Molecular diagnostics of rare inherited SYNDROMES with a view on diagnostic test development

CHARGE syndrome, Sotos syndrome and 3p deletion syndrome are examples of rare inherited syndromes that have been recognized for decades but for which the molecular diagnostics only have been made possible by recent advances in genomic research. Despite these advances, development of diagnostic tests for rare syndromes has been hindered by diagnostic laboratories having limited funds for test development, and their prioritization of tests for which a (relatively) high demand can be expected. In this study, the molecular diagnostic tests for CHARGE syndrome and Sotos syndrome were developed, resulting in their successful translation into routine diagnostic testing in the laboratory of Medical Genetics (UTUlab). In the CHARGE syndrome group, mutation was identified in 40.5% of the patients and in the Sotos syndrome group, in 34%, reflecting the use of the tests in routine diagnostics in differential diagnostics. In CHARGE syndrome, the low prevalence of structural aberrations was also confirmed. In 3p deletion syndrome, it was shown that small terminal deletions are not causative for the syndrome, and that testing with arraybased analysis provides a reliable estimate of the deletion size but benign copy number variants complicate result interpretation. During the development of the tests, it was discovered that finding an optimal molecular diagnostic strategy for a given syndrome is always a compromise between the sensitivity, specificity and feasibility of applying a new method. In addition, the clinical utility of the test should be considered prior to test development: sometimes a test performing well in a laboratory has limited utility for the patient, whereas a test performing poorly in the laboratory may have a great impact on the patient and their family. At present, the development of next generation sequencing methods is changing the concept of molecular diagnostics of rare diseases from single tests towards whole-genome analysis.

Side impact sub-system test development: MVMA thoracic impactor test procedure and evaluation. Final report.

Mode of access: Internet.

Development of a penetration test for timber impregnation products for use in old buildings

This paper studies the application of commercial biocides to old maritime pine timber structures (Pinus pinaster Ait.) that have previously been impregnated with other products. A method was developed in the laboratory to be used in situ to determine the impregnation depth achieved by a new generation biocide product applied to timber from an old building. This timber had once been treated with an unknown product difficult to characterize without extensive analysis. The test was initially developed in laboratory conditions and later tested on elements of the roof structure of an 18th century building. In both cases the results were promising and mutually consistent with penetration depths for some treatments reaching 2.0 cm. The application in situ proved the tests viability and simplicity of execution giving a clear indication on the feasibility of possible re-treatments.

Development of new dissolution test and HPLC-RP method for anti-parasitic ornidazole coated tablets

This work aimed the development and validation of a new dissolution test for ornidazole coated tablets. The dissolution conditions were determined after testing Sink conditions, dissolution medium, apparatus, stirring speed, 24 h stability and medium filtration influence. The best conditions were paddle at a stirring speed of 75 rpm and 900 mL of 0.1 M HCl. A new HPLC quantification method was developed and validated. The dissolution test and quantification method showed to be adequate for their purposes and could be applied for quality control of ornidazole coated tablets, since there is no official monograph.

Development of a rapid one-step immunochromatographic assay for HCV core antigen detection

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Exploration of the relationship between tacit knowledge and software system test complexity

This research has explored the relationship between system test complexity and tacit knowledge. It is proposed as part of this thesis, that the process of system testing (comprising of test planning, test development, test execution, test fault analysis, test measurement, and case management), is directly affected by both complexity associated with the system under test, and also by other sources of complexity, independent of the system under test, but related to the wider process of system testing. While a certain amount of knowledge related to the system under test is inherent, tacit in nature, and therefore difficult to make explicit, it has been found that a significant amount of knowledge relating to these other sources of complexity, can indeed be made explicit. While the importance of explicit knowledge has been reinforced by this research, there has been a lack of evidence to suggest that the availability of tacit knowledge to a test team is of any less importance to the process of system testing, when operating in a traditional software development environment. The sentiment was commonly expressed by participants, that even though a considerable amount of explicit knowledge relating to the system is freely available, that a good deal of knowledge relating to the system under test, which is demanded for effective system testing, is actually tacit in nature (approximately 60% of participants operating in a traditional development environment, and 60% of participants operating in an agile development environment, expressed similar sentiments). To cater for the availability of tacit knowledge relating to the system under test, and indeed, both explicit and tacit knowledge required by system testing in general, an appropriate knowledge management structure needs to be in place. This would appear to be required, irrespective of the employed development methodology.

