Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

Enhancing resolution of natural methylome reprogramming behavior in plants

We have developed a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Comparison with three commonly used programs and various available datasets to furnish a comparative measure of resolution by each method is included. To confirm results, methylation analysis was integrated with RNAseq and network enrichment analyses. Methyl-IT enhances resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods

"I Didn't Want To Be 'That Girl'": The Social Risks of Labeling, Telling, and Reporting Sexual Assault

This article deploys ethnographic data to explain why some students do not label experiences as sexual assault or report those experiences. Using ideas of social risks and productive ambiguities, it argues that not labeling or reporting assault can help students (1) sustain their current identities and allow for several future ones, (2) retain their social relationships and group affiliations while maintaining the possibility of developing a wider range of future ones, or (3) avoid derailing their current or future goals within the higher educational setting, or what we call "college projects." Conceptually, this work advances two areas of sociological research. First, it expands the framework of social risks, or culturally specific rationales for seemingly illogical behavior, by highlighting the interpersonal and institutional dimensions of such risks. Second, it urges researchers to be more attentive to contexts in which categorical ambiguity or denial is socially productive and to take categorical avoidance seriously as a subject of inquiry. Substantively, this work advances knowledge of why underreporting of campus sexual assault occurs, with implications for institutional policies to support students who have experienced unwanted nonconsensual sex regardless of how those students may label what happened

Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

<p>Abstract</p> <p>Background</p> <p>The mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ) activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene <it>MSH1 </it>(MutS 1 homolog), lending itself to detailed study of <it>de novo </it>mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution.</p> <p>Results</p> <p>We obtained evidence of double-strand break (DSB) repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and <it>msh1 </it>mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the <it>msh1 </it>mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. <it>De novo </it>asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes.</p> <p>Conclusions</p> <p>Extensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants.</p

Behavior problems and prevalence of asthma symptoms among Brazilian children.

OBJECTIVE: Asthma is the most common chronic disease in childhood and has been designated a public health problem due to the increase in its prevalence in recent decades, the amount of health service expenditure it absorbs and an absence of consensus about its etiology. The relationships among psychosocial factors and the occurrence, symptomatology, and severity of asthma have recently been considered. There is still controversy about the association between asthma and a child's mental health, since the pathways through which this relationship is established are complex and not well researched. This study aims to investigate whether behavior problems are associated with the prevalence of asthma symptoms in a large urban center in Latin America. METHODS: It is a cross-section study of 869 children between 6 and 12 years old, residents of Salvador, Brazil. The International Study of Allergy and Asthma in Childhood (ISAAC) instrument was used to evaluate prevalence of asthma symptoms. The Child Behavior Checklist (CBCL) was employed to evaluate behavioral problems. RESULTS: 19.26% (n=212) of the children presented symptoms of asthma. 35% were classified as having clinical behavioral problems. Poisson's robust regression model demonstrated a statistically significant association between the presence of behavioral problems and asthma symptoms occurrence (PR: 1.43; 95% CI: 1.10-1.85). CONCLUSION: These results suggest an association between behavioral problems and pediatric asthma, and support the inclusion of mental health care in the provision of services for asthma morbidity

Patients' experiences of illness, operation and outcome with reference to gastro-oesophageal reflux disease.

Background. Describing the illness-story from a patient perspective could increase understanding of living with a chronic disease for health professionals and others, facilitate decision-making about treatment and enhance information about the outcome from a patient perspective. Aim. To illuminate patients' illness experiences of having a gastro-oesophageal reflux disease (GORD), going through surgery and the outcome. Methods. Twelve patients were interviewed 5 years after having had the operation; six patients had had fundoplication via laparoscopy and six via open surgery. Each patient was asked to talk openly about their experiences, thoughts, feelings and consequences of living with the illness, going through surgery and the period from surgery to the day of interview. A qualitative content analysis was performed concerning the context of the data and its meaning. Findings. Three central categories were identified and nine subcategories: living with GORD- symptoms of the disease affecting daily living, taking medicines, work, family and social life; concerns related to surgery- decision-making about the operation, influence by physicians; life after the operation- outcomes and consequences, side-effects and complications of the operation, sick leave, information and sharing experiences with future patients. All patients were free from symptoms of the illness after surgery independent of type of surgery, but side-effects from surgical treatment varied individually. Interviewees would have liked information concerning side-effects after surgery from previous patients. Conclusions. This study contributes to knowledge about patients' long-term suffering, their control of symptoms and how they have tried to cure themselves, but also about their concerns about surgery and the importance of surgical treatment to their quality of life. They wanted information about treatment, outcome and consequences, not only from a health care perspective but also from previous patients having had the same treatment

The ‘T-Shaped Buyer’: a transactional perspective on supply chain relationships

This paper challenges the normative view of interdependent buyer-seller relationships and provides a more holistic perspective of the contextual reality that shapes buyer behaviour. By proposing an innovative qualitative methodology, which focusses on boundary-spanning, pre-sales interactions, the research penetrates complex and commercially sensitive buyer-seller relationships. The longitudinal research design uses web-based diaries and follow-up interviews to explore conditions of power based interdependence between buyers and sellers. The ensuing data is mapped using qualitative content analysis and the results are aggregated graphically for assessment. Using this approach the study develops a nuanced view of the dominant patterns of buyer behaviour, and challenges the opinion that a search for competitive advantage will strengthen cooperative relationships in conditions of power based interdependence. The paper introduces the metaphor of the 'T-Shaped Buyer' to explain the empirical findings and, while acknowledging the contextual limits of the study, suggests that this metaphor may cause both academics and practitioners to reflect on normative thinking

Psychological interventions in asthma

Asthma is a multifactorial chronic respiratory disease characterised by recurrent episodes of airway obstruction. The current management of asthma focuses principally on pharmacological treatments, which have a strong evidence base underlying their use. However, in clinical practice, poor symptom control remains a common problem for patients with asthma. Living with asthma has been linked with psychological co-morbidity including anxiety, depression, panic attacks and behavioural factors such as poor adherence and suboptimal self-management. Psychological disorders have a higher-than-expected prevalence in patients with difficult-to-control asthma. As psychological considerations play an important role in the management of people with asthma, it is not surprising that many psychological therapies have been applied in the management of asthma. There are case reports which support their use as an adjunct to pharmacological therapy in selected individuals, and in some clinical trials, benefit is demonstrated, but the evidence is not consistent. When findings are quantitatively synthesised in meta-analyses, no firm conclusions are able to be drawn and no guidelines recommend psychological interventions. These inconsistencies in findings may in part be due to poor study design, the combining of results of studies using different interventions and the diversity of ways patient benefit is assessed. Despite this weak evidence base, the rationale for psychological therapies is plausible, and this therapeutic modality is appealing to both patients and their clinicians as an adjunct to conventional pharmacological treatments. What are urgently required are rigorous evaluations of psychological therapies in asthma, on a par to the quality of pharmaceutical trials. From this evidence base, we can then determine which interventions are beneficial for our patients with asthma management and more specifically which psychological therapy is best suited for each patient