tbuckley/cabot-search huggingface dataset:
Congenital Tooth Agenesis and Risk of Early-Onset Cancer
Authors: Saga Elise Eiset, Jeremy Schraw, Gitte Vrelits Sørensen, Pernille Axél Gregersen, Sonja A. Rasmussen, Cecilia H. Ramlau-Hansen, Philip J. Lupo, Henrik Hasle
Journal: JAMA Network Open (2024)

Importance There is some evidence that tooth agenesis (congenital absence of 1 or more teeth) is associated with cancer risk, especially carcinomas of the colon and ovaries, but results of previous studies are conflicting, and associations have not yet been evaluated in a population-based setting. Objective To examine the association between tooth agenesis and specific cancer types before 40 years of age. Design, Setting, and Participants This population-based cohort study used linking data from nationwide registries in Denmark to assess all Danish live-born singletons born from January 1, 1977, to December 31, 2018, and followed up for up to 40 years. Data were analyzed from January through June 2023. Exposure Tooth agenesis as documented by the Danish Central Registry of Odontology (Danish municipal pediatric dental care) from January 1, 1988, to December 31, 2018, and from hospital encounters in the Danish National Patient Registry within the entire study period. Main Outcome and Measures The primary outcome was first cancer diagnosis before 40 years of age obtained from the Danish Cancer Registry. Associations between tooth agenesis and specific cancers were estimated by Cox proportional hazards regression as hazard ratios (HRs) with 95% CIs. Analyses were split into age groups: younger than 1 year, 1 to younger than 3 years, 3 to younger than 10 years, 10 to younger than 20 years, 20 to younger than 30 years, and 30 to younger than 40 years. Associations with nonsyndromic tooth agenesis were evaluated after exclusion of individuals with known syndromes. Results Among 2 501 715 included individuals (1 284 292 [51.3%] male), 70 288 (2.8%) had a diagnosis of tooth agenesis (mean [SD] age at diagnosis, 13.2 [4.1] years) and 26 308 (1.1%) had a diagnosis of early-onset cancer within the study period; 778 individuals had co-occurrence of tooth agenesis and cancer. Overall, tooth agenesis was positively associated with several cancer types, including neuroblastoma (age 1 to &amp;amp;lt;3 years; HR, 4.20; 95% CI, 2.24-7.88), nephroblastoma (age 1 to &amp;amp;lt;3 years; HR, 4.59; 95% CI, 2.37-8.91), hepatoblastoma (age 1 to &amp;amp;lt;3 years; HR, 7.10; 95% CI, 2.70-18.68), osteosarcoma (age 10 to &amp;amp;lt;20 years; HR, 2.19; 95% CI, 1.11-4.32), colorectal carcinomas (age 30 to &amp;amp;lt;40 years; HR, 2.81; 95% CI, 1.38-5.71), and carcinomas of bladder (age 20 to &amp;amp;lt;30 years; HR, 3.35; 95% CI, 1.35-8.30). Conclusions and Relevance This cohort study found associations between congenital tooth agenesis and several cancer types, from childhood to early adulthood. Further evaluation of these associations is needed to assess possible clinical implications.
Stage-Stratified Incidence Rates of Colorectal Adenocarcinoma Among Patients Aged 46 to 49 in the United States
Authors: Eric M. Montminy, Meijiao Zhou, Jerome C. Edelson, Jordan J. Karlitz
Journal: JAMA Network Open (2024)

This cross-sectional study uses Surveillance, Epidemiology, and End Results registry data to analyze colorectal adenocarcinoma staging incidence of patients aged 46 to 49 years from 2000 to 2020.
Meta-Analysis: Females at Higher Risk of Death From Staph Infection
Authors: Samantha Anderer
Journal: JAMA (2024)

