bluuebunny/crossref_metadata_2025 huggingface dataset:
A Quantitative Trait Locus on Chromosome 5p Influences D-Dimer Levels in the San Antonio Family Heart Study
Authors: Diego V. P. , Almasy L. , Rainwater D. L. , Mahaney M. C. , Comuzzie A. G. , Cole S. A. , Tracy R. P. , Stern M. P. , MacCluer J. W. , Blangero J.
Published: June 2010

Background. D-dimer is associated with increasing severity of atherosclerosis and with increased risk of a cardiovascular disease (CVD).Methods and Results. To better understand this risk factor, we performed a genome scan on 803 (301 males and 502 females) Mexican Americans in the San Antonio Family Heart Study (SAFHS). The SAFHS is ideal for the discovery of quantitative trait loci (QTLs) influencing CVD because CVD risk factors are prevalent in Mexican Americans of San Antonio and because the study design involves large families, which is optimal for QTL discovery. D-dimer levels were normalized in our study. We found that D-dimer levels were heritable, at about 23% heritability (P≈.00001). In a linkage analysis employing 432 microsatellite markers, we found strong evidence of a QTL on chromosome 5p with a lod score of 3.32 at 21 centiMorgans (cM). We also found suggestive evidence of a QTL on chromosome 2q with a lod score of 2.33 at 207 cM.Conclusions. To our knowledge, the putative QTL on chromosome 5p is novel. The possible QTL on chromosome 2q is discussed in relation to a recent report of linkage of a related hemostatic factor to the same location. These results warrant further investigation.
Modeling DV/DVCPRO Standards on Reconfigurable Video Coding Framework
Authors: Li Jianjun , Abdel-Raheem Esam
Published: June 2010

After more than 20 years, several video coding standards
and technologies have been delivered. Less consideration is
taken on their commonalities and interoperations. Specification
and reference code of case by case is time consuming. The MPEG
reconfigurable video coding (RVC) framework is a new standard
under development by MPEG. It aims to provide a unified high‐level
specification of current MPEG video coding technologies.
In this framework, the decoder is built as a configuration of
video coding tools taken from MPEG toolbox library. Up to
now, MPEG‐4 simple profile and China audio video coding
standard (AVS) decoders have been successfully modeled with
RVC framework. In this paper, we examine another video
standard, that is, DV/DVCPRO, and model it with RVC‐CAL. The
flexibility and ease of RVC‐CAL is demonstrated as well as the
validation of RVC modeling.
Decrease of Klotho in the Kidney of Streptozotocin-Induced Diabetic Rats
Authors: Cheng Meng-Fu , Chen Li-Jen , Cheng Juei-Tang
Published: June 2010

Theklothogene is expressed in a limited number of tissues, most notably in distal convoluted tubules in the kidney and choroid plexus in the brain. A previous study suggested that Klotho increases resistance to oxidative stress. However, changes of Klotho expression in high glucose-induced oxidative stress remain unclear. In the present study, we used streptozotocin-induced diabetic rats (STZ rats) to examine the effects of insulin, phloridzin or antioxidant, tiron on diabetic nephropathy. Both insulin and phloridzin reversed the lower Klotho expression levels in kidneys of STZ rats by the correction of hyperglycemia. Also, renal functions were improved by these treatments. In addition to the improvement of renal functions, the decrease of Klotho expression in kidney of STZ rats was also reversed by tiron without changing blood glucose levels. The reduction of oxidative stress induced by high glucose can be considered for this action of tiron. This view was further confirmed in vitro using high glucose-exposed Madin-Darby canine kidney (MDCK) epithelial cells. Thus, we suggest that decrease of oxidative stress is not only responsible for the improvement of renal function but also for the recovery of Klotho expression in kidney of STZ rats.
The Association of Weight Status with Physical Fitness among Chinese Children
Authors: Shang Xianwen , Liu Ailing , Li Yanping , Hu Xiaoqi , Du Lin , Ma Jun , Xu Guifa , Li Ying , Guo Hongwei , Ma Guansheng
Published: June 2010

Objective. To investigate the association of weight status with physical fitness among Chinese children.Methods. A total of 6929 children aged 6–12 years were selected from 15 primary schools of 5 provincial capital cities in eastern China. The height and fasting body weight were measured. The age-, sex-specific BMI WHO criteria was used to define underweight, overweight and obesity. Physical fitness parameters including standing broad jump, 50 m sprint, and 50 m∗8 shuttle run were tested.Results. The prevalence of underweight, overweight, and obesity was 3.1%, 14.9%, and 7.8%, respectively. Boys performed better than girls, and the older children performed better than their younger counterparts for all physical fitness tests. No significant difference in all three physical fitness tests were found between children with underweight and with normal weight, and they both performed better than their counterparts with overweight and obese in all three physical fitness tests. The likelihood of achieving good performance was much lower among overweight and obese children in comparison with their counterparts with normal weight (OR=0.13–0.54).Conclusions. An inverse association of obesity with cardiorespiratory fitness, muscle explosive strength, and speed was identified among Chinese children.
Elk Distributions Relative to Spring Normalized Difference Vegetation Index Values
Authors: Smallidge Samuel T. , Baker Terrell T. , VanLeeuwen Dawn , Gould William R. , Thompson Bruce C.
Published: June 2010

