EpiJen:a server for multistep T cell epitope prediction

Background - The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. Results - To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. Conclusion - EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction.

Visualisation of bioinformatics datasets

Analysing the molecular polymorphism and interactions of DNA, RNA and proteins is of fundamental importance in biology. Predicting functions of polymorphic molecules is important in order to design more effective medicines. Analysing major histocompatibility complex (MHC) polymorphism is important for mate choice, epitope-based vaccine design and transplantation rejection etc. Most of the existing exploratory approaches cannot analyse these datasets because of the large number of molecules with a high number of descriptors per molecule. This thesis develops novel methods for data projection in order to explore high dimensional biological dataset by visualising them in a low-dimensional space. With increasing dimensionality, some existing data visualisation methods such as generative topographic mapping (GTM) become computationally intractable. We propose variants of these methods, where we use log-transformations at certain steps of expectation maximisation (EM) based parameter learning process, to make them tractable for high-dimensional datasets. We demonstrate these proposed variants both for synthetic and electrostatic potential dataset of MHC class-I. We also propose to extend a latent trait model (LTM), suitable for visualising high dimensional discrete data, to simultaneously estimate feature saliency as an integrated part of the parameter learning process of a visualisation model. This LTM variant not only gives better visualisation by modifying the project map based on feature relevance, but also helps users to assess the significance of each feature. Another problem which is not addressed much in the literature is the visualisation of mixed-type data. We propose to combine GTM and LTM in a principled way where appropriate noise models are used for each type of data in order to visualise mixed-type data in a single plot. We call this model a generalised GTM (GGTM). We also propose to extend GGTM model to estimate feature saliencies while training a visualisation model and this is called GGTM with feature saliency (GGTM-FS). We demonstrate effectiveness of these proposed models both for synthetic and real datasets. We evaluate visualisation quality using quality metrics such as distance distortion measure and rank based measures: trustworthiness, continuity, mean relative rank errors with respect to data space and latent space. In cases where the labels are known we also use quality metrics of KL divergence and nearest neighbour classifications error in order to determine the separation between classes. We demonstrate the efficacy of these proposed models both for synthetic and real biological datasets with a main focus on the MHC class-I dataset.

Molecular studies in gorgonian alloimmunity : search for gene homologs of the immunoglobulin gene superfamily in Swiftia exserta

Humoral and cells surface molecules of the mammalian immune system, grouped into the Immunoglobulin Gene Superfamily, share protein structure and gene sequence homologies with molecules found among diverse phylogenetic groups. In histocompatibility studies, the gorgonian coral Swiftia exserta has recently demonstrated specific alloimmunity with memory (Salter-Cid and Bigger, 1991. Biological Bulletin Vol 181). In an attempt to shed light on the origins of this gene family and the evolution of the vertebrate immune response, genomic DNA from Swiftia exserta was isolated, purified, and analyzed by Southern blot hybridization with mouse gene probes corresponding to two molecules of the Immunoglobulin Gene Superfamily, the Thy-1 antigen, and the alpha-3 domain of the MHC Class I histocompatibility marker. Hybridizations were conducted under low to non-stringent conditions to allow binding of mismatched homologs that may exist between the mouse gene probes and the Swiftia DNA. Removal of non-specific binding (sequences less than 70% homologous) occurred in washing steps. Results show that with the probes selected, the method chosen, and the conditions applied, no evidence of sequences of 70% or greater homology to the mouse Thy-1 or MHC Class I alpha-3 genes exist in Swiftia exserta genome.

