tbuckley/cabot-search huggingface dataset:
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
Authors: Xuehuan Feng, Jinfang Zheng, Iker Irisarri, Huihui Yu, Bo Zheng, Zahin Ali, Sophie de Vries, Jean Keller, Janine M R Fürst-Jansen, Armin Dadras, Jaccoline M S Zegers, Tim P Rieseberg, Amra Dhabalia Ashok, Tatyana Darienko, Maaike J Bierenbroodspot, Lydia Gramzow, Romy Petroll, Fabian B Haas, Noe Fernandez-Pozo, Orestis Nousias, Tang Li, Elisabeth Fitzek, W Scott Grayburn, Nina Rittmeier, Charlotte Permann, Florian Rümpler, John M Archibald, Günter Theißen, Jeffrey P Mower, Maike Lorenz, Henrik Buschmann, Klaus von Schwartzenberg, Lori Boston, Richard D Hayes, Chris Daum, Kerrie Barry, Igor V Grigoriev, Xiyin Wang, Fay-Wei Li, Stefan A Rensing, Julius Ben Ari, Noa Keren, Assaf Mosquna, Andreas Holzinger, Pierre-Marc Delaux, Chi Zhang, Jinling Huang, Marek Mutwil, Jan de Vries, Yanbin Yin
Journal: Nature Genetics (2024)

Abstract Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum . We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
A critical assessment of using ChatGPT for extracting structured data from clinical notes
Authors: Jingwei Huang, Donghan M. Yang, Ruichen Rong, Kuroush Nezafati, Colin Treager, Zhikai Chi, Shidan Wang, Xian Cheng, Yujia Guo, Laura J. Klesse, Guanghua Xiao, Eric D. Peterson, Xiaowei Zhan, Yang Xie
Journal: npj Digital Medicine (2024)

Abstract Existing natural language processing (NLP) methods to convert free-text clinical notes into structured data often require problem-specific annotations and model training. This study aims to evaluate ChatGPT’s capacity to extract information from free-text medical notes efficiently and comprehensively. We developed a large language model (LLM)-based workflow, utilizing systems engineering methodology and spiral “prompt engineering” process, leveraging OpenAI’s API for batch querying ChatGPT. We evaluated the effectiveness of this method using a dataset of more than 1000 lung cancer pathology reports and a dataset of 191 pediatric osteosarcoma pathology reports, comparing the ChatGPT-3.5 (gpt-3.5-turbo-16k) outputs with expert-curated structured data. ChatGPT-3.5 demonstrated the ability to extract pathological classifications with an overall accuracy of 89%, in lung cancer dataset, outperforming the performance of two traditional NLP methods. The performance is influenced by the design of the instructive prompt. Our case analysis shows that most misclassifications were due to the lack of highly specialized pathology terminology, and erroneous interpretation of TNM staging rules. Reproducibility shows the relatively stable performance of ChatGPT-3.5 over time. In pediatric osteosarcoma dataset, ChatGPT-3.5 accurately classified both grades and margin status with accuracy of 98.6% and 100% respectively. Our study shows the feasibility of using ChatGPT to process large volumes of clinical notes for structured information extraction without requiring extensive task-specific human annotation and model training. The results underscore the potential role of LLMs in transforming unstructured healthcare data into structured formats, thereby supporting research and aiding clinical decision-making.
Targeted desialylation and cytolysis of tumour cells by fusing a sialidase to a bispecific T-cell engager
Authors: Zhuo Yang, Yingqin Hou, Geramie Grande, Jong Hyun Cho, Chao Wang, Yujie Shi, Jaroslav Zak, Yue Wan, Ke Qin, Dongfang Liu, John R. Teijaro, Richard A. Lerner, Peng Wu
Journal: Nature Biomedical Engineering (2024)
Colon Volume by Computed Tomography and Scintigraphic Colonic Transit in Constipated Patients With or Without Redundant Colon
Authors: Saam Dilmaghani, Camille Lupianez-Merly, Jeffrey Fetzer, Joelle BouSaba, Houssam Halawi, Michael Camilleri
Journal: Clinical Gastroenterology and Hepatology (2024)
Correction: Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Alyssa C. Flint, Dana K. Mitchell, Steven P. Angus, Abbi E. Smith, Waylan Bessler, Li Jiang, Henry Mang, Xiaohong Li, Qingbo Lu, Brooke Rodriguez, George E. Sandusky, Andi R. Masters, Chi Zhang, Pengtao Dang, Jenna Koenig, Gary L. Johnson, Weihua Shen, Jiangang Liu, Amit Aggarwal, Gregory P. Donoho, Melinda D. Willard, Shripad V. Bhagwat, D. Wade Clapp, Steven D. Rhodes
Journal: Clinical Cancer Research (2024)
“Myeloid” Mutations in ALL Are Not Uncommon: Implications for Etiology and Therapies
Authors: Ilaria Iacobucci
Journal: Blood Cancer Discovery (2024)

