tbuckley/cabot-search huggingface dataset:
Cross-scale multi-instance learning for pathological image diagnosis
Authors: Ruining Deng, Can Cui, Lucas W. Remedios, Shunxing Bao, R. Michael Womick, Sophie Chiron, Jia Li, Joseph T. Roland, Ken S. Lau, Qi Liu, Keith T. Wilson, Yaohong Wang, Lori A. Coburn, Bennett A. Landman, Yuankai Huo
Journal: Medical Image Analysis (2024)

Analyzing high resolution whole slide images (WSIs) with regard to information across multiple scales poses a significant challenge in digital pathology. Multi-instance learning (MIL) is a common solution for working with high resolution images by classifying bags of objects (i.e. sets of smaller image patches). However, such processing is typically performed at a single scale (e.g., 20× magnification) of WSIs, disregarding the vital inter-scale information that is key to diagnoses by human pathologists. In this study, we propose a novel cross-scale MIL algorithm to explicitly aggregate inter-scale relationships into a single MIL network for pathological image diagnosis. The contribution of this paper is three-fold: (1) A novel cross-scale MIL (CS-MIL) algorithm that integrates the multi-scale information and the inter-scale relationships is proposed; (2) A toy dataset with scale-specific morphological features is created and released to examine and visualize differential cross-scale attention; (3) Superior performance on both in-house and public datasets is demonstrated by our simple cross-scale MIL strategy. The official implementation is publicly available at https://github.com/hrlblab/CS-MIL.
Trickle-Down Medicaid
Authors: Laura A. Hatfield
Journal: JAMA (2024)

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 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 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
Cefepime vs Piperacillin-Tazobactam for Acute Infection in Hospitalized Adults
Authors: Rishi Chanderraj, Robert P. Dickson, Michael W. Sjoding
Journal: JAMA (2024)

To the Editor We applaud the execution and reporting of the Antibiotic Choice on Renal Outcomes (ACORN) pragmatic, randomized clinical trial1 of cefepime vs piperacillin-tazobactam in hospitalized adults with suspected infection in the emergency department or medical intensive care unit.
Cefepime vs Piperacillin-Tazobactam for Acute Infection in Hospitalized Adults
Authors: Dayu Chen, Haozhen Ren, Yuanjin Zhao
Journal: JAMA (2024)

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 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 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
Review of Evaluation and Treatment of Knee Pain
Authors: Giovanni Misseri, Cesare Gregoretti, Giuliano Lo Bianco
Journal: JAMA (2024)

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 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 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
Phase 3 Randomized Clinical Trial of the Safety and Efficacy of Travoprost Intraocular Implant in Patients with Open-Angle Glaucoma or Ocular Hypertension
Authors: Steven R. Sarkisian, Robert E. Ang, Andy M. Lee, John P. Berdahl, Sebastian B. Heersink, James H. Burden, Long V. Doan, Kerry G. Stephens, Angela C. Kothe, Dale W. Usner, L. Jay Katz, Tomas Navratil, Robert E. Ang, Sebastian B. Heersink, Steven Vold, Neil Atodaria, Jacob Brubaker, Damien Goldberg, Christopher Lin, Betsy Nguyen, Mitchell Schultz, Bruce Silverstein, Robert Sorenson, Kent Bashford, James H. Burden, Mohammed ElMallah, Joshua Kim, Benjamin Lambright, Cathleen McCabe, Rajesh Shetty, Steven Smith, Farrell Tyson, Jason Jones, Francis D’Ambrosio, Bin Wu, Mahdi Basha, Ralph Chu, Joseph Gira, Russell Swan, Brandon Baartman, Kent Wellish
Journal: Ophthalmology (2024)
Framework for in vivo T cell screens
Authors: Lauren E. Milling, Samuel C. Markson, Qin Tjokrosurjo, Nicole M. Derosia, Ivy S.L. Streeter, Grant H. Hickok, Ashlyn M. Lemmen, Thao H. Nguyen, Priyamvada Prathima, William Fithian, Marc A. Schwartz, Nir Hacohen, John G. Doench, Martin W. LaFleur, Arlene H. Sharpe
Journal: The Journal of Experimental Medicine (2024)

