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Article ; Online: Notice of Retraction and Replacement. Chaarani B, et al. Association of Video Gaming With Cognitive Performance Among Children. JAMA Network Open. 2022;5(10):e2235721.

Chaarani, Bader / Ortigara, Joseph / Yuan, DeKang / Loso, Hannah / Potter, Alexandra / Garavan, Hugh P

JAMA network open

2023 Volume 6, Issue 4, Page(s) e236895

Language	English
Publishing date	2023-04-03
Publishing country	United States
Document type	Journal Article ; Retraction of Publication
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2023.6895
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Terahertz parametric amplification as a reporter of exciton condensate dynamics.

Haque, Sheikh Rubaiat Ul / Michael, Marios H / Zhu, Junbo / Zhang, Yuan / Windgätter, Lukas / Latini, Simone / Wakefield, Joshua P / Zhang, Gu-Feng / Zhang, Jingdi / Rubio, Angel / Checkelsky, Joseph G / Demler, Eugene / Averitt, Richard D

Nature materials

2024

Abstract: Condensates are a hallmark of emergence in quantum materials such as superconductors and charge density waves. Excitonic insulators are an intriguing addition to this library, exhibiting spontaneous condensation of electron-hole pairs. However, ... ...

Abstract	Condensates are a hallmark of emergence in quantum materials such as superconductors and charge density waves. Excitonic insulators are an intriguing addition to this library, exhibiting spontaneous condensation of electron-hole pairs. However, condensate observables can be obscured through parasitic coupling to the lattice. Here we employ nonlinear terahertz spectroscopy to disentangle such obscurants through measurement of the quantum dynamics. We target Ta
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2088679-2
ISSN	1476-4660 ; 1476-1122
ISSN (online)	1476-4660
ISSN	1476-1122
DOI	10.1038/s41563-023-01755-2
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Article ; Online: scPerturb: harmonized single-cell perturbation data.

Peidli, Stefan / Green, Tessa D / Shen, Ciyue / Gross, Torsten / Min, Joseph / Garda, Samuele / Yuan, Bo / Schumacher, Linus J / Taylor-King, Jake P / Marks, Debora S / Luna, Augustin / Blüthgen, Nils / Sander, Chris

Nature methods

2024 Volume 21, Issue 3, Page(s) 531–540

Abstract: Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation- ... ...

Abstract	Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform quality control pipelines and harmonize feature annotations. The resulting information resource, scPerturb, enables development and testing of computational methods, and facilitates comparison and integration across datasets. We describe energy statistics (E-statistics) for quantification of perturbation effects and significance testing, and demonstrate E-distance as a general distance measure between sets of single-cell expression profiles. We illustrate the application of E-statistics for quantifying similarity and efficacy of perturbations. The perturbation-response datasets and E-statistics computation software are publicly available at scperturb.org. This work provides an information resource for researchers working with single-cell perturbation data and recommendations for experimental design, including optimal cell counts and read depth.
MeSH term(s)	Software ; Proteomics ; Gene Expression Profiling/methods ; Epigenomics ; Single-Cell Analysis
Language	English
Publishing date	2024-01-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-023-02144-y
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Article ; Online: Association of Video Gaming With Cognitive Performance Among Children.

Chaarani, Bader / Ortigara, Joseph / Yuan, DeKang / Loso, Hannah / Potter, Alexandra / Garavan, Hugh P

publication RETRACTED

JAMA network open

2022 Volume 5, Issue 10, Page(s) e2235721

Abstract: Importance: Although most research has linked video gaming to subsequent increases in aggressive behavior in children after accounting for prior aggression, findings have been divided with respect to video gaming's association with cognitive skills.: ... ...

