tbuckley/cabot-search huggingface dataset:
The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis
Authors: Darragh Duffy, Rasha Mamdouh, Melissa Laird, Charlotte Soneson, Lenaig Le Fouler, Maï El-Daly, Armanda Casrouge, Jérémie Decalf, Amal Abbas, Noha Sharaf Eldin, Magnus Fontes, Mohamed Abdel-Hamid, Mostafa K. Mohamed, Mona Rafik, Arnaud Fontanet, Matthew L. Albert
Journal: Hepatology (2013)

Viral hepatitis is the leading cause of liver disease worldwide and can be caused by several agents, including hepatitis A (HAV), B (HBV), and C (HCV) virus. We employed multiplexed protein immune assays to identify biomarker signatures of viral hepatitis in order to define unique and common responses for three different acute viral infections of the liver. We performed multianalyte profiling, measuring the concentrations of 182 serum proteins obtained from acute HAV- (18), HBV- (18), and HCV-infected (28) individuals, recruited as part of a hospital-based surveillance program in Cairo, Egypt. Virus-specific biomarker signatures were identified and validation was performed using a unique patient population. A core signature of 46 plasma proteins was commonly modulated in all three infections, as compared to healthy controls. Principle component analysis (PCA) revealed a host response based upon 34 proteins, which could distinguish HCV patients from HAV- and HBV-infected individuals or healthy controls. When HAV and HBV groups were compared directly, 34 differentially expressed serum proteins allowed the separation of these two patient groups. A validation study was performed on an additional 111 patients, confirming the relevance of our initial findings, and defining the 17 analytes that reproducibly segregated the patient populations.This combined discovery and biomarker validation approach revealed a previously unrecognized virus-specific induction of host proteins. The identification of hepatitis virus specific signatures provides a foundation for functional studies and the identification of potential correlates of viral clearance.
Advances in Cognitive Theory and Therapy: The Generic Cognitive Model
Authors: Aaron T. Beck, Emily A.P. Haigh
Journal: Annual Review of Clinical Psychology (2014)

For over 50 years, Beck's cognitive model has provided an evidence-based way to conceptualize and treat psychological disorders. The generic cognitive model represents a set of common principles that can be applied across the spectrum of psychological disorders. The updated theoretical model provides a framework for addressing significant questions regarding the phenomenology of disorders not explained in previous iterations of the original model. New additions to the theory include continuity of adaptive and maladaptive function, dual information processing, energizing of schemas, and attentional focus. The model includes a theory of modes, an organization of schemas relevant to expectancies, self-evaluations, rules, and memories. A description of the new theoretical model is followed by a presentation of the corresponding applied model, which provides a template for conceptualizing a specific disorder and formulating a case. The focus on beliefs differentiates disorders and provides a target for treatment. A variety of interventions are described.
Structure and function of Cas-L, a 105-kD Crk-associated substrate-related protein that is involved in beta 1 integrin-mediated signaling in lymphocytes.
Authors: M Minegishi, K Tachibana, T Sato, S Iwata, Y Nojima, C Morimoto
Journal: The Journal of Experimental Medicine (1996)

Integrin/ligand binding evokes tyrosine phosphorylation of various proteins. We reported previously that a 105 kD protein (pp105) was tyrosine phosphorylated by the engagement of beta 1 integrins in T lymphocytes. We show here that pp105 is a novel p130Cas (Crk-associated substrate)-related protein. Deduced amino acid sequence revealed that pp105 contains conserved motifs with p130Cas, and both pp105 and p130Cas bind to focal adhesion kinase (pp125FAK) and Crk. However, pp105 has a clearly distinct structure from p130Cas, and pp105 is preferentially expressed in lymphocytes, whereas p130Cas is expressed in adherent cells. With these findings, we designate pp105 as Cas-L, lymphocyte-type Cas. Furthermore, we demonstrate that integrin/ligand binding results in the recruitment of Crk, Nck, and SHPTP2 to pp105. These findings further define the roles of pp105/Cas-L and pp125FAK in the integrin-mediated signaling pathways.
Analgo-Sedation of Patients with Burns Outside the Operating Room
Authors: Cesare Gregoretti, Daniela Decaroli, Quirino Piacevoli, Alice Mistretta, Nicoletta Barzaghi, Nicola Luxardo, Irene Tosetti, Luisa Tedeschi, Laura Burbi, Paolo Navalesi, Fabio Azzeri
Journal: Drugs (2008)
How to minimise the health risks to athletes who compete in weight-sensitive sports review and position statement on behalf of the Ad Hoc Research Working Group on Body Composition, Health and Performance, under the auspices of the IOC Medical Commission
Authors: Jorunn Sundgot-Borgen, Nanna L Meyer, Timothy G Lohman, Timothy R Ackland, Ronald J Maughan, Arthur D Stewart, Wolfram Müller
Journal: British Journal of Sports Medicine (2013)

