Gene trajectory inference for single-cell data by optimal transport metrics.

Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied.

HIF-1 regulates pathogenic cytotoxic T cells in lupus skin disease.

Cutaneous lupus erythematosus (CLE) is a disfiguring autoimmune skin disease characterized by an inflammatory infiltrate rich in T cells, which are strongly implicated in tissue damage. How these cells adapt to the skin environment and promote tissue inflammation and damage is not known. In lupus nephritis, we previously identified an inflammatory gene program in kidney-infiltrating T cells that is dependent on HIF-1, a transcription factor critical for the cellular and developmental response to hypoxia as well as inflammation-associated signals.

Grading system for medullary thyroid carcinoma; an institutional experience.

Objective: Medullary thyroid carcinoma (MTC) is a rare type of thyroid malignancy. Recently, a two-tier grading system (GS) for MTC has been suggested. We conducted this study to evaluate the generalizability, as well as application of recently proposed GS to our cohort of Medullary thyroid carcinoma (MTC) cases.

On the efficient evaluation of the azimuthal Fourier components of the Green's function for Helmholtz's equation in cylindrical coordinates.

In this paper, we develop an efficient algorithm to evaluate the azimuthal Fourier components of the Green's function for the Helmholtz equation in cylindrical coordinates. A computationally efficient algorithm for this modal Green's function is essential for solvers for electromagnetic scattering from bodies of revolution (e.g.

Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.

Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns in a way that informs tissue biology are major computational and epistemological challenges. Here, we present Connectome, a software package for R which facilitates rapid calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data.

RAS mutation and associated risk of malignancy in the thyroid gland: An FNA study with cytology-histology correlation.

Background: Activating point mutations of the RAS gene (NRAS, HRAS, and KRAS) can be seen in benign and malignant thyroid tumors; among these, NRAS mutations are more commonly seen. This study was conducted to evaluate the thyroid risk of malignancy (ROM) associated with RAS mutations in thyroid fine-needle aspiration (FNA) at the authors' institution.

Methods: The authors searched their electronic database system between January 2015 and May 2021 for thyroid FNA cases with any type of RAS mutation.

Anaplastic Thyroid Carcinoma: Cytomorphologic Features on Fine-Needle Aspiration and Associated Diagnostic Challenges.

Objectives: Anaplastic thyroid carcinoma (ATC) is an aggressive malignancy, and early diagnosis, often aided by fine-needle aspiration (FNA), is key to improving patient prognosis. While the current literature describes some of the cytologic features (CFs) of this entity, a comprehensive examination of the CFs has not yet been performed.

Methods: We retrospectively searched our electronic database for ATC cases with available slides between January 2008 and December 2019.

Histopathologic and Machine Deep Learning Criteria to Predict Lymphoma Transformation in Bone Marrow Biopsies.

Context.—: Large cell transformation (LCT) of indolent B-cell lymphomas, such as follicular lymphoma (FL) and chronic lymphocytic leukemia (CLL), signals a worse prognosis, at which point aggressive chemotherapy is initiated. Although LCT is relatively straightforward to diagnose in lymph nodes, a marrow biopsy is often obtained first given its ease of procedure, low cost, and low morbidity.

Predictors of Family Dissatisfaction with Support During Neurocritical Care Shared Decision-Making.

Background: There is a critical need to improve support for families making difficult shared decisions about patient care with clinicians in the neuroscience ICU (neuro-ICU). The aim of this study is to identify patient- and family-related factors associated with dissatisfaction with shared decision-making support among families of neuro-critically ill patients.

Methods: We conducted a retrospective observational cohort study using survey data that had been collected from a consecutive sample of family members of patients in the neuro-ICU (one family member per patient) at two US academic centers.

Quantitative assessment of p16 expression in FNA specimens from head and neck squamous cell carcinoma and correlation with HPV status.

Background: This study investigated p16 by immunohistochemistry (IHC) on cellblocks (CBs) and human papillomavirus (HPV) by polymerase chain reaction (PCR) in fine-needle aspiration (FNA) of head and neck squamous cell carcinoma (HNSCC).

Methods: Receiver operating characteristic (ROC) curve analysis was used to assess test performance in CBs compared with p16 IHC in 42 surgical specimens from patients with HNSCC and in correlation with HPV by PCR in cytology specimens. The study assessed HPV by PCR in FNA specimens as a substitute for p16 IHC in surgical specimens.

Methods for registering and calibrating terahertz images of cutaneous burn wounds.

A method to register THz and visible images of cutaneous burn wounds and to calibrate THz image data is presented. Images of partial and full thickness burn wounds in 9 rats were collected over 435 mins. = 7.

Registration, results reporting, and publication bias of clinical trials supporting FDA approval of neuropsychiatric drugs before and after FDAAA: a retrospective cohort study.

Background: Mandatory trial registration, and later results reporting, were proposed to mitigate selective clinical trial publication and outcome reporting. The Food and Drug Administration (FDA) Amendments Act (FDAAA) was enacted by Congress on September 27, 2007, requiring the registration of all non-phase I clinical trials involving FDA-regulated medical interventions and results reporting for approved drugs. The association between FDAAA enactment and the registration, results reporting, and publication bias of neuropsychiatric trials has not been studied.

