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Background There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap. Conclusions Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.

Though clinical trials for medical applications of dimethyl sulfoxide (DMSO) reported toxicity in the 1960s, later, the FDA classified DMSO in the safest solvent category. DMSO became widely used in many biomedical fields and biological effects were overlooked. Meanwhile, biomedical science has evolved towards sensitive high-throughput techniques and new research areas, including epigenomics and microRNAs. Considering its wide use, especially for cryopreservation and in vitro assays, we evaluated biological effect of DMSO using these technological innovations. We exposed 3D cardiac and hepatic microtissues to medium with or without 0.1% DMSO and analyzed the transcriptome, proteome and DNA methylation profiles. In both tissue types, transcriptome analysis detected >2000 differentially expressed genes affecting similar biological processes, thereby indicating consistent cross-organ actions of DMSO. Furthermore, microRNA analysis revealed large-scale deregulations of cardiac microRNAs and smaller, though still massive, effects in hepatic microtissues. Genome-wide methylation patterns also revealed tissue-specificity. While hepatic microtissues demonstrated non-significant changes, findings from cardiac microtissues suggested disruption of DNA methylation mechanisms leading to genome-wide changes. The extreme changes in microRNAs and alterations in the epigenetic landscape indicate that DMSO is not inert. Its use should be reconsidered, especially for cryopreservation of embryos and oocytes, since it may impact embryonic development.

Im Falle des Prostatakarzinoms wird in der neueren Literatur der schadliche Effekt von Gewebe-NO und Malondialdehyd sowie oxidativer Stress durch freie Sauerstoffradikale als moglicher Ausloser genannt. Zusatzlich deuten aktuelle Forschungsergebnisse darauf hin, dass oxidativer Stress eindeutig mit Tumorprogression, Tumorstadium und zytologischer Differenzierung einhergeht. Gleichzeitig zeigen neuere Berichte, dass Chlorophyll in der Lage ist, sowohl den Effekt von oxidativem Stress, als auch den durch oxidativen Stress ausgelosten Zelltod (Apoptose) und Immunsuppression zu antizipieren. Aus diesem Grunde haben wir in einer Pilotstudie den Effekt von Chlorophyll auf klinische und laborchemische Parameter bei Patienten mit metastasiertem austherapiertem Prostatakarzinom und bei chronischer Prostatitis untersucht. Die Gabe von Chlorophyll fuhrt sowohl klinisch als auch laborchemisch zu einer deutlichen Verbesserung bei Patienten mit Prostatakarzinom. Die nebenwirkungsfreie Anwendung macht eine Supplementierung mit Chlorophyll unbedenklich. Die derzeitigen Ergebnisse sind Resultate aus einer Pilotstudie, die wegen der limitierten Patientenzahl in ihrer Aussage sehr eingeschrankt ist.

Actinobacillus pleuropneumoniae is among the most important pathogens worldwide in pig production. The agent can cause severe economic losses due to decreased performance, acute or chronic pleuropneumonia and an increased incidence of death. Therapeutics cannot be used in a sustainable manner, and vaccination is not always available, but discovering more about host defence and disease mechanisms might lead to new methods of prophylaxis. The aim of the present study was to detect quantitative trait loci (QTL) associated with resistance/susceptibility to A. pleuropneumoniae. Under controlled conditions, 170 F2 animals of a Hampshire/Landrace family, with known differences in founder populations regarding A. pleuropneumoniae resistance, were challenged with an A. pleuropneumoniae serotype 7 aerosol followed by a detailed clinical, radiographic, ultrasonographic, pathological and bacteriological examination. F2 pigs were genotyped with 159 microsatellite markers. Significant QTL were identified on Sus scrofa chromosomes (SSC) 2, 6, 12, 13, 16, 17 and 18. They explained 6–22 % of phenotypic variance. One QTL on SSC2 reached significance on a genome-wide level for five associated phenotypic traits. A multiple regression analysis revealed a combinatory effect of markers SWR345 (SSC2) and S0143 (SSC12) on Respiratory Health Score, Clinical Score and the occurrence of death. The results indicate the genetic background of A. pleuropneumoniae resistance in swine and provide new insights into the genetic architecture of resistance/susceptibility to porcine pleuropneumonia. The results will be helpful in identifying the underlying genes and mechanisms.

