tbuckley/cabot-search huggingface dataset:
RETRACTED: 6-month consequences of COVID-19 in patients discharged from hospital: a cohort study
Authors: Chaolin Huang, Lixue Huang, Yeming Wang, Xia Li, Lili Ren, Xiaoying Gu, Liang Kang, Li Guo, Min Liu, Xing Zhou, Jianfeng Luo, Zhenghui Huang, Shengjin Tu, Yue Zhao, Li Chen, Decui Xu, Yanping Li, Caihong Li, Lu Peng, Yong Li, Wuxiang Xie, Dan Cui, Lianhan Shang, Guohui Fan, Jiuyang Xu, Geng Wang, Ying Wang, Jingchuan Zhong, Chen Wang, Jianwei Wang, Dingyu Zhang, Bin Cao
Journal: The Lancet (2021)
Methods to investigate intrathecal adaptive immunity in neurodegeneration
Authors: Hamilton Oh, Olivia Leventhal, Divya Channappa, Victor W. Henderson, Tony Wyss-Coray, Benoit Lehallier, David Gate
Journal: Molecular Neurodegeneration (2021)

Abstract Background Cerebrospinal fluid (CSF) provides basic mechanical and immunological protection to the brain. Historically, analysis of CSF has focused on protein changes, yet recent studies have shed light on cellular alterations. Evidence now exists for involvement of intrathecal T cells in the pathobiology of neurodegenerative diseases. However, a standardized method for long-term preservation of CSF immune cells is lacking. Further, the functional role of CSF T cells and their cognate antigens in neurodegenerative diseases are largely unknown. Results We present a method for long-term cryopreservation of CSF immune cells for downstream single cell RNA and T cell receptor sequencing (scRNA-TCRseq) analysis. We observe preservation of CSF immune cells, consisting primarily of memory CD4 + and CD8 + T cells. We then utilize unbiased bioinformatics approaches to quantify and visualize TCR sequence similarity within and between disease groups. By this method, we identify clusters of disease-associated, antigen-specific TCRs from clonally expanded CSF T cells of patients with neurodegenerative diseases. Conclusions Here, we provide a standardized approach for long-term storage of CSF immune cells. Additionally, we present unbiased bioinformatic approaches that will facilitate the discovery of target antigens of clonally expanded T cells in neurodegenerative diseases. These novel methods will help improve our understanding of adaptive immunity in the central nervous system.
Patient pathway analysis of tuberculosis diagnostic delay: a multicentre retrospective cohort study in China
Authors: Lu Zhang, Tao-Ping Weng, Hong-Yu Wang, Feng Sun, Yuan-Yuan Liu, Ke Lin, Zhe Zhou, Yuan-Yuan Chen, Yong-Guo Li, Ji-Wang Chen, Li-Jun Han, Hui-Mei Liu, Fu-Li Huang, Cui Cai, Hong-Ying Yu, Wei Tang, Zheng-Hui Huang, Long-Zhi Wang, Lei Bao, Peng-Fei Ren, Guo-Fang Deng, Jian-Nan Lv, Yong-Lan Pu, Fan Xia, Tao Li, Qun Deng, Gui-Qing He, Yang Li, Wen-Hong Zhang
Journal: Clinical Microbiology and Infection (2021)