A focus on low body weight and body fat content, combined with regulations in some weight-sensitive sports, are considered risk factors for extreme dieting, eating disorders (EDs) and related health consequences among athletes. At present there are, from a health perspective, no generally accepted optimum values for body weight or percentage of fat mass in different sports and there is no ‘gold standard’ method for body composition assessment in athletes. On the basis of health considerations as well as performance, medical support teams should know how to approach elite athletes who seek to achieve an unrealistic body composition and how to prevent restrictive eating practices from developing into an ED. In addition, these teams must know when to raise the alarm and how to advice athletes who are affected by extreme dieting or clinical EDs. However, there is no consensus on when athletes struggling with extreme dieting or EDs should be referred for specialist medical treatment or removed from competition. Based on the present review, we conclude that there is a need for (1) sport-specific and gender-specific preventive programmes, (2) criteria for raising alarm and ‘does not start’ (DNS) for athletes with EDs and (3) modifications to the regulations in some sports. Further, the key areas for research identified include the development of standard methods for body composition assessment in elite athletes; screening measures for EDs among athletes; development and testing of prevention programmes; investigating the short and long-term effects of extreme dieting; and EDs on health and performance.
The bedside autofluorescence pleuroscopy for the undiagnosed lung cancer with pleural effusion in a intensive care unit
Authors: Hean Ooi, Shang-Miao Chang, Chien-Ming Liu, Kuo-Liang Chiu, Jeng-Yuan Wu, Nan-Yung Hsu
Journal: European Respiratory Journal (2012)

Introduction: Autofluorescence bronchoscopy was developed to enhance the detection of lung cancer in the airway. However, its role in evaluation of pleural space has not been published.  Aim: To assess the undiagnosed lung cancer with pleural effusion in a intensive care unit(ICU).  Methods: A flexible bronchoscope(SAFE 3000,Pentax,Tokyo) to entry to assess the pleural space. The evaluation of pleural space was started by Twin Mode and then completed by MIX. Then the specimens send for histological examination and the clinical data retrospectively stydied. The whole procedures were done in the ICU bedsides.  Results: 22 patients were recruited. There were 6 patients with cytology negative and normal finding in WLP or AFP but 2 of them were found to have lung cancer. Among the 16 patients with atypia or suspicious cells had abnormal finding in the WLP or AFP, 15 patients finally had lung cancer.  Conclusion: The AFP is useful for detecting the undiagnosed lung cancer with pleural effusion. This is a daily practice performed not only in endoscopic room but in the ICU bedsides.
Lung function trajectories from birth through puberty reflect atopic disease phenotypes
Authors: Karin C. Lødrup Carlsen, Vegard Hovland, Petter Mowinckel, Geir Håland, Kai-Håkon Carlsen
Journal: European Respiratory Journal (2013)

