6413
2011
eng
article
1
2013-02-11
--
--
CrossQuery : A Web Tool for Easy Associative Querying of Transcriptome Data
Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deepsequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.
urn:nbn:de:bvb:20-opus-76088
7608
In: PLoS ONE (2011) 6(12); e28990. doi:10.1371/journal.pone.0028990
Toni U. Wagner
Andreas Fischer
Eva C. Thoma
Manfred Schartl
deu
swd
CrossQuery
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/6413/Wagner_journal.pone.0028990.pdf
12068
2014
eng
191
4
article
1
2015-10-21
--
--
Salmonella—how a metabolic generalist adopts an intracellular lifestyle during infection
The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, “-omics” data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.
Frontiers in Cellular and Infection Microbiology
10.3389/fcimb.2014.00191
2235-2988
urn:nbn:de:bvb:20-opus-120686
Frontiers in Cellular and Infection Microbiology 4:191. doi:10.3389/fcimb.2014.00191
Thomas Dandekar
Astrid Fieselmann
Eva Fischer
Jasmin Popp
Michael Hensel
Janina Noster
eng
uncontrolled
regulation
eng
uncontrolled
virulence
eng
uncontrolled
"-omics"
eng
uncontrolled
metabolism
eng
uncontrolled
Salmonella-containing vacuole (SCV)
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12068/114_Dandekar_Frontiers_in_Cellular_and_Infection_Microbiology.pdf
13478
2011
eng
e28990
12
6
article
1
2016-06-13
--
--
CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data
Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.
PLoS ONE
10.1371/journal.pone.0028990
urn:nbn:de:bvb:20-opus-134787
PLoS ONE 6(12):e28990. doi:10.1371/journal.pone.0028990
false
true
Toni U. Wagner
Andreas Fischer
Eva C. Thoma
Manfred Schartl
eng
uncontrolled
Microarray data
eng
uncontrolled
Sprouting angiogenesis
eng
uncontrolled
Cell-line
eng
uncontrolled
Biology
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13478/032_Wagner_PLoSOne.PDF
13025
2012
eng
e37885
6
7
article
1
2016-03-18
--
--
A Randomized, Double Blind, Placebo-Controlled Trial of Pioglitazone in Combination with Riluzole in Amyotrophic Lateral Sclerosis
Background: Pioglitazone, an oral anti-diabetic that stimulates the PPAR-gamma transcription factor, increased survival of mice with amyotrophic lateral sclerosis (ALS).
Methods/Principal Findings: We performed a phase II, double blind, multicentre, placebo controlled trial of pioglitazone in ALS patients under riluzole. 219 patients were randomly assigned to receive 45 mg/day of pioglitazone or placebo (one: one allocation ratio). The primary endpoint was survival. Secondary endpoints included incidence of non-invasive ventilation and tracheotomy, and slopes of ALS-FRS, slow vital capacity, and quality of life as assessed using EUROQoL EQ-5D. The study was conducted under a two-stage group sequential test, allowing to stop for futility or superiority after interim analysis. Shortly after interim analysis, 30 patients under pioglitazone and 24 patients under placebo had died. The trial was stopped for futility; the hazard ratio for primary endpoint was 1.21 (95% CI: 0.71-2.07, p = 0.48). Secondary endpoints were not modified by pioglitazone treatment. Pioglitazone was well tolerated.
Conclusion/Significance: Pioglitazone has no beneficial effects on the survival of ALS patients as add-on therapy to riluzole.
PLoS One
10.1371/journal.pone.0037885
urn:nbn:de:bvb:20-opus-130255
PLoS ONE 7(6): e37885. doi:10.1371/journal.pone.0037885
Luc Dupuis
Reinhard Dengler
Michael T. Heneka
Thomas Meyer
Stephan Zierz
Jan Kassubek
Wilhelm Fischer
Franziska Steiner
Eva Lindauer
Markus Otto
Jens Dreyhaupt
Torsten Grehl
Andreas Hermann
Andrea S. Winkler
Ulrich Bogdahn
Reiner Benecke
Bertold Schrank
Carsten Wessig
Julian Grosskreutz
Albert C. Ludolph
eng
uncontrolled
ALS
eng
uncontrolled
transgenic mouse model
eng
uncontrolled
central nervous system
eng
uncontrolled
nonalcoholic steatohepatitis
eng
uncontrolled
PPAR-gamme
eng
uncontrolled
hexanucleotide repeat
eng
uncontrolled
disease progression
eng
uncontrolled
delays progression
eng
uncontrolled
SOD1 mutations
eng
uncontrolled
monocycline
Medizin und Gesundheit
open_access
Neurologische Klinik und Poliklinik
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/13025/journal.pone.0037885.pdf
7062
1993
eng
article
1
2013-08-09
--
--
Analysis of virulence factors of Legionella pneumophila.
