bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene set analysis in the cloud
Authors: Zhang Lu , Gu Shengchang , Liu Yuan , Wang Bingqiang , Azuaje Francisco 
Published: November 2011

Abstract
Summary: Cloud computing offers low cost and highly flexible opportunities in bioinformatics. Its potential has already been demonstrated in high-throughput sequence data analysis. Pathway-based or gene set analysis of expression data has received relatively less attention. We developed a gene set analysis algorithm for biomarker identification in the cloud. The resulting tool, YunBe, is ready to use on Amazon Web Services. Moreover, here we compare its performance to those obtained with desktop and computing cluster solutions.
Availability and implementation: YunBe is open-source and freely accessible within the Amazon Elastic MapReduce service at s3n://lrcv-crp-sante/app/yunbe.jar. Source code and user's guidelines can be downloaded from http://tinyurl.com/yunbedownload.
Contact: francisco.azuaje@crp-sante.lu
Missing and presumed lost: extinction in the ocean and its inference
Authors: Smith Woollcott K. , Solow Andrew R. 
Published: November 2011

Abstract
Smith, W. K., and Solow, A. R. 2012. Missing and presumed lost: extinction in the ocean and its inference. – ICES Journal of Marine Science, 69: 89–94. The number of modern extinctions in the ocean is unknown. The actual demise of the last individual of a species is essentially unobservable, so extinction can only be inferred. Statistical methods are described for inferring extinction from sighting records, species–area considerations, and taxonomic samples collected at two different times. The methods are illustrated using a variety of real datasets, including a sighting record of the Caribbean monk seal and results from three surveys of benthic invertebrates.
Feeding difficulties in children with cerebral palsy: low‐cost caregiver training in Dhaka, Bangladesh
Authors: Adams M. S. , Khan N. Z. , Begum S. A. , Wirz S. L. , Hesketh T. , Pring T. R. 
Published: November 2011

AbstractBackground The majority of children with cerebral palsy have feeding difficulties, which, if not managed, result in stressful mealtimes, chronic malnutrition, respiratory disease, reduced quality of life for caregiver and child, and early death. In well‐resourced countries, high‐ and low‐cost medical interventions, ranging from gastrostomy tube feeding to caregiver training, are available. In resource‐poor countries such as Bangladesh, the former is not viable and the latter is both scarce and its effectiveness not properly evaluated. The aim of this study was to evaluate the effectiveness of a low‐cost, low‐technology intervention to improve the feeding practices of carers of children with moderate–severe cerebral palsy and feeding difficulties in Bangladesh.Methods An opportunistic sample of 37 caregivers and their children aged 1–11 years were invited to a six‐session training programme following an initial feeding assessment with brief advice. During home visits, pre‐ and post‐measures of nutritional status, chest health and feeding‐related stress were taken and feeding practices were observed. A control phase was evaluated for 20 of the participant pairs following initial assessment with advice, while awaiting full training.Results A minimum of four training sessions showed significant improvements in the children's respiratory health (P= 0.005), cooperation during mealtimes (P= 0.003) and overall mood (P< 0.001). Improvements in growth were inconsistent. Dramatic reductions were observed in caregiver stress (P< 0.001). A significant difference in the outcomes following advice only compared with advice plus training was also observed.Conclusions In situations of poverty, compliance is restricted by lack of education, finances and time. Nonetheless, carers with minimal formal education, living in conditions of extreme poverty were able to change feeding practices after a short, low‐cost training intervention, with highly positive consequences. The availability of affordable food supplementation for this population, however, requires urgent attention.
Evaluation of yield and chemical composition of a halophyte (Suaeda glauca) and its feeding value for lambs
Authors: Sun H. X. , Zhou D. W. , Zhao C. S. , Wang M. L. , Zhong R. Z. , Liu H. W. 
Published: November 2011

