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The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

Jurgen F. Doreleijers, Wim F. Vranken, Christopher Schulte, Jundong Lin, Jonathan R. Wedell, Christopher J. Penkett, Geerten W. Vuister, Gert Vriend, John L. Markley, Eldon L. Ulrich
2009 Journal of Biomolecular NMR  
(f) Last but not least, the NRG data should be integrated with the main BMRB data on chemical shifts that will soon be mandatory for PDB submission.  ... 
doi:10.1007/s10858-009-9378-z pmid:19809795 pmcid:PMC2777234 fatcat:gdnkbqlzivebvfy3s6kksbuvem

NEW BIOINFORMATICS RESOURCES FOR METABOLOMICS

JOHN L. MARKLEY, MARK E. ANDERSON, QIU CUI, HAMID R. EGHBALNIA, IAN A. LEWIS, ADRIAN D. HEGEMAN, JING LI, CHRISTOPHER F. SCHULTE, MICHAEL R. SUSSMAN, WILLIAM M. WESTLER, ELDON L. ULRICH, ZSOLT ZOLNAI
2006 Biocomputing 2007  
We recently developed two databases and a laboratory information system as resources for the metabolomics community. These tools are freely available and are intended to ease data analysis in both MS and NMR based metabolomics studies. The first database is a metabolomics extension to the BioMagResBank (BMRB, http://www.bmrb.wisc.edu), which currently contains experimental spectral data on over 270 pure compounds. Each small molecule entry consists of five or six one-and two-dimensional NMR
more » ... sets, along with information about the source of the compound, solution conditions, data collection protocol and the NMR pulse sequences. Users have free access to peak lists, spectra, and original time-domain data. The BMRB database can be queried by name, monoisotopic mass and chemical shift. We are currently developing a deposition tool that will enable people in the community to add their own data to this resource. Our second database, the Madison Metabolomics Consortium Database (MMCD, available from http://mmcd.nmrfam.wisc.edu/), is a hub for information on over 10,000 metabolites. These data were collected from a variety of sites with an emphasis on metabolites found in Arabidopsis. The MMC database supports extensive search functions and allows users to make bulk queries using experimental MS and/or NMR data. In addition to these databases, we have developed a new module for the Sesame laboratory information management system (http://www.sesame.wisc.edu) that captures all of the experimental protocols, background information, and experimental data associated with metabolomics samples. Sesame was designed to help coordinate research efforts in laboratories with high sample throughput and multiple investigators and to track all of the actions that have taken place in a particular study.
doi:10.1142/9789812772435_0016 fatcat:dywllrjv3jbszfnys5petgnxtq

Bond behaviour of thin concrete overlays for maintenance of concrete pavements

Rolf Breitenbücher, Christoph Schulte-Schrepping, Sebastian Kunz, M.G. Alexander, H. Beushausen, F. Dehn, P. Moyo
2018 MATEC Web of Conferences  
Concrete pavements are exposed to a number of stresses during their service life, mostly resulting from traffic and climate conditions. In consideration of the continuously rising traffic volume, the durability requirements of concrete pavements become more and more significant. In this context, maintenance and repair become increasingly important. Small-scale repairs like spalling at edges up to the replacement of whole slabs are proven in several cases. In contrast, largescale maintenance
more » ... niques for partial repairs of whole pavement sections are not available, yet. If the upper layer concrete is deteriorated, while the lower layer and the base course are still intact, the whole pavement needs to be replaced, due to a lack of alternatives. Therefore new maintenance techniques like the application of concrete overlays are needed for an economic rehabilitation and the prevention of an unnecessarily long traffic disruption by time-consuming maintenance of complete pavements. The relevant questions how a durable bond between old and new concrete can be ensured and which parameters affect this bond, were investigated in representative studies on large-scale concrete beams with a thin concrete overlay on existing concrete.
doi:10.1051/matecconf/201819908005 fatcat:w5io25p6unhk7dgxk7po7ddmpy

