bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ship Management Attitudes and Their Relation to Behavior and Performance
Authors: Röttger Stefan , Vetter Saskia , Kowalski Jens T. 
Published: October 2012

Objective: The aim of this study was to adapt the Crew Resource Management (CRM) Attitudes Questionnaire (CMAQ) to the maritime domain, to assess the ship management attitudes of junior naval officers, and to determine the extent to which these attitudes correlate with behavior and performance in a naval exercise. Background: CRM attitudes have been shown to be associated with performance in aviation, but it is unclear whether this construct is applicable and relevant to the maritime domain. Method: Participants were 121 active seafarers and 101 junior officers of the German Navy who completed the Ship Management Attitudes Questionnaire–German Navy (SMAQ-GN). Ratings of nontechnical skills and ratings of mission success of the junior officers were collected during a real-world naval exercise. Results: Internal consistencies of SMAQ-GN were similar to those of the original CMAQ and retest reliability was rather high. Attitudes of junior officers toward communication and coordination were positive. Regarding command responsibility and the recognition of stressor effects, positive as well as neutral and negative attitudes were found. Overall, attitudes did not correlate with behavior and performance. Separate analysis of those participants reporting negative to neutral ship management attitudes showed substantial positive correlations of attitudes with behavior and performance. Conclusion: Ship management attitudes play a significant role in commanding ships. The attitude–performance linkage is not linear. Behavior and perfor-mance are less effective in officers with negative attitudes and equally effective in officers with slightly positive and very positive attitudes. Application: Ship management attitudes can be used to assess training needs for nautical teams.
Water and Coffee
Authors: Silverstein Barbara A. , Bao Stephen S. , Russell Steven , Stewart Kate 
Published: October 2012

Objective: The aim of this study was to reduce the physical load on coffee-harvesting workers while maintaining productivity. Background: Coffee is second to oil in commodity trading. Water is becoming scarce worldwide. The global virtual water footprint for one cup of coffee is 140 liters. Shade-grown coffee is one approach to reducing the water footprint. Method: A participatory ergonomics approach was used during two Nicaraguan shade-grown coffee harvesting seasons to reduce the physical load on harvesters with the use of a newly designed bag instead of a basket strapped around the waist. Results: Productivity in the mountainous, shade-grown coffee farms was maintained while physical load on the worker was improved somewhat. Among basket users, 84.2% reported pain in at least one body area compared with 78.9% of bag users ( ns). Nonetheless, 74% of participants liked the bag “much better” than the basket. Workers identified ways the bag could be improved further with the use of local materials. These suggestions included (a) reducing the horizontal distance of the bag to reduce reach and (b) having waterproof material on the bag between the worker and the bag to reduce moisture and damage to the berries. There was no difference in productivity between using the bag and using the small basket. Conclusions: Workers are extending this partici-patory approach to how to get the harvested coffee cherries down the mountain other than carrying 40-kg bags on their backs. The ultimate goal is to make the coffee-harvesting bag design available to harvesters around the world.
A Community-Based Participatory Diabetes Prevention and Management Intervention in Rural India Using Community Health Workers
Authors: Balagopal Padmini , Kamalamma N. , Patel Thakor G. , Misra Ranjita , Misra Ranjita , Balagopal Padmini , Patel Thakor G. , Kamalamma N. 
Published: October 2012

Purpose The purpose of this study was to test the effectiveness of a 6-month community-based diabetes prevention and management program in rural Gujarat, India. Methods A community-based participatory research method was used to plan and tailor the intervention by engaging trained community health workers as change agents to provide lifestyle education, serve as community advocates, and collect data from 1638 rural Indians (81.9% response rate). Ten culturally and linguistically appropriate health education messages were provided in face-to-face individual and group sessions (demonstrations of model meals and cooking techniques). Results Mean age was 41.9 ± 15.9 years. Overall point prevalence of diabetes, prediabetes, obesity, and hypertension were 7.2%, 19.3%, 16.7%, and 28%, respectively, with significant differences between the low socioeconomic status (SES) participants (agricultural workers) and the high SES participants (business community) due to differing diet and activity levels. The intervention significantly reduced blood glucose levels by 5.7 and 14.9 mg/dL for individuals with prediabetes and diabetes, respectively, and systolic and diastolic blood pressure by 8 mm Hg and 4 mm Hg, respectively, in the overall population. Knowledge of diabetes and cardiovascular disease improved by 50% in the high SES group and doubled in the low SES group; general and abdominal obesity also decreased by ≤ 1%. High rates of undiagnosed hypertension (26.1%) were surprising. Among individuals with diabetes, metabolic complications such as diabetic nephropathy and chronic kidney disease were noted. Conclusions Through collective engagement of the community, participatory programs can serve as a prototype for future prevention and management efforts, which are rare and underutilized in India.
Low concentration of mercury induces autophagic cell death in rat hepatocytes
Authors: Chatterjee Sarmishtha , Ray Atish , Mukherjee Sandip , Agarwal Soumik , Kundu Rakesh , Bhattacharya Shelley 
Published: October 2012

