Energy Landscapes of Model Knotted Polymers.

The energy landscape of a model knotted ring polymer, consisting of 100 Lennard-Jones particles connected by harmonic springs, is extensively characterized for three topologies. Basin-hopping global optimization with unrestricted perturbation moves for the geometry can efficiently locate the global minimum of the topologically unconstrained energy landscape. We show that an isotropic radial potential to expand the structure provides a robust way to assign the crossing number and topology of each configuration.

Determination of the performance of a novel diagnostic test for toxins A and B using latent class analysis.

Unlabelled: The diagnosis of infection (CDI) remains challenging. Nucleic acid amplification tests (NAAT) targeting the (CD) toxin B gene suffer from suboptimal specificity for CDI due to CD asymptomatic colonization. Enzyme immunoassays (EIAs) that detect the presence of CD toxins are more specific for CDI but suffer from low sensitivity.

Predicting aquatic toxicity of anionic hydrocarbon and perfluorinated surfactants using membrane-water partition coefficients from coarse-grained simulations.

Anionic surfactants are widely used in commercial and industrial applications. For assessment of their environmental fate and effects, it is highly desirable to quantify the membrane-water partition/distribution coefficient (/). Here, we further develop a computational route to for anionic surfactants based on coarse-grained molecular dynamics simulations, validating it against new and existing experimental measurements.

Numerical methods for unraveling inter-particle potentials in colloidal suspensions: A comparative study for two-dimensional suspensions.

We compare three model-free numerical methods for inverting structural data to obtain interaction potentials, namely, iterative Boltzmann inversion (IBI), test-particle insertion (TPI), and a machine-learning (ML) approach called ActiveNet. Three archetypal models of two-dimensional colloidal systems are used as test cases: Weeks-Chandler-Anderson short-ranged repulsion, the Lennard-Jones potential, and a repulsive shoulder interaction with two length scales. Additionally, data on an experimental suspension of colloidal spheres are acquired by optical microscopy and used to test the inversion methods.

Concurrent myelomeningocele and sagittal craniosynostosis: illustrative case.

Background: Myelomeningocele and sagittal craniosynostosis are 2 neurosurgical pathologies with complications such as increased intracranial pressure (ICP) and hydrocephalus. While the 2 defects commonly occur independently, their simultaneous occurrence is exceptionally rare.

Observations: The authors report the case of a newborn male diagnosed with a simultaneous myelomeningocele and sagittal craniosynostosis.

Re-entrant percolation in active Brownian hard disks.

Non-equilibrium clustering and percolation are investigated in an archetypal model of two-dimensional active matter using dynamic simulations of self-propelled Brownian repulsive particles. We concentrate on the single-phase region up to moderate levels of activity, before motility-induced phase separation (MIPS) sets in. Weak activity promotes cluster formation and lowers the percolation threshold.

Peri-operative zoledronic acid attenuates peri-prosthetic osteolysis in a rat model of cemented knee replacement.

Progressive osteolysis can occur at the cement-bone interface of joint replacements and the associated loss of fixation can lead to clinical loosening. We previously developed a rat hemiarthroplasty model that exhibited progressive loss of fixation with the development of cement-bone gaps under the tibial tray that mimicked patterns found in human arthroplasty retrievals. Here we explored the ability of a bisphosphonate (zoledronic acid, ZA) to attenuate cement-bone osteolysis and maintain implant stability.

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P.

Partitioning into phosphatidylcholine-cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation.

Membrane-water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field.

Modification to Mirels scoring system location component improves fracture prediction for metastatic disease of the proximal femur.

Background: Correctly identifying patients at risk of femoral fracture due to metastatic bone disease remains a clinical challenge. Mirels criteria remains the most widely referenced method with the advantage of being easily calculated but it suffers from poor specificity. The purpose of this study was to develop and evaluate a modified Mirels scoring system through scoring modification of the original Mirels location component within the proximal femur.

Potential for supraphysiologic fluid shear stresses in a rat cemented knee replacement model.

The mechano-biologic environment associated with aseptic loosening of cemented joint replacements is not fully understood. The goal of this study was to use a preclinical rat knee arthroplasty model to explore the changes in cement-bone morphology and micromotion that occur with in vivo service. Narrow gaps between cement and bone under the tibial tray were present at early time points, and with even small magnitude micromotion, resulted in large micromotion-to-gap width ratios.

Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning.

With a view to high-throughput simulations, we present an automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field. The method scales to larger molecules and a broader chemical space than existing schemes. The core of the mapping process is a graph-based analysis of the molecule's bonding network, which has the advantages of being fast, general, and preserving symmetry.

Differing susceptibility of C57BL/6J and DBA/2J mice-parents of the murine BXD family, to severe acute respiratory syndrome coronavirus infection.

The ongoing coronavirus disease-2019 (COVID-19) pandemic, caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that is closely related to SARS-CoV, poses a grave threat to global health and has devastated societies worldwide. One puzzling aspect of COVID-19 is the impressive variation in disease manifestations among infected individuals, from a majority who are asymptomatic or exhibit mild symptoms to a smaller, largely age-dependent fraction who develop life-threatening conditions. Some of these differences are likely the consequence of host genetic factors.

Standardization of assay representation in the Ontology for Biomedical Investigations.

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

Predicting Fracture Risk in Patients with Metastatic Bone Disease of the Femur: A Pictorial Review Using Three Different Techniques.

One of the key roles of an orthopedic surgeon treating metastatic bone disease (MBD) is fracture risk prediction. Current widely used impending fracture risk tools such as Mirels scoring lack specificity. Two newer methods of fracture risk prediction, CT-based structural rigidity analysis (CTRA) and finite element analysis (FEA), have each been shown to be more accurate than Mirels.

Nearest-neighbor connectedness theory: A general approach to continuum percolation.

We introduce a method to estimate continuum percolation thresholds and illustrate its usefulness by investigating geometric percolation of noninteracting line segments and disks in two spatial dimensions. These examples serve as models for electrical percolation of elongated and flat nanofillers in thin film composites. While the standard contact volume argument and extensions thereof in connectedness percolation theory yield accurate predictions for slender nanofillers in three dimensions, they fail to do so in two dimensions, making our test a stringent one.

Control of Superselectivity by Crowding in Three-Dimensional Hosts.

Motivated by the fine compositional control observed in membraneless droplet organelles in cells, we investigate how a sharp binding-unbinding transition can occur between multivalent client molecules and receptors embedded in a porous three-dimensional structure. In contrast to similar superselective binding previously observed at surfaces, we have identified that a key effect in a three-dimensional environment is that the presence of inert crowding agents can significantly enhance or even introduce superselectivity. In essence, molecular crowding initially suppresses binding via an entropic penalty, but the clients can then more easily form many bonds simultaneously.

Progressive loss of implant fixation in a preclinical rat model of cemented knee arthroplasty.

Aseptic loosening of total knee arthroplasty continues to be a challenging clinical problem. The progression of the loosening process, from the initial well-fixed component, is not fully understood. In this study, loss of fixation of cemented hemiarthroplasty was explored using 9-month-old Sprague-Dawley rats with 0, 2, 6, 12, 26 week end points.

Potential COVID-19 papain-like protease PL inhibitors: repurposing FDA-approved drugs.

Using the crystal structure of SARS-CoV-2 papain-like protease (PL) as a template, we developed a pharmacophore model of functional centers of the PL inhibitor-binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. This search identified 147 compounds that can be potential inhibitors of SARS-CoV-2 PL.

Radiographic and Biomechanical Assessment of Three Implant Designs for Canine Cementless Total Hip Replacement.

Objective:  The aim of this study was to evaluate the relationship between radiographic fit/fill measurements and biomechanical performance of three canine cementless total hip implant designs using an biomechanical testing protocol that replicates compression and torsion.

Study Design:  Eighteen (six/group) canine cadaveric femurs were implanted with one of three cementless total hip implant designs: (1) collarless, (2) collared or (3) lateral bolt stems. Femoral length, canal flare index (CFI), canal fill, stem fit, stem level and stem angle were measured as independent variables.

Phase transitions on non-uniformly curved surfaces: coupling between phase and location.

For particles confined to two dimensions, any curvature of the surface affects the structural, kinetic and thermodynamic properties of the system. If the curvature is non-uniform, an even richer range of behaviours can emerge. Using a combination of bespoke Monte Carlo, molecular dynamics and basin-hopping methods, we show that the stable states of attractive colloids confined to non-uniformly curved surfaces are distinguished not only by the phase of matter but also by their location on the surface.

Similitude of cement-bone micromechanics in cemented rat and human knee replacement.

A preclinical rat knee replacement model was recently developed to explore the biological and mechanobiological changes of trabecular resorption for cement-bone interdigitated regions. The goal here was to evaluate the relevance of this model compared with human knee replacement with regards to functional micromechanics. Eight nonsurvival, cemented knee replacement surgeries were performed, the interdigitated gap morphology was quantified, and interface micromotion between cement and bone was measured for 1 to 5 bodyweight loading.