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Article ; Online: Consumption of foods and beverages rich in added sugar associated with incident metabolic syndrome: Coronary Artery Risk Development in Young Adults (CARDIA) study.

Goins, Rae K / Steffen, Lyn M / Yi, So-Yun / Zhou, Xia / Van Horn, Linda / Shikany, James M / Terry, James G / Jacobs, David R

European journal of preventive cardiology

2024

Abstract: Aims: Numerous studies report positive associations between total carbohydrate (CHO) intake and incident metabolic syndrome (MetS), but few differentiate quality or type of CHO relative to MetS. We examined source of CHO intake, including added sugar ( ... ...

Abstract	Aims: Numerous studies report positive associations between total carbohydrate (CHO) intake and incident metabolic syndrome (MetS), but few differentiate quality or type of CHO relative to MetS. We examined source of CHO intake, including added sugar (AS), AS-rich CHO foods and sugar-sweetened beverages (SSBs) associated with incident MetS in adults enrolled in the Coronary Artery Risk Development in Young Adults (CARDIA) study. Methods: Among 3154 Black American and White American women and men aged 18-30 years at baseline, dietary intake was assessed by diet history three times over 20 years. Sources of AS-rich CHO foods and beverages include sugar-rich refined grain products, candy, sugar products, and SSBs. Incident MetS was created according to standard criteria. Time-dependent Cox proportional-hazards regression analysis evaluated the associations of incident MetS across quintiles of cumulative intakes of AS-rich CHO foods and beverages, AS, and SSBs adjusted for potential confounding factors over 30 years of follow-up. Results: The associations of AS-rich CHO foods and beverages, AS, and SSB intakes with incident MetS were consistent. Compared to the lowest intake, the greatest intake of AS-rich CHOs, AS, and SSBs were associated with 59% (ptrend<0.001), 44% (ptrend=0.01), and 34% (ptrend=0.03) higher risk of developing MetS, respectively. As expected, diet quality was lower across increasing quintiles of AS-rich CHO foods and beverages, AS, and SSBs (all ptrend<0.001). Conclusion: Our study findings are consistent with an elevated risk of developing MetS with greater consumption of AS, AS-rich CHO foods, and SSBs which support consuming fewer AS-rich CHO foods and SSBs.
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2626011-6
ISSN	2047-4881 ; 2047-4873
ISSN (online)	2047-4881
ISSN	2047-4873
DOI	10.1093/eurjpc/zwad409
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Zs.A 4686: Show issues

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Article ; Online: Correction: Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient.

Jiang, Xiaoben / Van Horn, David J / Okie, Jordan G / Buelow, Heather N / Schwartz, Egbert / Colman, Daniel R / Feeser, Kelli L / Takacs-Vesbach, Cristina D

Extremophiles : life under extreme conditions

2024 Volume 28, Issue 1, Page(s) 13

Language	English
Publishing date	2024-01-22
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	1481278-2
ISSN	1433-4909 ; 1431-0651
ISSN (online)	1433-4909
ISSN	1431-0651
DOI	10.1007/s00792-023-01325-z
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Book ; Online: Human in-the-Loop Estimation of Cluster Count in Datasets via Similarity-Driven Nested Importance Sampling

Perez, Gustavo / Sheldon, Daniel / Van Horn, Grant / Maji, Subhransu

2023

Abstract: ... A common approach to this problem is to vary the number of clusters in a clustering algorithm (e.g., 'k' ...

