julilili42/papers huggingface dataset:
Solitons and black holes in a generalized Skyrme model with dilaton-quarkonium field
2011-06-01

Skyrme theory is among the viable effective theories which emerge from\\nlow-energy limit of quantum chromodynamics. Many of its generalizations include\\nalso a dilaton. Here we find new self-gravitating solutions, both solitons and\\nblack holes, in a Generalized Skyrme Model (GSM) in which a dilaton is present.\\nThe investigation of the properties of the solutions is done numerically. We\\nfind that the introduction of the dilaton in the theory does not change the\\npicture qualitatively, only quantitatively. The model considered here has one\\nfree parameter more than the Einstein-Skyrme model which comes from the\\npotential of the dilaton. We have applied also the turning point method to\\nestablish that one of the black-hole branches of solutions is unstable. The\\nturning point method here is based on the first law of black-hole\\nthermodynamics a detailed derivation of which is given in the Appendix of the\\npaper.\\n
Multipath mitigation for indoor localization based on IEEE 802.11 time-of-flight measurements
2011-06-01

There are two major approaches to wireless LAN-based indoor localization. One is based on received signal strength indication (RSSI). The other one measures the time of flight (TOF), i.e. the time a network frame needs for propagation in space. To both methods multipath effects pose a significant problem. A well-known mitigation approach for RSSI-based methods is location fingerprinting. This paper investigates the application of fingerprinting to TOF-based localization. In addition, we provide a comparison of RSSI-and TOF-based approaches by applying the same algorithms under the same conditions. Finally, we demonstrate that finger-printing improves TOF-based localization accuracy and even allows for a RSSI-TOF-hybrid approach with low additional effort.
Measurement error in footwear research biomechanics
2011-06-01

Study designs for the biomechanical evaluation of running footwear often encompass repeated measurements of subjects running in a laboratory setup. During post-processing, within-subject variance is usually discarded by pooling subjects' data, although it can be used in a beneficial way to derive intervals for relevant effect magnitudes. These are essentially required for the a priori calculation of sample size as well as the interpretation of statistical test results. Based on the calculation of the random error component of repeated measurements, a sample dataset on rearfoot eversion measurements was used to demonstrate the concept of detecting practically relevant effect magnitudes. This paper provides calculation procedures as well as the interpretational concept, which can both be easily adapted to many other research scenarios.
Merkmalloses versus pluralisches/distributives/intensives Partizip
2011-06-01

Abstract Traditionally (Sethe/Gardiner), the difference between reduplicated (formerly ‘geminated’) and non-reduplicated participles is seen to lie in tense/ aspect. According to more recent interpretations, the choice of the reduplicated participle is determined by the aspect of plurality (Schenkel), distributivity (Allen) and/or intensification (Jansen-Winkeln). The observation that provided a point of departure (Schenkel), and which now forms the basis for a refutation (Depuydt), is the juxtaposition of phrases such as mr.y it(i)=f “beloved of his father” and mrr.w sn(·w.w)=f “beloved of his brothers”. The thesis presented here is that in the case of mr.y as opposed to mrr.w , for example, we are dealing not with a simple paradigmatic opposition of participles but rather that mr.y , which lexicographers have classified as a participle, is in fact a substantivized participle, i.e. is a substantive, whereas mrr.w , which pre-Polotsky, when used in relative constructions, was considered to be a participle, should, according to Polotsky, be understood as a Relative Form and not a participle. As a consequence, the juxtaposition of mr.y and mrr.w alone does not enable one to prove either the contextual (paradigmatic) relevance or irrelevance of the aspects of plurality, distributivity or intensification. Not affected is the co-textual relevance of plurality, distributivity or intensification since the choice of reduplicated Relative Forms obviously (also) depends on co-textual factors.
Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization
2011-06-01

