tbuckley/cabot-search huggingface dataset:
A medical multimodal large language model for future pandemics
Authors: Fenglin Liu, Tingting Zhu, Xian Wu, Bang Yang, Chenyu You, Chenyang Wang, Lei Lu, Zhangdaihong Liu, Yefeng Zheng, Xu Sun, Yang Yang, Lei Clifton, David A. Clifton
Journal: npj Digital Medicine (2023)

Deep neural networks have been integrated into the whole clinical decision procedure which can improve the efficiency of diagnosis and alleviate the heavy workload of physicians. Since most neural networks are supervised, their performance heavily depends on the volume and quality of available labels. However, few such labels exist for rare diseases (e.g., new pandemics). Here we report a medical multimodal large language model (Med-MLLM) for radiograph representation learning, which can learn broad medical knowledge (e.g., image understanding, text semantics, and clinical phenotypes) from unlabelled data. As a result, when encountering a rare disease, our Med-MLLM can be rapidly deployed and easily adapted to them with limited labels. Furthermore, our model supports medical data across visual modality (e.g., chest X-ray and CT) and textual modality (e.g., medical report and free-text clinical note); therefore, it can be used for clinical tasks that involve both visual and textual data. We demonstrate the effectiveness of our Med-MLLM by showing how it would perform using the COVID-19 pandemic "in replay". In the retrospective setting, we test the model on the early COVID-19 datasets; and in the prospective setting, we test the model on the new variant COVID-19-Omicron. The experiments are conducted on 1) three kinds of input data; 2) three kinds of downstream tasks, including disease reporting, diagnosis, and prognosis; 3) five COVID-19 datasets; and 4) three different languages, including English, Chinese, and Spanish. All experiments show that our model can make accurate and robust COVID-19 decision-support with little labelled data.
Acknowledgement to Referees
Authors: Archana Agarwal, Abdul Aleem, Mansour Alotaibi, Carlos Alves, Danieli Andrade, Mariano Andres, Erick Argueta, Sally Awad, Arata Azuma, James Backes, Stephen Bain, Dipika Bansal, Francis Berenbaum, George Bertsias, Evandro Greece, Daniel Bezerra, George Blackburn
Journal: Drugs (2023)
Telehealth interventions for transition to self‐management in adolescents with allergic conditions: A systematic review
Authors: Meg O' Sullivan, Margaret Curtin, Rachel Flynn, Caoimhe Cronin, James O' Mahony, Juan Trujillo
Journal: Allergy (2023)

Abstract Telehealth is an emerging approach that uses technology to provide healthcare remotely. Recent publications have outlined the importance of supporting the transition to self‐management of adolescents with allergic conditions. However, no synthesis of the evidence base on the use and impact of telehealth interventions for this purpose has been conducted to date. This review achieves these aims, in addition to exploring the language use surrounding these interventions, and their implementation. Four databases were searched systematically. References were independently screened by two reviewers. Methodological quality was assessed using the Mixed Methods Appraisal Tool. A narrative synthesis was undertaken. Eighteen articles were included, reporting on 15 telehealth interventions. A total of 86% targeted adolescents with asthma. Mobile applications were the most common telehealth modality used, followed by video‐conferencing, web‐based, virtual reality and artificial intelligence. Five intervention content categories were identified; educational, monitoring, behavioural, psychosocial and healthcare navigational. Peer and/or healthcare professional interaction, gamification and tailoring may increase engagement. The studies showed positive effects of the interventions or no difference from active controls, in self‐management outcomes such as knowledge, health outcomes such as quality‐of‐life, and economic outcomes such as healthcare utilization. The most common implementation outcomes reported were acceptability, appropriateness, feasibility and fidelity.
Low local recurrence rates after Mohs micrographic surgery for cutaneous squamous cell carcinoma of the nail unit
Authors: Surya A. Veerabagu, Junqian Zhang, Aimee E. Krausz, William C. Fix, Brian Cheng, Joseph F. Sobanko, Jeremy R. Etzkorn, Thuzar M. Shin, H. William Higgins, Cerrene N. Giordano, Stacy L. McMurray, Joanna L. Walker, Christopher J. Miller
Journal: Journal of the American Academy of Dermatology (2023)
Cover Image, Volume 43, Issue 12
Authors: Yuting Li, Hanhao Zheng, Yuming Luo, Yan Lin, Mingjie An, Yao Kong, Yue Zhao, Yina Yin, Le Ai, Jian Huang, Changhao Chen
Journal: Cancer Communications (2023)

