tbuckley/cabot-search huggingface dataset:
Racial/Ethnic Disparities in Survival Among Patients With Young-Onset Colorectal Cancer
Authors: Andreana N. Holowatyj, Julie J. Ruterbusch, Laura S. Rozek, Michele L. Cote, Elena M. Stoffel
Journal: Journal of Clinical Oncology (2016)

Racial disparities in colorectal cancer (CRC) persist, despite overall reductions in morbidity and mortality. In addition, incidence is rising among individuals younger than 50 years of age. We compared the survival of young-onset CRC among non-Hispanic black (NHB), non-Hispanic white (NHW), and Hispanic individuals.Using the National Cancer Institute's Surveillance, Epidemiology, and End Results program data, we identified individuals between the ages of 20 and 49 years, diagnosed with CRC between 2000 and 2009. Survival rates and Cox proportional hazards models were used to compare stage-specific 5-year survival among NHBs, NHWs, and Hispanics.We identified 28,145 patients with young-onset CRC (19,497 NHW; 4,384 NHB; 4,264 Hispanic) during the 10-year study period. Overall survival at 5 years after CRC diagnosis was 54.9% among NHB, 68.1% among NHW, and 62.9% among Hispanic individuals (P < .001). NHB individuals had a significantly higher hazard of cancer-specific death compared with NHWs after adjusting for age, sex, race, stage, county-level poverty, and treatment history in cases of colon (hazard ratio [HR], 1.35; 95% CI 1.26 to 1.45) and rectum/rectosigmoid junction (HR, 1.51; 95% CI, 1.37 to 1.68) cancers, whereas there was no significant difference in survival between NHWs and Hispanics. The greatest racial disparities in cancer-specific survival were observed among NHB and NHW patients diagnosed with stage II cancers of the colon (HR, 1.69; 95% CI, 1.33 to 2.14) and stage III cancers of the rectum (HR, 1.98; 95% CI, 1.63 to 2.40).Survival after CRC diagnosis at a young age is significantly worse among NHBs compared with NHWs, even among patients with early-stage disease. Further study is needed to determine whether differences in tumor biology and/or treatment are associated with racial disparities in outcomes, which would have implications for CRC treatment and prevention.
Case 35-1976
Authors: Richard C. Cabot, Robert E. Scully, James J. Galdabini, Betty U. McNeely, Robert H. Schapiro, Peter Dervan
Journal: New England Journal of Medicine (1976)

Presentation of CaseA 62-year-old woman was admitted to the hospital because of recurrent jaundice.She was well until one year previously, when fever developed, with rise of the temperature to 38.9°C, accompanied by chills, jaundice, dark urine, light stools, fatigue, weakness and anorexia. Three weeks later she entered another hospital, where a cholecystectomy and an incidental appendectomy were performed. An operative cholangiographic study (Fig. 1) showed narrowing of the distal portion of the common bile duct, with dilatation and several small irregular defects in the proximal portion; the right hepatic duct was poorly filled. The gallbladder contained "ash" but . . .
Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using Antioxidant Response Element Reporter Gene Assay Models and Big Data
Authors: Marlene Thai Kim, Ruili Huang, Alexander Sedykh, Wenyi Wang, Menghang Xia, Hao Zhu
Journal: Environmental Health Perspectives (2015)

