tbuckley/cabot-search huggingface dataset:
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration
Authors: Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Höffner, Marcus Krüger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun
Journal: Genome biology (2013)

Notophthalmus viridescens, an urodelian amphibian, represents an excellent model organism to study regenerative processes, but mechanistic insights into molecular processes driving regeneration have been hindered by a paucity and poor annotation of coding nucleotide sequences. The enormous genome size and the lack of a closely related reference genome have so far prevented assembly of the urodelian genome.We describe the de novo assembly of the transcriptome of the newt Notophthalmus viridescens and its experimental validation. RNA pools covering embryonic and larval development, different stages of heart, appendage and lens regeneration, as well as a collection of different undamaged tissues were used to generate sequencing datasets on Sanger, Illumina and 454 platforms. Through a sequential de novo assembly strategy, hybrid datasets were converged into one comprehensive transcriptome comprising 120,922 non-redundant transcripts with a N50 of 975. From this, 38,384 putative transcripts were annotated and around 15,000 transcripts were experimentally validated as protein coding by mass spectrometry-based proteomics. Bioinformatical analysis of coding transcripts identified 826 proteins specific for urodeles. Several newly identified proteins establish novel protein families based on the presence of new sequence motifs without counterparts in public databases, while others containing known protein domains extend already existing families and also constitute new ones.We demonstrate that our multistep assembly approach allows de novo assembly of the newt transcriptome with an annotation grade comparable to well characterized organisms. Our data provide the groundwork for mechanistic experiments to answer the question whether urodeles utilize proprietary sets of genes for tissue regeneration.
A hepatitis B virus mutant with a new hepatocyte nuclear factor 1 binding site emerging in transplant-transmitted fulminant hepatitis B
Authors: I Pult, T Chouard, S Wieland, R Klemenz, M Yaniv, H E Blum
Journal: Hepatology (1997)

Hepatitis B virus (HBV) DNA was cloned from serum of a heart transplant recipient who died from fulminant hepatitis B transmitted by the donor. Restriction enzyme analyses of the clones obtained by conventional cloning yielded six HBV variants: a major species (pF-1) representing 88% and five minor species (pF-2 to pF-6), each representing 2% to 4% of the clones. The complete nucleotide sequence of these six variants revealed that five of the six viral genomes, including pF-1, carried a novel 11 base pair (bp) insertion in the core promoter region as well as an 18 bp and an 108 bp in-frame deletion in the pre-S1 region not present in the donor. One genome was identical to the sequence of the donor. Functional analyses of HBV clones generated by in vitro mutagenesis and cassette exchange showed that the 11 bp insertion is a strong binding site for hepatocyte nuclear factor 1 (HNF-1). In transient transfection experiments, the novel HNF-1 sequence motif was shown to result in enhanced viral replication. Immunohistochemical analyses revealed high levels of cytoplasmic and nuclear hepatitis B core antigen (HBcAg) and only scattered hepatitis B surface antigen (HBsAg) expression in the liver. The data in our immunosuppressed patient showed that HBV variants can rapidly accumulate in severe hepatitis B and suggest that the novel HNF-1 binding site may have contributed to the fulminant clinical course, possibly via enhanced viral replication.
Foods and Nutrition 1981
Authors: Philip L. White
Journal: JAMA (1981)

<h3>Questions</h3> In these exciting times, when medical science is beginning to reap the benefits of years of physiological research and to understand the exquisite metabolic patterns in health, trauma, and the aging process, the public is asking the simple question: What should we eat? "If physicians and nutritionists would agree on what they tell the public about diet, my life would be a lot simpler." Thus chided a friend as he was deciding whether to partake of Baked Alaska or shaved chocolate cake during his birthday party. He had already enjoyed some wine, canapés, and an Italian dinner. "Eat both," I advised, "but in very small amounts." My friend, Larry, contemplating his birthday cake, is physically active and maintains appropriate weight, but he is worried. At age 50 years, he is beginning to think about the process of aging and is aware of much of what has been written in
AN EVALUATION OF HYPNOSIS IN THE TREATMENT OF ALCOHOLICS
Authors: STANLEY ABRAMS
Journal: American Journal of Psychiatry (1964)

