Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses

Paediatric preventative health care use by immigrants in Hong Kong: a pilot study

BACKGROUND: Over 14,000 children arrived in Hong Kong from Mainland China last year to join their recently immigrated parents. The aims of this pilot study were to explore immigrant parents' knowledge and perceptions of the accessibility of paediatric preventative health care services. METHOD: A descriptive survey was administered to parents. Participants (N=27) were grouped by their child's point of entry into the health care system. RESULTS: Most participants lacked knowledge about well-child care and health education. Participants whose children lived in Hong Kong for longer than one year used services for well-child care significantly more than those with shorter stays (χ2=4.50; p=0.03). The major barrier in accessing services was lack of knowledge. CONCLUSIONS: Although a preliminary study, the results suggest a population-based study is needed because lack of familiarity with available services was a reoccurring finding. A more comprehensive assessment of the learning needs of this population is needed so effective ways of familiarizing new immigrants and tracking these children can be developed.published_or_final_versio

The Prevalence and Risk Factors of Paternal Depression from the Antenatal to the Postpartum period and the Relationships between Antenatal and Postpartum Depression among Fathers in Hong Kong

Introduction. Despite the fact that maternal perinatal mental health problems have been extensively studied and addressed to be a significant health problem, the literature on paternal perinatal mental health problems is relatively scarce. The present study aims at determining the prevalence of paternal perinatal depression and identifying the risk factors and the relationship between antenatal and postpartum depression. Methodology. 622 expectant fathers were recruited from regional maternal clinics. The expectant fathers were assessed using standardized and validated psychological instruments on 3 time points including early pregnancy, late pregnancy, and six weeks postpartum. Results. Results showed that a significant proportion of expectant fathers manifested depressive symptoms during the perinatal period. Paternal antenatal depression could significantly predict higher level of paternal postpartum depression. Psychosocial risk factors were consistently associated with paternal depression in different time points. Conclusions. The present study points to the need for greater research and clinical attention to paternal depression given that it is a highly prevalent problem and could be detrimental to their spouse and children development. The present findings contribute to theoretical basis of the prevalence and risk factors of paternal perinatal depression and have implications of the design of effective identification, prevention, and interventions of these clinical problems.published_or_final_versio

Atom-by-Atom Substitution of Mn in GaAs and Visualization of their Hole-Mediated Interactions

The discovery of ferromagnetism in Mn doped GaAs [1] has ignited interest in the development of semiconductor technologies based on electron spin and has led to several proof-of-concept spintronic devices [2-4]. A major hurdle for realistic applications of (Ga,Mn)As, or other dilute magnetic semiconductors, remains their below room-temperature ferromagnetic transition temperature. Enhancing ferromagnetism in semiconductors requires understanding the mechanisms for interaction between magnetic dopants, such as Mn, and identifying the circumstances in which ferromagnetic interactions are maximized [5]. Here we report the use of a novel atom-by-atom substitution technique with the scanning tunnelling microscope (STM) to perform the first controlled atomic scale study of the interactions between isolated Mn acceptors mediated by the electronic states of GaAs. High-resolution STM measurements are used to visualize the GaAs electronic states that participate in the Mn-Mn interaction and to quantify the interaction strengths as a function of relative position and orientation. Our experimental findings, which can be explained using tight-binding model calculations, reveal a strong dependence of ferromagnetic interaction on crystallographic orientation. This anisotropic interaction can potentially be exploited by growing oriented Ga1-xMnxAs structures to enhance the ferromagnetic transition temperature beyond that achieved in randomly doped samples. Our experimental methods also provide a realistic approach to create precise arrangements of single spins as coupled quantum bits for memory or information processing purposes

Antenatal anxiety in the first trimester: Risk factors and effects on anxiety and depression in the third trimester and 6-week postpartum

