Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC.

Large-scale scATAC-seq experiments are challenging because of their costs, lengthy protocols, and confounding batch effects. Several sample multiplexing technologies aim to address these challenges, but do not remove batch effects introduced when performing transposition reactions in parallel. We demonstrate that sample-to-sample variability in nuclei-to-Tn5 ratios is a major cause of batch effects and develop MULTI-ATAC, a multiplexing method that pools samples prior to transposition, as a solution.

Linking volatile metabolites from bacterial pathogens to exhaled breath condensate of people with cystic fibrosis.

Obtaining sputum samples from people with cystic fibrosis (pwCF) for microbiology has become challenging due to the positive clinical effects of the cystic fibrosis transmembrane conductance regulator modulator therapy, elexacaftor-tezacaftor-ivacaftor (ETI). Although ETI improves lung function and reduces sputum production, recent data shows that bacterial pathogens persist, making continued monitoring of infection important. As an alternative to sputum sampling, this study developed a non-invasive technique called 'Cough Breath' (CB) to identify volatile organic compounds (VOCs) in exhaled breath condensate (EBC) and link them to cystic fibrosis (CF) bacterial pathogens using purge and trap GC-MS.

SATINN v2: automated image analysis for mouse testis histology with multi-laboratory data integration.

Analysis of testis histology is fundamental to the study of male fertility, but it is a slow task with a high skill threshold. Here, we describe new neural network models for the automated classification of cell types and tubule stages from whole-slide brightfield images of mouse testis. The cell type classifier recognizes 14 cell types, including multiple steps of meiosis I prophase, with an external validation accuracy of 96%.

Deletion of an evolutionarily conserved TAD boundary impacts spermatogenesis in mice†.

Spermatogenesis is a complex process that can be disrupted by genetic and epigenetic changes, potentially leading to male infertility. Recent research has rapidly increased the number of protein coding mutations causally linked to impaired spermatogenesis in humans and mice. However, the role of non-coding mutations remains largely unexplored.

Exploring the Scholarly Value and Impact of DNP-Prepared Nurses Through the Lens of Nursing Leaders.

Objective: To explore organizational nursing leaders' perceptions of impact, value, and support for doctor of nursing practice (DNP)-prepared nurses engaging in practice scholarship.

Background: DNP nurses are educated to lead change at the system level and direct practice-based initiatives to enhance health outcomes. Organizational support and the value of DNP scholarship need to be better understood.

Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments.

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of identical-by-descent DNA segments (IBD) yield the most precise relatedness estimates.

Diminished DNA binding affinity of DMRT1 caused by heterozygous DM domain mutations is a cause of male infertility.

The most severe form of male infertility is idiopathic non-obstructive azoospermia (NOA), a complete sperm absence in the ejaculate. We performed exome sequencing in the Croatian infertile brothers with NOA and found a variant in DMRT1 (Doublesex and mab-3 related transcription factor 1) gene that was further assessed by the EMSA assay and molecular dynamic simulations. We additionally screened for DMRT1 mutations in 1940 infertile men diagnosed with spermatogenic failure, 644 normozoospermic controls, and 105 females with primary ovarian insufficiency (POI) recruited to the GEnetics of Male INfertility Initiative (GEMINI) or Estonian Andrology (ESTAND) cohorts.

The effect of antibiotic prophylaxis duration on infection rates and outcomes after head and neck reconstruction with bony free flaps and hardware.

Background: Although the literature supports a shorter course of 24 h of prophylaxis after head and neck free flap reconstruction, studies supporting this duration do not differentiate between flap types. There is a paucity of evidence on the optimal duration of prophylaxis for osteocutaneous free flaps with hardware, which may have higher rates of post-operative complications compared to other free flaps. This study aimed to examine the effect of different lengths of antibiotic prophylaxis on surgical site infection (SSI) rates after head and neck reconstruction with osteocutaneous free flaps and hardware.

T helper 2 cell-directed immunotherapy eliminates precancerous skin lesions.

The continuous rise in skin cancer incidence highlights an imperative for improved skin cancer prevention. Topical calcipotriol-plus-5-fluorouracil (calcipotriol-plus-5-FU) immunotherapy effectively eliminates precancerous skin lesions and prevents squamous cell carcinoma (SCC) in patients. However, its mechanism of action remains unclear.

Association between microvascular free-flap arterial anastomosis caliber and risk for development of osteoradionecrosis.

Objectives: Osteoradionecrosis (ORN) following radiation therapy (RT) is a serious complication for patients undergoing head and neck cancer treatment. Recent literature has found an association between ipsilateral external carotid artery (ECA) diameter and the development of ORN. This study evaluates microvascular free-flap arterial anastomosis diameter and the development of ORN.

