tbuckley/cabot-search huggingface dataset:
Novel Lipid-Lowering Therapies to Reduce Cardiovascular Risk
Authors: John T. Wilkins, Donald M. Lloyd-Jones
Journal: JAMA (2021)

This JAMA Insights Clinical Update reviews lipid-lowering therapies prescribed to reduce cardiovascular risk, including statins and ezetimibe, as well as novel therapies such as PCSK-9 inhibitors, bempedoic acid, icosapent ethyl, and inclisiran.
MO8-5 Planned drug holidays during treatment with lenvatinib for radioiodine-refractory differentiated thyroid cancer
Authors: Chihiro Matsuyama, Yuri Ueda, Shinya Suzuki, Takao Fujisawa, Kazue Ito, Tomohiro Enokida, Susumu Okano, Makoto Tahara
Journal: Annals of Oncology (2021)
MO16-3 Results of the first survey using EORTC QLQ INFO25 on information acquisition and satisfaction of lung cancer patients
Authors: Hidefumi Shimizu, Takayuki Takahama, Hiroyasu Kaneda, Hidehito Horinouchi, Takeshi Yoshida, Kiyotaka Watanabe, Kazuo Hasegawa, Kouji Onishi, Kenichi Yoshimura, Toshiyuki Sawa, Akihiko Gemma
Journal: Annals of Oncology (2021)
Bodily Changes in Pain, Hunger, Fear and Rage. An Account of Recent Researches into the Function of Emotional Excitement.
Journal: JAMA (1920)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Long-term Outcomes of Laparoscopic Lavage for Perforated Diverticulitis Remain Unfavorable
Authors: Sergio A. Acuna, Fahima Dossa, Tyler R. Chesney
Journal: JAMA Surgery (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Surgery HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Surgery journal
sTREM-1 is a specific biomarker of TREM-1 pathway activation
Authors: Lucie Jolly, Kévin Carrasco, Margarita Salcedo-Magguilli, Jean-Jacques Garaud, Simon Lambden, Tom van der Poll, Alexandre Mebazaa, Pierre-François Laterre, Sebastien Gibot, Amir Boufenzer, Marc Derive
Journal: Cellular and Molecular Immunology (2021)
Abstract 14323: Enhanced Oxidative Stress is Correlated With Skeletal Muscle Abnormalities in Patients With Metabolic Syndrome
Authors: Shintaro Kinugawa, Takashi Yokota, Kagami Hirabayashi, Tadashi Suga, Masashige Takahashi, Shingo Takada, Koichi Okita, Hiroyuki Tsutsui
Journal: Circulation (2011)

Background: We have previously reported that intramyocellular lipid (IMCL) is increased and high-energy phosphate metabolism is impaired in the skeletal muscle in patients with metabolic syndrome (...
Resistin deletion protects against heart failure injury by targeting DNA damage response
Authors: Baoyin Zhao, Rihab Bouchareb, Djamel Lebeche
Journal: Cardiovascular Research (2021)

Abstract Aims Increased resistin (Retn) levels are associated with development of cardiovascular diseases. However, the role of Retn in heart failure (HF) is still unclear. Here we probed the functional and molecular mechanism underlying the beneficial effect of Retn deletion in HF. Methods and results Wild-type (WT) and adipose tissue-specific Retn-knockout (RKO) mice were subjected to transverse aortic constriction (TAC)-induced HF. Cardiac function and haemodynamic changes were measured by echocardiography and left ventricular catheterization. Adipose tissue Retn deletion attenuated while Retn cardiac-selective overexpression, via a recombinant adeno-associated virus-9 vector, exacerbated TAC-induced hypertrophy, cardiac dysfunction, and myocardial fibrosis in WT and RKO mice. Mechanistically, we showed that Gadd45α was significantly increased in RKO HF mice while cardiac overexpression of Retn led to its downregulation. miR148b-3p directly targets Gadd45α and inhibits its expression. Retn overexpression upregulated miR148b-3p expression and triggered DNA damage response (DDR) in RKO-HF mice. Inhibition of miR148b-3p in vivo normalized Gadd45α expression, decreased DDR, and reversed cardiac dysfunction and fibrosis. In vitro Retn overexpression in adult mouse cardiomyocytes activated miR148b-3p and reduced Gadd45α expression. Gadd45α overexpression in H9C2-cardiomyoblasts protected against hydrogen peroxide- and Retn-induced DDR. Conclusion These findings reveal that diminution in circulating Retn reduced myocardial fibrosis and apoptosis, and improved heart function in a mouse model of HF, at least in part, through attenuation of miR148b-3p and DDR. The results of this study indicate that controlling Retn levels may provide a potential therapeutic approach for treating pressure overload-induced HF.
Combining sonodynamic therapy with chemoradiation for the treatment of pancreatic cancer
Authors: Richard J. Browning, Sarah Able, Jia-Ling Ruan, Luca Bau, Philip D. Allen, Veerle Kersemans, Sheena Wallington, Paul Kinchesh, Sean Smart, Christiana Kartsonaki, Sukanta Kamila, Keiran Logan, Mark A. Taylor, Anthony P. McHale, John F. Callan, Eleanor Stride, Katherine A. Vallis
Journal: Journal of Controlled Release (2021)
PCI for Nonculprit Lesions in Patients with STEMI — No Role for FFR
Authors: Peter Jüni
Journal: New England Journal of Medicine (2021)

