Article
Biotechnology & Applied Microbiology
Nawazish Khan, Andrew C. Peterson, Benjamin Aubert, Alan Morris, Penny R. Atkins, Amy L. Lenz, Andrew E. Anderson, Shireen Y. Elhabian
Summary: Statistical shape modeling is essential for quantitative analysis of anatomies. Particle-based shape modeling allows learning of population-level shape representation from medical imaging data. However, global multi-organ models have limitations, such as scalability issues and anatomical inconsistencies. This paper proposes a new approach that overcomes these limitations by optimizing correspondence-points and capturing inter-organ relations.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Matthew R. Willman, Jill M. Bushakra, Nahla Bassil, Chad E. Finn, Michael Dossett, Penelope Perkins-Veazie, Christine M. Bradish, Gina E. Fernandez, Courtney A. Weber, Joseph C. Scheerens, Lisa Dunlap, Jonathan Fresnedo-Ramirez
Summary: The analysis of the genetic variation and stability of black raspberry traits provides insights into improving black raspberry germplasm and cultivars.
Article
Multidisciplinary Sciences
Yipin Lei, Shuya Li, Ziyi Liu, Fangping Wan, Tingzhong Tian, Shao Li, Dan Zhao, Jianyang Zeng
Summary: The authors proposed a deep learning framework CAMP for predicting peptide-protein interactions and identifying important binding residues. Comprehensive evaluation showed that CAMP outperformed other methods in predicting peptide-protein interactions. CAMP serves as a significant tool in facilitating peptide drug discovery.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Interdisciplinary Applications
Vandana Dwarka, Cornelis Vuik
Summary: Recent research efforts have focused on iteratively solving time-harmonic waves by accelerating convergence techniques. Deflation techniques, particularly for the Helmholtz equation, have been studied to speed up the convergence of Krylov subspace methods. This work introduces a multilevel deflation method for (heterogeneous) Helmholtz and elastic wave problems, utilizing higher-order deflation vectors to maintain spectrum stability at the coarse-grid linear systems' indefinite level.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Plant Sciences
Camille Branchereau, Craig Hardner, Elisabeth Dirlewanger, Benedicte Wenden, Loick Le Dantec, David Alletru, Julien Parmentier, Anton Ivancic, Daniela Giovannini, Federica Brandi, Gregorio Lopez-Ortega, Federico Garcia-Montiel, Benedicte Quilot-Turion, Jose Quero-Garcia
Summary: Flowering date in sweet cherry is strongly influenced by environmental conditions and can be impacted by genotype-by-environment interaction (GxE) and QTL-by-environment interaction (QTLxE). This study conducted a multi-environment trial to explore the effects of environment on flowering date in sweet cherry and identified significant QTLxE. The findings provide valuable insights into the genetic control of flowering date and offer a strategy for marker-assisted selection in sweet cherry breeding.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Computer Science, Theory & Methods
Diego Serrano, Eleni Stroulia
Summary: The number of Web APIs is increasing, yet tools to automate the process of invoking APIs and composing responses are lacking. The LRA methodology relies on RDF service specifications to automate Web API development, with the LRAWbench simplifying the formulation of LRA-compliant SPARQL queries. Empirical evaluation shows that the LRAWbench significantly improves developers' performance in formulating SPARQL queries for LRA.
JOURNAL OF BIG DATA
(2021)
Article
Computer Science, Artificial Intelligence
Xin Shu, Guoying Zhao
Summary: In this paper, a novel framework is proposed to integrate semantic correlation and feature correlation for cross-modal retrieval. By using semantic transformation, the model avoids explicitly computing the covariance matrix, which leads to a huge saving of computational cost. Experimental results demonstrate the accuracy and efficiency of the proposed method on three multi-label datasets.
PATTERN RECOGNITION
(2021)
Article
Biology
Jaclyn Smith, Yao Shi, Michael Benedikt, Milos Nikolic
Summary: In the field of biomedicine, there is a need for scalable data integration solutions due to limitations in large-scale data processing frameworks in analyzing complex data types. TraNCE is an automated framework designed to address the challenges of designing distributed analyses with complex biomedical data types, demonstrating its ability to outperform common alternatives.