In an attempt to determine the effectiveness of hypnotic techniques in the treatment of alcoholism, the literature was reviewed. The findings regarding the value of a hypnotically induced conditioned aversion reflex indicated that considerable success had been attained with this method. Moreover, less risk was involved and conditioning was reported to be instilled more deeply in the hypnotic in contrast to the drug induced conditioning. The findings regarding the degree of success were definitely equivocal. Some therapists reported that no treatment of the alcoholic was complete without the employment of hypnosis, while others indicated that it was of little value. Further investigation is needed to clarify these findings and to determine the value of hypnotic methods in the treatment of the alcoholic patient.
TCT-85 Ventricular and Atrial Remodeling after the Percutaneous MitraClip: 4 year Follow-up Data from the EVEREST II Randomized Controlled Trial
Authors: Atif Qasim, Laura Mauri, Patricia Apruzzese, Lori Crosson, Jeffrey Ellis, Peter S. Fail, Andrew Wang, William A. Gray, Ted Feldman, Elyse Foster
Journal: Journal of the American College of Cardiology (2013)
The Treatment of Mild Hypertension Study-Reply
Authors: James D. Neaton
Journal: JAMA (1993)

<h3>In Reply.</h3> —Although the nutritional-hygienic advice given participants in TOMHS was targeted at weight loss, reduction in sodium and alcohol intake, and increase in physical activity and not specifically at smoking cessation,<sup>1</sup>27% of the smokers at entry reported smoking cessation after 4 years of follow-up. Cessation rates were similar for those given placebo (28%) and those in a drug treatment group (27%). We attribute this cessation in part to the general emphasis of our intervention, which sought to increase health awareness and to promote sustained changes in lifestyle, and in part to changes in smoking behavior that were taking place in the US population during the time of our study.<sup>2</sup> Consistent with a large body of data, a higher percentage of smokers than nonsmokers experienced at least one major clinical event (6.1% vs 5.6%). Similarly, the incidence of first major or other clinical events was higher among
Can morbidity associated with untreated asthma in primary school children be reduced?: a controlled intervention study.
Authors: R Hill, J Williams, J Britton, A Tattersfield
Journal: BMJ (1991)

OBJECTIVE--To determine whether an intervention programme based on existing school and community resources can reduce school absence and improve participation in games lessons and sport in children with unrecognised or undertreated asthma. DESIGN--Parallel group controlled intervention study. SETTING--102 primary schools in Nottingham: 49 were randomised to receive the intervention and 53 to be control schools. SUBJECTS--All children aged 5 to 10 years with parent reported absence from school because of wheezing in the previous year and taking no treatment or beta agonists only. INTERVENTIONS--Children with asthma were referred to their general practitioner for assessment of symptoms and treatment. Teachers were given education on asthma by the school nurse in 44 of the 49 intervention schools. MAIN OUTCOME MEASURES--Changes in school absence and missed games and swimming lessons because of wheezing, and schools9 policy towards management of asthma in school. RESULTS--Of 17,432 children screened, 451 met the entry criteria--228 in intervention schools and 223 in control schools. 152 (67%) children in intervention schools visited their general practitioner, of whom 39 (26%) were given a new diagnosis of asthma and 58 (38%) had treatment for asthma increased or changed. Over the next academic year mean (SE) parent reported school absence due to wheezing fell significantly, but to a similar extent, in both intervention and control schools (0.82 (0.11) and 1.09 (0.21) weeks respectively). There was little change in school recorded absence or participation in games lessons and swimming lessons in either group. At the end of the study intervention schools were more likely to have improved aspects of management of asthma in school. CONCLUSION--The intervention resulted in a majority of children being assessed by their general practitioner and improved teachers9 understanding and management of asthma, but it did not result in any appreciable reduction in morbidity.
Centenarians: Miss Hastings, who Died Aged 104
Authors: G. M. Humphry
Journal: BMJ (1886)