Approximately 50% of patients with acute ST-segment elevation myocardial infarction (STEMI) have multivessel disease.1 For such patients, a major clinical question has been whether percutaneous coronary intervention (PCI) should be performed only on the coronary occlusion causing the infarct (the culprit lesion) or whether other stenoses (nonculprit lesions) should also be treated during, or soon after, the culprit-lesion procedure. Seven small or midsize trials involving a total of 1939 patients with STEMI that were published through 2015 suggested that early PCI of nonculprit lesions was associated with a lower risk of major adverse cardiac events than culprit-lesion-only PCI, driven by . . .
The potential of SARS-CoV-2 antigen-detection tests in the screening of asymptomatic persons
Authors: Jonas Wachinger, Ioana Diana Olaru, Susanne Horner, Paul Schnitzler, Klaus Heeg, Claudia M. Denkinger
Journal: Clinical Microbiology and Infection (2021)

The aim was to assess the performance of antigen-based rapid diagnostic tests (Ag-RDTs) for SARS CoV-2 when implemented for large-scale universal screening of asymptomatic individuals. This study was a pragmatic implementation study for universal Ag-RDT-based screening at a tertiary care hospital in Germany where patients presenting for elective procedures and selected personnel without symptoms suggestive of SARS-CoV-2 were screened with an Ag-RDT since October 2020. Test performance was calculated on an individual patient level. In total, 49 542 RDTs were performed in 27 421 asymptomatic individuals over a duration of 5 and a half months. Out of 222 positive results, 196 underwent in-house confirmatory testing with PCR, out of which 170 were confirmed positive, indicating a positive predictive value of 86.7% (95% CI 81.2-91.1%). Negative Ag-RDTs were not routinely tested with PCR, but a total of 94 cases of false negative Ag-RDTs were detected due to PCR tests being performed within the following 5 days with a median cycle threshold value of 33 (IQR 29-35). This study provides evidence that Ag-RDTs can have a high diagnostic yield for transmission relevant infections with limited false positives when utilized at the point of care on asymptomatic patients and thus can be a suitable public health test for universal screening.
Covid-19 Breakthrough Infections in Vaccinated Health Care Workers
Authors: Moriah Bergwerk, Tal Gonen, Yaniv Lustig, Sharon Amit, Marc Lipsitch, Carmit Cohen, Michal Mandelboim, Einav Gal Levin, Carmit Rubin, Victoria Indenbaum, Ilana Tal, Malka Zavitan, Neta Zuckerman, Adina Bar-Chaim, Yitshak Kreiss, Gili Regev-Yochay
Journal: New England Journal of Medicine (2021)

