Utility of temporal artery biopsy samples for genome-wide analysis of giant cell arteritis

Giant Cell Arteritis (GCA) is the most common vasculitis affecting the elderly. Archived formalin-fixed paraffin-embedded (FFPE) temporal artery biopsy (TAB) specimens potentially represent a valuable resource for large-scale genetic analysis of this disease. FFPE TAB samples were obtained from 12 patients with GCA. Extracted TAB DNA was assessed by real time PCR before restoration using the Illumina HD FFPE Restore Kit. Paired FFPE-blood samples were genotyped on the Illumina OmniExpress FFPE microarray. The FFPE samples that passed stringent quality control measures had a mean genotyping success of >97%. When compared with their matching peripheral blood DNA, the mean discordant heterozygote and homozygote single nucleotide polymorphisms calls were 0.0028 and 0.0003, respectively, which is within the accepted tolerance of reproducibility. This work demonstrates that it is possible to successfully obtain high-quality microarray-based genotypes FFPE TAB samples and that this data is similar to that obtained from peripheral blood.

Utility of magnetic resonance imaging-based finite element analysis for the biomechanical stress analysis of hemorrhagic and non-hemorrhagic carotid plaques

Background: Biomechanical stress analysis has been used for plaque vulnerability assessment. The presence of plaque hemorrhage (PH) is a feature of plaque vulnerability and is associated with thromboembolic ischemic events. The purpose of the present study was to use finite element analysis (FEA) to compare the stress profiles of hemorrhagic and non-hemorrhagic profiles. Methods and Results: Forty-five consecutive patients who had suffered a cerebrovascular ischemic event with an underlying carotid artery disease underwent high-resolution magnetic resonance imaging (MRI) of their symptomatic carotid artery in a 1.5-T MRI system. Axial images were manually segmented for various plaque components and used for FEA. Maximum critical stress (M-CstressSL) for each slice was determined. Within a plaque, the maximum M-CstressSL for each slice of a plaque was selected to represent the maximum critical stress of that plaque (M-CstressPL) and used to compare hemorrhagic and non-hemorrhagic plaques. A total of 62% of plaques had hemorrhage. It was observed that plaques with hemorrhage had significantly higher stress (M-CstressPL) than plaques without PH (median [interquartile range]: 315 kPa [247-434] vs. 200 kPa [171-282], P=0.003). Conclusions: Hemorrhagic plaques have higher biomechanical stresses than non-hemorrhagic plaques. MRI-based FEA seems to have the potential to assess plaque vulnerability.

Utility of USPIO-enhanced MR imaging to identify inflammation and the fibrous cap: A comparison of symptomatic and asymptomatic individuals

Background and purpose: Inflammation is a risk factor the vulnerable atheromatous plaque. This can be detected in vivo on high-resolution magnetic resonance (MR) imaging using a contrast agent, Sinerem™, an ultra-small super-paramagnetic iron oxide (USPIO). The aim of this study was to explore whether there is a difference in the degree of MR defined inflammation using USPIO particles, between symptomatic and asymptomatic carotid plaques. We report further on its T1 effect of enhancing the fibrous cap, which may allow dual contrast resolution of carotid atheroma. Methods: Twenty patients with carotid stenosis (10 symptomatic and 10 asymptomatic) underwent multi-sequence MR imaging before and 36 h post-USPIO infusion. Images were manually segmented into quadrants and signal change in each quadrant was calculated following USPIO administration. Mean signal change across all quadrants were compared between the two groups. Results: Symptomatic patients had significantly more quadrants with a signal drop than asymptomatic individuals (75% vs. 32%, p < 0.01). Asymptomatic plaques had more quadrants with signal enhancement than symptomatic ones (68% vs. 25%, p < 0.05); their mean signal change was also higher (46% vs. 15%, p < 0.01) and this appeared to correlate with a thicker fibrous cap on histology. Conclusions: Symptomatic patients had more quadrants with signal drop suggesting larger inflammatory infiltrates. Asymptomatic individuals showed significantly more enhancement possibly suggesting greater stability as a result of thicker fibrous caps. However, some asymptomatic plaques also had focal areas of signal drop, suggesting an occult macrophage burden. If validated by larger studies, USPIO may be a useful dual contrast agent able to improve risk stratification of patients with carotid stenosis and inform selection for intervention.