TH-R BRIVIIIY 1 cJ4-f-JiQJR4 }¢; 1S8.& gram,the identical plate of Braune's taken from his frozen sections; T~~~~~~ã ' k~~a 1. (Esophagus. 2. Aorta.4. Liver, right and left lobes.5. Pericardial layer of diaphragm.5. Stomuach.[Section at the level of the fifth rib in front.Braune.]and it will be seen that the only part of the diaphragm upon which tUe,jhart rests (5) which can comne into contact with the stomach, is the sMall triangular portion marked off by dotted lines.This corre-911onds in its thoracic aspect to the under surface of the left ventricle, an on its abdominal to the anterior wall of the stomach, two inches ad a half from the cardiac orifice, aud two from the lesser curvature -points which strikinglv correspond with the situation of the t.wo pathological conditions which exist in the case I have recorded.Ihadlan opportunity of verifying this anatomical relation in one .rentsubject.A pin passed through the chest.wall, in the left fifth intercostal space inside the nipple, and directed downwards, traversed the,ericardial aspect, of the diaphragm, and impinged on the anterior waIl of the stomach in the situation pointed out.It would, therefore, appear as an anatomical -condition to permit a perforation of the pericardium and heart from the stomach, that the left lobe of the liver should be smaller and narrower tbaii it is 3known to be in the majority-or any way in a very large-number-- of iastances.
Epstein-Barr virus-related primary cutaneous amyloidosis. Successful treatment with acyclovir and interferon-alpha
Authors: F. DRAGO, E. RANIERI, A. PASTORINO, S. CASAZZA, F. CROVATO, A. REBORA
Journal: British Journal of Dermatology (1996)

Cutaneous lesions related to chronic active Epstein-Barr virus (EBV) infection have been rarely documented in immunocompetent patients. A 30-year-old woman, fulfilling the diagnostic criteria for the chronic fatigue syndrome, had a 10-year history of pruritic brownish macules and papules on her chest and back. Her EBV serology was abnormal; the EBV genome was present in the epidermis of lesions, in oral secretions, and in peripheral mononuclear cells (PMC). Her blood lymphocytes spontaneously outgrew in culture. Histology revealed deposits of amyloid in the papillary dermis. Treatment with acyclovir and interferon-alpha rapidly improved her condition, stopped the lymphocyte outgrowth in culture, and reduced the EBV DNA content in oral secretions and in PMC. These data support an endogenous reactivation of EBV infection and suggest a causal relationship with primary amyloidosis.
Urine Mutagenicity as a Measure of Exposure to Tar
Authors: David J. Doolittle
Journal: JAMA (1987)

To the Editor.—  In the recent article by Benowitz et al1entitled Reduced Tar, Nicotine, and Carbon Monoxide Exposure While Smoking Ultralow- but Not Low-Yield Cigarettes, the authors suggest that   may be quantitatively measured as urine mutagenicity. Neither the literature2-4nor the authors' own data support this assumption.  The authors state that relative tar exposure was estimated by urine mutagenicity, simply assuming that urine mutagenicity offers a predictive measure of tar exposure. The validity of this assumption is called into question by the authors' own data. The authors state that group 1 smokers tended to be heavier smokers, based on higher admission blood levels of cotinine... and plasma thiocyanate. Yet, when the mutagenic activity of the two groups when smoking their usual brand of cigarette is compared, the urine of the heavier smokers is substantially less mutagenic (Table).  Differences in urine mutagenic activity can be due
Iron Nutrition and the Fortification of Food With Iron
Authors: Clement A. Finch
Journal: JAMA (1972)

At present, a high incidence of iron deficiency prevails in the infant and female population. Improvement in iron balance through fortification of food with additional iron is needed to prevent such deficiency. In the infant, this may be accomplished through the fortification of special food items whose use is confined to infancy. In the adult woman, an increase in fortification of flour and flour products to 40 mg/lb is proposed to accomplish this. Such manipulation of the public diet carries with it the responsibility of monitoring its effects on the iron balance of the population, and on the prevalence of iron deficiency and iron overload.
Staining of Pneumocystis carinii in Lung Imprints
Authors: ABRAHAM VERGHESE
Journal: Annals of Internal Medicine (1984)

