QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes.

Deciphering the fine-scale molecular mechanisms that shape the genetic effects at disease-associated loci from genome-wide association studies (GWAS) remains challenging. The key avenue is to identify the essential molecular phenotypes that mediate the causal variant and disease under particular biological conditions. Therefore, integrating GWAS signals with context-specific quantitative trait loci (QTLs) (such as different tissue/cell types, disease states, and perturbations) from extensive molecular phenotypes would present important strategies for full understanding of disease genetics. Via persistent curation and systematic data processing of large-scale human molecular trait QTLs (xQTLs), we updated our previous QTLbase database (now QTLbase2, http://mulinlab.org/qtlbase) to comprehensively analyze and visualize context-specific QTLs across 22 molecular phenotypes and over 95 tissue/cell types. Overall, the resource features the following major updates and novel functions: (i) 960 more genome-wide QTL summary statistics from 146 independent studies; (ii) new data for 10 previously uncompiled QTL types; (iii) variant query scope expanded to fit 195 QTL datasets based on whole-genome sequencing; (iv) supports filtering and comparison of QTLs for different biological conditions, such as stimulation types and disease states; (v) a new linkage disequilibrium viewer to facilitate variant prioritization across tissue/cell types and QTL types.

EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material.

The European Search Catalogue for Plant Genetic Resources (EURISCO) is a central entry point for information on crop plant germplasm accessions from institutions in Europe and beyond. In total, it provides data on more than two million accessions, making an important contribution to unlocking the vast genetic diversity that lies deposited in >400 germplasm collections in 43 countries. EURISCO serves as the reference system for the Plant Genetic Resources Strategy for Europe and represents a significant approach for documenting and making available the world's agrobiological diversity. EURISCO is well established as a resource in this field and forms the basis for a wide range of research projects. In this paper, we present current developments of EURISCO, which is accessible at http://eurisco.ecpgr.org.

A catalogue of the types of rove beetles (Coleoptera: Staphylinidae) deposited in the collection of Johan Heinrich Hochhuth in the National Museum of Natural History of the National Academy of Sciences of Ukraine.

Type specimens of Staphylinidae (Coleoptera) from the collection of J.H. Hochhuth (18101872) deposited in National Museum of Natural History of the National Academy of Sciences of Ukraine (Kyiv) are currently being catalogued and illustrated. This catalogue presents information about 103 type specimens (14 holotypes, 80 lecto- and paratypes, and nine syntypes) belonging to 67 nominal species. Several lectotypes are designated: Conurus erythrocephalus Hochhuth, 1849, Aleochara solida Hochhuth, 1849, Trogophloeus kiesenwetterii Hochhuth, 1851, Ocypus pullus Hochhuth, 1849, Philonthus armeniacus Hochhuth, 1851, P. interpunctatus Hochhuth, 1860, and P. subopacus Hochhuth, 1851.

A catalog of validity indices for step counting wearable technologies during treadmill walking: the CADENCE-Kids study.

BACKGROUND: Wearable technologies play an important role in measuring physical activity (PA) and promoting health. Standardized validation indices (i.e., accuracy, bias, and precision) compare performance of step counting wearable technologies in young people. PURPOSE: To produce a catalog of validity indices for step counting wearable technologies assessed during different treadmill speeds (slow [0.8-3.2 km/h], normal [4.0-6.4 km/h], fast [7.2-8.0 km/h]), wear locations (waist, wrist/arm, thigh, and ankle), and age groups (children, 6-12 years; adolescents, 13-17 years; young adults, 18-20 years). METHODS: One hundred seventeen individuals (13.1 ± 4.2 years, 50.4% female) participated in this cross-sectional study and completed 5-min treadmill bouts (0.8 km/h to 8.0 km/h) while wearing eight devices (Waist: Actical, ActiGraph GT3X+, NL-1000, SW-200; Wrist: ActiGraph GT3X+; Arm: SenseWear; Thigh: activPAL; Ankle: StepWatch). Directly observed steps served as the criterion measure. Accuracy (mean absolute percentage error, MAPE), bias (mean percentage error, MPE), and precision (correlation coefficient, r; standard deviation, SD; coefficient of variation, CoV) were computed. RESULTS: Five of the eight tested wearable technologies (i.e., Actical, waist-worn ActiGraph GT3X+, activPAL, StepWatch, and SW-200) performed at < 5% MAPE over the range of normal speeds. More generally, waist (MAPE = 4%), thigh (4%) and ankle (5%) locations displayed higher accuracy than the wrist location (23%) at normal speeds. On average, all wearable technologies displayed the lowest accuracy across slow speeds (MAPE = 50.1 ± 35.5%), and the highest accuracy across normal speeds (MAPE = 15.9 ± 21.7%). Speed and wear location had a significant effect on accuracy and bias (P < 0.001), but not on precision (P > 0.05). Age did not have any effect (P > 0.05). CONCLUSIONS: Standardized validation indices focused on accuracy, bias, and precision were cataloged by speed, wear location, and age group to serve as important reference points when selecting and/or evaluating device performance in young people moving forward. Reduced performance can be expected at very slow walking speeds (0.8 to 3.2 km/h) for all devices. Ankle-worn and thigh-worn devices demonstrated the highest accuracy. Speed and wear location had a significant effect on accuracy and bias, but not precision. TRIAL REGISTRATION: Clinicaltrials.gov NCT01989104 . Registered November 14, 2013.