Background:Hepatotoxicity accounts for a substantial number of drugs being withdrawn from the market. Using traditional animal models to detect hepatotoxicity is expensive and time-consuming. Alternative in vitro methods, in particular cell-based high-throughput screening (HTS) studies, have provided the research community with a large amount of data from toxicity assays. Among the various assays used to screen potential toxicants is the antioxidant response element beta lactamase reporter gene assay (ARE-bla), which identifies chemicals that have the potential to induce oxidative stress and was used to test &gt; 10,000 compounds from the Tox21 program.Objective:The ARE-bla computational model and HTS data from a big data source (PubChem) were used to profile environmental and pharmaceutical compounds with hepatotoxicity data.Methods:Quantitative structure–activity relationship (QSAR) models were developed based on ARE-bla data. The models predicted the potential oxidative stress response for known liver toxicants when no ARE-bla data were available. Liver toxicants were used as probe compounds to search PubChem Bioassay and generate a response profile, which contained thousands of bioassays (&gt; 10 million data points). By ranking the in vitro–in vivo correlations (IVIVCs), the most relevant bioassay(s) related to hepatotoxicity were identified.Results:The liver toxicants profile contained the ARE-bla and relevant PubChem assays. Potential toxicophores for well-known toxicants were created by identifying chemical features that existed only in compounds with high IVIVCs.Conclusion:Profiling chemical IVIVCs created an opportunity to fully explore the source-to-outcome continuum of modern experimental toxicology using cheminformatics approaches and big data sources.Citation:Kim MT, Huang R, Sedykh A, Wang W, Xia M, Zhu H. 2016. Mechanism profiling of hepatotoxicity caused by oxidative stress using antioxidant response element reporter gene assay models and big data. Environ Health Perspect 124:634–641; http://dx.doi.org/10.1289/ehp.1509763
Filgrastim–Induced Crescentic Transformation of Recurrent IgG2λ GN
Authors: Ibrahim Batal, Glen S. Markowitz, Waichi Wong, Rupali Avasare, Markus Y. Mapara, Gerald B. Appel, Vivette D. D'Agati
Journal: Journal of the American Society of Nephrology (2016)

Proliferative GN with monoclonal IgG deposits is an increasingly recognized form of GN, but its relation to hematologic malignancy remains poorly understood. Filgrastim, an analog for granulocyte colony–stimulating factor produced by recombinant DNA technology, is frequently used to stimulate bone marrow release of hematopoietic progenitor cells in preparation for stem cell transplant. We report an exceptional case of proliferative GN with monoclonal IgG2 λ deposits in a young man whose disease progressed slowly to CKD, which was followed by a preemptive kidney transplant. The patient developed recurrent GN in the allograft and clinically detectable plasma cell neoplasm 9 years after the first renal manifestations. Contemporaneous with filgrastim administration for stem cell mobilization, the patient’s slowly progressive GN underwent severe crescentic transformation, leading to rapidly progressive and irreversible allograft failure. This report explores the spectrum of GN with monoclonal IgG deposits and the pathophysiologic role of granulocyte colony–stimulating factor in exacerbation of preexisting GN.
Ewing's sarcoma oncogene structure: a novel prognostic marker?
Authors: J A Fletcher
Journal: Journal of Clinical Oncology (1998)

Article Tools Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.1998.16.4.1241 Journal of Clinical Oncology - published online before print September 21, 2016 PMID: 9552020 Ewing's sarcoma oncogene structure: a novel prognostic marker? J A FletcherxJ A FletcherSearch for articles by this author https://doi.org/10.1200/JCO.1998.16.4.1241 First Page PDF © 1998 by American Society of Clinical Oncology
Treatment of alcohol use disorders in patients with alcoholic liver disease
Authors: Giovanni Addolorato, Antonio Mirijello, Pablo Barrio, Antoni Gual
Journal: Journal of Hepatology (2016)

SummaryAlcohol use disorders (AUDs) is one of the leading causes of disease and disability in almost all European countries. Among the alcohol-related diseases, alcoholic liver disease (ALD) is the most common. At present, alcohol is the most frequent cause of liver cirrhosis in the Western world. The cornerstone of treatment for ALD is achieving total alcohol abstinence and preventing relapse; medical and surgical treatments for ALD are limited when drinking continues.This narrative review summarizes current treatments for AUDs with a particular emphasis to the treatment of AUDs in patients with ALD. Medical management, psychosocial and pharmacological interventions are analyzed, underlying limits and options in AUD patients. Finally, this review discusses the most appropriate setting for the management of AUD patients with advanced liver disease as well as the indications for liver transplantation in AUD patients.
Determining Electroconvulsive Therapy Response With Machine Learning
Authors: Christopher C. Abbott, Dyani Loo, Jing Sui
Journal: JAMA Psychiatry (2016)

