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Baal N, Cunningham S, Obermann HL, Thomas J, Lippitsch A, Dietert K, Gruber AD, Kaufmann A, Michel G, Nist A, Stiewe T, Rupp O, Goesmann A, Zukunft S, Fleming I, Bein G, Lohmeyer J, Bauer S, Hackstein H. ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function. THE JOURNAL OF IMMUNOLOGY 2019; 202:1099-1111. [DOI: 10.4049/jimmunol.1800269] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 12/07/2018] [Indexed: 11/19/2022]
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Farbmacher E, Bregolin T, Friedrich LM, Mechtcheriakov S, Kaufmann A, Hausmann A, Weiner R, Hofer A, Zernig G. Optimization of a combined therapeutic drug monitoring – pharmacogenetic (TDMPG) approach to explain subtherapeutic, therapeutic and supratherapeutic concentrations of neuropsychopharmacologic medications. PHARMACOPSYCHIATRY 2018. [DOI: 10.1055/s-0038-1649530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Kaufmann A. [Urodynamic studies prior to urinary incontinence surgery : What is useful?]. Urologe A 2017; 56:1539-1547. [PMID: 29079907 DOI: 10.1007/s00120-017-0530-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Surgery is often necessary after failure of conservative therapy for urinary incontinence. Guidelines recommend urodynamic studies before surgery. A distinction is made between non-invasive (uroflowmetry) and invasive methods (cystometry and pressure-flow study, if necessary as combined videourodynamics, as well as urethral pressure profile). All examinations serve to objectify and quantify the symptoms, to correctly assign symptoms to the pathophysiology and anatomy as well as to identify risk factors, which often have a significant influence on the success of surgical therapy. Given appropriate experience, complications and often significant sequelae of bladder dysfunction affecting the patient's quality of life and life expectancy can be recognized. Urodynamic studies are performed to help narrow down potential diagnoses, to develop therapeutic strategies, and to obtain prognostic parameters. The following article is intended to provide some support.
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Edmondson R, Crosbie E, Nickkho-Amiry M, Kaufmann A, Stelloo E, Nijman H, Leary A, Auguste A, Mileshkin L, Pollock P, MacKay H, Powell M, Bosse T, Creutzberg C, Kitchener H. Markers of the p53 pathway further refine molecular profiling in high-risk endometrial cancer: A Trans PORTEC initiative. Gynecol Oncol 2017; 146:327-333. [DOI: 10.1016/j.ygyno.2017.05.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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Bremer J, Domurath B, Böthig R, Kaufmann A, Geng V. [Medical quality standards for selected urological aids and devices : Consensus for patients with neurogenic urinary bladder dysfunction]. Urologe A 2017; 57:155-163. [PMID: 28707096 DOI: 10.1007/s00120-017-0457-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Using the CE mark of therapeutic appliances is, on its own, not sufficient enough for their appropriate and effective application. In order to treat the patient successfully, not jeopardizing the success of the treatment, medical quality criteria for therapeutic appliances care are necessary to acceptably compensate for a patient's disabilities. OBJECTIVES Medical quality criteria are formulated for the most frequently used urological aids and devices, considering hygienic requirements, international literature and the practical experience of physicians and nurses with regard to the care of patients with neurogenic urinary bladder dysfunction. METHODS An expert group of urologists, surgeons, rehabilitation physicians and nurses has developed medical quality criteria via a structured consensus procedure. Developing these criteria, the group has taken into account current jurisprudence, the current resource directory of neurourological relevant aids, data from international literature and hygiene requirements. RESULTS Medical quality requirements are discussed and defined for selected groups of urological devices (single use catheters, indwelling catheters, external catheters, urine bags, templates and diapers as well as devices for the electrostimulation of nerves). CONCLUSION The presented quality requirements offer the possibility to stabilize quality of care with neurourological relevant therapeutic appliances. The catalogue of therapeutic appliances must be urgently updated. Urinal catheters for single use must be classified as an individual product group. Devices for anterior root stimulation and neuromodulation must be included in the resource directory. The incontinence severity classification needs to be reviewed.
