GENCODE 2025: reference gene annotation for human and mouse.

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result.

Assessing hip joint-related structure and patient-reported outcomes in people with Marfan syndrome.

Objective: People with Marfan syndrome (MFS) have clinical symptoms of hip pain, but to date, there is limited knowledge about hip-related structural abnormalities in these patients. Therefore, the purpose of this cross-sectional study was to assess hip-related structural abnormalities and patient-reported outcomes (PRO) in a cohort of patients with MFS compared to healthy controls.

Methods: Nineteen individuals with MFS (17 females, 39.

Dissecting the -regulatory syntax of transcription initiation with deep learning.

Despite extensive characterization of mammalian Pol II transcription, the DNA sequence determinants of transcription initiation at a third of human promoters and most enhancers remain poorly understood. We trained and interpreted a neural network called ProCapNet that accurately models base-resolution initiation profiles from PRO-cap experiments using local DNA sequence. ProCapNet learns sequence motifs with distinct effects on initiation rates and TSS positioning and uncovers context-specific cryptic initiator elements intertwined within other TF motifs.

Use of plasmapheresis to lower anti-AAV antibodies in nonhuman primates with pre-existing immunity to AAVrh74.

Patients with pre-existing immunity to adeno-associated virus (AAV) are currently unable to receive systemic gene transfer therapies. In this nonhuman primate study, we investigated the impact of immunosuppression strategies on gene transfer therapy safety and efficacy and analyzed plasmapheresis as a potential pretreatment for circumvention of pre-existing immunity or redosing. In part 1, animals received delandistrogene moxeparvovec (SRP-9001), an AAVrh74-based gene transfer therapy for Duchenne muscular dystrophy.

Chlorination of Emerging Contaminants for Application in Potable Wastewater Reuse: Disinfection Byproduct Formation, Estrogen Activity, and Cytotoxicity.

With increasing water scarcity, many utilities are considering the potable reuse of wastewater as a source of drinking water. However, not all chemicals are removed in conventional wastewater treatment, and disinfection byproducts (DBPs) can form from these contaminants when disinfectants are applied during or after reuse treatment, especially if applied upstream of advanced treatment processes to control biofouling. We investigated the chlorination of seven priority emerging contaminants (17β-estradiol, estrone, 17α-ethinylestradiol, bisphenol A (BPA), diclofenac, -nonylphenol, and triclosan) in ultrapure water, and we also investigated the impact of chlorination on real samples from different treatment stages of an advanced reuse plant to evaluate the role of chlorination on the associated cytotoxicity and estrogenicity.

The effects of IPV and mental health symptoms on HPA axis functioning during early pregnancy.

Maternal HPA axis dysregulation during early pregnancy can negatively affect maternal functioning. However, findings are mixed regarding how intimate partner violence (IPV), a common traumatic stressor, impacts HPA axis regulation during pregnancy. Interactions between IPV and mental health symptoms as they influence cortisol production are rarely examined, especially among pregnant women.

Economic Hardship Predicts Intimate Partner Violence Victimization During Pregnancy.

Objective: Intimate partner violence (IPV) during pregnancy is associated with negative physical and mental health consequences for both mothers and infants. Economic hardship is often exacerbated during pregnancy and is associated with increased rates of IPV in non-pregnant samples. However, temporal associations between economic hardship and IPV victimization have not been well characterized during pregnancy.

Off the shelf: Investigating transfer of learning using commercially available virtual reality equipment.

The evolution of virtual reality (VR) has created the opportunity for a relatively low-cost and accessible method to practice motor skills. Previous studies have demonstrated how motor skill practice in non-immersive virtual environments transfers to physical environments. Though minimal research has investigated motor learning and transfer within immersive VR, multiple experiments provide empirical evidence of positive transfer effects.

An Evaluation of a Narrative Expressive Writing Program for Nurses During the COVID-19 Pandemic.

Objective: This study aimed to evaluate a writing program targeted to reduce stress and improve resilience in nurses during the coronavirus pandemic (COVID-19).

Background: Occupational hazards often result in poor mental health outcomes. The pandemic highlighted this problem.

Defining the value of faculty primary care clinical pharmacists.

Background: Demonstrating the value of comprehensive medication management (CMM) within clinical faculty sites is a challenge when balancing patient volume with academic responsibilities. Utilizing an evidence-based implementation system for CMM, faculty primary care clinical pharmacists (PCCPs) standardized CMM within their practice sites.

Objective: The primary objective of this project was to define the value of faculty PCCPs.

