Generalized Path Integral Energy and Heat Capacity Estimators of Quantum Oscillators and Crystals Using Harmonic Mapping.

Imaginary-time path integral (PI) is a rigorous tool to treat nuclear quantum effects in static properties. However, with its high computational demand, it is crucial to devise precise estimators. We introduce generalized PI estimators for the energy and heat capacity that utilize coordinate mapping.

Methodical evaluation of Boyle temperatures using Mayer sampling Monte Carlo with application to polymers in implicit solvent.

The Boyle temperature, TB, for an n-segment polymer in solution is the temperature where the second osmotic virial coefficient, A2, is zero. This characteristic is of interest for its connection to the polymer condensation critical temperature, particularly for n → ∞. TB can be measured experimentally or computed for a given model macromolecule.

Cell identity revealed by precise cell cycle state mapping links data modalities.

Several methods for cell cycle inference from sequencing data exist and are widely adopted. In contrast, methods for classification of cell cycle state from imaging data are scarce. We have for the first time integrated sequencing and imaging derived cell cycle pseudo-times for assigning 449 imaged cells to 693 sequenced cells at an average resolution of 3.

Harmonic Oscillator Staging Coordinates for Efficient Path Integral Simulations of Quantum Oscillators and Crystals.

Imaginary-time path integral (PI) is a rigorous quantum mechanical tool to compute static properties at finite temperatures. However, the stiff nature of the internal PI modes poses a sampling challenge. This is commonly tackled using staging coordinates, in which the free particle (FP) contribution of the PI action is diagonalized.

Efficient single-run implementation of generalized Einstein relation to compute transport coefficients: A binary-based time sampling.

A robust and simple implementation of the generalized Einstein formulation using single equilibrium molecular dynamics simulation is introduced to compute diffusion and shear viscosity. The unique features underlying this framework are as follows: (1) The use of a simple binary-based method to sample time-dependent transport coefficients results in a uniform distribution of data on a logarithmic time scale. Although we sample "on-the-fly," the algorithm is readily applicable for post-processing analysis.

Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma.

Glioblastoma (GBM) is the most aggressive form of primary brain tumor. Complete surgical resection of GBM is almost impossible due to the infiltrative nature of the cancer. While no evidence for recent selection events have been found after diagnosis, the selective forces that govern gliomagenesis are strong, shaping the tumor's cell composition during the initial progression to malignancy with late consequences for invasiveness and therapy response.

Mathematical Modeling of Clonal Interference by Density-Dependent Selection in Heterogeneous Cancer Cell Lines.

Many cancer cell lines are aneuploid and heterogeneous, with multiple karyotypes co-existing within the same cell line. Karyotype heterogeneity has been shown to manifest phenotypically, thus affecting how cells respond to drugs or to minor differences in culture media. Knowing how to interpret karyotype heterogeneity phenotypically would give insights into cellular phenotypes before they unfold temporally.

Probabilistic computations of virial coefficients of polymeric structures described by rigid configurations of spherical particles: A fundamental extension of the ZENO program.

We describe an extension of the ZENO program for polymer and nanoparticle characterization that allows for precise calculation of the virial coefficients, with uncertainty estimates, of polymeric structures described by arbitrary rigid configurations of hard spheres. The probabilistic method of virial computation used for this extension employs a previously developed Mayer-sampling Monte Carlo method with overlap sampling that allows for a reduction of bias in the Monte Carlo averaging. This capability is an extension of ZENO in the sense that the existing program is also based on probabilistic sampling methods and involves the same input file formats describing polymer and nanoparticle structures.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt.

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left-right asymmetry and anomalous crystalline polymorphs (i.

Virial equation of state as a new frontier for computational chemistry.

The virial equation of state (VEOS) provides a rigorous bridge between molecular interactions and thermodynamic properties. The past decade has seen renewed interest in the VEOS due to advances in theory, algorithms, computing power, and quality of molecular models. Now, with the emergence of increasingly accurate first-principles computational chemistry methods, and machine-learning techniques to generate potential-energy surfaces from them, VEOS is poised to play a larger role in modeling and computing properties.

The EcpD Tip Adhesin of the Common Pilus Mediates Binding of Enteropathogenic to Extracellular Matrix Proteins.

The attachment of enteropathogenic (EPEC) to intestinal epithelial cells is facilitated by several adhesins; however, the individual host-cell receptors for pili-mediated adherence have not been fully characterized. In this study, we evaluated the hypothesis that the common pilus (ECP) tip adhesin protein EcpD mediates attachment of EPEC to several extracellular matrix (ECM) glycoproteins (fibronectin, laminin, collagens I and IV, and mucin). We found that the Δ mutant, which lacks production of the EcpA filament but retains EcpD on the surface, adhered to these glycoproteins below the wild-type levels, while the Δ mutant, which does not display EcpA or EcpD, bound significantly less to these host glycoproteins.

Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance.

Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus, an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought.

Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish.

Background: The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species' vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration.

Reduced Follicular Regulatory T Cells in Spleen and Pancreatic Lymph Nodes of Patients With Type 1 Diabetes.

In the attempt to understand the origin of autoantibody (AAb) production in patients with and at risk for type 1 diabetes (T1D), multiple studies have analyzed and reported alterations in T follicular helper (Tfh) cells in presymptomatic AAb subjects and patients with T1D. Yet, whether the regulatory counterpart of Tfh cells, represented by T follicular regulatory (Tfr) cells, is similarly altered is still unclear. To address this question, we performed analyses in peripheral blood, spleen, and pancreatic lymph nodes (PLN) of organ donor subjects with T1D.

Coupled Monte Carlo and Molecular Dynamics Simulations on Interfacial Properties of Antifouling Polymer Membranes.

We use molecular simulation to study the wetting behavior of antifouling polymer-tethered membranes. We obtain the interfacial properties (e.g.

RASAL2 Confers Collateral MEK/EGFR Dependency in Chemoresistant Triple-Negative Breast Cancer.

Purpose: While chemotherapy remains the standard treatment for triple-negative breast cancer (TNBC), identifying and managing chemoresistant tumors has proven elusive. We sought to discover hallmarks and therapeutically actionable features of refractory TNBC through molecular analysis of primary chemoresistant TNBC specimens.

Experimental Design: We performed transcriptional profiling of tumors from a phase II clinical trial of platinum chemotherapy for advanced TNBC (TBCRC-009), revealing a gene expression signature that identified chemorefractory tumors.

Evaluation of Osmotic Virial Coefficients via Restricted Gibbs Ensemble Simulations, with Support from Gas-Phase Mixture Coefficients.

We present a method for computing osmotic virial coefficients in explicit solvent via simulation in a restricted Gibbs ensemble. Two equivalent phases are simulated at once, each in a separate box at constant volume and temperature and each in equilibrium with a solvent reservoir. For osmotic coefficient , a total of solutes are individually exchanged back and forth between the boxes, and the average distribution of solute numbers between the boxes provides the key information needed to compute .

Systemic Disease Associations with Disorders of Gut-Brain Interaction and Gastrointestinal Transit: A Review.

Functional gastrointestinal disorders (FGID) are now classified within the Rome IV framework as disorders of gut-brain interaction (DGBI). Disorders of gastrointestinal transit (as defined by abnormalities on contemporary gastrointestinal motility testing) frequently are associated with symptoms that are also characteristic of DGBIs. In this narrative review, we outline a non-inclusive set of systemic diseases or risk factors that have been classically associated with DGBIs and disorders of gastrointestinal transit; these include diabetes mellitus, paraneoplastic syndromes, surgery, Parkinson's disease, systemic sclerosis, endocrinopathies, polypharmacy, and post-infectious syndromes.

Brahma-Related Gene-1 (BRG1) promotes the malignant phenotype of glioblastoma cells.

Glioblastoma multiforme (GBM) is an aggressive malignant brain tumour that is resistant to existing therapeutics. Identifying signalling pathways deregulated in GBM that can be targeted therapeutically is critical to improve the present dismal prognosis for GBM patients. In this report, we have identified that the BRG1 (Brahma-Related Gene-1) catalytic subunit of the SWI/SNF chromatin remodelling complex promotes the malignant phenotype of GBM cells.

The health and condition responses of Delta Smelt to fasting: A time series experiment.

There is an extensive literature establishing, validating, and quantifying a wide range of responses of fishes to fasting. Our study complements this work by comparing fed and unfed treatments of hatchery-raised Delta Smelt (Hypomesus transpacificus)-an imperiled fish that is endemic to the San Francisco Estuary and its tributaries in California, USA-across a diverse suite of endpoints over a two-month time series. The experiment was conducted at 15.

Dissecting the Financial Relationship Between Industry and Academic Neurosurgery.

Background: Established by the Centers for Medicare and Medicaid Services (CMS), the Open Payments Database (OPD) has reported industry payments to physicians since August 2013.

Objective: To evaluate the frequency, type, and value of payments received by academic neurosurgeons in the United States over a 5-yr period (2014-2018).

Methods: The OPD was queried for attending neurosurgeons from all neurosurgical training programs in the United States (n = 116).

Cluster integrals and virial coefficients for realistic molecular models.

We present a concise, general, and efficient procedure for calculating the cluster integrals that relate thermodynamic virial coefficients to molecular interactions. The approach encompasses nonpairwise intermolecular potentials generated from quantum chemistry or other sources; a simple extension permits efficient evaluation of temperature and other derivatives of the virial coefficients. We demonstrate with a polarizable model of water.