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Abstract: The hippocampus has been hypothesized to function as a “spatial” or “cognitive” map, however, the functional cellular organization of the spatial map remains a mystery. The majority of electrophysiological studies, thus far, have supported the view of a random-type organization in the hippocampus. However, using immediate early genes (IEGs) as an indicator of neuronal activity, we recently observed a cluster-type organization of hippocampal principal cells, whereby a small number (∼4) of nearby cells were activated in rats exposed to a restricted part of an environment. To determine the fine structure of these clusters and to provide a 3D image of active hippocampal cells that encode for different parts of an environment, we established a functional mapping of IEGs zif268 and Homer1a, using in situ hybridization and 3D-reconstruction imaging methods. We found that, in rats exposed to the same location twice, there were significantly more double IEG-expressing cells, and the clusters of nearby cells were more “tightly” formed, in comparison to rats exposed to two different locations. We propose that spatial encoding recruits specific cell ensembles in the hippocampus and that with repeated exposure to the same place the ensembles become better organized to more accurately represent the “spatial map.” [Copyright &y& Elsevier]

This paper introduces methods for the detection of anisotropies which are caused by compression of regular 3D point patterns. Isotropy tests based on directional summary statistics and estimators for the compression factor are developed. Using simulated data, the dependence of the power of these methods on the intensity, the degree of regularity, and the compression strength is studied. Finally, our methods are applied to the point patterns of centers of air pores extracted from tomographic images of ice cores. This way the presence of anisotropies in the ice caused by the compression of the ice sheet and an increase of their strength with increasing depth are shown. [ABSTRACT FROM AUTHOR]

Simple Summary: A majority of breast cancer deaths are caused by aggressive molecular subtypes that are at high risk of progression. Patients with high-risk breast cancer commonly receive first-line systemic chemotherapy. Chemotherapy exerts direct cytotoxic effects on proliferating cancer cells. In addition, significant effects of chemotherapy are mediated through immune-boosting anti-cancer mechanisms that counteract immunosuppressive tumor-associated macrophages (TAMs). The aim of our study was to evaluate the potential prognostic value of the prevalence and the spatial localization of CD 163 + TAMs in tumor tissue from breast cancer patients treated with chemotherapy after surgery. We developed a novel algorithm that identifies CD 163 + TAMs in an objective manner and quantifies spatial interactions between CD 163 + TAMs and cancer cells using distance-based metrics. Our results demonstrate that close spatial proximity of CD 163 + TAMs to cancer cells and the average number of CD 163 + cells either directly adjacent to or within communicating distance of each cancer cell are independent predictors of unfavorable prognosis in breast cancer. Tumor-associated macrophages (TAMs) promote progression of breast cancer and other solid malignancies via immunosuppressive, pro-angiogenic and pro-metastatic effects. Tumor-promoting TAMs tend to express M2-like macrophage markers, including CD163. Histopathological assessments suggest that the density of CD163-positive TAMs within the tumor microenvironment is associated with reduced efficacy of chemotherapy and unfavorable prognosis. However, previous analyses have required research-oriented pathologists to visually enumerate CD 163 + TAMs, which is both laborious and subjective and hampers clinical implementation. Objective, operator-independent image analysis methods to quantify TAM-associated information are needed. In addition, since M2-like TAMs exert local effects on cancer cells through direct juxtacrine cell-to-cell interactions, paracrine signaling, and metabolic factors, we hypothesized that spatial metrics of adjacency of M2-like TAMs to breast cancer cells will have further information value. Immunofluorescence histo-cytometry of CD 163 + TAMs was performed retrospectively on tumor microarrays of 443 cases of invasive breast cancer from patients who subsequently received adjuvant chemotherapy. An objective and automated algorithm was developed to phenotype CD 163 + TAMs and calculate their density within the tumor stroma and derive several spatial metrics of interaction with cancer cells. Shorter progression-free survival was associated with a high density of CD 163 + TAMs, shorter median cancer-to-CD 163 + nearest neighbor distance, and a high number of either directly adjacent CD 163 + TAMs (within juxtacrine proximity <12 μm to cancer cells) or communicating CD 163 + TAMs (within paracrine communication distance <250 μm to cancer cells) after multivariable adjustment for clinical and pathological risk factors and correction for optimistic bias due to dichotomization. [ABSTRACT FROM AUTHOR]