Abstract	Identifying the number of clusters serves as a preliminary goal for many data analysis tasks. A common approach to this problem is to vary the number of clusters in a clustering algorithm (e.g., 'k' in $k$-means) and pick the value that best explains the data. However, the count estimates can be unreliable especially when the image similarity is poor. Human feedback on the pairwise similarity can be used to improve the clustering, but existing approaches do not guarantee accurate count estimates. We propose an approach to produce estimates of the cluster counts in a large dataset given an approximate pairwise similarity. Our framework samples edges guided by the pairwise similarity, and we collect human feedback to construct a statistical estimate of the cluster count. On the technical front we have developed a nested importance sampling approach that yields (asymptotically) unbiased estimates of the cluster count with confidence intervals which can guide human effort. Compared to naive sampling, our similarity-driven sampling produces more accurate estimates of counts and tighter confidence intervals. We evaluate our method on a benchmark of six fine-grained image classification datasets achieving low error rates on the estimated number of clusters with significantly less human labeling effort compared to baselines and alternative active clustering approaches.
Keywords	Computer Science - Computer Vision and Pattern Recognition
Subject code	004
Publishing date	2023-12-08
Publishing country	us
Document type	Book ; Online
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Article ; Online: Evaluation of Glial Fibrillary Acidic Protein and Ubiquitin C-Terminal Hydrolase-L1 Using a Rapid Point of Care Test for Predicting Head Computed Tomography Lesions After Mild Traumatic Brain Injury in a Dutch Multi-Center Cohort.

Chayoua, Walid / Visser, Koen / de Koning, Myrthe E / Beishuizen, Albertus / IJmker, Rein / van der Naalt, Joukje / Krabbe, Johannes G / van der Horn, Harm Jan

Journal of neurotrauma

2024

Abstract: Mild traumatic brain injury (mTBI) is a common condition seen in emergency departments worldwide. Blood-based biomarkers glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase-L1 (UCH-L1) are recently U.S. Food and Drug Administration- ... ...

Abstract	Mild traumatic brain injury (mTBI) is a common condition seen in emergency departments worldwide. Blood-based biomarkers glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase-L1 (UCH-L1) are recently U.S. Food and Drug Administration-approved for the prediction of intracranial lesions on head computed tomography (CT) scans in mTBI. We evaluated the diagnostic performance of GFAP and UCH-L1 in a Dutch cohort using the i-STAT TBI assay. In a multi-center observational study, we enrolled 253 mTBI patients. Head CT scans were scored using the Marshall classification system. Logistic regression models were used to assess the contribution of biomarkers and clinical parameters to diagnostic performance. Detection of UCH-L1 and GFAP resulted in a sensitivity of 97% and specificity of 19% for CT positivity in mTBI patients, along with a negative predictive value of 95% (88-100%) and a positive predictive value of 27% (21-33%). Combining biomarker testing with loss of consciousness and time to sample increased specificity to 46%. Combined testing of UCH-L1 and GFAP testing resulted in possibly more unnecessary CT scans compared with GFAP testing alone, with only limited increase in sensitivity. This study confirmed high sensitivity of GFAP and UCH-L1 for CT abnormalities in mTBI patients using the i-STAT TBI test. The results support the potential use of GFAP and UCH-L1 as tools for determining the indication for CT scanning in mTBI patients, possibly offering a cost- and time-effective approach to management of patients with mTBI. Prospective studies in larger cohorts are warranted to validate our findings.
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	645092-1
ISSN	1557-9042 ; 0897-7151
ISSN (online)	1557-9042
ISSN	0897-7151
DOI	10.1089/neu.2023.0491
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Article ; Online: Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller.

Saccuzzo, Emily G / Mebrat, Mubark D / Scelsi, Hailee F / Kim, Minjoo / Ma, Minh Thu / Su, Xinya / Hill, Shannon E / Rheaume, Elisa / Li, Renhao / Torres, Matthew P / Gumbart, James C / Van Horn, Wade D / Lieberman, Raquel L

Nature communications

2024 Volume 15, Issue 1, Page(s) 155

Abstract: Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma- ... ...

Abstract	Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma-associated myocilin. Mutations within the olfactomedin domain of myocilin (OLF) cause a gain-of-function, namely cytotoxic intracellular aggregation, which hastens disease progression. Aggregation by wild-type OLF (OLF
MeSH term(s)	Humans ; Amyloid/metabolism ; Glaucoma/genetics ; Mutation ; Amyloid beta-Peptides/genetics ; Amyloidogenic Proteins/genetics ; Protein Folding
Chemical Substances	Amyloid ; Amyloid beta-Peptides ; Amyloidogenic Proteins
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44479-2
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Article ; Online: Granulocytic myeloid-derived suppressor cell activity during biofilm infection is regulated by a glycolysis/HIF1a axis.

