julilili42/papers huggingface dataset:
Pursuing Credibility in Performance Evaluation of VoIP over Wireless Mesh Networks
2011-01-14

There has been an increasingly interest in real-time multimedia services over wireless networks in the last few years, for the most part due to the proliferation of powerful mobile devices, and the potential ubiquity of wireless networks. Nevertheless, there are some constraints that make their deployment over Wireless Mesh Networks (WMNs) somewhat difficult. Due to the dynamics of WMNs, there are significant challenges in the design and optimization of such services. Impairments like packet loss, delay and jitter affects the end-to-end speech quality (Carvalho, 2004). Experimenters have been proposing solutions to the challenges found so far, and comparing them before implementation is a mandatory task. There exists a necessity of designing efficient tools for enhancing the computational effort of the performance modeling and analysis of VoIP over WMNs. Structural complexity of such highly dynamic systems causes that in many situations computer simulation is the only way of investigating their behavior in a controllable manner, allowing the experimenter to conduct independent and repeatable experiments, in addition to the comparison of a large number of system alternatives. Stochastic simulation is a flexible, yet powerful tool for scientifically getting insight into the characteristics of a system being investigated. However, to ensure reproducible results, stochastic simulation imposes its own set of rules. The credibility of a performance evaluation study is greatly affected by the problem formulation, model validation, experimental design, and proper analysis of simulation outcomes. Therefore, a fine-tuning of the parameters within a simulator is indispensable, so that it closely tracks the behavior of a real network. However, the lack of rigor in following the simulation methodology threatens the credibility of the published research (Pawlikowski et al., 2002; Andel & Yasinac, 2006; Kurkowski et al., 2005). The aim of this chapter is to provide a detailed discussion of these aspects. To do so, we used as a starting point the observation that the optimized use of the bandwidth of wireless networks definitely affects the quality of VoIP calls over WMN. Since the payload size of VoIP packets is usually smaller than the header size, much network resource is spent for conveying control information instead of data information. Hence, VoIP header compression is an alternative to reduce the use of the bandwidth needed to transmit control information, thereby increasing the percentage of bandwidth used to carry payload information. 9
Phylogenetic Networks: Concepts, Algorithms and Applications
2011-01-17

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org
Reference values for pulse oximetry recordings in healthy term neonates during their first 5 days of life
2011-01-17

Objective To determine reference values for pulse oximeter saturation (SpO 2 ) variables and desaturation event indices in healthy term neonates during their first 5 days of life, and to compare two definitions for the identification of desaturation events. Design Observational study (case series). Setting Maternity ward, Department of Neonatology, University Children's Hospital, Tuebingen, Germany. Patients 209 healthy term neonates (50% boys), median (minimum–maximum) age 2 (0–5) days. Main outcome measures SpO 2 variables (eg, median SpO 2 ) and desaturation events obtained by motion-resistant pulse oximetry (VitaGuard 310; Getemed, incorporating Masimo SET). Desaturation events were identified based either on a good signal quality (SIQ) provided by the device or on the combination of a good SIQ and an undisturbed pulse waveform (SIQ+PW). Desaturation event indices were calculated as desaturation events divided by hour of artefact-free recording time. Results The mean (SD) of the obtained median SpO 2 was 97.3% (1.4%). There were 36 (17%) subjects with desaturation events to &lt;80% SpO 2 based on SIQ, and 26 (12%) based on SIQ+PW. Median desaturation event rate to &lt;80% SpO 2 /h (75th centile; 95th centile; maximum) was 0 (0; 0.6; 2.3) based on SIQ, and 0 (0; 0.4; 1.7) based on SIQ+PW. Conclusions Desaturation events to &lt;80% SpO 2 were rare in our sample of healthy term neonates during their first 5 days of life. Analysis of SIQ alone could be a quick and simple alternative to traditional analysis of PW. The presented reference values may be used for clinical decision making.
A self-reported long-term follow-up of patients operated with either shortening techniques or a TachoSil grafting procedure
2011-01-17

