tbuckley/cabot-search huggingface dataset:
Public good or climate washing? A guideline for climate and health researchers considering funding from carbon-intensive industries
Authors: Connie Hoe, Aditi Bunker, Cristina Arnés-Sanz, Joacim Rocklöv, Kirsty Wild, Wallis Turner Holmes, Alistair Woodward
Journal: The Lancet Planetary Health (2024)

Should climate and health researchers accept funding from industries that profit from climate-damaging consumption? In this Personal View, we aim to ignite discussions on this key topic and to introduce a guideline to possibly help climate and health researchers grappling with this complex question. Drawing from existing tools focused on other public health issues and the conclusions of the 2023 Lancet Series on commercial determinants of health, we propose a guideline comprising six parts: meeting public health and climate goals; building credibility and trust; avoiding undue dependence on particular sources of funding; not inflating without good reason the public image of industry; embedding processes to ensure transparency and independence; and protecting the freedom to publish. We invite other climate and public health scientists to report their own experiences and provide feedback on this guideline.
Faecal (or intestinal) microbiota transplant: a tool for repairing the gut microbiome
Authors: Rohma Ghani, Despoina Chrysostomou, Lauren A Roberts, Madhumitha Pandiaraja, Julian R. Marchesi, Benjamin H. Mullish
Journal: Gut Microbes (2024)

Faecal/intestinal microbiota transplant (FMT/IMT) is an efficacious treatment option for recurrent Clostridioides difficile infection, which has prompted substantial interest in FMT's potential role in the management of a much broader range of diseases associated with the gut microbiome. Despite its promise, the success rates of FMT in these other settings have been variable. This review critically evaluates the current evidence on the impact of clinical, biological, and procedural factors upon the therapeutic efficacy of FMT, and identifies areas that remain nebulous. Due to some of these factors, the optimal therapeutic approach remains unclear; for example, the preferred timing of FMT administration in a heavily antibiotic-exposed hematopoietic cell transplant recipient is not standardized, with arguments that can be made in alternate directions. We explore how these factors may impact upon more informed selection of donors, potential matching of donors to recipients, and aspects of clinical care of FMT recipients. This includes consideration of how gut microbiome composition and functionality may strategically inform donor selection criteria. Furthermore, we review how the most productive advances within the FMT space are those where clinical and translational outcomes are assessed together, and where this model has been used productively in recent years to better understand the contribution of the gut microbiome to human disease, and start the process toward development of more targeted microbiome therapeutics.
SATB2 is an Emergent Biomarker of Anaplastic Thyroid Carcinoma: A Series with Comprehensive Biomarker and Molecular Studies
Authors: Dingani Nkosi, William E. Crowe, Brian J. Altman, Zoltán N. Oltvai, Ellen J. Giampoli, Moises J. Velez
Journal: Endocrine Pathology (2024)

Anaplastic thyroid carcinoma (ATC) is a rare and aggressive thyroid malignancy typically comprised of undifferentiated tumor cells with various histologic morphologies, which makes the diagnosis challenging. These tumors commonly show loss of thyroglobulin and TTF1 with preservation of cytokeratin (67%) and Paired Box Gene 8 (PAX8) (55%) expression. Identification of a sensitive immunohistochemical stain to aid in the diagnosis of ATC would be beneficial. Immunohistochemistry (IHC) against special AT-rich sequence-binding protein 2 (SATB2) protein is a sensitive and specific marker expressed in colorectal adenocarcinoma and bone or soft tissue tumors with osteoblastic differentiation. However, SATB2 is also expressed in other sarcomatous/undifferentiated neoplasms lacking osteoblastic differentiation. Using quantitative reverse transcription PCR (RT-qPCR) we showed that there is variable expression of SATB2 mRNA expression in ATCs. To evaluate the role of SATB2 protein expression in ATC, we performed PAX8, SATB2, pancytokeratin (AE1/AE3 & CAM5.2), claudin-4 and TTF1 immunostaining on 23 cases. ATCs showed retained expression of PAX8 in 65% (15/23); SATB2 was detected in 74% (17/23); pancytokeratin was expressed in 65% (15/23); claudin-4 was expressed in 35% (8/23) and TTF1 showed expression in 13% (3/23) of cases. Furthermore, 83% (5/6) of ATCs which lacked SATB2 expression, retained PAX8 expression, while 88% (7/8) of the tumors without PAX8 expression were positive for SATB2. Differentiated follicular cell-derived thyroid cancers (n = 30), differentiated high grade thyroid carcinoma (n = 3), and poorly differentiated thyroid carcinoma (n = 8) were negative for SATB2 immunoreactivity. Next-generation selected cases detected the commonly identified oncogenic variants including those in BRAF, RAS, TP53, and TERT promoter. Overall, we hereby demonstrate that SATB2 IHC may be used to support the diagnosis of ATC.
WWOX tuning of oleic acid signaling orchestrates immunosuppressive macrophage polarization and sensitizes hepatocellular carcinoma to immunotherapy
Authors: Shaoqing Liu, Shiguang Yang, Min Xu, Qiang Zhou, Jialei Weng, Zhiqiu Hu, Minghao Xu, Wenxin Xu, Yong Yi, Yi Shi, Qiongzhu Dong, Mien-Chie Hung, Ning Ren, Chenhao Zhou
Journal: Journal for ImmunoTherapy of Cancer (2024)