ObjectivesDelay in diagnosis of tuberculosis (TB) is an important but under-appreciated problem. Our study aimed to analyse the patient pathway and possible risk factors of long diagnostic delay (LDD).MethodsWe enrolled 400 new bacteriologically diagnosed patients with pulmonary TB from 20 hospitals across China. LDD was defined as an interval between the initial care visit and the confirmation of diagnosis exceeding 14 days. Its potential risk factors were investigated by multivariate logistic regression and multilevel logistic regression. Hospitals in China were classified by increasing size, from level 0 to level 3. TB laboratory equipment in hospitals was also evaluated.ResultsThe median diagnostic delay was 20 days (IQR: 7–72 days), and 229 of 400 patients (57.3%, 95%CI 52.4–62.1) had LDD; 15% of participants were diagnosed at the initial care visit. Compared to level 0 facilities, choosing level 2 (OR 0.27, 95%CI 0.12–0.62, p 0.002) and level 3 facilities (OR 0.34, 95%CI 0.14–0.84, p 0.019) for the initial care visit was independently associated with shorter LDD. Equipping with smear, culture, and Xpert at initial care visit simultaneously also helped to avoid LDD (OR 0.28, 95%CI 0.09–0.82, p 0.020). The multilevel logistic regression yielded similar results. Availability of smear, culture, and Xpert was lower in level 0–1 facilities than in level 2–3 facilities (p < 0.001, respectively).ConclusionsMost patients failed to be diagnosed at the initial care visit. Patients who went to low-level facilities initially had a higher risk of LDD. Improvement of TB laboratory equipment, especially at low-level facilities, is urgently needed.
An advanced optical clearing protocol allows label-free detection of tissue necrosis <i>via</i> multiphoton microscopy in injured whole muscle
Authors: Dominik Schneidereit, Anita Bröllochs, Paul Ritter, Lucas Kreiß, Zeinab Mokhtari, Andreas Beilhack, Gerhard Krönke, Jochen A Ackermann, Maria Faas, Anika Grüneboom, Sebastian Schürmann, Oliver Friedrich
Journal: Theranostics (2021)

Rationale: Structural remodeling or damage as a result of disease or injury is often not evenly distributed throughout a tissue but strongly depends on localization and extent of damaging stimuli. Skeletal muscle as a mechanically active organ can express signs of local or even systemic myopathic damage, necrosis, or repair. Conventionally, muscle biopsies (patients) or whole muscles (animal models) are mechanically sliced and stained to assess structural alterations histologically. Three-dimensional tissue information can be obtained by applying deep imaging modalities, e.g. multiphoton or light-sheet microscopy. Chemical clearing approaches reduce scattering, e.g. through matching refractive tissue indices, to overcome optical penetration depth limits in thick tissues. Methods: Here, we optimized a range of different clearing protocols. We find aqueous solution-based protocols employing (20-80%) 2,2'-thiodiethanol (TDE) to be advantageous over organic solvents (dibenzyl ether, cinnamate) regarding the preservation of muscle morphology, ease-of-use, hazard level, and costs. Results: Applying TDE clearing to a mouse model of local cardiotoxin (CTX)-induced muscle necrosis, a complete loss of myosin-II signals was observed in necrotic areas with little change in fibrous collagen or autofluorescence (AF) signals. The 3D aspect of myofiber integrity could be assessed, and muscle necrosis in whole muscle was quantified locally via the ratios of detected AF, forward- and backward-scattered Second Harmonic Generation (fSHG, bSHG) signals. Conclusion: TDE optical clearing is a versatile tool to study muscle architecture in conjunction with label-free multiphoton imaging in 3D in injury/myopathy models and might also be useful in studying larger biofabricated constructs in regenerative medicine.
Myocardial Infarction incidence during national lockdown in two French provinces unevenly affected by COVID-19 outbreak: An observational study
Authors: Eric Van Belle, Thibault Manigold, Adeline Piérache, Alain Furber, Nicolas Debry, Anne Luycx-Bore, Jean-Jacques Bauchart, Olivier Nugue, François Huchet, Mathieu Bic, François Vinchon, Smaïn Sayah, Alexandre Fournier, Eric Decoulx, Usman Mouhammad, Jérôme Clerc, Aurélie Manchuelle, Tahar Lazizi, Akram Chmait, Julien Jeannetteau, Pierre Hénon, Mickael Bonin, Marie Dupret-Minet, Ashok Tirouvanziam, David Molcard, Fabien Arabucki, Antoine Py, Fabrice Prunier, Cédric Delhaye, Gilles Lemesle, Guillaume Schurtz, Alessandro Cosenza, Hugues Spillemaeker, Basile Verdier, Tom Denimal, Thibault Pamart, Habib Sylla, Dany Janah, David Aouate, Sina Porouchani, Valérie Guillez, Guillaume Bonnet, Julien Ternacle, Julien Labreuche, Guillaume Cayla, Flavien Vincent
Journal: The Lancet Regional Health - Europe (2021)
An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes
Authors: Saba Ghaffari, Casey Hanson, Remington E. Schmidt, Kelly J. Bouchonville, Steven M. Offer, Saurabh Sinha
Journal: Genome biology (2021)

Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to systematically integrate transcriptomic, epigenomic, and cistromic information to accurately define the regulatory networks critical for metastasis.To address this limitation, we use a purposefully generated cellular model of colon cancer invasiveness to generate multi-omics data, including expression, accessibility, and selected histone modification profiles, for increasing levels of invasiveness. We then adopt a rigorous probabilistic framework for joint inference from the resulting heterogeneous data, along with transcription factor binding profiles. Our approach uses probabilistic graphical models to leverage the functional information provided by specific epigenomic changes, models the influence of multiple transcription factors simultaneously, and automatically learns the activating or repressive roles of cis-regulatory events. Global analysis of these relationships reveals key transcription factors driving invasiveness, as well as their likely target genes. Disrupting the expression of one of the highly ranked transcription factors JunD, an AP-1 complex protein, confirms functional relevance to colon cancer cell migration and invasion. Transcriptomic profiling confirms key regulatory targets of JunD, and a gene signature derived from the model demonstrates strong prognostic potential in TCGA colorectal cancer data.Our work sheds new light into the complex molecular processes driving colon cancer metastasis and presents a statistically sound integrative approach to analyze multi-omics profiles of a dynamic biological process.
Tissue-resident CD4 <sup>+</sup> T helper cells assist the development of protective respiratory B and CD8 <sup>+</sup> T cell memory responses
Authors: Young Min Son, In Su Cheon, Yue Wu, Chaofan Li, Zheng Wang, Xiaochen Gao, Yao Chen, Yoshimasa Takahashi, Yang-Xin Fu, Alexander L. Dent, Mark H. Kaplan, Justin J. Taylor, Weiguo Cui, Jie Sun
Journal: Science Immunology (2021)

Identification of a CD4 + helper T cell population providing in situ help to B and CD8 + T cells in the respiratory mucosa.
Abstract 10262: Radial versus Femoral Access for Percutaneous Coronary Intervention in Patients With St-segment Elevation Myocardial Infarction: Trial Sequential Analysis
Authors: Mohammed Osman, Maryam Saleem, Khansa Osman, Babikir Kheiri, Sean Regner, Qais Radaideh, Jason A Moreland, Sunil V Rao, Samir R Kapadia
Journal: Circulation (2019)

Introduction: Percutaneous coronary intervention (PCI) is the gold standard for management of ST-segment elevation myocardial infarction(STEMI). Randomized controlled trials (RCTs) yielded conflict...
MO01.01 Durvalumab for Patients with Stage III EGFR-Mutated Non-Small Cell Lung Cancer Receiving Definitive Chemoradiotherapy
Authors: J.V. Aredo, J.A. Hellyer, J.W. Neal, S.K. Padda, C.E. McCoach, J.W. Riess, E.C. Cabebe, B.W. Loo, M. Diehn, H.A. Wakelee
Journal: Journal of Thoracic Oncology (2021)
Extreme Weather and Climate Change: Population Health and Health System Implications
Authors: Kristie L. Ebi, Jennifer Vanos, Jane W. Baldwin, Jesse E. Bell, David M. Hondula, Nicole A. Errett, Katie Hayes, Colleen E. Reid, Shubhayu Saha, June Spector, Peter Berry
Journal: Annual Review of Public Health (2021)

