Microarray missing data imputation based on a set theoretic framework and biological knowledge

Gene expressions measured using microarrays usually suffer from the missing value problem. However, in many data analysis methods, a complete data matrix is required. Although existing missing value imputation algorithms have shown good performance to deal with missing values, they also have their limitations. For example, some algorithms have good performance only when strong local correlation exists in data while some provide the best estimate when data is dominated by global structure. In addition, these algorithms do not take into account any biological constraint in their imputation. In this paper, we propose a set theoretic framework based on projection onto convex sets (POCS) for missing data imputation. POCS allows us to incorporate different types of a priori knowledge about missing values into the estimation process. The main idea of POCS is to formulate every piece of prior knowledge into a corresponding convex set and then use a convergence-guaranteed iterative procedure to obtain a solution in the intersection of all these sets. In this work, we design several convex sets, taking into consideration the biological characteristic of the data: the first set mainly exploit the local correlation structure among genes in microarray data, while the second set captures the global correlation structure among arrays. The third set (actually a series of sets) exploits the biological phenomenon of synchronization loss in microarray experiments. In cyclic systems, synchronization loss is a common phenomenon and we construct a series of sets based on this phenomenon for our POCS imputation algorithm. Experiments show that our algorithm can achieve a significant reduction of error compared to the KNNimpute, SVDimpute and LSimpute methods

A One Stop 3D Target Reconstruction and multilevel Segmentation Method

3D object reconstruction and multilevel segmentation are fundamental to computer vision research. Existing algorithms usually perform 3D scene reconstruction and target objects segmentation independently, and the performance is not fully guaranteed due to the challenge of the 3D segmentation. Here we propose an open-source one stop 3D target reconstruction and multilevel segmentation framework (OSTRA), which performs segmentation on 2D images, tracks multiple instances with segmentation labels in the image sequence, and then reconstructs labelled 3D objects or multiple parts with Multi-View Stereo (MVS) or RGBD-based 3D reconstruction methods. We extend object tracking and 3D reconstruction algorithms to support continuous segmentation labels to leverage the advances in the 2D image segmentation, especially the Segment-Anything Model (SAM) which uses the pretrained neural network without additional training for new scenes, for 3D object segmentation. OSTRA supports most popular 3D object models including point cloud, mesh and voxel, and achieves high performance for semantic segmentation, instance segmentation and part segmentation on several 3D datasets. It even surpasses the manual segmentation in scenes with complex structures and occlusions. Our method opens up a new avenue for reconstructing 3D targets embedded with rich multi-scale segmentation information in complex scenes. OSTRA is available from https://github.com/ganlab/OSTRA

Trajetórias Familiares e Práticas de Gestão: Estudo de Caso da Família Gotardo em Guarapari.

Inserido em uma perspectiva subjetiva de pesquisa sobre empresas familiares, este trabalho, busca somar-se ao o esforço para interpretação de dinâmicas sócio-culturais, contrapondo-se aos que tratam apenas assuntos referentes à sucessão. A pesquisa tem caráter qualitativo e investiga como as práticas sócio-culturais de gestão da família Gotardo configuraram as suas trajetórias empresariais. Para tal, utiliza como procedimento metodológico à análise da história oral desenvolvida sobre a transcrição de entrevistas com os gestores de empresas pertencentes à referida família, em Guarapari-ES. O referencial teórico é desenvolvido em temáticas essenciais para direcionar a pesquisa: gestão como prática social; estudos sobre empresas familiares e trajetórias empresariais e; estudos sobre famílias.Inserted in a subjective perspective of research on family companies, this work search to add to the effort for interpretation of partner-cultural dynamics, opposing to the that just treat referring subjects about the succession. The research has qualitative character and investigates as the social practices of the Gotardo family set its businesses trajectory. For such, it uses as methodological procedure the analysis of the oral history developed about the transcription of interviews with the managers of the companies that belong the referred family in Guarapari-ES. The theoretical thought is developed in essential thematic to set the research: management as social practice; studies on family companies; managerial paths and studies on families

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

Summary: The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome‐wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher‐level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants

Photoreceptor Activity Contributes to Contrasting Responses to Shade in Cardamine and Arabidopsis Seedlings

Plants have evolved two major ways to deal with nearby vegetation or shade: avoidance and tolerance. Moreover, some plants respond to shade in different ways; for example, Arabidopsis thaliana undergoes an avoidance response to shade produced by vegetation, but its close relative Cardamine hirsuta tolerates shade. How plants adopt opposite strategies to respond to the same environmental challenge is unknown. Here, using a genetic strategy, we identified the C. hirsuta slender in shade1 (sis1) mutants, which produce strongly elongated hypocotyls in response to shade. These mutants lack the phytochrome A (phyA) photoreceptor. Our findings suggest that C. hirsuta has evolved a highly efficient phyA-dependent pathway that suppresses hypocotyl elongation when challenged by shade from nearby vegetation. This suppression relies, at least in part, on stronger phyA activity in C. hirsuta; this is achieved by increased ChPHYA expression and protein accumulation combined with a stronger specific intrinsic repressor activity. We suggest that modulation of photoreceptor activity is a powerful mechanism in nature to achieve physiological variation (shade tolerance vs. avoidance) for species to colonize different habitats

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species

Morphomechanical Innovation Drives Explosive Seed Dispersal

How mechanical and biological processes are coordinated across cells, tissues, and organs to produce complex traits is a key question in biology. Cardamine hirsuta, a relative of Arabidopsis thaliana, uses an explosive mechanism to disperse its seeds. We show that this trait evolved through morphomechanical innovations at different spatial scales. At the organ scale, tension within the fruit wall generates the elastic energy required for explosion. This tension is produced by differential contraction of fruit wall tissues through an active mechanism involving turgor pressure, cell geometry, and wall properties of the epidermis. Explosive release of this tension is controlled at the cellular scale by asymmetric lignin deposition within endocarp b cells-a striking pattern that is strictly associated with explosive pod shatter across the Brassicaceae plant family. By bridging these different scales, we present an integrated mechanism for explosive seed dispersal that links evolutionary novelty with complex trait innovation