tbuckley/cabot-search huggingface dataset:
Epidemiology of pertussis in Denmark, 1995 to 2013
Authors: Tine Dalby, Peter Henrik Andersen, Steen Hoffmann
Journal: Eurosurveillance (2016)

We describe incidence and age distribution of laboratory-confirmed pertussis in Denmark from 1995 to 2013. Notification has been mandatory since 2007. Since 1997, an acellular monocomponent vaccine has been used. The latest epidemic occurred in 2002 with an incidence of 36 per 100,000; since 1995, only six infant deaths have been recorded. The inter-epidemic incidence lies below 10 per 100,000. In 1995, the mean age of confirmed cases was 9.2 years (95% confidence interval (CI): 7.9-10.5; median: 5.1), this gradually increased to 23.9 years in 2013 (95% CI: 22.0-25.8; median: 15.7). In 1995, 14% of laboratory-confirmed cases were 20 years and older, 43% in 2013. In the study period, the highest incidence among children was among those younger than one year with incidences between 84 and 331 per 100,000 in inter-epidemic periods (mean: 161/100,000) and 435 for the epidemic in 2002. After introduction of a preschool booster in 2003, the highest incidence among children one year and older changed gradually from three to five-year-olds in 2003 to 12 to 14-year-olds in 2013. In 2013, PCR was the primary method used for laboratory-diagnosis of pertussis in Denmark, while serology was the method with the highest percentage of positive results.
CEP-701 Is a JAK2 Inhibitor Which Attenuates JAK2/STAT5 Signaling Pathway and the Proliferation of Primary Cells from Patients with Myeloproliferative Disorders.
Authors: Pawel Dobrzanski, Elizabeth Hexner, Cynthia Serdikoff, Mahfuza Jan, Cezary Swider, Candy Robinson, Shi Yang, Thelma Angeles, Stephen G. Emerson, Martin Carroll, Bruce Ruggeri
Journal: Blood (2006)
Pathways for Oxygen Regulation and Homeostasis
Authors: William G. Kaelin, Peter J. Ratcliffe, Gregg L. Semenza
Journal: JAMA (2016)

In this Viewpoint, 2016 Lasker Award winners William Kaelin, Peter Ratcliffe, and Gregg Semenza discuss their discovery of pathways by which humans and other multicellular organisms sense and respond to changes in oxygen availability.
Differential Activation of a Mouse Estrogen Receptor <b>β</b> Isoform (mER <b>β</b> 2) with Endocrine-Disrupting Chemicals (EDCs)
Authors: Lauren J. Donoghue, Thomas I. Neufeld, Yin Li, Yukitomo Arao, Laurel A. Coons, Kenneth S. Korach
Journal: Environmental Health Perspectives (2016)

Endocrine-disrupting chemicals (EDCs) are suspected of altering estrogenic signaling through estrogen receptor (ER) α or β (mERβ1 in mice). Several EDC effects have been reported in animal studies and extrapolated to human studies. Unlike humans, rodents express a novel isoform of ERβ (mERβ2) with a modified ligand-binding domain sequence. EDC activity through this isoform remains uncharacterized.We identified the expression pattern of mERβ2 in mouse tissues and assessed the estrogenic activity of EDCs through mERβ2.mERβ2 mRNA expression was measured in mouse tissues. HepG2 cells were used to assess the transactivation activity of mERβ isoforms with EDCs and ER co-activators. 293A cells transiently transfected with mER isoforms were used to detect EDC-mediated changes in endogenous ER target gene expression.Expression of mERβ2 mRNA was detected in mouse reproductive tissues (ovary, testis, and prostate) and lung and colon tissues from both female and male mice. Five (E2, DES, DPN, BPAF, Coum, 1-BP) of 16 compounds tested by reporter assay had estrogenic activity through mERβ2. mERβ2 had a compound-specific negative effect on ERβ/ligand-mediated activity and ER target genes when co-expressed with mERβ1. mERβ2 recruited coactivators SRC2 or SRC3 in the presence of EDCs, but showed less recruitment than mERβ1.mERβ2 showed weaker estrogenic activity than mERβ1 in our in vitro system, and can dampen mERβ1 activity. In vivo models of EDC activity and ER-mediated toxicity should consider the role of mERβ2, as rodent tissue responses involving mERβ2 may not be reproduced in human biology.
Comparative Genomic Hybridization on Immunophenotypically Pure, Flow Sorted Plasmocyte Populations Shows an Improved Detection of Chromosomal Abnormalities in Monoclonal Gammopathy of Undetermined Significance and Multiple Myeloma.
Authors: Brigitte Maes, Sabine Franke, Greet Voets, Karen Hensen, Hanne Jongen, Veerle Peeters, Reinoud Cartuyvels, Greet Bries, Gregor Verhoef, Jean-Luc Rummens
Journal: Blood (2006)
An alternative novel tool for DNA editing without target sequence limitation: the structure-guided nuclease
Authors: Shu Xu, Shasha Cao, Bingjie Zou, Yunyun Yue, Chun Gu, Xin Chen, Pei Wang, Xiaohua Dong, Zheng Xiang, Kai Li, Minsheng Zhu, Qingshun Zhao, Guohua Zhou
Journal: Genome biology (2016)

