bluuebunny/crossref_metadata_2025 huggingface dataset:
Convergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach
Authors: Kravchenko-Balasha Nataly , Remacle F , Gross Ayelet , Rotter Varda , Levitzki Alexander , Levine RD
Published: March 2011

Background

Surprisal analysis is a thermodynamic-like molecular level approach that identifies biological constraints that prevents the entropy from reaching its maximum. To examine the significance of altered gene expression levels in tumorigenesis we apply surprisal analysis to the WI-38 model through its precancerous states. The constraints identified by the analysis are transcription patterns underlying the process of transformation. Each pattern highlights the role of a group of genes that act coherently to define a transformed phenotype.

Results

We identify a major transcription pattern that represents a contraction of signaling networks accompanied by induction of cellular proliferation and protein metabolism, which is essential for full transformation. In addition, a more minor, "tumor signature" transcription pattern completes the transformation process. The variation with time of the importance of each transcription pattern is determined. Midway through the transformation, at the stage when cells switch from slow to fast growth rate, the major transcription pattern undergoes a total inversion of its weight while the more minor pattern does not contribute before that stage.

Conclusions

A similar network reorganization occurs in two very different cellular transformation models: WI-38 and the cervical cancer HF1 models. Our results suggest that despite differences in a list of transcripts expressed in different cancer models the rationale of the network reorganization remains essentially the same.
Gene networks associated with conditional fear in mice identified using a systems genetics approach
Authors: Park Christopher C , Gale Greg D , de Jong Simone , Ghazalpour Anatole , Bennett Brian J , Farber Charles R , Langfelder Peter , Lin Andy , Khan Arshad H , Eskin Eleazar , Horvath Steve , Lusis Aldons J , Ophoff Roel A , Smith Desmond J
Published: March 2011

Background

Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution.

Results

A total of 27 behavioral quantitative trait loci were mapped with a false discovery rate of 5%. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and also genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. Highly connected genes in the context fear modules includedPsmd6,Ube2aandUsp33, suggesting an important role for ubiquitination in learning and memory. In addition, we surveyed the architecture of brain transcript regulation and demonstrated preservation of gene co-expression modules in hippocampus and striatum, while also highlighting important differences.Rps15a, Kif3a, Stard7, 6330503K22RIK, andPlvapwere among the individual genes whose transcript abundance were strongly associated with fear phenotypes.

Conclusion

Application of our multi-faceted mapping strategy permits an increasingly detailed characterization of the genetic networks underlying behavior.
Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment
Authors: Okulski Helena , Druck Birgit , Bhalerao Sheetal , Ringrose Leonie
Published: March 2011

Background

Polycomb/Trithorax response elements (PREs) are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position.

Results

We adapted the ΦC31 site-specific integration tool to enable systematic quantitative comparison of PREs and sequence variants at identical genomic locations. In this adaptation, a miniwhite (mw) reporter in combination with eye-pigment analysis gives a quantitative readout of PRE function. We compared the Hox PRE Frontabdominal-7 (Fab-7) with a PRE from the vestigial (vg) gene at four landing sites. The analysis revealed that the Fab-7 and vg PREs have fundamentally different properties, both in terms of their interaction with the genomic environment at each site and their inherent silencing abilities. Furthermore, we used the ΦC31 tool to examine the effect of deletions and mutations in the vg PRE, identifying a 106 bp region containing a previously predicted motif (GTGT) that is essential for silencing.

Conclusions

This analysis showed that different PREs have quantifiably different properties, and that changes in as few as four base pairs have profound effects on PRE function, thus illustrating the power and sensitivity of ΦC31 site-specific integration as a tool for the rapid and quantitative dissection of elements of PRE design.
Stem cell factor and granulocyte colony-stimulating factor reduce β-amyloid deposits in the brains of APP/PS1 transgenic mice
Authors: Li Bin , Gonzalez-Toledo Maria E , Piao Chun-Shu , Gu Allen , Kelley Roger E , Zhao Li-Ru
Published: March 2011

Introduction

Alzheimer's disease (AD) is widely recognized as a serious public health problem and heavy financial burden. Currently, there is no treatment that can delay or stop the progressive brain damage in AD. Recently, we demonstrated that stem cell factor (SCF) in combination with granulocyte colony-stimulating factor (G-CSF) (SCF+G-CSF) has therapeutic effects on chronic stroke. The purpose of the present study is to determine whether SCF+G-CSF can reduce the burden of β-amyloid deposits in a mouse model of AD.

Methods

APP/PS1 transgenic mice were used as the model of AD. To track bone marrow-derived cells in the brain, the bone marrow of the APP/PS1 mice was replaced with the bone marrow from mice expressing green fluorescent protein (GFP). Six weeks after bone marrow transplantation, mice were randomly divided into a saline control group and a SCF+G-CSF-treated group. SCF in combination with G-CSF was administered subcutaneously for 12 days. Circulating bone marrow stem cells (CD117+ cells) were quantified 1 day after the final injection. Nine months after treatment, at the age of 18 months, mice were sacrificed. Brain sections were processed for immunohistochemistry to identify β-amyloid deposits and GFP expressing bone marrow-derived microglia in the brain.

Results

Systemic administration of SCF+G-CSF to APP/PS1 transgenic mice leads to long-term reduction of β-amyloid deposition in the brain. In addition, we have also observed that the SCF+G-CSF treatment increases circulating bone marrow stem cells and augments bone marrow-derived microglial cells in the brains of APP/PS1 mice. Moreover, SCF+G-CSF treatment results in enhancement of the co-localization of bone marrow-derived microglia and β-amyloid deposits in the brain.

