bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications
Authors: He Ziwen , Li Xinnian , Ling Shaoping , Fu Yun-Xin , Hungate Eric , Shi Suhua , Wu Chung-I 
Published: August 2013

Abstract

Background
As the error rate is high and the distribution of errors across sites is non-uniform in next generation sequencing (NGS) data, it has been a challenge to estimate DNA polymorphism (θ) accurately from NGS data.

Results
By computer simulations, we compare the two methods of data acquisition - sequencing each diploid individual separately and sequencing the pooled sample. Under the current NGS error rate, sequencing each individual separately offers little advantage unless the coverage per individual is high (>20X). We hence propose a new method for estimating θ from pooled samples that have been subjected to two separate rounds of DNA sequencing. Since errors from the two sequencing applications are usually non-overlapping, it is possible to separate low frequency polymorphisms from sequencing errors. Simulation results show that the dual applications method is reliable even when the error rate is high and θ is low.

Conclusions
In studies of natural populations where the sequencing coverage is usually modest (~2X per individual), the dual applications method on pooled samples should be a reasonable choice.
Association of biomarkers of inflammation and cell adhesion with lung function in the elderly: a population-based study
Authors: Kuhlmann Antje , Ólafsdóttir Inga Sif , Lind Lars , Sundström Johan , Janson Christer 
Published: August 2013

AbstractBackgroundLow lung function is associated with increased morbidity and mortality. It is therefore of interest to identify biomarkers that are associated with impaired lung function. The aim of the study was to analyse associations of biomarkers and combinations of biomarkers with lung function in an elderly general population.MethodsLung function (FEV1and FVC) and a panel of 15 inflammatory markers from blood samples were analysed in 888 subjects aged 70 years. Biomarkers included cytokines, chemokines, adhesion molecules, C-reactive protein (CRP) and leukocyte count.ResultsLeukocyte count and CRP were independently associated with FEV1after adjustments for other inflammatory markers, sex, BMI, current smoking and pack-years of smoking. In a similar model, leukocyte count and vascular cell adhesion protein 1 (VCAM-1) were the biomarkers that were significantly associated with FVC. Subjects that had both leukocyte count and CRP in the lowest tertile had a FEV1that was 9% of predicted higher than subjects with leukocyte count and CRP in the highest tertile (103±16 vs. 94±21% of predicted, p=0.0002) (mean±SD). A difference of 8% of predicted in FVC was found between subjects with leukocyte count and VCAM-1 in the lowest and highest tertiles, respectively (106±18 vs. 98±19% of predicted, p=0.002).ConclusionLeucocyte count, CRP and VCAM-1 were found to relate to poorer lung function. A dose related association was found for the combination leukocyte count and CRP towards FEV1and leukocyte and VCAM-1 towards FVC. This indicates that combination of two biomarkers yielded more information than assessing them one by one when analysing the association between systemic inflammation and lung function.
Incidence of pneumonia and risk factors among patients with head and neck cancer undergoing radiotherapy
Authors: Chu Chin-Nan , Muo Chih-Hsin , Chen Shang-Wen , Lyu Shu-Yu , Morisky Donald E 
Published: August 2013

Abstract

Background
This study investigated the incidence and patient- and treatment-related risk factors related to pneumonia acquired during radiotherapy (PNRT) in head and neck cancer (HNC) patients.

Methods
Using the universal insurance claims data, 15,894 total HNC patients between 1998 and 2007 were included in this analysis. PNRT was defined as the occurrence of pneumonia within 90 days of the commencement of radiotherapy. Information also included some demographic characteristics, treatment-related factors, and comorbidities. Appropriate statistical tests were performed to assess the difference between patients with and those without PNRT. A logistic regression was used to estimate the odds ratio (OR) of PNRT among the variables examined.