Immune checkpoint inhibitors (ICIs) are therapeutically effective for hepatocellular carcinoma (HCC) but are individually selective. This study examined the role of specific common fragile sites (CFSs) related gene in HCC immunotherapy.
In situ endoscopic photodynamic therapy combined with immature DC vaccination induces a robust T cell response against peritoneal carcinomatosis
Authors: Charline Degavre, Anouk Lepez, Sebastien Ibanez, Clémence François, Katarzyna Głowacka, Céline Guilbaud, Florine Laloux-Morris, Hrag Esfahani, Davide Brusa, Caroline Bouzin, Olivier Feron
Journal: Journal for ImmunoTherapy of Cancer (2024)

Immunogenic cell death (ICD) and ferroptosis have recently emerged as key factors in the anticancer immune response. Among the treatments able to induce ICD and the associated release of danger signals is photodynamic therapy (PDT). Ferroptosis for its part results from lipid peroxidation and is induced by CD8
Role of<i>CD47</i>gene expression in colorectal cancer: a comprehensive molecular profiling study
Authors: Hiroyuki Arai, Nishant Gandhi, Francesca Battaglin, Jingyuan Wang, Sandra Algaze, Priya Jayachandran, Shivani Soni, Wu Zhang, Yan Yang, Joshua Millstein, Jae Ho Lo, Davendra Sohal, Richard Goldberg, Michael J Hall, Aaron James Scott, Jimmy J Hwang, Emil Lou, Benjamin A Weinberg, John Marshall, Sanjay Goel, Joanne Xiu, W Michael Korn, Heinz-Josef Lenz
Journal: Journal for ImmunoTherapy of Cancer (2024)

Background In patients with colorectal cancer (CRC), the therapeutic effects of conventional immune checkpoint inhibitors targeting the adaptive immune system are largely limited to those with microsatellite instability-high tumors. Meanwhile, new immunotherapies targeting the innate immune system are attracting increasing attention. CD47 is a representative innate immune checkpoint involved in the evasion of tumor cell phagocytosis by macrophages. This large-scale study comprehensively examined the molecular significance of CD47 gene expression in CRC. Methods We analyzed the next-generation sequencing data of DNA and RNA from 14,287 CRC cases included in the data set of a commercial Clinical Laboratory Improvement Amendments-certified laboratory (Caris Life Sciences). The cases were divided into two groups based on the median value of CD47 gene expression levels. The molecular and immune profiles between the groups were compared, and the relationship between CD47 expression and survival outcomes was further examined. Results In CD47 -high tumors, the proportion of consensus molecular subtypes 1 and 4 was significantly higher than in CD47 -low tumors. The expression levels of damage-associated molecular pattern-related genes showed a positive correlation with CD47 expression levels. Major oncogenic pathways, such as mitogen-activated protein kinase, phosphoinositide 3-kinase, angiogenesis, and transforming growth factor beta, were significantly activated in CD47 -high tumors. Additionally, the expression levels of a panel of adaptive immune checkpoint genes and estimates of immune cells constituting the tumor microenvironment (TME) were significantly higher in CD47 -high tumors. Conclusions CD47 expression in CRC was associated with the activation of several oncogenic pathways and an immune-engaged TME. Our findings may provide valuable information for considering new therapeutic strategies targeting innate immune checkpoints in CRC.
Intratumoral and peritumoral radiomics of MRIs predicts pathologic complete response to neoadjuvant chemoimmunotherapy in patients with head and neck squamous cell carcinoma
Authors: Peiliang Lin, Wenqian Xie, Yong Li, Chenjia Zhang, Huiqian Wu, Huan Wan, Ming Gao, Faya Liang, Ping Han, Renhui Chen, Gui Cheng, Xuekui Liu, Song Fan, Xiaoming Huang
Journal: Journal for ImmunoTherapy of Cancer (2024)