The cover image is based on the Original Article An HGF-dependent positive feedback loop between bladder cancer cells and fibroblasts mediates lymphangiogenesis and lymphatic metastasis by Yuting Li et al., https://doi.org/10.1002/cac2.12470.
Biomarkers and experimental models for cancer immunology investigation
Authors: Hengyi Xu, Ziqi Jia, Fengshuo Liu, Jiayi Li, Yansong Huang, Yiwen Jiang, Pengming Pu, Tongxuan Shang, Pengrui Tang, Yongxin Zhou, Yufan Yang, Jianzhong Su, Jiaqi Liu
Journal: MedComm (2023)

Abstract The rapid advancement of tumor immunotherapies poses challenges for the tools used in cancer immunology research, highlighting the need for highly effective biomarkers and reproducible experimental models. Current immunotherapy biomarkers encompass surface protein markers such as PD‐L1, genetic features such as microsatellite instability, tumor‐infiltrating lymphocytes, and biomarkers in liquid biopsy such as circulating tumor DNAs. Experimental models, ranging from 3D in vitro cultures (spheroids, submerged models, air–liquid interface models, organ‐on‐a‐chips) to advanced 3D bioprinting techniques, have emerged as valuable platforms for cancer immunology investigations and immunotherapy biomarker research. By preserving native immune components or coculturing with exogenous immune cells, these models replicate the tumor microenvironment in vitro. Animal models like syngeneic models, genetically engineered models, and patient‐derived xenografts provide opportunities to study in vivo tumor‐immune interactions. Humanized animal models further enable the simulation of the human‐specific tumor microenvironment. Here, we provide a comprehensive overview of the advantages, limitations, and prospects of different biomarkers and experimental models, specifically focusing on the role of biomarkers in predicting immunotherapy outcomes and the ability of experimental models to replicate the tumor microenvironment. By integrating cutting‐edge biomarkers and experimental models, this review serves as a valuable resource for accessing the forefront of cancer immunology investigation.
Accuracy of the Enhanced Liver Fibrosis Test in Patients With Type 2 Diabetes Mellitus and Its Clinical Implications
Authors: Taeang Arai, Hirokazu Takahashi, Yuya Seko, Hidenori Toyoda, Hideki Hayashi, Kanji Yamaguchi, Michihiro Iwaki, Masato Yoneda, Toshihide Shima, Hideki Fujii, Asahiro Morishita, Kazuhito Kawata, Kengo Tomita, Miwa Kawanaka, Yuichi Yoshida, Tadashi Ikegami, Kazuo Notsumata, Satoshi Oeda, Masanori Atsukawa, Yoshihiro Kamada, Yoshio Sumida, Hideaki Fukushima, Eiji Miyoshi, Shinichi Aishima, Takeshi Okanoue, Yoshito Itoh, Atsushi Nakajima
Journal: Clinical Gastroenterology and Hepatology (2023)
Characterization of Chitosan‐Gallic Acid Graft Copolymer for Periodontal Dressing Hydrogel Application
Authors: Mengge Feng, Xuelian Zeng, Quan Lin, Yunxiao Wang, Hongjiang Wei, Shanyi Yang, Guangwei Wang, Xingyu Chen, Mengqin Guo, Xin Yang, Jun Hu, Yufeng Zhang, Xiangliang Yang, Yangge Du, Yanbing Zhao
Journal: Advanced Healthcare Materials (2023)

