Obtenció de jerarquies d'estats cel·lulars via web

Hi ha diversos mètodes d'anàlisi que duen a terme una agrupació global de la sèries de mostres de microarrays, com SelfOrganizing Maps, o que realitzen agrupaments locals tenint en compte només un subconjunt de gens coexpressats, com Biclustering, entre d'altres. En aquest projecte s'ha desenvolupat una aplicació web: el PCOPSamplecl, és una eina que pertany als mètodes d'agrupació (clustering) local, que no busca subconjunts de gens coexpresats (anàlisi de relacions linials), si no parelles de gens que davant canvis fenotípics, la seva relació d'expressió pateix fluctuacions. El resultats del PCOPSamplecl seràn les diferents distribucions finals de clusters i les parelles de gens involucrades en aquests canvis fenotípics. Aquestes parelles de gens podràn ser estudiades per trobar la causa i efecte del canvi fenotípic. A més, l'eina facilita l'estudi de les dependències entre les diferents distribucions de clusters que proporciona l'aplicació per poder estudiar la intersecció entre clusters o l'aparició de subclusters (2 clusters d'una mateixa agrupació de clusters poden ser subclusters d'altres clusters de diferents distribucions de clusters). L'eina és disponible al servidor: http://revolutionresearch.uab.es/

Segmentació d'imatge de ressonància magnètica de pit utilitzant atlas probabilístic

La localització d'òrgans és un tòpic important en l'àmbit de la imatge mèdica per l'ajuda del tractament i diagnosi del càncer. Un exemple es pot trobar en la cal•libració de models farmacoquinètics. Aquesta pot ésser realitzada utilitzant un teixit de referència, on, per exemple en imatges de ressonància magnètica de pit, una correcta segmentació del múscul pectoral és necessària per a la detecció de signes de malignitat. Els mètodes de segmentació basat en atlas han estat altament avaluats en imatge de ressonància magnètica de cervell, obtenint resultats satisfactoris. En aquest projecte, en col•laboració amb el el Diagnostic Image Analysis Group de la Radboud University Nijmegen Medical Centre i la supervisió del Dr. N.Karssemeijer, es presenta la primera aproximació d'un mètode de segmentació basat en atlas per segmentar els diferents teixits visibles en imatges de ressonància magnètica (T1) del pit femení. L'atlas consisteix en 5 estructures (teixit greixòs, teixit dens, cor, pulmons i múscul pectoral) i ha estat utilitzat en un algorisme de segmentació Bayesià per tal de delinear les esmentades estructures. A més a més, s'ha dut a terme una comparació entre un mètode de registre global i un de local, utilitzats tant en la construcció de l'atlas com en la fase de segmentació, essent el primer el que ha presentat millors resultats en termes d'eficiència i precisió. Per a l'avaluació, s'ha dut a terme una comparació visual i numèrica entre les segmentacions obtingudes i les realitzades manualment pels experts col•laboradors. Pel que fa a la numèrica, s'ha emprat el coeficient de similitud de Dice ( mesura que dóna valors entre 0 i 1, on 0 significa no similitud i 1 similitud màxima) i s'ha obtingut una mitjana general de 0.8. Aquest resultat confirma la validesa del mètode presentat per a la segmentació d'imatges de ressonància magnètica del pit.

Is hospital discharge administrative data an appropriate source of information for cancer registries purposes? Some insights from four Spanish registries

