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1. Integrating Data Across Misaligned Spatial Units

   https://doi.org/10.1017/pan.2023.5  

   Zhukov, Yuri M.; Byers, Jason S.; Davidson, Marty A.; Kollman, Ken (January 2024, Political Analysis)

   Abstract Theoretical units of interest often do not align with the spatial units at which data are available. This problem is pervasive in political science, particularly in subnational empirical research that requires integrating data across incompatible geographic units (e.g., administrative areas, electoral constituencies, and grid cells). Overcoming this challenge requires researchers not only to align the scale of empirical and theoretical units, but also to understand the consequences of this change of support for measurement error and statistical inference. We show how the accuracy of transformed values and the estimation of regression coefficients depend on the degree of nesting (i.e., whether units fall completely and neatly inside each other) and on the relative scale of source and destination units (i.e., aggregation, disaggregation, and hybrid). We introduce simple, nonparametric measures of relative nesting and scale, asex anteindicators of spatial transformation complexity and error susceptibility. Using election data and Monte Carlo simulations, we show that these measures are strongly predictive of transformation quality across multiple change-of-support methods. We propose several validation procedures and provide open-source software to make transformation options more accessible, customizable, and intuitive. 

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2. Tools for Integrating Data by Complex, Dynamic Categories

   https://doi.org/10.1002/pra2.1145  

   Hruschka, Daniel; Cheng, Yi‐Yun; Hsiao, I‐Han; Bischoff, Robert; Peeples, Matthew; Kasi, Harsha; Huang, Cindy (October 2024, Proceedings of the Association for Information Science and Technology)

   ABSTRACT A key challenge in conducting comparative analyses across social units, such as religions, ethnicities, or cultures, is that data on these units is often encoded in distinct and incompatible formats across diverse datasets. This can involve simple differences in the variables and values used to encode these units (e.g., Roman Catholic is V130 = 1 vs. Q98A = 2 in two different datasets) or differences in the resolutions at which units are encoded (Maya vs. Kaqchikel Maya). These disparate encodings can create substantial challenges for the efficiency and transparency of data syntheses across diverse datasets. We introduce a user‐friendly set of tools to help users translate four kinds of categories (religion, ethnicity, language, and subdistrict) across multiple, external datasets. We outline the platform's key functions and current progress, as well as long‐range goals for the platform. 

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3. Exploring the association of Brownfield remediation status with socioeconomic conditions in Wayne County, MI

   https://doi.org/10.1007/s11356-023-26666-2  

   O’Leary, Brendan F.; Hill, Alex B.; Linn, Colleen; Lu, Mei; Miller, Carol J.; Newman, Andrew; Sperone, F. Gianluca; Zhang, Qiong (May 2023, Environmental Science and Pollution Research)

   Abstract Urban neighborhoods with locations of environmental contamination, known as brownfields, impact entire neighborhoods, but corrective environmental remedial action on brownfields is often tracked on an individual property basis, neglecting the larger neighborhood-level impact. This study addresses this impact by examining spatial differences between brownfields with unmitigated environmental concerns (open site) and sites that are considered fully mitigated or closed in urban neighborhoods (closed site) on the US census tract scale in Wayne County, MI. Michigan’s Department of Environment, Great Lakes, and Energy’s leaking underground storage tank (LUST) database provided brownfield information for Wayne County. Local indicators of spatial association (LISA) produced maps of spatial clustering and outliers. A McNemar’s test demonstrated significant discordances in LISA categories between LUST open and closed sites ( p  < 0.001). Geographically weighted regressions (GWR) evaluated the association between open and closed site spatial density (open-closed) with socioeconomic variables (population density, proportion of White or Black residents, proportion of college educated populations, the percentage of owner-occupied units, vacant units, rented units, and median household value). Final multivariate GWR showed that population density, being Black, college education, vacant units, and renter occupied units were significantly associated ( p  < 0.05) with open-closed, and that those associations varied across Wayne County. Increases in Black population was associated with increased open-closed. Increases in vacant units, renter-occupied units, and college education were associated with decreased open-closed. These results provide input for environmental justice research to identify inequalities and discover the distribution of environmental hazards among urban neighborhoods. 

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4. Distinct attentional characteristics of neurons with visual feature coding in the primate brain

   https://doi.org/10.1126/sciadv.adq0332  

   Zhang, Jie; Cao, Runnan; Zhu, Xiaocang; Zhou, Huihui; Wang, Shuo (March 2025, Science Advances)

   Visual attention and object recognition are two critical cognitive functions that shape our perception of the world. While these neural processes converge in the temporal cortex, the nature of their interactions remains largely unclear. Here, we systematically investigated the interplay between visual attention and stimulus feature coding by training macaques to perform a free-gaze visual search task with natural stimuli. Recording from a large number of units across multiple brain areas, we found that units exhibiting visual feature coding showed stronger attentional modulation of responses and spike–local field potential coherence than units without feature coding. Across brain areas, attention directed toward search targets enhanced the neuronal pattern separation of stimuli, with this enhancement more pronounced for units encoding visual features. Together, our results suggest a complex interplay between visual feature and attention coding in the primate brain, likely driven by interactions between brain areas engaged in these processes. 

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5. A natural ANI gap that can define intra-species units of bacteriophages and other viruses

   https://doi.org/10.1128/mbio.01536-24  

   Aldeguer-Riquelme, Borja; Conrad, Roth E; Antón, Josefa; Rossello-Mora, Ramon; Konstantinidis, Konstantinos T (August 2024, mBio)

   Cooper, Vaughn S (Ed.)

   ABSTRACT Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage (Caudoviricetes) species revealed a region of low frequency of ANI values around 99.2%–99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars. IMPORTANCEViral species are composed of an ensemble of intra-species variants whose individual dynamics may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of mostly bacteriophage genomes, we show that there is a widely distributed natural gap in whole-genome average nucleotide identity values in most, but not all, of these species that can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies. 

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