Neighborhood Composition Research Articles (Page 1)

Gene co-expression networks based on RNA abundance have identified genes with shared biological functions, common regulatory elements, and physical interactions among their protein products. Although thousands of ribosome profiling datasets are publicly available, they have not been leveraged to construct networks to characterize translation efficiency covariation (TEC) to quantify how translation of different transcripts co-varies across conditions. We construct and analyze a human TEC network, revealing topological and functional properties distinct from RNA co-expression networks. The TEC network displays modular structure, small-world characteristics, and rich-club organization but differs substantially in node connectivity and neighborhood composition. Comparative analyses show that genes such as PKM, which are central in the TEC network due to their role in translational regulation, are peripheral in RNA co-expression networks. Tissue-specific TEC networks further uncover context-dependent translation patterns. These results suggest that TEC networks provide a complementary framework for understanding gene regulation. The code for this study is archived on https://zenodo.org/records/17275939 and publicly available at https://github.com/CenikLab/TEC-Network-Analyses. The associated data can be accessed at https://zenodo.org/records/17275970.

PURPOSE Lack of race- and age-diversity in clinical trials adversely affects generalizability of trial results and equity of trial access. Research on barriers to representative accrual has focused on patient-level factors. We aimed to define site-level factors affecting the diversity of accrual to a multicenter clinical trial. METHODS Alliance 191901 (GETSET) is a national randomized controlled trial testing interventions to promote breast cancer endocrine therapy adherence, which oversamples Black women and those under age 50 years at 30% thresholds. A secondary study objective is to examine site-level factors associated with accrual of Black and younger participants. At 50% accrual to the parent study, we performed prespecified analyses of association between site characteristics (region, neighborhood racial composition, Alliance membership type, number of recent accruals to cooperative research group trials) and the proportion of Black patients and younger patients accrued. We also examined trajectories of accrual over time for race- and age-specified subgroups. RESULTS The analysis included 124 sites. Among 590 participants, 9.7% were Black, and 22.4% were age <50 years. Neither site type nor historical accrual volume was associated with Black participant recruitment. Southern sites recruited higher proportions of Black participants (19.0% v 7.3% for West, P < .001). Neighborhood racial composition was positively associated with recruitment of Black participants (16.2% at sites from highest Black composition v 1.4% in lowest, P < .01). Recruitment trajectories of Black participants were slower than target rates, whereas those among non-Black participants were faster. CONCLUSION Neighborhood composition and geographic region were predictors of proportions of Black participants accrued to A191901 sites, but site type and historical accrual volume were not. When trials must limit site selection, identifying sites based on neighborhood composition and geography may be an appropriate tool for increasing trial diversity.

Characterizing the Consumer Food Environment of Dollar Stores and Exploring Differences by Neighborhood Racial Composition.

While biodiversity has been widely shown to promote tree growth in forests, the effects of diversity at the cellular level remain unclear. This hinders a deeper understanding of how diversity influences wood production. Here, we investigated the influence of neighbourhood composition on wood formation processes at the cellular level. We found that neighbourhood diversity significantly increased both the number and wall thickness of xylem fibre cells generated during the growing season, resulting in enhanced biomass growth. Compared with monocultures, woody biomass production at the highest neighbourhood species richness (NSR = 4) increased by an average of 19%-29% across the studied species. Neighbourhood diversity also led to a shift in cambium phenology. An earlier start of cambium activity and an extended duration of wall thickening were observed under higher tree species richness. Furthermore, neighbourhood competition decreased vessel area, which was closely associated with cell wall thickness. Our study offers a microscopic perspective on the effects of diversity and competition on wood formation and woody biomass production. We highlight that the contribution of diversity to woody biomass accumulation may be underestimated when variation in cell wall thickness is ignored.

Concentrated Affluence and Deprivation and Spatial Distribution of Firearm Violence: Racial/Ethnic Disparities Across Urban Neighborhoods in the U.S.

ABSTRACT Previous studies have exhaustedly tested whether neighborhood migrant concentration affects migrants’ intergroup relations but rarely explored how such neighborhood effects may vary by generations. The residual neighborhood thesis suggests that the neighborhood is more important for the elderly since they cannot access broader social networks due to their limited mobility or retirement. However, this may not apply to the old-generation internal migrants, who are usually physically unrestricted and still work. Drawing upon semi-structured interviews with migrants in Beijing, this study investigates the role of neighborhood in the development of new- and old-generation migrants’ intergroup relations in urban China. The results indicate that the neighborhood is more relevant to old-generation migrants than to new-generation migrants. Living in less migrant-concentrated neighborhoods helps old-generation migrants foster intergroup relations. Many old-generation migrants reach the later life stage with less financial pressure and lower work commitment, so they engage more in neighboring and are more affected by neighborhood composition. Moreover, they are more willing to develop neighborly relations as they grew up before or shortly after market-oriented reforms. In contrast to the residual neighborhood thesis, this paper shows that old-generation migrants may actively invest in neighboring rather than being confined to their neighborhoods.

