tbuckley/cabot-search huggingface dataset:
Ten-Year Monitored Natural Recovery of Lead-Contaminated Mine Tailing in Klity Creek, Kanchanaburi Province, Thailand
Authors: Tanapon Phenrat, Ashijya Otwong, Aphichart Chantharit, Gregory V. Lowry
Journal: Environmental Health Perspectives (2016)

Klity Creek has become Thailand's first official remediation ordered by the court in 2013, 15 years after the spill of lead (Pb)-contaminated mine tailing into the creek. The Pollution Control Department (PCD) decided to restore the creek through monitored natural recovery (MNR) since 2006 but has not been successful. Interestingly, the most recent remediation plan in 2015 will still apply MNR to five out of the seven portions of the creek, despite no scientific feasibility evaluation of using MNR to restore the creek.This study qualitatively and quantitatively evaluated the feasibility of using MNR to clean up the creek in order to protect the Klity children from excess Pb exposure.We analyzed the physical and chemical transformation of Pb contaminated sediment in the creek and developed a remedial action goal and cleanup level using the Integrated Exposure Uptake Biokinetic model (IEUBK). We empirically determined the natural recovery (NR) potentials and rates using 10 years of data monitoring the water and sediment samples from eight monitoring stations (KC1 to KC8).Klity Creek has NR potential for water except at KC2, which is closest to the spill and the other improperly managed Pb sources. However, the creek has no NR potential for sediment except at the KC8 location (NR rate = 11.1 ± 3.0 × 10-3 month-1) farthest from the spill.The MNR method is not suitable to use as the sole remedial approach for Klity Creek (KC2 to KC7). Although MNR is applicable at KC8, it may require up to 377 ± 76 years to restore the sediment to the background Pb concentration.Phenrat T, Otwong A, Chantharit A, Lowry GV. 2016. Ten-year monitored natural recovery of lead-contaminated mine tailing in Klity Creek, Kanchanaburi Province, Thailand. Environ Health Perspect 124:1511-1520; http://dx.doi.org/10.1289/EHP215.
High-performance web services for querying gene and variant annotation
Authors: Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, Nikhil Gopal, Gregory S. Stupp, Timothy E. Putman, Benjamin J. Ainscough, Obi L. Griffith, Ali Torkamani, Patricia L. Whetzel, Christopher J. Mungall, Sean D. Mooney, Andrew I. Su, Chunlei Wu
Journal: Genome biology (2016)

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.
Imaging of Inflammation in Unexplained Cardiomyopathy
Authors: Ana Kadkhodayan, Panithaya Chareonthaitawee, Subha V. Raman, Leslie T. Cooper
Journal: JACC. Cardiovascular imaging (2016)

Myocarditis is a recognized but underdiagnosed cause of cardiomyopathy due to its wide clinical spectrum and nonspecific presentation. Accurate diagnosis is important because 25% of patients with acute myocarditis develop cardiomyopathy, and of those, approximately 5% per year require heart transplantation or die. Current guidelines for the recognition and treatment of the inflammatory cardiomyopathies are limited. The gold standard for diagnosis, endomyocardial biopsy, has low sensitivity, and thus, multimodality imaging of inflammation plays a crucial role in defining the cardiac abnormalities and in assisting with diagnosis and management. The literature on inflammatory cardiomyopathies is limited to small studies of selected populations due to the diverse etiologies and inherent difficulties in definitive diagnosis. This review focuses on the current and projected use of various imaging modalities, including echocardiography, cardiac magnetic resonance, and nuclear imaging to better define inflammatory cardiomyopathies and aid in their management; it specifically focuses on cardiac sarcoidosis, and giant cell, eosinophilic, and lymphocytic myocarditis.
Treatment of Gilles de la Tourette syndrome with pimozide
Authors: A K Shapiro, E Shapiro, G J Eisenkraft
Journal: American Journal of Psychiatry (1983)

The results of this clinical study of 31 patients with Tourette syndrome suggest that pimozide is more effective and induces fewer side effects than haloperidol in some patients. The clinical advantages of pimozide may be associated with its more specific dopamine-blocking properties and the absence of significant norepinephrine effects. The authors recommend further controlled study of exclusive dopamine antagonists in the treatment of Tourette syndrome.
Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish
Authors: Finola E. Moore, Elaine G. Garcia, Riadh Lobbardi, Esha Jain, Qin Tang, John C. Moore, Mauricio Cortes, Aleksey Molodtsov, Melissa Kasheta, Christina C. Luo, Amaris J. Garcia, Ravi Mylvaganam, Jeffrey A. Yoder, Jessica S. Blackburn, Ruslan I. Sadreyev, Craig J. Ceol, Trista E. North, David M. Langenau
Journal: The Journal of Experimental Medicine (2016)

