tbuckley/cabot-search huggingface dataset:
Predictive role of natural killer cells in bronchoalveolar lavage fluid of patients with sarcoidosis
Authors: L. Bergantini, M. Spalletti, M. d'Alessandro, M. Genovese, E. Masotto, P. Cameli, A. Prasse, E. Bargagli
Journal: Pulmonology (2024)

Sarcoidosis is a rare granulomatous disease of unknown aetiology belonging to the wide group of interstitial lung diseases.). Although the limitlessness of BAL fluid is debated, it remains one of the best matrices for studying the pathogenesis of sarcoidosis. Natural killer (NK) cells have been described in BAL fluid from sarcoidosis patients. Elevated NK cells in BAL fluid from sarcoidosis patients have been found to be associated with poor outcomes. In this study, NK cells were evaluated in BAL samples from sarcoidosis patients at the time of diagnosis and associated with clinical characteristics in order to evaluate their prognostic role. Of the 276 patients suspected to have sarcoidosis on the basis of clinical and radiological findings, 248 had a final diagnosis of sarcoidosis. Clinical parameters, Scadding stage, and extrapulmonary localization were collected in a database. It resulted in fibrotic sarcoidosis patients being associated with an increase in lymphocyte percentages in BAL samples, particularly NK cells when compared with other groups. From ROC analysis, NK cell percentages in BAL samples resulted as being the best predictive markers in discriminating stage 4 of sarcoidosis from other RX stages (AUC=0.85, p<0.0001). Furthermore, after the stratification of patients on the basis of the number of extrapulmonary localizations, patients with an higher number of extrapulmonary localizations also showed higher percentages of NK cells in BAL fluid. In conclusion, NK cell percentages in BAL fluid can be considered a good prognostic marker of fibrotic phenotypes of sarcoidosis and involvement of other organs, although their diagnostic utility was poor.
Exercise induces tissue-specific adaptations to enhance cardiometabolic health
Authors: Stephen P. Ashcroft, Ben Stocks, Brendan Egan, Juleen R. Zierath
Journal: Cell Metabolism (2024)

The risk associated with multiple cancers, cardiovascular disease, diabetes, and all-cause mortality is decreased in individuals who meet the current recommendations for physical activity. Therefore, regular exercise remains a cornerstone in the prevention and treatment of non-communicable diseases. An acute bout of exercise results in the coordinated interaction between multiple tissues to meet the increased energy demand of exercise. Over time, the associated metabolic stress of each individual exercise bout provides the basis for long-term adaptations across tissues, including the cardiovascular system, skeletal muscle, adipose tissue, liver, pancreas, gut, and brain. Therefore, regular exercise is associated with a plethora of benefits throughout the whole body, including improved cardiorespiratory fitness, physical function, and glycemic control. Overall, we summarize the exercise-induced adaptations that occur within multiple tissues and how they converge to ultimately improve cardiometabolic health.
Publisher Correction: Interim survival analysis of the randomized phase III GEMSTONE-302 trial: sugemalimab or placebo plus chemotherapy as first-line treatment for metastatic NSCLC
Authors: Caicun Zhou, Ziping Wang, Meili Sun, Lejie Cao, Zhiyong Ma, Rong Wu, Yan Yu, Wenxiu Yao, Si Sun, Jianhua Chen, Wu Zhuang, Jiuwei Cui, Xueqin Chen, You Lu, Hong Shen, Chunhong Hu, Jiwei Liu, Yunpeng Liu, Mengzhao Wang, Xingya Li, Ping Sun, Yongqian Shu, Jianying Zhou, Jingzhang Li, Kangsheng Gu, Changli Wang, Hui Zhao, Yiping Zhang, Chunling Liu, Jingru Wang, Rumei Chen, Mengmeng Qin, Hao Wang, Jason Yang
Journal: Nature Cancer (2024)
Comparison of US Oncologist Rurality by Practice Setting and Patients Served
Authors: Sarah L. Cornelius, Andrew P. Shaefer, Sandra L. Wong, Erika L. Moen
Journal: JAMA Network Open (2024)