Background. The use of hospital discharge administrative data (HDAD) has been recommended for automating, improving, even substituting, population-based cancer registries. The frequency of false positive and false negative cases recommends local validation. Methods. The aim of this study was to detect newly diagnosed, false positive and false negative cases of cancer from hospital discharge claims, using four Spanish population-based cancer registries as the gold standard. Prostate cancer was used as a case study. Results. A total of 2286 incident cases of prostate cancer registered in 2000 were used for validation. In the most sensitive algorithm (that using five diagnostic codes), estimates for Sensitivity ranged from 14.5% (CI95% 10.3-19.6) to 45.7% (CI95% 41.4-50.1). In the most predictive algorithm (that using five diagnostic and five surgical codes) Positive Predictive Value estimates ranged from 55.9% (CI95% 42.4-68.8) to 74.3% (CI95% 67.0-80.6). The most frequent reason for false positive cases was the number of prevalent cases inadequately considered as newly diagnosed cancers, ranging from 61.1% to 82.3% of false positive cases. The most frequent reason for false negative cases was related to the number of cases not attended in hospital settings. In this case, figures ranged from 34.4% to 69.7% of false negative cases, in the most predictive algorithm. Conclusions. HDAD might be a helpful tool for cancer registries to reach their goals. The findings suggest that, for automating cancer registries, algorithms combining diagnoses and procedures are the best option. However, for cancer surveillance purposes, in those cancers like prostate cancer in which care is not only hospital-based, combining inpatient and outpatient information will be required.

Can 3T multiparametric magnetic resonance imaging accurately detect prostate cancer extracapsular extension?

BACKGROUND: Accurate staging is essential to determine the correct management of patients diagnosed with prostate cancer. We assess the accuracy of 3T multiparametric magnetic resonance imaging (MRI) with endorectal coil (3TemMRI) in detecting prostate cancer local extension. METHODS: We retrospectively reviewed charts from January 2008 to July 2012 from all patients undergoing radical prostatectomy. Patients were only included if 3TemMRI and radical prostatectomy were performed at our institution. Based on the presence of extracapsular extension (ECE) at 3TemMRI, prostate cancer was dichotomized into locally advanced or organ-confined disease. The accuracy of 3TemMRI local staging was then evaluated using definitive pathology as a reference. RESULTS: Overall, 177 radical prostatectomies were performed within the timeframe. After applying exclusion criteria, 60 patients were included in the final analysis. The mean patient age was 67 ± 7 (standard deviation) years. Mean prostate-specific antigen value was 12.7 ± 12.7 ng/L. Based on preoperative characteristics, we considered 38 of the 60 patients (63%) patients high risk. 3TemMRI identified an organ-confined tumour in 46 patients and locally advanced disease in 14 patients. When correlated to final pathology, 3TemMRI specificity, sensitivity, negative and positive predictive values, and accuracy in detecting locally advanced prostate cancer were 90%, 35%, 57%, 79% and 62%, respectively. INTERPRETATION: This study shows that the use of preoperative 3TemMRI can be used to identify organ-confined prostate cancer when locally advanced disease is suspected.

An epidemiologic study to determine the prevalence of the HLA-B*5701 allele among HIV-positive patients in Europe.

OBJECTIVES: HLA-B*5701 is a major histocompatibility complex class I allele associated with an immunologically-mediated hypersensitivity reaction to abacavir. The objectives of this study were to evaluate HLA-B*5701 prevalence among European, HIV-1-infected patients and to compare the local and central laboratory screening results. METHODS: Data were combined from six multicentre, prospective studies involving 10 European countries in which HIV-1-infected patients (irrespective of treatment experience or previous HLA-B*5701 screening), >or=18 years of age, were evaluated for HLA-B*5701 carriage, determined by the central and local laboratory methods. RESULTS: A total of 9720 patients from 272 centres were included in the analysis. The overall estimate of HLA-B*5701 prevalence in Europe was 4.98%, with country-specific estimates ranging from 1.53 to 7.75%. HLA-B*5701 prevalence was highest in the self-reported white population (6.49%) and lowest in the black population (0.39%). Local laboratory results had a high specificity (99.9%) and sensitivity (99.2%) when compared with the central laboratory results. CONCLUSION: This study supports data from previous studies regarding the prevalence of HLA-B*5701 in the HIV population and the variation of HLA-B*5701 prevalence between different racial groups. The high specificity and sensitivity of local laboratory results, suggests that clinicians can be confident in using local laboratories for pretreatment HLA-B*5701 screening. However, it is essential that local laboratories participate in HLA-B*5701-specific quality assurance programs to maintain 100% sensitivity. In HIV-infected patients, pretreatment HLA-B*5701 screening may allow more informed decisions regarding abacavir use and has the potential to significantly reduce the frequency of abacavir-related hypersensitivity reactions and costs associated with managing these reactions.