AbstractSuaeda glauca is a potential feedstock for ruminants in north‐east China in areas of increasing salinity. The characteristics of S. glauca pasture from June to October and effects on intake, digestion and blood metabolites in lambs given increasing proportions of S. glauca in the forage component of a mixed hay/concentrate (50/50) diet were evaluated. Harvest date had a significant effect on dry matter (DM) yield. There were significant increases in DM content, total energy, neutral detergent fibre and acid detergent fibre (ADF), but declines in leaf proportion, crude protein, total ash and sodium contents with maturity. Inclusion of 25%S. glauca hay in a diet significantly improved daily intake of DM, organic matter (OM) and energy compared with T0% and T50% groups. Supplementation at 25 or 50% significantly increased the digestibility of energy, DM, OM and ADF compared with the T0% group. Water intake, urinary excretion, water content of fresh faeces and sodium excretion from urine linearly increased with increasing S. glauca content, but potassium excretion from urine decreased. K and Mg serum contents were significantly increased compared with T0% group when S. glauca made up 50% of diet. This study indicates that S. glauca is a suitable hay when added as 25% of the lamb diet.
Cytoplasmic expression of oestrogen receptor beta (ERβ) as a prognostic factor in vulvar squamous cell carcinoma in elderly women
Authors: Zannoni Gian F , Prisco Maria G , Vellone Valerio G , De Stefano Ilaria , Vizzielli Giuseppe , Tortorella Lucia , Fagotti Anna , Scambia Giovanni , Gallo Daniela 
Published: November 2011

Zannoni G F, Prisco M G, Vellone V G, De Stefano I, Vizzielli G, Tortorella L, Fagotti A, Scambia G & Gallo D  (2011) Histopathology 59, 909–917Cytoplasmic expression of oestrogen receptor beta (ERβ) as a prognostic factor in vulvar squamous cell carcinoma in elderly womenAims:  To investigate the prognostic value of cytoplasmic oestrogen receptor beta (ERβ) expression in a series of untreated patients with non‐human papillomavirus (HPV)‐related vulvar cancer.Methods and results:  Immunohistochemistry was carried out using a polyclonal rabbit anti‐human ERβ antibody. The nuclear and cytoplasmic expression of ERβ was evaluated in 33 patients. Cytoplasmic immunoreactivity was correlated with histopathological and molecular parameters (Ki67, p21), disease‐free survival (DFS) and overall survival (OS). The expression of cytoplasmic ERβ was found to be associated with grade (P = 0.006), while no association was found with any of the remaining variables examined. Cases with high cytoplasmic ERβ expression showed lower DFS and OS compared to cases with low cytoplasmic ERβ (P = 0.007, P = 0.01, respectively). There was also a progressive decline in both the DFS and OS with increasing tumour size (P = 0.05, P = 0.07, respectively) and with increasing depth of infiltration (P = 0.14, P = 0.07, respectively). On multivariate analysis, only tumour size and cytoplasmic ERβ staining retained an independent negative prognostic role for DFS and OS.Conclusions:  The assessment of cytoplasmic ERβ expression could be helpful to identify poor prognosis in elderly patients with non‐HPV‐related vulvar squamous cell carcinoma (SCC).
The effect of an intervention combining self‐efficacy theory and pedometers on promoting physical activity among adolescents
Authors: Lee Ling‐Ling , Kuo Yu‐Chi , Fanaw Dilw , Perng Shoa‐Jen , Juang Ian‐Fei 
Published: November 2011

