tbuckley/cabot-search huggingface dataset:
Histology differentiation in non-small cell lung cancer using matrix-assisted laser desorption/ionization mass spectrometry.
Authors: Jun Won Park, Geon Kook Lee, Hee Seok Lee, Jae Ill Zo, Young Hwan Kim, Kwang Pyo Kim, Hark K. Kim
Journal: Journal of Clinical Oncology (2012)

e21043 Background: New developments in the treatment of lung cancer have necessitated the correct histologic differentiation between two major histologic types of NSCLC. Methods: Histology-directed tissue matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of common solid tumors. In this approach, mass spectra are obtained from discrete locations on the thin sections of frozen tissues sections. In this study, we evaluated various MALDI MS protocols for the histopathologic classification of NSCLC. Results: When adenocarcinoma and squamous cell carcinoma biopsy samples were compared for protein profile using standard sinapinic acid matrix, the median prediction accuracy of the best histology classifier in test sets was 83.3% in 100 random training-to-test partitions (feature selection P &lt;0.05). When 2,5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid matrices were used for lipid MALDI MS, the median prediction accuracy of the best histology classifier in test sets was 85.7% in 100 random partitions (feature selection P&lt;0.01). We then validated the discriminatory lipid profile using independent set of 51 NSCLC surgical samples. Eleven discriminatory lipids correctly classified the histology of 80.4% of independent NSCLC surgical tissue samples (41 out of 51) in validation set. Phosphatidylcholine 32:0 (m/z 756.68) was overexpressed in adenocarcinomas. Conclusions: Due to the small amount of tissue required for MALDI analysis, rapid experimental procedure, and high predictive values documented in this study, histology-directed MALDI MS, especially lipid profiling, may be a promising approach to the histologic classification of NSCLC (This work was supported by Converging Research Center Program through the Ministry of Education, Science and Technology of Korea (2010K001121)).
Relationship of <i>CUL4A </i>gene underexpression and prognosis in localized high-risk soft tissue sarcoma (STS) patients of limbs or trunk wall.
Authors: Javier Martin Broto, Antonio Lopez-Pousa, Rafael Ramos, Alessandro Gronchi, Paolo Giovanni Casali, Antonio Gutierrez, Piero Picci, Stefano Ferrari, Josefina Cruz, Pablo Luna Fra, Antonio Casado, Ricardo Cubedo, Roberto Lasso, Andres Poveda, Ana De Juan, Carmen Balana, Silvia Calabuig, Antonia Obrador, Jose Antonio Lopez-Guerrero
Journal: Journal of Clinical Oncology (2012)

