Resource requirements to accelerate clinical applications of next-generation sequencing and radiomics: workshop commentary and review.

The National Institutes of Health-US Food and Drug Administration Joint Leadership Council Next-Generation Sequencing and Radiomics Working Group was formed by the National Institutes of Health-Food and Drug Administration Joint Leadership Council to promote the development and validation of innovative next-generation sequencing tests, radiomic tools, and associated data analysis and interpretation enhanced by artificial intelligence and machine learning technologies. A 2-day workshop was held on September 29-30, 2021, to convene members of the scientific community to discuss how to overcome the "ground truth" gap that has frequently been acknowledged as 1 of the limiting factors impeding high-quality research, development, validation, and regulatory science in these fields. This report provides a summary of the resource gaps identified by the working group and attendees, highlights existing resources and the ways they can potentially be employed to accelerate growth in these fields, and presents opportunities to support next-generation sequencing and radiomic tool development and validation using technologies such as artificial intelligence and machine learning.

Why Should Pharmacy Students Take Biochemistry?

The role of biochemistry in the pharmacy curriculum has recently been questioned based on its relevance to the career of a working pharmacist. This commentary explores the historical background of pharmacy education and the central role of chemistry since the 19th century. Reasons for the importance of biochemistry and other sciences are introduced to demonstrate their role in the practice of pharmacy.

Management of paroxysmal nocturnal hemoglobinuria in CALR mutated post-essential thrombocythemia myelofibrosis: A case report.

Paroxysmal nocturnal hemoglobinuria (PNH) results from the loss of erythrocyte surface proteins, leading to complement activation and its spectrum of effects. We explore this case of a 57-year-old man with post-essential thrombocythemia (ET) myelofibrosis (MF) who developed symptomatic anemia with evidence of hemolysis on lab work. While hemolysis was localized to be intramedullary based on workup, the exact diagnosis was undetermined, leading to a prolonged course of steroid therapy to control anemia.

ATP Redux.

The renaissance of interest in metabolism has focused mostly on techniques to measure massive numbers of metabolites. Yet, established metabolic theory has been abandoned. Here, I highlight one misconception: how ATP (and ADP and AMP) are currently understood.

Revisiting prochirality.

We propose a new model for prochirality that satisfies all known examples: the prochiral plane. This plane contains the prochiral carbon and defines two separate faces for chemical modification. We extend this to enzyme catalysis, replacing the "three point attachment" hypothesis and its variants.

Impact of prevalence and case distribution in lab-based diagnostic imaging studies.

We investigated effects of prevalence and case distribution on radiologist diagnostic performance as measured by area under the receiver operating characteristic curve (AUC) and sensitivity-specificity in lab-based reader studies evaluating imaging devices. Our retrospective reader studies compared full-field digital mammography (FFDM) to screen-film mammography (SFM) for women with dense breasts. Mammograms were acquired from the prospective Digital Mammographic Imaging Screening Trial.

An Idea to Explore: Understanding Redox Reactions in Biochemistry.

Understanding redox reactions in biochemistry requires a clear grasp of three definitions: electron exchange, oxidation number, and oxygen atom insertion. Here, the electrochemical cell is explained for redox-active ions, introducing a new comparison between the measurement of midpoint potential and the measurement of initial velocity for enzymes. Oxygen atom insertion is shown to be of use in readily classifying oxidation states.

Covalently deposited dyes: a new chromogen paradigm that facilitates analysis of multiple biomarkers in situ.

Multiplexed analysis of multiple biomarkers in a tissue sample requires use of reporter dyes with specific spectral properties that enable discrimination of signals. Conventional chromogens with broad absorbance spectra, widely used in immunohistochemistry (IHC), offer limited utility for multiplexed detection. Many dyes with narrow absorbance spectra, eg rhodamines, fluoresceins, and cyanines, potentially useful for multiplexed detection are well-characterized; however, generation of a chromogenic reagent useful for IHC analysis has not been demonstrated.

