julilili42/papers huggingface dataset:
Shared Cell Surface Marker Expression in Mesenchymal Stem Cells and Adult Sarcomas
2012-12-19

Abstract Advanced adult soft-tissue sarcomas (STSs) are rare tumors with a dismal prognosis and limited systemic treatment options. STSs may originate from mesenchymal stem cells (MSCs); the latter have mainly been isolated from adult bone marrow as plastic-adherent cells with differentiation capacity into mesenchymal tissues. Recently, a panel of antibodies has been established that allows for the prospective isolation of primary MSCs with high selectivity. Similar to cancer stem cells in other malignancies, sarcoma stem cells may bear immunophenotypic similarity with the corresponding precursor, that is, MSCs. We therefore set out to establish the expression pattern of MSC markers in sarcoma cell lines and primary tumor samples by flow cytometry. In addition, fibroblasts from different sources were examined. The results document a significant amount of MSC markers shared by sarcoma cells. The expression pattern includes uniformly expressed markers, as well as MSC markers that only stained subpopulations of sarcoma cells. Expression of W5C5, W8B2 (tissue nonspecific alkaline phosphatase [TNAP]), CD344 (frizzled-4), and CD271 marked subpopulations displaying increased proliferation potential. Moreover, CD271+ cells displayed in vitro doxorubicin resistance and an increased capacity to form spheres under serum-free conditions. Interestingly, another set of antigens, including the bona fide progenitor cell markers CD117 and CD133, were not expressed. Comparative expression patterns of novel MSC markers in sarcoma cells, as well as fibroblasts and MSCs, are presented. Our data suggest a hierarchical cytoarchitecture of the most common adult type sarcomas and introduce W5C5, TNAP, CD344, and CD271 as potential sarcoma progenitor cell markers.
Metaspin and dirishonic dark matter
2012-12-19

The antisymmetry requirement of rishon bound state wave functions suggests a\\nnew rishon quantum number called M spin. From M spin conservation and the\\nNussinov-Weingarten-Witten theorem we predict the existence of a stable\\npseudoscalar dirishonic meson, called zeta, that is lighter than the lightest\\nneutrino. Its mass is estimated as m(zeta) = 10^{-9} eV. This particle could\\nmake up the major part of cold dark matter in the Universe.\\n
Spinal Robotics
2012-12-20

Even though robotic technology holds great potential for performing spinal surgery and advancing neurosurgical techniques, it is of utmost importance to establish its practicality and to demonstrate better clinical outcomes compared with traditional techniques, especially in the current cost-effective era. Several systems have proved to be safe and reliable in the execution of tasks on a routine basis, are commercially available, and are used for specific indications in spine surgery. However, workflow, usability, interdisciplinary setups, efficacy, and cost-effectiveness have to be proven prospectively. This article includes a short description of robotic structures and workflow, followed by preliminary results of a randomized prospective study comparing conventional free-hand techniques with routine spine navigation and robotic-assisted procedures. Additionally, we present cases performed with a spinal robotic device, assessing not only the accuracy of the robotic-assisted procedure but also other factors (eg, minimal invasiveness, radiation dosage, and learning curves). Currently, the use of robotics in spinal surgery greatly enhances the application of minimally invasive procedures by increasing accuracy and reducing radiation exposure for patients and surgeons compared with standard procedures. Second-generation hardware and software upgrades of existing devices will enhance workflow and intraoperative setup. As more studies are published in this field, robot-assisted therapies will gain wider acceptance in the near future.
CCND2 rearrangements are the most frequent genetic events in cyclin D1− mantle cell lymphoma
2012-12-20

Key Points This report describes a multidisciplinary study characterizing the largest series of cyclin D1− MCL patients. CCND2 translocations are the most frequent genetic event (55%) in cyclin D1− MCL.
Comparison of Sedimentary PAHs in the Rivers of Ammer (Germany) and Liangtan (China): Differences between Early- and Newly-Industrialized Countries
2012-12-20