Item and task difficulty in a B2 reading examination: perceptions of test-takers and CEFR alignment experts compared with psychometric measurements

The article presents a study of a CEFR B2-level reading subtest that is part of the Slovenian national secondary school leaving examination in English as a foreign language, and compares the test-taker actual performance (objective difficulty) with the test-taker and expert perceptions of item difficulty (subjective difficulty). The study also analyses the test-takers’ comments on item difficulty obtained from a while-reading questionnaire. The results are discussed in the framework of the existing research in the fields of (the assessment of) reading comprehension, and are addressed with regard to their implications for item-writing, FL teaching and curriculum development.

Do Larvae and Ovipositing Chironomus riparius (Diptera: Chironomidae) Females Avoid Copper-Contaminated Environments?

Studies on the avoidance behavior of aquatic organisms to contaminants have confirmed that such behavior can be relevant in field situations. However, almost all toxicity tests involve the forced exposure of organisms to toxicants. In particular, despite the importance of Chironomus riparius Meigen larvae in sediment toxicity testing, only a few studies on avoidance behavior have been performed. This study investigated the ability of different life stages of C. riparius, including ovipositing females, first-, second-, and fourth-instar larvae, to avoid copper-contaminated environments. Ovipositing females were given a choice between a control and copper solution (1.3 mg Cu l(-1)). First-instar larvae were provided with a choice between a control and a copper (2.0 mg Cu l(-1))-spiked sediment. Both second- and fourth-instars were exposed to a copper gradient (0.38-3.4 mg Cu l(-1)) in a flow-through system. None of the life stages avoided copper, even though the highest concentrations caused lethal effects on midges. The avoidance behavior of C. riparius is not a sensitive endpoint to assess copper sublethal toxicity.

Desenvolupament d'una aplicació per ajudar a detectar la dislèxia

S’ha creat un portal informatiu sobre la dislèxia. També s’ha programat el test de detecció de dislèxia Bangor i s’ha deixat allotjat a internet, de manera que pugui ser utilitzat en qualsevol ordinador. S’ha creat una part dedicada a centres docents perquè puguin portar un control sobre els resultats dels alumnes que han dut a terme el test.

Systematic review of meaning in life assessment instruments.

BACKGROUND: The construct of "meaning in life" (MiL) has raised the interest of clinicians working in psycho-oncology and end-of-life care. It has become a topic of scientific investigation where diverse assessment approaches have been applied. Aims: We present a comprehensive systematic review of existing MiL assessment instruments. METHODS: Electronic searches of articles published in English peer-reviewed journals were performed in Psycinfo, Medline, Embase and Cinahl. Instruments are appraised with regard to ten measurement properties. RESULTS: In total, 59 nomothetic and idiographic MiL instruments were identified. Most instruments were developed in North America and meet basic psychometric criteria. They assess presence of and search for MiL, crisis and sources of MiL, meaning making, meaningful activity, MiL in the context of illness, breadth, depth, and other structural indicators. These aspects are largely consistent with existing MiL definitions. Nine out of 59 instruments included cancer populations in test development. CONCLUSIONS: This overview of available instruments underscores the complexity of the construct and might assist researchers to select an appropriate instrument for their research needs. Finally, it points to the need for more integrative theorizing and research on MiL. Copyright © 2012 John Wiley & Sons, Ltd.