Summary: In Blood Cancer Discovery, Saygin and colleagues report that somatic variants that are recurrent in myeloid malignancies can also occur with high frequency (16%) in adult acute lymphoblastic leukemia (ALL) where they correlate with older age, diagnosis following genotoxic therapy for a prior malignancy and worse outcome to chemotherapy. Mutations in these “myeloid” genes can precede ALL diagnosis and arise in hematopoietic stem or progenitor cells that clonally expand and differentiate into both lymphoblasts and nonmalignant myeloid cells, supporting a role for clonal hematopoiesis as premalignant state outside the context of myeloid malignancies and providing implications for both ALL etiology and therapeutic intervention. See related article by Saygin et al., p. 164 (4).
False-Negative Neuroendocrine Tumor Identified With 68Ga-DOTATOC PET/CT
Authors: Aurélie Moreau, Charlotte Chaouat, Thomas Walter, Aurélien Dupré, David Kryza
Journal: Clinical Nuclear Medicine (2024)

Abstract We report the case of a 25-year-old man who was undergoing follow-up for neurofibromatosis type 1. The man underwent 68 Ga-DOTATOC PET/CT for a suspected well-differentiated duodenal neuroendocrine tumor. This examination did not reveal any significant uptake, whereas complementary 18 F-FDG PET/CT showed moderate 18 F-FDG uptake in the primary tumor as well as the adenopathy. Histology, a well-differentiated duodenal neuroendocrine tumor was confirmed, consistent with the diagnosis of somatostatinoma. Although rare, this well-differentiated neuroendocrine tumor should be kept in mind as a possible source of false-negative somatostatin receptor PET/CT findings.
Intramuscular Granular Cell Tumor Detected on 68Ga-PSMA PET/CT
Authors: Muge N. Engin, Adil Boz
Journal: Clinical Nuclear Medicine (2024)

Abstract Finding of the prostate-specific membrane antigen (PSMA) is highly expressed in prostate cancer (PC) cells that have made it possible to evaluate the patients with PC with a single imaging method. 68 Ga-PSMA PET/CT is now part of the routine in patients with PC. After several years of clinical experience with PSMA tracers, the specificity is satisfactory; however, concerns about the specificity are raising day by day due to the newly laid out nonprostatic malignant and benign lesions with high PSMA expression. Herein, we present an incidental 68 Ga-PSMA uptake in an intramuscular granular cell tumor.
Bilateral Adrenal Metastasis of Prostatic Adenocarcinoma on 68Ga-PSMA PET/CT Imaging
Authors: Ediz Beyhan, Ceyda Turan Bektaş, Mehmet Can Baloğlu, Zehranur Tosunoğlu, Tevfik Fikret Çermik
Journal: Clinical Nuclear Medicine (2024)

Abstract An 84-year-old man with prostate adenocarcinoma underwent 68 Ga-PSMA PET/CT due to PSA recurrence. Foci of 68 Ga-PSMA uptake were observed in bilateral adrenal glands. Adrenal MRI showed metastasis only in the left adrenal gland. Metastatic 68 Ga-PSMA uptake was also observed in the mediastinum and bone. Enzalutamide treatment was started. Follow-up 68 Ga-PSMA PET/CT scan showed regression in both adrenal gland metastases and other metastases.
68Ga-DOTATOC Pictorial Essay of Various Recurrent Meningiomas Rejected for Treatment With 177Lu-DOTATATE
Authors: Aurélie Moreau, Aurélien Maureille, David Kryza
Journal: Clinical Nuclear Medicine (2024)

