Publications by authors named "Rotman J"

Article Synopsis
  • * RNA-seq allows researchers to investigate various aspects of gene expression, such as identifying new exons, measuring gene expression levels, and studying alternative splicing, but challenges persist in extracting meaningful data due to the complexity and size of the datasets.
  • * The review aims to clarify essential concepts and terminology related to RNA-seq data analysis, highlighting the evolution of computational tools as technology advances and the importance of researchers’ computational skills.
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Elder abuse, defined as "harm inflicted on an older person in a relationship where there is an expectation of trust, and/or when the person is targeted based on age or disability," can be challenging for clinicians to identify. Radiologists can help raise appropriate suspicion for elder abuse based on a patient's imaging. This article reviews common distributions and radiographic patterns of injury sustained in physical elder abuse.

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Understanding the pathophysiology of a disease allows physicians to make a diagnosis, alter its natural course, and develop and implement appropriate preventative and management strategies. With ballistic injuries, an understanding of how the mechanism of injury translates to the injuries observed makes it possible to make sense of what can, at times be a complex imaging appearance and mitigate against the long-term complications of gunshot wounds. In this article, the authors describe the different types of ballistic projectiles, their mechanism of injury as well as the injury patterns they cause.

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Purpose: The aim of this study was to demonstrate that the transition from a stand-alone radiology clerkship block to a longitudinally integrated radiology curriculum leverages newer teaching tools favored by today's learners.

Methods: In 2013 and 2014, medical students attended a dedicated 1-week radiology clerkship course. In 2015, the block clerkship model for radiology transitioned to a vertically integrated curriculum.

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Purpose: To determine the incidence and clinical predictors of intrathoracic complications in COVID-19 patients, and the association with outcomes.

Methods: In this retrospective cross-sectional study, we included 976 patients (age 61 ± 17 years, 62% male) who tested positive for SARS-CoV-2 between March 3-April 4, 2020 and underwent chest imaging. 3836 radiographs from 976 patients and 105 CTs from 88 patients were reviewed for intrathoracic complications, including pneumothorax, pneumomediastinum, pneumopericardium, lobar collapse, pleural effusion, and pneumatocele formation.

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Human papillomavirus (HPV) infection drives tumorigenesis in almost all cervical cancers and a fraction of vulvar and penile cancers. Due to increasing incidence and low vaccination rates, many will still have to face HPV-related morbidity and mortality in the upcoming years. Current treatment options (i.

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Background: Therapeutic immune intervention is highly dependent on the T-cell priming and boosting capacity of tumor-draining lymph nodes (TDLN). In vulvar cancer, in-depth studies on the immune status of (pre)metastatic TDLN is lacking.

Methods: We have phenotyped and enumerated various T-cell and myeloid subsets in tumor-free (LN-, n=27) and metastatic TDLN (LN+, n=11) using flow cytometry.

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Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads.

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Unlabelled: Pelvic fracture patients were randomized to blinded daily subcutaneous teriparatide (TPTD) or placebo to assess healing and functional outcomes over 3 months. With TPTD, there was no evidence of improved healing by CT or pain reduction; however, physical performance improved with TPTD but not placebo (group difference p < 0.03).

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Background: Usual vulvar intraepithelial neoplasia (uVIN) is a premalignancy caused by persistent infection with high-risk types of human papillomavirus (HPV), mainly type 16. Even though different treatment modalities are available (eg, surgical excision, laser evaporation or topical application of imiquimod), these treatments can be mutilating, patients often have recurrences and 2%-8% of patients develop vulvar carcinoma. Therefore, immunotherapeutic strategies targeting the pivotal oncogenic HPV proteins E6 and E7 are being explored to repress carcinogenesis.

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Background: Human papillomavirus (HPV) infection is known to promote the development of mucosal squamous cell carcinoma (mSCC), including pathologically high-grade lesions, but its role in cutaneous squamous cell carcinoma (cuSCC) remains unclear, particularly in lesions that are considered high risk.

Objective: We aimed to determine whether enhanced HPV transcriptional activity can be detected in high-risk cuSCC samples compared with low-grade SCC samples or normal skin.

Methods: We performed RNA sequencing of cuSCC across 23 risk-stratified skin lesions.

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Background: Coronavirus disease 2019 (COVID-19) affects vulnerable populations (VP) adversely.

Purpose: To evaluate overall imaging utilization in vulnerable subgroups (elderly, racial/ethnic minorities, socioeconomic status [SES] disadvantage) and determine if a particular subgroup has worse outcomes from COVID-19.