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.

Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.

A genomic catalog of Earth's microbiomes.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

An atlas of personality, emotion and behaviour.

A novel two-dimensional matrix taxonomy, or atlas, of personality, emotion and behaviour is presented. The two dimensions of the atlas, affiliation and dominance, are demonstrated to have theoretical foundations in neurobiology and social psychology. Both dimensions are divided into five ordinal categories, creating a square matrix of 25 cells. A new catalogue of 20,669 English words descriptive of personality, emotion, behaviour, and power is also presented. The catalogue is more comprehensive than previous catalogues, and is novel in its inclusion of intrapersonal, group, and societal behaviours. All words in the catalogue were scored according to the atlas, facilitating visualisation in two dimensions. This enabled a contiguous and novel comparison of existing psychological taxonomies, as well as broader societal concepts such as leadership, ethics, and crime. Using the atlas, a novel psychological test is developed with improved sensitivity and specificity.

A Catalog of GAL4 Drivers for Labeling and Manipulating Circadian Clock Neurons in Drosophila melanogaster.

Daily rhythms of physiology, metabolism, and behavior are orchestrated by a central circadian clock. In mice, this clock is coordinated by the suprachiasmatic nucleus, which consists of 20,000 neurons, making it challenging to characterize individual neurons. In Drosophila, the clock is controlled by only 150 clock neurons that distribute across the fly's brain. Here, we describe a comprehensive set of genetic drivers to facilitate individual characterization of Drosophila clock neurons. We screened GAL4 lines that were obtained from Drosophila stock centers and identified 63 lines that exhibit expression in subsets of central clock neurons. Furthermore, we generated split-GAL4 lines that exhibit specific expression in subsets of clock neurons such as the 2 DN2 neurons and the 6 LPN neurons. Together with existing driver lines, these newly identified ones are versatile tools that will facilitate a better understanding of the Drosophila central circadian clock.

Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus.

Nematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C. elegans facilitate the evolutionary study of biological functions using reverse genetics. However, the ability to identify orthologs of candidate genes in other species can be hampered by erroneous gene annotations. To improve gene annotation in the nematode model organism Pristionchus pacificus, we performed a genome-wide screen for C. elegans genes with potentially incorrectly annotated P. pacificus orthologs. We initiated a community-based project to manually inspect more than two thousand candidate loci and to propose new gene models based on recently generated Iso-seq and RNA-seq data. In most cases, misannotation of C. elegans orthologs was due to artificially fused gene predictions and completely missing gene models. The community-based curation raised the gene count from 25,517 to 28,036 and increased the single copy ortholog completeness level from 86% to 97%. This pilot study demonstrates how even small-scale crowdsourcing can drastically improve gene annotations. In future, similar approaches can be used for other species, gene sets, and even larger communities thus making manual annotation of large parts of the genome feasible.

Annotated catalogue of species of Angiostrongylus and the related genera Gallegostrongylus, Rodentocaulus and Stefanskostrongylus (Nematoda: Metastrongyloidea, Angiostrongylidae).

