Determinants of Surgical Outcomes in Tricuspid Valve Endocarditis.

Background: Current treatment guidelines for infective endocarditis focus on left-sided infective endocarditis. Because right-sided infective endocarditis has different presentations and outcomes, it is crucial to further delineate surgical outcomes for isolated tricuspid valve endocarditis (TVE).

Methods: This retrospective study reviewed 374 surgically treated patients with isolated TVE from January 2012 through April 2022 who underwent isolated tricuspid valve surgical procedures.

Development of a Human Recombinant Collagen for Vat Polymerization-Based Bioprinting.

In light-based 3D-bioprinting, gelatin methacrylate (GelMA) is one of the most widely used materials, as it supports cell attachment, and shows good biocompatibility and degradability in vivo. However, as an animal-derived material, it also causes safety concerns when used in medical applications. Gelatin is a partial hydrolysate of collagen, containing high amounts of hydroxyproline.

Higher-order correction of persistent batch effects in correlation networks.

Motivation: Systems biology analyses often use correlations in gene expression profiles to infer co-expression networks that are then used as input for gene regulatory network inference or to identify functional modules of co-expressed or putatively co-regulated genes. While systematic biases, including batch effects, are known to induce spurious associations and confound differential gene expression analyses (DE), the impact of batch effects on gene co-expression has not been fully explored. Methods have been developed to adjust expression values, ensuring conditional independence of mean and variance from batch or other covariates for each gene, resulting in improved fidelity of DE analysis.

Treatment patterns, resource utilization and clinical outcomes in patients with higher risk myelodysplastic syndromes (MDS) in United States community practices.

Management of higher-risk myelodysplastic syndromes (HR-MDS) is challenging in the real world. We studied 200 patients with HR-MDS within a large US community hospital network. We describe the clinical presentation, patient-related factors, prognostic characteristics, treatment patterns, clinical outcomes and resource utilization.

Extracorporeal Membrane Oxygenation for Acute Respiratory Failure Due to COVID-19: A Multicenter Matched Cohort Study.

Mechanical ventilation for respiratory failure due to COVID-19 is associated with significant morbidity and mortality. Veno-venous extracorporeal membrane oxygenation (ECMO) is an attractive management option. This study sought to determine the effect of ECMO on hospital mortality and discharge condition in this population.

The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.

Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; netzoo.github.

A real-world retrospective study of the use of Ki-67 testing and treatment patterns in patients with HR+, HER2- early breast cancer in the United States.

Background: The National Comprehensive Cancer Network recommends that patients with hormone receptor-positive early breast cancer be considered for adjuvant endocrine therapy (ET) after primary treatment like surgical excision. Adjuvant chemotherapy (CT) use primarily depends on risk of recurrence. Biomarkers such as Ki-67 potentially have most value in patients with intermediate risk factors, such as involvement of 1-3 positive nodes.

Discordance in Tumor Mutation Burden from Blood and Tissue Affects Association with Response to Immune Checkpoint Inhibition in Real-World Settings.

Background: Tumor mutation burden (TMB), a biomarker for immune checkpoint inhibitor (CPI) response, is reported by both blood- and tissue-based next-generation sequencing (NGS) vendors. However, the agreement between TMB from blood (bTMB) and tissue (tTMB) in real-world settings, both in absolute value and association with CPI response, is not known.

Materials And Methods: This study utilizes Sarah Cannon's precision medicine platform, Genospace, to harmonize clinico-genomic data from 17 206 patients with cancer with NGS results from September 2015 to August 2021.

Tumor-Specific and Tumor-Agnostic Molecular Signatures Associated With Response to Immune Checkpoint Inhibitors.

Purpose: Next-generation sequencing (NGS) testing is being incorporated into routine standard of care for patients with cancer. Immune checkpoint inhibitors (CPIs) are approved for use in both tumor-specific and tumor-agnostic indications. We sought to determine tumor type-specific or tumor-agnostic correlations between mutations detected by NGS and response to CPIs.

Next-Generation Sequencing of Patients With Breast Cancer in Community Oncology Clinics.

Purpose: Molecular biomarkers informing disease diagnosis, prognosis, and treatment decisions in patients with breast cancer are being uncovered by next-generation sequencing (NGS) technologies. In this study, we survey how NGS is used for patients with breast cancer in real-world settings with a focus on physician behaviors and sequencing results.

