tbuckley/cabot-search huggingface dataset:
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
Authors: Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop
Journal: Genome biology (2011)

A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences in the copy number of the gene between even closely related organisms, and due to PCR artifacts. The taxonomic composition can also be determined from metagenomic shotgun sequencing data by matching individual reads against a database of reference sequences. One major limitation of prior computational methods used for this purpose is the use of a universal classification threshold for all genes at all taxonomic levels. We propose that better classification results can be obtained by tuning the taxonomic classifier to each matching length, reference gene, and taxonomic level. We present a novel taxonomic classifier MetaPhyler (
                  http://metaphyler.cbcb.umd.edu
                                  ), which uses phylogenetic marker genes as a taxonomic reference. Results on simulated datasets demonstrate that MetaPhyler outperforms other tools commonly used in this context (CARMA, Megan and PhymmBL). We also present interesting results by analyzing a real metagenomic dataset. We have introduced a novel taxonomic classification method for analyzing the microbial diversity from whole-metagenome shotgun sequences. Compared with previous approaches, MetaPhyler is much more accurate in estimating the phylogenetic composition. In addition, we have shown that MetaPhyler can be used to guide the discovery of novel organisms from metagenomic samples.
TCT-600 Distinct Vascular Response between Vulnerable and Stable Coronary Plaques after the Second Generation Drug-eluting Stents Implantation: One-year Angioscopic Comparison
Authors: Kenji Kawai, Minoru Ichikawa, Takashi Takagi, Mitsutoshi Asai, Yoshizumi Takei, Kenji Fukuda, Shohei Yoshima, Takeshi Oshita, Yoshiyuki Kijima
Journal: Journal of the American College of Cardiology (2014)
Use of Chlorpromazine in the Withdrawal of Addicting Drugs
Authors: Charles E. Friedgood, Charles B. Ripstein
Journal: New England Journal of Medicine (1955)

THE abrupt withdrawal of addicting drugs gives rise to well defined symptoms, including restlessness, nausea, emesis, insomnia and perspiration. Many of these effects, as Himmelsbach1 has pointed out, are manifestations of disturbances that are autonomic in origin. His findings and those of others2 3 4 indicate that the use of opiates, by upsetting homeostatic equilibrium, calls into play autonomic compensatory action, which then becomes a hyper-reaction requiring these drugs to preserve the quasi equilibrium. Consequently, withholding opiates from addicts temporarily produces an autonomic imbalance that results in the manifestations of the abstinence syndrome.Investigators5 , 6 in Europe have reported that a new phenothiazine . . .
Vacant spots for stem cells
Authors: Amy Maxmen
Journal: The Journal of Experimental Medicine (2009)

Like cars circling city blocks on Saturday night, stem cells stand a good chance of finding a parking spot in bone marrow if they circulate long enough. Hematopoietic stem cells frequently leave their niches, freeing up space for other stem cells to enter, report [Bhattacharya et al.][1]

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On the biological basis of human laterality: II. The mechanisms of inheritance
Authors: Michael J. Morgan, Michael C. Corballis
Journal: Behavioral and Brain Sciences (1978)

Abstract This paper focuses on the inheritance of human handedness and cerebral lateralization within the more general context of structural biological asymmetries. The morphogenesis of asymmetrical structures, such as the heart in vertebrates, depends upon a complex interaction between information coded in the cytoplasm and in the genes, but the polarity of asymmetry seems to depend on the cytoplasmic rather than the genetic code. Indeed it is extremely difficult to find clear-cut examples in which the direction of an asymmetry is under genetic control. As one possible case, there is some evidence that the direction, clockwise or counterclockwise, of rotation of the abdomen in certain mutant strains of Drosophila is controlled by a particular gene locus, although there appears to be some degree of confusion on this point. By contrast, it is much easier to find examples in which the degree but not the direction of asymmetry is under genetic control. For instance, there is a mutant strain of mice in which half of the animals display situs inversus of the viscera. The proportion has remained at one half despite many years of inbreeding, suggesting that the mutant allele effectively cancels the normal situs and allows the asymmetry to be specified in random fashion. Although this account does not deny that the right hemisphere of humans may be the more specialized for certain functions, it does attribute a leading or dominant role to the left hemisphere (at least in most individuals). We suggest that so-called “right-hemisphere” functions are essentially acquired by default, due to the left hemisphere's prior involvement with speech and skilled motor acts; we note, for instance, that these right-hemisphere functions include rather elementary perceptual processes. But perhaps the more critical prediction from our account is that the phenomenon of equipotentiality should be unidirectional: the right (lagging) hemisphere should be more disposed to take over left-hemisphere functions following early lesions than is the left (leading) hemisphere to take over right-hemisphere functions. We note preliminary evidence that this may be so.
Clouds on the 'Private Medicare' Horizon
Authors: Bernard R. Tresnowski
Journal: JAMA (1986)

