Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Lipid coated liquid crystal droplets for the on-chip detection of antimicrobial peptides

We describe a novel biosensor based on phospholipid-coated nematic liquid crystal (LC) droplets and demonstrate the detection of Smp43, a model antimicrobial peptide (AMP) from the venom of North African scorpion Scorpio maurus palmatus. Mono-disperse lipid-coated LC droplets of diameter 16.7 ± 0.2 μm were generated using PDMS microfluidic devices with a flow-focusing configuration and were the target for AMPs. The droplets were trapped in a bespoke microfluidic trap structure and were simultaneously treated with Smp43 at gradient concentrations in six different chambers. The disruption of the lipid monolayer by the Smp43 was detected (<6 μM) at concentrations well within its biologically active range, indicated by a dramatic change in the appearance of the droplets associated with the transition from a typical radial configuration to a bipolar configuration, which is readily observed by polarizing microscopy. This suggests the system has feasibility as a drug-discovery screening tool. Further, compared to previously reported LC droplet biosensors, this LC droplet biosensor with a lipid coating is more biologically relevant and its ease of use in detecting membrane-related biological processes and interactions has the potential for development as a reliable, low-cost and disposable point of care diagnostic tool

Temocillin: a new candidate antibiotic for local antimicrobial delivery in orthopaedic surgery?

Objectives - To assess the performance of the Gram-negative-specific antibiotic temocillin in polymethylmethacrylate bone cement pre-loaded with gentamicin, as a strategy for local antibiotic delivery. Methods - Temocillin was added at varying concentrations to commercial gentamicin-loaded bone cement. The elution of the antibiotic from cement samples over a 2 week period was quantified by LC-MS. The eluted temocillin was purified by fast protein liquid chromatography and the MICs for a number of antibiotic-resistant Escherichia coli were determined. The impact strength of antibiotic-loaded samples was determined using a Charpy-type impact testing apparatus. Results - LC-MS data showed temocillin eluted to clinically significant concentrations within 1 h in this laboratory system and the eluted temocillin retained antimicrobial activity against all organisms tested. Impact strength analysis showed no significant difference between cement samples with or without temocillin. Conclusions - Temocillin can be added to bone cement and retains its antimicrobial activity after elution. The addition of up to 10% temocillin did not affect the impact strength of the cement. The results show that temocillin is a promising candidate for use in antibiotic-loaded bone cement.</p

The central density of a neutron star is unaffected by a binary companion at linear order in μ/R\mu/R

Recent numerical work by Wilson, Mathews, and Marronetti [J. R. Wilson, G. J. Mathews and P. Marronetti, Phys. Rev. D 54, 1317 (1996)] on the coalescence of massive binary neutron stars shows a striking instability as the stars come close together: Each star's central density increases by an amount proportional to 1/(orbital radius). This overwhelms any stabilizing effects of tidal coupling [which are proportional to 1/(orbital radius)^6] and causes the stars to collapse before they merge. Since the claimed increase of density scales with the stars' mass, it should also show up in a perturbation limit where a point particle of mass $\mu$ orbits a neutron star. We prove analytically that this does not happen; the neutron star's central density is unaffected by the companion's presence to linear order in $\mu/R$. We show, further, that the density increase observed by Wilson et. al. could arise as a consequence of not faithfully maintaining boundary conditions.Comment: 3 pages, REVTeX, no figures, submitted to Phys Rev D as a Rapid Communicatio

Living with Traumatic Brain Injury in a Rural Setting: Supports and Barriers Across the Continuum of Care

Purpose: Traumatic brain injury (TBI) is prevalent in Kentucky and comes with a high cost in care and quality of life for individuals and caregivers affected. Many people living with the condition of TBI have unmet needs. Research among people living with TBI in rural areas is limited. The purposes of this study were to (1) increase understanding of the lived experience of people with TBI and caregivers in rural regions of Kentucky across the continuum of their care and (2) provide their perspectives on barriers and facilitators of optimal function and well-being. Methods: A qualitative descriptive interview study was conducted by a multidisciplinary team. Content analysis was completed with data-derived coding and iterative modifications to analysis, coalescing codes into categories and themes. Results: Thirteen people with TBI and six caregivers participated in the interview. Categories that emerged in analysis included the experiences under each locus of care; themes included relationships, functional competence, and participation in meaningful activity. Conclusion: Relationships represented both barriers and facilitators of well-being. Major unmet needs persisted in terms of medical problems, support for caregivers, community linkages, and participation in meaningful activities. Recommendations are made regarding avenues for addressing unmet needs

Comparative hazards of chrysotile asbestos and its substitutes: A European perspective.

Although the use of amphibole asbestos (crocidolite and amosite) has been banned in most European countries because of its known effects on the lung and pleura, chrysotile asbestos remains in use in a number of widely used products, notably asbestos cement and friction linings in vehicle brakes and clutches. A ban on chrysotile throughout the European Union for these remaining applications is currently under consideration, but this requires confidence in the safety of substitute materials. The main substitutes for the residual uses of chrysotile are p-aramid, polyvinyl alcohol (PVA), and cellulose fibers, and it is these materials that are evaluated here. Because it critically affects both exposure concentrations and deposition in the lung, diameter is a key determinant of the intrinsic hazard of a fiber; the propensity of a material to release fibers into the air is also important. It is generally accepted that to be pathogenic to the lung or pleura, fibers must be long, thin, and durable; fiber chemistry may also be significant. These basic principles are used in a pragmatic way to form a judgement on the relative safety of the substitute materials, taking into account what is known about their hazardous properties and also the potential for uncontrolled exposures during a lifetime of use (including disposal). We conclude that chrysotile asbestos is intrinsically more hazardous than p-aramid, PVA, or cellulose fibers and that its continued use in asbestos-cement products and friction materials is not justifiable in the face of available technically adequate substitutes

Primary palliative care research: opportunities and challenges.

INTRODUCTION: Primary care has a central role in palliative and end of life care: 45.6% of deaths in England and Wales occur under the care of primary care teams at home or in care homes. The Community Care Pathways at the End of Life (CAPE) study investigated primary care provided for patients in the final 6 months of life. This paper highlights the opportunities and challenges associated with primary palliative care research in the UK, describing the methodological, ethical, logistical and gatekeeping challenges encountered in the CAPE study and how these were addressed. THE STUDY METHODS: Using a mixed-methods approach, quantitative data were extracted from the general practitioner (GP) and district nurse (DN) records of 400 recently deceased patients in 20 GP practices in the East of England. Focus groups were conducted with some GPs and DNs, and individual interviews held with bereaved carers and other GPs and DNs. THE CHALLENGES ADDRESSED: Considerable difficulties were encountered with ethical permissions, with GP, DN and bereaved carer recruitment and both quantitative and qualitative data collection. These were overcome with flexibility of approach, perseverance of the research team and strong user group support. This enabled completion of the study which generated a unique primary palliative care data set.National Institute for Health Research (NIHR) Research for Patient Benefit Programme. National Institute for Health Research (NIHR) School for Primary Care Research (SPCR). National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care (CLAHRC) East of Englan

Cerium dioxide, a Jekyll and Hyde nanomaterial, can increase basal and decrease elevated inflammation and oxidative stress

It was hypothesized that the catalyst nanoceria can increase oxidative stress/inflammation from the basal state and reduce it from the elevated state . Nanoceria are cleared by macrophages. To test the hypothesis, M0 (non-polarized), M1- (classically activated, pro-inflammatory), and M2-like (alternatively activated, regulatory phenotype) RAW 264.7 macrophages were nanoceria exposed. Responses were quantified by arginase activity, IL-1ß level, cell oxygen consumption rate (OCR), the glycolysis stress test (GST), morphology determined by light microscopy, macrophage phenotype marker expression and morphology using a novel three dimensional immunohistochemical method, and RT-qPCR. Nanoceria blocked arginase and IL-1ß effects, increased M0 cell OCR and GST toward the M2 phenotype and altered multiple M1- and M2-like cell endpoints toward the M0 level. M1-like cells had greater volume and less circularity/roundness, and the M2-like cells had greater volume than M0 macrophages. Nanoceria converted M1- and M2-like cells toward M0 morphology. The results are overall consistent with the hypothesis

Peripheral killer cells do not differentiate between asthma patients with or without fixed airway obstruction

Objective: The three main types of killer cells – CD8+ T cells, NK cells and NKT cells – have been linked to asthma and chronic obstructive pulmonary disease (COPD). However, their role in a small subset of asthma patients displaying fixed airway obstruction (FAO), similar to that seen in COPD, has not been explored. The objective of the present study was to investigate killer cell numbers, phenotype and function in peripheral blood from asthma patients with FAO, asthma patients without FAO, and healthy individuals. Methods: Peripheral CD8+ T cells (CD8+CD3+CD56−), NK cells (CD56+CD3−) and NKT-like cells (CD56+CD3+) of 14 asthma patients with FAO (post-bronchodilator FEV/FVC <0.7, despite clinician-optimised treatment), 7 asthma patients without FAO (post-bronchodilator FEV/FVC ≥0.7), and 9 healthy individuals were studied. Results: No significant differences were seen between the number, receptor expression, MAPK signalling molecule expression, cytotoxic mediator expression, and functional cytotoxicity of peripheral killer cells from asthma patients with FAO, asthma patients without FAO and healthy individuals. Conclusions: Peripheral killer cell numbers or functions do not differentiate between asthma patients with or without fixed airway obstruction

Elevated Phospholipase A2 Activities in Plasma Samples from Multiple Cancers.

Only in recent years have phospholipase A2 enzymes (PLA2s) emerged as cancer targets. In this work, we report the first detection of elevated PLA2 activities in plasma from patients with colorectal, lung, pancreatic, and bladder cancers as compared to healthy controls. Independent sets of clinical plasma samples were obtained from two different sites. The first set was from patients with colorectal cancer (CRC; n = 38) and healthy controls (n = 77). The second set was from patients with lung (n = 95), bladder (n = 31), or pancreatic cancers (n = 38), and healthy controls (n = 79). PLA2 activities were analyzed by a validated quantitative fluorescent assay method and subtype PLA2 activities were defined in the presence of selective inhibitors. The natural PLA2 activity, as well as each subtype of PLA2 activity was elevated in each cancer group as compared to healthy controls. PLA2 activities were increased in late stage vs. early stage cases in CRC. PLA2 activities were not influenced by sex, smoking, alcohol consumption, or body-mass index (BMI). Samples from the two independent sites confirmed the results. Plasma PLA2 activities had approximately 70% specificity and sensitivity to detect cancer. The marker and targeting values of PLA2 activity have been suggested