Rocky Mountain elk (Cervus elaphus) that winter near San Antonio Mountain in northern New Mexico provide important recreational and economic benefits while creating management challenges related to temporospatial variation in their spring movements. Our objective was to examine spring distributions of elk in relation to vegetative emergence as it progresses across the landscape as measured by remote sensing. Spring distributions of elk were closely associated with greater photosynthetic activity of spring vegetation in 2 of 3 years as determined using NDVI values derived from AVHRR datasets. Observed elk locations were up to 271% greater than expected in the category representing the most photosynthetic activity. This association was not observed when analyses at a finer geographic scale were conducted. Managers facing challenges involving human-wildlife interactions and land-use issues should consider environmental conditions that may influence variation in elk association with greener portions of the landscape.
A Zero‐Dissipative Runge‐Kutta‐Nyström Method with Minimal Phase‐Lag
Authors: Senu Norazak , Suleiman Mohamed , Ismail Fudziah , Othman Mohamed
Published: June 2010

An explicit Runge‐Kutta‐Nyström method is developed for solving second‐order
differential equations of the form q′′ = f(t, q) where the solutions are oscillatory. The method has zero‐dissipation with minimal phase‐lag at a cost of three‐function
evaluations per step of integration. Numerical comparisons with RKN3HS, RKN3V, RKN4G, and RKN4C methods show the preciseness and effectiveness of the method developed.
Stability of Ranked Gene Lists in Large Microarray Analysis Studies
Authors: Stiglic Gregor , Kokol Peter
Published: June 2010

This paper presents an empirical study that aims to explain the relationship between the number of samples and stability of different gene selection techniques for microarray datasets. Unlike other similar studies where number of genes in a ranked gene list is variable, this study uses an alternative approach where stability is observed at different number of samples that are used for gene selection. Three different metrics of stability, including a novel metric in bioinformatics, were used to estimate the stability of the ranked gene lists. Results of this study demonstrate that the univariate selection methods produce significantly more stable ranked gene lists than the multivariate selection methods used in this study. More specifically, thousands of samples are needed for these multivariate selection methods to achieve the same level of stability any given univariate selection method can achieve with only hundreds.
Hydrogen‐Bonded Networks Based on Cobalt(II), Nickel(II), and Zinc(II) Complexes of N,N′‐Diethylurea
Authors: Drakopoulou Labrini , Raptopoulou Catherine P. , Terzis Aris , Papaefstathiou Giannis S.
Published: June 2010

N,N′‐diethylurea (DEU) was employed as a ligand to form the octahedral complexes (M=Co, Ni and Zn). Compounds [Co(DEU)6] (1), [Co(DEU)6] (2), (3), and [Zn(DMU)6] (4) have been prepared from the reactions of DEU and the appropriate hydrated metal(II) salts in EtOH in the presence of 2,2‐dimethoxypropane. Crystal structure determinations demonstrate the existence of cations and (in 2–4) or (in 1) counterions. The cations in the solid state are stabilized by a pseudochelate effect due to the existence of six strong intracationic N‐H ⋯ O(DEU)
hydrogen bonds. The cations and counterions self‐assemble to form hydrogen‐bonded 2D architectures in 2–4 that conform to the kgd (kagome dual) network, and a 3D hydrogen‐bonded rtl (rutile) network in 1. The nature of the resulting supramolecular structures is influenced by the nature of the counter‐ion. The complexes were also characterized by vibrational spectroscopy (IR).
Generalised Filtering
Authors: Friston Karl , Stephan Klaas , Li Baojuan , Daunizeau Jean
Published: June 2010

We describe a Bayesian filtering scheme for nonlinear state‐space models in continuous time. This scheme is called Generalised Filtering and furnishes posterior (conditional) densities on hidden states and unknown parameters generating observed data. Crucially, the scheme operates online, assimilating data to optimize the conditional density on time‐varying states and time‐invariant parameters. In contrast to Kalman and Particle smoothing, Generalised Filtering does not require a backwards pass. In contrast to variational schemes, it does not assume conditional independence between the states and parameters. Generalised Filtering optimises the conditional density with respect to a free‐energy bound on the model′s log‐evidence. This optimisation uses the generalised motion of hidden states and parameters, under the prior assumption that the motion of the parameters is small. We describe the scheme, present comparative evaluations with a fixed‐form variational version, and conclude with an illustrative application to a nonlinear state‐space model of brain imaging time‐series.
Qualitative Simulation of Photon Transport in Free Space Based on Monte Carlo Method and Its Parallel Implementation
Authors: Chen Xueli , Gao Xinbo , Qu Xiaochao , Chen Duofang , Ma Bin , Wang Lin , Peng Kuan , Liang Jimin , Tian Jie
Published: June 2010

