tbuckley/cabot-search huggingface dataset:
A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals
Authors: D. Penny, W. T. White, M. D. Hendy, M. J. Phillips
Journal: Molecular Biology and Evolution (2007)

Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.
A possible link between Trousseau's syndrome and tissue factor producing plasma cells
Authors: Kazuyuki Shimizu, Junji Itoh
Journal: American Journal of Hematology (2009)

increase has been previously reported only in three transplanted sickle cell disease patients after graft failure [6], suggesting that such an event may occur in different genetic diseases.In the absence of a definite explanation, only a series of hypotheses can be discussed.It is possible that, after myeloablative treatment, the vast majority of committed autologous erythroid progenitors were destroyed, and autologous hematopoietic stem cells alone survived in marrow niches, restoring the ontological HbF regulation mechanisms [7] with a complete reversal of ggene silencing.In such a case, it is questionable whether this long-lasting effect on full HbF synthesis will be permanent.Otherwise, the increased HbF may be due to a new status, induced by modulations and influences operating in the setting of the BMT (microenvironment and stage-specific cytokines), able to re-program globin-gene expression or to select the ''fetal clones'' proliferation.Such a possibility is supported by the fact that the environment is known to influence globin synthesis [8].Moreover, it remains to be determined whether the favorable genetic predisposition for a deregulated g-globin gene transcription (homozygosity for Gg-158) observed in our patient concurred with the full HbF production.
Bone marrow cytogenetic abnormalities of aplastic anemia
Authors: Yi-Kong Keung, Mark J. Pettenati, Julia M. Cruz, Bayard L. Powell, Ralph D. Woodruff, David H. Buss
Journal: American Journal of Hematology (2001)

Cytogenetic abnormalities in association with aplastic anemia have been reported fairly infrequently. Clonal cytogenetic abnormalities at initial diagnosis are uncommon. A retrospective study was performed of the cytogenetic findings in patients with typical morphological and clinical features of severe aplastic anemia from a single institution for the years 1988 through 1998. A total of 30 cases of aplastic anemia, 16 men and 14 women, were identified. The median age was 60 with females being significantly older (67.5 years) in comparison to males (44 years). Bone marrow specimens failed to yield metaphases in 16 cases and normal karyotypes were detected in 11 cases. Cytogenetic abnormalities were detected in 3 cases. Clonal abnormalities, as defined, occurred in only 2 cases (6.7%). A review of the literature identified a total of 24 cases of aplastic anemia with abnormal cytogenetic findings. Overall, the most common chromosome abnormalities are trisomies of 6 and 8 and loss of chromosome 7. Trisomy 6 is more common at diagnosis while loss of chromosome 7 is more common after therapy. Am. J. Hematol. 66:167–171, 2001. © 2001 Wiley-Liss, Inc.
ELLIPTICAL REGIONS OF INTEREST (ROI) IMPROVE ACCURACY OF MYOCARDIAL IMAGING
Authors: A. C. Civelek, K. Durski, J. Links, P. Cole, H. N. Wagner
Journal: Clinical Nuclear Medicine (1988)

A circular ROI is often used to quantify the tracer distribution within the left ventricular myocardium in SPECT long and short axis views. We have found that an ellipse, rather than a circle, is better for the long axis views, especially with new Tc-99m labelled tracers with considerable hepatic uptake. In studies of 15 normal persons and 12 patients with coronary artery disease, we found the ellipse to provide better positioning and quantification of regional tracer uptake, percent washout of T1–201, and differences between rest and exercise Tc-99m isonitrile studies. The use of an elliptical ROI made it possible to exclude nearby non-myocardial soft tissue activity. Inclusion of this neighboring activity, which changed with the degree of exercise, caused errors in quantification that can result in false positive and false negative interpretations. 30 randomly selected long axis slices with circumferential profiles were visually compared by two observers. Based on 5 point score, all circle ROI generated profiles ranged between 1 and 3; all elliptical ROI profiles scored between 4 and 5. The elliptical ROI permitted more accurate superimposition of left ventricular regions in pairs of images during TI-201 redistribution or rest and exercise Tc-99m isonitrile studies. The positioning of circular ROIs was not sufficiently unique because of rotation around the same center. With elliptical ROIs any mismatch was easily recognized. Even prominent mispositioning was not detected with circular ROIs. In conclusion elliptical ROIs more accurately fit the left ventricle and have a true representation of the distribution of left ventricular activity.
Britain sets first standards for benzene levels
Authors: F Godlee
Journal: BMJ (1994)

Britain will become the first country to establish an environmental standard for benzene, which is known to cause leukaemia, after air quality guidelines were published last week. The guidelines, in a report commissioned by the Department of the Environment, set 5 parts per billion (ppb) as the standard - 100 times less than the current occupational exposure standard - and call on the government to work towards 1 ppb.