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Indigenous data governance approaches applied in research using routinely collected health data: a scoping review
Authors: Teyl Engstrom, Elton H. Lobo, Kristie Watego, Carmel Nelson, Jinxiang Wang, Howard Wong, Sungkyung Linda Kim, Soo In Oh, Michael Lawley, Alain-Dominique Gorse, James Ward, Clair Sullivan
Journal: npj Digital Medicine (2024)

Globally, there is a growing acknowledgment of Indigenous Peoples' rights to control data related to their communities. This is seen in the development of Indigenous Data Governance standards. As health data collection increases, it's crucial to apply these standards in research involving Indigenous communities. Our study, therefore, aims to systematically review research using routinely collected health data of Indigenous Peoples, understanding the Indigenous Data Governance approaches and the associated advantages and challenges. We searched electronic databases for studies from 2013 to 2022, resulting in 85 selected articles. Of these, 65 (77%) involved Indigenous Peoples in the research, and 60 (71%) were authored by Indigenous individuals or organisations. While most studies (93%) provided ethical approval details, only 18 (21%) described Indigenous guiding principles, 35 (41%) reported on data sovereignty, and 28 (33%) addressed consent. This highlights the increasing focus on Indigenous Data Governance in utilising health data. Leveraging existing data sources in line with Indigenous data governance principles is vital for better understanding Indigenous health outcomes.
Bispecific immune cell engager enhances the anticancer activity of CD16+ NK cells and macrophages in vitro, and eliminates cancer metastasis in NK humanized NOG mice
Authors: Shahryar Khoshtinat Nikkhoi, Ge Yang, Hajar Owji, Mayara Grizotte-Lake, Rick I Cohen, Lazaro Gil Gonzalez, Mohammad Massumi, Arash Hatefi
Journal: Journal for ImmunoTherapy of Cancer (2024)

Background In a prior report, we detailed the isolation and engineering of a bispecific killer cell engager, referred to as BiKE:E5C1. The BiKE:E5C1 exhibits high affinity/specificity for the CD16a activating receptor on natural killer (NK) cells and human epidermal growth factor receptor 2 (HER2) on cancer cells. In vitro studies have demonstrated that BiKE:E5C1 can activate the NK cells and induce the killing of HER2+ ovarian and breast cancer cells, surpassing the performance of the best-in-class monoclonal antibody, Trazimera (trastuzumab). To advance this BiKE technology toward clinical application, the objective of this research was to demonstrate the ability of BiKE:E5C1 to activate CD16+ immune cells such as NK cells and macrophages to kill cancer cells, and eradicate metastatic HER2+ tumors in NK humanized NOG mice. Methods We assessed BiKE:E5C1’s potential to activate CD16-expressing peripheral blood (PB)-NK cells, laNK92 cells, and THP-1-CD16A monocyte-macrophages through flowcytometry and antibody-dependent cell-mediated cytotoxicity/phagocytosis (ADCC) assays. Subsequently, laNK92 cells were selected as effector cells and genetically modified to express the nanoluciferase gene, enabling the monitoring of their viability in NK humanized NOG mice using quantitative bioluminescent imaging (qBLI). To evaluate the functionality of BiKE:E5C1 in vivo, we introduced firefly luciferase-expressing ovarian cancer cells via intraperitoneal injection into hIL-15 and hIL-2 NOG mice, creating a model of ovarian cancer metastasis. Once tumor establishment was confirmed, we treated the mice with laNK92 cells plus BiKE:E5C1 and the response to therapy was assessed using qBLI. Results Our data demonstrate that BiKE:E5C1 activates not only laNK92 cells but also PB-NK cells and macrophages, significantly enhancing their anticancer activities. ADCC assay demonstrated that IgG 1 Fc region had no impact on BiKE:E5C1’s anticancer activity. In vivo results reveal that both hIL-15 and hIL-2 NOG mouse models support the viability and proliferation of laNK92 cells. Furthermore, it was observed that BiKE:E5C1 activates laNK92 cells in mice, leading to eradication of cancer metastasis in both NK humanized hIL-15 and hIL-2 NOG mouse models. Conclusions Collectively, our in vivo findings underscore BiKE:E5C1’s potential as an immune cell engager capable of activating immune cells for cancer cell elimination, thereby expanding the arsenal of available BiKEs for cancer immunotherapy.
Effect of Patient Navigation on Completion of Lung Cancer Screening in Vulnerable Populations
Authors: Sheena Bhalla, Vijaya Natchimuthu, Jessica L. Lee, Urooj Wahid, Hong Zhu, Noel O. Santini, Travis Browning, Heidi A. Hamann, David H. Johnson, Hsienchang Chiu, Simon J. Craddock Lee, David E. Gerber
Journal: Journal of the National Comprehensive Cancer Network (2024)

