Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

BACKGROUND: The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS: We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. CONCLUSION: Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements, and then send those annotations to any database in the world. Textpresso Central URL: http://www.textpresso.org/tpc.

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is 'hidden' from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to reduce the workload of the curators, it has resulted in valuable analytic by-products that address accessibility, use and citation of resources that can now be shared with resource owners and the larger scientific community. DATABASE URL: http://neuinfo.org.

TROP2 expression as prognostic marker for gastric carcinoma.

BACKGROUND: In gastric cancer the recurrence rate is unacceptably high, even after R0 resection and (neo)adjuvant chemotherapy. Therefore, there is an urgent need for identification of predictive and/or prognostic biomarkers to select high-risk patients who might benefit from additional therapies. Expression of TROP2 has been shown to be associated with tumour aggressiveness and poor prognosis in patients with various epithelial cancers. AIMS: To investigate TROP2 expression in gastric cancer and its correlation with clinicopathological features and disease outcome. METHODS: Expression of TROP2 was investigated by immunohistochemistry of tumour specimens from 104 patients who underwent resection for gastric cancer. Parameters found to be of prognostic significance in univariate analysis were verified in a multivariate Cox regression model. RESULTS: TROP2 was found to be overexpressed in 58 (56%) tumour samples. Significantly higher expression of TROP2 could be detected in intestinal-type carcinomas (p = 0.03). In intestinal-type gastric cancer, TROP2 overexpression was significantly correlated with shorter disease-free survival (DFS) (p = 0.03). Among the total group, TROP2 overexpression was predictive for poor disease-free (p<0.01) and overall (p = 0.03) survival in lymph node positive patients. Multivariate Cox regression analysis revealed TROP2 overexpression to be an independent prognostic marker for poor DFS in the subgroup of patients with intestinal-type gastric cancer irrespective of lymph node involvement. CONCLUSION: Results show that TROP2 is an independent prognostic marker for disease recurrence in intestinal type gastric cancer. Due to its wide distribution TROP2 may become an attractive therapeutic target in a subgroup of patients with gastric cancer.

Natural occurrence of Fusarium toxins in soy food marketed in Germany.

A total of 45 samples of soy food including whole beans, roasted soy nuts, flour and flakes, textured soy protein, tofu, proteinisolate including infant formulas and fermented products (soy sauce) were randomly collected in food and health food stores and analysed for Fusarium toxins. A spectrum of 13 trichothecenes of the A-type as well as of the B-type were determined by gas chromatography/mass spectrometry, zearalenone (ZEA), alpha- and beta-zearalenol (alpha- and beta-ZOL) by high performance liquid chromatography (HPLC) with fluorescence and UV-detection. Detection limits ranged between 1 and 19 microg/kg. At least one of the toxins investigated was detected in 11 out of a total of 45 samples of soy food belonging to different commodities. Scirpentriol (SCIRP), 15-monoacetoxyscirpenol, 4,15-diacetoxyscirpenol, T-2 tetraol, HT-2 toxin, deoxynivalenol (DON), 15- and 3-acetyldeoxynivalenol, ZEA, alpha- and beta-ZOL were detected in at least one sample, T-2 triol, T-2, NEO, NIV and FUS-X were not detected in any sample. Five out of 11 samples were positive for one toxin, one sample for two, three, six or seven toxins, two samples for 5 toxins, demonstrating the possibility of a contamination of soy food with a spectrum of Fusarium toxins. SCIRP, DON and ZEA were found up to 108, 260 and 214 microg/kg, the other toxins did not exceed 61 microg/kg. A first insight into the contamination of soy food with a broad spectrum of Fusarium toxins is provided.

Gene methylation data--a new challenge for bioinformaticians?

OBJECTIVES: Changes in the status of DNA methylation, known as epigenetic alterations, are among the most common molecular alterations in human neoplasia. For the first time, we reported on the analysis of fecal DNA from patients with CRC to determine the feasibility, sensitivity and specificity of this approach. We want to present basic information about DNA methylation analysis in the context of bioinformatics, the study design and several statistical experiences with gene methylation data. Additionally we outline chances and new research questions in the field of DNA methylation. METHODS: We present current approaches to DNA methylation analysis based on one reference study. Its study design and the statistical analysis is reflected in the context of biomarker development. Finally we outline perspectives and research questions for statisticians and bioinformaticians. RESULTS: Identification of at least three genes as potential DNA methylation-based tumor marker genes (SFRP2, SFRP5, PGR). CONCLUSIONS: DNA methylation analysis is a rising topic in molecular genetics. Gene methylation will push the extension of biobanks to include new types of genetic data. Study design and statistical methods for the detection of methylation biomarkers must be improved. For the purpose of establishing methylation analysis as a new diagnostic/prognostic tool the adaptation of several approaches has become a challenging field of research activity.