Methods: We conducted a retrospective analysis of patients with breast cancer who received NGS testing from commercial vendors as part of standard of care from 2014 to 2019.

Pilot investigation on the dose-dependent impact of irradiation on primary human alveolar osteoblasts in vitro.

Radiotherapy of head and neck squamous cell carcinoma can lead to long-term complications like osteoradionecrosis, resulting in severe impairment of the jawbone. Current standard procedures require a 6-month wait after irradiation before dental reconstruction can begin. A comprehensive characterization of the irradiation-induced molecular and functional changes in bone cells could allow the development of novel strategies for an earlier successful dental reconstruction in patients treated by radiotherapy.

Convalescent plasma associates with reduced mortality and improved clinical trajectory in patients hospitalized with COVID-19.

BACKGROUNDEvidence supporting convalescent plasma (CP), one of the first investigational treatments for coronavirus disease 2019 (COVID-19), has been inconclusive, leading to conflicting recommendations. The primary objective was to perform a comparative effectiveness study of CP for all-cause, in-hospital mortality in patients with COVID-19.METHODSThe multicenter, electronic health records-based, retrospective study included 44,770 patients hospitalized with COVID-19 in one of 176 HCA Healthcare-affiliated community hospitals.

Comparison of the Translational Potential of Human Mesenchymal Progenitor Cells from Different Bone Entities for Autologous 3D Bioprinted Bone Grafts.

Reconstruction of segmental bone defects by autologous bone grafting is still the standard of care but presents challenges including anatomical availability and potential donor site morbidity. The process of 3D bioprinting, the application of 3D printing for direct fabrication of living tissue, opens new possibilities for highly personalized tissue implants, making it an appealing alternative to autologous bone grafts. One of the most crucial hurdles for the clinical application of 3D bioprinting is the choice of a suitable cell source, which should be minimally invasive, with high osteogenic potential, with fast, easy expansion.

Outcomes of COVID-19 in hospitalized solid organ transplant recipients compared to a matched cohort of non-transplant patients at a national healthcare system in the United States.

Data describing outcomes of solid organ transplant (SOT) recipients with coronavirus disease 2019 (COVID-19) are variable, and the association between SOT status and mortality remains unclear. In this study, we compare clinical outcomes of SOT recipients hospitalized with COVID-19 between March 10, and September 1, 2020, to a matched cohort of non-SOT recipients at a national healthcare system in the United States (US). From a population of 43 461 hospitalized COVID-19-positive patients, we created a coarsened exact matched cohort of 4035 patients including 128 SOT recipients and 3907 weighted matched non-SOT controls.

Estimating drivers of cell state transitions using gene regulatory network models.

Background: Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks.

Estimating gene regulatory networks with pandaR.

Contact: johnq@jimmy.harvard.edu or dschlauch@fas.

Identification of genetic outliers due to sub-structure and cryptic relationships.

Motivation: In order to minimize the effects of genetic confounding on the analysis of high-throughput genetic association studies, e.g. (whole-genome) sequencing (WGS) studies, genome-wide association studies (GWAS), etc.

Short-term triple therapy with lansoprazole 30 mg or 60 mg, amoxycillin and clarithromycin to eradicate Helicobacter pylori.

Background: We investigated the efficacy of 30 vs. 60 mg lansoprazole daily in a 1-week triple therapy for eradication of Helicobacter pylori in a prospective randomized study.

Methods: Two hundred and fifteen consecutive out-patients with peptic ulcer disease or non-ulcer dyspepsia, in whom H.

Direct dissolution of gallstones with methyl tert-butyl ether by endoscopic cannulation of the gallbladder.

Methyl tert-butyl ether (MTBE) rapidly and effectively dissolves cholesterol gallbladder stones. Due to the invasive nature of transhepatic catheterization, we studied the safety and efficacy of MTBE stone dissolution, delivered by endoscopic, retrograde cannulation of the gallbladder. Extracorporeal shock-wave lithotripsy (ESWL) was employed in patients with multiple stones, to increase contact surface area and facilitate dissolution.

[Enteroscopy--expansion of the diagnostic spectrum. Review and personal results].

The source of blood loss remains undetermined in 5% of patients with chronic gastrointestinal bleeding. Small bowel enteroscopy using a prototype of a sonde-type enteroscope was performed in 27 patients with chronic or subacute gastrointestinal bleeding of obscure origin. The procedure time ranged between 1.