tbuckley/cabot-search huggingface dataset:
On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain
Authors: V. Berry, O. Gascuel
Journal: Molecular Biology and Evolution (1996)

In this study we address the problem of interpreting a bootstrap tree. The main issue is choosing the threshold of clade selection in order to separate reliable clades from unreliable ones, depending on their bootstrap proportion. This threshold depends on the chosen error measure. We investigate error measures that stem from a generalization of Robinson and Foulds’ (1981) distance, used to quantify the divergence between the true phylogeny and the estimated trees. We propose two analytical approximations of the optimum threshold of clade selection to interpret (i.e., reduce) the bootstrap tree. We performed extensive simulations along the lines of Kuhner and Felsenstein (1994) using the neighbor-joining and the maximum-parsimony methods. These simulations show that our approximations cause only small losses in quality when compared to the optimum threshold resulting from empirical observation. Next, we measured the error reduction achieved when estimating the true phylogeny by the properly reduced bootstrap tree rather than by the complete original tree, obtained with a classical tree-building method. Our simulations on short sequences show that an error reduction of 39% is achieved with the parsimony method and an error reduction of 33% is achieved with the distance method when the error is measured with the standard Robinson and Foulds distance. The observed error reduction is shown to originate from an important decrease in Type I error (wrong inferences), while Type II error (omitted correct clades) is only slightly increased. Greater error reduction is achieved when shorter sequences are used, and when more importance is given to Type I error than to Type II error. To investigate the causes of error from another point of view, we propose a general decomposition of the error expectation in two terms of bias, and one of variance. Results for these terms show that no fundamental bias is introduced by the bootstrap process, the only source of bias being structural (lack of resolution). Moreover, the variance in the estimations is greatly reduced, providing another explanation for the better results of the reduced bootstrap tree compared with the original tree estimate.
Pheochromocytoma Presenting With Remote Bony Recurrence Twenty Years After Initial Surgery
Authors: Girish Kumar Parida, Varun Singh Dhull, Punit Sharma, Chandrasekhar Bal, Rakesh Kumar
Journal: Clinical Nuclear Medicine (2013)

Pheochromocytomas are rare tumors which can be malignant in 10% of cases. We present the case of a 75-year-old woman who presented with headache and palpitation for 1 year. She had a past history of right adrenalectomy for pheochromocytoma 20 years back. In between, the patient was asymptomatic. Twenty-four-hour urinary vanillylmandelic acid was raised. Noncontrast CT and ultrasound of abdomen were unremarkable. The patient underwent 68Ga-DOTANOC PET/CT that showed metastasis to left ilium, which was confirmed on biopsy.
Commentary: Health Costs of a Reduced Energy Supply
Authors: James R. McCarroll
Journal: Environmental Health Perspectives (1983)

Health effects associated with electricity production, especially air pollution from fossil fuel combustion, have received much attention in the past 30 years. Virtually no attention has been paid to the health costs of a reduced or overpriced energy supply although these are real and formidable. Stringent regulations mandating control technology on stack emissions and/or burning of low sulfur fuels have been promulgated which cost the American public billions of dollars. These have indeed alleviated some health problems, but pressures to further tighten regulations offer little chance of further health benefits commensurate with their cost and are most likely to produce a new series of problems.
Early Gene Defect Implicated in Non-Hereditary Colon Cancer
Authors: J. Bowersox
Journal: JNCI Journal of the National Cancer Institute (1992)

Journal Article Early Gene Defect Implicated in Non-Hereditary Colon Cancer Get access John Bowersox John Bowersox Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 84, Issue 20, 21 October 1992, Pages 1551–1552, https://doi.org/10.1093/jnci/84.20.1551 Published: 21 October 1992
AB0714 Psychiatric Symptoms in Patients with Ankylosing Spondylitis
Authors: D. Durmus, G. Sarisoy, G. Alayli, H. Kesmen, A. Bilgici, O. Kuru
Journal: Annals of the Rheumatic Diseases (2014)

