julilili42/papers huggingface dataset:
Fully coupled hydrogeophysical inversion of a laboratory salt tracer experiment monitored by electrical resistivity tomography
2011-11-09

We perform a salt tracer experiment, monitored by time‐lapse electrical resistivity tomography, in a quasi‐two‐dimensional sandbox with the aim of determining the hydraulic conductivity distribution in the domain. We use sodium chloride as a tracer, together with cochineal red for visual monitoring. The time series of observed resistance for each electrode configuration is characterized by its temporal moments. We invert the mean arrival time of electrical potential perturbations and a few steady state hydraulic head measurements using the fully coupled hydrogeophysical approach recently introduced by Pollock and Cirpka (2010). This is the first application of the approach to experimental data. The results obtained show a reasonable agreement between the estimated hydraulic conductivity field and the pattern of the actual sandbox filling. Using this estimation, a transient simulation is performed to compute the propagation of the salt tracer plume through the sandbox. The latter is compared to pictures taken during the experiment. These results show an even better agreement, indicating that the lenses of different sand types are not entirely homogeneous and some unexpected preferential flow paths are present. We conclude that temporal moments of potential perturbations obtained during salt tracer tests provide a good basis for inferring the hydraulic conductivity distribution by fully coupled hydrogeophysical inversion.
Diagnostic Evaluation of Diffuse Gliomas
2011-11-09

Diffuse gliomas are preferentially located in the subcortical or deep white matter of the cerebral hemispheres and are the most frequent CNS neoplasms accounting for approximately 60 per cent of all CNS tumors (CBTRUS 2011). This definition excludes the circumscribed and biological different pilocytic astrocytoma and pilomyxoid astrocytoma which are covered in a separate chapter in this book. Other rare distinct glial neoplasms with a favourable prognosis such as the subependymal giant cell astrocytoma of lateral ventricles and the pleomorphic xanthoastrocytoma of children and young adults also do not belong into the group of diffuse gliomas. Ependymomas indeed are diffuse growing glial neoplasms but are biologically different. Moreover they appear in a different population as astrocytic and oligodendroglial neoplasms. Because of space limitations the current chapter deals only with astrocytomas, oligodendrogliomas, oligoastrocytomas and glioblastomas. These tumors are grouped here under the umbrella term “diffuse gliomas”. They have a predilection for frontal and temporal lobes accounting together for more than two third of all cases. However diffuse astrocytomas may be seen in any other region of the brain including cerebellum and spinal cord (Louis et al., 2007a). Although serious advances in neuroimaging of these brain tumors have been made in the past, histopathologic evaluation of neurosurgically removed tumor specimens is still required for definite diagnosis of diffuse gliomas. These CNS tumors show an extensive variety of histologcial and cytological appearance making diagnosis somewhat difficult for those who are not familiar in working with brain tumors. The current chapter focuses on neuropathological features of the different types of diffusely infiltrating gliomas based on the latest World Health Organization (WHO) classification of tumors of the nervous system. Core features and distinct pattern and variants are also introduced and illustrated. Immunohistochemistry and molecular biology have contributed to an improved classification and shown in some cases to be of prognostic value. The advantages and limitations of the most commonly used antibodies such as GFAP, WT1, MAP2, MIB-1, P53, IDH1R132H; NOGO-A are discussed in the current chapter. Molecular analysis of 1p19q codeletion, MGMT promoter methylation, Tp53 and isocitrate dehydrogenase mutations are presented in detail and their implications are discussed.
Creativity, Analytical Skills, Personality Traits, and Innovation Game Behavior in the Lab: An Experiment
2011-11-09

Innovative behavior is mostly studied theoretically, e.g., in models of patent races, and empirically, e.g., by using R&amp;D or patent data. This research, however, is only poorly informed about the psychological tradition of creativity research. Our study is an attempt to experimentally collect behavioral data revealing in how far creativity, analytical skills, personality traits and innovation game behavior in the lab are interrelated. With the help of a within-subject design we find that participants' performance in the innovation games is in fact related to their creativity, risk tolerance and self-control. Other personality traits such participants' anxiety, independence, tough-mindedness and extraversion, if any, only play a minor role, and the same is true for participants' analytical skills.
Visualization and Photodynamic Therapy in Malignant Glioma - An Overview and Perspectives
2011-11-09