During the past decade, Monte Carlo method has obtained wide applications in optical imaging to simulate photon transport process inside tissues. However, this method has not been effectively extended to the simulation of free‐space photon transport at present. In this paper, a uniform framework for noncontact optical imaging is proposed based on Monte Carlo method, which consists of the simulation of photon transport both in tissues and in free space. Specifically, the simplification theory of lens system is utilized to model the camera lens equipped in the optical imaging system, and Monte Carlo method is employed to describe the energy transformation from the tissue surface to the CCD camera. Also, the focusing effect of camera lens is considered to establish the relationship of corresponding points between tissue surface and CCD camera. Furthermore, a parallel version of the framework is realized, making the simulation much more convenient and effective. The feasibility of the uniform framework and the effectiveness of the parallel version are demonstrated with a cylindrical phantom based on real experimental results.
Daylight Saving Time Transitions and Road Traffic Accidents
Authors: Lahti Tuuli , Nysten Esa , Haukka Jari , Sulander Pekka , Partonen Timo
Published: June 2010

Circadian rhythm disruptions may have harmful impacts on health. Circadian rhythm disruptions caused by jet lag compromise the quality and amount of sleep and may lead to a variety of symptoms such as fatigue, headache, and loss of attention and alertness. Even a minor change in time schedule may cause considerable stress for the body. Transitions into and out of daylight saving time alter the social and environmental timing twice a year. According to earlier studies, this change in time-schedule leads to sleep disruption and fragmentation of the circadian rhythm. Since sleep deprivation decreases motivation, attention, and alertness, transitions into and out of daylight saving time may increase the amount of accidents during the following days after the transition. We studied the amount of road traffic accidents one week before and one week after transitions into and out of daylight saving time during years from 1981 to 2006. Our results demonstrated that transitions into and out of daylight saving time did not increase the number of traffic road accidents.
Efficacy and Cytokine Modulating Effects of Tacrolimus in Systemic Lupus Erythematosus: A Review
Authors: Yoon Kam Hon
Published: June 2010

Systemic lupus erythematosus (SLE) is a complex systemic autoimmune disease with involvement of both B cells and cytotoxic T lymphocytes and several cytokines aberrations. Standard therapy for SLE has its limitations. Tacrolimus, a novel calcineurin inhibitor with potent immunosuppressive effects, has been shown in the recent years to be effective in SLE therapy. This paper serves to collate the experimental and clinical data on the efficacy of tacrolimus in the treatment of SLE and lupus nephritis. Tacrolimus as a key component of multitarget therapy in SLE is also discussed. The immunocytokine modulatory effects of tacrolimus are also reviewed with reference to SLE. It can be concluded that tacrolimus has an established role in the management of SLE.
A 12 dB 0.7 V W CMOS LNA for 866 MHz UHF RFID Reader
Authors: Li Jie , Hasan S. M. Rezaul
Published: June 2010

The design of a narrow-band cascode CMOS inductive source-degenerated low noise amplifier (LNA) for 866 MHz UHF RFID reader is presented. Compared to other previously reported narrow-band LNA designs, in this paper the finite    effect has been considered to improve the nanometric design, achieving simultaneous impedance and minimum noise matching at a very low power drain of 850  from a 0.7 V supply voltage. The LNA was fabricated using the IBM 130 nm CMOS process delivering a forward power gain () of , a reverse isolation () of , an output power reflection ( @866 MHz) of , and an input power reflection ( @866 MHz) of . It had a minimum pass-band of around 2.2 dB and a third-order input referred intercept point (IIP3) of .
Scattering Amplitudes, the AdS/CFT Correspondence, Minimal Surfaces, and Integrability
Authors: Alday Luis F.
Published: June 2010

We focus on the computation of scattering amplitudes of planar maximally supersymmetric Yang‐Mill in four dimensions at strong coupling by means of the AdS/CFT correspondence and explain how the problem boils down to the computation of minimal surfaces in AdS in the first part of this paper. In the second part of this review we explain how integrability allows to give a solution to the problem in terms of a set of integral equations. The intention of the review is to give a pedagogical, rather than very detailed, exposition.
Smart Sensing Technologies for Structural Health Monitoring of Civil Engineering Structures
Authors: Sun M. , Staszewski W. J. , Swamy R. N.
Published: June 2010

Structural Health Monitoring (SHM) aims to develop automated systems for the continuous monitoring, inspection, and damage detection of structures with minimum labour involvement. The first step to set up a SHM system is to incorporate a level of structural sensing capability that is reliable and possesses long term stability. Smart sensing technologies including the applications of fibre optic sensors, piezoelectric sensors, magnetostrictive sensors and self-diagnosing fibre reinforced composites, possess very important capabilities of monitoring various physical or chemical parameters related to the health and therefore, durable service life of structures. In particular, piezoelectric sensors and magnetorestrictive sensors can serve as both sensors and actuators, which make SHM to be an active monitoring system. Thus, smart sensing technologies are now currently available, and can be utilized to the SHM of civil engineering structures. In this paper, the application of smart materials/sensors for the SHM of civil engineering structures is critically reviewed. The major focus is on the evaluations of laboratory and field studies of smart materials/sensors in civil engineering structures.
Debundling and Selective Enrichment of SWNTs for Applications in Dye-Sensitized Solar Cells
Authors: Bonaccorso F.
Published: June 2010

We present an overview of the recent developments in de-bundling and sorting of Single-Wall Carbon Nanotubes (SWNTs), which are useful for hi-tech applications in dye sensitized solar cells (DSSCs). Applications of SWNTs as transparent and conductive films, catalyst, and scaffold in DSSCs are also reviewed.
Nonlinear Dynamic Response of Functionally Graded Rectangular Plates under Different Internal Resonances
Authors: Hao Y. X. , Zhang W. , Ji X. L.
Published: June 2010