Epstein-Barr-viruksen antigeeniosoitustestin kehittäminen

Epstein-Barr-virus (EBV) aiheuttaa mononukleoosia eli pusutautia, joka ilmenee yleensä murrosiällä tai nuorella aikuisiällä. Mononukleoosissa on tyypilliset nielutulehduksen oireet, minkä takia sitä on vaikea erottaa muiden taudinaiheuttajien aiheuttamista nielutulehduksista. Erotusdiagnostiikan käyttö nielutulehduksessa on oleellista, koska vain Streptokokki-bakteerien aiheuttamat nielutulehdukset vaativat antibioottihoitoa. Akuutin EBV-infektion pikadiagnostiikka perustuu nykyisellään infektion seurauksena muodostuvien heterofiilisten vasta-aineiden mittaamiseen verestä. Niiden mittaamisessa on useita ongelmia, koska useilla lapsilla niitä ei muodostu lainkaan ja vanhemmillakin niitä muodostuu yleensä vasta viikon päästä mononukleoosin oireiden alkamisesta. Mittaamalla EBV:n antigeeneja saataisiin positiivinen testitulos vasta-ainetestiä nopeammin. EBV:lle ei ole kuitenkaan kehitetty antigeeniosoitustestiä todennäköisesti siksi, että EBV:n erittymisen terveiden viruksen kantajien limakalvoille uskotaan olevan ongelma antigeenitestauksessa. Diplomityön tavoitteena oli kehittää akuutin EBV-infektion pikadiagnostiikkaan soveltuva limakalvonäytteestä tehtävä immunometrinen antigeeniosoitustesti. Työssä kehitettiin uusia polyklonaalisia vasta-aineita sekä testattiin kaupallisia vasta-aineita. Vasta-aineiden toimintaa tutkittiin immunomäärityksissä kokonaista EBV:ta ja puhdistettuja proteiiniantigeeneja vastaan. Monoklonaalisten vasta-aineiden kehitys lopetettiin ennen varsinaista tuottoa, koska ensin kehitetyt polyklonaaliset vasta-aineet eivät tunnistaneet natiivia virusta vaan pelkästään immunisointeihin käytetyt rekombinanttiset kohdeproteiinit. Kaupallisista vasta-aineista yhdellä onnistuttiin kehittämään tiettävästi maailman ensimmäinen immunometrinen EBV-antigeeniosoitustesti, jossa saatiin tunnistus sekä natiivilla EBV:lla että puhdistetulla proteiiniantigeenilla. Testin herkkyys proteiiniantigeenilla oli hyvä (4 pM) ja puhdistetulla EBV-virusvalmisteellakin todennäköisesti riittävä (6,2×106 viruspartikkelia/ml) kliiniseen diagnostiikkaan. Testillä ei kuitenkaan saatu suppeasta mononukleoosipotilaiden nielunäyteaineistosta yhtään EBV-positiivista tulosta. Referenssiksi tilatut PCR-testit osoittivat näytteiden EBV-pitoisuuksien olevan liian alhaisia osoitettavaksi kehitetyllä EBV-antigeeniosoitustestillä. PCR-testauksessa mononukleoosipotilaiden nielunäytteistä osoitettujen alhaisten EBV-määrien perusteella spekuloitiin, että olisiko edustavin näytteenottopaikka akuutissa EBV-infektiossa sittenkin nielun sijaan nenänielu. Myös kirjallisuudesta löytyi tälle tukea. EBV-antigeeniosoitustestin osoitettiin toimivan hyvin standardinäyte-materiaalilla. Testikehitysprojektin jatkon kannalta oleellista on kuitenkin vielä selvittää laajemmalla kliinisellä näyteaineistolla, mistä EBV:n antigeeneja pitäisi osoittaa akuutissa EBV-infektiossa ja ovatko niiden pitoisuudet riittävän korkeita.