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Chatzistamatiou K, Moysiadis T, Angelis E, Kaufmann A, Skenderi A, Jansen-Duerr P, Lekka I, Kilintzis V, Angelidou S, Katsiki E, Hagemann I, Tsertanidou A, Koch I, Boecher O, Soutschek E, Maglaveras N, Agorastos T. Diagnostic accuracy of high-risk HPV DNA genotyping for primary cervical cancer screening and triage of HPV-positive women, compared to cytology: preliminary results of the PIPAVIR study. Arch Gynecol Obstet 2017; 295:1247-1257. [DOI: 10.1007/s00404-017-4324-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/07/2017] [Indexed: 11/29/2022]
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Böthig R, Domurath B, Kaufmann A, Bremer J, Vance W, Kurze I. [Neuro-urological diagnosis and therapy of lower urinary tract dysfunction in patients with spinal cord injury : S2k Guideline of the German-Speaking Medical Society of Paraplegia (DMGP), AWMF register no. 179/001]. Urologe A 2017; 56:785-792. [PMID: 28314966 DOI: 10.1007/s00120-017-0354-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Most patients with spinal cord injury (SCI) suffer from neurogenic lower urinary tract dysfunction (NLUTD), bowel dysfunction and sexual dysfunction. If these remain untreated, severe medical complications and serious limitations (restrictions) in quality of life are imminent. OBJECTIVES In the long term, there are considerable differences in the treatment results of highly specialized centers versus other treatment facilities. MATERIALS AND METHODS Against this background, a consensus-based guideline, according to the AWMF (Association of the Scientific Medical Societies in Germany) criteria (S2k), was developed by the neuro-urology working group of the DMPG (German-Speaking Medical Society of Paraplegia). RESULTS The guideline defines the principles and objectives of the neuro-urological care of patients with SCI and discusses in detail the principles of diagnosis and therapy of NLUTD. The need for video-urodynamic studies as a basis for the classification of the NLUTD and as a foundation for the development of a treatment strategy is emphasized. Both conservative and surgical therapy options and their indications are explained in detail. Possible complications and their prevention in the long-term course of SCI are presented with a particular consideration of the specific features of urinary tract infections and autonomic dysreflexia. Finally, the principles of the provision of urological appliances are discussed. CONCLUSIONS The presented S2k guideline provides the current standards in the neuro-urological care of patients with NLUTD due to SCI. Their consistent implementation both in the acute and chronic phase as well as in the context of lifelong surveillance of SCI patients should prevent the impending complications of NLUTD.
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Bremer J, Böthig R, Domurath B, Kutzenberger J, Kaufmann A, Pretzer J, Klask JP, Geng V, Vance W, Kurze I. [Objective and subjective requirement of aids and appliances in patients with neurogenic lower urinary tract dysfunction : Multicenter study to determinate the daily necessity of urological aids and appliances]. Urologe A 2016; 55:1553-1563. [PMID: 27725995 DOI: 10.1007/s00120-016-0250-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The provision of urological appliances for patients with neurogenic lower urinary tract dysfunction (NLUTD) is essential. Hitherto existing standard guidelines for the estimation of monthly material requirements are based solely on estimates. OBJECTIVE The goal of this work was to define the objective and subsequently subjective requirements for urological appliances on a scientifically validated basis. MATERIALS AND METHODS Data concerning bladder management and daily consumption of urological appliances for patients with NLUTD were collected through a standardized survey at six different centers in Germany during the period of October to December 2014 and statistically evaluated. RESULTS In all, 767 patient records were analyzed: 543 men and 221 woman (N/A = 3). The daily disposable catheter consumption of 577 patients who exclusively used intermittent catheterization was 5.13. Patients who used other means of bladder emptying (n = 31) in addition to catheterization consumed on average 3.17 catheters. The margin of deviation was larger for children. Of the 608 patients with intermittent catheterization, 94 (15.5 %) required additional paddings as absorbent aids (on average 2.29 paddings per day), 34 patients (5.6 %) additionally used pants (2.55 per day) and 46 patients (7.6 %) utilized condom catheters (3.81 per day) between catheterization. Among all surveyed patients, 126 (16.4 %) used paddings (5.03 per day) and 51 patients (6.6 %) pants (3.03 per day). Of all male respondents 82 (15.1 %) used condom catheters (2.80 urinary sheaths per day). CONCLUSION Applying twice the standard deviation of the mean as a measure of assessing the objective requirement of urological appliances and aids for adult patients with NLUTD allows the following daily thresholds to be defined: 1-9 disposable catheters, 0-7 urinary sheaths, 1-9 paddings and 0-7 pants. These thresholds can serve as a basis for estimating the subjective need. They allow for a scientifically validated benchmark for an economically feasible and patient-tailored supply with urological aids and appliances. Individually required appliances and aids have to be recognized. Verifiable quality standards need to be developed.
