tbuckley/cabot-search huggingface dataset:
Five-year changes in school recess and lunchtime and the contribution to children's daily physical activity
Authors: Nicola D Ridgers, Anna Timperio, David Crawford, Jo Salmon
Journal: British Journal of Sports Medicine (2011)

Objective To investigate the longitudinal changes in children's recess and lunchtime physical activity levels and in the contribution of recess and lunchtime to daily physical activity levels over 5 years among 5–6- and 10–12-year olds. Methods Data were drawn from two longitudinal studies that were conducted in metropolitan Melbourne, Australia. Boys and girls (n=2782) aged 5–6 years and 10–12 years participated in baseline (T0) measures. Physical activity (n=2490) was measured every 60 s for eight consecutive days using hip-mounted accelerometry. Subsequent measurements were taken at 3-year (T1; n=773) and 5-year (T2; n=634) follow-up. Physical activity intensities were derived using age-adjusted cut-points. Sedentary time was defined as 100 counts/min. Longitudinal data were analysed using three-level (time, child, school) multilevel analyses, stratified by sex and cohort, and adjusted for potential confounding variables. Results Significant decreases in recess and lunchtime moderate and vigorous physical activity were observed (p&lt;0.001), with larger decreases occurring in the older cohort. Associated increases were observed in sedentary time over time (p&lt;0.01). Although the contribution of recess to daily moderate intensity physical activity increased in the younger cohort over time (p&lt;0.001), significant decreases were observed in the older cohort (p&lt;0.001). Conclusion Physical activity levels during recess and lunchtime decreased in both cohorts over time. Decreases in the contribution of recess and lunchtime to older children's daily physical activity were also observed. Interventions are needed in both primary and secondary schools to promote physical activity levels during recess and lunchtime, particularly during the early years of secondary school.
Bacterial transposon Tn5: evolutionary inferences.
Authors: D E Berg, C M Berg, C Sasakawa
Journal: Molecular Biology and Evolution (1984)

Transposable elements induce spontaneous mutations, promote genome rearrangements, regulate gene expression, and participate in the horizontal spread of genes encoding traits such as antibiotic resistance among bacterial genera too distantly related to undergo homologous recombination. Here we review the bacterial transposon Tn5 and focus on those aspects of its functional organization and transposition which provide insights into how it and other elements may have arisen, proliferated, and evolved.
Genome-Wide Association Analysis of Blood Biomarkers in Chronic Obstructive Pulmonary Disease
Authors: Deog Kyeom Kim, Michael H. Cho, Craig P. Hersh, David A. Lomas, Bruce E. Miller, Xiangyang Kong, Per Bakke, Amund Gulsvik, Alvar Agustí, Emiel Wouters, Bartolome Celli, Harvey Coxson, Jørgen Vestbo, William MacNee, Julie C. Yates, Stephen Rennard, Augusto Litonjua, Weiliang Qiu, Terri H. Beaty, James D. Crapo, John H. Riley, Ruth Tal-Singer, Edwin K. Silverman
Journal: American Journal of Respiratory and Critical Care Medicine (2012)

