tbuckley/cabot-search huggingface dataset:
TransUNet: Rethinking the U-Net architecture design for medical image segmentation through the lens of transformers
Authors: Jieneng Chen, Jieru Mei, Xianhang Li, Yongyi Lu, Qihang Yu, Qingyue Wei, Xiangde Luo, Yutong Xie, Ehsan Adeli, Yan Wang, Matthew P. Lungren, Shaoting Zhang, Lei Xing, Le Lu, Alan Yuille, Yuyin Zhou
Journal: Medical Image Analysis (2024)

Medical image segmentation is crucial for healthcare, yet convolution-based methods like U-Net face limitations in modeling long-range dependencies. To address this, Transformers designed for sequence-to-sequence predictions have been integrated into medical image segmentation. However, a comprehensive understanding of Transformers' self-attention in U-Net components is lacking. TransUNet, first introduced in 2021, is widely recognized as one of the first models to integrate Transformer into medical image analysis. In this study, we present the versatile framework of TransUNet that encapsulates Transformers' self-attention into two key modules: (1) a Transformer encoder tokenizing image patches from a convolution neural network (CNN) feature map, facilitating global context extraction, and (2) a Transformer decoder refining candidate regions through cross-attention between proposals and U-Net features. These modules can be flexibly inserted into the U-Net backbone, resulting in three configurations: Encoder-only, Decoder-only, and Encoder+Decoder. TransUNet provides a library encompassing both 2D and 3D implementations, enabling users to easily tailor the chosen architecture. Our findings highlight the encoder's efficacy in modeling interactions among multiple abdominal organs and the decoder's strength in handling small targets like tumors. It excels in diverse medical applications, such as multi-organ segmentation, pancreatic tumor segmentation, and hepatic vessel segmentation. Notably, our TransUNet achieves a significant average Dice improvement of 1.06% and 4.30% for multi-organ segmentation and pancreatic tumor segmentation, respectively, when compared to the highly competitive nn-UNet, and surpasses the top-1 solution in the BrasTS2021 challenge. 2D/3D Code and models are available at https://github.com/Beckschen/TransUNet and https://github.com/Beckschen/TransUNet-3D, respectively.
Frequency of lymph node metastases at different neck levels in patients with oral squamous cell carcinoma: a systematic review and meta-analysis
Authors: Yi-Fu Yu, Lei-Ming Cao, Zi-Zhan Li, Nian-Nian Zhong, Guang-Rui Wang, Yao Xiao, Qiu-Ji Wu, Bing Liu, Lin-Lin Bu
Journal: International Journal of Surgery (2024)

Background: Currently, neck dissection is a standard treatment for the majority of oral squamous cell carcinoma (OSCC) patients. However, the procedure can lead to a series of complications, significantly reducing patient quality of life and even affecting the antitumor immune response in patients undergoing immunotherapy. Therefore, in the era of precision surgery, gaining a deeper understanding of the patterns of lymph node metastasis (LNM) in OSCC is crucial. Materials and Methods: Literature searches were performed on PubMed, Embase, Web of Science, Cochrane Library, WANFANGDATA and China National Knowledge Infrastructure (CNKI) (inception to April 10, 2024). In addition, a manual searching was conducted in Scopus, Google Scholar, and Education Resources Information Center (ERIC). We included observational studies that evaluated the frequency of LNM in OSCC patients. Systematic review and a random effects model meta-analysis were performed. Results: The search identified 4694 articles, of which 17 studies included in our study. We calculated the frequency of LNM according to the data reported in the articles. Frequency of LNM=number of patients with positive lymph node / number of patients with OSCC. The frequency of LNM was 12% in level I (95%CI: 0.11 to 0.15, I 2 =38.01%), 20% in level II (95%CI: 0.17 to 0.22, I 2 =47.71%), 10% in level III (95%CI: 0.08 to 0.12, I 2 =49.10%), 2% in level VI (95%CI: 0.01 to 0.03, I 2 =27.58%), 1% in level V (95%CI: 0.00 to 0.01, I 2 =11.37%). Conclusion: The frequency of LNM is consistent with the “cascade theory” and appears to be no significant difference from different primary sites. The frequency of LNM were low in levels I-III and were very low in level IV-V which implicated that more conservative treatments may be considered for OSCC in the future. This study will help clinicians better determine the extent of surgery and preserve lymph nodes during neck dissection.
A systematic review and meta-analysis of morbidity and pancreatic fistula after distal pancreatectomy with versus without prophylactic intra-abdominal drainage
Authors: Ulla Klaiber, Philip M. Collins, Simon Trinkler, Charlotte Gustorff, Martin Schindl, Klaus Sahora, Carl-Stephan Leonhardt, Oliver Strobel
Journal: International Journal of Surgery (2024)