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 Psychiatry 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 Psychiatry journal
Targeted Ablation of Periostin-Expressing Activated Fibroblasts Prevents Adverse Cardiac Remodeling in Mice
Authors: Harmandeep Kaur, Mikito Takefuji, C.Y. Ngai, Jorge Carvalho, Julia Bayer, Astrid Wietelmann, Ansgar Poetsch, Soraya Hoelper, Simon J. Conway, Helge Möllmann, Mario Looso, Christian Troidl, Stefan Offermanns, Nina Wettschureck
Journal: Circulation Research (2016)

Rationale: Activated cardiac fibroblasts (CF) are crucial players in the cardiac damage response; excess fibrosis, however, may result in myocardial stiffening and heart failure development. Inhibition of activated CF has been suggested as a therapeutic strategy in cardiac disease, but whether this truly improves cardiac function is unclear. Objective: To study the effect of CF ablation on cardiac remodeling. Methods and Results: We characterized subgroups of murine CF by single-cell expression analysis and identified periostin as the marker showing the highest correlation to an activated CF phenotype. We generated bacterial artificial chromosome–transgenic mice allowing tamoxifen-inducible Cre expression in periostin-positive cells as well as their diphtheria toxin-mediated ablation. In the healthy heart, periostin expression was restricted to valvular fibroblasts; ablation of this population did not affect cardiac function. After chronic angiotensin II exposure, ablation of activated CF resulted in significantly reduced cardiac fibrosis and improved cardiac function. After myocardial infarction, ablation of periostin-expressing CF resulted in reduced fibrosis without compromising scar stability, and cardiac function was significantly improved. Single-cell transcriptional analysis revealed reduced CF activation but increased expression of prohypertrophic factors in cardiac macrophages and cardiomyocytes, resulting in localized cardiomyocyte hypertrophy. Conclusions: Modulation of the activated CF population is a promising approach to prevent adverse cardiac remodeling in response to angiotensin II and after myocardial infarction.
Prediction of Response of Primary Tumors to Neoadjuvant Sunitinib Using Perfusion (Dce) Computed Tomography (Ct) in Metastatic Renal Cell Carcinoma (Mrcc) Patients (Preinsut Trial)
Authors: M. Bouaboula, L. Fournier, Y. Vano, H. Pereira, L. Albiges Sauvin, L. Salomon, S. Taieb, E. Anglade, S. Abadie-Lacourtoisie, A. Scherrer, C. Theodore, C. De Bazelaire, S. Culine, L.M. Caquot, J. Eymard, C. Le Rest, G. Chatellier, A. Mejean, C.A. Cuenod, S. Oudard
Journal: Annals of Oncology (2014)
Nanoparticle Strategy Enhances Delivery of Cancer Drugs
Authors: Tracy Hampton
Journal: JAMA (2016)

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 HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Case 52-1965
Authors: John H. Knowles, Benjamin Castleman
Journal: New England Journal of Medicine (1965)

Presentation of CaseA fifty-year-old woman was admitted to the hospital because of pain in the abdomen.She had been well until fifteen years previously, when there was the onset of a cough that became productive of yellow sputum. Three months later x-ray films of the chest taken at another hospital revealed "diffuse mottling" in both lungs. Because of increased severity of the cough and the development of bilateral pain in the chest she came to the clinic. There was no history of dyspnea, edema, cyanosis, anorexia, chills, fever, sweats, weight loss or exposure to tuberculosis. At the age of . . .
Human Tumor Cell Migration2
Authors: Alistair J. Cochran, Rolf Kiessling, Eva Klein, Peter Gunvén, Alan K. Foulis
Journal: JNCI Journal of the National Cancer Institute (1973)

