tbuckley/cabot-search huggingface dataset:
Abstract LB-267: Detection of lung cancer by metabolomics of exhaled breath and machine learning
Authors: Mantang Qiu, Hang Li, Shushi Meng, Qingyun Li, Zuli Zhou, Jun Wang
Journal: Cancer Research (2020)

Abstract Background: Exhaled breath-based test is an attractive option for cancer detection due to it is non-invasive and feasible nature. Here, we reported an effective approach to detect early-stage lung cancer (LC) by integration of metabolomics of exhaled breath and machine learning. Methods: Healthy controls (HC) were adults who received low-dose CT for annual physical examination with no calcified pulmonary nodules and without history of cancer within 5 years. Treatment-naïve LC patients without history of cancer were enrolled. Exhaled breath samples of LC patients were collected before surgery. Exhaled breath samples were collected and stored in Tedla bags and detected by a high-pressure photon ionization time-of-flight mass spectrometry (HPPI-TOFMS). A CO2 sensor was applied during exhaled breath collection to ensure only “alveolar air” was collected. Detection model construction and feature selection were performed by support vector machine (SVM). Results: Firstly, an exploratory cohort of 119 HC and 118 LC was set up. Exhaled breath samples were directly detected by HPPI-TOFMS and 32500 features were extracted from each sample. 22 features were selected and subjected to SVM to construct detection model in the exploratory cohort, which was randomly divided into training (n=159) and test (n=78) set. This model achieved a sensitivity of 89.74%, specificity of 92.31%, and accuracy of 89.74% in the test set, suggesting exhaled breath is accurate for LC detection. Secondly, a quantitative detection method was established by introducing mixed internal standard gas at 15 mL/min controlled by a mass flow meter, by which individual violate organic compound could be quantified. Then, a prospective cohort of 53 LC and 129 HC was set up and detected by the quantitative method. For mass spectrometry data with inner standard gas, 21 features were selected by SVM. Similarly, the prospective cohort was randomly divided into training (n=122) and test (n=60) set. The 21 features-based quantified model was trained and tested in the prospective cohort and achieved a sensitivity of 88.24%, specificity of 100%, and accuracy of 96.67% in the test dataset. Conclusions: Exhaled breath with machine learning is a highly accurate approach for early-stage LC detection and inner standard gas could improve detection performance. Citation Format: Mantang Qiu, Hang Li, Shushi Meng, Qingyun Li, Zuli Zhou, Jun Wang. Detection of lung cancer by metabolomics of exhaled breath and machine learning [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-267.
Recovery of endoscopy services in the era of COVID-19: recommendations from an international Delphi consensus
Authors: Pradeep Bhandari, Sharmila Subramaniam, Michael J Bourke, Asma Alkandari, Philip Wai Yan Chiu, James F Brown, Rajesh N Keswani, Raf Bisschops, Cesare Hassan, Gottumukkala S Raju, V Raman Muthusamy, Amrita Sethi, Gary R May, Eduardo Albéniz, Marco Bruno, Michal Filip Kaminski, Maryam Alkhatry, Majid Almadi, Mostafa Ibrahim, Fabian Emura, Eduardo Moura, Claudio Navarrete, Adolfo Wulfson, Christopher Khor, Ryan Ponnudurai, Haruhiro Inoue, Yutaka Saito, Naohisa Yahagi, Sergey Kashin, Evgeniy Nikonov, Honggang Yu, Amit P Maydeo, D Nageshwar Reddy, Michael B Wallace, Mark Bennett Pochapin, Thomas Rösch, Prateek Sharma, Alessandro Repici
Journal: Gut (2020)