Photodynamic therapy (PDT) is a relatively new modality of cancer treatment.Actual ongoing clinical era started with the studies of Dougherty in the 1970s.PDT is based on the application of a so called photosensitizer (PS), which preferably enriches in the tumor tissue.The application of light at an appropriate wavelength excites the PS molecules from their ground state S 0 to an electronically excited singlet state S x .The energy of the excited state can be dissipated via several relaxation pathways.By this, so called cytotoxic reactive oxygen species (ROS) are generated.ROS react with various biomolecules inducing cell death by different mechanims.(Dougherty et al. 1998b) History of PDTThe newer history of PDT starts with the observations of Von Tappeiner and Raab at the Maximilian Ludwig University in Munich.In 1900, Raab first reported on the chemical sensitisation of tissue by light.(Raab1900) Von Tappeiner described in 1904 the so called "photodynamic reaction".(Tappeiner& Jodlbauer 1904) He believed that this effect was based on fluorescence.In contrast Neiser (Breslau) and Dreyer (Finsen Institue in Kopenhagen) described a sensitisation by light for photodynamic reaction.(Dreyer1903;Neisser & Halberstaedtter 1904) At this time Ledoux-Lebards already proved the concept of the presence of oxygen as a condition for PDT at the Institute Pasteur in Paris (1902).(Ledoux-Lebards1902) In this era skin diseases were treated with chinidin, acridin and eosin with unsatisfying results.Already from the beginning of PDT, haematoporphyrin (Hp) was of special interest.Hausmann used Hp for photodynamic investigations in mice in 1911.(Hausmann1911) In 1913, Meyer-Betz studied Hp to determine its biological effects on himself.After exposition to sunlight he suffered from extensive phototoxic reactions.(Meyer-Betz1913) Policard detected 1924 in rat sarcoma a red fluorescence after Hp administration.(Policard1924) In 1942 Auler and Banzer reported on the affinity of neoplastic tissues for Hp in tumor, metastases and lymphatic vessels in patients suffering cancer.(Auler& Banzer 1942) Further investigations were performed by Figge et al. in 1948; they demonstrated the properties of Hp to localize tumors.(Figge,Weiland, & Manganiello 1948) Due to high toxic reactions of www.intechopen.com
Resolution adapted finite element modeling of radio frequency interactions on conductive resonant structures in MRI
2011-11-10

Abstract Prediction of interactions between the radiofrequency electromagnetic field in magnetic resonance scanners and electrically conductive material surrounded by tissue plays an increasing role for magnetic resonance safety. Testing of conductive implants or instruments is usually performed by standardized experimental setups and temperature measurements at distinct geometrical points, which cannot always reflect worst‐case situations. A finite element method based on Matlab (The Mathworks, Natick, MA) and the finite element method program Comsol Multiphysics (Stockholm, Sweden) with a spatially highly variable mesh size solving Maxwell's full‐wave equations was applied for a comprehensive simulation of the complete geometrical arrangement of typical birdcage radiofrequency coils loaded with small conductive structures in a homogenous medium. Conductive implants like rods of variable length and closed and open ring structures, partly exhibiting electromagnetic resonance behavior, were modeled and evaluated regarding the distribution of the B 1 ‐ and E ‐field, induced currents and specific absorption rates. Numerical simulations corresponded well with experiments using a spin‐echo sequence for visualization of marked B 1 ‐field inhomogeneities. Even resonance effects in conductive rods and open rings with suitable geometry were depicted accurately. The proposed method has high potential for complementation or even replacement of common experimental magnetic resonance compatibility measurements. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Intra‐ and interoperator reliability of manual and semi‐automated measurements of intracranial translucency
2011-11-11