The aim of this article is to analyse the long-term results of different surgical techniques for correction of penile deviations in Peyronie's disease. Patients who underwent surgery for a penile deviation in Peyronie's disease between 1997 and 2007 were included into this study. Cases were retrospectively analysed by chart review. The current situation was evaluated by a 16-item standardized questionnaire addressing penile straightness, sensation, length, sexual function and satisfaction. Ninety patients were contacted with a return rate of 75 (83%) evaluable questionnaires. Thirty-two patients were operated by shortening techniques (STs) with either Schroeder-Essed (n=16) or Nesbit (n=16). Forty-three were operated by a plaque in-/excision and defect covering by TachoSil method (TM). Both groups were similar regarding age (ST 56 years, TM 57 years), comorbidities, mean preoperative erection hardness score (EHS; 3.1 ST, 3.4 TM) and time of follow-up (total mean, 63 months). Preoperatively ST patients had significantly less plaques (P<0.05) and a lower deviation angle in comparison to TM patients (ST 56° versus TM 74°; P< 0.001). Still TM patients reported slightly better straightening results, but a significantly lower mean EHS (ST 3.3 versus TM 2.6; P<0.001) during the follow-up. Satisfaction rates were similar in both groups. In conclusion, both techniques revealed to be safe and sustainable successful in penile straightening with better functional outcome of patients operated by STs.
Nonliteral Language in Alzheimer Dementia: A Review
2011-01-18

Abstract The use of nonliteral language in clinical assessment, especially testing the patients’ ability to interpret proverbs, has a long tradition in psychiatry. However, its diagnostic sensitivity and specificity in dementias is not yet clear. The aim of this review article is to examine the current evidence on nonliteral/figurative language (proverb, metaphor, metonymy, idiom, irony, sarcasm) comprehension in Alzheimer's disease and related disorders. A comprehensive literature search identified 25 studies (16 proverb, 3 metaphor, 0 metonymy, 5 idiom, 3 sarcasm) on nonliteral language comprehension in dementia. Studies predominantly indicate a deficit. Most studies investigated Alzheimer's dementia. Applied correctly, nonliteral language is a worthwhile diagnostic tool to evaluate language and abstract thinking in dementias. During assessment, familiarity testing (e.g., by asking “are you familiar with the proverb XY”) is obligatory. Still, future research is needed in several areas: evidence on decline of nonliteral language over the course of the illness is limited. So far, almost no studies delineated proverb comprehension in high risk populations such as patients with mild cognitive impairment. Currently, there is a lack of studies addressing performance in direct comparison to relevant differential diagnosis like older-age depression, delirium, brain lesion, or other psychiatric conditions. ( JINS , 2011, 17 , 207–218)
Proteins encoded by the mre gene cluster in Streptomyces coelicolor A3(2) cooperate in spore wall synthesis
2011-01-18

Summary It is still an open question how an intracellular cytoskeleton directs the synthesis of the peptidoglycan exoskeleton. In contrast to MreB of rod‐shaped bacteria, which is essential for lateral cell wall synthesis, MreB of Streptomyces coelicolor has a role in sporulation. To study the function of the S. coelicolor mre gene cluster consisting of mreB, mreC, mreD, pbp2 and sfr , we generated non‐polar replacement mutants. The individual mutants were viable and growth of substrate mycelium was not affected. However, all mutants produced enlarged spores, which frequently germinated prematurely and were sensitive to heat, high osmolarity and cell wall damaging agents. Protein–protein interaction assays by bacterial two‐hybrid analyses indicated that the S. coelicolor Mre proteins form a spore wall synthesizing complex, which closely resembles the lateral wall synthesizing complex of rod‐shaped bacteria. Screening of a genomic library identified several novel putative components of this complex. One of them ( sco2097 ) was deleted. The Δsco2097 mutant formed sensitive spores with an aberrant morphology, demonstrating that SCO2097 is a new player in cell morphogenesis of Streptomyces . Our results suggest that all Mre proteins cooperate with the newly identified proteins in the synthesis of the thickened spore wall required to resist detrimental environmental conditions.
Bayesian timing analysis of giant flare of SGR  180620 by RXTE PCA
2011-01-18