Abstract: Birds frequently interrupt feeding to scan their surrounding environment. Usually an inverse correlation between scan rate and flock size exists. The ‘many-eyes’ hypothesis suggests that more eyes are able to detect a predator earlier. Due to the ‘dilution-effect’ animals in larger groups experience ‘safety in numbers’, while the ‘scramble competition’ hypothesis suggests that individuals reduce their vigilance in larger groups since they compete for a limited amount of scarce resources. Here, I induced competition in natural coot populations. Coots preferred feeding on grass and were occasionally fed by passers-by at the study sites. However, this resource was scarce and coots experienced additional food as a very limited resource. I sampled coots prior and after an experimental treatment with an additional food supply. Correlations between vigilance rate (number of scans during 1min of foraging), nearest neighbor distance and flock size existed before the experimental treatment but afterwards the correlation between vigilance and nearest neighbor distance faded. I found a significantly lower vigilance rate and nearest neighbor distance after inducing competition. This study provided experimental evidence for the ‘scramble competition’ hypothesis namely that individuals in groups lowered their vigilance when faced with competition for a limited amount of food resources given similar flock sizes. [Copyright &y& Elsevier]

Development of schooling behavior was studied in hatchery-reared Spanish mackerel Scomberomorus niphonius . Behavior of larvae and juveniles was video recorded from above in a 500-L rearing tank from day 7 up to day 23 at 1–2-day intervals. For the video image analysis, separation angle (SA), nearest neighbor distance (NND), separation swimming angle (SSA) and separation swimming index (SSI) were defined and measured. Schooling behavior developed from day 17 (15.9 mm in standard length (SL)) to day 19 (19.6 mm in SL). During this period, SA and NND decreased significantly, suggesting that they started aggregation forming parallel orientation. Separation swimming angle and SSI also decreased dramatically in this period. After day 17 and up to day 23 (26.6 mm in SL), these parameters of schooling behavior did not show much change, suggesting that schooling behavior of Spanish mackerel juveniles was completed by day 19. Relatively high values of NND (1.2–1.5-fold SL compared to < 1.0 in most other species) and SSI (0.6–0.8 compared to 0.15–0.29 in chub mackerel Scomber japonicus ) reflected a loose school as pelagic fish juveniles, and in this way they might have been minimizing the risk of cannibalism in this piscivorous species. [ABSTRACT FROM AUTHOR]

The tendency to aggregate with conspecifics is a common type of social behavior, and interspecific differences in degree of sociality may indicate that evolutionary changes in sociality have been shaped by past selection pressures. A pre-requisite for such evolutionary change is that the behavior in question has an additive genetic basis. I investigated parent-offspring resemblance in two characteristics of sociality (colony size and nearest neighbor distance) in the semi-colonial barn swallow Hirundo rustica. Heritability estimates of these phenotypic characters were statistically significant. Offspring that were transferred to foster nests as part of brood size manipulation or cross-fostering experiments resembled their original parents more than their foster parents with respect to sociality. There was little evidence of phenotypic characteristics of mothers being significantly related to colony size or nearest neighbor distance of their offspring. Maintenance of genetic variation in sociality in this species may be related to the facts that the relationship between reproductive success and colony size differs among years, and that individuals differing in phenotypic quality have different optimal colony sizes. [ABSTRACT FROM AUTHOR]