Article
Construction & Building Technology
Mohammadreza Shirzadi, Yoshihide Tominaga
Summary: This study proposes a multi-fidelity shape optimization framework for the pedestrian-level wind environment. By integrating low-fidelity and high-fidelity CFD models, the optimization reliability is improved, the high-wind-speed area is reduced, and the importance of considering local wind climates in architectural design is highlighted.
BUILDING AND ENVIRONMENT
(2021)
Article
Agriculture, Multidisciplinary
Chao Kai-xiang, Wu Cai-juan, Li Juan, Wang Wen-li, Wang Bao-tong, Li Qiang
Summary: The study found that Wudubaijian, a wheat landrace in China, exhibits resistance to stripe rust, and two stable quantitative trait loci (QTLs) were identified through genetic mapping and molecular markers.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Biochemistry & Molecular Biology
Marius Alfred Dieckmann, Sebastian Beyvers, Rudel Christian Nkouamedjo-Fankep, Patrick Harald Georg Hanel, Lukas Jelonek, Jochen Blom, Alexander Goesmann
Summary: The EDGAR platform is a web server offering precomputed orthology data for thousands of microbial genomes, playing a crucial role in comparative genomics and phylogenomics research. With advanced technical infrastructure and features like Venn diagrams and phylogenetic trees, EDGAR 3.0 introduces scalable infrastructure for comprehensive microbial comparative gene content analysis, accommodating the increasing number of genomes analyzed in projects.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Nanoscience & Nanotechnology
Stefania Sciara, Piotr Roztocki, Bennet Fischer, Christian Reimer, Luis Romero Cortes, William J. Munro, David J. Moss, Alfonso C. Cino, Lucia Caspani, Michael Kues, Jose Azana, Roberto Morandotti
Summary: Multi-level entangled photon states are a key resource for quantum technologies, offering unique advantages in boosting the performance of advanced applications. Research focuses on the generation and processing methods of multi-level photon states, as well as the experimental feasibility and noise robustness of entanglement states.
Article
Ecology
Adam Z. Hasik, Adam M. Siepielski
Summary: The extent and magnitude of parasitism vary among closely related host species and populations within species. Host identity and local abiotic conditions play important roles in shaping parasitism, while host density and resource abundance have limited effects. The findings highlight the significance of the local environment in host-parasite interactions.
FRESHWATER BIOLOGY
(2022)
Article
Engineering, Electrical & Electronic
Michael I. -C. Wang, Charles H. -P. Wen, H. Jonathan Chao
Summary: This paper proposes a holistic solution for scalable CAV routing by enabling hierarchical cooperation and load balancing in the Multi-Access Edge Computing (MEC) environment. The system cooperatively plans CAV routes and dynamically balances loads in MECs to handle massive requests.
IEEE TRANSACTIONS ON VEHICULAR TECHNOLOGY
(2023)
Article
Computer Science, Theory & Methods
Wenyu Li, Chenglin Feng, Lei Zhang, Hao Xu, Bin Cao, Muhammad Ali Imran
Summary: The article proposes a scalable multi-layer PBFT-based consensus mechanism for large systems, such as IoT ecosystems and blockchain, by hierarchically grouping nodes and limiting communication within groups. The optimal double-layer PBFT is introduced to minimize communication complexity, with security threshold analyzed based on faulty probability models. Practical protocols for the proposed double-layer PBFT system are provided, extending the results to arbitrary-layer PBFT systems with communication complexity and security analysis verified through simulation results.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2021)
Article
Endocrinology & Metabolism
Manuel Delpero, Danny Arends, Maximilian Sprechert, Florian Krause, Oliver Kluth, Annette Schuermann, Gudrun A. Brockmann, Deike Hesse
Summary: The study aimed to identify genetic variants associated with impaired glucose metabolism using obese lines BFMI861-S1 and BFMI861-S2. QTL mapping revealed overlapping QTL for gonadal adipose tissue weight and blood glucose concentration on Chr 3 and Chr 17, with additional QTL detected on Chr 15 and Chr 16. The study provided evidence for direct and indirect genetic effects on blood glucose concentration in the insulin-resistant mouse line BFMI861-S1.