Patch dynamics in ecology have been useful for understanding the functioning of diverse biomes, focusing primarily on how processes maintain the vegetation mosaic. However, less is known about how the mosaic structure influences processes within each patch, completing the pattern–process feedback. We present a conceptual framework exploring the importance of neighborhood structure and composition on patch dynamics. We described the neighborhood for each focal patch based on the neighbor's distance (Voronoi area), the size of the neighbors, and the neighborhood species composition. We tested this model in grazed and ungrazed Patagonian steppes, where mosaic structure and patch dynamics are associated to shrub life stages. Using field data spanning 26 years, we evaluated how mosaic attributes influence the establishment, growth and mortality of long‐lived dominant shrub species, while considering climate variability and the effect of grazing by domestic livestock. Our results show that larger neighborhood areas and lower intraspecific ratios reduced shrub establishment and growth, while increasing mortality. Therefore, the neighborhood structure and composition alter patch dynamics. Grazing had species‐specific effects on establishment and growth but did not alter the relationship between neighborhood variables and focal shrubs. Our results demonstrate that shrub population dynamics – and thus patch dynamics – are influenced by the structure and composition of the vegetation mosaic. This long‐term study enhances our understanding of the mosaic maintenance feedback involving patterns and processes in ecosystems where woody species play a significant role in its dynamics, and in a context of increasing environmental pressures.

e16029 Background: Immune Checkpoint Blockade (ICB) is established in many solid cancers often lacking robust biomarkers for response stratification. We explored the predictive role of neutrophil and lymphocyte counts as well as the immune-cell composition of the tumor neighborhood in patients with solid tumors. Methods: Clinical data, including neutrophil-to-lymphocyte ratio (NLR), from seven prospective trials investigating ICB in solid tumors were pooled (NCT03416244, NCT03409848, NCT03620123, NCT03193931, NCT03044626, NCT02917772 and NCT03219775). Tumor biopsies and peripheral blood samples were collected from 21 patients with esophageal squamous cell carcinoma (ESCC) before ICB (Nivolumab +/- Ipilimumab; NCT03416244). Tumor sections were stained by a 40-plex immunofluorescence panel (Akoya PhenoCycler) to examine spatial tumor-immune interactions associated with clinical outcomes as overall (OS) or progression-free survival (PFS) and best overall response (RECIST version 1.1). Peripheral blood mononuclear cells (PBMCs) were isolated and profiled by 10x single-cell RNA-sequencing to compare cellular (sub)types between ICB responders and non-responders. Results: Higher pretreatment NLR, defined as NLR > 3, predicted poorer OS (HR 0.4; 95% CI 0.30-0.53; p < 0.0001) in multivariate analysis of 693 patients, as well as worse PFS (HR 0.55; 95% CI 0.43-0.71; p < 0.0001), overall response rate (OR 2.01; 95% CI 1.32-3.05; p = 0.0012) and disease control rate (OR 2.31; 95% CI 1.34-3.99; p = 0.0026). Spatial analysis of ESCC patients´ tissue discovered the enrichment of a neutrophil-CD4 + regulatory T cell neighborhood in the tumor-adjacent tissue of ICB non-responders (p < 0.05, n = 6), while intratumoral macrophages, CD4 + /CD8 + T cells and dendritic cells were more abundant in responders (p = 0.0245, n = 9). scRNA sequencing of PBMCs validated correlation of T cell abundance with better survival (p < 0.05, responders vs non-responders), while myeloid cell abundance was reversely correlated (p < 0.05, responders vs non-responders). The myeloid cells showed significant differential expression of G0S2, BASP1, CXCL8, LYN , confirming prominent neutrophil presence in non-responders. Conclusions: Pro-tumoral inflammation and a lack of anti-tumoral immune response, reflected by a higher NLR in peripheral blood, and a neutrophil-CD4 + regulatory T cell neighborhood in the tumor-adjacent tissue can be used to predict ICB response in solid cancers, such as ESCC. A deeper understanding of underlying mechanisms of neutrophil activation in ICB might help to stratify patients in the future.