10079 Background: Genes involved in cell cycle checkpoints and chromosome stability seem to be relevant in distant metastases appearance in STS. CUL4A is an E3 ubiquitin ligase that has been related to both p16 activation and maintenance of genomic stability. Expression of CUL4A has been scarcely described in some tumors with divergent outcome and there are no publications regarding its expression in STS patients. We previously showed that protein underexpression of CUL4A in metastatic STS was related to poor survival. Methods: The expression level of CUL4A was determined by quantitative qPCR and was retrospectively performed in a subset of 39 high-risk (grade 3, deep tumours and &gt; than 5 cm) localized STS of limbs or trunk wall patients for which histological material and clinical data were available. Patients of this series were enrolled prospectively into a randomized clinical trial conducted by the Italian and Spanish sarcoma groups (ISG-GEIS 0101) comparing 3 vs 5 cycles of epirrubicin and ifosfamide. Differences in PFS, RFS, and OS were calculated using log-rank test Results: The median age was 51 years with a median follow-up of 52 months. The pathologic subtypes were undifferentiated pleomorphic sarcoma (35.3%), synovial sarcoma (23.5%) and mixed subtypes (41.2%). Location was distributed as inferior limbs (66.6%), upper limbs (25.5%) and trunk wall (7.9%). No relationship was seen between CUL4A expression and clinical variables (histologic types, location, size or response to neoadjuvant treatment). The expression level of CUL4A was significantly associated with events of progression, 65% vs 32%, p =0.037, for expression values under and over the median respectively. Regarding 4 y actuarial survival, there was a significant worse PFS and RFS for patients underexpressing CUL4A (p=0.041 and 0.009 respectively) and a trend towards worse OS (p=0.056). Conclusions: Expression of CUL4A gene shows a prognostic role in sarcomas within this high risk localized subset of STS patients. The outcome of this exploratory analysis is aligned with our hypothesis that genes implicated in cell cycle regulation and chromosome stability could play a relevant prognostic role in STS.
FACTORS THAT INFLUENCE BEMPEDOIC ACID-MEDIATED REDUCTIONS IN HIGH-SENSITIVITY C-REACTIVE PROTEIN: ANALYSIS OF POOLED PATIENT-LEVEL DATA FROM PHASE 3 CLINICAL TRIALS
Authors: Erik S. G Stroes, Harold Bays, Maciej Banach, Alberico Catapano, P. Barton Duell, Ulrich Laufs, G.B. John Mancini, Kausik Kumar Ray, William Sasiela, Zhan Ye, Antonio M. Gotto
Journal: Journal of the American College of Cardiology (2020)
BPI20-022: Use of Cyclin Dependent Kinase 4/6 Inhibitors in Hormone Receptor Positive HER2 Negative Metastatic Breast Cancer. Experience in a Third Level Hospital in Mexico City
Authors: Benigno Emmanuel Rodriguez Soto, Lorena López Zepeda, Alejandro Noguez Ramos, Daniela Vázquez Juarez, Daniela Shveid Gerson, Yazmin Carolina Blanco Vázquez, Samuel Rivera Rivera, Alberto Villalobos Prieto, Gabriela Olivia Regalado Porras, Ivonne Salcedo Sullk, Fernando Pérez Zincer, Christian Patricio Camacho Limas, Juan Alberto Serrano Olvera, Álvaro Aguayo González, Guillermo Manuel Olivares Beltrán, Raquel Gerson Cwilich
Journal: Journal of the National Comprehensive Cancer Network (2020)

"BPI20-022: Use of Cyclin Dependent Kinase 4/6 Inhibitors in Hormone Receptor Positive HER2 Negative Metastatic Breast Cancer. Experience in a Third Level Hospital in Mexico City" published on 20 Mar 2020 by National Comprehensive Cancer Network.
COMPARISON BETWEEN HEART SCORE AND REST MYOCARDIAL PERFUSION IMAGING IN THE EVALUATION OF ACUTE CHEST PAIN AT THE EMERGENCY DEPARTMENT
Authors: Lucas Cronemberger Maia Mendes, Sebastiao L. Lacerda Filho, Heleno R. Reis, Edmur C. Araujo, Ludmilla R.A. Silva, Mariana B. Guedes, Patrícia B.M.R. Germano, Guilherme E.V. Silva, Carlos J.D.G. Barbosa
Journal: Journal of the American College of Cardiology (2020)
Performance of late pregnancy biometry for gestational age dating in low-income and middle-income countries: a prospective, multicountry, population-based cohort study from the WHO Alliance for Maternal and Newborn Health Improvement (AMANHI) Study Group
Authors: Saikat Deb, Mohammad Said Mohammed, Usha Dhingra, Arup Dutta, Syed Mohammed Ali, Pratibha Dixit, Mohammed Hamad Juma, Massoud Juma Hassan, Sunil Sazawal, Imran Nisar, Muhammad Ilyas, Usma Mehmood, Farzana Kausar, Shamim Jaweed, Muhammad Karim, Atiya Hussain, Naila Nadeem, Fyezah Jehan, Sayedur Rahman, Nasreen Islam, Ruksana Azad, Syed Mamum Ibne Moin, Mahmoodur Rahman, Salahuddin Ahmed, Abdul Quiayum, Rasheda Khanam, Abdullah H. Baqui, Sachido Yoshida, Alexander Manu, Rajiv Bahl, Anne CC Lee, Mariam Naqvi, Lauren E. Schaeffer, Rachel Whelan, Blair J. Wylie
Journal: The Lancet Global Health (2020)