Results
In total, 772 patients (4.86%) were identified with PNRT as the case group, whereas 15,122 subjects of the same cancer without PNRT formed the control group. Of patients with PNRT, 632 (81.9%) were hospitalized with a mean length of stay of 25.9 days. Results from the multiple logistic regression showed that an older age and certain comorbidities were associated with an increased risk of PNRT. Patients with cancer of the tongue, buccal mucosa, oropharynx, and hypopharynx/larynx were at particularly higher risk (OR = 1.28, 1.28, 1.67, and 1.74, respectively). Compared to radiotherapy alone, concurrent chemoradiotherapy had no effect on the PNRT. Patients in the PNRT group had higher overall medical costs and length of stay.

Conclusion
The incidence of PNRT in HNC patients receiving radiotherapy was approximately 5%. Notably, an older age, certain comorbidities, and certain specific tumor sites were associated with an increased risk.
An economic evaluation for prevention of diabetes mellitus in a developing country: a modelling study
Authors: Liu Xiaoqian , Li Changping , Gong Hui , Cui Zhuang , Fan Linlin , Yu Wenhua , Zhang Cui , Ma Jun 
Published: August 2013

AbstractBackgroundThe serious consequences of diabetes mellitus, and the subsequent economic burden, call for urgent preventative action in developing countries. This study explores the clinical and economic outcomes of strategies that could potentially prevent diabetes based on Chinese circumstances. It aims to provide indicators for the long-term allocation of healthcare resources for authorities in developing countries.MethodsA representative sample of Chinese adults was used to create a simulated population of 20,000 people aged 25 years and above. The hybrid decision tree Markov model was developed to compare the long-term clinical and economic outcomes of four simulated diabetes prevention strategies with a control group, where no prevention applied. These preventive strategies were the following: (i) one-off screening for undiagnosed diabetes and impaired glucose tolerance (IGT), with lifestyle interventions on diet, (ii) on exercise, (iii) on diet combined exercise (duo-intervention) respectively in those with IGT, and (iv) one-off screening alone. Independent age-specific models were simulated based on diverse incidences of diabetes, mortalities and health utilities. The reported outcomes were the following: the remaining survival years, the quality-adjusted life years (QALYs) per diabetes or IGT subjects, societal costs per simulated subject and the comparisons between preventions and control over 40 years. Sensitivity analyses were performed based on variations of all assumptions, in addition to the performance and the compliance of screening.ResultsCompared with the control group, all simulated screening programmes prolonged life expectancy at the initiation ages of 25 and 40 years, postponed the onset of diabetes and increased QALYs at every initiation age. Along with an assumption of six years intervention, prevention programmes were associated with cost-saving compared with the control group, especially in the population aged 25 years. The savings were at least US$2017 per subject, but no statistically significant difference was observed among the intervention strategies within each age groups. The cost savings were reduced when screening was affected by poor performance and noncompliance.ConclusionsDeveloping countries have few effective strategies to manage the prevention of diabetes. One-off screening for undiagnosed diabetes and IGT, with appropriate lifestyle interventions for those with IGT are cost saving in China, especially in young adults.
Prevalence of cardiovascular risk factors and socioeconomic level among public-sector workers in Angola
Authors: Capingana Daniel P , Magalhães Pedro , Silva Amílcar BT , Gonçalves Mauer AA , Baldo Marcelo P , Rodrigues Sérgio L , Simões Cristóvão CF , Ferreira Albano VL , Mill José G 
Published: August 2013

Abstract

Background
Cardiovascular diseases are the leading cause of death in the majority of developed and developing countries. African countries are currently facing an increase in both cardiovascular and transmitted diseases. In addition, cardiovascular risk varies among different socioeconomic groups. Thus, we determined the prevalence of modifiable cardiovascular risk factors in apparently healthy public-sector workers and investigated possible relationships with socioeconomic status.

Methods
We employed a cross-sectional study comprising 42.2% (n = 615) of the public-sector workers at Agostinho Neto University, 48% (n = 294) male and 52% (n= 321) female, with ages between 20 and 72 years and from various socioeconomic groups. The study was conducted from February 2009 to December 2010. Personal, anthropometric, biochemical, hemodynamic, socioeconomic, and physical activity data were collected.