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Abstract
The syndrome of overactive bladder (OAB) with the symptoms of frequency, urgency and nocturia is often seen. After the diagnosis has been made by careful exclusion of other conditions, there are different symptomatic treatment strategies available. These include drug treatment as well as minimally invasive local surgical treatments and treatments which intervene with the control of the bladder by modulating central nervous areas. Alternative methods such as acupuncture may help in individual cases; the placebo effect is high and there is a lack of controlled studies.
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Scheerer C, Bauer P, Chiantera V, Sehouli J, Kaufmann A, Mechsner S. Characterization of endometriosis-associated immune cell infiltrates (EMaICI). Arch Gynecol Obstet 2016; 294:657-64. [DOI: 10.1007/s00404-016-4142-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/24/2016] [Indexed: 11/25/2022]
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Kaufmann A, Walker S. Extension of the Q Orbitrap intrascan dynamic range by using a dedicated customized scan. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1087-1095. [PMID: 27003046 DOI: 10.1002/rcm.7530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE The intrascan dynamic range of modern Orbitrap instrumentation is specified to reach 1:5000, while the interscan dynamic range is significantly larger due to the utilization of the automatic gain control feature. There are some applications (e.g. residue analysis in complex matrices, metabolomics or structural elucidation) where a wider intrascan dynamic range is desirable. METHODS The Application Programming Interface (API) of the Q Exactive Orbitrap mass spectrometer has been used to program a customized scan in order to cover a larger intrascan dynamic range. Different approaches were used, which were all based on the variation of the isolation time of low-abundance versus high-abundance mass range segments. The differently attenuated mass range segments isolated by the quadrupole were sequentially forwarded to the C-trap. Finally, the accumulated mass segments were measured within the Orbitrap analyzer. RESULTS The spectra obtained by the customized scans show an enlarged dynamic range. This has been demonstrated by monitoring the higher isotope mass peaks (first and second isotope) of a low intensity analyte. Furthermore, a practical application (veterinary drugs in bovine kidney) has been investigated with the proposed customized scan. Analytes eluting within the retention time region of very intense matrix peaks (e.g. peptides) showed improved detectability when utilizing the customized scan. CONCLUSIONS The extension of the intrascan dynamic range by a customized scan is helpful when analyzing residues which happen to elute together with a dominating matrix peak or within a high ion abundance region (e.g. dead volume). Furthermore, this feature helps in the process of determining the elemental composition of compounds by permitting the investigation of low-abundance ions (e.g. belonging to the isotopic fine structure of the investigated compound).
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Kaufmann A, Walker S, Mol G. Product ion isotopologue pattern: A tool to improve the reliability of elemental composition elucidations of unknown compounds in complex matrices. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:791-799. [PMID: 26969920 DOI: 10.1002/rcm.7476] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/19/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Elucidation of the elemental compositions of unknown compounds (e.g., in metabolomics) generally relies on the availability of accurate masses and isotopic ratios. This study focuses on the information provided by the abundance ratio within a product ion pair (monoisotopic versus the first isotopic peak) when isolating and fragmenting the first isotopic ion (first isotopic mass spectrum) of the precursor. METHODS This process relies on the capability of the quadrupole within the Q Orbitrap instrument to isolate a very narrow mass window. Selecting only the first isotopic peak (first isotopic mass spectrum) leads to the observation of a unique product ion pair. The lighter ion within such an isotopologue pair is monoisotopic, while the heavier ion contains a single carbon isotope. The observed abundance ratio is governed by the percentage of carbon atoms lost during the fragmentation and can be described by a hypergeometric distribution. RESULTS The observed carbon isotopologue abundance ratio (product ion isotopologue pattern) gives reliable information regarding the percentage of carbon atoms lost in the fragmentation process. It therefore facilitates the elucidation of the involved precursor and product ions. Unlike conventional isotopic abundances, the product ion isotopologue pattern is hardly affected by isobaric interferences. Furthermore, the appearance of these pairs greatly aids in cleaning up a 'matrix-contaminated' product ion spectrum. CONCLUSIONS The product ion isotopologue pattern is a valuable tool for structural elucidation. It increases confidence in results and permits structural elucidations for heavier ions. This tool is also very useful in elucidating the elemental composition of product ions. Such information is highly valued in the field of multi-residue analysis, where the accurate mass of product ions is required for the confirmation process. Copyright © 2016 John Wiley & Sons, Ltd.