Cities worldwide increasingly adopt social resilience strategies, yet their implementation often obscures real drivers of urban renovation with ambiguous indicators. This study examines Rotterdam’s 'balanced neighbourhoods' policy, based on property values, and its claimed contribution to urban social resilience. Using empirical data and structural equation modelling, we investigate how housing value mix affects social cohesion and informal support in 'balanced neighbourhood' configurations. Only 2.1% of possible configurations fit Rotterdam’s urban policy claims, and even those yield counterproductive associations. We argue that the ambiguous definition of 'balanced neighbourhoods' obscures policy goals, allowing areas in Rotterdam North to meet 'balance' criteria without reflecting the municipality’s long-term composition targets, while the South—dominated by social housing—faces demolition. Our study highlights the need for more nuanced measures of resilience and calls for shifting from interventions that alter the physical composition of neighbourhoods to enhancing social cohesion as a key factor promoting resilient actions.

Effects of Neighborhood Composition and the COVID-19 Pandemic on Emergency Department Visits for Asthma

BackgroundGovernments worldwide have implemented various interventions to improve the healthiness of food offered by out-of-home outlets. However, there is limited evidence on whether healthier menus would influence individual dietary behaviours and quality. In this cross-sectional study, we investigated associations between different measures of the neighbourhood out-of-home food environment, incorporating menu healthiness, and out-of-home meal purchasing and diet quality.MethodsWe used a sample of 3,481 adults in Great Britain (GB) with valid home postcodes from the 2021 International Food Policy Study. We linked this sample to a national database of food outlet geographical locations to characterise individuals’ exposure to the out-of-home food environment. The exposure metrics included menu healthiness scores, availability, proximity, and relative composition of out-of-home food outlets in various neighbourhood buffers around the home (i.e., 500 - 1600 m). Outcomes considered were out-of-home meal consumption and overall diet quality. Using multiverse analyses, where multiple reasonable analytical choices can be tested, we investigated the associations between different exposure measures and these outcomes.ResultsGB adults had access to an average of 97 (95% CI 91, 104) out-of-home food outlets within 1600 m of their homes. The number of both healthier and less healthy out-of-home food outlets was positively associated with the number of meals purchased out-of-home across all neighbourhood buffers, e.g., every 10 additional less healthy out-of-home food outlets within 500 m of the home corresponded to a 6% (95% CI = 2, 11) increase in the frequency of out-of-home meal purchases in the previous week. Proximity, relative composition, and menu healthiness of neighbourhood out-of-home outlets were not associated with out-of-home meal purchase frequency after adjusting for multiple comparisons. There were no consistent associations between out-of-home food environment exposures and diet quality.ConclusionThe only aspect of the neighbourhood out-of-home food environment associated with out-of-home meal purchase frequency was the number of out-of-home food outlets. Menu healthiness of out-of-home food outlets was not associated with how often people purchased out-of-home meals or overall diet quality. Interventions focusing on mitigating the proliferation of out-of-home food outlets may be more effective in changing individual dietary behaviour than those focusing on food served.

The effect of neighborhood composition on ethnic discrimination in the labor market

Exploring the impact of the built environment on street vitality is essential for enhancing urban public spaces. Using the central urban area of Nanchang City as a case study, multi-temporal street vitality is measured with popula-tion heat data. A multi-dimensional built environment indicator system is de-veloped based on macro-scale neighborhood composition and micro-scale street characteristics, using street view imagery, POI data, and OSM road network data. The spatiotemporal variations in the influence of built envi-ronment factors on street vitality are examined through a multiscale geo-graphically weighted regression (MGWR) model. Results reveal that: (1) Street vitality is most prominent between 10:00 and 20:00, with a spatial pattern of "eastern core, western belt, and multiple clustered points" across all time periods. (2) Macro-scale neighborhood composition generally has a stronger impact on street vitality than micro-scale street characteristics. (3) The influence of various built environment factors on street vitality exhibits significant spatiotemporal heterogeneity. Factors like sky view openness and parking lot density show robust spatiotemporal variations, while con-nectivity, facility densities, walkability, street ratio, and green view index have localized spatiotemporal effects.