Although the World …
Intestinal disease and the urban environment.
Authors: H P Schedl
Journal: Environmental Health Perspectives (1979)

Factors in the urban environments of highly industralized societies are important causes of disease. This review examines urban diseases of small and large intestine. The urban environment is pervaded by chemicals including drugs, food additives, pesticides, industrial products, etc., which are potential causes of disease. Examples of typical urban, as contrasted with rural, intestinal disease are considered in terms of differing etiological factors. Urban intestinal disease is examined from the following standpoints: the population at risk; the chemical agents to which the population is exposed; a model for the physiology of distribution and metabolism of chemicals in relation to the alimentary tract; the application of this model to treatment of an industrial disease; a major urban disease of the alimentary tract, carcinoma of the colon, considered in terms of this model; approaches to characterizing, identifying, and controlling urban intestinal disease.
Abstract 5494: The development and validation of risk predictive models for cervical low-grade and high-grade squamous intraepithelial lesions
Authors: Ming-Tsang Wu
Journal: Cancer Research (2012)

Abstract Aim To develop and validate a risk predictive model for cervical high-grade squamous intraepithelial lesions (HGSIL; CIN2/CIN3). Materials and Methods Study women were from a community survey network for cervical cytological screening to evaluate and develop a simplified risk-score system (Jan., 2003-Feb., 2009, Kaohsiung county). Two other series of study participants obtained, respectively, from a follow-up of disease-free women in the community (followed from Apr., 2004-Feb., 2010) and from a hospital screening (Nov., 2008-Aug. 2011, KMUH) for cervical lesions were used to validate the risk-score system. Kaplan-Meier failure functions and the Cox proportional hazards model were used to evaluate the cervical precancerous risk for women with high-risk scores. Results Women who have a risk score of ≥5 obtained from the HGSIL model were defined as high risk subjects for the cervical lesion. The sensitivity and specificity of the risk-score system were 76.3% and 88.1%. The results of validation showed that the HGSIL model had high sensitivity and specificity (100% and 89.6%) for the community follow-up samples. We also evaluated the incidences of HGSIL among women with a high risk-score using the community follow-up cohort. The first and second-year cumulative incidences of HGSIL among women with the score of ≥5 were 1.05% and 3.63%, respectively. Conclusion With an acceptable accuracy, our data suggest that the HGSIL risk predictive model can be used to assist the screening of HGSIL. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5494. doi:1538-7445.AM2012-5494
Vascular Type 1A Angiotensin II Receptors Control BP by Regulating Renal Blood Flow and Urinary Sodium Excretion
Authors: Matthew A. Sparks, Johannes Stegbauer, Daian Chen, Jose A. Gomez, Robert C. Griffiths, Hooman A. Azad, Marcela Herrera, Susan B. Gurley, Thomas M. Coffman
Journal: Journal of the American Society of Nephrology (2015)

Inappropriate activation of the type 1A angiotensin (AT1A) receptor contributes to the pathogenesis of hypertension and its associated complications. To define the role for actions of vascular AT1A receptors in BP regulation and hypertension pathogenesis, we generated mice with cell-specific deletion of AT1A receptors in smooth muscle cells (SMKO mice) using Loxp technology and Cre transgenes with robust expression in both conductance and resistance arteries. We found that elimination of AT1A receptors from vascular smooth muscle cells (VSMCs) caused a modest (approximately 7 mmHg) yet significant reduction in baseline BP and exaggerated sodium sensitivity in mice. Additionally, the severity of angiotensin II (Ang II)-dependent hypertension was dramatically attenuated in SMKO mice, and this protection against hypertension was associated with enhanced urinary excretion of sodium. Despite the lower BP, acute vasoconstrictor responses to Ang II in the systemic vasculature were largely preserved (approximately 80% of control levels) in SMKO mice because of exaggerated activity of the sympathetic nervous system rather than residual actions of AT1B receptors. In contrast, Ang II-dependent responses in the renal circulation were almost completely eliminated in SMKO mice (approximately 5%-10% of control levels). These findings suggest that direct actions of AT1A receptors in VSMCs are essential for regulation of renal blood flow by Ang II and highlight the capacity of Ang II-dependent vascular responses in the kidney to effect natriuresis and BP control.
279 BONE MORPHOGENETIC PROTEIN (BMP)-9: A NEW MEMBER OF THE TGF-β SUPERFAMILY WHICH IS SECRETED BY ACTIVATED HEPATIC STELLATE CELLS
Authors: K. Breitkopf, A. Müller, L. Ciuclan, E. Wiercinska, P. Ten Dijke, S. Dooley
Journal: Journal of Hepatology (2009)
Effect of Vitamin D on Bone Mineral Mass in Normal Subjects and in Epileptic Patients on Anticonvulsants: A Controlled Therapeutic Trial
Authors: C. Christiansen, P. Rodbro, M. Lund
Journal: BMJ (1973)

The bone mineral mass was estimated by photon absorptiometry in 23 epileptic patients on long-term treatment with phenytoin and in 20 normal subjects before and during treatment with vitamin D or placebo.Initially, subnormal values of bone mineral mass were found in the epileptic patients. The group of epileptic patients treated with vitamin D showed a significant increase in bone mineral mass. The group of epileptic patients treated with placebo and the normal subjects treated with vitamin D or placebo showed no change in bone mineral mass.
Presentation of AIDS-related pulmonary Kaposi's sarcoma diagnosed by bronchoscopy.
Authors: L Huang, L M Schnapp, J F Gruden, P C Hopewell, J D Stansell
Journal: American Journal of Respiratory and Critical Care Medicine (1996)

Kaposi's sarcoma (KS) is the most common neoplasm in persons infected with the human immunodeficiency virus (HIV). However, information about the presenting features of pulmonary KS is limited. To describe the clinical, laboratory, and radiographic features of pulmonary KS, medical records and chest radiographs of 168 patients with pulmonary KS diagnosed by bronchoscopy during a 7-yr period were reviewed. All of the patients were HIV-seropositive males, of whom 95% identified homosexual or bisexual sex as a risk factor for HIV infection. The median CD4 lymphocyte count was 19 cells/microliter. The most common symptoms were cough, dyspnea, and fever. Patients with a concurrent opportunistic pneumonia had a higher median serum lactate dehydrogenase (LDH) concentration than did those with pulmonary KS alone (p<0.001). The most common chest radiograph findings were bronchial-wall thickening, nodules, Kerley B lines, and pleural effusions. The presence of granular opacities or cystic spaces usually indicated concomitant Pneumocystitis carinii pneumonia (p < 0.001). Twenty-six patients (15.5%, 95% CI = 10.2% to 20.8%) had pulmonary KS in the absence of mucocutaneous involvement. The presentation of pulmonary KS is characterized by symptoms that cannot be distinguished from those of a superimposed infection. An elevated serum LDH concentration or a chest radiograph with granular opacities or cystic spaces should raise the suspicion of concurrent opportunistic pneumonia. The diagnosis of pulmonary KS should be considered in an HIV-infected homosexual or bisexual male with respiratory symptoms even in the absence of mucocutaneous lesions.
Assessment of Myocardial Scarring Improves Risk Stratification in Patients Evaluated for Cardiac Defibrillator Implantation
Authors: Igor Klem, Jonathan W. Weinsaft, Tristram D. Bahnson, Don Hegland, Han W. Kim, Brenda Hayes, Michele A. Parker, Robert M. Judd, Raymond J. Kim
Journal: Journal of the American College of Cardiology (2012)
How To Build and Interpret a Nomogram for Cancer Prognosis
Authors: Alexia Iasonos, Deborah Schrag, Ganesh V. Raj, Katherine S. Panageas
Journal: Journal of Clinical Oncology (2008)

Nomograms are widely used for cancer prognosis, primarily because of their ability to reduce statistical predictive models into a single numerical estimate of the probability of an event, such as death or recurrence, that is tailored to the profile of an individual patient. User-friendly graphical interfaces for generating these estimates facilitate the use of nomograms during clinical encounters to inform clinical decision making. However, the statistical underpinnings of these models require careful scrutiny, and the degree of uncertainty surrounding the point estimates requires attention. This guide provides a nonstatistical audience with a methodological approach for building, interpreting, and using nomograms to estimate cancer prognosis or other health outcomes.
HISTOPATHOLOGIC EVALUATION OF PATENT DUCTUS ARTERIOSUS STENTS AFTER HYBRID PALLIATION OF HYPOPLASTIC LEFT HEART SYNDROME
Authors: Matthew Egan, Aaron J. Trask, Peter B. Baker, Jonathan Lawrence, Elena Ladich, Renu Virmani, Sharon L. Hill, Pamela A. Lucchesi, Mark Galantowicz, John P. Cheatham, John P. Kovalchin
Journal: Journal of the American College of Cardiology (2010)
Allogeneic Hematopoietic Stem-Cell Transplantation for Chronic Lymphocytic Leukemia With 17p Deletion: A Retrospective European Group for Blood and Marrow Transplantation Analysis
Authors: Johannes Schetelig, Anja van Biezen, Ronald Brand, Dolores Caballero, Rodrigo Martino, Maija Itala, José A. García-Marco, Liisa Volin, Norbert Schmitz, Rainer Schwerdtfeger, Arnold Ganser, Francesco Onida, Brigitte Mohr, Stephan Stilgenbauer, Martin Bornhäuser, Theo de Witte, Peter Dreger
Journal: Journal of Clinical Oncology (2008)

Patients with chronic lymphocytic leukemia (CLL) and 17p deletion (17p-) have a poor prognosis. Although allogeneic hematopoietic stem-cell transplantation (HCT) has the potential to cure patients with advanced CLL, it is not known whether this holds true for patients with 17p-CLL.Baseline data from patients, for whom information on the presence of 17p-CLL was available, were downloaded from the European Group for Blood and Marrow Transplantation database. Additional information on the course of CLL and follow-up was collected with a questionnaire.A total of 44 patients with 17p-CLL received allogeneic HCT between March 1995 and July 2006 from a matched sibling (n = 24) or an alternative donor (n = 20). 17p-CLL had been diagnosed by fluorescent in situ hybridization in 82% of patients and by conventional banding in 18% of patients. The median age was 54 years. Before HCT, a median of three lines of chemotherapy had been administered. At HCT, 53% of patients were in remission. Reduced-intensity conditioning was applied in 89% of patients. Acute, grade 2 to 4 graft-versus-host disease (GVHD) occurred in 43% of patients, and extensive chronic GVHD occurred in 53% of patients. At last follow-up, 19 patients were alive, with a median observation time of 39 months (range, 18 to 101 months). Three-year overall survival and progression-free survival rates were 44% and 37%, respectively. The cumulative incidence of progressive disease at 4 years was 34%. No late relapse occurred in nine patients with a follow-up longer than 4 years.Allogeneic HCT has the potential to induce long-term disease-free survival in patients with 17p-CLL.
Evaluation of a Model for Efficient Screening of Tuberculosis Contact Subjects
Authors: Khaoula Aissa, Fouad Madhi, Nathalie Ronsin, France Delarocque, Aurélie Lecuyer, Bénédicte Decludt, Natacha Remus, Laurent Abel, Christine Poirier, Christophe Delacourt
Journal: American Journal of Respiratory and Critical Care Medicine (2008)

