Convergent adaptation of the genomes of woody plants at the land-sea interface

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P-true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence

Deficient supplies of drugs for life threatening diseases in an African community

<p>Abstract</p> <p>Background</p> <p>In Malawi essential drugs are provided free of charge to patients at all public health facilities in order to ensure equitable access to health care. The country thereby spends about 30% of the national health budget on drugs. In order to investigate the level of drug shortages and eventually find the reasons for the drugs shortages in Malawi, we studied the management of the drug supplies for common and life threatening diseases such as pneumonia and malaria in a random selection of health centres.</p> <p>Methods</p> <p>In July and August 2005 we visited eight out of a total of 37 health centres chosen at random in the Lilongwe District, Malawi. We recorded the logistics of eight essential and widely used drugs which according to the treatment guidelines should be available at all health centres. Five drugs are used regularly to treat pneumonia and three others to treat acute malaria. Out-of-stock situations in the course of one year were recorded retrospectively. We compared the quantity of each drug recorded on the Stock Cards with the actual stock of the drug on the shelves at the time of audit. We reviewed 8,968 Patient Records containing information on type and amount of drugs prescribed during one month.</p> <p>Results</p> <p>On average, drugs for treating pneumonia were out of stock for six months during one year of observation (median value 167 days); anti-malarial drugs were lacking for periods ranging from 42 to138 days. The cross-sectional audit was even more negative, but here too the situation was more positive for anti-malarial drugs. The main reason for the shortage of drugs was insufficient deliveries from the Regional Medical Store. Benzyl penicillin was in shortest supply (4% received). The median value for non-availability was 240 days in the course of a year. The supply was better for anti-malarial drugs, except for quinine injections (9 %). Only 66 % of Stock Card records of quantities received were reflected in Patient Records showing quantities dispensed.</p> <p>Conclusion</p> <p>We conclude that for the eight index drugs the levels of supply are unacceptable. The main reason for the observed shortage of drugs at the health centres was insufficient deliveries from the Regional Medical Store. A difference between the information recorded on the Stock Cards at the health centres and that recorded in the Patient Records may have contributed to the overall poor drug supply situation. In order to ensure equitable access to life saving drugs, logistics in general should be put in order before specific disease management programmes are initiated.</p

Cross-national variations in reported discrimination among people treated for major depression worldwide : the ASPEN/INDIGO international study

No study has so far explored differences in discrimination reported by people with major depressive disorder (MDD) across countries and cultures. To (a) compare reported discrimination across different countries, and (b) explore the relative weight of individual and contextual factors in explaining levels of reported discrimination in people with MDD. Cross-sectional multisite international survey (34 countries worldwide) of 1082 people with MDD. Experienced and anticipated discrimination were assessed by the Discrimination and Stigma Scale (DISC). Countries were classified according to their rating on the Human Development Index (HDI). Multilevel negative binomial and Poisson models were used. People living in ‘very high HDI’ countries reported higher discrimination than those in ‘medium/low HDI’ countries. Variation in reported discrimination across countries was only partially explained by individual-level variables. The contribution of country-level variables was significant for anticipated discrimination only. Contextual factors play an important role in anticipated discrimination. Country-specific interventions should be implemented to prevent discrimination towards people with MDD

Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice

Diatoms are significant primary producers in sea ice, an ephemeral habitat with steep vertical gradients of temperature and salinity characterizing the ice matrix environment. To cope with the variable and challenging conditions, sea ice diatoms produce polysaccharide-rich extracellular polymeric substances (EPS) that play important roles in adhesion, cell protection, ligand binding and as organic carbon sources. Significant differences in EPS concentrations and chemical composition corresponding to temperature and salinity gradients were present in sea ice from the Weddell Sea and Eastern Antarctic regions of the Southern Ocean. To reconstruct the first metabolic pathway for EPS production in diatoms, we exposed Fragilariopsis cylindrus, a key bi-polar diatom species, to simulated sea ice formation. Transcriptome profiling under varying conditions of EPS production identified a significant number of genes and divergent alleles. Their complex differential expression patterns under simulated sea ice formation was aligned with physiological and biochemical properties of the cells, and with field measurements of sea ice EPS characteristics. Thus, the molecular complexity of the EPS pathway suggests metabolic plasticity in F. cylindrus is required to cope with the challenging conditions of the highly variable and extreme sea ice habitat

Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study

Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully revealed common variants associated with disease risk, the role of common variation in partial epilepsies has not yet been explored in a well-powered study. We undertook a genome-wide association-study to identify common variants which influence risk for epilepsy shared amongst partial epilepsy syndromes, in 3445 patients and 6935 controls of European ancestry. We did not identify any genome-wide significant association. A few single nucleotide polymorphisms may warrant further investigation. We exclude common genetic variants with effect sizes above a modest 1.3 odds ratio for a single variant as contributors to genetic susceptibility shared across the partial epilepsies. We show that, at best, common genetic variation can only have a modest role in predisposition to the partial epilepsies when considered across syndromes in Europeans. The genetic architecture of the partial epilepsies is likely to be very complex, reflecting genotypic and phenotypic heterogeneity. Larger meta-analyses are required to identify variants of smaller effect sizes (odds ratio <1.3) or syndrome-specific variants. Further, our results suggest research efforts should also be directed towards identifying the multiple rare variants likely to account for at least part of the heritability of the partial epilepsies. Data emerging from genome-wide association-studies will be valuable during the next serious challenge of interpreting all the genetic variation emerging from whole-genome sequencing studies

Childhood poly-victimization and children's health: A nationally representative study

Background Although research on the negative effects of childhood poly-victimization is substantial, few studies have examined the relationship between poly-victimization and younger children’s physical health and diseases. Objective This study examines the associations between poly-victimization and children’s health problems requiring medical attention. Methods A national stratified cluster random sampling was used to select and approach 25% of the total primary schools in Taiwan, and 49% of the approached schools agreed to participate in this study. We collected data with a self-report questionnaire from 6233 (4th-grade) students aged 10–11, covering every city and county in Taiwan. Results Logistic regression analyses demonstrate a significant dose-response relationship between children’s poly-victimization exposure and their health problems including hospitalization, serious injury, surgery, daily-medication requirements, heart murmurs, asthma, dizziness or fainting, allergies, kidney disease, therapies for special needs, smoking, and alcohol use. The results indicate that children’s risk of having a health problem grew significantly with each increase in the number of victimization types that children experienced. Conclusions These research findings underscore the effect of poly-victimization on children’s health problems requiring medical attention, and stress the need for both proper screening methods for children’s exposure to poly-victimization and stronger awareness of poly-victimization’s effects on health conditions in healthcare clinics

Problematic smartphone use: an empirically validated model

Given the prominent role that smartphones have in everyday life, research in the field has proliferated. From a theoretical perspective, problematic smartphone use (PSPU) is described as a multi-faceted phenomenon entailing a variety of dysfunctional manifestations (e.g., addictive, antisocial and dangerous use). To date, however, there is still a lack of empirical evidence supporting the identification of PSPU as a potential behavioural addiction. Driven by theory, the aim of the present study was to provide an empirically validated model by testing the contribution of specific factors leading to PSPU. Relationships among individual characteristics (internalised psychopathology, impulsivity and personality traits) and PSPU uses (addictive, antisocial and dangerous) were investigated according to the updated version of the theoretical framework provided by the Pathway Model of problematic smartphone use (Billieux et al., 2015). An online survey was administered to a convenience sample (N = 511) of smartphone users in order to examine their daily engagement, problematic usage patterns and related psychological correlates. Path analysis revealed important information about different PSPU components and results are discussed in light of the available literature. Recommendations for future research are proposed to further investigate the problematic behaviour, including the study of additional variables, such as the fear of missing out (FoMO), nomophobia and excessive social media use

Psychometric properties of the Adverse Childhood Experiences Abuse Short Form (ACE-ASF) among Romanian high school students

Objective: Child abuse is a major public health problem. In order to establish the prevalence of abuse exposure among children, measures need to be age appropriate, sensitive, reliable and valid. This study aimed to investigate the psychometric properties of the Adverse Childhood Experiences Questionnaire Abuse Short Form (ACE-ASF). Methods: The ACE-ASF is an 8-item retrospective self-report questionnaire measuring lifetime physical, emotional and sexual abuse. Data from a nationally representative sample of 15-year-old school-going adolescents (n=1733, 55.5% female) from the Romanian Health Behavior in School-based Children Study 2014 (HBSC) was analyzed. The factorial structure of the ACE-ASF was tested with Exploratory Factor Analysis (EFA) and confirmed using Confirmatory Factor Analysis (CFA). Measurement invariance was examined across boys and girls and internal reliability and concurrent criterion validity were established. Results: Violence exposure was high: 39.7% physical, 32.2% emotional and 13.1% sexual abuse. EFA established a two factor structure: physical/emotional abuse and sexual abuse. CFA confirmed this model fitted the data well [χ 2 (df)=60.526(19); RMSEA=.036; CFI/TLI=.990/.986]. Metric invariance was supported across genders. Internal consistency was good (.83) for the sexual abuse scale and poor (.57) for the physical/emotional abuse scale. Concurrent criterion validity confirmed hypothesized relationships between childhood abuse and health-related quality of life, life satisfaction, self-perceived health, bullying victimization and perpetration, externalizing and internalizing behaviors and multiple health complaints. Conclusions: Results support the ACE-ASF as a valid measure of physical, emotional and sexual abuse in school-aged adolescents. Future research is needed to replicate findings in other youth populations and across different age groups