Importance Studies of the oncology workforce most often classify physician rurality by their practice location, but this could miss the true extent of physicians involved in rural cancer care. Objective To compare a method for identifying oncology physicians involved in rural cancer care that uses the proportion of rural patients served with the standard method based on practice location. Design, Setting, and Participants This cross-sectional study used retrospective Centers for Medicare &amp;amp;amp; Medicaid Services encounter data on medical oncologists, radiation oncologists, and surgeons treating Medicare beneficiaries diagnosed with breast, colorectal, or lung cancer from January 1 to December 31, 2019. Data were analyzed from May to September 2023. Main Outcomes and Measures The standard method of classifying oncologist physician rurality based on practice location was compared with a novel method of classification based on proportion of rural patients served. Results The study included 27 870 oncology physicians (71.3% male), of whom 835 (3.0%) practiced in a rural location. Physicians practicing in a rural location treated a high proportion of rural patients (median, 50.0% [IQR, 16.7%-100%]). When considering the rurality of physicians’ patient panels, 5123 physicians (18.4%) whose patient panel included at least 20% rural patients, 3199 (11.5%) with at least 33% rural patients, and 1996 (7.2%) with at least 50% rural patients were identified. Using a physician’s patient panel to classify physician rurality revealed a higher number and greater spread of oncology physicians involved in rural cancer care in the US than the standard method, while maintaining high performance (area under the curve, 0.857) and fair concordance (κ, 0.346; 95% CI, 0.323-0.369) with the method based on practice setting. Conclusions and Relevance In this cross-sectional study, classifying oncologist rurality by the proportion of rural patients served identified more oncology physicians treating patients living in rural areas than the standard method of practice location and may more accurately capture the rural cancer physician workforce, as many hospitals have historically been located in more urban areas. This new method may be used to improve future studies of rural cancer care delivery.
Treatment completion, asparaginase completion, and oncologic outcomes among children, adolescents and young adults with acute lymphoblastic leukemia treated with DFCI Consortium Protocols
Authors: Yannis K. Valtis, Yael Flamand, Shai Shimony, Andrew E. Place, Lewis B. Silverman, Lynda M. Vrooman, Andrew M. Brunner, Stephen E. Sallan, Martha Wadleigh, Richard M. Stone, Daniel J. DeAngelo, Marlise R. Luskin
Journal: Leukemia (2024)
History of Infertility and Midlife Cardiovascular Health in Female Individuals
Authors: Amy R. Nichols, Sheryl L. Rifas-Shiman, Karen M. Switkowski, Mingyu Zhang, Jessica G. Young, Marie-France Hivert, Jorge E. Chavarro, Emily Oken
Journal: JAMA Network Open (2024)

Importance Fertility status is a marker for future health, and infertility has been associated with risk for later cancer and diabetes, but associations with midlife cardiovascular health (CVH) in female individuals remain understudied. Objective To evaluate the association of infertility history with CVH at midlife (approximately age 50 years) among parous individuals. Design, Setting, and Participants Project Viva is a prospective cohort study of pregnant participants enrolled between 1999 and 2002 who delivered a singleton live birth in the greater Boston, Massachusetts, area. Infertility history was collected at a midlife visit between 2017 and 2021, approximately 18 years after enrollment. Data analysis was performed from January to June 2023. Exposures The primary exposure was any lifetime history of infertility identified by self-report, medical record, diagnosis, or claims for infertility treatment. Main Outcomes and Measures The American Heart Association’s Life’s Essential 8 (LE8) is a construct for ranking CVH that includes scores from 0 to 100 (higher scores denote better health status) in 4 behavioral (diet, physical activity, sleep, and smoking status) and 4 biomedical (body mass index, blood pressure, blood lipids, and glycemia) domains to form an overall assessment of CVH. Associations of a history of infertility (yes or no) with mean LE8 total, behavioral, biomedical, and blood biomarker (lipids and glycemia) scores were examined, adjusting for age at outcome (midlife visit), race and ethnicity, education, household income, age at menarche, and perceived body size at age 10 years. Results Of 468 included participants (mean [SD] age at the midlife visit, 50.6 [5.3] years) with exposure and outcome data, 160 (34.2%) experienced any infertility. Mean (SD) LE8 scores were 76.3 (12.2) overall, 76.5 (13.4) for the behavioral domain, 76.0 (17.5) for the biomedical domain, and 78.9 (19.2) for the blood biomarkers subdomain. In adjusted models, the estimated overall LE8 score at midlife was 2.94 points lower (95% CI, −5.13 to −0.74 points), the biomedical score was 4.07 points lower (95% CI, −7.33 to −0.78 points), and the blood subdomain score was 5.98 points lower (95% CI, −9.71 to −2.26 points) among those with vs without history of infertility. The point estimate also was lower for the behavioral domain score (β = −1.81; 95% CI, −4.28 to 0.66), although the result was not statistically significant. Conclusions and Relevance This cohort study of parous individuals found evidence for an association between a history of infertility and lower overall and biomedical CVH scores. Future study of enhanced cardiovascular preventive strategies among those who experience infertility is warranted.
Sociodemographic inequities in the burden of carcinogenic industrial air emissions in the United States
Authors: Jessica M Madrigal, Abigail Flory, Jared A Fisher, Elizabeth Sharp, Barry I Graubard, Mary H Ward, Rena R Jones
Journal: JNCI Journal of the National Cancer Institute (2024)