The omission of a prophylactic intra-abdominal drainage has been under debate in pancreatic surgery due to the high risk of complications and especially of postoperative pancreatic fistula (POPF). Recently, the second randomized controlled trial (RCT) and two propensity score-matched comparative studies assessing risks and benefits of a no-drainage policy versus prophylactic drainage after distal pancreatectomy (DP) have been published. This systematic review with meta-analysis provides an updated summary of the available evidence on this topic.
Update on Genetic Counselor Practice and Recommendations for Pediatric Cancer Predisposition Evaluation and Surveillance
Authors: Kristin Zelley, Jaclyn Schienda, Bailey Gallinger, Wendy K. Kohlmann, Rose B. McGee, Sarah R. Scollon, Kami Wolfe Schneider
Journal: Clinical Cancer Research (2024)

In July 2023, the American Association for Cancer Research held the second Childhood Cancer Predisposition Workshop, at which international experts in pediatric cancer predisposition met to update the previously published 2017 consensus statements on pediatric cancer predisposition syndromes. Since 2017, advances in tumor and germline genetic testing and increased understanding of cancer predisposition in patients with pediatric cancer have led to significant changes in clinical care. Here, we provide an updated genetic counseling framework for pediatric oncology professionals. The framework includes referral indications and timing, somatic and germline genetic testing options, testing for adult-onset cancer predisposition syndromes in children with and without cancer, evolving genetic counseling models to meet the increased demand for genetic testing, barriers to cancer genetic testing and surveillance in children, and psychosocial and equity considerations regarding cancer genetic testing and surveillance in children. Adaptable genetic counseling services are needed to provide support to pediatric oncology provider teams and diverse patients with pediatric cancer, cancer predisposition, and their families.
Scribble Deficiency Promotes Pancreatic Ductal Adenocarcinoma Development and Metastasis
Authors: Camino Bermejo-Rodriguez, Joaquín Araos Henríquez, Giuseppina Caligiuri, Sara Pinto Teles, Youngkyu Park, Anthony Evans, Lawrence N. Barrera, Albrecht Neesse, Robert Grützmann, Daniela Aust, Petra Rümmele, Thomas Knösel, Masako Narita, Masashi Narita, Fiona Campbell, Daniel Öhlund, Christian Pilarsky, Lukas E. Dow, Patrick O. Humbert, Giulia Biffi, David A. Tuveson, Pedro A. Perez-Mancera
Journal: Cancer Research (2024)

Perturbation of cell polarity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) progression. Scribble (SCRIB) is a well-characterized polarity regulator that has diverse roles in the pathogenesis of human neoplasms. To investigate the impact of SCRIB deficiency in PDAC development and progression, Scrib expression was genetically ablated in well-established mouse models of PDAC. Scrib loss in combination with KrasG12D did not influence development of pancreatic intraepithelial neoplasms in mice. However, Scrib deletion cooperated with KrasG12D and concomitant Trp53 heterozygous deletion to promote invasive PDAC and metastatic dissemination, leading to reduced overall survival. Immunohistochemical and transcriptome analyses revealed that Scrib-null tumors display a pronounced reduction of collagen content and an abundance of cancer-associated fibroblasts (CAF). Mechanistically, IL1α levels were reduced in Scrib-deficient tumors, and Scrib knockdown downregulated IL1α in mouse PDAC organoids (mPDO), which impaired CAF activation. Furthermore, Scrib loss increased YAP activation in mPDOs and established PDAC cell lines, enhancing cell survival. Clinically, SCRIB expression was decreased in human PDAC, and SCRIB mislocalization was associated with poorer patient outcome. These results indicate that SCRIB deficiency enhances cancer cell survival and remodels the tumor microenvironment to accelerate PDAC development and progression, establishing the tumor suppressor function of SCRIB in advanced pancreatic cancer. Significance: SCRIB loss promotes invasive pancreatic cancer development via both cell-autonomous and non-cell-autonomous processes and is associated with poorer outcomes, denoting SCRIB as a tumor suppressor and potential biomarker for the prediction of recurrence.
FANCI Inhibition Induces PARP1 Redistribution to Enhance the Efficacy of PARP Inhibitors in Breast Cancer
Authors: Yu-Zhou Huang, Ming-Yi Sang, Pei-Wen Xi, Ruo-Xi Xu, Meng-Yuan Cai, Zi-Wen Wang, Jian-Yi Zhao, Yi-Han Li, Ji-Fu Wei, Qiang Ding
Journal: Cancer Research (2024)