Journal Article Human Tumor Cell Migration Get access Alistair J. Cochran, Alistair J. Cochran 3University Department of Pathology, The Western Infirmary, Glasgow, G11 6NT, Scotland Search for other works by this author on: Oxford Academic PubMed Google Scholar Rolf Kiessling, Rolf Kiessling 5Department of Tumor Biology, The Karolinska Institute, Stockholm S104-01, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar Eva Klein, Eva Klein 5Department of Tumor Biology, The Karolinska Institute, Stockholm S104-01, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar Peter Gunvén, Peter Gunvén 5Department of Tumor Biology, The Karolinska Institute, Stockholm S104-01, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar Alan K. Foulis Alan K. Foulis 3University Department of Pathology, The Western Infirmary, Glasgow, G11 6NT, Scotland Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 51, Issue 4, October 1973, Pages 1109–1111, https://doi.org/10.1093/jnci/51.4.1109 Published: 01 October 1973 Article history Received: 23 March 1973 Accepted: 31 May 1973 Published: 01 October 1973
Multimedia: WEBSITE OF THE WEEK
Authors: Richard Harling
Journal: BMJ (1999)

www.netlink.de/gen/home.html Biotechnology companies trying to introduce genetically modified food into Europe have found themselves up against well organised resistance. The battle for minds and stomachs continues, and on the internet the environmental and food safety lobby seem to be winning.

The Campaign to Ban Genetically Engineered Foods offers access in four languages to the latest news from across the world, with links to a vast network of sites from over 12 countries. The sheer scale of their web presence means that groups opposed to genetically modified foods provide most of the easily available information. The range of groups involved serves to make their message more powerful: if physicians (www.psagef.org/indexgen.htm), mothers (www.safe-food.org/), and students (www.sage-intl.org) can all agree then surely they must have a point?

The biotechnology industry is also accused of cynically manipulating public and political opinion in order to enhance the image of its products. The website home.intekom.com/tm_info/geleak1.htm contains what is claimed to be a leaked document that describes this strategy. If genuine, it is chilling reading: the intricacy of the propaganda exercise required is breathtaking.

Up against powerful multinational organisations, the more extreme environmental and food safety groups have resorted to direct action. Their exploits make interesting reading, and anarchists do seem to design attractive websites. Try the Super Heroes Against Genetix campaign (www.enviroweb.org/shag/) or the Natural Reality SuperWeed Kit (pages.hotbot.com/politics/superweed/), a genetically engineered “superweed” designed to “attack corporate monoculture.”
In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians
Authors: Alyssa M. Molinaro, Bret J. Pearson
Journal: Genome biology (2016)

The planarian Schmidtea mediterranea is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal has hindered the study of lineage progression and has made understanding the mechanisms of tissue regeneration a challenge. However, recent advances in single-cell transcriptomics and analysis methods allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell.Here we apply pseudotime analysis and single-cell transcriptomics to identify adult stem cells belonging to specific cellular lineages and identify novel candidate genes for future in vivo lineage studies. We purify 168 single stem and progeny cells from the planarian head, which were subjected to single-cell RNA sequencing (scRNAseq). Pseudotime analysis with Waterfall and gene set enrichment analysis predicts a molecularly distinct neoblast sub-population with neural character (νNeoblasts) as well as a novel alternative lineage. Using the predicted νNeoblast markers, we demonstrate that a novel proliferative stem cell population exists adjacent to the brain.scRNAseq coupled with in silico lineage analysis offers a new approach for studying lineage progression in planarians. The lineages identified here are extracted from a highly heterogeneous dataset with minimal prior knowledge of planarian lineages, demonstrating that lineage purification by transgenic labeling is not a prerequisite for this approach. The identification of the νNeoblast lineage demonstrates the usefulness of the planarian system for computationally predicting cellular lineages in an adult context coupled with in vivo verification.
A hydrophobic peptide fraction that enhances the water dispersibility of curcumin
Authors: Risa Yamashita, Tatsuya Oshima, Yoshinari Baba
Journal: Asian Journal of Pharmaceutical Sciences (2016)

