bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conceptual Combination: Extension and Intension. Commentary on Aerts, Gabora, and Sozzo
Authors: Hampton James A. 
Published: November 2013

AbstractAerts et al. provide a valuable model to capture the interactive nature of conceptual combination in conjunctions and disjunctions. The commentary provides a brief review of the interpretation of these interactions that has been offered in the literature, and argues for a closer link between the more traditional account in terms of concept intensions, and the parameters that emerge from the fitting of the Quantum Probability model.
THE METAPHOR OF THE ARCHITECT IN DARWIN: CHANCE AND FREE WILL
Authors: Noguera‐Solano Ricardo 
Published: November 2013

AbstractIn The Variation of Animals and Plants under Domestication, published in 1868, Darwin used the metaphor of the architect to argue in favor of natural autonomy and to clarify the role of chance in his theory of adaptive change by variation and natural selection. In this article, I trace the history of this important heuristic instrument in Darwin's writings and letters and suggest that this metaphor was important to Darwin because it helps him to explain the role of chance, and gives an argument in favor of the free will.
THE RELEVANCE OF EMERGENCE THEORY IN THE SCIENCE–RELIGION DIALOGUE
Authors: Leidenhag Mikael 
Published: November 2013

AbstractIn this article, I call into question the relevance of emergence theories as presently used by thinkers in the science–religion discussion. Specifically, I discuss theories of emergence that have been used by both religious naturalists and proponents of panentheism. I argue for the following conclusions: (1) If we take the background theory to be metaphysical realism, then there seems to be no positive connection between the reality of emergent properties and the validity of providing reality with a religious interpretation, though one could perhaps construe an argument for the positive ontological status of emergence as a negative case for a religious worldview. (2) To be considered more plausible, religious naturalism should interpret religious discourse from the perspective of pragmatic realism. (3) Panentheistic models of divine causality are unable to avoid ontological dualism. (4) It is not obvious that emergent phenomena and/or properties are nonreducible in the ontological sense of the terms; indeed, the tension between weak and strong emergence makes it difficult for the emergentist to make ontological judgments. My general conclusion is that the concept of emergence has little metaphysical significance in the dialogue between science and theology.
GUILT AND THE SCIENCE OF EMOTION: HOW DOES PRAYER FIT?
Authors: Tsakiridis George 
Published: November 2013

AbstractThis article engages sources regarding evolutionary development of guilt (Richard Joyce's The Evolution of Morality, Jesse Prinz's Gut Reactions, and others) and how they can be used to dialogue with material on the alleviation of guilt in the Christian tradition using examples in the work of Anselm of Canterbury and John Chrysostom. This raises a few key questions. If guilt is an evolutionary trait created to build reputation and relationship, how does this mesh with some theological approaches to solutions for guilt? To be more precise, guilt possibly evolved to create a motivation for beneficial communal actions, and necessitates belief in the authority of the rules that one breaks to induce it. That said, does religion play a role in awareness of one's guilt, while also providing a solution to that guilt? The possibilities are explored in this article as they relate to issues of repentance, atonement, and prayer.
Monte Carlo calculations for reference dosimetry of electron beams with the PTW Roos and NE2571 ion chambers
Authors: Muir B. R. , Rogers D. W. O. 
Published: November 2013

