INFO2009 Coursework 1 2012-13 Annotated Bibliography Specification and Assessment Criteria

This the coursework specification as a single file including assessment criteria which also appear on the ECS handin page. The collection of associated handouts and links along with the coursework specification can be found at http://www.edshare.soton.ac.uk/6041/

Immunohistochemistry as a fundamental tool for the differential diagnosis of polymorphous low-grade adenocarcinoma

Polymorphous low-grade adenocarcinoma (PLGA) is a subtype of salivary gland carcinoma with a marked predilection for the minor salivary glands. The diagnosis of this lesion can be a challenge in incisional biopsies because of its similarity to other salivary neoplasms and the difficulty of analyzing its infiltrative nature and neurotropism. Diagnosis can be facilitated, however, by immunohistochemistry, a technique that has become a fundamental tool to the pathologist. The purpose of this study was analyze the immunohistochemical aspects of 4 cases that were examined in the São José dos Campos School of Dentistry. The patients included 4 women, ages 32 to 57 years (mean, 50 years), who reported an intraoral painless lesion, ranging in size from 1 to 3 cm (mean, 1.75 cm) with a variable evolution period. Histologically, the lesions showed similar aspects, characterized by polymorphous growth pattern, including solid, cribriform, trabecular, papillary, and single-file arrays. The tumors showed positivity to cytokeratins (Cks) 7 and 8 and vimentin, variable expression for Ck 14, and a negative reaction to Cks 13 and 19 and muscle-specific actin. PLGA is a tumor of the salivary gland that must be distinguished from other neoplasms for therapeutic and prognostic considerations, and the panel of antibodies employed in this study was effective for its diagnosis.

Endodontic retreatment: clinical comparison of reciprocating systems versus rotary system in disinfecting root canals

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Glutamic acid inducing kidney stone biomimicry by a brushite/gelatin composite

Brushite is a well known precursor of calcium oxalate monohydrate, the main mineral found in kidney stones having a monoclinic crystal structure. Here, we present a new method for biomimicking brushite using a single tube diffusion technique for gel growth. Brushite crystals were grown by precipitation of calcium hydrogen phosphate hydrate in a gelatin/glutamic acid network. They are compared with those produced in gel in the presence of urea. The aggregates were analyzed by scanning electron microscopy (SEM), X-ray diffraction (XRD), infrared spectroscopy (IR) and thermal gravimetric analysis (TGA). SEM revealed a change of morphology by glutamic acid from spherulitic growth to plate-shaped and mushroom-like forms consisting of crystal plates and highly ordered prismatic needles, respectively. Furthermore, brushite crystals grown in a gelatin/glutamic acid/urea network showed needle-shaped morphology being different from other brushite growth forms. The XRD method showed that cell parameters for brushite specimens were slightly larger than those of the American Mineral Society reference structure. The mushroom-like biomimetic composite bears a strong resemblance to the brushite kidney stones which may open up new future treatment options for crystal deposition diseases. Hence, suitable diets from glutamic acid rich foods could be recommended to inhibit and control brushite kidney stones.

The conducting form of gramicidin A is a right-handed double-stranded double helix

The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDHℛ) reported here agree with 15N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs+ and K+ salts may be in error and that our evidence points to the DSDHℛ as the major conformer responsible for ion transport in membranes.

Streaming potential measurements in αβγ-rat epithelial Na+ channel in planar lipid bilayers