Extreme weather and climate events, such as heat waves, cyclones, and floods, are an expression of climate variability. These events and events influenced by climate change, such as wildfires, continue to cause significant human morbidity and mortality and adversely affect mental health and well-being. Although adverse health impacts from extreme events declined over the past few decades, climate change and more people moving into harm's way could alter this trend. Long-term changes to Earth's energy balance are increasing the frequency and intensity of many extreme events and the probability of compound events, with trends projected to accelerate under certain greenhouse gas emissions scenarios. While most of these events cannot be completely avoided, many of the health risks could be prevented through building climate-resilient health systems with improved risk reduction, preparation, response, and recovery. Conducting vulnerability and adaptation assessments and developing health system adaptation plans can identify priority actions to effectively reduce risks, such as disaster risk management and more resilient infrastructure. The risks are urgent, so action is needed now.
Abstract 16252: In vivo β1 Adrenergic Receptor Blockade Reverses an Oxidative Modification Inhibiting the Na+-K+ Pump of Cardiac Myocytes in Heart Failure
Authors: Natasha A Fry, Alvaro Garcia, Keyvan Karimi, Craig McLachlan, Chia-Chi Liu, Gemma A Figtree, Helge H Rasmussen
Journal: Circulation (2012)

Identifying mechanisms for beneficial effect of β1 adrenergic receptor (AR) blockade in heart failure may be useful for developing new treatments. Since a raised Na+ concentration ([Na+]i) in myocy...
NK cell-based cancer immunotherapy: from basic biology to clinical development
Authors: Sizhe Liu, Vasiliy Galat, Yekaterina Galat4, Yoo Kyung Annie Lee, Derek Wainwright, Jennifer Wu
Journal: Journal of Hematology & Oncology (2021)

Abstract Natural killer (NK) cell is a specialized immune effector cell type that plays a critical role in immune activation against abnormal cells. Different from events required for T cell activation, NK cell activation is governed by the interaction of NK receptors with target cells, independent of antigen processing and presentation. Due to relatively unsophisticated cues for activation, NK cell has gained significant attention in the field of cancer immunotherapy. Many efforts are emerging for developing and engineering NK cell-based cancer immunotherapy. In this review, we provide our current understandings of NK cell biology, ongoing pre-clinical and clinical development of NK cell-based therapies and discuss the progress, challenges, and future perspectives.
Effectiveness of a Nurse-Led Multidisciplinary Intervention vs Usual Care on Advance Care Planning for Vulnerable Older Adults in an Accountable Care Organization
Authors: Jennifer Gabbard, Nicholas M. Pajewski, Kathryn E. Callahan, Ajay Dharod, Kristie L. Foley, Keren Ferris, Adam Moses, James Willard, Jeff D. Williamson
Journal: JAMA Internal Medicine (2021)

Advance care planning (ACP), especially among vulnerable older adults, remains underused in primary care. Additionally, many ACP initiatives fail to integrate directly into the electronic health record (EHR), resulting in infrequent and disorganized documentation.To determine whether a nurse navigator-led ACP pathway combined with a health care professional-facing EHR interface improves the occurrence of ACP discussions and their documentation within the EHR.This was a randomized effectiveness trial using the Zelen design, in which patients are randomized prior to informed consent, with only those randomized to the intervention subsequently approached to provide informed consent. Randomization began November 1, 2018, and follow-up concluded November 1, 2019. The study population included patients 65 years or older with multimorbidity combined with either cognitive or physical impairments, and/or frailty, assessed from 8 primary care practices in North Carolina.Participants were randomized to either a nurse navigator-led ACP pathway (n = 379) or usual care (n = 380).The primary outcome was documentation of a new ACP discussion within the EHR. Secondary outcomes included the usage of ACP billing codes, designation of a surrogate decision maker, and ACP legal form documentation. Exploratory outcomes included incident health care use.Among 759 randomized patients (mean age 77.7 years, 455 women [59.9%]), the nurse navigator-led ACP pathway resulted in a higher rate of ACP documentation (42.2% vs 3.7%, P < .001) as compared with usual care. The ACP billing codes were used more frequently for patients randomized to the nurse navigator-led ACP pathway (25.3% vs 1.3%, P < .001). Patients randomized to the nurse navigator-led ACP pathway more frequently designated a surrogate decision maker (64% vs 35%, P < .001) and completed ACP legal forms (24.3% vs 10.0%, P < .001). During follow-up, the incidence of emergency department visits and inpatient hospitalizations was similar between the randomized groups (hazard ratio, 1.17; 95% CI, 0.92-1.50).A nurse navigator-led ACP pathway integrated with a health care professional-facing EHR interface increased the frequency of ACP discussions and their documentation. Additional research will be required to evaluate whether increased EHR documentation leads to improvements in goal-concordant care.ClinicalTrials.gov Identifier: NCT03609658.
Abstract 12128: Frailty in Patients With Heart Failure May be Caused by Catabolic Anabolic Imbalance and Ventricular Vascular Stiffening
Authors: Tatsuji Kono, Akiko Soyama, Kaoru Otsuka, Tomohiro Matsuoka, Shogo Murakami
Journal: Circulation (2017)