Letters and Corrections1 February 1984Staining of Pneumocystis carinii in Lung ImprintsABRAHAM VERGHESE, M.D., ALFRED DEMARIA JR., M.D.ABRAHAM VERGHESE, M.D.Search for more papers by this author, ALFRED DEMARIA JR., M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-100-2-321_2 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editors: Of relevance to the recent paper of Macher and coworkers (1) on Pneumocystis carinii identified by Gram stain of lumg imprints is a case of a male narcotic addict recently seen by us in whom a diagnosis of pneumocystis pneumonia was made by the method described and was confirmed by conventional stains of both lung imprints and lung tissue. In addition to the Gram staining, the cysts could be stained with Kinyoun acid-fast basic fuschin or methylene blue.Thus,P. cariniimay be visible on slides of lung imprints stained with many of the stains a clinician...Reference1. MACHERSHELHAMERMACLOWRYPARKERMASUR AJJMH. Pneumocystis carinii identified by Gram stain of lung imprints. Ann Intern Med. 1983;99:484-5. LinkGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: Boston University School of Medicine Boston, MA 02118 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 1 February 1984Volume 100, Issue 2Page: 321-321KeywordsAddictsGram stainingLungsMethylene bluePneumocystisPneumonia Issue Published: 1 February 1984 PDF DownloadLoading ...
A prospective comparative study of narrow-band imaging, chromoendoscopy, and conventional colonoscopy in the diagnosis of colorectal neoplasia
Authors: H.-M. Chiu, C.-Y. Chang, C.-C. Chen, Y.-C. Lee, M.-S. Wu, J.-T. Lin, C.-T. Shun, H.-P. Wang
Journal: Gut (2006)

Background: Discrimination between neoplastic and non-neoplastic lesions is crucial in colorectal cancer screening. Application of narrow-band imaging (NBI) in colonoscopy visualises mucosal vascular networks in neoplastic lesions and may improve diagnostic accuracy. Aim: To compare the diagnostic efficacy of NBI in differentiating neoplastic from non-neoplastic colorectal lesions with diagnostic efficacies of standard modalities, conventional colonoscopy, and chromoendoscopy. Methods: In this prospective study, 180 colorectal lesions from 133 patients were observed with conventional colonoscopy, and under low-magnification and high-magnification NBI and chromoendoscopy. Lesions were resected for histopathological analysis. Endoscopic images were stored electronically and randomly allocated to two readers for evaluation. Sensitivity, specificity and diagnostic accuracy of each endoscopic modality were assessed by reference to histopathology. Results: NBI and chromoendoscopy scored better under high magnification than under low magnification in comparison with conventional colonoscopy. The diagnostic accuracy of NBI with low or high magnification was significantly higher than that of conventional colonoscopy (low magnification: p = 0.0434 for reader 1 and p = 0.004 for reader 2; high magnification: p<0.001 for both readers) and was comparable to that of chromoendoscopy. Conclusion: Both low-magnification and high-magnification NBI were capable of distinguishing neoplastic from non-neoplastic colorectal lesions; the diagnostic accuracy of NBI was better than that of conventional colonoscopy and equivalent to that of chromoendoscopy. The role of NBI in screening colonoscopy needs further evaluation.
The "Controlled" Use of New Tuberculin in the Treatment of Pulmonary Tuberculosis
Authors: A. C. Watkin
Journal: BMJ (1913)

some ailment, and many for various reasons are disinclined to go back to work, or in some cases, having lost their job from sickness, to find another.From every person I inquire what wages they were receiving when at work, and one can see without much trouble how little induceinent there is to go back and work hard for perhaps 6d. or ls. a week more; one youth told me he only got 6d.more when at work, and with many women the difference is
Prolactin Release After Mating and Genitosensory Stimulation in Females*
Authors: MARY S. ERSKINE
Journal: Endocrine Reviews (1995)

