tbuckley/cabot-search huggingface dataset:
Equity considerations in clinical practice guidelines for traumatic brain injury and the criminal justice system: A systematic review
Authors: Zoe Colclough, Maria Jennifer Estrella, Julie Michele Joyce, Sara Hanafy, Jessica Babineau, Angela Colantonio, Vincy Chan
Journal: PLoS Medicine (2024)

Background Traumatic brain injury (TBI) is disproportionately prevalent among individuals who intersect or are involved with the criminal justice system (CJS). In the absence of appropriate care, TBI-related impairments, intersecting social determinants of health, and the lack of TBI awareness in CJS settings can lead to lengthened sentences, serious disciplinary charges, and recidivism. However, evidence suggests that most clinical practice guidelines (CPGs) overlook equity and consequently, the needs of disadvantaged groups. As such, this review addressed the research question “To what extent are (1) intersections with the CJS considered in CPGs for TBI, (2) TBI considered in CPGs for CJS, and (3) equity considered in CPGs for CJS?”. Methods and findings CPGs were identified from electronic databases (MEDLINE, Embase, CINAHL, PsycINFO), targeted websites, Google Search, and reference lists of identified CPGs on November 2021 and March 2023 (CPGs for TBI) and May 2022 and March 2023 (CPGs for CJS). Only CPGs for TBI or CPGs for CJS were included. We calculated the proportion of CPGs that included TBI- or CJS-specific content, conducted a qualitative content analysis to understand how evidence regarding TBI and the CJS was integrated in the CPGs, and utilised equity assessment tools to understand if and how equity was considered. Fifty-seven CPGs for TBI and 6 CPGs for CJS were included in this review. Fourteen CPGs for TBI included information relevant to the CJS, but only 1 made a concrete recommendation to consider legal implications during vocational evaluation in the forensic context. Two CPGs for CJS acknowledged the prevalence of TBI among individuals in prison and one specifically recommended considering TBI during health assessments. Both CPGs for TBI and CPGs for CJS provided evidence specific to a single facet of the CJS, predominantly in policing and corrections. The use of equity best practices and the involvement of disadvantaged groups in the development process were lacking among CPGs for CJS. We acknowledge limitations of the review, including that our searches were conducted in English language and thus, we may have missed other non-English language CPGs in this review. We further recognise that we are unable to comment on evidence that is not integrated in the CPGs, as we did not systematically search for research on individuals with TBI who intersect with the CJS, outside of CPGs. Conclusions Findings from this review provide the foundation to consider CJS involvement in CPGs for TBI and to advance equity in CPGs for CJS. Conducting research, including investigating the process of screening for TBI with individuals who intersect with all facets of the CJS, and utilizing equity assessment tools in guideline development are critical steps to enhance equity in healthcare for this disadvantaged group.
Antibody persistence and safety of a live-attenuated chikungunya virus vaccine up to 2 years after single-dose administration in adults in the USA: a single-arm, multicentre, phase 3b study
Authors: Robert McMahon, Sebastian Toepfer, Natascha Sattler, Martina Schneider, Marivic Narciso-Abraham, Sandra Hadl, Romana Hochreiter, Karin Kosulin, Robert Mader, Oliver Zoihsl, Nina Wressnigg, Katrin Dubischar, Vera Buerger, Susanne Eder-Lingelbach, Juan-Carlos Jaramillo
Journal: The Lancet Infectious Diseases (2024)
Comprehensive review on single-cell RNA sequencing: A new frontier in Alzheimer's disease research
Authors: Wengang Jin, JinJin Pei, Jeane Rebecca Roy, Selvaraj Jayaraman, Rathi Muthaiyan Ahalliya, Gopalakrishnan Velliyur Kanniappan, Monica Mironescu, Chella Perumal Palanisamy
Journal: Ageing Research Reviews (2024)
Exposure to doxycycline increases risk of carrying a broad range of enteric antimicrobial resistance determinants in an elderly cohort
Authors: Lucy Carpenter, Sophie Miller, Erin Flynn, Jocelyn M. Choo, Josephine Collins, Andrew P. Shoubridge, David Gordon, David J. Lynn, Craig Whitehead, Lex E.X. Leong, Kerry L. Ivey, Steve L. Wesselingh, Maria C. Inacio, Maria Crotty, Lito E. Papanicolas, Steven L. Taylor, Geraint B. Rogers
Journal: Journal of Infection (2024)