Assessment of inflammatory Bowel Disease patient's needs and problems from a nursing perspective

BACKGROUND: In this study, we aimed at assessing Inflammatory Bowel Disease patients' needs and current nursing practice to investigate to what extent consensus statements (European Crohn's and Colitis Organization) on the nursing roles in caring for patients with IBD concur with local practice. METHODS: We used a mixed-method convergent design to combine quantitative data prospectively collected in the Swiss IBD cohort study and qualitative data from structured interviews with IBD healthcare experts. Symptoms, quality of life, and anxiety and depression scores were retrieved from physician charts and patient self-reported questionnaires. Descriptive analyses were performed based on quantitative and qualitative data. RESULTS: 230 patients of a single center were included, 60% of patients were males, and median age was 40 (range 18-85). The prevalence of abdominal pain was 42%. Self-reported data were obtained from 75 out of 230 patients. General health was perceived significantly lower compared with the general population (p < 0.001). Prevalence of tiredness was 73%; sleep problems, 78%; issues related to work, 20%; sexual constraints, 35%; diarrhea, 67%; being afraid of not finding a bathroom, 42%; depression, 11%; and anxiety symptoms, 23%. According to experts' interviews, the consensus statements are found mostly relevant with many recommendations that are not yet realized in clinical practice. CONCLUSION: Identified prevalence may help clinicians in detecting patients at risk and improve patient management. © 2015 S. Karger AG, Basel.

Wind gust estimation for Mid-European winter storms: towards a probabilistic view

Three wind gust estimation (WGE) methods implemented in the numerical weather prediction (NWP) model COSMO-CLM are evaluated with respect to their forecast quality using skill scores. Two methods estimate gusts locally from mean wind speed and the turbulence state of the atmosphere, while the third one considers the mixing-down of high momentum within the planetary boundary layer (WGE Brasseur). One hundred and fifty-eight windstorms from the last four decades are simulated and results are compared with gust observations at 37 stations in Germany. Skill scores reveal that the local WGE methods show an overall better behaviour, whilst WGE Brasseur performs less well except for mountain regions. The here introduced WGE turbulent kinetic energy (TKE) permits a probabilistic interpretation using statistical characteristics of gusts at observational sites for an assessment of uncertainty. The WGE TKE formulation has the advantage of a ‘native’ interpretation of wind gusts as result of local appearance of TKE. The inclusion of a probabilistic WGE TKE approach in NWP models has, thus, several advantages over other methods, as it has the potential for an estimation of uncertainties of gusts at observational sites.

Stromal-derived factor-1 alpha (CXCL12) levels increase in periodontal disease

Background: The CXC chemokine receptor 4 (CXCR4) and its ligand, stromal cell-derived factor-1 (SDF-1 alpha or CXC chemokine ligand 12) are involved in the trafficking of leukocytes into and out of extravascular tissues. The purpose of this study was to determine whether SDF-1 alpha secreted by host cells plays a role in recruiting inflammatory cells into the periodontia during local inflammation. Methods: SDF-1 alpha levels were determined by enzyme-linked immunosorbent assay in gingival crevicular fluid (GCF) of 24 individuals with periodontitis versus healthy individuals in tissue biopsies and in a preclinical rat model of Porphyromonas gingivalis lipopolysaccharide-induced experimental bone loss. Neutrophil chemotaxis assays were also used to evaluate whether SDF-1 alpha plays a role in the recruitment of host cells at periodontal lesions. Results: Subjects with periodontal disease had higher levels of SDF-1 alpha in their GCF compared to healthy subjects. Subjects with periodontal disease who underwent mechanical therapy demonstrated decreased levels of SDF-1 alpha. Immunohistologic staining showed that SDF-1 alpha and CXCR4 levels were elevated in samples obtained from periodontally compromised individuals. Similar results were observed in the rodent model. Neutrophil migration was enhanced in the presence of SDF-1 alpha, mimicking immune cell migration in periodontal lesions. Conclusions: SDF-1 alpha may be involved in the immune defense pathway activated during periodontal disease. Upon the development of diseased tissues, SDF-1 alpha levels increase and may recruit host defensive cells into sites of inflammation. These studies suggest that SDF-1 alpha may be a useful biomarker for the identification of periodontal disease progression.