This catalogue is concerned with the closely related angiostrongylid genera Angiostrongylus, Gallegostrongylus, Rodentocaulus and Stefanskostrongylus. Three species, Angiostrongylus cantonensis, A. costaricensis and A. vasorum, have attracted most attention because of their importance in human and domestic animal disease. Many of the remaining species are poorly known and the number of valid taxa is unclear. The catalogue lists all nomenclaturally available and unavailable genus-group and species-group names that have been applied to the above genera and the species included in them, indicating their current nomenclatural status and providing the rigorous nomenclatural basis for future work. The catalogue lists 14 published and nomenclaturally available genus-group names, with the above four treated as valid, the other ten being junior synonyms. There are 42 published species-group names: 36 are valid, two are junior synonyms, four are nomenclaturally unavailable. One additional species, described in Chabaudistrongylus (synonym of Angiostrongylus), is listed as incertae sedis in Angiostrongylidae. Also listed are two unpublished collection names. The catalogue provides bibliographic details for all published names, and for available names provides locations of type material, details of type localities, geographic distributions and details of type and other hosts, both definitive and intermediate, to the extent known. The catalogue is a work of nomenclature, not a revisionary taxonomic work. No new names or new combinations are proposed. The apparently new family-group synonymy of Cardionematinae with Angiostrongylidae is introduced, as are four genus-group synonymies, three with Angiostrongylus and one with Stefaskostrongylus.

[Development of a national competency-based learning objective catalogue for undergraduate medical education in Germany]. / Entwicklung eines kompetenzbasierten Lernzielkatalogs Nuklearmedizin für das Studium der Humanmedizin in Deutschland.

AIMS: Implementation of the guidelines on the Competency-based Learning Objective Catalogue for Undergraduate Medical Education for a Nuclear Medicine curriculum on behalf of the committee on professional training and continuing education of the German Association of Nuclear Medicine (DGN) METHODS:: In 7 domains 100 learning objectives (LOs) were subject to a prioritization in 3 categories (A, B and C) by means of a questionnaire as part of a Delphi method, in collaboration with all members of the DGN holding a "venia legendi" as experts. Category A defined the essential LOs for each medical practitioner. The prioritization was made by ranking the frequency of the A-classifications. In the 2nd step of the Delphi method, a list of LOs with the ranking positions 1-5 in each domain was presented to the first round's experts as a core curriculum, asking either for acceptance or modifications. RESULTS: The results of the 1st step of the Delphi method deliver a return rate of 29% of the questionnaires (55 out of 184). The 2nd round shows a return rate of 30.9% (57 out of 184) and full approval of the proposed LOs in all LO domains by in median 72 % of the experts consulted (61%-81%). The present final version contains 37 competency-based LOs in the LO domains "legal basis and radiation protection", "basic science", indications and contra-indications for "PET/CT", "scintigraphy and SPECT", "patient preparation", "image interpretation" as well as "therapy". CONCLUSION: The Competency-based Learning Objective Catalogue for Nuclear Medicine describes the knowledge and competencies, every physician should have at the end of his medical studies. The LO catalogue is a living document, which needs to be adapted continuously to the progress of the medical and technological development.

Restoration of an academic historical gross pathology collection-refreshed impact on current medical teaching?

The declaration of Leiden pronounces the demand to conserve pathological-anatomical collections as cultural heritage. Likewise, the Institute of Pathology of the Friedrich-Alexander-University Erlangen-Nuremberg owns macroscopic pathological-anatomical specimens reaching back over 150 years. The purpose of this work is to examine the impact, meaning, and perception of such historical preparations during the current medical curriculum. Additionally, the experiences from the renovation process can be used as a template for other institutes. All preparations were documented, photographed, and catalogued in an electronic database. During a restoration period, a series of didactically suitable specimens were professionally restored. Hereby, the help of a special course of interested students was admitted. In a second step, the specimens were integrated into the regular teaching of students in macroscopic pathology. An evaluation was carried out on two student cohorts with and without historical specimens by means of a questionnaire with 23 items and two free text fields. In total, 1261 specimens were registered covering diseases from almost the complete human body with a strong representation of the cardiovascular, urinary, gastrointestinal, and central nervous systems. Hereby, exceptional rare and untreated cases with medical relevance could be found and stepwise implemented into the curriculum. The student evaluation positively addressed that the courses became livelier and interactive. Furthermore, a more comprehensive overview and a better understanding of the macroscopic pathology were appreciated. However, more self-study time with the specimen was demanded. The authenticity of historical specimens contrasts with the tendency to carry out virtual "online" didactic methods. The stereoscopic view on often untreated and, therefore, unbiased cases enhances a skill-oriented deeper understanding of diseases. In conclusion, historical specimens regain interest and even didactic value, especially in an era of declining autopsy rates.