Purpose:To investigate recommendations for reference dosimetry of electron beams and gradient effects for the NE2571 chamber and to provide beam quality conversion factors using Monte Carlo simulations of the PTW Roos and NE2571 ion chambers.Methods:The EGSnrc code system is used to calculate the absorbed dose‐to‐water and the dose to the gas in fully modeled ion chambers as a function of depth in water. Electron beams are modeled using realistic accelerator simulations as well as beams modeled as collimated point sources from realistic electron beam spectra or monoenergetic electrons. Beam quality conversion factors are calculated with ratios of the doses to water and to the air in the ion chamber in electron beams and a cobalt‐60 reference field. The overall ion chamber correction factor is studied using calculations of water‐to‐air stopping power ratios.Results:The use of an effective point of measurement shift of 1.55 mm from the front face of the PTW Roos chamber, which places the point of measurement inside the chamber cavity, minimizes the difference betweenR50, the beam quality specifier, calculated from chamber simulations compared to that obtained using depth‐dose calculations in water. A similar shift minimizes the variation of the overall ion chamber correction factor with depth to the practical range and reduces the root‐mean‐square deviation of a fit to calculated beam quality conversion factors at the reference depth as a function of R50. Similarly, an upstream shift of 0.34 rcav allows a more accurate determination of R50 from NE2571 chamber calculations and reduces the variation of the overall ion chamber correction factor with depth. The determination of the gradient correction using a shift of 0.22 rcav optimizes the root‐mean‐square deviation of a fit to calculated beam quality conversion factors if all beams investigated are considered. However, if only clinical beams are considered, a good fit to results for beam quality conversion factors is obtained without explicitly correcting for gradient effects. The inadequacy of R50 to uniquely specify beam quality for the accurate selection of kQ factors is discussed. Systematic uncertainties in beam quality conversion factors are analyzed for the NE2571 chamber and amount to between 0.4% and 1.2% depending on assumptions used.Conclusions:The calculated beam quality conversion factors for the PTW Roos chamber obtained here are in good agreement with literature data. These results characterize the use of an NE2571 ion chamber for reference dosimetry of electron beams even in low‐energy beams.
Measuring uncertainty in dose delivered to the cochlea due to setup error during external beam treatment of patients with cancer of the head and neck
Authors: Yan M. , Lovelock D. , Hunt M. , Mechalakos J. , Hu Y. , Pham H. , Jackson A. 
Published: November 2013

Purpose:To use Cone Beam CT scans obtained just prior to treatments of head and neck cancer patients to measure the setup error and cumulative dose uncertainty of the cochlea.Methods:Data from 10 head and neck patients with 10 planning CTs and 52 Cone Beam CTs taken at time of treatment were used in this study. Patients were treated with conventional fractionation using an IMRT dose painting technique, most with 33 fractions. Weekly radiographic imaging was used to correct the patient setup. The authors used rigid registration of the planning CT and Cone Beam CT scans to find the translational and rotational setup errors, and the spatial setup errors of the cochlea. The planning CT was rotated and translated such that the cochlea positions match those seen in the cone beam scans, cochlea doses were recalculated and fractional doses accumulated. Uncertainties in the positions and cumulative doses of the cochlea were calculated with and without setup adjustments from radiographic imaging.Results:The mean setup error of the cochlea was 0.04 ± 0.33 or 0.06 ± 0.43 cm for RL, 0.09 ± 0.27 or 0.07 ± 0.48 cm for AP, and 0.00 ± 0.21 or −0.24 ± 0.45 cm for SI with and without radiographic imaging, respectively. Setup with radiographic imaging reduced the standard deviation of the setup error by roughly 1–2 mm. The uncertainty of the cochlea dose depends on the treatment plan and the relative positions of the cochlea and target volumes. Combining results for the left and right cochlea, the authors found the accumulated uncertainty of the cochlea dose per fraction was 4.82 (0.39–16.8) cGy, or 10.1 (0.8–32.4) cGy, with and without radiographic imaging, respectively; the percentage uncertainties relative to the planned doses were 4.32% (0.28%–9.06%) and 10.2% (0.7%–63.6%), respectively.Conclusions:Patient setup error introduces uncertainty in the position of the cochlea during radiation treatment. With the assistance of radiographic imaging during setup, the standard deviation of setup error reduced by 31%, 42%, and 54% in RL, AP, and SI direction, respectively, and consequently, the uncertainty of the mean dose to cochlea reduced more than 50%. The authors estimate that the effects of these uncertainties on the probability of hearing loss for an individual patient could be as large as 10%.
The Pathogenesis of Severe Fever with Thrombocytopenia Syndrome Virus Infection in Alpha/Beta Interferon Knockout Mice: Insights into the Pathologic Mechanisms of a New Viral Hemorrhagic Fever
Authors: Liu Yan , Wu Bin , Paessler Slobodan , Walker David H. , Tesh Robert B. , Yu Xue-jie 
Published: November 2013

