tbuckley/cabot-search huggingface dataset:
Rebalancing Iron Homeostasis and Erythropoiesis through <i>Tfr2</i> Inhibition for Correction of Anemia in CKD
Authors: Violante Olivari, Maria Rosa Lidonnici, Mariam Aghajan, Mariateresa Pettinato, Simona Maria Di Modica, Alessia Pagani, Francesca Tiboni, Shuling Guo, Laura Silvestri, Giuliana Ferrari, Antonella Nai
Journal: Blood (2021)
Genomic Profiling of Smoldering Multiple Myeloma Classifies Molecular Groups with Distinct Pathogenic Phenotypes and Clinical Outcomes
Authors: Shankara Anand, Mark Bustoros, Romanos Sklavenitis-Pistofidis, Robert A. Redd, Eileen M Boyle, Yu-Tzu Tai, Carl J Neuse, Selina J Chavda, Cody J. Boehner, Mahshid Rahmat, Benny Zhitomirsky, Andrew Dunford, Ankit K. Dutta, Chip Stewart, Lorenzo Trippa, Tineke Casneuf, Efstathios Kastritis, Brian A Walker, Faith E Davies, Meletios A. Dimopoulos, P. Leif Bergsagel, Kwee Yong, Gareth J. Morgan, François Aguet, Gad Getz, Irene M. Ghobrial
Journal: Blood (2021)
Corrigendum to Heybeli C, Bentall A, Wen J, et al. A study from The Mayo Clinic evaluated long-term outcomes of kidney transplantation in patients with immunoglobulin light chain amyloidosis. Kidney Int. 2021;99:707–715
Authors: Cihan Heybeli, Andrew Bentall, Jiqiu Wen, Mariam Priya Alexander, Francis K. Buadi, Fernando G. Cosio, Patrick G. Dean, Angela Dispenzieri, David Dingli, Mireille El Ters, Morie A. Gertz, Hatem Amer, Prashant Kapoor, Hasan Khamash, Taxiarchis Kourelis, Shaji Kumar, Elizabeth C. Lorenz, Martin Mai, Eli Muchtar, David L. Murray, Mikel Prieto, Carrie A. Schinstock, Mark D. Stegall, Rahma Warsame, Nelson Leung
Journal: Kidney International (2021)
Magnetically Controlled Capsule Endoscopy for Assessment of Antiplatelet Therapy–Induced Gastrointestinal Injury
Authors: Yaling Han, Zhuan Liao, Yi Li, Xianxian Zhao, Shuren Ma, Dan Bao, Miaohan Qiu, Jie Deng, Jinhai Wang, Peng Qu, Chunmeng Jiang, Shaobin Jia, Shaoqi Yang, Leisheng Ru, Jia Feng, Wei Gao, Yonghui Huang, Ling Tao, Ying Han, Kan Yang, Xiaoyan Wang, Wenjuan Zhang, Bangmao Wang, Yue Li, Youlin Yang, Junxia Li, Jiangqiu Sheng, Yitong Ma, Min Cui, Sicong Ma, Xiaozeng Wang, Zhaoshen Li, Gregg W. Stone
Journal: Journal of the American College of Cardiology (2021)
Combining the Expression of CD33.CAR and CXCR4 to Increase CAR-CIK Cell Homing to Bone Marrow Niche and Leukemic Stem Cell Eradication in Acute Myeloid Leukemia
Authors: Marta Biondi, Beatrice Cerina, Chiara Tomasoni, Gianpietro Dotti, Sarah Tettamanti, Andrea Biondi, Alice Pievani, Marta Serafini
Journal: Blood (2021)
The SARS-CoV-2 Lambda variant and its neutralisation efficiency following vaccination with Comirnaty, Israel, April to June 2021
Authors: Neta Zuckerman, Ital Nemet, Limor Kliker, Nofar Atari, Yaniv Lustig, Efrat Bucris, Dana Bar Ilan, Miranda Geva, Reut Sorek-Abramovich, Chen Weiner, Nir Rainy, Adina Bar-Chaim, Patricia Benveniste-Levkovitz, Ramzia Abu Hamed, Gili Regev-Yochay, Ofra Hevkin, Orna Mor, Sharon Alroy-Preis, Ella Mendelson, Michal Mandelboim
Journal: Eurosurveillance (2021)