[Competence Based Catalogue of Learning Objectives for Rehabilitation, Physical Medicine, Naturopathic Treatment - Revised Version - Joint Recommendations of the German Society of Rehabilitation Science and the German Society of Physical Medicine and Rehabilitation]. / Kompetenzbasierter Lernzielkatalog "Rehabilitation, Physikalische Medizin, Naturheilverfahren" (RPMN) ­ revidierte Fassung.

Since the first publication of learning objectives for the interdisciplinary subject "Rehabilitation, Physical Medicine, Naturopathic Treatment" in undergraduate medical education in 2004 a revision is reasonable due to heterogenous teaching programmes in the faculties and the introduction of the National Competence Based Catalogue of Learning Objectives in Medicine as well as the "Masterplan Medical Education 2020". Therefore the German Society of Rehabilitation Science and the German Society of Physical Medicine and Rehabilitation started a structured consensus process using the DELPHI-method to reduce the learning objectives and arrange them more clearly. Objectives of particular significance are emphasised. All learning objectives are assigned to the cognitive and methodological level 1 or to the action level 2. The learning objectives refer to the less detailed National Competence Based Catalogue of Learning Objectives in Medicine. The revised learning objectives will contribute to further progress in competence based and more homogenous medical teaching in core objectives of Rehabilitation, Physical Medicine, and Naturopathic Treatment in the faculties.

Checklist of Gymnotiformes (Osteichthyes: Ostariophysi) and catalogue of primary types

A list of all valid names of species of Neotropical electric fishes (Gymnotiformes) is presented herein. The list is arranged by family and genus and includes all available synonyms. The list is comprehensive through 2016 and includes 240 valid species distributed among 34 genera and five families, including one monotypic genus known only from the fossil record. The presented classification reflects recently published interpretations about the validity of the included names which, in general, are widely accepted. When the validity of a particular name is disputed in recent literature, we followed one of the published interpretations and provide relevant information on the alternate interpretation(s) in the remarks section of that name. Synonymies of some names need to be considered tentative, inasmuch as the types underlying those names are either absent or appear to be based on more than one taxon. First reviser actions (e.g., lectotype and neotype designations, resolution of simultaneous synonyms, etc.) are reported and include erroneous subsequent attempts at problem resolutions. Herein, we include one new first reviser action by selecting Gymnotus aequilabiatus Humboldt, 1805, as type species of Sternopygus because previous attempts to select a type did not follow the provisions of the Code of Zoological Nomenclature.(AU)

Uma lista de todas as espécies válidas de peixes elétricos neotropicais (Gymnotiformes) é apresentada. A lista é organizada por família e gênero, e inclui todos os sinônimos válidos. A lista encontra-se atualizada até 2016 e inclui 240 espécies válidas viventes distribuídas entre os 34 gêneros e cinco famílias, e um gênero monotípico conhecido apenas por registros fósseis. A presente classificação reflete as recentes interpretações publicadas sobre a validade dos nomes incluídos, nos quais, em geral, são amplamente aceitos. Quando a validade de um nome em particular é disputada na literatura recente, nós seguimos uma das interpretações publicadas, e fornecemos informações relevantes sobre a(s) interpretação(ões) na seção de comentários do nome em questão. Sinônimos de alguns nomes precisam ser considerados com cautela, tendo em vista que os tipos para estes nomes são ausentes, ou parecem ser baseados em mais de um táxon. As primeira ações de revisão (e.g., designação de lectótipos e neótipos, resolução na designação simultânea de sinônimos, etc.) são registradas e incluem os esforços errôneos subsequentes para a solução do problema. Aqui, nós incluímos uma primeira ação de revisão selecionando Gymnotus aequilabiatus Humboldt, 1805, como a espécie-tipo de Sternopygus, porque os esforços prévios para selecionar o tipo não seguiram as recomendações do Código de Nomenclatura Zoológica.(AU)

Catalogue of the Teratomyzidae (Diptera, Opomyzoidea) of the World.

A catalogue of Teratomyzidae of the world is presented comprising 23 described species in seven genera. Geographic records for nine undescribed species are also listed. All valid names and synonyms are presented, totaling 34 names. All references known to us from the taxonomic and biological literature, including information about name, author, year of publication, page number, type genus, type species, type locality and references are given to the categories of family, genus and species. Camur willii McAlpine has its distributional record enlarged to Paraná (Brazil).

