tbuckley/cabot-search huggingface dataset:
Contrasting approaches to a theory of learning
Authors: Timothy D. Johnston
Journal: Behavioral and Brain Sciences (1981)

Abstract The general process view of learning, which guided research into learning for the first half of this century, has come under attack in recent years from several quarters. One form of criticism has come from proponents of the so-called biological boundaries approach to learning. These theorists have presented a variety of data showing that supposedly general laws of learning may in fact be limited in their applicability to different species and learning tasks, and they argue that the limitations are drawn by the nature of each species' adaptation to the particular requirements of its natural environment. The biological boundaries approach has served an important critical function in the move away from general process learning theory, but it is limited in its ability to provide an alternative to the general process approach. In particular, the biological boundaries approach lacks generality, it is in some respects subservient to the general process tradition, and its ecological content is in too many cases limited to ex post facto adaptive explanations of learning skills. A contrasting, ecological approach to learning, which can provide a true alternative to general process theory, is presented. The ecological approach begins by providing an ecological task description for naturally occurring instances of learning; this step answers the question: What does this animal learn to do? The next step is an analysis of the means by which learning occurs in the course of development, answering the question: How does the animal learn to do this? On the basis of such analyses, local principles of adaptation are formulated to account for the learning abilities of individual species. More global principles are sought by generalization among these local principles and may form the basis for a general ecological theory of learning.
Human plasmacytoid dendritic cells efficiently cross-present exogenous Ags to CD8+ T cells despite lower Ag uptake than myeloid dendritic cell subsets
Authors: Jurjen Tel, Gerty Schreibelt, Simone P. Sittig, Till S. M. Mathan, Sonja I. Buschow, Luis J. Cruz, Annechien J. A. Lambeck, Carl G. Figdor, I. Jolanda M. de Vries
Journal: Blood (2012)
Presence of a mobilizable intracellular pool of hepatocyte growth factor in human polymorphonuclear neutrophils
Authors: Alain Grenier, Sylvie Chollet-Martin, Bruno Crestani, Charlotte Delarche, Jamel El Benna, Anne Boutten, Valérie Andrieu, Geneviève Durand, Marie-Anne Gougerot-Pocidalo, Michel Aubier, Monique Dehoux
Journal: Blood (2002)
Inflammatory and Coagulation Biomarkers and Mortality in Patients with HIV Infection
Authors: Lewis H Kuller, Russell Tracy, Waldo Belloso, Stephane De Wit, Fraser Drummond, H. Clifford Lane, Bruno Ledergerber, Jens Lundgren, Jacqueline Neuhaus, Daniel Nixon, Nicholas I Paton, James D Neaton
Journal: PLoS Medicine (2008)

Background In the Strategies for Management of Anti-Retroviral Therapy trial, all-cause mortality was higher for participants randomized to intermittent, CD4-guided antiretroviral treatment (ART) (drug conservation [DC]) than continuous ART (viral suppression [VS]). We hypothesized that increased HIV-RNA levels following ART interruption induced activation of tissue factor pathways, thrombosis, and fibrinolysis. Methods and Findings Stored samples were used to measure six biomarkers: high sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), amyloid A, amyloid P, D-dimer, and prothrombin fragment 1+2. Two studies were conducted: (1) a nested case–control study for studying biomarker associations with mortality, and (2) a study to compare DC and VS participants for biomarker changes. For (1), markers were determined at study entry and before death (latest level) for 85 deaths and for two controls (n = 170) matched on country, age, sex, and date of randomization. Odds ratios (ORs) were estimated with logistic regression. For each biomarker, each of the three upper quartiles was compared to the lowest quartile. For (2), the biomarkers were assessed for 249 DC and 250 VS participants at study entry and 1 mo following randomization. Higher levels of hsCRP, IL-6, and D-dimer at study entry were significantly associated with an increased risk of all-cause mortality. Unadjusted ORs (highest versus lowest quartile) were 2.0 (95% confidence interval [CI], 1.0–4.1; p = 0.05), 8.3 (95% CI, 3.3–20.8; p < 0.0001), and 12.4 (95% CI, 4.2–37.0; p < 0.0001), respectively. Associations were significant after adjustment, when the DC and VS groups were analyzed separately, and when latest levels were assessed. IL-6 and D-dimer increased at 1 mo by 30% and 16% in the DC group and by 0% and 5% in the VS group (p < 0.0001 for treatment difference for both biomarkers); increases in the DC group were related to HIV-RNA levels at 1 mo (p < 0.0001). In an expanded case–control analysis (four controls per case), the OR (DC/VS) for mortality was reduced from 1.8 (95% CI, 1.1–3.1; p = 0.02) to 1.5 (95% CI, 0.8–2.8) and 1.4 (95% CI, 0.8–2.5) after adjustment for latest levels of IL-6 and D-dimer, respectively. Conclusions IL-6 and D-dimer were strongly related to all-cause mortality. Interrupting ART may further increase the risk of death by raising IL-6 and D-dimer levels. Therapies that reduce the inflammatory response to HIV and decrease IL-6 and D-dimer levels may warrant investigation. Trial Registration: ClinicalTrials.gov (NCT00027352).
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Authors: Christopher S Miller, Brett J Baker, Brian C Thomas, Steven W Singer, Jillian F Banfield
Journal: Genome biology (2011)

Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://doi.org/github.com/csmiller/EMIRGE .
Different combined oral contraceptives and the risk of venous thrombosis: systematic review and network meta-analysis
Authors: B. H. Stegeman, M. de Bastos, F. R. Rosendaal, A. van Hylckama Vlieg, F. M. Helmerhorst, T. Stijnen, O. M. Dekkers
Journal: BMJ (2013)

<h3>Abstract</h3> Mass vaccination is effective in reducing SARS-CoV-2 infections among vaccinated individuals. However, it remains unclear how effectively Covid-19 vaccines prevent people from spreading the virus to their close contacts in real-world circumstances. Here, using nationwide administrative datasets on SARS-CoV-2 infections, vaccination records, demographics, and unique household IDs, we provide evidence about the direct and indirect effectiveness of Covid-19 vaccines in reducing infections among vaccinated individuals and their unvaccinated household members. Our estimates for adults imply indirect effectiveness of 8.7% (95% CI: -28.9 to 35.4) two weeks and 42.9% (95% CI: 22.3 to 58.1) 10 weeks after the first dose. We find that the indirect effect of Covid-19 vaccines is smaller and less precise for unvaccinated children aged between 3 to 18 years than for adults. These results provide household-level evidence that vaccines do not only protect vaccinated individuals but provide indirect protection to unvaccinated individuals in a real-world setting.
Positron Emission Tomography in Oncology
Authors: George M. Bohigian
Journal: JAMA (1988)

This report describes the current and potential uses of positron emission tomography in clinical medicine and research related to oncology. Assessment will be possible of metabolism and physiology of tumors and their effects on adjacent tissues. Specific probes are likely to be developed for target sites on tumors, including monoclonal antibodies and specific growth factors that recognize tumors. To date, most oncological applications of positron emission tomography tracers have been qualitative; in the future, quantitative metabolic measurements should aid in the evaluation of tumor biology and response to treatment. (<i>JAMA</i>1988;259:2126-2131)
Effect of cancer-associated mutations in the PlexinB1 gene
Authors: Chun Zhou, Oscar Gee-Wan Wong, John R Masters, Magali Williamson
Journal: Molecular Cancer (2012)

Abstract Background Semaphorins act as chemotactic cues for cell movement via their transmembrane receptors, plexins. Somatic missense mutations in the plexinB1 gene coupled with overexpression of the protein frequently occur in prostate tumours, indicating a role for plexinB1 in the pathogenesis of prostate cancer. Results Two specific mutations found in prostate cancer enhance RhoD binding and one other mutation results in loss of inhibition of Rac-dependent Pak1 phosphorylation and lamellipodia formation and in impairment of trafficking of plexinB1 to the membrane. None of the three characterised mutations affect PDZRhoGEF binding, RhoA activity, the interaction of plexinB1with the oncogenes ErbB2 or c-Met or ErbB2 phosphorylation. The mutations have the net effect of increasing cell motility by blocking plexinB1-mediated inhibition of Rac while enhancing the interaction with RhoD, an anti-migratory factor. Conclusions PlexinB1 mutations block plexinB1-mediated signalling pathways that inhibit cell motility.
Fibrillar collagen and myocardial stiffness in the intact hypertrophied rat left ventricle.
Authors: J E Jalil, C W Doering, J S Janicki, R Pick, S G Shroff, K T Weber
Journal: Circulation Research (1989)