The COVID-19 pandemic has had a profound impact on provision of endoscopy services globally as staff and real estate were repurposed. As we begin to recover from the pandemic, a cohesive international approach is needed, and guidance on how to resume endoscopy services safely to avoid unintended harm from diagnostic delays. The aim of these guidelines is to provide consensus recommendations that clinicians can use to facilitate the swift and safe resumption of endoscopy services. An evidence-based literature review was carried out on the various strategies used globally to manage endoscopy during the COVID-19 pandemic and control infection. A modified Delphi process involving international endoscopy experts was used to agree on the consensus statements. A threshold of 80% agreement was used to establish consensus for each statement. 27 of 30 statements achieved consensus after two rounds of voting by 34 experts. The statements were categorised as pre-endoscopy, during endoscopy and postendoscopy addressing relevant areas of practice, such as screening, personal protective equipment, appropriate environments for endoscopy and infection control precautions, particularly in areas of high disease prevalence. Recommendations for testing of patients and for healthcare workers, appropriate locations of donning and doffing areas and social distancing measures before endoscopy are unique and not dealt with by any other guidelines. This international consensus using a modified Delphi method to produce a series of best practice recommendations to aid the safe resumption of endoscopy services globally in the era of COVID-19.
Abstract 14156: Impact of Concomitant Tricuspid Regurgitation on Long Term Outcomes in Patients With Severe Aortic Stenosis
Authors: Masashi Amano, Chisato Izumi, Makoto Miyake, Tomohiko Taniguchi, Takeshi Morimoto, Shunsuke Nishimura, Maiko Muroda, Takeshi Harita, Suguru Nishiuchi, Jiro Sakamoto, Yodo Tamaki, Soichiro Enomoto, Toshihiro Tamura, Hirokazu Kondo, Yoshihisa Nakagawa, Takeshi Kimura
Journal: Circulation (2017)

Introduction: Tricuspid regurgitation (TR) is a common echocardiographic finding and it is well known that increasing TR severity is associated with worse survival in patients with cardiac disease....
FRI0129 Lupus and pure red cell aplasia
Authors: GS Habib, W Saliba, P Froom
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> Pure Red CEll Aplasia (PRCA) is characterised by normochromic normocytic anaemia, reticulocytopenia and aplasia or severe hypoplasia of the red cell line with normal white cell and megakaryocyte lines in the bone marrow.<sup>1</sup> PRCA may be associated with other conditions,<sup>2</sup> but the association with systemic lupus erythematosus (SLE) is rare. Here we summarise our case and the previous cases of PRCA and SLE reported in the English literature. <h3>Objectives</h3> To evaluate the clinical and laboratory features of all the patients reported with both SLE and PRCA. <h3>Methods</h3> In addition to case, cases were identified from the English literature through a search using the Medline from the year 1966 till December 2000, and also through references of relevant publications. <h3>Results</h3> Twenty-four cases, including our case were identified. The association between SLE and PRCA is relatively rare. However it may be underdiagnosed. In most of the cases SLE was diagnosed prior to or concomitantly with the diagnosis of PRCA. The clinical and laboratory features relevant to SLE in our patients are similar to the general patients of SLE, except for significantly less pleuritis and a trend for less nephritis, hallucinations, thrombopenia and leukopenia. Most of the patients had no clinical or laboratory activity at the time of PRCA diagnosis. In some patients as in the general patients with PRCA, inhibitory effect of the patient's serum against erythroid progenitor cells and against erythropoietin (EPO) were identified. In most of the patients PRCA responded to corticosteroid (CS) treatment, and in some of the non-responders other modalities of treatment like intravenous gammaglobulins and even EPO were helpful. <h3>Conclusion</h3> The association between PRCA and SLE is relatively rare. The clinical and laboratory features relevant to SLE in our patients are similar to the general patients with SLE, and the spectrum of inhibitory effect on the erythroid progenitor cells and EPO are similar to the general patients with PRCA. Most patients had favourable response to CS treatment. <h3>References</h3> Schmid JR, Kiely JM, Pease GL, Hargraves MM. Acquired pure red cell aplasia. Acta Haematol. 1963;30:325 Amus SS, Yunis AA. Aqcuired pure red cell aplasia. Am J Med. 1987;24:311–26
Abstract 12934: Aggressive Stent Sizing Can Avoid Stent Under-Expansion: An Optical Coherence Tomography Analysis
Authors: Yutaka Matsuhiro, Masami Nishino, Yasuyuki Egami, Ryu Shutta, Jun Tanouti
Journal: Circulation (2019)

Background: Stent under-expansion remains a concern as a cause of target lesion failure. Optical coherence tomography (OCT) guided percutaneous coronary intervention (PCI) has become popular, but t...
Improved Detection of Abnormal Glucose Tolerance in Africans: The Value of Combining Hemoglobin A1c With Glycated Albumin
Authors: Arsene F. Hobabagabo, Nana H. Osei-Tutu, Thomas Hormenu, Elyssa M. Shoup, Christopher W. DuBose, Lilian S. Mabundo, Joon Ha, Arthur Sherman, Stephanie T. Chung, David B. Sacks, Anne E. Sumner
Journal: Diabetes Care (2020)