Legionella pneumophila, the causative agent of Legionnaires' disease is a facultative intracellular bacterium, which in the course of human infection multiplies in lung macrophages predominantly manifesting as pneumonia. The natural habitat of Legionella is found in sweet water reservoirs and man-made water systems. Virulent L. pneumophila spontaneously convert to an avirulent status at a high frequency. Genetic approaches have led to the identification of various L. pneumophila genes. The mip (macrophage infectivity potentiator) determinant remains at present the sole established virulence factor. The Mip protein exhibits activity of a peptidyl prolyl cis trans isomerase (PPiase), an enzyme which is able to bind the immunosuppressant FK506 and is involved in protein folding. The recently cloned major outer membrane protein (MOMP) could play a role in the uptake of legionellae by macrophages. Cellular models are useful in studying the intracellular replication of legionellae in eukaryotic cells. Human celllines and protozoan models are appropriate for this purpose. By using U 937 macrophage-like cells and Acanthamoeba castellanii as hosts, we could discriminate virulent and avirulent L. pneumophila variants since only the virulent strain was capable of intracellular growth at 37 oc. By using these systems we further demonstrated that a hemolytic factor cloned and characterized in our laboratory, legiolysin (lly), had no influence on the intracellular growth of L. pneumophila.
7942
urn:nbn:de:bvb:20-opus-70620
Zbl. Bakt., 1993, 278, 348-358
Deutsches Urheberrecht
Jörg Hacker
Manfred Ott
Eva Wintermeyer
Birgit Ludwig
Gunter Fischer
deu
swd
Legionella pneumophila
Medizin und Gesundheit
open_access
Institut für Molekulare Infektionsbiologie
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/7062/Hacker_7062.pdf
14902
2015
eng
191
4
article
1
2017-05-22
--
--
Salmonella - how a metabolic generalist adopts an intracellular lifestyle during infection
The human-pathogenic bacterium Salmonella enterica adjusts and adapts to different environments while attempting colonization. In the course of infection nutrient availabilities change drastically. New techniques, "-omics" data and subsequent integration by systems biology improve our understanding of these changes. We review changes in metabolism focusing on amino acid and carbohydrate metabolism. Furthermore, the adaptation process is associated with the activation of genes of the Salmonella pathogenicity islands (SPIs). Anti-infective strategies have to take these insights into account and include metabolic and other strategies. Salmonella infections will remain a challenge for infection biology.
Frontiers in Cellular and Infection Microbiology
10.3389/fcimb.2014.00191
urn:nbn:de:bvb:20-opus-149029
Frontiers in Cellular and Infection Microbiology 4:191 (2015). DOI: 10.3389/fcimb.2014.00191
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Thomas Dandekar
Astrid Fieselmann
Eva Fischer
Jasmin Popp
Michael Hensel
Janina Noster
eng
uncontrolled
enterica serovar Typhimurium
eng
uncontrolled
bacterial invasion
eng
uncontrolled
mouse model
eng
uncontrolled
defenses
eng
uncontrolled
regulation
eng
uncontrolled
"-omics"
eng
uncontrolled
virulence
eng
uncontrolled
Salmonella-containing vacuole (SCV)
eng
uncontrolled
metabolism
eng
uncontrolled
nitric oxide
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14902/054_Dandekar_Frontiers_in_Cellular_and_Infection_Microbiology.pdf
15780
2017
eng
275
11
article
1
2018-02-21
--
--
The effect of agomelatine and melatonin on sleep-related eating: a case report
Background:
Sleep-related eating may occur in the context of mental illness, sleep disorders, or psychopharmacological treatment. Frequently, sleep-related eating leads to severe weight gain and, so far, there are no treatment options for the condition.
Case presentation:
We report the case of a 54-year-old white woman with depression, panic disorder, and sleep apnea under treatment with various antidepressants who developed severe sleep-related eating. Her sleep-related eating completely vanished after addition of agomelatine, it reoccurred after cessation of agomelatine, and vanished again after her re-exposure to another melatonergic drug, extended melatonin.
Conclusions:
This case suggests that melatonergic drugs lead to relief from sleep-related eating, even when the condition occurs in the context of physical and mental disorders as well as psychopharmacological treatment.
Journal of Medical Case Reports
10.1186/s13256-017-1438-5
urn:nbn:de:bvb:20-opus-157805
Journal of Medical Case Reports (2017) 11:275. DOI: 10.1186/s13256-017-1438-5
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Angela Alexandra Zapp
Eva Caroline Fischer
Michael Deuschle
eng
uncontrolled
sleep-related eating
eng
uncontrolled
agomelatine
eng
uncontrolled
melatonin
eng
uncontrolled
weight loss
eng
uncontrolled
parasomn
Medizin und Gesundheit
open_access
Medizinische Fakultät
Förderzeitraum 2017
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/15780/Zapp_Journal_of_Medical_Case_Reports.pdf