Although low-dose, CT-based lung cancer screening (LCS) can decrease lung cancer mortality in high-risk individuals, the process may be complex and pose challenges to patients, particularly those from minority underinsured and uninsured populations. We conducted a randomized controlled trial of telephone-based navigation for LCS within an integrated, urban, safety-net health care system.
Drug stewardship in chronic kidney disease to achieve effective and safe medication use
Authors: Rasheeda K. Hall, Rümeyza Kazancıoğlu, Teerawat Thanachayanont, Germaine Wong, Dharshana Sabanayagam, Marisa Battistella, Sofia B. Ahmed, Lesley A. Inker, Erin F. Barreto, Edouard L. Fu, Catherine M. Clase, Juan J. Carrero
Journal: Nature Reviews Nephrology (2024)
Proteomic characterization of esophageal squamous cell carcinoma response to immunotherapy reveals potential therapeutic strategy and predictive biomarkers
Authors: Fahan Ma, Yan Li, Chan Xiang, Bing Wang, Jie Lv, Jinzhi Wei, Zhaoyu Qin, Yan Pu, Kai Li, Haohua Teng, Subei Tan, Jinwen Feng, Zhanxian Shang, Yunzhi Wang, Sha Tian, Changsheng Du, Yuchen Han, Chen Ding
Journal: Journal of Hematology & Oncology (2024)

Immunotherapy is the first-line therapy for esophageal squamous cell carcinoma (ESCC), yet many patients do not respond due to drug resistance and the lack of reliable predictive markers. We collected 73 ESCC patients (including discovery cohort and validation cohort) without immune thrombocytopenia and undergoing anti-PD1 immunotherapy. Proteomic and phosphoproteomic analysis of 73 ESCC treatment-naive samples by mass spectrometry-based label-free quantification were applied to explore the potential resistant and sensitive mechanisms, and identify predictive markers of ESCC immunotherapy. Comparative analysis found the pathways related to immune and mitochondrial functions were associated with ESCC immunotherapy sensitivity; while platelet activation bioprocess showed negative correlation with CD8+ T cells and related to ESCC immunotherapy non-sensitivity. Finally, we identified 10 ESCC immunotherapy predictive biomarkers with high accuracy (≥ 0.90) to predict the immunotherapeutic response, which was validated in the independent cohort.
Re: Annika Herlemann, Janet E. Cowan, Samuel L. Washington 3rd, et al. Long-term Prostate Cancer-specific Mortality After Prostatectomy, Brachytherapy, External Beam Radiation Therapy, Hormonal Therapy, or Monitoring for Localized Prostate Cancer. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2023.09.024
Authors: Olivier Cussenot, Antoine Chambaz, Freddie C. Hamdy
Journal: European Urology (2024)
NCI Cancer Research Data Commons: Cloud-Based Analytic Resources
Authors: David Pot, Zelia Worman, Alexander Baumann, Shirish Pathak, Rowan Beck, Erin Beck, Katherine Thayer, Tanja M. Davidsen, Erika Kim, Brandi Davis-Dusenbery, John Otridge, Todd Pihl, the CRDC Program, Jill S. Barnholtz-Sloan, Anthony R. Kerlavage
Journal: Cancer Research (2024)