[Criteria catalogue to systematize conceptual approaches in universal prevention of childhood overweight : Methodological approach and first results]. / Kriterienkatalog zur Systematisierung konzeptioneller Ansätze in der universellen Prävention von Kinderübergewicht : Methodische Vorgehensweise und erste Ergebnisse.

BACKGROUND: Overweight and obesity are serious health risks for children and adolescents. Hence, various prevention projects have been initiated and implemented. Until now, a systematic overview of interventions in different settings has been lacking. AIM(S)/RESEARCH QUESTION: The aim of the "Prevention of child overweight" project (SkAP-project) is to prepare a systematic overview of the conceptual approaches used in universal prevention of overweight among children and adolescents. First of all, a comprehensive criteria catalogue will be developed based on systematic searches. In the next step the criteria catalogue will be applied to identify and characterize conceptual approaches. DATA AND METHODS: Criteria to describe conceptual approaches as well as determinants of childhood overweight were determined by systematic searches. The searches included relevant data bases and were further expanded by internet and hand search. Three settings (kindergarten, school and communities) and families are addressed by the systematic searches. Additional non-setting specific searches were conducted. RESULTS: A comprehensive criteria catalogue was developed, which allows a detailed analysis of conceptual approaches. This catalogue covers further quality criteria as well as determinants of childhood overweight. DISCUSSION: Currently, the criteria catalogue is being employed. Although the detailed analysis of conceptual approaches can be regarded as advantage of the criteria catalogue, there are also some limitations, such as the lack of necessary information provided in publications. Overall, the application will reveal an overview regarding universal prevention in childhood overweight, which is still lacking, and will support development in this field.

Catalogue of snout mites (Acariformes: Bdellidae) of the world.

Bdellidae (Trombidiformes: Prostigmata) are moderate to large sized predatory mites that inhabit soil, leaves, leaf litter, and intertidal rocks. They are readily recognized by an elongated, snout-like gnathosoma and by elbowed pedipalps bearing two (one in Monotrichobdella Baker & Balock) long terminal setae. Despite being among the first mites ever described, with species described by Carl Linnaeus, the knowledge about bdellids has never been compiled into a taxonomic catalogue. Here we present a catalogue listing 278 valid species; for each species we include distribution information, taxonomic literature, and type depository institutions. The genus Rigibdella Tseng, 1978 is considered a junior synonym of Cyta von Heyden, 1826, and Bdellodes Oudemans, 1937 is considered a junior synonym of Odontoscirus Tohr, 1913. Illustrated keys to subfamilies and genera are presented, as well as keys to species of each genus.

Modeling Requirements for Cohort and Register IT.

BACKGROUND: The project KoRegIT (funded by TMF e.V.) aimed to develop a generic catalog of requirements for research networks like cohort studies and registers (KoReg). The catalog supports such kind of research networks to build up and to manage their organizational and IT infrastructure. OBJECTIVES: To make transparent the complex relationships between requirements, which are described in use cases from a given text catalog. By analyzing and modeling the requirements a better understanding and optimizations of the catalog are intended. There are two subgoals: a) to investigate one cohort study and two registers and to model the current state of their IT infrastructure; b) to analyze the current state models and to find simplifications within the generic catalog. METHODS: Processing the generic catalog was performed by means of text extraction, conceptualization and concept mapping. Then methods of enterprise architecture planning (EAP) are used to model the extracted information. To work on objective a) questionnaires are developed by utilizing the model. They are used for semi-structured interviews, whose results are evaluated via qualitative content analysis. Afterwards the current state was modeled. Objective b) was done by model analysis. RESULTS: A given generic text catalog of requirements was transferred into a model. As result of objective a) current state models of one existing cohort study and two registers are created and analyzed. An optimized model called KoReg-reference-model is the result of objective b). CONCLUSION: It is possible to use methods of EAP to model requirements. This enables a better overview of the partly connected requirements by means of visualization. The model based approach also enables the analysis and comparison of the empirical data from the current state models. Information managers could reduce the effort of planning the IT infrastructure utilizing the KoReg-reference-model. Modeling the current state and the generation of reports from the model, which could be used as requirements specification for bids, is supported, too.