The SARS-CoV-2 Lambda (Pango lineage designation C.37) variant of interest, initially identified in Peru, has spread to additional countries. First detected in Israel in April 2021 following importations from Argentina and several European countries, the Lambda variant infected 18 individuals belonging to two main transmission chains without further spread. Micro-neutralisation assays following Comirnaty (BNT162b2 mRNA, BioNTech-Pfizer) vaccination demonstrated a significant 1.6-fold reduction in neutralising titres compared with the wild type virus, suggesting increased susceptibility of vaccinated individuals to infection.
Abstract 17893: Deficiency of Yes-Associated Protein (YAP) Promotes Structural and Functional Cardiac Maladaptation in Response to Acute Pressure Overlaod
Authors: Jaemin Byun, Dominic P Del Re, Peiyong Zhai, Shohei Ikeda, Akihiro Shirakabe, Junichi Sadoshima
Journal: Circulation (2017)

Yes-Associated Protein (YAP), a downstream effector of the Hippo pathway, regulates cell proliferation and survival. Cardiac-specific loss of YAP leads to increased cardiomyocyte (CM) apoptosis and...
Abstract PO-014: VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts
Authors: Luke Ternes, Ge Huang, Christian Lanciault, Guillaume Thibault, Rachelle Riggers, Joe Gray, John Muschler, Young Hwan Chang
Journal: Cancer Research (2021)

Abstract Objective and quantifiable assessment of tissue pathology is necessary to study mechanistic disease progression; however, current quantification methods based on tissue staining have many drawbacks including cost, time, labor, batch effects, as well as uneven staining which can result in misinterpretation and investigator bias. Here we present VISTA, an automated deep learning tool for semantic segmentation and quantification of histologic features from hematoxylin and eosin (H&amp;E) stained pancreatic tissue sections. VISTA is trained to identify four key tissue types in developing murine PDAC samples: normal acinar, acinar-to-ductal metaplasia (ADM), dysplasia, and other normal tissue. Predicted segmentations were quantitatively evaluated against pathologist annotation with Dice Coefficients, achieving scores of 0.79, 0.70, 0.79 for normal acinar, ADM, and dysplasia, respectively. Predictions were evaluated against biological ground truth using the mean structural similarity index to immunostainings amylase and pan-keratin (0.925 and 0.920, respectively). The total area of feature prediction was also correlated to the area of immunostaining in whole tissue sections using spearman correlation (0.86, 0.97, and 0.92 for DAPI, amylase, and cytokeratins, respectively). Importantly, our tool is not only able to predict staining information, but it is able to distinguish between ADM and dysplasia, which are not reliably distinguished with common immunostaining methods, showing VISTA’s potential to expand research beyond what is capable with current standards. As a use case example of VISTA, we quantified abundance of histologic features in murine cohorts with oncogenic Kras-driven disease. We observed stromal expansion, a reduction in normal acinar, and an increase in both ADM and dysplasia as the disease progresses, which matches known biology. Since VISTA is an automated algorithm, it can accelerate histological analysis and improve the consistency of quantification between laboratories and investigators. This work has been published in Nature Scientific Reports, and the code is available on github at https://github.com/GelatinFrogs/MicePan-Segmentation. Citation Format: Luke Ternes, Ge Huang, Christian Lanciault, Guillaume Thibault, Rachelle Riggers, Joe Gray, John Muschler, Young Hwan Chang. VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-014.
Evaluation of Pulmonary Toxicities in Lymphoma Patients Receiving Brentuximab Vedotin
Authors: Tiffany Guan, Mimi Lo, Rebecca Young, Fouad Boulbol, Hanson Mouanoutoua, Raymond Chu, Weiyun Z. Ai, Haifaa Abdulhaq, Bita Fakhri
Journal: Blood (2021)
Outcomes Are Similar Following Allogeneic Hematopoietic Stem Cell Transplant for Newly Diagnosed Patients Who Received Venetoclax + Azacitidine Versus Intensive Chemotherapy
Authors: Amanda C. Winters, Grace Bosma, Diana Abbott, Mohd Minhajuddin, Craig T Jordan, Daniel A. Pollyea, Jonathan A. Gutman
Journal: Blood (2021)
Epithelial barrier dysfunction in ocular allergy
Authors: Neera Singh, Yolanda Diebold, Srikant K. Sahu, Andrea Leonardi
Journal: Allergy (2021)