We aimed to evaluate and improve the accuracy of the ultrasound scan in estimating gestational age in late pregnancy (ie, after 24 weeks' gestation) in low-income and middle-income countries (LMICs), where access to ultrasound in the first half of pregnancy is rare and where intrauterine growth restriction is prevalent.
PROSPECTIVE SINGLE CENTER EXPERIENCE OF PULMONARY EMBOLISM MANAGEMENT AND OUTCOMES IN THE ERA OF PULMONARY EMBOLISM RESPONSE TEAMS
Authors: Matthew J. Lacey, Tarek Hammad, Jun Li, Leben Tefera, Robert Schilz, Teresa Carman, Rebecca Kahl, Amanda Zemko, Mehdi Shishehbor
Journal: Journal of the American College of Cardiology (2020)
PREDICTING CARDIOVASCULAR OUTCOMES BY BASELINE LIPOPROTEIN(A) CONCENTRATIONS: A LARGE COHORT AND LONG-TERM STUDY ON REAL WORLD PATIENTS RECEIVING PCI
Authors: Hui-Hui Liu, Ye-Xuan Cao, Jing-Lu Jin, Hui-Wen Zhang, Qi Hua, Yan-Fang Li, Yuan-Lin Guo, Cheng-Gang Zhu, Na-Qiong Wu, Rui-Xia XU, Xie-Hui Chen, Jian-Jun Li
Journal: Journal of the American College of Cardiology (2020)
Charles George McEwen: visionary ophthalmologist
Authors: John Illman
Journal: BMJ (2020)

Operating microscopes have become as standard in ophthalmology as antibiotics in treating infection. But magnification in ophthalmology has a controversial history. In the 1950s and ’60s many clinicians struggling with lengthy lists complained about how long it took to use the new cumbersome devices. Not knowing what they could not see, they swore by their old fashioned loupes or magnifiers.

Charles McEwen (“Charlie”) played a prominent part in the revolution that consigned the loupe to the museum and brought the operating microscope into the clinical mainstream. He was also part of a new generation driven by the dream of making the world a better place …
Covid-19: BMA calls for rapid testing and appropriate protective equipment for doctors
Authors: Abi Rimmer
Journal: BMJ (2020)

The BMA has said that it is working to ensure that all doctors have appropriate protective equipment and that those who are self-isolating with minor respiratory symptoms have access to rapid testing.

In a letter sent to BMA members on 16 March, BMA council chair Chaand Nagpaul said that, in response to the covid-19 pandemic, the association was working to tackle the issues affecting doctors, across the nations, and in each branch of practice.

“We will all be naturally worried about how this will impact on our ability to provide vital care for patients,” Nagpaul said. “We are also concerned about the need for healthcare workers to …
What do patients with cancer think of the use of their tumor tissue for medical research?
Authors: Christos Stelios Karapetis, Rajiv Kumar, Quek Timothy, Shawgi Sukumaran, Ganessan Kichenadasse, Divyanshu Dua, Harminder Singh Takhar, Alison Richards, Kelly Mead, Marleesa Ly, Bogda Koczwara
Journal: Journal of Clinical Oncology (2013)