High rates of antibiotic prescription in residential aged care are likely to promote enteric carriage of antibiotic-resistant pathogens and increase the risk of antibiotic treatment failure. Despite their importance, relationships between antibiotic exposures and patterns of enteric resistance carriage in this population remain poorly understood.
Genetic Risk Stratification and Outcomes Among Treatment-Naive Patients With AML Treated With Venetoclax and Azacitidine
Authors: Hartmut Döhner, Keith W. Pratz, Courtney D. DiNardo, Andrew H. Wei, Brian A. Jonas, Vinod A. Pullarkat, Michael J. Thirman, Christian Récher, Andre C. Schuh, Sunil Babu, Xiaotong Li, Grace Ku, Zihuan Liu, Yan Sun, Jalaja Potluri, Monique Dail, Brenda Chyla, Daniel A. Pollyea
Journal: Blood (2024)

Abstract The European LeukemiaNet (ELN) acute myeloid leukemia (AML) genetic risk classification systems are based on response to intensive chemotherapy; their ability to discriminate outcomes in older patients treated with venetoclax-azacitidine may be suboptimal. This pooled analysis of the phase 3 VIALE-A trial (NCT02993523) and phase 1b study (NCT02203773) examined prognostic stratification according to the 2017 and 2022 ELN risk classifications and derived new molecular signatures differentiating venetoclax-azacitidine–treated patients based on overall survival (OS). Overall, 279 patients treated with venetoclax-azacitidine and 113 patients treated with placebo-azacitidine were analyzed. The ELN 2017 or 2022 prognostic criteria classified most patients as adverse-risk AML (60.2% and 72.8% for venetoclax-azacitidine and 65.5% and 75.2% for placebo-azacitidine, respectively). Although outcomes with venetoclax-azacitidine improved across all ELN risk groups compared with placebo-azacitidine, ELN classification systems poorly discriminated venetoclax-azacitidine outcomes. By applying a bioinformatic algorithm, new molecular signatures were derived differentiating OS outcomes with venetoclax-azacitidine. The mutational status of TP53, FLT3 internal tandem duplication (FLT3-ITD), NRAS, and KRAS categorized patients into higher-, intermediate-, and lower-benefit groups (52%, 25%, and 23% of patients, respectively), each associated with a distinct median OS (26.5 months [95% confidence interval (CI), 20.2-32.7]; 12.1 months [95% CI, 7.3-15.2]; and 5.5 months [95% CI, 2.8-7.6], respectively). ELN prognostic classifiers did not provide clinically meaningful risk stratification of OS outcomes in patients treated with venetoclax-azacitidine. TP53, FLT3-ITD, NRAS, and KRAS mutation status allows the classification of these patients into 3 risk groups with distinct differences in median OS. These trials were registered at www.clinicaltrials.gov as #NCT02993523 and #NCT02203773.
The Impact of TIGAR on Prognosis in Hepatocellular Carcinoma; Association with Tumor Microenvironment and Ferroptosis
Authors: Katsuya Toshida, Shinji Itoh, Norifumi Iseda, Shugo Tanaka, Kensuke Nakazono, Takahiro Tomiyama, Shohei Yoshiya, Takeo Toshima, Noboru Harada, Kenichi Kohashi, Koji Taniguchi, Yoshinao Oda, Tomoharu Yoshizumi
Journal: Liver Cancer (2024)