Higher organisms are able to respond to continuously changing external conditions by transducing cellular signals into specific regulatory programs, which control gene expression states of thousands of different genes. One of the central problems in understanding gene regulation is to decipher how combinations of transcription factors control sets of co expressed genes under specific experimental conditions. Existing methods in this field mainly focus on sequence aspects and pattern recognition, e.g., by detecting cis-regulatory modules (CRMs) based on gene expression profiling data. We propose a novel approach by combining experimental data with a priori knowledge of respective experimental conditions. These various sources of evidence are likewise considered using multi-objective evolutionary optimization. In this work, we present three objective functions that are especially designed for stimulus-response experiments and can be used to integrate a priori knowledge into the detection of gene regulatory modules. This method was tested and evaluated on whole-genome microarray measurements of drug-response in human hepatocytes.
Towards quantification of biocompatibility: Monitoring ingrowth behavior of biomaterials in tissue with a microsensor implant
2011-06-01

We introduce a microsensor implant (MSI) comprising microsensors for dissolved oxygen, pH and electrical impedance to monitor ingrowth behavior of biomaterial coatings into tissue. The chorioallantoic membrane (CAM) of ex ovo transferred avian embryos served as a physiological tissue environment. Here, different signal progressions during ingrowth could be observed in a time period of 3-4 days. We tested biodegradable poly(DL-lactide-co-glycolide) and biostable plasma-polymerized coatings compared to an uncoated MSI.
Runtime-datapath-remapping for fault-tolerant coarse-grained reconfigurable architectures
2011-06-01

In this contribution we present an approach which significantly enhances the reliability of coarse-grained reconfigurable architectures by applying a novel remapping strategy. If a component of the architecture is affected by a permanent failure, it will be deactivated and the architecture is reconfigured to relinquish the concerned resource. In our experiments, we have regarded the failure of each single component in the PE array. All of the failures were successfully repaired by applying our remapping method. In average, the repair of one failure took 6 minutes, and the clock frequency had to be reduced by just 0.6% to enable the execution of the changed application mapping.
A DTN mode for reliable internet telephony
2011-06-01

IP telephony suffers from the well-known fact that the Internet does only provide a best-effort service. Thus, minimum transmission quality cannot be guaranteed and, especially during times of network congestion or occasional link failures, UDP-based VoIP becomes unusable. To overcome these limitations, we have developed a rate-adaptive transmission system for highly scalable speech and audio codecs that uses the Delay Tolerant Networking (DTN) approach for very low bit rates. In this way, as soon as the available transmission capacity falls below the minimum coding rate, our system switches to a Push-To-Talk (PTT) like conversational mode. Subjective conversational quality tests have shown that the algorithm allows for a good and effective conversation (MOS-CQS is 3.5) even in cases where traditional UDP based VoIP telephony fails (MOS-CQS is 1).
Magnetic survey of soil pollution around meishan steel mill in Nanjing, China
2011-06-01

High resolution magnetic survey around Meishan steel mill in Nanjing (SE China) was carried out after a preliminary magnetic study which proved that paddy soil could be a suitable target for environmental study on heavy metal pollution. Magnetic susceptibilities were measured on the surface and along down holes at 100 soil sites around Meishan steel mill. In vertical profiles, geochemical and magnetic results show an obvious boundary at a depth of 20cm or so (plough pan). It means there is no transmission of heavy metals below plough pan. The low susceptibility blow plough pan can be taken as background, and the high susceptibility in the upper part can be thought as an average polluted signal. Surface measurement of magnetic susceptibility at paddy field around the steel mill shows a decreasing trend with the increasing distance from the main emission zone of steel mill. With the help of geochemistry, correlation between zinc content and magnetic susceptibility of top soil is proved to be significant. It indicates paddy soil can be used as an effective object to map heavy metal pollution. To some extent, our research expands the magnetic object for heavy metal pollution, and makes it possible to carry out a large scale magnetic scanning for heavy metal pollution in China, since undisturbed soil with low magnetic background is not easy to find.
Ceramide formation as a target in beta-cell survival and function
2011-06-02

