---------- Forwarded message ---------- From: Mehdi Najafi <sm.najaf...@gmail.com> Date: Fri, Aug 5, 2016 at 9:17 AM Subject: pubmed.mineR To: r...@igib.in
Hi dear helper, it has been a pleasure to read magnificat paper titled "pubmed.mineR: An R package with text-mining algorithms to analyse PubMed abstracts". I encuntered a problem using it.I wish you could help me with that. favorite <http://stackoverflow.com/questions/38781115/cant-find-objects-using-pubmed-miner-package#> I have downloaded abstracts of interest from pubmed.com then read them using pubmed.mineR package with readabs() function, which is supposed to create object of class "Abstracs", but when I type in ls(), it gives me character(0), which as far as i know implies that there is no object in the memory. I want to search abstracts using searchabsL(x,include="term"), Here x is the object of class Abstracts containing data.though i don't know how? after readabs() i face these lines: > readabs("b.txt") An object of class "Abstracts" Slot "Journal": [1] "1. Alzheimers Res Ther. 2015 Dec 18;7(1):75. doi: 10.1186/s13195-015-0159-5." [2] "2. J Cereb Blood Flow Metab. 2016 Mar;36(3):621-8. doi: 10.1177/0271678X15606141." Slot "Abstract": [1] " Diagnostic value of cerebrospinal fluid Aβ ratios in preclinical Alzheimer's disease. Adamczuk K(1,)(2), Schaeverbeke J(3,)(4), Vanderstichele HM(5), Lilja J(6,)(7), Nelissen N(8,)(9), Van Laere K(10,)(11), Dupont P(12,)(13), Hilven K(14), Poesen K(15,)(16), Vandenberghe R(17,)(18,)(19). Author information: (1)Laboratory for Cognitive Neurology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. kate.adamc...@med.kuleuven.be. (2)Alzheimer Research Centre KU Leuven, Leuven Institute of Neuroscience and Disease, Herestraat 49, 3000, Leuven, Belgium. kate.adamc...@med.kuleuven.be. (3)Laboratory for Cognitive Neurology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. jolien.schaeverb...@med.kuleuven.be. (4)Alzheimer Research Centre KU Leuven, Leuven Institute of Neuroscience and Disease, Herestraat 49, 3000, Leuven, Belgium. jolien.schaeverb...@med.kuleuven.be. (5)ADx NeuroSciences, Technologiepark 4, 9052, Gent, Belgium. hugo.vanderstichele@ adxneurosciences.com. (6)GE Healthcare, Björkgatan 30, 751 25, Uppsala, Sweden. johan.li...@radiol.uu.se. (7)Nuclear Medicine and PET, Department of Surgical Sciences, Uppsala University, 751 85, Uppsala, Sweden. johan.li...@radiol.uu.se. (8)Laboratory for Cognitive Neurology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. natalie.nelis...@psych.ox.ac. uk. (9)Department of Psychiatry, Oxford University, Oxford, OX3 7JX, UK. natalie.nelis...@psych.ox.ac.uk. (10)Alzheimer Research Centre KU Leuven, Leuven Institute of Neuroscience and Disease, Herestraat 49, 3000, Leuven, Belgium. koen.vanla...@uzleuven.be. (11)Nuclear Medicine and Molecular Imaging Department, KU Leuven and University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium. koen.vanla...@uzleuven.be. (12)Laboratory for Cognitive Neurology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. patrick.dup...@med.kuleuven.be. (13)Alzheimer Research Centre KU Leuven, Leuven Institute of Neuroscience and Disease, Herestraat 49, 3000, Leuven, Belgium. patrick.dup...@med.kuleuven.be. (14)Laboratory for Neuroimmunology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. kelly.hil...@med.kuleuven.be. (15)Laboratory for Molecular Neurobiomarker Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. koen.poe...@uzleuven.be. (16)Laboratory Medicine, UZ Leuven, Herestraat 49, 3000, Leuven, Belgium. koen.poe...@uzleuven.be. (17)Laboratory for Cognitive Neurology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium. rik.vandenber...@uz.kuleuven.ac.be. (18)Alzheimer Research Centre KU Leuven, Leuven Institute of Neuroscience and Disease, Herestraat 49, 3000, Leuven, Belgium. rik.vandenber...@uz.kuleuven.ac.be. (19)Neurology Department, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium. rik.vandenber...