tbuckley/cabot-search huggingface dataset:
Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies
Authors: Shaolin Wang, Eric Peatman, Jason Abernathy, Geoff Waldbieser, Erika Lindquist, Paul Richardson, Susan Lucas, Mei Wang, Ping Li, Jyothi Thimmapuram, Lei Liu, Deepika Vullaganti, Huseyin Kucuktas, Christopher Murdock, Brian C Small, Melanie Wilson, Hong Liu, Yanliang Jiang, Yoona Lee, Fei Chen, Jianguo Lu, Wenqi Wang, Peng Xu, Benjaporn Somridhivej, Puttharat Baoprasertkul, Jonas Quilang, Zhenxia Sha, Baolong Bao, Yaping Wang, Qun Wang, Tomokazu Takano, Samiran Nandi, Shikai Liu, Lilian Wong, Ludmilla Kaltenboeck, Sylvie Quiniou, Eva Bengten, Norman Miller, John Trant, Daniel Rokhsar, Zhanjiang Liu
Journal: Genome biology (2010)

Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification.A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis.This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.
The Negative Is Not So Negative: What Do We Learn From Trials With Orteronel?
Authors: Kevin Lu
Journal: Journal of Clinical Oncology (2015)

alone(medianOS,17.0[95%CI,15.2to19.9]months v15.2[95%CI, 13.5to16.9]months;hazardratio,0.886[95%CI,0.739to1.062]; P .1989). Similar to previous studies that assessed the efficacy of androgen signaling pathway inhibitors in patients with mCRPC after docetaxel therapy, 2,3 the ELM-PC 5 trial was another attempt to investigate androgen biosynthesis inhibitors in a modestly selected population. Despite an improvement in radiographic progressionfree survival (rPFS), this study did not meet its OS end point. The ELM-PC 5 trial is a failed trial. However, is this negative result meaningless? Is there potential value in sharing this negative result with researchers and communities that can inspire new directions for additional studies? WhatcanwelearnfromthisstudypublishedbyFizazietal? 1 One
Risk Factors for and Impact of Online Sexual Solicitation of Youth
Authors: Kimberly J. Mitchell
Journal: JAMA (2001)

ContextHealth care professionals, educators, and others are increasingly called upon to advise parents and policymakers about risks posed to children by Internet use. However, little scientific information exists on the experiences of children online.ObjectiveTo assess the risk factors surrounding online sexual solicitations of youth and distress due to solicitation.Design, Setting, and ParticipantsTelephone survey (August 1999–February 2000) of a random sample of 1501 youth aged 10 through 17 years who were regular Internet users.Main Outcome MeasuresDemographic and behavioral characteristics associated with solicitation risk and distress due to solicitation.ResultsNineteen percent of youth who used the Internet regularly were the targets of unwanted sexual solicitation in the last year. Girls (P&lt;.001), older teens (P = .005), troubled youth (P = .004), frequent Internet users (P = .01), chat room participants (P&lt;.001), and those who communicated online with strangers (P&lt;.001) were at greater risk. Twenty-five percent of the solicited youth reported high levels of distress after solicitation incidents. Risk of distress was more common among the younger youth (P = .005), those who received aggressive solicitations (the solicitor attempted or made offline contact) (P = .001), and those who were solicited on a computer away from their home (P = .001).ConclusionsMany young people who use the Internet encounter unwanted sexual overtures. Health care professionals, educators, and parents should be prepared to educate youth about how to respond to online sexual solicitations, including encouraging youth to disclose and report such encounters and to talk about them.
The effect of GSK2190915, a 5-lipoxygenase activating protein inhibitor, on the early asthmatic response to inhaled allergen
Authors: Virginia Norris, Jane Bentley, Sandra Kent, Dave Singh, Malcolm Boyce, Brian Leaker
Journal: European Respiratory Journal (2011)