6541 Background: Research involving archival tumor tissue has become increasingly important in molecular oncology and has led to improved therapeutics. There are important ethical considerations for such research. We examined the attitudes of patients with cancer toward research that used their tumor tissue. Methods: From January to April 2012, consecutive patients with cancer attending the outpatient clinic of the Flinders Cancer Centre were asked to complete a 27-item investigator-developed questionnaire. The questionnaire included 4 sections: 1) demographics, 2) understanding of cancer research, 3) donation of tumor tissue and 4) ethical issues. Results: 118 patients completed the questionnaire, 53% male and mean age 61. 95% stated that they believed that research involving tumor tissue was beneficial to the public and to cancer patients in the future. 72% responded such research could have a direct benefit for them. 94% would allow their tissue to be used for future research. 86% stated that nothing would prevent them from allowing tissue research. Only14% believed that they needed to be informed about the research. Only 5% were of the opinion that the tissue still belonged to them after it had been removed from their body. 72% were not concerned where their tissue was sent for research, whilst 19% preferred that the research be conducted in Australia. When asked about the use of tissue for research after death, 10% stated that their prior approval was required, less than 1% wanted their family members to approve the research whilst 80% felt that ethics committee approval without individual consent was acceptable. Less than 1% stated that the tissue should be destroyed after death. 69% expressed a preference for the research findings to be available to everyone without commercialisation. Conclusions: The majority of patients permit the use of their tumor tissue for research with ethical approval but without the expectation of individual consent. After death, most patients did not want to have their tissue discarded and were accepting of research without the need for prior consent or family approval. We need to understand the preferences of the majority of patients in determining optimal policy for correlative tumor tissue research.
Gene expression analytics identify tissue of origin of unspecified metastatic cancers
Authors: T. Rigl, L. Buturovic, A. Pattin, Q. Tran, L. Nguyen
Journal: Journal of Clinical Oncology (2006)

20082 Background: Identification of the tissue of origin for unspecified metastatic cancers is associated with improved outcomes. To aid in determining the origin of these cancers, we designed a semi-quantitative test that uses proprietary analytics and a companion genomic microarray to compare the expression signature of a biopsy specimen with those of the following types of cancers: bladder, breast, colorectal, gastroesophageal, germ line, hepatocellular, kidney, lung, lymphoma, melanoma, ovarian, pancreatic, prostate, soft tissue-sarcoma, and thyroid. More than 5,500 human specimens processed on Affymetrix HG U133A microarrays were analyzed to determine the test’s standardization algorithm. Methods: Studies across nine different laboratories were conducted to demonstrate the reproducibility required to support the potential clinical application of the test. Biopsy specimens of 604 metastatic cancers of known origin (by conventional pathological testing) were used to “train” the algorithm. An additional 636 samples then were tested. Diagnostic odds ratio (OR), sensitivity, specificity, positive likelihood ratio (LR+), and negative likelihood ratio (LR−) were determined for individual all-against-one tests. Results: Robust standardization, which involves 121 “house-keeping genes”, enabled the tissue of origin test to demonstrate reproducibility across nine different laboratories. Identification of the correct tissue of origin was associated with OR values ranging from 23 to &gt;500, with averages for sensitivity of 83%, specificity of 99%, LR+ of 210, and LR− of 0.17. Conclusions: The PathWork Oncology Suite: Tissue of Origin (POS:TOO) test uses methods that are reproducible across laboratories. By analyzing microarray data with the POS:TOO algorithm, the test can identify the origin of metastatic tumors. Preparations for clinical validation studies are in progress and results will be submitted to FDA for clearance. [Table: see text]
Using antagonistic pleiotropy to design a chemotherapy-induced evolutionary trap to target drug resistance in cancer
Authors: Kevin H. Lin, Justine C. Rutter, Abigail Xie, Bryann Pardieu, Emily T. Winn, Reinaldo Dal Bello, Antoine Forget, Raphael Itzykson, Yeong-Ran Ahn, Ziwei Dai, Raiyan T. Sobhan, Gray R. Anderson, Katherine R. Singleton, Amy E. Decker, Peter S. Winter, Jason W. Locasale, Lorin Crawford, Alexandre Puissant, Kris C. Wood
Journal: Nature Genetics (2020)
RELATIONSHIP BETWEEN LIPOPROTEIN (A) AND GENETIC POLYMORPHISMS OF PLASMINOGEN ACTIVATOR INHIBITOR-1 WITH CORONARY ARTERY DISEASE EXTENSION, PRESENCE OF INTRACORONARY THROMBUS, ABNORMAL TIMI FLOW AND TYPE OF ACUTE CORONARY SYNDROMES
Authors: Gastón Guzmán Souto, Julio O. Bono, Eduardo Moreyra
Journal: Journal of the American College of Cardiology (2020)
VARIABLE LEFT VENTRICULAR EJECTION FRACTION ON MULTIGATED RADIONUCLIDE IMAGING ANALYZED BY DIFFERENT SOFTWARE PACKAGES IN PATIENTS WITH CANCER
Authors: Anoshia Raza, Giselle Suero-Abreu, Phillip Lim, Khyati Mehta, Hector Salcedo, Joshua Kra, Anupama Hooda-Nehra, Julius Gardin, Yiyan Liu, Marc Klapholz, Alfonso Waller
Journal: Journal of the American College of Cardiology (2020)
How safe is surgery in obese lung cancer patients?
Authors: Binod Dhakal, Sunitha Sukumaran, Rafael Santana-Davila, George Haasler, Daniel Eastwood, William Tisol, Mario Gasparri, Nicholas W. Choong
Journal: Journal of Clinical Oncology (2012)