Streaming potentials across cloned epithelial Na+ channels (ENaC) incorporated into planar lipid bilayers were measured. We found that the establishment of an osmotic pressure gradient (Δπ) across a channel-containing membrane mimicked the activation effects of a hydrostatic pressure differential (ΔP) on αβγ-rENaC, although with a quantitative difference in the magnitude of the driving forces. Moreover, the imposition of a Δπ negates channel activation by ΔP when the Δπ was directed against ΔP. A streaming potential of 2.0 ± 0.7 mV was measured across αβγ-rat ENaC (rENaC)-containing bilayers at 100 mM symmetrical [Na+] in the presence of a 2 Osmol/kg sucrose gradient. Assuming single file movement of ions and water within the conduction pathway, we conclude that between two and three water molecules are translocated together with a single Na+ ion. A minimal effective pore diameter of 3 Å that could accommodate two water molecules even in single file is in contrast with the 2-Å diameter predicted from the selectivity properties of αβγ-rENaC. The fact that activation of αβγ-rENaC by ΔP can be reproduced by the imposition of Δπ suggests that water movement through the channel is also an important determinant of channel activity.

Data compilation of dinoflagellates growth rate, grazing rate and gross gowth efficiency from field and labratory experiments

The present data compilation includes dinoflagellates growth rate, grazing rate and gross growth efficiency determined either in the field or in laboratory experiments. From the existing literature, we synthesized all data that we could find on dinoflagellates. Some sources might be missing but none were purposefully ignored. We did not include autotrophic dinoflagellates in the database, but mixotrophic organisms may have been included. This is due to the large uncertainty about which taxa are mixotrophic, heterotrophic or symbiont bearing. Field data on microzooplankton grazing are mostly comprised of grazing rate using the dilution technique with a 24h incubation period. Laboratory grazing and growth data are focused on pelagic ciliates and heterotrophic dinoflagellates. The experiment measured grazing or growth as a function of prey concentration or at saturating prey concentration (maximal grazing rate). When considering every single data point available (each measured rate for a defined predator-prey pair and a certain prey concentration) there is a total of 801 data points for the dinoflagellates, counting experiments that measured growth and grazing simultaneously as 1 data point.

Data compilation of ciliates growth rate, grazing rate and gross gowth efficiency from field and labratory experiments

The present data compilation includes ciliates growth rate, grazing rate and gross growth efficiency determined either in the field or in laboratory experiments. From the existing literature, we synthesized all data that we could find on cilliate. Some sources might be missing but none were purposefully ignored. Field data on microzooplankton grazing are mostly comprised of grazing rate using the dilution technique with a 24h incubation period. Laboratory grazing and growth data are focused on pelagic ciliates and heterotrophic dinoflagellates. The experiment measured grazing or growth as a function of prey concentration or at saturating prey concentration (maximal grazing rate). When considering every single data point available (each measured rate for a defined predator-prey pair and a certain prey concentration) there is a total of 1485 data points for the ciliates, counting experiments that measured growth and grazing simultaneously as 1 data point.

Caracterização da produção científica portuguesa da área da saúde indexada na Scopus