INTERNATIONAL JOURNAL OF OBESITY
(2022)
Article
Biochemistry & Molecular Biology
Florian Krause, Kourosh Mohebian, Manuel Delpero, Deike Hesse, Ralf Kuehn, Danny Arends, Gudrun A. Brockmann
Summary: The Berlin Fat Mouse Inbred (BFMI) line serves as a model for juvenile obesity with a recessive defect causing obesity identified on chromosome 3 (jObes1). Bbs7 was determined as a candidate gene for this effect. By introducing a specific deletion into B6N mice using CRISPR/Cas9, partial complementation of the jObes1 allele from BFMI was achieved. This suggests the presence of additional variants near Bbs7 interacting with the deletion in intron 8.
Article
Agriculture, Dairy & Animal Science
Salma Elzaki, Paula Korkuc, Danny Arends, Monika Reissmann, Siham A. Rahmatalla, Gudrun A. Brockmann
Summary: This study investigated the association between somatic cell score (SCS) and single nucleotide polymorphisms (SNPs) in Butana and Butana x Holstein cattle in Sudan. The results showed significant association between two SNPs and SCS, with the minor allele being associated with increased SCS.
TROPICAL ANIMAL HEALTH AND PRODUCTION
(2022)
Article
Genetics & Heredity
Karl W. Broman
Summary: A common step in the analysis of multiparent populations is genotype reconstruction, which involves identifying the origin of haplotypes using dense marker data. This process often utilizes a probability model to represent the distribution of founder alleles along chromosomes, considering their relative frequencies and the likelihood of exchanges among them. The model relies on the meiotic recombination process and mating design for the population. We present an approximate model that can be applied to various multiparent populations, implemented in the R/qtl2 software and demonstrated using publicly available data on Diversity Outbred and Collaborative Cross mice.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Danny Arends, Stefan Kaerst, Sebastian Heise, Paula Korkuc, Deike Hesse, Gudrun A. Brockmann
Summary: The study reveals the genetic mechanisms underlying the heterogeneity of complex traits through genetic incompatibilities, distortion of protein-protein interactions, and meiotic drive. Genes in TRD regions can serve as new targets for investigating genetic adaptation and determinants of complex traits.
Review
Biochemical Research Methods
Axel Kowald, Israel Barrantes, Steffen Moeller, Daniel Palmer, Hugo Murua Escobar, Anne Schwerk, Georg Fuellen
Summary: Accurate transfer learning of clinical outcomes is highly useful for transferring prediction tasks from one cellular context to another. Transductive transfer learning focuses on learning the predictor in the source domain and transferring its label calculations to the target domain, while inductive transfer learning considers cases where the target predictor performs a different yet related task compared with the source predictor. Mapping variables may also be required. Various transfer learning approaches have been discussed and compared in the context of predicting clinical outcomes based on preclinical molecular data.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Kathryn J. Michel, Dayane C. Lima, Hope Hundley, Vasanth Singan, Yuko Yoshinaga, Chris Daum, Kerrie Barry, Karl W. Broman, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler
Summary: The Stiff Stalk heterotic pool is an important germplasm resource in US maize breeding and has been widely used. Significant loci for flowering time and plant height traits were identified in a multi-parent population. Genomic prediction was used to effectively predict hybrid phenotypes without hybrid data.
Article
Agriculture, Dairy & Animal Science
Shijie Lyu, Danny Arends, Mostafa K. Nassar, Annett Weigend, Steffen Weigend, Eryao Wang, Gudrun A. Brockmann
Summary: This study identified genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens through a genome-wide association study and principal component analysis. The investigated Asian Game type chicken breeds were found to be genetically different from the Asian Bantam breeds. A region on chromosome 4 (17.3-21.3 Mb) was identified as potentially contributing to the phenotypic difference, although further validation of candidate genes is necessary.