The nonlinear dynamic response of functionally graded rectangular plates under combined transverse and in‐plane excitations is investigated under the conditions of 1 : 1, 1 : 2 and 1 : 3 internal resonance. The material properties are assumed to be temperature‐dependent and vary along the thickness direction. The thermal effect due to one‐dimensional temperature gradient is included in the analysis. The governing equations of motion for FGM rectangular plates are derived by using Reddy′s third‐order plate theory and Hamilton′s principle. Galerkin′s approach is utilized to reduce the governing differential equations to a two‐degree‐of‐freedom nonlinear system including quadratic and cubic nonlinear terms, which are then solved numerically by using 4th‐order Runge‐Kutta algorithm. The effects of in‐plane excitations on the internal resonance relationship and nonlinear dynamic response of FGM plates are studied.
Effects of HIF-1 and HIF2 on Growth and Metabolism of Clear-Cell Renal Cell Carcinoma 786-0 Xenografts
Authors: Biswas Swethajit , Troy Helen , Leek Russell , Chung Yuen-Li , Li Ji-liang , Raval Raju R. , Turley Helen , Gatter Kevin , Pezzella Francesco , Griffiths John R. , Stubbs Marion , Harris Adrian L.
Published: June 2010

In cultured clear-cell renal carcinoma (CCRCC) 786-0 cells transfected with HIF1 (HIF-1+), HIF-2 (HIF-2+), or empty vector (EV), no significant differences were observed in the growth ratesin vitro, but when grownin vivoas xenografts HIF-2 significantly increased, and HIF-1 significantly decreased growth rates, compared to EV tumors. Factors associated with proliferation were increased and factors associated with cell death were decreased in HIF-2+ tumors. Metabolite profiles showed higher glucose and lower lactate and alanine levels in the HIF-2+ tumors whilst immunostaining demonstrated higher pyruvate dehydrogenase and lower pyruvate dehydrogenase kinase 1, compared to control tumors. Taken together, these results suggest that overexpression of HIF-2 in CCRCC 786-0 tumors regulated growth both by maintaining a low level of glycolysis and by allowing more mitochondrial metabolism and tolerance to ROS induced DNA damage. The growth profiles observed may be mediated by adaptive changes to a more oxidative phenotype.
Postnatal BDNF Expression Profiles in Prefrontal Cortex and Hippocampus of a Rat Schizophrenia Model Induced by MK-801 Administration
Authors: Guo Chunmei , Yang Yang , Su Yun'ai , Si Tianmei
Published: June 2010

Neonatal blockade of N-methyl-D-aspartic acid (NMDA) receptors represents one of experimental animal models for schizophrenia. This study is to investigate the long-term brain-derived neurotrophic factor (BDNF) expression profiles in different regions and correlation with “schizophrenia-like” behaviors in the adolescence and adult of this rat model. The NMDA receptor antagonist MK801 was administered to female Sprague-Dawley rats on postnatal days (PND) 5 through 14. Open-field test was performed on PND 42, and PND 77 to examine the validity of the current model. BDNF protein levels in hippocampus and prefrontal cortex (PFC) were analyzed on PND 15, PND 42, and PND 77. Results showed that neonatal challenge with MK-801 persistently elevated locomotor activity as well as BDNF expression; the alterations in BDNF expression varied at different developing stages and among brain regions. However, these findings provide neurochemical evidence that the blockade of NMDA receptors during brain development results in long-lasting alterations in BDNF expression and might contribute to neurobehavioral pathology of the present animal model for schizophrenia. Further study in the mechanisms and roles of the BDNF may lead to better understanding of the pathophysiology of schizophrenia.
A 3.5‐Dimensional Variational Method for Doppler Radar Data Assimilation and Its Application to Phased‐Array Radar Observations
Authors: Xu Qin , Wei Li , Gu Wei , Gong Jiandong , Zhao Qingyun
Published: June 2010

A 3.5‐dimensional variational method is developed for Doppler radar data assimilation. In this method, incremental analyses are performed in three steps to update the model state upon the background state provided by the model prediction. First, radar radial‐velocity observations from three consecutive volume scans are analyzed on the model grid. The analyzed radial‐velocity fields are then used in step 2 to produce incremental analyses for the vector velocity fields at two time levels between the three volume scans. The analyzed vector velocity fields are used in step 3 to produce incremental analyses for the thermodynamic fields at the central time level accompanied by the adjustments in water vapor and hydrometeor mixing ratios based on radar reflectivity observations. The finite element B‐spline representations and recursive filter are used to reduce the dimension of the analysis space and enhance the computational efficiency. The method is applied to a squall line case observed by the phased‐array radar with rapid volume scans at the National Weather Radar Testbed and is shown to be effective in assimilating the phased‐array radar observations and improve the prediction of the subsequent evolution of the squall line.
Krammer′s Representation of the Pure Braid Group, P3
Authors: Abdulrahim Mohammad N. , Al-Tahan Madline
Published: June 2010

