Dielectric Response of Periodic Systems from Quantum Monte Carlo Calculations

We present a novel approach that allows to calculate the dielectric response of periodic systems in the quantum Monte Carlo formalism. We employ a many-body generalization for the electric enthalpy functional, where the coupling with the field is expressed via the Berry-phase formulation for the macroscopic polarization. A self-consistent local Hamiltonian then determines the ground-state wavefunction, allowing for accurate diffusion quantum Monte Carlo calculations where the polarization's fixed point is estimated from the average on an iterative sequence, sampled via forward-walking. This approach has been validated for the case of an isolated hydrogen atom, and then applied to a periodic system, to calculate the dielectric susceptibility of molecular-hydrogen chains. The results found are in excellent agreement with the best estimates obtained from the extrapolation of quantum-chemistry calculations.Comment: 5 page 2figure

Phylogenetic analysis of three genes of Penguinpox virus corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L reveals that it is most closely related to Turkeypox virus, Ostrichpox virus and Pigeonpox virus

Phylogenetic analysis of three genes of Penguinpox virus, a novel Avipoxvirus isolated from African penguins, reveals its relationship to other poxviruses. The genes corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L were sequenced and phylogenetic trees (Neighbour-Joining and UPGMA) constructed from MUSCLE nucleotide and amino acid alignments of the equivalent sequences from several different poxviruses. Based on this analysis, PEPV was confirmed to belong to the genus Avipoxvirus, specifically, clade A, subclade A2 and to be most closely related to Turkeypox virus (TKPV), Ostrichpox virus (OSPV)and Pigeonpox virus (PGPV)

A novel candidate HIV vaccine vector based on the replication deficient Capripoxvirus, Lumpy skin disease virus (LSDV)

<p>Abstract</p> <p>Background</p> <p>The <it>Capripoxvirus</it>, Lumpy skin disease virus (LSDV) has a restricted host-range and is being investigated as a novel HIV-1 vaccine vector. LSDV does not complete its replication cycle in non-ruminant hosts.</p> <p>Methods</p> <p>The safety of LSDV was tested at doses of 10⁴and 10⁶plaque forming units in two strains of immunocompromised mice, namely RAG mice and CD4 T cell knockout mice. LSDV expressing HIV-1 subtype C Gag, reverse transcriptase (RT), Tat and Nef as a polyprotein (Grttn), (rLSDV-grttn), was constructed. The immunogenicity of rLSDV-grttn was tested in homologous prime-boost regimens as well as heterologous prime-boost regimes in combination with a DNA vaccine (pVRC-grttn) or modified vaccinia Ankara vaccine (rMVA-grttn) both expressing Grttn.</p> <p>Results</p> <p>Safety was demonstrated in two strains of immunocompromised mice.</p> <p>In the immunogenicity experiments mice developed high magnitudes of HIV-specific cells producing IFN-gamma and IL-2. A comparison of rLSDV-grttn and rMVA-grttn to boost a DNA vaccine (pVRC-grttn) indicated a DNA prime and rLSDV-grttn boost induced a 2 fold (p < 0.01) lower cumulative frequency of Gag- and RT-specific IFN-γ CD8 and CD4 cells than a boost with rMVA-grttn. However, the HIV-specific cells induced by the DNA vaccine prime rLSDV-grttn boost produced greater than 3 fold (p < 0.01) more IFN- gamma than the HIV-specific cells induced by the DNA vaccine prime rMVA-grttn boost. A boost of HIV-specific CD4 cells producing IL-2 was only achieved with the DNA vaccine prime and rLSDV-grttn boost. Heterologous prime-boost combinations of rLSDV-grttn and rMVA-grttn induced similar cumulative frequencies of IFN- gamma producing Gag- and RT-specific CD8 and CD4 cells. A significant difference (p < 0.01) between the regimens was the higher capacity (2.1 fold) of Gag-and RT-specific CD4 cells to produce IFN-γ with a rMVA-grttn prime - rLSDV-grttn boost. This regimen also induced a 1.5 fold higher (p < 0.05) frequency of Gag- and RT-specific CD4 cells producing IL-2.</p> <p>Conclusions</p> <p>LSDV was demonstrated to be non-pathogenic in immunocompromised mice. The rLSDV-grttn vaccine was immunogenic in mice particularly in prime-boost regimens. The data suggests that this novel vaccine may be useful for enhancing, in particular, HIV-specific CD4 IFN- gamma and IL-2 responses induced by a priming vaccine.</p

Outcomes in Trials for Management of Caries Lesions (OuTMaC):protocol

Background Clinical trials on caries lesion management use an abundance of outcomes, hampering comparison or combination of different study results and their efficient translation into clinical practice. Core outcome sets are an agreed standardized collection of outcomes which should be measured and reported in all trials for a specific clinical area. We aim to develop a core outcome set for trials investigating management of caries lesions in primary or permanent teeth conducted in primary or secondary care encompassing all stages of disease. Methods To identify existing outcomes, trials on prevention and trials on management of caries lesions will be screened systematically in four databases. Screening, extraction and deduplication will be performed by two researchers until consensus is reached. The definition of the core outcome set will by based on an e-Delhi consensus process involving key stakeholders namely patients, dentists, clinical researchers, health economists, statisticians, policy-makers and industry representatives. For the first stage of the Delphi process, a patient panel and a separate panel consisting of researchers, clinicians, teachers, industry affiliated researchers, policy-makers, and other interested parties will be held. An inclusive approach will be taken to involve panelists from a wide variety of socio-economic and geographic backgrounds. Results from the first round will be summarized and fed back to individuals for the second round, where panels will be combined and allowed to modify their scoring in light of the full panel’s opinion. Necessity for a third round will be dependent on the outcome of the first two. Agreement will be measured via defined consensus rules; up to a maximum of seven outcomes. If resources allow, we will investigate features that influence decision making for different groups. Discussion By using an explicit, transparent and inclusive multi-step consensus process, the planned core outcome set should be justifiable, relevant and comprehensive. The dissemination and application of this core outcome set should improve clinical trials on managing caries lesions and allow comparison, synthesis and implementation of scientific data. Trial registration Registered 12 April 2015 at COMET (http://www.comet-initiative.org

A survey of cancer patients undergoing a radical course of radiotherapy to establish levels of anxiety and depression.

This research aims to establish the prevalence and aetiology of anxiety and depression in cancer patients within their first 2 weeks of a radical course of radiotherapy. Depression followed by anxiety is the two most frequent psychological disorders experienced by cancer patients. However, these two disorders are frequently undiagnosed and untreated in patients undergoing a course of radiotherapy possibly because the treatment side effects often simulate those of anxiety and depression; the consequences of this can be reduced patient prognosis and increased health care costs. A questionnaire was administered to a sample of 100 eligible cancer patients and this yielded a 68% response rate. The Hospital Anxiety and Depression (HAD) scale was integrated into the questionnaire to accurately establish levels of anxiety and depression in the respondents of the study. The study identified six respondents with clinically significant levels of anxiety (9%) and six with depression (9%); 21% (n ¼ 14) of participants had higher than normal levels of anxiety and 21% for depression (n ¼ 14). Correlations were then identified between levels of psychological distress and the four independent variables; age, diagnosis, adjuvant medication and pain. Four predisposing factors were established—breast cancer diagnosis, age range 40"50 years, the presence of pain and adjuvant chemotherapy regime

Six host-range restricted poxviruses from three genera induce distinct gene expression profiles in an in vivo mouse model

BACKGROUND: Host-range restricted poxviruses make promising vaccine vectors due to their safety profile and immunogenicity. An understanding of the host innate immune responses produced by different poxvirus vectors would aid in the assessment, selection and rational design of improved vaccines for human and veterinary applications. Novel avipoxviruses are being assessed to determine if they are different from other poxvirus vectors. Analysis of the transcriptome induced in a mouse model would aid in determining if there were significant differences between different poxvirus vectors which may reflect different adjuvant potential as well as establish if they should be further evaluated as vaccine vectors. RESULTS: We compared host transcript abundance in the spleens of BALB/c mice twenty four hours after intravenous infection (10 5 pfu/mouse) with six host-restricted poxvirus species from three genera, namely Lumpy Skin Disease virus (LSDV), Canarypox virus (CNPV), Fowlpox virus (FWPV), modified vaccinia Ankara (MVA) and two novel South African avipoxviruses, Feral Pigeonpox virus (FeP2) and Penguinpox virus (PEPV). These six viruses produced qualitatively and quantitatively distinct host responses with LSDV, followed by MVA, inducing the greatest interferon (IFN) response. FeP2 and PEPV caused very little change to host transcript abundance compared to the other 4 viruses tested. CNPV and FWPV induced the up regulation of two immunoglobulin genes (Ighg and Ighg3 (IgG3)) with CNPV inducing a third, Ighm (IgM). HIV-1-specific IgG3 antibodies have been correlated with decreased risk of HIV-1 infection in the RV144 trial, which included a CNPV-based vector (Yates et al. (Sci Transl Med, 6(228) p228, 2014). Up regulation of IgG3 by CNPV and FWPV but not the other poxviruses tested in vivo, implies that these two avipoxvirus-vector backbones may be involved in stimulation of the clinically important IgG3 antibody subclass. Differential transcript abundance associated with the different poxviruses is further discussed with particular emphasis on responses related to immune responses. CONCLUSION: Six, genetically diverse host-restricted poxviruses produce different responses in a mouse model early after infection. These differences may affect the immune response induced to vaccine antigen in vectors based on these viruses. The two novel avipoxviruses were clearly distinguishable from the other viruses

Qualitative Assessment of the Symptoms and Impact of Pancreatic Exocrine Insufficiency (PEI) to Inform the Development of a Patient-Reported Outcome (PRO) Instrument

Background: Pancreatic exocrine insufficiency (PEI) affects patients with chronic pancreatitis (CP) and cystic fibrosis (CF) who produce insufficient digestive pancreatic enzymes. Common symptoms include steatorrhoea, diarrhea, and abdominal pain. Objective: The objective of the study was to develop and test the content validity of a patient-reported outcome (PRO) instrument assessing PEI symptoms and their impact on health-related quality of life. Methods: Instrument development was supported by a literature review, expert physician interviews (n = 10: Germany 4, UK 3, France 3), and exploratory, qualitative, concept-elicitation interviews with patients with CF and CP with PEI (n = 61: UK 29, Germany 18, France 14) and expert physicians (n = 10). Cognitive debriefing of the draft instrument was then performed with patients with PEI (n = 37: UK 24, Germany 8, France 5), and feasibility was assessed with physicians (n = 3). For all interviews, verbatim transcripts were qualitatively analysed using thematic analysis methods and Atlas.ti computerized qualitative software. All themes were data driven rather than a priori. Results: Patient interviews elicited symptoms and impacts not reported in the literature. Six symptom concepts emerged: pain, bloating, bowel symptoms, nausea/vomiting, eating problems, and tiredness/fatigue. Six impact domains were also identified. A 45-item instrument was developed in English, French, and German for testing in cognitive debriefing patient interviews. Following cognitive debriefing, 18 items were deleted. Conclusion: Rigorous qualitative patient research and expert clinical input supported development of a PEI-specific PRO with the potential to aid management and monitoring of unmet needs among patients with PEI. The next step is to perform psychometric evaluation of the resulting instrument.</p

SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications.

We present the SSIPTools suite of programs. SSIPTools is a collection of software modules enabling the use of the Surface Site Interaction Point (SSIP) molecular descriptors, used for the modeling of noncovalent interactions in neutral organic molecules. It contains an implementation of the workflow for the generation of the SSIP descriptors, as well as the Functional Group Interaction Profiles (FGIPs) and Solvent Similarity Indexes (SSIs) applications, based on the SSIMPLE (Surface Site Interaction model for the Properties of Liquids at Equilibria) approach.Engineering and Physical Sciences Research Council (EP/M506485/1

HIV-1 subtype C mosaic Gag expressed by BCG and MVA elicits persistent effector t cell responses in a prime-boost regimen in mice

Over 90% of HIV/AIDS positive individuals in sub-Saharan Africa are infected with highly heterogeneous HIV-1 subtype C (HIV-1C) viruses. One of the best ways to reduce the burden of this disease is the development of an affordable and effective prophylactic vaccine. Mosaic immunogens are computationally designed to overcome the hurdle of HIV diversity by maximizing the expression of potential T cell epitopes. Mycobacterium bovis BCG Δ panCD auxotroph and modified vaccinia Ankara (MVA) vaccines expressing HIV-1C mosaic Gag (Gag M ) were tested in a prime-boost regimen to demonstrate immunogenicity in a mouse study. The BCG-Gag M vaccine was stable and persisted 11.5 weeks post vaccination in BALB/c mice. Priming with BCG-Gag M and boosting with MVA-Gag M elicited higher Gag-specific IFN-γ ELISPOT responses than the BCG-Gag M only and MVA-Gag M only homologous vaccination regimens. The heterologous vaccination also generated a more balanced and persistent CD4 + and CD8 + T cell Gag-specific IFN-γ ELISPOT response with a predominant effector memory phenotype. A Th1 bias was induced by the vaccines as determined by the predominant secretion of IFN-γ, TNF-α, and IL-2. This study shows that a low dose of MVA (10 4 pfu) can effectively boost a BCG prime expressing the same mosaic immunogen, generating strong, cellular immune responses against Gag in mice. Our data warrants further evaluation in non-human primates. A low dose vaccine would be an advantage in the resource limited countries of sub-Saharan Africa and India (where the predominating virus is HIV-1 subtype C)