bluuebunny/crossref_metadata_2025_split huggingface dataset:
The application of pangenomics and machine learning in genomic selection in plants
Authors: Bayer Philipp E. , Petereit Jakob , Danilevicz Monica Furaste , Anderson Robyn , Batley Jacqueline , Edwards David 
Published: July 2021

AbstractGenomic selection approaches have increased the speed of plant breeding, leading to growing crop yields over the last decade. However, climate change is impacting current and future yields, resulting in the need to further accelerate breeding efforts to cope with these changing conditions. Here we present approaches to accelerate plant breeding and incorporate nonadditive effects in genomic selection by applying state‐of‐the‐art machine learning approaches. These approaches are made more powerful by the inclusion of pangenomes, which represent the entire genome content of a species. Understanding the strengths and limitations of machine learning methods, compared with more traditional genomic selection efforts, is paramount to the successful application of these methods in crop breeding. We describe examples of genomic selection and pangenome‐based approaches in crop breeding, discuss machine learning‐specific challenges, and highlight the potential for the application of machine learning in genomic selection. We believe that careful implementation of machine learning approaches will support crop improvement to help counter the adverse outcomes of climate change on crop production.
A systems‐biology clinical trial of a personalized multimodal lifestyle intervention for early Alzheimer's disease
Authors: McEwen Sarah C. , Merrill David A. , Bramen Jennifer , Porter Verna , Panos Stella , Kaiser Scott , Hodes John , Ganapathi Aarthi , Bell Lesley , Bookheimer Tess , Glatt Ryan , Rapozo Molly , Ross Mary Kay , Price Nathan D. , Kelly Daniel , Funk Cory C. , Hood Leroy , Roach Jared C. 
Published: July 2021

AbstractIntroductionThere is an urgent need to develop effective interventional treatments for people with Alzheimer's disease (AD). AD results from a complex multi‐decade interplay of multiple interacting dysfunctional biological systems that have not yet been fully elucidated. Epidemiological studies have linked several modifiable lifestyle factors with increased incidence for AD. Because monotherapies have failed to prevent or ameliorate AD, interventional studies should deploy multiple, targeted interventions that address the dysfunctional systems that give rise to AD.MethodsThis randomized controlled trial (RCT) will examine the efficacy of a 12‐month personalized, multimodal, lifestyle intervention in 60 mild cognitive impairment (MCI) and early stage AD patients (aged 50+, amyloid positivity). Both groups receive data‐driven, lifestyle recommendations designed to target multiple systemic pathways implicated in AD. One group receives these personalized recommendations without coaching. The other group receives personalized recommendations with health coaching, dietary counseling, exercise training, cognitive stimulation, and nutritional supplements. We collect clinical, proteomic, metabolomic, neuroimaging, and genetic data to fuel systems‐biology analyses. We will examine effects on cognition and hippocampal volume. The overarching goal of the study is to longitudinally track biological systems implicated in AD to reveal the dynamics between these systems during the intervention to understand differences in treatment response.ResultsWe have developed and implemented a protocol for a personalized, multimodal intervention program for early AD patients. We began enrollment in September 2019; we have enrolled a third of our target (20 of 60) with a 95% retention and 86% compliance rate.DiscussionThis study presents a paradigm shift in designing multimodal, lifestyle interventions to reduce cognitive decline, and how to elucidate the biological systems being targeted. Analytical efforts to explain mechanistic or causal underpinnings of individual trajectories and the interplay between multi‐omic variables will inform the design of future hypotheses and development of effective precision medicine trials.
Effects of climate change on depression‐focused groundwater recharge in the Canadian Prairies
Authors: Negm Amro , Abdrakhimova Polina , Hayashi Masaki , Rasouli Kabir 
Published: July 2021

AbstractSmall topographic depressions are ubiquitous in the glaciated terrain of the Northern Prairies characterized by a cold semiarid climate. Groundwater recharge in this region is focused in topographic depressions, which receive lateral inputs of snowmelt runoff in addition to vertical inputs of precipitation. The response of depression‐focused recharge to climate change is largely unknown due to the difficulty of representing the complex interaction between depressions and surrounding uplands in hydrological models. This study evaluates climate change effects on recharge using a process‐based hydrological model and the pseudo‐global warming (PGW) approach representing a climate of 2092–2100, which has a higher mean annual temperature (+4.9 °C) and precipitation (+135 mm or +27%) compared with the present climate. The recharge model is conditioned using field data from an instrumented grassland site in the Canadian Prairies. Under the present climate, snowmelt runoff occurred in March–April over frozen soil, which accounted for the majority of water transfer from the upland to the depression. Under the PGW scenario, the amount of snowmelt runoff in March–April decreased due to lower snow accumulation and shorter periods of frozen soil. Instead, runoff occurred in midwinter and also in summer months due to increased intensity and duration of summer storms. Despite the increased precipitation, mean annual recharge rates decreased from 10.2 to 3.2 mm yr–1, indicating the importance of considering the complex effects of warmer and wetter climate on hydrological processes in cold semiarid regions.
Providing Outdoor Experiences for Infants and Toddlers: Pedagogical Possibilities and Challenges from a Brazilian Early Childhood Education Centre Case Study
Authors: da Costa Natália Meireles Santos , Rossetti-Ferreira Maria Clotilde , de Araujo Mello Ana Maria 
Published: July 2021