Abstract Background Industrial facilities are not located uniformly across communities in the United States, but how the burden of exposure to carcinogenic air emissions may vary across population characteristics is unclear. We evaluated differences in carcinogenic industrial pollution among major sociodemographic groups in the United States and Puerto Rico. Methods We evaluated cross-sectional associations of population characteristics including race and ethnicity, educational attainment, and poverty at the census tract level with point-source industrial emissions of 21 known human carcinogens using regulatory data from the US Environmental Protection Agency. Odds ratios and 95% confidence intervals comparing the highest emissions (tertile or quintile) to the referent group (zero emissions [ie, nonexposed]) for all sociodemographic characteristics were estimated using multinomial, population density–adjusted logistic regression models. Results In 2018, approximately 7.4 million people lived in census tracts with nearly 12 million pounds of carcinogenic air releases. The odds of tracts having the greatest burden of benzene, 1,3-butadiene, ethylene oxide, formaldehyde, trichloroethylene, and nickel emissions compared with nonexposed were 10%-20% higher for African American populations, whereas White populations were up to 18% less likely to live in tracts with the highest emissions. Among Hispanic and Latino populations, odds were 16%-21% higher for benzene, 1,3-butadiene, and ethylene oxide. Populations experiencing poverty or with less than high school education were associated with up to 51% higher burden, irrespective of race and ethnicity. Conclusions Carcinogenic industrial emissions disproportionately impact African American and Hispanic and Latino populations and people with limited education or experiencing poverty thus representing a source of pollution that may contribute to observed cancer disparities.
Regulatory T-cell dysfunction and cutaneous exposure to Staphylococcus aureus underlie eczema in DOCK8 deficiency
Authors: Hazel Wilkie, Mrinmoy Das, Tyler Pelovitz, Wayne Bainter, Brian Woods, Mohammed Alasharee, Ali Sobh, Safa Baris, Sevgi Bilgic Eltan, Waleed Al-Herz, Mohamed-Ridha Barbouche, Imen Ben-Mustapha, Meriem Ben-Ali, Mohamed T.H. Sallam, Amany Awad, Sohilla Lotfy, Aisha El Marsafy, Moushira Ezzelarab, Michael Farrar, Brigitta A.R. Schmidt, Monali NandyMazumdar, Emma Guttman-Yassky, Anthony Sheets, Katie Maria Vidic, George Murphy, Patrick M. Schlievert, Janet Chou, Juan Manuel Leyva-Castillo, Erin Janssen, Maheshwor Timilshina, Raif S. Geha
Journal: Journal of Allergy and Clinical Immunology (2024)
Looking to the future—Enhancing engagement with the publishing enterprise and peer review
Authors: Susan M Chang, Roy E Strowd
Journal: Neuro-Oncology (2024)

Journal Article Looking to the future—Enhancing engagement with the publishing enterprise and peer review Get access Susan M Chang, Susan M Chang Department of Neurological Surgery, University of California at San Francisco, San Francisco, California, USA Corresponding Author: Susan M. Chang, MD, Department of Neurological Surgery, University of California at San Francisco, 505 Parnassus Ave., M774, San Francisco, CA 94143-0112, USA (Susan.Chang@ucsf.edu) Search for other works by this author on: Oxford Academic PubMed Google Scholar Roy E Strowd, III Roy E Strowd, III Department of Neurology, Wake Forest University School of Medicine, Winston Salem, North Carolina , USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Neuro-Oncology, Volume 26, Issue 1, January 2024, Page 1, https://doi.org/10.1093/neuonc/noad246 Published: 05 January 2024 Article history Corrected and typeset: 05 January 2024 Published: 05 January 2024
Social network analysis of cell networks improves deep learning for prediction of molecular pathways and key mutations in colorectal cancer
Authors: Neda Zamanitajeddin, Mostafa Jahanifar, Mohsin Bilal, Mark Eastwood, Nasir Rajpoot
Journal: Medical Image Analysis (2024)