Oregovomab Maintenance Monoimmunotherapy Does Not Improve Outcomes in Advanced Ovarian Cancer

Jonathan Berek, Peyton Taylor, William McGuire, L. Mary Smith, Birgit Schultes, Christopher F. Nicodemus
2009 Journal of Clinical Oncology  
Mary Smith, Birgit Schultes, and Christopher F.  ...  Mary Smith, Birgit Schultes, Christopher F. Nicodemus 12.  ... 
doi:10.1200/jco.2008.17.8400 pmid:19075271 fatcat:lyqmvsfgofderpbbywetvjs5gy

Microbiomarkers in inflammatory bowel diseases: caveats come with caviar

Felix Sommer, Malte Christoph Rühlemann, Corinna Bang, Marc Höppner, Ateequr Rehman, Christoph Kaleta, Phillippe Schmitt-Kopplin, Astrid Dempfle, Stephan Weidinger, Eva Ellinghaus, Susanne Krauss-Etschmann, Dirk Schmidt-Arras (+10 others)
2017 Gut  
Pascal et al replicate the findings of Gevers et al 16 that F. prausnitzii is reduced/absent in patients with CD and that patients have a higher abundance of Escherichia and Fusobacterium.  ... 
doi:10.1136/gutjnl-2016-313678 pmid:28733278 pmcid:PMC5595102 fatcat:z4wb6mn2rvcp5dy5cqkzsqe5ce

Wilms Tumor 1bdefines a wound-specific sheath cell subpopulation associated with notochord repair [article]

Juan Carlos Lopez-Baez, Zhiqiang Zeng, Witold Rybski, Leonie F. A. Huitema, Alessandro Brombin, Rodney M. Dale, Koichi Kawakami, Christoph Englert, Stefan Schulte-Merker, Nicholas D. Hastie, E. Elizabeth Patton
2017 bioRxiv   pre-print
, A., Schulte-Merker, S,. and Witten, P.E. (2011) Not all bones are created equal -387 using zebrafish and other teleost species in osteogenesis research.  ...  (f) Confocal imaging highlights the overlapping presence of bone (alizarin red stained) and wt1b:GFP cells at the wound in 18 dpi larvae (arrow). n >10; experimental replicates = 3.  ... 
doi:10.1101/172288 fatcat:fmrlzlloofgyxljkntzaijmn2a

Targeting HER2/neu with a fully human IgE to harness the allergic reaction against cancer cells

Tracy R. Daniels, Richard K. Leuchter, Rafaela Quintero, Gustavo Helguera, José A. Rodríguez, Otoniel Martínez-Maza, Birgit C. Schultes, Christopher F. Nicodemus, Manuel L. Penichet
2011 Cancer Immunology and Immunotherapy  
© Springer-Verlag 2011 Breast and ovarian cancer are two of the leading causes of cancer deaths among women in the United States. Overexpression of the HER2/neu oncoprotein has been reported in patients affected with breast and ovarian cancers, and is associated with poor prognosis. To develop a novel targeted therapy for HER2/neu expressing tumors, we have constructed a fully human IgE with the variable regions of the scFv C6MH3-B1 specific for HER2/neu. This antibody was expressed in murine
more » ... eloma cells and was properly assembled and secreted. The Fc region of this antibody triggers in vitro degranulation of rat basophilic cells expressing human FcεRI (RBL SX-38) in the presence of murine mammary carcinoma cells that express human HER2/neu (D2F2/E2), but not the shed (soluble) antigen (ECD HER2 ) alone. This IgE is also capable of inducing passive cutaneous anaphylaxis in a human FcεRIα transgenic mouse model, in the presence of a crosslinking antibody, but not in the presence of soluble ECD HER2 . Additionally, IgE enhances antigen presentation in human dendritic cells and facilitates cross-priming, suggesting that the antibody is able to stimulate a secondary T-cell antitumor response. Furthermore, we show that this IgE significantly prolongs survival of human FcεRIα transgenic mice bearing D2F2/E2 tumors. We also report that the anti-HER2/neu IgE is well tolerated in a preliminary study conducted in Macaca fascicularis (cynomolgus) monkeys. In summary, our results suggest that this IgE should be further explored as a potential therapeutic against HER2/ neu overexpressing tumors, such as breast and ovarian cancers.
doi:10.1007/s00262-011-1150-z pmid:22127364 pmcid:PMC3719406 fatcat:ln4m5py66vhkdbq2x7i6vfurhy

