julilili42/papers huggingface dataset:
Steady‐State and Time‐Resolved Photophysical Studies on a Series of Gallium Phthalocyanine Monomers and Dimers
2005-10-10

Abstract Intramolecular interaction between coplanar‐stacked phthalocyanine (Pc) and porphyrin molecules plays an importantrole in the energy‐ and electron‐transfer process. A series of results from different photophysical experiments on gallium phthalocyanine compounds are initially described. The PcGa dimer with a direct gallium–gallium bond, i.e. [ t Bu 4 PcGa] 2 · 2dioxane, may exist in two different conformations: one in which the two phthalocyanines are poorly interacting and the other in which they are very close and strongly interacting. In the former, the emission lifetime is quite close to that of the monomer model compounds; in the latter, it is much shorter probably due to different radiative and nonradiative deactivation constants from those of the monomers. Because no significant difference between the absorption spectra of the monomer and dimer was observed in the photophysical experiments, implying that no ground‐state interaction can be assessed, the results regarding triplet excited state lifetimes of [ t Bu 4 PcGa] 2 · 2dioxane can be attributed to strong intramolecular interactions existing only in the excited state. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Framework for evaluation of networked mobile games
2005-10-10

In this position paper we propose an evaluation framework for networked mobile gaming, consisting of user, group, communication, and environment models. Each of these components acts as a detailed representation of real-world characteristics. The combination of these models allows a realistic modeling of mobile gaming scenarios. The main contribution of our approaches is a new class of mobility models, which are purely based on strategies derived from real-world scenarios. This allows us to simulate the behavior and the movement of users and groups, and the communication aspects, and thus, it facilitates a creation of test beds for mobile applications. These simulated users interact, e.g. communicate, with each other and are able to move purposeful as well as to build groups spontaneously depending on the similarity of their goals or individual strategies. The paper presents an analytic discussion of the framework, its architecture, and the current state of its implementation.
Primary central nervous system lymphomas (PCNSL): MRI response criteria revised
2005-10-11

The authors investigated the applicability of Macdonald response criteria to patients with primary CNS lymphoma (PCNSL). Four of 68 patients with persisting contrast-enhancing lesions after primary therapy did not receive further therapy, and none showed tumor progression after up to 54 months. Because contrast enhancement may not necessarily indicate residual, biologically active lymphoma, the authors propose a modification of the Macdonald response criteria.
Monoamine receptors in human corneal epithelium and endothelium
2005-10-11

Abstract. Purpose: Monoamine receptors are found throughout the body. Reports about the presence of monoamine receptors in the human cornea are inconsistent. Methods: Immunohistochemistry, immunofluorescence and immunoblotting were used to localize monoamine receptor sites on human corneal epithelium and endothelium. Results: Antibodies to alpha‐1, beta‐1 and beta‐2 adrenergic receptors and to D1‐like and 5HT‐7 receptors were bound in corneal epithelium. Antibodies to alpha‐1, alpha‐2A, beta‐1 and beta‐2 adrenergic receptors and to 5HT‐7 receptors were bound in corneal endothelium. Conclusions: Our data demonstrate the presence of several monoamine receptors in the human cornea. These receptors may play a role in the regulation of fluid transport or corneal homeostasis.
Diameter of the human internal acoustic meatus and sex determination
2005-10-11

Abstract We report the results of testing the diameter of the internal opening of the acoustic canal in the petrous part of the temporal bone for sex determination of skeletal remains. The method involves measuring the diameter using a suite of ordinary drills. The method is very simple and has the great advantage of utilising one of the sturdiest bone elements of the human skeleton. The method may be especially useful for the analyses of very fragmented skeletal remains or cremated bones, where the petrous bone may still be readily recognisable. The method was tested using a forensic sample of 113 left petrous bones with known sex. Intra‐ and inter‐observer testing was also performed. We found a statistically significant difference in diameter between males and females (means: males: 3.7 mm; females: 3.4 mm; P &lt; 0.009). However, the low predictive value (70%) for correct sexing using two sectioning points ( &lt; 3.0 mm = female; &gt;3.5 mm = male) was disappointing. No additional accuracy was gained by employing both left and right petrous bones (a bilateral sample of 60 petrous bones was also tested), although left and right side diameter is highly correlated (R = 0.778; P = 0.0001). Copyright © 2005 John Wiley &amp; Sons, Ltd.
Transfection of Dendritic Cells with in Vitro-Transcribed CMV RNA Induces Polyclonal CD8+- and CD4+-Mediated CMV-Specific T Cell Responses
2005-10-11