Objective: Anxiety is common among pregnant women. However, research attention in the area of reproductive mental health has mainly focused on postpartum depression in past decades. Given adverse outcomes of antenatal anxiety, there is an urgent need to fill the research gaps. The objectives of the present study were to determine the prevalence of antenatal anxiety symptoms and examine the risk factors and effects of anxiety symptoms in early pregnancy on anxiety and depressive symptoms in later pregnancy and early postpartum period. Methodology: A prospective longitudinal design with quantitative approach was adopted. A consecutive sample of 1470 Chinese pregnant women from hospitals in Hong Kong was invited to participate in the study and was assessed using standardized instruments on 3 time points including first and third trimesters of pregnancy and 6-week postpartum. Results: The results showed that 17.7% of pregnant women manifested anxiety symptoms in the first trimester of pregnancy. Single mothers, younger mothers, mothers who smoked before pregnancy and mothers who received low education level reported significantly higher levels of anxiety symptoms in the first trimester. Unwanted pregnancy, low self esteem, low marital satisfaction and perceived low social support were significant psychosocial risk factors for anxiety symptoms in the first trimester. Anxiety symptoms in the first trimester were independent predictors for anxiety symptoms in the third trimester ( QUOTE β = 0.26, t = 5.74, p < 0.001), however anxiety symptoms in the first trimester no longer significantly predicted anxiety and depressive symptoms in 6 weeks postpartum after adjusting for the effects of potential confounders. Discussions: The present study points to the need for greater research and clinical attention to antenatal anxiety given that antenatal anxiety is a prevalent problem and has serious impacts on maternal well-being. Such findings also contribute to the understanding of maternal anxiety and have implications for the design of effective identification, prevention and treatment of these significant clinical problemspublished_or_final_versio

InAs/GaAs quantum dot solar cells with quantum dots in the base region

In this work, the influence of quantum dot (QD) position on the performance of solar cells was studied. The presence of QDs within the base regions leads to improved open circuit voltage ( V oc) from 0.73 to 0.90 V. Despite a slight reduction in short-circuit current ( J sc) due to carrier collection loss, the enhancement of the V oc of QDSCs with QDs in base region is significant enough to ensure that power conversion efficiencies ( η) are higher than the reference quantum dot solar cell (QDSC) of which QDs are embedded in the intrinsic region. Moreover, sample with QDs in deep base region achieved the highest η of 9.75%, an increase of 29% with regard to the reference quantum dot solar cell

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

BACKGROUND: Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. RESULTS: We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels) in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs) with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. CONCLUSION: QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at and as Additional files

Succession of microfungal communities on decaying leaves of Castanopsis fissa

A total of 38 fungal taxa were identified on senescent untreated and autoclaved Castanopsis fissa leaves during a 4-month study period. Seventy-six percent of the fungal genera found in this survey have not previously been recorded from Castanopsis. Frequency and time of occurrence of fungal taxa occurring on untreated senescent leaves were clustered into four groups when analyzed by cluster analysis, suggesting the replacement of microfungi in stages of succession on naturally senescent leaves. Autoclaved leaves revealed significantly different fungal communities, with only 26% of overlap with the natural ones and no clear patterns of replacement of fungal communities. Factors regulating the rates of decomposition are also discussed.published_or_final_versio

Atmospheric carbon dioxide, ice sheet and topographic constraints on palaeo moisture availability in Asia

Today, the hydrological regime in East and South Asia is dominated by the monsoons, whilst central Asia is characterized as arid. Studies that have examined the onset of aridity and the intensification of the monsoons in Asia have generated significant debate, especially in respect to the timing of monsoon onset and how this relates to the potential causal mechanisms. The uplift of the Tibetan Plateau, the retreat of the Paratethys Sea, and the global cooling after the Eocene/Oligocene transition are all considered major drivers of Asian aridity and monsoonal intensification. However, little is known about each of these factor's contribution to the development of modern monsoon behaviour. Here, for the first time, we perform sensitivity simulations of a fully coupled ocean–atmosphere climate model (HadCM3) to investigate the effect of the Greenland and Antarctic ice-sheets formation, atmospheric carbon dioxide (CO2) variability, and Tibetan Plateau uplift on East Central Asian aridity and monsoon driven precipitation. We focus on three individual regions, the South Asian Monsoon, the East Asian Monsoon and the Arid East Central Asia and we present the annual precipitation cycle and the moisture availability over each region. Our results show that of the parameters investigated the primary control on Asian hydroclimate is the topography of the Tibetan Plateau. Furthermore, our results highlight that the significance of each forcing depends on the component of the hydrological region and factors studied, a factor that proxy interpretation need to take into consideration