Identification of Gene Regulatory Networks Associated with Breast Cancer Patient Survival Using an Interpretable Deep Neural Network Model.

Artificial neural networks have recently gained significant attention in biomedical research. However, their utility in survival analysis still faces many challenges. In addition to designing models for high accuracy, it is essential to optimize models that provide biologically meaningful insights.

DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain.

DNA transposons have emerged as promising tools in both gene therapy and functional genomics. In particular, the Sleeping Beauty (SB) DNA transposon has advanced into clinical trials due to its ability to stably integrate DNA sequences of choice into eukaryotic genomes. The efficiency of the DNA transposon system depends on the interaction between the transposon DNA and the transposase enzyme that facilitates gene transfer.

Enhanced pollen tube performance at high temperature contributes to thermotolerant fruit and seed production in tomato.

Rising temperature extremes during critical reproductive periods threaten the yield of major grain and fruit crops. Flowering plant reproduction depends on the ability of pollen grains to generate a pollen tube, which elongates through the pistil to deliver sperm cells to female gametes for double fertilization. We used tomato as a model fruit crop to determine how high temperature affects the pollen tube growth phase, taking advantage of cultivars noted for fruit production in exceptionally hot growing seasons.

Single-shot quantitative phase microscopy: a multi-functional tool for cell analysis.

This study showcases the multifunctionality of a single-shot quantitative phase microscopy (QPM) system for comprehensive cell analysis. The system captures four high-contrast images in one shot, enabling tasks like cell segmentation, measuring cell confluence, and estimating cell mass. We demonstrate the usability of the QPM system in routine biological workflows, showing how its integration with computational algorithms enables automated, precise analysis, achieving accuracy scores between 85% and 97% across samples with varying cell densities, even those with low signal-to-noise ratios.

Patient-Reported Outcome Measures and Biomechanical Variables That May Be Related to Knee Functions Following Total Knee Arthroplasty.

Total knee arthroplasty (TKA) is a commonly performed surgery aimed at alleviating pain and improving functionality. However, patients often face uncertainties in selecting the timing, location, and type of TKA implant that best meets their needs. This study aims to comprehensively compare various variables, explore trends, and identify factors potentially influencing TKA outcomes.

Affordable Care Act Medicaid expansion, access to health care, and financial behavior of the United States adults.

The access to care benefits of Affordable Care Act (ACA) Medicaid expansions are important for 45-64-year-old adults who are living below 100% of the Federal Poverty Level, a particularly vulnerable group in the United States (US). Gaining coverage from Medicaid expansions should improve access to healthcare and affect social determinants of health, including financial behavior. We analyzed data from 2009 to 2018 from the National Financial Capability Survey (NFCS) and utilize a difference-in-differences model to compare outcomes changes in states with and without expansion before and after the ACA Medicaid expansions.

The Relationship between HERV, Interleukin, and Transcription Factor Expression in ZIKV Infected versus Uninfected Trophoblastic Cells.

Zika virus (ZIKV) is an arbovirus with maternal, sexual, and TORCH-related transmission capabilities. After 2015, Brazil had the highest number of ZIVK-infected pregnant women who lost their babies or delivered them with Congenital ZIKV Syndrome (CZS). ZIKV triggers an immune defense in the placenta.

Depressive Symptoms Affect Cognitive Functioning from Middle to Late Adulthood: Ethnoracial Minorities Experience Greater Repercussions.

Cognitive deficits, a diagnostic criterion for depressive disorders, may precede or follow the development of depressive symptoms and major depressive disorder. However, an individual can report an increase in depressive symptoms without any change in cognitive functioning. While ethnoracial minority group differences exist, little is known to date about how the relationship between depressive symptoms and cognitive function may differ by ethnoracial minority status.

Promoting vigorous intermittent lifestyle physical activity (vilpa) in middle-aged adults: an evaluation of the movsnax mobile app.

Background: Most adults fail to meet the moderate to vigorous physical activity-based recommendations needed to maintain or improve health. Vigorous Intermittent Lifestyle Physical Activity (VILPA) refers to short (1-2 min) high-intensity activities that are integrated into activities of daily living. VILPA has shown strong potential to improve health and addresses commonly reported barriers to physical activity.

Examining emotion regulation and inflammation as predictors of maternal mental health after fetal anomaly diagnosis.

Objective: Fetal anomalies occur in approximately 3% of pregnancies and receiving the diagnosis may be a potentially traumatic experience for families. The mental health of mothers receiving diagnoses and what predicts resilience or poor mental health is understudied. Emotion regulation is an important, modifiable, transdiagnostic factor of mental health, and may be protective post-diagnosis.

