tbuckley/cabot-search huggingface dataset:
Abstract 4879: Reducing amplification artifacts in highly multiplex amplicon sequencing by using molecular barcodes
Authors: Quan Peng, Ravi Vijaya Satya, Marcus Lewis, Pranay Randad, John DiCarlo, Yexun Wang
Journal: Cancer Research (2015)

Abstract Background PCR amplicon sequencing has been widely used as a targeted approach for both DNA and RNA sequence analysis. Highly multiplex PCR has further enabled the enrichment of hundreds of amplicons in one simple reaction. At the same time, the performance of PCR amplicon sequencing can be negatively affected by issues such as high duplicate reads, polymerase artifacts and PCR amplification bias. Recently, people have made good progress at addressing those shortcomings by incorporating molecular barcodes into PCR primer design. So far, most work has been demonstrated using one to a few pairs of primers, which limits the size of the region one can analyze at one time. Results We described a simple protocol, which enables the use of molecular barcodes in highly multiplex PCR with hundreds of amplicons. Using this protocol and reference materials, we studied how molecular barcodes can increase the accuracy of variant calling at very low allelic frequency and reduce PCR amplification bias. We also evaluated its utility in profiling FFPE samples. Conclusions We demonstrated the successful implementation of molecular barcodes in highly multiplex PCR, at a scale many folds beyond earlier work. We showed that the new protocol combined the benefits of both highly multiplex PCR and molecular barcodes, i.e. the analysis of a very large region, low DNA input requirement, very good reproducibility and the ability to detect as low as 1% mutation with minimal false positives. Citation Format: Quan Peng, Ravi Vijaya Satya, Marcus Lewis, Pranay Randad, John DiCarlo, Yexun Wang. Reducing amplification artifacts in highly multiplex amplicon sequencing by using molecular barcodes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4879. doi:10.1158/1538-7445.AM2015-4879
HYPERTHYROIDISM AND THE SYMPATHETIC NERVOUS SYSTEM
Authors: M LOPEZ ESNAURRIZAR
Journal: JAMA (1964)

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 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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
Inhibition by interleukin-10 of inducible cyclooxygenase expression in lipopolysaccharide-stimulated monocytes: its underlying mechanism in comparison with interleukin-4
Authors: H Niiro, T Otsuka, T Tanabe, S Hara, S Kuga, Y Nemoto, Y Tanaka, H Nakashima, S Kitajima, M Abe
Journal: Blood (1995)
Enhancement of release from MHC class II antigen-positive monocytes of hematopoietic colony stimulating factors CSF-1 and G-CSF by recombinant human tumor necrosis factor-alpha: synergism with recombinant human interferon-gamma
Authors: L Lu, D Walker, CD Graham, A Waheed, RK Shadduck, HE Broxmeyer
Journal: Blood (1988)
Abstract IA09: Imaging to guide genomics and epigenomics of glioma
Authors: Joseph F. Costello
Journal: Cancer Research (2015)