Results
The prevalence rates of cardiovascular risk factors were as follows: hypertension, 45.2% (men 46.3%, women 44.2%, P > 0.05); hypercholesterolemia, 11.1% (men 10.5%, women 11.5%, P > 0.05); low high-density lipoprotein (HDL) cholesterol, 50.1% (men 36.9%, women 62.3%; P < 0.05); hypertriglyceridemia, 10.6% (men 12.6%, women 8.7%, P > 0.05); smoking, 7.2% (men 10.2%, women 4.4%; P < 0.05); diabetes, 5.7% (men 5.5%, women 5.9%, P > 0.05); overweight, 29.3% (men 27.3%, women 31.2%, P > 0.05); obesity, 19.6% (men 9.2%, women 29.0%; P < 0.05); sedentary lifestyle, 87.2% (men 83.0%, women 91,0%, P < 0.05); and left ventricular hypertrophy, 20% (men 32.0%, women 9.0%; P < 0.05). At least one risk factor was present in 27.7% of the sample; 15.2% had two risk factors, and 31.4% had three or more risk factors. Among the individuals with low socioeconomic status, 41.0% had three or more risk factors.

Conclusions
The results of this study suggest the existence of a high prevalence of multiple risk factors for cardiovascular disease in apparently healthy public-sector workers in Angola. The workers in lower socioeconomic groups had higher incidences of hypertension, smoking, and left ventricular hypertrophy.
Kinetics of drug selection systems in mouse embryonic stem cells
Authors: Nakatake Yuhki , Fujii Setsuko , Masui Shinji , Sugimoto Toshimi , Torikai-Nishikawa Satomi , Adachi Kenjiro , Niwa Hitoshi 
Published: August 2013

Abstract

Background
Stable expression of transgenes is an important technique to analyze gene function. Various drug resistance genes, such as neo, pac, hph, zeo, bsd, and hisD, have been equally used as selection markers to isolate a transfectant without considering their dose-dependent characters.

Results
We quantitatively measured the variation of transgene expression levels in mouse embryonic stem (mES) cells, using a series of bi-cistronic expression vectors that contain Egfp expression cassette linked to each drug resistant gene via IRES with titration of the selective drugs, and found that the transgene expression levels achieved in each system with this vector design are in order, in which pac and zeo show sharp selection of transfectants with homogenously high expression levels. We also showed the importance of the choice of the drug selection system in gene-trap or gene targeting according to this order.

Conclusions
The results of the present study clearly demonstrated that an appropriate choice of the drug resistance gene(s) is critical for a proper design of the experimental strategy.
Neuritogenic effect of standardized extract of Centella asiatica ECa233 on human neuroblastoma cells
Authors: Wanakhachornkrai Oraphan , Pongrakhananon Varisa , Chunhacha Preedakorn , Wanasuntronwong Aree , Vattanajun Anusara , Tantisira Boonyong , Chanvorachote Pithi , Tantisira Mayuree H 
Published: August 2013

Abstract

Background
In order to gain insight into neuroprotective effects of ECa 233, a standardized extract of Centella asiatica, previously demonstrated in animal models of memory impairment induced by transient global ischemia or intracerebroventricular injection of β-amyloid, the effect of ECa 233 on neurite outgrowth of human IMR-32 neuroblastoma cell line was investigated.

Methods
Cells were seeded and incubated with various concentrations of ECa 233. Morphometric analysis was carried out by a measurement of the longest neurite growth of cells at 24 and 48 h. Contributing signaling pathways possibly involved were subsequently elucidated by western blot analysis.

Results
While ECa 233 had only limited effects on cell viability, it significantly enhanced neurite outgrowth of IMR-32 cells at the concentrations of 1–100 μg/ml. Western blot analysis revealed that ECa 233 significantly upregulated the level of activated ERK1/2 and Akt of the treated cells suggesting their involvement in the neuritogenic effect observed, which was subsequently verified by the finding that an addition of their respective inhibitors could reverse the effect of ECa 233 on these cells.

