julilili42/papers huggingface dataset:
Comparative Transcriptome and Proteome Analysis of Ha-ras and B-raf Mutated Mouse Liver Tumors
2009-05-28

Mouse liver tumors frequently harbor activating mutations in the Ha-ras protooncogene. In addition, mutations are also found in the B-raf gene leading to constitutive activation of the B-Raf kinase. In two previous studies, we have investigated by microarray analysis the effect of the mutations on the mRNA expression patterns of the respective tumors. In the present study, we analyzed proteome changes in Ha-ras and B-raf mutated liver tumors by 2-D gel-electrophoretic separation of proteins followed by their identification by mass spectrometry. In total, 104 significantly altered protein spots were identified in Ha-ras mutated tumors and 111 in B-raf mutated tumors when compared to the corresponding normal liver tissue. The changes in protein expression patterns were highly correlated between Ha-ras and B-raf mutated tumors, and in the majority of the cases, both tumor types showed the respective alteration. Most of the tumor-specific changes in protein expression were reflected by similar changes in their mRNAs except for some up-regulated proteins without accompanying changes in mRNA levels. Interestingly, Ha-ras but not B-raf mutated tumors showed high levels of the phosphorylated (activated) form of the Ras/Raf/MEK effector kinase ERK which was, however, not associated with any detectable difference in the transcriptome or protein setup of the tumors.
Nucleation in Organic Thin Film Growth: Perylene on Al2O3/Ni3Al(111)
2009-05-29

The molecular orientation of perylene thin films has been investigated using near-edge X-ray absorption fine structure spectroscopy. The presence of different molecular orientations in the monolayer, ranging from flat-lying to more upright-standing molecules, has been found and related with the different sets of growth parameters used for each sample preparation. The same molecular tuning has been observed in the multilayer regime. It is shown that it is possible to explain these results by using concepts of the atomistic theory of nucleation. Regarding perylene on Al2O3/Ni3Al(111) as a model system for organic layers in, for example, organic field effect transistors, our findings raise some questions about the suitability of perylene as an active layer in a real device.
Diet and feeding behaviour of the leaf-litter frogIschnocnema henselii(Anura: Brachycephalidae) inAraucariarain forests on the Serra Geral of Rio Grande do Sul, Brazil†
2009-05-29

Dietl, Jörn, Engels, Wolf, Solé, Mirco (2009): Diet and feeding behaviour of the leaf-litter frog Ischnocnema henselii (Anura: Brachycephalidae) in Araucaria rain forests on the Serra Geral of Rio Grande do Sul, Brazil. Journal of Natural History 43 (23-24): 1473-1483, DOI: 10.1080/00222930902898709, URL: http://dx.doi.org/10.1080/00222930902898709
Detection of High Levels of European Bat Lyssavirus Type‐1 Viral RNA in the Thyroid Gland of Experimentally‐Infected Eptesicus fuscus Bats
2009-05-29

Summary Two common bat lyssavirus species have been identified in many European countries: European bat lyssavirus type‐1 and ‐2 (EBLV‐1 and EBLV‐2). Only limited knowledge on the susceptibility of the natural EBLV‐hosts, insectivorous bats, to lyssavirus infection is available. Our study was undertaken to evaluate the susceptibility and pathology associated with an EBLV‐1 infection in Eptesicus fuscus following different routes of virus inoculation including intracranial ( n = 6 ), intramuscular ( n = 14 ), oral ( n = 7 ) and intranasal ( n = 7 ). Blood and saliva samples were collected from all bats on a monthly basis. Four bats inoculated intracranially developed rabies with a mean of 11 days to death, whilst seven bats inoculated intramuscularly developed rabies, with an extended incubation period prior to death. We did not observe any mortality in the oral (p.o.) or intranasal (i.n.) groups and both groups had detectable levels of virus neutralizing antibodies (data not shown). Virus shedding was demonstrated in the saliva by virus isolation and the detection of viral RNA in ill bats, particularly immediately prior to the development of disease. In addition, the presence of virus and viral RNA was detected in the thyroid gland in bats challenged experimentally with EBLV‐1, which exceeded that detected in all other extra‐neural tissue. The significance of detecting EBLV‐1 in the thyroid gland of rabid bats is not well understood. We speculate that the infection of the thyroid gland may cause subacute thyroiditis, a transient form of thyroiditis causing hyperthyroidism, resulting in changes in adrenocortical activity that could lead to hormonal dysfunction, thereby distinguishing the clinical presentation of rabies in the rabid host.
Nonlinear effects at high flux-flow electric fields
2009-05-29

