IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.

A Scoping Review of Self-Care Within the Context of Obesity-Related Outcomes Among Faith Leaders.

OBJECTIVE: Faith leaders often serve as health-related role models yet many struggle with obesity and self-care engagement. The purpose of this scoping review was to examine how the faith leader literature has defined self-care and examined obesity and obesity-related chronic disease. DATA SOURCE: Studies were identified through database (eg, PubMed, CINAHL, PsycINFO), backward, and grey literature (eg, dissertations) searches. INCLUSION/EXCLUSION CRITERIA: Studies published in English with participants who were 18 years or older and examined leaders across all faiths. Studies also included an examination of self-care behaviors among faith leaders within the context of obesity or obesity-related chronic diseases. DATA EXTRACTION/SYNTHESIS: Data synthesis was qualitative and informed by the six-step framework developed by Arksey and O'Malley (2005) as well as updated recommendations by Daudt et al (2013). Of the 418 studies identified and screened, 20 met the eligibility criteria. RESULTS: Studies were primarily cross-sectional and participants Christian faith-leaders in the US. Most studies did not define self-care or incorporate theory, but focused on vegetarian diets and physical activity engagement. Other self-care related behaviors (eg, sleep, days off), some unique to faith leaders (eg, sabbatical), were included but not systematically. CONCLUSIONS: Research with more diverse faith leaders and that uses theory is needed to guide development of strategies for engaging this population in self-care to reduce obesity and related chronic diseases.

Taylor's law for exponentially growing local populations linked by migration.

We consider the dynamics of a collection of n>1 populations in which each population has its own rate of growth or decay, fixed in continuous time, and migrants may flow from one population to another over a fixed network, at a rate, fixed over time, times the size of the sending population. This model is represented by an ordinary linear differential equation of dimension n with constant coefficients arrayed in an essentially nonnegative matrix. This paper identifies conditions on the parameters of the model (specifically, conditions on the eigenvalues and eigenvectors) under which the variance of the n population sizes at a given time is asymptotically (as time increases) proportional to a power of the mean of the population sizes at that given time. A power-law variance function is known in ecology as Taylor's Law and in physics as fluctuation scaling. Among other results, we show that Taylor's Law holds asymptotically, with variance asymptotically proportional to the mean squared, on an open dense subset of the class of models considered here.

Fit with Faith: An Exploratory Study Examining a Behavior Change Intervention for African-American Clergy and Their Spouses.

Fit with Faith is a 10-week, diet, physical activity, and stress reduction intervention for African-American clergy and spouses, which included: meetings, phone calls, a behavior tracking app. Survey, 24-h recall, accelerometer, anthropometric, and blood pressure data were collected. Wilcoxon signed ranked tests were used for analyses. In this one-arm study, clergy and spouses (n = 20) attended most meetings and calls, but only half posted daily goals or tracked behaviors using the app. Spouses' body mass index (BMI) decreased and physical activity self-regulation cognitive scores increased pre-post intervention. Statistically significant changes in BMI, systolic blood pressure, and self-regulations scores also were seen among younger (< 51 years) participants (n = 8). As positive changes were seen mostly among women and younger participants, more research is needed on how to engage all clergy in behavior change programs.

The persistent homology of genealogical networks.

Genealogical networks (i.e. family trees) are of growing interest, with the largest known data sets now including well over one billion individuals. Interest in family history also supports an 8.5 billion dollar industry whose size is projected to double within 7 years [FutureWise report HC-1137]. Yet little mathematical attention has been paid to the complex network properties of genealogical networks, especially at large scales. The structure of genealogical networks is of particular interest due to the practice of forming unions, e.g. marriages, that are typically well outside one's immediate family. In most other networks, including other social networks, no equivalent restriction exists on the distance at which relationships form. To study the effect this has on genealogical networks we use persistent homology to identify and compare the structure of 101 genealogical and 31 other social networks. Specifically, we introduce the notion of a network's persistence curve, which encodes the network's set of persistence intervals. We find that the persistence curves of genealogical networks have a distinct structure when compared to other social networks. This difference in structure also extends to subnetworks of genealogical and social networks suggesting that, even with incomplete data, persistent homology can be used to meaningfully analyze genealogical networks. Here we also describe how concepts from genealogical networks, such as common ancestor cycles, are represented using persistent homology. We expect that persistent homology tools will become increasingly important in genealogical exploration as popular interest in ancestry research continues to expand.

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.

Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

Using social networks to improve team transition prediction in professional sports.

