tbuckley/cabot-search huggingface dataset:
Differential role of HLA-A and HLA-B, C expression levels as prognostic markers in colon and rectal cancer
Authors: Theodoros Michelakos, Filippos Kontos, Tomohiro Kurokawa, Lei Cai, Ananthan Sadagopan, Danielle Krijgsman, Wilko Weichert, Lindy G Durrant, Peter J K Kuppen, Cristina R Ferrone, Soldano Ferrone
Journal: Journal for ImmunoTherapy of Cancer (2022)

Purpose The association of human leucocyte antigen (HLA) class I expression levels with the clinical course of many malignancies reflects their crucial role in the recognition and elimination of malignant cells by cognate T cells and NK cells. In colorectal cancer, results regarding this association are conflicting. The potential pathogenetic and therapeutic implications of this association prompted us to perform a large patient-level pooled analysis assessing the role of the expression level of HLA class I loci gene products in colon and rectal cancer. Experimental design Included studies provided patient-level data on HLA class I expression levels determined by immunohistochemistry on surgical specimens. Expression levels of the HLA class I loci gene products (HLA-A, HLA-B/C) were correlated with common genetic events and survival. Results Data from 5 studies including 2863 patients were used. In the 1620 colon cancer patients, lower HLA-A, HLA-B/C and total HLA class I expression levels were associated with microsatellite instability (p=0.044, p=0.008 and p=0.022, respectively), higher frequency of BRAF mutations (p&lt;0.001, p=0.021 and p&lt;0.001, respectively) and lower frequency of KRAS mutations (p=0.001, ns and p=0.002, respectively). In the 1243 rectal cancer patients, HLA-A expression was higher in tumors treated with neoadjuvant radiation (p=0.024). High HLA-B/C, but not HLA-A, expression level was an independent predictor of favorable overall survival in colon (p=0.006) and rectal (p&lt;0.001) cancer. Conclusions T-cells and HLA-B/C antigens, rather than NK cells and HLA-A antigens, likely play an important role in controlling colon/rectal cancer growth. Colon/rectal cancer patients may benefit from strategies that upregulate HLA-B/C and trigger or enhance T cell immunity.
Generation of Alveolar Epithelium Using Reconstituted Basement Membrane and hiPSC‐Derived Organoids (Adv. Healthcare Mater. 6/2022)
Authors: Yong He, Elrade Rofaani, Xiaochen Huang, Boxin Huang, Feng Liang, Li Wang, Jian Shi, Juan Peng, Yong Chen
Journal: Advanced Healthcare Materials (2022)
Abstract P2-11-14: Pathology AI features and immune biomarkers of postpartum involution: Implications for postpartum breast cancer
Authors: Joshua Were Ogony, Thomas De Bel, Derek Radisky, Jeroen VanderLaak, Mark Sherman
Journal: Cancer Research (2022)

Abstract Breast cancer risk is increased in parous women in the period following childbirth, peaking at five years. After weaning or in the absence of lactation, the breast undergoes postpartum involution (PPI), a process characterized by epithelial cell death and tissue remodeling that returns the mammary gland to a baseline state, and has previously been associated with increased inflammation and breast cancer development and progression in preclinical models. Features of PPI and determinants of related inflammation have been incompletely characterized among women. In this study, we performed visual and AI analysis of 725 digitized H&amp;E images of normal breast tissues donated to the Komen Tissue Bank (KTB) by parous and nulliparous women ≤45 years, and further investigated the immune microenvironment in specimens from 23 women (also from KTB, 13 parous, 10 nulliparous) using NanoString RNA immuno oncology (IO) 360 panels and immune protein biomarkers by NanoString GeoMx Digital Spatial Profiling (DSP). We found that recently parous women (≤5 years of a last birth) had higher numbers of terminal duct lobular units (TDLUs), immune cells, and plasma cells as compared with nulliparous women, and that beyond 5 years of a last birth, TDLU numbers were still higher in parous women, but the immune and plasma cell content of the breast of parous and nulliparous women were not significantly different. Our gene expression analysis revealed differential expression of genes that clustered according to parity status, with interferon stimulated genes; STAT1 and IFITM1, and interferon alpha receptor 1 (IFNAR1), and MHC class II genes (HLA-DMA, HLA-DPA,HLA-DPB1, and HLA-DRA) elevated in parous women. Our DSP analysis revealed that immune biomarkers with immunosuppressive functions, including ARG1, VISTA, CTLA-4, and CD68 were significantly higher in parous women as compared with nulliparous women. Breast tissues of parous women show lobular expansion and alterations in immune cell components compared with nulliparous tissues. Further research is needed to assess how these alterations may impact risk. Citation Format: Joshua Were Ogony, Thomas De Bel, Derek Radisky, Jeroen VanderLaak, Mark Sherman. Pathology AI features and immune biomarkers of postpartum involution: Implications for postpartum breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-11-14.
