bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying ecological models to communities of genetic elements: the case of neutral theory
Authors: Linquist Stefan , Cottenie Karl , Elliott Tyler A. , Saylor Brent , Kremer Stefan C. , Gregory T. Ryan 
Published: April 2015

AbstractA promising recent development in molecular biology involves viewing the genome as a mini‐ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome‐level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational‐hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub ‘fitness neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size.
Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity
Authors: Lahrmann Urs , Strehmel Nadine , Langen Gregor , Frerigmann Henning , Leson Lisa , Ding Yi , Scheel Dierk , Herklotz Siska , Hilbert Magdalena , Zuccaro Alga 
Published: April 2015

SummaryDuring a compatible interaction, the sebacinoid root‐associated fungiPiriformospora indicaandSebacina vermiferainduce modification of root morphology and enhance shoot growth inArabidopsis thaliana.The genomic traits common in these two fungi were investigated and compared with those of other root‐associated fungi and saprotrophs. The transcriptional responses of the two sebacinoid fungi and of Arabidopsis roots to colonization at three different symbiotic stages were analyzed by custom‐designed microarrays.We identified key genomic features characteristic of sebacinoid fungi, such as expansions for gene families involved in hydrolytic activities, carbohydrate‐binding and protein–protein interaction. Additionally, we show that colonization of Arabidopsis correlates with the induction of salicylic acid catabolism and accumulation of jasmonate and glucosinolates (GSLs). Genes involved in root developmental processes were specifically induced byS. vermiferaat later stages during interaction.Using different Arabidopsis indole‐GSLs mutants and measurement of secondary metabolites, we demonstrate the importance of the indolic glucosinolate pathway in the growth restriction ofP. indicaandS. vermiferaand we identify indole‐phytoalexins and specifically indole‐carboxylic acids derivatives as potential key players in the maintenance of a mutualistic interaction with root endophytes.
Combined genetic and transcriptomic analysis reveals three major signalling pathways activated by Myc‐LCOs in Medicago truncatula
Authors: Camps Céline , Jardinaud Marie‐Françoise , Rengel David , Carrère Sébastien , Hervé Christine , Debellé Frédéric , Gamas Pascal , Bensmihen Sandra , Gough Clare 
Published: April 2015

Summary

Myc‐LCOs are newly identified symbiotic signals produced by arbuscular mycorrhizal (AM) fungi. Like rhizobial Nod factors, they are lipo‐chitooligosaccharides that activate the common symbiotic signalling pathway (CSSP) in plants. To increase our limited understanding of the roles of Myc‐LCOs we aimed to analyse Myc‐LCO‐induced transcriptional changes and their genetic control.

Whole genome RNA sequencing (RNA‐seq) was performed on roots of Medicago truncatula wild‐type plants, and dmi3 and nsp1 symbiotic mutants affected in nodulation and mycorrhizal signalling. Plants were treated separately with the two major types of Myc‐LCOs, sulphated and nonsulphated.

Generalized linear model analysis identified 2201 differentially expressed genes and classified them according to genotype and/or treatment effects. Three genetic pathways for Myc‐LCO‐regulation of transcriptomic reprogramming were highlighted: DMI3‐ and NSP1‐dependent; DMI3‐dependent and NSP1‐independent; and DMI3‐ and NSP1‐independent. Comprehensive analysis revealed overlaps with previous AM studies, and highlighted certain functions, especially signalling components and transcription factors.

These data provide new insights into mycorrhizal signalling mechanisms, supporting a role for NSP1, and specialisation for NSP1‐dependent and ‐independent pathways downstream of DMI3. Our data also indicate significant Myc‐LCO‐activated signalling upstream of DMI3 and/or parallel to the CSSP and some constitutive activity of the CSSP.
Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.)
Authors: Wang Maojun , Yuan Daojun , Tu Lili , Gao Wenhui , He Yonghui , Hu Haiyan , Wang Pengcheng , Liu Nian , Lindsey Keith , Zhang Xianlong 
Published: April 2015

Summary

Long noncoding RNAs (lncRNAs) are transcripts of at least 200 bp in length, possess no apparent coding capacity and are involved in various biological regulatory processes. Until now, no systematic identification of lncRNAs has been reported in cotton (Gossypium spp.).