Purpose: The Post-Ureteroscopic Lesion Scale (PULS) offers a simple grading system for the description of ureteral lesions after ureteroscopy. In this article, we present the results of a video-based multicenter evaluation of the inter-rater reliability of clinically important PULS grades 0-3. Methods: Video sequences at the end of ureteroscopy (final passage) were recorded for 100 consecutive patients at a single institution and assessed by experienced urologists (n = 20) and senior residents (n = 17) at 19 international centers. The cohort included only patients with lesions grades 0-3 (with grades 2 and 3 subsumed as 2 + since distinction is defined by an extravasation of contrast medium in fluoroscopy). The gradings were evaluated for inter-rater reliability and in terms of simplicity, validity, comprehensibility, reproducibility, and usefulness. Results: Overall, inter-rater reliability was high (Kendall's W = 0.69, p < 0.001) and was comparable between specialists (Kendall's W = 0.69, p < 0.001) and residents (Kendall's W = 0.71, p < 0.001). The matched ratings showed grade 0 in 43.0 % of patients and grades 1 or 2 + in 44.0 and 13.0 % of patients, respectively. Results of the questionnaires indicated a high degree of acceptance, with an overall rating of 1.76 (1.64-1.93 for different items, scale 1-6). Conclusions: Inter-rater reliability of the endoscopically assessable PULS was high among urologists with different levels of experience in different countries worldwide. The validated PULS system may be used for standardized reporting of ureteral lesions/injuries after ureteroscopy. In addition, PULS will enable more selective standardization of indications for postoperative DJ stenting based on the randomized controlled trials.

In der transrektalen dreidimensionalen Sonographie ist es erstmals moglich, das zu untersuchende Areal gleichzeitig in 3 Schnittebenen zu analysieren. Dadurch kann eine sehr genaue Beurteilung der anatomischen Strukturen des kleinen Beckens und der Beckenbodenregion durchgefuhrt werden. Mit Hilfe dieser neuen Untersuchungstechnik konnen die Glandulae bulbourethrales routinemasig untersucht sowie Zysten dieser Drusen diagnostiziert werden. Die Zonen der Prostata und ihre Relationen zueinander, insbesondere das Wachstum der Transitionalzone im Rahmen der benignen Prostathyperplasie, konnen exakt bestimmt werden. Die transrektale 3D-Sonographie ermoglicht auch, die Morphologie und die Funktion des Rhabdosphinkters zu untersuchen und zu quantifizieren. Die 3D-sonographisch gezielte Punktion und Drainage von Prostataabszessen stellt ein attraktives und minimal-invasives Behandlungsverfahren dar. Diese Methode kann generell zur Punktion und zur Applikation von Nadeln oder Implantaten im unteren Harntrakt eingesetzt werden. Die transrektale dreidimensionale Sonographie bietet somit neue diagnostische und therapeutische Moglichkeiten bei der Beurteilung von Veranderungen des unteren Harntraktes.

Patients: In order to determine if there are areas of major and minor perfusion in a single testicle and if the quality of sperm is correlated with quantity of perfusion we collected testicle tissue for TESE in accordance to the local testicle tissue perfusion. Methods: A patient undergoing TESE underwent testicular perfusion mapping using contrast enhanced ultrasound. The exposed tissue was scanned with a Laser Doppler scanner and perfusion rates were determined measuring tissue perfusion units (TPUs). Tissue was biopsied and sperm were selected and prepared for assisted reproduction. Results: The total amount of isolated sperm correlated highly with the intensity of tissue perfusion showing high number of sperm in areas with high TPUs. Conclusions: This is the first demonstration that sperm quality and quantity is depending on tissue perfusion within the testicle. To further improve infertility treatment we propose that random biopsies could be replaced by perfusion-dependent collection of testicular tissue.

Die interstitielle Zystitis (IC) ist eine seltene, komplexe Form der Harnblasenentzundung, deren Diagnostik Probleme bereiten kann. Die fur Forschungszwecke festgelegten strengen NIH-Kriterien zur IC-Diagnostik sind in der Routine ungeeignet, da ein Grosteil von IC-Patienten ubersehen wird. Bei IC-Verdacht wird nach Anamnese und korperlicher Untersuchung ein mehrtagiges Miktionsprotokoll gefordert. Grosere Miktionsvolumina (funktionelle Blasenkapazitat >250 ml) oder langere Miktionsintervalle (>2 h), fehlende Nykturie oder symptomfreie Phasen sprechen gegen eine IC. Die weiterfuhrende Ausschlussdiagnostik umfasst Urinuntersuchungen (Infekt), Zytologie (Carcinoma in situ), Harntraktsonographie (Steine, Raumforderungen, Anomalien) und in Sonderfallen Urodynamik. Blasenkapazitatsbestimmungen in Sedoanalgesie sind ungeeignet, da funktionell kleine Blasen mechanisch dehnbar sein konnen. Standardverfahren der IC-Diagnostik ist die Zystoskopie in Narkose, bei der 90% der IC-Patienten nach Blasendistension charakteristische Schleimhautglomerulationen entwickeln. Blasenbiopsien zum Malignitatsausschluss sind empfehlenswert. Kaliuminstillationstests haben bei der Routinediagnostik wegen geringer Spezifitat keinen Stellenwert. Gleichermasen sind aufwendige Bestimmugen neuartiger IC-Marker (Histamin, Tryptase, Zytokine, Wachstumsfaktoren, Substanz-P, Stickoxid) Forschungszentren vorbehalten und ohne Relevanz im Klinikalltag.