Ohm's law with the linear relation between resistive voltage and electric current is strictly valid only in the limit of infinitesimally small voltages. On the other hand, at finite electric voltages nonlinearities in the electric resistance can develop due to the energy picked up by the charge carriers in the electric field. This can lead to important effects both in the case of semiconductors and of superconductors, where the energy rise of the charge carriers or the quasiparticles can become relatively large. In this paper we limit our discussion to the flux-flow voltage in the mixed state of a type-II superconductor. At sufficiently low temperatures the energy dependence of the quasiparticle density of states and, hence, of the quasiparticle scattering rate can cause distinct nonlinear effects in the flux-flow resistance. The recent advances in thin-film sample preparation provided new opportunities for observing nonlinear effects of the latter kind.
1-[2-(Benzylamino)-4-pyridyl]-2-(4-fluorophenyl)ethane-1,2-dione
2009-05-29

The crystal structure of the title compound, C 20 H 15 FN 2 O 2 , contains two crystallographically independent molecules, which are related by a pseudo-inversion center and linked into dimers via intermolecular N—H...N hydrogen bonds. The 4-fluorophenyl ring of molecule A makes dihedral angles of 17.17 (16) and 62.25 (15)°, respectively, with the phenyl and pyridine rings. The 4-fluorophenyl ring of molecule B makes dihedral angles of 8.50 (16) and 64.59 (15)°, respectively, with the phenyl and pyridine rings. The dihedral angle between the pyridine ring and the phenyl ring of molecule A [60.97 (15)°] is bigger than in molecule B [59.49 (15)°]. The dihedral angle between the two pyridine rings is 1.37 (14)° and between the two phenyl rings is 3.64 (16)°.
Representation of Number in the Brain
2009-06-01

Number symbols have allowed humans to develop superior mathematical skills that are a hallmark of technologically advanced cultures. Findings in animal cognition, developmental psychology, and anthropology indicate that these numerical skills are rooted in nonlinguistic biological primitives. Recent studies in human and nonhuman primates using a broad range of methodologies provide evidence that numerical information is represented and processed by regions of the prefrontal and posterior parietal lobes, with the intraparietal sulcus as a key node for the representation of the semantic aspect of numerical quantity.
Tyrosine Kinase Inhibitors – A Review on Pharmacology, Metabolism and Side Effects
2009-06-01

Tyrosine kinase inhibitors (TKI) are effective in the targeted treatment of various malignancies. Imatinib was the first to be introduced into clinical oncology, and it was followed by drugs such as gefitinib, erlotinib, sorafenib, sunitinib, and dasatinib. Although they share the same mechanism of action, namely competitive ATP inhibition at the catalytic binding site of tyrosine kinase, they differ from each other in the spectrum of targeted kinases, their pharmacokinetics as well as substance-specific adverse effects. With variations from drug to drug, tyrosine kinase inhibitors cause skin toxicity, including folliculitis, in more than 50% of patients. Among the tyrosine kinase inhibitors that are commercially available as yet, the agents that target EGFR, erlotinib and gefitinib, display the broadest spectrum of adverse effects on skin and hair, including folliculitis, paronychia, facial hair growth, facial erythema, and varying forms of frontal alopecia. In contrast, folliculitis is not common during administration of sorafenib and sunitinib, which target VEGFR, PDGFR, FLT3, and others, whereas both agents have been associated with subungual splinter hemorrhages. Periorbital edema is a common adverse effect of imatinib. Besides the haematological side effects of most of TKIs like anemia, thrombopenia and neutropenia, the most common extra-heamatologic adverse effects are edema, nausea, hypothyroidism, vomiting and diarrhea. Regarding possible long term effects, recently cardiac toxicity with congestive heart failure is under debate in patients receiving imatinib and sunitinib therapy; however, this observation was probably relate to patients selection, although, TKIs overall appear to be a very well tolerated drug class.
A Noninvasive Brain-Actuated Wheelchair Based on a P300 Neurophysiological Protocol and Automated Navigation
2009-06-01