Qualitative analysis of two reconstruction techniques and their application in dentistry

Although visualization in the field of dentistry has some of the same requirements as the medicine field, the differences in goal demand specific approaches. This paper reports on the implementation of two fundamentally different approaches to reconstruction of structures from planar cross sections and their application to dentistry data. One of the approaches was an implementation of a distance-based sampling technique, and the other is a new algorithm, based on the Delaunay triangulation. Both were tested using contour data of teeth and the results are compared here in the light of the target applications, which are teaching and training dentistry, as well as simulation of dental procedures and illnesses. Widely mentioned problems encountered in local reconstruction methods such as marching cubes for these cases are clearly illustrated in this paper, and a very satisfactory alternative is given. © 2000 SPIE and IS&T.

Modeling of a MIT for the application of a frequency inverter of the electric vehicle

Nowadays, drives that use a combination of induction motors and frequency inverters are very common, a fact due to the financial practicality and viability in purchasing and operating that system. This system modeling and simulation becomes important when it wants to evaluate the performance, to calculate and correct parameters, and it has a fundamental role in functionality and viability analysis for application of new configurations and technologies. This work is about to elaborate a simple induction motor model based in the torque versus speed characteristic, using the linearization method for application in a specific operation range to be controlled by a frequency inverter. © 2011 Springer-Verlag Berlin Heidelberg.

Knowledge and use of wild edible plants in rural communities along Paraguay River, Pantanal, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