In vivo T cell screens are a powerful tool for elucidating complex mechanisms of immunity, yet there is a lack of consensus on the screen design parameters required for robust in vivo screens: gene library size, cell transfer quantity, and number of mice. Here, we describe the Framework for In vivo T cell Screens (FITS) to provide experimental and analytical guidelines to determine optimal parameters for diverse in vivo contexts. As a proof-of-concept, we used FITS to optimize the parameters for a CD8+ T cell screen in the B16-OVA tumor model. We also included unique molecular identifiers (UMIs) in our screens to (1) improve statistical power and (2) track T cell clonal dynamics for distinct gene knockouts (KOs) across multiple tissues. These findings provide an experimental and analytical framework for performing in vivo screens in immune cells and illustrate a case study for in vivo T cell screens with UMIs.
Nanomaterial‐Based Strategies for Preventing Tumor Metastasis by Interrupting the Metastatic Biological Processes
Authors: Qingjin Cai, Yijia He, Yang Zhou, Ji Zheng, Jun Deng
Journal: Advanced Healthcare Materials (2024)

Tumor metastasis is the primary cause of cancer-related deaths. The prevention of tumor metastasis has garnered notable interest and interrupting metastatic biological processes is considered a potential strategy for preventing tumor metastasis. The tumor microenvironment (TME), circulating tumor cells (CTCs), and premetastatic niche (PMN) play crucial roles in metastatic biological processes. These processes can be interrupted using nanomaterials due to their excellent physicochemical properties. However, most studies have focused on only one aspect of tumor metastasis. Here, the hypothesis that nanomaterials can be used to target metastatic biological processes and explore strategies to prevent tumor metastasis is highlighted. First, the metastatic biological processes and strategies involving nanomaterials acting on the TME, CTCs, and PMN to prevent tumor metastasis are briefly summarized. Further, the current challenges and prospects of nanomaterials in preventing tumor metastasis by interrupting metastatic biological processes are discussed. Nanomaterial-and multifunctional nanomaterial-based strategies for preventing tumor metastasis are advantageous for the long-term fight against tumor metastasis and their continued exploration will facilitate rapid progress in the prevention, diagnosis, and treatment of tumor metastasis. Novel perspectives are outlined for developing more effective strategies to prevent tumor metastasis, thereby improving the outcomes of patients with cancer.
Sexual-biased necroinflammation is revealed as a predictor of bevacizumab benefit in glioblastoma
Authors: Sara Hiller-Vallina, Lucia Mondejar-Ruescas, Marta Caamaño-Moreno, Blanca Cómitre-Mariano, Denisse Alcivar-López, Juan M Sepulveda, Aurelio Hernández-Laín, Ángel Pérez-Núñez, Berta Segura-Collar, Ricardo Gargini
Journal: Neuro-Oncology (2024)

Glioblastoma (GBM) is a highly malignant brain tumor that affects men more often than women. In addition, the former shows a poorer survival prognosis. To date, the reason for this sex-specific aggressiveness remains unclear. Therefore, the aim of this study is to investigate tumor processes that explain these sex differences.
Periodontitis and rheumatoid arthritis—Global efforts to untangle two complex diseases
Authors: Isabel Lopez‐Oliva, Jennifer Malcolm, Shauna Culshaw
Journal: Periodontology 2000 (2024)

Abstract Understanding the impact of oral health on rheumatoid arthritis (RA) will inform how best to manage patients with both periodontitis and RA. This review seeks to provide an update on interventional and mechanistic investigations, including a brief summary of European Research programs investigating the link between periodontitis and RA. Recent clinical studies are described that evaluate how the treatment of one disease impacts on the other, as are studies in both humans and animal models that have sought to identify the potential mechanisms linking the two diseases.
Germline variants in patients developing second malignant neoplasms after therapy for pediatric acute lymphoblastic leukemia—a case-control study
Authors: Stefanie V. Junk, Alisa Förster, Gunnar Schmidt, Martin Zimmermann, Birthe Fedders, Bernd Haermeyer, Anke K. Bergmann, Anja Möricke, Gunnar Cario, Bernd Auber, Martin Schrappe, Christian P. Kratz, Martin Stanulla
Journal: Leukemia (2024)