The epithelial barrier is the first line of defense that forms a protective barrier against pathogens, pollutants, and allergens. Epithelial barrier dysfunction has been recently implicated in the development of allergic diseases such as asthma, atopic dermatitis, food allergy, and rhinitis. However, there is limited knowledge on epithelial barrier dysfunction in ocular allergy (OA). Since the ocular surface is directly exposed to the environment, it is important to understand the role of ocular epithelia and their dysfunction in OA. Impaired epithelial barrier enhances allergen uptake, which lead to activation of immune responses and development of chronic inflammation as seen in allergies. Abnormal expression of tight junction proteins that helps to maintain epithelial integrity has been reported in OA but sufficient data not available in chronic atopic (AKC) and vernal keratoconjunctivitis (VKC), the pathophysiology of which is not just complex, but also the current treatments are not completely effective. This review provides an overview of studies, which indicates the role of barrier dysfunction in OA, and highlights how ocular barrier dysfunction possibly contributes to the disease pathogenesis. The review also explores the potential of ocular epithelial barrier repair strategies as preventive and therapeutic approach.
Dendrocalamus latiflorus and its component rutin exhibit glucose-lowering activities by inhibiting hepatic glucose production via AKT activation
Authors: Kun Luo, Wenting Huang, Liansheng Qiao, Xiaoling Zhang, Di Yan, Zhiyu Ning, Chengmei Ma, Honglei Dang, Dong Wang, Hongyan Guo, Lan Xie, Jing Cheng
Journal: Acta Pharmaceutica Sinica B (2021)

The potential medicinal value of Ma bamboo (Dendrocalamus latiflorus), one of the most popular and economically important bamboo species in China, has been underestimated. In the present study, we found that D. latiflorus leaf extract (DLE) reduced fasting blood glucose levels, body weight, and low-density lipoprotein cholesterol with low liver toxicity in db/db mice. In addition, gene expression profiling was performed and pathway enrichment analysis showed that DLE affected metabolic pathways. Importantly, DLE activated the AKT signaling pathway and reduced glucose production by downregulating glucose-6-phosphatase (G6PC) and phosphoenolpyruvate carboxykinase 1 (PCK1) expression. Moreover, network pharmacology analysis identified rutin as an active component in DLE through targeting insulin growth factor 1 receptor (IGF1R), an upstream signaling transducer of AKT. Due to its hypoglycemic effects and low toxicity, DLE may be considered an adjuvant treatment option for type 2 diabetes patients.
7 Analytical comparison of a PD-L1 22C3 antibody laboratory-developed test protocol on the Benchmark XT and PD-L1 IHC 22C3 pharmDx: pan-tumor and triple-negative breast cancer samples
Authors: Gilad Vainer, Ghadeer Zatara, Lingkang Huang, Shanthy Nuti, Shanthy Nuti, Kenneth Emancipator
Journal: Journal for ImmunoTherapy of Cancer (2021)