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; &lt;i&gt;TP53&lt;/i&gt;-induced glycolysis and apoptosis regulator (TIGAR) is a p53 target protein that has critical roles in glycolysis and redox balance. The reports about the effect of TIGAR on prognosis and its biological role in hepatocellular carcinoma (HCC) are limited. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; A total of 386 patients with HCC who had undergone hepatic resection were enrolled. Immunohistochemical staining for TIGAR was performed. Additionally, the regulation of malignant activity and ferroptosis by TIGAR was investigated in vitro. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; Patients were divided into TIGAR-positive (&lt;i&gt;n&lt;/i&gt; = 80, 20.7%) and -negative (&lt;i&gt;n&lt;/i&gt; = 306, 79.3%) groups. TIGAR positivity was significantly correlated with lower albumin, higher α-fetoprotein/ &lt;i&gt;des&lt;/i&gt;-gamma-carboxyprothrombin, larger tumor size/number of tumors, and greater proportions of BCLC staging C/single nodular type/poor differentiation/microscopic vascular invasion/microscopic intrahepatic metastasis. In multivariate analysis, TIGAR positivity was an independent prognostic factor (&lt;i&gt;p&lt;/i&gt; &amp;lt; 0.0001). In addition, TIGAR positivity was significantly associated with a smaller number of cluster of differentiation (CD) 8-positive T cells (&lt;i&gt;p&lt;/i&gt; = 0.0450), larger number of CD68-positive macrophages (&lt;i&gt;p&lt;/i&gt; = 0.0058), larger number of programmed death-ligand 1-positive cases (&lt;i&gt;p&lt;/i&gt; = 0.0002), and larger number of vessels that encapsulate tumor cluster-positive cases (&lt;i&gt;p&lt;/i&gt; = 0.0004). In vitro, &lt;i&gt;TIGAR&lt;/i&gt; knockdown decreased cell motility and induced ferroptosis. &lt;i&gt;TIGAR&lt;/i&gt; knockdown inhibited the phosphorylation of adenosine monophosphate-activated protein kinase and acetyl-CoA carboxylase. Ferroptosis induced by &lt;i&gt;TIGAR&lt;/i&gt; knockdown was inhibited by liproxstatin and baicalein treatment. The combination of &lt;i&gt;TIGAR&lt;/i&gt; knockdown and lenvatinib further induced ferroptosis. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; High expression of TIGAR impacted the clinical outcome of HCC patients and TIGAR was associated not only with tumor microenvironment but also with resistance to ferroptosis.
Epidemiology of Homebound Population Among Beneficiaries of a Large National Medicare Advantage Plan
Authors: Bruce Leff, Christine Ritchie, Sarah Szanton, Oren Shapira, Amanda Sutherland, Andrew Lynch, Brian W. Powers, Mona Siddiqui, Katherine A. Ornstein
Journal: Annals of Internal Medicine (2024)

Interest in home-based care is increasing among Medicare Advantage (MA) plans. The epidemiology of homebound MA beneficiaries is unknown.
Reply to Bihari <i>et al.</i>: Alveolar Collapse Is a Threat in Injured Lungs but What About the Airway Opening Pressure
Authors: Mayson L. A. Sousa, Bhushan H Katira, Sheena Bouch, Vanessa Hsing, Doreen Engelberts, Marcelo B. P. Amato, Martin Post, Laurent Brochard
Journal: American Journal of Respiratory and Critical Care Medicine (2024)
Gastroesophageal Reflux Disease
Authors: Kerry B. Dunbar
Journal: Annals of Internal Medicine (2024)

Gastroesophageal reflux disease (GERD) is a condition that occurs when reflux of gastric contents into the esophagus causes symptoms and/or complications. The prevalence of GERD in Western societies has been estimated at 30%, making it one of the most commonly encountered disorders in primary care. The spectrum of GERD includes typical symptoms of esophageal reflux (heartburn and/or regurgitation); esophageal injury (erosive esophagitis; stricture; Barrett esophagus; and, rarely, adenocarcinoma); and extraesophageal symptoms, such as hoarseness and chronic cough. Proper diagnosis and treatment of GERD includes symptom control, exclusion of other disorders, avoiding overuse of medications and invasive testing, and minimizing complications.
How Would You Treat This Inpatient With Type 2 Diabetes Mellitus? Grand Rounds Discussion From Beth Israel Deaconess Medical Center
Authors: Zahir Kanjee, Florence M. Brown, Zachary H. Taxin, Gerald W. Smetana
Journal: Annals of Internal Medicine (2024)

