of CBC marks a new clinical situation in terms of investigations for metastases, treatment considerations, and follow-up strategy.