IN THIS issue ofThe Journal, the American Medical Association's Council on Medical Service publishes a detailed description of a Board of Trustees-proposed conversion of the federal Medicare program to private insurers, at a rate that includes prefunding of benefits for future generations.<sup>1</sup>The goals of the program are ambitious: prefunded, affordable accessibility of comprehensive protection for an increasing cohort of the elderly in a system rationalized by means testing. The system would depend on the private market to underwrite the benefits, which are defined as "all services presently covered by Medicare Parts A and B, with additional benefits including periodic health examinations and other preventive services" and catastrophic expense "above a specified beneficiary cost sharing limit." Presumably there are statistics that would suggest the extent to which the proposed increase in the age of eligibility would limit liability, but this feature of the proposal may not go as
Women in Science
Authors: Marjorie S. Sirridge
Journal: JAMA (2006)

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
Tc-99m Depreotide Detecting Malignant Pulmonary Nodules
Authors: Wei-Jen Shih, Luis Samayoa
Journal: Clinical Nuclear Medicine (2004)

Tc-99m depreotide is a synthetic somatostatin analog with a low molecular weight of 1358 and binding domains for somatostatin receptors (SSTRs) subtypes 2, 3, and 5. This agent has been used for imaging pulmonary nodules in an effort to differentiate malignancies from infectious processes. To investigate whether there is significant ratio variability predicting a specific lung cancer type, we undertook this study. We analyzed the semiquantitative tumor-to-normal lung ratios among 23 patients with histopathologically proven lung carcinoma. Eleven patients with squamous cell carcinoma had 14 nodular lesions (n = 14); the ratios ranged from 6.0 to 1.4; the mean was 3.500. Nine patients with adenocarcinoma had 9 nodular lesions (n = 9); the ratios ranged from 3.2 to 1.0; mean was 1.89. Three patients with large cell carcinoma had 3 nodular lesions (n = 3); mean was 1.2. There were significantly different ratio values between squamous cell carcinoma and nonsquamous cell carcinoma. On a statistical analysis by t test, this difference proved to have a statistically significant value of P < 0.038. For patients with lung cancer, we could predict the tumor most likely to be squamous cell carcinoma if the uptake ratio was greater than 3.5. Otherwise, the lower ratio appeared to be either the result of large cell carcinoma or adenocarcinoma. High tumor uptake of Tc-99m depreotide reflecting abundant SSTRs of a tumor and/or peritumoral neovasculature such as squamous cell carcinoma could be potentially useful in diagnostic and therapeutic guidance.
Abstract 4729: Expression of lumican is negatively associated with the risk of biochemical recurrence in human prostate cancer
Authors: Marco A. De Velasco, Yuji Hatanaka, Takashi Oki, Yurie Kura, Yutaka Yamamoto, Kazuhiro Yoshimura, Nobutaka Shimizu, Masahiro Nozawa, Kazuhiro Yoshikawa, Kazuto Nishio, Hirotsugu Uemura
Journal: Cancer Research (2014)

Abstract We used DNA chip technology in a genetically engineered mouse model of prostate cancer, and identified lumican as a candidate biomarker in prostate cancer progression. Lumican is a small leucine-rich extracellular matrix protein that has been shown to modulate cell migration and proliferation during embryonic development, and tissue repair. Expression and distinct glycosylation patterns of lumican in several tumor and stromal tissues has been shown to play important roles in vascular invasion, differentiation, proliferation, and invasion. Our goal was to determine the clinical value of lumican as a biomarker for human prostate cancer. In order to do so, we examined gene expression in publicly available databases and confirmed the protein expression in tissue microarrays constructed from prostatectomy cases. Protein expression was examined by immunohistochemistry and expression scores were compared with clinicopathological features and disease progression. Our analysis shows that in human prostate cancer, stromal expression of lumican correlated inversely with clinicopathological features associated with disease progression. In addition, biochemical recurrence was significantly longer for patients with high expression of stromal lumican. Our findings suggest that lumican may be a strong candidate prognostic biomarker and warrants prospective validation. Citation Format: Marco A. De Velasco, Yuji Hatanaka, Takashi Oki, Yurie Kura, Yutaka Yamamoto, Kazuhiro Yoshimura, Nobutaka Shimizu, Masahiro Nozawa, Kazuhiro Yoshikawa, Kazuto Nishio, Hirotsugu Uemura. Expression of lumican is negatively associated with the risk of biochemical recurrence in human prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4729. doi:10.1158/1538-7445.AM2014-4729
Hypoproteinaemia during Recovery from Severe Anaemia
Authors: T. Davies
Journal: BMJ (1945)

