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Article ; Online: Remarkable Rate Enhancement of Ligand Substitution Promoted by Geometrical Arrangement of Tridentate "Spectator" Ligands K.J.T. acknowledges Arco Chemical and the National Science Foundation for support of this research. M.H.V.H. gratefully acknowledges postdoctoral fellowship support from the Director's Office of Los Alamos National Laboratory. Los Alamos National Laboratory is operated by the University of California for the U.S. Department of Energy under Contract W-7405-ENG-36. M.H.V.H. also thanks Dr. Beverly K. Hartline (Deputy Laboratory Director, Argonne National Laboratory), Dr. Donald G. Lee (Chemistry Professor, University of Regina, Saskatchewan, Canada, S4S0A2), Dr. R. Thomas Baker (Los Alamos National Laboratory), and Dr. David E. Morris (Los Alamos National Laboratory) for their suggestions and discussions.

Huynh, My Hang V. / Smyth, Jennifer / Wetzler, Modi / Mort, Brendan / Gong, Paul K. / Witham, Laura M. / Jameson, Donald L. / Geiger, David K. / Lasker, Joanne M. / Charepoo, Mina / Gornikiewicz, Michelle / Cintron, Jose M. / Imahori, Gretchen / Sanchez, Roberto R. / Marschilok, Amy C. / Krajkowski, Lynn M. / Churchill, David G. / Churchill, Melvyn Rowen / Takeuchi, Kenneth J.

Angewandte Chemie (International ed. in English)

2001 Volume 40, Issue 23, Page(s) 4469–4473

Language	English
Publishing date	2001-12-03
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/1521-3773(20011203)40:23<4469::aid-anie4469>3.0.co;2-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Evaluation of a Radiological Tool for Semiautomatic Scalar Translocation Detection After Cochlear Implantation.

Arends, Sebastiaan R S / Briaire, Jeroen J / Geiger, Stephan / Nauwelaers, Tim / Frijns, Johan H M

Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology

2024 Volume 45, Issue 4, Page(s) e322–e327

Abstract: Objective: To evaluate the clinical applicability of a semiautomatic radiological tool for scalar translocation detection.: Study design: Retrospective study.: Setting: Tertiary care academic center.: Patients: We included 104 patients ... ...

Abstract	Objective: To evaluate the clinical applicability of a semiautomatic radiological tool for scalar translocation detection. Study design: Retrospective study. Setting: Tertiary care academic center. Patients: We included 104 patients implanted with 116 HiFocus Mid-Scala electrode arrays between January 2013 and September 2016. Intervention: Cochlear implantation. Main outcome measures: The tool's scalar position assessments were compared with manual ones by calculating intraclass coefficient (ICC) for individual contacts and sensitivity and specificity for translocation detection of the whole array. In addition, ICC was calculated for diameters A and B, ratio A/B, and angular insertion depth (AID). Results: Nine-one percent of cases could be processed, which took 5 to 10 minutes per case. Comparison of manual and semiautomatic scalar position showed for individual contacts an ICC of 0.89 and for the whole array a sensitivity of 97% and a specificity of 96%. ICCs for A, B, and A/B were 0.82, 0.74, and 0.39 respectively. For AID, ICC of each of the 16 contacts was 0.95 or higher. Conclusions: The semiautomatic radiological tool could analyze most cases and showed good to excellent agreement with manual assessments for translocation detection, diameter A, diameter B, and AID. The variability between semiautomatic and manual measurements is comparable to interobserver variability, indicating that clinical implementation of the tool is feasible.
MeSH term(s)	Humans ; Cochlear Implantation ; Cochlear Implants ; Retrospective Studies ; Radiography ; Cochlea/surgery
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2036790-9
ISSN	1537-4505 ; 1531-7129
ISSN (online)	1537-4505
ISSN	1531-7129
DOI	10.1097/MAO.0000000000004161
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Article ; Online: Upscaling the porosity-permeability relationship of a microporous carbonate for Darcy-scale flow with machine learning.

Menke, H P / Maes, J / Geiger, S

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2625

Abstract: The permeability of a pore structure is typically described by stochastic representations of its geometrical attributes (e.g. pore-size distribution, porosity, coordination number). Database-driven numerical solvers for large model domains can only ... ...