Engineered endonucleases are a powerful tool for editing DNA. However, sequence preferences may limit their application. We engineer a structure-guided endonuclease (SGN) composed of flap endonuclease-1 (FEN-1), which recognizes the 3′ flap structure, and the cleavage domain of Fok I (Fn1), which cleaves DNA strands. The SGN recognizes the target DNA on the basis of the 3′ flap structure formed between the target and the guide DNA (gDNA) and cut the target through its Fn1 dimerization. Our results show that the SGN, guided by a pair of gDNAs, cleaves transgenic reporter gene and endogenous genes in zebrafish embryonic genome.
Associations Between Free Protein S and Factor VIII Levels with Traditional Arterial Thrombotic Risk Factors and Their Risk On Arterial Thrombosis. Results From a Retrospective Family Cohort Study.
Authors: René Mulder, Inge M van Schouwenburg, Bakhtawar Khan Mahmoodi, Nic J.G.M. Veeger, André B Mulder, Saskia Middeldorp, Hanneke C. Kluin-Nelemans, Willem M Lijfering
Journal: Blood (2009)
eFT508, a Potent and Selective Mitogen-Activated Protein Kinase Interacting Kinase (MNK) 1 and 2 Inhibitor, Is Efficacious in Preclinical Models of Diffuse Large B-Cell Lymphoma (DLBCL)
Authors: Kevin R. Webster, Vikas K Goel, Ivy NJ Hung, Gregory S Parker, Jocelyn Staunton, Melissa Neal, Jolene Molter, Gary G Chiang, Katti A. Jessen, Christopher J Wegerski, Samuel Sperry, Vera Huang, Joan Chen, Peggy A Thompson, James R Appleman, Stephen E Webber, Paul A Sprengeler, Siegfried H Reich
Journal: Blood (2015)
Retrospective analysis of anti-allergy prophylaxis for infusion reactions of cetuximab in head and neck cancer patients
Authors: Kiwako Ikegawa, Shinya Suzuki, Hayato Kamata, Hisanaga Nomura, Tomohiro Enokida, Tetsuro Wakasugi, Tomoko Yamazaki, Makoto Tahara, Shinichiro Saito
Journal: Annals of Oncology (2015)
Coronary ultrasound thrombolysis in acute coronary syndromes: The first 100 patients from the acolysis registry
Authors: J Fajadet, L Caleron, Moly Thomas, F Amann, Walter Desmet, F Ozman, J Gasper, R Erbel, I Hertz, G Gaul, HI Miller, U Rosenschein
Journal: Circulation (1998)
Differential response of primary cultures of breast carcinomas to lapatinib in an in vitro chemoresponse assay
Authors: L. M. Hancher, P. R. Ervin, S. L. Brower
Journal: Journal of Clinical Oncology (2009)