Transfection of dendritic cells (DCs) with RNA was shown to be effective in the generation of antigen-specific T cells, probably due to the induction of a polyclonal T cell response directed against multiple antigens. To verify this assumption we used DCs, generated from cytomegalovirus (CMV)-negative or -positive donors, that were electroporated with in vitro-transcribed RNA (in vitro transcript, IVT) coding for the CMV pp65 antigen. We found that transfection of DCs with pp65 IVT induces an expansion of polyclonal CD8(+) T lymphocytes that recognize peptide antigens presented on different HLA molecules. These T lymphocytes are able to lyse DCs pulsed with pp65-derived peptides or transfected with the cognate IVT. Furthermore, this approach allowed the identification of immunodominant epitopes presented upon IVT transfection. Interestingly, transfection of DCs with pp65 IVT resulted in the induction of CD4(+)-specific T cells. Cotransfection of DCs with IVTs coding for the CMV antigens pp65 and IE1 elicited polyclonal T lymphocytes specific for peptides derived from both antigens. More importantly, cytotoxic T cells could be generated in two of three CMV-negative donors. Finally, functional CMV-specific autologous cytotoxic T lymphocytes were successfully generated from immunosuppressed patients after allogeneic hematopoietic stem cell transplantation.
Teaching Neuro Image : Thromboembolic stroke in ICA stenosis
2005-10-11

A 74-year-old man with right-sided amaurosis fugax had an ultrasound examination revealing right internal carotid artery (ICA) stenosis (figure 1, A and B). Angiography (figure 2A) showed a proximal ICA stenosis of approximately 90% according to NASCET criteria1 and a distal thrombus. The patient was anticoagulated with heparin. Invasive treatment options were discussed, but ...
Application of Phylogenetic Networks in Evolutionary Studies
2005-10-12

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)
2005-10-12

We present a new support vector machine (SVM)-based approach to predict the substrate specificity of subtypes of a given protein sequence family. We demonstrate the usefulness of this method on the example of aryl acid-activating and amino acid-activating adenylation domains (A domains) of nonribosomal peptide synthetases (NRPS). The residues of gramicidin synthetase A that are 8 A around the substrate amino acid and corresponding positions of other adenylation domain sequences with 397 known and unknown specificities were extracted and used to encode this physico-chemical fingerprint into normalized real-valued feature vectors based on the physico-chemical properties of the amino acids. The SVM software package SVM(light) was used for training and classification, with transductive SVMs to take advantage of the information inherent in unlabeled data. Specificities for very similar substrates that frequently show cross-specificities were pooled to the so-called composite specificities and predictive models were built for them. The reliability of the models was confirmed in cross-validations and in comparison with a currently used sequence-comparison-based method. When comparing the predictions for 1230 NRPS A domains that are currently detectable in UniProt, the new method was able to give a specificity prediction in an additional 18% of the cases compared with the old method. For 70% of the sequences both methods agreed, for <6% they did not, mainly on low-confidence predictions by the existing method. None of the predictive methods could infer any specificity for 2.4% of the sequences, suggesting completely new types of specificity.
Central Signals Rapidly Switch Tactile Processing in Rat Barrel Cortex during Whisker Movements
2005-10-12

Palpatory movements ('active' touch) are an integral part of tactile sensing. It is known that tactile signals can be modulated in certain behavioral contexts, but it is still unresolved to what degree this modulation is related to movement kinematics and whether it stems from tactile receptors or from central sources. Using awake, head-fixed rats, trained to contact an object, we measured trajectories of muscle-propelled whisker movement precisely and compared tactile responses to contacts thus accomplished with 'passive' contacts (motionless whisker contacted by object). Multielectrode extracellular recordings in deep layers of barrel cortex revealed that when the animals moved their whiskers actively, tactile processing switched from high response amplitudes, wide cortical representation and low background firing, to low response amplitudes, narrow spatial representation and elevated background firing. Switching was fast (<100 ms) and unrelated to the degree of alertness as assessed by spectral analysis of pre-contact field potentials. Switching persisted when information about whisker kinematics was interrupted by transection of the infraorbital nerve and contacts were mimicked by peripheral electrical stimulation. Taken together, these characteristics render central signals derived from the motor system a likely contributor to the processing of active touch.
Genetic heterogeneity of deafness phenotypes linked to DFNA4
2005-10-12

Abstract Mutations in the heavy chain of the class II nonmuscle myosin, MYH14 , cause autosomal dominant hearing loss in families linked to the DFNA4 locus. Consistent with this discovery, we identified an S120L mutation in MYH14 in a large German family segregating deafness that links to DFNA4. However, complete screening of the American family that originally defined the DFNA4 locus revealed no mutations in this gene. Furthermore, haplotyping of a single nucleotide polymorphism (SNP) 5′ to MYH14 excludes this gene from the critical region in this family. Our results imply that mutations in another gene result in deafness at the DFNA4 locus. The newly defined candidate region encompasses a region of approximately 19 cM. Several candidate genes have been screened for disease‐causing mutations. © 2005 Wiley‐Liss, Inc.
Evaluation of ray casting on processor-like reconfigurable architectures
2005-10-12