<h3>Objectives</h3> This study was intended to identify general psychiatric symptoms in patients with ankylosing spondylitis (AS) and to determine the distribution of these psychiatric symptoms by degree of disease activity. <h3>Methods</h3> One hundred sixty volunteers, 80 AS patients and 80 healthy controls, matched in terms of age, gender, education and job, were included. Spinal pain by visual analogue scale (pain VAS-rest), disease activity by Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), functional capacity by Bath Ankylosing Spondylitis Functional Index (BASFI), and quality of life by short form-36 (SF-36) were assessed in patients. Psychiatric symptoms were measured using the Symptom Checklist-90-R, Beck Depression Inventory, State–Trait Anxiety Inventory, Pittsburgh Sleep Quality Index, and Rosenberg Self-Esteem Scale. Correlations were determined between BASDAI, BASFI scores and psychiatric scale scores. <h3>Results</h3> In addition to symptoms of depression, anxiety, decreased quality of life and sleep impairment in AS patients, we also determined that less studied symptoms such as somatization, obsession, compulsion, anger–hostility, paranoid ideation, psychoticism, and low self-esteem were also more frequent compared to the healthy controls. Some symptoms were also more prevalent in AS patients with high disease activity compared to patients with low disease activity. In AS patients, while there was positive correlation between disease activity and psychiatric symptoms, there was negative correlation between functional capacity and psychiatric symptoms. <h3>Conclusions</h3> Depressive, anxious and sleep impairment symptoms are not the only ones seen in AS patients; other psychiatric symptoms are also common. Further studies are needed to investigate the frequency and causes of these symptoms. As seen in patients with a progressive course and lower functional capacity, more psychiatric symptoms develop in patients with more severe disease. <h3>Disclosure of Interest</h3> None declared <h3>DOI</h3> 10.1136/annrheumdis-2014-eular.5156
Abstract SY27-01: Colon commensals and cancer
Authors: Cynthia L. Sears
Journal: Cancer Research (2011)

Abstract A clear intersection between the infectious diseases and oncology fields has emerged from our understanding that many cancers arise in the setting of chronic infection. Roughly one-third of cancers worldwide, particularly epithelial cancers, are associated with identified single microbial infections, leading to the conceptual paradigm that chronic infection with specific microbes cause these cancers independent of other components of the ambient microbial community. Among epithelial cancers, colon cancer is the second leading cancer killer of adults in the United States but specific microbial contributors have not yet been identified. Rather, we now understand that the colon is home to one of the most dense and diverse communities of bacteria in the body and that we are each remarkably unique in our bacterial makeup, reinforcing the contrasting view that the microbial contribution to colon cancer pathogenesis may lie in the composition of the colon microbiome. This talk will explore the scientific data supporting differing paradigms for how the colonic flora may contribute to colon oncogenesis. Specific, usually commensal, members of the colonic microbiome and the mechanisms by which they may initiate and/or promote colon tumors with be discussed with a particular emphasis on enterotoxigenic Bacteroides fragilis (ETBF). B. fragilis not only colonizes most humans but is the leading anaerobe in human disease. ETBF is a molecular subset of B. fragilis distinguished by secretion of a zinc-dependent metalloprotease toxin. In murine models, ETBF is a potent inducer of colonic tumors. Tumor induction by ETBF is dependent, in part, on a specific host immune response involving IL-17-producing CD3+CD4+ T cells. A framework for utilizing this knowledge to better understand the pathogenesis of colon cancer and to develop new approaches to colon cancer prevention and/or therapy will be discussed. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr SY27-01. doi:10.1158/1538-7445.AM2011-SY27-01
Abstract LB-198: Collagen remodeling and tissue mechanics at different stages of mammary tumor development
Authors: Hongmei Yu, Valerie M. Weaver
Journal: Cancer Research (2010)

Abstract Discussion Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-198.
S71 Ambulatory oxygen improves the effectiveness of Pulmonary Rehabilitation (PR) in selected patients
Authors: F. J. Dyer
Journal: Thorax (2010)

