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Article ; Online: Re: Decision Support with the Personal Patient Profile-Prostate: A Multicenter Randomized Trial: D. L. Berry, F. Hong, T. M. Blonquist, B. Halpenny, C. P. Filson, V. A. Master, M. G. Sanda, P. Chang, G. W. Chien, R. A. Jones, T. L. Krupski, S. Wolpin, L. Wilson, J. H. Hayes, Q.-D. Trinh, M. Sokoloff and P. Somayaji J Urol 2018;199:89-97.

Vickers, Andrew / Weber, Ryan

2018 Volume 199, Issue 6, Page(s) 1632–1633

MeSH term(s)	Humans ; Male ; Prostate
Language	English
Publishing date	2018-03-16
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	3176-8
ISSN	1527-3792 ; 0022-5347
ISSN (online)	1527-3792
ISSN	0022-5347
DOI	10.1016/j.juro.2017.12.064
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Ui VI Zs.91: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MO 331: Show issues

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Article: Mutations in Ig V(D)J genes are distributed asymmetrically and independently of the position of V(D)J.

Weber, J S / Berry, J / Manser, T / Claflin, J L

Journal of immunology (Baltimore, Md. : 1950)

1994 Volume 153, Issue 8, Page(s) 3594–3602

Abstract: ... genes, the 5' region of 14 to 21 mutant forms of three different V(D)J were sequenced. These were ... compared with a fourth V(D)J for which the flanking sequences of 10 mutant forms are known. The leader ... that: 1) The mutation frequency is distributed asymmetrically with respect to the V(D)J exon with skewing ...

Abstract	To study the distribution of somatic mutations in the DNA flanking the 5' side of rearranged Ig V genes, the 5' region of 14 to 21 mutant forms of three different V(D)J were sequenced. These were compared with a fourth V(D)J for which the flanking sequences of 10 mutant forms are known. The leader intron of these four V genes varied from 82 to 365 nucleotides in length. Analysis of the data showed that: 1) The mutation frequency is distributed asymmetrically with respect to the V(D)J exon with skewing in the 3' direction. 2) The distribution of mutations 5' of V(D)J seems to be related to the size of the leader intron. The significance of these findings for models of hypermutation is discussed.
MeSH term(s)	Animals ; Base Sequence ; DNA Primers/chemistry ; Gene Rearrangement, B-Lymphocyte, Heavy Chain ; Gene Rearrangement, B-Lymphocyte, Light Chain ; Genes, Immunoglobulin ; Immunoglobulin Heavy Chains/genetics ; Immunoglobulin Variable Region/genetics ; Immunoglobulin kappa-Chains/genetics ; Mice ; Molecular Sequence Data ; Mutation
Chemical Substances	DNA Primers ; Immunoglobulin Heavy Chains ; Immunoglobulin Variable Region ; Immunoglobulin kappa-Chains
Language	English
Publishing date	1994-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
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Ud II Zs.37: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MG 28: Show issues

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Book ; Thesis: Pulmonale Hypertonie und Nierentransplantation bei Kindern

Leyendecker, Jannik / Weber, Lutz T. / Stippel, Dirk

2020

Institution	Klinik und Poliklinik für Kinder- und Jugendmedizin
Author's details	vorgelegt von Jannik Leyendecker ; 1. Gutachter: Professor Dr. med. L.T. Weber, 2. Gutachter: Universitätsprofessor Dr. med. D. Stippel ; aus dem Zentrum für Kinder- und Jugendmedizin der Universität zu Köln, Klinik und Poliklinik für Kinder- und Jugendmedizin
Subject code	610
Language	German
Size	111 Seiten, Illustrationen, Diagramme
Publishing place	Köln
Publishing country	Germany
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Dissertation, Universität zu Köln, 2020
HBZ-ID	HT020671336
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2020 D 971	order for loan	Magazin

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Article ; Online: Competition between Water-Water Hydrogen Bonds and Water-π Bonds in Pyrene-Water Cluster Anions.

Salzmann, Heinrich / Rasmussen, Anne P / Eaves, Joel D / Weber, J Mathias

The journal of physical chemistry. A

2024 Volume 128, Issue 14, Page(s) 2772–2781

Abstract: We present infrared spectra and density functional theory calculations of hydrated pyrene anion clusters with up to four water molecules. The experimental spectra were acquired by using infrared Ar messenger photodissociation spectroscopy. Water ... ...