We examine whether social data can be used to predict how members of Major League Baseball (MLB) and members of the National Basketball Association (NBA) transition between teams during their career. We find that incorporating social data into various machine learning algorithms substantially improves the algorithms' ability to correctly determine these transitions in the NBA but only marginally in MLB. We also measure the extent to which player performance and team fitness data can be used to predict transitions between teams. This data, however, only slightly improves our predictions for players for both basketball and baseball players. We also consider whether social, performance, and team fitness data can be used to infer past transitions. Here we find that social data significantly improves our inference accuracy in both the NBA and MLB but player performance and team fitness data again does little to improve this score.

Integration of software tools for integrative modeling of biomolecular systems.

Integrative modeling computes a model based on varied types of input information, be it from experiments or prior models. Often, a type of input information will be best handled by a specific modeling software package. In such a case, we desire to integrate our integrative modeling software package, Integrative Modeling Platform (IMP), with software specialized to the computational demands of the modeling problem at hand. After several attempts, however, we have concluded that even in collaboration with the software's developers, integration is either impractical or impossible. The reasons for the intractability of integration include software incompatibilities, differing modeling logic, the costs of collaboration, and academic incentives. In the integrative modeling software ecosystem, several large modeling packages exist with often redundant tools. We reason, therefore, that the other development groups have similarly concluded that the benefit of integration does not justify the cost. As a result, modelers are often restricted to the set of tools within a single software package. The inability to integrate tools from distinct software negatively impacts the quality of the models and the efficiency of the modeling. As the complexity of modeling problems grows, we seek to galvanize developers and modelers to consider the long-term benefit that software interoperability yields. In this article, we formulate a demonstrative set of software standards for implementing a model search using tools from independent software packages and discuss our efforts to integrate IMP and the crystallography suite Phenix within the Bayesian modeling framework.

New system for archiving integrative structures.

Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined. A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, PDB-Dev ensures that the results of integrative structure determinations are freely accessible to everyone.

Impact of Menopause and Body Composition Status on Dyslipidemia in Women.

Objective: The aim of this study was to identify the effects of menopausal and body composition statuses on measures of total and regional body composition and dyslipidemia in women. Methods: Sedentary, non-smoking women (N = 212), not currently treated for dyslipidemia were grouped based on 2 categories: (1) menstrual status: premenopausal or postmenopausal and (2) body composition status: normal weight (NW; BMI < 25 kg/m² and body fat (BF) < 36%), normal weight obese (NWO; BMI < 25 kg/m² and BF > 36%), or obese (BMI > 25 kg/m² and BF > 36%), to determine differences in total and regional body composition and measures of lipid and lipoprotein-cholesterol concentrations. Results: Overall, a greater prevalence of NWO was observed in postmenopausal versus premenopausal women. Being postmenopausal was associated with higher TC, LDL-C, non-HDL-C, HDL-C, and HDL3-C. Premenopausal NWO women had elevated LDL-C and VLDL-C comparable to obese women. Postmenopausal NWO women had elevated Tg and VLDL-C and lower HDL-C similar to obese women. Conclusions: Menopausal status was not associated with differences in fat distribution, however, the age-related differences in lipids and lipoproteins appear to be due to a difference in menopausal status exacerbated in women who are NWO.

Strategies for Designing Clergy and Spouse Obesity-Related Programs.

PURPOSE: Clergy have influence on the health of congregations and communities yet struggle with health behaviors. Interventions tailored to their occupation-specific demands and unique needs may provide a solution. Qualitative methods were used to identify opportunities and resources for the development of an effective obesity-related program for clergy. APPROACH: Ninety-minute focus groups were held with clergy (3 groups) and spouses (3 separate groups). Discussion explored: Program target(s); Opportunities and barriers that influence diet, physical activity, and stress-reduction practices; Empowering and culturally relevant health promotion strategies. SETTING: All study activities took place in Memphis, TN. PARTICIPANTS: Eighteen clergy and fourteen spouses participated. All clergy were male, all spouses were female. METHOD: Previous research with clergy informed the interview guide and the PEN-3 framework aided in organizing the coding of clergy and spouse focus groups. Focus groups were audio recorded and transcripts analyzed using NVivo® 12. RESULTS: Themes included: 1) Intervention targets-clergy, spouses, congregations; 2) Opportunities and barriers-making time, establishing boundaries, church traditions, individuals who support and hinder behavior change; 3) Intervention strategies-tools for healthy eating, goal setting, camaraderie, combining face-to-face with eHealth modalities. CONCLUSION: The relationship between clergy, spouse, and congregation make it important for obesity-related programs to target the unique needs of both clergy and spouses. Strategies should focus on healthy eating and personal connections no matter the modality used.