Clozapine and COVID-19: The authors respond

Dan Siskind, William G. Honer, Scott Clark, Christoph U. Correll, Alkomiet Hasan, Oliver Howes, John M. Kane, Deanna L. Kelly, Robert Laitman, Jimmy Lee, James H. MacCabe, Nick Myles (+6 others)
2020 Journal of Psychiatry & Neuroscience  
doi:10.1503/jpn.2045302 pmid:32584530 pmcid:PMC7828928 fatcat:pv4qgqawq5f45mffoo5eab6dgu

A novel IgE antibody targeting the prostate-specific antigen as a potential prostate cancer therapy

Tracy R Daniels-Wells, Gustavo Helguera, Richard K Leuchter, Rafaela Quintero, Maggie Kozman, José A Rodríguez, Elizabeth Ortiz-Sánchez, Otoniel Martínez-Maza, Birgit C Schultes, Christopher F Nicodemus, Manuel L Penichet
2013 BMC Cancer  
Prostate cancer (PCa) is the second leading cause of cancer deaths in men in the United States. The prostate-specific antigen (PSA), often found at high levels in the serum of PCa patients, has been used as a marker for PCa detection and as a target of immunotherapy. The murine IgG1 monoclonal antibody AR47.47, specific for human PSA, has been shown to enhance antigen presentation by human dendritic cells and induce both CD4 and CD8 T-cell activation when complexed with PSA. In this study, we
more » ... plored the properties of a novel mouse/human chimeric anti-PSA IgE containing the variable regions of AR47.47 as a potential therapy for PCa. Our goal was to take advantage of the unique properties of IgE in order to trigger immune activation against PCa. Methods: Binding characteristics of the antibody were determined by ELISA and flow cytometry. In vitro degranulation was determined by the release of β-hexosaminidase from effector cells. In vivo degranulation was monitored in human FcεRIα transgenic mice using the passive cutaneous anaphylaxis assay. These mice were also used for a vaccination study to determine the in vivo anti-cancer effects of this antibody. Significant differences in survival were determined using the Log Rank test. In vitro T-cell activation was studied using human dendritic cells and autologous T cells. Results: The anti-PSA IgE, expressed in murine myeloma cells, is properly assembled and secreted, and binds the antigen and FcεRI. In addition, this antibody is capable of triggering effector cell degranulation in vitro and in vivo when artificially cross-linked, but not in the presence of the natural soluble antigen, suggesting that such an interaction will not trigger systemic anaphylaxis. Importantly, the anti-PSA IgE combined with PSA also triggers immune activation in vitro and in vivo and significantly prolongs the survival of human FcεRIα transgenic mice challenged with PSA-expressing tumors in a prophylactic vaccination setting. Conclusions: The anti-PSA IgE exhibits the expected biological properties and is capable of triggering immune activation and anti-tumor protection. Further studies on this antibody as a potential PCa therapy are warranted.
doi:10.1186/1471-2407-13-195 pmid:23594731 pmcid:PMC3651304 fatcat:p7dzxrt7yrchrhf6st3xuz7yv4

Randomized, Placebo-Controlled Study of Oregovomab for Consolidation of Clinical Remission in Patients With Advanced Ovarian Cancer