1115 Background: Lapatinib (Tykerb) is a small molecule tyrosine kinase inhibitor that targets the intracellular domain of the epidermal growth factor receptor and HER-2, thereby inhibiting both growth and survival signaling pathways. Lapatinib is currently FDA-approved to treat HER-2-positive breast cancer previously treated with anthracycline and taxane therapies and trastuzumab. Due to the low population response rate of lapatinib, an integrated biomarker that can identify patients with an increased likelihood for response would be of great clinical utility. The current study describes an in vitro chemoresponse assay developed to predict sensitivity and resistance of primary cultures of human breast tumor specimens to lapatinib. Methods: The chemoresponse assay (ChemoFx) for lapatinib was developed using four different immortalized carcinoma cell lines (SK-OV3, BT474, MDA-MB-231, MCF7). In addition to cell lines, the chemoresponse assay was also performed on 55 first passage primary cultures of human breast carcinomas. All cultures were confirmed to contain keratin-positive epithelial cells using fluorescence immunocytochemistry. Cell lines and specimens were treated with a 10 dose concentration range of lapatinib for 72 hours and stained with DAPI; remaining live cells were counted on an inverted fluorescent imaging system. Resulting dose-response curves were analyzed and categorized as responsive, intermediate responsive, or non-responsive using a proprietary scoring algorithm. Results: All four cell lines (BT474, MDA-MB-231, MCF7, SK-OV3) were responsive to lapatinib treatment, with EC50 values of approximately 10 uM. Dose-response curves of the 55 primary breast cultures revealed that 9% of the specimens tested were responsive to lapatinib, 15% had an intermediate response, and 76% were non-responsive. These results are consistent with a reported clinical response rate of 10% for lapatinib. Conclusions: Initial results with the described integrated cell-based assay demonstrate that in vitro chemoresponse testing may be useful in predicting patient response to lapatinib. This type of in vitro biomarker is likely to increase the efficacy of the current chemotherapy decision-making process for oncologists and their patients. No significant financial relationships to disclose.
Clinical performance of FXG: RESP (Asp+) assay for Pneumocystis jirovecii on respiratory specimens
Authors: P. Hauser, Katrien Lagrou, X. Cui, C. Lass-Florl, D. S. Perlin, S. Park, Johan Maertens, M. Hughes, P. Bowyer, D. W. Denning, J. Billie
Journal: Clinical Microbiology and Infection (2008)
Vital Signs: Disparities in Antihypertensive Medication Nonadherence Among Medicare Part D Beneficiaries — United States, 2014
Authors: Matthew Ritchey, Anping Chang, Christopher Powers, Fleetwood Loustalot, Linda Schieb, Michelle Ketcham, Jeffrey Durthaler, Yuling Hong
Journal: MMWR Morbidity and Mortality Weekly Report (2016)

Nonadherence to taking prescribed antihypertensive medication (antihypertensive) regimens has been identified as a leading cause of poor blood pressure control among persons with hypertension and an important risk factor for adverse cardiovascular disease outcomes. CDC and the Centers for Medicare and Medicaid Services analyzed geographic, racial-ethnic, and other disparities in nonadherence to antihypertensives among Medicare Part D beneficiaries in 2014.Antihypertensive nonadherence, defined as a proportion of days a beneficiary was covered with antihypertensives of <80%, was assessed using prescription drug claims data among Medicare Advantage or Medicare fee-for-service beneficiaries aged ≥65 years with Medicare Part D coverage during 2014 (N = 18.5 million). Analyses were stratified by antihypertensive class, beneficiaries' state and county of residence, type of prescription drug plan, and treatment and demographic characteristics.Overall, 26.3% (4.9 million) of Medicare Part D beneficiaries using antihypertensives were nonadherent to their regimen. Nonadherence differed by multiple factors, including medication class (range: 16.9% for angiotensin II receptor blockers to 28.9% for diuretics); race-ethnicity (24.3% for non-Hispanic whites, 26.3% for Asian/Pacific Islanders, 33.8% for Hispanics, 35.7% for blacks, and 38.8% for American Indians/Alaska Natives); and state of residence (range 18.7% for North Dakota to 33.7% for the District of Columbia). Considerable county-level variation in nonadherence was found; the highest nonadherence tended to occur in the southern United States (U.S. Census region nonadherence = 28.9% [South], 26.7% [West], 24.1% [Northeast], and 22.8% [Midwest])More than one in four Medicare Part D beneficiaries using antihypertensives were nonadherent to their regimen, and certain racial/ethnic groups, states, and geographic areas were at increased risk for nonadherence. These findings can help inform focused interventions among these groups, which might improve blood pressure control and cardiovascular disease outcomes.
P3-202: Patterns of radiotherapy practice in non-metastatic non-small cell lung cancer: results of web-based patterns of care study in Korea
Authors: Hong-Gyun Wu, Keun Yong Eom, Do Hoon Oh, Il Han Kim, Mi Yeon Lee, Eui Kyu Chie, Charn Il Park
Journal: Journal of Thoracic Oncology (2007)
Response by Chao et al to Letters Regarding Article, “Use of Oral Anticoagulants for Stroke Prevention in Patients With Atrial Fibrillation Who Have a History of Intracranial Hemorrhage”
Authors: Tze-Fan Chao, Chia-Jen Liu, Jo-Nan Liao, Kang-Ling Wang, Yenn-Jiang Lin, Shih-Lin Chang, Li-Wei Lo, Yu-Feng Hu, Ta-Chuan Tuan, Fa-Po Chung, Tzeng-Ji Chen, Gregory Y.H. Lip, Shih-Ann Chen
Journal: Circulation (2016)
B2-01: The NATCH trial: chemotherapy toxicity and response on the neoadjuvant arm
Authors: Enriqueta Felip, Rafael Rosell, Bartomeu Massuti, Guillermo Alonso, Jose-Luis Gonzalez-Larriba, Carlos Camps, Dolores Isla, Cristina Mas, Jose Javier Sanchez, Jose Antonio Maestre
Journal: Journal of Thoracic Oncology (2007)
B4-04: Detection of peripheral lung cancer in the bronchial washing specimen using MAGE A1-6 RT-PCR
Authors: Hyeong Ryul Kim, Qwanwoo Ku, Chang Hyun Kang, Young Tae Kim, Sanghoon Jheon, Sook Whan Sung, Jin-Haeng Chung, Ho Il Yoon, Choon Taek Lee, Changho Jheon
Journal: Journal of Thoracic Oncology (2007)
Immunogenicity evaluation of subcutaneous administration of peptide hydrolysate from Lolium perenne (gpASIT plus TM) in combination with bacterial HSP70 (DnaK) in patients with seasonal allergic rhinitis
Authors: M. H Shamji, Jan Ceuppens, Peter Hellings, S. R Durham, J Duchateau, T Legon, S Pirotton
Journal: Allergy (2014)
Treatment delays in non-small cell lung cancer (NSCLC) and their prognostic implications.
Authors: R. Diaconescu, C. Lafond, L. Choiniere, C. Sirois, B. Laliberte, M. Doyon, R. Whittom
Journal: Journal of Clinical Oncology (2010)