Here, we describe the identification of 30 550 long intergenic noncoding RNA (lincRNA) loci (50 566 transcripts) and 4718 long noncoding natural antisense transcript (lncNAT) loci (5826 transcripts). LncRNAs are rich in repetitive sequences and preferentially expressed in a tissue‐specific manner. The detection of abundant genome‐specific and/or lineage‐specific lncRNAs indicated their weak evolutionary conservation. Approximately 76% of homoeologous lncRNAs exhibit biased expression patterns towards the At or Dt subgenomes. Compared with protein‐coding genes, lncRNAs showed overall higher methylation levels and their expression was less affected by gene body methylation.

Expression validation in different cotton accessions and coexpression network construction helped to identify several functional lncRNA candidates involved in cotton fibre initiation and elongation. Analysis of integrated expression from the subgenomes of lncRNAs generating miR397 and its targets as a result of genome polyploidization indicated their pivotal functions in regulating lignin metabolism in domesticated tetraploid cotton fibres.

This study provides the first comprehensive identification of lncRNAs in Gossypium.
Conserved V‐ATPase c subunit plays a role in plant growth by influencing V‐ATPase‐dependent endosomal trafficking
Authors: Zhou Aimin , Bu Yuanyuan , Takano Tetsuo , Zhang Xinxin , Liu Shenkui 
Published: April 2015

SummaryIn plant cells, the vacuolar‐type H+‐ATPases (V‐ATPase) are localized in the tonoplast, Golgi, trans‐Golgi network and endosome. However, little is known about how V‐ATPase influences plant growth, particularly with regard to the V‐ATPase c subunit (VHA‐c). Here, we characterized the function of a VHA‐c gene from Puccinellia tenuiflora (PutVHA‐c) in plant growth. Compared to the wild‐type, transgenic plants overexpressing PutVHA‐c in Arabidopsis thaliana exhibit better growth phenotypes in root length, fresh weight, plant height and silique number under the normal and salt stress conditions due to noticeably higher V‐ATPase activity. Consistently, the Arabidopsis atvha‐c5 mutant shows reduced V‐ATPase activity and retarded plant growth. Furthermore, confocal and immunogold electron microscopy assays demonstrate that PutVHA‐c is mainly localized to endosomal compartments. The treatment of concanamycin A (ConcA), a specific inhibitor of V‐ATPases, leads to obvious aggregation of the endosomal compartments labelled with PutVHA‐c‐GFP. Moreover, ConcA treatment results in the abnormal localization of two plasma membrane (PM) marker proteins Pinformed 1 (AtPIN1) and regulator of G protein signalling‐1 (AtRGS1). These findings suggest that the decrease in V‐ATPase activity blocks endosomal trafficking. Taken together, our results strongly suggest that the PutVHA‐c plays an important role in plant growth by influencing V‐ATPase‐dependent endosomal trafficking.
Verifying the Indonesian version of the Child Behavior Checklist
Authors: Hartini Sri , Hapsara Sunartini , Herini Siti E. , Takada Satoshi 
Published: April 2015

AbstractBackgroundThe Child Behavior Checklist for Ages 6–18 (CBCL/6‐18) is widely used to assess emotional and behavioral problems in children in the USA and Europe. Given that Indonesia has a more traditional culture that is different from the USA and Europe, it is possible that the CBCL is not effective in assessing the emotional and behavioral problems of Indonesian children, due to a difference in culture. Moreover, the validity and reliability of the Indonesian version of the CBCL/6‐18 have not been tested. The purpose of this study was therefore to test the validity and reliability of the Indonesian version of the CBCL/6‐18.MethodsThree hundred and eight mothers of children attending public primary schools participated in this study by completing the self‐administered questionnaire.ResultsAll items of the CBCL were positively correlated with total score (0.15–0.59), and total problems score had high internal consistency (r = 0.94). The correlations between questionnaire items and the eight subscales of the CBCL ranged from 0.10 to 0.74 and from 0.12 to 0.64 for the internalizing and externalizing scales, respectively (P < 0.01). The eight subscales of the CBCL had good internal consistency (0.61–0.87).ConclusionsThe CBCL/6‐18 is a valid and reliable instrument to measure emotional and behavioral problems in Indonesian children aged 6–12 years.
Prediction of medication non‐adherence and associated outcomes in pediatric kidney transplant recipients
Authors: Connelly James , Pilch N. , Oliver M. , Jordan C. , Fleming J. , Meadows H. , Baliga P. , Nadig S. , Twombley K. , Shatat I. , Taber D. 
Published: April 2015