Colorectal cancer (CRC) is a primary global health concern, and identifying the molecular pathways, genetic subtypes, and mutations associated with CRC is crucial for precision medicine. However, traditional measurement techniques such as gene sequencing are costly and time-consuming, while most deep learning methods proposed for this task lack interpretability. This study offers a new approach to enhance the state-of-the-art deep learning methods for molecular pathways and key mutation prediction by incorporating cell network information. We build cell graphs with nuclei as nodes and nuclei connections as edges of the network and leverage Social Network Analysis (SNA) measures to extract abstract, perceivable, and interpretable features that explicitly describe the cell network characteristics in an image. Our approach does not rely on precise nuclei segmentation or feature extraction, is computationally efficient, and is easily scalable. In this study, we utilize the TCGA-CRC-DX dataset, comprising 499 patients and 502 diagnostic slides from primary colorectal tumours, sourced from 36 distinct medical centres in the United States. By incorporating the SNA features alongside deep features in two multiple instance learning frameworks, we demonstrate improved performance for chromosomal instability (CIN), hypermutated tumour (HM), TP53 gene, BRAF gene, and Microsatellite instability (MSI) status prediction tasks (2.4%-4% and 7-8.8% improvement in AUROC and AUPRC on average). Additionally, our method achieves outstanding performance on MSI prediction in an external PAIP dataset (99% AUROC and 98% AUPRC), demonstrating its generalizability. Our findings highlight the discrimination power of SNA features and how they can be beneficial to deep learning models' performance and provide insights into the correlation of cell network profiles with molecular pathways and key mutations.
A Systematic Review of Ophthalmology Education in Medical Schools
Authors: Sascha K.R. Spencer, Patrick A. Ireland, Jorja Braden, Jenny L. Hepschke, Michael Lin, Helen Zhang, Jessie Channell, Hessom Razavi, Angus W. Turner, Minas T. Coroneo, Boaz Shulruf, Ashish Agar
Journal: Ophthalmology (2024)
Conbercept versus Laser for the Treatment of Infants with Zone II Retinopathy of Prematurity
Authors: Yong Cheng, Kailin Liu, Manhong Li, Zifeng Zhang, Wensi Chen, Xuemei Zhu, Dandan Linghu, Xun Deng, Daoman Xiang, Yusheng Wang, Jianhong Liang
Journal: Ophthalmology (2024)
Physiological 68Ga-PSMA-11 Uptake in Dural Venous Sinuses
Authors: Mukta Kulkarni, Prathamesh Vijay Joshi, Kritik Kumar
Journal: Clinical Nuclear Medicine (2024)

We describe hitherto unreported physiological low-grade 68Ga-PSMA-11 uptake in dural sinuses of patients who underwent 68Ga-PSMA-11 PET/CT for evaluation of prostate carcinoma. A strong positive correlation was found between SUVmax of tracer uptake in dural sinuses and SUVmax of blood pool activity in superior vena cava. Low-grade 68Ga-PSMA-11 uptake seen in dural sinuses is physiological and is most likely result of venous blood pool activity. Such uptake should not be interpreted as pathological. Knowledge of such physiological uptake is essential for optimal interpretation of PSMA PET/CT images and differentiating physiological versus pathological uptake.
NET-Induced Carcinoid Heart Disease Affecting Both Tricuspid and Aortic Valves Due to Patent Foramen Ovale and Right/Left Shunt
Authors: Christina Laschinsky, Matthias Welsner, Amir A. Mahabadi, Harald Lahner, Hubertus Hautzel
Journal: Clinical Nuclear Medicine (2024)