Background:  GSK2190915 is a potent 5-lipoxygenase activating protein inhibitor, thereby inhibiting the synthesis of leukotrienes and 5-oxo-ETE.   Objective:  To assess the effects of GSK2190915 on the allergen induced early asthmatic response (EAR).   Methods:  19 patients with mild asthma were enrolled in this 3-centre, double- blind, 3-way crossover study. They took 10 and 50 mg GSK2190915 and placebo orally, once daily for 3 days, in randomised order. On Day 3 they had an inhaled allergen challenge.   Results:  GSK2190915 had a significant effect on the EAR, the treatment difference from placebo for 10 mg was 0.212 L (0.044, 0.379) and for 50 mg was 0.409 L (0.242, 0.576) for minimum FEV 1  in the 2 hours after allergen inhalation. The magnitude of the effect with 50 mg GSK2190915 in this study was comparable to that observed with 100 mg on the EAR in a separate study [1]. Safety and tolerability were good.   Conclusion:  GSK2190915 has shown a significant, dose related, inhibition of the EAR to inhaled allergen.   References:   1V Norris et al. ERS conference 2011.  ClinicalTrials.gov identifier NCT00812773
Nanotherapeutics for inhibition of atherogenesis and modulation of inflammation in atherosclerotic plaques
Authors: Daniel R. Lewis, Latrisha K. Petersen, Adam W. York, Sonali Ahuja, Hoonbyung Chae, Laurie B. Joseph, Saum Rahimi, Kathryn E. Uhrich, Paul B. Haser, Prabhas V. Moghe
Journal: Cardiovascular Research (2015)

Atherosclerotic development is exacerbated by two coupled pathophysiological phenomena in plaque-resident cells: modified lipid trafficking and inflammation. To address this therapeutic challenge, we designed and investigated the efficacy in vitro and ex vivo of a novel 'composite' nanotherapeutic formulation with dual activity, wherein the nanoparticle core comprises the antioxidant α-tocopherol and the shell is based on sugar-derived amphiphilic polymers that exhibit scavenger receptor binding and counteract atherogenesis. Amphiphilic macromolecules were kinetically fabricated into serum-stable nanoparticles (NPs) using a core/shell configuration. The core of the NPs comprised either of a hydrophobe derived from mucic acid, M12, or the antioxidant α-tocopherol (α-T), while an amphiphile based on PEG-terminated M12 served as the shell. These composite NPs were then tested and validated for inhibition of oxidized lipid accumulation and inflammatory signalling in cultures of primary human macrophages, smooth muscle cells, and endothelial cells. Next, the NPs were evaluated for their athero-inflammatory effects in a novel ex vivo carotid plaque model and showed similar effects within human tissue. Incorporation of α-T into the hydrophobic core of the NPs caused a pronounced reduction in the inflammatory response, while maintaining high levels of anti-atherogenic efficacy. Sugar-based amphiphilic macromolecules can be complexed with α-T to establish new anti-athero-inflammatory nanotherapeutics. These dual efficacy NPs effectively inhibited key features of atherosclerosis (modified lipid uptake and the formation of foam cells) while demonstrating reduction in inflammatory markers based on a disease-mimetic model of human atherosclerotic plaques.
The Flashlight Test Lacks Validity as a Screen for Nocturnal Hypoglycemia
Authors: Bruce B Duncan, Maria I Schmidt, Jay S Skyler, George J Ellis, Adrienne Keller, Michael H Rathjens
Journal: Diabetes Care (1984)

Though never validated, the flashlight test is a commonly used screen for nocturnal hypoglycemia. Between 2 a.m. and 4 a.m., we applied the test to 107 children at Eagle's Nest Camp for Children with Diabetes. We validated the test against simultaneously determined capillary blood glucose values (Glucoscan). An eyelid squint in response to the flashlight was considered an intact test. No significant difference existed between mean glucoses for intact and nonintact responses. Both sensitivity and positive predictive value are too low for the flashlight test to be useful in screening for nocturnal hypoglycemia.
Targeting dexamethasone to Kupffer cells: Effects on liver inflammation and fibrosis in rats
Authors: Barbro N. Melgert, Peter Olinga, Judith M.S. Van Der Laan, Betty Weert, Jaejin Cho, Detlef Schuppan, Geny M. M. Groothuis, Dirk K.F. Meijer, Klaas Poelstra
Journal: Hepatology (2001)