Abstract Objectives To assess the reproducibility of fetal intracranial translucency (IT) measurements performed manually or with SonoNT ® , a semi‐automated caliper placement technique recently introduced for nuchal translucency thickness (NT) measurement. Methods This was a retrospective study using 116 stored images of the head (mid‐sagittal plane) from normal fetuses in dorsoposterior position at 11–13 weeks. Two experienced operators each measured the IT separately, twice manually and twice using the semi‐automated software. Intraoperator and interoperator repeatability were assessed. The mean of the two manual measurements of the more experienced Operator 2 was considered as the ‘gold standard’. Results Seven cases were excluded as the IT could not be recognized by the semi‐automated software. In the remaining 109 cases, the interquartile range of the mean IT measurement was 1.9–2.4 mm for Operator 1 and 1.8–2.3 mm for Operator 2 for both the manual and the semi‐automated IT measurements. The intraoperator SD for manual measurements was 0.091 mm for Operator 1 and 0.088 mm for Operator 2, and for semi‐automated measurements it was 0.054 mm for Operator 1 and 0.067 mm for Operator 2. Concerning interoperator bias of the manual measurements, the mean difference between Operator 1 and Operator 2 was − 0.09 (95% CI, − 0.11 to − 0.07) mm. With respect to the gold standard, the mean bias of the semi‐automated measurements was 0.01 (95% CI − 0.01 to 0.03) mm for Operator 1 and − 0.09 (95% CI − 0.11 to − 0.07) mm for Operator 2, indicating good agreement. Conclusions Manual IT measurements are reproducible. In addition, IT can be assessed reliably using the semi‐automated NT algorithm, leading to standardization of the IT assessment process. Copyright © 2012 ISUOG. Published by John Wiley &amp; Sons, Ltd.
Continental Europe
2011-11-11

This chapter contains sections titled: Mapping the Territory: Different Traditions in Continental Europe The Emergence of Practical Theology as a Discipline The Foundational Contribution of Friedrich Schleiermacher Institutionalization of Practical Theology in the Twentieth Century Contemporary Developments: Practical Theology as a Discipline Internationalization Interdisciplinary Relationships The Methodology of Practical Theology Expanding the Scope of Practical Theology References
Regulation of coronary venular barrier function by blood borne inflammatory mediators and pharmacological tools: insights from novel microvascular wall models
2011-11-12

We hypothesized that postcapillary venules play a central role in the control of the tightness of the coronary system as a whole, particularly under inflammatory conditions. Sandwich cultures of endothelial cells and pericytes of precapillary arteriolar or postcapillary venular origin from human myocardium as models of the respective vascular walls (sandwich cultures of precapillary arteriolar or postcapillary venular origin) were exposed to thrombin and components of the acutely activatable inflammatory system, and their hydraulic conductivity ( L P ) was registered. L P of SC-PAO remained low under all conditions (3.24 ± 0.52·10 −8 cm·s −1 ·cmH 2 O −1 ). In contrast, in the venular wall model, PGE 2 , platelet-activating factor (PAF), leukotriene B 4 (LTB 4 ), IL-6, and IL-8 induced a prompt, concentration-dependent, up to 10-fold increase in L P with synergistic support when combined. PAF and LTB 4 released by metabolically cooperating platelets, and polymorphonuclear leucocytes (PMNs) caused selectively venular endothelial cells to contract and to open their clefts widely. This breakdown of the barrier function was preventable and even reversible within 6–8 h by the presence of 50 μM quercetin glucuronide (QG). LTB 4 synthesis was facilitated by biochemical involvement of erythrocytes. Platelets segregated in the arterioles and PMNs in the venules of blood-perfused human myocardium (histological studies on donor hearts refused for heart transplantation). Extrapolating these findings to the coronary microcirculation in vivo would imply that the latter's complex functionality after accumulation of blood borne inflammatory mediators can change rapidly due to selective breakdown of the postcapillary venular barrier. The resulting inflammatory edema and venulo-thrombosis will severely impair myocardial performance. The protection afforded by QG could be of particular relevance in the context of cardiosurgical intervention.
Computation of measures of effect size for neuroscience data sets
2011-11-14

Abstract The overwhelming majority of research in the neurosciences employs P ‐values stemming from tests of statistical significance to decide on the presence or absence of an effect of some treatment variable. Although a continuous variable, the P ‐value is commonly used to reach a dichotomous decision about the presence of an effect around an arbitrary criterion of 0.05. This analysis strategy is widely used, but has been heavily criticized in the past decades. To counter frequent misinterpretations of P ‐values, it has been advocated to complement or replace P ‐values with measures of effect size (MES). Many psychological, biological and medical journals now recommend reporting appropriate MES. One hindrance to the more frequent use of MES may be their scarcity in standard statistical software packages. Also, the arguably most widespread data analysis software in neuroscience, matlab , does not provide MES beyond correlation and receiver‐operating characteristic analysis. Here we review the most common criticisms of significance testing and provide several examples from neuroscience where use of MES conveys insights not amenable through the use of P ‐values alone. We introduce an open‐access matlab toolbox providing a wide range of MES to complement the frequently used types of hypothesis tests, such as t ‐tests and analysis of variance. The accompanying documentation provides calculation formulae, intuitive explanations and example calculations for each measure. The toolbox described is usable without sophisticated statistical knowledge and should be useful to neuroscientists wishing to enhance their repertoire of statistical reporting.
Enlightening the past: Analytical proof for the use of Pistacia exudates in ancient Egyptian embalming resins
2011-11-14