• Spatial patterns of living and dead small Norway spruce trees in two mountain forest reserves contribute to explain tree mortality and regeneration processes. • Local density of juvenile trees varies with topography and is driven by special site conditions. • Juvenile living (and dead) trees (tend to) cluster around large living (and dead) neighbors at short distances. • Clustering of tree regeneration decreases with increasing distance from large trees. Spatial patterns can reveal a lot about ecological processes, but our knowledge of the spatial ecology of tree regeneration at a fine scale is quite limited. Therefore, we studied the spatial patterns of living and dead small trees in two subalpine Norway spruce forest reserves in Switzerland (Scatlè and Bödmerenwald) using three types of analyses. First, we investigated the distances of small trees to the nearest large neighboring tree and, by using maximum distances as indicator, inferred the size of forest gaps, detecting mainly forest gaps of small size, although with two exceptions that were driven by large-scale disturbances. Second, we accounted for spatial inhomogeneity in the pattern of small and large trees (i.e., variations in local tree densities) by including environmental covariates in point pattern models. Latitude (within the forest reserve), elevation and aspect contributed significantly to explaining the density of living and dead small trees, and partly of living and dead large trees. Yet, the influence of these environmental covariates varied between the two reserves due to their different topography and peculiar site conditions. Third, we analyzed neighborhood interactions between small and large trees based on the vicinity and size of trees. In both forest reserves, small living trees were randomly dispersed around large dead trees over a broad range of distances and, at certain distances in one reserve, even dispersed away from them. Small living trees further showed clustering around large living trees at short distances and dispersion at large distances. Small dead trees featured mainly a random pattern, although with a tendency to cluster around large neighbors at short distances, irrespective whether these were living or dead. Yet, the weakening of clustering with increasing distances indicates that the influence of large trees on small trees varies with spatial scale and thus that these neighborhood interactions are scale-dependent. Overall, our study contributes to a better understanding of the spatial ecology of mortality in small trees and ultimately of tree regeneration processes and stand dynamics in mountain forests. [ABSTRACT FROM AUTHOR]

When heterospecific seabirds are part of a nesting colony, there may be less opportunity for conspecifics to come in direct contact with each other, resulting in lower intraspecific aggressiveness. To determine if individuals spend less time in aggressive behavior when nesting in conspecific rather than heterospecific groups, we compared the behavior of black skimmers ( Rhynchops niger) nesting with gull-billed terns ( Sterna nilotica) in three mixed species subcolonies to those of black skimmers in three single species subcolonies. In contrast to our predictions, black skimmers spent significantly less time in aggressive behaviors when nesting in single species subcolonies than when nesting with heterospecifics. Although skimmers in mixed species subcolonies tended to have more aggressive interactions with skimmers than terns, this may be a function of subcolony composition; the proportions of aggressive interactions with conspecifics were similar to the proportions of conspecifics in each subcolony. However, within the mixed species subcolonies, skimmers that nested nearer to terns were involved in aggressive interactions significantly less than skimmers that nested closer to conspecifics. Also, skimmers nested closer to their nearest neighbor when it was a gull-billed tern than when it was another skimmer. Regardless of which species they nested closest to, skimmers were more aggressive towards other skimmers than to terns within the mixed species subcolonies. Distance to nearest neighbor's nest did not differ significantly between the colony types, and did not seem to influence the duration of aggressive activity in the single species subcolonies. In the mixed species subcolonies, however, the time spent in aggressive behavior increased as the distance to nearest neighbor increased. It appears that of the several benefits that have been proposed of mixed species colonies, reduced time spent in conspecific aggression is not among them. However, within a mixed species colony, an individual can reduce time spent in aggressive interactions by nesting near heterospecifics. [ABSTRACT FROM AUTHOR]