Abstract The postoperative periodontal wound is in a complex physiological environment; the bacteria accumulation, the saliva stimulation, and the food residues retention will aggravate the wound deterioration. Commercial periodontal dressings have been widely used for postoperative periodontal treatment, and there still exists some problems, such as poor biocompatibility, weak adhesion, insufficient antibacterial, and anti‐inflammatory properties. In this study, a chitosan‐gallic acid graft copolymer (CS‐GA) is synthesized as a potential periodontal dressing hydrogel. CS‐GA possesses high swelling rate, adjustable degradability, self‐healing ability, biocompatibility, strong adhesion ability, high mechanical properties and toughness. Furthermore, CS‐GA has good scavenging ability for ·OH, O 2 − , and 1 O 2. And CS‐GA has good inhibition effect on different bacterial through bacterial membranes damage. CS‐GA can stop bleeding in a short time and adsorb erythrocytes to form physical blood clots to enhance the hemostatic performance. In addition, CS‐GA can reduce inflammatory factors expressions, increase collagen fibers deposition, and neovascularization to promote wounds healing, which makes it as a potential periodontal dressing for postoperative tissue restoration.
Oncofetal reprogramming in tumor development and progression: novel insights into cancer therapy
Authors: Jiangjun Cao, Zhe Zhang, Li Zhou, Maochao Luo, Lei Li, Bowen Li, Edouard C. Nice, Weifeng He, Shaojiang Zheng, Canhua Huang
Journal: MedComm (2023)

Abstract Emerging evidence indicates that cancer cells can mimic characteristics of embryonic development, promoting their development and progression. Cancer cells share features with embryonic development, characterized by robust proliferation and differentiation regulated by signaling pathways such as Wnt, Notch, hedgehog, and Hippo signaling. In certain phase, these cells also mimic embryonic diapause and fertilized egg implantation to evade treatments or immune elimination and promote metastasis. Additionally, the upregulation of ATP‐binding cassette (ABC) transporters, including multidrug resistance protein 1 (MDR1), multidrug resistance‐associated protein 1 (MRP1), and breast cancer‐resistant protein (BCRP), in drug‐resistant cancer cells, analogous to their role in placental development, may facilitate chemotherapy efflux, further resulting in treatment resistance. In this review, we concentrate on the underlying mechanisms that contribute to tumor development and progression from the perspective of embryonic development, encompassing the dysregulation of developmental signaling pathways, the emergence of dormant cancer cells, immune microenvironment remodeling, and the hyperactivation of ABC transporters. Furthermore, we synthesize and emphasize the connections between cancer hallmarks and embryonic development, offering novel insights for the development of innovative cancer treatment strategies.
Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare
Authors: David Oniani, Jordan Hilsman, Yifan Peng, Ronald K. Poropatich, Jeremy C. Pamplin, Gary L. Legault, Yanshan Wang
Journal: npj Digital Medicine (2023)