A New Approach for Managing Bovine Tuberculosis: Veterinary Services’ Proposed Action Plan

Bovine tuberculosis (TB) is a serious disease with animal health, public health, and international trade consequences. The cooperative Federal-State-industry effort to eradicate bovine TB from cattle in the United States has made significant progress since the program’s inception in 1917. However, the goal of eradication remains elusive. This proposed action plan presents Veterinary Services’ (VS’) current thinking about changes we are considering for the TB program to address our current challenges. This action plan will: 1. Reduce the introduction of TB into the U.S. national herd from imported animals and wildlife by: o Applying additional requirements to cattle imports from Mexico o Enhancing efforts to mitigate risks from wildlife 2. Enhance TB surveillance by: o Crafting a comprehensive national surveillance plan o Accelerating diagnostic test development to support surveillance 3. Increase options for managing TB-affected herds by: o Conducting epidemiological investigations and assessing individual herd risk o Applying whole-herd depopulation judiciously and developing alternative control strategies o Applying animal identification (ID) standards to meet animal ID needs 4. Modernize the regulatory framework to allow VS to focus resources where the disease exists 5. Transition the TB program from a State classification system to a science-based zoning approach to address disease risk To succeed, this new approach will require VS’ continued partnership with State animal health and wildlife officials, other Federal agencies, industry, international partners, academia, and other stakeholders. Successful partnerships will allow us to use available resources efficiently to achieve program objectives and protect our nation’s herd. Implementation of the VS proposed action plan will benefit Federal and State animal health officials, the regulated industries, and producers by allowing a more rapid response that employs up-to-date science and can adapt rapidly to changing situations.

Prediction of clinical toxicity in localized cervical carcinoma by radio-induced apoptosis study in peripheral blood lymphocytes (PBLs)

[EN] Background: Cervical cancer is treated mainly by surgery and radiotherapy. Toxicity due to radiation is a limiting factor for treatment success. Determination of lymphocyte radiosensitivity by radio-induced apoptosis arises as a possible method for predictive test development. The aim of this study was to analyze radio-induced apoptosis of peripheral blood lymphocytes. Methods: Ninety four consecutive patients suffering from cervical carcinoma, diagnosed and treated in our institution, and four healthy controls were included in the study. Toxicity was evaluated using the Lent-Soma scale. Peripheral blood lymphocytes were isolated and irradiated at 0, 1, 2 and 8 Gy during 24, 48 and 72 hours. Apoptosis was measured by flow cytometry using annexin V/propidium iodide to determine early and late apoptosis. Lymphocytes were marked with CD45 APC-conjugated monoclonal antibody. Results: Radiation-induced apoptosis (RIA) increased with radiation dose and time of incubation. Data strongly fitted to a semi logarithmic model as follows: RIA = βln(Gy) + α. This mathematical model was defined by two constants: α, is the origin of the curve in the Y axis and determines the percentage of spontaneous cell death and β, is the slope of the curve and determines the percentage of cell death induced at a determined radiation dose (β = ΔRIA/Δln(Gy)). Higher β values (increased rate of RIA at given radiation doses) were observed in patients with low sexual toxicity (Exp(B) = 0.83, C.I. 95% (0.73-0.95), p = 0.007; Exp(B) = 0.88, C.I. 95% (0.82-0.94), p = 0.001; Exp(B) = 0.93, C.I. 95% (0.88-0.99), p = 0.026 for 24, 48 and 72 hours respectively). This relation was also found with rectal (Exp(B) = 0.89, C.I. 95% (0.81-0.98), p = 0.026; Exp(B) = 0.95, C.I. 95% (0.91-0.98), p = 0.013 for 48 and 72 hours respectively) and urinary (Exp(B) = 0.83, C.I. 95% (0.71-0.97), p = 0.021 for 24 hours) toxicity. Conclusion: Radiation induced apoptosis at different time points and radiation doses fitted to a semi logarithmic model defined by a mathematical equation that gives an individual value of radiosensitivity and could predict late toxicity due to radiotherapy. Other prospective studies with higher number of patients are needed to validate these results.