Management of hospitalized patients with type 2 diabetes mellitus (T2DM) presents unique challenges. Two recently released guidelines, one from the American Diabetes Association and the other from the Endocrine Society, provide useful recommendations and evidence review to inform the care of medical inpatients with T2DM. These guidelines mostly agree, although there are slight differences in their recommendations. In these rounds, 2 expert diabetologists discuss their approach to inpatient management of T2DM, specifically regarding inpatient glycemic goals on the medical ward, the use of noninsulin antihyperglycemic medications, and patient safety strategies for patients receiving long-acting insulin. They conclude with recommendations for Mr. D, a real patient with T2DM admitted with a recurrent foot infection.
Unbalanced MYC break-apart FISH patterns indicate the presence of a MYC rearrangement in HGBCL-DH-BCL2.
Authors: Brett J Collinge, Susana Ben-Neriah, Laura K Hilton, Waleed Alduaij, Tracy Tucker, Graham W. Slack, Pedro Farinha, Jeffrey W Craig, Merrill Boyle, Barbara Meissner, Diego Villa, Alina S. Gerrie, Laurie H. Sehn, Kerry J. Savage, Ryan D Morin, Andrew J Mungall, Christian Steidl, David W. Scott
Journal: Blood (2024)
Genetic risk classification for adults with AML receiving less-intensive therapies: the 2024 ELN recommendations
Authors: Hartmut Döhner, Courtney D. DiNardo, Frederick Appelbaum, Charles Craddock, Hervé Dombret, Benjamin L Ebert, Pierre Fenaux, Lucy A Godley, Robert P Hasserjian, Richard A Larson, Ross L Levine, Yasushi Miyazaki, Dietger Niederwieser, Gert J Ossenkoppele, Christoph Röllig, Jorge Sierra, Eytan M. Stein, Martin S. Tallman, Hwei-Fang Tien, Jianxiang Wang, Agnieszka Wierzbowska, Andrew H. Wei, Bob Löwenberg
Journal: Blood (2024)
Integrative plasma and fecal metabolomics identify functional metabolites in adenoma-colorectal cancer progression and as early diagnostic biomarkers
Authors: Yang Sun, Xiang Zhang, Dong Hang, Harry Cheuk-Hay Lau, Jie Du, Chuanfa Liu, Mingxu Xie, Yasi Pan, Le Wang, Cong Liang, Xingyu Zhou, Danyu Chen, Jiamei Rong, Zengren Zhao, Alvin Ho-Kwan Cheung, Yuet Wu, Hongyan Gou, Chi Chun Wong, Lingbin Du, Junliang Deng, Zhibin Hu, Hongbing Shen, Yinglei Miao, Jun Yu
Journal: Cancer Cell (2024)

Changes in plasma and fecal metabolomes in colorectal cancer (CRC) progression (normal-adenoma-CRC) remain unclear. Here, plasma and fecal samples were collected from four independent cohorts of 1,251 individuals (422 CRC, 399 colorectal adenoma [CRA], and 430 normal controls [NC]). By metabolomic profiling, signature plasma and fecal metabolites with consistent shift across NC, CRA, and CRC are identified, including CRC-enriched oleic acid and CRC-depleted allocholic acid. Oleic acid exhibits pro-tumorigenic effects in CRC cells, patient-derived organoids, and two murine CRC models, whereas allocholic acid has opposing effects. By integrative analysis, we found that oleic acid or allocholic acid directly binds to α-enolase or farnesoid X receptor-1 in CRC cells, respectively, to modulate cancer-associated pathways. Clinically, we establish a panel of 17 plasma metabolites that accurately diagnoses CRC in a discovery and three validation cohorts (AUC = 0.848–0.987). Overall, we characterize metabolite signatures, mechanistic significance, and diagnostic potential of plasma and fecal metabolomes in CRC.
Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD
Authors: Mayra Shanley, May Daher, Jinzhuang Dou, Sufang Li, Rafet Basar, Hind Rafei, Merve Dede, Joy Gumin, Jezreel Pantaleόn Garcίa, Ana Karen Nunez Cortes, Shan He, Corry M. Jones, Sunil Acharya, Natalie W. Fowlkes, Donghai Xiong, Sanjay Singh, Hila Shaim, Samantha Claire Hicks, Bin Liu, Abhinav Jain, Mohammad Fayyad Zaman, Qi Miao, Ye Li, Nadima Uprety, Enli Liu, Luis Muniz-Feliciano, Gary M. Deyter, Vakul Mohanty, Patrick Zhang, Scott E. Evans, Elizabeth J. Shpall, Frederick F. Lang, Ken Chen, Katayoun Rezvani
Journal: Cancer Cell (2024)