Kupffer cells (KC) play an important role in the pathogenesis of inflammatory liver diseases leading to fibrosis. Anti-inflammatory drugs are only effective when administered at high doses that may cause side effects. Therefore, dexamethasone coupled to mannosylated albumin (Dexa(5)-Man(10)-HSA) was designed by us to selectively deliver this anti-inflammatory drug to the KC. The effectiveness of Dexa(5)-Man(10)-HSA was studied both in organ cultures and fibrosis induced by bile duct ligation (BDL) in rats. Dexa(5)-Man(10)-HSA accumulated in livers of both healthy and fibrotic rats (67% +/- 5% and 70% +/- 9% of the dose, respectively) and uptake was found almost exclusively in KC. Active dexamethasone was liberated from its carrier, because Dexa(5)-Man(10)-HSA could effectively inhibit nitric oxide (NO) and tumor necrosis factor alpha (TNF-alpha) release in endotoxin-activated liver slices. In vivo, however, this was associated with increased collagen I and III depositions and enhanced tissue inhibitor of metalloproteinase-1 (TIMP-1) mRNA expression. This was accompanied by a decreased influx of reactive oxygen species (ROS) producing cells in the livers of BDL animals treated with Dexa(5)-Man(10)-HSA as compared with untreated BDL rats. Dexa(5)-Man(10)-HSA treatment also replenished the depleted glycogen stores in hepatocytes of BDL livers. In conclusion, our studies showed selective delivery of dexamethasone to KC with Dexa(5)-Man(10)-HSA. This conjugate reduced intrahepatic ROS in vivo and TNF-alpha production in vitro and prevented glycogen depletion in vivo, indicating effective pharmacologic targeting. Dexa(5)-Man(10)-HSA, however, also accelerated fibrogenesis, which was paralleled by TIMP-1 mRNA induction. Targeting of dexamethasone to KC provides evidence for a dual role of this cell type in fibrogenesis of BDL rats.
Effect of Propranolol on Systemic and Coronary Hemodynamics at Rest and during Simulated Exercise
Authors: DAVID H. MCKENNA, ROBERT J. CORLISS, SALVADOR SIALER, WILLIAM C. ZARNSTORFF, CHARLES W. CRUMPTON, GEORGE G. ROWE
Journal: Circulation Research (1966)

The systemic and coronary hemodynamic effects of relatively large doses of propranolol have been studied following its infusion into intact anesthetized dogs at rest and during simulated exercise. At rest, the administration of propranolol was associated with decreased cardiac output and ventricular work and increased peripheral, pulmonary, and coronary vascular resistances. Coronary blood flow and coronary sinus oxygen content decreased while myocardial oxygen consumption and the index of cardiac efficiency were unchanged. The usual hemodynamic response to mild exercise was obtained, with increased cardiac output, cardiac work, body oxygen consumption, and a modest but insignificant increase in coronary blood flow. When propranolol was given and the same exercise continued, body oxygen consumption, cardiac output, and left ventricular work significantly decreased. Insignificant decreases occurred in coronary blood flow, left ventricular oxygen usage, and coronary sinus oxygen content. The present observations are consistent with the thesis that beta-adrenergic blockade induced by propranolol decreases cardiac work at rest and reduces the cardiovascular response to exercise.
Adult Nephrology Fellowship Training in the United States
Authors: Mark E. Rosenberg
Journal: Journal of the American Society of Nephrology (2007)

This article reviews trends and issues related to adult nephrology fellowship education in the United States. The number of nephrology fellowship programs and trainees has continued to increase slowly despite limitations in funding of graduate medical education. The use of the Electronic Residency Application System has provided information for the first time on the number, demographics, and behavior of applicants that can be used as baseline data for tracking trends in fellowship applications and for formulating training policies. Issues that nephrology training programs face are discussed in this review: (1) A more stringent graduate medical education regulatory environment, (2) the use of the National Resident Matching Program to enhance the nephrology fellowship applicant selection process, (3) future nephrology workforce shortages, and (4) the continued subspecialization of nephrology. By working together, nephrology fellowship programs can overcome barriers that are raised by these issues and improve the fellowship training experience.
THE ASSOCIATION OF ANTHROPOMETRIC OBESITY MEASURES WITH CT-MEASURED NON-ALCOHOLIC FATTY LIVER DISEASE IN THE MULTI-ETHNIC STUDY OF ATHEROSCLEROSIS
Authors: Geoffrey H. Tison, Michael Blaha, Khurram Nasir, Roger Blumenthal, Moyses Szklo, Jingzhong Ding, Matthew Budoff
Journal: Journal of the American College of Cardiology (2012)
THE ENHANCEMENT OF BACTERIAL PHAGOCYTOSIS BY SERUM
Authors: Richard B. Johnston, Martin R. Klemperer, Chester A. Alper, Fred S. Rosen
Journal: The Journal of Experimental Medicine (1969)

