Catalyzing computational biology research at an academic institute through an interest network.

Biology has been transformed by the rapid development of computing and the concurrent rise of data-rich approaches such as, omics or high-resolution imaging. However, there is a persistent computational skills gap in the biomedical research workforce. Inherent limitations of classroom teaching and institutional core support highlight the need for accessible ways for researchers to explore developments in computational biology.

The Pandemic Journaling Project: A new dataset of first-person accounts of the COVID-19 pandemic.

Background: The rapid global spread of the COVID-19 pandemic affected different regions, communities, and individuals in vastly different ways that interdisciplinary social scientists are well-positioned to document and investigate. This paper describes an innovative mixed-methods dataset generated by a research study that was designed to chronicle and preserve evidence of the pandemic's divergent effects: the Pandemic Journaling Project (PJP). The dataset was generated by leveraging digital technology to invite ordinary people around the world to document the impact of the COVID-19 pandemic on their everyday lives over a two-year period (May 2020-May 2022) using text, images, and audio.

Challenges in the return of molecular tumor profiling results.

Next-generation sequencing (NGS) has transformed cancer care by providing essential insights for diagnosis, prognosis, and treatment. However, variability in testing timing, reporting practices, and interpretation challenges limits its clinical impact. This manuscript highlights key opportunities to optimize somatic reporting, emphasizing the importance of timely testing throughout the cancer care continuum to maximize the diagnostic and therapeutic relevance of findings.

Sirolimus for Venous Malformations: A Systematic Review of Efficacy and Safety.

Venous malformations can cause substantial morbidity and long-term complications. There are no Food and Drug Administration (FDA)-approved therapies for the treatment of venous malformations. However, off-label use of sirolimus has demonstrated clinical benefit in these patients.

Prolonging All-Optical Molecular Electron Spin Coherence in the Tissue Transparency Window.

Coherent electron spin states within paramagnetic molecules hold significant potential for microscopic quantum sensing. However, all-optical coherence measurements amenable to high spatial and temporal resolution under ambient conditions remain a significant challenge. Here we conduct room-temperature, picosecond time-resolved Faraday ellipticity/rotation (TRFE/R) measurements of the electron spin decoherence time in [IrBr].

Approach to the Postmarket Evaluation of Consumer Wearable Technologies.

Importance: Consumer wearable technologies have wide applications, including some that have US Food and Drug Administration clearance for health-related notifications. While wearable technologies may have premarket testing, validation, and safety evaluation as part of a regulatory authorization process, information on their postmarket use remains limited. The Stanford Center for Digital Health organized 2 pan-stakeholder think tank meetings to develop an organizing concept for empirical research on the postmarket evaluation of consumer-facing wearables.

Efficient production of sodium Bose-Einstein condensates in a hybrid trap.

We describe an apparatus that efficiently produces 23Na Bose-Einstein condensates (BECs) in a hybrid trap that combines a quadrupole magnetic field with a far-detuned optical dipole trap. Using a Bayesian optimization framework, we systematically optimize all BEC production parameters in modest-sized batches of highly correlated parameters. Furthermore, we introduce a Lagrange multiplier-based technique to optimize the duration of different evaporation stages constrained to have a fixed total duration; this enables the progressive creation of increasingly rapid experimental sequences that still generate high-quality BECs.

A New Family of Ternary Intermetallic Compounds with Dualistic Atomic Ordering - The ZIP Phases.

A new family of nanostructured ternary intermetallic compounds - named the ZIP phases - is introduced in this work. The ZIP phases exhibit dualistic atomic ordering, i.e.

Microautophagy: definition, classification, and the complexity of the underlying mechanisms.

Recently, rapid progress in the field of microautophagy (MI-autophagy) revealed the existence of multiple subtypes that differ in both intracellular membrane dynamics and molecular mechanisms. As a result, a single umbrella term "microautophagy" has become too vague, even creating some confusion among researchers both within and outside the field. We herein describe different subtypes of MI-autophagic processes and propose a systematic approach for naming them more accurately.

Genome sequencing reveals the impact of pseudoexons in rare genetic disease.

Purpose: Advancements in sequencing technologies have significantly improved clinical genetic testing, yet the diagnostic yield remains around 30-40%. Emerging technologies are now being deployed to address the remaining diagnostic gap.

Methods: We tested whether short-read genome sequencing could increase the diagnostic yield in individuals enrolled into the UCI-GREGoR research study, who had suspected Mendelian conditions and prior inconclusive testing.

Toward Health Equity: A Workshop Report on the State of the Science of Obesity Interventions for Adults.

Objective: From October 18-20, 2022, the National Institutes of Health held a workshop to examine the state of the science concerning obesity interventions in adults to promote health equity. The workshop had three objectives: (1) Convene experts from key institutions and the community to identify gaps in knowledge and opportunities to address obesity, (2) generate recommendations for obesity prevention and treatment to achieve health equity, and (3) identify challenges and needs to address obesity prevalence and disparities, and develop a diverse workforce.

Methods: A three-day virtual convening.

Age-related amyloid beta dynamics modeled with the generalized additive model for location, scale, and shape (GAMLSS) across diverse populations: Cross-sectional trajectories and longitudinal validation.

Introduction: We developed and validated age-related amyloid beta (Aβ) positron emission tomography (PET) trajectories using a statistical model in cognitively unimpaired (CU) individuals.

