bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress
Authors: Kido Ederson A , Ferreira Neto José RC , Silva Roberta LO , Belarmino Luis C , Bezerra Neto João P , Soares-Cavalcanti Nina M , Pandolfi Valesca , Silva Manassés D , Nepomuceno Alexandre L , Benko-Iseppon Ana M 
Published: January 2013

Abstract

Background
Despite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources.

Methods
A curated set of osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome.

Results
The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo- inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs.

Conclusions
Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.
Finding reproducible cluster partitions for the k-means algorithm
Authors: Lisboa Paulo JG , Etchells Terence A , Jarman Ian H , Chambers Simon J 
Published: January 2013

Abstract
K-means clustering is widely used for exploratory data analysis. While its dependence on initialisation is well-known, it is common practice to assume that the partition with lowest sum-of-squares (SSQ) total i.e. within cluster variance, is both reproducible under repeated initialisations and also the closest that k-means can provide to true structure, when applied to synthetic data. We show that this is generally the case for small numbers of clusters, but for values of k that are still of theoretical and practical interest, similar values of SSQ can correspond to markedly different cluster partitions.
This paper extends stability measures previously presented in the context of finding optimal values of cluster number, into a component of a 2-d map of the local minima found by the k-means algorithm, from which not only can values of k be identified for further analysis but, more importantly, it is made clear whether the best SSQ is a suitable solution or whether obtaining a consistently good partition requires further application of the stability index. The proposed method is illustrated by application to five synthetic datasets replicating a real world breast cancer dataset with varying data density, and a large bioinformatics dataset.
Young aboriginals are less likely to receive a renal transplant: a Canadian national study
Authors: Promislow Steven , Hemmelgarn Brenda , Rigatto Claudio , Tangri Navdeep , Komenda Paul , Storsley Leroy , Yeates Karen , Mojica Julie , Sood Manish M 
Published: January 2013

Abstract

Background
Previous studies have demonstrated Aboriginals are less likely to receive a renal transplant in comparison to Caucasians however whether this applies to the entire population or specific subsets remains unclear. We examined the effect of age on renal transplantation in Aboriginals.

Methods
Data on 30,688 dialysis (Aboriginal 2,361, Caucasian 28, 327) patients obtained between Jan. 2000 and Dec. 2009 were included in the final analysis. Racial status was self-reported. Cox proportional hazards, the Fine and Grey sub-distribution method and Poisson regression were used to determine the association between race, age and transplantation.

Results
In comparison to Caucasians, Aboriginals were less likely to receive a renal transplant (Adjusted HR 0.66 95% CI 0.57-0.77, P < 0.0001) however after stratification by age and treating death as a competing outcome, the effect was more predominant in younger Aboriginals (Age 18–40: 20.6% aboriginals vs. 48.3% Caucasians transplanted; aHR 0.50(0.39-0.61), p < 0.0001, Age 41–50: 10.2% aboriginals vs. 33.9% Caucasians transplanted; aHR 0.46(0.32-0.64), p = 0.005, Age 51–60: 8.2% aboriginals vs. 19.5% Caucasians transplanted; aHR0.65(0.49-0.88), p = 0.01, Age >60: 2.7% aboriginals vs. 2.6% Caucasians transplanted; aHR 1.21(0.76-1.91), P = 0.4, Age X race interaction p < 0.0001). Both living and deceased donor transplants were lower in Aboriginals under the age of 60 compared to Caucasians.

Conclusion
Younger Aboriginals are less likely to receive a renal transplant compared to their Caucasian counterparts, even after adjustment for comorbidity. Determination of the reasons behind these discrepancies and interventions specifically targeting the Aboriginal population are warranted.
Selecting renal replacement therapies: what do African American and non-African American patients and their families think others should know? A mixed methods study
Authors: DePasquale Nicole , Ephraim Patti L , Ameling Jessica , Lewis-Boyér Lapricia , Crews Deidra C , Greer Raquel C , Rabb Hamid , Powe Neil R , Jaar Bernard G , Gimenez Luis , Auguste Priscilla , Jenckes Mollie , Boulware L Ebony 
Published: January 2013

Abstract

Background
Little is known regarding the types of information African American and non-African American patients with chronic kidney disease (CKD) and their families need to inform renal replacement therapy (RRT) decisions.

Methods
In 20 structured group interviews, we elicited views of African American and non-African American patients with CKD and their families about factors that should be addressed in educational materials informing patients’ RRT selection decisions. We asked participants to select factors from a list and obtained their open-ended feedback.

Results
Ten groups of patients (5 African American, 5 non-African American; total 68 individuals) and ten groups of family members (5 African American, 5 non-African American; total 62 individuals) participated. Patients and families had a range (none to extensive) of experiences with various RRTs. Patients identified morbidity or mortality, autonomy, treatment delivery, and symptoms as important factors to address. Family members identified similar factors but also cited the effects of RRT decisions on patients’ psychological well-being and finances. Views of African American and non-African American participants were largely similar.