OBJECTIVE In African-born Blacks living in America, we determined by BMI category 1) prevalence of abnormal glucose tolerance (Abnl-GT) and 2) diagnostic value and reproducibility of hemoglobin A1c (HbA1c), fructosamine, and glycated albumin (GA). RESEARCH DESIGN AND METHODS Participants (n = 416; male, 66%; BMI 27.7 ± 4.5 kg/m2 [mean ± SD]) had an oral glucose tolerance test with HbA1c, GA, and fructosamine assayed. These glycemic markers were repeated 11 ± 7 days later. Abnl-GT diagnosis required 0 h ≥5.6 mmol/L (≥100 mg/dL) and/or 2 h ≥7.8 mmol/L (≥140 mg/dL). Thresholds for HbA1c, GA, and fructosamine were the values at the 75th percentile for the population (39 mmol/mol [5.7%], 14.2%, and 234 μmol/L, respectively). RESULTS Abnl-GT prevalence in the nonobese was 34% versus 42% in the obese (P = 0.124). Reproducibility was excellent for HbA1c and GA (both κ ≥ 0.8), but moderate for fructosamine (κ = 0.6). Focusing on HbA1c and GA in the nonobese, we found as single tests the sensitivities of HbA1c and GA were 36% versus 37% (P = 0.529). Combining HbA1c and GA, sensitivity increased to 58% because GA identified 37% of Africans with Abnl-GT not detected by HbA1c (P value for both tests vs. HbA1c alone was &amp;lt;0.001). For the obese, sensitivities for HbA1c, GA, and the combined tests were 60%, 27%, and 67%, respectively. Combined test sensitivity did not differ from HbA1c alone (P = 0.25) because GA detected only 10% of obese Africans with Abnl-GT not detected by HbA1c. CONCLUSIONS Adding GA to HbA1c improves detection of Abnl-GT in nonobese Africans.
Abstract 309: Mapping oncogenic signal transduction in PKA-driven cancers
Authors: Gary Kwan Leung Chan, Samantha M. Maisel, Y. Christina Hwang, Rebecca Wolber, Danielle L. Swaney, Nabeel Bardeesy, John D. Gordan
Journal: Cancer Research (2020)

Abstract Protein Kinase A (PKA) is a major effector of cyclic-AMP (cAMP) signaling and has recently been appreciated to play a role in multiple malignancies. Mutations of its catalytic subunit (PRKACA) have been identified in a substantial proportion of adrenocortical tumors, and are also detected in a wide spectrum of tumor types in the TCGA dataset, although at a low frequency. A unique fusion protein of PRKACA and DNAJB1 is seen in the majority of fibrolamellar liver cancers (FLC), a rare malignancy of young adults, where it is suspected to be the primary oncogenic driver. However, the key effectors of oncogenic signaling in FLC and other PRKACA driven cancers remain unknown. To understand PKA's downstream targets, we generated genetic cell models with doxycycline-inducible PRKACA or its dominant negative counterpart, a mutant form of the PRKAR1A regulatory subunit. These cell models were then subjected to mass spectrometry for kinome profiling in order to detect kinases with significant altered activity following PKA modulation. This was integrated with small molecule inhibition and siRNA knockdown to identify PKA-regulated kinases that impact cell proliferation. Our analysis revealed activation of the aurora-family kinase AURKA, with preferential sensitivity to the confirmation-disrupting AURKA inhibitor (CD-AURKAi) CD532 compared to other AURKA inhibitors. CD-AURKAi not only selectively inhibit AURKA's kinase activity, but also disrupt its interaction with MYC-family transcription factors. These key oncogenic mediators are necessary to drive the proliferation of multiple tumor types, although they have not yet been connected with oncogenic PKA signaling. Our follow up quantitative PCR experiments confirm that CD-532 treatment results in reduced expression of MYC family members and their transcriptional targets. We next confirmed that MYC family members support the proliferation of PKA-driven cell models with live cell imaging. Finally, we have begun to investigate other kinases identified in our siRNA screen for potential effects on MYC, and have identified several potential combination partners to augment the activity of CD-532 and other CD-AURKAi. These data suggest that CD-AURKAi, either alone or in combination, have the potential to serve as therapeutic agents for PKA-driven cancers. Citation Format: Gary Kwan Leung Chan, Samantha M. Maisel, Y. Christina Hwang, Rebecca Wolber, Danielle L. Swaney, Nabeel Bardeesy, John D. Gordan. Mapping oncogenic signal transduction in PKA-driven cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 309.
Recapitulation of cartilage/bone formation using iPSCs via biomimetic 3D rotary culture approach for developmental engineering
Authors: Maolin Zhang, Junfeng Shi, Ming Xie, Jin Wen, Kunimichi Niibe, Xiangkai Zhang, Jiaxin Luo, Ran Yan, Zhiyuan Zhang, Hiroshi Egusa, Xinquan Jiang
Journal: Biomaterials (2020)
Chilblains and COVID‐19: why SARS‐CoV‐2 endothelial infection is questioned. Reply from the authors
Authors: I. Colmenero, C. Santonja, M. Alonso‐Riaño, D. Andina, J.L. Rodríguez‐Peralto, L. Requena, A. Torrelo
Journal: British Journal of Dermatology (2020)