Abstract	Importance: Although most research has linked video gaming to subsequent increases in aggressive behavior in children after accounting for prior aggression, findings have been divided with respect to video gaming's association with cognitive skills. Objective: To examine the association between video gaming and cognition in children using data from the Adolescent Brain Cognitive Development (ABCD) study. Design, setting, and participants: In this case-control study, cognitive performance and blood oxygen level-dependent (BOLD) signal were compared in video gamers (VGs) and non-video gamers (NVGs) during response inhibition and working memory using task-based functional magnetic resonance imaging (fMRI) in a large data set of 9- and 10-year-old children from the ABCD study, with good control of demographic, behavioral, and psychiatric confounding effects. A sample from the baseline assessment of the ABCD 2.0.1 release in 2019 was largely recruited across 21 sites in the US through public, private, and charter elementary schools using a population neuroscience approach to recruitment, aiming to mirror demographic variation in the US population. Children with valid neuroimaging and behavioral data were included. Some exclusions included common MRI contraindications, history of major neurologic disorders, and history of traumatic brain injury. Exposures: Participants completed a self-reported screen time survey including an item asking children to report the time specifically spent on video gaming. All fMRI tasks were performed by all participants. Main outcomes and measures: Video gaming time, cognitive performance, and BOLD signal assessed with n-back and stop signal tasks on fMRI. Collected data were analyzed between October 2019 and October 2020. Results: A total of 2217 children (mean [SD] age, 9.91 [0.62] years; 1399 [63.1%] female) participated in this study. The final sample used in the stop signal task analyses consisted of 1128 NVGs (0 gaming hours per week) and 679 VGs who played at least 21 hours per week. The final sample used in the n-back analyses consisted of 1278 NVGs who had never played video games (0 hours per week of gaming) and 800 VGs who played at least 21 hours per week. The VGs performed better on both fMRI tasks compared with the NVGs. Nonparametric analyses of fMRI data demonstrated a greater BOLD signal in VGs in the precuneus during inhibitory control. During working memory, a smaller BOLD signal was observed in VGs in parts of the occipital cortex and calcarine sulcus and a larger BOLD signal in the cingulate, middle, and frontal gyri and the precuneus. Conclusions and relevance: In this study, compared with NVGs, VGs were found to exhibit better cognitive performance involving response inhibition and working memory as well as altered BOLD signal in key regions of the cortex responsible for visual, attention, and memory processing. The findings are consistent with videogaming improving cognitive abilities that involve response inhibition and working memory and altering their underlying cortical pathways.
MeSH term(s)	Adolescent ; Child ; Humans ; Female ; Male ; Case-Control Studies ; Video Games ; Memory, Short-Term/physiology ; Magnetic Resonance Imaging/methods ; Cognition/physiology
Language	English
Publishing date	2022-10-03
Publishing country	United States
Document type	Journal Article ; Retracted Publication
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2022.35721
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Article ; Online: Small molecule inhibitors of 15-PGDH exploit a physiologic induced-fit closing system

Wei Huang / Hongyun Li / Janna Kiselar / Stephen P. Fink / Sagar Regmi / Alexander Day / Yiyuan Yuan / Mark Chance / Joseph M. Ready / Sanford D. Markowitz / Derek J. Taylor

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 13

Abstract: Inhibition of 15-prostaglandin dehydrogenase (15-PGDH) is a promising therapeutic target for regenerative medicine. We report the structure of 15-PGDH in complex with two different inhibitors. Unexpectedly, access to the binding pocket is regulated by a ... ...

Abstract	Inhibition of 15-prostaglandin dehydrogenase (15-PGDH) is a promising therapeutic target for regenerative medicine. We report the structure of 15-PGDH in complex with two different inhibitors. Unexpectedly, access to the binding pocket is regulated by a dynamic “lid” of the enzyme.
Keywords	Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Prognostic Value of CT-FFR-Based Functional Duke Jeopardy Score in Patients With Suspected CAD.

JACC. Cardiovascular imaging

2023 Volume 16, Issue 9, Page(s) 1227–1229

MeSH term(s)	Humans ; Fractional Flow Reserve, Myocardial ; Prognosis ; Predictive Value of Tests ; Coronary Artery Disease/diagnostic imaging ; Coronary Artery Disease/therapy ; Coronary Stenosis ; Tomography, X-Ray Computed ; Coronary Angiography ; Computed Tomography Angiography ; Severity of Illness Index
Language	English
Publishing date	2023-04-12
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2491503-8
ISSN	1876-7591 ; 1936-878X
ISSN (online)	1876-7591
ISSN	1936-878X
DOI	10.1016/j.jcmg.2023.02.012
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Article ; Online: Trends in Medical Management of Moderately to Severely Active Ulcerative Colitis: A Nationwide Retrospective Analysis.

Yuan, William / Marwaha, Jayson S / Rakowsky, Shana T / Palmer, Nathan P / Kohane, Isaac S / Rubin, David T / Brat, Gabriel A / Feuerstein, Joseph D

Inflammatory bowel diseases

2022 Volume 29, Issue 5, Page(s) 695–704

Abstract: ... use of biologics in patient trajectories (762 days earlier relative to UC diagnosis, 2018 vs 2008; P ... < .001) and greater overall use of biologics over time (2.53× more in 2018 vs 2008; P < .00001 ... with infliximab or vedolizumab (odds ratio, 0.92; P < .005). Comparisons of patients with early biologic ...

Abstract	Background: With an increasing number of therapeutic options available for the management of ulcerative colitis (UC), the variability in treatment and prescribing patterns is not well known. While recent guidelines have provided updates on how these therapeutic options should be used, patterns of long-term use of these drugs over the past 2 decades remain unclear. Methods: We analyzed a retrospective, nationwide cohort of more than 1.7 million prescriptions for trends in prescribing behaviors and to evaluate practices suggested in guidelines relating to ordering biologics, step-up therapy, and combination therapy. The primary outcome was 30-day steroid-free remission and secondary outcomes included hospitalization, cost, and additional steroid usage. A pipeline was created to identify cohorts of patients under active UC medical management grouped by prescribing strategies to evaluate comparative outcomes between strategies. Cox proportional hazards and multivariate regression models were utilized to assess postexposure outcomes and adjust for confounders. Results: Among 6 major drug categories, we noted major baseline differences in patient characteristics at first exposure corresponding to disease activity. We noted earlier use of biologics in patient trajectories (762 days earlier relative to UC diagnosis, 2018 vs 2008; P < .001) and greater overall use of biologics over time (2.53× more in 2018 vs 2008; P < .00001) . Among biologic-naive patients, adalimumab was associated with slightly lower rates of remission compared with infliximab or vedolizumab (odds ratio, 0.92; P < .005). Comparisons of patients with early biologic initiation to patients who transitioned to biologics from 5-aminosalicylic acid suggest lower steroid consumption for early biologic initiation (-761 mg prednisone; P < .001). Combination thiopurine-biologic therapy was associated with higher odds of remission compared with biologic monotherapy (odds ratio, 1.36; P = .01). Conclusions: As biologic drugs have become increasingly available for UC management, they have increasingly been used at earlier stages of disease management. Large-scale analyses of prescribing behaviors provide evidence supporting early use of biologics compared with step-up therapy and use of thiopurine and biologic combination therapy.
MeSH term(s)	Humans ; Colitis, Ulcerative/drug therapy ; Retrospective Studies ; Infliximab/therapeutic use ; Adalimumab/therapeutic use ; Biological Factors/therapeutic use ; Immunologic Factors/therapeutic use ; Biological Products/therapeutic use
Chemical Substances	Infliximab (B72HH48FLU) ; Adalimumab (FYS6T7F842) ; Biological Factors ; Immunologic Factors ; Biological Products
Language	English
Publishing date	2022-07-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1340971-2
ISSN	1536-4844 ; 1078-0998
ISSN (online)	1536-4844
ISSN	1078-0998
DOI	10.1093/ibd/izac134
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Article: SIRT5

bioRxiv : the preprint server for biology

2023

Abstract: SIRT5 is a sirtuin deacylase that represents the major activity responsible for removal of negatively-charged lysine modifications, in the mitochondrial matrix and elsewhere in the cell. In benign cells and mouse models, under basal non-stressed ... ...

Abstract	SIRT5 is a sirtuin deacylase that represents the major activity responsible for removal of negatively-charged lysine modifications, in the mitochondrial matrix and elsewhere in the cell. In benign cells and mouse models, under basal non-stressed conditions, the phenotypes of SIRT5 deficiency are generally quite subtle. Here, we identify two homozygous
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.12.06.570371
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Article ; Online: Dose-response of benazepril on biomarkers of the classical and alternative pathways of the renin-angiotensin-aldosterone system in dogs.

Sotillo, Samantha / Ward, Jessica L / Guillot, Emilie / Domenig, Oliver / Yuan, Lingnan / Smith, Joseph S / Gabriel, Vojtech / Iennarella-Servantez, Chelsea A / Mochel, Jonathan P

Scientific reports

2023 Volume 13, Issue 1, Page(s) 2684

Abstract: ... P = 0.004), Ang1-5 (- 53%, P = 0.001), ACE-S (surrogate for ACE activity; - 59%, P = 0.0002), and ... ALT-S (surrogate for alternative RAAS activity; - 22%, P = 0.004), and higher values of AngI (+ 78%, P ... 0.014) and PRA-S (surrogate for plasma renin activity; + 58%, P = 0.040). There were no relevant ...

Abstract	Angiotensin-converting enzyme inhibitors (ACEI) such as benazepril are commonly prescribed in both humans and dogs with heart disease to mitigate the renin-angiotensin-aldosterone system (RAAS); however, the dose-dependent effects of benazepril on comprehensive RAAS components remain unknown. In this study, nine purpose-bred healthy dogs received three different dosages of oral benazepril (0.125 mg/kg, 0.25 mg/kg, or 0.5 mg/kg) in a randomized crossover design following induction of RAAS activation by consuming a low-sodium diet. Blood samples were collected at serial time intervals after benazepril dosing to measure plasma benazeprilat (active metabolite of benazepril) and serum RAAS biomarkers. Blood pressure and echocardiogram were performed at baseline and after each benazepril administration. Time-weighted averages for RAAS biomarkers for 12 h post-dose and hemodynamic variables were compared between dosing groups using Wilcoxon rank-sum testing. Compared to the lowest dosage of benazepril (0.125 mg/kg), the highest dosage (0.5 mg/kg) resulted in lower time-weighted average values of angiotensin (Ang) II (- 38%, P = 0.004), Ang1-5 (- 53%, P = 0.001), ACE-S (surrogate for ACE activity; - 59%, P = 0.0002), and ALT-S (surrogate for alternative RAAS activity; - 22%, P = 0.004), and higher values of AngI (+ 78%, P = 0.014) and PRA-S (surrogate for plasma renin activity; + 58%, P = 0.040). There were no relevant differences between dosing groups for blood pressure or echocardiographic variables. Knowledge of dose-dependent alterations in biomarkers of the classical and alternative RAAS pathways could help inform clinical trials for dosage optimization in both dogs and humans.
MeSH term(s)	Animals ; Dogs ; Aldosterone/pharmacology ; Angiotensin II/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Biomarkers ; Renin-Angiotensin System
Chemical Substances	Aldosterone (4964P6T9RB) ; Angiotensin II (11128-99-7) ; Angiotensin-Converting Enzyme Inhibitors ; benazepril (UDM7Q7QWP8) ; Biomarkers
Language	English
Publishing date	2023-02-15
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial, Veterinary ; 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/s41598-023-29771-x
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Article ; Online: Saline irrigation for reducing the recurrence of common bile duct stones after lithotripsy: a randomized controlled trial.

Lin, Yanyan / Yang, Man / Cao, Jie / Zhang, Xianzhuo / Mi, Ningning / Yang, Xiao / Wang, Haiping / Gao, Long / Bai, Mingzhen / Fu, Wenkang / Li, Xun / Yue, Ping / Yuan, Jinqiu / Meng, Wenbo / Leung, Joseph W

EClinicalMedicine

2023 Volume 59, Page(s) 101978

Abstract: ... CI], 11.35%-35.32%, p < 0.001). Multivariable Cox proportional hazards analyses showed ... that constipation (hazard risk [HR] 2.42; 95% CI, 1.22-4.80, p = 0.012), periampullary diverticulum (PAD) (HR 3.06 ... 95% CI, 1.62-5.79, p < 0.001), and total to direct bilirubin ratio (HR 1.48; 95% CI, 1.21-1.81, p < 0 ...

Abstract	Background: Mechanical lithotripsy produces stone fragments that are not easily detected by cholangiography and is a potential cause of recurrence of common bile duct stones (CBDS). This study aims to clarify whether 100 ml saline irrigation after mechanical lithotripsy reduces the recurrent rate of CBDS. Methods: In this randomized controlled trial performed at the Surgical Endoscopy Center, the First Hospital of Lanzhou University between May 10, 2019, and Dec 31, 2020, patients undergoing endoscopic mechanical lithotripsy were randomly assigned to receive saline irrigation (study group) or no irrigation (control group). The saline irrigation was given 100 ml saline pulse irrigation after cholangiography showed no residual stones. Patients were followed up for at least 24 months after endoscopic stone removal to assess the recurrence of CBDS. This study was registered with ClinicalTrials.gov (NCT03937037). Findings: During the median follow-up period of 35.6 months (interquartile range, 26.0-40.7), 43 of the 180 patients had stone recurrence (24%). The frequency of recurrence of CBD stones was 12.22% in the saline irrigation group and 35.56% in the control group, with a difference of 23.33% between the two groups (95% confidence interval [CI], 11.35%-35.32%, p < 0.001). Multivariable Cox proportional hazards analyses showed that constipation (hazard risk [HR] 2.42; 95% CI, 1.22-4.80, p = 0.012), periampullary diverticulum (PAD) (HR 3.06; 95% CI, 1.62-5.79, p < 0.001), and total to direct bilirubin ratio (HR 1.48; 95% CI, 1.21-1.81, p < 0.001) were independent risk factors for the recurrence of CBDS. Saline irrigation was the only preventive factor for the recurrence of CBDS (HR 0.22; 95% CI, 0.11-0.44, p < 0.001). Interpretation: For patients with CBDS requiring mechanical lithotripsy, 100 ml saline irrigation effectively reduces the recurrent rate of CBDS after endoscopic stone removal. Funding: This work was supported by National Natural Science Foundation of China (32160255); Natural Science Foundation of Gansu Province (22JR5RA898, 20JR10RA676); Science and Technology Planning Project of Chengguan District in Lanzhou (2020JSCX0043).
Language	English
Publishing date	2023-04-27
Publishing country	England
Document type	Journal Article
ISSN	2589-5370
ISSN (online)	2589-5370
DOI	10.1016/j.eclinm.2023.101978
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