Abstract	The permeability of a pore structure is typically described by stochastic representations of its geometrical attributes (e.g. pore-size distribution, porosity, coordination number). Database-driven numerical solvers for large model domains can only accurately predict large-scale flow behavior when they incorporate upscaled descriptions of that structure. The upscaling is particularly challenging for rocks with multimodal porosity structures such as carbonates, where several different type of structures (e.g. micro-porosity, cavities, fractures) are interacting. It is the connectivity both within and between these fundamentally different structures that ultimately controls the porosity-permeability relationship at the larger length scales. Recent advances in machine learning techniques combined with both numerical modelling and informed structural analysis have allowed us to probe the relationship between structure and permeability much more deeply. We have used this integrated approach to tackle the challenge of upscaling multimodal and multiscale porous media. We present a novel method for upscaling multimodal porosity-permeability relationships using machine learning based multivariate structural regression. A micro-CT image of Estaillades limestone was divided into small 60
Language	English
Publishing date	2021-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-82029-2
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Article: Are current cut-points for passive transfer of immunity appropriate for dairy calves fed colostrum replacers?

Geiger, A.J / Lago, A

Applied animal science. 2021 June, v. 37, no. 3

2021

Abstract: ... replacer supplying 150 g of IgG (CR). Serum samples were collected at 0 and 24 h of life to determine serum ...

Abstract	Passive transfer of immunity (PTI) is a metric used on farm to assess colostrum management. With multiple colostrum replacers available differing in composition, classical total serum protein cut points may not apply to all products. The aim of this analysis was to determine whether calves fed a whey-based colostrum replacer that successfully achieved PTI (serum IgG ≥10 mg/mL) would have been classified as having PTI using typical benchmarks (total serum protein <5.0, 5.2, or 5.5 g/dL or Brix% <8.4).In total, 1,220 calves were assigned to 1 of 2 treatments: (1) maternal colostrum (MC) or (2) whey-based colostrum replacer supplying 150 g of IgG (CR). Serum samples were collected at 0 and 24 h of life to determine serum IgG, total serum protein, Brix%, and apparent absorption efficiency.When comparing serum IgG values with current on-farm cut points, the proportion of calves incorrectly classified as having PTI failure was greater (P < 0.01) for the CR treatment compared with the MC treatment. The proportion of calves incorrectly classified for CR versus MC using current total serum protein or Brix% cut points were as follows: 5.0 g/dL (31.2 vs. 8.8%, P < 0.001), 5.2 g/dL (52.5 vs. 15.5%; P < 0.001), and 5.5 g/dL (82.0 vs. 34.0%, P < 0.001) or serum Brix 8.4% (73.2 vs. 29.2%; P < 0.01).These data suggest when analyzing serum on farm from calves fed a whey-based colostrum replacer, traditional cut points for PTI should be revised.
Keywords	absorption ; animal science ; blood serum ; brix ; colostrum ; farms ; immunity
Language	English
Dates of publication	2021-06
Size	p. 353-356.
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ISSN	2590-2865
DOI	10.15232/aas.2021-02151
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Unanticipated Hydrophobicity Increases of Squalene and Human Skin Oil Films Upon Ozone Exposure.

Butman, Jana L / Thomson, Regan J / Geiger, Franz M

The journal of physical chemistry. B

2022 Volume 126, Issue 45, Page(s) 9417–9423

Abstract: The C-H and O-H oscillators on the surfaces of thin films of human-derived skin oil and squalene ... H stretching region, while exposure to ozone results in surface spectra for both materials that is ... consistent with a loss of C-H oscillators. The measured contact angles show that the hydrophobicity ...

Abstract	The C-H and O-H oscillators on the surfaces of thin films of human-derived skin oil and squalene are probed under ambient conditions (300 K, 1 atm total pressure, 40% RH) using second-order vibrational spectroscopy and contact angle goniometry before and after exposure to ppb amounts of ozone. Skin oil and squalene are found to produce different vibrational sum frequency generation spectra in the C-H stretching region, while exposure to ozone results in surface spectra for both materials that is consistent with a loss of C-H oscillators. The measured contact angles show that the hydrophobicity of the films increases following exposure to ozone, consistent with the reduction in C═C···H
MeSH term(s)	Humans ; Squalene/chemistry ; Air Pollution, Indoor/analysis ; Ozone/analysis ; Ozone/chemistry ; Skin/chemistry ; Hydrophobic and Hydrophilic Interactions
Chemical Substances	Squalene (7QWM220FJH) ; Ozone (66H7ZZK23N)
Language	English
Publishing date	2022-11-04
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c04849
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Article ; Online: Unifying Flow, Stereo and Depth Estimation.