Linked Articles: Baeck et al. Br J Dermatol 2020; 183:1152–1153. Colmenero et al. Br J Dermatol 2020; 183:729–737
Normalization of Preexposure Prophylaxis for Adolescents
Authors: Jessica Londeree Saleska, Sung-Jae Lee
Journal: JAMA Pediatrics (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Cardiovascular outcomes trials with incretin-based medications: a critical review of data available on GLP-1 receptor agonists and DPP-4 inhibitors
Authors: Alexandros Sachinidis, Dragana Nikolic, Anca Pantea Stoian, Nikolaos Papanas, Omer Tarar, Ali A. Rizvi, Manfredi Rizzo
Journal: Metabolism (2020)
During the COVID-19 Pandemic, Lung Specialists of the World Implore You: Inhale Only Clean Air
Authors: Lekshmi Santhosh, Abdullah Alismail, Anna Breiburg, Graham Carlos, Shazia Jamil
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

"During the COVID-19 Pandemic, Lung Specialists of the World Implore You: Inhale Only Clean Air." American Journal of Respiratory and Critical Care Medicine, 202(6), pp. P19–P20
Activated Protein Phosphatase 2A Disrupts Nutrient Sensing Balance Between Mechanistic Target of Rapamycin Complex 1 and Adenosine Monophosphate–Activated Protein Kinase, Causing Sarcopenia in Alcohol‐Associated Liver Disease
Authors: Gangarao Davuluri, Nicole Welch, Jinendiran Sekar, Mahesha Gangadhariah, Khaled Alsabbagh Alchirazi, Maradumane L. Mohan, Avinash Kumar, Sashi Kant, Samjhana Thapaliya, McKenzie Stine, Megan R. McMullen, Rebecca L. McCullough, George R. Stark, Laura E. Nagy, Sathyamangla V. Naga Prasad, Srinivasan Dasarathy
Journal: Hepatology (2020)