As a proxy to trace the impact of anthropogenic activity, sedimentary polycyclic aromatic hydrocarbons (PAHs) are compared between the early industrialized and newly industrialized countries of Germany and China, respectively. Surface sediment samples in the Ammer River of Germany and the Liangtan River of China were collected to compare concentration levels, distribution patterns, and diagnostic plots of sedimentary PAHs. Total concentrations of 16 PAHs in Ammer sediments were significantly higher by a factor of ~4.5 than those in Liangtan. This contrast agrees with an extensive literature survey of PAH levels found in Chinese versus European sediments. Distribution patterns of PAHs were similar across sites in the Ammer River, whereas they were highly varied in the Liangtan River. Pyrogenic sources dominated in both cases. Strong correlations of the sum of 16 PAHs and PAH groups with TOC contents in the Liangtan River may indicate coemission of PAHs and TOC. Poor correlations of PAHs with TOC in the Ammer River indicate that other factors exert stronger influences. Sedimentary PAHs in the Ammer River are primarily attributed to input of diffuse sources or legacy pollution, while sediments in the Liangtan River are probably affected by ongoing point source emissions. Providing further evidence of a more prolonged anthropogenic influence are the elevated black carbon fractions in sedimentary TOC in the Ammer compared to the Liangtan. This implies that the Liangtan River, like others in newly industrialized regions, still has a chance to avoid legacy pollution of sediment which is widespread in the Ammer River and other European waterways.
Source Reconstruction Accuracy of MEG and EEG Bayesian Inversion Approaches
2012-12-20

Electro- and magnetoencephalography allow for non-invasive investigation of human brain activation and corresponding networks with high temporal resolution. Still, no correct network detection is possible without reliable source localization. In this paper, we examine four different source localization schemes under a common Variational Bayesian framework. A Bayesian approach to the Minimum Norm Model (MNM), an Empirical Bayesian Beamformer (EBB) and two iterative Bayesian schemes (Automatic Relevance Determination (ARD) and Greedy Search (GS)) are quantitatively compared. While EBB and MNM each use a single empirical prior, ARD and GS employ a library of anatomical priors that define possible source configurations. The localization performance was investigated as a function of (i) the number of sources (one vs. two vs. three), (ii) the signal to noise ratio (SNR; 5 levels) and (iii) the temporal correlation of source time courses (for the cases of two or three sources). We also tested whether the use of additional bilateral priors specifying source covariance for ARD and GS algorithms improved performance. Our results show that MNM proves effective only with single source configurations. EBB shows a spatial accuracy of few millimeters with high SNRs and low correlation between sources. In contrast, ARD and GS are more robust to noise and less affected by temporal correlations between sources. However, the spatial accuracy of ARD and GS is generally limited to the order of one centimeter. We found that the use of correlated covariance priors made no difference to ARD/GS performance.
Treatment of Visceral Leishmaniasis: Model-Based Analyses on the Spread of Antimony-Resistant L. donovani in Bihar, India
2012-12-20

Both hypotheses can potentially explain the Bihar observations. However, increased transmissibility as an explanation appears more plausible because it can occur in the background of asymptomatically transmitted infection whereas disease-related factors would most probably be observable. Irrespective of the cause of fitness, parasites with a higher fitness will finally replace sensitive parasites, even if antimonials are replaced by another drug.
One Size Fits All? Slow Cortical Potentials Neurofeedback
2012-12-20

Objective: The intent of this manuscript was to review all published studies on slow cortical potentials (SCP) neurofeedback for the treatment of ADHD, with emphasis on neurophysiological rationale, study design, protocol, outcomes, and limitations. Method: For review, PubMed, MEDLINE, ERIC, and Google Scholar searches identified six studies and six subsequent publications. In addition to five studies focusing on children with Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) –diagnosed ADHD, one study reports on adults. Results: SCP protocols utilize unipolar-electrode placement at Cz, randomized bidirectional signal regulation, feedback/transfer trials, and discrete feedback/rewards. Results demonstrated learning of SCP self-regulation, moderate to large within group effect sizes for core ADHD symptom reduction, and enhancement of event-related potentials/electroencephalogram components. Neurophysiological and session variables were predictive of treatment outcome, but open questions of specific and nonspecific effects remain. Study limitations and future directions are discussed. Conclusion: SCP is an efficacious and standardized neurofeedback protocol that addresses behavioral and neurophysiological deficits in ADHD.
InCroMAP: integrated analysis of cross-platform microarray and pathway data
2012-12-20