Abstract Genomic analysis of cancer is typically conducted at a single time point and on a single piece of tumor tissue without knowledge of its original context within the heterogeneous tumor. Glioma tissue biopsies guided by distinct physiologic and metabolic imaging parameters can enrich for tumor regions with elevated levels of cycling cells, differences in blood vessels, and increased presence of hypoxic regions, and an increased probability of malignant transformation. An imaging guided approach to biopsy allows the tumor genomic and transcriptome evolution to be focused on malignant transformation. I will describe the use of novel quantitative imaging methods to guide biopsies to biologically distinct regions of brain tumors for targeted genomic, epigenomic and transcriptome analysis. The clonal evolution of tumor cell populations can be reconstructed from patterns of genetic alterations. In contrast, tumor epigenetic states are reversible and sensitive to the tumor microenvironment, presumably precluding the use of epigenetics to discover the clonal and sub-clonal evolution of tumors. We recently used mutation patterns to learn how low grade brain tumors evolve over time, and also discovered that temozolomide treatment of LGG is associated with TMZ-induced hypermutation and malignant progression to GBM (BE Johnson et al, Science, 2014). I will present an update to these results, and our follow up analysis of the spatial and temporal dynamics of DNA methylation in this clinically and genetically characterized cohort and in imaging guided biopsies. Citation Format: Joseph F. Costello. Imaging to guide genomics and epigenomics of glioma. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr IA09.
Synthesis and Preliminary Assessment of 99m tc-HYNIC-Fab´s (Rituximab) for Non-Hodgkin Lymphoma Diagnosis
Authors: Ximena Camacho, Camila Machado, Agustina Banchero, Maria Fernanda García, Victoria Calzada, Marcelo Fernández, María Moreno, Juan Pablo Gambini, Omar Alonso, Roger Chammas, Pablo Cabral, Eloísa Riva
Journal: Blood (2014)
Abstract IA02: Molecular pathogenesis of IDH mutant cancers and evolving treatment strategies
Authors: William G. Kaelin
Journal: Cancer Research (2015)

Abstract IDH1 and IDH2 mutations have now been described in a variety of cancers including gliomas, acute myelogenous leukemias, chondrosarcomas, cholangiocarcinomas, and angioimmunoblastic T-cell lymphoma. Tumor-associated IDH1 and IDH2 mutants produce large amounts of the R enantiomer of 2-hydroxyglutarate (R-2HG), which accumulates to mM levels in IDH mutant tumor cells. R-2HG modulates (usually inhibits) various 2-oxoglutarate-dependent enzymes, including various 2-oxoglutarate-dependent dioxygenases. Examples of such dioxygenases include the JmjC family of histone demethylases and the TET methylcytosine hydroxylases. The challenge for the field has been to determine which enzymes, when modulated by R-2HG, drive transformation and which are simply bystanders. We developed a cell-based assay for hematopoietic transformation by mutant IDH and showed that transformation in this setting is indeed mediated by R-2HG and that its effects are reversible. Moreover, we and others provided evidence that inhibition of TET2 by R-2HG contributes to leukemic transformation in cells carrying IDH mutations. Small molecules that block R-2HG production appear promising based on early Phase 1 data in IDH1 and IDH2 mutant leukemias. We also developed a model of astrocytic transformation by IDH. We found that activation of the EglN prolyl hydroxylases, which target the HIF transcription factor for destruction, by R-2HG promotes soft agar growth by immortalized astrocytes but is not sufficient to promote tumor growth in immunocompromised mice. More recently we have developed an oncogene cooperation assay in which mutant IDH promotes tumor growth in mice. In addition, we have identified an enzyme in glioma cells that, when inhibited by R-2HG, creates a distinctive metabolic profile and renders IDH mutant cells dependent on glutaminase activity for survival. Citation Format: William G. Kaelin, Jr. Molecular pathogenesis of IDH mutant cancers and evolving treatment strategies. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr IA02.
Pharmacokinetics and Pharmacodynamics of Dabigatran 75 mg b.i.d. in Patients With Severe Chronic Kidney Disease
Authors: Judith Kooiman, Tom van der Hulle, Hugo Maas, Sabrina Wiebe, Stephan Formella, Andreas Clemens, Marjolijn van Buren, Martien Janssen, Ton J. Rabelink, Menno V. Huisman
Journal: Journal of the American College of Cardiology (2016)
Withdrawal of alclofenac (Prinalgin)
Authors: R D Mann
Journal: BMJ (1979)

days after the onset of symptoms showed a large, superficial ulcer in the mid-oesophagus.She responded well to withdrawal of emepronium bromide and to oral analgesics and nine days later repeat oesophagoscopy showed that the ulcer had healed.There have been a number of reports of oesophageal ulceration with emepronium bromide,'-4 as well as a report of mouth ulcers,; thought to be caused by prolonged contact of the tablet with the mucosa.The data sheet on this drug now suggests that the tablets should be swallowed with a glass of water, but it is apparent that this instruction is not always stressed by the doctor or followed by the patient.The tablet is formulated to distintegrate rapidly on contact with water but its hygroscopic nature can cause it to stick to the oesophageal mucosa if it is swallowed with too little water.Perhaps the time has come for the manufacturers to redevelop the presen- tation of this drug.Surely it will not be long before oesophageal perforation due to emepronium bromide is recorded.
Abstract IA24: Computational dissection of phenotypic and functional heterogeneity in cancer
Authors: Dana Pe'er
Journal: Cancer Research (2015)

Abstract Cells within a single tumor are known to display extensive phenotypic and functional heterogeneity. Many life-threatening features of cancer, including drug resistance, metastasis and relapse, are facets of intratumor heterogeneity. With emerging single-cell measurement technologies, the field is poised to make important strides in understanding and controlling this heterogeneity. However, these technologies require advances in analytical methods to interpret the complex data they produce. Using mass cytometry, which measures single cells in ~31 simultaneous proteomic features, we developed novel methods for analyzing phenotypic heterogeneity in cancer. We use AML as an example to demonstrate the power of our approach. The heart of our approach is Phenograph, a graph-based representation of single-cells which represents the phenotypic structure of the sample and can be partitioned into subsets of densely interconnected nodes, called communities. Using Phenograph, we deconstructed several AML samples into discrete phenotypes. Analyzing the resulting subpopulations provided insights into functional heterogeneity of AML. Phenograph can be applied to characterize heterogeneity and primitive subpopulations in additional cancers. Citation Format: Dana Pe'er. Computational dissection of phenotypic and functional heterogeneity in cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr IA24.
Abstract PR07: Synchronous ovarian and endometrial carcinomas: The case for pseudo-metastasis.
Authors: Michael S. Anglesio, Yi Kan Wang, Madlen Maassen, Hugo M. Horlings, Ali Bashashati, Blake Gilks, Stefan Kommoss, David G. Huntsman
Journal: Clinical Cancer Research (2016)

Abstract Background: Almost half of ovarian endometrioid histotype carcinomas present with concurrent endometrial carcinoma or pre-cancerous lesions. These “synchronous” ovarian and endometrial (SEO) tumors, when organ-confined and low-grade, consistently behave as two independent primary tumors, rather than a tumor-metastasis pair typical of advanced-stage carcinoma. Our study aims to investigate the ancestral relationship between ovarian and endometrial components of SEOs. Methods: We identified a cohort of SEOs and performed targeted, with the Illumina Truseq Custom Amplicon assay, and exome-level, with Nugen Ovation Library System and Agilent SureSelect XT2 capture, library construction followed by massively parallel sequencing on illumina MiSeq or HiSeq. Results: Despite complexities introduced as a result of sampling formalin fixed and paraffin embedded archival specimens we were able to confirm shared identical mutations, and thus a clonal relationship, between ovarian and endometrial tumors in all but one case. Discussion: In simultaneous presentation of cancer of the endometrium and ovary from our series we observed strong evidence of a primary tumor and metastasis relationship. However, the clinical behavior of this series, and SEOs in general, defies the basic tenant of cancer metastasis as a dire prognosis. Curiously similar anomalies, where there is advanced stage yet favorable outcome, occur in other organ systems. We therefore suggest a generalizable process “pseudo-metastasis” through which cells can spread to microenvironment-compatible and physically accessible sites. This restricted metastatic process can occur in cells that lack the full complement of cancer-associated transformation hallmarks required for tissue invasion and hematogenous or lymphatic metastasis. This phenomenon may be an important early step in dissemination of apparent multi-focal benign lesions, pre-malignant lesions, and low-grade carcinomas. This abstract is also presented as Poster B07. Citation Format: Michael S. Anglesio, Yi Kan Wang, Madlen Maassen, Hugo M. Horlings, Ali Bashashati, Blake Gilks, Stefan Kommoss, David G. Huntsman. Synchronous ovarian and endometrial carcinomas: The case for pseudo-metastasis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr PR07.
Review: After lower-extremity DVT, compression stockings do not reduce postthrombotic syndrome or recurrence
Authors: Brian P. Schmitt
Journal: Annals of Internal Medicine (2016)