BackgroundDespite the high efficacy of the BNT162b2 messenger RNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rare breakthrough infections have been reported, including infections among health care workers. Data are needed to characterize these infections and define correlates of breakthrough and infectivity.MethodsAt the largest medical center in Israel, we identified breakthrough infections by performing extensive evaluations of health care workers who were symptomatic (including mild symptoms) or had known infection exposure. These evaluations included epidemiologic investigations, repeat reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assays, antigen-detecting rapid diagnostic testing (Ag-RDT), serologic assays, and genomic sequencing. Correlates of breakthrough infection were assessed in a case–control analysis. We matched patients with breakthrough infection who had antibody titers obtained within a week before SARS-CoV-2 detection (peri-infection period) with four to five uninfected controls and used generalized estimating equations to predict the geometric mean titers among cases and controls and the ratio between the titers in the two groups. We also assessed the correlation between neutralizing antibody titers and N gene cycle threshold (Ct) values with respect to infectivity.Download a PDF of the Research Summary.ResultsAmong 1497 fully vaccinated health care workers for whom RT-PCR data were available, 39 SARS-CoV-2 breakthrough infections were documented. Neutralizing antibody titers in case patients during the peri-infection period were lower than those in matched uninfected controls (case-to-control ratio, 0.361; 95% confidence interval, 0.165 to 0.787). Higher peri-infection neutralizing antibody titers were associated with lower infectivity (higher Ct values). Most breakthrough cases were mild or asymptomatic, although 19% had persistent symptoms (>6 weeks). The B.1.1.7 (alpha) variant was found in 85% of samples tested. A total of 74% of case patients had a high viral load (Ct value, <30) at some point during their infection; however, of these patients, only 17 (59%) had a positive result on concurrent Ag-RDT. No secondary infections were documented.ConclusionsAmong fully vaccinated health care workers, the occurrence of breakthrough infections with SARS-CoV-2 was correlated with neutralizing antibody titers during the peri-infection period. Most breakthrough infections were mild or asymptomatic, although persistent symptoms did occur. Quick Take Covid-19 in Vaccinated Health Care Workers 1m 58s
Activation of Autophagy in Models of SF3B1 Mutant MDS
Authors: Valeria Visconte, Vera Adema, Bartlomiej P. Przychodzen, Allison Noe, Rachel Toth, Yasmine Hirbawi, Cassandra M. Hirsch, Jack Khouri, Elise LeMelle, Suresh K. Balasubramanian, Hetty E. Carraway, Daniel Lindner, Anjali S. Advani, Heesun J. Rogers, James G Phillips, Tomas Radivoyevitch, Kevin R Kelly, Steffan T. Nawrocki, Mikkael A. Sekeres, Jaroslaw P. Maciejewski, Jennifer Carew
Journal: Blood (2017)
IL-23/IL-17A/TRPV1 axis produces mechanical pain via macrophage-sensory neuron crosstalk in female mice
Authors: Xin Luo, Ouyang Chen, Zilong Wang, Sangsu Bang, Jasmine Ji, Sang Hoon Lee, Yul Huh, Kenta Furutani, Qianru He, Xueshu Tao, Mei-Chuan Ko, Andrey Bortsov, Christopher R Donnelly, Yong Chen, Andrea Nackley, Temugin Berta, Ru-Rong Ji
Journal: Neuron (2021)

Although sex dimorphism is increasingly recognized as an important factor in pain, female-specific pain signaling is not well studied. Here we report that administration of IL-23 produces mechanical pain (mechanical allodynia) in female but not male mice, and chemotherapy-induced mechanical pain is selectively impaired in female mice lacking Il23 or Il23r. IL-23-induced pain is promoted by estrogen but suppressed by androgen, suggesting an involvement of sex hormones. IL-23 requires C-fiber nociceptors and TRPV1 to produce pain but does not directly activate nociceptor neurons. Notably, IL-23 requires IL-17A release from macrophages to evoke mechanical pain in females. Low-dose IL-17A directly activates nociceptors and induces mechanical pain only in females. Finally, deletion of estrogen receptor subunit α (ERα) in TRPV1+ nociceptors abolishes IL-23- and IL-17-induced pain in females. These findings demonstrate that the IL-23/IL-17A/TRPV1 axis regulates female-specific mechanical pain via neuro-immune interactions. Our study also reveals sex dimorphism at both immune and neuronal levels.
2014 AHA/ACC Guideline for the Management of Patients With Non–ST-Elevation Acute Coronary Syndromes
Authors: Ezra A. Amsterdam, Nanette K. Wenger, Ralph G. Brindis, Donald E. Casey, Theodore G. Ganiats, David R. Holmes, Allan S. Jaffe, Hani Jneid, Rosemary F. Kelly, Michael C. Kontos, Glenn N. Levine, Philip R. Liebson, Debabrata Mukherjee, Eric D. Peterson, Marc S. Sabatine, Richard W. Smalling, Susan J. Zieman
Journal: Circulation (2014)
Distinct transcription factor networks control neutrophil-driven inflammation
Authors: Tariq E. Khoyratty, Zhichao Ai, Ivan Ballesteros, Hayley L. Eames, Sara Mathie, Sandra Martín-Salamanca, Lihui Wang, Ashleigh Hemmings, Nicola Willemsen, Valentin von Werz, Annette Zehrer, Barbara Walzog, Erinke van Grinsven, Andres Hidalgo, Irina A. Udalova
Journal: Nature Immunology (2021)
Antimicrobial Peptides: Delivery by Dendritic Mesoporous Silica Nanoparticles Enhances the Antimicrobial Activity of a Napsin‐Derived Peptide Against Intracellular <i>Mycobacterium tuberculosis</i> (Adv. Healthcare Mater. 14/2021)
Authors: Bastian Beitzinger, Fabian Gerbl, Thomas Vomhof, Roman Schmid, Reiner Noschka, Armando Rodriguez, Sebastian Wiese, Gilbert Weidinger, Ludger Ständker, Paul Walther, Jens Michaelis, Mika Lindén, Steffen Stenger
Journal: Advanced Healthcare Materials (2021)