Abstract Summary: Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that offer visualization, statistical analysis and more sophisticated analysis methods. Most of these tools are designed specifically for messenger RNA microarrays. However, today, more and more different microarray platforms are available. Changes in DNA methylation, microRNA expression or even protein phosphorylation states can be detected with specialized arrays. For these microarray technologies, the number of available tools is small compared with mRNA analysis tools. Especially, a joint analysis of different microarray platforms that have been used on the same set of biological samples is hardly supported by most microarray analysis tools. Here, we present InCroMAP, a tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways. Availability: InCroMAP is freely available as JavaTM application at www.cogsys.cs.uni-tuebingen.de/software/InCroMAP, including a comprehensive user’s guide and example files. Contact: clemens.wrzodek@uni-tuebingen.de or andreas.zell@uni-tuebingen.de
Bethe-Salpeter equation at leading order in Coulomb gauge
2012-12-20

The Bethe-Salpeter equation and leptonic decay constants for pseudoscalar and vector quark-antiquark mesons with arbitrary quark masses are studied in Coulomb gauge, under a leading order truncation. As input, we use a pure linear rising potential, supplemented by a contact term arising from the conservation of total color charge. It is shown how the equations can be written in terms of manifestly finite functions, despite the infrared singular interaction. The resulting equations are solved numerically. Both the pattern of dynamical chiral symmetry breaking and the leading order heavy quark limit are visible.
The Guanine Nucleotide Exchange Factor Kalirin-7 Is a Novel Synphilin-1 Interacting Protein and Modifies Synphilin-1 Aggregate Transport and Formation
2012-12-20

Synphilin-1 has been identified as an interaction partner of α-synuclein, a key protein in the pathogenesis of Parkinson disease (PD). To further explore novel binding partners of synphilin-1, a yeast two hybrid screening was performed and kalirin-7 was identified as a novel interactor. We then investigated the effect of kalirin-7 on synphilin-1 aggregate formation. Coexpression of kalirin-7 and synphilin-1 caused a dramatic relocation of synphilin-1 cytoplasmic small inclusions to a single prominent, perinuclear inclusion. These perinuclear inclusions were characterized as being aggresomes according to their colocalization with microtubule organization center markers, and their formation was microtubule-dependent. Furthermore, kalirin-7 increased the susceptibility of synphilin-1 inclusions to be degraded as demonstrated by live cell imaging and quantification of aggregates. However, the kalirin-7-mediated synphilin-1 aggresome response was not dependent on the GEF activity of kalirin-7 since various dominant negative small GTPases could not inhibit the formation of aggresomes. Interestingly, the aggresome response was blocked by HDAC6 catalytic mutants and the HDAC inhibitor trichostatin A (TSA). Moreover, kalirin-7 decreased the level of acetylated α-tubulin in response to TSA, which suggests an effect of kalirin-7 on HDAC6-mediated protein transportation and aggresome formation. In summary, this is the first report demonstrating that kalirin-7 leads to the recruitment of synphilin-1 into aggresomes in a HDAC6-dependent manner and also links kalirin-7 to microtubule dynamics.
Gauge fixing using overrelaxation and simulated annealing on GPUs
2012-12-20

We adopt CUDA-capable Graphic Processing Units (GPUs) for Coulomb, Landau and maximally Abelian gauge fixing in 3+1 dimensional SU(3) lattice g auge field theories. The local overrelaxation algorithm is perfectly suited for highly pa rallel architectures. Simulated annealing preconditioning strongly increases the probability to reach the global maximum of the gauge functional. We give performance results for single and double precision. To obtain our maximum performance of 300 GFlops on NVIDIA’s GTX 580 a very fine grain ed degree of parallelism is required due to the register limits of NVIDIA’s Fermi GPUs: w e use eight threads per lattice site, i.e., one thread per SU(3) matrix that is involved in the computation of a site update.
Neurophonetics
2012-12-20