Today, most children treated for acute lymphoblastic leukemia (ALL) can be cured by the application of intensive combination chemotherapy regimens [1,2].However, within 20 years, up to 10% develop a second malignant neoplasm (SMN) with cure rates often being dismal [3,4].Therefore, strategies are needed for an early identification of patients at risk for SMN development, an improved understanding of the underlying pathobiology and, ideally, the development of preventive actions.In this study, we analyzed genetic variation in 159 selected cancer predisposition genes (CPG) to determine their potential association with SMN.Patients included were 1-22 years of age at diagnosis of ALL and enrolled in the German part of the European AIEOP-BFM ALL 2000 multicenter clinical trial for frontline treatment of pediatric ALL [5].Median follow-up for the entire patient group was 14.8 (4.6-19.2) years as of November, 2020.Treatment details were described previously [6].We identified 75 SMN patients with sufficient DNA available, representing 94% of all 80 SMN cases observed in the entire AIEOP-BFM ALL 2000 study population up to this follow-up date.In a matched case-control approach, we analyzed germline DNA obtained from remission bone marrow samples of 223 individuals (75 cases, 148 controls); see Supplementary Methods section for sequencing details and Supplementary Table 1 for clinical background information.Matching criteria were sex, age at diagnosis of ALL, immunophenotype, and treatment.Candidate genes included genes based on own work and/or genes recommended by Byrjalsen et al. 2021; [7] variant pathogenicity was assessed according to standard interpretation guidelines (see Supplementary Table 2 for details).Statistical analyses and plotting were conducted with SAS (SAS-PC, Version 9.1, Cary, NC: SAS Institute Inc.), SPSS (IBM Deutschland GmbH, Ehningen, Germany) or R (4.0.5), and Rstudio (1.0.153); see Supplementary Methods section.Overall we observed 31 conspicuous findings in 22 genes: 17 (6 likely pathogenic and 11 pathogenic) in 16 (21%) cases with ALL
Inhibition of S6K lowers age-related inflammation and increases lifespan through the endolysosomal system
Authors: Pingze Zhang, James H. Catterson, Sebastian Grönke, Linda Partridge
Journal: Nature Aging (2024)

Suppression of target of rapamycin complex 1 (TORC1) by rapamycin ameliorates aging in diverse species. S6 kinase (S6K) is an essential mediator, but the mechanisms involved are unclear. Here we show that activation of S6K specifically in Drosophila fat-body blocked extension of lifespan by rapamycin, induced accumulation of multilamellar lysosomes and blocked age-associated hyperactivation of the NF-κB-like immune deficiency (IMD) pathway, indicative of reduced inflammaging. Syntaxin 13 mediated the effects of TORC1-S6K signaling on lysosome morphology and inflammaging, suggesting they may be linked. Inflammaging depended on the IMD receptor regulatory isoform PGRP-LC, and repression of the IMD pathway from midlife extended lifespan. Age-related inflammaging was higher in females than in males and was not lowered in males by rapamycin treatment or lowered S6K. Rapamycin treatment also elevated Syntaxin 12/13 levels in mouse liver and prevented age-related increase in noncanonical NF-κB signaling, suggesting that the effect of TORC1 on inflammaging is conserved from flies to mammals.
Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression
Authors: Leah A. Gates, Bernardo Sgarbi Reis, Peder J. Lund, Matthew R. Paul, Marylene Leboeuf, Annaelle M. Djomo, Zara Nadeem, Mariana Lopes, Francisca N. Vitorino, Gokhan Unlu, Thomas S. Carroll, Kivanç Birsoy, Benjamin A. Garcia, Daniel Mucida, C. David Allis
Journal: Nature Metabolism (2024)
PMF-seq: a highly scalable screening strategy for linking genetics to mitochondrial bioenergetics
Authors: Tsz-Leung To, Jason G. McCoy, Naomi K. Ostriker, Lev S. Sandler, Carmen A. Mannella, Vamsi K. Mootha
Journal: Nature Metabolism (2024)