Factors Influencing Perioperative Nurse Turnover: A Classic Grounded Theory Study.

Perioperative nurse turnover rates range from 12% to 18.8%, and approximately 75% of perioperative managers reported at least one vacancy in 2021. Perioperative leaders are challenged to mitigate nurse turnover effectively because factors contributing to a nurse's decision to leave their job are not well defined.

Developmental Consequences of Intimate Partner Violence on Children.

Numerous studies associate childhood exposure to intimate partner violence (IPV) with adverse adjustment in the domains of mental health, social, and academic functioning. This review synthesizes this literature and highlights the critical role of child self-regulation in mediating children's adjustment outcomes. We discuss major methodological problems of the field, including failure to consider the effects of prenatal IPV exposure and the limitations of variable-oriented and cross-sectional approaches.

Conducting Virtual Assessments in Developmental Research: COVID-19 Restrictions as a Case Example.

Developmental researchers face considerable challenges regarding maximizing data collection and reducing participant attrition. In this article, we use our experiences implementing our study on the effects of timing of prenatal stress on maternal and infant outcomes during the COVID-19 pandemic as a framework to discuss the difficulties and solutions for these challenges, including the development of two types of virtual assessments. Specific information regarding use of virtual platforms, confidentiality, engaging children during video conferencing, and modifying the major assessments of our research are discussed.

Guidelines in Practice: Prevention of Unintentionally Retained Surgical Items.

Retained surgical items (RSIs) are adverse events that can affect patients, surgeons, and nurses. Interdisciplinary teams should work to standardize surgical item accounting processes and help all perioperative team members prevent RSIs. AORN recently revised the "Guideline for prevention of unintentionally retained surgical items," which provides background information on RSIs and ways to prevent them.

Curtobacterium allii sp. nov., the actinobacterial pathogen causing onion bulb rot.

A Gram-stain-positive, aerobic, and non-spore-forming bacterial strain, 20TX0166, was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it first species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium flaccumfaciens LMG 3645 (100%), C.

The strawberry-derived permeation enhancer pelargonidin enables oral protein delivery.

Although patients generally prefer oral drug delivery to injections, low permeability of the gastrointestinal tract makes this method impossible for most biomacromolecules. One potential solution is codelivery of macromolecules, including therapeutic proteins or nucleic acids, with intestinal permeation enhancers; however, enhancer use has been limited clinically by modest efficacy and toxicity concerns surrounding long-term administration. Here, we hypothesized that plant-based foods, which are well tolerated by the gastrointestinal tract, may contain compounds that enable oral macromolecular absorption without causing adverse effects.

A multimodal sensor dataset for continuous stress detection of nurses in a hospital.

Advances in wearable technologies provide the opportunity to monitor many physiological variables continuously. Stress detection has gained increased attention in recent years, mainly because early stress detection can help individuals better manage health to minimize the negative impacts of long-term stress exposure. This paper provides a unique stress detection dataset created in a natural working environment in a hospital.

Bioinformatic Analysis of CircRNA from RNA-seq Datasets.

Circular RNAs (circRNAs) are a vast class of covalently closed, noncoding RNAs expressed in specific tissues and developmental stages. The molecular, cellular, and pathophysiologic roles of circRNAs are not fully known, but their impact on gene expression programs is beginning to emerge, as circRNAs often associate with RNA-binding proteins and nucleic acids. With rising interest in identifying circRNAs associated with disease processes, it has become particularly important to identify circRNAs in RNA sequencing (RNA-seq) datasets, either generated by the investigator or reported in the literature.

sp. nov., a bacterial pathogen causing onion bulb rot.

A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172, was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus and had the greatest sequence similarities with 520-20 (99.3 %), CFBP 2431 (99.

Conflict Appraisals and Trauma Symptoms in Children Exposed to Intimate Partner Violence.

Children exposed to intimate partner violence (IPV) are at risk for posttraumatic stress symptoms (PTSS) and alterations in hypothalamic-pituitary-adrenal (HPA) axis functioning. The current study investigated children's threat and self-blame appraisals about parental conflict as potential mechanisms leading to these adverse outcomes. Parent-child relationships were also examined.

Practical strategies to enhance resident engagement in clinical quality improvement.

Background: Engaging residents in meaningful quality improvement (QI) is difficult. Challenges include competing demands, didactics which lack connection to meaningful work, suboptimal experiential learning, unclear accountability, absence of timely and relevant data, and lack of faculty coaches and role models. Various strategies to address these challenges for engagement have been described, but not as a unified approach.