e17555 Background: Obesity is a risk factor for increased peri-operative morbidity and mortality in surgery. There have been limited studies to correlate morbidity of lung cancer resection with obesity. Methods: We performed a retrospective study of patients who underwent surgical resection for lung cancer at the Medical College of Wisconsin from 2006 to 2010. Data on patient demographics, weight, pathology findings and hospital course were abstracted after appropriate IRB approval. Peri-operative morbidity was defined as atrial fibrillation, heart failure, respiratory failure, pulmonary embolism or any medical complications arising within 30 days after surgery. Fisher’s exact test was used to test the association between BMI and perioperative morbidities. Results: Between 2006 and 2010, 320 lung resections were performed for lung cancer. Median age was 67 (25-88) years and 185 (57.8%) were females. The body mass index (BMI) distribution was 121 (37.8%) in BMI&lt;25 and 199(62.18%) in BMI≥25. In patients with BMI &lt; 25, surgical procedures consisted 76 (23.75%) lobectomy, 38 (11.8%) wedge resection and 7 (2.18%) pneumonectomy. In patients with BMI ≥ 25, surgical procedures consisted: 131 (40.93%) lobectomy, 61 (19.06%) wedge resection and 7 (2.18%) pneumonectomy. Tumor histology was: adenocarcinoma 138 (42.9%), squamous cell cancer 107 (33.3%), bronchoalveolar 25 (7.7%), large cell 19 (5.9%) and mixed 31 (9.68%). The 30-day mortality rate was 1.8 % (6 patients), out of which only 2 had BMI ≥ 25. Peri-operative morbidity occurred in 28 (23.14%) of normal BMI patients and 47 (23.6%) of BMI ≥ 25 patients (p=0.54). Specific morbidities encountered by patients with normal vs. BMI ≥ 25 were: atrial fibrillation 11(9.09%) vs. 24(12.06%) (p=0.46), pulmonary embolism 1(0.83%) vs. 3(1.51%) (p=1.0), congestive heart failure 2(1.65%) vs. 2(1.01%) (p=0.63), respiratory failure 12(9.92%) vs. 17(8.54%) (p=0.69) and ARDS 2(1.65%) vs. 1(0.50%) (p=0.55).Median hospital stay was 5 days in lower BMI group and 4 days in BMI ≥25 groups (p=0.52). Conclusions: Potential curative surgical resections can be offered to even significantly overweight patients as there is no significant difference in the peri-operative morbidities and length of stay as compared to normal BMI patients.
CircMRPS35 suppresses gastric cancer progression via recruiting KAT7 to govern histone modification
Authors: Mengmeng Jie, Yaran Wu, Mengyuan Gao, Xinzhe Li, Cheng Liu, Qin Ouyang, Qingyun Tang, Changyu Shan, Yangfan Lv, Kebin Zhang, Qian Dai, Yang Chen, Shuo Zeng, Chenglin Li, Liting Wang, Fengtian He, Changjiang Hu, Shiming Yang
Journal: Molecular Cancer (2020)