Abstract In 2020, the U.S. Department of Defense officially disclosed a set of ethical principles to guide the use of Artificial Intelligence (AI) technologies on future battlefields. Despite stark differences, there are core similarities between the military and medical service. Warriors on battlefields often face life-altering circumstances that require quick decision-making. Medical providers experience similar challenges in a rapidly changing healthcare environment, such as in the emergency department or during surgery treating a life-threatening condition. Generative AI, an emerging technology designed to efficiently generate valuable information, holds great promise. As computing power becomes more accessible and the abundance of health data, such as electronic health records, electrocardiograms, and medical images, increases, it is inevitable that healthcare will be revolutionized by this technology. Recently, generative AI has garnered a lot of attention in the medical research community, leading to debates about its application in the healthcare sector, mainly due to concerns about transparency and related issues. Meanwhile, questions around the potential exacerbation of health disparities due to modeling biases have raised notable ethical concerns regarding the use of this technology in healthcare. However, the ethical principles for generative AI in healthcare have been understudied. As a result, there are no clear solutions to address ethical concerns, and decision-makers often neglect to consider the significance of ethical principles before implementing generative AI in clinical practice. In an attempt to address these issues, we explore ethical principles from the military perspective and propose the “GREAT PLEA” ethical principles, namely Governability, Reliability, Equity, Accountability, Traceability, Privacy, Lawfulness, Empathy, and Autonomy for generative AI in healthcare. Furthermore, we introduce a framework for adopting and expanding these ethical principles in a practical way that has been useful in the military and can be applied to healthcare for generative AI, based on contrasting their ethical concerns and risks. Ultimately, we aim to proactively address the ethical dilemmas and challenges posed by the integration of generative AI into healthcare practice.
Toward low-cost gene therapy: mRNA-based therapeutics for treatment of inherited retinal diseases
Authors: Pedro Antas, Cláudia Carvalho, Joaquim Cabral-Teixeira, Luísa de Lemos, Miguel C. Seabra
Journal: Trends in Molecular Medicine (2023)

Inherited retinal diseases (IRDs) stem from genetic mutations that result in vision impairment. Gene therapy shows promising therapeutic potential, exemplified by the encouraging initial results with voretigene neparvovec. Nevertheless, the associated costs impede widespread access, particularly in low-to-middle income countries. The primary challenge remains: how can we make these therapies globally affordable? Leveraging advancements in mRNA therapies might offer a more economically viable alternative. Furthermore, transitioning to nonviral delivery systems could provide a dual benefit of reduced costs and increased scalability. Relevant stakeholders must collaboratively devise and implement a research agenda to realize the potential of mRNA strategies in equitable access to treatments to prevent vision loss.
The determinants associated with zoonotic potential of influenza A viruses: BTN3A3 evasion mediated by residue mutation in the nucleoprotein
Authors: Lili Tian, Maochen Li, Huahao Fan
Journal: MedComm (2023)

Mutation of residue 313 in the viral nucleoprotein from F/L to Y/V (or substitutions to N, H, or Q in the nucleoprotein residue 52 adjacent to residue 313) facilitates IAVs to escape from BTN3A3 restriction on virus replication.
CNS Efficacy of Osimertinib With or Without Chemotherapy in Epidermal Growth Factor Receptor–Mutated Advanced Non–Small-Cell Lung Cancer
Authors: Pasi A. Jänne, David Planchard, Kunihiko Kobayashi, Ying Cheng, Chee Khoon Lee, Natalia Valdiviezo, Konstantin Laktionov, Tsung-Ying Yang, Yan Yu, Terufumi Kato, Liyan Jiang, Busyamas Chewaskulyong, Sarayut Lucien Geater, Jean-Marc Maurel, Carlos Rojas, Toshiaki Takahashi, Libor Havel, Frances A. Shepherd, Kentaro Tanaka, Dana Ghiorghiu, Neha P. Amin, Elena Armenteros-Monterroso, Xiangning Huang, Ammar Ahmed Chaudhry, James Chih-Hsin Yang
Journal: Journal of Clinical Oncology (2023)

We report CNS efficacy of first-line osimertinib plus chemotherapy versus osimertinib monotherapy in patients with epidermal growth factor receptor (
Proinflammatory cytokines driving cardiotoxicity in COVID-19
Authors: Maria Colzani, Johannes Bargehr, Federica Mescia, Eleanor C Williams, Vincent Knight-Schrijver, Jonathan Lee, Charlotte Summers, Irina Mohorianu, Kenneth G C Smith, Paul A Lyons, Sanjay Sinha
Journal: Cardiovascular Research (2023)