We consider Krammer′s representation of the pure braid group on three strings: P3 → GL(3, Z[t±1, q±1]), where t and q are indeterminates. As it was done in the case of the braid group, B3, we specialize the indeterminates t and q to nonzero complex numbers. Then we present our main theorem that gives us a necessary and sufficient condition that guarantees the irreducibility of the complex specialization of Krammer′s representation of the pure braid group, P3.
Involvement of Aberrant Glycosylation in Thyroid Cancer
Authors: Miyoshi Eiji , Ito Yasuhiro , Miyoshi Yoko
Published: June 2010

Glycosylation is one of the most common posttranslational modification reactions and nearly half of all known proteins in eukaryotes are glycosylated. In fact, changes in oligosaccharides structures are associated with many physiological and pathological events, including cell growth, migration and differentiation, and tumor invasion. Therefore, functional glycomics, which is a comprehensive study of the structures and functions of glycans, is attracting the increasing attention of scientists in various fields of life science. In cases of thyroid cancer, the biological characters and prognosis are completely different in each type of histopathology, and their oligosaccharide structures as well as the expression of glycosyltransferases are also different. In this review, we summarized our previous papers on oligosaccharides and thyroid cancers and discussed a possible function of oligosaccharides in the carcinogenesis in thyroid cancer.
Nitrogen Uptake in the Northeastern Arabian Sea during Winter Cooling
Authors: Kumar S. , Ramesh R. , Dwivedi R. M. , Raman M. , Sheshshayee M. S. , D'Souza W.
Published: June 2010

The uptake of dissolved inorganic nitrogen by phytoplankton is an important aspect of the nitrogen cycle of oceans. Here, we present nitrate (NO3-) and ammonium (NH4+) uptake rates in the northeastern Arabian Sea using 15N tracer technique. In this relatively underexplored region, productivity is high during winter due to supply of nutrients by convective mixing caused by the cooling of the surface by the northeast monsoon winds. Studies done during different months (January and late February-early March) of the northeast monsoon 2003 revealed a fivefold increase in the average euphotic zone integrated NO3- uptake from January (2.3 mmolN m−2d−1) to late February-early March (12.7 mmolN m−2d−1). The f-ratio during January appeared to be affected by the winter cooling effect and increased by more than 50% from the southernmost station to the northern open ocean stations, indicating hydrographic and meteorological control. Estimates of NO3- residence time suggested that NO3- entrained in the water column during January contributed to the development of blooms during late February-early March.
Benefits of Neuropsychiatric Phenomics: Example of the 5-Lipoxygenase-Leptin-Alzheimer Connection
Authors: Manev Hari , Manev Radmila
Published: June 2010

Phenomics is a systematic study of phenotypes on a genomewide scale that is expected to unravel, as of yet, unsuspected functional roles of the genome. It remains to be determined how to optimally approach and analyze the available phenomics databases to spearhead innovation in neuropsychiatry. By serendipitously connecting two unrelated phenotypes of increased blood levels of the adipokine leptin, a molecule that regulates appetite, in 5-lipoxygenase- (5-LOX) deficient mice and patients with a lower risk for Alzheimer's disease (AD), we postulated a leptin-mediated basis for beneficial effects of ALOX5 (a gene encoding 5-LOX) gene-deficiency in AD. We suggest that it might be possible to avoid relying on serendipity and develop data-mining tools capable of extracting from phenomics databases indications for such novel hypotheses. Hence, we provide an example of using a free-access Arrowsmith two-node search interface to identify ALOX5 as unsuspected putative mechanisms for the previously described clinical association between increased plasma levels of leptin and a lower risk of incident dementia and AD.
Prefrontal Cortex Modulation during Anticipation of Working Memory Demands as Revealed by Magnetoencephalography
Authors: Altamura Mario , Goldberg Terry E. , Elvevåg Brita , Holroyd Tom , Carver Frederick W. , Weinberger Daniel R. , Coppola Richard
Published: June 2010

During the anticipation of task demands frontal control is involved in the assembly of stimulus‐response mappings based on current goals. It is not clear whether prefrontal modulations occur in higher‐order cortical regions, likely reflecting cognitive anticipation processes. The goal of this paper was to investigate prefrontal modulation during anticipation of upcoming working memory demands as revealed by magnetoencephalography (MEG). Twenty healthy volunteers underwent MEG while they performed a variation of the Sternberg Working Memory (WM) task. Beta band (14–30 Hz) SAM (Synthetic Aperture Magnetometry) analysis was performed. During the preparatory periods there was an increase in beta power (event‐related synchronization) in dorsolateral prefrontal cortex (DLPFC) bilaterally, left inferior prefrontal gyrus, left parietal, and temporal areas. Our results provide support for the hypothesis that, during preparatory states, the prefrontal cortex is important for biasing higher order brain regions that are going to be engaged in the upcoming task.
Uncovering the Complexity of Transcriptomes with RNA-Seq
Authors: Costa Valerio , Angelini Claudia , De Feis Italia , Ciccodicola Alfredo
Published: June 2010

In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
Hybrid ICA‐Seed‐Based Methods for fMRI Functional Connectivity Assessment: A Feasibility Study
Authors: Kelly Robert E. , Wang Zhishun , Alexopoulos George S. , Gunning Faith M. , Murphy Christopher F. , Morimoto Sarah Shizuko , Kanellopoulos Dora , Jia Zhiru , Lim Kelvin O. , Hoptman Matthew J.
Published: June 2010

