tbuckley/cabot-search huggingface dataset:
Outpatient Administration of First Cycle Azacitidine-Venetoclax in Acute Myeloid Leukemia Patients Compared to Inpatient Care: Preliminary Results of a Single-Center Retro-Prospective Study
Authors: Arianna Zappaterra, Caterina Brambilla, Beatrice Manghisi, Stefano Bonfanti, Maria Kogan, Paola Perfetti, Lorenza Maria Borin, Andrea Carrer, Luisa Verga, Carlo Gambacorti-Passerini, Monica Fumagalli
Journal: Blood (2024)
Overcoming Stress Response-Induced Drug Resistance through Targeting CDK9 in Ph+ Leukemia
Authors: Melina Vogt, Marie Kemkes, Berna-Selin Bilen, Julian Schliehe-Diecks, Katerina Scharov, Jia-Wey Tu, Ute Fischer, Aleksandra A. Pandyra, Arndt Borkhardt, Sanil Bhatia
Journal: Blood (2024)
The Association between Cumulative Excess Body Mass Index Exposure and Change in Monoclonal Protein Level in Veterans Diagnosed with Monoclonal Gammopathy of Undetermined Significance
Authors: Lawrence W Liu, Ekaterina Proskuriakova, Mei Wang, Murali Janakiram, Martin William Schoen, Kristen M. Sanfilippo, Theodore Thomas, Su-Hsin Chang
Journal: Blood (2024)
High-Dimensional Single-Cell Analysis of Clinical-Grade Flow Cytometry Explains the Unpredictable Complex Shifts of Patient-Specific Immunophenotypes during B-ALL Relapse Progression
Authors: Nina Rolf, Lorraine YT Liu, Pascal LeClair, Tanmaya Atre, Suzanne Vercauteren, Chinten James Lim, Gregor S. D. Reid
Journal: Blood (2024)
Safety and Efficacy of Ivosidenib Based Regimen in Patients with IDH1 Mutanted Acute Myeloid Leukemia: A Retrospective Case Series
Authors: Limin Zhao, Ligen Liu, Li Yang, Fangli Chen, Xuewei Jiang, Tinghua Zhang, Zhizhi Zhang, Xiang Zhou, Li Chang, Xinying Zhu, Chao Du, Chunrong Ying
Journal: Blood (2024)
Secure: A Prospective Long-Term Observational Study in Patients with Monoclonal Gammopathy of Undetermined Significance
Authors: Karthik Ramasamy, Elizabeth Knight, Sulgi Byun, Earnest Heartin, Victoria Garvey, Supratik Basu, Jacqueline Stones, Roderick Oakes, Grace Killingsworth, Patricia Nicholls, Samiya Mahmood, Stella Bowcock, Rachel Ryan, Sarah Essex, Arun Alfred, Dawn Collier, Lally De soysa, Rachel Bradley, Rowena Thomas-Dewing, Kathryn Cawley, Richard Kaczmarski, Magda Al-Obaidi, Freter Cubos, Charlotte Bomken, Simon Stern, Tiina Elonen, Parizade Raymode, Dinusha Chathurani, Louise Jenkins, Ceri Bygrave, Roberto Garcia Consuegra, Wendy Harrison, Fenella Willis, Richard Brouwer, Constantinos Koshiaris, Grant Vallance, Vicki Gamble, Kassim Javaid, Ross Sadler, Guy Pratt
Journal: Blood (2024)
Safety and Efficacy of R-PAD Regimen in Patients with Severe Multiple Center Idiopathic Castleman Disease: A Retrospective Case Series
Authors: Yingting Lu, Chunrong Ying, Ligen Liu, Limin Zhao, Xuewei Jiang, Tinghua Zhang, Zhizhi Zhang, Xiang Zhou, Li Chang, Xinying Zhu, Chao Du, Li Yang
Journal: Blood (2024)
Phase II Clinical Trial on Chidamide, Rituximab and High-Dose Methotrexate (C-R-HDMTX) in Newly Diagnosed Primary CNS Lymphoma
Authors: Guang-Liang Chen, Jia Jin, Hui Sun, Yizhen Liu, Qunling Zhang, Zuguang Xia, Junning Cao, Xiaonan Hong, Fangfang Lv
Journal: Blood (2024)
Efficacy of Isatuximab Combination Regimens in Patients with Newly Diagnosed Multiple Myeloma: A Systematic Review and Meta-Analysis of Phase III Randomized Controlled Trials
Authors: Hazem Aboaid, Ramaditya Srinivasmurthy, Daniel Thomas Jones, Kevin Nguyen, Rishi Kumar Nanda, Kyaw Zin Thein, Thura Win Htut
Journal: Blood (2024)
Modulatory Effects of Voxelotor and 5-HMF on Hemoglobin Affinity, Heme-Heme Cooperativity and Bohr Effect - Prospecting the Use of These Compounds in Cases of Hypoxemia, Such As in the Acute Respiratory Distress Syndrome (ARDS)
Authors: Diogo Grangani Lopes, Thaís Traina Jorge, Fernando Ferreira Costa, Susan Elisabeth Jorge
Journal: Blood (2024)
Next-Generation Sequencing-Based T-Cell Receptor (TR) Measurable Residual Disease Monitoring Does Not Predict Relapse in T-Lineage Acute Lymphoblastic Leukemia
Authors: Rafael Madero-Marroquin, Adnan Askari, Yenny Vanegas Moreno, Clare E Anderson, Talha Badar, Guru Subramanian Guru Murthy, Chenyu Lin, Alexander Coltoff, Adam S. Duvall, Richard A. Larson, Olatoyosi Odenike, Wendy Stock, Anand Ashwin Patel, Caner Saygin
Journal: Blood (2024)
Tasquinimod, an S100A9 Inhibitor, in Combination with Ixazomib, Lenalidomide, and Dexamethasone for Relapsed and Refractory Multiple Myeloma
Authors: Dan T. Vogl, Yulia Nefedova, E. Paul Wileyto, Chau Nguyen, Cynthia Diaczynsky, Inna Strakovsky, Eva Bondesson, Helen Tuvesson, Erik Vahtola, Adam D. Cohen, Sandra Susanibar-Adaniya, Adam Waxman, Shivani Kapur, Alfred L. Garfall, Edward A. Stadtmauer
Journal: Blood (2024)
Adult Hispanic Patients Receiving Pediatric-Inspired Asparaginase-Containing ALL Regimens Have High Rates of Hepatotoxicity, Pancreatitis, and Treatment Change
Authors: Ahmad Nassar, Ivan Arnaud Borboa, Alexander Krule, Jessica Zalapa, Noor Naffakh, Ryan Sun, Roberta Demichelis, John G Quigley
Journal: Blood (2024)
<i>ASXL1</i> As a Potential Genetic Modifier in a Family with <i>GATA2</i> Deficiency
Authors: Madeline VanDerGraaf, Kyle Dillahunt, Georgianne Younger, Diana K Bayer, Michael Halyko, Margarida Magalhaes-Silverman, Moon Ley Tung
Journal: Blood (2024)
Impact of Donor Age and Donor-Recipient Sex Mismatch on HLA-Matched Related and Unrelated Donor Hematopoietic Cell Transplantation Outcomes
Authors: Yosra M. Aljawai, George Chen, Betul Oran, Warren B. Fingrut, Amin M. Alousi, Qaiser Bashir, Chitra Hosing, Partow Kebriaei, David Marin, Uday Popat, Muzaffar H. Qazilbash, Jeremy Ramdial, Portia Smallbone, Katayoun Rezvani, Richard E. Champlin, Elizabeth J. Shpall, Rohtesh S. Mehta
Journal: Blood (2024)
Peptide‐Induced Hydrogelation with Ordered Metal‐Organic Framework Nanoparticles Generating Reactive Oxygen Species for Integrated Wound Repair
Authors: Ping Li, Yiying Li, Jiahui Yao, Li‐Li Li
Journal: Advanced Healthcare Materials (2024)