Aim.  To study the effect of an intervention combining self‐efficacy theory and pedometers on promoting physical activity among adolescents.Background.  The beneficial effects of regular physical activity on health in youths are well‐documented. However, adolescence is found to be the age of greatest decline in physical activity participation. Physical activity participation among girls was generally less frequent and less intense than boys. Therefore, there is a strong need for effective interventions that can help promote physical activity in this population.Design.  An experimental design.Methods. Two classes of female junior college students (mean age = 16) were randomly sampled from a total of four classes and, of those, one each was randomly assigned to either the intervention (n = 46) or the control group (n = 48). Self‐efficacy was used as a core theoretical foundation of the intervention design, and pedometers were provided to the students in the intervention group. Distances between each domestic scenic spot were illustrated graphically in a walking log for students to mark the extent of their walking or running. Students in the control group participated in a usual physical education programme. The primary outcome was a change in the number of aerobic steps. The secondary outcomes were changes in cardiopulmonary endurance and exercise self‐efficacy.Results.  At 12‐week follow‐up, the mean change in aerobic steps was 371 steps and 108 steps in the intervention and control group, respectively. The difference in mean change between the two groups was 467 steps. Effects of the intervention on changes of cardiopulmonary endurance and perceived exercise self‐efficacy scores were not found.Conclusions.  Among adolescent girls, a 12‐week intervention designed on the theoretical foundation of self‐efficacy theory and provision of pedometers was found to have an effect on increasing their physical activity. The intervention, using graphs of domestic scenic spots to represent the distance of walking or running as monitored by pedometers, might enhance motivation regarding physical activity.Relevance to clinical practice.  It is important for health professionals, including school health nurses, involved in the care of adolescent health, to design and provide a physical activity intervention combining self‐efficacy theory and provision of pedometer to promote physical activity.
Developing a minimum data set for electronic nursing handover
Authors: Johnson Maree , Jefferies Diana , Nicholls Daniel 
Published: November 2011

Aims and objectives.  This study presents a minimum data set designed for an electronic system to complement verbal nursing handover.Background.  Poor communication of patient information at handover has been implicated in adverse events with changes to clinical handover being proposed as a solution. This study developed a minimum data set for an electronic patient summary tool.Design.  Using an observational design the scope of information being presented by nurses at handover was identified in relation to a generic Nursing Handover Minimum Data Set.Method.  Patient handovers (n = 195) were observed and digitally recorded across diverse specialties.Results.  Content analysis confirmed the frequent use of the Nursing Handover Minimum Data Set items across all specialties. The use of the items was affected by the patient context and the clinical setting. Aged care patients often had several clinical alerts reported (pressure areas, falls risk). Rapid changes in patient condition in emergency emphasised the need for a focus on observations and presenting problems. Mental health and maternity required further refinement of the items.Conclusion.  The generic Nursing Handover Minimum Data Set can direct nurses to give a comprehensive account of their patient’s condition and care. The data set needs to be flexible and adaptable to the patient context and setting and complements structured content verbal handover. This minimum data set provides an excellent framework for system development by clinicians, managers and information technologists. Educators can use this tool to teach student nurses, new graduates and experienced staff, about the patient information to be presented at handover.Relevance to clinical practice.  The Nursing Handover Minimum Data Set for electronic nursing handover complements verbal handover and provides a tool to give clinicians access to comprehensive information about all patients within the ward area.
The experience of empowerment in the patient–staff encounter: the patient's perspective
Authors: Nygårdh Annette , Malm Dan , Wikby Kerstin , Ahlström Gerd 
Published: November 2011

Aim and objective.  The aim was to explore empowerment within the patient–staff encounter as experienced by out‐patients with chronic kidney disease.Background.  Empowerment has an important role to play in the patient–staff relationship in the case of patients with a chronic disease. When it comes to patients with chronic kidney disease, there has been little research on empowerment, for which reason interviewing such patients about their experiences of empowerment will provide useful knowledge within the context of out‐patient care.Design.  A qualitative interview study was chosen to gain an understanding of empowerment from the patient perspective.Method.  The study was carried out at an out‐patient clinic in Sweden and involved 20 patients with chronic kidney disease. The interviews were subjected to latent content analysis.Results.  Five of the seven sub‐themes emerging from the analysis represented empowerment: Accessibility according to need, Confirming encounter, Trust in the competence of the healthcare staff, Participation in decision‐making, Learning enables better self‐management. The other two represented non‐empowerment: Meeting with nonchalance, Lack of dialogue and influence. From the seven sub‐themes, one comprehensive theme was generated: Creation of trust and learning through encounter.Conclusion.  The main finding regarding the central role of the creation of trust and learning through the patient–staff encounter underlines the importance of understanding empowerment from the patient’s perspective.Relevance to clinical practice.  Nursing and other healthcare staff need knowledge and understanding of the meaning of empowerment from the patients’ perspective to meet their needs in out‐patient care.
The effect of cold application on pain due to chest tube removal
Authors: Ertuğ Nurcan , Ülker Saadet 
Published: November 2011

Aim and objectives.  The aim of the research is to determine the effect of cold application on the pain owing to chest tube removal for patients with single pleural chest tube.Background.  Removal of chest tubes causes patients to feel pain and interventions used for reducing the pain owing to the removal of chest tubes are not sufficient.Design.  Controlled clinical trial with repeated measures.Methods.  This study was conducted with 140 patients, of whom 70 patients were in the experimental group and 70 patients were in the control group, in a thoracic hospital in Turkey. Data were collected using a data collection form consisting of patients’ demographic and health history and Visual Analogue Scale. Cold was applied to patients in the experimental group prior to chest tube removal. In the experimental group, skin temperature and pain intensity was measured for each patient at four time points. In the control group, pain intensity was evaluated for each patient at three time points. Data were evaluated using Chi‐square and Repeated Measurements two‐way anova tests.Results.  The Visual Analogue Scale score was measured immediately after the chest tube removal in the experimental group was 3·85, compared with 5·60 in the control group. There were significant differences on pain with cold application between the two groups prior and after the intervention. Age, gender, the number of days the chest tube was inserted and the chest tube insertion indication had no effect on the pain owing to chest tube removal.Conclusion.  Cold application is effective in reducing the pain owing to chest tube removal.Relevance to clinical practice.  Cold application was recommended prior to chest tube removal to reduce the pain owing to removal of chest tube.
Studies on the inactivation of selected viral and bacterial fish pathogens at high pH for waste disposal purposes
Authors: Dixon P F , Algoët M , Bayley A , Dodge M , Joiner C , Roberts E 
Published: November 2011

AbstractThis study investigated the use of alkaline hydrolysis at ambient temperature for inactivation of selected fish pathogens in fish tissues under conditions approximating those that are likely to be found in the aquaculture industry. Infectious salmon anaemia virus (ISAV) and Lactococcus garvieae have been determined in a previous study to be the most resistant virus and bacteria to pH 12 from a wide range of viruses and bacteria tested. They were spiked at high titres into fish extracts that were then treated with 1 m sodium hydroxide (NaOH). Viable L. garvieae was not detected in the treated fish extract after 1 h, and ISAV was not detected after 24‐h exposure. Field mortalities of Atlantic salmon, Salmo salar L., caused by infectious pancreatic necrosis virus were treated by alkaline hydrolysis at ambient temperature. The macerated fish mortalities contained a high titre of virus (3.38 × 108 TCID50 g−1) that was reduced to approximately 2.2 × 103 TCID50 g−1 after 24‐h exposure to NaOH, and virus was not detected after exposure for 48 h. The results suggest that alkaline hydrolysis at ambient temperature has potential as a biosecure treatment method for fish by‐products containing fish pathogens.
The relation between coronary artery calcification in asymptomatic subjects and both traditional risk factors and living in the city centre: a DanRisk substudy
Authors: Lambrechtsen J. , Gerke O. , Egstrup K. , Sand N. P. , Nørgaard B. L. , Petersen H. , Mickley H. , Diederichsen A. C. P. 
Published: November 2011

Abstract.  Lambrechtsen J, Gerke O, Egstrup K, Sand NP, Nørgaard BL, Petersen H, Mickley H, Diederichsen ACP (Svendborg Hospital, Svendborg; Odense University Hospital, Odense; SVS, Esbjerg; Institute of Regional Health Services Research, University of Southern Denmark; Vejle Hospital, Vejle; and Odense University Hospital, Odense, Denmark). The relation between coronary artery calcification in asymptomatic subjects and both traditional risk factors and living in the city centre: a DanRisk substudy. J Intern Med 2012; 271: 444–450.Objective.  To evaluate the association between the risk factor for living in the city centre as a surrogate for air pollution and the presence of coronary artery calcification (CAC) in a population of asymptomatic Danish subjects.Design and subjects.  A random sample of 1825 men and women of either 50 or 60 years of age were invited to take part in a screening project designed to assess risk factors for cardiovascular disease (CVD). Noncontrast cardiac computed tomography was performed on all subjects, and their Agatston scores were calculated to evaluate the presence of subclinical coronary atherosclerosis. The relationship between CAC and several demographic and clinical parameters was evaluated using multivariate logistic regression.Results.  A total of 1225 individuals participated in the study, of whom 250 (20%) were living in the centres of major Danish cities. Gender and age showed the greatest association with the presence of CAC: the odds ratio (OR) for men compared with women was 3.2 [95% confidence interval (CI) 2.5–4.2; P < 0.0001], and the OR for subjects aged 60 versus those aged 50 years was 2.2 (95% CI 1.7–2.8; P < 0.0001). Other variables independently associated with the presence of CAC were diabetes and smoking with ORs of 2.0 (95% CI 1.1–3.5; P = 0.03) and 1.9 (95% CI 1.4–2.5, P < 0.0001), respectively. The adjusted OR for subjects living in city centres compared to those living outside was 1.8 (95% CI 1.3–2.4; P = 0.0003).Conclusion.  Both conventional risk factors for CVD and living in a city centre are independently associated with the presence of CAC in asymptomatic middle‐aged subjects.
Potential limitations in the use of KillerRed for fluorescence microscopy
Authors: NORDGREN M. , WANG B. , APANASETS O. , BREES C. , VAN VELDHOVEN P.P. , FRANSEN M. 
Published: November 2011

SummaryKillerRed, a bright red fluorescent protein, is a genetically encoded photosensitizer, which generates radicals and hydrogen peroxide upon green light illumination. The protein is a potentially powerful tool for selective light‐induced protein inactivation and cell killing, and can also be used to study downstream effects of locally increased levels of reactive oxygen species. The initial aim of this study was to investigate whether or not KillerRed‐mediated reactive oxygen species production inside peroxisomes could trigger the sequestration of these organelles into autophagosomes. Green fluorescent protein‐tagged microtubule‐associated protein 1 light chain 3 was used as autophagosome marker. We observed that KillerRed also emits weak green fluorescence upon excitation at 480 nm, and this may lead to erroneous data interpretation in conditions where green fluorophores are used. We discuss this potential pitfall of KillerRed for biological imaging and formulate recommendations to avoid misinterpretation of the data.
Successful serology‐based intervention to increase protection against vaccine‐preventable diseases in liver‐transplanted children: A 19‐yr review of the Swiss national reference center
Authors: L’Huillier A. G. , Wildhaber B. E. , Belli D. C. , Diana A. , Rodriguez M. , Siegrist C. A. , Posfay‐Barbe K. M. 
Published: November 2011

L’Huillier AG, Wildhaber BE, Belli DC, Diana A, Rodriguez M, Siegrist CA, Posfay‐Barbe KM. Successful serology‐based intervention to increase protection against vaccine‐preventable diseases in liver‐transplanted children: A 19‐yr review of the Swiss national reference center.  Pediatr Transplantation 2012: 16: 50–57. © 2011 John Wiley & Sons A/S.Abstract:  As children referred for OLT in Switzerland were not vaccinated optimally, new guidelines were developed and recommended to base catch‐up immunization on serum antibody titers against vaccine‐preventable diseases, before and after OLT. We measure the results of this serology‐based intervention by comparing vaccine coverage and antibody titers in the pre‐ (1990–2002, P1) and post‐intervention (2003–2008, P2) cohorts in a quality control project. Forty‐four P1 and 30 P2 children were evaluated. At pre‐OLT visit, D, T, SPn, and MMR serologies were checked more frequently in P2 than P1 (p < 0.05). More P2 children were up‐to‐date for DTaP and MMR (p < 0.05) or had received ≥1 dose of HBV, HAV, SPn, and VZV vaccines (p < 0.05). One yr post‐OLT, DT, SPn, MMR, and VZV serologies were more frequently checked (p < 0.05), and antibody titers were higher for DT and HAV (p < 0.05) in P2. Gender, age, or diagnosis did not explain these differences. Among P2 patients, pre‐ and post‐OLT titers for D, T, Hib, HBV, SPn14, and SPn19 were correlated (p < 0.05 for all). Protection against vaccine‐preventable diseases of high‐risk children like OLT patients can be significantly improved by serology‐based intervention for vaccine‐preventable diseases.