Rationale: A genome-wide association study (GWAS) for circulating chronic obstructive pulmonary disease (COPD) biomarkers could identify genetic determinants of biomarker levels and COPD susceptibility.Objectives: To identify genetic variants of circulating protein biomarkers and novel genetic determinants of COPD.Methods: GWAS was performed for two pneumoproteins, Clara cell secretory protein (CC16) and surfactant protein D (SP-D), and five systemic inflammatory markers (C-reactive protein, fibrinogen, IL-6, IL-8, and tumor necrosis factor-α) in 1,951 subjects with COPD. For genome-wide significant single nucleotide polymorphisms (SNPs) (P < 1 × 10−8), association with COPD susceptibility was tested in 2,939 cases with COPD and 1,380 smoking control subjects. The association of candidate SNPs with mRNA expression in induced sputum was also elucidated.Measurements and Main Results: Genome-wide significant susceptibility loci affecting biomarker levels were found only for the two pneumoproteins. Two discrete loci affecting CC16, one region near the CC16 coding gene (SCGB1A1) on chromosome 11 and another locus approximately 25 Mb away from SCGB1A1, were identified, whereas multiple SNPs on chromosomes 6 and 16, in addition to SNPs near SFTPD, had genome-wide significant associations with SP-D levels. Several SNPs affecting circulating CC16 levels were significantly associated with sputum mRNA expression of SCGB1A1 (P = 0.009–0.03). Several SNPs highly associated with CC16 or SP-D levels were nominally associated with COPD in a collaborative GWAS (P = 0.001–0.049), although these COPD associations were not replicated in two additional cohorts.Conclusions: Distant genetic loci and biomarker-coding genes affect circulating levels of COPD-related pneumoproteins. A subset of these protein quantitative trait loci may influence their gene expression in the lung and/or COPD susceptibility.Clinical trial registered with www.clinicaltrials.gov (NCT 00292552).
Stromal gene expression predicts clinical outcome in breast cancer
Authors: Greg Finak, Nicholas Bertos, Francois Pepin, Svetlana Sadekova, Margarita Souleimanova, Hong Zhao, Haiying Chen, Gulbeyaz Omeroglu, Sarkis Meterissian, Atilla Omeroglu, Michael Hallett, Morag Park
Journal: Nature Medicine (2008)
Analysis of inherited MYH/(MutYH) mutations in British Asian patients with colorectal cancer
Authors: S Dolwani, G T Williams, K P West, J Newman, D Stock, A P Griffiths, J Best, J P Cheadle, J R Sampson
Journal: Gut (2007)

Biallelic inherited mutations of the MYH gene (also known as MutYH or human MutY homologue) are associated with multiple colorectal adenomas and a high risk of colorectal cancer that approaches 100%.1,2 This recessive disorder has become known as MYH-associated polyposis (MAP) to distinguish it from dominantly inherited familial adenomatous polyposis. The risk of colorectal cancer in heterozygotes seems to be only marginally increased, if at all.2 During a review of the Wales Polyposis Register we noted that although only 4 of the 115 recorded families were of Asian origin, all four had MAP. This was in contrast to the 111 indigenous families, only 12 of which had MAP. All affected members of three unrelated British Indian families were homozygous for the mutation E466X and one patient of Pakistani descent was homozygous for Y90X.3 These mutations have not been observed in other ethnic groups. As the overall incidence of colorectal cancer among Asians living in England and Wales is markedly below that of the general population,4 we postulated that MYH mutations might contribute more significantly to colorectal cancer among British Asians than among indigenous northern Europeans. We conducted a retrospective study to assess the contribution of MYH mutations to colorectal cancer among British Asians.
AN INFECTIOUS OPHTHALMIA OF CATTLE
Authors: F. S. Jones, Ralph B. Little
Journal: The Journal of Experimental Medicine (1923)

Twenty-four cases of an acute ophthalmia of cattle have been observed. The infection is characterized by photophobia, severe congestion of the vessels of the eyeball, conjunctivitis, congestion and edema of the membrana nictitans, edema of the eyelids, accompanied by a thick, yellowish white mucus or mucopurulent exudate. In certain cases corneal ulcers and extensive corneal opacities developed. From all cases a characteristic diplobacillus was obtained. The organism was usually observed in the exudate in large numbers. The morphology, the hemolytic properties, and the proteolytic activities readily assist in its identification. Instillation of a few drops of bouillon suspensions of pure cultures beneath the eyelids of normal cattle gave rise to characteristic inflammations. The organism is not pathogenic for laboratory animals.
Lipids, adiposity and tendinopathy: is there a mechanistic link? Critical review
Authors: Alex Scott, Johannes Zwerver, Navi Grewal, Agnetha de Sa, Thuraya Alktebi, David J Granville, David A Hart
Journal: British Journal of Sports Medicine (2014)