Ampliação do Setor de Aulas Teóricas IV - UFRN: proposta arquitetônica baseada no conceito da flexibilidade e adaptabilidade, utilizando os parâmetros de conforto ambiental

In recent years, the Universidade Federal do Rio Grande do Norte (UFRN) has come through an intense process of expansion, common for the Instituições Federais de Ensino Superior (IFES) - Higher Education Institutions – since the implantation of the Programa de Reestruturação e Expansão das Universidades Federais (REUNI), a program of restructuring and expansion of the federal universities. The incentives made at UFRN can be seen into the expansion of the fields of teaching, research and extension, besides hiring human resources and adaptation / expansion of physical spaces. The focus of the UFRN at the technological area through the project (REUNI) has reflected in a significant expansion of the physical structure of the Center of Technology, area where the section of classes IV remains being the main set of rooms that supports the demand of the courses in the technological area, in which highlights the lack of classrooms. In this sense, the work presented here, proposes an architectural blueprint for expanding the physical space of this sector, based in this main parameters: (i) the spatial flexibility that attends the varying numbers of students per class; (ii) the environmental comfort, using the parameters and guidelines constructive for the Bioclimatic Zone 8; (iii) the requirements contained in the rules of ABNT NBR 9050:2004, 9077:2001 and NBR NBR 15220-3:2003. The architectural proposal used the maximum template allowed by the UFRN Central Campus Master Plan, four floors, considering the existing building (area equal to 7413.95 m²) as the ground floor and the extension proposed distributed on three floors, with an area of around 2,535, 00 m² each, making up a total of 7602.65 m² of total area built

Tratamento de cascalho de perfuração utilizando sistemas microemulsionados

The oil industry is one of the activities that generates more waste to the environment. The drill cuttings is a waste generated in large quantities in the drilling process and that may cause environmental damage such as soil contamination and consequently the contamination of groundwater if disposed of without prior treatment. Arises the need to develop scientific activities and research ways to adapt these wastes the current environmental standards. In the case of solid wastes, the NBR 10004: 2004 of the Brazilian Association of Technical Standards (ABNT) classifies them into class I waste (hazardous) and class II (not dangerous), which determines which wastes may or may not be discarded in the environment without causing environmental impact. This study presents a novel alternative for treating drill cuttings, where this waste was classified as class I (Abreu & Souza, 2005), mainly by removing the n-paraffin present in it, since this arises when using drilling fluids base oil. Using microemulsion systems promotes the removal of this contaminant drill cuttings samples from wells located in Alto do Rodrigues - RN. Initially, we determined the concentration of paraffin using infrared method in samples were extracted with ultrasound, we obtained a paraffin concentration in the range from 36.59 to 43.52 g of paraffin per kilogram of cuttings. Used two microemulsion systems containing two nonionic surfactants from different classes, one is an alcohol ethoxylated (UNTL-90) and the other an nonylphenol ethoxylated (RNX 110). The results indicated that the system UNTL-90 surfactant has better efficiency than the system with RNX 110. The study of the influence of contact time at the extraction showed that for times greater than 25 minutes has a tendency to increase the percentage extraction with increasing contact time. It was also observed that the extraction is fast because at 1 minute contact has 22.7% extraction. The reuse of the microemulsion system without removing the paraffin extracted in previous steps, showed reduction of 29.32 in percentage of extraction by comparing the first and third extraction, but by comparing the first and second extractions reduction is 8.5 in percentage extraction, so the systems reuse optimization can be an option for economically viable removing paraffin from cuttings. The extraction with shaking is more effective in the treatment of cuttings, reaching the extraction percentage of 87.04%, that is, obtaining a drill cuttings with 0.551% paraffin. Using the percentage of paraffin employed in non-aqueous drilling fluids and fluid maximum limit on cuttings for disposal established by the Environmental Protection Agency of the United States (US EPA), one arrives at the conclusion that the level of paraffin on gravel cannot exceed 3.93%. Conclude that the amount of paraffin in the treated cuttings with the microemulsion system with shaking is below the established by US EPA, showing that the system used was efficient in removing the paraffin from the drill cuttings.