<h3>Rationale</h3> The acute effect of supplemental oxygen on exertion is well documented although its use in PR has not yet been clearly established. Two small studies have previously shown no benefit; this may have been due to study power or methodology. Our study investigated whether ambulatory oxygen provides additional benefit to patients undergoing PR who meet the 2006 UK Department of Health criteria for ambulatory oxygen use. <h3>Methods</h3> A single blind (researcher) randomised controlled trial compared the effect of a 6 week PR programme either with or without ambulatory oxygen. The study was powered to show an 80% difference between groups. Eligible patients were those who desaturated on baseline exercise testing by &gt;4% to &lt;90% and whose exercise tolerance improved by &gt;10% with ambulatory oxygen. Outcome measures included the Endurance Shuttle Walk Test (ESWT) and the self report Chronic Respiratory Questionnaire (CRQ-SR). <h3>Results</h3> Between September 2007 and June 2009 62 patients consented; one patient withdrew choosing to use ambulatory oxygen, ten dropped out of PR. The majority of subjects had Chronic Obstructive Pulmonary Disease; eight had another chronic respiratory condition. Groups were similar at baseline except for weight and BMI (higher in the room air (RA) group). A far greater improvement in ESWT was found in the oxygen group (p=0.000) (Abstract S71 Table 1). When the acute effect of oxygen is excluded the oxygen group improved by 75% more than the RA group; this did not meet statistical significance since the study was powered to show an 80% improvement. The oxygen group gained improvements in three CRQ-SR domains (emotion, fatigue and mastery) above the minimally clinically important difference (MCID) but this was not the case for the RA group; the difference between groups for these domains also reached the MCID. Improvements in the dyspnoea domain were similar between groups, although the oxygen group walked 490 m (122%) further. <h3>Conclusion</h3> For patients who desaturate and with an acute positive response to oxygen, ambulatory oxygen significantly enhances the effect of PR.
INFLUENCE OF PATIENT FACTORS ON UTILIZATION OF INITIAL OUTPATIENT PEDIATRIC ECHOCARDIOGRAPHY
Authors: Kenan W.D. Stern, Talin Gulesserian, Sean Lang, Christopher Statile, Erik Michelfelder, Ericka McLaughlin, Tuan Nguyen, Leo Lopez, George Verghese, Daphne Hsu, Jaeun Choi, Ritu Sachdeva
Journal: Journal of the American College of Cardiology (2016)
Abstract 5415: Expression of immunosuppressive leukocyte inhibitory immunoglobulin like transcript 3(ILT3) receptors increases with the development and progression of ovarian tumors
Authors: Mohammad F. Khan, Aparna Yellapa, Janice Bahr, Pincas Bitterman, Jacques Abramowicz, Sanjib Basu, Seby Edassery, Animesh Barua
Journal: Cancer Research (2012)

Abstract Background: Immunosuppressive tumor microenvironment has been suggested as one of the barriers to anti-tumor immune response in patient with ovarian cancer (OVCA). Leukocyte Inhibitory Receptor Immunoglobulin-like Transcript 3 (ILT3) has been proposed as a factor involved in the suppression of immune response in several malignancies. However, the expression and role of ILT3 in the development and progression of ovarian tumors has not yet been studied. Objective: The goal of this study was to examine the expression and association of ILT3 in ovarian tumors in laying hen, a preclinical model of OVCA in humans. Methods: A cohort of mature White Leghorn laying hens with normal or low egg laying rates were evaluated by transvaginal ultrasound scan (15 normal hens and 30 hens with OVCA).All hens were euthanized and serum and ovarian tissues from all hens were collected and processed for immunohistochemistry (IHC), Western blotting (WB) and RT-PCR. Presence of tumors and tumor staging were confirmed by gross morphology and histology. Expression of ILT3 was examined by IHC, WB and RT-PCR. Results: Immune cell like cells in the ovarian stroma as well as epithelium of the normal ovaries and ovarian tumors expressed ILT3. The intensity of ILT3 expression was significantly higher in hens with OVCA than normal hens. Moreover, the intensity of ILT3 expression varied with histological subtypes of ovarian tumors and was significantly higher in serous OVCA than endometrioid OVCA. A band of approximately 55kDa of ILT3 protein was detected in the homogenates of normal ovarian surface epithelium or tumor epithelium as well as whole normal or ovarian tumor extracts. Similar to IHC observations, protein expression was stronger in hens with OVCA than in normal hens. Conclusion: This is the first study to show that immunosuppressive ILT3 is expressed by ovarian tumor epithelium and the intensity of expression increases as the disease progresses. Thus the results are consistent with the hypothesis that ILT3 may be involved in the suppression of anti-tumor immunity in OVCA. The laying hens may be a useful model to understand the OVCA-associated expression of ILT3. This animal model also offers the opportunity to develop and test anti-ILT3 therapy to enhance anti-tumor immunity against OVCA in humans. Support: Department of Defense (OC#93303) and Elmer Sylvia and Sramek Foundation. 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 5415. doi:1538-7445.AM2012-5415
Primary signet-ring cell carcinoma of the pancreas diagnosed by endoscopic retrograde pancreatic duct biopsy: a case report with an immunohistochemical study
Authors: T. Terada
Journal: Endoscopy (2012)