Abstract We report the cases of 4 patients treated for recurrent meningiomas of various grades. Pretreatment 68 Ga-DOTATOC PET/CT was performed prior to screening for vectorized internal radiotherapy with 177 Lu-DOTATATE or prior external radiotherapy to aid contouring. None of these patients had sufficient uptake to be eligible for 177 Lu-DOTATATE or reliable contouring. Most recurrences were grades II and III, suggesting a loss of physiological somatostatin receptor overexpression in these tumors. Therefore, the benefit of treatment with 177 Lu-DOTATATE in the current indication is questionable. In the absence of a validated systemic treatment, and considering a few case reports, treatment with 177 Lu-PSMA could be investigated as an additional vectorized internal radiotherapy option.
PSMA and FDG PET/CT Findings in Patient With Dedifferentiated Liposarcoma and Prostate Cancer Metastases
Authors: Xuhe Liao, Hongwei Sun, Xueqi Chen, Yan Fan, Jianhua Zhang
Journal: Clinical Nuclear Medicine (2024)

Abstract Dedifferentiated liposarcoma is an extremely rare and highly malignant tumor. We demonstrated a case of a 75-year-old man with significantly PSMA-avid and mildly FDG uptake–dedifferentiated liposarcoma in the retroperitoneal area. The double-tracer (PSMA and FDG) PET scans could further contribute to differential diagnosis and the following treatment strategy for patients who were suspected with prostate cancer metastases and other malignant tumors simultaneously.
177Lu-FAP-2286 Therapy in a Patient With Metastatic Rhabdoid Meningioma
Authors: Zibei Wan, Wei Wang, Yue Chen, Wenlu Zheng, Zhanwen Huang
Journal: Clinical Nuclear Medicine (2024)

Abstract Rhabdoid meningioma is a rare subtype of meningioma and has a poor prognosis. Herein, we reported a patient of rhabdoid meningioma with multiple liver, pancreas, and bone metastases, who received 177 Lu-FAP-2286 therapy. After 1 treatment cycle, 68 Ga-FAP-2286 PET/CT revealed partial remission of the lesions.
Two Cases of Synchronous Hodgkin Lymphoma and Papillary Thyroid Carcinoma in 18F-FDG PET/CT
Authors: Ru Wang, Haidong Cai, Changcun Liu, Zhongwei LV, Chao Ma
Journal: Clinical Nuclear Medicine (2024)

The concurrence of Hodgkin lymphoma and papillary thyroid carcinoma is a rare clinical event. Two women presented with a painless mass in the neck that was suspected malignancy by ultrasonography. Both cases shown in the 18 F-FDG PET/CT images demonstrated multiple foci of increased FDG uptake in the neck, mimicking thyroid carcinoma with contralateral cervical lymph node metastases. Unexpectedly, the postoperative pathologies confirmed the thyroid lesion of papillary carcinoma and contralateral cervical lymph nodes of classical Hodgkin lymphoma.
Chlorin e6 and BLZ945 Based Self‐Assembly for Photodynamic Immunotherapy Through Immunogenic Tumor Induction and Tumor‐Associated Macrophage Depletion
Authors: Chu‐Yu Huang, Lin‐Ping Zhao, Xiao‐Na Rao, Rong‐Rong Zheng, Zhi‐Shan Liu, Hua Cai, Wei Zhang, A‐Li Chen, Lin Xu, Shiying Li
Journal: Advanced Healthcare Materials (2024)

Immunotherapeutic effect is restricted by the nonimmunogenic tumor phenotype and immunosuppression behaviors of tumor-associated macrophages (TAMs). In this work, a drug self-assembly (designated as CeBLZ) is fabricated based on chlorin e6 (Ce6) and BLZ945 to activate photodynamic immunotherapy through tumor immunogenic induction and tumor-associated macrophage depletion. It is found that Ce6 tends to assemble with BLZ945 without any drug excipients, which can enhance the cellular uptake, tumor penetration, and blood circulation behaviors. The robust photodynamic therapy effect of CeBLZ efficiently suppresses the primary tumor growth and also triggers immunogenic cell death to reverse the nonimmunogenic tumor phenotype. Moreover, CeBLZ can deplete TAMs in tumor tissues to reverse the immunosuppression microenvironment, activating abscopal effect for distant tumor inhibition. In vitro and in vivo results confirm the superior antitumor effect of CeBLZ with negligible side effect, which might promote the development of sophisticated drug combinations for systematic tumor management.
Best practices for government agencies to publish data: lessons from COVID-19
Authors: Bastian Herre, Lucas Rodés-Guirao, Edouard Mathieu, Hannah Ritchie, Charlie Giattino, Joe Hasell, Saloni Dattani, Esteban Ortiz-Ospina, Max Roser
Journal: The Lancet Public Health (2024)

Without data, knowing how to respond to the COVID-19 pandemic would have been impossible. Data were crucial to understanding how the disease spread and which efforts successfully protected people. Yet, national agencies often did not publish their data in an optimal way, which made responding to the pandemic challenging. Therefore, learning from what went well and what did not for the future is crucial. Drawing on our first-hand experience of republishing COVID-19 data, we identify seven best practices for how to publish data in an optimal way: collect the data that are relevant; make them comparable; clearly document the data; share them frequently and promptly; publish data at a stable location; choose a reusable format; and license others to reuse the data. These best practices are straightforward, inexpensive, and achievable, with some countries already having implemented most of them during the COVID-19 pandemic. More government agencies following these best practices will enable others to access their data and address the world's public health challenges—including the next pandemic.
Immunopeptidome mining reveals a novel ERS-induced target in T1D
Authors: Lina Wang, Shushu Yang, Gaohui Zhu, Jie Li, Gang Meng, Xiaoling Chen, Mengjun Zhang, Shufeng Wang, Xiangqian Li, Yu Pan, Yi Huang, Li Wang, Yuzhang Wu
Journal: Cellular and Molecular Immunology (2024)
Enhanced Molecular Response in Myeloproliferative Neoplasms with Complete JAK2V617F Inhibition
Authors: Hamza Celik, Grant A. Challen
Journal: Cancer Discovery (2024)

Dunbar, Bowman, and colleagues present here a novel genetic mouse model with inducible and reversible expression of the JAK2V617F mutation in the endogenous locus. Results from this study clearly demonstrate an absolute requirement for myeloproliferative neoplasm-initiating cells for this mutation in their survival and imply that more efficacious inhibitors could be curative for these patients even in the setting of additional cooperating mutations. See related article by Dunbar et al., p. 737 (8).
Reverse total shoulder replacement versus anatomical total shoulder replacement for osteoarthritis: population based cohort study using data from the National Joint Registry and Hospital Episode Statistics for England
Authors: Epaminondas Markos Valsamis, Albert Prats-Uribe, Ian Koblbauer, Sophie Cole, Adrian Sayers, Michael R Whitehouse, Gillian Coward, Gary S Collins, Rafael Pinedo-Villanueva, Daniel Prieto-Alhambra, Jonathan L Rees
Journal: BMJ (2024)

To answer a national research priority by comparing the risk-benefit and costs associated with reverse total shoulder replacement (RTSR) and anatomical total shoulder replacement (TSR) in patients having elective primary shoulder replacement for osteoarthritis. Population based cohort study using data from the National Joint Registry and Hospital Episode Statistics for England. Public hospitals and publicly funded procedures at private hospitals in England, 2012-20. Adults aged 60 years or older who underwent RTSR or TSR for osteoarthritis with intact rotator cuff tendons. Patients were identified from the National Joint Registry and linked to NHS Hospital Episode Statistics and civil registration mortality data. Propensity score matching and inverse probability of treatment weighting were used to balance the study groups. The main outcome measure was revision surgery. Secondary outcome measures included serious adverse events within 90 days, reoperations within 12 months, prolonged hospital stay (more than three nights), change in Oxford Shoulder Score (preoperative to six month postoperative), and lifetime costs to the healthcare service. The propensity score matched population comprised 7124 RTSR or TSR procedures (126 were revised), and the inverse probability of treatment weighted population comprised 12 968 procedures (294 were revised) with a maximum follow-up of 8.75 years. RTSR had a reduced hazard ratio of revision in the first three years (hazard ratio local minimum 0.33, 95% confidence interval 0.18 to 0.59) with no clinically important difference in revision-free restricted mean survival time, and a reduced relative risk of reoperations at 12 months (odds ratio 0.45, 95% confidence interval 0.25 to 0.83) with an absolute risk difference of -0.51% (95% confidence interval -0.89 to -0.13). Serious adverse events and prolonged hospital stay risks, change in Oxford Shoulder Score, and modelled mean lifetime costs were similar. Outcomes remained consistent after weighting. This study's findings provide reassurance that RTSR is an acceptable alternative to TSR for patients aged 60 years or older with osteoarthritis and intact rotator cuff tendons. Despite a significant difference in the risk profiles of revision surgery over time, no statistically significant and clinically important differences between RTSR and TSR were found in terms of long term revision surgery, serious adverse events, reoperations, prolonged hospital stay, or lifetime healthcare costs.
Editor's Note: Tumor Resection Recruits Effector T Cells and Boosts Therapeutic Efficacy of Encapsulated Stem Cells Expressing IFNβ in Glioblastomas
Authors: Sung Hugh Choi, Daniel W. Stuckey, Sara Pignatta, Clemens Reinshagen, Jasneet Kaur Khalsa, Nicolaas Roozendaal, Jordi Martinez-Quintanilla, Kaoru Tamura, Erhan Keles, Khalid Shah
Journal: Clinical Cancer Research (2024)
Pre-diagnostic plasma proteomics profile for hepatocellular carcinoma
Authors: Xinyuan Zhang, Longgang Zhao, Long H Ngo, Simon T Dillon, Xuesong Gu, Michelle Lai, Tracey G Simon, Andrew T Chan, Edward L Giovannucci, Towia A Libermann, Xuehong Zhang
Journal: JNCI Journal of the National Cancer Institute (2024)

Proteomics may discover pathophysiological changes related to hepatocellular carcinoma, an aggressive and lethal type of cancer with low sensitivity for early stage diagnosis.
Ertugliflozin for Functional Mitral Regurgitation Associated With Heart Failure: EFFORT Trial
Authors: Duk-Hyun Kang, Sung-Ji Park, Sung-Hee Shin, In-Chang Hwang, Yeonyee Elizabeth Yoon, Hyung-Kwan Kim, Mijin Kim, Min-Seok Kim, Sung-Cheol Yun, Jong-Min Song, Seok-Min Kang
Journal: Circulation (2024)

BACKGROUND: The morbidity and mortality rates of patients with heart failure (HF) and functional mitral regurgitation (MR) remain substantial despite guideline-directed medical therapy for HF. We evaluated the efficacy of ertugliflozin for reduction of functional MR associated with HF with mild to moderately reduced ejection fraction. METHODS: The EFFORT trial (Ertugliflozin for Functional Mitral Regurgitation) was a multicenter, double-blind, randomized trial to examine the hypothesis that the sodium-glucose cotransporter 2 inhibitor ertugliflozin is effective for improving MR in patients with HF with New York Heart Association functional class II or III, 35%≤ejection fraction&lt;50%, and effective regurgitant orifice area of chronic functional MR &gt;0.1 cm 2 on baseline echocardiography. We randomly assigned 128 patients to receive either ertugliflozin or placebo in addition to guideline-directed medical therapy for HF. The primary end point was change in effective regurgitant orifice area of functional MR from baseline to the 12-month follow-up. Secondary end points included changes in regurgitant volume, left ventricular (LV) volume indices, left atrial volume index, LV global longitudinal strain, and NT-proBNP (N-terminal pro-B-type natriuretic peptide). RESULTS: The treatment groups were generally well-balanced with regard to baseline characteristics: mean age, 66±11 years; 61% men; 13% diabetes; 51% atrial fibrillation; 43% use of angiotensin receptor-neprilysin inhibitor; ejection fraction, 42±8%; and effective regurgitant orifice area, 0.20±0.12 cm 2 . The decrease in effective regurgitant orifice area was significantly greater in the ertugliflozin group than in the placebo group (−0.05±0.06 versus 0.03±0.12 cm 2 ; P &lt;0.001). Compared with placebo, ertugliflozin significantly reduced regurgitant volume by 11.2 mL (95% CI, −16.1 to −6.3; P =0.009), left atrial volume index by 6.0 mL/m 2 (95% CI, −12.16 to 0.15; P =0.005), and LV global longitudinal strain by 1.44% (95% CI, −2.42% to −0.46%; P =0.004). There were no significant between-group differences regarding changes in LV volume indices, ejection fraction, or NT-proBNP levels. Serious adverse events occurred in one patient (1.6%) in the ertugliflozin group and 6 (9.2%) in the placebo group ( P =0.12). CONCLUSIONS: Among patients with functional MR associated with HF, ertugliflozin significantly improved LV global longitudinal strain and left atrial remodeling, and reduced functional MR. Sodium-glucose cotransporter 2 inhibitors may be considered for patients with functional MR. REGISTRATION: URL: https://www.clinicaltrials.gov ; Unique identifier: NCT04231331.
Injectable hydrogel harnessing foreskin mesenchymal stem cell-derived extracellular vesicles for treatment of chronic diabetic skin wounds
Authors: Chang Xu, Jin-Feng Cao, Yue Pei, Yujin Kim, Huiyeon Moon, Chui-Qin Fan, Mao-Chuan Liao, Xing-Yu Wang, Fei Yao, Yu-Jun Zhang, Shao-Hui Zhang, Jian Zhang, Jian-Zhang Li, Jong Seung Kim, Lian Ma, Zhong-Jian Xie
Journal: Journal of Controlled Release (2024)