Background: Asthma heterogeneity challenges identification of scientifically and clinically meaningful childhood asthma phenotypes. We asked if lung function trajectories from birth to 16 years reflected time-based (TBP) or atopic-disease (ADP) phenotypes.  Methods: Lung function (z-scores) was measured in the “Environment and Childhood Asthma” birth cohort study in Oslo by tidal flow-volume ratios (time to peak expiratory flow by total expiratory time (tPTEF/tE)) in awake neonates (mean age 2 days) and by forced expiratory flow-volume loops at 10 and 16 years. Data from the 0-2, 10 and 16-years investigations were used to classify all 550 children (52% boys) by recurrent (≥2) bronchial obstruction (rBO) 0-2 years, or asthma (≥2 of doctor diagnosis, asthma symptoms or –medication use) from 2-10 and 10-16 years for the TBP and rBO/asthma with atopic dermatitis and/or allergic rhinitis from 10-16 years as ADP.  Results: Compared to children without asthma 10-16 years, the lung function trajectory for the phenotype asthma, AD and AR from 10-16 years, but not for TCP (figure 1) was significantly reduced from birth (p  Conclusions: Persistently reduced lung function through childhood was reflected in atopic disease- but not time of symptom presentation based phenotypes.
Identification of mutations in CUL7 in 3-M syndrome
Authors: Céline Huber, Dora Dias-Santagata, Anna Glaser, James O'Sullivan, Raja Brauner, Kenneth Wu, Xinsong Xu, Kerra Pearce, Rong Wang, Maria Luisa Giovannucci Uzielli, Nathalie Dagoneau, Wassim Chemaitilly, Andrea Superti-Furga, Heloisa Dos Santos, André Mégarbané, Gilles Morin, Gabriele Gillessen-Kaesbach, Raoul Hennekam, Ineke Van der Burgt, Graeme C M Black, Peter E Clayton, Andrew Read, Martine Le Merrer, Peter J Scambler, Arnold Munnich, Zhen-Qiang Pan, Robin Winter, Valérie Cormier-Daire
Journal: Nature Genetics (2005)
Parent-mediated communication-focused treatment in children with autism (PACT): a randomised controlled trial
Authors: Jonathan Green, Tony Charman, Helen McConachie, Catherine Aldred, Vicky Slonims, Pat Howlin, Ann Le Couteur, Kathy Leadbitter, Kristelle Hudry, Sarah Byford, Barbara Barrett, Kathryn Temple, Wendy Macdonald, Andrew Pickles
Journal: The Lancet (2010)
Sensitivity and specificity of the histamine challenge test for the diagnosis of asthma in an unselected sample of children and adolescents
Authors: V Backer, S Groth, A Dirksen, N Bach-Mortensen, KK Hansen, EM Laursen, D Wendelboe
Journal: European Respiratory Journal (1991)

The purpose of this investigation was to study factors of importance for the degree of bronchial responsiveness and, furthermore, to evaluate the sensitivity, specificity and predictive value of a bronchial challenge test with histamine for the diagnosis of asthma in 495 randomly selected children and adolescents, aged 7-16 yrs, from Copenhagen, Rigshospitalet. Detailed history about allergic symptoms, physical examination and bronchial histamine challenge tests were performed at the out-patient clinic. Asthma, atopic disease and height were found to be of great importance for the degree of bronchial responsiveness, whereas the age, sex and smoking habits were of no significance. The percentage of asthmatics with bronchial hyperresponsiveness, i.e. sensitivity to the test, increased towards 100% on inhaling increasing concentrations of histamine, but this was accompanied by a decrease in specificity and predictive values of positive test in regard to the diagnosis of asthma. However, lower concentrations of histamine may be preferable in order to distinguish between asthma and non-asthma in population samples, as inhalation of 2.4 mg.ml-1 and provocative concentration producing a 20% fall in forced expiratory volume in one second (FEV1) (PC20) provided an acceptable sensitivity (57%), specificity (98%), and predictive value of a positive test (60%). We conclude that as regards the diagnosis of asthma, a low predictive value confirms that the bronchial challenge test plays only a supplementary, but valuable, role in detecting the disease in population samples.
Mutations in the gene encoding fibroblast growth factor 10 are associated with aplasia of lacrimal and salivary glands
Authors: Miriam Entesarian, Hans Matsson, Joakim Klar, Birgitta Bergendal, Lena Olson, Rieko Arakaki, Yoshio Hayashi, Hideyo Ohuchi, Babak Falahat, Anne Isine Bolstad, Roland Jonsson, Marie Wahren-Herlenius, Niklas Dahl
Journal: Nature Genetics (2005)
Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the<i>Drosophila</i>X Chromosome
Authors: Joseph D Coolon, Kraig R Stevenson, C Joel McManus, Bing Yang, Brenton R Graveley, Patricia J Wittkopp
Journal: Molecular Biology and Evolution (2015)