Primary signet-ring cell carcinoma (SRCC) of the pancreas is extremely rare [1]; only three cases have been reported in the literature [2] [3] [4].
Megaloblastic Hematopoiesis in Uremia and in Patients on Long-Term Hemodialysis
Authors: Constantine L. Hampers, Richard Streiff, David G. Nathan, Donald Snyder, John P. Merrill
Journal: New England Journal of Medicine (1967)

SEVERE chronic renal failure has an adverse effect on hematopoiesis.1 The major defect appears to be one of relative bone-marrow failure in that the marrow of the patient with uremia does not respond to anemic stress to the same extent as normal marrow.2 The role of erythropoietin in this bone-marrow failure is in doubt.2 It may be that circulating "toxins" play a major part and depress the marrow directly.3 , 4 Another possibility is nutritional deficiency or a deranged metabolism of vitamins in uremic patients. Many marrows that we have examined in patients with chronic renal failure appear megaloblastic, particularly in the . . .
P681The IgCAM CAR regulates calcium homeostasis in the developing heart and nervous system
Authors: C Matthaeus, R Juettner, F Rathjen
Journal: Cardiovascular Research (2014)

CAR is a transmembrane protein of the Ig superfamily which serves as receptor for different adenoviruses. Due to the strong expression of CAR in brain and heart during embryonic development, the physiological function is of great interest. CAR knockout animal models show malformation of the heart which leads to death during development between days E11.5 and E13.5. This observation indicates an important function of CAR during heart development. Up to date, the cellular mechanism of CAR is not well understood. Therefore we studied the signaling pathway of CAR in cardiomyocytes and neurons. The Ad2 fiber knob is the binding part of the Ad2 adenovirus to CAR and it initiates the virus uptake. Here, we demonstrated in cardiomyocytes and neurons an increase in cytosolic Ca2+ concentration from intracellular Ca2+ stores upon application of the Ad2 fiber knob. Ad2 induced Ca2+ increase was blocked by wortmannin suggesting that CAR signaling triggers Ca2+ release from intracellular stores via PI3K. CAR knockout mice at E10.5 show a significant higher beating rate of the cardiomyocytes and Ca2+ transients compared to wild type. Further investigation of Ca2+ transients in CAR knockout cardiomyocytes revealed a significant faster calcium decline and decay time constant. Inhibition of SERCA2 by thapsigargin or CPA did not show the strong decrease in beating frequency in CAR knockout cardiomyocytes like observed in wild type cardiomyocytes. Therefore we suggest that in CAR knockout cardiomyocytes SERCA2 activity is enhanced.
Utility of intrapapillary capillary loops seen on magnifying narrow-band imaging in estimating invasive depth of esophageal squamous cell carcinoma
Authors: Hiroki Sato, Haruhiro Inoue, Haruo Ikeda, Chiaki Sato, Manabu Onimaru, BuHussain Hayee, Chainarong Phlanusi, Esperanza Santi, Yasutoshi Kobayashi, Shin-ei Kudo
Journal: Endoscopy (2015)