Jonathan S. Berek, Peyton T. Taylor, Alan Gordon, Mary J. Cunningham, Neil Finkler, James Orr, Saul Rivkin, Birgit C. Schultes, Theresa L. Whiteside, Christopher F. Nicodemus
2004 Journal of Clinical Oncology  
Schultes, Theresa L. Whiteside, and Christopher F.  ...  Schultes, Unither Pharmaceuticals; Christopher F. Nicodemus, Unither Pharmaceuticals. significant activity in advanced ovarian epithelial neoplasms. Ann Intern Med 111:273-279, 1989 21.  ... 
doi:10.1200/jco.2004.09.016 pmid:15337799 fatcat:ezy4rgjacbcvteyxb6sbrxyqba

Relationship Between Galectin-3 Levels and Mineralocorticoid Receptor Antagonist Use in Heart Failure: Analysis From HF-ACTION

Mona Fiuzat, Phillip J. Schulte, Michael Felker, Tariq Ahmad, Megan Neely, Kirkwood F. Adams, Mark P. Donahue, William E. Kraus, Ileana L. Piña, David J. Whellan, Christopher M. O'Connor
2014 Journal of Cardiac Failure  
Galectin-3 (Gal-3) is a marker of myocardial fibrosis, and elevated levels are associated with adverse outcomes. Mineralocorticoid receptor antagonists (MRAs) modulate cardiac fibrosis in heart failure (HF) patients and have been shown to improve long-term outcomes. We examined whether treatment effects from MRA use differed by Gal-3 levels in ambulatory heart failure patients enrolled in HF-ACTION. HF-ACTION was a randomized controlled trial of exercise training versus usual care in patients
more » ... th HF due to LV systolic dysfunction (New York Heart Association functional class II-IV, left ventricular ejection fraction ≤ 0.35, median follow-up 2.5 years). Galectin-3 was assessed at baseline in 895 patients. The end point was all-cause mortality or all-cause hospitalization (ACM+ACH); all-cause mortality (ACM) was a key secondary end point. A differential association of MRA use by increasing Gal-3 concentration was tested with the use of interaction terms in Cox proportional hazards models, adjusted for covariates previously identified in this cohort as well as age, sex, and race. Inverse propensity-weighted (IPW) methods were also used to assess this association. Approximately one-half (n = 401) of the patients were on an MRA. There was no significant interaction for the associations of Gal-3 levels and MRA use for either end point (adjusted interaction P = .76 for ACM+ACH; P = .26 for ACM). There was no evidence of improved outcomes for patients on an MRA compared with those not on MRA for either end point (hazard ratio [HR] 1.02, 95% confidence interval [CI] 0.85-1.23, P = .8; and HR = 1.15, 95% CI [0.82-1.61], P = .4; respectively). IPW analysis was consistent with the results of the adjusted analysis. Our study showed no evidence of interaction between Gal-3 and treatment effect of MRA. Whether biomarkers may be used to predict which patients may benefit from an mineralocorticoid receptor antagonist in HF requires further investigation.
doi:10.1016/j.cardfail.2013.11.011 pmid:24304938 pmcid:PMC3930443 fatcat:qhi5ijwnrrfbhfhnkdweyfjeki

Wilms Tumor 1b defines a wound-specific sheath cell subpopulation associated with notochord repair

Juan Carlos Lopez-Baez, Daniel J Simpson, Laura LLeras Forero, Zhiqiang Zeng, Hannah Brunsdon, Angela Salzano, Alessandro Brombin, Cameron Wyatt, Witold Rybski, Leonie F A Huitema, Rodney M Dale, Koichi Kawakami (+5 others)
2018 eLife  
(f, g) Results of quantitative real-time PCR (qRT-PCR) of mgp and sox9b.  ...  (f) WT1 and p53 shared gene targets DOI: https://doi.org/10.7554/eLife.30657.023 . Supplementary file 2. List of primers used for qRT-PCR and genotyping.  ... 
doi:10.7554/elife.30657 pmid:29405914 pmcid:PMC5811212 fatcat:fonydr2j6jeilpoelqmhzlogle