\\n Aims. By detecting high-frequency quasi-periodic oscillations (QPOs) and estimating their frequencies during the decaying tail of giant flares from soft gamma-ray repeaters (SGRs) useful constraints for the equation of state (EoS) of superdense matter may be obtained via comparison with theoretical predictions of eigenfrequencies.\\n Methods. We used the data collected by the Rossi X-Ray Timing Explorer (RXTE/XTE) Proportional Counter Array (PCA) of a giant flare of <ext-link ext-link-type="aoi">SGR 1806−20</ext-link> on 2004 Dec. 27 and applied an existing Bayesian periodicity detection method to search for oscillations of a transient nature.\\n Results. In addition to the already detected frequencies, we found a few new frequencies (fQPOs ~ 16.9,21.4,36.4,59.0,116.3 Hz) of predicted oscillations based on the APR14 EoS for <ext-link ext-link-type="aoi">SGR 1806−20</ext-link>. \\n
Three-quark confinement potential from the Faddeev equation
2011-01-18

In the heavy quark limit of Coulomb gauge QCD and by truncating the Yang-Mills sector to include only dressed two-point functions, an analytic nonperturbative solution to the Faddeev equation for three-quark bound states in the case of equal quark separations is presented. A direct connection between the temporal gluon propagator and the three-quark confinement potential is provided and it is shown that only color singlet qqq (baryon) states are physically allowed.
Current conservation and analytic determination of the magnetic moment of the Δ resonance in the πNbremsstrahlung: II. Formulation with quark degrees of freedom. III. Magnetic moment of the Δoand Δ−resonances
2011-01-18

Our previous paper \\\\cite{MFNEW} is generalized within the field theoretical\\nformulation with the quark degrees of freedom \\\\cite{HW,H,N,Z}, where pions and\\nnucleons are treated as the bound systems of quarks. It is shown that relations\\ngenerated by current conservation for the on shell bremsstrahlung\\namplitude with composite nucleons and pions have the same form as in the usual\\nquantum field theory \\\\cite{IZ,BD} without quark degrees of freedom\\n\\\\cite{MFNEW}. Consequently, the model independent relations for the magnetic\\ndipole moments of the and resonances in \\\\cite{MFNEW}\\nremain be the same in the quantum field theory with the quark degrees of\\nfreedom. These relations are extended for the magnetic dipole moments of the\\n and resonances which are determined via the anomalous\\nmagnetic moment of the neutron as and .\\n
Theoretical and Instructional Aspects of Learning with Visualizations
2011-01-18

Multimedia environments consist of verbal and visual representations that, if appropriately processed, allow for the construction of an integrated mental model of the content. Whereas much is known on how students learn from verbal representations, there are fewer insights regarding the processing of visual information, alone or in conjunction with text. This chapter uses a semiotics approach to provide a defi- nition of visualizations as a specific form of external representation, and then discusses the differences between verbal and visual representations in how they represent information. Finally, it discusses how meaning is achieved when learning with them. The next section discusses basic perceptual and cognitive processes relevant to learning with visualizations. This background is used to specify the instructional functions that visualizations have either as self-contained instructional messages or as text adjuncts. Moreover, the role of individual differences in processing visualizations is highlighted. The chapter ends with methodological suggestions concerning the important role of interdisciplinary research and assessment methods in this area. Request access from your librarian to read this chapter's full text.
Large-Scale Co-Phylogenetic Analysis on the Grid
2011-01-18

