Nearest Neighbor Classification Rule for Mixtures of Discrete and Continuous Random Variables

In this paper very simple nonparametric classification rule for mixtures of discrete and continuous random variables is described. It is based on the method of nearest neighbor proposed by Cover and Hart (1967). The bounds on the limit of the nearest neighbor rule risks are given. Both lower and upper bound depend on the Bayes risk and the loss function. Finally the method is compared with other existing methods on some practical data set.     

The pattern and meaning of neighbor relations in high-rise housing in Israel

This paper deals with the behavioral pattern of neighbor relations and their relationships to the subjective attitudes and expectations of the residents. The sample was 318 middle-class women living in eight-to 20-story buildings. The findings indicate that respondents so desiring were able to develop active social ties with their neighbors. Moreover, they interacted with neighbors despite the fact that the majority had opportunities for alternative social relations. The distinction between localized and nonlocalized high-rise residents does not seem meaningful in this case. Actual social ties with neighbors were related to norms and expectations regarding neighbor relations. Despite active neighboring, respondents did not have difficulties obtaining privacy.     

Pervasive migration of organellar DNA to the nucleus in plants

A surprisingly large number of plant nuclear DNA sequences inferred to be remnants of chloroplast and mitochondrial DNA migration events were detected through computer-assisted database searches. Nineteen independent organellar DNA insertions, with a median size of 117 by (range of 38 to >785 bp), occur in the proximity of 15 nuclear genes. One fragment appears to have been passed through a RNA intermediate, based on the presence of an edited version of the mitochondrial gene in the nucleus. Tandemly arranged fragments from disparate regions of organellar genomes and from different organellar genomes indicate that the fragments joined together from an intracellular pool of RNA and/or DNA before they integrated into the nuclear genome. Comparisons of integrated sequences to genes lacking the insertions, as well as the occurrence of coligated fragments, support a model of random integration by end joining. All transferred sequences were found in noncoding regions, but the positioning of organellar-derived DNA in introns, as well as regions 5 and 3 to nuclear genes, suggests that the random integration of organellar DNA has the potential to influence gene expression patterns. A semiquantitative estimate was performed on the amount of organellar DNA being transferred and assimilated into the nucleus. Based on this database survey, we estimate that 3–7% of the plant nuclear genomic sequence files contain organellar-derived DNA. The timing and the magnitude of genetic flux to the nuclear genome suggest that random integration is a substantial and ongoing process for creating sequence variation.Correspondence to: J.L. Blanchard     

A method for determining the position and size of optimal sequence regions for phylogenetic analysis

The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent. Correspondence to: J. Dopazo     

Advanced Cell Mapping Visualizations for Single Cell Functional Proteomics Enabling Patient Stratification

Highly multiplexed single‐cell functional proteomics has emerged as one of the next‐generation toolkits for a deeper understanding of functional heterogeneity in cell. Different from the conventional population‐based bulk and single‐cell RNA‐Seq assays, the microchip‐based proteomics at the single‐cell resolution enables a unique identification of highly polyfunctional cell subsets that co‐secrete many proteins from live single cells and most importantly correlate with patient response to a therapy. The 32‐plex IsoCode chip technology has defined a polyfunctional strength index (PSI) of pre‐infusion anti‐CD19 chimeric antigen receptor (CAR)‐T products, that is significantly associated with patient response to the CAR‐T cell therapy. To complement the clinical relevance of the PSI, a comprehensive visualization toolkit of 3D uniform manifold approximation and projection (UMAP) and t‐distributed stochastic neighbor embedding (t‐SNE) in a proteomic analysis pipeline is developed, providing more advanced analytical algorithms for more intuitive data visualizations. The UMAP and t‐SNE of anti‐CD19 CAR‐T products reveal distinct cytokine profiles between nonresponders and responders and demonstrate a marked upregulation of antitumor‐associated cytokine signatures in CAR‐T cells from responding patients. Using this powerful while user‐friendly analytical tool, the multi‐dimensional single‐cell data can be dissected from complex immune responses and uncover underlying mechanisms, which can promote correlative biomarker discovery, improved bioprocessing, and personalized treatment development.     