This paper describes a new noninvasive brain-actuated wheelchair that relies on a P300 neurophysiological protocol and automated navigation. When in operation, the user faces a screen displaying a real-time virtual reconstruction of the scenario and concentrates on the location of the space to reach. A visual stimulation process elicits the neurological phenomenon, and the electroencephalogram (EEG) signal processing detects the target location. This location is transferred to the autonomous navigation system that drives the wheelchair to the desired location while avoiding collisions with obstacles in the environment detected by the laser scanner. This concept gives the user the flexibility to use the device in unknown and evolving scenarios. The prototype was validated with five healthy participants in three consecutive steps: screening (an analysis of three different groups of visual interface designs), virtual-environment driving, and driving sessions with the wheelchair. On the basis of the results, this paper reports the following evaluation studies: 1) a technical evaluation of the device and all functionalities; 2) a users’ behavior study; and 3) a variability study. The overall result was that all the participants were able to successfully operate the device with relative ease, thus showing a great adaptation as well as a high robustness and low variability of the system.
Critical features for the perception of emotion from gait
2009-06-01

Human observers readily recognize emotions expressed in body movement. Their perceptual judgments are based on simple movement features, such as overall speed, but also on more intricate posture and dynamic cues. The systematic analysis of such features is complicated due to the difficulty of considering the large number of potentially relevant kinematic and dynamic parameters. To identify emotion-specific features we motion-captured the neutral and emotionally expressive (anger, happiness, sadness, fear) gaits of 25 individuals. Body posture was characterized by average flexion angles, and a low-dimensional parameterization of the spatio-temporal structure of joint trajectories was obtained by approximation with a nonlinear mixture model. Applying sparse regression, we extracted critical emotion-specific posture and movement features, which typically depended only on a small number of joints. The features we extracted from the motor behavior closely resembled features that were critical for the perception of emotion from gait, determined by a statistical analysis of classification and rating judgments of 21 observers presented with avatars animated with the recorded movements. The perceptual relevance of these features was further supported by another experiment showing that artificial walkers containing only the critical features induced high-level after-effects matching those induced by adaptation with natural emotional walkers.
Transformation of vivianite by anaerobic nitrate‐reducing iron‐oxidizing bacteria
2009-06-01

Abstract In phosphate‐rich environments, vivianite (Fe II 3 (PO 4 ) 2 , 8H 2 O) is an important sink for dissolved Fe(II) and is considered as a very stable mineral due to its low solubility at neutral pH. In the present study, we report the mineralogical transformation of vivianite in cultures of the nitrate‐reducing iron‐oxidizing bacterial strain BoFeN1 in the presence of dissolved Fe(II). Vivianite was first transformed into a greenish phase consisting mostly of an amorphous mixed valence Fe‐phosphate. This precipitate became progressively orange and the final product of iron oxidation consisted of an amorphous Fe(III)‐phosphate. The sub‐micrometer analysis by scanning transmission X‐ray microscopy of the iron redox state in samples collected at different stages of the culture indicated that iron was progressively oxidized at the contact of the bacteria and at a distance from the cells in extracellular minerals. Iron oxidation in the extracellular minerals was delayed by a few days compared with cell‐associated Fe‐minerals. This led to strong differences of Fe redox in between these two types of minerals and finally to local heterogeneities of redox within the sample. In the absence of dissolved Fe(II), vivianite was not significantly transformed by BoFeN1. Whereas Fe(II) oxidation at the cell contact is most probably directly catalyzed by the bacteria, vivianite transformation at a distance from the cells might result from oxidation by nitrite. In addition, processes leading to the export of Fe(III) from bacterial oxidation sites to extracellular minerals are discussed including some involving colloids observed by cryo‐transmission electron microscopy in the culture medium.
Isometric registration of ambiguous and partial data
2009-06-01