The role of serum factors in the phagocytosis of pneumococci was studied employing a spectrophotometric assay which measures reduced nitro blue tetrazolium (NBT) dye. Dye reduction occurs within the phagocyte shortly after bacterial ingestion as measured by the phagocytic index technique and by the uptake of (125)I-pneumococci. Bacteria prepared with gammaG antibody were not phagocytosed unless a small volume of fresh normal serum was added. Using fresh sera deficient in single complement components, it was demonstrated that the first four components are necessary for optimal bacterial phagocytosis. When highly purified complement components were added to the antibody-coated pneumococci, enhancement of phagocytosis was achieved only with the sequential addition of C1, C4, C2, and C3. Evidence has been presented that human C3 bound to an immune complex exhibits peptidase activity and that this activity is essential for phagocytosis. A heat-labile, dialyzable serum cofactor which enhances C3 peptidase activity enhanced the phagocytosis of pneumococci prepared with purified complement components. A second phagocytosis-promoting cofactor, which is not a complement component, was found to be a heat-labile, 5-6S, beta pseudoglobulin. This protein may stabilize C3 peptidase activity or inhibit enzymatic inactivation of C3.
Phenotypic identification of over 1000 isolates of anaerobic bacteria recovered between 1999 and 2008 in a major Costa Rican hospital
Authors: E. Rodríguez-Cavallini, P. Vargas, C. Rodríguez, C. Quesada-Gómez, M.-M. Gamboa-Coronado
Journal: Clinical Microbiology and Infection (2010)
Interleukin 13: novel role in direct regulation of proliferation and differentiation of primitive hematopoietic progenitor cells.
Authors: S E Jacobsen, C Okkenhaug, O P Veiby, D Caput, P Ferrara, A Minty
Journal: The Journal of Experimental Medicine (1994)

The recently cloned interleukin 13 (IL-13) shares most investigated biological activities on B lymphocytes and monocytes with IL-4. In this study we investigated for the first time the potential role of IL-13 in the regulation of the growth of hematopoietic progenitor cells. IL-13 enhanced stem cell factor (SCF)-induced proliferation of Lin-Sca-1+ bone marrow progenitor cells more potently than IL-4. The effect of IL-13 was purely synergistic, since IL-13 alone stimulated no colony formation. Single cell experiments suggested that the synergistic effect of IL-13 on Lin-Sca-1+ progenitors was directly mediated. In contrast, IL-13 had no synergistic activity on SCF-induced proliferation of the more mature Lin-Sca-1- progenitor cells. Thus, the cloning frequency in response to SCF + IL-13 was at least 20-fold higher in the Lin-Sca-1+ than the Lin-Sca-1- progenitor cell population. Furthermore, IL-13 but not IL-4 synergistically enhanced colony formation of Lin-Sca-1+ progenitors in response to granulocyte/macrophage colony-stimulating factor (GM-CSF) (threefold), whereas both IL-4 and IL-13 enhanced G-CSF-induced colony formation (threefold), and neither of the two significantly affected CSF-1 and IL-3-induced proliferation. Finally, whereas stimulation of Lin-Sca-1+ progenitors by SCF + G-CSF resulted in the formation of 90% granulocytes, the addition of IL-13 resulted in the production of macrophages exclusively. This novel effect on differentiation was directly mediated, shared with IL-4, and could not be observed on Lin-Sca-1- progenitor cells. Collectively, these findings indicate a novel role of IL-13 in early myelopoiesis, partially overlapping but also different from that of IL-4.
LUMBO-PELVIC ANGULAR KINEMATICS IN YOUTH BASEBALL PITCHERS AFTER A SIMULATED GAME
Authors: R Johnson
Journal: British Journal of Sports Medicine (2014)