Comprehensive proteomic profiling of serum extracellular vesicles in patients with colorectal liver metastases identifies a signature for non-invasive risk stratification and early-response evaluation
Authors: Kuailu Lin, Franziska Baenke, Xixi Lai, Martin Schneider, Dominic Helm, Heike Polster, Venkatesh S. Rao, Nicole Ganig, Fang Cheng Wong, Lena Seifert, Adrian M. Seifert, Beatrix Jahnke, Nicole Kretschmann, Tjalf Ziemssen, Fee Klupp, Thomas Schmidt, Martin Schneider, Yi Han, Tim F. Weber, Verena Plodeck, Heiner Nebelung, Nathalie Schmitt, Felix Korell, Bruno C. Köhler, Carina Riediger, Jürgen Weitz, Nuh N. Rahbari, Christoph Kahlert
Journal: Molecular Cancer (2022)
Vaccine based on folded receptor binding domain‐PreS fusion protein with potential to induce sterilizing immunity to SARS‐CoV‐2 variants
Authors: Pia Gattinger, Bernhard Kratzer, Inna Tulaeva, Katarzyna Niespodziana, Anna Ohradanova‐Repic, Laura Gebetsberger, Kristina Borochova, Erika Garner‐Spitzer, Doris Trapin, Gerhard Hofer, Walter Keller, Isabella Baumgartner, Ivan Tancevski, Musa Khaitov, Alexander Karaulov, Hannes Stockinger, Ursula Wiedermann, Winfried F. Pickl, Rudolf Valenta
Journal: Allergy (2022)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global COVID-19 pandemic. One possibility to control the pandemic is to induce sterilizing immunity through the induction and maintenance of neutralizing antibodies preventing SARS-CoV-2 from entering human cells to replicate in.
HSR22-129: The Cost of Treatment of HR+/HER2- Early Breast Cancer and Implications for the Cost-Effectiveness of Multigene Assays in the US
Authors: Vladislav Berdunov, Gebra Cuyun Carter, Ewan Laws, Roger Luo, Christy Russell, Sara Campbell, Yara Abdou, Jeremy Force
Journal: Journal of the National Comprehensive Cancer Network (2022)

"HSR22-129: The Cost of Treatment of HR+/HER2- Early Breast Cancer and Implications for the Cost-Effectiveness of Multigene Assays in the US" published on 31 Mar 2022 by National Comprehensive Cancer Network.