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Wolff S, Groseth A, Meyer B, Jackson D, Strecker T, Kaufmann A, Becker S. The New World arenavirus Tacaribe virus induces caspase-dependent apoptosis in infected cells. J Gen Virol 2016; 97:855-866. [PMID: 26769540 DOI: 10.1099/jgv.0.000403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Arenaviridae is a diverse and growing family of viruses that already includes more than 25 distinct species. While some of these viruses have a significant impact on public health, others appear to be non-pathogenic. At present little is known about the host cell responses to infection with different arenaviruses, particularly those found in the New World; however, apoptosis is known to play an important role in controlling infection of many viruses. Here we show that infection with Tacaribe virus (TCRV), which is widely considered the prototype for non-pathogenic arenaviruses, leads to stronger induction of apoptosis than does infection with its human-pathogenic relative Junín virus. TCRV-induced apoptosis occurred in several cell types during late stages of infection and was shown to be caspase-dependent, involving the activation of caspases 3, 7, 8 and 9. Further, UV-inactivated TCRV did not induce apoptosis, indicating that the activation of this process is dependent on active viral replication/transcription. Interestingly, when apoptosis was inhibited, growth of TCRV was not enhanced, indicating that apoptosis does not have a direct negative effect on TCRV infection in vitro. Taken together, our data identify and characterize an important virus-host cell interaction of the prototypic, non-pathogenic arenavirus TCRV, which provides important insight into the growing field of arenavirus research aimed at better understanding the diversity in responses to different arenavirus infections and their functional consequences.
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Hecker A, Küllmar M, Wilker S, Richter K, Zakrzewicz A, Atanasova S, Mathes V, Timm T, Lerner S, Klein J, Kaufmann A, Bauer S, Padberg W, Kummer W, Janciauskiene S, Fronius M, Schweda EKH, Lochnit G, Grau V. Phosphocholine-Modified Macromolecules and Canonical Nicotinic Agonists Inhibit ATP-Induced IL-1β Release. THE JOURNAL OF IMMUNOLOGY 2015. [PMID: 26202987 DOI: 10.4049/jimmunol.1400974] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
IL-1β is a potent proinflammatory cytokine of the innate immune system that is involved in host defense against infection. However, increased production of IL-1β plays a pathogenic role in various inflammatory diseases, such as rheumatoid arthritis, gout, sepsis, stroke, and transplant rejection. To prevent detrimental collateral damage, IL-1β release is tightly controlled and typically requires two consecutive danger signals. LPS from Gram-negative bacteria is a prototypical first signal inducing pro-IL-1β synthesis, whereas extracellular ATP is a typical second signal sensed by the ATP receptor P2X7 that triggers activation of the NLRP3-containing inflammasome, proteolytic cleavage of pro-IL-1β by caspase-1, and release of mature IL-1β. Mechanisms controlling IL-1β release, even in the presence of both danger signals, are needed to protect from collateral damage and are of therapeutic interest. In this article, we show that acetylcholine, choline, phosphocholine, phosphocholine-modified LPS from Haemophilus influenzae, and phosphocholine-modified protein efficiently inhibit ATP-mediated IL-1β release in human and rat monocytes via nicotinic acetylcholine receptors containing subunits α7, α9, and/or α10. Of note, we identify receptors for phosphocholine-modified macromolecules that are synthesized by microbes and eukaryotic parasites and are well-known modulators of the immune system. Our data suggest that an endogenous anti-inflammatory cholinergic control mechanism effectively controls ATP-mediated release of IL-1β and that the same mechanism is used by symbionts and misused by parasites to evade innate immune responses of the host.