Abstract	We present infrared spectra and density functional theory calculations of hydrated pyrene anion clusters with up to four water molecules. The experimental spectra were acquired by using infrared Ar messenger photodissociation spectroscopy. Water molecules form clusters on the surface of the pyrene, forming hydrogen bonds with the π-system. The structures of the water clusters and their interaction with the π-system are encoded in OH stretching vibrational modes. We find that the interactions between water molecules are stronger than the interactions between water molecules and the π-system. While all clusters show multiple conformers, three- and four-membered rings are the lowest energy structures in the larger hydrates.
Language	English
Publishing date	2024-04-02
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.4c00997
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Article ; Online: Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation.

Yu, Wenbo / Weber, David J / MacKerell, Alexander D

Journal of chemical theory and computation

2023 Volume 19, Issue 10, Page(s) 3007–3021

Abstract: Covalent drug design is an important component in drug discovery. Traditional drugs interact with their target in a reversible equilibrium, while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with ... ...

Abstract	Covalent drug design is an important component in drug discovery. Traditional drugs interact with their target in a reversible equilibrium, while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with targeted residues and thus may offer a more effective therapeutic approach. To facilitate the design of this class of ligands, computational methods can be used to help identify reactive nucleophilic residues, frequently cysteines, on a target protein for covalent binding, to test various warhead groups for their potential reactivities, and to predict noncovalent contributions to binding that can facilitate drug-target interactions that are important for binding specificity. To further aid covalent drug design, we extended a functional group mapping approach based on explicit solvent all-atom molecular simulations (SILCS: site identification by ligand competitive saturation) that intrinsically considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. Through docking of a library of representative warhead fragments using SILCS-Monte Carlo (SILCS-MC), reactive cysteines can be correctly identified for proteins being tested. Furthermore, a machine learning model was trained to quantify the effectiveness of various warhead groups for proteins using metrics from SILCS-MC as well as experimental model compound warhead reactivity data. The ability to rank covalent molecular binders with similar warheads using SILCS ligand grid free energy (LGFE) ranking was also tested for several proteins. Based on these tools, an integrated SILCS-based workflow was developed, named SILCS-Covalent, which can both qualitatively and quantitatively inform covalent drug discovery.
MeSH term(s)	Ligands ; Workflow ; Proteins/chemistry ; Binding Sites ; Drug Design
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2023-04-28
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.3c00232
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Article ; Online: Water-Hydrocarbon Interactions in Anionic Pyrene Monohydrate.

LeMessurier, Natalie / Salzmann, Heinrich / Leversee, River / Weber, J Mathias / Eaves, Joel D

The journal of physical chemistry. B

2024 Volume 128, Issue 13, Page(s) 3200–3210

Abstract: Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the ... ...

Abstract	Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to the water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond time scales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the line width and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.
Language	English
Publishing date	2024-03-25
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c07777
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Article ; Online: Author Correction: A pilot study on the efficacy of GPT-4 in providing orthopedic treatment recommendations from MRI reports.

Truhn, Daniel / Weber, Christian D / Braun, Benedikt J / Bressem, Keno / Kather, Jakob N / Kuhl, Christiane / Nebelung, Sven

Scientific reports

2024 Volume 14, Issue 1, Page(s) 5431

Language	English
Publishing date	2024-03-05
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-56029-x
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Article ; Online: Boron coordination change in barium borate melts and glasses and its contribution to configurational heat capacity, entropy, and fragility.

Alderman, O L G / Benmore, C J / Holland, D / Weber, J K R

The Journal of chemical physics

2023 Volume 158, Issue 22

Abstract: ... of isomerization between sp2 and sp3 boron. The results for BaB4O7, ΔH = 22(3) kJ mol-1 boron, ΔS = 19(2) J mol-1 ... boron K-1, agree quantitatively with those found previously for Na2B4O7. Analytical expressions for N4(J ... T) and associated configurational heat capacity, CPconf(J, T), and entropy, Sconf(J, T ...