Abstract The NCI's Cloud Resources (CR) are the analytical components of the Cancer Research Data Commons (CRDC) ecosystem. This review describes how the three CRs (Broad Institute FireCloud, Institute for Systems Biology Cancer Gateway in the Cloud, and Seven Bridges Cancer Genomics Cloud) provide access and availability to large, cloud-hosted, multimodal cancer datasets, as well as offer tools and workspaces for performing data analysis where the data resides, without download or storage. In addition, users can upload their own data and tools into their workspaces, allowing researchers to create custom analysis workflows and integrate CRDC-hosted data with their own. See related articles by Brady et al., p. 1384, Wang et al., p. 1388, and Kim et al., p. 1404
Corrigendum to “European Association of Urology Guidelines on Muscle-invasive and Metastatic Bladder Cancer: Summary of the 2023 Guidelines” [Eur. Urol. 85 (2024) 17–31]
Authors: J. Alfred Witjes, Harman Max Bruins, Albert Carrión, Richard Cathomas, Eva Compérat, Jason A. Efstathiou, Rainer Fietkau, Georgios Gakis, Anja Lorch, Alberto Martini, Laura S. Mertens, Richard P. Meijer, Matthew I. Milowsky, Yann Neuzillet, Valeria Panebiaco, John Redlef, Michael Rink, Mathieu Rouanne, George N. Thalmann, Sæbjørn Sæbjørnsen, Erik Veskimäe, Paramananthan Mariappan, Antoine G. van der Heijden
Journal: European Urology (2024)
NCI Cancer Research Data Commons: Resources to Share Key Cancer Data
Authors: Zhining Wang, Tanja M. Davidsen, Gina R. Kuffel, KanakaDurga Addepalli, Amanda Bell, Esmeralda Casas-Silva, Hayley Dingerdissen, Keyvan Farahani, Andrey Fedorov, Sharon Gaheen, Robert L. Grossman, Ron Kikinis, Erika Kim, John Otridge, Todd Pihl, Melissa Porter, Henry Rodriguez, Louis M. Staudt, Ratna R. Thangudu, Sudha Venkatachari, Jean Claude Zenklusen, Xu Zhang, Jill S. Barnholtz-Sloan, Anthony R. Kerlavage
Journal: Cancer Research (2024)

Abstract Since 2014, the NCI has launched a series of data commons as part of the Cancer Research Data Commons (CRDC) ecosystem housing genomic, proteomic, imaging, and clinical data to support cancer research and promote data sharing of NCI-funded studies. This review describes each data commons (Genomic Data Commons, Proteomic Data Commons, Integrated Canine Data Commons, Cancer Data Service, Imaging Data Commons, and Clinical and Translational Data Commons), including their unique and shared features, accomplishments, and challenges. Also discussed is how the CRDC data commons implement Findable, Accessible, Interoperable, Reusable (FAIR) principles and promote data sharing in support of the new NIH Data Management and Sharing Policy. See related articles by Brady et al., p. 1384, Pot et al., p. 1396, and Kim et al., p. 1404
Local origin of excitatory–inhibitory tuning equivalence in a cortical network
Authors: Adrian J. Duszkiewicz, Pierre Orhan, Sofia Skromne Carrasco, Eleanor H. Brown, Eliott Owczarek, Gilberto R. Vite, Emma R. Wood, Adrien Peyrache
Journal: Nature Neuroscience (2024)

