TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.

Clinical Perspectives from Randomized Phase 3 Trials on Prostate Cancer: An Analysis of the ClinicalTrials.gov Database

AbstractBackground It is not easy to overview pending phase 3 trials on prostate cancer (PCa), and awareness of these trials would benefit clinicians. Objective To identify all phase 3 trials on {PCa} registered in the ClinicalTrials.gov database with pending results. Design and setting On September 29, 2014, a database was established from the records for 175 538 clinical trials registered on ClinicalTrials.gov. A search of this database for the substring “prostat” identified 2951 prostate trials. Phase 3 trials accounted for 441 studies, of which 333 concerned only PCa. We selected only ongoing or completed trials with pending results, that is, for which the primary endpoint had not been published in a peer-reviewed medical journal. Results and limitations We identified 123 phase 3 trials with pending results. Trials were conducted predominantly in North America (n = 63; 51) and Europe (n = 47; 38). The majority were on nonmetastatic disease (n = 82; 67), with 37 (30) on metastatic disease and four trials (3) including both. In terms of intervention, systemic treatment was most commonly tested (n = 71; 58), followed by local treatment 34 (28), and both systemic and local treatment (n = 11; 9), with seven (6) trials not classifiable. The 71 trials on systemic treatment included androgen deprivation therapy (n = 34; 48), chemotherapy (n = 15; 21), immunotherapy (n = 9; 13), other systemic drugs (n = 9; 13), radiopharmaceuticals (n = 2; 3), and combinations (n = 2; 3). Local treatments tested included radiation therapy (n = 27; 79), surgery (n = 5; 15), and both (n = 2; 2). A limitation is that not every clinical trial is registered on ClinicalTrials.gov. Conclusion There are many {PCa} phase 3 trials with pending results, most of which address questions regarding systemic treatments for both nonmetastatic and metastatic disease. Radiation therapy and androgen deprivation therapy are the interventions most commonly tested for local and systemic treatment, respectively. Patient summary This report describes all phase 3 trials on prostate cancer registered in the ClinicalTrials.gov database with pending results. Most of these trials address questions regarding systemic treatments for both nonmetastatic and metastatic disease. Radiation therapy and androgen deprivation therapy are the interventions most commonly tested for local and systemic treatment, respectively.

The TREAT-NMD DMD Global Database: analysis of more than 7,000 Duchenne muscular dystrophy mutations.

Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations).

Concepts of Bitemporal Database Theory and the Evolution of Web-Documents

A vast amount of temporal information is provided on the Web. Even though many facts expressed in documents are time-related, the temporal properties of Web presentations have not received much attention. In database research, temporal databases have become a mainstream topic in recent years. In Web documents, temporal data may exist as meta data in the header and as user-directed data in the body of a document. Whereas temporal data can easily be identified in the semi-structured meta data, it is more difficult to determine temporal data and its role in the body. We propose procedures for maintaining temporal integrity of Web pages and outline different approaches of applying bitemporal data concepts for Web documents. In particular, we regard desirable functionalities of Web repositories and other Web-related tools that may support the Webmasters in managing the temporal data of their Web documents. Some properties of a prototype environment are described.

Incidence and predictors of cutaneous manifestations during the early course of systemic sclerosis: a 10-year longitudinal study from the EUSTAR database.

OBJECTIVES To longitudinally map the onset and identify risk factors for skin sclerosis and digital ulcers (DUs) in patients with systemic sclerosis (SSc) from an early time point after the onset of Raynaud's phenomenon (RP) in the European Scleroderma Trials and Research (EUSTAR) cohort. METHODS 695 patients with SSc with a baseline visit within 1 year after RP onset were followed in the prospective multinational EUSTAR database. During the 10-year observation period, cumulative probabilities of cutaneous lesions were assessed with the Kaplan-Meier method. Cox proportional hazards regression analysis was used to evaluate risk factors. RESULTS The median modified Rodnan skin score (mRSS) peaked 1 year after RP onset, and was 15 points. The 1-year probability to develop an mRSS ≥2 in at least one area of the arms and legs was 69% and 25%, respectively. Twenty-five per cent of patients developed diffuse cutaneous involvement in the first year after RP onset. This probability increased to 36% during the subsequent 2 years. Only 6% of patients developed diffuse cutaneous SSc thereafter. The probability to develop DUs increased to a maximum of 70% at the end of the 10-year observation. The main factors associated with diffuse cutaneous SSc were the presence of anti-RNA polymerase III autoantibodies, followed by antitopoisomerase autoantibodies and male sex. The main factor associated with incident DUs was the presence of antitopoisomerase autoantibodies. CONCLUSION Early after RP onset, cutaneous manifestations exhibit rapid kinetics in SSc. This should be accounted for in clinical trials aiming to prevent skin worsening.

Days spent in acute care hospitals at the end of life of cancer patients in four Swiss cantons: a retrospective database study (SAKK 89/09).