Abstract Background Aberrant expression of circular RNAs contributes to the initiation and progression of cancers, but the underlying mechanism remains elusive. Methods RNA-seq and qRT-PCR were performed to screen differential expressed circRNAs between gastric cancer tissues and adjacent normal tissues. Candidate circRNA (circMRPS35) was screened out and validated by qRT-PCR. Cell proliferation and invasion ability were determined by CCK-8 and cell invasion assays. RNA-seq, GO-pathway, RNA pull-down and ChIRP were further applied to search for detailed mechanism. Results Here, a novel circRNA named circMRPS35, was screened out by RNA-seq in gastric cancer tissues, whose expression is related to clinicopathological characteristics and prognosis in gastric cancer patients. Biologically, circMRPS35 suppresses the proliferation and invasion of gastric cancer cells in vitro and in vivo. Mechanistically, circMRPS35 acts as a modular scaffold to recruit histone acetyltransferase KAT7 to the promoters of FOXO1 and FOXO3a genes, which elicits acetylation of H4K5 in their promoters. Particularly, circMRPS35 specifically binds to FOXO1/3a promoter regions directly. Thus, it dramatically activates the transcription of FOXO1/3a and triggers subsequent response of their downstream target genes expression, including p21, p27, Twist1 and E-cadherin, resulting in the inhibition of cell proliferation and invasion. Moreover, circMRPS35 expression positively correlates with that of FOXO1/3a in gastric cancer tissues. Conclusions Our findings not only reveal the pivotal roles of circMRPS35 in governing histone modification in anticancer treatment, but also advocate for triggering circMRPS35/KAT7/FOXO1/3a pathway to combat gastric cancer.
The use of serum interleukin-2 receptor value for diagnosis of malignant lymphoma.
Authors: Masanobu Nakata, Takahide Ara, Kanako Shima, Koichiro Minauchi, Shuichi Ota, Kiyotoshi Imai, Teiichi Hirano, Yoshio Kiyama, Naoki Kobayashi, Masahiro Imamura
Journal: Journal of Clinical Oncology (2013)

e19507 Background: Serum soluble interleukin-2 receptor (sIL2R) has been anecdotally used for diagnosis of malignant lymphoma (ML). However, sensitivity and specificity have not been evaluated; therefore, there is no consensus for the appropriate cut-off value for diagnosis of ML. Methods: We retrospectively analyzed sIL2R values at initial presentation in the patients who were diagnosed with ML. We compared them with the sIL2R values in the patients who presented with lymphadenopathy but were not diagnosed with ML. Results: In 496 patients with ML, 232 patients were diagnosed with diffuse large B-cell lymphoma (DLBCL), 109 with follicular lymphoma (FL), 40 with T-cell lymphoma (TCL), 39 with Hodgkin lymphoma (HL), 16 with marginal zone B-cell lymphoma (MZBCL), 12 with mantle cell lymphoma (MCL) and 21 with others. In the 69 control patients who did not have ML, 22 patients were diagnosed with metastatic lymph nodes of cancer, 14 with reactive lymph nodes, 12 with Kikuchi’s disease (histiocytic necrotizing lymphadenitis), 6 with granulomatous lymphadenitis (including mycobacterial infection), 3 with sarcoidosis, 2 with infectious mononucleosis (in combination with clinical diagnosis), 1 with Castleman’s disease and 9 with others. Mean value of sIL2R in the patients with ML was 4223U/ml (95% confidence interval, CI: 3251-5196). It was significantly higher than that in patients not having ML (mean: 1072U/ml, 95%CI: 788-1356, p&lt;0.0001, t-test). The sensitivity and specificity were calculated based on our results. When the cut-off value was set at 1000U/ml, sensitivity for diagnosis of ML was 64% and specificity was 68%. When the cut-off value was set at 2000U/ml, sensitivity was 41% and specificity was 86%. According to histologic subtypes, mean sIL2R values were 4592U/ml (95%CI: 3690-6088) in DLBCL, 2166U/ml (95%CI: 1669-2664) in FL, 6510U/ml (95%CI: 3692-9329) in TCL, 1395U/ml (95%CI: 550-2240) in MZBCL, 2956U/ml (95%CI: 1736-4175) in HL and 3264U/ml (95%CI: 1734-4795) in MCL. Mean sIL2R value in each histologic subtype, except for MZBCL, was significantly higher than that in patients not having ML. Conclusions: Our study suggests that sIL2R value is useful for diagnosis of ML other than MZBCL.