Background PD-L1 IHC 22C3 pharmDx is an FDA-approved companion diagnostic for pembrolizumab across multiple tumor types designed for use on the Autostainer Link 48 (AL48). Many pathology laboratories do not have access to the AL48 and therefore do not use PD-L1 IHC 22C3 pharmDx but instead assess PD-L1 using laboratory-developed tests (LDTs) on the Ventana BenchMark platform. We compared our PD-L1 22C3 antibody-based LDT on the BenchMark XT platform with PD-L1 IHC 22C3 pharmDx using cervical cancer (CC), head and neck squamous cell carcinoma (HNSCC), urothelial carcinoma (UC), esophageal SCC (ESCC), and triple-negative breast cancer (TNBC) samples. Methods Tumor specimens from patients with CC, HNSCC, UC, ESCC, and TNBC were stained with the 22C3 antibody, scored using the LDT on the BenchMark XT as previously described, 1 and compared with PD-L1 IHC 22C3 pharmDx scored by a trained pathologist, who measured PD-L1 with the use of combined positive score (CPS) and standard cutoffs (HNSCC and CC, ≥1; UC, ESCC, and TNBC, ≥10). Agreement in PD-L1 CPS as determined using the LDT and the PD-L1 IHC 22C3 pharmDx was evaluated. Results 423 samples with CC (n = 77), HNSCC (n = 126), UC (n = 121), ESCC (n = 80), and TNBC (n = 19) were evaluated in this study. The pan-tumor (CC, HNSCC, UC, and ESCC) intraclass correlation coefficient (ICC) of PD-L1 CPS as a continuous variable was 0.95 (95% CI, 0.94%–0.96%); Spearman correlations were 0.95. ICC (95% CI) was 0.92 (0.88–0.95) for CC, 0.97 (0.96–0.98) for HNSCC, 0.95 (0.92–0.97) for UC, and 0.92 (0.88–0.95) for ESCC; Spearman correlation was 0.93, 0.96, 0.92, and 0.89, respectively. The overall percentage agreement at the respective CPS cutoff was 96% (CC), 96% (HNSCC), 96% (UC), and 90% (ESCC). Staining patterns by 22C3 LDT and PD-L1 IHC 22C3 pharmDx were also very similar in our TNBC pilot study; however, correlation was not calculated because of the small sample numbers. Conclusions The PD-L1 22C3 antibody-based LDT on the BenchMark XT demonstrated high concordance with PD-L1 IHC 22C3 pharmDx. These findings suggest the comparability of PD-L1 IHC 22C3 pharmDx with an LDT based on the 22C3 antibody across several tumor types. Further validation for TNBC is ongoing to confirm the data from the pilot run. Reference Neuman T, et al . J Thorac Oncol . 2016; 11 :1863–1868.
Pregnant and Peripartum Women with COVID-19 Have High Survival with Extracorporeal Membrane Oxygenation: An Extracorporeal Life Support Organization Registry Analysis
Authors: Erika R. O’Neil, Huiming Lin, Amir A. Shamshirsaz, Emily E. Naoum, Peter R. Rycus, Peta M. A. Alexander, Jamel P. Ortoleva, Meng Li, Marc M. Anders
Journal: American Journal of Respiratory and Critical Care Medicine (2021)
Plaque Rupture, Compared With Plaque Erosion, Is Associated With a Higher Level of Pancoronary Inflammation
Authors: Akihiro Nakajima, Tomoyo Sugiyama, Makoto Araki, Lena Marie Seegers, Damini Dey, Iris McNulty, Hang Lee, Taishi Yonetsu, Yumi Yasui, Yun Teng, Tatsuhiro Nagamine, Sunao Nakamura, Stephan Achenbach, Tsunekazu Kakuta, Ik-Kyung Jang
Journal: JACC. Cardiovascular imaging (2021)
Impact of Thrombus Aspiration one-year Cardiac Mortality During Primary PCI in STEMI Patients with total Occlusion; from Korea Acute Myocardial Infarction Registry National Institute of Health
Authors: Kye Taek Ahn, Seok-Woo Seong, Mijoo Kim, Jin-Ok Jeong, Seon-Ah Jin
Journal: Clinical Cardiology and Cardiovascular Interventions (2020)