Hematopoiesis culminates in the production of functionally heterogeneous blood cell types. In zebrafish, the lack of cell surface antibodies has compelled researchers to use fluorescent transgenic reporter lines to label specific blood cell fractions. However, these approaches are limited by the availability of transgenic lines and fluorescent protein combinations that can be distinguished. Here, we have transcriptionally profiled single hematopoietic cells from zebrafish to define erythroid, myeloid, B, and T cell lineages. We also used our approach to identify hematopoietic stem and progenitor cells and a novel NK-lysin 4+ cell type, representing a putative cytotoxic T/NK cell. Our platform also quantified hematopoietic defects in rag2E450fs mutant fish and showed that these fish have reduced T cells with a subsequent expansion of NK-lysin 4+ cells and myeloid cells. These data suggest compensatory regulation of the innate immune system in rag2E450fs mutant zebrafish. Finally, analysis of Myc-induced T cell acute lymphoblastic leukemia showed that cells are arrested at the CD4+/CD8+ cortical thymocyte stage and that a subset of leukemia cells inappropriately reexpress stem cell genes, including bmi1 and cmyb. In total, our experiments provide new tools and biological insights into single-cell heterogeneity found in zebrafish blood and leukemia.
Contemporary Therapy for Advanced Soft-Tissue Sarcomas in Adults
Authors: Angela Pang, Mariana Carbini, Robert G. Maki
Journal: JAMA Oncology (2016)

Immune checkpoint inhibitors have shown promising results in several cancers and are now put to the test in sarcomas. This brief summary presents data regarding the previously approved and newer agents for more common sarcomas and focuses on specific sarcoma histologic subtypes or novel approaches for which there is particular optimism. Approaches involving epigenetic agents, metabolic therapy, and modulators of the tumor microenvironment represent other ways the field of sarcoma medical oncology will progress in 2016 and beyond.A recent series of successful randomized trials provides new systemic therapy options for patients with metastatic soft-tissue sarcomas in the United States, after a gap of more than 10 years in which no new drugs were approved. The agents with most recent approval include pazopanib, trabectedin, and eribulin. As a sign that progress is not linear, 2 cousins of ifosfamide failed to show benefit in phase 3 trials, despite prior positive results of randomized phase 2 trials.The biological features of each sarcoma subtype are associated with specific sensitivity patterns to chemotherapy, and despite their rarity, future trials will need to emphasize specific histologic subtypes (many with well-defined genetic alterations) to best fit diagnosis to therapy.
A 5-Year-Old Boy With Refractory Hypocalcemia
Authors: Sarah V. Kelley, Karen E. Jerardi
Journal: JAMA Pediatrics (2016)

A 5-year-old boy with global developmental delay presented with a 3-day history of vomiting, diarrhea, and refusing to bear weight. His parents said that he is a “picky eater,” with a diet consisting exclusively of orange soda, meat, and chili. What is your diagnosis?
The Case for a Revised Definition of Myocardial Infarction—The Ongoing Conundrum of Type 2 Myocardial Infarction vs Myocardial Injury
Authors: Joseph S. Alpert, Kristian A. Thygesen
Journal: JAMA Cardiology (2016)

more general definition for acute myocardial injury, whether ischemic or nonischemic in complex medical and surgical patients, requires serious further study and consideration.The term acute myocardial injury seems a likely solution that would narrow the definition of MI and would be similar to the terminology used with injury to other organs.
Acute Myeloid Leukemia: The Outcome Is Determined By Age, Genetic Group, White Blood Cell Count, Lactate Dehydrogenase, Rather Than By Chemotherapy Intensity
Authors: Thomas Buchner, Wolfgang E. Berdel, Utz Krug, Claudia Haferlach, Susanne Schnittger, Torsten Haferlach, Carsten Mueller-Tidow, Matthias Stelljes, Rolf M. Mesters, Hubert Serve, Jan Braess, Karsten Spiekermann, Peter Staib, Andreas Grueneisen, Albrecht Reichle, Leopold Balleisen, Hartmut Eimermacher, Aristoteles Giagounidis, Herbert Rasche, Eva Lengfelder, Andreas Faldum, Maria Cristina Sauerland, Achim Heinecke, Rüdiger Hehlmann, Bernhard J. Woermann, Wolfgang Hiddemann
Journal: Blood (2013)
Prolonged Antitumor Effect of Indomethacin on Autochthonous Intestinal Tumors in Rats<xref ref-type="fn" rid="FN2">2</xref>
Authors: Morris Pollard, Phyllis H. Luckert
Journal: JNCI Journal of the National Cancer Institute (1983)