Ceramide participates in β-cell dysfunction and apoptosis after exposure to TNFα, IL-1β and IFN-γ, excessive amyloid and islet amyloid polypeptide or non-esterified fatty acids (lipotoxicity). Knockout of sphingomyelin synthase 1, which converts ceramide to sphingomyelin, leads to impairment of insulin secretion. Increased ceramidase activity or pharmacological inhibition of ceramide synthetase, inhibits β-cell apoptosis. Ceramide contributes to endoplasmatic reticulum (ER) stress, decreased mitochondrial membrane potential in insulin-secreting cells and mitochondrial release of cytochrome c into the cytosol, which are all triggers of apoptotic cell death. Ceramide-dependent signaling involves activation of extracellularly regulated kinases 1 and 2 (ERK1/2), downregulation of Period (Per)-aryl hydrocarbon receptor nuclear translocator (Arnt)-single-minded (Sim) kinase (PASK), activation of okadaic-acid-sensitive protein phosphatase 2A (PP2A) and stimulation of NADPH-oxidase with generation of superoxides and lipid peroxides. Ceramide reduces the activity of voltage gated potassium (Kv)-channels in insulin-secreting cells. The role of ceramide in β-cell survival and function may be therapeutically relevant, because ceramide formation can be suppressed by pharmacological inhibition of ceramide synthetase and/or sphingomyelinase.
Axonal Transmission in the Retina Introduces a Small Dispersion of Relative Timing in the Ganglion Cell Population Response
2011-06-02

Intraretinal conduction does not change the relative spike timing between ganglion cells of the same type but increases spike timing differences among ganglion cells of different type. The fastest retinal ganglion cells therefore act as indicators of new stimuli for postsynaptic neurons. The intraretinal dispersion of the population activity will not be compensated by variability in extraretinal conduction times, estimated from data in the literature.
Dealing with war crimes in Bosnia: retributive and restorative options through the eyes of the population
2011-06-02

The entry into force of the Rome Statute, on 1 July 2002, has been heralded by many observers as the final start of a new era, the era of international justice. The importance of the International Criminal Court (ICC) can indeed hardly be overstated. It is the first permanent international court in the world's history that is competent to judge individuals for having committed crimes in various parts of the globe. Some go even further and see it as the ultimate panacea that will not only react to crimes but also deter future crimes, promote reconciliation between former enemies and bring peace to the world. Both perspectives strongly rely on the ICC, and international criminal justice as a whole, as a new form of governance.
Rapid proteomic remodeling of cardiac tissue caused by total body ionizing radiation
2011-06-03

Abstract Accidental nuclear scenarios lead to environmental contamination of unknown level. Immediate radiation‐induced biological responses that trigger processes leading to adverse health effects decades later are not well understood. A comprehensive proteomic analysis provides a promising means to identify and quantify the initial damage after radiation exposure. Early changes in the cardiac tissue of C57BL/6 mice exposed to total body irradiation were studied, using a dose relevant to both intentional and accidental exposure (3 Gy gamma ray). Heart tissue protein lysates were analyzed 5 and 24 h after the exposure using isotope‐coded protein labeling (ICPL) and 2‐dimensional difference‐in‐gel‐electrophoresis (2‐D DIGE) proteomics approaches. The differentially expressed proteins were identified by LC‐ESI‐MS‐MS. Both techniques showed similar functional groups of proteins to be involved in the initial injury. Pathway analyses indicated that total body irradiation immediately induced biological responses such as inflammation, antioxidative defense, and reorganization of structural proteins. Mitochondrial proteins represented the protein class most sensitive to ionizing radiation. The proteins involved in the initial damage processes map to several functional categories involving cardiotoxicity. This prompts us to propose that these early changes are indicative of the processes that lead to an increased risk of cardiovascular disease after radiation exposure.
Automatic response activation in sequential affective priming: an ERP study
2011-06-03