AbstractIntense urbanization process in Brazil and Latin America has increasingly limited young children, since birth, to access outdoor spaces, especially green areas. Moreover, as conceptions of babies in domestic care support confinement practices, apprehending infants’ constitutive specificities as being intertwined with broader socio-cultural contexts requires further investigation. Notwithstanding the challenges, Early Childhood Education and Care (ECEC) institutions can be promising places to provide babies with daily contacts and appropriation of external areas amid an expanded collective experience. This chapter tackles the process of insertion and appropriation of outdoor spaces for infants and toddlers. We bring a case study from a Brazilian daycare centre with planned multiple outdoor environments, diversified spatial arrangements and natural elements. The empirical material, referring to the transition year of a group of under-twos, includes monthly recordings of everyday routine, interviews, field notes, institutional documents. We describe and analyze various outdoor spaces and socio-spatial practices of the daycare centre based on the cultural-historical perspective of the Network of Meanings. In the first semester, environments organized in semi-open areas connected to closed spaces were more frequently used. Whereas mainly in the second semester, given walking onset and greater motor resourcefulness, the going and appropriation of green areas unfolded as a gradual process not short of struggles. Substantial planning, projects and educational situations put forward by multiple social actors within a multidisciplinary approach modulated alternation of spaces and facilitated exchanges with peers, older children and adults – including family members.
Children’s Play and Social Relations in Nature and Kindergarten Playgrounds: Examples from Norway
Authors: Sørensen Hanne Værum 
Published: July 2021

AbstractIn kindergarten, outdoor playtime is usually a break from more structured activities. It is leisure time and an opportunity for children to engage in free play with friends. Previous research indicates that time spent outdoors facilitates playful physical activity and that playing in nature inspires children’s creativity, imaginations and play across age and gender. In short, play and social relations are crucial for young children’s development and cultural formation. This study investigated children’s play activities duringoutdoor playtimein nature and on kindergarten playgrounds. Its empirical materials consisted of video observations of 12 four-year-old’s activities in nature and on a kindergarten playground and interviews with two kindergarten teachers. One child, Benjamin was the primary focus, and five more were also included. Two examples of one child’s social play in nature and on the playground were analysed to illuminate the different conditions and challenges he encountered. The findings indicate that children’s play in nature tends to be more creative and inclusive than that on kindergarten playgrounds, that kindergarten teachers participate more in children’s play in nature than on playgrounds and that children are sensitive to and try to engage in what they view as a correct form of discourse with their teachers. The author argues for further research on the subject to learn more about children’s social relations, creativity and cultural formation during outdoor playtime in nature.
Time Regulation as Institutional Condition for Children’s Outdoor Play and Cultural Formation in Kindergarten
Authors: Birkeland Åsta , Sørensen Hanne Værum 
Published: July 2021

AbstractTime regulation is an important aspect of the everyday life in any kindergarten and has an impact on which activities are given priority. In this case study, the outdoor playtime in one kindergarten in China and one in Norway is compared based on the understanding that children’s cultural formation develops in a dialectical relationship between children’s interests and motives and societal, institutional, and weather conditions. The aim of the article is to identify how time regulations provide conditions for children’s play and cultural formation during outdoor playtime. The research question is: How does institutional time regulation interplay with the pedagogical practice and children’s activities in the outdoor playtime? Employing a cultural-historical approach, drawing on Hedegaard’s concepts of development and cultural formation as an individual, institutional and societal process, the dialectical interplay between institutional time regulation and children’s engagement in outdoor activities is the unit of analysis in this study. Our findings indicate that the kindergarten teachers in the Chinese kindergarten as well as the Norwegian kindergarten aim to adjust the pedagogical content and time schedule to the traditions, values, and conditions in both countries. This chapter contributes to knowledge about the interplay between institutional conditions and children’s activities and cultural formation in outdoor play.
Exploring the Taken-for-Granted Advantage of Outdoor Play in Norwegian Early Childhood Education
Authors: Grindheim Liv Torunn 
Published: July 2021