Correlation of carotid atheromatous plaque inflammation with biomechanical stress: Utility of USPIO enhanced MR imaging and finite element analysis

Objective: The aim of this study was to explore whether there is a relationship between the degree of MR-defined inflammation using ultra small super-paramagnetic iron oxide (USPIO) particles, and biomechanical stress using finite element analysis (FEA) techniques, in carotid atheromatous plaques. Methods and Results: 18 patients with angiographically proven carotid stenoses underwent multi-sequence MR imaging before and 36 h after USPIO infusion. T2 * weighted images were manually segmented into quadrants and the signal change in each quadrant normalised to adjacent muscle was calculated after USPIO administration. Plaque geometry was obtained from the rest of the multi-sequence dataset and used within a FEA model to predict maximal stress concentration within each slice. Subsequently, a new statistical model was developed to explicitly investigate the form of the relationship between biomechanical stress and signal change. The Spearman's rank correlation coefficient for USPIO enhanced signal change and maximal biomechanical stress was -0.60 (p = 0.009). Conclusions: There is an association between biomechanical stress and USPIO enhanced MR-defined inflammation within carotid atheroma, both known risk factors for plaque vulnerability. This underlines the complex interaction between physiological processes and biomechanical mechanisms in the development of carotid atheroma. However, this is preliminary data that will need validation in a larger cohort of patients.

Design studio terrains: Mapping the learning landscapes of Australian architectural education

It has been nearly 25 years since the problems associated with passive learning in large undergraduate classes were first established by McDermott (1991). STEM education, for example North Carolina State University’s SCALE-UP project, has subsequently been influenced by some unique aspects of design studio education. While there are now many institutions applying SCALE-UP or similar approaches to enable lively interaction, enhanced learning, increased student engagement, and to teach many different content areas to classes of all sizes, nearly all of these have remained in the STEM fields (Beichner, 2008). Architectural education, although originally at the forefront of this field, has arguably been left behind. Architectural practice is undergoing significant change, globally. Access to new technology and the development of specialised architectural documentation software has scaffolded new building procurement methods and allowed consultant teams to work more collaboratively, efficiently and even across different time zones. Up until recently, the spatial arrangements, pedagogical approaches, and project work outcomes in the architectural design studio, have not been dissimilar to its inception. It is not possible to keep operating architectural design studios the same way that they have for the past two hundred years, with this new injection of high-end technology and personal mobile Wi-Fi enabled devices. Employing a grounded theory methodology, this study reviews the current provision of architectural design learning terrains across a range of tertiary institutions, in Australia. Some suggestions are provided for how these spaces could be modified to address the changing nature of the profession, and implications for how these changes may impact the design of future SCALE-UP type spaces outside of the discipline of architecture, are also explored.

The utility of near infrared spectroscopy for age estimation of deepwater sharks

Reliable age information is vital for effective fisheries management, yet age determinations are absent for many deepwater sharks as they cannot be aged using traditional methods of growth bands counts. An alternative approach to ageing using near infrared spectroscopy (NIRS) was investigated using dorsal fin spines, vertebrae and fin clips of three species of deepwater sharks. Ages were successfully estimated for the two dogfish, Squalus megalops and Squalus montalbani, and NIRS spectra were correlated with body size in the catshark, Asymbolus pallidus. Correlations between estimated-ages of the dogfish dorsal fin spines and their NIRS spectra were good, with S. megalops R2=0.82 and S. montalbani R2=0.73. NIRS spectra from S. megalops vertebrae and fin clips that have no visible growth bands were correlated with estimated-ages, with R2=0.89 and 0.76, respectively. NIRS has the capacity to non-lethally estimate ages from fin spines and fin clips, and thus could significantly reduce the numbers of sharks that need to be lethally sampled for ageing studies. The detection of ageing materials by NIRS in poorly calcified deepwater shark vertebrae could potentially enable ageing of this group of sharks that are vulnerable to exploitation.

