Implementing an accelerated three-year MD curriculum at NYU Grossman School of Medicine.

Over the last decade there has been tremendous growth in the development of accelerated MD pathways that allow medical students to graduate in three years. Developing an accelerated pathway program requires commitment from students and faculty with intensive re-thinking and altering of the curriculum to ensure adequate content to achieve competency in an accelerated timeline. A re-visioning of assessment and advising must follow and the application of AI and new technologies can be added to support teaching and learning.

Towards Preanalytical Best Practices for Liquid Biopsy Studies: A BLOODPAC Landscape Analysis.

BLOODPAC is a public-private consortium that develops best practices, coordinates clinical and translational research, and manages the BLOODPAC Data Commons to broadly support the liquid biopsy community and accelerate regulatory review to aid patient accessibility. BLOODPAC previously recommended 11 preanalytical minimal technical data elements (MTDEs) for BLOODPAC-sponsored studies and data submitted to BLOODPAC Data Commons. The current landscape analysis evaluates the overlap of the BLOODPAC MTDEs with current best practices, guidelines, and standards documents related to clinical and research liquid biopsy applications.

An Unusual Ferryl Intermediate and Its Implications for the Mechanism of Oxacyclization by the Loline-Producing Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, LolO.

-Acetylnorloline synthase (LolO) is one of several iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases that catalyze sequential reactions of different types in the biosynthesis of valuable natural products. LolO hydroxylates C2 of 1--acetamidopyrrolizidine before coupling the C2-bonded oxygen to C7 to form the tricyclic loline core. Each reaction requires cleavage of a C-H bond by an oxoiron(IV) (ferryl) intermediate; however, different carbons are targeted, and the carbon radicals have different fates.

The Pandemic Response Commons.

Objectives: A data commons is a software platform for managing, curating, analyzing, and sharing data with a community. The Pandemic Response Commons (PRC) is a data commons designed to provide a data platform for researchers studying an epidemic or pandemic.

Methods: The PRC was developed using the open source Gen3 data platform and is based upon consortium, data, and platform agreements developed by the not-for-profit Open Commons Consortium.

A Framework for the Interoperability of Cloud Platforms: Towards FAIR Data in SAFE Environments.

As the number of cloud platforms supporting scientific research grows, there is an increasing need to support interoperability between two or more cloud platforms. A well accepted core concept is to make data in cloud platforms Findable, Accessible, Interoperable and Reusable (FAIR). We introduce a companion concept that applies to cloud-based computing environments that we call a ecure and uthorized AIR nvironment (SAFE).

Primary Hepatic EBV-DLBCL Lymphoma in the Setting of COVID-19 Infection.

This case study describes an instance of primary hepatic diffuse large B cell lymphoma (DLBCL) in a patient who had prolonged coronavirus disease 2019 (COVID-19). DLBCL rarely presents as a primary hepatic mass. The 53-year-old man sought emergency care because of fatigue and weight loss.

An open-source platform for pediatric cancer data exploration: a report from Data for the Common Good.

Objective: The Pediatric Cancer Data Commons (PCDC)-a project of Data for the Common Good-houses clinical pediatric oncology data and utilizes the open-source Gen3 platform. To meet the needs of end users, the PCDC development team expanded the out-of-box functionality and developed additional custom features that should be useful to any group developing similar data commons.

Materials And Methods: Modifications of the PCDC data portal software were implemented to facilitate desired functionality.

Transfer Learning for Mortality Prediction in Non-Small Cell Lung Cancer with Low-Resolution Histopathology Slide Snapshots.

High-resolution whole slide image scans of histopathology slides have been widely used in recent years for prediction in cancer. However, in some cases, clinical informatics practitioners may only have access to low-resolution snapshots of histopathology slides, not high-resolution scans. We evaluated strategies for training neural network prognostic models in non-small cell lung cancer (NSCLC) based on low-resolution snapshots, using data from the Veterans Affairs Precision Oncology Data Repository.

ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning.

Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting these data is challenging without expert input. We present Automated Tissue Alignment and Traversal (ATAT), a novel computational framework designed to enhance ST analysis in the context of multiple and complex tissue architectures and morphologies, such as those found in biopsies of the gastrointestinal tract. ATAT utilizes self-supervised contrastive learning on hematoxylin and eosin (H&E) stained images to automate the alignment and traversal of ST data.

Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons.

Veterans are at an increased risk for prostate cancer, a disease with extraordinary clinical and molecular heterogeneity, compared with the general population. However, little is known about the underlying molecular heterogeneity within the veteran population and its impact on patient management and treatment. Using clinical and targeted tumor sequencing data from the National Veterans Affairs health system, we conducted a retrospective cohort study on 45 patients with advanced prostate cancer in the Veterans Precision Oncology Data Commons (VPODC), most of whom were metastatic castration-resistant.

Optimizing Contrast Resolution in Digital Chest Radiography by Varying Copper Filtration and kVp.

Purpose: To measure the effect of increasing kilovoltage peak (kVp) and copper filtration thickness on entrance skin exposure and contrast resolution for chest radiography performed using digital flat-panel detectors.

Methods: A phantom-based experiment was conducted in which 24 radiographs of a quality control chest phantom were obtained at varying kVp levels and copper filtration thicknesses. The entrance skin exposure was measured and analyzed for each exposure.