Single molecule localization microscopy (SMLM) provided an unprecedented insight into the sub-nuclear organization of proteins and nucleic acids but apart from the nuclear envelope the role of the nuclear lipids in the functional organization of the cell nucleus was less studied. Nevertheless, nuclear lipids and specifically phosphatidylinositol phosphates (PIPs) play increasingly evident roles in gene expression. Therefore, here we provide the SMLM-based approach for the quantitative evaluation of the nuclear PIPs distribution while preserving the context of nuclear architecture. Specifically, on the example of phosphatidylinositol 4,5-bisphosphate (PIP2) we have:•Implemented and optimized the dual-color dSTORM imaging of nuclear PIP2.•Customized the Nearest Neighbor Distance analysis using ImageJ2 plug-in ThunderSTORM to quantitatively evaluate the spatial distribution of nuclear PIP2.•Developed an ImageJ2 tool for the visualization of the Nearest Neighbor Distance analysis results in cellulo .Our customization of the dual-color dSTORM imaging and quantitative analysis provide a tool that is independent of but complementary to the biochemical and lipidomic analyses of the nuclear PIPs. Contrary to the biochemical and lipidomic analyses, the advantage of our analysis is that it preserves the spatial context of the nuclear PIP distribution., Competing Interests: X The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)

The study aims to investigate spatial distribution pattern and age structure of wild Angelica sinensis in Gansu province.Ten plots each with an area of 100 m2 were set and the spatial coordinates of all wild A. sinensis individuals were measured within each plot. Based on plant individual mapping data,we explored the spatial distribution pattern and its differences between different life history stages of wild A. sinensis in Gansu province by using nearest neighbor distance statistics. Correlation analysis were carried out to explore the relationship between spatial aggregation degree and topographic factors. We also distinguished individuals to three life history stages( i.e. seedlings,adults and boltings) and then test the differences among/between them using nonparametric test.(1)We found that the dominant spatial distribution pattern of wild A. sinensis population in Gansu was aggregated distribution. There was no significant correlation between spatial aggregation degree of wild A. sinensis and altitude,slope and aspect. There was no significant difference between the average distance from seedlings to their nearest bolting individuals; the average distance from adult individuals to their nearest seedlings was significantly larger than the average distance from adult individuals to their nearest adult individuals; and the average distance from bolting individuals to their nearest adult individuals was significantly smaller than the average distance from bolting individuals to their nearest bolting individuals.(2)The age structure was showed as a declining population,characterized by less seedlings and bolting individuals,while more adult individuals within population. The population characteristics of wild A. sinensis,characterized by aggregated distribution pattern and senescent type of age structure,are disadvantage to its population development. The factors,such as habitat specialization,human activities and intraspecific competition,which shapes the current population characteristics,may increase the threatened status of wild A. sinensis. We suggest to strengthen the protection of wild A. sinensis.

Since the entropy is a popular randomness measure, there are many studies for the estimation of entropies for given random samples. In this paper, we propose an estimation method of the Rényi entropy of order α. Since the Rényi entropy of order α is a generalized entropy measure including the Shannon entropy as a special case, the proposed estimation method for Rényi entropy can detect any significant deviation of an ergodic stationary random source's output. It is shown that the expected test value of the proposed scheme is equivalent to the Rényi entropy of order α. After deriving a general representation of parameters of the proposed estimator, we discuss on the particular orders of Rényi entropy such as α → 1 , α = 1 / 2 , and α = 2 . Because the Rényi entropy of order 2 is the most popular one, we present an iterative estimation method for the application with stringent resource restrictions. [ABSTRACT FROM AUTHOR]

Modeling the random fiber distribution of a fiber-reinforced composite is of great importance for studying the progressive failure behavior of the material on the micro scale. In this paper, we develop a new algorithm for generating random representative volume elements (RVEs) with statistical equivalent fiber distribution against the actual material microstructure. The realistic statistical data is utilized as inputs of the new method, which is archived through implementation of the probability equations. Extensive statistical analysis is conducted to examine the capability of the proposed method and to compare it with existing methods. It is found that the proposed method presents a good match with experimental results in all aspects including the nearest neighbor distance, nearest neighbor orientation, Ripley's K function, and the radial distribution function. Finite element analysis is presented to predict the effective elastic properties of a carbon/epoxy composite, to validate the generated random representative volume elements, and to provide insights of the effect of fiber distribution on the elastic properties. The present algorithm is shown to be highly accurate and can be used to generate statistically equivalent RVEs for not only fiber-reinforced composites but also other materials such as foam materials and particle-reinforced composites.