Glutamate Transport Proteins and Metabolic Enzymes are Poor Prognostic Factors in Invasive Lobular Carcinoma.

Invasive Lobular Carcinoma (ILC) is a subtype of breast cancer characterized by distinct biological features, and limited glucose uptake coupled with increased reliance on amino acid and lipid metabolism. Our prior studies highlight the importance of glutamate as a key regulator of ILC tumor growth and therapeutic response. Here we examine the expression of four key proteins involved in glutamate transport and metabolism - SLC3A2, SLC7A11, GPX4, and GLUD1/2 - in a racially diverse cohort of 72 estrogen receptor-positive (ER+) ILC and 50 ER+ invasive ductal carcinoma, no special type (IDC/NST) patients with primary disease.

Frameshift mutations in peripheral blood as a biomarker for surveillance of Lynch syndrome.

Background: Lynch syndrome is a hereditary cancer predisposition syndrome caused by germline mutations in DNA mismatch repair genes, which lead to high microsatellite instability and frameshift mutations at coding mononucleotide repeats in the genome. Recurrent frameshift mutations in these regions are thought to play a central role in the increased risk of various cancers, but no biomarkers are currently available for the surveillance of high microsatellite instability-associated cancers.

Methods: A frameshift mutation-based biomarker panel was developed and validated by targeted next-generation sequencing of supernatant DNA from cultured high microsatellite instability colorectal cancer cells.

Organoids and metastatic orthotopic mouse model for mismatch repair-deficient colorectal cancer.

Background: Genome integrity is essential for the survival of an organism. DNA mismatch repair (MMR) genes (e.g.

Leishmaniasis: Recent epidemiological studies in the Middle East.

Leishmaniasis, one of the most neglected tropical diseases (NTDs), is the third most important vector-borne disease worldwide. This disease has a global impact and severity of the infection and is greatest in the Middle East. The agent of infection is a protozoan parasite of the genus, , and is generally transmitted by blood-sucking female sandflies.

Mesothelioma Mouse Models with Mixed Genomic States of Chromosome and Microsatellite Instability.

Malignant mesothelioma (MMe) is a rare malignancy originating from the linings of the pleural, peritoneal and pericardial cavities. The best-defined risk factor is exposure to carcinogenic mineral fibers (e.g.

Universality of stable multi-cluster periodic solutions in a population model of the cell cycle with negative feedback.

We study a population model where cells in one part of the cell cycle may affect the progress of cells in another part. If the influence, or feedback, from one part to another is negative, simulations of the model almost always result in multiple temporal clusters formed by groups of cells. We study regions in parameter space where periodic '-cyclic' solutions are stable.

Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection.

Background: Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented.

Methods: In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture.

Limitations of Transformers on Clinical Text Classification.

Bidirectional Encoder Representations from Transformers (BERT) and BERT-based approaches are the current state-of-the-art in many natural language processing (NLP) tasks; however, their application to document classification on long clinical texts is limited. In this work, we introduce four methods to scale BERT, which by default can only handle input sequences up to approximately 400 words long, to perform document classification on clinical texts several thousand words long. We compare these methods against two much simpler architectures - a word-level convolutional neural network and a hierarchical self-attention network - and show that BERT often cannot beat these simpler baselines when classifying MIMIC-III discharge summaries and SEER cancer pathology reports.

Real-Time and Wireless Assessment of Adherence to Antiretroviral Therapy With Co-Encapsulated Ingestion Sensor in HIV-Infected Patients: A Pilot Study.

Adherence with antiretroviral therapy is important for preventing disease progression and HIV transmission. The co-encapsulated pill sensor system sends a signal through a cutaneous patch and allows real-time monitoring of pill ingestion. A 16-week pilot study used a sensor system in 15 HIV-infected individuals with real-time monitoring of pill-taking with a personalized short message system text.

Pharmacokinetics of Coencapsulated Antiretrovirals with Ingestible Sensors.

We investigated the use of a system with an ingestible sensor (Proteus Digital Health Feedback system) coencapsulated with antiretrovirals (ARVs) to measure real-time adherence. To assess the safety and impact, if any, coencapsulation might have on ARV concentrations, we evaluated the pharmacokinetics of ARVs coencapsulated with an ingestible sensor for eight commonly used fixed-dose combination ARVs: emtricitabine (FTC)/tenofovir disoproxil fumarate (TDF); FTC/tenofovir alafenamide (TAF); efavirenz (EFV)/FTC/TDF; abacavir (ABC)/lamivudine (3TC); dolutegravir (DTG)/ABC/3TC; rilpivirine (RPV)/TAF/FTC; elvitegravir (EVG)/cobicistat (COBI)/FTC/TAF; and bictegravir (BIC)/FTC/TAF. The steady-state apparent peak plasma concentration (Cmax) and area under the concentration-time curve (AUC) were determined from plasma concentrations measured at predose, 1, 2, 4, and 6 h postdose, and compared with literature values.

Instability of the steady state solution in cell cycle population structure models with feedback.

We show that when cell-cell feedback is added to a model of the cell cycle for a large population of cells, then instability of the steady state solution occurs in many cases. We show this in the context of a generic agent-based ODE model. If the feedback is positive, then instability of the steady state solution is proved for all parameter values except for a small set on the boundary of parameter space.

Early treatment gains for antibiotic administration and within human host time series data.