Breast cancer is a global public health concern with high mortality rates, necessitating the development of innovative treatment strategies. PARP inhibitors have shown efficacy in certain patient populations, but their application is largely limited to cancers with homologous recombination deficiency. Here, we identified the suppression of FANCI as a therapeutic strategy to enhance the efficacy of PARP inhibitors in breast cancer. Elevated FANCI expression in breast cancer was associated with poor prognosis and increased cell proliferation and migration. FANCI interacted with PARP1, and suppressing FANCI limited the nuclear localization and functionality of PARP1. Importantly, FANCI inhibition sensitized breast cancer cells to the PARP inhibitor talazoparib in the absence of BRCA mutations. Additionally, the CDK4/6 inhibitor palbociclib enhanced the sensitivity of breast cancer cells to talazoparib through FANCI inhibition. These findings highlight the potential of targeting FANCI to enhance the efficacy of PARP inhibitors in treating breast cancer. Significance: Targeting FANCI is a promising therapeutic strategy for enhancing PARP inhibitor sensitivity in breast cancer that holds potential for broader therapeutic applications beyond cancers harboring BRCA mutations.
War, Bioethics, and Public Health
Authors: Nancy S. Jecker, Caesar Atuire, Vardit Ravitsky, Kevin Behrens, Mohammed Ghaly
Journal: The American Journal of Bioethics (2024)

This paper argues that bioethics as a field should broaden its scope to include the ethics of war, focusing on war's public health effects. The "Introduction" section describes the bioethics literature on war, which emphasizes clinical and research topics while omitting public health. The section, "War as a public health crisis" demonstrates the need for a public health ethics approach by framing war as a public health crisis. The section, "Bioethics principles for war and public health" proposes six bioethics principles for war that address its public health dimensions: health justice, accountability, dignified lives, public health sustainability, nonmaleficence, and public health maximization. The section, "Justifying and applying bioethical principles" shows how these principles inform ethical analysis, including just war theory and military ethics. The section, "From principles to practice" envisions ways in which bioethicists can promote these principles in practice through research, teaching, and service. The "Conclusion" section urges bioethicists to engage with war as a public health crisis, including calling attention to war's impact on civilians, especially women, children, and other vulnerable groups.
Targeting YES1 Disrupts Mitotic Fidelity and Potentiates the Response to Taxanes in Triple-Negative Breast Cancer
Authors: Katrina M. Piemonte, Natasha N. Ingles, Kristen L. Weber-Bonk, Mitchell J. Valentine, Parth R. Majmudar, Salendra Singh, Ruth A. Keri
Journal: Cancer Research (2024)

Clinical trials examining broad-spectrum Src family kinase (SFK) inhibitors revealed significant dose-limiting toxicities, preventing advancement for solid tumors. SFKs are functionally heterogeneous, thus targeting individual members is a potential strategy to elicit antitumor efficacy while avoiding toxicity. Here, we identified that YES1 is the most highly overexpressed SFK in triple-negative breast cancer (TNBC) and is associated with poor patient outcomes. Disrupting YES1, genetically or pharmacologically, induced aberrant mitosis, centrosome amplification, multipolar spindles, and chromosomal instability. Mechanistically, YES1 sustained FOXM1 protein levels and elevated expression of FOXM1 target genes that control centrosome function and are essential for effective and accurate mitotic progression. In both in vitro and in vivo TNBC models, YES1 suppression potentiated the efficacy of taxanes, cornerstone drugs for TNBC that require elevated chromosomal instability for efficacy. Clinically, elevated expression of YES1 was associated with worse overall survival of patients with TNBC treated with taxane and anthracycline combination regimens. Together, this study demonstrates that YES1 is an essential regulator of genome stability in TNBC that can be leveraged to improve taxane efficacy. Significance: YES1 is a sentinel regulator of genomic maintenance that controls centrosome homeostasis and chromosome stability through FOXM1, revealing this pathway as a therapeutic vulnerability for enhancing taxane efficacy in triple-negative breast cancer.
Opioid Overdose After Medication for Opioid Use Disorder Initiation Following Hospitalization or ED Visit
Authors: Scott G. Weiner, Kacey Little, Jiah Yoo, Diana P. Flores, Christi Hildebran, Dagan A. Wright, Grant A. Ritter, Sanae El Ibrahimi
Journal: JAMA Network Open (2024)