Intraoperative neurophysiological monitoring in neuroanesthesia.

Purpose Of Review: The purpose of this review is to highlight the importance of making informed choices of anesthetics and evaluating the impact of depth of anesthesia, hemodynamic status and other factors capable of interfering with signal capture during intraoperative neurophysiological monitoring (IONM).

Recent Findings: Over the last decades, neuromonitoring has advanced considerably, allowing for insights into neurological function during anesthesia and making it possible to assess intraoperative consciousness and neural integrity in real time. IONM is indicated in surgeries posing risk to targeted neural tissues and adjacent structures.

Optical System Design for Noncontact, Normal Incidence, THz Imaging of Human Cornea.

Reflection mode Terahertz (THz) imaging of corneal tissue water content (CTWC) is a proposed method for early, accurate detection and study of corneal diseases. Despite promising results from and cornea studies, interpretation of the reflectivity data is confounded by the contact between corneal tissue and dielectric windows used to flatten the imaging field. Herein, we present an optical design for non-contact THz imaging of cornea.

THz imaging system for human cornea.

Terahertz (THz) imaging of corneal tissue water content (CTWC) is a proposed method for early, accurate detection and study of corneal diseases. Despite promising results from and cornea studies, interpretation of the reflectivity data is confounded by the contact between corneal tissue and rigid dielectric window used to flatten the imaging field. This work develops a novel imaging system and image reconstruction methods specifically for nearly spherical targets such as human cornea.

Dynamic Optical Contrast Imaging.

The variable location and indistinct features of parathyroid glands can make their intraoperative identification challenging. Currently, there exists no routine use of localization methods during surgery. Dynamic optical contrast imaging (DOCI) leverages a novel realization of temporally dependent measurements of tissue autofluorescence that allows the acquisition of specific tissue properties.

Dynamic optical contrast imaging as a novel modality for rapidly distinguishing head and neck squamous cell carcinoma from surrounding normal tissue.

Background: Head and neck squamous cell carcinomas (HNSCCs) are debilitating diseases for which a patient's prognosis depends heavily on complete tumor resection. Currently, the surgeon's fingers determine the location of tissue margins. This study evaluated the diagnostic utility of a novel imaging modality, dynamic optical contrast imaging (DOCI), in the detection of HNSCC.

Focal Laser Ablation of Prostate Cancer: Phase I Clinical Trial.

Purpose: Focal laser ablation is an investigational technique to treat prostate cancer in a region confined manner via coagulative necrosis. This phase I trial primarily examines the safety of transrectal magnetic resonance imaging guided (in-bore) focal laser ablation in men with intermediate risk prostate cancer. An exploratory end point is cancer control after 6 months.

THz and mm-Wave Sensing of Corneal Tissue Water Content: Electromagnetic Modeling and Analysis.

Terahertz (THz) spectral properties of human cornea are explored as a function of central corneal thickness (CCT) and corneal water content, and the clinical utility of THz-based corneal water content sensing is discussed. Three candidate corneal tissue water content (CTWC) perturbations, based on corneal physiology, are investigated that affect the axial water distribution and total thickness. The THz frequency reflectivity properties of the three CTWC perturbations were simulated and explored with varying system center frequency and bandwidths (Q-factors).

Preliminary results of non-contact THz imaging of cornea.

This paper presents a novel THz optical design that allows the acquisition of THz reflectivity maps of cornea without the need for a field flattening window and preliminary imaging results of in vivo rabbit cornea. The system's intended use is to sense small changes in corneal tissue water content (CTWC) that can be precursors for a host of diseases and pathologies. Unique beam optics allows the scanning of a curved surface at normal incidence while keeping the source detector and target stationary.

THz and mm-Wave Sensing of Corneal Tissue Water Content: Sensing and Imaging Results.

A pulsed terahertz (THz) imaging system and millimeter-wave reflectometer were used to acquire images and point measurements, respectively, of five rabbit cornea . These imaging results are the first ever produced of cornea. A modified version of a standard protocol using a gentle stream of air and a Mylar window was employed to slightly dehydrate healthy cornea.

A system for evaluating magnetic resonance imaging of prostate cancer using patient-specific 3D printed molds.

We have developed a system for evaluating magnetic resonance imaging of prostate cancer, using patient-specific 3D printed molds to facilitate MR-histology correlation. Prior to radical prostatectomy a patient receives a multiparametric MRI, which an expert genitourinary radiologist uses to identify and contour regions suspicious for disease. The same MR series is used to generate a prostate contour, which is the basis for design of a patient-specific mold.

Ultrasound-stimulated vibro-acoustography for high-resolution differentiation based on viscoelastic properties of tissue mimicking phantoms.

In the absence of an imaging technique that provides imagery of diseased tissue with high diagnostic accuracy and contrast, surgeons must often excise excess healthy tissue surrounding neoplasms to ensure complete removal of malignant tissues. Additional approaches that are commonly used in the detection of tumor regions include palpation and conventional ultrasound to locate the affected area. However, these techniques suffer from limitations such as minimal specificity and lack of depth penetration.