The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial
Authors: Ehud Rinott, Anat Yaskolka Meir, Gal Tsaban, Hila Zelicha, Alon Kaplan, Dan Knights, Kieran Tuohy, Matthias Uwe Scholz, Omry Koren, Meir J. Stampfer, Dong D. Wang, Iris Shai, Ilan Youngster
Journal: Genome Medicine (2022)

Previous studies have linked the Mediterranean diet (MED) with improved cardiometabolic health, showing preliminary evidence for a mediating role of the gut microbiome. We recently suggested the Green-Mediterranean (Green-MED) diet as an improved version of the healthy MED diet, with increased consumption of plant-based foods and reduced meat intake. Here, we investigated the effects of MED interventions on the gut microbiota and cardiometabolic markers, and the interplay between the two, during the initial weight loss phase of the DIRECT-PLUS trial.In the DIRECT-PLUS study, 294 participants with abdominal obesity/dyslipidemia were prospectively randomized to one of three intervention groups: healthy dietary guidelines (standard science-based nutritional counseling), MED, and Green-MED. Both isocaloric MED and Green-MED groups were supplemented with 28g/day walnuts. The Green-MED group was further provided with daily polyphenol-rich green tea and Mankai aquatic plant (new plant introduced to a western population). Gut microbiota was profiled by 16S rRNA for all stool samples and shotgun sequencing for a select subset of samples.Both MED diets induced substantial changes in the community structure of the gut microbiome, with the Green-MED diet leading to more prominent compositional changes, largely driven by the low abundant, "non-core," microorganisms. The Green-MED diet was associated with specific microbial changes, including enrichments in the genus Prevotella and enzymatic functions involved in branched-chain amino acid degradation, and reductions in the genus Bifidobacterium and enzymatic functions responsible for branched-chain amino acid biosynthesis. The MED and Green-MED diets were also associated with stepwise beneficial changes in body weight and cardiometabolic biomarkers, concomitantly with the increased plant intake and reduced meat intake. Furthermore, while the level of adherence to the Green-MED diet and its specific green dietary components was associated with the magnitude of changes in microbiome composition, changes in gut microbial features appeared to mediate the association between adherence to the Green-MED and body weight and cardiometabolic risk reduction.Our findings support a mediating role of the gut microbiome in the beneficial effects of the Green-MED diet enriched with Mankai and green tea on cardiometabolic risk factors.The study was registered on ClinicalTrial.gov ( NCT03020186 ) on January 13, 2017.
Tailored Immunotherapy Approach With Nivolumab in Advanced Transitional Cell Carcinoma
Authors: Marc-Oliver Grimm, Bernd Jürgen Schmitz-Dräger, Uwe Zimmermann, Christine Barbara Grün, Gustavo Bruno Baretton, Marc Schmitz, Susan Foller, Katharina Leucht, Martin Schostak, Friedemann Zengerling, Ulrike Schumacher, Wolfgang Loidl, Johannes Meran
Journal: Journal of Clinical Oncology (2022)

Several anti-programmed cell death (ligand)-1 (PD-[L]1) immune checkpoint inhibitors are approved in advanced/metastatic urothelial carcinoma (mUC). Recently, improved activity of an anti-PD-1/anticytotoxic T-cell lymphocyte-4 (CTLA-4) combination versus anti-PD-1 monotherapy has been reported. We report a response-based approach starting treatment with nivolumab monotherapy with nivolumab/ipilimumab as immunotherapeutic boost.After four doses of nivolumab induction, responders continued with nivolumab maintenance therapy. Patients with stable/progressive disease received nivolumab 3 mg/kg plus ipilimumab 1 mg/kg once every 3 weeks for 2 doses followed by nivolumab 1 mg/kg plus ipilimumab 3 mg/kg once every 3 weeks for 2 doses, if not responding to the initial boost. Responders to boosts continued with nivolumab maintenance. Between July 2017 and April 2019, 86 patients were enrolled. The median follow-up is 7.7 months. The primary end point is objective response rate (ORR) per RECIST1.1. Secondary end points include efficacy of nivolumab induction, remission rate with nivolumab/ipilimumab boosts, overall survival, and safety.Of all patients, 42, 39, and five were first- (1L), second- (2L), and third-line (3L), respectively. The median age was 68 years. The ORR with nivolumab monotherapy (assessed at week 8) was 29% in 1L and 23% in 2/3L, respectively. Forty-one patients received early (week 8) and 11 received later nivolumab/ipilimumab boosts. ORRs with nivolumab with or without nivolumab/ipilimumab (best overall response) were 45% and 27% in 1L and 2/3L, respectively. In 1L, 7 of 17 patients receiving boosts at week 8 improved, compared with 2 of 24 in 2/3L.The tailored approach of TITAN-TCC shows meaningful clinical activity supporting dual checkpoint inhibition in 1L mUC. However, starting therapy with nivolumab exclusively appears inadequate given the aggressive nature of mUC. In 2/3L, nivolumab/ipilimumab boosts with escalating ipilimumab dose did not improve efficacy outcomes versus nivolumab monotherapy. An independent 2L cohort of TITAN-TCC receiving nivolumab 1 mg/kg plus ipilimumab 3 mg/kg once every 3 weeks for 4 doses is ongoing.