Abstract Hydrogels, with their high water content and flexible nature, are a promising class of medical dressings for combating bacterial wound infections. However, their development has been hindered by low sterilization efficiency. Here, this issue is addressed by designing a peptide hydrogel that assembles ordered metal‐organic framework (MOF) nanoparticles with photocatalytic bactericidal activity. Specifically, a short peptide, Nap‐Gly‐Phe‐Phe‐His (Nap‐GFFH), is used to induce the assembly of zinc‐imidazolate MOF (ZIF‐8) into a hydrogel (NHZ gel). This innovative structure integrates three key features: 1) ZIF‐8 nanoparticles are encapsulated within the hydrogel, overcoming their inherent brittleness, insolubility, and limited moldability; 2) the ordered ZIF‐8 structure enhances charge transfer, enabling efficient generation of reactive oxygen species (ROS); and 3) ZIF‐8 simultaneously improves the photocatalytic bactericidal efficiency and mechanical properties of the hydrogel. The NHZ gel demonstrates remarkable antibacterial performance, achieving &gt;99.9% and 99.99% inactivation of Escherichia coli and Staphylococcus aureus , respectively, within 15 min of simulated solar radiation. Additionally, the NHZ gel exhibits excellent biocompatibility, water retention, and exudate absorption, highlighting its broad potential for wound healing.
International Delphi consensus on bone stress injuries in athletes
Authors: Tim Hoenig, Karsten Hollander, Kristin L Popp, Michael Fredericson, Emily A Kraus, Stuart J Warden, Adam S Tenforde
Journal: British Journal of Sports Medicine (2024)

Bone stress injuries, commonly referred to as stress reactions and stress fractures, represent overuse injuries to bone. These injuries result in physical limitations in activity and can be career-ending for high-level athletes. While bone stress injuries have received increased attention in recent years, international consensus is lacking on definitions, risk factors and strategies for management and prevention. This study aimed to ascertain and improve the level of agreement on bone stress injuries by utilising a three-part modified Delphi approach on (1) pathophysiology, diagnosis, terminology and classification systems; (2) risk factors, screening and prevention; and (3) management and return to sport. A multidisciplinary steering committee initiated the consensus process. A panel of 41 members from six continents was formed to complete three rounds of voting, including experts (scientists and clinicians) and representatives (athletes and coaches). Thirty-three, 28 and 28 panel members completed Delphi rounds 1, 2 and 3, respectively. Consensus was reached on 41 out of 58 statements. Findings from this Delphi study outline a multifactorial approach to identify and manage bone stress injuries and to promote bone health in athletes. This includes recommendations for diagnostic workup and treatment to assist clinicians in caring for patients with bone stress injuries. Finally, this consensus process identifies knowledge gaps and provides a framework for future research to advance the clinical care and prevention of bone stress injuries.
spatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis
Authors: Oscar E. Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Y. Tsai, Joseph Markowitz, Ethan Vallebuona, Anders E. Berglund, Steven A. Eschrich, Xiaoqing Yu, Brooke L. Fridley
Journal: Cancer Research (2024)

Abstract Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing of the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying the tumor microenvironment of two data sets: 10X Visium samples from a cohort of melanoma metastasis and Nanostring CosMx fields of vision from a cohort of Merkel cell carcinoma samples. These results support the ability of spatialGE to identify spatial gene expression patterns that provide valuable insights into the tumor microenvironment and highlight its utility in democratizing ST data analysis for the wider scientific community.
AI-enabled wearable cameras for assisting dietary assessment in African populations
Authors: Frank P.-W. Lo, Jianing Qiu, Modou L. Jobarteh, Yingnan Sun, Zeyu Wang, Shuo Jiang, Tom Baranowski, Alex K. Anderson, Megan A. McCrory, Edward Sazonov, Wenyan Jia, Mingui Sun, Matilda Steiner-Asiedu, Gary Frost, Benny Lo
Journal: npj Digital Medicine (2024)

Abstract We have developed a population-level method for dietary assessment using low-cost wearable cameras. Our approach, EgoDiet, employs an egocentric vision-based pipeline to learn portion sizes, addressing the shortcomings of traditional self-reported dietary methods. To evaluate the functionality of this method, field studies were conducted in London (Study A) and Ghana (Study B) among populations of Ghanaian and Kenyan origin. In Study A, EgoDiet’s estimations were contrasted with dietitians’ assessments, revealing a performance with a Mean Absolute Percentage Error (MAPE) of 31.9% for portion size estimation, compared to 40.1% for estimates made by dietitians. We further evaluated our approach in Study B, comparing its performance to the traditional 24-Hour Dietary Recall (24HR). Our approach demonstrated a MAPE of 28.0%, showing a reduction in error when contrasted with the 24HR, which exhibited a MAPE of 32.5%. This improvement highlights the potential of using passive camera technology to serve as an alternative to the traditional dietary assessment methods.
Association between automatic AI-based quantification of airway-occlusive mucus plugs and all-cause mortality in patients with COPD
Authors: Tjeerd van der Veer, Eleni-Rosalina Andrinopoulou, Gert-Jan Braunstahl, Jean Paul Charbonnier, Victor Kim, Rudolfs Latisenko, David A Lynch, Harm Tiddens
Journal: Thorax (2024)

In this cohort study involving 9399 current and former smokers from the Genetic Epidemiology of Chronic Obstructive Pulmonary Disease study, we assessed the relationship between artificial intelligence-quantified mucus plugs on chest CTs and all-cause mortality. Our results revealed a significant positive association, particularly for those with COPD GOLD stages 1-4, with HRs of 1.18 for 1-2 mucus-obstructed bronchial segments and 1.27 for ≥3 obstructed segments. This corroborates previous visual mucus plug counting research and demonstrates the relevance of mucus plugs in COPD pathology and as a marker for risk assessment. Automated mucus plug quantification methods may provide an efficient tool for both clinical evaluations and research.
Energy Stress-induced CircEPB41(2) Promotes Lipogenesis in Hepatocellular Carcinoma
Authors: Yang Yang, Jingjing Luo, Zhongyu Wang, Kaiyue Liu, Keyi Feng, Fang Wang, Yide Mei
Journal: Cancer Research (2024)

Abstract The tumor microenvironment plays a pivotal role in the metabolic reprogramming of cancer cells. A better understanding of the underlying mechanisms regulating cancer metabolism could help identify potential therapeutic targets. Here, we identified circEPB41(2) as a metabolically regulated circular RNA that mediates lipid metabolism in hepatocellular carcinoma (HCC). CircEPB41(2) was induced in response to glucose deprivation via HNRNPA1-dependent alternative splicing. Upregulation of circEPB41(2) led to enhanced lipogenic gene expression that promoted lipogenesis. Mechanistically, circEPB41(2) cooperated with the m6A demethylase FTO to decrease the mRNA stability of the histone deacetylase SIRT6, thereby increasing H3K9ac and H3K27ac levels to activate lipogenic gene expression. Silencing of circEPB41(2) inhibited both in vitro proliferation of HCC cells and in vivo growth of tumor xenografts. Clinically, circEPB41(2) was elevated in HCC, and high circEPB41(2) expression was associated with poor patient prognosis. Overall, this study reveals that circEPB41(2) is an important regulator of lipid metabolic reprogramming and indicates that targeting the circEPB41(2)-FTO-SIRT6 axis could represent a promising anti-cancer strategy for treating HCC.
Targeting the PREX2/RAC1/PI3Kβ Signaling Axis Confers Sensitivity to Clinically Relevant Therapeutic Approaches in Melanoma
Authors: Catriona A. Ford, Dana Koludrovic, Patricia P. Centeno, Mona Foth, Elpida Tsonou, Nikola Vlahov, Nathalie Sphyris, Kathryn Gilroy, Courtney Bull, Colin Nixon, Bryan Serrels, Alison F. Munro, John C. Dawson, Neil O. Carragher, Valeria Pavet, David C. Hornigold, Philip D. Dunne, Julian Downward, Heidi C. Welch, Simon T. Barry, Owen J. Sansom, Andrew D. Campbell
Journal: Cancer Research (2024)

Abstract Metastatic melanoma remains a major clinical challenge. Large-scale genomic sequencing of melanoma has identified bona fide activating mutations in RAC1, which are associated with resistance to BRAF-targeting therapies. Targeting the RAC1-GTPase pathway, including the upstream activator PREX2 and the downstream effector PI3Kβ, could be a potential strategy for overcoming therapeutic resistance, limiting melanoma recurrence, and suppressing metastatic progression. Here, we used genetically engineered mouse models and patient-derived BRAFV600E-driven melanoma cell lines to dissect the role of PREX2 in melanomagenesis and response to therapy. While PREX2 was dispensable for the initiation and progression of melanoma, its loss conferred sensitivity to clinically relevant therapeutics targeting the MAPK pathway. Importantly, genetic and pharmacological targeting of PI3Kβ phenocopied PREX2 deficiency, sensitizing model systems to therapy. These data reveal a druggable PREX2/RAC1/PI3Kβ signaling axis in BRAF-mutant melanoma that could be exploited clinically.
MHC-Hammer decodes HLA disruption in tumors
Authors: Timothy Sears, Hannah Carter
Journal: Cancer Research (2024)