Fusarium toxin contents of maize and maize products purchased in the years 2000 and 2001 in Germany.

Samples (n=106) of maize and maize products were analysed for 13 trichothecene toxins and zearalenone (ZON). All 14 toxins examined were detected, although with varying frequency. Cooccurrence of two or more toxins was observed in 96% of samples. The toxins of the scirpenol group scirpentriol, 15-monoacetoxyscirpenol and diacetoxyscirpenol were detected in 14, 27 and 3% of the samples analysed, the toxins of the T-2 group T-2 toxin, HT-2 toxin, T-2 triol und T-2 tetraol were found in 33, 66, 2 and 7%. Toxin content was higher in feeds than in foods (semolina and flour). In food samples, the German regulatory level for DON (500 µg/kg) was not exceeded, three samples of maize flour contained ZON above the regulatory level (50 µg/kg).

Intake estimates for trichothecene toxins of the population in Southwest Germany in 1998 and in 1999.

The intake of theFusarium toxins deoxynivalenol (DON), nivalenol (NIV), HT-2 and T-2 toxin (HT-2, T-2), 3-, 15-acetyldeoxynivalenol (3-, 15- ADON), and fusarenon-X (FUS-X) was calculated for adults, children and babies, for an area of southwest Germany and two years (1998, 1999). Estimates were based on consumption data of bread and pasta by both adults and children and of infant food by babies, reported for the German population in a study on behalf of the European Union, and on toxin contents of a total of 208 samples of these commodities. No exceeding of the tolerable daily intake (TDI) of DON, NIV and the sum of HT-2 and T-2, as stated by the EU, was found for adults (70 kg body weight (BW)) and for babies (10 kg BW), independent of year and level of consumption. For children (20 kg BW) the intake of DON exceeded the TDI in 1998 for high, and in 1999 for both mean and high consumers. For both years the intake of the sum of HT-2 and T-2 was below the TDI following mean but above this value following high consumption. The intake of NIV was far below the TDI for both levels of ingestion. The daily intake of each of the three toxins 3-, 15- ADON and FUS-X was below 0.03, 0.11 and 0.05 µg/kg/BW for adults, children and babies, respectively.

Survey of Fusarium toxins in foodstuffs of plant origin marketed in Germany.

A total of 219 samples of foodstuffs of plant origin, consisting of grain-based food, pseudocereals and gluten-free food as well as vegetables, fruits, oilseeds and nuts, were randomly collected during 2000 and 2001 in food and health food stores. A spectra of 13 trichothecene toxins including diacetoxyscirpenol (DAS), 15-monoacetoxyscirpenol (MAS), scirpentriol (SCIRP), T-2 and HT-2 toxins (T-2, HT-2), T-2 triol, T-2 tetraol, neosolaniol (NEO) of the A-type as well as deoxynivalenol (DON), 3- and 15-acetyl-DON (3-, 15-ADON), nivalenol (NIV), and fusarenon-X (FUS-X) of the B-type were determined by gas chromatography/mass spectrometry. Analysis of zearalenone (ZEA), alpha- and beta-zearalenol (alpha- and beta-ZOL) was made by high-performance liquid chromatography with fluorescence and UV-detection. Detection limits ranged between 1 and 19 microg/kg. Out of 84 samples of cereal-based including gluten-free foods, 60 samples were positive for at least one of the toxins DON, 15-ADON, 3-ADON, NIV, T-2, HT-2, T-2 tetraol and ZEA, with incidences at 57%, 13%, 1%, 10%, 12%, 37%, 4% and 38%, respectively, whereas SCIRP and its derivatives MAS and DAS, T-2 triol, Fus-X as well as alpha- and beta-ZOL were not detected in any sample of this subgroup. Contents of DON ranged between 8 and 389 microg/kg, for all other toxins determined concentrations were below 100 microg/kg. The pseudocereals amaranth, quinoa and buckwheat were free of the toxins investigated. Ten of 85 samples of vegetables and fruits were toxin positive. ZEA and the type A trichothecenes MAS, SCIRP, DAS, HT-2 were detected in 7, 3, 2, 1 and 1 samples, respectively. Out of 35 samples of oilseeds and nuts, 7 samples were toxin positive. HT-2, T-2 and ZEA were detected in 4, 3 and 4 samples, respectively. In vegetables and fruits as well as in oilseeds and nuts, toxin levels were below 50 microg/kg. None of the B-type trichothecenes analysed was found for both subgroups.