Biochemical recognition in seeds: Germination of Rumex obtusifolius is promoted by leaves of facilitative adult conspecifics

Seeds express various germination behaviors in response to competitor plants. However, germination behaviors in response to facilitator plants are not yet well understood. Rumex obtusifolius seedlings usually appear on the ground near adult conspecific plants, and their survival rate under the canopy of adult conspecifics is higher than that outside the canopy, indicating that adult R. obtusifolius plants facilitate their seedling establishments. We hypothesized that emergence of R. obtusifolius seedlings is promoted by cues from adult conspecifics, but emergence of heterospecific seedlings is not. To test this, we investigated emergence responses of seedlings of R. obtusifolius and three other species that grow with R. obtusifolius in the presence of R. obtusifolius leaf phytochemicals. Emergence of R. obtusifolius seedlings was promoted by the presence of R. obtusifolius leaves. In contrast, emergence of other species seedlings was not promoted by R. obtusifolius leaves. We conclude that germination of R. obtusifolius seeds is facilitated in the presence of conspecifics, via water-soluble chemical exposure, and that recognizing these chemicals has adaptive value.     

猫儿山铁杉相邻植株冠层机械磨损对枝叶性状的影响

机械磨损是邻体植物冠层接壤区域的重要生态过程之一, 对枝叶生理和形态特征具有重要影响。但是, 当前非常缺乏邻体植物冠层机械磨损对枝叶功能性状影响特征和权衡机制的深入研究。该研究以广西猫儿山的铁杉(Tsuga chinensis)为对象, 通过比较邻体冠层间机械磨损区优势枝、劣势枝与非机械磨损区的叶面积、叶长、叶宽、叶厚、比叶面积、叶干物质含量、叶干质量、末端枝含水率和枝直径的差异, 分析枝叶功能性状在机械磨损影响下的变异和权衡关系。结果显示: 机械磨损显著影响邻体冠层叶干物质含量、比叶面积和叶干质量。具体而言, 机械磨损区优势枝叶干物质含量显著大于劣势枝和非机械磨损区, 优势枝比叶面积显著低于劣势枝和非机械磨损区, 劣势枝叶干质量显著低于优势枝和非机械磨损区。其次, 机械磨损对枝叶性状关系的影响格局不同。叶面积-叶长在机械磨损区优势枝、劣势枝和非机械磨损区间表现出一致的正向关系; 叶面积-叶宽、叶面积-叶干质量、叶宽-叶厚、叶厚-末端枝直径和叶长-叶宽仅在机械磨损区优势枝显著正相关; 叶面积-末端枝直径和末端枝直径-末端枝含水率仅在劣势枝显著负相关; 叶干物质含量-叶厚仅在劣势枝显著正相关。其余性状关系在机械磨损区优势枝、劣势枝和非机械磨损区均不显著。以上结果表明, 森林植物邻体间的冠层机械磨损可显著改变枝叶功能性状的权衡关系。     

DNA repair mechanisms in dividing and non-dividing cells

DNA damage created by endogenous or exogenous genotoxic agents can exist in multiple forms, and if allowed to persist, can promote genome instability and directly lead to various human diseases, particularly cancer, neurological abnormalities, immunodeficiency and premature aging. To avoid such deleterious outcomes, cells have evolved an array of DNA repair pathways, which carry out what is typically a multiple-step process to resolve specific DNA lesions and maintain genome integrity. To fully appreciate the biological contributions of the different DNA repair systems, one must keep in mind the cellular context within which they operate. For example, the human body is composed of non-dividing and dividing cell types, including, in the brain, neurons and glial cells. We describe herein the molecular mechanisms of the different DNA repair pathways, and review their roles in non-dividing and dividing cells, with an eye toward how these pathways may regulate the development of neurological disease.