ABSTRACT

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a newly discovered
Phlebovirus
causing an emerging hemorrhagic fever in East Asia, with reported case fatality rates up to 30%. Despite the high case fatality rate and large number of persons at risk of infection, the pathobiology of the disease is unknown, and no effective animal model has been available for investigating its pathogenesis. We have studied mice and hamsters as potential small-animal models of SFTSV infection following subcutaneous, intraperitoneal, or intracerebral inoculation. Animal tissues were processed for viral load determination, histopathology, immunohistochemistry, and confocal microscopic studies. We found that immunocompetent adult mice and hamsters did not become ill after SFTSV infection. However, alpha/beta interferon receptor knockout (IFNAR
−/−
) mice were highly susceptible to SFTSV infection, and all mice died within 3 to 4 days after subcutaneous inoculation of 10
6
focus-forming units of SFTSV. Histologic examination of tissues of IFNAR
−/−
mice infected with SFTSV showed no detectable lesions. In contrast, by immunohistochemistry virus antigen was found in liver, intestine, kidney, spleen, lymphoid tissue, and brain, but not in the lungs. Mesenteric lymph nodes and spleen were the most heavily infected tissues. Quantitative reverse transcription-PCR (RT-PCR) confirmed the presence of virus in these tissues. Confocal microscopy showed that SFTSV colocalized with reticular cells but did not colocalize with dendritic cells, monocytes/macrophages, neutrophils, or endothelium. Our results indicate that SFTSV multiplied in all organs except for lungs and that mesenteric lymph nodes and spleen were the most heavily infected tissues. The major target cells of SFTSV appear to be reticular cells in lymphoid tissues of intestine and spleen.
The Canarypox Virus Vector ALVAC Induces Distinct Cytokine Responses Compared to the Vaccinia Virus-Based Vectors MVA and NYVAC in Rhesus Monkeys
Authors: Teigler Jeffrey E. , Phogat Sanjay , Franchini Genoveffa , Hirsch Vanessa M. , Michael Nelson L. , Barouch Dan H. 
Published: November 2013

ABSTRACT
Despite the growing use of poxvirus vectors as vaccine candidates for multiple pathogens and cancers, their innate stimulatory properties remain poorly characterized. Here we show that the canarypox virus-based vector ALVAC induced distinct systemic proinflammatory and antiviral cytokine and chemokine levels following the vaccination of rhesus monkeys compared to the vaccinia virus-based vectors MVA and NYVAC. These data suggest that there are substantial biological differences among leading poxvirus vaccine vectors that may influence resultant adaptive immune responses following vaccination.
Differential
In Vitro
Immortalization Capacity of Eleven, Probable High-Risk Human Papillomavirus Types
Authors: Schütze Denise M. , Snijders Peter J. F. , Bosch Leontien , Kramer Duco , Meijer Chris J. L. M. , Steenbergen Renske D. M. 
Published: November 2013

ABSTRACT

Epidemiological studies identified 12 high-risk HPV (hrHPV) types and 8 probable/possible hrHPV types that display different cancer risks. Functional studies on transforming properties of hrHPV are mainly limited to HPV16 and -18, which induce immortalization of human foreskin keratinocytes (HFKs) by successive bypass of two proliferative life span barriers, senescence and crisis. Here, we systematically compared the
in vitro
immortalization capacities, as well as influences on p53, pRb, hTERT, growth behavior, and differentiation capacity, of nine hrHPV types (HPV16, -18, -31, -33, -35, -45, -51, -52, and -59), and two probable hrHPV types (HPV66 and -70). By retroviral transduction, the respective E6/E7 coding sequences were expressed in HFKs from two or three independent donors. Reduced p53 levels and low-level hTERT expression in early-passage cells, as seen in HPV16-, -31-, -33-, and -35-, and to a lesser extent HPV18-transduced HFKs, was associated with continuous growth and an increased immortalization capacity. Less frequent immortalization by HPV45 and -51 and immortalization by HPV66 and -70 was preceded by an intervening period of strongly reduced growth (crisis) without prior increase in hTERT expression. Immortalization by HPV59 was also preceded by a period crisis, despite the onset of low hTERT expression at early passage. HPV52 triggered an extended life span but failed to induce immortality. Variations in p53 and pRb levels were not correlated with differences in alternative E6/E7 mRNA splicing in all hrHPV-transduced HFKs. On collagen rafts, transductants showed disturbed differentiation reminiscent of precancerous lesions. In conclusion,
in vitro
oncogenic capacities differ between the established hrHPV types, and both some established and probable hrHPV types display weak or moderate immortalization potential.
Adenosine Deaminase Acts as a Natural Antagonist for Dipeptidyl Peptidase 4-Mediated Entry of the Middle East Respiratory Syndrome Coronavirus
Authors: Raj V. Stalin , Smits Saskia L. , Provacia Lisette B. , van den Brand Judith M. A. , Wiersma Lidewij , Ouwendijk Werner J. D. , Bestebroer Theo M. , Spronken Monique I. , van Amerongen Geert , Rottier Peter J. M. , Fouchier Ron A. M. , Bosch Berend Jan , Osterhaus Albert D.M.E. , Haagmans Bart L. 
Published: November 2013