Conclusions
The present study clearly demonstrated neurite outgrowth promoting activity of ECa 233. ERK1/2 and Akt signaling pathways seemed to account for the neurotrophic effect observed. In conjunction with in vivo neuroprotective effect of ECa 233 previously reported, the results obtained support further development of ECa 233 for clinical use in neuronal injury or neurodegenerative diseases.
How do medical doctors use a web-based oncology protocol system? A comparison of Australian doctors at different levels of medical training using logfile analysis and an online survey
Authors: Langton Julia M , Blanch Bianca , Pesa Nicole , Park Jae Min , Pearson Sallie-Anne 
Published: August 2013

Abstract

Background
Electronic decision support is commonplace in medical practice. However, its adoption at the point-of-care is dependent on a range of organisational, patient and clinician-related factors. In particular, level of clinical experience is an important driver of electronic decision support uptake. Our objective was to examine the way in which Australian doctors at different stages of medical training use a web-based oncology system (http://www.eviq.org.au).

Methods
We used logfiles to examine the characteristics of eviQ registrants (2009–2012) and patterns of eviQ use in 2012, according to level of medical training. We also used a web-based survey to evaluate the way doctors at different levels of medical training use the online system and to elicit perceptions of the system’s utility in oncology care.

Results
Our study cohort comprised 2,549 eviQ registrants who were hospital-based medical doctors across all levels of training. 65% of the cohort used eviQ in 2012, with 25% of interns/residents, 61% of advanced oncology trainees and 47% of speciality-qualified oncologists accessing eviQ in the last 3 months of 2012. The cohort accounted for 445,492 webhits in 2012. On average, advanced trainees used eviQ up to five-times more than other doctors (42.6 webhits/month compared to 22.8 for specialty-qualified doctors and 7.4 webhits/month for interns/residents). Of the 52 survey respondents, 89% accessed eviQ’s chemotherapy protocols on a daily or weekly basis in the month prior to the survey. 79% of respondents used eviQ at least weekly to initiate therapy and to support monitoring (29%), altering (35%) or ceasing therapy (19%). Consistent with the logfile analysis, advanced oncology trainees report more frequent eviQ use than doctors at other stages of medical training.

Conclusions
The majority of the Australian oncology workforce are registered on eviQ. The frequency of use directly mirrors the clinical role of doctors and attitudes about the utility of eviQ in decision-making. Evaluations of this kind generate important data for system developers and medical educators to drive improvements in electronic decision support to better meet the needs of clinicians. This end-user focus will optimise the uptake of systems which will translate into improvements in processes of care and patient outcomes.
Integrated wall stress: a new methodological approach to assess ventricular workload and myocardial contractile reserve
Authors: Dong Hailong , Mosca Heather , Gao Erhe , Akins Robert E , Gidding Samuel S , Tsuda Takeshi 
Published: August 2013

Abstract

Background
Wall stress is a useful concept to understand the progression of ventricular remodeling. We measured cumulative LV wall stress throughout the cardiac cycle over unit time and tested whether this “integrated wall stress (IWS)” would provide a reliable marker of total ventricular workload.

Methods and results
We applied IWS to mice after experimental myocardial infarction (MI) and sham-operated mice, both at rest and under dobutamine stimulation. Small infarcts were created so as not to cause subsequent overt hemodynamic decompensation. IWS was calculated over one minute through simultaneous measurement of LV internal diameter and wall thickness by echocardiography and LV pressure by LV catheterization. At rest, the MI group showed concentric LV hypertrophy pattern with preserved LV cavity size, LV systolic function, and IWS comparable with the sham group. Dobutamine stimulation induced a dose-dependent increase in IWS in MI mice, but not in sham mice; MI mice mainly increased heart rate, whereas sham mice increased LV systolic and diastolic function. IWS showed good correlation with a product of peak-systolic wall stress and heart rate. We postulate that this increase in IWS in post- MI mice represents limited myocardial contractile reserve.