Affective priming effects denote faster responses when two successively presented affective stimuli match in valence than when they mismatch. Two mechanisms have been proposed for their explanation: (i) Priming of affective information within a semantic network or distributed memory system (semantic priming). (ii) Automatic activation of the evaluative response through the affective prime (response priming). In this experiment, we sought more direct evidence for prime-induced response activations with measurement of the lateralized readiness potential (LRP). Onset of the stimulus-locked LRP was earlier in affectively congruent trials than in incongruent trials. In addition, priming modulated the LRP-amplitude of slow responses, indicating greater activation of the incorrect response hand in affectively incongruent trials. Onset of the response-locked LRP and peak latency of the P300 component were not modulated by priming but the amplitude of the N400 component was. In combination, these results suggest that both, semantic priming and response priming constitute affective priming effects in the evaluative categorization task.
Addressing Methionine in Molecular Design through Directed Sulfur–Halogen Bonds
2011-06-03

Halogen bonds are directional interactions involving an electron donor as binding partner. Employing quantum chemical calculations, we explore how they can be used in molecular design to address the sulfur atom in a methionine residue in a previously neglected, directed manner. We characterize energetics and directionality of these halogen bonds and elucidate their spatial variability in suboptimal geometries that are expected to occur in protein-ligand complexes featuring a multitude of concomitant interactions. We derive simple rules allowing medicinal chemists and chemical biologists to easily determine preferred areas of interaction within a binding site and to exploit them for scaffold decoration and design. Our work shows that sulfur-halogen bonds may be used to expand the patentable medicinal chemistry space. We demonstrate their potential to increase binding affinities and suggest that they can significantly contribute to inducing and tuning subtype selectivities.
Site‐specific analysis of bacterial phosphoproteomes
2011-06-03

Abstract Protein phosphorylation on serine, threonine and tyrosine is established as an important regulatory modification in bacteria. A growing number of studies employing mass spectrometry‐based proteomics report large protein phosphorylation datasets, providing precise evidence for in‐vivo phosphorylation that is especially suitable for functional follow‐up. Here, we provide an overview of the strategies currently used in bacterial phosphoproteomics, with an emphasis on gel‐free proteomics and approaches that enable global detection of phosphorylation sites in bacterial proteins. The proteomics technology has matured sufficiently to permit routine characterization of phosphoproteomes and phosphopeptides with high sensitivity; we argue that the next challenge in the field will be the large‐scale detection of protein kinase and phosphatase substrates and their integration into regulatory networks of the bacterial cell.
The otoferlin interactome in neurosensory hair cells: Significance for synaptic vesicle release and trans-Golgi network (Review)
2011-06-03

Sound perception in terrestrial vertebrates relies on a structure in the inner ear consisting of the utriculus, sacculus and lagena. In mammals, the lagena has developed into the cochlea where mechanotransduction at ciliated cells leads to ion influx via regulated ion channels. To maintain proper Ca2+ concentration many cellular systems use a variety of functional proteins; the neurosensory systems use calcium-sensors like hippocalcin, visinin or recoverin. In cochlear hair cells the 230 kDa protein otoferlin has been suggested to play this role. While several observations support this hypothesis additional data argue for a more expanded functional profile of otoferlin. Evidence for otoferlin's multiple roles and newer results on otoferlin's interacting partners are presented and the existence of a protein complex as a functional unit ('interactome') in the cochlea and further tissues is suggested.
Wall Teichoic Acid-Dependent Adsorption of Staphylococcal Siphovirus and Myovirus
2011-06-04

ABSTRACT The molecular interactions between staphylococcal phages and host cell surfaces are poorly understood. Employing Staphylococcus aureus teichoic acid mutants, we demonstrate that wall teichoic acid (WTA), but not lipoteichoic acid, serves as a receptor for staphylococcal siphovirus and myovirus, while only the siphovirus requires glycosylated WTA.
Involvement of Multiple Loci in Quorum Quenching of Autoinducer I Molecules in the Nitrogen-Fixing Symbiont Rhizobium (Sinorhizobium) sp. Strain NGR234
2011-06-04