Abiotic environments and biotic neighbourhoods interact to influence plant growth and community assembly. However, the nature of this interaction depends very much on how biotic neighbourhoods are measured, including their relatedness to focal plants. In a tropical seasonal rainforest, we examine the growth of a dominant canopy species in response to environmental factors, the densities and relatedness of conspecific and heterospecific neighbours, and their interactions. We find significant environmental effects and conspecific negative density dependence on growth. Furthermore, conspecific neighbour density has stronger negative effects on growth under high light and soil water resource levels, but weaker negative effects under low light and soil water resource levels. In addition, more closely related heterospecifics in the neighbourhood have negative effects on growth under high soil phosphorus availability, but positive effects under low soil phosphorus availability. In contrast, more closely related conspecifics in the neighbourhood have negative effects on growth under low soil potassium availability, but positive effects under high soil potassium availability. Our study emphasizes the importance of both intra- and interspecific neighbourhood composition and their interactions with resource levels for understanding tree growth. This enhances our understanding of the complex processes in community assembly and species coexistence within forest communities.

Given the successful graft-versus-leukemia cell treatment effect observed with allogeneic hematopoietic stem cell transplant for patients with refractory or relapsed acute myeloid leukemia, immunotherapies have also been investigated in the nontransplant setting. Here, we use a multi-omic approach to investigate spatiotemporal interactions in the bone marrow niche between leukemia cells and immune cells in patients with refractory or relapsed acute myeloid leukemia treated with a combination of the immune checkpoint inhibitor pembrolizumab and hypomethylating agent decitabine. We derived precise segmentation data by extensively training nuclear and membrane cell segmentation models, which enabled accurate transcript assignment and deep learning-feature-based image analysis. To overcome read-depth limitations, we integrated the single-cell RNA sequencing data with single-cell-resolution spatial transcriptomic data from the same sample. Quantifying cell-cell distances between cell edges rather than cell centroids allowed us to conduct a more accurate downstream analysis of the tumor microenvironment, revealing that multiple cell types of interest had global enrichment or local enrichment proximal to leukemia cells after pembrolizumab treatment, which could be associated with their clinical responses. Furthermore, ligand-receptor analysis indicated a potential increase in TWEAK signaling between leukemia cells and immune cells after pembrolizumab treatment.

Tumor-infiltrating lymphocytes are considered clinically beneficial in breast cancer, but the significance of natural killer (NK) cells is less well characterized. As increasing evidence has demonstrated that the spatial organization of immune cells in tumor microenvironments is a significant parameter for impacting disease progression as well as therapeutic responses, an improved understanding of tumor-infiltrating NK cells and their location within tumor contextures is needed to improve the design of effective NK cell-based therapies. In this study, we developed a multiplex immunohistochemistry (mIHC) antibody panel designed to quantitatively interrogate leukocyte lineages, focusing on NK cells and their phenotypes, in two independent breast cancer patient cohorts (n = 26 and n = 30). Owing to the clinical evidence supporting a significant role for NK cells in HER2+ breast cancer in mediating responses to Trastuzumab, we further evaluated HER2- and HER2+ specimens separately. Consistent with literature, we found that CD3+ T cells were the dominant leukocyte subset across breast cancer specimens. In comparison, NK cells, identified by CD56 or NKp46 expression, were scarce in all specimens with low granzyme B expression indicating reduced cytotoxic functionality. Whereas NK cell density and phenotype did not appear to be influenced by HER2 status, spatial analysis revealed distinct NK cells phenotypes regarding their proximity to neoplastic tumor cells that associated with HER2 status. Spatial cellular neighborhood analysis revealed multiple unique neighborhood compositions surrounding NK cells, where NK cells from HER2- tumors were more frequently found proximal to neoplastic tumor cells, whereas NK cells from HER2+ tumors were instead more frequently found proximal to CD3+ T cells. This study establishes the utility of quantitative mIHC to evaluate NK cells at the single-cell spatial proteomics level and illustrates how spatial characteristics of NK cell neighborhoods vary within the context of HER2- and HER2+ breast cancers.