Ca effects on glucose transport and fatty acid oxidation in L6 skeletal muscle cell cultures.

We examined the effect of Ca on skeletal muscle glucose transport and fatty acid oxidation using L6 cell cultures. Ca stimulation of glucose transport is controversial. We found that caffeine (a Ca secretagogue) stimulation of glucose transport was only evident in a two-part incubation protocol ("post-incubation").

Membrane depolarization increases ryanodine sensitivity to Ca2+ release to the cytosol in L6 skeletal muscle cells: Implications for excitation-contraction coupling.

The dihydropyridine receptor in the plasma membrane and the ryanodine receptor in the sarcoplasmic reticulum are known to physically interact in the process of excitation-contraction coupling. However, the mechanism for subsequent Ca(2+) release through the ryanodine receptor is unknown. Our lab has previously presented evidence that the dihydropyridine receptor and ryanodine receptor combine as a channel for the entry of Ca(2+) under resting conditions, known as store operated calcium entry.

The significance of autoantibodies to DFS70/LEDGFp75 in health and disease: integrating basic science with clinical understanding.

Antinuclear autoantibodies (ANAs) displaying the nuclear dense fine speckled immunofluorescence (DFS-IIF) pattern in HEp-2 substrates are commonly observed in clinical laboratory referrals. They target the dense fine speckled autoantigen of 70 kD (DFS70), most commonly known as lens epithelium-derived growth factor p75 (LEDGFp75). Interesting features of these ANAs include their low frequency in patients with systemic autoimmune rheumatic diseases (SARD), elevated prevalence in apparently healthy individuals, IgG isotype, strong trend to occur as the only ANA specificity in serum, and occurrence in moderate to high titers.

De novo acute myeloid leukemia with 20-29% blasts is less aggressive than acute myeloid leukemia with ≥30% blasts in older adults: a Bone Marrow Pathology Group study.

It is controversial whether acute myeloid leukemia (AML) patients with 20-29% bone marrow (BM) blasts, formerly referred to as refractory anemia with excess blasts in transformation (RAEBT), should be considered AML or myelodysplastic syndrome (MDS) for the purposes of treatment and prognostication. We retrospectively studied 571 de novo AML in patients aged >50 years, including 142 RAEBT and 429 with ≥30% blasts (AML30), as well as 151 patients with 10-19% BM blasts (RAEB2). RAEBT patients were older and had lower white blood count, but higher hemoglobin, platelet count, and karyotype risk scores compared to AML30, while these features were similar to RAEB2.

Metformin increases mitochondrial energy formation in L6 muscle cell cultures.

A popular hypothesis for the action of metformin, the widely used anti-diabetes drug, is the inhibition of mitochondrial respiration, specifically at complex I. This is consistent with metformin stimulation of glucose uptake by muscle and inhibition of gluconeogenesis by liver. Yet, mitochondrial inhibition is inconsistent with metformin stimulation of fatty acid oxidation in both tissues.

Structural brain alterations can be detected early in HIV infection.

Objective: Brain changes occurring early in HIV infection are not well characterized. The Chicago Early HIV Infection Study aimed to evaluate the presence and extent of structural brain alterations using quantitative MRI.

Methods: Forty-three HIV and 21 control subjects were enrolled.

A comparative evaluation of quantitative neuroimaging measurements of brain status in HIV infection.

Diffusion tensor imaging (DTI), magnetization transfer imaging (MT) and automated brain volumetry were used to summarize brain involvement in human immunodeficiency virus (HIV) infection. A multiparametric neuroimaging protocol was implemented at 1.5 T in 10 HIV+ and 24 controls.

Molecular genetic characterization of lymphoma: application to cytology diagnosis.

Mature B- and T-cell lymphomas are increasingly being associated with specific genetic alterations; characterization of these changes can sometimes be crucial to both diagnosis and prognosis. Molecular testing encompasses fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR)-based assays, as well as classical cytogenetics. FISH and PCR-based assays can be performed on cytology material without the need for advanced planning for testing with fresh tissue.