Abstract Neurophonetics aims at the elucidation of the brain mechanisms underlying speech communication in our species. Clinical observations in patients with speech impairments following cerebral disorders provided the initial vantage point of this research area and indicated distinct functional‐neuroanatomic systems to support human speaking and listening. Subsequent approaches—considering speech production a motor skill—investigated vocal tract movements associated with spoken language by means of kinematic and electromyographic techniques—allowing, among other things, for the evaluation of computational models suggesting elementary phonological gestures or a mental syllabary as basic units of speech motor control. As concerns speech perception, the working characteristics of auditory processing were first investigated based upon psychoacoustic techniques such as dichotic listening and categorical perception designs. More recently, functional hemodynamic neuroimaging and electrophysiological methods opened the door to the delineation of multiple stages of central auditory processing related to signal detection, classification, sensory memory processes, and, finally, lexical access. Beyond the control mechanisms in a stricter sense, both speech articulation and auditory processing represent examples of ‘grounded cognition’. For example, both domains cannot be restricted to text‐to‐speech translation processes, but are intimately interwoven with neuropsychological aspects of speech prosody, including the vocal expression of affects and the actual performance of speech acts, transforming propositional messages to ‘real’ utterances. Furthermore, during language acquisition, the periphery of language—i.e., hearing and speaking behavior—plays a dominant role for the construction of a language‐specific mental lexicon as well as language‐specific action plans for the production of a speech message. WIREs Cogn Sci 2013, 4:191–200. doi: 10.1002/wcs.1211 This article is categorized under: Linguistics &gt; Language in Mind and Brain
Transcranial magnetic stimulation and amyotrophic lateral sclerosis: pathophysiological insights
2012-12-21

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disorder of the motor neurons in the motor cortex, brainstem and spinal cord. A combination of upper and lower motor neuron dysfunction comprises the clinical ALS phenotype. Although the ALS phenotype was first observed by Charcot over 100 years ago, the site of ALS onset and the pathophysiological mechanisms underlying the development of motor neuron degeneration remain to be elucidated. Transcranial magnetic stimulation (TMS) enables non-invasive assessment of the functional integrity of the motor cortex and its corticomotoneuronal projections. To date, TMS studies have established motor cortical and corticospinal dysfunction in ALS, with cortical hyperexcitability being an early feature in sporadic forms of ALS and preceding the clinical onset of familial ALS. Taken together, a central origin of ALS is supported by TMS studies, with an anterograde transsynaptic mechanism implicated in ALS pathogenesis. Of further relevance, TMS techniques reliably distinguish ALS from mimic disorders, despite a compatible peripheral disease burden, thereby suggesting a potential diagnostic utility of TMS in ALS. This review will focus on the mechanisms underlying the generation of TMS measures used in assessment of cortical excitability, the contribution of TMS in enhancing the understanding of ALS pathophysiology and the potential diagnostic utility of TMS techniques in ALS.
Multimodal Therapy Concept and Aerobic Training in Breast Cancer Patients With Chronic Cancer-Related Fatigue
2012-12-21