Protein Structure Modeling with MODELLER.

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

High Prevalence of Cannabidiol Use Within Male Professional Rugby Union and League Players: A Quest for Pain Relief and Enhanced Recovery.

Rugby is characterized by frequent high-intensity collisions, resulting in muscle soreness. Players consequently seek strategies to reduce soreness and accelerate recovery, with an emerging method being cannabidiol (CBD), despite anti-doping risks. The prevalence and rationale for CBD use in rugby has not been explored; therefore, we recruited professional male players to complete a survey on CBD. Goodness of fit chi-square (χ2) was used to assess CBD use between codes and player position. Effects of age on use were determined using χ2 tests of independence. Twenty-five teams provided 517 player responses. While the majority of players had never used CBD (p < .001, V = 0.24), 26% had either used it (18%) or were still using it (8%). Significantly more CBD use was observed in rugby union compared with rugby league (p = .004, V = 0.13), but player position was not a factor (p = .760, V = 0.013). CBD use increased with players' age (p < .001, V = 0.28), with mean use reaching 41% in the players aged 28 years and older category (p < .0001). The players using CBD primarily used the Internet (73%) or another teammate (61%) to obtain information, with only 16% consulting a nutritionist. The main reasons for CBD use were improving recovery/pain (80%) and sleep (78%), with 68% of players reporting a perceived benefit. These data highlight the need for immediate education on the risks of CBD, as well as the need to explore the claims regarding pain and sleep.

The Provision of Clergy Health Resources by Faith-Based Organizations in the USA.

The purpose of this study was to describe practices and perceptions related to promoting clergy health among a national sample of denomination-level faith-based organizations (FBOs) (N = 154). Stress was identified as the top health-related issue facing clergy. The most commonly offered health resource was employer-sponsored health insurance. Lack of financial resources was the most common barrier to providing health resources for clergy. This study highlights potential priorities for denomination-level FBOs interested in providing health resources for clergy.

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.

Archiving and disseminating integrative structure models.

Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format.

An Examination of Denomination-Level Efforts in Congregation Health Programming.

Large denominational faith-based organizations (FBOs, e.g., conferences, dioceses) have potential to impact population health, though current activities are largely unknown. This study examined how large denominational FBOs approach health promotion programming and relevant barriers and issues related to capacity. A self-report survey via email and mail collected responses from representatives of FBOs about their health programming. The sample (n = 154) was diverse and included Catholic, Presbyterian, and Lutheran traditions. The most common activities were inclusion of health-related topics at organizational events and the provision of educational resources. Working with FBOs at a macro-level has potential implications for population-level health improvements.

Structure of the sensory domain of McpX from Sinorhizobium meliloti, the first known bacterial chemotactic sensor for quaternary ammonium compounds.

The α-proteobacterium Sinorhizobium meliloti can live freely in the soil or engage in a symbiosis with its legume host. S. meliloti facilitates nitrogen fixation in root nodules, thus providing pivotal, utilizable nitrogen to the host. The organism has eight chemoreceptors, namely McpT to McpZ and IcpA that facilitate chemotaxis. McpX is the first known bacterial sensor of quaternary ammonium compounds (QACs) such as choline and betaines. Because QACs are exuded at chemotaxis-relevant concentrations by germinating alfalfa seeds, McpX has been proposed to contribute to host-specific chemotaxis. We have determined the crystal structure of the McpX periplasmic region (McpXPR) in complex with the proline betaine at 2.7 Å resolution. In the crystal, the protein forms a symmetric dimer with one proline betaine molecule bound to each monomer of McpXPR within membrane-distal CACHE module. The ligand is bound through cation-πinteractions with four aromatic amino acid residues. Mutational analysis in conjunction with binding studies revealed that a conserved aspartate residue is pivotal for ligand binding. We discovered that, in a striking example of convergent evolution, the ligand-binding site of McpXPR resembles that of a group of structurally unrelated betaine-binding proteins including ProX and OpuAC. Through this comparison and docking studies, we rationalized the specificity of McpXPR for this specific group of ligands. Collectively, our structural, biochemical, and molecular docking data have revealed the molecular determinants in McpX that are crucial for its rare ligand specificity for QACs.

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions.