tbuckley/cabot-search huggingface dataset:
YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Authors: Christopher M. Colangelo, Mark Shifman, Kei-Hoi Cheung, Kathryn L. Stone, Nicholas J. Carriero, Erol E. Gulcicek, TuKiet T. Lam, Terence Wu, Robert D. Bjornson, Can Bruce, Angus C. Nairn, Jesse Rinehart, Perry L. Miller, Kenneth R. Williams
Journal: Genomics Proteomics & Bioinformatics (2015)

Abstract We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry (LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED’s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
Hyperglycemie and Microvascular and Macrovascular Disease in Diabetes
Authors: Ronald Klein
Journal: Diabetes Care (1995)

In summary, over the past 16 years, since the publication of Kelly West's book, epidemiological study has provided better insight into the relation of hyperglycemia and diabetic complications. Data from the WESDR demonstrate a strong consistent relationship between hyperglycemia and the incidence and progression of microvascular (diabetic retinopathy, loss of vision, and nephropathy) and macrovascular (amputation and cardiovascular disease mortality) complications in people with IDDM and NIDDM (Figs. 19 and 20). The DCCT has demonstrated that intensive insulin therapy will reduce the incidence and progression of microvascular complications in people with IDDM (22). A number of further challenges await laboratory scientists and epidemiologists regarding hyperglycemia in people with diabetes. There is a need to understand the relation of hyperglycemia to pathogenetic mechanisms that lead to the development of specific complications, to develop new methods to detect and physiologically treat hyperglycemia, and to develop better methods of primary and secondary prevention of diabetic complications in people with IDDM and NIDDM.
Effects of aspirin and prostaglandin E1 on in vitro thrombolysis with urokinase. Evidence for a possible role of inhibiting platelet activity in thrombolysis.
Authors: W Terres, C Beythien, W Kupper, W Bleifeld
Journal: Circulation (1989)

The formation of thrombi in vivo includes the activation of both platelets and the coagulation cascade. Conventional thrombolytic therapy is primarily directed toward the dissolution of fibrin. To evaluate the possibility that platelet activity impairs the lysis of thrombi, we studied the effects of aspirin and platelet-deaggregating prostaglandin E1 on thrombolysis with urokinase. Combined platelet and fibrin thrombi were produced in vitro by adding CaCl2 and collagen (1 microgram/ml) to citrated platelet-rich plasma (250,000 platelets per microliters). Urokinase (500-10,000 units/ml) caused a dose-dependent weight loss of the thrombi that was maximal at 2,000 units/ml. The addition of aspirin (10-200 micrograms/ml) to platelet-rich plasma before thrombus formation markedly enhanced thrombolysis with urokinase. This effect was most pronounced at 20 micrograms/ml aspirin. However, when aspirin was added after completion of thrombus formation, no significant effect on thrombolysis was noted. Prostaglandin E1 (1-100 mumol/l) improved the lysis with urokinase of the combined platelet and fibrin thrombi. This effect was maximal at 20 mumol/l prostaglandin E1. When pure fibrin thrombi were produced in platelet-free plasma, prostaglandin E1 was without effect on lysis. Thus, in vitro lysis with urokinase of combined platelet and fibrin thrombi was enhanced by the addition of platelet-deaggregating prostaglandin E1 and by pretreatment with aspirin.
Insights from studying prejudice in the context of American atheists
Authors: Eric P. Charles, Nicholas J. Rowland, Brooke Long, Fritz Yarrison
Journal: Behavioral and Brain Sciences (2012)

Abstract Our research on non-religion supports the proposed shift toward more interactive models of prejudice. Being nonreligious is easily hideable and, increasingly, of low salience, leading to experiences not easily understood via traditional or contemporary frameworks for studying prejudice and prejudice reduction. This context affords new opportunity to observe reverse forms of interactive prejudice, which can interfere with prejudice reduction.
PUERPERAL SEPTICEMIA AND ENDOCARDITIS CAUSED BY PSEUDOMONAS AERUGINOSA
Authors: Robert M. Hodges
Journal: JAMA (1960)

This report adds a 12th case to 11 documented cases of septicemia due to Pseudomonas in association with acute bacterial endocarditis. The patient, an Alaskan Indian woman, delivered a stillborn infant spontaneously under sterile controlled conditions. On the third postpartum day, treatment with procaine penicillin in doses of 600,000 (later increased to 1,000,000) units every six hours was instituted to treat infection. Pseudomonas as well as nonhemolytic staphylococci was cultured from the blood on the 30th postpartum day. Death occurred on the 59th postpartum day. Among other autopsy findings were Pseudomonas aeruginosa urinary infection, endometritis, septicemia, endocarditis, and meningitis. In addition there was adrenal necrosis with probable terminal failure. The increasing incidence of Pseudomonas aeruginosa septicemia, with acute endocarditis, is related to the use of antibiotics. The mortality of Pseudomonas septicemia is over 50%.
Alteration of drug metabolism in Gilbert's syndrome.
Authors: N Carulli, M Ponz de Leon, E Mauro, F Manenti, A Ferrari
Journal: Gut (1976)

The pathophysiology of Gilbert's syndrome was studied by investigating the metabolism of the drug tolbutamide, which is metabolised by the liver but does not undergo glucuronidation. Using rat liver cell supernatant, tolbutamide was shown to bind to the hepatic cytoplasmic Y protein in a manner similar to other organic anions, but not to Z protein. In 31 patients with Gilbert's syndrome the plasma disappearance (plasma half-life, mean +/- SD: 628+/-84 min) and metabolic clearance (7-9+/-1-8 ml/min) were significantly (P less than 0-0005) altered compared with the 13 controls (mean half-life 393+/-26 and mean clearance 13-4+/-1-5). The eight patients with hyperbilirubinaemia due to haemolytic disease showed no difference from the normal control subjects. In three patients with Gilbert's syndrome the cumulative urinary excretion of tolbutamide metabolites, 24 hours after the administration of the drug, was 30% lower than in the controls. In the five patients with Gilbert's syndrome, phenobarbital administration (100 mg/day) produced a significant increase in clearance of the drug from 8-8+/-0-8 to 13-4+/-1-9 ml/min; this was paralleled by a fall in serum bilirubin concentration. The plasma half-life of tolbutamide was similar in Gunn rats and Wistar rats. The results suggest that the metabolic defect(s) of Gilbert's syndrome affects compounds other than bilirubin and that defective uptake is probably the major factor.
ECCENTRIC POSES OF THE HEAD.Read in the Section on Ophthalmology at the Forty-fourth Annual Meeting of the American Medical Association.
Authors: J. ELLIOTT COLBURN
Journal: JAMA (1893)

should not consider he has confounded meningitis with typhoid fever.Case ®.-R.H. S., age 28, of Clifton Forge, Va., was sent to me by his physician on April 24, 1893, for treatment of his eyes which had become defective during an attack of typhoid fever, commencing July 4, 1892, and from which he did not fully recover until October, 1892, nearly four months.His sight continued to grow worse in spite of his steady improvement in general health.When I first saw him, both optic nerves showed decided atrophy of the discs.His vision was right 5-200, left % 200.I put him on strychnia sulp.and dil.phosphoric acid, grains two to the ounce.He commenced with 10 drops of tûis mixture after meals, and increased one drop each dose without showing any toxic symptoms until he was taking 52 drops, or one-fifth of a grain of sulphate of strychnia at a dose.On May 4 vision was, right, 12-200, left 5-200; May 10, right 14-200, left May 13, ; May 18, right 20-200, left 17-200, which indicated a steady improvement, as the right eye had four times as much vision and the left thirty-four times as much as at the first examination three weeks pre¬ viously. The type was changed at each examination so that he could not bring his memory to aiti his sight and give false results. When he reached th dose of one-fifth of a grain three times daily he showed decided toxic symptoms, when it was reduced to one-seventh of a grain, and he still continues the treatment.
A Bedside Decision Instrument To Elicit a Patient's Preference Concerning Adjuvant Chemotherapy for Breast Cancer
Authors: Mark N. Levine, Amiram Gafni, Barbara Markham, Dawn MacFarlane
Journal: Annals of Internal Medicine (1992)