Horn, Christopher M / Arumugam, Prabhakar / Van Roy, Zachary / Heim, Cortney E / Fallet, Rachel W / Bertrand, Blake P / Shinde, Dhananjay / Thomas, Vinai C / Romanova, Svetlana G / Bronich, Tatiana K / Hartman, Curtis W / Garvin, Kevin L / Kielian, Tammy

The Journal of clinical investigation

2024 Volume 134, Issue 8

Abstract: ... cells (G-MDSCs), which are critical for orchestrating the antiinflammatory biofilm milieu. Single-cell ... sequencing and bioinformatic metabolic algorithms were used to explore the link between G-MDSC metabolism and ... in G-MDSCs. Interfering with both pathways in vivo, using a 2-deoxyglucose nanopreparation and ...

Abstract	Staphylococcus aureus is a leading cause of biofilm-associated prosthetic joint infection (PJI). A primary contributor to infection chronicity is an expansion of granulocytic myeloid-derived suppressor cells (G-MDSCs), which are critical for orchestrating the antiinflammatory biofilm milieu. Single-cell sequencing and bioinformatic metabolic algorithms were used to explore the link between G-MDSC metabolism and S. aureus PJI outcome. Glycolysis and the hypoxia response through HIF1a were significantly enriched in G-MDSCs. Interfering with both pathways in vivo, using a 2-deoxyglucose nanopreparation and granulocyte-targeted Hif1a conditional KO mice, respectively, attenuated G-MDSC-mediated immunosuppression and reduced bacterial burden in a mouse model of S. aureus PJI. In addition, single-cell RNA-Seq (scRNA-Seq) analysis of granulocytes from PJI patients also showed an enrichment in glycolysis and hypoxia-response genes. These findings support the importance of a glycolysis/HIF1a axis in promoting G-MDSC antiinflammatory activity and biofilm persistence during PJI.
MeSH term(s)	Humans ; Mice ; Animals ; Myeloid-Derived Suppressor Cells/physiology ; Staphylococcus aureus ; Biofilms ; Granulocytes ; Hypoxia
Language	English
Publishing date	2024-02-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI174051
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Article ; Online: Assessment of porphyrogenicity of drugs and chemicals in selected hepatic cell culture models through a fluorescence-based screening assay.

Ma, Christopher D / Van Horn, Cynthia G / Wan, Meimei / Bishop, Colin / Bonkovsky, Herbert L

Pharmacology research & perspectives

2022 Volume 10, Issue 3, Page(s) e00951

Abstract: Compounds that induce 5-aminolevulinic acid [ALA] synthase-1 and/or cytochromes P-450 may induce acute porphyric attacks in patients with the acute hepatic porphyrias [AHPs]. Currently, there is no simple, robust model used to assess and predict the ... ...