PurposeThe prevalence of obesity, a crucial risk factor for breast cancer, is markedly higher among Hispanic women. The interaction between ethnic enclaves and neighborhood socioeconomic status (SES) as a determinant of this disparity warrants further research. We aimed to identify neighborhood profiles based on ethnic enclaves and socioeconomic status to evaluate the association with obesity among Hispanic women in the metropolitan Chicago region.MethodsWe used a convenience sample of 24,884 Hispanic women over age 40 who obtained breast imaging from the largest healthcare organization in Chicago between 2010 and 2017. We conducted LPA to characterize neighborhood composition based on tract indicators of ethnic enclaves, disadvantage, and affluence. Multivariate linear and multinomial logistic regression models were used to evaluate the association of neighborhood profiles with BMI.ResultsThe LPA model identified four latent profiles, labeled based on their most significant characteristic as “middling,” “disadvantage” “ethnic enclaves,” and “affluent”. Close to 50% of women in the disadvantage profile were obese and obese class II. Women in the disadvantage profile had the highest relative risk of being obese II (OR: 2.74 CI 95% 2.23, 3.36), compared to women in the middling profile. Women in the ethnic enclave and affluent profile were positively and negatively associated with obesity, respectively.DiscussionUsing LPA to group individuals according to their combined traits provides empirical evidence to strengthen our understanding of how neighborhoods influence obesity in Hispanic women. The study findings suggest that ethnic enclaves, that are also disadvantage, are associated with obesity in Hispanic women.

The composition of a plant's neighbourhood shapes its competitive interactions. Neighbours may be related individuals due to limited seed dispersal or clonal growth, so that the ability to recognize and respond to the presence of kin is beneficial. Here, we ask whether plants plastically adjust their floral and clonal allocation in response to their neighbour's identity. In a species that reproduces both sexually and clonally, we test the following predictions in response to neighbouring kin: (i) a reduction in floral display will occur to minimize costly floral structures and pollinator competition, as well as to mitigate inbreeding; and (ii) a decrease in clonality will occur to minimize resource competition and overcrowding among kin. We grew focal individuals of Mimulus guttatus (syn. Erythranthe guttata) surrounded by neighbours of varying relatedness (non-kin, outcross siblings or self siblings) and measured a suite of vegetative, floral and clonal traits. Consistent with our predictions, focal plants reduced floral and clonal allocation in the presence of kin. Moreover, focal plants increased their floral and clonal allocation when surrounded by non-kin neighbours that were high-performing. Together, we demonstrate a clear and predictable response to kin, which has general implications for the structure and function of plant neighbourhoods.

We incorporate the endogenous feedback loop at the core of the seminal Schelling (1969) model of segregation into a dynamic model of neighborhood choice and use it to study the forces that shaped racial and income segregation in the San Francisco Bay area from 1990 to 2004. Such an analysis requires causal identification of households' responses to the socioeconomic composition of their neighbors. We achieve this with novel instrumental variables that can be rationalized with a dynamic choice model with frictions. These IVs have potentially broad application: studying sorting along any observable demographic dimension, estimating the effects of neighborhood composition on outcomes such as house prices, or identifying other network externalities. We find that discriminatory (taste‐based and statistical) sorting by race and by income is widespread and complex: almost all households respond positively to similar neighbors and negatively to different neighbors, although at varying degrees of intensity. In spite of these discriminatory responses, frictions—moving costs and uncertainty—mitigate their impact on segregation. This implies that sorting on the basis of other neighborhood amenities may have a large impact on segregation and may justify place‐based desegregation policies. Because of these frictions, there is also scope for desegregation policies based on the reallocation of households to succeed.

Livestock grazing in North American rangelands has the capacity both to promote and control the spread of undesirable plant species. Within California annual grasslands, desirable forage peaks in spring and supports considerable livestock grazing. However, spring grazing appears to promote the invasion and spread of two late-season and unpalatable non-native annual grasses, Aegilops triuncialis and Elymus caput-medusae. We tested the hypothesis that grazing reduces the leaf area and water use of early-spring annuals, thus increasing residual soil water availability for the late-season species. We used grazing-exclosure experiments to examine the interactive effects of simulated grazing (i.e., clipping) and competition on soil moisture availability, and on physiological, phenological, and demographic responses. When compared to unclipped controls, spring clipping significantly increased late-season volumetric soil moisture by 13–24% in the top 7 cm of soil, and 8–11% in the top 20 cm of soil (p < 0.05, all sites), which supported significantly higher rates of stomatal conductance (73–100% increase) in both late-season invading species (p < 0.01, all sites). Flowering was significantly delayed in clipped plots for both invader species suggesting these species experienced a longer growing period (p < 0.0001 in all cases). In competition plots, the effects of clipping on the demographic response depended on neighborhood composition. When invaders were grown together, no significant effect of clipping on survival or reproduction was detected in either invader. However, when growing in mixtures with early-spring forage annuals or native species, clipping increased survival and reproductive output in late-season invader species by 3-fold. We suggest that strategies for arresting or reversing the dominance of these late-season invasive annuals must recognize the influence of current biomass management strategies on late-season resource availability.