LONG TERM MORTALITY IN HEART FAILURE WITH PRESERVED &amp; MID-RANGE EJECTION FRACTION: AN ASIAN PERSPECTIVE
Authors: Quah Wy Jin, Aslannif Roslan, Maizatu Akma Sulong, Koh Hui Beng, Ong Siew Hoon, Teoh Chee Kiang, Azmee Mohd Ghazi
Journal: Journal of the American College of Cardiology (2022)
Climate change and mental health research methods, gaps, and priorities: a scoping review
Authors: Alison R Hwong, Margaret Wang, Hammad Khan, D Nyasha Chagwedera, Adrienne Grzenda, Benjamin Doty, Tami Benton, Jonathan Alpert, Diana Clarke, Wilson M Compton
Journal: The Lancet Planetary Health (2022)

Research on climate change and mental health is a new but rapidly growing field. To summarise key advances and gaps in the current state of climate change and mental health studies, we conducted a scoping review that comprehensively examined research methodologies using large-scale datasets. We identified 56 eligible articles published in Embase, PubMed, PsycInfo, and Web of Science between Jan 1, 2000, and Aug 9, 2020. The primary data collection method used was surveys, which focused on self-reported mental health effects due to acute and subacute climate events. Other approaches used administrative health records to study the effect of environmental temperature on hospital admissions for mental health conditions, and national vital statistics to assess the relationship between environmental temperature and suicide rates with regression analyses. Our work highlights the need to link population-based mental health outcome databases to weather data for causal inference. Collaborations between mental health providers and data scientists can guide the formation of clinically relevant research questions on climate change.
INTRACARDIAC ECHOCARDIOGRAPHY AS AN ADJUNCT FOR OFF-LABEL EDGE-TO-EDGE REPAIR OF THE TRICUSPID VALVE
Authors: Gregory Judson, David Blusztein, Punita Kaveti, Tom C. Nguyen, Tobias Deuse, Hope Caughron, Atif Qasim, Kirsten Tolstrup, Vaikom S. Mahadevan
Journal: Journal of the American College of Cardiology (2022)
NON-INVASIVE ASSESSMENT OF MYOCARDIAL ENERGETICS USING 11-C ACETATE POSITRON EMISSION TOMOGRAPHY: SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Kartik Gupta, Mike Pate, Tanya Singh Kakar, Marcelo F. Di Carli, Karthikeyan Ananthasubramaniam, Sumanth Damodar Prabhu, Navkaranbir S. Bajaj
Journal: Journal of the American College of Cardiology (2022)
DAILY PVC VARIABILITY AFFECTS 2014 EHRA/HRS/APHRS EXPERT CONSENSUS CUTOFF
Authors: Richard Amara, Jason Appelbaum, Ameer Abutaleb, Muhammad Haq, Calvin M. Kagan, Rama Vunnam, Vincent Y. See, Stephen Ross Shorofsky, Jeffrey Rottman, Timm Dickfeld
Journal: Journal of the American College of Cardiology (2022)
The evolution and competitive strategies of <i>Akkermansia muciniphila</i> in gut
Authors: Ji-Sun Kim, Se Won Kang, Ju Huck Lee, Seung-Hwan Park, Jung-Sook Lee
Journal: Gut Microbes (2022)

Akkermansia muciniphila is a commensal bacterium using mucin as its sole carbon and nitrogen source. A. muciniphila is a promising candidate for next-generation probiotics to prevent inflammatory and metabolic disorders, including diabetes and obesity, and to increase the response to cancer immunotherapy. In this study, a comparative pan-genome analysis was conducted to investigate the genomic diversity and evolutionary relationships between complete genomes of 27 A. muciniphila strains, including KGMB strains isolated from healthy Koreans. The analysis showed that A. muciniphila strains formed two clades of group A and B in a phylogenetic tree constructed using 1,219 orthologous single-copy core genes. Interestingly, group A comprised of strains from human feces in Korea, whereas most of group B comprised strains from human feces in Europe and China, and from mouse feces. As group A and B branched, mucin hydrolysis played an important role in the stability of the core genome and drove evolution in the direction of defense against invading pathogens, survival in, and colonization in the mucus layer. In addition, WapA and anSME, which function in competition and post-translational modification of sulfatase, respectively, have been a particularly important selective pressure in the evolution of group A. KGMB strains in group A with anSME gene showed sulfatase activity, but KCTC 15667T in group B without anSME did not. Our findings revealed that KGMB strains evolved to gain an edge in the competition with other gut bacteria by increasing the utilization of sulfated mucin, which will allow it to become highly colonized in the gut environment.