Abstract Mastic, the resinous exudate of the evergreen shrub Pistacia lentiscus , is frequently discussed as one of the ingredients used for embalming in ancient Egypt. We show the identification of mastic in ancient Egyptian embalming resins by an unambiguous assignment of the mastic triterpenoid fingerprint consisting of moronic acid, oleanonic acid, isomasticadienonic and masticadienonic acid through the consolidation of NMR and GC/MS analysis. Differences in the observed triterpenoid fingerprints between mummy specimens suggest that more than one plant species served as the triterpenoid resin source. Analysis of the triterpenoid acids of ancient embalming resin samples in the form of their methyl‐ and trimethylsilyl esters is compared. In addition we show a simple way to differentiate between residues of mastic from its use as incense during embalming or from direct mastic application in the embalming resin.
Quasi-periodic flares in EXO 2030+375 observed with INTEGRAL
2011-11-14

Context: Episodic flaring activity is a common feature of X-ray pulsars in HMXBs. In some Be/X-ray binaries flares were observed in quiescence or prior to outbursts. EXO 2030+375 is a Be/X-ray binary showing "normal" outbursts almost every ~46 days, near periastron passage of the orbital revolution. Some of these outbursts were occasionally monitored with the INTEGRAL observatory. Aims: The INTEGRAL data revealed strong quasi-periodic flaring activity during the rising part of one of the system's outburst. Such activity has previously been observed in EXO 2030+375 only once, in 1985 with EXOSAT. (Some indications of single flares have also been observed with other satellites.) Methods: We present the analysis of the flaring behavior of the source based on INTEGRAL data and compare it with the flares observed in EXO 2030+375 in 1985. Results: Based on the observational properties of the flares, we argue that the instability at the inner edge of the accretion disk is the most probable cause of the flaring activity.
POPISK: T-cell reactivity prediction using support vector machines and string kernels
2011-11-15

Abstract Background Accurate prediction of peptide immunogenicity and characterization of relation between peptide sequences and peptide immunogenicity will be greatly helpful for vaccine designs and understanding of the immune system. In contrast to the prediction of antigen processing and presentation pathway, the prediction of subsequent T-cell reactivity is a much harder topic. Previous studies of identifying T-cell receptor (TCR) recognition positions were based on small-scale analyses using only a few peptides and concluded different recognition positions such as positions 4, 6 and 8 of peptides with length 9. Large-scale analyses are necessary to better characterize the effect of peptide sequence variations on T-cell reactivity and design predictors of a peptide's T-cell reactivity (and thus immunogenicity). The identification and characterization of important positions influencing T-cell reactivity will provide insights into the underlying mechanism of immunogenicity. Results This work establishes a large dataset by collecting immunogenicity data from three major immunology databases. In order to consider the effect of MHC restriction, peptides are classified by their associated MHC alleles. Subsequently, a computational method (named POPISK) using support vector machine with a weighted degree string kernel is proposed to predict T-cell reactivity and identify important recognition positions. POPISK yields a mean 10-fold cross-validation accuracy of 68% in predicting T-cell reactivity of HLA-A2-binding peptides. POPISK is capable of predicting immunogenicity with scores that can also correctly predict the change in T-cell reactivity related to point mutations in epitopes reported in previous studies using crystal structures. Thorough analyses of the prediction results identify the important positions 4, 6, 8 and 9, and yield insights into the molecular basis for TCR recognition. Finally, we relate this finding to physicochemical properties and structural features of the MHC-peptide-TCR interaction. Conclusions A computational method POPISK is proposed to predict immunogenicity with scores which are useful for predicting immunogenicity changes made by single-residue modifications. The web server of POPISK is freely available at http://iclab.life.nctu.edu.tw/POPISK .
p38α mitogen-activated protein kinase inhibitors, a patent review (2005 – 2011)
2011-11-15