Being overweight or obese is associated with an elevated risk of tendon pathology. However, for sportspeople the epidemiological data linking weight or adiposity on one hand, and risk of tendon pathology on the other, are less consistent. Indeed, the mechanistic links between diet, adiposity and tendon pathology remain largely unexamined. Recent studies have begun to examine the effects of dietary interventions on outcomes such as tendon biomechanics or pain. Oxidised low-density lipoprotein has been shown to (A) accumulate in the tendon tissues of mice that eat a fatty diet and (B) induce a pathological phenotype in human tendon cells. This paper addresses the current debate: is excessive body mass index (causing increased load and strain on tendon tissue) per se the underlying mechanism? Or do local or systemic influences of fat on tendons predispose to tendon pathology? This narrative review argues that excessive blood lipids may be an important avenue for clinical investigations.
Bone marrow augmentation of donor-cell chimerism in kidney, liver, heart, and pancreas islet transplantation
Authors: P Fontes, A.S Rao, P Carroll, F Dodson, R Shapiro, A Tzakis, S Todo, K Abu-Elmagd, M Jordon, J.J Fung, T.E Starzl, A.J Demetris, A Zeevi, M Trucco, W.A Rudert, W Rybka, C Ricordi
Journal: The Lancet (1994)
Oral lichen planus pathogenesis: A role for the HCV-specific cellular immune response
Authors: M Pilli
Journal: Hepatology (2002)

Hepatitis C virus infection can be associated with different extrahepatic manifestations, including lichen planus; however, no clear role for HCV in their pathogenesis has been established. T cells were isolated from lichen biopsy specimens of 7 HCV positive patients with oral lichen planus. HCV-specific CD4(+) T-cell lines were obtained in 4 patients from lichen lesions but only in 2 of them from the peripheral blood. Different clonal populations were found in oral tissue and peripheral blood of individual patients, as shown by TCR-Vbeta analysis of antigen-specific T cells. Frequency of HCV-specific CD8(+) cells tested with 4 different HCV tetramers was significantly higher in the lichen tissue than in the circulation; moreover, lichen-derived HCV-specific CD8(+) T cells showed the phenotype of recently activated T cells because most of them were CD69(+) and produced interferon gamma (IFN-gamma) but expanded poorly in vitro upon antigen stimulation. The specificity of HCV-reactive T-cell recruitment into the lichen tissue was further confirmed by the absence of HBV-specific T cells within lichen lesions in 3 additional patients with lichen planus associated with HBV infection. Our study shows HCV-specific T-cell responses at the site of the lesions of an HCV-associated dermatologic disease, sustained by HCV-specific T cells with phenotypic and functional characteristics of terminally differentiated effector cells. In conclusion, this finding and the detection of HCV RNA strands in the lichen tissue strongly suggest a role for HCV-specific T-cell responses in the pathogenesis of oral lichen planus associated with HCV infection.
Three Lectures on the Principle of Least Action in Nature, Illustrated by Animal Mechanics
Authors: S. Haughton
Journal: BMJ (1871)

Geometrical Classiftcatioz of Muscles founid in Anitals.-Application oy theprinciple of Least Action to severalforms of Muscle, demonstratinig the possibility of "predicting" Animal Structures by JMathematical Calculationts similato those used in Astrono7ny and the other exact Sciences.
Recursive Partitioning Identifies Patients at High and Low Risk for Ipsilateral Tumor Recurrence After Breast-Conserving Surgery and Radiation
Authors: G. M. Freedman, A. L. Hanlon, B. L. Fowble, P. R. Anderson, N. Nicoloau
Journal: Journal of Clinical Oncology (2002)