6068 Background: The impact of treatment delays on NSCLC patients' survival is uncertain. While later treatment could negatively affect their psychological wellbeing, the maximum acceptable waiting time has not been determined. Methods: We analyzed consecutive patients diagnosed with NSCLC between January 2005 and May 2007 who received standard treatment at Hôpital du Sacré-Coeur de Montréal. Treatment delay was calculated from the first abnormal radiographic study. Patients were classified into three groups, based on TNM staging and the treatment received: localized (stages I and II), regional (most of stage III) and advanced (stages IIIB and IV). Cox proportional hazards analysis was used to identify predictive factors for survival among the following parameters: age, gender, histology, smoking status, type of treatment, tumor board discussion and treatment delay. Kaplan-Meier curves were used to estimate survival. Results: Three hundred twenty eight patients were identified. Their median treatment delay was 72 days (25%-75% interquartile range = 37-110 days), and distributed as follows: 85 (56-130) days for localized, 91 (37-120) days for regional and 50 (30-76) days for advanced stages (p < 0.01 for the latter). Treatment delay did not have a significant prognostic meaning for localized or regional stages. The opposite was true for advanced disease, both in univariate (p = 0.006) as well as multivariate (p = 0.009) analysis; for each week that the treatment could be delayed, the hazard ratio for mortality was improved at 0.93 (95% confidence interval 0.89-0.98). Survival of advanced patients who began treatment earlier versus later than 50 days was 6.8 months compared to 11.6 months (p = 0.027). None of the other factors were significant in uni or multivariate analyses. Conclusions: Treatment delays did not impact outcome in patients having localized or regional stage NSCLC in our cohort. For advanced stages, shorter treatment delays were associated with shorter survival. Rather than having a direct negative impact, this likely reflects that urgent treatment carried a negative prognostic meaning, as it was preferentially offered to patients having more aggressive disease. No significant financial relationships to disclose.
CD117 (c-kit) Expression On CD34+ Cells Participates In The Cytogenetic Response To Imatinib In CML Patients In First Chronic Phase
Authors: Jaroslaw Dybko, Ewa Medras, Olga Haus, Bozena Jazwiec, Joanna Urbaniak, Mieczyslaw Wozniak, Kazimierz Kuliczkowski
Journal: Blood (2013)
Romosozumab Treatment in Postmenopausal Women with Osteoporosis
Authors: Felicia Cosman, Daria B. Crittenden, Jonathan D. Adachi, Neil Binkley, Edward Czerwinski, Serge Ferrari, Lorenz C. Hofbauer, Edith Lau, E. Michael Lewiecki, Akimitsu Miyauchi, Cristiano A.F. Zerbini, Cassandra E. Milmont, Li Chen, Judy Maddox, Paul D. Meisner, Cesar Libanati, Andreas Grauer
Journal: New England Journal of Medicine (2016)