Barrett's Esophagus and Associated Adenocarcinoma : studies on pathogenesis, clinical staging and cost-utility of cancer treatment

Esophageal and gastroesophageal junction (GEJ) adenocarcinoma is rapidly increasing disease with a pathophysiology connected to oxidative stress. Exact pre-treatment clinical staging is essential for optimal care of this lethal malignancy. The cost-effectiviness of treatment is increasingly important. We measured oxidative metabolism in the distal and proximal esophagus by myeloperoxidase activity (MPA), glutathione content (GSH), and superoxide dismutase (SOD) in 20 patients operated on with Nissen fundoplication and 9 controls during a 4-year follow-up. Further, we assessed the oxidative damage of DNA by 8-hydroxydeoxyguanosine (8-OHdG) in esophageal samples of subjects (13 Barrett s metaplasia, 6 Barrett s esophagus with high-grade dysplasia, 18 adenocarcinoma of the distal esophagus/GEJ, and 14 normal controls). We estimated the accuracy (42 patients) and preoperative prognostic value (55 patients) of PET compared with computed tomography (CT) and endoscopic ultrasound (EUS) in patients with adenocarcinoma of the esophagus/GEJ. Finally, we clarified the specialty-related costs and the utility of either radical (30 patients) or palliative (23 patients) treatment of esophageal/GEJ carcinoma by the 15 D health-related quality-of-life (HRQoL) questionnaire and the survival rate. The cost-utility of radical treatment of esophageal/GEJ carcinoma was investigated using a decision tree analysis model comparing radical, palliative, and hypothetical new treatment. We found elevated oxidative stress ( measured by MPA) and decreased antioxidant defense (measured by GSH) after antireflux surgery. This indicates that antireflux surgery is not a perfect solution for oxidative stress of the esophageal mucosa. Elevated oxidative stress in turn may partly explain why adenocarcinoma of the distal esophagus is found even after successful fundoplication. In GERD patients, proximal esophageal mucosal anti-oxidative defense seems to be defective before and even years after successful antireflux surgery. In addition, antireflux surgery apparently does not change the level of oxidative stress in the proximal esophagus, suggesting that defective mucosal anti-oxidative capacity plays a role in development of oxidative damage to the esophageal mucosa in GERD. In the malignant transformation of Barrett s esophagus an important component appears to be oxidative stress. DNA damage may be mediated by 8-OHdG, which we found to be increased in Barrett s epithelium and in high-grade dysplasia as well as in adenocarcinoma of the esophagus/GEJ compared with controls. The entire esophagus of Barrett s patients suffers from increased oxidative stress ( measured by 8-OhdG). PET is a useful tool in the staging and prognostication of adenocarcinoma of the esophagus/GEJ detecting organ metastases better than CT, although its accuracy in staging of paratumoral and distant lymph nodes is limited. Radical surgery for esophageal/GEJ carcinoma provides the greatest benefit in terms of survival, and its cost-utility appears to be the best of currently available treatments.

Interculturality in Theory and Practice in the Master's Programme of Intercultural Bilingual Education in Bolivia