In article number 2100453 by Steffen Stenger, Mika Lindén, and co-workers, the activity of the antimicrobial peptide NapFab against intracellular Mycobacterium tuberculosis (Mtb) is significantly increased by loading onto dendritic mesoporous silica nanoparticles (DMSN). This enhanced activity is based on a 30-fold increased, DMSN-mediated peptide uptake. Livecell fluorescence microscopy and electron microscopy reveal fast DMSN uptake in endosomal vesicles, intracellular degradation of the carrier, and a continuous peptide release.
Beware of regional heterogeneity when assessing the role of schools in the SARS-CoV-2 second wave in Italy
Authors: Simona Bignami-Van Assche, Yacine Boujija, Daniela Ghio, Nikolaos I. Stilianakis
Journal: The Lancet Regional Health - Europe (2021)

opening regional heterogeneity disease incidenceGandini et al. [1] argue that school opening was not a driver of the SARS-CoV-2 second wave in Italy.We contend this is an overreaching interpretation of their results.First, contrary to what indicated by the authors, cross-sectionally the incidence of SARS-CoV-2 among students age 14À18 is higher than the general population in 8 out of 18 regions considered (see Fig. 1.b in Gandini et al. [1]).Second, Gandini et al. [1]'s prospective analysis focuses on the temporal relationship between school opening and COVID-19 transmission in the Veneto region until November 7, 2020.However, consistently with the different implementation of public health measures at the sub-national level and the distinctive pandemic evolution and management in the Veneto region, evidence for 12 regions under monitoring by the Italian Epidemiological Association reveals substantial geographic variation in the role of school opening for Italy's second wave.Notably, at the end of September 2020, the rise in incidence among high school students age 14À18 preceded that of adults age 25+ in Emilia-Romagna, Lazio, Lombardy, Marche, Piemonte, and Tuscany [2] À the same regions (except for Lombardy) where Gandini et al. [1] find a higher incidence of SARS-CoV-2 among students age 14À18 than the general population (see Fig. 1.b).Official data from the Istituto Superiore di Sanit a confirm that, nationally, the rise in incidence among 10À19 years old has preceded that of adults age 30+ after school opening in Fall 2020 [3].The role of school openings on the second COVID-19 wave in Italy should thus not be minimized.
Probing the fluorination effect on the self-assembly characteristics, <i>in vivo</i> fate and antitumor efficacy of paclitaxel prodrug nanoassemblies
Authors: Xin Wang, Bin Yang, Lingxiao Li, Tian Liu, Shiyi Zuo, Dongxu Chi, Zhonggui He, Bingjun Sun, Jin Sun
Journal: Theranostics (2021)