Introdução – É particularmente importante uma avaliação objetiva e imparcial da qualidade da atividade científica dos investigadores, mas também do comportamento científico e pedagógico das instituições de ensino superior, as quais, por sua vez, são o espelho do empenho de um país na sua componente de I&D. Objetivo – O presente estudo bibliométrico pretende caracterizar a presença portuguesa na Scopus e analisar a produção científica portuguesa classificada na área da saúde e indexada nesta base de dados. Métodos – Analisou-se a produção científica portuguesa referente ao período de janeiro de 2000 a dezembro de 2015. A abordagem centrou-se nas seguintes variáveis: categorias de classificação da Scopus; tipologia de documentos indexados; títulos de revistas; autores; distribuição por anos de publicação; afiliação institucional e países de origem dos autores com quem foram estabelecidas relações de parceria científica. Consideraram-se três grandes categorias de classificação na Scopus (Life Sciences, Health Sciences e Social Sciences & Humanities, usando filtros temáticos), porque a área da saúde tanto assume componentes exatas como transversais. Conjugou-se o descritor Portugal com a modalidade affiliation country. Os dados foram alinhados pela terminologia das variáveis em estudo (affiliation, author, country, doctype, source, subject, year) e fundidos num só ficheiro por variável. Resultados – A Scopus contempla 198.749 resultados com afiliação em Portugal. Na área da saúde contabilizaram-se, no total, 71.232 trabalhos, o que significa uma percentagem de 35,8%. Estes encontram-se distribuídos pelos três grupos de classificação: Health Sciences (59,1%), Life Sciences (34%) e Social Sciences & Humanities (6,9%). O artigo original (78,1%) consubstancia a forma mais usada pelos autores portugueses para a divulgação dos resultados de investigação, logo seguido do artigo de revisão (8,9%), dos paper (3,9%) e das letter (3,1%). Os últimos cinco anos são os mais representativos na produção científica (58,4%). Analisando as revistas onde os investigadores portugueses mais publicam, constata-se que são portuguesas sete das primeiras dez. A maioria da produção científica com visibilidade internacional é oriunda das universidades, sendo a Universidade do Porto a que mais se destaca. A parceria científica com outros investigadores destaca a colaboração nacional, mas também com os Estados Unidos, Espanha, Reino Unido, Alemanha, França, Itália, Países Baixos e Brasil, por esta ordem. De destacar que é a Universidade de São Paulo (no Brasil) a maior instituição parceira com 788 trabalhos. Discussão e Conclusões – Na informação da área da saúde indexada na Scopus, as universidades desempenham um papel fundamental, destacando-se a Universidade do Porto. Também os índices de coautoria e sobretudo a colaboração internacional com investigadores de outras nacionalidades têm aumentado ao longo dos anos. Os benefícios e os méritos desta colaboração internacional ao nível da investigação incluem a partilha e a transferência de conhecimento e equipamento, associando os investigadores a uma grande rede científica, bem como o acelerar do processo de investigação, aumentando a visibilidade dos artigos. A produção científica portuguesa da saúde evidencia a existência de vínculos com diversos países, produto das parcerias, dos projetos globais e dos financiamentos.

Single molecule simulation of diffusion and enzyme kinetics

This work presents a molecular-scale agent-based model for the simulation of enzymatic reactions at experimentally measured concentrations. The model incorporates stochasticity and spatial dependence, using diffusing and reacting particles with physical dimensions. We developed strategies to adjust and validate the enzymatic rates and diffusion coefficients to the information required by the computational agents, i.e., collision efficiency, interaction logic between agents, the time scale associated with interactions (e.g., kinetics), and agent velocity. Also, we tested the impact of molecular location (a source of biological noise) in the speed at which the reactions take place. Simulations were conducted for experimental data on the 2-hydroxymuconate tautomerase (EC 5.3.2.6, UniProt ID Q01468) and the Steroid Delta-isomerase (EC 5.3.3.1, UniProt ID P07445). Obtained results demonstrate that our approach is in accordance to existing experimental data and long-term biophysical and biochemical assumptions.

Combining multiple files in to a single PDF file using Adobe Pro X

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Combining multiple files in to a single PDF file using Adobe Acrobat XI Pro

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Diffusion ability of endotoxin through dentinal tubules

The aim of this study was to evaluate the ability of endotoxin to diffuse through dentinal tubules towards the cement and to observe the period of time needed for it to reach the external root surface. Thirty single-rooted human teeth had their crowns and apices removed in order to standardize the root length to 15 mm. Teeth were instrumented until #30 K-file and made externally impermeable with epoxy adhesive, leaving 10 mm of the exposed root (middle third). The specimens were placed in plastic vials and irradiated (60Co gamma-rays). Then, they were divided into 2 groups (n = 15): G1) Escherichia coli endotoxin was inoculated into the root canal of the specimens and 1 ml of pyrogen-free water was put in the tubes; G2) (control): pyrogen-free water was inoculated into the root canals and 1 ml of pyrogen-free water was put in each tube. After 30 min, 2 h, 6 h, 12 h, 24 h, 48 h, 72 h and 7 days, the water of the tubes was removed and replaced. The removed aliquot was tested for the presence of endotoxin. Considering that the endotoxin is a B-lymphocyte polyclonal activator, at each experimental period, B-lymphocyte culture was stimulated with a sample of water removed from each tube and antibody (IgM) production was detected by ELISA technique. The results of IgM production were higher in groups of 24 h, 48 h, 72 h and 7 days in relation to the other studied groups, with statistically significant differences (ANOVA and Tukey's test p < 0.05). Endotoxin was able to diffuse through the dentinal tubules towards the cement, reaching the external root surface after the period of 24 h.