The present study describes the complexation between curcumin (Cur) and a peptide mixture (Pep). Pep was prepared by enzymatic hydrolysis of casein and used as an excipient for poorly water-soluble Cur. An aqueous solution of Pep and an acetone solution of Cur were mixed and lyophilized to obtain a white-yellow powder of the peptide and Cur complex (Cur-Pep). The water dispersibility of Cur was enhanced by the complexation with Pep. Pep was fractionated using ammonium sulfate precipitation and ultrafiltration to identify which peptides preferentially interact with Cur. Relatively hydrophobic peptides with high molecular weights (>5 kDa) were more effective in enhancing the water dispersibility of Cur than other fractions. Cur-Pep dispersed under acidic and neutral conditions, at which amphoteric Pep is positively or negatively charged. Cur-Pep exists as a hydrocolloid with particle size 160–330 nm in aqueous media.
Authors’ reply to Barbieri and Kovarik, Mariani, and Waxman and Kanzaria
Authors: Anupam B Jena, Lena Schoemaker, Jay Bhattacharya, Seth A Seabury
Journal: BMJ (2015)

Barbieri and Kovarik raise several interesting points regarding our study and the empirical malpractice literature in general.1 2 It is important to note that our study intended to explore the positive question of how physicians’ use of resources relates to subsequent malpractice risk rather than whether physicians “should” spend more to reduce liability. This last question relies on notions of causality and economic welfare that we could not answer. However, we recognise the implications of our findings for physicians’ behaviour, particularly given the important role that malpractice plays in physicians’ practice. …
Progranulin Plays a Central Role in Host Defense during Sepsis by Promoting Macrophage Recruitment
Authors: Zhixin Song, Xuemei Zhang, Liping Zhang, Fang Xu, Xintong Tao, Hua Zhang, Xue Lin, Lihua Kang, Yu Xiang, Xaiofei Lai, Qun Zhang, Kun Huang, Yubing Dai, Yibing Yin, Ju Cao
Journal: American Journal of Respiratory and Critical Care Medicine (2016)

Progranulin, a widely expressed protein, has multiple physiological functions. The functional role of progranulin in the host response to sepsis remains unknown.To assess the role of progranulin in the host response to sepsis.Effects of progranulin on host response to sepsis were determined.Progranulin concentrations were significantly elevated in adult (n = 74) and pediatric (n = 26) patients with sepsis relative to corresponding healthy adult (n = 36) and pediatric (n = 17) control subjects, respectively. By using a low-lethality model of nonsevere sepsis, we observed that progranulin deficiency not only increased mortality but also decreased bacterial clearance during sepsis. The decreased host defense to sepsis in progranulin-deficient mice was associated with reduced macrophage recruitment, with correspondingly impaired chemokine CC receptor ligand 2 (CCL2) production in peritoneal lavages during the early phase of sepsis. Progranulin derived from hematopoietic cells contributed to host defense in sepsis. Therapeutic administration of recombinant progranulin not only rescued impaired host defense in progranulin-deficient mice after nonsevere sepsis but also protected wild-type mice against a high-lethality model of severe sepsis. Progranulin-mediated protection against sepsis was closely linked to improved peritoneal macrophage recruitment. In addition, CCL2 treatment of progranulin-deficient mice improved survival and decreased peritoneal bacterial loads during sepsis, at least in part through promotion of peritoneal macrophage recruitment.This proof-of-concept study supports a central role of progranulin-dependent macrophage recruitment in host defense to sepsis, opening new opportunities to host-directed therapeutic strategy that manipulate host immune response in the treatment of sepsis.