Phylogenetic data analysis represents an extremely compute-intensive area of Bioinformatics and thus requires high-performance technologies. Another compute- and memory-intensive problem is that of host-parasite co-phylogenetic analysis: given two phylogenetic trees, one for the hosts (e.g., mammals) and one for their respective parasites (e.g., lice) the question arises whether host and parasite trees are more similar to each other than expected by chance alone. CopyCat is an easy-to-use tool that allows biologists to conduct such co-phylogenetic studies within an elaborate statistical framework based on the highly optimized sequential and parallel AxParafit program. We have developed enhanced versions of these tools that efficiently exploit a Grid environment and therefore facilitate large-scale data analyses. Furthermore, we developed a freely accessible client tool that provides co-phylogenetic analysis capabilities. Since the computational bulk of the problem is embarrassingly parallel, it fits well to a computational Grid and reduces the response time of large scale analyses.Request access from your librarian to read this chapter's full text.
Clinical presentation and management of dermatological toxicities of epidermal growth factor receptor inhibitors
2011-01-19

Abstract The last decade in oncology has been highlighted by the emergence of novel, highly specific anti‐cancer agents, targeting a variety of molecular structures and able to inhibit aberrantly activated oncogenic pathways. Epidermal growth factor receptor inhibitors (EGFRIs) represent one type of such “targeted” agents. Their use made treatment more tolerable and resulted in significant reduction of systemic adverse effects. However, EGFRIs are associated with toxicities affecting the skin and adnexal structures, and mucosal surfaces that affect the majority of treated patients. Significant dermatologic toxicities have changed the role and involvement of dermatologists in their care. It is essential to be familiar with these adverse effects, potential complications, long‐term sequelae, and available effective treatment strategies in order to appropriately manage these patients. This review will describe the clinical presentation, histopathology, underlying mechanisms, and management options, emphasizing evidence‐based approaches.
The morphogene AmiC2 is pivotal for multicellular development in the cyanobacterium Nostoc punctiforme
2011-01-19

Summary Filamentous cyanobacteria of the order Nostocales are primordial multicellular organisms, a property widely considered unique to eukaryotes. Their filaments are composed of hundreds of mutually dependent vegetative cells and regularly spaced N 2 ‐fixing heterocysts, exchanging metabolites and signalling molecules. Furthermore, they may differentiate specialized spore‐like cells and motile filaments. However, the structural basis for cellular communication within the filament remained elusive. Here we present that mutation of a single gene, encoding cell wall amidase AmiC2, completely changes the morphology and abrogates cell differentiation and intercellular communication. Ultrastructural analysis revealed for the first time a contiguous peptidoglycan sacculus with individual cells connected by a single‐layered septal cross‐wall. The mutant forms irregular clusters of twisted cells connected by aberrant septa. Rapid intercellular molecule exchange takes place in wild‐type filaments, but is completely abolished in the mutant, and this blockage obstructs any cell differentiation, indicating a fundamental importance of intercellular communication for cell differentiation in Nostoc . AmiC2–GFP localizes in the cell wall with a focus in the cross walls of dividing cells, implying that AmiC2 processes the newly synthesized septum into a functional cell–cell communication structure during cell division. AmiC2 thus can be considered as a novel morphogene required for cell–cell communication, cellular development and multicellularity.
Metamorphism and diachronous cooling in a contractional orogen: the Strandja Massif, NW Turkey
2011-01-19