Our current understanding of mitochondrial organelle physiology has benefited from two broad approaches: classically, cuvette-based measurements with suspensions of isolated mitochondria, in which bioenergetic parameters are monitored acutely in response to respiratory chain substrates and inhibitors
Adapted large language models can outperform medical experts in clinical text summarization
Authors: Dave Van Veen, Cara Van Uden, Louis Blankemeier, Jean-Benoit Delbrouck, Asad Aali, Christian Bluethgen, Anuj Pareek, Malgorzata Polacin, Eduardo Pontes Reis, Anna Seehofnerová, Nidhi Rohatgi, Poonam Hosamani, William Collins, Neera Ahuja, Curtis P. Langlotz, Jason Hom, Sergios Gatidis, John Pauly, Akshay S. Chaudhari
Journal: Nature Medicine (2024)
Targeting PRMT9-mediated arginine methylation suppresses cancer stem cell maintenance and elicits cGAS-mediated anticancer immunity
Authors: Haojie Dong, Xin He, Lei Zhang, Wei Chen, Yi-Chun Lin, Song-Bai Liu, Huafeng Wang, Le Xuan Truong Nguyen, Min Li, Yinghui Zhu, Dandan Zhao, Lucy Ghoda, Jonathan Serody, Benjamin Vincent, Leo Luznik, Ivana Gojo, Joshua Zeidner, Rui Su, Jianjun Chen, Ritin Sharma, Patrick Pirrotte, Xiwei Wu, Weidong Hu, Weidong Han, Binghui Shen, Ya-Huei Kuo, Jie Jin, Amandeep Salhotra, Jeffrey Wang, Guido Marcucci, Yun Lyna Luo, Ling Li
Journal: Nature Cancer (2024)

Abstract Current anticancer therapies cannot eliminate all cancer cells, which hijack normal arginine methylation as a means to promote their maintenance via unknown mechanisms. Here we show that targeting protein arginine N -methyltransferase 9 (PRMT9), whose activities are elevated in blasts and leukemia stem cells (LSCs) from patients with acute myeloid leukemia (AML), eliminates disease via cancer-intrinsic mechanisms and cancer-extrinsic type I interferon (IFN)-associated immunity. PRMT9 ablation in AML cells decreased the arginine methylation of regulators of RNA translation and the DNA damage response, suppressing cell survival. Notably, PRMT9 inhibition promoted DNA damage and activated cyclic GMP-AMP synthase, which underlies the type I IFN response. Genetically activating cyclic GMP-AMP synthase in AML cells blocked leukemogenesis. We also report synergy of a PRMT9 inhibitor with anti-programmed cell death protein 1 in eradicating AML. Overall, we conclude that PRMT9 functions in survival and immune evasion of both LSCs and non-LSCs; targeting PRMT9 may represent a potential anticancer strategy.
mPAP/CO Slope and Oxygen Uptake Add Prognostic Value in Aortic Stenosis
Authors: Sarah Hoedemakers, Nicola Riccardo Pugliese, Jan Stassen, Arnaud Vanoppen, Jade Claessens, Tin Gojevic, Youri Bekhuis, Maarten Falter, Sara Moura Ferreira, Sebastiaan Dhont, Nicolò De Biase, Lavinia Del Punta, Valerio Di Fiore, Marco De Carlo, Cristina Giannini, Andrea Colli, Raluca Elena Dulgheru, Jolien Geers, Alaaddin Yilmaz, Guido Claessen, Philippe Bertrand, Steven Droogmans, Patrizio Lancellotti, Bernard Cosyns, Frederik H. Verbrugge, Lieven Herbots, Stefano Masi, Jan Verwerft
Journal: Circulation (2024)

Recent guidelines redefined exercise pulmonary hypertension as a mean pulmonary artery pressure/cardiac output (mPAP/CO) slope >3 mm Hg·L
68Ga-PSMA Uptake in the Testis
Authors: Merve Nida Calderon Tobar, Hasan Önner
Journal: Clinical Nuclear Medicine (2024)

Abstract Although abnormal 68 Ga-PSMA uptake in the prostate and its metastases can be seen in a variety of diseases, it is rare to see in the testis. In these 2 cases, 68 Ga-PSMA PET/CT revealed unilateral 68 Ga-PSMA uptake in the testis of 2 patients. One of these patients was diagnosed with testis metastases from prostate cancer after an orchiectomy. The other patient was diagnosed with an orchitis. 68 Ga-PSMA uptake should be considered as an infection, as well as a malignancy in the initial differential diagnosis.
Cutaneous Metastasis From Prostate Cancer on Posttherapeutic 177Lu–Prostate-Specific Membrane Antigen Scan
Authors: Mohammad Taghavi, Reyhane Ahmadi, Mohsen Qutbi
Journal: Clinical Nuclear Medicine (2024)