In species with a heterogametic sex, population genetics theory predicts that DNA sequences on the X chromosome can evolve faster than comparable sequences on autosomes. Both neutral and nonneutral evolutionary processes can generate this pattern. Complex traits like gene expression are not predicted to have accelerated evolution by these theories, yet a “faster-X” pattern of gene expression divergence has recently been reported for both Drosophila and mammals. Here, we test the hypothesis that accelerated adaptive evolution of cis-regulatory sequences on the X chromosome is responsible for this pattern by comparing the relative contributions of cis- and trans-regulatory changes to patterns of faster-X expression divergence observed between strains and species of Drosophila with a range of divergence times. We find support for this hypothesis, especially among male-biased genes, when comparing different species. However, we also find evidence that trans-regulatory differences contribute to a faster-X pattern of expression divergence both within and between species. This contribution is surprising because trans-acting regulators of X-linked genes are generally assumed to be randomly distributed throughout the genome. We found, however, that X-linked transcription factors appear to preferentially regulate expression of X-linked genes, providing a potential mechanistic explanation for this result. The contribution of trans-regulatory variation to faster-X expression divergence was larger within than between species, suggesting that it is more likely to result from neutral processes than positive selection. These data show how accelerated evolution of both coding and noncoding sequences on the X chromosome can lead to accelerated expression divergence on the X chromosome relative to autosomes.
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets.
Authors: Xiu-Jie Wang, José L Reyes, Nam-Hai Chua, Terry Gaasterland
Journal: Genome biology (2004)

Abstract Background A class of eukaryotic non-coding RNAs termed microRNAs (miRNAs) interact with target mRNAs by sequence complementarity to regulate their expression. The low abundance of some miRNAs and their time- and tissue-specific expression patterns make experimental miRNA identification difficult. We present here a computational method for genome-wide prediction of Arabidopsis thaliana microRNAs and their target mRNAs. This method uses characteristic features of known plant miRNAs as criteria to search for miRNAs conserved between Arabidopsis and Oryza sativa . Extensive sequence complementarity between miRNAs and their target mRNAs is used to predict miRNA-regulated Arabidopsis transcripts. Results Our prediction covered 63% of known Arabidopsis miRNAs and identified 83 new miRNAs. Evidence for the expression of 25 predicted miRNAs came from northern blots, their presence in the Arabidopsis Small RNA Project database, and massively parallel signature sequencing (MPSS) data. Putative targets functionally conserved between Arabidopsis and O. sativa were identified for most newly identified miRNAs. Independent microarray data showed that the expression levels of some mRNA targets anti-correlated with the accumulation pattern of their corresponding regulatory miRNAs. The cleavage of three target mRNAs by miRNA binding was validated in 5' RACE experiments. Conclusions We identified new plant miRNAs conserved between Arabidopsis and O. sativa and report a wide range of transcripts as potential miRNA targets. Because MPSS data are generated from polyadenylated RNA molecules, our results suggest that at least some miRNA precursors are polyadenylated at certain stages. The broad range of putative miRNA targets indicates that miRNAs participate in the regulation of a variety of biological processes.
THE ELECTROENCEPHALOGRAM IN POST-TRAUMATIC EPILEPSY
Authors: FREDERIC A. GIBBS, WALTER R. WEGNER, ERNA L. GIBBS
Journal: American Journal of Psychiatry (1944)

The electroencephalograms of 175 cases of post-traumatic epilepsy and of 215 cases of head injury without epilepsy were compared. The group of head injury patients without epilepsy was subdivided into 113 cases of mild injury and 102 cases of severe injury. In all cases the electroencephalogram was taken three months or more after the injury so that only the chronic post-traumatic state was considered. Comparisons were made between the electroencephalograms of these three post-traumatic groups, a group of 1,161 unselected epileptics and a group of 1,000 normal control subjects. On the basis of differences between the five groups, the following conclusions are drawn with regard to the electroencephalogram in the chronic post-traumatic state: 1. Among patients with severe head injuries but no seizures, the incidence of abnormal electroencephalograms continues to decrease from three months to two years after injury. 2. Among post-traumatic epileptics, there is a relatively slight decrease in the incidence of abnormalities from three months to two years after injury. 3. Mild head injuries do not greatly increase the incidence of abnormal electroencephalograms above the level encountered in the normal control series. 4. In severe head injuries without seizures, the incidence of electroencephalographic abnormalities is more than twice as high as in the normal control group. 5. After head injury, children are slightly more likely to show abnormalities than adults. They are especially likely to show focal abnormalities. 6. Focal electroencephalographic abnormality is four times as common in post-traumatic epileptics as in unselected epileptics. 7. Focal electroencephalographic abnormality correlates with focal seizures. It strongly suggests localized brain damage. 8. Focal paroxysmal electroencephalograms, i. e., those manifesting focal seizure-discharges, are twenty-one times as common among post-traumatic epileptics as among head injury patients without seizures. 9. Subjective complaints after head injury do not correlate significantly with electroencephalographic abnormalities.
Direct Anti-Inflammatory Mechanisms Contribute to Attenuation of Experimental Allograft Arteriosclerosis by Statins
Authors: Koichi Shimizu, Masanori Aikawa, Kiyoshi Takayama, Peter Libby, Richard N. Mitchell
Journal: Circulation (2003)