Ray casting, a real-life application for the visualization of 3D scientific and medical data, demands both high performance and high flexibility, and is likely to be used in future mobile devices, where low power is an important issue. In this paper, we show that implementing ray casting on coarse-grained, highly reconfigurable architectures satisfies these conflicting requirements much better than traditional architectures.
Comment on "The Brain of LB1, Homo floresiensis "
2005-10-13

Falk et al. ([ 1 ][1]) presented new data on the 18,000-year-old type specimen LB1 of the dwarf hominin Homo floresiensis ([ 2 ][2], [ 3 ][3]) with regard to cranial capacity and its implications for human evolution. They revised the originally determined brain size of only 380 cm3 ([ 2 ][2])
Life history variation in an annual plant under two opposing environmental constraints along an aridity gradient
2005-10-14

Environmental gradients represent an ideal framework for studying adaptive variation in the life history of plant species. However, on very steep gradients, largely contrasting conditions at the two gradient ends often limit the distribution of the same species across the whole range of environmental conditions. Here, we study phenotypic variation in a winter annual crucifer Biscutella didyma persisting along a steep gradient of increasing rainfall in Israel. In particular, we explored whether the life history at the arid end of the gradient indicates adaptations to drought and unpredictable conditions, while adaptations to the highly competitive environment prevail at the mesic Mediterranean end. We examined several morphological and reproductive traits in four natural populations and in populations cultivated in standard common environment. Plants from arid environments were faster in phenological development, more branched in architecture and tended to maximize reproduction, while the Mediterranean plants invested mainly in vertical vegetative growth. Differences between cultivation and field in diaspore production were very large for arid populations as opposed to Mediterranean ones, indicating a larger potential to increase reproduction under favorable conditions. Our overall findings indicate two strongly opposing selective forces at the two extremes of the aridity gradient, which result in contrasting strategies within the studied annual plant species.
Technical Report and Preliminary Clinical Data of a Novel Catheter for Luminal Re-Entry After Subintimal Dissection
2005-10-14

Although the Outback catheter is safe, the percentage of intraluminal reaccess should be ameliorated through engineering improvements because there is some evidence to suggest that subintimal recanalization could produce improved long-term results.
High anti‐inflammatory activity of harpagoside‐enriched extracts obtained from solvent‐modified super‐ and subcritical carbon dioxide extractions of the roots of Harpagophytum procumbens
2005-10-14

Abstract Solvent‐modified carbon dioxide extractions of the roots of Harpagophytum procumbens have been investigated with respect to extraction efficiency and content of harpagoside, and compared with a conventional extract. The effects of pressure, temperature, type and concentration of the modifier have been examined. Two extraction steps were necessary in order to achieve high anti‐inflammatory harpagoside‐enriched extracts. The first extraction step was carried out in the supercritical state using carbon dioxide modified with n ‐propanol to remove undesired lipophilic substances. The main extraction was performed either in the supercritical or in the subcritical state with carbon dioxide modified with ethanol. The supercritical fluid extraction resulted in extracts containing up to 30% harpagoside. The subcritical extracts showed a harpagoside content of ca. 20%, but the extraction yield was nearly three times greater compared with supercritical conditions. The total harpagoside recovery resulting from the sum of the extract and the crude drug residue was greater than 99% in all experiments. The conventional extract and two carbon dioxide extracts were tested for in‐vitro inhibition of 5‐lipoxygenase or cyclooxygenase‐2 biosynthesis. Both carbon dioxide extracts showed total inhibition on 5‐lipoxygenase biosynthesis at a concentration of 51.8 mg/L. In contrast, the conventional extract failed to show any inhibition of 5‐lipoxygenase biosynthesis. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Age-related prevalence of dermoscopy patterns in acquired melanocytic naevi
2005-10-18

The predominance of dermoscopic types of melanocytic naevi varies according to the individual's age. Awareness of the age-related dermoscopic predominance of melanocytic naevi might allow more accurate recognition of dermoscopic patterns of melanocytic skin lesions that are unusual with respect to the individual's age. This observation may help in the early recognition of some 'banal'-appearing melanomas. Furthermore, the observations made in this study raise interesting questions regarding naevus evolution.
Ca2+‐dependent lipid binding and membrane integration of PopA, a harpin‐like elicitor of the hypersensitive response in tobacco
2005-10-18