Two-dimensional relaxation-diffusion analysis to study water compartmentalization in cells by a single-sided NMR device

In questo lavoro di tesi è presentato un metodo per lo studio della compartimentalizzazione dell’acqua in cellule biologiche, mediante lo studio dell’autodiffusione delle molecole d’acqua tramite uno strumento NMR single-sided. Le misure sono state eseguite nel laboratorio NMR all’interno del DIFA di Bologna. Sono stati misurati i coefficienti di autodiffusione di tre campioni in condizione bulk, ottenendo risultati consistenti con la letteratura. È stato poi analizzato un sistema cellulare modello, Saccharomyces cerevisiae, allo stato solido, ottimizzando le procedure per l’ottenimento di mappe di correlazione 2D, aventi come assi il coefficiente di autodiffusione D e il tempo di rilassamento trasversale T2. In questo sistema l’acqua è confinata e l’autodiffusione è ristretta dalle pareti cellulari, si parla quindi di coefficiente di autodiffusione apparente, Dapp. Mediante le mappe sono state individuate due famiglie di nuclei 1H. Il campione è stato poi analizzato in diluizione in acqua distillata, confermando la separazione del segnale in due distinte famiglie. L’utilizzo di un composto chelato, il CuEDTA, ha permesso di affermare che la famiglia con il Dapp maggiore corrisponde all’acqua esterna alle cellule. L’analisi dei dati ottenuti sulle due famiglie al variare del tempo lasciato alle molecole d’acqua per la diffusione hanno portato alla stima del raggio dei due compartimenti: r=2.3±0.2µm per l’acqua extracellulare, r=0.9±0.1µm per quella intracellulare, che è probabilmente acqua scambiata tra gli organelli e il citoplasma. L’incertezza associata a tali stime tiene conto soltanto dell’errore nel calcolo dei parametri liberi del fit dei dati, è pertanto una sottostima, dovuta alle approssimazioni connesse all’utilizzo di equazioni valide per un sistema poroso costituito da pori sferici connessi non permeabili. Gli ordini di grandezza dei raggi calcolati sono invece consistenti con quelli osservabili dalle immagini ottenute con il microscopio ottico.

Dynamic contrast-enhanced and diffusion-weighted MRI for early detection of tumoral changes in single-dose and fractionated radiotherapy: evaluation in a rat rhabdomyosarcoma model

We aimed to examine different intratumoral changes after single-dose and fractionated radiotherapy, using diffusion-weighted (DW) and dynamic contrast-enhanced (DCE) MRI in a rat rhabdomyosarcoma model. Four WAG/Rij rats with rhabdomyosarcomas in the flanks received single-dose radiotherapy of 8 Gy, and four others underwent fractionated radiotherapy (five times 3 Gy). In rats receiving single-dose radiotherapy, a significant perfusion decrease was found in the first 2 days post-treatment, with slow recuperation afterwards. No substantial diffusion changes could be seen; tumor growth delay was 12 days. The rats undergoing fractionated radiotherapy showed a similar perfusion decrease early after the treatment. However, a very strong increase in apparent diffusion coefficient occurred in the first 10 days; growth delay was 18 days. DW-MRI and DCE-MRI can be used to show early tumoral changes induced by radiotherapy. Single-dose and fractionated radiotherapy induce an immediate perfusion effect, while the latter induces more intratumoral necrosis.