Brain functional connectivity (FC) is often assessed from fMRI data using seed‐based methods, such as those of detecting temporal correlation between a predefined region (seed) and all other regions in the brain; or using multivariate methods, such as independent component analysis (ICA). ICA is a useful data‐driven tool, but reproducibility issues complicate group inferences based on FC maps derived with ICA. These reproducibility issues can be circumvented with hybrid methods that use information from ICA‐derived spatial maps as seeds to produce seed‐based FC maps. We report results from five experiments to demonstrate the potential advantages of hybrid ICA‐seed‐based FC methods, comparing results from regressing fMRI data against task‐related a priori time courses, with “back‐reconstruction” from a group ICA, and with five hybrid ICA‐seed‐based FC methods: ROI‐based with (1) single‐voxel, (2) few‐voxel, and (3) many‐voxel seed; and dual‐regression‐based with (4) single ICA map and (5) multiple ICA map seed.
Recurrent Urinary Bladder Paraganglioma
Authors: Al-Zahrani Ali A.
Published: June 2010

A 39-year-old male presented with recurrent attacks of painless haematuria. The patient has a history of partial cystectomy for bladder paraganglioma 10 years prior to the presentation. Imaging study and cystoscopic examination revealed a small anterior wall bladder tumor. The histological examination of the lesion confirmed that it was a urinary paraganglioma. Partial cystectomy was performed to this recurrent lesion. This case report stresses the importance of life-long follow-up of these lesions.
Fixed Point Results for Multivalued Maps in Cone Metric Spaces
Authors: Latif Abdul , Shaddad FawziaY
Published: June 2010

We prove some fixed point theorems for multivalued maps in cone metric spaces. We improve and extend a number of known fixed point results including the corresponding recent fixed point results of Feng and Liu (1996) and Chifu and Petrusel (1997). The remarks and example provide improvement in the mentioned results.
Elastic Membrane That Undergoes Mechanical Deformation Enhances Osteoblast Cellular Attachment and Proliferation
Authors: Toworfe G. K. , Composto R. J. , Lee M. H. , Ducheyne P.
Published: June 2010

The main objective of this paper was to investigate the effect of transmission of force on bone cells that were attached to a deformable membrane. We functionalized a silastic membrane that measured 0.005 inches thickness and coated it with an extra cellular matrix (ECM) protein, fibronectin (FN). MC3T3-E1 osteoblast-like cells were cultured on the functionalized FN-coated membrane after which cell attachment and proliferation were evaluated. We observed an immediate attachment and proliferation of the bone cells on the functionalized membrane coated with FN, after 24 hours. Upon application of a mechanical force to cells cultured on the functionalized silicone membrane in the form of a dynamic equibiaxial strain, 2% magnitude; at 1-Hz frequency for 2 h, the osteoblast cells elicited slightly elevated phalloidin fluorescence, suggesting that there was reorganization of the cytoskeleton. We concluded from this preliminary data obtained that the engineered surface transduced applied mechanical forces directly to the adherent osteoblast cells via integrin binding tripeptide receptors, present in the FN molecules, resulting in the enhanced cellular attachment and proliferation.
The Modification of Sodium Polyacrylate Water Solution Cooling Properties by AL2O3
Authors: Gęstwa Wojciech , Przyłęcka Małgorzata
Published: June 2010

This paper presents a preliminary examination of water cooling ability as a result of its modification by the addition of sodium polyacrylate and AL2O3nanoparticles. (AL2O3) alumina oxide was present in gamma phase as a form of nanopowder whose particle size was less than 50 nm. Cooling curves in the temperature-time system were marked for the three cooling media: water, 10% water solution of sodium polyacrylate, and 10% water solution of sodium polyacrylate with 1% addition of AL2O3nanoparticles. Based on cooling curves, it can be concluded that for the water solution of sodium polyacrylate with AL2O3nanoparticles in comparison to water and 10% polymer water solution lower cooling speed is obtained. The cooling medium containing nanoparticles provides lower cooling speed in the smallest surface austenite occurance (500–600 C) in the charts of the CTP for most nonalloy structural steels and low-alloy steels. However lower cooling temperature at the beginning of martensitic transformation causes the formation of smaller internal stresses, leading to smaller dimensional changes and hardening deformation. For the quenching media the wetting angle was appointed by the drop-shape method. These studies showed the best wettability of polymer water solution (sodium polyacrylate) with the addition of AL2O3nanoparticles, whose wetting angle was about 65 degrees. Obtaining the smallest wetting angle for the medium containing nanoparticles suggests that the heat transfer to the cooling medium is larger. This allows slower cooling at the same time ensuring its homogeneity. The obtained values of wetting angle confirm the conclusions drawn on the basis of cooling curves and allowus to conclude that in the case of the heat transfer rate it will have a lower value than for water and 10% polymer water solution. In the research on hardened carburized steel samples C10 and 16MnCr5 surface hardness, impact strength and changes in the size of cracks in Navy C-ring sample are examined. On this basis of the obtained results it can be concluded that polymer water solution with nanoparticles allows to obtain a better impact strength at comparable hardness on the surface. Research on the dimensional changes on the basis of the sample of Navy C-ring also shows small dimensional changes for samples carburized and hardened in 10% polymer water solution with the addition of nanoparticles AL2O3. Smaller dimensional changes were obtained for samples of steel 16MnCr5 thanfar C10. The results allowus to conclude that by the addition of solid nanoparticles to water based quenching media their cooling properties which are not inferior to mineral oils and polymer water solutions can be shaped.
Infliximab for Idiopathic Deep Cutaneous Vasculitis Refractory to Cyclophosphamide
Authors: Schafranski Marcelo Derbli , Campanari Giuliano Doretto
Published: June 2010