Intestinal tumors were induced in randomly propagated Lobund Sprague-Dawley rats by dimethylhydrazine dihydrochloride and by methylazoxymethanol acetate. At 14, 63, and 77 days after exposure to a carcinogen, rats were fed, ad libitum, indomethacin in the drinking water (20 mg/liter) for 20 and 40 weeks. The development of intestinal tumors was prevented or retarded significantly compared to that of control animals. Among control rats at 20, 40, and 52 weeks, the numbers of tumors per rat were relatively constant, but the individual tumors were increased in size.
BMJ Awards 2016 honour doctor behind “Hello, my name is” campaign
Authors: Zosia Kmietowicz
Journal: BMJ (2016)

Kate Granger, a doctor and the founder of the successful “Hello, my name is” campaign, which encourages medical staff to introduce themselves to patients, won a Special Achievement Award at The BMJ Awards 2016 in London on 5 May.

Granger, a consultant in geriatric medicine at Mid Yorkshire Hospitals NHS Trust, whose experiences as a patient with cancer led to the campaign, was the first recipient of this one-off award. Her campaign now has 42 000 Twitter followers globally.

Granger was joined by doctors and teams who have excelled in their fields, such as anaesthesia, diabetes, cancer care, cardiology, clinical leadership, dermatology, and gastroenterology.

Competition for this year’s BMJ Awards, now in their eighth …
Prevalence of Inappropriate Antibiotic Prescriptions Among US Ambulatory Care Visits, 2010-2011
Authors: Katherine E. Fleming-Dutra, Adam L. Hersh, Daniel J. Shapiro, Monina Bartoces, Eva A. Enns, Thomas M. File, Jonathan A. Finkelstein, Jeffrey S. Gerber, David Y. Hyun, Jeffrey A. Linder, Ruth Lynfield, David J. Margolis, Larissa S. May, Daniel Merenstein, Joshua P. Metlay, Jason G. Newland, Jay F. Piccirillo, Rebecca M. Roberts, Guillermo V. Sanchez, Katie J. Suda, Ann Thomas, Teri Moser Woo, Rachel M. Zetts, Lauri A. Hicks
Journal: JAMA (2016)

<h3>Importance</h3> The National Action Plan for Combating Antibiotic-Resistant Bacteria set a goal of reducing inappropriate outpatient antibiotic use by 50% by 2020, but the extent of inappropriate outpatient antibiotic use is unknown. <h3>Objective</h3> To estimate the rates of outpatient oral antibiotic prescribing by age and diagnosis, and the estimated portions of antibiotic use that may be inappropriate in adults and children in the United States. <h3>Design, Setting, and Participants</h3> Using the 2010-2011 National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey, annual numbers and population-adjusted rates with 95% confidence intervals of ambulatory visits with oral antibiotic prescriptions by age, region, and diagnosis in the United States were estimated. <h3>Exposures</h3> Ambulatory care visits. <h3>Main Outcomes and Measures</h3> Based on national guidelines and regional variation in prescribing, diagnosis-specific prevalence and rates of total and appropriate antibiotic prescriptions were determined. These rates were combined to calculate an estimate of the appropriate annual rate of antibiotic prescriptions per 1000 population. <h3>Results</h3> Of the 184 032 sampled visits, 12.6% of visits (95% CI, 12.0%-13.3%) resulted in antibiotic prescriptions. Sinusitis was the single diagnosis associated with the most antibiotic prescriptions per 1000 population (56 antibiotic prescriptions [95% CI, 48-64]), followed by suppurative otitis media (47 antibiotic prescriptions [95% CI, 41-54]), and pharyngitis (43 antibiotic prescriptions [95% CI, 38-49]). Collectively, acute respiratory conditions per 1000 population led to 221 antibiotic prescriptions (95% CI, 198-245) annually, but only 111 antibiotic prescriptions were estimated to be appropriate for these conditions. Per 1000 population, among all conditions and ages combined in 2010-2011, an estimated 506 antibiotic prescriptions (95% CI, 458-554) were written annually, and, of these, 353 antibiotic prescriptions were estimated to be appropriate antibiotic prescriptions. <h3>Conclusions and Relevance</h3> In the United States in 2010-2011, there was an estimated annual antibiotic prescription rate per 1000 population of 506, but only an estimated 353 antibiotic prescriptions were likely appropriate, supporting the need for establishing a goal for outpatient antibiotic stewardship.
Burden of Cancer in a Large Consortium of Prospective Cohorts in Europe
Authors: Konstantinos K Tsilidis, Nikos Papadimitriou, Despoina Capothanassi, Christina Bamia, Vassiliki Benetou, Mazda Jenab, Heinz Freisling, Frank Kee, Annemarie Nelen, Mark G O'Doherty, Angela Scott, Isabelle Soerjomataram, Anne Tjønneland, Anne M May, J Ramón Quirós, Ulrika Pettersson-Kymmer, Hermann Brenner, Ben Schöttker, José M Ordóñez-Mena, Aida Karina Dieffenbach, Sture Eriksson, Ellisiv Bøgeberg Mathiesen, Inger Njølstad, Galatios Siganos, Tom Wilsgaard, Paolo Boffetta, Dimitrios Trichopoulos, Antonia Trichopoulou
Journal: JNCI Journal of the National Cancer Institute (2016)