Abstract In this note, we aim to present a patient with a known case of prostate cancer with widespread metastasis to the skeleton and liver who has undergone several cycles of chemoradiotherapy. The patient received 2 doses of 177 Lu–prostate-specific membrane antigen therapy, in which several zones of uptake were detected on the thoracic wall compatible with cutaneous metastatic lesions of prostate cancer.
18F-FDG PET/CT in Synovial Anaplastic Large Cell Lymphoma
Authors: Ka Lun Chiu, Tsz Kit Chow, Wai Han Ma, Kwok Man Ma
Journal: Clinical Nuclear Medicine (2024)

Abstract Anaplastic large cell lymphoma is an uncommon and aggressive form of peripheral T-cell lymphoma. Synovial anaplastic large cell lymphoma is very rare. We present PET/CT findings in a patient with synovial anaplastic large cell lymphoma. Intense FDG accumulation was found in irregular synovial thickening of the right knee. Biopsy of the synovium was performed and revealed anaplastic large cell lymphoma. This case demonstrates that anaplastic large cell lymphoma should be included as one of the differential diagnoses of FDG-avid synovial lesions.
Clinical Feasibility of Deep Learning–Based Attenuation Correction Models for Tl-201 Myocardial Perfusion SPECT
Authors: Sungjoo Lim, Yong-Jin Park, Su Jin Lee, Young-Sil An, Joon-Kee Yoon
Journal: Clinical Nuclear Medicine (2024)

Purpose We aimed to develop deep learning (DL)–based attenuation correction models for Tl-201 myocardial perfusion SPECT (MPS) images and evaluate their clinical feasibility. Patients and Methods We conducted a retrospective study of patients with suspected or known coronary artery disease. We proposed a DL-based image-to-image translation technique to transform non–attenuation-corrected images into CT-based attenuation-corrected (CT AC ) images. The model was trained using a modified U-Net with structural similarity index (SSIM) loss and mean squared error (MSE) loss and compared with other models. Segment-wise analysis using a polar map and visual assessment for the generated attenuation-corrected (GEN AC ) images were also performed to evaluate clinical feasibility. Results This study comprised 657 men and 328 women (age, 65 ± 11 years). Among the various models, the modified U-Net achieved the highest performance with an average mean absolute error of 0.003, an SSIM of 0.990, and a peak signal-to-noise ratio of 33.658. The performance of the model was not different between the stress and rest datasets. In the segment-wise analysis, the myocardial perfusion of the inferior wall was significantly higher in GEN AC images than in the non–attenuation-corrected images in both the rest and stress test sets ( P &lt; 0.05). In the visual assessment of patients with diaphragmatic attenuation, scores of 4 (similar to CT AC images) or 5 (indistinguishable from CT AC images) were assigned to most GEN AC images (65/68). Conclusions Our clinically feasible DL-based attenuation correction models can replace the CT-based method in Tl-201 MPS, and it would be useful in case SPECT/CT is unavailable for MPS.
Dual 177Lu–Prostate-Specific Membrane Antigen and 177Lu-DOTATATE Therapy in Metastatic Castration-Resistant Prostate Cancer With Neuroendocrine Differentiation
Authors: Ediz Beyhan, Özge Erol Fenercioğlu, Rahime Şahin, Tevfik Fikret Çermik, Nurhan Ergül
Journal: Clinical Nuclear Medicine (2024)

Abstract We present an 87-year-old man diagnosed with prostate cancer and neuroendocrine differentiation, posttherapy results to consecutive 177 Lu–prostate-specific membrane antigen and 177 Lu-DOTATATE. Despite hormonal therapy and chemoradiotherapy, the patient progressed rapidly, and multiple liver and bone metastases showed regression after 177 Lu–prostate-specific membrane antigen and 177 Lu-DOTATATE treatment. Prostate cancer with neuroendocrine differentiation is resistant to treatments; however, treatment with the combination of 177 Lu-DOTATATE therapy may be promising.