This study tested the hypothesis that with hypertrophy, the proportion, distribution, and structural alignment of fibrillar collagen are important determinants of myocardial stiffness. Toward this end, the collagen volume fraction (morphometry), the transmural or subendocardial distribution of collagen, and the structural arrangement of fibrillar collagens (picrosirius red) were examined in the hypertrophied ventricle secondary to pressure overload (abdominal aorta banding or perinephritis), isoproterenol, and pressure overload plus isoproterenol. In the same hearts, the slopes of the systolic and diastolic stress-strain relations of the left ventricle, representing its active and passive stiffness, respectively, were obtained. In comparison with controls, we found 1) for a moderate rise in transmural collagen, active and passive stiffness increased with pressure-overload hypertrophy; 2) following isoproterenol alone there was a marked increase in subendocardial collagen, and active and passive stiffness increased; 3) in pressure-overload hypertrophy plus isoproterenol, active stiffness declined. Passive stiffness was increased except when fibrosis and thinning of the interventricular septum occurred, in which case it decreased; and 4) fibrillar collagens involved in remodeling included the formation of either collagen strands and fibers in a greater number of previously collagen-free intermuscular spaces in pressure-overload hypertrophy, or a dense crisscrossing latticework of fibers that encircled muscle fibers after isoproterenol. Thus, an increase in fibrillar collagen in pressure-overload hypertrophy is partially adaptive in that it enhances the tensile strength and three-dimensional delivery of force by the myocardium, but at the expense of reducing distensibility. The appearance of a dense collagen meshwork within the subendocardium after isoproterenol can be considered pathological in that it entraps muscle fibers causing active stiffness to fall while impairing distensibility. Finally, fibrosis may paradoxically reduce passive stiffness if it leads to a thinning of the interventricular septum.
Rapid Progression of Left Ventricular Hypertrophy
Authors: Takuya Taniguchi, Tatsuya Kawasaki, Nobuyuki Miyai, Shigeyuki Miki, Tadaaki Kamitani, Shingo Kawasaki, Hiroaki Matsubara, Chikao Yutani, Hiroki Sugihara
Journal: Circulation (2006)
Biological Gene Delivery Vehicles: Beyond Viral Vectors
Authors: Yiqi Seow, Matthew J Wood
Journal: Molecular Therapy (2009)

Gene therapy covers a broad spectrum of applications, from gene replacement and knockdown for genetic or acquired diseases such as cancer, to vaccination, each with different requirements for gene delivery. Viral vectors and synthetic liposomes have emerged as the vehicles of choice for many applications today, but both have limitations and risks, including complexity of production, limited packaging capacity, and unfavorable immunological features, which restrict gene therapy applications and hold back the potential for preventive gene therapy. While continuing to improve these vectors, it is important to investigate other options, particularly nonviral biological agents which include bacteria, bacteriophage, virus-like particles (VLPs), erythrocyte ghosts, and exosomes. Exploiting the natural properties of these biological entities for specific gene delivery applications will expand the repertoire of gene therapy vectors available for clinical use. Here, we review the prospects for nonviral biological delivery vehicles as gene therapy agents with focus on their unique evolved biological properties and respective limitations and potential applications. The potential of these nonviral biological entities to act as clinical gene therapy delivery vehicles has already been shown in clinical trials using bacteria-mediated gene transfer and with sufficient development, these entities will complement the established delivery techniques for gene therapy applications. Gene therapy covers a broad spectrum of applications, from gene replacement and knockdown for genetic or acquired diseases such as cancer, to vaccination, each with different requirements for gene delivery. Viral vectors and synthetic liposomes have emerged as the vehicles of choice for many applications today, but both have limitations and risks, including complexity of production, limited packaging capacity, and unfavorable immunological features, which restrict gene therapy applications and hold back the potential for preventive gene therapy. While continuing to improve these vectors, it is important to investigate other options, particularly nonviral biological agents which include bacteria, bacteriophage, virus-like particles (VLPs), erythrocyte ghosts, and exosomes. Exploiting the natural properties of these biological entities for specific gene delivery applications will expand the repertoire of gene therapy vectors available for clinical use. Here, we review the prospects for nonviral biological delivery vehicles as gene therapy agents with focus on their unique evolved biological properties and respective limitations and potential applications. The potential of these nonviral biological entities to act as clinical gene therapy delivery vehicles has already been shown in clinical trials using bacteria-mediated gene transfer and with sufficient development, these entities will complement the established delivery techniques for gene therapy applications.
Stroke Complicating Percutaneous Coronary Interventions
Authors: Shmuel Fuchs, Eugenio Stabile, Timothy D. Kinnaird, Gary S. Mintz, Luis Gruberg, Daniel A. Canos, Ellen E. Pinnow, Ran Kornowski, William O. Suddath, Lowell F. Satler, Augusto D. Pichard, Kenneth M. Kent, Neil J. Weissman
Journal: Circulation (2002)