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Janko M, Spiegl B, Kaufmann A, Lucyshyn T, Holzer C. Weld line improvement of short fiber reinforced thermoplastics with a movable flow obstacle. J Appl Polym Sci 2015. [DOI: 10.1002/app.42025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Jung S, von Thülen T, Laukemper V, Pigisch S, Hangel D, Wagner H, Kaufmann A, Bauer S. A single naturally occurring 2'-O-methylation converts a TLR7- and TLR8-activating RNA into a TLR8-specific ligand. PLoS One 2015; 10:e0120498. [PMID: 25785446 PMCID: PMC4364935 DOI: 10.1371/journal.pone.0120498] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/23/2015] [Indexed: 12/20/2022] Open
Abstract
TLR7 and TLR8 recognize RNA from pathogens and lead to subsequent immune stimulation. Here we demonstrate that a single naturally occurring 2’-O-methylation within a synthetic 18s rRNA derived RNA sequence prevents IFN-α production, however secretion of proinflammatory cytokines such as IL-6 is not impaired. By analysing TLR-deficient plasmacytoid dendritic cells and performing HEK293 genetic complementation assays we could demonstrate that the single 2’-O-methylation containing RNA still activated TLR8 but not TLR7. Therefore this specific 2’-O-ribose methylation in rRNA converts a TLR7 / TLR8 ligand to an exclusively TLR8-specific ligand. Interestingly, other modifications at this position such as 2’-O-deoxy or 2’-fluoro had no strong modulating effect on TLR7 or TLR8 activation suggesting an important role of 2’-O-methylation for shaping differential TLR7 or TLR8 activation.
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Tinhofer I, Jöhrens K, Keilholz U, Kaufmann A, Lehmann A, Weichert W, Stenzinger A, Stromberger C, Klinghammer K, Becker ET, Dommerich S, Stölzel K, Hofmann V, Hildebrandt B, Moser L, Ervens J, Böttcher A, Albers A, Stabenow R, Reinecke A, Budach V, Hoffmeister B, Raguse J. Contribution of human papilloma virus to the incidence of squamous cell carcinoma of the head and neck in a European population with high smoking prevalence. Eur J Cancer 2015; 51:514-521. [DOI: 10.1016/j.ejca.2014.12.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 12/20/2014] [Indexed: 11/24/2022]
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Kaufmann A, Butcher P, Maden K, Walker S, Widmer M. Determination of nitrofuran and chloramphenicol residues by high resolution mass spectrometry versus tandem quadrupole mass spectrometry. Anal Chim Acta 2015; 862:41-52. [DOI: 10.1016/j.aca.2014.12.036] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
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Rämö P, Drewek A, Arrieumerlou C, Beerenwinkel N, Ben-Tekaya H, Cardel B, Casanova A, Conde-Alvarez R, Cossart P, Csúcs G, Eicher S, Emmenlauer M, Greber U, Hardt WD, Helenius A, Kasper C, Kaufmann A, Kreibich S, Kühbacher A, Kunszt P, Low SH, Mercer J, Mudrak D, Muntwiler S, Pelkmans L, Pizarro-Cerdá J, Podvinec M, Pujadas E, Rinn B, Rouilly V, Schmich F, Siebourg-Polster J, Snijder B, Stebler M, Studer G, Szczurek E, Truttmann M, von Mering C, Vonderheit A, Yakimovich A, Bühlmann P, Dehio C. Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC Genomics 2014; 15:1162. [PMID: 25534632 PMCID: PMC4326433 DOI: 10.1186/1471-2164-15-1162] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/12/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries. RESULTS We show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied. CONCLUSIONS Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
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Gross G, Becker N, Brockmeyer N, Esser S, Freitag U, Gebhardt M, Gissmann L, Hillemanns P, Grundhewer H, Ikenberg H, Jessen H, Kaufmann A, Klug S, Klussmann J, Nast A, Pathirana D, Petry K, Pfister H, Röllinghof U, Schneede P, Schneider A, Selka E, Singer S, Smola S, Sporbeck B, von Knebel Doeberitz M, Wutzler P. Impfprävention HPV-assoziierter Neoplasien. Laryngorhinootologie 2014; 93:848-56. [DOI: 10.1055/s-0034-1382013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kaufmann A. Combining UHPLC and high-resolution MS: A viable approach for the analysis of complex samples? Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.06.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Kaufmann A, Butcher P, Maden K, Walker S, Widmer M. Reliability of veterinary drug residue confirmation: high resolution mass spectrometry versus tandem mass spectrometry. Anal Chim Acta 2014; 856:54-67. [PMID: 25542358 DOI: 10.1016/j.aca.2014.11.034] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/10/2014] [Accepted: 11/25/2014] [Indexed: 11/19/2022]