showing retardation of thought, drowsiness, mild disorientation, and slow response to questioning.Objective signs were present in 10 cases of this type, and included nystagmus, pupillary dilatation with sluggish reflexes to light, diminution of vision, cerebellar ataxia and dysarthria, and loss of vibration and position sense.Centrally, therefore, the main incidence seems to be on the optic nerves, oculomotor nerves, cerebellar con- nexions, and posterior columns, with occasional involvement of the higher centres producing psychic disturbances.Treatment up to the present has been only symptomatic, as these cases improve with rest in bed and removal from exposure to the gas, and no great increase in blood or cerebro- spinal fluid bromide has been found (up to 27 mg. of sodium bromide per 100 c.cm.).It is presumably the methyl combina- tion that does the damage, as bromide poisoning is not clinically apparent until blood concentrations of above 100 mg. per 100 c.cm. are reached.Convalescence is prolonged, with persistence of some ataxia, undue fatigue, and nystagmus long after the disappearance of the peripheral neuritis, but most of the cases seem to have recovered within a year.Two patients were returned to employment where the risk of exposure to methyl bromide was still present, and both relapsed within six months and had lost time from work owing to residual and recrudescing symptoms.SummaryThe effects of chronic methyl bromide poisoning on the nervous system are described, with a review of the literature and an illustra- tive case history.These effects, on analysis, form a pattern of dysfunction mainly affecting the peripheral and optic nerves, cerebellar connexions, and certain spinal cord tracts, although the material available is not sufficient to postulate a definite syndrome associated with methyl bromide poisoning.On removal of the patient from the toxic hazard the symptoms slowly clear up without any specific treatment and apparently with- out permanent sequelae, but it is inadvisable to allow return to further exposure.
Surveillance for Recurrence of Colorectal Cancer
Authors: Tetsuji Fujita
Journal: JAMA (2014)

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
Benign Leptospirosis: First Reported Outbreak in British Isles due to Strains Belonging to the Hebdomadis Serogroup of Leptospira Interrogans
Authors: A. Sakula, W. Moore
Journal: BMJ (1969)

The clinical and epidemiological features associated with the first reported outbreak in the British Isles of benign anicteric leptospirosis, due to strains belonging to the hebdomadis subgroup, are described. Four cowherdsmen working in two dairy farms in Surrey developed a febrile illness which was not associated with jaundice, but aseptic meningitis was a feature. Microscopic agglutination tests with formolized antigen suspensions revealed a significant rise in the agglutinin titres against various serotypes belonging to the hebdomadis serogroup of Leptospira interrogans. The probable source was eventually traced to the cattle, which showed serological evidence of infection with the same serogroup.
Chemical Manipulation of Food
Authors: E. Mellanby
Journal: BMJ (1951)

Present PracticeAt the present time, both in the U.S.A. and in this country, it is possible for chemical substances to be used in food manipulation and production which ultimately prove to be harmful and deleterious.This does not mean that substances known to be harmful can be added to food but only that chemicals are often assumed to be harmless and, after being used for a longer or shorter time, are then proved to have harmful properties.
Carrier-bound, nonallergenic Ole e 1 peptides for vaccination against olive pollen allergy
Authors: Teresa E. Twaroch, Margit Focke, Vera Civaj, Milena Weber, Nadja Balic, Adriano Mari, Rosetta Ferrara, Santiago Quirce, Susanne Spitzauer, Ines Swoboda, Rudolf Valenta
Journal: Journal of Allergy and Clinical Immunology (2011)
Heritability and Genome-Wide Association Study to Assess Genetic Differences between Advanced Age-related Macular Degeneration Subtypes
Authors: Lucia Sobrin, Stephan Ripke, Yi Yu, Jesen Fagerness, Tushar R. Bhangale, Perciliz L. Tan, Eric H. Souied, Gabriëlle H.S. Buitendijk, Joanna E. Merriam, Andrea J. Richardson, Soumya Raychaudhuri, Robyn Reynolds, Kimberly A. Chin, Aaron Y. Lee, Nicolas Leveziel, Donald J. Zack, Peter Campochiaro, R. Theodore Smith, Gaetano R. Barile, Ruth E. Hogg, Usha Chakravarthy, Timothy W. Behrens, André G. Uitterlinden, Cornelia M. van Duijn, Johannes R. Vingerling, Milam A. Brantley, Paul N. Baird, Caroline C.W. Klaver, Rando Allikmets, Nicholas Katsanis, Robert R. Graham, John P.A. Ioannidis, Mark J. Daly, Johanna M. Seddon
Journal: Ophthalmology (2012)
Helper signals in the plaque-forming cell response to protein-bound haptens.
Authors: N W Roehm, P Marrack, J W Kappler
Journal: The Journal of Experimental Medicine (1983)