Hypothese: Cancer-related fatigue (CRF) and sleep disorders are some of the most wearing and common symptoms in disease-free breast cancer patients (BC). Aerobic training (AT) is the treatment with the best available evidence, even though it seems to be insufficient with regards to improvements in cognitive fatigue. We introduced a new multimodal therapy concept (MM) consisting of psycho-, sleep-education and new approaches based on anthroposophic medicine such as eurythmy and painting therapy. Study design: This pilot study will test the implementation of MM and yield first results of the MM and AE in our centres. Methods: 31 out of 34 patients suffering from BC and CRF were fully assessed in a ten-week intervention study. 21 patients chose MM and 10 decided on AT. CRF was measured with the help of the Cancer Fatigue Scale (CFS-D), and the global quality of sleep was measured with the Pittsburgh Sleep Quality Index (PSQI). We also captured autonomic regulation (aR) and patients’ satisfaction with questionnaires. Statistical analysis was done with SAS 9.1.3 for windows. Results: The new MM therapy can be implemented with high satisfaction among patients. Significant improvements were found in the MM group with regards to CFS-D, global quality of sleep, sleep efficiency (PSQI), aR and rest/activity regulation compared to baseline (all p&lt;0.05). In the AT group aR orthostatic-circulatory and rest/activity regulation improved significantly (p&lt;0.05), too. However, no improvement in cognitive fatigue was seen in either group. Conclusion: The multimodal therapy concept was feasible and improved cancer fatigue, sleep quality, autonomic and rest-/activity regulation in breast cancer patients. It may therefore constitute a valuable treatment option in addition to aerobic training for BC patients with CRF. A further study with larger sample size needs to be carried out to assess the efficacy of combined multimodal-aerobic therapy.
On the complexity of computing the temporal hybridization number for two phylogenies
2012-12-21

Phylogenetic networks are now frequently used to explain the evolutionary history of a set of species for which a collection of gene trees, reconstructed from genetic material of different parts of the species’ genomes, reveal inconsistencies. However, in the context of hybridization, the reconstructed networks are often not temporal. If a hybridization network is temporal, then it satisfies the time constraint of instantaneously occurring hybridization events; i.e. all species that are involved in such an event coexist in time. Furthermore, although a collection of phylogenetic trees can often be merged into a hybridization network that is temporal, many algorithms do not necessarily find such a network since their primary optimization objective is to minimize the number of hybridization events. In this paper, we present a characterization for when two rooted binary phylogenetic trees admit a temporal hybridization network. Furthermore, we show that the underlying optimization problem is APX-hard and, therefore, NP-hard. Thus, unless P=NP, it is unlikely that there are efficient algorithms for either computing an exact solution or approximating it within a ratio arbitrarily close to one.
Release of Matrix Metalloproteinase-8 During Physiological Trafficking and Induced Mobilization of Human Hematopoietic Stem Cells
2012-12-23

Previous studies indicate that the release of proteases, including the gelatinase matrix metalloproteinase (MMP)-9, from mature granulocytes plays a crucial role in cytokine-induced hematopoietic stem and progenitor cell (HSPC) mobilization. However, studies with MMP-9-deficient mice revealed that HSPC mobilization was normal in these animals, suggesting that additional proteases must be active at clinically relevant cytokine concentrations. In the present study, we provide evidence that the collagenase MMP-8 is involved in stem cell mobilization. A rapid release of MMP-8 from isolated neutrophil granulocytes can be observed during an in vitro culture. During granulocyte colony-stimulating factor-induced HSPC mobilization, highly elevated serum concentrations of MMP-8 were observed on days 4 to 6 of the mobilization regimen, concomitantly with elevated MMP-9 serum levels and higher numbers of circulating CD34(+) cells. Elevated serum concentrations of both proteases were also found in umbilical cord blood serum. In functional assays, adhesion of HSPC to osteoblasts as an essential component of the endosteal stem cell niche is negatively influenced by MMP-8. The chemokine CXCL12, which is critically involved in stem cell trafficking, can be proteolytically processed by MMP-8 treatment. This degradation has a strong inhibitory influence on HSPC migration. Taken together, our data strongly suggest that MMP-8 can be directly involved in hematopoietic stem cell mobilization and trafficking.
Effect of small changes in natural origin-based emulsion systems on hydrocortisone skin absorption and performance: a comparison of twoin vivomethods
2012-12-24

Although the performed in vivo methods cannot be considered alternative, skin stripping technique proved to be a cost-efficient mode of percutaneous penetration assessment, providing additional information on vehicle-skin interactions.
Parallel video-based traffic sign recognition on the Intel SCC many-core platform
2012-12-24

This paper presents a demonstrator for a largely task-parallel implementation of an automotive Advanced-Driver-Assistance-System (ADAS). Targeting the Intel SCC1 [1] 48-core chip, we show the scalability of this application towards a configurable number of cores up to 25.