Glioblastoma (GBM) is an aggressive brain cancer with limited therapeutic options. Natural killer (NK) cells are innate immune cells with strong anti-tumor activity and may offer a promising treatment strategy for GBM. We compared the anti-GBM activity of NK cells engineered to express interleukin (IL)-15 or IL-21. Using multiple in vivo models, IL-21 NK cells were superior to IL-15 NK cells both in terms of safety and long-term anti-tumor activity, with locoregionally administered IL-15 NK cells proving toxic and ineffective at tumor control. IL-21 NK cells displayed a unique chromatin accessibility signature, with CCAAT/enhancer-binding proteins (C/EBP), especially CEBPD, serving as key transcription factors regulating their enhanced function. Deletion of CEBPD resulted in loss of IL-21 NK cell potency while its overexpression increased NK cell long-term cytotoxicity and metabolic fitness. These results suggest that IL-21, through C/EBP transcription factors, drives epigenetic reprogramming of NK cells, enhancing their anti-tumor efficacy against GBM.
Foundation models in gastrointestinal endoscopic AI: Impact of architecture, pre-training approach and data efficiency
Authors: Tim G.W. Boers, Kiki N. Fockens, Joost A. van der Putten, Tim J.M. Jaspers, Carolus H.J. Kusters, Jelmer B. Jukema, Martijn R. Jong, Maarten R. Struyvenberg, Jeroen de Groof, Jacques J. Bergman, Peter H.N. de With, Fons van der Sommen
Journal: Medical Image Analysis (2024)

Pre-training deep learning models with large data sets of natural images, such as ImageNet, has become the standard for endoscopic image analysis. This approach is generally superior to training from scratch, due to the scarcity of high-quality medical imagery and labels. However, it is still unknown whether the learned features on natural imagery provide an optimal starting point for the downstream medical endoscopic imaging tasks. Intuitively, pre-training with imagery closer to the target domain could lead to better-suited feature representations. This study evaluates whether leveraging in-domain pre-training in gastrointestinal endoscopic image analysis has potential benefits compared to pre-training on natural images. To this end, we present a dataset comprising of 5,014,174 gastrointestinal endoscopic images from eight different medical centers (GastroNet-5M), and exploit self-supervised learning with SimCLRv2, MoCov2 and DINO to learn relevant features for in-domain downstream tasks. The learned features are compared to features learned on natural images derived with multiple methods, and variable amounts of data and/or labels (e.g. Billion-scale semi-weakly supervised learning and supervised learning on ImageNet-21k). The effects of the evaluation is performed on five downstream data sets, particularly designed for a variety of gastrointestinal tasks, for example, GIANA for angiodyplsia detection and Kvasir-SEG for polyp segmentation. The findings indicate that self-supervised domain-specific pre-training, specifically using the DINO framework, results into better performing models compared to any supervised pre-training on natural images. On the ResNet50 and Vision-Transformer-small architectures, utilizing self-supervised in-domain pre-training with DINO leads to an average performance boost of 1.63% and 4.62%, respectively, on the downstream datasets. This improvement is measured against the best performance achieved through pre-training on natural images within any of the evaluated frameworks. Moreover, the in-domain pre-trained models also exhibit increased robustness against distortion perturbations (noise, contrast, blur, etc.), where the in-domain pre-trained ResNet50 and Vision-Transformer-small with DINO achieved on average 1.28% and 3.55% higher on the performance metrics, compared to the best performance found for pre-trained models on natural images. Overall, this study highlights the importance of in-domain pre-training for improving the generic nature, scalability and performance of deep learning for medical image analysis. The GastroNet-5M pre-trained weights are made publicly available in our repository: huggingface.co/tgwboers/GastroNet-5M_Pretrained_Weights.
A Research Agenda to Improve Outcomes in Patients with Chronic Obstructive Pulmonary Disease and Cardiovascular Disease. An Official American Thoracic Society Research Statement
Authors: Laura C. Myers, Jennifer K Quint, Nathaniel M Hawkins, Nirupama Putcha, Alan Hamilton, Peter Lindenauer, J. Michael Wells, Leah J Witt, Sagar P Shah, Todd Lee, Huong Nguyen, Caroline Gainer, Allan Walkey, David M. Mannino, Surya P Bhatt, R. Graham Barr, Richard Mularski, Mark Dransfield, Sadiya S Khan, Andrea S Gershon, Miguel Divo, Valerie G Press
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Individuals with chronic obstructive pulmonary disease (COPD) are often at risk for or have comorbid cardiovascular disease and are likely to die of cardiovascular-related causes.
External validation of serum biomarkers predicting short-term and mid/long-term relapse in patients with Crohn’s disease stopping infliximab
Authors: Nicolas Pierre, Vân Anh Huynh-Thu, Dominique Baiwir, Gabriel Mazzucchelli, Maximilien Fléron, Lisette Trzpiot, Gauthier Eppe, Edwin De Pauw, David Laharie, Jack Satsangi, Peter Bossuyt, Lucine Vuitton, Sophie Vieujean, Jean-Frédéric Colombel, Marie-Alice Meuwis, Edouard Louis
Journal: Gut (2024)

