ELLA: Modeling Subcellular Spatial Variation of Gene Expression within Cells in High-Resolution Spatial Transcriptomics.

Spatial transcriptomic technologies are becoming increasingly high-resolution, enabling precise measurement of gene expression at the subcellular level. Here, we introduce a computational method called subcellular expression localization analysis (ELLA), for modeling the subcellular localization of mRNAs and detecting genes that display spatial variation within cells in high-resolution spatial transcriptomics. ELLA creates a unified cellular coordinate system to anchor diverse cell shapes and morphologies, utilizes a nonhomogeneous Poisson process to model spatial count data, leverages an expression gradient function to characterize subcellular expression patterns, and produces effective control of type I error and high statistical power.

Surveillance strategies for the detection of new pathogen variants across epidemiological contexts.

Surveillance systems that monitor pathogen genome sequences are critical for rapidly detecting the introduction and emergence of pathogen variants. To evaluate how interactions between surveillance capacity, variant properties, and the epidemiological context influence the timeliness of pathogen variant detection, we developed a geographically explicit stochastic compartmental model to simulate the transmission of a novel SARS-CoV-2 variant in New York City. We measured the impact of (1) testing and sequencing volume, (2) geographic targeting of testing, (3) the timing and location of variant emergence, and (4) the relative variant transmissibility on detection speed and on the undetected disease burden.

Endoscopic Ultrasound-guided Transmural Biliary Drainage With 6 mm and 8 mm Cautery-enhanced Lumen-apposing Metal Stents: A Multicenter Collaborative Study.

Objective: Endoscopic retrograde cholangiopancreatography (ERCP) may be unsuccessful in patients with duodenal stenosis or malignant ampullary infiltration. Endoscopic ultrasound-guided biliary drainage (EUS-BD) has been proposed as an alternative. We aimed to assess the efficacy and safety of EUS-BD for malignant distal bile duct obstruction using the newly introduced smaller caliber 6 or 8 mm cautery-enhanced lumen-apposing metal stent.

The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021.

Socio-economic disparities were associated with disproportionate viral incidence between neighborhoods of New York City (NYC) during the first wave of SARS-CoV-2. We investigated how these disparities affected the co-circulation of SARS-CoV-2 variants during the second wave in NYC. We tested for correlation between the prevalence, in late 2020/early 2021, of Alpha, Iota, Iota with E484K mutation (Iota-E484K), and B.

Reasons for Discordance between Ga-PSMA-PET and Magnetic Resonance Imaging in Men with Metastatic Prostate Cancer.

Background: PSMA PET has emerged as a "gold standard" imaging modality for assessing prostate cancer metastases. However, it is not universally available, and this limits its impact. In contrast, whole-body MRI is much more widely available but misses more lesions.

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.

With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine-learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome.

Association between neighbourhood composition, kindergarten educator-reported distance learning barriers, and return to school concerns during the first wave of the COVID-19 pandemic in Ontario, Canada.

Introduction: Research to date has established that the COVID-19 pandemic has not impacted everyone equitably. Whether this unequitable impact was seen educationally with regards to educator reported barriers to distance learning, concerns and mental health is less clear.

Objective: The objective of this study was to explore the association between the neighbourhood composition of the school and kindergarten educator-reported barriers and concerns regarding children's learning during the first wave of COVID-19 related school closures in Ontario, Canada.

Travel history among persons infected with SARS-CoV-2 variants of concern in the United States, December 2020-February 2021.

The first three SARS-CoV-2 phylogenetic lineages classified as variants of concern (VOCs) in the United States (U.S.) from December 15, 2020 to February 28, 2021, Alpha (B.

A high-dimensional mediation model for a neuroimaging mediator: Integrating clinical, neuroimaging, and neurocognitive data to mitigate late effects in pediatric cancer.

Pediatric cancer treatment, especially for brain tumors, can have profound and complicated late effects. With the survival rates increasing because of improved detection and treatment, a more comprehensive understanding of the impact of current treatments on neurocognitive function and brain structure is critically needed. A frontline medulloblastoma clinical trial (SJMB03) has collected data, including treatment, clinical, neuroimaging, and cognitive variables.

The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B.

Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021.

Background: Monitoring the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified.

Methods: We performed phylogeographic analysis on 15 967 Gamma sequences sampled between 10 March and 1 May 2021, to identify geographic sources of Gamma lineages introduced into NYC.

Epidemiological characteristics of the B.1.526 SARS-CoV-2 variant.

To characterize the epidemiological properties of the B.1.526 SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) variant of interest, here we used nine epidemiological and population datasets and model-inference methods to reconstruct SARS-CoV-2 transmission dynamics in New York City, where B.

From Full Day Learning to 30 Minutes a Day: A Descriptive Study of Early Learning During the First COVID-19 Pandemic School Shutdown in Ontario.

Unlabelled: When the COVID-19 pandemic was declared in March 2020, the lives of families all over the world were disrupted. Many adults found themselves working from home while their children were unable to go to school. To better understand the potential impact of these educational disruptions, it is important to establish what learning looked like during the first school shutdown in the spring of 2020, particularly for the youngest learners who may feel the longest lasting impacts from this pandemic.

Magnetic Resonance Imaging Radiomics-Based Machine Learning Prediction of Clinically Significant Prostate Cancer in Equivocal PI-RADS 3 Lesions.

Background: While Prostate Imaging Reporting and Data System (PI-RADS) 4 and 5 lesions typically warrant prostate biopsy and PI-RADS 1 and 2 lesions may be safely observed, PI-RADS 3 lesions are equivocal.

Purpose: To construct and cross-validate a machine learning model based on radiomics features from T -weighted imaging (T WI) of PI-RADS 3 lesions to identify clinically significant prostate cancer (csPCa), that is, pathological Grade Group ≥ 2.

Study Type: Single-center retrospective study.