Disability-adjusted life-years (DALYs) are an indicator of mortality, morbidity, and disability. We calculated DALYs for cancer in middle-aged and older adults participating in the Consortium on Health and Ageing Network of Cohorts in Europe and the United States (CHANCES) consortium.A total of 90 199 participants from five European cohorts with 10 455 incident cancers and 4399 deaths were included in this study. DALYs were calculated as the sum of the years of life lost because of premature mortality (YLLs) and the years lost because of disability (YLDs). Population-attributable fractions (PAFs) were also estimated for five cancer risk factors, ie, smoking, adiposity, physical inactivity, alcohol intake, and type II diabetes.After a median follow-up of 12 years, the total number of DALYs lost from cancer was 34 474 (382 per 1000 individuals) with a similar distribution by sex. Lung cancer was responsible for the largest number of lost DALYs (22.9%), followed by colorectal (15.3%), prostate (10.2%), and breast cancer (8.7%). Mortality (81.6% of DALYs) predominated over disability. Ever cigarette smoking was the risk factor responsible for the greatest total cancer burden (24.0%, 95% confidence interval [CI] = 22.2% to 26.0%), followed by physical inactivity (4.9%, 95% CI = 0.8% to 8.1%) and adiposity (1.8%, 95% CI = 0.2% to 2.8%).DALYs lost from cancer were substantial in this large European sample of middle-aged and older adults. Even if the burden of disease because of cancer is predominantly caused by mortality, some cancers have sizeable consequences for disability. Smoking remained the predominant risk factor for total cancer burden.
Survival Analysis over 28 Years of 173,378 Patients with Hepatocellular Carcinoma in Japan
Authors: Masatoshi Kudo, Namiki Izumi, Michiie Sakamoto, Yutaka Matsuyama, Takafumi Ichida, Osamu Nakashima, Osamu Matsui, Yonson Ku, Norihiro Kokudo, Masatoshi Makuuchi
Journal: Liver Cancer (2016)

&lt;b&gt;&lt;i&gt;Background: &lt;/i&gt;&lt;/b&gt;Beginning in 1967, the Liver Cancer Study Group of Japan (LCSGJ) started a nationwide prospective registry of all patients with hepatocellular carcinoma (HCC) diagnosed at more than 700 institutions. To determine the effectiveness of surveillance and treatment methods longitudinally, we analyzed improvements over time in overall survival (OS) of 173,378 patients with HCC prospectively entered into the LCSGJ registry between 1978 and 2005. &lt;b&gt;&lt;i&gt;Methods: &lt;/i&gt;&lt;/b&gt;All patients from more than 700 institutions throughout Japan with HCC were entered into the LCSGJ registry. Patients were grouped by years of diagnosis, with OS and 5-year OS rates being calculated. We also assessed OS and 5-year OS rates in patients who underwent resection, local ablation, transarterial chemoembolization (TACE), and hepatic arterial infusion chemotherapy (HAIC) and in those with baseline serum alpha-fetoprotein (AFP) levels ≥400 ng/ml. &lt;b&gt;&lt;i&gt;Results: &lt;/i&gt;&lt;/b&gt;The 5- and 10-year OS rates in the cohort of 173,378 patients were 37.9% and 16.5%, respectively. However, over time, the mean maximum tumor size decreased significantly, whereas 5-year OS rates and median survival time increased significantly. Similar findings were observed separately in patients who underwent resection, local ablation, TACE, and HAIC, as well as in patients with AFP levels ≥400 ng/ml. &lt;b&gt;&lt;i&gt;Conclusion: &lt;/i&gt;&lt;/b&gt;The establishment of a nationwide HCC surveillance program in Japan has contributed to longer median OS and increased OS rates in patients diagnosed with this disease. These findings suggest that the establishment of a surveillance program in other countries with patients at risk for HCC may provide significant survival benefits.
Abstract 20552: Comparison of Outcome in Patients With ST-Elevation Myocardial Infarction Treated with Drug-Eluting Stents versus Bare Metal Stents in Eastern Denmark and Southern Sweden
Authors: Homa Waziri, Erik Jorgensen, Henning Kelbaek, Martin Stagmo, Frants Pedersen, Stefan James, Bo Lagerqvist, Lars Kober, Kristian wachtell
Journal: Circulation (2014)