RAPID ATRIAL PACING IMMEDIATELY BEFORE AND AFTER TAVR FOR PREDICTION OF PACEMAKER IMPLANTATION: A PROSPECTIVE SINGLE-CENTER STUDY
Authors: Bryan E-Xin Tan, Leela Krishna Teja Boppana, Anas Mohamad Hashem, Mohammed Faisaluddin, Samarthkumar Thakkar, Akbar Khurshid Ahmed, Bipul Baibhav, Cameron Hall, Farhad Abtahian, Mohan Rao, Jeremiah Peter Depta
Journal: Journal of the American College of Cardiology (2022)
SLAMF7 engagement superactivates macrophages in acute and chronic inflammation
Authors: Daimon P. Simmons, Hung N. Nguyen, Emma Gomez-Rivas, Yunju Jeong, A. Helena Jonsson, Antonia F. Chen, Jeffrey K. Lange, George S. Dyer, Philip Blazar, Brandon E. Earp, Jonathan S. Coblyn, Elena M. Massarotti, Jeffrey A. Sparks, Derrick J. Todd, Deepak A. Rao, Edy Y. Kim, Michael B. Brenner
Journal: Science Immunology (2022)

Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a superactivated macrophage state in rheumatoid arthritis. We implicated IFN-γ as a key regulator of SLAMF7 expression and engaging SLAMF7 drove a strong wave of inflammatory cytokine expression. Induction of TNF-α after SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients but also in gut macrophages from patients with active Crohn's disease and in lung macrophages from patients with severe COVID-19. This suggests a central role for SLAMF7 in macrophage superactivation with broad implications in human disease pathology.
EXTRACELLULAR GLYCOPROTEINS AND ADVANCED GLYCATION END PRODUCTS ASSOCIATE WITH CALCIFICATION DEVELOPMENT IN HUMAN AND RABBIT CALCIFIED AORTIC VALVES
Authors: Nikolaos Anousakis-Vlachochristou, Dimitra Athanasiadou, Manolis Mavroidis, Antigoni Miliou, Manousos Makridakis, Loukas Kaklamanis, Stamatis Adamopoulos, Antonia Vlahou, Dennis V. Cokkinos, Karina Carneiro, Konstantinos P. Toutouzas
Journal: Journal of the American College of Cardiology (2022)
SERUM BIOMARKERS IN MORTALITY RISK STRATIFICATION IN PATIENTS, HOSPITALIZED WITH COVID-19 PNEUMONIA IN EARLY AND REMOTE PERIOD
Authors: Naufal Zagidullin, Gumerov Ruslan, Tyurin Anton, Davtayn Paruir, Dozhdev Sergey, Lakman Irina, Pavlov Valentin
Journal: Journal of the American College of Cardiology (2022)
PROGNOSTIC CONCORDANCE OF COMPUTED TOMOGRAPHY DERIVED FRACTIONAL FLOW RESERVE AND MYOCARDIAL PERFUSION IMAGING IN PATIENTS WITH SUSPECTED CORONARY ARTERY DISEASE
Authors: Ahmed Ibrahim Ahmed, Yushui Han, Jean Michel Saad, Mahmoud Al Rifai, Myra Cocker, Chris Schwemmer, Juan Carlos Ramirez Giraldo, Faisal Nabi, Mouaz H. Al-Mallah
Journal: Journal of the American College of Cardiology (2022)
EICOSAPENTAENOIC ACID (EPA) REDUCES J774 MACROPHAGE ACTIVATION AND CYCLOOXYGENASE (COX-1) EXPRESSION