Materials/methods: Of 4110 patients who underwent COVID-19 testing from March 3-April 4, 2020 at NewYork-Presbyterian Hospital (NYP) health system, we included 1121 COVID-19 positive adults (mean age 59±18 years, 59% male) from two academic hospitals and evaluated imaging utilization rates and outcomes, including mortality.

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Human papillomavirus (HPV) drives high-grade intraepithelial neoplasia and cancer; for unknown reasons, this occurs most often in the cervical transformation zone. Either mutation or HPV E6-driven inhibition of Notch1 can drive neoplastic development in stratified squamous epithelia. However, the contribution of Notch1 and its Delta-like ligands (DLL) to site susceptibility remains poorly understood.

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PD-1/PD-L1 immune checkpoint inhibitors show potential for cervical cancer treatment. However, low response rates suggest that patient selection based on PD-L1 protein expression is not optimal. Here, we evaluated different PD-L1 detection methods and studied transcriptional regulation of PD-L1/PD-L2 expression by The Cancer Genome Atlas (TCGA) mRNAseq analysis.

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While initial reports regarding coronavirus disease 2019 (COVID-19) focused on its pulmonary manifestations, more recent literature describes multisystem abnormalities related to its associated microvascular angiopathy. Calciphylaxis is a rare systemic condition characterized by tissue necrosis in the setting of systemic microvascular calcifications. Both COVID-19 and calciphylaxis are procoagulant diagnoses associated with vascular-mediated cutaneous findings.

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Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.

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Purpose: Adenocarcinoma of the uterine cervix is the second most common type of cervical cancer after squamous cell carcinoma (SCC). Although both subtypes are treated similarly, patients with adenocarcinoma have a worse prognosis. In this study, immunologic features of the tumor microenvironment in these two subsets were pursued with potential therapeutic implications.

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Aim: To test whether alerting clinicians to severe weight loss in older patients leads to higher dietitian visit rates, to higher body mass index (BMI) levels and, mainly, to lower annual death risk.

Methods: The randomized controlled trial included patients aged ≥75 years, with BMI ≤23 kg/m that decreased ≥2 kg/m during the previous 2 years. All participants received usual care.

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Background: In today's world of big data, computational analysis has become a key driver of biomedical research. High-performance computational facilities are capable of processing considerable volumes of data, yet often lack an easy-to-use interface to guide the user in supervising and adjusting bioinformatics analysis via a tablet or smartphone.

Results: To address this gap we proposed Telescope, a novel tool that interfaces with high-performance computational clusters to deliver an intuitive user interface for controlling and monitoring bioinformatics analyses in real-time.

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Chronic pelvic pain is an important but underrecognized cause of morbidity in men. While there is abundant literature discussing female pelvic pain and the diagnostic role of imaging, much less attention has been given to imaging of non-gynecologic causes of chronic pelvic pain. Chronic pelvic pain in men can be a challenge to diagnose as pain may arise from visceral, musculoskeletal, or neurovascular pathology.

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Objectives: The benefit of alerting clinical staff to drug-induced hypocholesterolemia in patients aged 75 years and older remains uncertain.

Design, Setting, And Participants: The study included 1791 patients with serum cholesterol <160 mg/dL and on cholesterol-lowering drugs who were assigned to have an e-mail alert sent to their physician, and 1804 patients who were assigned to receive usual clinical care (control group). The primary outcome of the trial was annual death rate.

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Objectives: The benefit of alerting clinical staff to low plasma glycated hemoglobin (HbA1c) in patients aged 75 years and older who receive antidiabetic drugs remains uncertain.

Design, Setting, And Participants: In a randomized controlled trial, 1684 patients with HbA1c ≤ 6.5% who received antidiabetic drugs were assigned to have an e-mail alert sent to their physician, and 1643 were assigned to have no such alert (control group).

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Juvenile granulosa cell tumor (JGCT) is an extremely rare ovarian tumor that has been associated with Maffucci syndrome. It both secretes hormone and has been postulated to grow in response to hormone. We present a case of a 33-year-old G1P0 asymptomatic woman with a history of Maffucci syndrome found to have a left adnexal mass on routine ultrasonography at 13 weeks gestation.

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Lymph nodes draining the primary tumor are essential for the initiation of an effective anti-tumor T-cell immune response. However, cancer-derived immune suppressive factors render the tumor-draining lymph nodes (TDLN) immune compromised, enabling tumors to invade and metastasize. Unraveling the different mechanisms underlying this immune escape will inform therapeutic intervention strategies to halt tumor spread in early clinical stages.

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