Source Citation Berntsen CF, Kristiansen A, Akl EA, et al. Compression stockings for preventing the postthrombotic syndrome in patients with deep vein thrombosis. Am J Med. 2016;129:447.e1-e20. 26747198
Gaucher Disease
Authors: John L. Zeller, Alison E. Burke, Richard M. Glass
Journal: JAMA (2007)

A blood test to measure glucocerebrosidase enzyme activity is currently used to determine whether a person has Gaucher disease or may be a carrier.With a confirmation of the diagnosis, disease management has shifted to disease-specific therapies:• Enzyme replacement therapy (ERT)-The goal of ERT is to provide an appropriate amount of needed enzyme.• Substrate reduction therapy (SRT)-The goal is to minimize the amount of production and accumulation of waste material within cells.• Symptom management-Treatment includes pain reduction therapies, blood transfusions, orthopedic surgery, and possible splenectomy (removal of the spleen).• Psychological care-Professional counseling can help patients better manage the difficulties of their disease and the lifestyle changes that might be required.
Measles in Europe in 2001-2002
Authors: M Muscat, S Glismann, H Bang
Journal: Eurosurveillance (2003)

A total of 17 928 measles cases were reported to EUVAC.NET in 2001-02, with a 41% increase between the 2 years, giving a crude incidence of 2.36 and 3.37 per 100 000 population respectively. Most reported cases were aged 1-9 years. Outbreak related measles cases amounted to 18% of reported cases in 2001 and 20% in 2002. Less than 1% of cases were known to be imported in 2001 and 2002. Encephalitis as a severe complication was reported in 21 in 2001 and 6 cases 2002. One death attributed to measles was reported in 2001. The proportion of reported cases with known vaccination status increased from 56% of cases in 2001 to 72% in 2002. Overall, the proportion of reported measles cases that were unvaccinated rose from 50% in 2001 to 66% in 2002.
Natural Man
Authors: Lewis Thomas
Journal: New England Journal of Medicine (1973)

THE social scientists, especially the economists, are moving deeply into ecology and the environment these days, with disquieting results. It goes somehow against the grain to learn that cost-benefit analyses can be done neatly on lakes, meadows, nesting gannets, and even whole oceans. It is hard enough to confront the environmental options ahead, and the hard choices, but even harder when the price tags are so visible. Even the new jargon is disturbing: it hurts the spirit, somehow, to read the word "environments," when the plural means that there are so many alternatives there to be sorted through, as in . . .
RHEUMATOLOGY: SPECIALTY WITH A FUTURE
Authors: J DURIVAGE
Journal: JAMA (1961)

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 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) Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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
Safety and clinical outcomes of abiraterone acetate (aa) after docetaxel (doc) in octogenarians with metastatic castration-resistant prostate cancer (mcrpc)
Authors: O. Caffo, F. Maines, U. De Giorgi, L. Fratino, G. Lo Re, V. Zagonel, A. D'Angelo, M. Donini, F. Verderame, R. Ratta, G. Procopio, E. Campadelli, F. Massari, D. Gasparro, P. Ermacora, C. Messina, M. Giordano, D. Alesini, V. Conteduca, A. Veccia, E. Galligioni
Journal: Annals of Oncology (2015)
Ultrastructural Insights into the Biological Significance of Persisting DNA Damage Foci after Low Doses of Ionizing Radiation
Authors: Yvonne Lorat, Stefanie Schanz, Claudia E. Rübe
Journal: Clinical Cancer Research (2016)