The prognosis of patients with ST-elevation myocardial infarction (STEMI) has improved significantly in the era of mechanical revascularization. Regional differences exist in the choice of stents. The aim of this study was to assess whether differences in preference of stents effect outcome in Danish and Swedish STEMI patients treated with either drug-eluting stents (DES) or bare metal stents (BMS) during percutaneous coronary intervention (PCI) in Eastern Denmark and Southern Sweden, respectively. Methods: We included 14,260 consecutive STEMI patients from 2003-2012 (59,708 patient-years of follow-up) treated in Eastern Denmark and Southern Sweden with either DES or BMS. Data were obtained from the Eastern Danish Heart Registry and the Swedish Coronary Angiography and Angioplasty Registry. Results: We identified 7828 (54.9%) Danish and 6,432 (45.1%) Swedish patients. Among Danish patients 76% (n=5966) received DES whereas 82% (n= 5254) of the Swedish patients received BMS. Overall 7116 (49.9%) patients were treated with DES and 7144 (50.1%) with BMS. Patients who received BMS were older (65.9 vs. 63.0) with a higher prevalence of hypertension (38.9 % vs. 36.3%) and history of myocardial infarction (13.0% vs. 9.2%) but with a lower prevalence of smoking (42.1% vs. 50.7%) and hyperlipidemia (20.7% vs. 24.3%, all p&lt;0.01). Patients with BMS had a higher risk adjusted 30-day mortality (hazard ratio [HR] =1.3, CI 1.02-1.68, p&lt;0.001) compared with DES. There was no statistically significant difference in mortality after 30 days and onwards (HR=0.96, CI 0.83-1.1, p=0.59) Conclusions: The use of DES is associated with a significantly lower 30-day mortality compared with BMS. After 30-days there is no difference in mortality between DES and BMS.
P0153 : Insulin-like growth factor-binding protein 3 (IGFBP3) serum levels are associated with prognosis in patients admitted for acute decompensation of cirrhosis
Authors: C.G. Correa, B.S. Colombo, M.F. Ronsoni, P.E. Soares e Silva, L. Fayad, L.M. Wildner, M.L. Bazzo, E. Dantas-Correa, J.L. Narciso-Schiavon, L.L. Schiavon
Journal: Journal of Hepatology (2015)
Detection of cancer cells using SapC-DOPS nanovesicles
Authors: Harold W. Davis, Nida Hussain, Xiaoyang Qi
Journal: Molecular Cancer (2016)

Unlike normal cells, cancer cells express high levels of phosphatidylserine on the extracellular leaflet of their cell membrane. Exploiting this characteristic, our lab developed a therapeutic agent that consists of the fusogenic protein, saposin C (SapC) which is embedded in dioleoylphosphatidylserine (DOPS) vesicles. These nanovesicles selectively target cancer cells and induce apoptosis. Here we review the data supporting use of SapC-DOPS to locate tumors for surgical resection or for treatment. In addition, there is important evidence suggesting that SapC-DOPS may also prove to be an effective novel cancer therapeutic reagent. Given that SapC-DOPS is easily labeled with lipophilic dyes, it has been combined with the far-red fluorescent dye, CellVue Maroon (CVM), for tumor targeting studies. We also have used contrast agents incorporated in the SapC-DOPS nanovesicles for computed tomography and magnetic resonance imaging, and review that data here. Administered intravenously, the fluorescently labeled SapC-DOPS traversed the blood–brain tumor barrier enabling identification of brain tumors. SapC-DOPS-CVM also detected a variety of other mouse tumors in vivo, rendering them observable by optical imaging using IVIS and multi-angle rotational optical imaging. Dye is detected within 30 min and remains within tumor for at least 7 days, whereas non-tumor tissues were unstained (some dye observed in the liver was transient, likely representing degradation products). Additionally, labeled SapC-DOPS ex vivo delineated tumors in human histological specimens. SapC-DOPS can also be labeled with contrast reagents for computed tomography or magnetic resonance imaging. In conclusion, labeled SapC-DOPS provides a convenient, specific, and nontoxic method for detecting tumors while concurrently offering a therapeutic benefit.