Background: Frailty is common in older adults with heart failure (HF), with a recent study suggesting it may be present in ≥ 70% of patients with HF and ≥ 80 years of age. The aim of this study was...
A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection
Authors: Cornelia Blume, Claire L. Jackson, Cosma Mirella Spalluto, Jelmer Legebeke, Liliya Nazlamova, Franco Conforti, Jeanne-Marie Perotin, Martin Frank, John Butler, Max Crispin, Janice Coles, James Thompson, Robert A. Ridley, Lareb S. N. Dean, Matthew Loxham, Stephanie Reikine, Adnan Azim, Kamran Tariq, David A. Johnston, Paul J. Skipp, Ratko Djukanovic, Diana Baralle, Christopher J. McCormick, Donna E. Davies, Jane S. Lucas, Gabrielle Wheway, Vito Mennella
Journal: Nature Genetics (2021)
The Leeds Risk Profile Predicts Outcome for Older Myeloma Patients: A Prognostic Score Using Frailty Biomarkers Derived and Tested Using 2371 Clinical Trial Patients
Authors: Gordon Cook, Kara-Louise Royle, Charlotte Pawlyn, Anna Hockaday, Walter M Gregory, J Anthony Child, Faith E Davies, Gareth J. Morgan, David Cairns, Graham Jackson
Journal: Blood (2017)
XPO1 Inhibition Targets Transcriptional Vulnerability of FLT3-ITD+D835 Double Mutant AML through p53 Accumulation and Inhibition of Oncogenic Transcription Factors: Lesson Learned from Cage Sequencing of Primary AML Cells
Authors: Kotoko Yamatani, Yoko Tabe, Kazumasa Sekihara, Haeun Yang, Kaori Saito, Weiguo Zhang, Kazuho Ikeo, Sonoko Kinjo, Kaoru Mogushi, Masaki Hosoya, Yoshihide Hayashizaki, Yasunari Yamanaka, Hironori Harada, Takashi Miida, Marina Konopleva, Michael Andreeff
Journal: Blood (2017)
Beyond Age—Improvement of Prognostication Through Physical and Cognitive Functioning for Nursing Home Residents With COVID-19
Authors: Márlon Juliano Romero Aliberti, Thiago Junqueira Avelino-Silva
Journal: JAMA Internal Medicine (2021)

Orestis A. Panagiotou, MD, PhD; Cyrus M. Kosar, MA; Elizabeth M. White, PhD, APRN; Leonidas E. Bantis, PhD; Xiaofei Yang, ScM; Christopher M. Santostefano, BSN, RN; Richard A. Feifer, MD, MPH; Carolyn Blackman, MD; James L. Rudolph, MD; Stefan Gravenstein, MD, MPH; Vincent Mor, PhD
CXCL12-mediated HOXB5 overexpression facilitates Colorectal Cancer metastasis through transactivating CXCR4 and ITGB3
Authors: Weibo Feng, Wenjie Huang, Jie Chen, Chenyang Qiao, Danfei Liu, Xiaoyu Ji, Meng Xie, Tongyue Zhang, Yijun Wang, Mengyu Sun, Dean Tian, Daiming Fan, Yongzhan Nie, Kaichun Wu, Limin Xia
Journal: Theranostics (2021)