Conclusions
Educational resources addressing the influence of RRT selection on patients’ morbidity and mortality, autonomy, treatment delivery, and symptoms could help patients and their families select RRT options closely aligned with their values. Including information about the influence of RRT selection on patients’ personal relationships and finances could enhance resources’ cultural relevance for African Americans.
Gender difference in the characteristics of and high-risk behaviours among non-injecting heterosexual methamphetamine users in Qingdao, Shandong Province, China
Authors: Liu Dianchang , Wang Zhenhong , Chu Tongsheng , Chen Shumin 
Published: January 2013

Abstract

Background
Despite the increasing risk of HIV infections, few studies concerning the characteristics of non-injecting heterosexual methamphetamine (MA) users and related risk behaviours have been conducted in China.

Methods
Gender differences in socio-demographic characteristics, perception of MA and STD/HIV, MA use practices, and sexual behaviours related to MA use were examined among 398 non-injecting heterosexual MA users (288 males, 110 females).

Results
Male MA users were more likely to be married, local, and self-employed; female MA users were more likely to be young, single, engaged in commercial service or unemployed. Female MA users usually start MA use at an earlier age than males (24.3 vs. 31.3 years old), with shorter abuse durations (2.6 vs. 2.9 years), higher frequency of MA use (3.6 vs. 2.4 times per week), and higher likelihood of using MA with heterosexual partners (100% vs. 78.1%). More male MA users have had multiple sex partners (96.9% vs. 77.3%) and sex exchanges (72.9% vs. 46.4%). Among 277 males who had had sex with commercial sex workers (CSW), 69.4% never used condoms, and among 77 males who had had sex with multiple partners who are commercial sex workers and always or usually used condoms, 87.0% never changed condoms when changing partners.

Conclusion
There may be gender difference in the characteristics of high-risk behaviours among non-injecting heterosexual MA users. The findings suggest the integration of specific risk reduction strategies into intervention programs for non-injecting heterosexual MA user populations may significantly improve program goals.
Gamified physical activation of young men – a Multidisciplinary Population-Based Randomized Controlled Trial (MOPO study)
Authors: Ahola Riikka , Pyky Riitta , Jämsä Timo , Mäntysaari Matti , Koskimäki Heli , Ikäheimo Tiina M , Huotari Maija-Leena , Röning Juha , Heikkinen Hannu I , Korpelainen Raija 
Published: January 2013

Abstract

Background
Inactive and unhealthy lifestyles are common among adolescent men. The planned intervention examines the effectiveness of an interactive, gamified activation method, based on tailored health information, peer networks and participation, on physical activity, health and wellbeing in young men. We hypothesize that following the intervention the physical activation group will have an improved physical activity, as well as self-determined and measured health compared with the controls.

Methods/design
Conscription-aged men (18 years) attending compulsory annual call-ups for military service in the city of Oulu in Finland (n = 1500) will be randomized to a 6-months intervention (n = 640) or a control group (n = 640) during the fall 2013. A questionnaire on health, health behaviour, diet and wellbeing is administered in the beginning and end of the intervention. In addition, anthropometric measures (height, weight and waist circumference), body composition, grip strength, heart rate variability and aerobic fitness will be measured. The activation group utilizes an online gamified activation method in combination with communal youth services, objective physical activity measurement, social networking, tailored health information and exercise programs according to baseline activity level and the readiness of changes of each individual. Daily physical activity of the participants is monitored in both the activation and control groups. The activation service rewards improvements in physical activity or reductions in sedentary behaviour. The performance and completion of the military service of the participants will also be followed.

Discussion
The study will provide new information of physical activity, health and health behaviour of young men. Furthermore, a novel model including methods for increasing physical activity among young people is developed and its effects tested through an intervention. This unique gamified service for activating young men can provide a translational model for community use. It can also be utilized as such or tailored to other selected populations or age groups.

Trial registration
ClinicalTrials.gov Identifier: NCT01376986
Vitamin D deficiency among healthy adolescents in Al Ain, United Arab Emirates
Authors: Muhairi Shamma J , Mehairi Aaesha E , Khouri Aysha A , Naqbi Muna M , Maskari Fatima A , Kaabi Juma Al , Dhaheri Ayesha S Al , Nagelkerke Nico , Shah Syed M 
Published: January 2013

Abstract

Background
Although vitamin D deficiency has been studied in various adult populations, there are few data on the prevalence of this nutritional deficiency among healthy adolescents in the United Arab Emirates (UAE). This study was conducted to determine the prevalence of vitamin D deficiency and to examine its correlates in adolescents aged 15 to 18 years.