Abstract The southern part of the Strandja Massif, northern Thrace, Turkey, comprises a basement of various gneisses, micaschists and rare amphibolite, and a cover of metaconglomerate and metasandstone, separated from each other by a pre-metamorphic unconformity. Metamorphic grade decreases from the epidote–amphibolite facies in the south to the albite–epidote–amphibolite/greenschist-facies transition in the north. Estimated P – T conditions are 485–530°C and 0.60–0.80 GPa in the epidote–amphibolite facies domain, and decrease towards the transitional domain between greenschist- and epidote–amphibolite facies. Rb–Sr muscovite ages range from 162.9 ± 1.6 Ma to 149.1 ± 2.1 Ma, and are significantly older (279–296 Ma) in the northernmost part of the study area. The Rb–Sr biotite ages decrease from 153.9 ± 1.5 Ma in the south to 134.4 ± 1.3 Ma in the north. These age values in conjunction with the attained temperatures suggest that the peak metamorphism occurred at around 160 Ma and cooling happened diachronously, and Rb–Sr muscovite ages were not reset during the metamorphism in the northernmost part. Structural features such as (i) consistent S-dipping foliation and SW to SE-plunging stretching lineation, (ii) top-to-the-N shear sense, and (iii) N-vergent ductile shear zones and brittle thrusts suggest a N-vergent compressional deformation coupled with exhumation. We tentatively ascribe this metamorphism and subsequent diachronous cooling to the northward propagation of a thrust slice. The compressional events in the Strandja Massif were most probably related to the coeval N-vergent subduction/collision system in the southerly lying Rhodope Massif.
Oncogenetics of melanoma: basis for molecular diagnostics and therapy
2011-01-19

Summary Our understanding of oncogenetics and of the molecular mechanisms involved in melanoma development and signaling has dramatically changed in recent years. Today, melanomas are also classified based on molecular alterations. Emerging molecular therapies are targeted against specific mutations in melanoma. An example of targeted therapies is the successful treatment of KIT ‐mutant melanoma with the kinase inhibitor imatinib. Highly selective BRAF ‐inhibitors are likewise under clinical development and show encouraging clinical responses. An increasing number of targeted drugs will emerge in the coming years, based on molecular diagnostics and classification. The present article reviews signaling pathways in melanocytes and alterations in melanoma that are a prerequisite to understanding modern cancer therapies in melanoma.
Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution
2011-01-20

Sec14-superfamily proteins integrate the lipid metabolome with phosphoinositide synthesis and signaling via primed presentation of phosphatidylinositol (PtdIns) to PtdIns kinases. Sec14 action as a PtdIns-presentation scaffold requires heterotypic exchange of phosphatidylcholine (PtdCho) for PtdIns, or vice versa, in a poorly understood progression of regulated conformational transitions. We identify mutations that confer Sec14-like activities to a functionally inert pseudo-Sec14 (Sfh1), which seemingly conserves all of the structural requirements for Sec14 function. Unexpectedly, the “activation” phenotype results from alteration of residues conserved between Sfh1 and Sec14. Using biochemical and biophysical, structural, and computational approaches, we find the activation mechanism reconfigures atomic interactions between amino acid side chains and internal water in an unusual hydrophilic microenvironment within the hydrophobic Sfh1 ligand-binding cavity. These altered dynamics reconstitute a functional “gating module” that propagates conformational energy from within the hydrophobic pocket to the helical unit that gates pocket access. The net effect is enhanced rates of phospholipid-cycling into and out of the Sfh1* hydrophobic pocket. Taken together, the directed evolution approach reveals an unexpectedly flexible functional engineering of a Sec14-like PtdIns transfer protein—an engineering invisible to standard bioinformatic, crystallographic, and rational mutagenesis approaches.
Molecular Phylogenetic Analysis of Enterobius vermicularis and Development of an 18S Ribosomal DNA-Targeted Diagnostic PCR
2011-01-20

ABSTRACT We genetically characterized pinworms obtained from 37 children from different regions of Germany and established new species-specific molecular diagnostic tools. No ribosomal DNA diversity was found; the phylogenetic position of Enterobius vermicularis within the Oxyurida order and its close relationship to the Ascaridida and Spirurida orders was confirmed.
Prognostic value of computed tomography coronary angiography in patients with known or suspected coronary artery disease: A 12-month follow-up study
2011-01-20

Objectives: The aim of our study was to determine the prognostic value of coronary computed tomography angiography (CCTA) for major adverse cardiac events (MACE) in patients with known or suspected coronary artery disease (CAD).