Xu, Haofei / Zhang, Jing / Cai, Jianfei / Rezatofighi, Hamid / Yu, Fisher / Tao, Dacheng / Geiger, Andreas

IEEE transactions on pattern analysis and machine intelligence

2023 Volume 45, Issue 11, Page(s) 13941–13958

Abstract: We present a unified formulation and model for three motion and 3D perception tasks: optical flow, rectified stereo matching and unrectified stereo depth estimation from posed images. Unlike previous specialized architectures for each specific task, we ... ...

Abstract	We present a unified formulation and model for three motion and 3D perception tasks: optical flow, rectified stereo matching and unrectified stereo depth estimation from posed images. Unlike previous specialized architectures for each specific task, we formulate all three tasks as a unified dense correspondence matching problem, which can be solved with a single model by directly comparing feature similarities. Such a formulation calls for discriminative feature representations, which we achieve using a Transformer, in particular the cross-attention mechanism. We demonstrate that cross-attention enables integration of knowledge from another image via cross-view interactions, which greatly improves the quality of the extracted features. Our unified model naturally enables cross-task transfer since the model architecture and parameters are shared across tasks. We outperform RAFT with our unified model on the challenging Sintel dataset, and our final model that uses a few additional task-specific refinement steps outperforms or compares favorably to recent state-of-the-art methods on 10 popular flow, stereo and depth datasets, while being simpler and more efficient in terms of model design and inference speed.
Language	English
Publishing date	2023-10-03
Publishing country	United States
Document type	Journal Article
ISSN	1939-3539
ISSN (online)	1939-3539
DOI	10.1109/TPAMI.2023.3298645
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Article: Complementary Effects of Surgery and Pexidartinib in the Management of Patients with Complex Diffuse-Tenosynovial Giant Cell Tumor.

Bernthal, Nicholas M / Randall, R Lor / Zeitlinger, Lauren N / Geiger, Erik J / Healey, John H

Case reports in orthopedics

2022 Volume 2022, Page(s) 7768764

Abstract: Tenosynovial giant cell tumor (TGCT) is a rare neoplasm of the joint synovium that has a wide clinical spectrum including pain and stiffness in the affected joint, joint swelling, periarticular erosions, and cartilage loss, which can severely impact ... ...

Abstract	Tenosynovial giant cell tumor (TGCT) is a rare neoplasm of the joint synovium that has a wide clinical spectrum including pain and stiffness in the affected joint, joint swelling, periarticular erosions, and cartilage loss, which can severely impact quality of life. The mainstay treatment for TGCT has been surgery involving partial or total synovectomy using arthroscopic or open techniques. However, surgical resection alone is associated with high recurrence rates, particularly in diffuse-TGCT (D-TGCT) cases. The 3 cases presented here summarize a combination approach (surgery+pexidartinib [tyrosine kinase inhibitor]) in patients with previously unresectable or inoperable D-TGCT.
Language	English
Publishing date	2022-12-03
Publishing country	United States
Document type	Case Reports
ZDB-ID	2684648-2
ISSN	2090-6757 ; 2090-6749
ISSN (online)	2090-6757
ISSN	2090-6749
DOI	10.1155/2022/7768764
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Article ; Online: Accurate and sensitive mutational signature analysis with MuSiCal.

Jin, Hu / Gulhan, Doga C / Geiger, Benedikt / Ben-Isvy, Daniel / Geng, David / Ljungström, Viktor / Park, Peter J

Nature genetics

2024 Volume 56, Issue 3, Page(s) 541–552

Abstract: Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to ... ...

Abstract	Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
MeSH term(s)	Humans ; Music ; Neoplasms/genetics ; Mutation ; Carcinogenesis/genetics ; INDEL Mutation
Language	English
Publishing date	2024-02-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-024-01659-0
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Article ; Online: Drug-induced phospholipidosis is not correlated with the inhibition of SARS-CoV-2 - inhibition of SARS-CoV-2 is cell line-specific.

Diesendorf, Viktoria / Roll, Valeria / Geiger, Nina / Fähr, Sofie / Obernolte, Helena / Sewald, Katherina / Bodem, Jochen

Frontiers in cellular and infection microbiology

2023 Volume 13, Page(s) 1100028

Abstract: Recently, Tummino et al. reported that 34 compounds, including Chloroquine and Fluoxetine, inhibit SARS-CoV-2 replication by inducing phospholipidosis, although Chloroquine failed to suppress viral replication in Calu-3 cells and patients. In contrast, ... ...