AbstractIt is claimed that nature is given temporal and cultural dimensions in Norway, in a transgression of the distinction between nature and culture. The overall emphasis on nature in the Nordic countries may represent an unconscious taken-for-granted understanding of nature as the best place for children’s play, learning and cultural formation. Understandings of a strong Norwegian cultural connection to nature, and thereby outdoor life, as an important arena for children’s cultural formation may be challenged by changes in Early Childhood Education (ECE) institutions and the contemporary society. Such changes can force conflicts that help in depicting what is taken for granted. This chapter is therefore structured around the research question: What conflicts can be found between ECE teachers’ values and motives for outdoor play versus contextual conditions and demands in personal, institutional and cultural perspectives and in the perception of nature? By exploring conflicts between contextual conditions and demands and ECE teachers’ values and motives, the aim is to get a broader insight into perspectives and conditions for children’s cultural formation. The analysis draws on 15 interviews with ECE teachers, political documents and earlier research. The analysis reveals that nature as a valued arena for cultural formation, through play, may not be as apparent as expected in Norwegian ECE.
Usage and Scaling of an Open-Source Spiking Multi-Area Model of Monkey Cortex
Authors: van Albada Sacha J. , Pronold Jari , van Meegen Alexander , Diesmann Markus 
Published: July 2021

AbstractWe are entering an age of ‘big’ computational neuroscience, in which neural network models are increasing in size and in numbers of underlying data sets. Consolidating the zoo of models into large-scale models simultaneously consistent with a wide range of data is only possible through the effort of large teams, which can be spread across multiple research institutions. To ensure that computational neuroscientists can build on each other’s work, it is important to make models publicly available as well-documented code. This chapter describes such an open-source model, which relates the connectivity structure of all vision-related cortical areas of the macaque monkey with their resting-state dynamics. We give a brief overview of how to use the executable model specification, which employs NEST as simulation engine, and show its runtime scaling. The solutions found serve as an example for organizing the workflow of future models from the raw experimental data to the visualization of the results, expose the challenges, and give guidance for the construction of an ICT infrastructure for neuroscience.
Aspekte des Wahrscheinlichkeitsbegriffs
Authors: Kalisch Markus , Meier Lukas 
Published: July 2021

ZusammenfassungAusgehend von dem Begriff der Wahrscheinlichkeit werden die Begriffe der Odds (Chance) und Log-Odds eingeführt und anhand von einem Beispiel illustriert. Beide Größen werden später bei der Interpretation des logistischen Regressionsmodells eine zentrale Rolle spielen. Neben exakten Definitionen wird Wert auf ein intuitives Verständnis der Zusammenhänge gelegt. Die Begriffe Risk-Ratio und Odds-Ratio erlauben es, Wahrscheinlichkeiten bzw. Odds für ein Ereignis in zwei verschiedenen Situationen zu vergleichen.
Logistische Regression in R
Authors: Kalisch Markus , Meier Lukas 
Published: July 2021

ZusammenfassungIn diesem Kapitel wird illustriert, wie die bis jetzt gelernten Konzepte mit der Statistiksoftware R umgesetzt werden können. Anhand eines Beispiels wird gezeigt, wie ein Modell ausgehend von Daten geschätzt werden kann. Anschließend wird die Effektstärke inkl. Vertrauensintervall auf der Skala der Log-Odds und der Odds bestimmt. Es folgen Vorhersagen auf der Skala der Log-Odds, der Odds und der Wahrscheinlichkeit. Den Abschluss bildet die effiziente Bearbeitung von gruppierten Daten.
Expanding on the Cardy-like limit of the SCI of 4d $$ \mathcal{N} $$ = 1 ABCD SCFTs
Authors: Amariti Antonio , Fazzi Marco , Segati Alessia 
Published: July 2021

Abstract
We study the Cardy-like limit of the superconformal index of generic $$ \mathcal{N} $$
N
= 1 SCFTs with ABCD gauge algebra, providing strong evidence for a universal formula that captures the behavior of the index at finite order in the rank and in the fugacities associated to angular momenta. The formula extends previous results valid at lowest order, and generalizes them to generic SCFTs. We corroborate the validity of our proposal by studying several examples, beyond the well-understood toric class. We compute the index also for models without a weakly-coupled gravity dual, whose gravitational anomaly is not of order one.
The canonical formulation of E6(6) exceptional field theory
Authors: Kreutzer Lars T. 
Published: July 2021