Abstract The interplay between excitation and inhibition determines the fidelity of cortical representations. The receptive fields of excitatory neurons are often finely tuned to encoded features, but the principles governing the tuning of inhibitory neurons remain elusive. In this study, we recorded populations of neurons in the mouse postsubiculum (PoSub), where the majority of excitatory neurons are head-direction (HD) cells. We show that the tuning of fast-spiking (FS) cells, the largest class of cortical inhibitory neurons, was broad and frequently radially symmetrical. By decomposing tuning curves using the Fourier transform, we identified an equivalence in tuning between PoSub-FS and PoSub-HD cell populations. Furthermore, recordings, optogenetic manipulations of upstream thalamic populations and computational modeling provide evidence that the tuning of PoSub-FS cells has a local origin. These findings support the notion that the equivalence of neuronal tuning between excitatory and inhibitory cell populations is an intrinsic property of local cortical networks.
GDF1 ameliorates cognitive impairment induced by hearing loss
Authors: Lina Pan, Chunrui Li, Lanxia Meng, Guoxin Zhang, Li Zou, Ye Tian, Sen Chen, Yu Sun, Dandan Su, Xingyu Zhang, Min Xiong, Tingting Xiao, Danhao Xia, Zhengyuan Hong, Zhentao Zhang
Journal: Nature Aging (2024)
Bacteria-mediated resistance of neutrophil extracellular traps to enzymatic degradation drives the formation of dental calculi
Authors: Mei-chen Wan, Kai Jiao, Yi-na Zhu, Qian-qian Wan, Yi-peng Zhang, Long-zhang Niu, Chen Lei, Jing-han Song, Wei-cheng Lu, Hua-jie Liu, Zhao-yang Ren, Franklin Tay, Li-na Niu
Journal: Nature Biomedical Engineering (2024)
Surveillance of infections of surgical sites and lower respiratory tracts should be combined: experiences from the German surveillance module for operated patients (OP-KISS), 2018 to 2022
Authors: Seven Johannes Sam Aghdassi, Selin Saydan, Michael Behnke, Jörg Clausmeyer, Petra Gastmeier, Christine Geffers
Journal: Eurosurveillance (2024)

BackgroundSurveillance of lower respiratory tract infections (LRTI) of operated patients conventionally focuses on intubated patients in intensive care units (ICU). Post-operative immobilisation increases the risk of LRTI not associated with ventilators. Operated patients, however, have thus far not been a primary target for LRTI surveillance.AimWe aimed to describe the applied LRTI surveillance method in the German surveillance module for operated patients (OP-KISS) and to report data between 2018 and 2022.MethodsSurveillance of LRTI can be performed voluntarily in addition to surgical site infection (SSI) surveillance in OP-KISS. We calculated LRTI rates per 100 operations for all procedures combined, as well as for individual surgical groups and procedures. Additionally, a combined post-operative infection rate (SSI and LRTI) was calculated.ResultsSurveillance of LRTI was performed in 4% of all participating OP-KISS departments and for 2% (23,239 of 1,332,438) of all procedures in the OP-KISS database. The pooled LRTI rate was 0.9 per 100 operations, with marked differences between different types of surgery (3.6 for lobectomies, 0.1 for traumatology and orthopaedics). The share of LRTI among all post-operative infections was highly variable. For lobectomies, the LRTI rate was higher than the SSI rate (3.6 vs 1.5 per 100 operations).ConclusionSurveillance of post-operative LRTI is not yet widely adopted by German hospitals. Based on the data in this study, lobectomies represent a prime target for post-operative LRTI surveillance.
Regional dissemination of NDM-1 producing Enterobacter hormaechei ST1740, with a subset of strains co-producing VIM-4 or IMP-13, France, 2019 to 2022
Authors: Inès Rezzoug, Cécile Emeraud, Christophe Rodriguez, Jean-Michel Pawlotsky, Rémy A. Bonnin, Laurent Dortet
Journal: Eurosurveillance (2024)