This paper introduces a new shape matching algorithm for computing correspondences between 3D surfaces that have undergone (approximately) isometric deformations. The new approach makes two main contributions: First, the algorithm is, unlike previous work, robust to "topological noise" such as large holes or "false connections", which is both observed frequently in real-world scanner data. Second, our algorithm samples the space of feasible solutions such that uncertainty in matching can be detected explicitly. We employ a novel randomized feature matching algorithm in order to find robust subsets of geodesics to verify isometric consistency. The paper shows shape matching results for real world and synthetic data sets that could not be handled using previous deformable matching algorithms.
Cortical hypometabolism assessed by a metabolic ratio in Parkinson's disease primarily reflects cognitive deterioration—[18F]FDG‐PET
2009-06-01

Abstract In Parkinson's disease patients with cognitive deterioration, regional cortical hypometabolism has been observed with [ 18 F]fluorodeoxyglucose‐positron emission tomography (FDG‐PET). Our aim was to develop a robust method to subsume the overall degree of metabolic deterioration in Parkinson's disease by means of a single index and to investigate which of the clinical features correlates best with hypometabolism. Twenty‐two Parkinson's patients (10 demented) and seven controls underwent FDG‐PET. A metabolic index (mean relative uptake in typically affected regions) was calculated for each patient and compared with scores for cognition [Minimental State Examination (MMSE)], motor performance [Unified Parkinson's Disease Rating Scale (UPDRS III)” and behavior (Neuropsychiatric Inventory). In stepwise linear regression analysis, MMSE ( P &lt; 0.001) score showed the only significant effect. Estimated sensitivity and specificity for DSM‐IV diagnosis of dementia were high for the metabolic index (MI), with 91 and 100%. Taken together, the presented data indicate that cerebral hypometabolism in Parkinson's disease is primarily associated with cognitive impairment. © 2009 Movement Disorder Society
DARC on RBC limits lung injury by balancing compartmental distribution of CXC chemokines
2009-06-01

Abstract The Duffy antigen receptor for chemokines (DARC) has a high affinity for CC and CXC chemokines. However, it lacks the ability to induce cell responses that are typical for classical chemokine receptors. The role of DARC in inflammatory conditions remains to be elucidated. We studied the role of DARC in a murine model of acute lung injury. We found that in Darc ‐gene‐deficient ( Darc −/− ) mice, LPS‐induced PMN migration into the alveolar space was elevated more than twofold. In contrast, PMN adhesion to endothelial cells and within the interstitial space was reduced in Darc −/− mice. Darc −/− mice also exhibited increased microvascular permeability. Elevated PMN migration in Darc −/− mice was associated with increased concentrations of two essential CXCR2 ligands, CXCL1 and CXCL2/3 in the alveolar space. In the blood, CXCL1 was mostly associated with RBC in WT mice and with plasma in Darc −/− mice. We found that DARC on RBC prevented excessive PMN migration into the alveolar space. In contrast, DARC on non‐hematopoietic cells appeared to have only minor effects on leukocyte trafficking in this model. These findings show how DARC regulates lung inflammation by controlling the distribution and presentation of chemokines that bind CXCR2.
Effect of genetic variation in Kv1.3 on olfactory function
2009-06-01

Abstract Background Olfactory function is reduced in aged humans and diabetes mellitus patients. However, little is known about the pathogenic mechanisms leading to olfactory dysfunction. Recently, it has been shown that the voltage‐gated potassium channel Kv1.3 is regulated by insulin and is highly expressed in the olfactory bulb. Furthermore, the function of this channel is associated with olfaction in mice and with glucose metabolism in mice and men. We therefore hypothesized that a functionally relevant polymorphism in Kv1.3 might alter olfactory function. Methods We investigated a group of 94 healthy subjects (male: n = 58, female: n = 36) for olfactory function and genotyped them for rs2821557 in the human Kv1.3 gene. Olfactory function was tested using standardised sniffing sticks, and parameters of glucose metabolism were assessed. Results We found a significant olfactory impairment in male homozygous carriers of the Kv1.3 polymorphism rs2821557 (recessive model, p = 0.018, adjusted for age) that could not be determined in female subjects due to the very small number of homozygous minor allele carriers ( n = 1). In addition, we found a significant correlation of olfactory dysfunction with higher HbA1c and fasting plasma glucose ( p = 0.004 and p = 0.001, both adjusted for age). We also found a loss of olfactory function with age ( p = 0.006). Gender, body mass index and insulin sensitivity did not alter smelling function. Conclusions The presence of genetic variation in Kv1.3 is associated with decreased olfactory function in healthy subjects. As olfactory function, glucose metabolism and genetic variation in Kv1.3 seem to be associated, further studies are needed to clarify the underlying mechanisms. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Dynamic foot scanning: A new approach for measurement of the human foot shape while walking
2009-06-01