Abstract	Compounds that induce 5-aminolevulinic acid [ALA] synthase-1 and/or cytochromes P-450 may induce acute porphyric attacks in patients with the acute hepatic porphyrias [AHPs]. Currently, there is no simple, robust model used to assess and predict the porphyrogenicity of drugs and chemicals. Our aim was to develop a fluorescence-based in vitro assay for this purpose. We studied four different hepatic cell culture models: HepG2 cells, LMH cells, 3D HepG2 organoids, and 3D organoids of primary liver cells from people without known disease [normal human controls]. We took advantage of the fluorescent properties of protoporphyrin IX [PP], the last intermediate of the heme biosynthesis pathway, performing fluorescence spectrometry to measure the intensity of fluorescence emitted by these cells treated with selected compounds of importance to patients with AHPs. Among the four cell culture models, the LMH cells produced the highest fluorescence readings, suggesting that these cells retain more robust heme biosynthesis enzymes or that the other cell models may have lost their inducibility of ALA synthase-1 [ALAS-1]. Allyl isopropyl acetamide [AIA], a known potent porphyrogen and inducer of ALAS-1, was used as a positive control to help predict porphyrogenicity for tested compounds. Among the tested compounds (acetaminophen, acetylsalicylic acid, β-estradiol, hydroxychloroquine sulfate, alpha-methyldopa, D (-) norgestrel, phenobarbital, phenytoin, sulfamethoxazole, sulfisoxazole, sodium valproate, and valsartan), concentrations greater than 0.314 mM for norgestrel, phenobarbital, phenytoin, and sodium valproate produced fluorescence readings higher than the reading produced by the positive AIA control. Porphyrin accumulation was also measured by HPLC to confirm the validity of the assay. We conclude that LMH cell cultures in multi-well plates are an inexpensive, robust, and simple system to predict the porphyrogenicity of existing or novel compounds that may exacerbate the AHPs.
MeSH term(s)	Cell Culture Techniques ; Heme ; Hepatocytes/metabolism ; Humans ; Liver/metabolism ; Norgestrel/metabolism ; Phenobarbital/metabolism ; Phenobarbital/pharmacology ; Phenytoin/metabolism ; Porphobilinogen Synthase/deficiency ; Porphyrias, Hepatic ; Valproic Acid/metabolism
Chemical Substances	Norgestrel (3J8Q1747Z2) ; Heme (42VZT0U6YR) ; Valproic Acid (614OI1Z5WI) ; Phenytoin (6158TKW0C5) ; Porphobilinogen Synthase (EC 4.2.1.24) ; Phenobarbital (YQE403BP4D)
Language	English
Publishing date	2022-04-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2740389-0
ISSN	2052-1707 ; 2052-1707
ISSN (online)	2052-1707
ISSN	2052-1707
DOI	10.1002/prp2.951
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Article ; Online: Parkinson's disease cerebrovascular reactivity pattern: A feasibility study.

van der Horn, Harm Jan / Vakhtin, Andrei A / Julio, Kayla / Nitschke, Stephanie / Shaff, Nicholas / Dodd, Andrew B / Erhardt, Erik / Phillips, John P / Pirio Richardson, Sarah / Deligtisch, Amanda / Stewart, Melanie / Suarez Cedeno, Gerson / Meles, Sanne K / Mayer, Andrew R / Ryman, Sephira G

Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism

2024 , Page(s) 271678X241241895

Abstract: A mounting body of research points to cerebrovascular dysfunction as a fundamental element in the pathophysiology of Parkinson's disease (PD). In the current feasibility study, blood-oxygen-level-dependent (BOLD) MRI was used to measure cerebrovascular ... ...

Abstract	A mounting body of research points to cerebrovascular dysfunction as a fundamental element in the pathophysiology of Parkinson's disease (PD). In the current feasibility study, blood-oxygen-level-dependent (BOLD) MRI was used to measure cerebrovascular reactivity (CVR) in response to hypercapnia in 26 PD patients and 16 healthy controls (HC), and aimed to find a multivariate pattern specific to PD. Whole-brain maps of CVR amplitude (i.e., magnitude of response to CO
Language	English
Publishing date	2024-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	604628-9
ISSN	1559-7016 ; 0271-678X
ISSN (online)	1559-7016
ISSN	0271-678X
DOI	10.1177/0271678X241241895
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Zs.A 1663: Show issues

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Article: A Decentralized ComBat Algorithm and Applications to Functional Network Connectivity.

Bostami, Biozid / Hillary, Frank G / van der Horn, Harm Jan / van der Naalt, Joukje / Calhoun, Vince D / Vergara, Victor M

Frontiers in neurology

2022 Volume 13, Page(s) 826734

Abstract: Recent studies showed that working with neuroimage data collected from different research facilities or locations may incur additional source dependency, affecting the overall statistical power. This problem can be mitigated with data harmonization ... ...