ABSTRACT
Middle East respiratory syndrome coronavirus (MERS-CoV) replicates in cells of different species using dipeptidyl peptidase 4 (DPP4) as a functional receptor. Here we show the resistance of ferrets to MERS-CoV infection and inability of ferret DDP4 to bind MERS-CoV. Site-directed mutagenesis of amino acids variable in ferret DPP4 thus revealed the functional human DPP4 virus binding site. Adenosine deaminase (ADA), a DPP4 binding protein, competed for virus binding, acting as a natural antagonist for MERS-CoV infection.
Global Bidirectional Transcription of the Epstein-Barr Virus Genome during Reactivation
Authors: O'Grady Tina , Cao Subing , Strong Michael J. , Concha Monica , Wang Xia , Splinter BonDurant Sandra , Adams Marie , Baddoo Melody , Srivastav Sudesh K. , Lin Zhen , Fewell Claire , Yin Qinyan , Flemington Erik K. 
Published: November 2013

ABSTRACT
Epstein-Barr virus (EBV) reactivation involves the ordered induction of approximately 90 viral genes that participate in the generation of infectious virions. Using strand-specific RNA-seq to assess the EBV transcriptome during reactivation, we found extensive bidirectional transcription extending across nearly the entire genome. In contrast, only 4% of the EBV genome is currently bidirectionally annotated. Most of the newly identified transcribed regions show little evidence of coding potential, supporting noncoding roles for most of these RNAs. Based on previous cellular long noncoding RNA size calculations, we estimate that there are likely hundreds more EBV genes expressed during reactivation than was previously known. Limited 5′ and 3′ rapid amplification of cDNA ends (RACE) experiments and findings of novel splicing events by RNA-seq suggest that the complexity of the viral genome during reactivation may be even greater. Further analysis of antisense transcripts at some of the EBV latency gene loci showed that they are “late” genes, they are nuclear, and they tend to localize in areas of the nucleus where others find newly synthesized viral genomes. This raises the possibility that these transcripts perform functions such as new genome processing, stabilization, organization, etc. The finding of a significantly more complex EBV transcriptome during reactivation changes our view of the viral production process from one that is facilitated and regulated almost entirely by previously identified viral proteins to a process that also involves the contribution of a wide array of virus encoded noncoding RNAs.

IMPORTANCE
Epstein-Barr virus (EBV) is a herpesvirus that infects the majority of the world's population, in rare cases causing serious disease such as lymphoma and gastric carcinoma. Using strand-specific RNA-seq, we have studied viral gene expression during EBV reactivation and have discovered hundreds more viral transcripts than were previously known. The finding of alternative splicing and the prevalence of overlapping transcripts indicate additional complexity. Most newly identified transcribed regions do not encode proteins but instead likely function as noncoding RNA molecules which could participate in regulating gene expression, gene splicing or even activities such as viral genome processing. These findings broaden the scope of what we need to consider to understand the viral manufacturing process. As more detailed studies are undertaken they will likely change the way we view this process as a whole.
Weekly sport practice and adolescent well-being
Authors: Merglen Arnaud , Flatz Aline , Bélanger Richard E , Michaud Pierre-André , Suris Joan-Carles 
Published: November 2013

ObjectiveSport practice is widely encouraged, both in guidelines and in clinical practice, because of its broad range of positive effects on health. However, very limited evidence directly supports this statement among adolescents and the sport duration that we should recommend remains unknown. We aimed to determine sport durations that were associated with poor well-being.MethodsWe conducted a survey including 1245 adolescents (16–20 years) from the general Swiss population. Participants were recruited from various settings (sport centres, peers of sport practicing adolescents, websites) and asked to complete a web-based questionnaire. Weekly sport practice was categorised into four groups: low (0–3.5 h), average (≈ recommended 7 h (3.6–10.5)), high (≈14 h (10.6–17.5)) and very high (>17.5 h). We assessed well-being using the WHO-5 Well-Being Index.ResultsCompared with adolescents in the average group, those in the very high group had a higher risk of poor well-being (OR 2.29 (95% CI 1.11 to 4.72)), as did those in the low group (OR 2.33 (1.58 to 3.44)). In contrast, those in the high group had a lower risk of poor well-being than those in the average group (OR 0.46 (0.23 to 0.93)).ConclusionsWe found an inverted, U-shaped relationship between weekly sport practice duration and well-being among adolescents. The peak scores of well-being were around 14 h per week of sport practice, corresponding to twice the recommended 7 h. Practicing higher sport durations was an independent risk factor of poor well-being.
Anthracycline-induced cardiotoxicity: prospective cohort study from Pakistan
Authors: Shaikh Abdul Sattar , Saleem Ali Faisal , Mohsin Shazia Samad , Alam Muhammad Matloob , Ahmed Mehnaz Atiq 
Published: November 2013