Abstract	High-energy x-ray diffraction from molten and glassy BaB2O4 and BaB4O7 has been performed using aerodynamic levitation and laser heating over a wide range of temperatures. Remarkably, even in the presence of a heavy metal modifier dominating x-ray scattering, it was possible to extract accurate values for the tetrahedral, sp3, boron fraction, N4, which declines with increasing temperature, using bond valence-based mapping from the measured mean B-O bond lengths while accounting for vibrational thermal expansion. These are used within a boron-coordination-change model to extract enthalpies, ΔH, and entropies, ΔS, of isomerization between sp2 and sp3 boron. The results for BaB4O7, ΔH = 22(3) kJ mol-1 boron, ΔS = 19(2) J mol-1 boron K-1, agree quantitatively with those found previously for Na2B4O7. Analytical expressions for N4(J, T) and associated configurational heat capacity, CPconf(J, T), and entropy, Sconf(J, T), contributions are extended to cover a wide composition range 0 ≤ J = BaO/B2O3 ≤ 3 using a model for ΔH(J) and ΔS(J) derived empirically for lithium borates. Maxima in the CPconf(J, Tg) and fragility index contributions are thereby predicted for J ≲ 1, higher than the maximum observed and predicted in N4(J, Tg) at J ≃ 0.6. We discuss the utility of the boron-coordination-change isomerization model in the context of borate liquids containing other modifiers and the prospect of neutron diffraction to aid in empirical determinations of modifier-dependent effects, illustrated by new neutron diffraction data on Ba11B4O7 glass, its well-known α-polymorph, and lesser-known δ-phase.
MeSH term(s)	Entropy ; Borates/chemistry ; Boron ; Barium ; Hot Temperature
Chemical Substances	Borates ; Boron (N9E3X5056Q) ; Barium (24GP945V5T)
Language	English
Publishing date	2023-06-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0153282
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Article ; Online: Distinguishing cells using electro-acoustic spinning.

Saghaei, Tayebeh / Weber, Andreas / Reimhult, Erik / van Oostrum, Peter D J

Scientific reports

2023 Volume 13, Issue 1, Page(s) 20466

Abstract: Many diseases, including cancer and covid, result in altered mechanical and electric properties of the affected cells. These changes were proposed as disease markers. Current methods to characterize such changes either provide very limited information on ...

Abstract	Many diseases, including cancer and covid, result in altered mechanical and electric properties of the affected cells. These changes were proposed as disease markers. Current methods to characterize such changes either provide very limited information on many cells or have extremely low throughput. We introduce electro-acoustic spinning (EAS). Cells were found to spin in combined non-rotating AC electric and acoustic fields. The rotation velocity in EAS depends critically on a cell's electrical and mechanical properties. In contrast to existing methods, the rotation is uniform in the field of view and hundreds of cells can be characterized simultaneously. We demonstrate that EAS can distinguish cells with only minor differences in electric and mechanical properties, including differences in age or the number of passages.
MeSH term(s)	Electricity ; Rotation ; Acoustics ; Acoustic Stimulation ; Electric Stimulation ; Cochlear Implants ; Cochlear Implantation
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-46550-w
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Article ; Online: Computer-Aided Drug Design: An Update.

Yu, Wenbo / Weber, David J / MacKerell, Alexander D

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2601, Page(s) 123–152

Abstract: Computer-aided drug design (CADD) approaches are playing an increasingly important role in understanding the fundamentals of ligand-receptor interactions and helping medicinal chemists design therapeutics. About 5 years ago, we presented a chapter ... ...

Abstract	Computer-aided drug design (CADD) approaches are playing an increasingly important role in understanding the fundamentals of ligand-receptor interactions and helping medicinal chemists design therapeutics. About 5 years ago, we presented a chapter devoted to an overview of CADD methods and covered typical CADD protocols including structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches that were frequently used in the antibiotic drug design process. Advances in computational hardware and algorithms and emerging CADD methods are enhancing the accuracy and ability of CADD in drug design and development. In this chapter, an update to our previous chapter is provided with a focus on new CADD approaches from our laboratory and other peers that can be employed to facilitate the development of antibiotic therapeutics.
MeSH term(s)	Ligands ; Drug Design ; Algorithms ; Anti-Bacterial Agents/pharmacology ; Laboratories
Chemical Substances	Ligands ; Anti-Bacterial Agents
Language	English
Publishing date	2022-12-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2855-3_7
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