Background: The clinical impact of intracoronary thrombus aspiration (TA) during primary percutaneous coronary intervention (PCI) in patients with ST-segment elevation myocardial infarction (STEMI) is unclear. We investigated to evaluate whether TA during primary PCI reduces one-year mortality. Methods: From the Korea Acute Myocardial Infarction Registry-National Institute of Health, 3749 patients with STEMI who were undergoing primary PCI within 12 hours (60.8±12.9 years, 18.7% women) and shown pre-procedural Thrombolysis In Myocardial Infarction (TIMI) flow 0, 1 in coronary angiography were enrolled between November 2011 and November 2015 during one-year follow up. The patients were divided into two groups according to TA during primary PCI: PCI with TA (n=1630) and PCI alone (n=2119). The primary end-point was major adverse cardiac events (MACE), defined as the composite of cardiovascular death (CVD), stroke or recurrent MI at one-year. The secondary efficacy end-point were all-cause of mortality and CVD at one-year. Results: PCI with TA did not reduce the risk of MACE (OR: 0.598, 95% CI: 0.737-1.160, p=0.499), all-cause mortality (OR: 0.898, 95% CI: 0.705-1.144, p=0.383) and CVD (OR: 0.893, 95% CI: 0.683-1.168, p=0.408) in all patients during one-year follow up. The trend did not change after propensity score matching. In subgroup analysis, there was no efficacy of clinical outcome during one-year follow up. Conclusions: Primary PCI with TA did not reduce MACE and all-cause mortality among patients with STEMI and pre-procedural TIMI flow 0,1 during one-year follow up.
Intravenous Iron and Infection Risk—Still an Unanswered Question
Authors: Deborah Rund
Journal: JAMA Network Open (2021)

Akshay A. Shah, MSc; Killian Donovan, BM, BCh; Claire Seeley, MBBS; Edward A. Dickson, BMBS; Antony J. R. Palmer, DPhil; Carolyn Doree, PhD; Susan Brunskill, MSc; Jack Reid, MBBS; Austin G. Acheson, MD; Anita Sugavanam, MBBS; Edward Litton, PhD; Simon J. Stanworth, DPhil
Medical Therapy of Acute Myocardial Infarction by Application of Hemodynamic Subsets
Authors: James S. Forrester, George Diamond, Kanu Chatterjee, H. J. C. Swan
Journal: New England Journal of Medicine (1976)

Physiologic Basis for Therapeutic Decisions — Effects of Drugs on Cardiac FunctionThe selection of therapy for a patient with disordered function in acute myocardial infarction involves both assessment of the level of cardiac performance and prediction of the response to therapy. Table 5 summarizes the reported hemodynamic effects of commonly used therapeutic methods in acute myocardial infarction. The effects of therapeutic agents on cardiac function in acute myocardial infarction are usefully considered in four classes: diuretics, vasodilators, inotropes and others. This classification is of particular value in clinical practice, for although there are substantial variations in the magnitude of effects, the . . .
Sequential Conditioning Regimen with Thiotepa in Allogeneic Hematopoietic Cell Transplantation for the Treatment of Refractory Myeloid Malignancies
Authors: Rémy Duléry, Nadia Belmoufid, Florent Malard, Eolia Brissot, Anne Banet, Simona Sestili, Zoé Van De Wyngaert, Nicolas Stocker, Vera Radici, Michele Wieczorek, Ramdane Belhocine, Simona Lapusan, Mara Memoli, Alexis Genthon, Anne Vekhoff, Tounes Ledraa, Agnès Bonnin, Ollivier Legrand, Pierre Fenaux, Myriam Labopin, Mohamad Mohty
Journal: Blood (2021)
Single-Cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-Genesis in Pigs
Authors: Jianbo Li, Ligang Wang, Dawei Yu, Junfeng Hao, Longchao Zhang, Adeniyi C. Adeola, Bingyu Mao, Yun Gao, Shifang Wu, Chunling Zhu, Yongqing Zhang, Jilong Ren, Changgai Mu, David M. Irwin, Lixian Wang, Tang Hai, Haibing Xie, Yaping Zhang
Journal: Genomics Proteomics & Bioinformatics (2021)