ObjectivesTo identify anthracycline-induced acute (within 1 month) and early-onset chronic progressive (within 1 year) cardiotoxicity in children younger than 16 years of age with childhood malignancies at a tertiary care centre of Pakistan.DesignProspective cohort study.SettingAga Khan University, Karachi, Pakistan.Participants110 children (aged 1 month–16 years).InterventionAnthracycline (doxorubicin and/or daunorubicin).Outcome measurementsAll children who received anthracycline as chemotherapy and three echocardiographic evaluations (baseline, 1 month and 1 year) between July 2010 and June 2012 were prospectively analysed for cardiac dysfunction. Statistical analysis including systolic and diastolic functions at baseline, 1 month and 1 year was carried out by repeated measures analysis of variance.ResultsMean age was 74±44 months and 75 (68.2%) were males. Acute lymphoblastic leukaemia was seen in 70 (64%) patients. Doxorubicin alone was used in 59 (54%) and combination therapy was used in 35 (32%). A cumulative dose of anthracycline <300 mg/m2was used in 95 (86%). Fifteen (14%) children developed cardiac dysfunction within a month and 28 (25%) children within a year. Of these 10/15 (66.6%) and 12/28 (43%) had isolated diastolic dysfunction, respectively, while 5/15 (33.3%) and 16/28 (57%) had combined systolic and diastolic dysfunction. Seven (6.4%) patients expired due to severe cardiac dysfunction. Eight of 59 (13.5%) children showed dose-related cardiotoxicity (p=<0.001). Cardiotoxicity was also high when the combination of doxorubicin and daunorubicin was used (p=0.004).ConclusionsIncidence of anthracycline-induced cardiotoxicity is high. Long-term follow-up is essential to diagnose its late manifestations.
Additive roles of platelets and fibrinogen in whole-blood fibrin clot formation upon dilution as assessed by thromboelastometry
Authors: Ninivaggi Marisa , Feijge Marion A. H. , Baaten Constance C. F. M. J. , Kuiper Gerhardus J. A. J. M. , Marcus Marco A. E. , Cate Hugo ten , Lancé Marcus D. , Heemskerk Johan W. M. , van der Meijden Paola E. J. 
Published: November 2013

SummaryBlood dilution after transfusion fluids leads to diminished coagulant activity monitored by rotational thromboelastometry, assessing elastic fibrin clot formation, or by thrombin generation testing. We aimed to determine the contributions of blood cells (platelets, red blood cells) and plasma factors (fibrinogen, prothrombin complex concentrate) to fibrin clot formation under conditions of haemodilution in vitro or in vivo. Whole blood or plasma diluted in vitro was supplemented with platelets, red cells, fibrinogen or prothrombin complex concentrate (PCC). Thromboelastometry was measured in whole blood as well as plasma; thrombin generation was determined in parallel. Similar tests were performed with blood from 48 patients, obtained before and after massive fluid infusion during cardiothoracic surgery. Addition of platelets or fibrinogen, in additive and independent ways, reversed the impaired fibrin clot formation (thromboelastometry) in diluted whole blood. In contrast, supplementation of red blood cells or prothrombin complex concentrate was ineffective. Platelets and fibrinogen independently restored clot formation in diluted plasma, resulting in thromboelastometry curves approaching those in whole blood. In whole blood from patients undergoing dilution during surgery, elastic clot formation was determined by both the platelet count and the fibrinogen level. Thrombin generation in diluted (patient) plasma was not changed by fibrinogen, but improved markedly by prothrombin complex concentrate. In conclusion, in dilutional coagulopathy, platelets and fibrinogen, but not red blood cells or vitamin K-dependent coagulation factors, independently determine thromboelastometry parameters measured in whole blood and plasma. Clinical decisions for transfusion based on thromboelastometry should take into account the platelet concentration.