An investigation into complex inorganic materials with Mössbauer spectroscopy

Mössbauer Spektroskopie ist ein unverzichtbares Instrument für die Bestimmung von Oxidationszuständen und für die Analyse von lokalen Ordnungsphänomenen von Mössbauer aktiven Atomen. Weil es sich um eine lokale Methode handelt können sowohl kristalline als auch amorphe Materialien untersucht werden. Die Kombination von lokaler Prüfung mit Mössbauer Spektroskopie und globaler Untersuchung z.B. mit Röntgendiffraktometrie ermöglicht die Studie von Ordnungseffekten von statistisch besetzten Positionen in einer geordneten Matrix. Das wurde hier eingesetzt um die lokale Umgebung in zwei Serien von Heuslerverbindungen, Co2-xFe1+xSi and Co2Mn1-xFexAl zu untersuchen. Für die Co2Mn1-xFexAl Serie wurde eine L21 geordnete Phase in einer insgesamt B2 geordneten Probe detektiert. Ein Wechsel von der AlCu2Mn zu der CuHg2Ti Struktur wurde für die Co2-xFe1+xSi Proben gefunden. Die Transformation von einem Glas zu einem keramischen Material wurde mit 119Sn Mössbauer Spektroskopie untersucht. Die höhere Ordnung in der Keramik wurde von einer kleiner werdenden Mössbauerlinienbreite begleitet. Demzufolge geben die Modifikationen der Sn Umgebungen klar die Transformation des gesamten Materials wieder. Ist die lokale Umgebung von unregelmäßig auftretenden Atomen in einer amorphen Matrix von Interesse, sind lokal prüfende Methoden die zuverlässigsten Methoden die zur Verfügung stehen. In dieser Arbeit wurde 119Sn Mössbauer Spektroskopie eingesetzt um die Oxidationszustände, die lokalen Umgebungen und relativen Intensitäten von Zinn Atomen in einer Silikatmatrix zu bestimmen. Modifikationen dieser Parameter als Funktion von Prozess bestimmenden Parametern wie der Sauerstoffpartialdruck, die Temperatur, die Behandlungsdauer und der Abkühlprozess genauso wie der SnO2 Gehalt sind von Interesse, weil durch Reduktions- und Diffusionsprozesse Änderungen des Koordinations- und des Oxidationszustands der Zinnatome auftreten. Da diese Änderungen in der Glasmatrix verursachen, die das fertige Produkt im industriellen Fertigungsprozess ruinieren können sind diese feinen Veränderungen sehr wichtig. Wenigstens zwei Mössbauerlinien korrespondierend mit zwei verschiedenen Umgebungen für Sn2+ und Sn4+ sind für eine Analyse mit ausreichender Qualität notwendig. Durch Vergleich von den bestimmten Hyperfein Parametern mit den Parametern von Modelsubstanzen werden lokale Umgebungen der Zinnatome entworfen. Für Sn2+ werden zwei auf einer trigonalen Pyramide basierende Umgebungen mit variierender Anzahl von bindenden und nicht-bindenden Sauerstoffatomen formuliert. Für Sn4+ wurde eine tetraedrische und eine oktaedrische Umgebung postuliert. Die relativen Intensitäten der vier Mössbauerlinien wurden um ein Diffusions- und Reaktionsmodell zu entwickeln und um einen Satz von Diffusions- und Transferkoeffizienten zu bestimmen eingesetzt. Die bestimmten Diffusionskoeffizienten stimmen mit den Literaturdaten überein. Der Massentransferkoeffizient ist kleiner als der bestimmte Wert, aber immer noch in der gleichen Größenordnung. Im Gegensatz zu den Erwartungen ist der präsentierte Diffusionskoeffizient für Sn4+ bestimmt als der von Sn2+. Das wiederum kann durch Berücksichtigung von Elektronhoppingprozessen erklärt werden.

Experiences in Monitoring and Assessment of Sustainable Land Management

Although sustainable land management (SLM) is widely promoted to prevent and mitigate land degradation and desertification, its monitoring and assessment (M&A) has received much less attention. This paper compiles methodological approaches which to date have been little reported in the literature. It draws lessons from these experiences and identifies common elements and future pathways as a basis for a global approach. The paper starts with local level methods where the World Overview of Conservation Approaches and Technologies (WOCAT) framework catalogues SLM case studies. This tool has been included in the local level assessment of Land Degradation Assessment in Drylands (LADA) and in the EU-DESIRE project. Complementary site-based approaches can enhance an ecological process-based understanding of SLM variation. At national and sub-national levels, a joint WOCAT/LADA/DESIRE spatial assessment based on land use systems identifies the status and trends of degradation and SLM, including causes, drivers and impacts on ecosystem services. Expert consultation is combined with scientific evidence and enhanced where necessary with secondary data and indicator databases. At the global level, the Global Environment Facility (GEF) knowledge from the land (KM:Land) initiative uses indicators to demonstrate impacts of SLM investments. Key lessons learnt include the need for a multi-scale approach, making use of common indicators and a variety of information sources, including scientific data and local knowledge through participatory methods. Methodological consistencies allow cross-scale analyses, and findings are analysed and documented for use by decision-makers at various levels. Effective M&A of SLM [e.g. for United Nations Convention to Combat Desertification (UNCCD)] requires a comprehensive methodological framework agreed by the major players.