Abstract Tumors utilize various mechanisms of HLA disruption in order to evade immune surveillance. Previous computational tools have interrogated specific aspects of this process, yet a holistic picture of HLA loss of heterozygosity (LOH), transcriptomic suppression, and alternative splicing has remained challenging. In a recent Nature Genetics study, Puttick and colleagues introduced MHC Hammer, a robust computational toolkit designed to dissect the complexities of HLA disruptions that mediate immune evasion in cancer. By analyzing comprehensive genomic and transcriptomic data across several large cancer cohorts, the study highlights the prevalence of HLA disruptions–particularly alternative splicing events–across various tumor types and identifies HLA LOH as an important immune evasion mechanism during metastasis in lung adenocarcinoma.
Rare but elevated incidence of hematological malignancy after clozapine use in schizophrenia: A population cohort study
Authors: Yuqi Hu, Le Gao, Lingyue Zhou, Wenlong Liu, Cuiling Wei, Boyan Liu, Qi Sun, Wenxin Tian, Rachel Yui Ki Chu, Song Song, Franco Wing Tak Cheng, Joe Kwun Nam Chan, Amy Pui Pui Ng, Heidi Ka Ying Lo, Krystal Chi Kei Lee, Wing Chung Chang, William Chi Wai Wong, Esther Wai Yin Chan, Ian Chi Kei Wong, Yi Chai, Francisco Tsz Tsun Lai
Journal: PLoS Medicine (2024)

Background Clozapine is widely regarded as a highly efficacious psychotropic drug that is largely underused worldwide. Recent disproportionality analyses and nationwide case-control studies suggested a potential association between clozapine use and hematological malignancy (HM). Nevertheless, the absolute rate difference is not well-established due to the absence of analytic cohort studies. The clinical significance of such a potential risk remains unclear. Methods and findings We extracted data from a territory-wide public healthcare database from January 2001 to August 2022 in Hong Kong to conduct a retrospective cohort study of anonymized patients aged 18 + years with a diagnosis of schizophrenia who used clozapine or olanzapine (drug comparator with highly similar chemical structure and pharmacological mechanisms) for 90 + days, with at least 2 prior other antipsychotic use records within both groups. Weighted by inverse probability of treatment (IPTW) based on propensity scores, Poisson regression was used to estimate the incidence rate ratio (IRR) of HM between clozapine and olanzapine users. The absolute rate difference was also estimated. In total, 9,965 patients with a median follow-up period of 6.99 years (25th to 75th percentile: 4.45 to 10.32 years) were included, among which 834 were clozapine users. After IPTW, the demographic and clinical characteristics of clozapine users were comparable to those of olanzapine users. Clozapine users had a significant weighted IRR of 2.22 (95% confidence interval (CI) [1.52, 3.34]; p &lt; 0.001) for HM compared to olanzapine users. The absolute rate difference was estimated at 57.40 (95% CI [33.24, 81.55]) per 100,000 person-years. Findings were consistent across subgroups by age and sex. Sensitivity analyses all supported the robustness of the results and showed good specificity to HM but no other cancers. The main limitation of this observational study is the potential residual confounding effects that could have arisen from the lack of randomization in clozapine or olanzapine use. Conclusions Absolute rate difference in HM incidence associated with clozapine is small despite a 2-fold elevated rate. Given the rarity of HM and existing blood monitoring requirements, more restrictive indication for clozapine or special warnings may not be necessary.
Pertussis Immunity 5 Years After Booster Vaccination With Recombinant Pertussis Vaccines
Authors: Punnee Pitisuttithum, Chukiat Sirivichayakul, Jittima Dhitavat, Arom Pitisuthitham, Souad Mansouri, Hong Thai Pham
Journal: JAMA Network Open (2024)

This cohort study compares levels of immunity 5 years after vaccination among adolescents given genetically detoxified pertussis boosters with those given chemically inactivated pertussis boosters.
Natural potential difference induced functional optimization mechanism for Zn-based multimetal bone implants
Authors: Jing Xu, Zhenbao Zhang, Jianhui Wang, Yuhan Qi, Xiaohong Qi, Yijie Liang, Manxi Li, Haixia Li, Yantao Zhao, Zhuangzhuang Liu, Yanfeng Li
Journal: Bioactive Materials (2024)
Neoadjuvant Exercise Therapy in Patients With Prostate Cancer
Authors: Fabian Falkenbach, Lars Budäus
Journal: JAMA Oncology (2024)

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