IN many female mammals, vaginocervical stimulation (VCS) received during mating modifies sexual responsiveness and initiates or induces several neuroendocrine changes that influence reproductive success. VCS is particularly important in reflexively ovulating species such as the cat and rabbit in which mating directly induces ovulation by increasing hypothalamic LHRH secretion and pituitary LH release. In spontaneously ovulating species such as the rat, mating-induced changes in neuroendocrine function are no less important for reproductive success. In these cases, mating stimulation triggers the release of the PRL required for rescue of the short-lived corpus luteum of the estrous cycle and for the resulting prolongation of progesterone secretion that is necessary for uterine endometrial development and implantation of the blastocyst. The existence of the link between VCS and reproductive function has been known to endocrinologists since the 1930s (1), and there is substantial understanding of the neural and endocrine mechanisms involved in controlling mating-induced PRL secretion (see Refs. 2–6). In some respects, the requirement for VCS in initiating the endocrine changes necessary for pregnancy is similar to the more classic neuroendocrine reflexes such as suckling-induced oxytocin (OXY) and PRL secretion. Like these latter reflexes, neurogenic stimuli initiate pituitary hormone secretion. Unlike suckling-induced PRL and OXY release (7, 8), however, VCS-induced changes in PRL secretion persist over days rather than seconds/minutes, are associated with a circadian oscillatory mechanism, and are dependent upon establishment of a memory of the VCS. Despite major advances in our understanding of these factors, our knowledge remains incomplete, particularly in the area of the initiation phase of the PRL surges. The present article will review the information available about neural and endocrine changes that occur in response to VCS in the female with particular emphasis on what is known about the proximal responses to VCS that are important for establishment of PRL surges. Because the majority of work in this area has been performed in the rat, this review will focus on this species.
Multiple class I and class II major histocompatibility complex allospecificities are generated with T cell receptor variable (V) domains created by a single Ti beta V gene family.
Authors: O Acuto, R E Hussey, E L Reinherz
Journal: The Journal of Experimental Medicine (1985)

10 alloreactive cytotoxic T lymphocytes using REX Ti beta variable region (V) gene segments in formation of their antigen/major histocompatibility complex (MHC) T3-Ti receptor were selected, cloned, and characterized in an effort to examine the extent of receptor diversity created by this one V gene family. Multiple and distinct class II as well as class I allospecificities were generated from the formation of different Ti beta V domains. Five allospecificities were directed at various class I epitopes whereas the other five were directed at class II MHC gene products. The following conclusions were drawn: (a) Ti beta V genes do not segregate into those that encode class I and those that encode class II allospecificities; and (b) there is no restriction on the Ti beta V gene pool available to T4+ vs. T8+ T lymphocytes.
The Healing Touch
Authors: Robert C. Lusk
Journal: Annals of Internal Medicine (1997)

On Being a Doctor15 September 1997The Healing TouchRobert C. Lusk, MDRobert C. Lusk, MDSalem, OR 97301Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-127-6-199709150-00012 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Seven a.m. and the board's empty! You guys must have had a quiet night.”The sleepy intern nodded, “It was okay for me, but Tom was busy. He's still in the crash room.”My spirits sank. Mondays in the emergency department are never easy, and starting one with a train wreck was not a good omen. I entered the crash room and reached for the chart, but Tom held it back. “You don't want to see that yet. It isn't pretty. Let's talk outside while you finish your coffee.”“Nineteen-year-old male found down … Damn, the syringe was still in ... Author, Article, and Disclosure InformationAffiliations: Salem, OR 97301Corresponding Author: Robert C. Lusk, MD, 720 Winter Street Southeast, Suite 304, Salem, OR 97301. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 15 September 1997Volume 127, Issue 6Page: 486KeywordsBreathingChartsCoffeeEmergency departmentNursesPostural controlSleepTouchVeins Issue Published: 15 September 1997 CopyrightCopyright © 1997 by American College of Physicians. All Rights Reserved.PDF DownloadLoading ...