Recursive partitioning analysis (RPA), a method of building decision trees of significant prognostic factors for outcome, was used to determine subgroups at significantly different risk for ipsilateral breast tumor recurrence (IBTR) in early-stage breast cancer.Nine hundred twelve women underwent breast-conserving surgery, axillary dissection, and radiation. Systemic therapy was chemotherapy with or without tamoxifen in 32%, tamoxifen in 27%, or none in 41%. RPA was used to create a decision tree according to predictive variables that classify patients by IBTR risk, and the Kaplan-Meier method was used to calculate 10-year risks. Median follow-up was 5.9 years.Age was the first split in the partition tree. Patients more than 55 years old had a 4% 10-year IBTR, the only further division being use of tamoxifen or not (2% v 5%, P =.03). For patients </= 55 years old, extensive intraductal component (EIC) was the next significant split. For EIC-negative tumors, age </= 35 years and negative margins were associated with a 10-year IBTR of 3%; with close (</= 2 mm) or positive margins, 34%. Patients 36 to 55 years old with estrogen receptor-positive tumors receiving tamoxifen had a risk of IBTR of 5%, but had a 20% risk without tamoxifen.This RPA showed that age </= 55 versus more than 55 years was the most significant factor for IBTR. Patients </= 35 years old had a low risk of IBTR when tumors were EIC-negative with negative margins. EIC was an independent factor for IBTR for ages </= 55 years. Use of tamoxifen was the most significant factor for patients older than 55 years, but it resulted in a greater absolute decrease in risk of IBTR for patients 36 to 55 years old.
Recent advances in exacerbations of COPD
Authors: T. Seemungal, A. Sykes
Journal: Thorax (2008)

The First International Conference on Exacerbations of Airways Disease (ICEAD) brought together experts from both sides of the Atlantic to discuss problems in the management of exacerbations of both asthma and chronic obstructive pulmonary disease (COPD). A brief overview of these discussions on COPD exacerbations follows.

### Symptom and treatment based definitions

Up to 18 definitions of a COPD exacerbation have been advanced, from less explicit1 to very explicit symptom based criteria.2 3 However, large therapeutic trials in COPD have all used treatment based definitions.4 5 The first consensus definition was treatment based but the current GOLD guidelines accept a symptom based definition.6 7 Biochemical or physiological markers applied in studies using either definition8 9 have all shown significant changes, supporting the validity of these approaches to a definition but lack specificity and sensitivity. The healthcare utilisation approach to severity of exacerbation may be more robust as it has been related to mortality10 but does not allow for detection of untreated exacerbations, which may contribute to poor quality of life.

### Health burden

COPD patients have about 0.5–3.5 exacerbations/year, 0.09–2.4 hospitalisations/year and inhospital mortality varies between 10% and 60%, depending on the severity of COPD. Overall, the death rate varies from 5.4 per 1000 person years among normal subjects to 42.9 among subjects with GOLD stage 3 or 4.11 Thus COPD exacerbations are a significant cause of death, mainly in patients with more severe COPD. This leads to a high cost of COPD care which can be effectively reduced through decreasing hospitalisation.12

### Airway bacterial infection

Bacteria may be detected in up to 60% of exacerbations and viruses in 23–60%.13 14 A study of hospitalised patients found bacteria in 25%, bacteria and viruses in 25% and viruses alone in 25%, and no infectious agent in another 25%.14 The acquisition of new strains of bacteria …
Low Olfactory Bulb Volume in First-Degree Relatives of Patients With Schizophrenia
Authors: Bruce I Turetsky, Paul J Moberg, Steven E Arnold, Richard L Doty, Raquel E Gur
Journal: American Journal of Psychiatry (2003)