▪ The objective of this study was to develop an instrument to help clinicians inform patients with breast cancer of risks and benefits of adjuvant chemotherapy as derived from clinical trials and to help the informed patient decide whether she prefers treatment or no treatment. The instrument consists of a visual aid (called the decision board) and written material. It provides detailed information on a patient's choices (chemotherapy or no chemotherapy), outcomes (recurrence or not), probabilities of outcomes and their meaning, and quality of life associated with treatment choice and outcome. The validity and reliability of the instrument were evaluated in 30 healthy female volunteers. It was first administered using standard estimates of recurrence for node-negative breast cancer (15% risk of recurrence without treatment, which is reduced to 10% with chemotherapy). A preference for treatment (or no treatment) was then elicited. The validity was evaluated by changing the information provided on risks and benefits and determining whether the preference changed in a predictable manner. To test for reliability, the instrument was administered 2 weeks later. Seventeen women chose chemotherapy and 13 chose no chemotherapy. In the former group, 14 women (82%) switched preference when the magnitude of benefit was reduced, and 16 (94%) switched when the toxicity of treatment was increased. For those women who chose not to receive chemotherapy, 12 (92%) switched when the benefit was increased and 100% switched when toxicity was eliminated. The reliability was excellent (κ = 0.86). The instrument has been used to elicit treatment preferences in 37 newly presenting patients with high-risk, node-negative breast cancer and has been found to be acceptable and helpful to the patient.
US settlement harms rest of the world
Authors: R. Tomlinson
Journal: BMJ (1997)

The proposed $368.5bn (£230bn) legal settlement between 40 states and the tobacco industry in the United States was heavily criticised for doing nothing to limit the activities of the tobacco giants abroad.

The tobacco deal (26 April, p 1217) was the hottest political subject at the conference, and organisers said that no other topic had …
ACUTE PANCREATITIS: ITS CAUSES, SYMPTOMS, AND TREATMENT: WITH A DESCRIPTION OF THREE CASES
Authors: A. J. Evans
Journal: BMJ (1913)

THIE rapid developmuent of abdominal surgery in recent years, especially as regards the treatment of diseased organs lying in the upper abdomen, has in a large measure been due to tlle pioneer work of Mayo Robson and Moynilian, and to this must be added the no less important patlhological, chemical, and experimental work of Cammidge, Opie, Flexner, and others.We have now, therefore, a very precise knowledge of the intimate inter-relationslhip between the biliary passages, the duodenum and the pancreas, and lhow disease of one of these structures may affect the other, more especially so if it be of a catarrlhal or muicrobic nature.It lhas been my lot within the past eiglhteen montlhs to operate on three cases of acute pancreatitis, a condition which, not many years ago, often passed unrecognized, even on the operating table and somiietimes in the postmnortem room.Tlle recognition of acute pancreatitis from a clinical standpoint during life is still an exceedingly difficult mnatter, and in only one of my cases was tlle diagnosis suspected before the abdomen wvas opened.CASE I. E. J., male, aged 35, a dock labourer, was brought into hospitat in a state of collapse.He had been drinking heavily during the previous ten days, and had hardly been sober during that period.
Quantitation of cis-diamminedichloroplatinum II (cisplatin)-DNA-intrastrand adducts in testicular and ovarian cancer patients receiving cisplatin chemotherapy.
Authors: E Reed, S H Yuspa, L A Zwelling, R F Ozols, M C Poirier
Journal: Journal of Clinical Investigation (1986)

The antitumor activity of cis-diamminedichloroplatinum II (cisplatin) is believed to be related to its covalent interaction with DNA where a major DNA binding product is an intrastrand N7-bidentate adduct on adjacent deoxyguanosines. A novel immunoassay was used to quantitate this adduct in buffy coat DNA from testicular and ovarian cancer patients undergoing cisplatin therapy. 44 out of 120 samples taken from 45 cisplatin patients had detectable cisplatin-DNA adducts. No adducts were detected in 18 samples of DNA taken from normal controls, patients on other chemotherapy, or patients before treatment. The quantity of measurable adducts increased as a function of cumulative dose of cisplatin. This was observed both during repeated daily infusion of the drug and over long-term, repeated 21-28 d cycles of administration. These results suggested that adduct removal is slow even though the tissue has a relatively rapid turnover. Patients receiving cisplatin for the first time on 56-d cycles, and those given high doses of cisplatin as a "salvage" regimen, did not accumulate adducts as rapidly as patients on first time chemotherapy on 21- or 28-d cycles. Disease response data, evaluated for 33 cisplatin-treated patients, showed a positive correlation between the formation of DNA adducts and response to drug therapy. However, more data will be required to confirm this relationship. These data show that specific immunological probes can readily be applied to quantitate DNA adducts in patients undergoing cancer chemotherapy.
Beneficial Effects of Hepatitis in Patients with Acute Myelogenous Leukemia
Authors: JAMES C. BARTON
Journal: Annals of Internal Medicine (1979)

Of 50 consecutive patients admitted with acute myelogenous leukemia, 30 developed complete remissions on antileukemic therapy. Nineteen of the 30 repeatedly had elevated serum glutamic oxalacetic transaminase (SGOT) concentrations 3 to 14 weeks after the start of therapy. Patients with SGOT elevations had a significantly greater chance of remission and a longer survival (76 ± 11 weeks) than those with normal SGOT levels (39 ± 5 weeks), suggesting that hepatitis may have a beneficial effect in acute myelogenous leukemia. The hepatitis was mild in all patients. Review of patients at this institution alive 2 years after the diagnosis of acute myelogenous leukemia showed that they repeatedly had elevated SGOT levels. We believe that most had non-A, non-B post-transfusion hepatitis, which may have a beneficial effect on the leukemia or serve as an indicator of patients who have greater immunocompetence and thus a better prognosis.
Antibacterial effects and biocompatibility of titanium surfaces with graded silver incorporation in titania nanotubes
Authors: Shenglin Mei, Huaiyu Wang, Wei Wang, Liping Tong, Haobo Pan, Changshun Ruan, Qianli Ma, Mengyuan Liu, Huiling Yang, Liang Zhang, Yicheng Cheng, Yumei Zhang, Lingzhou Zhao, Paul K. Chu
Journal: Biomaterials (2014)
A Blind Spot in Preventive Medicine
Authors: Christine L. Williams
Journal: JAMA (1976)

PEDIATRICIANS have without doubt done exceptionally well in keeping our children healthy as children, but at the same time they have fallen far short of creating healthy adults. The result is a blind spot in preventive medicine, a gray zone in chronic disease prevention that needs elucidation before progress can be made against excessive mortality related to heart  cancer, and stroke.  Many pediatricians still consider chronic disease prevention in childhood controversial and intend to wait for absolute confirmation and clarification of the complex etiologic web surrounding the pathophysiology of these diseases. Cautiously worded articles have labeled atherosclerosis as a pediatric disease, but have advocated screening and intervention only among those children at high risk, 1 particularly those whose parents have suffered premature heart attacks (be-, fore 50 years of age) even though the children may be grown up by then. We have at least agreed that prevalence studies are
Serum ferritin is an independent predictor of histologic severity and advanced fibrosis in patients with nonalcoholic fatty liver disease
Authors: Kris V. Kowdley, Patricia Belt, Laura A. Wilson, Matthew M. Yeh, Brent A. Neuschwander–Tetri, Naga Chalasani, Arun J. Sanyal, James E. Nelson
Journal: Hepatology (2011)