Number of days spent in acute hospitals (DAH) at the end of life is regarded as an important care quality indicator for cancer patients. We analysed DAH during 90 days prior to death in patients from four Swiss cantons. Claims data from an insurance provider with about 20% market share and patient record review identified 2086 patients as dying of cancer. We calculated total DAH per patient. Multivariable generalised linear modelling served to evaluate potential explanatory variables. Mean DAH was 26 days. In the multivariable model, using complementary and alternative medicine (DAH = 33.9; +8.8 days compared to non-users) and canton of residence (for patient receiving anti-cancer therapy, Zürich DAH = 22.8 versus Basel DAH = 31.4; for other patients, Valais DAH = 22.7 versus Ticino DAH = 33.7) had the strongest influence. Age at death and days spent in other institutions were additional significant predictors. DAH during the last 90 days of life of cancer patients from four Swiss cantons is high compared to most other countries. Several factors influence DAH. Resulting differences are likely to have financial impact, as DAH is a major cost driver for end-of-life care. Whether they are supply- or demand-driven and whether patients would prefer fewer days in hospital remains to be established.

Special Tax Treatment as Trade Policy: A Database on Export Processing and Special Economic Zones

Many countries treat income generated via exports favourably, especially when production takes places in special zones known as export processing zones (EPZs). EPZs can be defined as specific, geographically defined zones or areas that are subject to special administration and that generally offer tax incentives, such as duty‐free imports when producing for export, exemption from other regulatory constraints linked to import for the domestic market, sometimes favourable treatment in terms of industrial regulation, and the streamlining of border clearing procedures. We describe a database of WTO Members that employ special economic zones as part of their industrial policy mix. This is based on WTO notification and monitoring through the WTO’s trade policy review mechanism (TPRM), supplemented with information from the ILO, World Bank, and primary sources. We also provide some rough analysis of the relationship between use of EPZs and the carbon intensity of exports, and relative levels of investment across countries with and without special zones.

VISUAL MEMORY PROCESSING BY PRIMATES AND AVIANS IN A RELATIONAL TASK

Three rhesus monkeys (Macaca mulatta) and four pigeons (Columba livia) were trained in a visual serial probe recognition (SPR) task. A list of visual stimuli (slides) was presented sequentially to the subjects. Following the list and after a delay interval, a probe stimulus was presented that could be either from the list (Same) or not from the list (Different). The monkeys readily acquired a variable list length SPR task, while pigeons showed acquisition only under constant list length condition. However, monkeys memorized the responses to the probes (absolute strategy) when overtrained with the same lists and probes, while pigeons compared the probe to the list in memory (relational strategy). Performance of the pigeon on 4-items constant list length was disrupted when blocks of trials of different list lengths were imbedded between the 4-items blocks. Serial position curves for recognition at variable probe delays showed better relative performance on the last items of the list at short delays (0-0.5 seconds) and better relative performance on the initial items of the list at long delays (6-10 seconds for the pigeons and 20-30 seconds for the monkeys and a human adolescent). The serial position curves also showed reliable primacy and recency effects at intermediate probe delays. The monkeys showed evidence of using a relational strategy in the variable probe delay task. The results are the first demonstration of relational serial probe recognition performance in an avian and suggest similar underlying dynamic recognition memory mechanisms in primates and avians. ^

Prognostic factors in desmoid tumors

Purpose. To evaluate the prognostic factors in desmoid tumors in the light of its possible use in standardizing the treatment strategy of an individual patient. ^ Patients and methods. A retrospective review of 189 consecutive patients who were treated at MD Anderson Cancer Center (MDACC) from January 1995 to December 2005 was done. Univariate and multivariate analysis of different prognostic factors was done on all patients, patients treated with surgery alone, subset of patients who came to MDACC with primary tumor. The median follow up was 63 months. Also the analysis of 189 desmoid patients treated at MDACC between 1995 and 2005 was compared to results of 189 desmoid patients treated at MDACC from 1965-1994 using data retrieved from a 150 field prospective relational soft tissue tumor database. ^ Results. 5-, and 10-year overall survival rate were 0.976 (95%CI 0.952, 0.999), and 0.966 (95% CI 0.935, 0.996), respectively. 5-, and 10-year recurrence free rate were 0.803 (95%CI 0.738, 0.868), and 0.793 (95% CI 0.726, 0.860), respectively. 5 year recurrence free survival for surgery alone, radiotherapy alone, chemotherapy alone and combination regimen were 0.759, 0.625, 0.933, and 0.802 respectively. Age (>30 vs. <=30) and primary tumor site (extremity vs visceral) were two prognostic factors significantly associated with local recurrence in all of the patients. ^ Conclusion. An increased awareness of the complex multidisciplinary management needed for successful control of desmoid tumor may underlie a significantly increased number of desmoid referrals, especially primary untreated desmoids, to UTMDACC. The careful prospective integration of multiple therapies has led to a significant recent improvement in desmoid patient outcome. These trends should be supported, particularly if personalized molecular-based therapies are to be rapidly and effectively deployed for the benefit of those afflicted by this rare and potentially devastating disease.^