For patients with locally advanced head and neck squamous cell carcinoma (HNSCC), combined programmed death receptor-1 inhibitor and chemotherapy improved response rate to neoadjuvant therapy. However, treatment response varies among patients. There is no tool to predict pathologic complete response (pCR) with high accuracy for now. To develop a tool based on radiomics features of MRI to predict pCR to neoadjuvant chemoimmunotherapy (NACI) may provide valuable assistance in treatment regimen determination for HNSCC.
Evolution of Plant Genome Size and Composition
Authors: Bing He, Wanfei Liu, Jianyang Li, Siwei Xiong, Jing Jia, Qiang Lin, Hailin Liu, Peng Cui
Journal: Genomics Proteomics & Bioinformatics (2024)

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we focus on changes in plant genome size and composition, examining the effects of polyploidy, whole-genome duplication, and alternations in transposable elements on plant genome architecture and evolution, respectively. In addition, to address gaps in the available information, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a comprehensive, up-to-date summary of information on plant genome architecture and evolution in this review.
CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants
Authors: Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Shafighi, Szymon M. Kiełbasa, Hugo W. van Kessel, Ruben A. L. de Groen, Joost S. P. Vermaat, Julieta H. Sepúlveda Yáñez, Marcelo A. Navarrete, Hendrik Veelken, Cornelis A. M. van Bergen, Ewa Szczurek
Journal: Genome biology (2024)

Abstract Tumours exhibit high genotypic and transcriptional heterogeneity. Both affect cancer progression and treatment, but have been predominantly studied separately in follicular lymphoma. To comprehensively investigate the evolution and genotype-to-phenotype maps in follicular lymphoma, we introduce CaClust, a probabilistic graphical model integrating deep whole exome, single-cell RNA and B-cell receptor sequencing data to infer clone genotypes, cell-to-clone mapping, and single-cell genotyping. CaClust outperforms a state-of-the-art model on simulated and patient data. In-depth analyses of single cells from four samples showcase effects of driver mutations, follicular lymphoma evolution, possible therapeutic targets, and single-cell genotyping that agrees with an independent targeted resequencing experiment.
The Genetic Basis of Sudden Cardiac Death: From Diagnosis to Emerging Genetic Therapies
Authors: Enya Dewars, Andrew Landstrom
Journal: Annual Review of Medicine (2024)

Sudden cardiac death (SCD) is an abrupt, tragic manifestation of a number of cardiovascular diseases, primarily ion channelopathies and heritable cardiomyopathies. Because these diseases are heritable, genetics play a key role in the diagnosis and management of SCD-predisposing diseases. Historically, genetics have been used to confirm a diagnosis and identify at-risk family members, but a deeper understanding of the genetic causes of SCD could pave the way for individualized therapy, early risk detection, and a transformative shift toward genetically informed therapies. This review focuses on the evolving genetic landscape of SCD-predisposing diseases, the current state of gene therapy and therapeutic development, and the promise of using predictive genetics to identify individuals at risk of SCD.
177Lu-FAP-2286 Therapy in a Case of Squamous Lung Cancer
Authors: Linwei Li, Lingzhi Chen, Yanlang Zhang, Yu Zhang, Yue Chen
Journal: Clinical Nuclear Medicine (2024)

Abstract We reported a 72-year-old man who was diagnosed with squamous lung cancer and received 2 cycles of 177 Lu-FAP-2286 treatment. Radiological remission was observed on follow-up FAP imaging 7 months later with squamous cell carcinoma antigen decreased to normal level. No other abnormality monitored by routine laboratory examination was noted.
Glucagon-Like Peptide-1 Receptor–Targeted PET/CT With 68Ga-HBED-CC-Exendin-4 in Localizing Insulinoma
Authors: Linlin Li, Guochang Wang, Jiarou Wang, Heng Ma, Jingci Chen, Rongxi Wang, Qingqing Pan, Haiyan Hong, Wenbin Jin, Hank F. Kung, Lin Zhu, Yaping Luo, Zhaohui Zhu
Journal: Clinical Nuclear Medicine (2024)