Ethics in the provision of removable partial dentures

Aim: To investigate the construction of cobalt-chromium removable partial dentures by commercial private dental laboratories. Methods: Ninety master casts for fabrication of cobalt-chromium removable partial dentures were obtained from three commercial laboratories randomly selected. Casts were assessed for dental arch treated, Kennedy classification, cast surveying, denture design information provided by the dentist, and mouth preparation (rest seat, guiding plane and retentive area). Dental technicians answered a questionnaire regarding qualification of assisted dentists, monthly number of framework castings, and use of dental surveyor. Mouth preparation was compared among laboratories using Kruskal-Wallis test (α=0.05). Results: The percentage of Kennedy class I was 16%, class II 19%, class III 56%, and class IV 9%. The majority of master cats (51%) examined was sent to dental laboratories without any design information and did not comply with ethical guidelines in the provision of RPD. Approximately half of the casts were considered “inappropriate” for guiding planes and retentive areas. One of the laboratories presented all casts “inappropriate” for rest seat distribution (p<0.001). Conclusions: Mouth preparation frequently failed for guiding planes, retentive areas and distribution of rest seats. It is necessary to provide students with adequate clinical experience at the dental school environment, which will actually be carried into the practice of dentistry.

Ethics in the provision of removable partial dentures

Aim: To investigate the construction of cobalt-chromium removable partial dentures by commercial private dental laboratories. Methods: Ninety master casts for fabrication of cobalt-chromium removable partial dentures were obtained from three commercial laboratories randomly selected. Casts were assessed for dental arch treated, Kennedy classification, cast surveying, denture design information provided by the dentist, and mouth preparation (rest seat, guiding plane and retentive area). Dental technicians answered a questionnaire regarding qualification of assisted dentists, monthly number of framework castings, and use of dental surveyor. Mouth preparation was compared among laboratories using Kruskal-Wallis test (α=0.05). Results: The percentage of Kennedy class I was 16%, class II 19%, class III 56%, and class IV 9%. The majority of master cats (51%) examined was sent to dental laboratories without any design information and did not comply with ethical guidelines in the provision of RPD. Approximately half of the casts were considered “inappropriate” for guiding planes and retentive areas. One of the laboratories presented all casts “inappropriate” for rest seat distribution (p<0.001). Conclusions: Mouth preparation frequently failed for guiding planes, retentive areas and distribution of rest seats. It is necessary to provide students with adequate clinical experience at the dental school environment, which will actually be carried into the practice of dentistry.

Prótese parcial removível retida por implantes: relato de caso

A ausência de dentes posteriores inferiores representa dificuldades no planejamento e controle de próteses parciais removíveis, pois o suporte é proporcionado por dentes e mucosa, que apresentam características anatômicas diferentes. O planejamento de próteses parciais removíveis apoiadas sobre implantes na região distal torna a prótese dento-implanto-suportada e não dento-muco-suportada sendo, uma opção aos casos de extremidade livre. Por meio deste relato de caso, um paciente portador de arco classe II de Kennedy foi reabilitado com prótese parcial removível apoiada sobre implante na região distal. A colocação do implante resultou em uma oclusão mais estável, o que melhorou a funcionalidade da prótese e proporcionou maior conforto ao paciente. Observou-se que esta resolução pode ser uma alternativa viável de tratamento, pois apresenta custo reduzido em relação à prótese fixa sobre implantes, entretanto, requer um acompanhamento em longo prazo com uma série de casos para tornar-se um método rotineiro de tratamento.

Prótese parcial removível retida por implantes: relato de caso

A ausência de dentes posteriores inferiores representa dificuldades no planejamento e controle de próteses parciais removíveis, pois o suporte é proporcionado por dentes e mucosa, que apresentam características anatômicas diferentes. O planejamento de próteses parciais removíveis apoiadas sobre implantes na região distal torna a prótese dento-implanto-suportada e não dento-muco-suportada sendo, uma opção aos casos de extremidade livre. Por meio deste relato de caso, um paciente portador de arco classe II de Kennedy foi reabilitado com prótese parcial removível apoiada sobre implante na região distal. A colocação do implante resultou em uma oclusão mais estável, o que melhorou a funcionalidade da prótese e proporcionou maior conforto ao paciente. Observou-se que esta resolução pode ser uma alternativa viável de tratamento, pois apresenta custo reduzido em relação à prótese fixa sobre implantes, entretanto, requer um acompanhamento em longo prazo com uma série de casos para tornar-se um método rotineiro de tratamento.