In the last few years, compounds have become more potent and more selective, for example, by induction of the so-called glycine flip. Furthermore, some companies are striving for selectivity with respect to isoforms. The increasing availability of rapid screening services, which include more than 400 kinases, has encouraged companies to reconsider traditional approaches. The most promising approach appears to be the development of linear binding molecules that feature a carbonyl oxygen that can enforce the glycine flip. Furthermore, recent projects increasingly target new fields of application, for example, pulmonary diseases. This might be the most important trend of the past few years.
Discus (Canaridiscus) rupivagus sp. nov., a rock-dwelling species from La Gomera, Canary Islands (Gastropoda: Pulmonata: Discidae)
2011-11-15

Yanes et al. (2011) assume that the endemic Discidae from the Madeiran and Canarian Islands are members of the single genus Atlantica Ancey, with Atlantica s.str. and Canaridiscus Alonso &amp; Ibañez as subgenera. As long as the anatomy of the type-species of Atlantica [Discus guerinianus (R.T. Lowe) from Madeira] is not known however, we do not follow this designation but maintain the genus Discus with the subgenera Atlantica and Canaridiscus. The subgenus Canaridiscus has been established by Alonso &amp; Ibañez (in Yanes et al. 2011) for two newly discovered Canarian species, anagaensis Ibañez &amp; D. Holyoak from the northeastern Anaga mountains (Tenerife), and saproxylophagus Alonso, G. Holyoak &amp; Yanes from the National Park of Garajonay (La Gomera). The most remarkable feature of the new taxon is the genital system with a long or very long penis, unknown in other Discidae. Here we deal with the occurence of an additional Canaridiscus species, living near Casas de Encherada in the eastern part of La Gomera, where it has been found hidden in narrow rock crevices.
Integrating GIVENness into a structured meaning approach in HPSG
2011-11-16

In this article we show how the HPSG approach to information structure of De Kuthy (2002) and De Kuthy and Meurers (2003) can be extended to capture givenness (Schwarzschild, 1999) and make the right predictions for so-called deaccenting of given information, a widespread phenomenon not previously dealt with in HPSG.
Poor Trail Making Test Performance Is Directly Associated with Altered Dual Task Prioritization in the Elderly – Baseline Results from the TREND Study
2011-11-16

Under most challenging conditions, the elderly with poor TMT performance prioritize the cognitive task at the expense of walking velocity. This indicates that poor cognitive flexibility and working memory are directly associated with altered prioritization.
CXCR1andCXCR2haplotypes synergistically modulate cystic fibrosis lung disease
2011-11-16

Cystic fibrosis (CF) lung disease severity is largely independent on the CF transmembrane conductance regulator ( CFTR ) genotype, indicating the contribution of genetic modifiers. The chemokine receptors CXCR1 and CXCR2 have been found to play essential roles in the pathogenesis of CF lung disease. Here, we determine whether genetic variation of CXCR1 and CXCR2 influences CF lung disease severity. Genomic DNA of CF patients in Germany (n=442) was analysed for common variations in CXCR1 and CXCR2 using a single-nucleotide polymorphism (SNP) tagging approach. Associations of CXCR1 and CXCR2 SNPs and haplotypes with CF lung disease severity, CXCR1 and CXCR2 expression, and neutrophil effector functions were assessed. Four SNPs in CXCR1 and three in CXCR2 strongly correlated with age-adjusted lung function in CF patients. SNPs comprising haplotypes CXCR1 _Ha and CXCR2 _Ha were in high linkage disequilibrium and patients heterozygous for the CXCR1-2 haplotype cluster ( CXCR1-2 _Ha) had lower lung function compared with patients with homozygous wild-type alleles (forced expiratory volume in 1 s ≤70% predicted, OR 7.24; p=2.30×10 −5 ). CF patients carrying CXCR1-2 _Ha showed decreased CXCR1 combined with increased CXCR2 mRNA and protein expression, and displayed disturbed antibacterial effector functions. CXCR1 and CXCR2 genotypes modulate lung function and antibacterial host defence in CF lung disease.