Background From 2019 to 2022, the French National Reference Centre for Antibiotic Resistance (NRC) received a total of 25 isolates of Enterobacter hormaechei subsp. hoffmannii sequence type (ST)1740. All produced metallo-β-lactamase(s) and were from the Lyon area. Aim To understand these strains’ spread and evolution, more extended microbiological and molecular analyses were conducted. Methods Patients’ demographics and specimen type related to isolates were retrieved. All strains underwent short-read whole genome sequencing, and for 15, long-read sequencing to understand carbapenemase-gene acquisition. Clonal relationships were inferred from core-genome single nt polymorphisms (SNPs). Plasmids and the close genetic environment of each carbapenemase-encoding gene were analysed. Results Patients (10 female/15 male) were on average 56.6 years old. Seven isolates were recovered from infections and 18 through screening. With ≤ 27 SNPs difference between each other’s genome sequences, the 25 strains represented a clone dissemination. All possessed a chromosome-encoded bla NDM-1 gene inside a composite transposon flanked by two IS 3000 . While spreading, the clone independently acquired a bla VIM-4 -carrying plasmid of IncHI2 type (n = 12 isolates), or a bla IMP-13 -carrying plasmid of IncP-1 type (n = 1 isolate). Of the 12 isolates co-producing NDM-1 and VIM-4, seven harboured the colistin resistance gene mcr9.2 ; the remaining five likely lost this gene through excision. Conclusion This long-term outbreak was caused by a chromosome-encoded NDM-1-producing ST1740 E. hormaechei subsp. hoffmannii clone, which, during its dissemination, acquired plasmids encoding VIM-4 or IMP-13 metallo-β-lactamases. To our knowledge, IMP-13 has not prior been reported in Enterobacterales in France. Epidemiological and environmental investigations should be considered alongside microbiological and molecular ones.
High proportion of post-migration HIV acquisition in migrant men who have sex with men receiving HIV care in the Paris region, and associations with social disadvantage and sexual behaviours: results of the ANRS-MIE GANYMEDE study, France, 2021 to 2022
Authors: Romain Palich, Andrés Arias-Rodríguez, Martin Duracinsky, Jean-Yves Le Talec, Olivia Rousset Torrente, Caroline Lascoux-Combe, Karine Lacombe, Jade Ghosn, Jean-Paul Viard, Gilles Pialoux, Michel Ohayon, Claudine Duvivier, Annie Velter, Mohamed Ben Mechlia, Lydie Beniguel, Sophie Grabar, Maria Melchior, Lambert Assoumou, Virginie Supervie
Journal: Eurosurveillance (2024)

Background Some migrant men who have sex with men (MSM) acquire HIV in France. Aims We investigated, in migrant MSM receiving HIV care in France, the (i) rate of post-migration-HIV acquisition in France, (ii) delay between arrival and HIV acquisition and (iii) factors affecting HIV acquisition within 1 year after migration. Methods This cross-sectional study focused on ≥ 18-year-old MSM born outside France, receiving HIV care in the Paris region. Information on migration history, socioeconomic condition, sexual activity, and health was collected in May 2021–June 2022 through self-administered questionnaires and medical records. Post-migration-HIV-acquisition rate and delay between arrival in France and HIV acquisition were estimated from biographical data and CD4 + T-cell counts. Predictors of HIV acquisition within 1 year after migration were determined using logistic regression. Results Overall post-migration HIV-acquisition rate was 61.7% (715/1,159; 95%CI: 61.2–62.2), ranging from 40.5% (95%CI: 39.6–41.6) to 85.4% (95%CI: 83.9–86.0) in participants from Latin America and North Africa. Among post-migration-HIV acquisitions, those within 1 year after migration represented 13.1% overall (95%CI: 11.6–14.6), being highest in participants from sub-Saharan Africa (25%; 95%CI: 21.5–28.3). Participants ≥ 15-years old at migration, with post-migration-acquired HIV, had a 7.5-year median interval from arrival in France to HIV acquisition (interquartile range (IQR): 3.50–14.75). Older age at arrival, region of origin (sub-Saharan Africa and Asia), degree of social disadvantage and numbers of sexual partners were independently associated with acquiring HIV within 1 year in France. Conclusion Our findings may guide HIV prevention policies for most vulnerable migrants to Europe.