In the present study, we attempted to elucidate the induction of autophagy in rat hepatocytes by a low concentration of mercury. Hepatocytes treated with different doses of mercuric chloride (HgCl2; 1, 2.5, 5 and 10 µM) and at different time intervals (0 min, 30 min, 1 h, 2 h and 4 h) show autophagic cell death only at 5 µM HgCl2 within 30 min of incubation. At 1 and 2.5 µM HgCl2, no cell death is recorded, while apoptosis is found at 10 µM HgCl2, as evidenced by the activation of caspase 3. Autophagic cell death is confirmed by the presence of monodansylcadaverine (MDC) positive hepatocytes which is found to be highest at 1 h. Atg5-Atg12 covalent-conjugation triggers the autophagic pathway within 30 min of 5 µM HgCl2 treatment and continues till 4 h of incubation. In addition, damage-regulated autophagy modulator (DRAM) expression gradually increases from 30 min to 4 h of treatment with mercury and a corresponding linear decrease in p53 has been observed. It is concluded that a low concentration (5 µM HgCl2) of mercury induces autophagy or nonapoptotic programmed cell death following an Atg5-Atg12 covalent-conjugation pathway, which is modulated by DRAM in a p53-dependent manner.
Characterization of serotonin transporter gene (SLC6A4) polymorphisms and its association with drug dependence in a Jordanian Arab population
Authors: Al-Eitan Laith Naser , Jaradat Saied Ali , Qin Wenwen , Wildenauer Diah Mutiara B , Wildenauer Dieter DB , Hulse Gary K , Tay Guan K 
Published: October 2012

Drug dependence is a pattern of repeated self-administration of a drug, which can result in tolerance, withdrawal and compulsive drug-taking behaviour. It has been recently suggested that 5-HTTLPR ( LL/ LS/ SS) variants and rs25531 (A/G) polymorphism in the serotonin transporter gene ( SLC6A4) may play a role in drug dependence. The current study aimed to (1) identify allelic, haplotypic and genotypic frequencies of the 5-HTTLPR variants and rs25531 polymorphisms of SLC6A4 gene in drug and nondrug-dependent Jordanian Arab population and (2) determine whether there is an association of these variants in a drug-dependent population from the same area. Jordanian drug male addicts of Arab descent ( n = 192) meeting the Diagnostic and Statistical Manual of Mental Disorders – Fourth edition criteria for drug dependence and 230 healthy male controls from an ethnically homogenous Jordanian Arab population were examined. Genotyping was performed using the restriction fragment length polymorphism–polymerase chain reaction-based method to genotype the 5-HTTLPR variants and detect the A/G polymorphism at position rs25531. The biallelic analysis revealed that the frequency of 5-HTTLPR ( LL/ LS/ SS) genotypes was statistically significant different between drug-dependent individuals and controls ( χ2 (2, N = 422), p = 0.04). Drug-dependent subjects had a higher frequency of ‘ L’ allele. However, using the triallelic approach, the estimated frequency of haplotypes ( SA, SG, LA and LG) and phased genotypes ( LA/ LA, LA/ SA, LA/ LG, SA/ SA and SA/ SG) did not show significant association with drug dependence ( χ2 (3, N = 422), p = 0.53 and χ2 (4, N = 422), p = 0.06, respectively). This study suggests a putative role of the 5-HTTLPR for drug dependence in the Jordanian Nationals of Arab ancestry.
Physical education teachers’ continuing professional development in health-related exercise
Authors: Alfrey Laura , Webb Louisa , Cale Lorraine 
Published: October 2012

This paper uses figurational sociology to explain why Secondary Physical Education teachers’ engagement with Health Related Exercise (HRE) is often limited. Historically-rooted concerns surround the teaching of HRE, and these have recently been linked to teachers’ limited continuing professional development (CPD) in HRE (HRE-CPD). A two-phase, mixed-method study involving a survey questionnaire ( n=124) and semi-structured interviews ( n=12) was conducted in the UK to explore Physical Education teachers’ engagement with HRE and HRE-CPD over time. The findings confirm that teachers’ engagement with HRE-CPD is often limited. Indeed, nearly three quarters of the teachers (73%) also felt that their tertiary education had failed to adequately prepare them to teach HRE. This paper argues that a range of interdependent processes are contributing towards teachers’ limited engagement with HRE, and that most of these processes – such as the marginalisation of HRE – are rooted in the privileging of sporting, individualised and performative ideologies within Physical Education. In conclusion, it is argued that informed and strategic action which addresses the above issues and which transcends all levels of the education figuration is needed if the concerns surrounding HRE are to be overcome.
Barriers to therapeutic clinical trials enrollment: Differences between African-American and white cancer patients identified at the time of eligibility assessment
Authors: Penberthy Lynne , Brown Richard , Wilson-Genderson Maureen , Dahman Bassam , Ginder Gordon , Siminoff Laura A 
Published: October 2012

Background Clinical trials (CTs) are the mechanism by which research is translated into standards of care. Low recruitment among underserved and minority populations may result in inequity in access to the latest technology and treatments, compromise the generalizability, and lead to failure in identification of important positive or negative treatment effects among under-represented populations. Methods Data were collected over a 39-month period on patient eligibility for available therapeutic cancer CTs. Reasons for ineligibility and refusal were collected. The data were captured using an automated software tool for tracking eligibility pre-enrollment. We examined characteristics associated with being evaluated for a trial, and reasons for ineligibility and refusal, overall and by patient race. Results African-Americans (AAs) were more likely than Whites to be ineligible (odds ratio, (OR) = 1.26, 95% confidence interval (CI) = 1.0–1.58) and if eligible, to refuse participation (OR = 1.79, 95% CI = 1.27–2.52), even after adjusting for insurance, age, gender, study phase, and cancer type. White patients were more likely to be ineligible due to study-specific or cancer characteristics. AAs were more likely to be ineligible due to mental status or perceived noncompliance. Whites were more likely to refuse due to extra burden, due to concerns with randomization and toxicity, or because they express a positive treatment preference. AAs were more likely to refuse because they were not interested in CTs, because of family pressures, or they felt overwhelmed (NS)). Discussion This study is the first to directly compare ineligibility and refusal rates and reasons captured prospectively in AA and White cancer patients. The data are consistent with earlier studies that indicated that AA patients more often are deemed ineligible and, when eligible, more often refuse participation. However, differences in reasons for ineligibility and refusal by race have implications for a cancer center to participate in CTs appropriate for the population of patients served. On a broader scale, consideration should be given to modifying eligibility criteria and other design aspects to permit broader participation of minority and other underserved groups.
Individuals with increased inflammatory response to ozone demonstrate muted signaling of immune cell trafficking pathways
Authors: Fry Rebecca C , Rager Julia E , Zhou Haibo , Zou Baiming , Brickey June W , Ting Jenny , Lay John C , Peden David B , Alexis Neil E 
Published: October 2012

Abstract

Background
Exposure to ozone activates innate immune function and causes neutrophilic (PMN) airway inflammation that in some individuals is robustly elevated. The interplay between immuno-inflammatory function and genomic signaling in those with heightened inflammatory responsiveness to ozone is not well understood.

Objectives
Determine baseline predictors and post exposure discriminators for the immuno-inflammatory response to ozone in inflammatory responsive adult volunteers.

Methods
Sputum induction was performed on 27 individuals before and after a two hour chamber exposure to 0.4 ppm ozone. Subjects were classified as inflammatory responders or non-responders to ozone based on their PMN response. Innate immune function, inflammatory cell and cytokine modulation and transcriptional signaling pathways were measured in sputum.

Results
Post exposure, responders showed activated innate immune function (CD16: 31,004 MFI vs 8988 MFI; CD11b: 44,986 MFI vs 24,770 MFI; CD80: 2236 MFI vs 1506 MFI; IL-8: 37,603 pg/ml vs 2828 pg/ml; and IL-1β: 1380 pg/ml vs 318 pg/ml) with muted signaling of immune cell trafficking pathways. In contrast, non-responders displayed decreased innate immune activity (CD16, CD80; phagocytosis: 2 particles/PMN vs 4 particles/PMN) post exposure that was accompanied by a heightened signaling of immune cell trafficking pathways.

Conclusions
Inflammatory responsive and non responsive individuals to ozone show an inverse relationship between immune cell trafficking and immuno-inflammatory functional responses to ozone. These distinct genomic signatures may further our understanding about ozone-induced morbidity in individuals with different levels of inflammatory responsiveness.
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees
Authors: Ramu Avinash , Kahveci Tamer , Burleigh J Gordon 
Published: October 2012

Abstract

Background
We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees.

Results
We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods.