Objective In patients with Crohn’s disease (CD) on combination therapy (infliximab and immunosuppressant) and stopping infliximab (cohort from the study of infliximab diSconTinuation in CrOhn’s disease patients in stable Remission on combined therapy with Immunosuppressors (STORI)), the risk of short-term (≤6 months) and mid/long-term relapse (&gt;6 months) was associated with distinct blood protein profiles. Our aim was to test the external validity of this finding in the SPARE cohort (A proSpective Randomized Controlled Trial comParing infliximAb-antimetabolites Combination Therapy to Anti-metabolites monotheRapy and Infliximab monothErapy in Crohn's Disease Patients in Sustained Steroid-free Remission on Combination Therapy). Design In SPARE, patients with CD in sustained steroid-free clinical remission and on combination therapy were randomly allocated to three arms: continuing combination therapy, stopping infliximab or stopping immunosuppressant. In the baseline serum of the STORI and SPARE (arm stopping infliximab) cohorts, we studied 202 immune-related proteins. The proteins associated with time to relapse (univariable Cox model) were compared between STORI and SPARE. The discriminative ability of biomarkers (individually and combined in pairs) was evaluated by the c-statistic (concordance analysis) which was compared with C-reactive protein (CRP), faecal calprotectin and a previously validated model (CEASE). Results In STORI and SPARE, distinct blood protein profiles were associated with the risk of short-term (eg, high level: CRP, haptoglobin, interleukin-6, C-type lectin domain family 4 member C) and mid/long-term relapse (eg, low level: Fms-related tyrosine kinase 3 ligand, kallistatin, fibroblast growth factor 2). At external validation, the top 10 biomarker pairs showed a higher c-statistic than the CEASE model, CRP and faecal calprotectin in predicting short-term (0.76–0.80 vs 0.74 vs 0.71 vs 0.69, respectively) and mid/long-term relapse (0.66–0.68 vs 0.61 vs 0.52 vs 0.59, respectively). Conclusion In patients with CD stopping infliximab, we confirm that the risk of short-term and mid/long-term relapse is associated with distinct blood protein profiles showing the potential to guide infliximab withdrawal. Trial registration number NCT00571337 and NCT02177071 .
Thyroid hormone suppresses medulloblastoma progression through promoting terminal differentiation of tumor cells
Authors: Yijun Yang, Silvia Anahi Valdés-Rives, Qing Liu, Tong Gao, Chakkapong Burudpakdee, Yuzhe Li, Jun Tan, Yinfei Tan, Christian A. Koch, Yuan Rong, Steven R. Houser, Shuanzeng Wei, Kathy Q. Cai, Jinhua Wu, Sheue-yann Cheng, Robert Wechsler-Reya, Zeng-jie Yang
Journal: Cancer Cell (2024)