Abstract	Recent studies showed that working with neuroimage data collected from different research facilities or locations may incur additional source dependency, affecting the overall statistical power. This problem can be mitigated with data harmonization approaches. Recently, the ComBat method has become commonly adopted for various neuroimage modalities. While open neuroimaging datasets are becoming more common, a substantial amount of data is still unable to be shared for various reasons. In addition, current approaches require moving all the data to a central location, which requires additional resources and creates redundant copies of the same datasets. To address these issues, we propose a decentralized harmonization approach that does not create redundant copies of the original datasets and performs remote operations on the datasets separately without sharing any individual subject data, ensuring a certain level of privacy and reducing regulatory hurdles. We proposed a novel approach called "Decentralized ComBat" which can harmonize datasets separately without combining the datasets. We tested our model by harmonizing functional network connectivity datasets from two traumatic brain injury studies in a decentralized way. Also, we used simulations to analyze the performance and scalability of our model when the number of data collection sites increases. We compare the output with centralized ComBat and show that the proposed approach produces similar results, increasing the sensitivity of the functional network connectivity analysis and validating our approach. Simulations show that our model can be easily scaled to many more datasets based on the requirement. In sum, we believe this provides a powerful tool, further complementing open data and allowing for integrating public and private datasets.
Language	English
Publishing date	2022-03-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2022.826734
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Article ; Online: An exploratory study on the association between blood-based biomarkers and subacute neurometabolic changes following mild traumatic brain injury.

Visser, Koen / de Koning, Myrthe E / Ciubotariu, Diana / Kok, Marius G J / Sibeijn-Kuiper, Anita J / Bourgonje, Arno R / van Goor, Harry / van der Naalt, Joukje / van der Horn, Harm Jan

Journal of neurology

2023 Volume 271, Issue 4, Page(s) 1985–1998

Abstract: Background and objectives: Blood-based biomarkers and advanced neuroimaging modalities such as magnetic resonance spectroscopy (MRS) or diffusion tensor imaging (DTI) have enhanced our understanding of the pathophysiology of mild traumatic brain injury ( ...

Abstract	Background and objectives: Blood-based biomarkers and advanced neuroimaging modalities such as magnetic resonance spectroscopy (MRS) or diffusion tensor imaging (DTI) have enhanced our understanding of the pathophysiology of mild traumatic brain injury (mTBI). However, there is limited published data on how blood biomarkers relate to neuroimaging biomarkers post-mTBI. Methods: To investigate this, 30 patients with mTBI and 21 healthy controls were enrolled. Data was collected at two timepoints postinjury: acute, < 24 h, (blood) and subacute, four-to-six weeks, (blood and imaging). Interleukin (IL) 6 and 10 (inflammation), free thiols (systemic oxidative stress) and neurofilament light (NF-L) (axonal injury) were quantified in plasma. The neurometabolites total N-acetyl aspartate (tNAA) (neuronal energetics), Myo-Inositol (Ins) and total Choline (tCh) (inflammation) and, Glutathione (GSH, oxidative stress) were quantified using MRS. Results: Concentrations of IL-6 and IL-10 were significantly elevated in the acute phase post-mTBI, while NF-L was elevated only in the subacute phase. Total NAA was lowered in patients with mTBI, although this difference was only nominally significant (uncorrected P < 0.05). Within the patient group, acute IL-6 and subacute tNAA levels were negatively associated (r = - 0.46, uncorrected-P = 0.01), albeit not at a threshold corrected for multiple testing (corrected-P = 0.17). When age was added as a covariate a significant increase in correlation magnitude was observed (ρ = - 0.54, corrected-P = 0.03). Conclusion: This study demonstrates potential associations between the intensity of the inflammatory response in the acute phase post-mTBI and neurometabolic perturbations in the subacute phase. Future studies should assess the longitudinal dynamics of blood-based and imaging biomarkers after injury.
MeSH term(s)	Humans ; Brain Concussion ; Diffusion Tensor Imaging/methods ; Interleukin-6 ; Biomarkers ; Aspartic Acid ; Inflammation ; Brain/pathology
Chemical Substances	Interleukin-6 ; Biomarkers ; Aspartic Acid (30KYC7MIAI)
Language	English
Publishing date	2023-12-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	187050-6
ISSN	1432-1459 ; 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
ISSN (online)	1432-1459
ISSN	0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
DOI	10.1007/s00415-023-12146-7
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