Abstract
Confirmation of suspected residues has been a long time domain of tandem triple quadrupole mass spectrometry (QqQ). The currently most widely used confirmation strategy relies on the use of two selected reaction monitoring signals (SRM). The details of this confirmation procedure are described in detail in the Commission Decision 93/256/EC (CD). On the other hand, high resolution mass spectrometry (HRMS) is nowadays increasingly used for trace analysis. Yet its utility for confirmatory purposes has not been well explored and utilized, since established confirmation strategies like the CD do not yet include rules for modern HRMS technologies. It is the focus of this paper to evaluate the likelihood of false positive and false negative confirmation results, when using a variety of HRMS based measurement modes as compared to conventional QqQ mass spectrometry. The experimental strategy relies on the chromatographic separation of a complex blank sample (bovine liver extract) and the subsequent monitoring of a number of dummy transitions respectively dummy accurate masses. The term "dummy" refers to precursor and derived product ions (based on a realistic neutral loss) whose elemental compositions (CxHyNzOdCle) were produced by a random number generator. Monitoring a large number of such hypothetical SRM's, or accurate masses inevitably produces a number of mass traces containing chromatographic peaks (false detects) which are caused by eluting matrix compounds. The number and intensity of these peaks were recorded and standardized to permit a comparison among the two employed MS technologies. QqQ performance (compounds which happen to produce a response in two SRM traces at identical retention time) was compared with a number of different HRMS(1) and HRMS(2) detection based modes. A HRMS confirmation criterion based on two full scans (an unfragmented and an all ion fragmented) was proposed. Compared to the CD criteria, a significantly lower probability of false positive and false negative findings is obtained by utilizing this criterion.
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Schwarz T, Spaczynski M, Kaufmann A, Wysocki J, Gałaj A, Schulze K, Suryakiran P, Thomas F, Descamps D. Persistence of immune responses to the HPV-16/18 AS04-adjuvanted vaccine in women aged 15-55 years and first-time modelling of antibody responses in mature women: results from an open-label 6-year follow-up study. BJOG 2014; 122:107-18. [PMID: 25208608 PMCID: PMC4489326 DOI: 10.1111/1471-0528.13070] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Evaluation of the long-term HPV-16/18 AS04-adjuvanted vaccine immunogenicity persistence in women. DESIGN Multicentre, open-label, long-term follow-up (NCT00947115) of a primary phase-III study (NCT00196937). SETTING Six centres in Germany and Poland. POPULATION 488 healthy women (aged 15-55 years, age-stratified into groups: 15-25, 26-45, and 46-55 years) who received three vaccine doses in the primary study. METHODS Immune responses were evaluated in serum and cervicovaginal secretion (CVS) samples 6 years after dose 1. Anti-HPV-16/18 geometric mean titres (GMTs) were measured by enzyme-linked immunosorbent assay (ELISA), and were used to fit the modified power-law and piecewise models, predicting long-term immunogenicity. Serious adverse events (SAEs) were recorded. MAIN OUTCOME MEASURES Anti-HPV-16/18 seropositivity rates and GMTs 6 years after dose 1. RESULTS At 6 years after dose 1, all women were seropositive for anti-HPV-16 and ≥97% were seropositive for anti-HPV-18 antibodies. GMTs ranged from 277.7 to 1344.6 EU/ml, and from 97.6 to 438.2 EU/ml, for anti-HPV-16 and anti-HPV-18, respectively. In all age groups, GMTs were higher (anti-HPV-16, 9.3-45.1-fold; anti-HPV-18, 4.3-19.4-fold) than levels associated with natural infection (29.8 EU/ml). A strong correlation between serum and CVS anti-HPV-16/18 levels was observed, with correlation coefficients of 0.81-0.96 (anti-HPV-16) and 0.69-0.84 (anti-HPV-18). Exploratory modelling based on the 6-year data predicted vaccine-induced anti-HPV-16/18 levels above natural infection levels for at least 20 years, except for anti-HPV-18 in the older age group (piecewise model). One vaccine-related and two fatal SAEs were reported. CONCLUSIONS At 6 years after vaccination, immune responses induced by the HPV-16/18 AS04-adjuvanted vaccine were sustained in all age groups.