Die Nachfrage nach alternativen Heilmethoden wird immer groser. Besonders Patienten, bei denen allopathische Methoden bisher ohne Erfolg angewendet wurden, sind an diesen Behandlungsstrategien interessiert. Im Folgenden werden alternative und additive Verfahren beschrieben und diskutiert, die wiederholt in der Behandlung der interstitiellen Zystitis (IC) als effektive additive Behandlungsformen beschrieben werden.

Endourologische Operationstechniken (transurethrale Resektion und Koagulation, Nd-YAG-Laser) zur Behandlung der interstitiellen Zystitis (IC) wurden nur in wenigen Studien wissenschaftlich untersucht. Nach Ausschopfen konservativer Behandlungsstrategien stellen sie theoretisch den nachsten Schritt im Therapiekonzept dar, bevor offen chirurgische Behandlungsansatze als Ultima ratio zum Einsatz kommen. Diese Ubersicht zeigt, dass nach Anwendung strenger Kriterien aus dem Bereich der evidenzbasierten Medizin, wissenschaftliche Grundlagen fur die Empfehlung endourologischer Techniken zur Behandlung der IC noch weitgehend fehlen.

Background Multiple functional genomics data for complex human diseases have been published and made available by researchers worldwide. The main goal of these studies is the detailed analysis of a particular aspect of the disease. Complementary, meta-analysis approaches try to extract supersets of disease genes and interaction networks by integrating and combining these individual studies using statistical approaches. Results Here we report on a meta-analysis approach that integrates data of heterogeneous origin in the domain of type-2 diabetes mellitus (T2DM). Different data sources such as DNA microarrays and, complementing, qualitative data covering several human and mouse tissues are integrated and analyzed with a Bootstrap scoring approach in order to extract disease relevance of the genes. The purpose of the meta-analysis is two-fold: on the one hand it identifies a group of genes with overall disease relevance indicating common, tissue-independent processes related to the disease; on the other hand it identifies genes showing specific alterations with respect to a single study. Using a random sampling approach we computed a core set of 213 T2DM genes across multiple tissues in human and mouse, including well-known genes such as Pdk4, Adipoq, Scd, Pik3r1, Socs2 that monitor important hallmarks of T2DM, for example the strong relationship between obesity and insulin resistance, as well as a large fraction (128) of yet barely characterized novel candidate genes. Furthermore, we explored functional information and identified cellular networks associated with this core set of genes such as pathway information, protein-protein interactions and gene regulatory networks. Additionally, we set up a web interface in order to allow users to screen T2DM relevance for any – yet non-associated – gene. Conclusion In our paper we have identified a core set of 213 T2DM candidate genes by a meta-analysis of existing data sources. We have explored the relation of these genes to disease relevant information and – using enrichment analysis – we have identified biological networks on different layers of cellular information such as signaling and metabolic pathways, gene regulatory networks and protein-protein interactions. The web interface is accessible via http://t2dm-geneminer.molgen.mpg.de.

Diabetes is a complex trait, reflecting interactions of a network of genes with environmental factors, such as obesity, age and nutrition [1]. The polygenic nature of type 2 diabetes is now well established. The individual contributions of each individual gene to the phenotype is likely to be small. The primary objective of our work is to provide identification and data integration for obesity and type 2 diabetes mellitus. Microarrays have become a standard technology platform for genome screening. This technique fails in the integration of other data sources relevant for diagnostic purposes. For these tasks, data integration methods are indispensable. In our poster we present strategies to incorporate these sources within the framework of R/BioConductor [2, 3]. To elucidate the most important genes for diabetes we employ scoring to gain new knowledge on the pathways and marker genes relevant. Pathway information from databases like KEGG [4] is comprised to map the genes into their function/framework. Ultimately, the proposed marker genes will enable us to develop models for the disease. Medical researcher can combine molecular biological data with clinically relevant parameters to predict quantitatively individual predispositions to type 2 diabetes and include physiological data.

Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analyses. However, the amount of work done to integrate and evaluate these tools and the corresponding experimental procedures is not high. Although complex hybridization experiments are based on a data production pipeline that incorporates a significant amount of error parameters, the evaluation of these parameters has not been studied yet in sufficient detail. In this paper we present simulation studies on several error parameters arising in complex hybridization experiments. A general tool was developed that allows the design of exactly defined hybridization data incorporating, for example, variations of spot shapes, spot positions and local and global background noise. The simulation environment was used to judge the influence of these parameters on subsequent data analysis, for example image analysis and the detection of differentially expressed genes. As a guide for simulating expression data real experimental data were used and model parameters were adapted to these data. Our results show how measurement error can be balanced by the analysis tools. We describe an implemented model for the simulation of DNA-array experiments. This tool was used to judge the influence of critical parameters on the subsequent image analysis and differential expression analysis. Furthermore the tool can be used to guide future experiments and to improve performance by better experimental design. Series of simulated images varying specific parameters can be downloaded from our web-site: http://www.molgen.mpg.de/~lh_bioinf/projects/simulation/biotech/