Conclusion
We hereby propose that IWS provides a useful estimate of total ventricular workload in the mouse model and that increased IWS indicates limited LV myocardial contractile reserve.
Compensatory regulation of Na+ absorption by Na+/H+ exchanger and Na+-Cl- cotransporter in zebrafish (Danio rerio)
Authors: Chang Wei-Jen , Wang Yi-Fang , Hu Huei-Jyun , Wang Jung-Hsuan , Lee Tsung-Han , Hwang Pung-Pung 
Published: August 2013

Abstract

Introduction
In mammals, internal Na+ homeostasis is maintained through Na+ reabsorption via a variety of Na+ transport proteins with mutually compensating functions, which are expressed in different segments of the nephrons. In zebrafish, Na+ homeostasis is achieved mainly through the skin/gill ionocytes, namely Na+/H+ exchanger (NHE3b)-expressing H+-ATPase rich (HR) cells and Na+-Cl- cotransporter (NCC)-expressing NCC cells, which are functionally homologous to mammalian proximal and distal convoluted tubular cells, respectively. The present study aimed to investigate whether or not the functions of HR and NCC ionocytes are differentially regulated to compensate for disruptions of internal Na+ homeostasis and if the cell differentiation of the ionocytes is involved in this regulation pathway.

Results
Translational knockdown of ncc caused an increase in HR cell number and a resulting augmentation of Na+ uptake in zebrafish larvae, while NHE3b loss-of-function caused an increase in NCC cell number with a concomitant recovery of Na+ absorption. Environmental acid stress suppressed nhe3b expression in HR cells and decreased Na+ content, which was followed by up-regulation of NCC cells accompanied by recovery of Na+ content. Moreover, knockdown of ncc resulted in a significant decrease of Na+ content in acid-acclimated zebrafish.

Conclusions
These results provide evidence that HR and NCC cells exhibit functional redundancy in Na+ absorption, similar to the regulatory mechanisms in mammalian kidney, and suggest this functional redundancy is a critical strategy used by zebrafish to survive in a harsh environment that disturbs body fluid Na+ homeostasis.
Evaluation of an intelligent wheelchair system for older adults with cognitive impairments
Authors: How Tuck-Voon , Wang Rosalie H , Mihailidis Alex 
Published: August 2013

AbstractBackgroundOlder adults are the most prevalent wheelchair users in Canada. Yet, cognitive impairments may prevent an older adult from being allowed to use a powered wheelchair due to safety and usability concerns. To address this issue, an add-on Intelligent Wheelchair System (IWS) was developed to help older adults with cognitive impairments drive a powered wheelchair safely and effectively. When attached to a powered wheelchair, the IWS adds a vision-based anti-collision feature that prevents the wheelchair from hitting obstacles and a navigation assistance feature that plays audio prompts to help users manoeuvre around obstacles.MethodsA two stage evaluation was conducted to test the efficacy of the IWS.Stage One: Environment of Use– the IWS’s anti-collision and navigation features were evaluated against objects found in a long-term care facility. Six different collision scenarios (wall, walker, cane, no object, moving and stationary person) and three different navigation scenarios (object on left, object on right, and no object) were performed. Signal detection theory was used to categorize the response of the system in each scenario.Stage Two: User Trials– single-subject research design was used to evaluate the impact of the IWS on older adults with cognitive impairment. Participants were asked to drive a powered wheelchair through a structured obstacle course in two phases: 1) with the IWS and 2) without the IWS. Measurements of safety and usability were taken and compared between the two phases. Visual analysis and phase averages were used to analyze the single-subject data.ResultsStage One:The IWS performed correctly for all environmental anti-collision and navigation scenarios.Stage Two:Two participants completed the trials. The IWS was able to limit the number of collisions that occurred with a powered wheelchair and lower the perceived workload for driving a powered wheelchair. However, the objective performance (time to complete course) of users navigating their environment did not improve with the IWS.ConclusionsThis study shows the efficacy of the IWS in performing with a potential environment of use, and benefiting members of its desired user population to increase safety and lower perceived demands of powered wheelchair driving.