Towards an Agile Biodigital Architecture: Supporting a Dynamic Evolutionary and Developmental View of Architecture

Architecture and biology are fields of high complexity. Generative design approaches provide access to continuously increasing complexity in design. Some of these methods are based on biological principles but usually do not communicate the conceptual base necessary to appropriately reflect the input from biology into architecture. To address this, we propose a model for analysis and design of architecture based on a multistaged integrated design process that extends the common morphological process in digital morphogenesis with a typology-based ontological model. Biomimetics, an emerging field to strategically search for information transfer from biology to technological application, will assist in delivering a frame of reference and methodology for establishing valid analogies between the different realms as well as integration of the biological concept into a larger framework of analogy to biological processes. As the biomimetic translation of process and systems information promises more radical innovation, this chapter focuses on the dynamic perspectives provided by biological development and evolution to model the complexity of architecture. The proposed process was used to inform five parallel workshops to explore dynamic biological concepts in design. The potential of the process to investigate biomimetic processes in architecture is then discussed, and future work is outlined

Estructuras inteligentes en proyectos arquitectónicos: Hacia un marco interactivo de diseño combinando optimización estructural multiescalar y nodos estructurales optimizados de manera personalizada para un diseño generativo

La personalización masiva interactiva está cambiando prácticas en arquitectura, ingeniería, y la industria de la construcción (AEC). Los flujos de trabajo de sistemas de software en el futuro podrían abordar las tecnologías que incluyen interacción con usuarios y así aumentar las capacidades creativas humanas. Las primeras etapas de diseño requieren decisiones rápidas e informadas por datos entregados por tecnología de modelado de información de construcción. El diseño arquitectónico se ha transformado por la introducción de software de diseño, pero hasta hace poco el diseño en sí ha seguido siendo realizado por el arquitecto. Eso ha comenzado a cambiar con la exploración de marcos de diseño interactivo. La optimización de estructuras en múltiples escalas afecta tanto a la estructura general en dependencia de la geometría arquitectónica y la expresión local de nodos estructurales impresos en 3D. La investigación reportada exploró el uso de un algoritmo para cerrar brechas geométricas en el diseño generativo de componentes estructurales. Este algoritmo similar a la espuma permitió al artista y arquitecto diseñar en el estilo del Nuevo Estructuralismo usando una combinación de diferentes rutinas de optimización. Como resultado, el algoritmo SPUME se investigó para integrar varias partes geométricas en una forma orgánica para el diseño de nodos estructurales optimizados de manera personalizada. Como parte del estudio de caso, un pabellón con una estructura teselada y nodos estructurales impresos en 3D y optimizados de manera personalizada fue diseñado por un artista y un arquitecto para mostrar el potencial de aplicación del marco conceptualizado. Finalmente, un prototipo para conectar soportes y la forma optimizada por BESO de los nudos estructurales fue producido para combinar todos los aspectos de la geometría del nodo local en la representación tectónica

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.This work was financially supported by the following grants: project GABI-BARLEX, German Federal Ministry of Education and Research (BMBF), #0314000 to MP, US, KFXM and NS; Triticeae Coordinated Agricultural Project, USDA-NIFA #2011-68002-30029 to GJM; and Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA’s Cooperative State Research and Extension Service, #2009-65300- 05645 to GJM

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND: There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS: A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS: We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes

TRITEX : chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.Peer reviewe

A chromosome conformation capture ordered sequence of the barley genome

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Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Modeling as a necessary step for understanding Internet-wide route progagation

Most of the insight we have today about the Internet-wide route propagation comes from studies performed more than 5 years ago [1], [2], [3]. Since then, insight about the routing system has largely focused on the behavior of individual ASes [4], [5], [6], [7] or particular prefixes [8]. The way BGP routes propagate across the Internet, how fast, and whether BGP does it reasonably well are largely open questions. To argue in favor or against potential alternatives to BGP, the research community must be able to provide answers to such questions. We argue that since measurements cannot reveal the whole picture of the Internet route propagation, building models of the Internet is one of the most reasonable ways to improve our understanding of this aspect of the interdomain routing system. [9] constitutes a first step in this direction.Steve Uhlig, Olaf Maennel, and Wolfgang Muelbaue

Patient Compliance in Assessing Electronic Patient-Reported Outcome Measures after Urologic Surgery

Introduction: This study aimed to assess patient compliance with a newly established electronic patient-reported outcome measure (ePROM) system after urologic surgery and to identify influencing factors. Methods: Digital surveys were provided to patients undergoing cystectomy, radical or partial nephrectomy, or transurethral resection of bladder tumor via a newly established ePROM system. Participants received a baseline survey preoperatively and several follow-up surveys postoperatively. Multivariable regression analysis was performed to identify factors predicting compliance. Results: Of N = 435 eligible patients, n = 338 completed the baseline survey (78.0%). Patients who did not participate were significantly more likely male (p = 0.004) and older than 70 years (p = 0.005). Overall, 206/337 patients (61.3%) completed the survey at 1-month, 167/312 (53.5%) at 3-month, and 142/276 (51.4%) at 6-month follow-up. Lower baseline quality of life (odds ratio: 2.27; p = 0.004) was a significant predictor for dropout at 1-month follow-up. Low educational level was significantly associated with low compliance at 3- (OR: 1.92; p = 0.01) and 6-month follow-up (OR: 2.88; p < 0.001). Conclusion: Acceptable compliance rates can be achieved with ePROMs following urologic surgery. Several factors influence compliance and should be considered when setting-up ePROM surveys