Importance Hospitalizations related to opioid use disorder (OUD) represent an opportunity to initiate medication for OUD (MOUD). Objective To assess whether starting MOUD after a hospitalization or emergency department (ED) visit is associated with the odds of fatal and nonfatal opioid overdose at 6 and 12 months. Design, Setting, and Participants This population-based cohort study used data from the Oregon Comprehensive Opioid Risk Registry, which links all payer claims data to other administrative health datasets, for individuals aged 18 years or older who had diagnosis codes related to OUD recorded at an index ED visit or hospitalization from January 2017 to December 2019. Data were analyzed between May 2023 and January 2024. Exposures Receipt of MOUD within the 7 days after an OUD-related hospital visit. Main Outcomes and Measures The primary outcome was fatal or nonfatal overdose at 6 and 12 months after discharge. Sample characteristics, including age, sex, insurance plan, number of comorbidities, and opioid-related overdose events, were stratified by receipt or nonreceipt of MOUD within 7 days after an OUD-related hospital visit. A logistic regression model was used to investigate the association between receipt of MOUD and having an opioid overdose event. Results The study included 22 235 patients (53.1% female; 25.0% aged 25-39 years) who had an OUD-related hospital visit during the study period. Overall, 1184 patients (5.3%) received MOUD within 7 days of their ED visit or hospitalization. Of these patients, 683 (57.7%) received buprenorphine, 463 (39.1%) received methadone, and 46 (3.9%) received long-acting injectable naltrexone. Patients who received MOUD within 7 days after discharge had lower adjusted odds of fatal or nonfatal overdose at 6 months compared with those who did not (adjusted odds ratio [AOR], 0.63; 95% CI, 0.41-0.97). At 12 months, there was no difference in adjusted odds of fatal or nonfatal overdose between these groups (AOR, 0.79; 95% CI, 0.58-1.08). Patients had a lower risk of fatal or nonfatal overdose at 6 months associated with buprenorphine use (AOR, 0.50; 95% CI, 0.27-0.95) but not with methadone use (AOR, 0.57; 95% CI, 0.28-1.17). Conclusions and Relevance In this cohort study of individuals with an OUD-related hospital visit, initiation of MOUD was associated with reduced odds of opioid-related overdose at 6 months. Hospitals should consider implementing programs and protocols to offer initiation of MOUD to patients with OUD who present for care.
EMR-Documented Contraception for Patients Prescribed Medications With Adverse Perinatal Outcomes
Authors: Joseph V. Nolan, Marisa A. Muhonen, Michael A. Jaeb, Michael G. Semanik, Wendy N. Nembhard, Zachary N. Stowe
Journal: JAMA Network Open (2024)

This cross-sectional study examines the rates of method of contraception documentation in the electronic medical record (EMR) for patients receiving 1 of 3 drugs known to be associated with adverse perinatal outcomes.
Stroke After Influenza Vaccines in Older Adults in the US, 2016 to 2019
Authors: Yun Lu, Kathryn Matuska, Yuxin Ma, Layo Laniyan, Yoganand Chillarige, Steven A. Anderson, Richard A. Forshee
Journal: JAMA Network Open (2024)

This case series investigates whether an increase in stroke risk occurred after influenza vaccination among fee-for-service Medicare beneficiaries during the influenza seasons from 2016 to 2019.
Itching Frequency and Neuroanatomic Correlates in Frontotemporal Lobar Degeneration
Authors: Rafi Hadad, Maria Luisa Mandelli, Katherine P. Rankin, Charlie Toohey, Virginia E. Sturm, Shireen Javandel, Andjelika Milicic, Marguerite Knudtson, Isabel Elaine Allen, Nathalia Hoffmann, Adit Friedberg, Katherine Possin, Victor Valcour, Bruce L. Miller
Journal: JAMA Neurology (2024)