Primary and secondary drug screening assays for Friedreich ataxia.

Friedreich ataxia (FRDA) is an autosomal recessive neuro- and cardiodegenerative disorder for which there are no proven effective treatments. FRDA is caused by decreased expression and/or function of the protein frataxin. Frataxin chaperones iron in the mitochondrial matrix for the assembly of iron-sulfur clusters (ISCs), which are prosthetic groups critical for the function of the Krebs cycle and the mitochondrial electron transport chain (ETC).

Marked relationship between matrix metalloproteinase 7 and brain atrophy in HIV infection.

Circulating levels of matrix metalloproteinases (MMP-1 and 7) have been found to correlate with the severity of brain injury in HIV-infected subjects. This study used high-resolution neuroanatomic imaging and automated segmentation algorithms to clarify this relationship. Both metalloproteinases were significantly correlated with increased cerebrospinal fluid volume fraction.

Abnormalities in resting-state functional connectivity in early human immunodeficiency virus infection.

Limited information is available concerning changes that occur in the brain early in human immunodeficiency virus (HIV) infection. This investigation evaluated resting-state functional connectivity, which is based on correlations of spontaneous blood oxygen level-dependent functional magnetic resonance imaging (fMRI) oscillations between brain regions, in 15 subjects within the first year of HIV infection and in 15 age-matched controls. Resting-state fMRI data for each session were concatenated in time across subjects to create a single 4D dataset and decomposed into 36 independent component analysis (ICA) using Multivariate Exploratory Linear Optimized Decomposition into Independent Components.

Biomarkers of neurological status in HIV infection: a 3-year study.

Purpose: To evaluate circulating cytokines and chemokines as correlates of the degree of brain injury in individuals with advanced human immunodeficiency virus (HIV) infection.

Experimental Design: Study participants included ten well-characterized subjects in advanced stage HIV infection. High-throughput multiplexed analysis was used to quantify markers of interest at baseline and 3 years later in the clinical course.

Metformin activates AMP kinase through inhibition of AMP deaminase.

The mechanism for how metformin activates AMPK (AMP-activated kinase) was investigated in isolated skeletal muscle L6 cells. A widely held notion is that inhibition of the mitochondrial respiratory chain is central to the mechanism. We also considered other proposals for metformin action.

Serum matrix metalloproteinase levels correlate with brain injury in human immunodeficiency virus infection.

Circulating levels of specific matrix metalloproteinases (MMPs; 1 and 7) were evaluated as correlates of brain injury in eight individuals in advanced human immunodeficiency virus (HIV) infection. Neurological status was quantified in vivo with automated segmentation algorithms and with diffusion tensor imaging. Both metalloproteinases correlated with microstructural brain alterations and the degree of atrophy.

Computer-aided detection of endobronchial valves using volumetric CT.

Rationale And Objectives: The ability to automatically detect and monitor implanted devices may serve an important role in patient care by aiding the evaluation of device and treatment efficacy. The purpose of this research was to develop a system for the automated detection of one-way endobronchial valves that were implanted for less invasive lung volume reduction.

Materials And Methods: Volumetric thin-section computed tomographic data was obtained for 194 subjects; 95 subjects implanted with 246 devices were used for system development and 99 subjects implanted with 354 devices were reserved for testing.

Prevalence of tracheal collapse in an emphysema cohort as measured with end-expiration CT.

Rationale And Objectives: To retrospectively investigate the prevalence of tracheal collapse in an emphysema cohort. The occurrence of a large degree of tracheal collapse may have important implications for the clinical management of respiratory symptoms and air trapping in patients with emphysema.

Materials And Methods: Paired full-inspiratory and end-expiratory thin-section volumetric computed tomographic scans were available for 1071 long-term smokers with clinically and physiologically confirmed emphysema.