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1. RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

   https://doi.org/10.1093/bioinformatics/btac317  

   Segura, Joan; Rose, Yana; Bittrich, Sebastian; Burley, Stephen K.; Duarte, Jose M.; Cowen, ed., Lenore (May 2022, Bioinformatics)

   Abstract MotivationMapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. ResultsWe present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies. Availability and implementationhttps://github.com/rcsb/rcsb-saguaro-3d. Supplementary informationSupplementary data are available at Bioinformatics online. 

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2. Population Atlas Analysis of Emerging Brain Structural Connections in the Human Fetus

   https://doi.org/10.1002/jmri.29057  

   Calixto, Camilo; Machado‐Rivas, Fedel; Karimi, Davood; Velasco‐Annis, Clemente; Cortes‐Albornoz, Maria Camila; Afacan, Onur; Warfield, Simon K.; Gholipour, Ali; Jaimes, Camilo (October 2023, Journal of Magnetic Resonance Imaging)

   BackgroundA lack of in utero imaging data hampers our understanding of the connections in the human fetal brain. Generalizing observations from postmortem subjects and premature newborns is inaccurate due to technical and biological differences. PurposeTo evaluate changes in fetal brain structural connectivity between 23 and 35 weeks postconceptional age using a spatiotemporal atlas of diffusion tensor imaging (DTI). Study TypeRetrospective. PopulationPublicly available diffusion atlases, based on 60 healthy women (age 18–45 years) with normal prenatal care, from 23 and 35 weeks of gestation. Field Strength/Sequence3.0 Tesla/DTI acquired with diffusion‐weighted echo planar imaging (EPI). AssessmentWe performed whole‐brain fiber tractography from DTI images. The cortical plate of each diffusion atlas was segmented and parcellated into 78 regions derived from the Edinburgh Neonatal Atlas (ENA33). Connectivity matrices were computed, representing normalized fiber connections between nodes. We examined the relationship between global efficiency (GE), local efficiency (LE), small‐worldness (SW), nodal efficiency (NE), and betweenness centrality (BC) with gestational age (GA) and with laterality. Statistical TestsLinear regression was used to analyze changes in GE, LE, NE, and BC throughout gestation, and to assess changes in laterality. Thet‐tests were used to assess SW.P‐values were corrected using Holm‐Bonferroni method. A correctedP‐value <0.05 was considered statistically significant. ResultsNetwork analysis revealed a significant weekly increase in GE (5.83%/week, 95% CI 4.32–7.37), LE (5.43%/week, 95% CI 3.63–7.25), and presence of SW across GA. No significant hemisphere differences were found in GE (P = 0.971) or LE (P = 0.458). Increasing GA was significantly associated with increasing NE in 41 nodes, increasing BC in 3 nodes, and decreasing BC in 2 nodes. Data ConclusionExtensive network development and refinement occur in the second and third trimesters, marked by a rapid increase in global integration and local segregation. Level of Evidence3 Technical EfficacyStage 2 

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3. Training the Future: Themes From a Content Analysis of Psychology Research Lab Manuals

   https://doi.org/10.1177/00986283241283057  

   Lilley, Malin_K; Castellanos, Isabella; Wicks, Anastacia; Raya, Alena; Weatherford, Dawn_R; Huynh, Ho_Phi (October 2024, Teaching of Psychology)

   BackgroundLab manuals help researchers and students share a common understanding of the rules, guidelines, and expectations related to being involved with a research laboratory. However, no formal guidelines direct the creation of lab manuals in psychology. ObjectiveIn this study, we conducted qualitative analyses of 10 psychology lab manuals to provide some broad guidelines for crafting a lab manual that would improve the research experience for undergraduate students. MethodTaking an inductive approach, a team of researchers created codes from the contents of the manuals, and then derived themes from those codes. ResultsThemes included lab philosophy and direction, expectations and roles in the lab, communication inside and outside the lab, ethics, preparing for research, conducting research, presenting research, networking, and benefits of undergraduate research. ConclusionWe defined and provided specific examples of each theme for consideration by educators and discussed limitations of our approach. Teaching ImplicationsUltimately, these themes could serve as a modest outline from which teacher-scholars can create their lab manuals from scratch or to revise/expand current manuals. 

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4. Low Levels of Neutralizing Antibodies After Natural Infection With Severe Acute Respiratory Syndrome Coronavirus 2 in a Community-Based Serological Study

   https://doi.org/10.1093/ofid/ofac055  

   McDade, Thomas W.; Sancilio, Amelia; D’Aquila, Richard; Mustanski, Brian; Vaught, Lauren A.; Reiser, Nina L.; Velez, Matthew E.; Hsieh, Ryan R.; Ryan, Daniel T.; Saber, Rana; et al (March 2022, Open Forum Infectious Diseases)

   Abstract BackgroundConfidence in natural immunity after infection with severe acute respiratory syndrome coronavirus 2 is one reason for vaccine hesitancy. MethodsWe measured antibody-mediated neutralization of spike protein-ACE2 receptor binding in a large community-based sample of seropositive individuals who differed in severity of infection (N = 790). ResultsA total of 39.8% of infections were asymptomatic, 46.5% were symptomatic with no clinical care, 13.8% were symptomatic with clinical care, and 3.7% required hospitalization. Moderate/high neutralizing activity was present after 41.3% of clinically managed infections, in comparison with 7.9% of symptomatic and 1.9% of asymptomatic infections. ConclusionsPrior coronavirus disease 2019 infection does not guarantee a high level of antibody-mediated protection against reinfection in the general population. 

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5. An offline coupling of fire spread models to simulate the 2021 Marshall Fire

   https://doi.org/10.1071/WF24027  

   Szasdi-Bardales, Fernando; Shamsaei, Kasra; Juliano, Timothy_W; Kosovic, Branko; Ebrahimian, Hamed; Elhami-Khorasani, Negar (January 2025, International Journal of Wildland Fire)

   BackgroundExisting fire spread models focus exclusively on wildland or urban fire simulation. AimsThis study aims at an offline coupling of two fire spread models to enable a continuous simulation of a wildfire incident transitioning from wildland into wildland–urban interface (WUI) communities, evaluate the effects of wind input on simulation results and study the influence of building types on fire spread patterns. MethodsThe selected models are WRF-Fire, a wildland fire behaviour simulation platform, and SWUIFT, a model for fire spread inside the WUI. The 2021 Marshall Fire serves as the case study. A map of the fire’s timeline and location is generated using public information. Three simulation scenarios are analysed to study the effects of wind input resolution and building type on the predicted fire spread and damage. Key resultsThe most accurate results are obtained using a high-resolution wind input and when incorporating different building types. ConclusionsThe offline coupling of models provides a reliable solution for fire spread simulation. Fire-resistant buildings likely helped limit community fire spread during the Marshall Fire. ImplicationsThe research is a first step toward developing simulation capabilities to predict the spread of wildfires within the wildland, WUI and urban environments. 

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