Rationale: Small-molecule prodrug nanoassembly is emerging as an efficient platform for chemotherapy.The self-assembly stability plays a vital role on the drug delivery efficiency of prodrug nanoassembly.It is reported that fluoroalkylation could improve the self-assembly stability of amphiphilic polymers by utilizing the unique fluorination effect.But the application of fluoroalkylation on small-molecule prodrug nanoassembly has never been reported.Methods: Here, fluoro-modified prodrug was developed by conjugating paclitaxel with perfluorooctanol (F8-SS-PTX), and the paclitaxel-octanol prodrug (C8-SS-PTX) was used as control.The fluoro-mediated self-assembly mechanisms were illustrated using molecular dynamics simulation.In addition, the impacts of fluoroalkylation on the pharmacy characters, in vivo fate and antitumor effect of small-molecule prodrug nanoassembly were investigated in details.Results: Fluoroalkylation significantly improved the self-assembly stability of F8-SS-PTX NPs both in vitro and in vivo, which could be attributed to the fluoro-mediated hydrophobic force and halogen bonds.The AUC0-24h and tumor accumulation of F8-SS-PTX NPs was 6-fold and 2-fold higher than that of C8-SS-PTX NPs, respectively.As a result, F8-SS-PTX NPs exhibited much better antitumor effect than C8-SS-PTX NPs and Abraxane.Conclusion: Fluoroalkylation could improve the self-assembly stability, in vivo fate, and antitumor efficacy of small-molecule prodrug nanoassemblies, which could be an effective strategy for the rational design of advanced nanomedicines.
Using Updated PubMed
Authors: Pauline Kang, Michael Kalloniatis, Gordon S. Doig
Journal: JAMA (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA HomeNew OnlineCurrent IssueFor Authors Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA journal
Frequency, clinical features and outcomes of COVID-19 in patients with IgG4-related hepato-pancreato-biliary disease: a collaborative European multi-centre study
Authors: G. A. Ramirez, M. Lanzillotta, M. Ebbo, A. Fernandez-Codina, G. Mancuso, F. Martinez-Valle, O. Orozco-Galvez, L. Smith, N. Schleinitz, L. Dagna, E. Della Torre, E. Culver
Journal: Journal of Hepatology (2021)
Onychomadesis and onycholysis associated with capecitabine
Authors: G-Y. Chen, Y-H. Chen, M.M.L. Hsu, C-J. Tsao, W-C. Chen
Journal: British Journal of Dermatology (2008)

Journal Article Onychomadesis and onycholysis associated with capecitabine Get access G‐Y. Chen, G‐Y. Chen Departments of Dermatology and *Haemato‐Oncology, College of Medicine, National Cheng Kung University Hospital, 138 Sheng‐Li Road, 704 Tainan, Taiwan Correspondence: W‐C.Chen.E‐mail: wchen@mail.ncku.edu.tw Search for other works by this author on: Oxford Academic Google Scholar Y‐H. Chen, Y‐H. Chen Departments of Dermatology and *Haemato‐Oncology, College of Medicine, National Cheng Kung University Hospital, 138 Sheng‐Li Road, 704 Tainan, Taiwan Correspondence: W‐C.Chen.E‐mail: wchen@mail.ncku.edu.tw Search for other works by this author on: Oxford Academic Google Scholar M.M.L. Hsu, M.M.L. Hsu Departments of Dermatology and *Haemato‐Oncology, College of Medicine, National Cheng Kung University Hospital, 138 Sheng‐Li Road, 704 Tainan, Taiwan Correspondence: W‐C.Chen.E‐mail: wchen@mail.ncku.edu.tw Search for other works by this author on: Oxford Academic Google Scholar C‐J. Tsao, C‐J. Tsao Departments of Dermatology and *Haemato‐Oncology, College of Medicine, National Cheng Kung University Hospital, 138 Sheng‐Li Road, 704 Tainan, Taiwan Correspondence: W‐C.Chen.E‐mail: wchen@mail.ncku.edu.tw Search for other works by this author on: Oxford Academic Google Scholar W‐C. Chen W‐C. Chen Departments of Dermatology and *Haemato‐Oncology, College of Medicine, National Cheng Kung University Hospital, 138 Sheng‐Li Road, 704 Tainan, Taiwan Correspondence: W‐C.Chen.E‐mail: wchen@mail.ncku.edu.tw Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 145, Issue 3, 1 September 2001, Pages 521–522, https://doi.org/10.1111/j.1365-2133.2001.04391.x Published: 01 September 2001
DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
Authors: Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Journal: Genome biology (2021)

Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells.