ROBUST DISCOVERY OF MUTATIONAL SIGNATURES USING POWER POSTERIORS.

Mutational processes, such as the molecular effects of carcinogenic agents or defective DNA repair mechanisms, are known to produce different mutation types with characteristic frequency profiles, referred to as mutational signatures. Non-negative matrix factorization (NMF) has successfully been used to discover many mutational signatures, yielding novel insights into cancer etiology and targeted therapies. However, the NMF model is only a rough approximation to reality, and even small departures from this assumed model can have large negative effects on the accuracy and reliability of the results.

Harvesting heterogeneity: Selective expertise versus machine learning.

The heterogeneity of outcomes in behavioral research has long been perceived as a challenge for the validity of various theoretical models. More recently, however, researchers have started perceiving heterogeneity as something that needs to be not only acknowledged but also actively addressed, particularly in applied research. A serious challenge, however, is that classical psychological methods are not well suited for making practical recommendations when heterogeneous outcomes are expected.

Gut Microbiome and Osteoarthritis: Insights From the Naturally Occurring Canine Model of Osteoarthritis.

Objective: The purpose of this study was to enhance the current knowledge of the relationship between the gut microbiome and osteoarthritis (OA) and associated pain using pet dogs as a clinically relevant translational model.

Methods: Fecal samples were collected from 93 owned pet dogs. Dogs were designated as either clinically healthy or OA pain using validated methods.

A Pilot Randomized Controlled Trial of Vaginal Cryotherapy for the Treatment of Pelvic Floor Myofascial Pain.

Introduction And Hypothesis: Pelvic floor myofascial pain (PFMP) is a common but underrecognized component of chronic pelvic pain and pelvic floor disorders symptoms with limited, well-studied treatment modalities. Our objective was to determine the effect of vaginal cryotherapy on PFMP with palpation.

Methods: Following a standardized PFMP screening examination, individuals with a pain score ≥4/10 in ≥1 of four muscle groups were invited to participate in a randomized controlled trial comparing patients undergoing vaginal cryotherapy with controls.

Patterns of emotion-network dynamics are orthogonal to mood disorder status: An experience sampling investigation.

Individuals differ markedly in how they experience the ebb and flow of emotions. In this study, we used daily experience sampling to examine whether these differences reflect the nature and presence of mood disorders or whether they can better be characterized as distinct dynamic emotion profiles that cut-across diagnostic boundaries. We followed 105 individuals in 2019-2020 with diagnoses of major depression, remitted major depression, bipolar disorder, or no history of disorder, over 14 days ( = 6,543 experience-sampling assessments).

Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases.

Purpose: Preclinical data showed that prophylactic, low-dose temozolomide (TMZ) significantly prevented breast cancer brain metastasis. We present results of a phase I trial combining T-DM1 with TMZ for the prevention of additional brain metastases after previous occurrence and local treatment in patients with HER2+ breast cancer.

Patients And Methods: Eligible patients had HER2+ breast cancer with brain metastases and were within 12 weeks of whole brain radiation therapy (WBRT), stereotactic radiosurgery, and/or surgery.

Sexual Orientation and Racial Bias in Relation to Medical Specialty.

Physician explicit and implicit biases involving race and sexual orientation (SO) affect patient and provider experiences in healthcare settings. An anonymous survey was disseminated nationally to graduating medical students, residents, and practicing physicians to evaluate SO and racial biases across medical specialties. SO explicit and implicit bias were measured with the Attitudes toward Lesbians and Gay Men Scale, short form (ATLG-S) and Gay-Straight Implicit Association Test (IAT).

Tangent normalization for somatic copy-number inference in cancer genome analysis.

Motivation: Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas, the Broad Institute Genome Characterization Center developed the Tangent normalization method to generate copy-number profiles using data from single-nucleotide polymorphism (SNP) arrays and whole-exome sequencing (WES) technologies for over 10 000 pairs of tumors and matched normal samples.

Microenvironmental Landscape of Human Melanoma Brain Metastases in Response to Immune Checkpoint Inhibition.

Melanoma-derived brain metastases (MBM) represent an unmet clinical need because central nervous system progression is frequently an end stage of the disease. Immune checkpoint inhibitors (ICI) provide a clinical opportunity against MBM; however, the MBM tumor microenvironment (TME) has not been fully elucidated in the context of ICI. To dissect unique elements of the MBM TME and correlates of MBM response to ICI, we collected 32 fresh MBM and performed single-cell RNA sequencing of the MBM TME and T-cell receptor clonotyping on T cells from MBM and matched blood and extracranial lesions.

Identification of Small Regions of Overlap from Copy Number Variable Regions in Patients with Hypospadias.

Hypospadias is a common form of congenital atypical sex development that is often associated with other congenital comorbidities. Many genes have been associated with the condition, most commonly single sequence variations. Further investigations of recurrent and overlapping copy number variations (CNVs) have resulted in the identification of genes and chromosome regions associated with various conditions, including differences of sex development (DSD).

Telemedicine: The New "Virtual Reality" of Female Pelvic Medicine and Reconstructive Surgery?

Importance: Understanding women's acceptance of telemedicine as a model of care for pelvic floor disorders (PFDs) allows for a more patient-centered approach to widespread implementation in female pelvic medicine and reconstructive surgery.

Objectives: The pandemic sparked rapid and widespread implementation of telemedicine. Our goal was to assess acceptance, satisfaction, and desire for future use of telemedicine among women seeking care for PFDs.

CNGPLD: case-control copy-number analysis using Gaussian process latent difference.

Motivation: Cross-sectional analyses of primary cancer genomes have identified regions of recurrent somatic copy-number alteration, many of which result from positive selection during cancer formation and contain driver genes. However, no effective approach exists for identifying genomic loci under significantly different degrees of selection in cancers of different subtypes, anatomic sites or disease stages.

Results: CNGPLD is a new tool for performing case-control somatic copy-number analysis that facilitates the discovery of differentially amplified or deleted copy-number aberrations in a case group of cancer compared with a control group of cancer.

Distinct genetic pathways define pre-malignant versus compensatory clonal hematopoiesis in Shwachman-Diamond syndrome.

To understand the mechanisms that mediate germline genetic leukemia predisposition, we studied the inherited ribosomopathy Shwachman-Diamond syndrome (SDS), a bone marrow failure disorder with high risk of myeloid malignancies at an early age. To define the mechanistic basis of clonal hematopoiesis in SDS, we investigate somatic mutations acquired by patients with SDS followed longitudinally. Here we report that multiple independent somatic hematopoietic clones arise early in life, most commonly harboring heterozygous mutations in EIF6 or TP53.

Effect of very low-protein diets supplemented with branched-chain amino acids on energy balance, plasma metabolomics and fecal microbiome of pigs.

Feeding pigs with very-low protein (VLP) diets while supplemented with limiting amino acids (AA) results in decreased growth. The objective of this study was to determine if supplementing VLP diets with branched-chain AA (BCAA) would reverse the negative effects of these diets on growth and whether this is associated with alterations in energy balance, blood metabolomics and fecal microbiota composition. Twenty-four nursery pigs were weight-matched, individually housed and allotted into following treatments (n = 8/group): control (CON), low protein (LP) and LP supplemented with BCAA (LP + BCAA) for 4 weeks.

Inactivation of Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade.

The molecular mechanisms leading to resistance to PD-1 blockade are largely unknown. Here, we characterize tumor biopsies from a patient with melanoma who displayed heterogeneous responses to anti-PD-1 therapy. We observe that a resistant tumor exhibited a loss-of-function mutation in the tumor suppressor gene , whereas a sensitive tumor from the same patient did not.

Temozolomide in secondary prevention of HER2-positive breast cancer brain metastases.

Brain metastases occur in up to 25-55% of patients with metastatic HER2-positive breast cancer. Standard treatment has high rates of recurrence or progression, limiting survival and quality of life in most patients. Temozolomide (TMZ) is known to penetrate the blood-brain barrier and is US FDA approved for treatment of glioblastoma.