Intensity-modulated radiotherapy (IMRT) enables the delivery of high doses to target volume while sparing surrounding nontargeted tissues. IMRT treatment, however, substantially increases the normal tissue volume receiving low-dose irradiation, but the biologic consequences are unclear.Using mouse strains that varied in genetic DNA repair capacity, we investigated the DNA damage response of cortical neurons during daily low-dose irradiation (0.1 Gy). Using light and electron microscopic approaches, we enumerated and characterized DNA damage foci as marker for double-strand breaks (DSBs).During repeated low-dose irradiation, cortical neurons in brain tissues of all mouse strains had a significant increase of persisting foci with cumulative doses, with the most pronounced accumulation of large-sized foci in repair-deficient mice. Electron microscopic analysis revealed that persisting foci in repair-proficient neurons reflect chromatin alterations in heterochromatin, but not persistently unrepaired DSBs. Repair-deficient SCID neurons, by contrast, showed high numbers of unrepaired DSBs in eu- and heterochromatin, emphasizing the fundamental role of DNA-PKcs in DSB rejoining, independent of chromatin status. In repair-deficient ATM-/- neurons, large persisting damage foci reflect multiple unrepaired DSBs concentrated at the boundary of heterochromatin due to disturbed KAP1 phosphorylation.Repeated low-dose irradiation leads to the accumulation of persisting DNA damage foci in cortical neurons and thus may adversely affect brain tissue and increase the risk of carcinogenesis. Multiple unrepaired DSBs account for large-sized foci in repair-deficient neurons, thus quantifying foci alone may underestimate extent and complexity of persistent DNA damage. Clin Cancer Res; 22(21); 5300-11. ©2016 AACR.
Serum hepatitis B virus RNA is encapsidated pregenome RNA that may be associated with persistence of viral infection and rebound
Authors: Jie Wang, Tao Shen, Xiangbo Huang, G. Renuka Kumar, Xiangmei Chen, Zhenzhen Zeng, Ruiyang Zhang, Ran Chen, Tong Li, Tianying Zhang, Quan Yuan, Pao-Chen Li, Qi Huang, Richard Colonno, Jidong Jia, Jinlin Hou, Malcolm A. McCrae, Zhiliang Gao, Hong Ren, Ningshao Xia, Hui Zhuang, Fengmin Lu
Journal: Journal of Hepatology (2016)

Hepatitis B virus (HBV) RNA in serum has recently been linked to efficacy and prognosis of chronic hepatitis B (CHB) treatment. This study explored the nature, origin, underlying mechanisms, and potential clinical significance of serum HBV RNA.The levels of HBV DNA and RNA were determined in the supernatant of induced HepAD38, HBV-expressing HepG2.2.15 cells and primary human hepatocytes (PHH), and in the serum of transgenic mice and CHB patients. NP-40 and proteinase K treatment, sucrose density gradient centrifugation, electron microscopy, northern blot, multiple identification PCRs and 5' rapid-amplification of cDNA ends were performed to identify the nature of serum HBV RNA.Although significantly lower than HBV DNA levels, abundant HBV RNA was present in the serum of CHB patients. A series of experiments demonstrated that serum HBV RNA was pregenome RNA (pgRNA) and present in virus-like particles. HBV pgRNA virion levels increased after blocking the reverse transcription activity of HBV DNA polymerase, and decreased after blocking the encapsidation of pgRNA. Furthermore, the presence of HBV pgRNA virion was associated with risk of viral rebound after discontinuation of nucleot(s)ide analogues (NAs) therapy in CHB patients.Serum HBV RNA was confirmed to be pgRNA present in virus-like particles. HBV pgRNA virions were produced from encapsidated particles in which the pgRNA was non- or partially reverse transcribed. Clinically, HBV pgRNA virion might be a potential biomarker for monitoring safe discontinuation of NA-therapy.HBV may have another virion form in which the nucleic acid is composed of RNA, not DNA. The level of HBV RNA virion in serum may be associated with risk of HBV viral rebound after withdrawal of treatment, and therefore, a potential predictive biomarker to monitor the safe discontinuation of nucleot(s)ide analogues-therapy.