Serum ferritin (SF) levels are commonly elevated in patients with nonalcoholic fatty liver disease (NAFLD) because of systemic inflammation, increased iron stores, or both. The aim of this study was to examine the relationship between elevated SF and NAFLD severity. Demographic, clinical, histologic, laboratory, and anthropometric data were analyzed in 628 adult patients with NAFLD (age, ≥ 18 years) with biopsy-proven NAFLD and an SF measurement within 6 months of their liver biopsy. A threshold SF >1.5 × upper limit of normal (ULN) (i.e., >300 ng/mL in women and >450 ng/mL in men) was significantly associated with male sex, elevated serum alanine aminotransferase, aspartate aminotransferase, iron, transferrin-iron saturation, iron stain grade, and decreased platelets (P < 0.01). Histologic features of NAFLD were more severe among patients with SF >1.5 × ULN, including steatosis, fibrosis, hepatocellular ballooning, and diagnosis of NASH (P < 0.026). On multiple regression analysis, SF >1.5 × ULN was independently associated with advanced hepatic fibrosis (odds ratio [OR], 1.66; 95% confidence interval [CI], 1.05-2.62; P = 0.028) and increased NAFLD Activity Score (NAS) (OR, 1.99; 95% CI, 1.06-3.75; P = 0.033).A SF >1.5 × ULN is associated with hepatic iron deposition, a diagnosis of NASH, and worsened histologic activity and is an independent predictor of advanced hepatic fibrosis among patients with NAFLD. Furthermore, elevated SF is independently associated with higher NAS, even among patients without hepatic iron deposition. We conclude that SF is useful to identify NAFLD patients at risk for NASH and advanced fibrosis.
Primary Tumour of Right Auricle of Heart, Rupture of Inferior Vena Cava
Authors: N. Raw
Journal: BMJ (1898)

PRIMARY TUMOUR OF RIGHT AURICLE.[rF1=.I= 'I335 of'a few teeth, which are connected with their neighbours by sh7arp points or hooks.In the case I record below the patient had been for many years in the habit of wearing three artificial incisors attached to a plate which had been broken some months previously, axid which from motives of economy she had neglected to get repaired.History.-E.R., aged 34, who was not in the habit of removing her teeth at night, woke up early in the morning of October 3oth, -x897, with a very sore throat, and found that she had loet her teeth.As she was subject to occasional epileptic attacks she concluded, " as she felt so baid," that she lad had one-during the night and had swallowed her teeth.She sent for her doctor, who advised her to take nothing but gruel, but she found that swallowing was so painful that she took " hardly anytlhing."Thirty- six hours afterwards her breath began to get short, and this graduall increased for the next twenty-four hours, when she applied at the hospital for admission.
Gaucher's Disease and Coagulation Factors
Authors: Arthur Sawitsky, Bruce F. Boklan
Journal: Annals of Internal Medicine (1972)

Letters, Comments and Corrections1 July 1972Gaucher's Disease and Coagulation FactorsARTHUR SAWITSKY, M.D., BRUCE F. BOKLAN, M.D.ARTHUR SAWITSKY, M.D.Search for more papers by this author, BRUCE F. BOKLAN, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-77-1-150_2 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editor: The concurrence of two unusual disorders in one patient has led us to investigate the relationship between them.Patient H.G. is a 52-year-old man with Gaucher's disease; the diagnosis made 35 years earlier in him and two of four siblings. He has had thrombocytopenia for many years. He was seen here by us because of a tender right lower-quadrant mass of 6 weeks' duration. He had a Grade III/IV holosystolic apical cardiac murmur, massive hepatosplenomegaly, and a firm mass in the right side of the abdomen, from the inguinal ligament to the liver and, laterally, to the... This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAuthors: ARTHUR SAWITSKY, M.D.; BRUCE F. BOKLAN, M.D. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited byPlatelet function and coagulation abnormalities in type 1 Gaucher disease patients: effects of enzyme replacement therapy (ERT)Gaucher's disease and acquired coagulopathyObstetric aspects of Gaucher diseaseAnticoagulant Monitoring 1 July 1972Volume 77, Issue 1Page: 150-151KeywordsCoagulation factorsHepatosplenomegalyLigamentsLiver ePublished: 1 December 2008 Issue Published: 1 July 1972 PDF downloadLoading ...
Campylobacter jejuni enteritis and reactive arthritis
Authors: C. D. Short, P. T. Klouda, L. Smith
Journal: Annals of the Rheumatic Diseases (1982)

A further case of reactive arthritis following <i>Campylobacter jejuni</i> enteritis is reported. The interim results of a small prospective study are discussed. It may be desirable to do serological studies for campylobacter infection in the investigation of mono- or polyarthritis of acute onset.
Authors' reply to Cottrell and Wittekind
Authors: L. Te Morenga, J. Mann, S. Mallard
Journal: BMJ (2013)

Thank you for your interest in spreading the word about The BMJ.NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address. Username * Your Email * Send To * You are going to email the following Authors' reply to Cottrell and Wittekind Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.