Carcinoid heart disease (Hedinger syndrome) is a long-term consequence in hormone-active neuroendocrine tumors with hepatic metastases and carcinoid syndrome. Because of serotonin, excess multiple cardiac and pulmonary symptoms evolve, which are further complicated by a patent foramen ovale due to right-left shunting. We present a 53-year-old man with an ileum-neuroendocrine tumor including gross liver metastases and long-term stable disease who subsequently developed Hedinger syndrome. Initially experiencing progressive dyspnea, he eventually experienced severe hypoxemia due to patent foramen ovale. 99mTc-MAA lung perfusion scintigraphy quantitatively identified the right-left shunting, whereas 68Ga-FAPI-46 PET/CT characterized the typical fibrous heart valve thickening due to serotonin-induced fibroblast proliferative properties.
Integrating coaxial electrospinning and 3D printing technologies for the development of biphasic porous scaffolds enabling spatiotemporal control in tumor ablation and osteochondral regeneration
Authors: Wenbao He, Chunlin Li, Shitong Zhao, Zhendong Li, Jing Wu, Junjun Li, Haichao Zhou, Yunfeng Yang, Yong Xu, Huitang Xia
Journal: Bioactive Materials (2024)

The osteochondral defects (OCDs) resulting from the treatment of giant cell tumors of bone (GCTB) often present two challenges for clinicians: tumor residue leading to local recurrence and non-healing of OCDs. Therefore, this study focuses on developing a double-layer PGPC-PGPH scaffold using shell-core structure nanofibers to achieve "spatiotemporal control" for treating OCDs caused by GCTB. It addresses two key challenges: eliminating tumor residue after local excision and stimulating osteochondral regeneration in non-healing OCD cases. With a shell layer of protoporphyrin IX (PpIX)/gelatin (GT) and inner cores containing chondroitin sulfate (CS)/poly(lactic-co-glycolic acid) (PLGA) or hydroxyapatite (HA)/PLGA, coaxial electrospinning technology was used to create shell-core structured PpIX/GT-CS/PLGA and PpIX/GT-HA/PLGA nanofibers. These nanofibers were shattered into nano-scaled short fibers, and then combined with polyethylene oxide and hyaluronan to formulate distinct 3D printing inks. The upper layer consists of PpIX/GT-CS/PLGA ink, and the lower layer is made from PpIX/GT-HA/PLGA ink, allowing for the creation of a double-layer PGPC-PGPH scaffold using 3D printing technique. After GCTB lesion removal, the PGPC-PGPH scaffold is surgically implanted into the OCDs. The sonosensitizer PpIX in the shell layer undergoes sonodynamic therapy to selectively damage GCTB tissue, effectively eradicating residual tumors. Subsequently, the thermal effect of sonodynamic therapy accelerates the shell degradation and release of CS and HA within the core layer, promoting stem cell differentiation into cartilage and bone tissues at the OCD site in the correct anatomical position. This innovative scaffold provides temporal control for anti-tumor treatment followed by tissue repair and spatial control for precise osteochondral regeneration.
Comparative Efficacy of Advanced Therapies for Achieving Endoscopic Outcomes in Crohn’s Disease: A Systematic Review and Network Meta-Analysis
Authors: Sudheer K. Vuyyuru, Tran M. Nguyen, Mohammad Hassan Murad, Neeraj Narula, Talat Bessissow, Guangyong Zou, Jeffrey D. McCurdy, Laurent Peyrin-Biroulet, Silvio Danese, Christopher Ma, Siddharth Singh, Vipul Jairath
Journal: Clinical Gastroenterology and Hepatology (2024)
Multilayer concept of autoimmune mechanisms and manifestations in inborn errors of immunity: Relevance for precision therapy
Authors: Markus G. Seidel, Fabian Hauck
Journal: Journal of Allergy and Clinical Immunology (2024)

Autoimmunity in inborn errors of immunity (IEI) has a multifactorial pathogenesis and develops upon a genetic predisposition in conjunction with gene regulation, environmental modifiers, and infectious triggers. Based on incremental data availability due to up-front application of omics-technologies, a more granular and dynamic view of mechanisms and manifestations is warranted. Here we present a comprehensive novel concept of autoimmunity in IEI that considers multiple layers of interdependent elements and connects 101 causative genes or deletions according to the quality of the allelic variants with 47 molecular pathways and 22 immune effector mechanisms. Furthermore, we list 50 resulting manifestations together with the corresponding human phenotype ontology (HPO) terms and review the types and frequencies of the most relevant clinical presentations. Together, this concept, i), extends the historical anatomical view of central versus peripheral tolerance towards multiple interdependent mechanisms of immune tolerance, ii), delineates the mechanisms underlying the protean clinical manifestations, and thereby, iii), points towards the most suitable precision therapy for autoimmunity in IEI. The multilayer concept of autoimmune mechanisms and manifestations in IEI will facilitate research design and provide clinical guidance on the use of precision medicine irrespective of the data depth available in each health care scenario.