Torsemide Versus Furosemide in Patients With Acute Heart Failure (from the ASCEND-HF Trial)

Robert J. Mentz, Vic Hasselblad, Adam D. DeVore, Marco Metra, Adriaan A. Voors, Paul W. Armstrong, Justin A. Ezekowitz, W.H. Wilson Tang, Phillip J. Schulte, Kevin J. Anstrom, Adrian F. Hernandez, Eric J. Velazquez (+1 others)
2016 American Journal of Cardiology  
Furosemide is the most commonly used loop diuretic in heart failure (HF) patients despite data suggesting potential pharmacologic and anti-fibrotic benefits with torsemide. We investigated HF patients in ASCEND-HF who were discharged on either torsemide or furosemide. Using inverse probability weighting to account for the non-random selection of diuretic, we assessed the relation between choice of diuretic at discharge with 30-day mortality or HF hospitalization and 180-day mortality. Of 7,141
more » ... atients in the trial, 4,177 patients were included in this analysis, of which 87% (n=3,620) received furosemide and 13% (n=557) received torsemide. Torsemide-treated patients had lower ejection fraction and blood pressure, and higher creatinine and natriuretic peptide level compared with furosemide. Torsemide was associated with similar outcomes on unadjusted analysis and nominally lower events on adjusted analysis [30-day mortality/HF hospitalization OR 0.89, 95% CI: 0.62-1.29, P=0.55 and 180-day mortality HR 0.86, 95% CI: 0.63-1.19, P=0.37]. In conclusion, these data are hypothesis-generating and randomized comparative-effectiveness trials are needed to investigate the optimal diuretic choice.
doi:10.1016/j.amjcard.2015.10.059 pmid:26704029 pmcid:PMC4718787 fatcat:frw4juguffcj7ipdajet3spk5a

Consensus statement on the use of clozapine during the COVID-19 pandemic

Dan Siskind, William G Honer, Scott Clark, Christoph U Correll, Alkomiet Hasan, Oliver Howes, John M Kane, Deanna L Kelly, Robert Laitman, Jimmy Lee, James H MacCabe, Nick Myles (+6 others)
2020 Journal of Psychiatry & Neuroscience  
He has provided expert testimony for Janssen and Otsuka. He served on a data safety monitoring board for Lundbeck, Rovi, Supernus and Teva. He has received grant support from the Berlin Institute of health, Janssen, the National Institute of Mental Health, Patient Centered Outcomes Research Institute, Takeda and the Thrasher Foundation. He has re-ceived royalties from UpToDate and is a stock option holder of LB Pharma. A. Hasan has been on the advisory boards and has received speaker fees from
more » ... anssen, Lundbeck and Otsuka. O. Howes reports receiving speaker fees, participating on advisory boards, and/or receiving investigator-initiated funding from manufacturers of antipsychotics, including clozapine. J. Kane declares consulting fees/
doi:10.1503/jpn.200061 pmid:32297722 pmcid:PMC7828973 fatcat:neff2t2efff37peipo5bbwyx7e

Epicutaneous sensitization results in IgE-dependent intestinal mast cell expansion and food-induced anaphylaxis

Lisa M. Bartnikas, Michael F. Gurish, Oliver T. Burton, Sabine Leisten, Erin Janssen, Hans C. Oettgen, Jacqueline Beaupré, Christopher N. Lewis, K. Frank Austen, Stephanie Schulte, Jason L. Hornick, Raif S. Geha (+1 others)
2013 Journal of Allergy and Clinical Immunology  
E, F. Core body temperature after i.v. challenge. n/ group= 10-12 in A-D and 4 in E, F. Columns and bars: mean and SEM. ** P<0.01, *** P <0.001. ns = not significant.  ... 
doi:10.1016/j.jaci.2012.11.032 pmid:23374269 pmcid:PMC3587010 fatcat:uj3jpmqeazgbhjnbulr5f4tefq
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