Tämän tutkielman aiheena on kulttuurienvälisyys kulttuurienvälisessä kaksikielisessä opetuksessa (Educación Intercultural Bilingüe, EIB) Boliviassa ja erityisesti kulttuurienvälisen kaksikielisen koulutuksen maisteriohjelmassa (Maestría en Educación Intercultural Bilingüe), jota koordinoi PROEIB Andes -järjestö yhteistyössä Cochabamban Universidad Mayor de San Simónin kanssa. Tutkielman tarkoituksena on selvittää, miten kulttuurienvälisyys määritellään ja mitä se käytännössä merkitsee opetuksen eri osa-alueilla: sisällöissä, opetusmetodeissa ja -materiaaleissa sekä arvioinnissa. Koska kulttuurienvälisen kaksikielisen opetuksen toteutus ja tutkiminen eri Latinalaisen Amerikan maissa on tähän asti painottunut lähes yksinomaan perusopetukseen, pyrin työssäni keskittymään kulttuurienvälisyyden ilmentymiin nimenomaan bolivialaisessa korkeakoulukontekstissa. Tutkielman aineistona on käytetty kahdeksaa EIB -asiantuntijoiden teemahaastattelua, jotka FM Eila Isotalus on tehnyt Boliviassa vuonna 2004. Haastatteluaineisto analysoitiin teoriasidonnaista eli abduktiivista sisällönanalyysiä käyttäen. Tutkielman teoriatausta koostuu yhtäältä kulttuurienvälisyyteen ja monikulttuurisuuteen liittyvien käsitteiden määrittelystä, ja toisaalta kulttuurienväliseen opetukseen liittyvien mallien esittelystä. Aineiston analyysissä avuksi on ollut etenkin James A. Banksin teoria monikulttuurisen opetuksen viidestä ulottuvuudesta, joiden kautta on voitu pohtia kulttuurienvälisyyden toteutumista opetuksen eri osa-alueilla ja nostaa esille bolivialaisen kulttuurienvälisen opetuksen erityispiirteitä. Aineiston analyysissä ilmenee, että kulttuurienvälisyyden käsitteen määrittely on vahvasti kontekstisidonnainen ja jatkuva prosessi, johon vaikuttavat eri toimijoiden näkemykset ja vaatimukset. EIB -asiantuntijoiden esittämät määrittelyt voidaan jakaa makro- ja mikrososiaaliseen kategoriaan sen mukaan, nähdäänkö kulttuurienvälisyys ensisijaisesti yhteiskunnallisena vai yksilötason käsitteenä. Aineistossa korostuu ajatus latinalaisamerikkalaisesta kulttuurienvälisyydestä poliittisena käsitteenä, jonka keskiössä on vaatimus yhteiskunnallisten valtasuhteiden muutoksesta. Yksi suurimmista haasteista kulttuurienvälisyyden toteuttamisessa bolivialaisessa korkeakouluopetuksessa ovat akateemiseen kulttuuriin liittyvät perinteet, jotka vaikeuttavat uusien toimintatapojen omaksumista. Kulttuurienvälisyys opetuksessa on toistaiseksi tarkoittanut etupäässä sisältöjen monipuolistamista lisäämällä opetusohjelmiin elementtejä paikallisista kulttuureista. Tärkeänä askeleena EIB:n kehityksessä voidaan pitää painopisteen siirtymistä sisältökysymyksistä kulttuurienvälisten opetusmetodien luomiseen. Näiden opetusmenetelmien tulisi pohjautua ymmärrykseen oppimisesta kokonaisvaltaisena, yhteisöllisenä prosessina ja siten kuroa umpeen kuilua koulun ja yhteisöjen arkielämän välillä. Opetusmenetelmien ja -materiaalien suhteen keskeinen kulttuurienvälisyyteen liittyvä kysymys on intiaanikansojen suullisen kulttuurin ja tiedon jakamisen perinteiden hyödyntäminen opetuksessa. Maisteriohjelman opiskelijoiden arvioinnissa pyritään huomioimaan yksilön kokonaisvaltainen kehitys pelkkien opintosuoritusten sijasta, mutta arvosanoihin pohjautuvasta arvostelukäytännöstä ei ole toistaiseksi voitu luopua yliopiston vaatimusten vuoksi. Kaiken kaikkiaan kulttuurienvälisyyden toteuttaminen EIB:ssä ja maisteriohjelmassa on pitkän tähtäimen prosessi, joka vaatii perinteisten opetuskäytäntöjen kyseenalaistamista ja korkeakouluopetuksessa myös akateemisen kulttuurin haastamista. On oleellisen tärkeää, että prosessiin osallistuvat asiantuntijoiden ohella myös esimerkiksi opiskelijat, intiaaniyhteisöt ja -järjestöaktiivit.

Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.