Methods: We analyzed 849 CU Korean and 521 CU non-Hispanic White (NHW) participants after propensity score matching. Aβ PET trajectories were modeled using the generalized additive model for location, scale, and shape (GAMLSS) based on baseline data and validated with longitudinal data.

Maximizing theoretical and practical storage capacity in single-layer feedforward neural networks.

Artificial neural networks are limited in the number of patterns that they can store and accurately recall, with capacity constraints arising from factors such as network size, architectural structure, pattern sparsity, and pattern dissimilarity. Exceeding these limits leads to recall errors, eventually leading to catastrophic forgetting, which is a major challenge in continual learning. In this study, we characterize the theoretical maximum memory capacity of single-layer feedforward networks as a function of these parameters.

The Case for Limiting "Sequences of Concern" to Those with Demonstrated Pathogenic Function.

Screening synthetic nucleic acid orders for sequences of concern is a necessary part of a healthy biosecurity regime, but it exacts costs for nucleic acid providers. Taxonomy is and will remain a critical part of the decision-making process for screening, especially for viral sequences. But, moving forward, the function of a sequence will also be determinative of its level of concern, or lack thereof.

Retinal progenitor cells (jCell) for retinitis pigmentosa.

Objective: To assess the safety and tolerability of intravitreal injection of human retinal progenitor cells (RPCs) at multiple dose levels in adults with non-syndromic retinitis pigmentosa (RP).

Design: A prospective, multicenter, open-label, single-arm, Phase I/IIa safety study of RPCs in adults with RP ( = 28). Two patient cohorts were studied: Cohort 1: BCVA no better than 20/200 and no worse than Hand Motions, and Cohort 2: BCVA no better than 20/40 and no worse than 20/200).

Improving Communication and Management Following a Positive Home HPV Self-Sampling Result: Comparing Intervention Strategies Between the HOME and STEP Trials.

Background: Mailed human papillomavirus (HPV) self-sampling kits improve cervical cancer screening adherence. The HOME trial found information needs and anxiety among HPV-positive patients. We designed a STEP trial to test optimized intervention strategies with bolstered educational materials and a centralized nurse communicating positive results.

Open-source models for development of data and metadata standards.

Machine learning and artificial intelligence promise to accelerate research and understanding across many scientific disciplines. Harnessing the power of these techniques requires aggregating scientific data. In tandem, the importance of open data for reproducibility and scientific transparency is gaining recognition, and data are increasingly available through digital repositories.

A view of the sustainable computing landscape.

This article presents a holistic research agenda to address the significant environmental impact of information and communication technology (ICT), which accounts for 2.1%-3.9% of global greenhouse gas emissions.

Single-Cell and Plasma Proteomics Do Not Differentiate Patients With and Without SARS-CoV-2 Antigenemia in Convalescence in a Cohort of 100 Patients.

Plasma samples obtained approximately 3 ( = 100) and 12 months ( = 78) after acute SARS-CoV-2 infection were tested for S1, spike, and N antigens. There were no significant differences in plasma proteins or single-cell protein expression levels on immune cells between those with and without plasma antigen detected.

Systematic review of prospective hazard analysis in radiation therapy.

Introduction: Prospective hazard analysis (PHA) was introduced to the wider medical physics community by the initiation of American association of physicists in medicine task group 100 in 2003. Since then, there has been increasing interest in the applicability of PHA to radiotherapy for the purpose of keeping patients safe and assessing the risks within the whole practice of radiotherapy. The purpose of this research was to review the PHA literature focusing on which techniques and technologies have been assessed, how they have been assessed, and what can be learnt.

Soil Carbon Availability Drives Depth-Dependent Responses of Microbial Nitrogen Use Efficiency to Warming.

Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N between microbial growth and N mineralization, which is crucial for assessing soil N retention. However, how warming affects NUE along soil depth remains unclear. Based on a whole-soil-profile warming experiment (0 to 100 cm, +4°C) on the Qinghai-Tibetan Plateau, combined with O and N isotope labeling techniques, we determined soil carbon (C) composition, edaphic properties, and microbial parameters.

The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.

Background: Recent advances in high-throughput sequencing technologies have enabled the collection and sharing of a massive amount of omics data, along with its associated metadata-descriptive information that contextualizes the data, including phenotypic traits and experimental design. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability and limit secondary analyses.

Structure, function and assembly of nuclear pore complexes.

The defining property of eukaryotic cells is the storage of heritable genetic material in a nuclear compartment. For eukaryotic cells to carry out the myriad biochemical processes necessary for their function, macromolecules must be efficiently exchanged between the nucleus and cytoplasm. The nuclear pore complex (NPC) - which is a massive assembly of ~35 different proteins present in multiple copies totalling ~1,000 protein subunits and architecturally conserved across eukaryotes - establishes a size-selective channel for regulated bidirectional transport of folded macromolecules and macromolecular assemblies across the nuclear envelope.

Durotaxis is a driver and potential therapeutic target in lung fibrosis and metastatic pancreatic cancer.

Durotaxis, cell migration along stiffness gradients, is linked to embryonic development, tissue repair and disease. Despite solid in vitro evidence, its role in vivo remains largely speculative. Here we demonstrate that durotaxis actively drives disease progression in vivo in mouse models of lung fibrosis and metastatic pancreatic cancer.