The Irish paradigm on the natural progression of hepatitis C virus infection: an investigation in a homogeneous patient population infected with HCV 1b (Review)

The aetiological agent of chronic hepatitis C is the hepatitis C virus. The hepatitis C virus is spread by parenteral transmission of body fluids, primarily blood or blood products. In 1989, after more than a decade of research, HCV was isolated and characterised. The hepatitis C viral genome is a positive-sense, single-stranded RNA molecule approximately 9.4 kb in length, which encodes a polyprotein of about 3100 amino acids. There are 6 main genotypes of HCV, each further stratified by subtype. In 1994, a cohort of women was identified in Ireland as having been iatrogenically exposed to the hepatitis C virus. The women were all young and exposed as a consequence of the receipt of HCV 1b contaminated anti-D immunoglobulin. The source of the infection was identified as an acutely infected female. As part of a voluntary serological screening programme involving 62,667 people, 704 individuals were identified as seropositive for exposure to the hepatitis C virus; 55.4% were found to be positive for the viral genome 17 years after exposure. Of these women 98% had evidence of inflammation, but suprisingly, a remarkable 49% showed no evidence of fibrosis. Clinicopathology and virological analysis has identified associations between viral load and the histological activity index for inflammation, and, between inflammation and levels of the liver enzyme alanine aminotransferase. Infection at a younger age appears to protect individuals from progression to advanced liver disease. Molecular analyses of host immunogenetic elements shows that particular class II human leukocyte associated antigen alleles are associated with clearance of the hepatitis C virus. Additional class II alleles have been identified that are associated with stable viraemia over an extended period of patient follow-up. Although, investigation of large untreated homogeneous cohorts is likely to become more difficult, as the efficacy of anti-viral therapy improves, further investigation of host and viral factors that influence disease progression will help provide an evidence based approach were realistic expectations regarding patient prognosis can be ascertained.

Adult orthodontics: internet information and a national survey

Aims: 1. To investigate the reliability and readability of information on the Internet on adult orthodontics. 2. To evaluate the profile and treatment of adults by specialist orthodontists in the Republic of Ireland (ROI). Materials and methods: 1. An Internet search was conducted in May 2015 using three search engines (Google, Yahoo and Bing), with two search terms (“adult orthodontics” and “adult braces”). The first 50 websites from each engine were screened and exclusion criteria applied. Included websites were then assessed for reliability using the JAMA benchmarks, the DISCERN and LIDA tools and the presence of the HON seal. Readability was assessed using the FRES. 2. A pilot-tested questionnaire about adult orthodontics was distributed to 122 eligible specialist orthodontists in the ROI. Questions addressed general and treatment information about adult orthodontic patients, methods of information provision and respondent demographics. Results: 1. Thirteen websites met the inclusion criteria. Three websites contained all JAMA benchmarks and one displayed the HON Seal. The mean overall score for DISCERN was 3.9/5 and the mean total LIDA score was 115/120. The average FRES score was 63.1. 2. The questionnaire yielded a response rate of 83%. The typical demographic profile of adult orthodontic patients was professional females between 25-35 years. The most common incisor relationship and skeletal base was Class II, division 1 (51%) and Class II (61%) respectively. Aesthetic upper brackets and metal lower brackets were the most frequently used appliances. Only 30% of orthodontists advise their adult patients to find extra information on the Internet. Conclusions: 1. The reliability and readability of information on the Internet on adult orthodontics is of moderate quality. 2. The provision of adult orthodontic treatment is common among specialist orthodontists in the Republic of Ireland.