Cutaneous vasculitis can be classified as primary or idiopathic; or secondary, when it presents as a manifestation of connective tissue diseases, infections, drug reactions or malignancies. Although most of the idiopathic cases are self-limited and responsive to supportive measures and nonsteroidal anti-inflammatory drugs, potent immunosuppressants are sometimes required for the management of the refractory situations. Here we describe a case of a 32-year-old Caucasian female patient with history of idiopathic cutaneous deep vasculitis unresponsive to methotrexate, dapsone, and cyclophosphamide who was effectively treated with infliximab.
A Model of Gear Transmission: Fractional Order System Dynamics
Authors: Hedrih Katica (Stevanović) , Nikolić-Stanojević Vera
Published: June 2010

A theoretical model of multistep gear transmission dynamics is presented. This model is based on the assumption that the connection between the teeth of the gears is with properties within the range from ideal clasic to viscoelastic so that a new model of connection between the teeth was expressed by means of derivative of fractional order. For this model a two‐step gear transmision with three degrees of freedom of motion has been used. The obtained solutions are in the analytic form of the expansion according to time. As boundary cases this model gives results for the case of ideally elastic connection of the gear teeth and for the case of viscoelastic connection of the gear teeth, as well. Eigen fractional modes are obtained and a vizualization is done.
Nerve Growth Factor Promotes the Survival of Goat Preantral Follicles Cultured in vitro
Authors: Chaves R.N. , Alves A.M.C.V. , Duarte A.B.G. , Araújo V.R. , Celestino J.J.H. , Matos M.H.T. , Lopes C.A.P. , Campello C.C. , Name K.P.O. , Báo S.N. , Figueiredo J.R.
Published: June 2010

The aim of this study was to investigate the effects of nerve growth factor (NGF) on the in vitro culture of goat preantral follicles. Ovarian cortex fragments were cultured in α-MEM+ supplemented with 0, 1, 10, 50, 100 or 200 ng/ml NGF for 1 or 7 days. Small fragments of noncultured ovarian tissue as well as those cultured for 1 or 7 days were processed for histology and transmission electron microscopy. The results showed that after 1 or 7 days of culture at all concentrations of NGF, except at 1 ng/ml after 1 day of culture, there was a significant reduction in the percentage of normal follicles compared to noncultured tissues. At higher NGF concentrations (100 and 200 ng/ml) after 7 days of culture, there was a significant reduction in the percentage of normal follicles compared to tissues cultured in α-MEM+ alone or at the other concentrations of NGF. It is important to note that ultrastructural and fluorescent analyses confirmed only the integrity of follicles cultured with 1 ng/ml of NGF after 7 days. In contrast to noncultured control tissues, the percentage of developing follicles was significantly increased at all concentrations of NGF after 1 or 7 days of culture. We observed that follicular diameter was greater at 1 and 10 ng/ml NGF after culture for 7 days than at the other concentrations but was similar to follicles cultured in α-MEM+ alone. In conclusion, NGF improved the survival of goat preantral follicles cultured in vitro in a dose-dependent manner.
Rapid Neutrophil Destruction following Phagocytosis of Staphylococcus aureus
Authors: Kobayashi Scott D. , Braughton Kevin R. , Palazzolo-Ballance Amy M. , Kennedy Adam D. , Sampaio Elizabeth , Kristosturyan Ervand , Whitney Adeline R. , Sturdevant Daniel E. , Dorward David W. , Holland Steven M. , Kreiswirth Barry N. , Musser James M. , DeLeo Frank R.
Published: June 2010

Mechanisms underlying the enhanced virulence phenotype of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are incompletely defined, but presumably include evasion of killing by human polymorphonuclear leukocytes (PMNs or neutrophils). To better understand this phenomenon, we investigated the basis of rapid PMN lysis after phagocytosis of USA300, a prominent CA-MRSA strain. Survival of USA300 clinical isolates after phagocytosis ultimately resulted in neutrophil lysis. PMNs containing ingested USA300 underwent morphological changes consistent with apoptosis, but lysed rapidly thereafter (within 6 h), whereas cells undergoing FAS-mediated apoptosis or phagocytosis-induced cell death remained intact. Phagosome membranes remained intact until the point of PMN destruction, suggesting lysis was not caused by escape of S. aureus from phagosomes or the cytolytic action of pore-forming toxins. Microarray analysis of the PMN transcriptome after phagocytosis of representative community-associated S. aureus and healthcare-associated MRSA strains revealed changes unique to community-associated S. aureus strains, such as upregulation of transcripts involved in regulation of calcium homeostasis. Collectively, the data suggest that neutrophil destruction after phagocytosis of USA300 is in part a form of programmed necrosis rather than direct lysis by S. aureus pore-forming toxins. We propose that the ability of CA-MRSA strains to induce programmed necrosis of neutrophils is a component of enhanced virulence.
Evolutionary Dynamics of Tag Mediated Cooperation with Multilevel Selection
Authors: Soule T.
Published: June 2010

Understanding the conditions and dynamics that produce cooperation in evolving systems remains a fundamental goal of evolutionary theory. Significant progress has been made in determining the conditions that support cooperation in simple models, but the evolutionary dynamics that lead from noncooperative conditions to cooperation are still poorly understood. And, in more complex models, even the conditions that support cooperation are not well defined.