Conclusions
Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses.
Construction and analysis of a high-density genetic linkage map in cabbage (Brassica oleracea L. var. capitata)
Authors: Wang Wanxing , Huang Shunmou , Liu Yumei , Fang Zhiyuan , Yang Limei , Hua Wei , Yuan Suxia , Liu Shengyi , Sun Jifeng , Zhuang Mu , Zhang Yangyong , Zeng Aisong 
Published: October 2012

AbstractBackgroundBrassica oleraceaencompass a family of vegetables and cabbage that are among the most widely cultivated crops. In 2009, theB. oleraceaGenome Sequencing Project was launched using next generation sequencing technology. None of the available maps were detailed enough to anchor the sequence scaffolds for the Genome Sequencing Project. This report describes the development of a large number of SSR and SNP markers from the whole genome shotgun sequence data ofB. oleracea, and the construction of a high-density genetic linkage map using a double haploid mapping population.ResultsTheB. oleraceahigh-density genetic linkage map that was constructed includes 1,227 markers in nine linkage groups spanning a total of 1197.9 cM with an average of 0.98 cM between adjacent loci. There were 602 SSR markers and 625 SNP markers on the map. The chromosome with the highest number of markers (186) was C03, and the chromosome with smallest number of markers (99) was C09.ConclusionsThis first high-density map allowed the assembled scaffolds to be anchored to pseudochromosomes. The map also provides useful information for positional cloning, molecular breeding, and integration of information of genes and traits inB. oleracea. All the markers on the map will be transferable and could be used for the construction of other genetic maps.
SERE: Single-parameter quality control and sample comparison for RNA-Seq
Authors: Schulze Stefan K , Kanwar Rahul , Gölzenleuchter Meike , Therneau Terry M , Beutler Andreas S 
Published: October 2012

Abstract

Background
Assessing the reliability of experimental replicates (or global alterations corresponding to different experimental conditions) is a critical step in analyzing RNA-Seq data. Pearson’s correlation coefficient r has been widely used in the RNA-Seq field even though its statistical characteristics may be poorly suited to the task.

Results
Here we present a single-parameter test procedure for count data, the Simple Error Ratio Estimate (SERE), that can determine whether two RNA-Seq libraries are faithful replicates or globally different. Benchmarking shows that the interpretation of SERE is unambiguous regardless of the total read count or the range of expression differences among bins (exons or genes), a score of 1 indicating faithful replication (i.e., samples are affected only by Poisson variation of individual counts), a score of 0 indicating data duplication, and scores >1 corresponding to true global differences between RNA-Seq libraries. On the contrary the interpretation of Pearson’s r is generally ambiguous and highly dependent on sequencing depth and the range of expression levels inherent to the sample (difference between lowest and highest bin count). Cohen’s simple Kappa results are also ambiguous and are highly dependent on the choice of bins. For quantifying global sample differences SERE performs similarly to a measure based on the negative binomial distribution yet is simpler to compute.

Conclusions
SERE can therefore serve as a straightforward and reliable statistical procedure for the global assessment of pairs or large groups of RNA-Seq datasets by a single statistical parameter.
Callose plug deposition patterns vary in pollen tubes of Arabidopsis thalianaecotypes and tomato species
Authors: Qin Peng , Ting Dylan , Shieh Andrew , McCormick Sheila 
Published: October 2012

Abstract

Background
The pollen grain contains the male gametophyte that extends a pollen tube that grows through female tissues in order to deliver sperm to the embryo sac for double fertilization. Growing pollen tubes form periodic callose plugs that are thought to block off the older parts of the tube and maintain the cytoplasm near the growing tip. The morphology of callose plugs and the patterns of their deposition were previously shown to vary among species, but variation within a species had not been examined. We therefore systematically examined callose plug deposition in Arabidopsis thaliana ecotypes, tested for heritability using reciprocal crosses between ecotypes that had differing deposition patterns, and investigated the relationship between callose plugs and pollen tube growth rate. We also surveyed callose plug deposition patterns in different species of tomato.

Results
We used in vitro grown pollen tubes of 14 different A. thaliana ecotypes and measured the distance from the pollen grain pore to the first callose plug (termed first interval). This distance varied among Arabidopsis ecotypes and in some cases even within an ecotype. Pollen tubes without a callose plug were shorter than those with a callose plug, and tubes with a callose plug near the grain were, on average, longer than those with the first callose plug farther from the grain. Variations in the first callose plug position were also observed between different species of tomato.

Conclusions
We showed that the position of the first callose plug varied among Arabidopsis ecotypes and in tomato species, and that callose plug deposition patterns were heritable. These findings lay a foundation for mapping genes that regulate callose plug deposition or that determine pollen tube length or growth rate.