Background and Aims Despite the high clinical significance of sarcopenia in alcohol‐associated cirrhosis, there are currently no effective therapies because the underlying mechanisms are poorly understood. We determined the mechanisms of ethanol‐induced impaired phosphorylation of mechanistic target of rapamycin complex 1 (mTORC1) and adenosine monophosphate–activated protein kinase (AMPK) with consequent dysregulated skeletal muscle protein homeostasis (balance between protein synthesis and breakdown). Approach and Results Differentiated murine myotubes, gastrocnemius muscle from mice with loss and gain of function of regulatory genes following ethanol treatment, and skeletal muscle from patients with alcohol‐associated cirrhosis were used. Ethanol increases skeletal muscle autophagy by dephosphorylating mTORC1, circumventing the classical kinase regulation by protein kinase B (Akt). Concurrently and paradoxically, ethanol exposure results in dephosphorylation and inhibition of AMPK, an activator of autophagy and inhibitor of mTORC1 signaling. However, AMPK remains inactive with ethanol exposure despite lower cellular and tissue adenosine triphosphate, indicating a “pseudofed” state. We identified protein phosphatase (PP) 2A as a key mediator of ethanol‐induced signaling and functional perturbations using loss and gain of function studies. Ethanol impairs binding of endogenous inhibitor of PP2A to PP2A, resulting in methylation and targeting of PP2A to cause dephosphorylation of mTORC1 and AMPK. Activity of phosphoinositide 3‐kinase‐γ (PI3Kγ), a negative regulator of PP2A, was decreased in response to ethanol. Ethanol‐induced molecular and phenotypic perturbations in wild‐type mice were observed in PI3Kγ−/− mice even at baseline. Importantly, overexpressing kinase‐active PI3Kγ but not the kinase‐dead mutant reversed ethanol‐induced molecular perturbations. Conclusions Our study describes the mechanistic underpinnings for ethanol‐mediated dysregulation of protein homeostasis by PP2A that leads to sarcopenia with a potential for therapeutic approaches by targeting the PI3Kγ‐PP2A axis.
An Instagram initiative for medical school applicants
Authors: Ayesha N Ahmed, Nawal Zia, Halimah Khalil, Adeolu Banjoko, Kirsty Morrison, Alexander Lawson, Vaibhi Dua, Pratyusha Saha
Journal: BMJ (2020)

The covid-19 pandemic has presented unique challenges to medical school applicants.1 These changes have particularly affected students from widening access backgrounds—that is, young people from under-represented groups such as those of a lower socioeconomic …
Abstract 15394: Visceral Adiposity is Increased in Patients With Heart Failure With Preserved Ejection Fraction
Authors: Wendy Ying, Kavita Sharma, Vinita Subramanya, Stephen J Dvorak, Megan E Bach, Sahar Soleimanifard, Dhananjay Vaidya, Erin D Michos, Sanjiv J Shah, Allison Hays
Journal: Circulation (2018)

Background: Obesity and body composition abnormalities are common in heart failure with preserved ejection fraction (HFpEF) and are associated with adverse cardiovascular outcomes. Accumulation of ...
Abstract 10079: Socioeconomic Status and the Development of Atrial Fibrillation in Hispanics, African Americans and non-Hispanic Whites
Authors: Eric Shulman, Philip Aagaard, Faraj Kargoli, Ethan Hoch, Scott Schafler, Luigi Di Biase, John D Fisher, Jay N Gross, Soo G Kim, Kevin J Ferrick, Andrew Krumerman
Journal: Circulation (2015)

Introduction: Atrial fibrillation (AF) is the most common arrhythmia and is associated with significant morbidity and mortality. Despite having a higher burden of traditional AF risk factors, African American and Hispanic minorities have a lower incidence of AF when compared to non-Hispanic Whites, referred to as the “racial paradox.” Hypothesis: We investigated if socioeconomic status (SES) could be an explanatory factor for the “racial paradox.” Methods: An ECG/EMR database from a tertiary-care center in New York State was interrogated for individuals free of AF for development of subsequent AF from 2000-2013. SES was assessed per zip code via a log composite of six measures Z-scored to the New York State average (income; value of housing unit; percentage of receiving interest/dividend/rental income; education; percentage completed college; individuals in professional positions). SES was reclassified into decile groups (1 lowest and 10 highest). The Log-Rank test was used to determine difference in survival times to develop AF by race/ethnicity stratified by SES decile. Cox regression analysis controlling for all baseline differences was used to estimate the independent predictive ability of SES for AF. P-trend was calculated by race/ethnicity to determine if there was a trend by SES decile to develop AF. Results: We identified 48,631 persons (43% Hispanic, 37% African Americans and 20% non-Hispanic White, mean age 59 years, mean follow-up of 3.2 years) of which 4,556 AF cases occurred. Hispanics and African Americans had lower AF risk than Whites in all SES deciles (p-value &lt; 0.001 by Log Rank Test). Higher SES was borderline associated with lower AF risk (HR=0.990, 95% CI 0.980-1.001, p=0.061). P-trend analysis was not significant by any race/ethnic group by SES deciles for AF (Figure 1). Conclusions: Our study suggests that non-Hispanic Whites are at higher risk for AF compared to non-Whites, and this is independent of socioeconomic status.