Abstract	Recently, Tummino et al. reported that 34 compounds, including Chloroquine and Fluoxetine, inhibit SARS-CoV-2 replication by inducing phospholipidosis, although Chloroquine failed to suppress viral replication in Calu-3 cells and patients. In contrast, Fluoxetine represses viral replication in human precision-cut lung slices (PCLS) and Calu-3 cells. Thus, it is unlikely that these compounds have similar mechanisms of action. Here, we analysed a subset of these compounds in the viral replication and phospholipidosis assays using the Calu-3 cells and PCLS as the patient-near system. Trimipramine and Chloroquine induced phospholipidosis but failed to inhibit SARS-CoV-2 replication in Calu-3 cells, which contradicts the reported findings and the proposed mechanism. Fluoxetine, only slightly induced phospholipidosis in Calu-3 cells but reduced viral replication by 2.7 orders of magnitude. Tilorone suppressed viral replication by 1.9 orders of magnitude in Calu-3 cells without causing phospholipidosis. Thus, induction of phospholipidosis is not correlated with the inhibition of SARS-CoV-2, and the compounds act via other mechanisms. However, we show that compounds, such as Amiodarone, Tamoxifen and Tilorone, with antiviral activity on Calu-3 cells, also inhibited viral replication in human PCLS. Our results indicate that antiviral assays against SARS-CoV-2 are cell-line specific. Data from Vero E6 can lead to non-transferable results, underlining the importance of an appropriate cell system for analysing antiviral compounds against SARS-CoV-2. We observed a correlation between the active compounds in Calu-3 cells and PCLS.
MeSH term(s)	Humans ; Tilorone ; COVID-19 ; Fluoxetine ; SARS-CoV-2 ; Antiviral Agents/pharmacology ; Cell Line ; Chloroquine
Chemical Substances	Tilorone (O6W7VEW6KS) ; Fluoxetine (01K63SUP8D) ; Antiviral Agents ; Chloroquine (886U3H6UFF)
Language	English
Publishing date	2023-08-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2023.1100028
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Article ; Online: Upscaling the porosity–permeability relationship of a microporous carbonate for Darcy-scale flow with machine learning

H. P. Menke / J. Maes / S. Geiger

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 10

Abstract: Abstract The permeability of a pore structure is typically described by stochastic representations of its geometrical attributes (e.g. pore-size distribution, porosity, coordination number). Database-driven numerical solvers for large model domains can ... ...

Abstract	Abstract The permeability of a pore structure is typically described by stochastic representations of its geometrical attributes (e.g. pore-size distribution, porosity, coordination number). Database-driven numerical solvers for large model domains can only accurately predict large-scale flow behavior when they incorporate upscaled descriptions of that structure. The upscaling is particularly challenging for rocks with multimodal porosity structures such as carbonates, where several different type of structures (e.g. micro-porosity, cavities, fractures) are interacting. It is the connectivity both within and between these fundamentally different structures that ultimately controls the porosity–permeability relationship at the larger length scales. Recent advances in machine learning techniques combined with both numerical modelling and informed structural analysis have allowed us to probe the relationship between structure and permeability much more deeply. We have used this integrated approach to tackle the challenge of upscaling multimodal and multiscale porous media. We present a novel method for upscaling multimodal porosity–permeability relationships using machine learning based multivariate structural regression. A micro-CT image of Estaillades limestone was divided into small 603 and 1203 sub-volumes and permeability was computed using the Darcy–Brinkman–Stokes (DBS) model. The microporosity–porosity–permeability relationship from Menke et al. (Earth Arxiv, https://doi.org/10.31223/osf.io/ubg6p , 2019) was used to assign permeability values to the cells containing microporosity. Structural attributes (porosity, phase connectivity, volume fraction, etc.) of each sub-volume were extracted using image analysis tools and then regressed against the solved DBS permeability using an Extra-Trees regression model to derive an upscaled porosity–permeability relationship. Ten test cases of 3603 voxels were then modeled using Darcy-scale flow with this machine learning predicted upscaled porosity–permeability relationship and benchmarked against full DBS simulations, a numerically upscaled Darcy flow model, and a Kozeny–Carman model. All numerical simulations were performed using GeoChemFoam, our in-house open source pore-scale simulator based on OpenFOAM. We found good agreement between the full DBS simulations and both the numerical and machine learning upscaled models, with the machine learning model being 80 times less computationally expensive. The Kozeny–Carman model was a poor predictor of upscaled permeability in all cases.
Keywords	Medicine ; R ; Science ; Q
Subject code	670
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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