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Karsenty G, Baverstock R, Carlson K, Diaz DC, Cruz F, Dmochowski R, Fulford S, Giannantoni A, Heesakkers J, Kaufmann A, Peyrat L, Thavaseelan J, Dasgupta P. Technical aspects of botulinum toxin type A injection in the bladder to treat urinary incontinence: reviewing the procedure. Int J Clin Pract 2014; 68:731-42. [PMID: 24472109 DOI: 10.1111/ijcp.12360] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
AIMS Standardise the injection technique with botulinum toxin type A (BoNT A) in the bladder of patients with overactive bladder (OAB) [idiopathic overactive bladder (iOAB) or neurogenic overactive bladder (nOAB) with urinary incontinence], using a literature review and a survey of an International expert panel. METHODS PubMed literature searches of BoNT A in adults with iOAB/nOAB together with a survey of 13 experts from 10 countries. RESULTS Data from 21 articles and completed questionnaires were collated. The procedure can be carried out in an out-/inpatient setting. Dose used in clinical studies vs. clinical practice was 300 and 200 U for nOAB and 200 and 100 U for iOAB. Recent studies have also demonstrated that there are no clinically relevant benefits between 100 and 150 U in iOAB or between 300 and 200 U in nOAB, though adverse effects are increased with higher doses. Usually, 30 sites for nOAB (range: 6.7-10 U/ml) and 20-30 sites for iOAB (range: 5-10 U/ml) are injected in clinical studies vs. 20-30 sites of 1 ml/injection for 200 U in nOAB and 10-20 sites of 0.5-1 ml/injection for 100 U in iOAB in clinical practice. BoNT A is usually injected directly into the detrusor, sparing the trigone. Flexible or rigid cystoscopes are used. The needle should be typically 22-27 gauge and 4 mm in length and should have a stopper to avoid any leakage or perforation of the bladder wall while ensuring a targeted injection. CONCLUSION Based on the literature and survey analysis, recommendations are proposed for the standardisation of the injection procedure.
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Patterson MJ, Sutton RE, Forrest I, Sharrock R, Lane M, Kaufmann A, O'Donnell R, Edmondson RJ, Wilson BT, Curtin NJ. Assessing the function of homologous recombination DNA repair in malignant pleural effusion (MPE) samples. Br J Cancer 2014; 111:94-100. [PMID: 24867690 PMCID: PMC4090730 DOI: 10.1038/bjc.2014.261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/20/2014] [Accepted: 04/23/2014] [Indexed: 12/02/2022] Open
Abstract
Background: Patients with malignant pleural effusions (MPEs) generally have advanced disease with poor survival and few therapeutic options. Cells within MPEs may be used to stratify patients for targeted therapy. Targeted therapy with poly(ADP ribose) polymerase inhibitors (PARPi) depends on identifying homologous recombination DNA repair (HRR)-defective cancer cells. We aimed to determine the feasibility of assaying HRR status in MPE cells. Methods: A total of 15 MPE samples were collected from consenting patients with non-small-cell lung cancer (NSCLC), mesothelioma and ovarian and breast cancer. Primary cultures were confirmed as epithelial by pancytokeratin, and HRR status was determined by the detection of γH2AX and RAD51 foci following a 24-h exposure to rucaparib, by immunofluorescence microscopy. Massively parallel next-generation sequencing of DNA repair genes was performed on cultured MPE cells. Results: From 15 MPE samples, 13 cultures were successfully established, with HRR function successfully determined in 12 cultures. Four samples – three NSCLC and one mesothelioma – were HRR defective and eight samples – one NSCLC, one mesothelioma, one sarcomatoid, one breast and four ovarian cancers – were HRR functional. No mutations in DNA repair genes were associated with HRR status, but there was probable loss of heterozygosity of FANCG, RPA1 and PARP1. Conclusions: HRR function can be successfully detected in MPE cells demonstrating the potential to stratify patients for targeted therapy with PARPi.
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