Authors: Samuel CR R. Sherratt, Peter Libby, Deepak L. Bhatt, Hazem Dawoud, Tadeusz Malinski, R. Preston Mason
Journal: Journal of the American College of Cardiology (2022)
IMAGE-BASED COMPUTATIONAL MODELING OF DYNAMIC SHAPE VARIATION IN TETRALOGY OF FALLOT
Authors: Justin Tso, Dylan N. Nguyen, Hengjie Liu, Takegawa Yoshida, Majid Husain, Gary M. Satou, J. Paul Finn, Peng Hu, Kim-Lien Nguyen
Journal: Journal of the American College of Cardiology (2022)
Biodigester Cookstove Interventions and Child Diarrhea in Semirural Nepal: A Causal Analysis of Daily Observations
Authors: Heather K. Amato, Caitlin Hemlock, Kristin L. Andrejko, Anna R. Smith, Nima S. Hejazi, Alan E. Hubbard, Sharat C. Verma, Ramesh K. Adhikari, Dhiraj Pokhrel, Kirk Smith, Jay P. Graham, Amod Pokhrel
Journal: Environmental Health Perspectives (2022)

Hundreds of thousands of biodigesters have been constructed in Nepal. These household-level systems use human and animal waste to produce clean-burning biogas used for cooking, which can reduce household air pollution from woodburning cookstoves and prevent respiratory illnesses. The biodigesters, typically operated by female caregivers, require the handling of animal waste, which may increase domestic fecal contamination, exposure to diarrheal pathogens, and the risk of enteric infections, especially among young children.
THE IMPLICATIONS OF COVID-19 VACCINATION ON HOSPITALIZATIONS AND CLINICAL OUTCOMES
Authors: Brian Case, Benjamin Rosenfeld, Corey Shea, Cheng Zhang, Giorgio Medranda, Lowell F. Satler, Itsik Ben-Dor, Hayder Dhafir Hashim, Toby Rogers, Ron Waksman
Journal: Journal of the American College of Cardiology (2022)
Comments on Surgeon-Patient Sex Concordance and Postoperative Outcomes
Authors: Jingcheng Zhao
Journal: JAMA Surgery (2022)

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DIAGNOSIS AND ROBOTIC-ASSISTED, MINIMALLY INVASIVE, AUTOLOGOUS PERICARDIAL PATCH REPAIR OF A SINUS VENOSUS ATRIAL SEPTAL DEFECT (ASD) WITH REPAIR OF PARTIAL ANOMALOUS PULMONARY VENOUS CONNECTION
Authors: Luke Joseph, James Barrios, Samuel McElwee, Jacob L. Roemen
Journal: Journal of the American College of Cardiology (2022)
CORONARY ARTERY PERFORATION AND TAMPONADE DUE TO PCI IN A PATIENT WITH STEMI DUE TO COVID-19: RESOLUTION OF THE COMPLICATION WITH COIL EMBOLIZATION AND AUTOTRANSFUSION.
Authors: Jose Ramon Benitez, Elizabeth Gomez Ureña, Juan Alan Fuentes Mendoza, Rafael Ignacio Aguilar Reynoso, Andrei Andrei Tort Hidalgo, Luis Enrique Berumen Dominguez, Cesar Gerardo Galvan Vargas
Journal: Journal of the American College of Cardiology (2022)