Three-dimensional outcomes of twin-block appliance treatment and the influence of the postured wax bite

Aims 1 To identify the 3D soft tissue volumetric and linear landmark changes following treatment with the Twin-Block Appliance TBA. 2 To estimate the TBA treatment outcome on the soft tissue facial profile volumetric and linear landmark changes from the Postured Wax Bite (PWB). 3 To identify if there is any association between certain soft tissue landmark variables and successful treatment outcome of the TBA as measured by the reduction in overjet. 4 To assess the effects of TBA treatment on facial expressions. Materials and Methods Forty-seven Caucasian subjects with Class II division 1 were recruited. 3D images captured of each subject, pre-treatment (T1), with the PWB (T2) and at the end of treatment (T3). Soft tissue volumetric and linear changes as well as the correlation between facial parameters and successful treatment were calculated. Results The mean soft tissue volumetric change from T1 to T3 was 22.24 ± 16.73 cm³. Soft tissue profile linear changes from T1-T3 for lower facial landmarks were 4-5 mm. From T1-T3, the mean soft tissue volumetric change of the total sample was 60% of the change produced by the PWB (T1 to T2). Correlations were weak for all 3D facial parameters and successful overjet reduction. Facial expression changes were only significant for the lower landmarks. Conclusions 1 TBA treatment, in growing subjects, increased the lower facial soft tissue volume and caused forward movement of the lower soft tissue facial profile landmarks.2 The PWB can be used to estimate the treatment outcome of the TBA on soft tissue profile changes.3 No association was found between soft tissue landmark variables and successful overjet reduction.4 TBA treatment had no effect on the upper facial landmarks for each facial expression but it changed the lower facial expressions significantly except for maximal smile in males.

PEG-based solid dispersions enhanced the solubility and dissolution of eprosartan mesylate in-vitro

Abstract - This study investigates the effect of solid dispersions prepared from of polyethylene glycol (PEG) 3350 and 6000 Da alone or combined with the non-ionic surfactant Tween 80 on the solubility and dissolution rate of a poorly soluble drug eprosartan mesylate (ESM) in attempt to improve its bioavailability following its oral administration.

INTRODUCTION

ESM is a potent anti-hypertension [1]. It has low water solubility and is classified as a Class II drug as per the Biopharmaceutical Classification Systems (BCS) leading to low and variable oral bioavailability (approximately 13%). [2]. Thus, improving ESM solubility and/or dissolution rate would eventually improve the drug bioavailability. Solid dispersion is widely used technique to improve the water solubility of poorly water-soluble drugs employing various biocompatible polymers. In this study, we aimed to enhance the solubility and dissolution of EMS employing solid dispersion (SD) formulated from two grades of poly ethylene glycol (PEG) polymers (i.e. PEG 3350 & PEG 6000 Da) either individually or in combination with Tween 80.

MATERIALS AND METHODS

ESM SDs were prepared by solvent evaporation method using either PEG 3350 or PEG 6000 at various (drug: polymer, w/w) ratios 1:1, 1:2, 1:3, 1:4, 1:5 alone or combined with Tween 80 added at fixed percentage of 0.1 of drug by weight?. Physical mixtures (PMs) of drug and carriers were also prepared at same ratios. Drug solid dispersions and physical mixtures were characterized in terms of drug content, drug dissolution using dissolution apparatus USP II and assayed using HPLC method. Drug dissolution enhancement ratio (ER %) from SD in comparison to the plain drug was calculated. Drug-polymer interactions were evaluated using Differential Scanning Calorimetry (DSC) and FT-IR.

RESULTS AND DISCUSSION

The in vitro solubility and dissolution studies showed SDs prepared using both polymers produced a remarkable improvement (p<0.05) in comparison to the plain drug which reached around 32% (Fig. 1). The dissolution enhancement ratio was polymer type and concentration-dependent. Adding Tween 80 to the SD did not show further dissolution enhancement but reduced the required amount of the polymer to get the same dissolution enhancement. The DSC and FT-IR studies indicated that using SD resulted in transformation of drug from crystalline to amorphous form.