Cardiac involvement is common in patients hospitalized with COVID-19 and correlates with an adverse disease trajectory. While cardiac injury has been attributed to direct viral cytotoxicity, serum-induced cardiotoxicity secondary to serological hyperinflammation constitutes a potentially amenable mechanism that remains largely unexplored.
Hypoxia-activated glutamine antagonist prodrug combined with combretastatin A4 nanoparticles for tumor-selective metabolic blockade
Authors: Mengfei Zheng, Hang Xu, Yue Huang, Jiali Sun, Honglei Zhang, Zheng Lv, Zhilin Liu, Zhaohui Tang, Xuesi Chen
Journal: Journal of Controlled Release (2023)
OX40L-expressing M1-like macrophage exosomes for cancer immunotherapy
Authors: Yongkang Yu, Tingxuan Li, Meitong Ou, Ran Luo, Hongzhong Chen, He Ren, Zimu Li, Jie Sun, Hanjie Zhang, Shaojun Peng, Yanli Zhao, Lin Mei
Journal: Journal of Controlled Release (2023)
Molluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum
Authors: Kyle E McElroy, Jorge A Audino, Jeanne M Serb
Journal: Molecular Biology and Evolution (2023)

Abstract In animals, opsins and cryptochromes are major protein families that transduce light signals when bound to light-absorbing chromophores. Opsins are involved in various light-dependent processes, like vision, and have been co-opted for light-independent sensory modalities. Cryptochromes are important photoreceptors in animals, generally regulating circadian rhythm, they belong to a larger protein family with photolyases, which repair UV-induced DNA damage. Mollusks are great animals to explore questions about light sensing as eyes have evolved multiple times across, and within, taxonomic classes. We used molluscan genome assemblies from 80 species to predict protein sequences and examine gene family evolution using phylogenetic approaches. We found extensive opsin family expansion and contraction, particularly in bivalve xenopsins and gastropod Go-opsins, while other opsins, like retinochrome, rarely duplicate. Bivalve and gastropod lineages exhibit fluctuations in opsin repertoire, with cephalopods having the fewest number of opsins and loss of at least 2 major opsin types. Interestingly, opsin expansions are not limited to eyed species, and the highest opsin content was seen in eyeless bivalves. The dynamic nature of opsin evolution is quite contrary to the general lack of diversification in mollusk cryptochromes, though some taxa, including cephalopods and terrestrial gastropods, have reduced repertoires of both protein families. We also found complete loss of opsins and cryptochromes in multiple, but not all, deep-sea species. These results help set the stage for connecting genomic changes, including opsin family expansion and contraction, with differences in environmental, and biological features across Mollusca.
pH-dependent pressure-sensitive colonic capsules for the delivery of aqueous bacterial suspensions
Authors: Fatma Abdi, Marina Green Buzhor, Nadia Zellweger, None Zhi-Luo, Jean-Christophe Leroux
Journal: Journal of Controlled Release (2023)

Microbiome-based therapies hold great promise for treating various diseases, but the efficient delivery of live bacteria to the colon remains a challenge. Furthermore, current oral formulations, such as lyophilized bacterial capsules or tablets, are produced using processes that can decrease bacterial viability. Consequently, high dosages are required to achieve efficacy. Herein, we report the design of pressure-sensitive colonic capsules for the encapsulation and delivery of aqueous suspensions of live bacteria. The capsules consisted of 2 functional thin-films (hydrophobic and enteric) of ethyl cellulose and Eudragit S100 dip-coated onto hydroxypropyl methylcellulose molds. The capsules could be loaded with aqueous media and provide protection against acidic fluids and, to some extent, oxygen diffusion, suggesting their potential suitability for delivering anaerobic bacterial strains. Disintegration and mechanical studies indicated that the capsules could withstand transit through the stomach and upper/proximal small intestinal segments and rupture in the ileum/colon. In vitro studies showed that bacterial cells (anaerobic and aerobic commensals) remained highly viable (74–98%) after encapsulation and exposure to the simulated GI tract conditions. In vivo studies with a beagle dog model revealed that 67% of the capsules opened after 3.5 h, indicating content release in the distal gastrointestinal tract. These data demonstrate that live aqueous bacterial suspensions comprised of both aerobic and anaerobic commensals can be encapsulated and in the future might be efficiently delivered to the distal gastrointestinal tract, suggesting the practical applications of these capsules in microbiome-based therapies.
Genetic Modification of a <i>Hox</i> Locus Drives Mimetic Color Pattern Variation in a Highly Polymorphic Bumble Bee
Authors: Wanhu Yang, Jixiang Cui, Yuxin Chen, Chao Wang, Yuanzhi Yin, Wei Zhang, Shanlin Liu, Cheng Sun, Hu Li, Yuange Duan, Fan Song, Wanzhi Cai, Heather M Hines, Li Tian
Journal: Molecular Biology and Evolution (2023)