MeCP2 and MBD2 expression in human neoplastic and non-neoplastic breast tissue and its association with oestrogen receptor status.

This study analysed mRNA expression of two members of the methyl-CpG-binding protein family - MeCP2 and MBD2 - in human non-neoplastic (n=11) and neoplastic (n=57) breast tissue specimens using a quantitative real-time PCR method. We observed higher expression levels of MeCP2 mRNA in neoplastic tissues than in non-neoplastic tissues (P=0.001), whereas no significant differences for MBD2 were detected. When studying the relations between the most important clinicopathologic features of breast cancer and the mRNA expression level of both MBDs, we found that oestrogen receptor (OR)-positive breast cancer specimens contained higher levels of MeCP2 mRNA than did OR-negative cancers (P=0.005). Furthermore, we observed statistically significantly higher levels of MeCP2 in non-neoplastic tissues expressing high levels of OR as compared to those expressing low levels (P=0.017). Finally, using a linear regression model, we identified a statistically significant association between OR expression and MeCP2 mRNA expression in neoplastic and non-neoplastic breast tissue specimens (P=0.003). In conclusion, we were able to demonstrate for the first time that there exists a strong association between OR status and MeCP2 mRNA expression. Furthermore, we speculate that MeCP2, regulated by OR, plays a key role in the differentiation processes in human breast tissues.

Vector space classification of DNA sequences.

Revisiting the problem of intron-exon identification, we use a principal component analysis (PCA) to classify DNA sequences and present first results that validate our approach. Sequences are translated into document vectors that represent their word content; a principal component analysis then defines Gaussian-distributed sequence classes. The classification uses word content and variation of word usage to distinguish sequences. We test our approach with several data sets of genomic DNA and are able to classify introns and exons with an accuracy of up to 96%. We compare the method with the best traditional coding measure, the non-overlapping hexamer frequency count, and find that the PCA method produces better results. We also investigate the degree of cross-validation between different data sets of introns and exons and find evidence that the quality of a data set can be detected.

Influence of training volume and acute physical exercise on the homocysteine levels in endurance-trained men: interactions with plasma folate and vitamin B12.

The interrelation between physical exercise and plasma levels of homocysteine (Hcy), vitamin B(12), and folic acid has not been examined. Therefore, we investigated the influence of extensive endurance training and acute intense exercise on plasma concentrations of total Hcy, vitamin B(12), and folic acid in 42 well-trained male triathletes. Examinations and blood sampling took place before and after a 30-day endurance training period as well as before and 1 and 24 h after a competitive exercise (sprint triathlon). Following the training period, no significant change in Hcy levels could be detected for the whole group. Subgroup analysis in quartiles of training volume revealed that - as compared with the lowest quartile (low-training group: 9.1 h training/week) - athletes in the highest training quartile (high-training group: 14.9 h training/week) exhibited a significant decrease in Hcy levels (from 12.7 +/- 2.3 to 11.7 +/- 2.4 micromol/l as compared with levels of 12.5 +/- 1.5 and 12.86 +/- 1.5 micromol/l in the low-training group; p < 0.05). The plasma folate levels were significantly higher in the high-training group at all points of examination (p < 0.05). 1 h and 24 h after competition, the Hcy concentration increased in all athletes independent of the previous training volume (24 h: 12.3 +/- 1.8 vs. 13.5 +/- 2.6 micromol/l; p < 0.001), although the increase was decisively stronger in the low-training group. 1 h after competition, the plasma folate concentration increased (7.03 +/- 2.1 vs. 8.33 +/- 2.1 ng/ml; p < 0.05) in all athletes. Multivariate analysis showed that the exercise-induced increase in the Hcy levels was dependent on baselines levels of folate and training volume, but not on the vitamin B(12) levels. In conclusion, although intense exercise acutely increased the Hcy levels, chronic endurance exercise was not associated with higher Hcy concentrations. Moreover, athletes with the highest training volume, exhibiting also the highest plasma folate levels, showed a decrease in Hcy levels following the training period as well as a much lower increase of the Hcy concentration after acute intense exercise. The combined effect of training and higher plasma folate levels to reduce Hcy should be investigated in future studies.

Deoxynivalenol contents in foodstuffs of organical and conventional production.