AbstractStudies have continued to evaluate risk factors associated with post‐transplant non‐adherence in pediatric patients. However, many of these studies fail to evaluate how risk factors can be utilized to predict MNA. The aims of this study were to (i) determine salient risk factors associated with MNA to develop an adequate predictive risk model and (ii) assess transplant outcomes based on the presence of MNA in a large, diverse cohort of pediatric KTX recipients. One hundred and seventy‐five solitary pediatric KTX recipients transplanted from 1999 to 2013 were included. AA, males, older patients, those who lived in urban environments, had legal issues, and lived shorter distances from the transplant center were more likely to have MNA. Using logistic regression, a parsimonious model applying nine risk factors together was developed for predicting MNA, demonstrating a PPV of 69% and a NPV of 81%. Patients with MNA had more than twice the risk of biopsy proven acute rejection, 1.6 times the risk of hospitalization, and 1.8 times the risk of graft loss. Utilization of a predictive model to determine risk of MNA after pediatric KTX may offer clinicians the ability to efficiently and effectively monitor MNA following transplant.
Ultraviolet B Inhibits Skin Wound Healing by Affecting Focal Adhesion Dynamics
Authors: Liu Han , Yue Jiping , Lei Qiang , Gou Xuewen , Chen Shao‐Yu , He Yu‐Ying , Wu Xiaoyang 
Published: April 2015

AbstractAs the most important interface between human body and external environment, skin acts as an essential barrier preventing various environmental damages, among which DNA‐damaging UV radiation from the sun remains the major environmental risk factor causing various skin diseases. It has been well documented that wavelengths in the ultraviolet B (UVB) radiation range (290–320 nm) of the solar spectrum can be absorbed by skin and lead to cutaneous injury and various other deleterious effects. During process such as wound healing, the orchestrated movement of cells in a particular direction is essential and highly regulated, integrating signals controlling adhesion, polarity and the cytoskeleton. Cell adhesion and migration are modulated through both of actin and microtubule cytoskeletons. However, little was known about how UVB affects skin wound healing and migration of epidermal keratinocytes. Here, we demonstrate that UVB can delay the wound healing progress in vivo with a murine model of full‐thickness skin wound. In addition, UVB significantly inhibited keratinocyte motility by altering focal adhesion turnover and cytoskeletal dynamics. Our results provide new insights into the etiology of UVB exposure‐induced skin damages.
Family caregivers' views on coordination of care in Huntington's disease: a qualitative study
Authors: Røthing Merete , Malterud Kirsti , Frich Jan C. 
Published: April 2015