Background: Metastasis is the major reason for the high mortality of colorectal cancer (CRC). However, the molecular mechanism underlying CRC metastasis remains unclear. Here, we report a novel role of homeobox B5 (HOXB5), a member of the HOX family, in promoting CRC metastasis. Method: The expression of HOXB5 and its target genes were examined by immunohistochemistry in human CRC. Chromatin immunoprecipitation and luciferase reporter assays were performed to measure the transcriptional regulation of target genes by HOXB5. The metastatic capacities of CRC cells were evaluated by in vivo lung and liver metastatic models. Results: The elevated expression of HOXB5 was positively correlated with distant metastasis, higher AJCC stage, and poor prognosis in CRC patients. HOXB5 expression was an independent and significant risk factor for the recurrence and survival in CRC patients. Overexpression of HOXB5 promoted CRC metastasis by transactivating metastatic related genes, C-X-C motif chemokine receptor 4 (CXCR4) and integrin subunit beta 3 (ITGB3). C-X-C motif chemokine ligand 12 (CXCL12), which is the ligand of CXCR4, upregulated HOXB5 expression through the extracellular regulated protein kinase (ERK)/ETS proto-oncogene 1, transcription factor (ETS1) pathway. The knockdown of HOXB5 decreased CXCL12-enhanced CRC metastasis. Furthermore, AMD3100, a specific CXCR4 inhibitor, significantly suppressed HOXB5-mediated CRC metastasis. HOXB5 expression was positively correlated with CXCR4 and ITGB3 expression in human CRC tissues, and patients with positive co-expression of HOXB5/CXCR4, or HOXB5/ITGB3 exhibited the worst prognosis. Conclusion: Our study implicates HOXB5 as a prognostic biomarker in CRC, and defines a CXCL12-HOXB5-CXCR4 positive feedback loop that plays an important role in promoting CRC metastasis.
PATH01.02 Diagnostic and Economic Value of Liquid vs. Solid Tissue Biopsy Procedures for the Detection of Targetable Mutations in Non-Small Cell Lung Cancer (NSCLC) Tumors: A Literature Review
Authors: Y. Zheng, H. Vioix, F.X. Liu, B. Singh, S. Sharma, D. Sharda
Journal: Journal of Thoracic Oncology (2021)
Evaluating Alzheimer Disease With Flortaucipir and Florbetapir PET
Authors: Olga G. James, Alexandra R. Linares, Caroline Hellegers, P. Murali Doraiswamy, Terence Z. Wong
Journal: Clinical Nuclear Medicine (2021)

Abstract Early, accurate diagnosis of Alzheimer disease (AD) is essential but remains challenging. Neuropathological hallmarks of AD are β-amyloid neuritic plaques and tau protein neurofibrillary tangles. 18 F-Florbetapir is one of several available PET tracers for imaging cortical fibrillary β-amyloid plaques. 18 F-Flortaucipir PET was recently approved for evaluating the distribution and density of aggregated neurofibrillary tangles. We present cases of mild cognitive impairment or suspected AD to depict the nuances of flortaucipir distribution and scan interpretation as well as how combined information from amyloid and tau PET may help with differential diagnosis and prognosis.
Abstract 14870: The Evaluation of Global Longitudinal Strain and the Ratio of Early Mitral Inflow Velocity to Global Longitudinal Strain Rate in Patients With Heart Failure With Preserved Ejection Fraction Treated by Sodium-Glucose Cotransporter 2 Inhibitors
Authors: Takaaki Sakai, Shinichiro Miura
Journal: Circulation (2018)

Hypothesis: Treatment with sodium-glucose cotransporter 2 (SGLT2) inhibitors may improve left ventricular (LV) diastolic function and endothelial function in patients with heart failure with preser...
MO01.36 Afatinib in Asian and Non-Asian Patients (pts) with EGFR Mutation-Positive (EGFRm+) NSCLC Harboring Major Uncommon Mutations
Authors: J. Chih-Hsin Yang, M. Schuler, S. Popat, S. Miura, S. Heeke, A. Passaro, F. de Marinis, K. Park, E.S. Kim
Journal: Journal of Thoracic Oncology (2021)
Should all patients with an acute myocardial infarction present to a hospital with revascularization capabilities?: The evidence is mounting that they need not**Editorials published in the Journal of the American College of Cardiology reflect the views of the authors and do not necessarily represent the views of JACC or the American College of Cardiology.
Authors: Vladimir Džavík, Jean-L.uçien Rouleau
Journal: Journal of the American College of Cardiology (2002)