@uz.kuleuven.ac.be. INTRODUCTION: In this study of preclinical Alzheimer's disease (AD) we assessed the added diagnostic value of using cerebrospinal fluid (CSF) Aβ ratios rather than Aβ42 in isolation for detecting individuals who are positive on amyloid positron emission tomography (PET). METHODS: Thirty-eight community-recruited cognitively intact older adults (mean age 73, range 65-80 years) underwent (18)F-flutemetamol PET and CSF measurement of Aβ1-42, Aβ1-40, Aβ1-38, and total tau (ttau). (18)F-flutemetamol retention was quantified using standardized uptake value ratios in a composite cortical region (SUVRcomp) with reference to cerebellar grey matter. Based on a prior autopsy validation study, the SUVRcomp cut-off was 1.57. Sensitivities, specificities and cut-offs were defined based on receiver operating characteristic analysis with CSF analytes as variables of interest and (18)F-flutemetamol positivity as the classifier. We also determined sensitivities and CSF cut-off values at fixed specificities of 90 % and 95 %. RESULTS: Seven out of 38 subjects (18 %) were positive on amyloid PET. Aβ42/ttau, Aβ42/Aβ40, Aβ42/Aβ38, and Aβ42 had the highest accuracy to identify amyloid-positive subjects (area under the curve (AUC) ≥ 0.908). Aβ40 and Aβ38 had significantly lower discriminative power (AUC = 0.571). When specificity was fixed at 90 % and 95 %, Aβ42/ttau had the highest sensitivity among the different CSF markers (85.71 % and 71.43 %, respectively). Sensitivity of Aβ42 alone was significantly lower under these conditions (57.14 % and 42.86 %, respectively). CONCLUSION: For the CSF-based definition of preclinical AD, if a high specificity is required, our data support the use of Aβ42/ttau rather than using Aβ42 in isolation. DOI: 10.1186/s13195-015-0159-5 PMCID: PMC4683859" [2] "Epub 2015 Sep 30. Cerebrospinal fluid profiles with increasing number of cerebral microbleeds in a continuum of cognitive impairment. Shams S(1), Granberg T(2), Martola J(2), Li X(3), Shams M(2), Fereshtehnejad SM(3), Cavallin L(2), Aspelin P(2), Kristoffersen-Wiberg M(2), Wahlund LO(3). Author information: (1)Department of Clinical Science, Intervention, and Technology, Division of Medical Imaging and Technology, Karolinska Institutet, Stockholm, Sweden Department of Radiology, Karolinska University Hospital, Stockholm, Sweden sara.sh...@ki.se. (2)Department of Clinical Science, Intervention, and Technology, Division of Medical Imaging and Technology, Karolinska Institutet, Stockholm, Sweden Department of Radiology, Karolinska University Hospital, Stockholm, Sweden. (3)Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Stockholm, Sweden Division of Clinical Geriatrics, Karolinska University Hospital, Stockholm, Sweden. Cerebral microbleeds (CMBs) are hypothesised to have an important yet unknown role in the dementia disease pathology. In this study we analysed increasing number of CMBs and their independent associations with routine cerebrospinal fluid (CSF) biomarkers in a continuum of cognitive impairment. A total of 1039 patients undergoing dementia investigation were analysed and underwent lumbar puncture, and an MRI scan. CSF samples were analysed for amyloid β (Aβ) 42, total tau (T-tau), tau phosphorylated at threonine 18 (P-tau) and CSF/serum albumin ratios. Increasing number of CMBs were independently associated with low Aβ42 levels, in the whole cohort, Alzheimer's disease and mild cognitive impairment (p < 0.05). CSF/serum albumin ratios were high with multiple CMBs (p < 0.001), reflecting accompanying blood-brain barrier dysfunction. T-tau and P-tau levels were lower in Alzheimer's patients with multiple CMBs when compared to zero CMBs, but did not change in the rest of the cohort. White matter hyperintensities were associated with low Aβ42 in the whole cohort and Alzheimer's disease (p < 0.05). Aβ42 is the routine CSF-biomarker mainly associated with CMBs in cognitive impairment, and there is an accumulative effect with increasing number of CMBs. © The Author(s) 2015. DOI: 10.1177/0271678X15606141 PMCID: PMC4794093 [Available on 2017-03-01]" Slot "PMID": [1] 26677842 26661151 I would be glad to hear from you. sincerely,Mehdi Najafi. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