BackgroundCollaboration between family caregivers and health professionals in specialised hospitals or community‐based primary healthcare systems can be challenging. During the course of severe chronic disease, several health professionals might be involved at a given time, and the patient's illness may be unpredictable or not well understood by some of those involved in the treatment and care.AimThe aim of this study was to explore the experiences and expectations of family caregivers for persons with Huntington's disease concerning collaboration with healthcare professionals.MethodsTo shed light on collaboration from the perspectives of family caregivers, we conducted an explorative, qualitative interview study with 15 adult participants experienced from caring for family members in all stages of Huntington's disease. Data were analysed with systematic text condensation, a cross‐case method for thematic analysis of qualitative data.ResultsWe found that family caregivers approached health services hoping to understand the illness course and to share their concerns and stories with skilled and trustworthy professionals. Family caregivers felt their involvement in consultations and access to ongoing exchanges of knowledge were important factors in improved health services. They also felt that the clarity of roles and responsibilities was crucial to collaboration.ConclusionsFamily caregivers should be acknowledged for their competences and should be involved as contributors in partnerships with healthcare professionals. Our study suggests that building respectful partnerships with family caregivers and facilitating the mutual sharing of knowledge may improve the coordination of care. It is important to establish clarity of roles adjusted to caregivers' individual resources for managing responsibilities in the care process.
Conversations between persons with dementia disease living in nursing homes and nurses – qualitative evaluation of an intervention with the validation method
Authors: Söderlund Mona , Cronqvist Agneta , Norberg Astrid , Ternestedt Britt‐Marie , Hansebo Görel 
Published: April 2015

Living with dementia disease (DD) can include difficulties describing experiences of everyday lives, which can lead to withdrawal, social isolation or existential homelessness. Persons with DD living in nursing homes are mainly dependent on the nurses for establishing and maintaining relationships with those around them. It can be challenging for nurses to understand what a person with DD is trying to express and to make themselves understood in turn. The validation method is intended to facilitate communication with persons with DD, but to our knowledge, there have been no qualitative studies of how this influences persons' communication. This study aimed to illuminate the actions and reactions of persons with DD living in nursing homes in one‐to‐one conversations with nurses during 1 year of validation method training, as observed in videotapes. Four persons with DD were involved in videotaped conversations with four nurses who were participating in a validation method training programme. Videotapes with at least 5 months between the first and last recording were analysed and compared qualitatively. The findings are presented in four categories that were identified to various degrees in conversations at the beginning and at the end of the programme: being uninterested in or unable to answer questions, talking about more than one topic of conversation at the same time, trying to talk about what is on one's mind and speaking more freely about what is on one's mind. In the videotaped conversations at the end of the programme, the persons had the opportunity to use their remaining communication abilities. This may have been related to the development of the nurses' communication skills during the training programme, and so it is possible that persons with DD could benefit from communicating with nurses trained in the validation method.
Views concerning patient dignity among relatives to patients experiencing psychosis
Authors: Skorpen Frode , Thorsen Arlene Arstad , Forsberg Christina , Rehnsfeldt Arne 
Published: April 2015

BackgroundMental illness influences not only the suffering patient but often changes family life forever and results in experience of reduced dignity for both patients and relatives.AimThe aim of this study was to reveal relatives’ opinions regarding what is important for taking care of patients’ dignity.ParticipantsThirteen relatives of patients experiencing psychosis were recruited through a relatives’ user organisation.Research designThe methodological approach is Q methodology. A Q sample of 51 statements was sorted in a quasinormal distribution curve. Postinterviews were conducted with all participants.ResultsFour viewpoints emerged described as ‘value based’, ‘expectations’, ‘asymmetric’ and ‘nuanced’.ConclusionFocus on overarching values such as honesty and respect, to involve patients and relatives in care, by reducing asymmetry between patients and staff, with staff taking total responsibility for a patient's situation when needed, all represent aspects of taking care of patient dignity.
“Voluntary PR Voting” in the Election of Swiss Regional Governments
Authors: Lachat Romain , Kriesi Hanspeter 
Published: April 2015

AbstractThis paper analyses citizens' voting behaviour in the April 2011 elections of the regional governments in the cantons of Zurich and Lucerne. These elections were conducted with a majoritarian electoral system in a multi‐member district. In both cantons, the number of candidates in competition is relatively limited due to “voluntary PR”, that is, a coordination effort among parties that aims to achieve a proportional distribution of government seats. If citizens cast all of their votes, they must support candidates from various ideological camps. Alternatively, they can limit the number of votes used to cast a more concentrated vote. This paper examines what factors lead citizens to cast an ideologically concentrated or dispersed vote. The results show that the degree of ideological concentration of citizens' votes is related to partisan preferences, strategic considerations, political knowledge, and the level of satisfaction with the government performance.
Phosphorus availability and environmental risks in potato fields in North Florida
Authors: Liao X. , Liu G. , Hogue B. , Li Y. 
Published: April 2015