Structure Revision of Type B Polycyclic Polyprenylated Acylphloroglucinols Fused to a Partly Reduced Furan Ring.

Four previous papers reported the isolation and structural determination of 10 polycyclic polyprenylated acylphloroglucinols (PPAPs), uraliones F, G, K, and O, attenuatumiones E and F, and scabrumiones A-D, from species. Their structures were identified as type B PPAPs that featured not only the characteristic acyl group at C-3 of the bicyclo[3.3.

A Conformationally Restricted Gold(III) Complex Elicits Antiproliferative Activity in Cancer Cells.

Diamine ligands are effective structural scaffolds for tuning the reactivity of transition-metal complexes for catalytic, materials, and phosphorescent applications and have been leveraged for biological use. In this work, we report the synthesis and characterization of a novel class of cyclometalated [C^N] Au(III) complexes bearing secondary diamines including a norbornane backbone, (2,3)-,-dibenzylbicyclo[2.2.

Mortality in ASIA Impairment Scale grade A to D Patients With Odontoid Fracture and Magnetic Resonance Imaging Evidence of Spinal Cord Injury.

Odontoid fractures are common, often presenting in the elderly after a fall and infrequently associated with traumatic spinal cord injury (tSCI). The goal of this study was to analyze predictors of mortality and neurological outcome when odontoid fractures were associated with signal change on magnetic resonance imaging (MRI) at admission. Over an 18-year period (2001-2019), 33 patients with odontoid fractures and documented tSCI on MRI were identified.

Riluzole in Spinal Cord Injury Study (RISCIS)-Pharmacokinetic (PK) Sub-Study: An Analysis of Pharmacokinetics, Pharmacodynamics, and Impact on Axonal Degradation of Riluzole in Patients With Traumatic Cervical Spinal Cord Injury Enrolled in the RISCIS Phase III Randomized Controlled Trial.

To date, no drug therapy has shown significant efficacy in improving functional outcomes in patients with acute spinal cord injury (SCI). Riluzole is an approved benzothiazole sodium channel blocker to attenuate neurodegeneration in amyotrophic lateral sclerosis (ALS) and is of interest for neuroprotection in SCI. In a Phase I clinical trial (ClinicalTrials.

Total synthesis and structural reassignment of garcinielliptone FC, a polycyclic polyprenylated acylphloroglucinol with diverse bioactivity.

Garcinielliptone FC (GFC) was assigned to be a type A polycyclic polyprenylated acylphloroglucinol (PPAP) and was found to exhibit diverse biological activities. Now we revise the structure of GFC to xanthochymol, a type B PPAP, NMR and total synthesis methods. The total syntheses of (±)-xanthochymol and (±)-cycloxanthochymol were accomplished in 12 and 13 steps, respectively.

Variability in Early Surgery for Acute Cervical Spinal Cord Injury Patients: An Opportunity for Enhanced Care Delivery.

Data supporting the benefits of early surgical intervention in acute spinal cord injury (SCI) is growing. For early surgery to be accomplished, understanding the causes of variabilities that effect the timing of surgery is needed to achieve this goal. The purpose of this analysis is to determine factors that affect the timing of surgery for acute cervical SCI within the North American Clinical Trials Network (NACTN) for SCI registry.

North American Clinical Trials Network for Spinal Cord Injury Registry: Methodology and Analysis.

The North American Clinical Trials Network (NACTN) for Spinal Cord Injury (SCI) is a consortium of neurosurgery departments at university affiliated hospitals with medical, nursing, and rehabilitation personnel who are skilled in the assessment, evaluation, and management of SCI. NACTN was established with the goal of consistently advancing the quality of life of people with SCI through clinical trials of new therapies that provide robust evidence of safety and effectiveness. A prospective multi-center Registry was created to collect the natural course of the acute traumatic SCI patient from time of injury to 12 months follow-up.

Lived experience-centred word clouds may improve research uncertainty gathering in priority setting partnerships.

Introduction: AO Spine RECODE-DCM was a multi-stakeholder priority setting partnership (PSP) to define the top ten research priorities for degenerative cervical myelopathy (DCM). Priorities were generated and iteratively refined using a series of surveys administered to surgeons, other healthcare professionals (oHCP) and people with DCM (PwDCM). The aim of this work was to utilise word clouds to enable the perspectives of people with the condition to be heard earlier in the PSP process than is traditionally the case.

Towards self-describing and FAIR bulk formats for biomedical data.

We introduce a self-describing serialized format for bulk biomedical data called the Portable Format for Biomedical (PFB) data. The Portable Format for Biomedical data is based upon Avro and encapsulates a data model, a data dictionary, the data itself, and pointers to third party controlled vocabularies. In general, each data element in the data dictionary is associated with a third party controlled vocabulary to make it easier for applications to harmonize two or more PFB files.

Artificial Intelligence Screening of Medical School Applications: Development and Validation of a Machine-Learning Algorithm.

Purpose: To explore whether a machine-learning algorithm could accurately perform the initial screening of medical school applications.

Method: Using application data and faculty screening outcomes from the 2013 to 2017 application cycles (n = 14,555 applications), the authors created a virtual faculty screener algorithm. A retrospective validation using 2,910 applications from the 2013 to 2017 cycles and a prospective validation using 2,715 applications during the 2018 application cycle were performed.