Stroke associated with percutaneous coronary intervention (PCI) is an infrequent although devastating complication. We investigated the incidence, predictors, and prognostic impact of periprocedural stroke in unselected patients undergoing PCI.A total of 9662 patients who underwent 12 407 PCIs between January 1990 and July 1999 were retrospectively studied. Stroke was diagnosed in 43 patients (0.38% of procedures). Patients with stroke were older (72+/-11 versus 64+/-11 years, P<0.001), had lower left ventricular ejection fraction (42+/-12 versus 46+/-13%, P=0.04) and more diabetes (39.5% versus 27.2%, P=0.07), and experienced a higher rate of intraprocedural complications necessitating emergency use of intra-aortic balloon pump (IABP) (23.3% versus 3.3%, P<0.001). In-hospital mortality (37.2% versus 1.1%, P<0.001) and 1-year mortality (56.1% versus 6.5%, P<0.001) were higher in patients with stroke. Compared with hemorrhagic stroke, patients with ischemic stroke had higher rate of in-hospital major adverse cardiac events (57.1% versus 25%, P=0.037). Multivariate logistic regression analysis identified emergency use of IABP as the strongest predictors for stroke (OR=9.6, CI 3.9 to 23.9, P<0.001), followed by prophylactic use of IABP (OR=5.1), age >80 years (OR=3.2, compared with age <50 years), and vein graft intervention (OR=2.7).Stroke associated with contemporary PCI is associated with substantial increased mortality. Elderly patients who experience intraprocedural complications necessitating the use of IABP are at particularly high risk.
Interferon- release assays for the diagnosis of active tuberculosis: sensible or silly?
Authors: C. Lange, M. Pai, F. Drobniewski, G. B. Migliori
Journal: European Respiratory Journal (2009)

Every time Mycobacterium tuberculosis is recovered from human specimens by microbiological culture, the diagnosis of active tuberculosis (TB) is definite 1. As culture growth of M. tuberculosis may take ≥2 weeks on average, clinicians need to rely on other methods to achieve rapid diagnosis of active TB and justify the decision to treat the patient. The decision to initiate anti-TB treatment can be difficult, especially in children, and is currently based on different criteria including: 1) medical history and local epidemiology; 2) chest radiography; 3) the microscopic detection of acid fast bacilli (AFB); 4) amplification of M. tuberculosis nucleic acids from biological specimens; 5) the detection of mycobacteria-specific immune responses in the tuberculin skin test (TST); and 6) interferon (IFN)-γ release assays (IGRAs). Furthermore, several scoring methods have been proposed to diagnose TB in children when microbiological evidence is lacking. While serological antibody-based tests have not been successful 2, novel methods for the diagnosis of TB are constantly being developed 3.

IGRAs, commercially available as the QuantiFERON-TB-Gold® In Tube (QFT-GIT) test (Cellestis, Carnegie, Australia) and as the T-SPOT.TB® test (Oxford Immunotec, Abingdon, UK), are now established in many countries as advanced tools for the immunodiagnosis of latent TB infection (LTBI). In contrast to the mixture of antigens in the purified protein derivate, which is used in the in vivo TST, the IGRA detects effector memory responses to a limited number of specific RD1 peptides by peripheral blood mononuclear cells (PBMC) ex vivo . The genes that encode for the RD1 proteins are absent in the bacille Calmette-Guerin (BCG) vaccine strain. Consequently, in BCG-vaccinated recent contacts of infectious cases, IGRA responses correlate better to M. tuberculosis exposure than the TST 4–8. Therefore, it is plausible that IGRAs are superior to the TST in predicting the development …
Influence of Paired Stimulation on the Electro-mechanical Dissociation During Low Calcium Perfusion of Isolated Rat Hearts
Authors: E. S. Nieuwendijk, F. L. Meijler, D. Durrer
Journal: Cardiovascular Research (1967)