Contact tracing is an important component of tuberculosis (TB) control programs. Standardization of contact investigation protocols can make them more efficient.To develop a model to select contact subjects for screening.We prospectively collected standardized data on 325 TB index cases and their 2,009 contacts. Factors that independently influenced the risk of TB infection were included in the model, which was then validated in a second prospective cohort of 88 cases of TB and their 618 contacts.A total of eight independent risk factors were identified (odds ratio; 95% confidence interval): age, with three subgroups: 6-14 years (3.6; 1.6-8.0); 15-29 years (3.7; 1.8-7.7); > or =30 years (4.1; 2.0-8.5); cavitation on the index case's chest radiograph (1.6; 1.1-2.2); an index case sputum smear with 100 or more acid-fast bacilli per field (1.8; 1.2-2.8); household contact at night (2.1; 1.3-3.2); first-degree family relationship with the index case (2.1; 1.3-3.3); active smoking by the contact (1.6; 1.1-2.4); free health care (2.0; 1.2-3.2); and birth in a country with TB incidence rate higher than 25 of 100,000 (2.2; 1.5-3.2). Predictive probabilities were chosen to ensure false-negative rates lower than estimated TB infection background. The number of contacts to be investigated was reduced by 26% while maintaining a false-negative rate of 8%.This study provides a standardized contact screening model which reduces resources required without negatively affecting disease control.
Sodium Phosphate Does Not Increase Risk for Acute Kidney Injury After Routine Colonoscopy, Compared With Polyethylene Glycol
Authors: J. Bradley Layton, Philip J. Klemmer, Christian F. Christiansen, Andrew S. Bomback, John A. Baron, Robert S. Sandler, Abhijit V. Kshirsagar
Journal: Clinical Gastroenterology and Hepatology (2014)
Role of TLR4 in allergic sensitization to food proteins in mice
Authors: M. C. Berin, Y. Zheng, M. Domaradzki, X.‐M. Li, H. A. Sampson
Journal: Allergy (2005)

Allergic sensitization to food proteins and other allergens is increasing in prevalence. One hypothesis for this increase is that the decreased rate of infections or exposure to microbial products leaves the immune system susceptible to inappropriate reactivity to innocuous antigens through the lack of development of regulatory cells. We hypothesized that constitutive Toll‐like receptor (TLR)4 signaling (presumably via the commensal flora) could inhibit the development of allergic sensitization to food proteins. We tested this hypothesis by sensitizing TLR4+ and TLR4− mice on two genetic backgrounds, C3H and BALB/c, to two common food allergens [ β ‐lactoglobulin ( β LG) and peanut (PN)]. B‐cell responses were not significantly influenced by TLR4 status. T‐cell responses were Th2 skewed in TLR4‐deficient C3H mice compared with TLR4 sufficient C3H mice, but this pattern of Th2 skewing was not observed in TLR4‐deficient mice on a BALB/c background. In anaphylaxis‐susceptible C3H mice, TLR4 deficiency was associated with increased severity of anaphylaxis to PN, and decreased severity of anaphylaxis to β LG. In anaphylaxis‐resistant BALB/c mice, TLR4 deficiency was not sufficient to render mice susceptible to PN‐induced anaphylaxis. We conclude that although TLR4 status can influence T‐cell responses and anaphylaxis severity, the nature of the influence is highly antigen‐ and strain‐dependent.
Funding will Continue for Neutron Therapy Trials Beyond 1989
Authors: F. Antoine
Journal: JNCI Journal of the National Cancer Institute (1988)

Journal Article Funding will Continue for Neutron Therapy Trials Beyond 1989 Get access Florence Antoine Florence Antoine Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 80, Issue 10, 20 July 1988, Pages 715–717, https://doi.org/10.1093/jnci/80.10.715 Published: 20 July 1988
James Jackson, Jr., and Emphysema
Authors: CHARLES MITTMAN
Journal: Annals of Internal Medicine (1973)

Comments and Corrections1 August 1973James Jackson, Jr., and EmphysemaCHARLES MITTMAN, M.D.CHARLES MITTMAN, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-79-2-283_1 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editor: Dr. William B. Spaulding's review of the life of James Jackson, Jr., in the March 1973 issue (pp. 429-435) reminded me of an earlier encounter with the work of this remarkable young man. In searching the literature for studies of the possible relation between heredity and emphysema, I found the following statement in a standard medical textbook of 1842 (1).The question as to its [emphysema] hereditary character was closely and ably investigated by a young American physician, too soon lost to sciences, (J. Jackson, Jr., of Boston,) who was a worthy pupil of a distinguished master,...References1. DUNGLISON R: The Practice of Medicine, or a Treatise on Special Pathology and Therapeutics. Philadelphia, Lea & Blanchard, 1842, pp. 326-327 Google Scholar2. LAURELL C and ERIKSSON S: The electrophoretic alpha1-globulin pattern of serum. Scand J Clin Lab Invest 15:132-140, 1963 CrossrefGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAuthors: CHARLES MITTMAN, M.D. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited byRadarmessungen zur Bestimmung von Fl�chenniederschl�gen 1 August 1973Volume 79, Issue 2Page: 283-283KeywordsEmphysemaHeredity ePublished: 1 December 2008 Issue Published: 1 August 1973 PDF downloadLoading ...