ABSTRACT Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales ) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. Since we have previously described the complete genome sequence of NGR234, we now report on a genome-wide functional analysis of the genes and enzymes involved in autoinducer I hydrolysis in this microbe. Altogether we identified five cosmid clones that repeatedly gave a positive result in our function-based approach for the detection of autoinducer I hydrolase genes. Of these five cosmid clones, two were located on pNGR234 b and three were on cNGR234. Subcloning and in vitro mutagenesis in combination with BLAST analyses identified the corresponding open reading frames (ORFs) of all cosmid clones: dlhR , qsdR1 , qsdR2 , aldR , and hitR-hydR . Analyses of recombinant DlhR and QsdR1 proteins by using high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrate that these enzymes function as acyl homoserine lactone (AHL) lactonases. Furthermore, we showed that these enzymes inhibited biofilm formation and other quorum-sensing-dependent processes in Pseudomonas aeruginosa , Chromobacterium violaceum , and Agrobacterium tumefaciens . Finally, our experimental data suggest that competitive colonization of roots in the rhizospheres of cowpea plants is affected by DlhR and QsdR1.
Increased palmitoyl-myristoyl-phosphatidylcholine in neonatal rat surfactant is lung specific and correlates with oral myristic acid supply
2011-06-04

Surfactant predominantly comprises phosphatidylcholine (PC) species, together with phosphatidylglycerols, phosphatidylinositols, neutral lipids, and surfactant proteins-A to -D. Together, dipalmitoyl-PC (PC16:0/16:0), palmitoyl-myristoyl-PC (PC16:0/14:0), and palmitoyl-palmitoleoyl-PC (PC16:0/16:1) make up 75–80% of mammalian surfactant PC, the proportions of which vary during development and in chronic lung diseases. PC16:0/14:0, which exerts specific effects on macrophage differentiation in vitro, increases in surfactant during alveolarization (at the expense of PC16:0/16:0), a prenatal event in humans but postnatal in rats. The mechanisms responsible and the significance of this reversible increase are, however, not understood. We hypothesized that, in rats, myristic acid (C14:0) enriched milk is key to lung-specific PC16:0/14:0 increases in surfactant. We found that surfactant PC16:0/14:0 in suckling rats correlates with C14:0 concentration in plasma chylomicrons and lung tissue triglycerides, and that PC16:0/14:0 fractions reflect exogenous C14:0 supply. Significantly, C14:0 was increased neither in plasma PC, nor in liver triglycerides, free fatty acids, or PC. Lauric acid was also abundant in triglycerides, but was not incorporated into surfactant PC. Comparing a C14:0-rich milk diet with a C14:0-poor carbohydrate diet revealed increased C14:0 and decreased C16:0 in plasma and lung triglycerides, respectively. PC16:0/14:0 enrichment at the expense of PC16:0/16:0 did not impair surfactant surface tension function. However, the PC profile of the alveolar macrophages from the milk-fed animals changed from PC16:0/16:0 rich to PC16:0/14:0 rich. This was accompanied by reduced reactive oxygen species production. We propose that nutritional supply with C14:0 and its lung-specific enrichment may contribute to decreased reactive oxygen species production during alveolarization.
Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation
2011-06-05

Vemurafenib produced improved rates of overall and progression-free survival in patients with previously untreated melanoma with the BRAF V600E mutation. (Funded by Hoffmann-La Roche; BRIM-3 ClinicalTrials.gov number, NCT01006980.).
Ipilimumab plus Dacarbazine for Previously Untreated Metastatic Melanoma
2011-06-05

Ipilimumab (at a dose of 10 mg per kilogram) in combination with dacarbazine, as compared with dacarbazine plus placebo, improved overall survival in patients with previously untreated metastatic melanoma. The types of adverse events were consistent with those seen in prior studies of ipilimumab; however, the rates of elevated liver-function values were higher and the rates of gastrointestinal events were lower than expected on the basis of prior studies. (Funded by Bristol-Myers Squibb; ClinicalTrials.gov number, NCT00324155.).