Background A growing body of evidence may indicate that the lumbo-pelvic-hip complex (LPHC) has an influence on the function of the scapular and shoulder in overhand throwing athletes. Dysfunction of the LPHC may be related to shoulder injuries. Objective The purpose of this study was to explore the effects of a simulated game on angular velocity and acceleration of the LPHC in youth baseball pitchers. Design Repeated measures within-subjects design (MANOVA). Setting Controlled laboratory setting. Youth sports. Participants 13 male baseball pitchers (11.2±1.0 years; 44.9±7.3 kg; 151.5±6.7 cm) volunteered for this study. Interventions The effects of a simulated baseball game without exceeding the participants' age-restricted pitch limit (35 to 65 pitches) under laboratory conditions formed the independent variable. Main outcome measurements The peak positive and negative velocities and accelerations of flexion/extension and axial rotation of the LPHC during the action (ACT) and follow through (FT) phase before and after the simulated game were the dependent measures. Results The main effect of the simulated game was not significant. Univariate measures indicated axial rotation velocity during the action phase increased, Pre ( M =540.2°/s, SD =97.8) Post ( M =626.7°/s, SD =101.0), F (1, 24)=4.34, P&gt;.049 game. All other LPHC axial rotation measures increased but were not significant at the P=.05 level. No significant change in the angular velocities or accelerations of LPHC flexion. Conclusions Increases in positive angular velocity and acceleration in axial rotation in both ACT and FT were accompanied by increased variation. This may indicate less LPHC control during pitches at the end of the simulated game. Further research on LPHC kinematics needs to be done to understand the role of the pelvis as it relates to the shoulder and kinetic chain.
S20 Time-resolved CT pulmonary angiography contrast transit time in patients with pulmonary embolism: a novel functional CT metric of right heart strain?
Authors: E. R. Swift, S. Rajaram, O. R. Byass, K. Chiu, A. J. Swift
Journal: Thorax (2011)

<h3>Introduction and Objectives</h3> Acute right ventricular (RV) failure is known to cause death in patients with pulmonary embolus due to circulatory collapse. CT pulmonary angiogram (CTPA) is now considered the gold standard test for the detection of pulmonary emboli, the technique provides excellent structural detail, however provides limited functional information. This aim of this was to assess time-resolved CTPA contrast transit times (TT) as a potential functional CT marker for the detection of right heart strain in patients with PE. <h3>Methods</h3> We retrospectively reviewed consecutive patients who underwent CTPA at our institution over a 2-month period. Scans were performed on a Phillips Brilliance 16-slice scanner with a 4 ml/s OptirayTM 300 pressure injection. TT was defined as the time from the start of the injection to the scan trigger at the threshold of 150 hounsfield units measured from ROI analysis at the main pulmonary artery. Established CT structural imaging metrics were scored for comparison. <h3>Results</h3> 56 consecutive patients were identified with evidence of pulmonary embolic disease or normal thoracic CT appearances from CTPA scans. One patient with PE was excluded as the CTPA scan was non-diagnostic. TT, RV septum to free wall distance, RV/LV ratio and PA diameter were all significantly elevated in patients with pulmonary embolus compared to patients with a normal CTPA. On analysis of bivariate correlation, TT had a statistically significant positive correlation with hepatic reflux, PA diameter and RV/LV ratio. Notably, the TT and RV/LV ratio demonstrated a significant direct linear correlation (p=0.001). <h3>Conclusions</h3> This study supports previous evidence of existing markers, such as RV/LV ratio, being useful imaging marker in pulmonary embolic disease. It also suggests that TT, could be a new useful functional marker of right heart strain. The importance of further research into this field is highlighted, and particularly into TT as a haemodynamic prognostic indicator in acute pulmonary embolism.
What is intermediate care?
Authors: René J F Melis, Marcel G M Olde Rikkert, Stuart G Parker, Monique I J van Eijken
Journal: BMJ (2004)

An international consensus on what constitutes intermediate care is needed 

I ntermediate care is an emerging concept in health care, which may offer attractive alternatives to hospital care for elderly patients. As little scientific evidence exists on the benefits of intermediate care, research is especially important.1–3 A prerequisite for research is agreement on the definition of a concept, which is lacking for intermediate care. The term intermediate care is often used as if its meaning is clear, but it conveys little meaning other than being about care that is “in between.” Commonly used definitions of intermediate care do not help much, and several very different definitions are in use. What is needed at the outset is a consensus on what constitutes intermediate care. Until this is agreed on, the concept of intermediate care will remain a mirage and its possibilities unknown.

The term intermediate care was introduced in the United Kingdom's NHS Plan and refined in the national service framework for older people.4 5 The concept seems to arise out of a policy imperative, rather than an analysis of the scientific evidence about effective models of care. Objectives such as “promotion of independence” and …