In this paper we study the dynamics of the evolution of cooperation in both a simple tag-mediated cooperation model and in a more complex version of the same system in which there is multilevel competition—competition between both individuals and populations of individuals. The results show that the inclusion of multilevel competition has both quantitative effects (increasing the frequency and duration of the periods of cooperation) and qualitative effects (introducing a new stable state) on the evolutionary dynamics of cooperation.
Twee Generaties Schortinghuis Catechese in Een Tijd Van Vroomheid En Verlichting
Authors: Bosch Roel A.
Published: July 2010

Two generations Schortinghuis catechesis in a time of Piety and Enlightenment. In the history of Dutch reformed pietism, the Midwolda reverend Wilhelmus Schortinghuis is best known for his book 'Het innige christendom'. In this article, however, we focus on his far less known catechism-book, Nodige waarheden in 't herte van een christen, 1738 (Necessary truths in the heart of a Christian), and on the summary of this work edited by his sons, Verkort opstel der noodige waarheden,1769 (Abbreviated text of necessary truths). Changes in contents will be found, as well as changes in the cultural context for which the booklets were meant, Midwolda-Groningen 1738 (father) and Koudekerke-Zeeland 1769-1780 (the sons). The real author of the Abbreviated text was his son Hendrikus. Comparing the work of two generations, we may conclude, that most important changes were from a more subjective to a more objective theology.
Children's Rights in Rwanda: A Hierarchical or Parallel Model of Implementation?
Authors: Murray Cathy
Published: June 2010

The paper reports on a qualitative study, entitled Children's Rights in Rwanda, which was conducted in Kigali, Rwanda in 2007. Qualitative interviews were conducted with government ministers, senior staff in non-governmental organisations, Human Rights Commissioners, a Senior Prosecutor and the Ombudsman. Two focus groups were held with teenage pupils. The study explores the key children's rights – provision, protection and participation – enshrined in the United Nations Convention on the Rights of the Child. The research question is whether children's participation rights feature in Rwanda, a country in which children's rights to provision and to protection are still being addressed. A parallel model and a hierarchical model of implementing children's rights are proposed and the use of elite interviews discussed. A key finding is that a parallel model of implementation of children's rights is evident, with children's right to participation (at least in the public sphere) being addressed alongside children's right to provision and protection. In the private sphere, children's participation rights lag behind.
The Voice of the Child in Family Mediation: Norway and England
Authors: Haugen Gry Mette , Marples Rebecca , James Adrian , Rantalaiho Minna
Published: June 2010

In the context of the growing use of mediation in many countries to resolve parental disputes in separation and divorce, this article considers the implications of mediation practice for the rights of the child and, in particular, the tension between Article 3 and Article 12. In order to highlight the potential influence of the UNCRC in ensuring that children's article 12 rights are not compromised by the practice of mediation, which revolves around adults and parental decision-making, recent developments in England and Norway are compared in order to consider the impact of Norway's recent incorporation of the UNCRC into its domestic law.
Implementing the Social and Economic Rights of Children in Developing Countries: The Place of International Assistance and Cooperation
Authors: Wabwile Michael
Published: June 2010

It is a common feature of the treaties on international protection of economic and social rights that all states, regardless of their resource capabilities, are invited to ratify these treaties. Although all developing countries except Somalia have ratified the Convention on the Rights of the Child, the macroeconomic conditions of systemic poverty and underdevelopment in these countries indicate that there are concerns as to whether and how such states can really perform their legal obligations and guarantee the fulfilment of the Convention's economic and social rights. This article examines the emerging patterns of recent state practice in this area, with a view to identifying the contribution of international cooperation and assistance in these processes. The gist of the discussion presented here is that despite their macro-economic disadvantages, developing countries can accelerate the processes of achieving full implementation of economic and social rights if they have access to appropriate arrangements for external technical and financial cooperation and assistance. In view of this, it is suggested that there may be a legal obligation on the part of the international community to render such assistance and cooperation.
The Status Shift of Refugee Children in Settlement: An Analysis of the Norwegian Context
Authors: Archambault Josée
Published: June 2010

Drawing on the Norwegian context of the settlement of refugee families who have been granted a residence permit after applying for asylum, this article looks at how the incorporation of children's rights into domestic immigration policies appears to offer asylum-seeking children a better entry as 'active citizens' than is offered to their parents in the early stages of asylum. Later on during the asylum process, once families obtain a residence permit along with the right to settle, the focus of welfare policies shifts toward the emancipation of adults' integration as active new citizens. The article explores the reasons for that shift and identifies how the special status of refugee children seems to go off at a tangent when their whole family officially settles in the country. This transitional process highlights the duality between the state's recognition of the responsibility of parents, and the recognition of the rights of children as individuals.