Samples of wheat flour, bread, noodles, rice, corn and corn based foods as well as oats and oats based foods of conventional and organical production were analysed for trichothecene toxins. In wheat flour, bread and noodels the median deoxynivalenol (DON) contents were lower in ecological than in conventional products with significant differences for what flour and bread. To estimate toxin uptake of the consumer a corrected mean of DON concentration was calculated, which was lower in wheat flour and bread for ecological than for conventional products. In noodles the corrected mean of organical products was higher than that of conventional ones.

Fusarium toxins in wheat flour collected in an area in southwest Germany.

A total of 60 samples of wheat flour were collected during the first 6 months of 1999 from mills and food stores in an area in southwest Germany. Samples included whole-grain and two types of white flour with these three groups characterized by a high, medium and low ash content. The contents of deoxynivalenol (DON), nivalenol (NIV), 3- and 15-acetyldeoxynivalenol, HT-2 toxin (HT-2), T-2 toxin (T-2) and fusarenon-X (FUS-X) were determined by gas chromatography/mass spectrometry, and those of zearalenone (ZEA), alpha- and beta-zearalenol (alpha- and beta-ZOL) by high performance liquid chromatography with fluorescence detection. FUS-X, alpha- and beta-ZOL were not detected in any sample. Based on incidence and level, DON was the predominant toxin followed by NIV and ZEA for all three flour types. The overall degree of toxin contamination was lower with decreasing ash content. This suggests a localization of the toxins analyzed primarily in the outer parts of the original wheat kernels. The median DON content was significantly (P<0.05) higher for wheat flour originating from wheat of conventional than of organic production.

Fusarium toxins in different food samples.

Samples of wheat for human nutrition, wheat flour, bread and noodles were analysed for different trichothecenes and partly for zearalenone (ZEA). The toxin contents for deoxynivalenol (DON) and ZEA were compared with the maximum tolerated levels recently discussed for foodstuffs in Germany. The limits for DON were exceeded in 20, 15, 5 and 9% of the samples of wheat, wheat flour, bread and noodles respectively, the limits for ZEA in 4 and 0% for wheat and wheat flour respectively.ZUSAMMENFASSUNG: Proben von Weizen für die menschliche Ernährung, Weizenmehl, Brot und Nudeln wurden auf verschiedene Trichothecene und z. T. auf Zearalenon (ZEA) untersucht und die ermittelten Gehalte an Deoxynivalenol (DON) und ZEA mit den in Deutschland zur Diskussion stehenden Höchstgehalten verglichen. Diese Werte wurden für DON in 20, 15, 5 und 9% der Weizen, Weizenmehl, Brot bzw. Nudelproben überschritten, für ZEA in 4% der Weizenproben und in 0% der Weizenmehlproben.

Gambicin: a novel immune responsive antimicrobial peptide from the malaria vector Anopheles gambiae.

A novel mosquito antimicrobial peptide, gambicin, and the corresponding gene were isolated in parallel through differential display-PCR, an expressed sequence tag (EST) project, and characterization of an antimicrobial activity in a mosquito cell line by reverse-phase chromatography. The 616-bp gambicin ORF encodes an 81-residue protein that is processed and secreted as a 61-aa mature peptide containing eight cysteines engaged in four disulfide bridges. Gambicin lacks sequence homology with other known proteins. Like other Anopheles gambiae antimicrobial peptide genes, gambicin is induced by natural or experimental infection in the midgut, fatbody, and hemocyte-like cell lines. Within the midgut, gambicin is predominantly expressed in the anterior part. Both local and systemic gambicin expression is induced during early and late stages of natural malaria infection. In vitro experiments showed that the 6.8-kDa mature peptide can kill both Gram-positive and Gram-negative bacteria, has a morphogenic effect on a filamentous fungus, and is marginally lethal to Plasmodium berghei ookinetes. An oxidized form of gambicin isolated from the cell line medium was more active against bacteria than the nonoxidized form from the same medium.

Characteristics and clinical relevance of chronic anemia in adult heart transplant recipients.