CONCLUSIONS

This study indicated that SDs prepared by using both polymers i.e. PEG 3350 and PEG 6000 improved the in-vitro solubility and dissolution of ESM remarkably which may result in improving the drug bioavailability in vivo.

Acknowledgments

This work is a part of MSc thesis of O.M. Ali at the Faculty of Pharmacy, Aleppo University, Syria.

REFERENCES

[1] Ruilope L, Jager B: Eprosartan for the treatment of hypertension. Expert Opin Pharmacother 2003; 4(1):107-14

[2] Tenero D, Martin D, Wilson B, Jushchyshyn J, Boike S, Lundberg, D, et al. Pharmacokinetics of intravenously and orally administered Eprosartan in healthy males: absolute bioavailability and effect of food. Biopharm Drug Dispos 1998; 19(6): 351- 6.

Development of Medical Devices

The medical devices sector helps save lives by providing innovative health care solutions regarding diagnosis, prevention, monitoring, treatment, and alleviation. Medical devices are classified into 1 of 3 categories in the order of increasing risk: Class I, Class II, and Class III.1 Medical devices are distinguished from drugs for regulatory purposes based on mechanism of action. Unlike drugs, medical devices operate via physical or mechanical means and are not dependent on metabolism to accomplish their primary intended effect.

Doença enxerto-versus hospedeiro: determinação da expressão de genes e alterações de vias associadas ao sistema imunológico usando metodos da biofísica

O transplante de medula óssea (TMO) é um procedimento terapêutico importante em casos relacionados à pacientes com leucemia ou linfoma. Em decorrência desse processo, uma reação conhecida como doença enxerto-versus-hospedeiro (GVHD) pode ocorrer em pacientes susceptíveis como conseqüência da presença de células imunocompetentes do doador. Entretanto, não existe um modelo para descrever completamente as ações relacionadas ao mecanismo imunológico da GVHD desde a fase que inicializa a doença até a fase efetora. O Objetivo geral deste estudo é a investigação da resposta imunológica considerando-se o sistema HLA (antígenos leucocitários humano) em pacientes que desenvolveram a GVHD em decorrência do TMO. O National Cancer Institute (NCI) – Pathway interaction Database e Reactome foram usados como bases de dados com o objetivo de se estudar a expressão de genes e vias relacionados às Classes I e II do sistema HLA (antígenos leucocitários humano). O estudo considerou a mudança de expressão de genes relacionados às 17 vias do sistema imunológico com potencialidade para se expressar em pacientes que desenvolveram a GVHD associada à TMO. Dados referentes aos transcriptomas foram obtidos utilizando-se a plataforma GPL570 Affymetrix Genoma Humano U133 Plus. A atividade relativa foi usada para determinar as alterações das vias em amostras de GVHD em relação ao controle. As análises foram realizadas utilizando-se o software Via Complex e Bioconductor. Observou-se aumento significativo da expressão de genes ralacionados às vias do sistema imune adaptativo, antígenos associados às Classe I e II do HLA, fosforilação de CD3 e CD247, sinalização dos receptores de células T em CD4+ nativas e ativação de NF-kapa β nas células B. Também observou-se alterações significativas na mudança de expressão dos genes associados às vias relacionadas à super família de moléculas B7:CD28\CTLA-4 quando comparadas ao controle. Isso pode indicar a necessidade de geração de um segundo sinal co-estimulador em GVHD, acionado pelas moléculas dessa super família. O aumento da expressão do gene CD69 nas amostras experimentais caracteriza a ativação celular e, portanto, a sinalização de estímulos em GVHD. Os achados obtidos neste estudo contribuem para melhor elucidar o mecanismo imunopatogênico associado à GVHD. P