Romosozumab, a monoclonal antibody that binds sclerostin, increases bone formation and decreases bone resorption.We enrolled 7180 postmenopausal women who had a T score of -2.5 to -3.5 at the total hip or femoral neck. Patients were randomly assigned to receive subcutaneous injections of romosozumab (at a dose of 210 mg) or placebo monthly for 12 months; thereafter, patients in each group received denosumab for 12 months, at a dose of 60 mg, administered subcutaneously every 6 months. The coprimary end points were the cumulative incidences of new vertebral fractures at 12 months and 24 months. Secondary end points included clinical (a composite of nonvertebral and symptomatic vertebral) and nonvertebral fractures.At 12 months, new vertebral fractures had occurred in 16 of 3321 patients (0.5%) in the romosozumab group, as compared with 59 of 3322 (1.8%) in the placebo group (representing a 73% lower risk with romosozumab; P<0.001). Clinical fractures had occurred in 58 of 3589 patients (1.6%) in the romosozumab group, as compared with 90 of 3591 (2.5%) in the placebo group (a 36% lower risk with romosozumab; P=0.008). Nonvertebral fractures had occurred in 56 of 3589 patients (1.6%) in the romosozumab group and in 75 of 3591 (2.1%) in the placebo group (P=0.10). At 24 months, the rates of vertebral fractures were significantly lower in the romosozumab group than in the placebo group after each group made the transition to denosumab (0.6% [21 of 3325 patients] in the romosozumab group vs. 2.5% [84 of 3327] in the placebo group, a 75% lower risk with romosozumab; P<0.001). Adverse events, including instances of hyperostosis, cardiovascular events, osteoarthritis, and cancer, appeared to be balanced between the groups. One atypical femoral fracture and two cases of osteonecrosis of the jaw were observed in the romosozumab group.In postmenopausal women with osteoporosis, romosozumab was associated with a lower risk of vertebral fracture than placebo at 12 months and, after the transition to denosumab, at 24 months. The lower risk of clinical fracture that was seen with romosozumab was evident at 1 year. (Funded by Amgen and UCB Pharma; FRAME ClinicalTrials.gov number, NCT01575834 .).
INTRAOPERATIVE DECREASES OF SELENIUM, ZINC AND COPPER ARE ASSOCIATED WITH THE DEVELOPMENT OF SEVERE SYSTEMIC INFLAMMATORY RESPONSE SYNDROME IMMEDIATELY AFTER OPEN-HEART SURGERY
Authors: C Stoppe, B Graf, R Kopp, R Dembinski, G Schaelte, C Hasenbank, J Spillner, G Marx, Steffen Rex
Journal: Intensive Care Medicine (2009)
Requirements for global elimination of hepatitis B: a modelling study
Authors: Shevanthi Nayagam, Mark Thursz, Elisa Sicuri, Lesong Conteh, Stefan Wiktor, Daniel Low-Beer, Timothy B Hallett
Journal: The Lancet Infectious Diseases (2016)

Despite the existence of effective prevention and treatment interventions, hepatitis B virus (HBV) infection continues to cause nearly 1 million deaths each year. WHO aspires to global control and elimination of HBV infection. We aimed to evaluate the potential impact of public health interventions against HBV, propose targets for reducing incidence and mortality, and identify the key developments required to achieve them.
Gut and liver T-cells of common clonal origin in primary sclerosing cholangitis-inflammatory bowel disease
Authors: Eva Kristine Klemsdal Henriksen, Kristin Kaasen Jørgensen, Fatemeh Kaveh, Kristian Holm, David Hamm, Johanna Olweus, Espen Melum, Brian K. Chung, Tor J. Eide, Knut E.A. Lundin, Kirsten Muri Boberg, Tom H. Karlsen, Gideon M. Hirschfield, Evaggelia Liaskou
Journal: Journal of Hepatology (2016)
An Updated Analysis of the Stratus Trial (MM-010): Safety and Efficacy of Pomalidomide Plus Low-Dose Dexamethasone (POM + LoDEX) in Patients (Pts) with Relapsed/Refractory Multiple Myeloma (RRMM)
Authors: Meletios A. Dimopoulos, Antonio Palumbo, Paolo Corradini, Michele Cavo, Michel Delforge, Katja C. Weisel, Enrique M. Ocio, Francesco Di Raimondo, Markus Hansson, Mathew Simcock, Neil Miller, Ana Slaughter, Teresa Peluso, Lars Sternas, Mohamed H Zaki, Philippe Moreau
Journal: Blood (2015)
Oxford Nanopore MinION Sequencing and Genome Assembly
Authors: Hengyun Lu, Francesca Giordano, Zemin Ning
Journal: Genomics Proteomics & Bioinformatics (2016)

The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT). MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.