<b>Background and study aims: </b>Intrapapillary capillary loops (IPCLs) have been used to estimate histopathological atypia and the invasion depth of squamous cell carcinoma (SCC). The aim of this study was to evaluate the clinical significance of IPCLs. <b>Patients and methods:</b> A total of 358 consecutive patients with esophageal neoplasia on magnifying narrow-band imaging (M-NBI) were studied. The lesions were categorized according to the IPCL classification of Inoue et al. and were subsequently resected. Resected specimens were histopathologically analyzed to determine the invasion depth. The inter- and intraobserver agreements in the interpretation of IPCL images were also investigated. <b>Results: </b>A total of 446 lesions were diagnosed on M-NBI as IPCL type V lesions, which were further classified as 185 IPCL type V1, 109 type V2, 104 type V3, and 48 type Vn. Sensitivity and specificity of IPCL type V1-2 for invasion confined to the epithelium or lamina propria mucosa (m1-2) were 89.5 % (95 % confidence interval [CI] 85.4 % – 92.7 %) and 79.6 % (95 %CI 72.3 % – 85.7 %), respectively. Sensitivity and specificity of IPCL type V3 for invasion confined to the muscularis mucosa or slight submucosal invasion (m3-sm1) were 58.7 % and 83.8 %, respectively. Sensitivity and specificity of IPCL type Vn for deeper invasion (sm2-3) were 55.8 % and 98.6 %, respectively. Interobserver agreement was substantial (κ = 0.609, 0.641, and 0.705), as was intraobserver agreement (κ = 0.705 and κ = 0.819). <b>Conclusion: </b>Changes in the morphology of IPCLs on M-NBI correlated with the depth of SCC invasion, and results were reproducible and reliable among observers. Identification of IPCL type V1-2 proved useful for the intraprocedural identification of m1-2 lesions, which are considered an absolute indication for endoscopic resection.
Abstract 4883: YM155 potentiates chemosensitivity to gemcitabine in human pancreatic cancer cell line, MiaPaCa-2
Authors: Kyungah Jung, Dokhyun Yoon, Jaesik Shin, Taewon Kim
Journal: Cancer Research (2012)

Abstract Pancreatic cancer is a highly aggressive malignancy with a median overall survival of less than 1 year. Although gemcitabine is a standard chemotherapeutic agent, response rates range only from 20% to 40% and ultimately all patients acquire resistance to the chemotherapy. In this study, we evaluated the potential efficacy of YM155, a selective survivin suppressant, in pancreatic cancer cell line, MiaPaCa-2 showing resistance to gemcitabine. YM155 inhibited the expression of survivin in the pancreatic cancer cell line and gemcitabine upregulated survivin on the contrary. However, YM155 enhanced chemosensitivity to gemcitabine resulting in apoptotic cell death, which accompanied a decrease in survivin expression. Knockdown of endogenous survivin via RNA interference also enhanced sensitivity to gemcitabine. In addition, YM155 potentiated the anti-tumor effect of gemcitabine in the xenograft tumors of MiaPaCa-2. While gemcitabine induced cell cycle arrest at S-phase, co-treatment of YM155 bypassed the cell cycle arrest resulting in apoptotic cell death. Therefore, our results suggest that YM155 potentiates chemosensitivity to gemcitabine in pancreatic cancer cells through suppression of survivin, which is induced by gemcitabine. Combination of gemcitabine and YM155 might be a potential therapeutic strategy for the treatment of pancreatic cancer to be explored in clinical investigation. 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 4883. doi:1538-7445.AM2012-4883
Induction of Donor-Type Chimerism and Transplantation Tolerance Across Major Histocompatibility Barriers in Sublethally Irradiated Mice by Sca-1+Lin− Bone Marrow Progenitor Cells: Synergism With Non-Alloreactive (Host × Donor)F1 T Cells
Authors: Esther Bachar-Lustig, Hong Wei Li, Hilit Gur, Rita Krauthgamer, Hadar Marcus, Yair Reisner
Journal: Blood (1999)
Evolving the future by creating and adapting to novel environments
Authors: Peter LaFreniere
Journal: Behavioral and Brain Sciences (2014)

Abstract Adaptation demands effective responses to both recurrent and novel environmental challenges. Developmental plasticity and domain-general mechanisms have important consequences with respect to our human capacity for imagining, creating, and adapting to novel environments. They facilitate the evolution of any cognitive mechanism, no matter how opportunistic, flexible, or domain-general, that is able to solve new problems or achieve new goals.