Müllerian mimicry provides natural replicates ideal for exploring mechanisms underlying adaptive phenotypic divergence and convergence, yet the genetic mechanisms underlying mimetic variation remain largely unknown. The current study investigates the genetic basis of mimetic color pattern variation in a highly polymorphic bumble bee, Bombus breviceps (Hymenoptera, Apidae). In South Asia, this species and multiple comimetic species converge onto local Müllerian mimicry patterns by shifting the abdominal setal color from orange to black. Genetic crossing between the orange and black phenotypes suggested the color dimorphism being controlled by a single Mendelian locus, with the orange allele being dominant over black. Genome-wide association suggests that a locus at the intergenic region between 2 abdominal fate-determining Hox genes, abd-A and Abd-B, is associated with the color change. This locus is therefore in the same intergenic region but not the same exact locus as found to drive red black midabdominal variation in a distantly related bumble bee species, Bombus melanopygus. Gene expression analysis and RNA interferences suggest that differential expression of an intergenic long noncoding RNA between abd-A and Abd-B at the onset setal color differentiation may drive the orange black color variation by causing a homeotic shift late in development. Analysis of this same color locus in comimetic species reveals no sequence association with the same color shift, suggesting that mimetic convergence is achieved through distinct genetic routes. Our study establishes Hox regions as genomic hotspots for color pattern evolution in bumble bees and demonstrates how pleiotropic developmental loci can drive adaptive radiations in nature.
111P Comparison of the efficacy and safety of fruquintinib and fruquintinib combined with immune checkpoint inhibitors in the treatment of metastatic microsatellite stable colorectal cancer: A real-world study
Authors: Z. Wang, H. Fu, L. Huiyan, F. Wang, F. Wang, D. Wang, Y. Li, D. Li, Y. Jin, D. Zhang, Z. Lu, J. Chen
Journal: Annals of Oncology (2023)
138MO Pembrolizumab (Pembro) or placebo (Pbo) plus chemotherapy (Chemo) for advanced HER2-negative gastric/gastroesophageal junction (G/GEJ) adenocarcinoma (KEYNOTE-859): Asia subgroup analysis
Authors: D-Y. Oh, Y. Bai, M.H. Ryu, J. Lee, J. Li, S. Luo, H. Pan, Y. Qu, J. Lu, L. Yang, H. Yasui, H. Yabusaki, C.J. Yen, W.W.L. Chan, K. Yamaguchi, K-H. Yeh, L. Yin, S. Bordia, P. Bhagia, S.Y. Rha
Journal: Annals of Oncology (2023)
89O Long-term outcomes of intraoperative chemotherapy with 5-FU for colorectal cancer patients receiving curative resection (IOCCRC): A randomized, multicenter, prospective, phase III trial
Authors: Z. Pan, R. Zhang, X. Wu, D-S. Wan, J-Z. Lin, P-R. Ding, L. Liao, J. Lei, Z. Lu, L. Li, G. Chen, L-H. Kong, F. Wang, W. Fan, W. Jiang, W. Zhou, C. Li, Y. Li, J. Peng
Journal: Annals of Oncology (2023)