We have demonstrated the ability of a series of murine T cell hybridomas to deliver an antigen-specific, B cell I-region-restricted helper signal in the generation of specific PFC responses to protein-bound haptens. With some hybridomas the elicitation of optimal PFC responses required the addition of nonspecific factors provided by culture supernatants of concanavalin A-stimulated (Con A SN) spleen cells. Using hapten-primed B cells depleted of both T cells and macrophages (Mphi) we have now demonstrated a requirement for three nonspecific factor preparations to substitute for spleen Con A SN in the elicitation of optimal PFC responses. The first preparation was the interleukin 1 containing culture supernatant of the Mphi tumor cell line P388D1, the second the interleukin 2 (IL-2) and B cell growth factor containing Con A SN of the T cell hybridoma FS6-14.13, and the third, the gamma interferon containing Con A SN of the T cell hybridoma FS7-20.6.18. The P388D1 and FS6-14.13 factor preparations were most effective when added at the initiation of culture, while the FS7-20.6.18 factor preparation was most effective when added at 24 h of culture. The activity of FS6-14.13 Con A SN was depleted by incubation with the IL-2-dependent T cell line HT-2. The activity of FS7-20.6.18 Con A SN was abrogated by incubation at pH 2. The results suggest that the generation of PFC responses to protein-bound haptens require at least three nonspecific factors in addition to an antigen/Ia specific helper signal.
The mitogen-activated protein kinases p38 and ERK1/2 are increased in lesional psoriatic skin
Authors: C. Johansen, K. Kragballe, M. Westergaard, J. Henningsen, K. Kristiansen, L. Iversen
Journal: British Journal of Dermatology (2005)

Journal Article The mitogen‐activated protein kinases p38 and ERK1/2 are increased in lesional psoriatic skin Get access C. Johansen, C. Johansen Department of Dermatology, Marselisborg Hospital, P.P. Orumsgade 11, University of Aarhus, DK‐8000 Aarhus C, Denmark *Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK‐5230 Odense M, Denmark Claus Johansen PhD. E‐mail: clausoglotte@hotmail.com Search for other works by this author on: Oxford Academic Google Scholar K. Kragballe, K. Kragballe Department of Dermatology, Marselisborg Hospital, P.P. Orumsgade 11, University of Aarhus, DK‐8000 Aarhus C, Denmark *Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK‐5230 Odense M, Denmark Search for other works by this author on: Oxford Academic Google Scholar M. Westergaard, M. Westergaard Department of Dermatology, Marselisborg Hospital, P.P. Orumsgade 11, University of Aarhus, DK‐8000 Aarhus C, Denmark *Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK‐5230 Odense M, Denmark Search for other works by this author on: Oxford Academic Google Scholar J. Henningsen, J. Henningsen Department of Dermatology, Marselisborg Hospital, P.P. Orumsgade 11, University of Aarhus, DK‐8000 Aarhus C, Denmark *Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK‐5230 Odense M, Denmark Search for other works by this author on: Oxford Academic Google Scholar K. Kristiansen, K. Kristiansen Department of Dermatology, Marselisborg Hospital, P.P. Orumsgade 11, University of Aarhus, DK‐8000 Aarhus C, Denmark *Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK‐5230 Odense M, Denmark Search for other works by this author on: Oxford Academic Google Scholar L. Iversen L. Iversen Department of Dermatology, Marselisborg Hospital, P.P. Orumsgade 11, University of Aarhus, DK‐8000 Aarhus C, Denmark *Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK‐5230 Odense M, Denmark Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 152, Issue 1, 1 January 2005, Pages 37–42, https://doi.org/10.1111/j.1365-2133.2004.06304.x Published: 01 January 2005 Article history Accepted: 14 June 2004 Published: 01 January 2005