OBJECTIVE: There is a substantial genetic contribution to schizophrenia but no way to readily identify individuals at risk. Biological abnormalities reflecting greater genetic vulnerability may be discovered by examining healthy family members of patients with schizophrenia. There is evidence that olfactory impairments are common in patients. The authors previously reported that patients have abnormal olfactory bulbs, assessed by magnetic resonance imaging (MRI). This study examined olfactory bulbs in patients' relatives to determine whether low bulb volume represents an endophenotypic marker of genetic vulnerability. METHOD: Olfactory psychophysical measures and MRI scans of olfactory bulbs were acquired from 19 healthy first-degree relatives, 20 healthy comparison subjects with similar age and gender distributions, and the 11 patient probands of these relatives. Olfactory bulb volumes were measured by using a reliable region-of-interest procedure. RESULTS: The patients had impaired ability to detect odors and had lower olfactory bulb volumes than the comparison subjects. Although the family members had normal olfactory ability, they exhibited low right bulb volume. The patients had smaller left, but not right, olfactory bulbs than their own healthy relatives. CONCLUSIONS: The findings in family members suggest that structural abnormalities of the olfactory system in schizophrenia may partly reflect preexisting genetic vulnerability to illness. Preliminary analyses suggest that right olfactory bulb volume may serve as an endophenotypic marker of genetic vulnerability, while left bulb volume may reflect overt disease among individuals who share genetic vulnerability. Bulb abnormalities in patients are consistent with reports of cellular abnormalities affecting peripheral olfactory receptor neurons.
Pharmacological Treatments of Non-Substance-Withdrawal Delirium: A Systematic Review of Prospective Trials
Authors: Joseph I. Friedman, Laili Soleimani, Daniel P. McGonigle, Claudine Egol, Jeffrey H. Silverstein
Journal: American Journal of Psychiatry (2013)

Most reviews of pharmacological strategies for delirium treatment evaluate the effectiveness of these interventions for delirium prevention, reduction in duration and severity of ongoing delirium, and other outcomes that extend beyond the recommendations of expert treatment guidelines. However, little if any attention is given to substantiating the potential benefits of such treatment or addressing the methodological weaknesses that, in part, limit the pharmacological recommendations made by expert treatment guidelines. Therefore, the authors conducted a systematic review to provide the most up-to-date and inclusive review of published prospective trials of potential pharmacological interventions for the prevention and treatment of delirium, and they discuss potential benefits of pharmacological prevention of delirium and/or reduction of ongoing delirium episode duration and severity.The analysis followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, including prospective randomized and nonrandomized double-blind, single-blind, and open-label clinical trials of any pharmacological agent for the prevention or treatment of delirium and reviewing them systematically for effectiveness on several predefined outcomes.The pharmacological strategies reviewed showed greater success in preventing delirium than in treating it. Significant delirium prevention effects are associated with haloperidol, second-generation antipsychotics, iliac fascia block, gabapentin, melatonin, lower levels of intraoperative propofol sedation, and a single dose of ketamine during anesthetic induction and with dexmedetomidine compared with other sedation strategies for mechanically ventilated patients.These promising results warrant further study with consideration of the methodological weaknesses and inconsistencies of studies to date.
Clinical experience of zinc supplementation during intravenous nutrition in Crohn's disease: value of serum and urine zinc measurements.
Authors: A N Main, M J Hall, R I Russell, G S Fell, P R Mills, A Shenkin
Journal: Gut (1982)

Serum zinc concentrations and urine zinc excretion have been studied in 10 patients with severe Crohn9s disease before and during 59 patient-weeks of intravenous nutrition. Before serum zinc concentrations (9.9 +/- 1.0 mumol/l: mean +/- SEM) and urine zinc excretion (3-3 +/- 0.6 mumol/24h) were less than controls (p less than 0.01). No patients had clinical signs of zinc deficiency before intravenous nutrition and none developed signs during it. There was no overall change in serum zinc concentrations, despite improvements in body weight, skinfold thickness, and mid-arm circumference in all patients, and increased serum albumin and serum transferrin concentrations during all but two periods of intravenous nutrition. Nor was there any relationship between serum zinc concentrations and zinc uptake (up to 220 mumol/day), serum zinc concentrations remaining significantly lower than control levels. Urine zinc excretion during the first week of intravenous nutrition showed a 1.2 to 53-fold increase (mean 11-fold) over pre-intravenous nutrition levels, and a positive relationship was demonstrated between zinc intake and urine zinc excretion. It is suggested that zinc supplied by the intravenous route is inefficiently transported to the tissues, and that some is excreted in the form of small molecular weight chelates into urine. Recommendations are made for the supply of intravenous zinc, based on monitoring urine zinc excretion in individual patients.