Summary PopA is released by type III secretion from the bacterial plant pathogen Ralstonia solanacearum and triggers the hypersensitive response (HR) in tobacco. The function of PopA remains obscure, mainly because mutants lacking this protein are not altered in their ability to interact with plants. In an attempt to identify the site of PopA activity in plant cells, we generated transgenic tobacco plants expressing the popA gene under the control of an inducible promoter. Immunocytologic analysis revealed that the HR phenotype of these plants correlated with the presence of PopA at the plant plasma membrane. Membrane localization was observed irrespective of whether the protein was designed to accumulate in the cytoplasm or to be secreted by the plant cell, suggesting a general lipid‐binding ability. We found that the protein had a high affinity for sterols and sphingolipids in vitro and that it required Ca 2+ for both lipid binding and oligomerization. In addition, the protein was integrated into liposomes and membranes from Xenopus laevis oocytes where it formed ion‐conducting pores. These characteristics suggest that PopA is part of a system that aims to attach the host cell plasma membrane and to allow molecules cross this barrier.
The kinase insert domain-containing receptor is an angiogenesis-associated antigen recognized by human cytotoxic T lymphocytes
2005-10-19

Antigen-specific cancer immunotherapy directed toward tumor-nourishing angiogenic blood vessels holds the promise of high efficacy, low toxicity, and ease of application. To evaluate whether the human angiogenic kinase insert domain-containing receptor (KDR) can serve as a target for cellular immunotherapy, 19 peptide sequences with HLA-A*0201 motifs were selected by computer-based algorithms. Five peptides (KDR82-90, KDR288-297, KDR766-774, KDR1093-1101, KDR1035-1044) stimulated specific cytotoxic T lymphocytes (CTLs) from peripheral-blood mononuclear cells (PBMCs) of 3 HLA-A*0201 donors. The decapeptide KDR288-297 was efficient in sensitizing target cells for recognition by a CTL clone at a concentration of 10 nM. More important, KDR288-297 - specific CTLs lysed target cells transfected with HLA-A2/KDR cDNAs and a range of HLA-matched KDR+ angiogenic endothelial cells (aECs) and also recognized CD34+ endothelial progenitor cells. The specificity of CTLs was further confirmed by tetramer assay and cold-target inhibition assay. In addition, ex vivo exposure of aECs to the inflammatory cytokines enhanced CTL reactivity, which is in keeping with up-regulated KDR and HLA class 1 expression. In Matrigel assays, recognition of aECs by specific CTLs triggered an antivascular effect. These findings provide the first proof of the antigenic property of KDR protein and may be useful for devising new immunotherapeutic approaches to human cancers.
Darwinian fitness, evolutionary entropy and directionality theory
2005-10-19

Two recent articles provide computational and empirical validation of the following analytical fact: the outcome of competition between an invading genotype and that of a resident population is determined by the rate at which the population returns to its original size after a random perturbation. This phenomenon can be quantitatively described in terms of the demographic parameter termed "evolutionary entropy", a measure of the variability in the age at which individuals produce offspring and die. The two articles also validate certain predictions of directionality theory, an evolutionary model that integrates demography and ecology with population genetics. In particular, directionality theory predicts that in populations that spend the greater part of their life cycle in the stationary growth phase, evolution will result in an increase in entropy. These species will be described by a late age of sexual maturity, small progeny sets and a broad reproductive time-span. In populations that undergo large fluctuations in size, however, the evolutionary outcome will be different. When the average size is large, evolution will result in a decrease in entropy-these populations will be described by early age of sexual maturity, large numbers of offspring and narrow reproductive span but when the average size is small, the evolutionary outcome will be random and non-directional.
Quantum-Degenerate Mixture of Fermionic Lithium and Bosonic Rubidium Gases
2005-10-20

We report on the observation of sympathetic cooling of a cloud of fermionic 6Li atoms which are thermally coupled to evaporatively cooled bosonic 87Rb. Using this technique we obtain a mixture of quantum-degenerate gases, where the Rb cloud is colder than the critical temperature for Bose-Einstein condensation and the Li cloud is colder than the Fermi temperature. From measurements of the thermalization velocity we estimate the interspecies s-wave triplet scattering length |amx|=20(+9)(-6)aB. We found that the presence of residual rubidium atoms in the |2, 1> and the |1, -1> Zeeman substates gives rise to important losses due to inelastic collisions.
Three-Junction SQUID Rocking Ratchet
2005-10-20

We investigate three-junction SQUIDs which show voltage rectification if biased with an ac current drive with zero mean value. The Josephson phase across the SQUID experiences an effective ratchet potential, and the device acts as an efficient rocking ratchet, as demonstrated experimentally for adiabatic and nonadiabatic drive frequencies. For high-frequency drives the rectified voltage is quantized due to synchronization of the phase dynamics with the external drive. The experimental data are in excellent agreement with numerical simulations including thermal fluctuations.