BACKGROUND: Mild chronic anemia following heart transplantation (HTX), with hemoglobin (Hb) values of 10-14 g/dL in men and 10-12 g/dL in women, is frequent. It has continued to be of uncertain etiology yet clinical relevance. Nonetheless, therapeutic immunosuppression has been regarded as a major cause of chronic anemia in HTX patients. METHODS: Sixty outpatients were observed over a period of 5 yr after HTX. Laboratory values related to anemia such as Hb, erythropoietin (EPO), ferritin, transferrin, iron, and vitamin levels were obtained and analyzed monthly. Patients were divided into two groups retrospectively. Patients with persistent anemia for more than 1 yr were compared with non-anemic patients. RESULTS: Forty-three (72%) of the 60 patients were anemic. Anemia was normochromic, normocytic, and slightly anisocytic. Anemic and non-anemic patients showed EPO levels within the expected range as defined by Erslev (Erythropoietin. N Engl J Med 1991: 324: 1339). Reticulocyte counts were found to be normal in all patients. Iron deficiency and deficiency of vitamin B12 or folic acid were not observed. Patients with persistent anemia showed a significantly shorter survival period than non-anemic patients (p<0.02). CONCLUSIONS: Mild anemia following HTX shows the same characteristics as anemia in chronic diseases. Persisting mild anemia used to be associated with a shorter life expectancy. There is no evidence that standard immunosuppression causes anemia.

Epigenetic downregulation of the retinoic acid receptor-beta2 gene in breast cancer.

A growing body of evidence supports the hypothesis that the retinoic acid receptor beta2 (RAR-beta2) gene is a tumor suppressor gene which induces apoptosis and that the chemopreventive and therapeutic effects of retinoids are due to induction of RAR-beta2. During breast cancer progression, RAR-beta2 is reduced or even lost. It is known from studies of other tumor-suppressor genes that methylation of the 5'-region is the cause of loss of expression. Several groups demonstrated that this is also true for the RAR-beta2 in breast cancer by treating breast cancer cell lines with a demethylating agent and examining expression of the RAR-beta2 gene in response to a challenge with retinoic acid. Studies using sodium bisulfite genomic sequencing as well as methylation specific PCR showed that a number of breast cancer cell lines as well as breast cancer tissue showed signs of methylation. The RAR-beta2 gene was unmethylated in non-neoplastic breast tissue as well as in other normal tissues. A combination of retinoic acid with demethylating agents as well as with histone deacetylase inhibitors acts synergistically to inhibit growth. This review presents data that suggest that treatment of cancer patients with demethylating agents followed by retinoic acid may offer a new therapeutic modality. Both the time of commencement of chemoprevention and the choice of substances that are able either to prevent de novo methylation or to reverse methylation-caused gene silencing may be important considerations.

Blood digestion in the malaria mosquito Anopheles gambiae: molecular cloning and biochemical characterization of two inducible chymotrypsins.

The elucidation of digestive processes in the Anopheles gambiae gut leading to the utilization of the blood meal will result in a deeper understanding of the physiology of blood digestion and its impact on parasite-vector interactions. Accordingly, the identification of digestive serine proteases in A. gambiae has implications for the development of alternative strategies for the control of mosquito-borne diseases. We report here on the cDNA and genomic cloning and on the expression analysis of two closely related chymotrypsin genes, Anchym1 and Anchym2. Genomic cloning revealed that Anchym1 and Anchym2, which map on chromosomal division 25D, are clustered in tandem within 6 kb, both genes being interrupted by two short introns. After blood feeding, transcription of Anchym1 and Anchym2 is induced in the midgut epithelium, followed by secretion of the translated products into the midgut lumen where the Anchym1 and Anchym2 zymogens are activated by partial tryptic digestion. The amino-acid residues forming the substrate pocket of Anchym1 and Anchym2 suggested chymotryptic cleavage specificity. This was confirmed by mass spectrometry analysis and Edman degradation sequencing of proteolytic products generated by the recombinant, trypsin-activated Anchym1.

Substitution of the thioredoxin system for glutathione reductase in Drosophila melanogaster.

The disulfide reducing enzymes glutathione reductase and thioredoxin reductase are highly conserved among bacteria, fungi, worms, and mammals. These proteins maintain intracellular redox homeostasis to protect the organism from oxidative damage. Here we demonstrate the absence of glutathione reductase in Drosophila melanogaster, identify a new type of thioredoxin reductase, and provide evidence that a thioredoxin system supports GSSG reduction. Our data suggest that antioxidant defense in Drosophila, and probably in related insects, differs fundamentally from that in other organisms.

Innate immune defense against malaria infection in the mosquito.

Anopheles gambiae, the most important vector of malaria, employs its innate immune system in the fight against Plasmodium. This can affect the propagative capacity of Plasmodium in the vector and, in some cases, leads to total refractoriness to the parasite. The components operating in the mosquito's innate immune system and their potential relevance to antimalarial responses are being systematically dissected.