Article
Multidisciplinary Sciences
Kathrin Jager, Juliane Mensch, Maria Elisabeth Grimmig, Bruno Neuner, Kerstin Gorzelniak, Seval Turkmen, Ilja Demuth, Alexander Hartmann, Christiane Hartmann, Felix Wittig, Anje Sporbert, Andreas Hermann, Georg Fuellen, Steffen Moller, Michael Walter
Summary: Telomeres are repetitive nucleotide sequences at the ends of chromosomes which can silence genes away from them to inhibit tumor growth. A study identified a set of highly conserved genes in replicatively aging animals and discovered that PPP2R2C gene, regulated by TPE-OLD, can suppress tumor-related signaling pathways.
Article
Genetics & Heredity
Guilherme B. Neumann, Paula Korkuc, Danny Arends, Manuel J. Wolf, Katharina May, Sven Koenig, Gudrun A. Brockmann
Summary: German Black Pied cattle (DSN) are an endangered dual-purpose cattle breed. This study aimed to characterize their genetic diversity and inbreeding, and detect selection signatures between DSN and Holstein. The results revealed a close genetic relationship between DSN and Holstein, and identified regions responsible for their specific traits.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Paula Korkuc, Guilherme B. Neumann, Deike Hesse, Danny Arends, Monika Reissmann, Siham Rahmatalla, Katharina May, Manuel J. Wolf, Sven Koenig, Gudrun A. Brockmann
Summary: The study identified 1980 associated variants for milk production traits in German Black Pied (DSN) cows. These variants were found in 13 genomic loci on 9 chromosomes. Selecting favorable alleles can improve milk yield and composition. Careful investigation is needed before applying the milk-associated variants to DSN cows due to their dual-purpose nature.
Article
Microbiology
Q. Zhang, V. Linke, K. A. Overmyer, L. L. Traeger, K. Kasahara, I. J. Miller, D. E. Manson, T. J. Polaske, R. L. Kerby, J. H. Kemis, E. A. Trujillo, T. R. Reddy, J. D. Russell, K. L. Schueler, D. S. Stapleton, M. E. Rabaglia, M. Seldin, D. M. Gatti, G. R. Keele, D. T. Pham, J. P. Gerdt, E. I. Vivas, A. J. Lusis, M. P. Keller, G. A. Churchill, H. E. Blackwell, K. W. Broman, A. D. Attie, J. J. Coon, F. E. Rey
Summary: By using a genetically diverse mouse population, this study revealed the molecular bases of how host genetic variation impacts the gut microbiome and identified interactions between host and microbe phenotypes. The study found that Akkermansia muciniphila plays a role in the production of immunomodulatory ornithine lipids, which are potentially important for host-microbe interactions. These findings highlight the importance of host genetics in determining responses to gut microbes and provide insights into the complex relationships between host and microbiome.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Anna C. Salvador, M. Nazmul Huda, Danny Arends, Ahmed M. Elsaadi, C. Anthony Gacasan, Gudrun A. Brockmann, William Valdar, Brian J. Bennett, David W. Threadgill
Summary: The gut microbiota is influenced by a combination of diet, host genetics, and sex effects. The study found that sex, diet, and genetic background have different magnitudes of effects on inter-individual differences in gut microbiota. Precision Nutrition integrating genetic variation, microbiota, and sex affecting microbiota variation will be important for predicting responses to diets varying in carbohydrate composition.
Article
Genetics & Heredity
Steffen Moeller, Nadine Saul, Elias Projahn, Israel Barrantes, Andras Gezsi, Michael Walter, Peter Antal, Georg Fuellen
Summary: This study utilized gene co-expression network analysis to study healthspan modules in human and animal models, identifying a set of candidate genes related to health(span) and finding functional associations through enrichment analysis. The meta-study of hub genes for complex healthspan phenotype across multiple species can provide insights into molecular mechanisms.
NAR GENOMICS AND BIOINFORMATICS
(2022)
Meeting Abstract
Environmental Sciences
Danila Cuomo, Danny Arends, David Threadgill
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)