Itching is common in geriatric populations and is frequently linked to dermatological or systemic conditions. Itching engages specific brain regions that are implicated in the pathogenesis of frontotemporal lobar degeneration spectrum disorders (FTLD-SD). Thus, itching of undetermined origin (IUO) may indicate the presence of a neurodegenerative process.
Prevalence of Epilepsy in People of Sexual and Gender Minoritized Groups
Authors: Emily L. Johnson, Esther Bui, Karina Tassiopoulos, Maya Overby Koretzky, Rodrigo Zepeda, Ernesto Gonzalez-Giraldo, Rebecca F. Gottesman
Journal: JAMA Neurology (2024)

Epilepsy is a highly treatable condition for many people, but there are large treatment gaps with suboptimal seizure control in minoritized groups. The sexual and gender minority (SGM) community is at risk for health disparities, yet the burden of epilepsy in this community is not known.
Change in Trust in US Government Health Agencies for Cancer Information in the COVID-19 Era
Authors: Onyema G. Chido-Amajuoyi, Rajesh Talluri, Henry K. Onyeaka, Itunu Sokale, Gideon T. Dosunmu, Noelle LoConte, Sanjay Shete
Journal: JAMA Network Open (2024)

This cross-sectional study assesses changes in levels of public trust in US government health agencies providing cancer information.
Overground Gait Training With a Wearable Robot in Children With Cerebral Palsy
Authors: Ja Young Choi, Seung Ki Kim, Juntaek Hong, Hankyul Park, Shin-seung Yang, Dongho Park, Min-Keun Song
Journal: JAMA Network Open (2024)

Importance Cerebral palsy (CP) is the most common developmental motor disorder in children. Robot-assisted gait training (RAGT) using a wearable robot can provide intensive overground walking experience. Objective To investigate the effectiveness of overground RAGT in children with CP using an untethered, torque-assisted, wearable exoskeletal robot. Design, Setting, and Participants This multicenter, single-blind randomized clinical trial was conducted from September 1, 2021, to March 31, 2023, at 5 rehabilitation institutions in Korea. Ninety children with CP in Gross Motor Function Classification System levels II to IV were randomized. Intervention The RAGT group underwent 18 sessions of RAGT during 6 weeks, whereas the control group received standard physical therapy for the same number of sessions during the same period. Main Outcome and Measures The primary outcome measure was the Gross Motor Function Measure 88 (GMFM-88) score. Secondary outcome measures were the GMFM-66, Pediatric Balance Scale, selective control assessment of the lower extremity, Pediatric Evaluation of Disability Inventory–Computer Adaptive Test (PEDI-CAT), 6-minute walking test scores (distance and oxygen consumption), muscle and fat mass via bioelectrical impedance analysis, and gait parameters measured via 3-dimensional analysis. All assessments were performed for all patients at baseline, at the end of the 6-week intervention, and after the 4-week follow-up. Results Of the 90 children (mean [SD] age, 9.51 [2.48] years; 49 [54.4%] male and 41 [45.6%] female) in the study, 78 (86.7%) completed the intervention, with 37 participants (mean [SD] age, 9.57 [2.38] years; 19 [51.4%] male) and 41 participants (mean [SD] age, 9.32 [2.37] years; 26 [63.4%] male) randomly assigned to the RAGT and control groups, respectively. Changes in the RAGT group significantly exceeded changes in the control group in GMFM-88 total (mean difference, 2.64; 95% CI, 0.50-4.78), GMFM-E (mean difference, 2.70; 95% CI, 0.08-5.33), GMFM-66 (mean difference, 1.31; 95% CI, 0.01-2.60), and PEDI-CAT responsibility domain scores (mean difference, 2.52; 95% CI, 0.42-4.63), indicating independence in daily living at postintervention assessment. At the 4-week follow-up, the RAGT group showed significantly greater improvements in balance control (mean difference, 1.48; 95% CI, 0.03-2.94) and Gait Deviation Index (mean difference, 6.48; 95% CI, 2.77-10.19) compared with the control group. Conclusions and Relevance In this randomized clinical trial, overground RAGT using a wearable robot significantly improved gross motor function and gait pattern. This new torque-assisted wearable exoskeletal robot, based on assist-as-needed control, may complement standard rehabilitation by providing adequate assistance and therapeutic support to children with CP. Trial Registration CRIS Identifier: KCT0006273