Pathobiont-driven antibody sialylation through IL-10 undermines vaccination.

The pathobiont Staphylococcus aureus (Sa) induces nonprotective antibody imprints that underlie ineffective staphylococcal vaccination. However, the mechanism by which Sa modifies antibody activity is not clear. Herein, we demonstrate that IL-10 is the decisive factor that abrogates antibody protection in mice.

Commensal papillomavirus immunity preserves the homeostasis of highly mutated normal skin.

Immunosuppression commonly disrupts the homeostasis of mutated normal skin, leading to widespread skin dysplasia and field cancerization. However, the immune system's role in maintaining the normal state of mutated tissues remains uncertain. Herein, we demonstrate that T cell immunity to cutaneotropic papillomaviruses promotes the homeostasis of ultraviolet radiation-damaged skin.

Comparison of Race-Neutral versus Race-Specific Spirometry Equations for Evaluation of Child Asthma.

Race-based estimates of pulmonary function in children could influence the evaluation of asthma in children from racial and ethnic minoritized backgrounds. To determine if race-neutral (Global Lung Function Initiative [GLI]-Global) versus race-specific (GLI-Race-Specific) reference equations differentially impact spirometry evaluation of childhood asthma. The analysis included 8,719 children aged 5 to <12 years from 27 cohorts across the United States grouped by parent-reported race and ethnicity.

A novel CCDC112-dependent process of sperm midpiece formation and epididymal maturation.

The sperm mitochondrial sheath has proposed functions in structural support and energy production for motility. Here we define coiled coil domain containing protein 112, CCDC112, as crucial for male fertility, specifically in the assembly and function of the mitochondrial sheath. We unveiled a previously unrecognised process of epididymal mitochondrial sheath maturation.

Free Flap Enhanced Recovery Protocols in Head and Neck Surgery.

Enhanced recovery after surgery (ERAS) protocols facilitates a standardized patient care regimen with a goal of reducing the metabolic stress of surgery. Adapted to head and neck free flap reconstructive surgery in 2017, these protocols focused on several key domains such as perioperative nutritional optimization, multimodal pain control, and early mobilization. Studies have shown that in addition to ERAS implementation, the maintenance and improvement of ERAS protocol compliance rates improve perioperative outcomes such as hospital length of stay and decrease major postoperative complications.

Selection promotes age-dependent degeneration of the mitochondrial genome.

Somatic mutations in mitochondrial genomes (mtDNA) accumulate exponentially during aging. Using single cell sequencing, we characterize the spectrum of age-accumulated mtDNA mutations in mouse and human liver and identify directional forces that accelerate the accumulation of mutations beyond the rate predicted by a neutral model. "Driver" mutations that give genomes a replicative advantage rose to high cellular abundance and carried along "passenger" mutations, some of which are deleterious.

Open Access Data Repository and Common Data Model for Pulse Oximeter Performance Data.

The OpenOximetry Repository is a structured database storing clinical and lab pulse oximetry data, serving as a centralized repository and data model for pulse oximetry initiatives. It supports measurements of arterial oxygen saturation (SaO2) by arterial blood gas co-oximetry and pulse oximetry (SpO2), alongside processed and unprocessed photoplethysmography (PPG) data and other metadata. This includes skin color measurements, finger diameter, vital signs (e.

Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility.

piRNAs are crucial for transposon silencing, germ cell maturation, and fertility in male mice. Here, we report on the genetic landscape of piRNA dysfunction in humans and present 39 infertile men carrying biallelic variants in 14 different piRNA pathway genes, including PIWIL1, GTSF1, GPAT2, MAEL, TDRD1, and DDX4. In some affected men, the testicular phenotypes differ from those of the respective knockout mice and range from complete germ cell loss to the production of a few morphologically abnormal sperm.

[Comparison of the preclinical quality of analgesia of emergency physicians and paramedics based on trauma patients].

Background: Adequate prehospital pain management is a critical component of emergency medical services. With the introduction of the paramedic profession and the Paramedics Act in Germany, the basis for more extensive competencies of paramedics was established. In many emergency medical service areas it is thus possible for paramedics to perform analgesia and sedation with esketamine/midazolam according to pre-established instructions and/or standard operating procedures.

Leveraging Doctor of Nursing Practice Scholarship to Meet Organizational Leaders' Expectations.

The Doctor of Nursing Practice (DNP) degree prepares nurses for engagement in practice scholarship to improve health outcomes at multiple system levels. Organizational leaders' and employers' perceptions and expectations of DNP-prepared nurses require further study. To explore the perception of organizational leaders regarding expectations and engagement of DNP-prepared nurses in practice scholarship activities.