Adverse and benevolent childhood experiences among adults in the United Kingdom: a latent class analysis.

Background: Adverse childhood experiences (ACEs) are important factors for population mental and physical health. While considerable public health literature demonstrates the global relevance of ACEs, more recent research shows that benevolent childhood experiences (BCEs) might be important to consider in their direct and mitigating roles for psychological distress and other mental health outcomes. There is little evidence of latent class examinations involving both ACEs and BCEs among adults in western nations.

Development of the Technical Assistance Engagement Scale: a modified Delphi study.

Background: Technical assistance (TA) is a tailored approach to capacity building that is commonly used to support implementation of evidence-based interventions. Despite its widespread applications, measurement tools for assessing critical components of TA are scant. In particular, the field lacks an expert-informed measure for examining relationship quality between TA providers and recipients.

A collective agenda: A qualitative study on Exercise is Medicine® On Campus gold-level institutions.

Objective: The Exercise is Medicine® On Campus (EIM-OC) international campaign leverages university resources (e.g., health centers, recreation, and kinesiology departments) to encourage students, faculty, and staff to integrate physical activity into campus culture.

A gold standard dataset and evaluation of methods for lineage abundance estimation from wastewater.

During the SARS-CoV-2 pandemic, genome-based wastewater surveillance sequencing has been a powerful tool for public health to monitor circulating and emerging viral variants. As a medium, wastewater is very complex because of its mixed matrix nature, which makes the deconvolution of wastewater samples more difficult. Here we introduce a gold standard dataset constructed from synthetic viral control mixtures of known composition, spiked into a wastewater RNA matrix and sequenced on the Oxford Nanopore Technologies platform.

NFDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs.

Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase () is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase () and (iii) iron nitrogenase (). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist.

"He gets mad that I'm sober": Experiences of substance use coercion among postpartum women in recovery.

Purpose: The number of women with substance use disorders (SUDs) is growing in the U.S. Many women with SUDs are of childbearing age, and studies show that women who abstain from substance use during pregnancy often relapse in the postpartum period.

Structure and agency in resistance to schooling: Class, race, and the reproduction of unequal outcomes.

For low-income and marginalized racialized minority youth, declining prospects of mobility can undermine favorable attitudes toward schooling if adolescents anticipate limited utility in schooling. We find that adolescents' awareness of race and class inequality affects a complex set of attitudes toward schooling, and that these attitudes contribute to outcomes varying by race/ethnicity and class. We capitalize on a unique longitudinal dataset with a random stratified sample of 1428 Black and White high school graduates from a large school system.

Triptolide Administration Alters Immune Responses to Mitigate Insulin Resistance in Obese States.

Individuals who are overweight or obese are at increased risk of developing prediabetes and type 2 diabetes, yet the direct molecular mechanisms that connect diabetes to obesity are not clear. Chronic, sustained inflammation is considered a strong risk factor in these interactions, directed in part by the short-lived gene expression programs encoding for cytokines and pro-inflammatory mediators. In this study, we show that triptolide administration in the C57BL/6 diet-induced obese mice at up to 10 μg/kg/day for 10 weeks attenuated the development of insulin resistance and diabetes, but not obesity, in these animals.

Forging just ecologies: 25 years of urban long-term ecological research collaboration.

We ask how environmental justice and urban ecology have influenced one another over the past 25 years in the context of the US Long-Term Ecological Research (LTER) program and Baltimore Ecosystem Study (BES) project. BES began after environmental justice emerged through activism and scholarship in the 1980s but spans a period of increasing awareness among ecologists and environmental practitioners. The work in Baltimore provides a detailed example of how ecological research has been affected by a growing understanding of environmental justice.

A transformative shift in urban ecology toward a more active and relevant future for the field and for cities.

This paper builds on the expansion of urban ecology from a biologically based discipline-ecology in the city-to an increasingly interdisciplinary field-ecology of the city-to a transdisciplinary, knowledge to action endeavor-an ecology for and with the city. We build on this "prepositional journey" by proposing a transformative shift in urban ecology, and we present a framework for how the field may continue this shift. We conceptualize that urban ecology is in a state of flux, and that this shift is needed to transform urban ecology into a more engaged and action based field, and one that includes a diversity of actors willing to participate in the future of their cities.

The relational shift in urban ecology: From place and structures to multiple modes of coproduction for positive urban futures.

This perspective emerged from ongoing dialogue among ecologists initiated by a virtual workshop in 2021. A transdisciplinary group of researchers and practitioners conclude that urban ecology as a science can better contribute to positive futures by focusing on relationships, rather than prioritizing urban structures. Insights from other relational disciplines, such as political ecology, governance, urban design, and conservation also contribute.