Methods
This was a cross-sectional study in urban schools. Healthy adolescents (N=315) from a sample of 8 schools were randomly selected from the 142 schools in Al Ain, Abu Dhabi Emirate. Outcomes measured included serum concentrations of 25-hydroxy vitamin D (25OHD), plasma lipids, blood sugar, blood pressure and anthropometric data, nutrition and lifestyle variables.

Results
Fourty-one participants (19.7%) were vitamin D deficient (serum 25OHD level ≤15 ng/mL [≤37.5 nmol/L]. Using a cutoff level of 25(OH) D of ≤20 ng/ml [≤50 nmol/l] 143 participants (45.4%) were vitamin D insufficient. Overall 65.1% of study participants were either vitamin D deficient or insufficient. The prevalence of vitamin D deficiency varied between boys (10%) and girls (28%). In a final multivariate model, serum 25(OH) D concentrations were inversely correlated with female gender, consumption of fast food per week, and body mass index and positively correlated with physical activity scores after adjustment for age.

Conclusions
Vitamin D deficiency and insufficiency were highly prevalent in adolescents, and more common in girls.
Obesity & hypertension are determinants of poor hemodynamic control during total joint arthroplasty: a retrospective review
Authors: Nwachukwu Benedict U , Collins Jamie E , Nelson Emily P , Concepcion Mercedes , Thornhill Thomas S , Katz Jeffrey N 
Published: January 2013

AbstractBackgroundProper blood pressure control during surgical procedures such as total joint arthroplasty (TJA) is considered critical to good outcome. There is poor understanding of the pre-operative risk factors for poor intra-operative hemodynamic control. The purpose of this study is to identify risk factors for poor hemodynamic control during TJA.MethodsWe performed a retrospective cohort analysis of 118 patients receiving TJA in the Dominican Republic. We collected patient demographic and comorbidity data. We developed an a priori definition for poor hemodynamic control: 1) Mean arterial pressure (MAP) <65% of preoperative MAP or 2) MAP >135% of preoperative MAP. We performed bivariate and multivariate analyses to identify risk factors for poor hemodynamic control during TJA.ResultsHypertension was relatively common in our study population (76 of 118 patients). Average preoperative mean arterial pressure was 109.0 (corresponding to an average SBP of 149 and DBP of 89). Forty-nine (41.5%) patients had intraoperative blood pressure readings consistent with poor hemodynamic control. Based on multi-variable analysis preoperative hypertension of any type (RR 2.9; 95% CI 1.3-6.3) and an increase in BMI (RR 1.2 per 5 unit increase; 95% CI 1.0-1.5) were significant risk factors for poor hemodynamic control.ConclusionsPreoperative hypertension and being overweight/obese increase the likelihood of poor blood pressure control during TJA. Hypertensive and/or obese patients warrant further attention and medical optimization prior to TJA. More work is required to elucidate the relationship between these risk factors and overall outcome.
ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Authors: Thomas Dennis G , Gaheen Sharon , Harper Stacey L , Fritts Martin , Klaessig Fred , Hahn-Dantona Elizabeth , Paik David , Pan Sue , Stafford Grace A , Freund Elaine T , Klemm Juli D , Baker Nathan A 
Published: January 2013

Abstract

Background and motivation
The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.

Results
We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.

Conclusion
The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.
Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)
Authors: Mason Mary E , Koch Jennifer L , Krasowski Marek , Loo Judy 
Published: January 2013

Abstract

Background
Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by one of the Neonectria species of fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees.

Results
Proteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified.

Conclusions
Further study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services.
TCR activation kinetics and feedback regulation in primary human T cells
Authors: Poltorak Mateusz , Arndt Boerge , Kowtharapu Bhavani S , Reddycherla Amarendra V , Witte Vanessa , Lindquist Jonathan A , Schraven Burkhart , Simeoni Luca 
Published: January 2013

AbstractBackgroundSignaling through the TCR is crucial for the generation of different cellular responses including proliferation, differentiation, and apoptosis. A growing body of evidence indicates that differences in the magnitude and the duration of the signal are critical determinants in eliciting cellular responses.ResultsHere, we have analyzed signaling dynamics correlating with either unresponsiveness or proliferation induced upon TCR/CD28 ligation in primary human T cells. We used two widely employed methods to stimulate T cellsin vitro, antibodies either cross-linked in solution (sAbs) or immobilized on microbeads (iAbs). A comparative analysis of the signaling properties of iAbs and sAbs revealed that, under proliferation-inducing conditions, feedback regulation is markedly different from that leading to an unresponsive state. In fact, upon iAbs stimulation TCR-mediated signaling is prolonged by a positive feedback loop involving Erk, whereas sAbs strongly activate inhibitory molecules that likely terminate signaling. We additionally found that, by enhancing the phosphorylation of Src family kinases under proliferation-inducing conditions, signaling and T-cell activation are terminated.ConclusionsIn summary, our analysis documents TCR signaling kinetics and feedback regulation under conditions of stimulation inducing either unresponsiveness or proliferation.