Development of thoracolumbar vertebra (TLV) and rib primordium (RP) is a common evolutionary feature across vertebrates, although whole-organism analysis of the expression dynamics of TLV- and RP-related genes has been lacking. Here, we investigated the single-cell transcriptome landscape of thoracic vertebra (TV), lumbar vertebra (LV), and RP cells from a pig embryo at 27 days post-fertilization (dpf) and identified six cell types with distinct gene expression signatures. In-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP development. Further analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA10 3'-UTR sequence specific to osteoblasts of LV cells, which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV transition. Thus, this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution, which serves as a comprehensive view on the transcriptional profile of animal embryo development.
Association of Rural and Critical Access Hospital Status With Patient Outcomes After Emergency Department Visits Among Medicare Beneficiaries
Authors: Margaret Greenwood-Ericksen, Neil Kamdar, Paul Lin, Naomi George, Larissa Myaskovsky, Cameron Crandall, Nicholas M. Mohr, Keith E. Kocher
Journal: JAMA Network Open (2021)

<h3>Importance</h3> Rural US residents disproportionately rely on emergency departments (ED), yet little is known about patient outcomes after ED visits to rural hospitals or critical access hospitals (CAHs). <h3>Objective</h3> To compare 30-day outcomes after rural vs urban ED visits and in CAHs, a subset of rural hospitals. <h3>Design, Setting, and Participants</h3> This propensity-matched, retrospective cohort study used a 20% sample of national Medicare fee-for-service beneficiaries from January 1, 2011, to October 31, 2015. Rural and urban ED visits were matched on demographics, patient prior use of EDs, comorbidities, and diagnoses. Thirty-day outcomes overall and stratified by 25 common ED diagnoses were evaluated, with similar analysis of CAHs vs non-CAHs. Data were analyzed from February 15, 2020, to May 17, 2021. <h3>Main Outcomes and Measures</h3> The primary outcome was 30-day all-cause mortality. Secondary outcomes were ED revisits with and without hospitalization. <h3>Results</h3> The matched cohort included 473 152 rural and urban Medicare beneficiaries with a mean (SD) age of 75.1 (7.9) years (59.1% and 59.3% women, respectively; 86.9% and 87.1% White, respectively). Medicare beneficiaries at rural vs urban EDs experienced similar all-cause 30-day mortality (3.9% vs 4.1%; effect size, 0.01), ED revisits (18.1% vs 17.8%; effect size, 0.00), and ED revisits with hospitalization (6.0% vs 8.1%; effect size, 0.00). Rural ED visits were associated with more transfer (6.2% vs 2.0%; effect size, 0.22) and fewer hospitalizations (24.7% vs 39.2; effect size, 0.31). Stratified by diagnosis, patients in rural EDs with life-threatening illnesses experienced more transfer with 30-day mortality similar to that of patients in urban EDs. In contrast, mortality differed for patients in rural EDs with symptom-based diagnoses, including chest pain (odds ratio [OR], 1.54 [95% CI, 1.25-1.89]), nausea and vomiting (OR, 1.68 [95% CI, 1.26-2.24), and abdominal pain (OR, 1.73 [95% CI, 1.42-2.10]). All findings were similar for CAHs. <h3>Conclusions and Relevance</h3> The findings of this cohort study of rural ED care suggest that patient mortality for potentially life-threatening conditions is comparable to that in urban settings. Further research is needed to understand the sources of greater rural ED mortality for symptom-based conditions. These findings underscore the importance of ensuring access to treatment of life-threatening conditions at local EDs in rural communities, which are increasingly endangered by hospital closures.
Clinical Administration Characteristics of Subcutaneous and Intravenous Administration of Daratumumab in Multiple Myeloma Patients at Mayo Clinic
Authors: Scott Soefje, Corinne Carpenter, Katherine Carlson, Samir Awasthi, Thomas S. Lin, Shuchita Kaila, Daniel Tarjan, Nikhil Kayal, Christian Kirkup, Tyler Wagner, Kathleen Gray, Shaji Kumar
Journal: Blood (2021)
Outcomes for Allogeneic Stem Cell Transplantation in Secondary AML Are Inferior to De Novo AML and Are Independent of the Disease Risk Index
Authors: Jacinta Perram, Eleni Mayson, Catherine Tang, Steven Tran, Donna Aarons, Anthony J Dodds, Keith Fay, Nada Hamad, David Ma, Sam Milliken, Barbara Withers, Matthew Greenwood, William S Stevenson, Christopher Kevin Arthur, Ian H Kerridge, John Moore
Journal: Blood (2021)