AbstractSoil phosphorus (P) availability was compared with Mehlich‐1 soil testing and P fractionation at a research farm (RF) and 32 private farms (PFs) in north Florida. The environmental risks caused by P release were evaluated using the P saturation ratio (PSR). Soil Mehlich‐1 P at the RF and the PFs was 41.9 ± 4.1 and 278 ± 13 mg/kg, respectively. The dominant inorganic P fraction for all farms was NaOH‐Pi (Al/Fe‐bound P) followed by HCl‐Pi (Ca/Mg‐bound P) at most of the PFs but by NaOH‐Po for the RF. Furthermore, the high PSR at the PFs indicated high risks of P loss from soil. To improve P use efficiency and enhance ecological sustainability, better P nutrient management should be implemented for Florida crop production.
Assessment of Risk Factors in Milk Contamination with Staphylococcus aureus in Urban and Peri‐Urban Small‐Holder Dairy Farming in Central Ethiopia
Authors: Tigabu E. , Asrat D. , Kassa T. , Sinmegn T. , Molla B. , Gebreyes W. 
Published: April 2015

SummaryAssessment of risk factors associated with milk production systems is central to ensuring quality and safety of milk and milk products. This study was aimed at identifying possible risk factors in milk contamination in urban and peri‐urban areas of the central high lands of Ethiopia. A total of 477 on‐farm pooled milk (n = 433) and combined bulk milk samples (n = 44) were collected and processed using standard microbiological techniques to isolate and characterize Staphylococcus aureus. In addition, 433 individual farm owners and 22 collection centre owners were interviewed using a structured and pre‐tested questionnaire. Multivariate logistic regression was used to determine risk factors. Of the total individual on‐farm pooled milk samples analysed (n = 433), it was found that 103 of the individual milk samples (24%) and 17 of the combined bulk milk (39%) were positive for S. aureus. This difference in prevalence was statistically significant. Even though there were a number of potential variables associated with the recovery of S. aureus in bovine milk, four variables including cleaning milk container with hot water and detergent [Adjusted OR: 0.342, 95% CI, (0.166, 0.701)], mastitis check [Adjusted OR: 3.019, 95% CI (1.542, 5.913)], travel time to collection centres [Adjusted OR: 4.932, 95% CI, (2.265, 10.739)] and amount of milk delivered by farmers to collection centres per day [Adjusted OR: 1.059 (1.032, 1.087 β = 0.057)] were found to be statistically significantly associated with isolation of S. aureus. We recommend a targeted educational intervention on defined risk factors to reduce the post‐harvest S. aureus contamination of raw milk in urban and peri‐urban milk shed areas of central Ethiopia.
Barriers to Physical Activity in Children With Autism Spectrum Disorders: Relationship to Physical Activity and Screen Time
Authors: Must Aviva , Phillips Sarah , Curtin Carol , Bandini Linda G. 
Published: April 2015

Background:Individual, social, and community barriers to physical activity (PA) experienced by children with autism spectrum disorder (ASD) make PA participation more difficult and may contribute to increased screen time.Methods:We compared the prevalence of parent-reported barriers to PA among 58 typically developing (TD) children and 53 children with an ASD, 3 to 11 years, and assessed the association between barriers and PA participation and screen time among children with ASD.Results:Parents of children with ASD reported significantly more barriers than parents of TD children. Based on parent-report, 60% of children with ASD required too much supervision compared with no TD children (P < .001). Parents of children with ASD were more likely to report that adults lack skills needed to include their child (58%), that their child has few friends (45%), and that other children exclude their child (23%). The number of parent-reported barriers to PA was inversely correlated with the hours spent in PA per year (r = −0.27, P = .05) and positively related to total screen time (r = .32, P < .03).Conclusions:These findings underscore the need for community-based PA programs designed to meet the special requirements of this population and policies that compel schools and other government-supported organizations for inclusion and/or targeted programming.