Purpose Modifying glucagon-like peptide-1 receptor (GLP-1R)–targeted PET agent to achieve faster renal clearance and preserved high affinity to GLP-1R is clinically relevant. The aim of this study is to assess the performance of a newly developed GLP-1R–targeted agent, 68 Ga-HBED-CC-exendin-4 in localizing insulinoma, and its biodistribution, as compared with previously introduced 68 Ga-NOTA-exendin-4. Patients and Methods Nineteen patients with endogenous hyperinsulinemic hypoglycemia were enrolled and referred for 68 Ga-HBED-CC-exendin-4 PET/CT and 68 Ga-NOTA-exendin-4 PET/CT within 2 consecutive days. Diagnostic performance of the 2 tracers in localizing insulinoma was evaluated, and SUV of the lesion, normal pancreas background, kidneys, and bladder were measured. Results 68 Ga-HBED-CC-exendin-4 and 68 Ga-NOTA-exendin-4 PET/CT exhibited an equivalent efficacy in detection rate (both sensitivity of 100%). Although SUV max of the tumor in 68 Ga-HBED-CC-exendin-4 was significantly lower than that in 68 Ga-NOTA-exendin-4 (20.01 ± 9.41 vs 31.78 ± 15.46, P &lt; 0.001) at 50 minutes postinjection, there was no significant difference in the tumor-to-background ratio between the 2 agents (8.61 ± 3.57 vs 8.18 ± 3.38, P = 0.326), and the lesions could be visible as early as 4 minutes postinjection for both agents in patients who underwent dynamic PET/CT. In addition, 68 Ga-HBED-CC-exendin-4 exhibited approximately 30% decrease of the renal accumulation compared with 68 Ga-NOTA-exendin-4 (SUV mean , 42.21 ± 5.79 vs 58.58 ± 10.06 at 50 minutes, P &lt; 0.001). Conclusions 68 Ga-HBED-CC-exendin-4 is an effective agent for localizing insulinoma showing similar detectability and tumor-to-background ratio compared with 68 Ga-NOTA-exendin-4. Notably, 68 Ga-HBED-CC-exendin-4 exhibits significantly lower renal uptake than 68 Ga-NOTA-exendin-4, which might potentially benefit the detection of the tumors adjacent to the left kidneys.
Cancer-Specific Integrin Imaging With 68Ga-Trivehexin
Authors: Tejasvini Singhal, Kanhaiyalal Agrawal, Srijani Mandal, Girish Kumar Parida
Journal: Clinical Nuclear Medicine (2024)

Abstract 68 Ga-Trivehexin is a novel radiotracer binding to “cancer-specific integrin αvβ6.” 68 Ga-Trivehexin has high specificity for tumor cells and, thus, has the potential to replace 18 F-FDG PET/CT due to its limited specificity in the head and neck cancer. Here, we present one case of papillary thyroid carcinoma, where 68 Ga-Trivehexin PET CT demonstrated accurate staging compared with 18 F-FDG PET/CT.
Intradermal Delivery of Cell Vaccine via Ice Microneedles for Cancer Treatment
Authors: Chunli Yang, Wei Zhao, Li Zhang, Liming He, Siyi Wang, Jie Wang, Maya Xiang, Xin Yuan, Maling Gou
Journal: Advanced Healthcare Materials (2024)

Abstract The living tumor cell vaccine (TCV) holds a promise for cancer immunotherapy. Microneedle arrays provide a tool to improve the immune response of vaccines by the intradermal administration in a painless manner. However, it remains challenges for microneedle arrays to deliver the living TCV intradermally. Here, an ice microneedle array delivered living TCVs is shown with sustained granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) secretion for cancer treatment. The ice microneedle array is composed of ice microneedles and a matching polymer holder, which are customized fabricated by a static optical projection lithography (SOPL) technique. The living TCV consisted of irradiated melanoma cells transfected with nanoparticle‐mediated GM‐CSF plasmids. After the living TCV is readily loaded into the ice microneedle via a cryopreservation process, it could be efficiently delivered into the dermis by the microneedle device. Compared to the subcutaneous injection, intradermal administration led to the recruitment of more dendritic cells at the vaccination site and the increased infiltration of CD8 + T cells in the tumor. The ice microneedle array deliveres intradermal TCVs significantly inhibited melanoma growth and effectively prevented melanoma recurrence without obvious side effects. This work demonstrates a promising TCVs for melanoma treatment, which will inspire the future of cancer immunotherapy.
Construction of Somatostatin‐Based Multiphase “Core–Shell” Coacervates as Photodynamic Biomimetic Organelles
Authors: Wenyu Sun, Hongjie Xiong, Jiajia Yin, Wenyan Yao, Xiaohui Liu, Liu Liu, Xuemei Wang, Hui Jiang
Journal: Advanced Healthcare Materials (2024)

