Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 1; peer review: 1 approved, 1 approved with reservations]

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.Bioarchaeolog

Handouts for “Pediatric school psychology service delivery: Benefits and barriers”

Handouts for “Pediatric school psychology service delivery: Benefits and barriers

The roles of school psychologists working within a pediatric setting.

• With an increasing number of children presenting with health conditions, pediatric care has expanded from solely a medical definition to a more comprehensive service delivery approach that includes psychology and education (Perrin, 1999). • An interdisciplinary, inter-systemic approach is necessary to meet the needs of children across systems (Power, Shapiro, & DuPaul, 2003). • School psychologists are uniquely qualified to facilitate collaboration between settings and systems due to their expertise in consultation and intervention. • Roles in pediatric school psychology include: advocating for children’s educational and social needs; consulting with care providers, families, and educators; and facilitating collaboration among these individuals (Power & Parrish, 1995). • Conjoint behavioral consultation (CBC): o A structured, indirect model wherein a consultant works with a parent and teacher to promote collaborative, problem-solving partnerships across home and school (Sheridan, Kratochwill, & Bergan, 1996). o Effective in addressing a range of concerns across home and school (Sheridan, et al., 2001); high levels of parent and teacher acceptability and satisfaction reported (Freer & Watson, 1999; Sheridan & Steck, 1995). • Other roles: Individualized Education Plan (IEP) consultation, parent- or teacher-only consultation, observations, and provision of resources/referrals. • To date, no research has explored the conditions in which CBC is warranted in a pediatric medical setting and ones in which other services are appropriate

Handouts for “The roles of school psychologists working within a pediatric setting”

RESEARCH QUESTIONS 1. What clinical services are pediatric school psychologists providing and for whom are they providing them? 2. What types of referral concerns are pediatric school psychologists addressing and which of those are associated with CBC service delivery? 3. Under what conditions are CBC services desirable and appropriate in medical settings and when are such services not warranted

Enzymatic activity and mineralization of carbon and nitrogen in soil cultivated with coffee and green manures Atividade enzimática e mineralização do carbono e nitrogênio sob solo cultivado com adubos verdes na cultura do cafeeiro

There are great concerns about degradation of agricultural soils. It has been suggested that cultivating different plant species intercropped with coffee plants can increase microbial diversity and enhance soil sustainability. The objective of this study was to evaluate enzyme activity (urease, arylsulfatase and phosphatase) and alterations in C and N mineralization rates as related to different legume cover crops planted between rows of coffee plants. Soil samples were collected in a field experiment conducted for 10 years in a sandy soil in the North of Paraná State, Brazil. Samples were collected from the 0-10 cm layer, both from under the tree canopy and in-between rows in the following treatments: control, Leucaena leucocephala, Crotalaria spectabilis, Crotalaria breviflora, Mucuna pruriens, Mucuna deeringiana, Arachis hypogaea and Vigna unguiculata. The soil was sampled in four stages of legume cover crops: pre-planting (September), after planting (November), flowering stage (February) and after plant residue incorporation (April), from 1997 to 1999. The green manure species influenced soil enzyme activity (urease, arylsulfatase and phosphatase) and C and N mineralization rates, both under the tree canopy and in-between rows. Cultivation of Leucaena leucocephala increased acid phosphatase and arilsulfatase activity and C and N mineralization both under the tree canopy and in-between rows. Intercropped L. leucocephala increased urease activity under the tree canopy while C. breviflora increased urease activity in-between rows.<br>Existe grande preocupação sobre a degradação dos solos agrícolas. Tem sido sugerido que o cultivo de plantas intercalares no cafeeiro aumenta a diversidade microbiana e a sustentabilidade do solo. No presente trabalho foi avaliada a alteração na atividade de enzimas do solo (urease, arilsulfatase e fosfatase) e na mineralização do C e N devido ao cultivo intercalar de diferentes leguminosas de verão na cultura do cafeeiro. Foram feitas amostragens em um experimento de campo de longa duração instalado em Latossolo Vermelho distrófico em Miraselva, PR, na profundidade de 0-10 cm, na projeção da copa e na entrelinha, nos seguintes tratamentos: testemunha, leucena (Leucaena leucocephala), Crotalaria spectabilis, Crotalaria breviflora, amendoim-cavalo (Arachis hypogaea tipo virginia), mucuna-cinza (Mucuna pruriens), mucuna-anã (Mucuna deeringiana) e caupi (Vigna unguiculata). As amostragens de solo foram feitas em quatros estádios de desenvolvimento dos adubos verdes: pré-plantio (setembro), pós-plantio (novembro), florescimento (fevereiro) e pós-incorporação (abril), de 1997 a 1999. O cultivo de adubos verdes influenciou a atividade das enzimas do solo (urease, arilsulfatase e fosfatase) e a mineralização do C e N tanto na projeção da copa como na entrelinha. O cultivo da leucena aumentou a atividade da fosfatase ácida e da arilsulfatase e a mineralização de C e N na projeção da copa e na entrelinha do cafeeiro. O cultivo de leucena aumentou a atividade da urease na projeção da copa, enquanto C. breviflora incrementou a atividade da urease na entrelinha