State-of-the-Art Multihoming Protocols and Support for Android

Il traguardo più importante per la connettività wireless del futuro sarà sfruttare appieno le potenzialità offerte da tutte le interfacce di rete dei dispositivi mobili. Per questo motivo con ogni probabilità il multihoming sarà un requisito obbligatorio per quelle applicazioni che puntano a fornire la migliore esperienza utente nel loro utilizzo. Sinteticamente è possibile definire il multihoming come quel processo complesso per cui un end-host o un end-site ha molteplici punti di aggancio alla rete. Nella pratica, tuttavia, il multihoming si è rivelato difficile da implementare e ancor di più da ottimizzare. Ad oggi infatti, il multihoming è lontano dall’essere considerato una feature standard nel network deployment nonostante anni di ricerche e di sviluppo nel settore, poiché il relativo supporto da parte dei protocolli è quasi sempre del tutto inadeguato. Naturalmente anche per Android in quanto piattaforma mobile più usata al mondo, è di fondamentale importanza supportare il multihoming per ampliare lo spettro delle funzionalità offerte ai propri utenti. Dunque alla luce di ciò, in questa tesi espongo lo stato dell’arte del supporto al multihoming in Android mettendo a confronto diversi protocolli di rete e testando la soluzione che sembra essere in assoluto la più promettente: LISP. Esaminato lo stato dell’arte dei protocolli con supporto al multihoming e l’architettura software di LISPmob per Android, l’obiettivo operativo principale di questa ricerca è duplice: a) testare il roaming seamless tra le varie interfacce di rete di un dispositivo Android, il che è appunto uno degli obiettivi del multihoming, attraverso LISPmob; e b) effettuare un ampio numero di test al fine di ottenere attraverso dati sperimentali alcuni importanti parametri relativi alle performance di LISP per capire quanto è realistica la possibilità da parte dell’utente finale di usarlo come efficace soluzione multihoming.

Potential Cost-effectiveness of Early Identification of Hospital-acquired Infection in Critically Ill Patients.

RATIONALE: Limitations in methods for the rapid diagnosis of hospital-acquired infections often delay initiation of effective antimicrobial therapy. New diagnostic approaches offer potential clinical and cost-related improvements in the management of these infections. OBJECTIVES: We developed a decision modeling framework to assess the potential cost-effectiveness of a rapid biomarker assay to identify hospital-acquired infection in high-risk patients earlier than standard diagnostic testing. METHODS: The framework includes parameters representing rates of infection, rates of delayed appropriate therapy, and impact of delayed therapy on mortality, along with assumptions about diagnostic test characteristics and their impact on delayed therapy and length of stay. Parameter estimates were based on contemporary, published studies and supplemented with data from a four-site, observational, clinical study. Extensive sensitivity analyses were performed. The base-case analysis assumed 17.6% of ventilated patients and 11.2% of nonventilated patients develop hospital-acquired infection and that 28.7% of patients with hospital-acquired infection experience delays in appropriate antibiotic therapy with standard care. We assumed this percentage decreased by 50% (to 14.4%) among patients with true-positive results and increased by 50% (to 43.1%) among patients with false-negative results using a hypothetical biomarker assay. Cost of testing was set at $110/d. MEASUREMENTS AND MAIN RESULTS: In the base-case analysis, among ventilated patients, daily diagnostic testing starting on admission reduced inpatient mortality from 12.3 to 11.9% and increased mean costs by $1,640 per patient, resulting in an incremental cost-effectiveness ratio of $21,389 per life-year saved. Among nonventilated patients, inpatient mortality decreased from 7.3 to 7.1% and costs increased by $1,381 with diagnostic testing. The resulting incremental cost-effectiveness ratio was $42,325 per life-year saved. Threshold analyses revealed the probabilities of developing hospital-acquired infection in ventilated and nonventilated patients could be as low as 8.4 and 9.8%, respectively, to maintain incremental cost-effectiveness ratios less than $50,000 per life-year saved. CONCLUSIONS: Development and use of serial diagnostic testing that reduces the proportion of patients with delays in appropriate antibiotic therapy for hospital-acquired infections could reduce inpatient mortality. The model presented here offers a cost-effectiveness framework for future test development.