During electro-mechanical dissociation in isolated rat hearts caused by low calcium perfusion, paired stimulation restored the contractions. The main factor determining the size of these contractions is the duration of the interval between the two stimuli forming a pair.
Effects of temperature on Vitalograph spirometer readings.
Authors: W H Perks, T Sopwith, D Brown, C H Jones, M Green
Journal: Thorax (1983)

Spirometric variables were obtained from nine symptomless subjects, who performed forced expiratory manoeuvres with three Vitalograph spirometers at three different ambient temperatures (36.5 degrees C, 24.1 degrees C, and - 7.3 degrees C) over three days according to a Latin square design. Analysis of variance showed no significant difference between values at different ambient temperatures when measured at ATPS. Correction of the results to BTPS resulted in a significant difference in values at the three ambient temperatures for all measurements other than the Vmax25. The mean error introduced by conversion to BTPS varied from 7% (SD 5%) for the FVC at 24.1 degrees C to 30% (21%) for Vmax50 at - 7.3 degrees C. Possible explanations for these observations include the increasing compliance of the spirometer bellows with increasing temperature, relatively slow cooling of gases within the spirometer, and a combination of these effects. We conclude that there is no evidence that conversion to BTPS improves the accuracy of measurements made on a Vitalograph spirometer. Further studies on other spirometers are needed to see whether conversion to BTPS is always appropriate.
Extrinsic allergic alveolitis induced by the yeast<i>Debaryomyces Hansenii</i>
Authors: Y. Yamamoto, S. Osanai, S. Fujiuchi, K. Yamazaki, H. Nakano, Y. Ohsaki, K. Kikuchi
Journal: European Respiratory Journal (2002)

A 65-yr-old female developed cough, fever and dyspnoea following repeated exposure to a home ultrasonic humidifier. High-resolution computed tomography showed ground-glass opacity in both lung fields. Arterial blood gas analysis gave an oxygen tension of 8.38 kPa (63 Torr). Pulmonary function testing revealed restrictive ventilatory impairment with a reduction in the diffusing capacity. The diagnosis of extrinsic allergic alveolitis (EAA) was confirmed by radiographic findings, pathological evidence of alveolitis and reproductive development by a provocation test to the humidifier water. The yeast Debaryomyces Hansenii was the only microorganism cultured from the water of the humidifier. The double diffusion precipitating test and lymphocyte proliferative response was positive for an extract of D. Hansenii , providing evidence to incriminate this fungus. This is the first described case of EAA caused by D. Hansenii .
Inactivation of Bradykinin in the Pulmonary Vascular Bed of Newborn and Fetal Lambs
Authors: BEAT FRIEDLI, GERALDINE KENT, PETER M. OLLEY
Journal: Circulation Research (1973)

Bradykinin is largely inactivated in one passage through the pulmonary vascular bed of adult animals. We studied pulmonary inactivation of bradykinin in newborn lambs, fetal lambs at term, fetal lambs preterm, and adult ewes by comparing the systemic pressure response to infusions proximal to the pulmonary vascular bed with the response to infusions distal to the pulmonary vascular bed. A high degree of inactivation was confirmed in mature ewes (93 ± 1.2%); newborn lambs showed significantly less pulmonary inactivation (68 ± 5.2%) and fetal lambs at term showed only 46 ± 4.8% inactivation. In the preterm fetuses (gestational age 110-128 days), no inactivation could be demonstrated in the pulmonary vascular bed. The return to base-line diastolic pressure after the infusion was discontinued was much slower in the fetus than it was in the newborn and the adult animal, indicating a prolonged effect of bradykinin. The results suggest that inactivation of bradykinin is a pulmonary function that develops late in fetal life and is still less than adult levels at birth. This finding could be of particular interest if bradykinin participates in mediating the circulatory changes occurring at birth.