Despite the development of effective immunosuppressive therapy, transplant graft arterial disease (GAD) remains the major limitation to long-term graft survival. The interplay between host inflammatory cells and donor vascular wall cells results in an intimal hyperplastic lesion, which leads to ischemia and graft failure. HMG-CoA reductase inhibitors (statins) reduce GAD in human cardiac allografts, although it is unclear whether this is secondary to cholesterol lowering or other mechanisms. This study tested the hypothesis that statins can suppress GAD by cholesterol-independent pathways.We performed heterotopic murine cardiac transplants in total allogeneic or major histocompatibility complex class II-mismatched combinations. Transplanted animals received either control chow, chow containing 25 ppm cerivastatin (low dose), or chow containing 125 ppm cerivastatin (high dose). Mean plasma cerivastatin concentrations were 0.0 (control), 10.1 (low dose), and 21.9 (high dose) nmol/L, respectively. Plasma cholesterol levels were the same in all groups. GAD scores decreased in low-dose (P<0.05) and high-dose (P<0.0001) cerivastatin groups compared with controls, with concomitant reduction in graft-infiltrating cells and significantly decreased intragraft RANTES and monocyte chemotactic protein-1 mRNA expression. Cerivastatin, as well as other statins, also reduced RANTES and monocyte chemotactic protein-1 production in mouse endothelial cells stimulated with interferon-gamma and tumor necrosis factor-alpha in vitro.Clinically achievable levels of an HMG-CoA reductase inhibitor attenuate GAD in murine heart transplants, diminish host inflammatory cell recruitment, and do not alter cholesterol levels. These results indicate that statins can affect arterial biology and inflammation independently of their effects on cholesterol metabolism.
Post-ejection wall thickening as a marker of successful short term hibernation
Authors: J. Rose, R. Schulz, C. Martin, G. Heusch
Journal: Cardiovascular Research (1993)

Short term hibernating myocardium is characterised by a decrease in contractile function in proportion to the reduced blood flow, the recovery of creatine phosphate despite ongoing ischaemia, a recruitable inotropic reserve, and the absence of necrosis. During acute myocardial ischaemia systolic wall thickening decreases and post-ejection wall thickening develops. The extent of post-ejection thickening during severe ischaemia correlates with the recovery of contractile function during reperfusion. Whether the extent of post-ejection wall thickening can also distinguish short term hibernating myocardium from more severely ischaemic, infarcting myocardium and thus predict the amount of viable tissue was tested in 13 anaesthetised pigs.The left anterior descending coronary artery (LAD) was cannulated and perfused at constant flow. After control measurements of regional myocardial blood flow (with radiolabelled microspheres) and wall thickening (sonomicrometry), coronary inflow was reduced to produce a reduction in regional contractile function by 60-100%. After 85 minutes of ischaemia, dobutamine was infused into the LAD for five minutes to determine the extent of inotropic reserve. Transmural biopsies were taken to measure regional myocardial creatine phosphate content and infarct size was determined after two hours of reperfusion by staining with triphenyl tetrazolium chloride.The extent of post-ejection wall thickening after 85-90 minutes of ischaemia correlated with the myocardial creatine phosphate content (r = 0.812, n = 11, p < 0.01) and the extent of the dobutamine recruitable inotropic reserve (r = 0.783, n = 7, p < 0.05). A negative correlation existed between the extent of post-ejection wall thickening and % infarct size (r = -0.699, n = 10, p < 0.05 for the transmural piece of tissue containing the ultrasonic crystals; r = -0.743, n = 10, p < 0.05 for the area of the left ventricle at risk). Finally, post-ejection wall thickening after 85-90 minutes of ischaemia correlated with the recovery of contractile function at 30 minutes reperfusion (r = 0.657, n = 10, p < 0.05).The extent of post-ejection wall thickening may indicate the amount of viable tissue after 85-90 minutes of low flow ischaemia. The greater the post-ejection wall thickening, the more myocardium is successfully hibernating.