As technological improvements continue to infiltrate and impact medical practice, it has become possible to non-invasively collect dense physiological time series data from individual patients in real time. These advances continue to improve physicians' ability to detect and to treat infections early. One important benefit of early detection and treatment of nascent infections is that it leads to earlier resolution.

Evidence for internuclear signaling in drosophila embryogenesis.

Background: Syncytial nuclei in Drosophila embryos undergo their first 13 divisions nearly synchronously. In the last several cell cycles, these division events travel across the anterior-posterior axis of the syncytial blastoderm in a wave. The phenomenon is well documented but the underlying mechanisms are not yet understood.

Cell cycle dynamics in a response/signalling feedback system with a gap.

We consider a dynamical model of cell cycles of n cells in a culture in which cells in one specific phase (S for signalling) of the cell cycle produce chemical agents that influence the growth/cell cycle progression of cells in another phase (R for responsive). In the case that the feedback is negative, it is known that subpopulations of cells tend to become clustered in the cell cycle; while for a positive feedback, all the cells tend to become synchronized. In this paper, we suppose that there is a gap between the two phases.

Cell cycle dynamics: clustering is universal in negative feedback systems.

We study a model of cell cycle ensemble dynamics with cell-cell feedback in which cells in one fixed phase of the cycle S (Signaling) produce chemical agents that affect the growth and development rate of cells that are in another phase R (Responsive). For this type of system there are special periodic solutions that we call k-cyclic or clustered. Biologically, a k-cyclic solution represents k cohorts of synchronized cells spaced nearly evenly around the cell cycle.

Noise-induced dispersion and breakup of clusters in cell cycle dynamics.

We study the effects of random perturbations on collective dynamics of a large ensemble of interacting cells in a model of the cell division cycle. We consider a parameter region for which the unperturbed model possesses asymptotically stable two-cluster periodic solutions. Two biologically motivated forms of random perturbations are considered: bounded variations in growth rate and asymmetric division.

Two classes of ODE models with switch-like behavior.

In cases where the same real-world system can be modeled both by an ODE system ⅅ and a Boolean system 𝔹, it is of interest to identify conditions under which the two systems will be consistent, that is, will make qualitatively equivalent predictions. In this note we introduce two broad classes of relatively simple models that provide a convenient framework for studying such questions. In contrast to the widely known class of Glass networks, the right-hand sides of our ODEs are Lipschitz-continuous.

Bevacizumab maintenance in patients with advanced non-small-cell lung cancer, clinical patterns, and outcomes in the Eastern Cooperative Oncology Group 4599 Study: results of an exploratory analysis.

Introduction: The Eastern Cooperative Oncology Group (ECOG) 4599 study showed a significant survival benefit with the use of bevacizumab (BV) in combination with carboplatin and paclitaxel (CP) in comparison with CP chemotherapy alone in patients with previously untreated advanced, metastatic or recurrent non-small-cell lung cancer (NSCLC). Such results were achieved using BV as maintenance therapy until progressive disease. Because current data on single-agent BV maintenance in non-small-cell lung cancer are limited, we present a retrospective analysis of safety and efficacy outcomes for patients who received maintenance BV after induction treatment and the maintenance-eligible population of the control arm in ECOG 4599.

Finite amplitude, horizontal motion of a load symmetrically supported between isotropic hyperelastic springs.

The undamped, finite amplitude horizontal motion of a load supported symmetrically between identical incompressible, isotropic hyperelastic springs, each subjected to an initial finite uniaxial static stretch, is formulated in general terms. The small amplitude motion of the load about the deformed static state is discussed; and the periodicity of the arbitrary finite amplitude motion is established for all such elastic materials for which certain conditions on the engineering stress and the strain energy function hold. The exact solution for the finite vibration of the load is then derived for the classical neo-Hookean model.

THE HOPF BIFURCATION WITH BOUNDED NOISE.

We study Hopf-Andronov bifurcations in a class of random differential equations (RDEs) with bounded noise. We observe that when an ordinary differential equation that undergoes a Hopf bifurcation is subjected to bounded noise then the bifurcation that occurs involves a discontinuous change in the Minimal Forward Invariant set.

Non-invasive detection of pulmonary pathogens in ventilator-circuit filters by PCR.

Ventilator associated pneumonia is a common and costly complication in critically ill and injured surgical patients. The diagnosis of pneumonia remains problematic and non-specific. Using clinical criteria, a diagnosis of pneumonia is typically not made until an infection is well established.

A low dimensional dynamical model of the initial pulmonary innate response to infection.

In order to gain a deeper understanding of the onset and progression of pulmonary infections we present and analyze a low dimensional, phenomenological model of infection and the innate immune response in the lungs. Because pulmonary innate immunity has features unique to itself, general mathematical models of the immune system may not be appropriate. The differential equations model that we propose is based on current knowledge of the biology of pulmonary innate immunity and accurately reproduces known features of the initial phase of the dynamics of pulmonary innate system as exhibited in recent experiments.

Clustering in cell cycle dynamics with general response/signaling feedback.

Motivated by experimental and theoretical work on autonomous oscillations in yeast, we analyze ordinary differential equations models of large populations of cells with cell-cycle dependent feedback. We assume a particular type of feedback that we call responsive/signaling (RS), but do not specify a functional form of the feedback. We study the dynamics and emergent behavior of solutions, particularly temporal clustering and stability of clustered solutions.