Abstract Biomimetic coacervates have recently attracted great interest in biomedical fields, especially for drug delivery and as protocells. However, these membraneless structures are easily coalesced and poorly targetable, limiting their real biomedical applications. Here multiphase “core–shell” coacervate (CSC) constructed by dsDNA and somatostatin (SST), a 14‐mer cyclopeptide is designed. The CSC shows enhanced tumor targetability through SST binding to SST receptors on the tumor cells' surface. G4 quadruplex‐hemin complex can be embedded in the CSC by interaction with SST, as demonstrated by molecular simulation and isothermal titration calorimetry. The G4‐hemin embedded CSC can further recruit photosensitizers such as tetracarboxyphenyl porphyrin to form the CSC‐GHT composite for photodynamic therapy (PDT). As photodynamic biomimetic organelles, CSC‐GHT can convert oxygen to singlet oxygen (catalyzed by the catalase‐mimetic activity of G4‐hemin), resulting in enhanced PDT effect, which allows the inhibition of cellular migration in vitro and tumor growth in vivo. Owing to high stability, targetability, and biosafety, the proposed CSC can recruit various cargos from small dyes to large biomacromolecules (up to 430 kDa), providing promising theranostic applications.
In vivo performance of lean bioabsorbable Mg–Ca alloy X0 and comparison to WE43: Influence of surface modification and alloying content
Authors: L Berger, S Dolert, T Akhmetshina, J-P Burkhard, M Tegelkamp, A M Rich, W Rubin, S Darwiche, G Kuhn, R E Schäublin, B von Rechenberg, B Schaller, K M Nuss, J F Löffler
Journal: Bioactive Materials (2024)
Increased BMP-Responsive Transcription Factors in Distinct Endothelial and Mesenchymal Cells in PAH
Authors: Adam Michael Andruska, Rodrigo Cantu Valadez, Kenzo Ichimura, Pauline Chu, Tianyi Zhang, Katharina Schimmel, Lingli Wang, Aiqin Cao, Micheala A Aldred, Edda Spiekerkoetter
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"Increased BMP-Responsive Transcription Factors in Distinct Endothelial and Mesenchymal Cells in PAH." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Enabling Demonstrated Consent for Biobanking with Blockchain and Generative AI
Authors: Caspar Barnes, Mateo Riobo Aboy, Timo Minssen, Jemima Winifred Allen, Brian D. Earp, Julian Savulescu, Sebastian Porsdam Mann
Journal: The American Journal of Bioethics (2024)

Participation in research is supposed to be voluntary and informed. Yet it is difficult to ensure people are adequately informed about the potential uses of their biological materials when they donate samples for future research. We propose a novel consent framework which we call "demonstrated consent" that leverages blockchain technology and generative AI to address this problem. In a demonstrated consent model, each donated sample is associated with a unique non-fungible token (NFT) on a blockchain, which records in its metadata information about the planned and past uses of the sample in research, and is updated with each use of the sample. This information is accessible to a large language model (LLM) customized to present this information in an understandable and interactive manner. Thus, our model uses blockchain and generative AI technologies to track, make available, and explain information regarding planned and past uses of donated samples.
Temporal changes in mediation effects on cardiovascular and microvascular outcomes with glucagon-like peptide-1 receptor agonist therapy: a post-hoc analysis of the LEADER trial
Authors: Zi-Yang Peng, Yu-Hsuan Lee, Huang-Tz Ou, Shihchen Kuo
Journal: Cardiovascular Research (2024)

Journal Article Accepted manuscript Temporal changes in mediation effects on cardiovascular and microvascular outcomes with glucagon-like peptide-1 receptor agonist therapy: a post-hoc analysis of the LEADER trial Get access Zi-Yang Peng, MS, Zi-Yang Peng, MS Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan Search for other works by this author on: Oxford Academic PubMed Google Scholar Yu-Hsuan Lee, MS, Yu-Hsuan Lee, MS Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan Search for other works by this author on: Oxford Academic PubMed Google Scholar Huang-Tz Ou, PhD, Huang-Tz Ou, PhD Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, TaiwanDepartment of Pharmacy, College of Medicine, National Cheng Kung University, Tainan, Taiwan Correspondence to: Huang-Tz Ou, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, 1 University Road, Tainan 701, Taiwan, Telephone: 886-6-2353535 ext.5685, Fax: 886-6-2373149, Email: huangtz@mail.ncku.edu.tw https://orcid.org/0000-0002-5475-7848 Search for other works by this author on: Oxford Academic PubMed Google Scholar Shihchen Kuo, RPh, PhD Shihchen Kuo, RPh, PhD Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, TaiwanDivision of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, cvae237, https://doi.org/10.1093/cvr/cvae237 Published: 05 November 2024 Article history Received: 26 July 2024 Revision received: 23 September 2024 Accepted: 03 November 2024 Published: 05 November 2024