Abstract
We investigate the canonical formulation of the (bosonic) E6(6) exceptional field theory. The explicit non-integral (not manifestly gauge invariant) topological term of E6(6) exceptional field theory is constructed and we consider the canonical formulation of a model theory based on the topological two-form kinetic term. Furthermore we construct the canonical momenta and the canonical Hamiltonian of the full bosonic E6(6) exceptional field theory. Most of the canonical gauge transformations and some parts of the canonical constraint algebra are calculated. Moreover we discuss how to translate the results canonically into the generalised vielbein formulation. We comment on the possible existence of generalised Ashtekar variables.
se-atlas.de – Versorgungsatlas für Menschen mit Seltenen Erkrankungen
Authors: Neff Michaela , Schaaf Jannik , Tegtbauer Niels , Schäfer Johanna , Till Manuela , Wagner Thomas O. F. , Graeßner Holm , Mundlos Christine , Storf Holger 
Published: July 2021

ZusammenfassungEine Erkrankung zählt in der Europäischen Union zu den Seltenen Erkrankungen (SE), wenn diese nicht mehr als 5 von 10.000 Menschen betrifft. Derzeit existiert mit mehr als 6000 SE eine sowohl große als auch heterogene Menge an unterschiedlichen Krankheitsbilder, die in ihrer Symptomatik komplex, vielschichtig und damit im medizinischen Alltag schwierig einzuordnen sind. Dies erschwert Diagnosefindung und Behandlung sowie das Auffinden eines passenden Ansprechpartners, da es nur wenige Experten für jede einzelne SE gibt. Der medizinische Versorgungsatlas für Seltene Erkrankungen www.se-atlas.de ermöglicht anhand von Erkrankungsnamen die Suche nach Versorgungseinrichtungen und Selbsthilfeorganisationen zu bestimmten SE und stellt die Suchergebnisse geografisch dar. Ebenso gibt er einen Überblick über alle deutschen Zentren für SE, die eine Anlaufstelle für betroffene Personen mit unklarer Diagnose darstellen. Der se-atlas dient als Kompass durch die heterogene Menge an Informationen über Versorgungseinrichtungen für SE und stellt niederschwellig Informationen für eine breite Nutzergruppe von Betroffenen bis hin zu Mitgliedern des medizinischen Versorgungsteams bereit.
Unraveling the genetics of tomato fruit weight during crop domestication and diversification
Authors: Pereira Lara , Zhang Lei , Sapkota Manoj , Ramos Alexis , Razifard Hamid , Caicedo Ana L. , van der Knaap Esther 
Published: July 2021

Abstract
Key Message
Six novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs.

Abstract
The size and weight of edible organs have been strongly selected during crop domestication. Concurrently, human have also focused on nutritional and cultural characteristics of fruits and vegetables, at times countering selective pressures on beneficial size and weight alleles. Therefore, it is likely that novel improvement alleles for organ weight still segregate in ancestral germplasm. To date, five domestication and diversification genes affecting tomato fruit weight have been identified, yet the genetic basis for increases in weight has not been fully accounted for. We found that fruit weight increased gradually during domestication and diversification, and semi-domesticated subpopulations featured high phenotypic and nucleotide diversity. Columella and septum fruit tissues were proportionally increased, suggesting targeted selection. We developed twenty-one F2 populations with parents fixed for the known fruit weight genes, corresponding to putative key transitions from wild to fully domesticated tomatoes. These parents also showed differences in fruit weight attributes as well as the developmental timing of size increase. A subset of populations was targeted for QTL-seq, leading to the identification of six uncloned fruit weight QTLs. Three QTLs, located on chromosomes 1, 2 and 3, were subsequently validated by progeny testing. By exploring the segregation of the known fruit weight genes and the identified QTLs, we estimated that most beneficial alleles in the newly identified loci arose in semi-domesticated subpopulations from South America and were not likely transmitted to fully domesticated landraces. Therefore, these alleles could be incorporated into breeding programs using the germplasm and genetic resources identified in this study.
Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat
Authors: Badaeva Ekaterina D. , Konovalov Fedor A. , Knüpffer Helmut , Fricano Agostino , Ruban Alevtina S. , Kehel Zakaria , Zoshchuk Svyatoslav A. , Surzhikov Sergei A. , Neumann Kerstin , Graner Andreas , Hammer Karl , Filatenko Anna , Bogaard Amy , Jones Glynis , Özkan Hakan , Kilian Benjamin 
Published: July 2021

Abstract
Key message
We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement.

Abstract
Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.