MSG-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs

Background: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes. Results: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (\u3e90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image. Conclusions: MGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy

Breast is best: Positive mealtime interactions in breastfeeding mothers from Israel and the United Kingdom

We examined mealtime interactions to assess whether they varied according to maternal body mass index, country and mode of feeding in 41 Israeli and UK mother–infant dyads. Feeding behaviours were coded using the Simple Feeding Element Scale. Significantly, more UK mothers breastfed during the filmed meal compared to Israeli mothers. Mealtime interactions did not vary according to maternal body mass index or country. Women who breastfed (as opposed to those who bottle fed or fed solids) provided fewer distractions during the meal, a more ideal feeding environment and fed more responsively

Measuring emotional and social wellbeing in Aboriginal and Torres Strait Islander populations: an analysis of a Negative Life Events Scale

Aboriginal and Torres Strait Islander Australians experience widespread socioeconomic disadvantage and health inequality. In an attempt to make Indigenous health research more culturally-appropriate, Aboriginal and Torres Strait Islander Australians have called for more attention to the concept of emotional and social wellbeing (ESWB). Although it has been widely recognised that ESWB is of crucial importance to the health of Aboriginal and Torres Strait Islander peoples, there is little consensus on how to measure in Indigenous populations, hampering efforts to better understand and improve the psychosocial determinants of health. This paper explores the policy and political context to this situation, and suggests ways to move forward. The second part of the paper explores how scales can be evaluated in a health research setting, including assessments of endorsement, discrimination, internal and external reliability

Temporal rarity is a better predictor of local extinction risk than spatial rarity

Spatial rarity is often used to predict extinction risk, but rarity can also occur temporally. Perhaps more relevant in the context of global change is whether a species is core to a community (persistent) or transient (intermittently present), with transient species often susceptible to human activities that reduce niche space. Using 5–12 yr of data on 1,447 plant species from 49 grasslands on five continents, we show that local abundance and species persistence under ambient conditions are both effective predictors of local extinction risk following experimental exclusion of grazers or addition of nutrients; persistence was a more powerful predictor than local abundance. While perturbations increased the risk of exclusion for low persistence and abundance species, transient but abundant species were also highly likely to be excluded from a perturbed plot relative to ambient conditions. Moreover, low persistence and low abundance species that were not excluded from perturbed plots tended to have a modest increase in abundance following perturbance. Last, even core species with high abundances had large decreases in persistence and increased losses in perturbed plots, threatening the long-term stability of these grasslands. Our results demonstrate that expanding the concept of rarity to include temporal dynamics, in addition to local abundance, more effectively predicts extinction risk in response to environmental change than either rarity axis predicts alone.Fil: Wilfahrt, Peter A.. University of Minnesota; Estados UnidosFil: Asmus, Ashley L.. University of Minnesota; Estados UnidosFil: Seabloom, Eric. University of Minnesota; Estados UnidosFil: Henning, Jeremiah A.. University of Minnesota; Estados UnidosFil: Adler, Peter. State University of Utah; Estados UnidosFil: Arnillas, Carlos A.. University of Toronto Scarborough; CanadáFil: Bakker, Jonathan. University of Washington; Estados UnidosFil: Biederman, Lori. University of Iowa; Estados UnidosFil: Brudvig, Lars A.. Michigan State University; Estados UnidosFil: Cadotte, Marc W.. University of Toronto Scarborough; CanadáFil: Daleo, Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Eskelinen, Anu. German Centre for Integrative Biodiversity Research; AlemaniaFil: Firn, Jennifer. University of Queensland; AustraliaFil: Harpole, W. Stanley. German Centre for Integrative Biodiversity Research; Alemania. Helmholtz Centre for Environmental Research; Alemania. Martin Luther University Halle-Wittenberg; AlemaniaFil: Hautier, Yann. Utrecht University; Países BajosFil: Kirkman, Kevin P.. University of KwaZulu-Natal; SudáfricaFil: Komatsu, Kimberly J.. Smithsonian Environmental Research Center; Estados UnidosFil: Laungani, Ramesh. Doane University; Estados UnidosFil: MacDougall, Andrew. University of Guelph; CanadáFil: McCulley, Rebecca L.. University of Kentucky; Estados UnidosFil: Moore, Joslin L.. Monash University; AustraliaFil: Morgan, John W.. La Trobe University; AustraliaFil: Mortensen, Brent. Benedictine College; Estados UnidosFil: Ochoa Hueso, Raul. Universidad de Cádiz; EspañaFil: Ohlert, Timothy. University of New Mexico; Estados UnidosFil: Power, Sally A.. University of Western Sydney; AustraliaFil: Price, Jodi. Charles Sturt University; AustraliaFil: Risch, Anita C.. Swiss Federal Institute for Forest, Snow and Landscape Research; SuizaFil: Schuetz, Martin. Swiss Federal Institute for Forest, Snow and Landscape Research; SuizaFil: Shoemaker, Lauren. University of Wyoming; Estados UnidosFil: Stevens, Carly. Lancaster University; Reino UnidoFil: Strauss, Alexander T.. University of Minnesota; Estados Unidos. University of Georgia; Estados UnidosFil: Tognetti, Pedro Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Virtanen, Risto. University of Oulu; FinlandiaFil: Borer, Elizabeth. University of Minnesota; Estados Unido

Healing through culturally embedded practice: an investigation of counsellors’ and clients’ experiences of Buddhist Counselling in Thailand

This thesis is concerned with an exploration of counsellors’ and clients’ lived experiences of Buddhist Counselling, an indigenous Buddhist-based counselling approach in Thailand. Over the past decade, Buddhist Counselling has received a growing interest from Thai counselling trainees and practitioners, and it has also expanded to serve Thai people in various settings. Research on Buddhist Counselling is very limited and most of the existing studies in the field have focused on measuring the effectiveness of the approach. While these studies have consistently indicated the positive effects of Buddhist Counselling on psychological improvement across several population groups, the significant questions of how Buddhist Counselling brings about such outcome and how it is experienced are still largely unanswered. Moreover, existing research is concentrated much more on clients’ views than counsellors’ views, although counsellors’ views of their counselling practice can also serve as a knowledge base of the field. This thesis thus sets out to contribute to rectifying this omission by exploring Buddhist Counselling from the perspectives of both counsellors and clients. The thesis is based on two qualitative studies. The first study addressed Buddhist Counselling from the perspective of five counsellors through a focus group and semi-structured interviews. The second study explored Buddhist Counselling from the perspective of three clients, using two semi-structured interviews with each of them. All data received were analysed using interpretative phenomenological analysis (IPA). The study reveals counsellors’ and clients’ overall positive experience of engaging in Buddhist Counselling. Central to the accounts of the counsellors are the following perceptions: that their practice of Buddhist Counselling is culturally congruent with the existing values and beliefs of both themselves and their clients; that their personal and professional congruence is key to their therapeutic efficacy; and that they enhance such congruence through their application of Buddhist ideas and practices in their daily lives. Key to the clients’ accounts is their emphasis on the significant roles of the counsellors’ Buddhist ideas and personal qualities, and of their religious practices in facilitating healing and change. Key shared findings from both studies reveal that the participants’ accounts of their cultural background and their experiences of Buddhist Counselling are intertwined. Adopting hermeneutics to address this intertwinement, I reveal the cultural and moral dimensions underlying the practice of Buddhist Counselling. Based on such revelation, I suggest that Buddhist Counselling in particular, as well as psychotherapy in general, should be better understood as a historically situated, culturally bound, and morally constituted activity of people who are concerned with improving the quality of their lives and their community, rather than the transcultural and merely relational work of morally-neutral practitioners