Click to increase image sizeClick to decrease image size Acknowledgements This project is funded by the German Federal Ministry of Economics and Technology. We would like to thank ViALUX GmbH (Chemnitz, Germany) for their cooperation.
Functions of Bat Social Calls: The Influence of Local Abundance, Interspecific Interactions and Season on the Production of Pipistrelle (Pipistrellus pipistrellus) Type D Social Calls
2009-06-01

We studied the social call rate of the common pipistrelle (Pipistrellus pipistrellus) in natural habitats in relation to the presence or absence of conspecifics and of other bat species by acoustical and behavioural monitoring and analyses. The relative frequency of type D social calls increased, when more than one individual of P. pipistrellus was present, compared to one individual. The data confirm the assumption that one function of social calls is repelling conspecifics (food patch defence hypothesis). In the presence of other species of the genus Pipistrellus or of other genera, the mean social call rate did not significantly increase, except when P. pygmaeus was present. Hence, social call production as a food patch defence typically is not significantly influenced by interspecific interactions. This directs to niche separation concerning the foraging mode of different species. The closely related species P. pipistrellus and P. pygmaeus may compete for resources and communicate by type D social calls. Pipistrelles are known to use a series of type D social calls during songflights. For instance, males use this calling behaviour to attract females and repel competing males. During the mating season P. pipistrellus produced social calls more frequently when other pipistrelle species were absent. This shows that interspecific recognition may influence the mating behaviour of P. pipistrellus. Competing for non-food resources like mating roosts may cause bats to keep calm in the presence of other species.
Voicing-aware parametric speech quality models over VoIP networks
2009-06-01

This paper describes novel parametric speech quality models which subsume the effect of packet loss distribution and voicing feature of missing signal waves. Speech quality estimate models for voiced and unvoiced loss location patterns are developed following multiple statistical regression analysis of measurements gathered from a built speech quality assessment framework. The overall speech quality is estimated by combining voiced and unvoiced speech quality estimate scores using an expression calibrated using a large number of speech samples. The input parameters namely, mean loss durations and ratios for voiced and unvoiced packets, of speech quality estimate models are extracted at run-time using a new voicing-aware packet loss Markov model. This chain, calibrated at run-time, finely models bursty packet loss behavior over voiced and unvoiced missing speech waves. Performance evaluation study shows that our voicing-aware speech quality estimate models clearly outperform voicing-agnostic speech quality models in terms of accuracy over a wide range of conditions.
Reo assessment to guide the ReoGo Therapy: Reliability and validity of novel robotic scores
2009-06-01

The ReoGo Therapy <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> system, is designed to provide robotic therapy for stroke victims. The success of robotic rehabilitation has called for the need to develop a tool that can quantitatively diagnose as well as monitor therapy of stroke victims. This poster evaluates the validity and reliability of the newly developed Reo Assessment. The Reo Assessment was found to be valid and reliable, and thus opens the path to the development of a standard assessment battery as an integral part of the ReoGotrade therapy.
Path Selection Techniques for SCTP Multihoming
2009-06-01

This paper proposes a new innovative concept for using machine learning techniques to optimize the overall data throughput over low bandwidth networks with several paths for a parallel transmission of data. The multihoming feature of the stream control transmission protocol is used to transfer user data parallel over several end-to-end paths. The work focuses on the selection of the actual best path, where the capacities of the present paths are not necessarily known in advance. The path selection is adapted in an autonomic and flexible way by a new network component, the so called intelligent network placed at the network layer. Using this adaptive mechanism it is possible to implement applications like long-distance medicine in mobile scenarios.