Off-pump extraanatomic aortic bypass for the treatment of complex aortic coarctation and hypoplastic aortic arch

BACKGROUND: Despite advances in surgical and interventional techniques, the optimal surgical treatment of severe aortic (re) coarctation and hypoplastic aortic arch is still controversial. Anatomic repair may require extensive dissection, cardiopulmonary bypass, and deep hypothermic circulatory arrest with their inherent risks. The aim of this study was to analyze the outcome of off-pump extraanatomic aortic bypass as a surgical alternative to local repair. METHODS: From February 2000 to December 2005, ten consecutive patients (median age 20 years; range, 11 to 38 years) with severe aortic (re) coarctation (n = 4) and (or) hypoplastic aortic arch (n = 7) underwent off-pump extraanatomic aortic bypass through median sternotomy. All but three patients had undergone previous surgery for coarctation and angioplasty or stenting. Three patients underwent concomitant replacement of the ascending aorta because of an aneurysm using cardiopulmonary bypass. RESULTS: Postoperative hospital course was uneventful in all patients. There was no perioperative mortality or significant morbidity. During a mean follow-up of 48 +/- 22 months no patient required additional procedures. All patients were free of symptoms; no patient showed signs of heart failure after follow-up. At last follow-up, no patient presented with claudication, nor any patient experienced orthostatic problems due to a steal phenomenon. During follow-up, hypertension resolved in all patients with residual mild hypertension in two patients. CONCLUSIONS: Off-pump extraanatomic aortic bypass is an attractive treatment option for complex aortic (re) coarctation and hypoplastic aortic arch. Perioperative risks are minimized, hypertension is influenced favorably, and midterm survival is event-free.

Risk factors for Clostridium difficile nosocomial diarrhea in patients at the Michael E. Debakey Veterans Affairs Medical Center, Houston, Texas

Background. Clostridium difficile is the leading cause of hospital associated infectious diarrhea and colitis. About 3 million cases of Clostridium difficile diarrhea occur each year with an annual cost of $1 billion. ^ About 20% of patients acquire C. difficile during hospitalization. Infection with Clostridium difficile can result in serious complications, posing a threat to the patient's life. ^ Purpose. The aim of this research was to demonstrate the uniqueness in the characteristics of C. difficile positive nosocomial diarrhea cases compared with C. difficile negative nosocomial diarrhea controls admitted to a local hospital. ^ Methods. One hundred and ninety patients with a positive test and one hundred and ninety with a negative test for Clostridium difficile nosocomial diarrhea, selected from patients tested between January 1, 2002 and December 31, 2003, comprised the study population. Demographic and clinical data were collected from medical records. Logistic regression analyses were conducted to determine the associated odds between selected variables and the outcome of Clostridium difficile nosocomial diarrhea. ^ Results. For the antibiotic classes, cephalosporins (OR, 1.87; CI 95, 1.23 to 2.85), penicillins (OR, 1.57; CI 95, 1.04 to 2.37), fluoroquinolones (OR, 1.65; CI 95, 1.09 to 2.48) and antifungals (OR, 2.17; CI 95, 1.20 to 3.94), were significantly associated with Clostridium difficile nosocomial diarrhea Ceftazidime (OR, 1.95; CI 95, 1.25 to 3.03, p=0.003), gatifloxacin (OR, 1.97; CI 95, 1.31 to 2.97, p=0.001), clindamycin (OR, 3.13; CI 95, 1.99 to 4.93, p<0.001) and vancomycin (OR, 1.77; CI 95, 1.18 to 2.66, p=0.006, were also significantly associated with the disease. Vancomycin was not statistically significant when analyzed in a multivariable model. Other significantly associated drugs were, antacids, laxatives, narcotics and ranitidine. Prolong use of antibiotics and an increased number of comorbid conditions were also associated with C. difficile nosocomial diarrhea. ^ Conclusion. The etiology for C. difficile diarrhea is multifactorial. Exposure to antibiotics and other drugs, prolonged antibiotic usage, the presence and severity of comorbid conditions and prolonged hospital stay were shown to contribute to the development of the disease. It is imperative that any attempt to prevent the disease, or contain its spread, be done on several fronts. ^