Conclusions

These data suggest that bone marrow-derived microglia play a role in SCF+G-CSF-induced long-term effects to reduce β-amyloid deposits. This study provides insights into the contribution of the hematopoeitic growth factors, SCF and G-CSF, to limit β-amyloid accumulation in AD and may offer a new therapeutic approach for AD.
Improving RNA-Seq expression estimates by correcting for fragment bias
Authors: Roberts Adam , Trapnell Cole , Donaghey Julie , Rinn John L , Pachter Lior
Published: March 2011

The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.
Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data
Authors: Wang Joanne H , Pappas Derek , De Jager Philip L , Pelletier Daniel , de Bakker Paul IW , Kappos Ludwig , Polman Chris H ,   Australian and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene), Chibnik Lori B , Hafler David A , Matthews Paul M , Hauser Stephen L , Baranzini Sergio E , Oksenberg Jorge R
Published: March 2011

Background

Multiple sclerosis (MS) is the most common cause of chronic neurologic disability beginning in early to middle adult life. Results from recent genome-wide association studies (GWAS) have substantially lengthened the list of disease loci and provide convincing evidence supporting a multifactorial and polygenic model of inheritance. Nevertheless, the knowledge of MS genetics remains incomplete, with many risk alleles still to be revealed.

Methods

We used a discovery GWAS dataset (8,844 samples, 2,124 cases and 6,720 controls) and a multi-step logistic regression protocol to identify novel genetic associations. The emerging genetic profile included 350 independent markers and was used to calculate and estimate the cumulative genetic risk in an independent validation dataset (3,606 samples). Analysis of covariance (ANCOVA) was implemented to compare clinical characteristics of individuals with various degrees of genetic risk. Gene ontology and pathway enrichment analysis was done using the DAVID functional annotation tool, the GO Tree Machine, and the Pathway-Express profiling tool.

Results

In the discovery dataset, the median cumulative genetic risk (P-Hat) was 0.903 and 0.007 in the case and control groups, respectively, together with 79.9% classification sensitivity and 95.8% specificity. The identified profile shows a significant enrichment of genes involved in the immune response, cell adhesion, cell communication/signaling, nervous system development, and neuronal signaling, including ionotropic glutamate receptors, which have been implicated in the pathological mechanism driving neurodegeneration. In the validation dataset, the median cumulative genetic risk was 0.59 and 0.32 in the case and control groups, respectively, with classification sensitivity 62.3% and specificity 75.9%. No differences in disease progression or T2-lesion volumes were observed among four levels of predicted genetic risk groups (high, medium, low, misclassified). On the other hand, a significant difference (F = 2.75, P = 0.04) was detected for age of disease onset between the affected misclassified as controls (mean = 36 years) and the other three groups (high, 33.5 years; medium, 33.4 years; low, 33.1 years).

Conclusions

The results are consistent with the polygenic model of inheritance. The cumulative genetic risk established using currently available genome-wide association data provides important insights into disease heterogeneity and completeness of current knowledge in MS genetics.
Latest developments in seismic texture analysis for subsurface structure, facies, and reservoir characterization: A review
Authors: Gao Dengliang
Published: March 2011

In exploration geology and geophysics, seismic texture is still a developing concept that has not been sufficiently known, although quite a number of different algorithms have been published in the literature. This paper provides a review of the seismic texture concepts and methodologies, focusing on latest developments in seismic amplitude texture analysis, with particular reference to the gray level co-occurrence matrix (GLCM) and the texture model regression (TMR) methods. The GLCM method evaluates spatial arrangements of amplitude samples within an analysis window using a matrix (a two-dimensional histogram) of amplitude co-occurrence. The matrix is then transformed into a suite of texture attributes, such as homogeneity, contrast, and randomness, which provide the basis for seismic facies classification. The TMR method uses a texture model as reference to discriminate among seismic features based on a linear, least-squares regression analysis between the model and the data within an analysis window. By implementing customized texture model schemes, the TMR algorithm has the flexibility to characterize subsurface geology for different purposes. A texture model with a constant phase is effective at enhancing the visibility of seismic structural fabrics, a texture model with a variable phase is helpful for visualizing seismic facies, and a texture model with variable amplitude, frequency, and size is instrumental in calibrating seismic to reservoir properties. Preliminary test case studies in the very recent past have indicated that the latest developments in seismic texture analysis have added to the existing amplitude interpretation theories and methodologies. These and future developments in seismic texture theory and methodologies will hopefully lead to a better understanding of the geologic implications of the seismic texture concept and to an improved geologic interpretation of reflection seismic amplitude.
High Growth Rate of Benign Thyroid Nodules Bearing RET/PTC Rearrangements
Authors: Sapio Maria Rosaria , Guerra Anna , Marotta Vincenzo , Campanile Elisabetta , Formisano Raffaele , Deandrea Maurilio , Motta Manuela , Limone Paolo Piero , Fenzi Gianfranco , Rossi Guido , Vitale Mario
Published: March 2011

Context:

Benign thyroid nodules display a broad range of behaviors from a stationary size to a progressive growth. The RET/PTC oncogene has been documented in a fraction of benign thyroid nodules, besides papillary thyroid carcinomas, and it might therefore influence their growth.

Objective:

The aim of the present work was to evaluate whether RET/PTC in benign thyroid nodules associates with a different nodular growth rate.

Study Design:

In this prospective multicentric study, 125 subjects with benign nodules were included. RET rearrangements were analyzed in cytology samples; clinical and ultrasonographic nodule characteristics were assessed at the start and at the end of the study.

Results:

RET/PTC was present in 19 nodules. The difference between the mean baseline nodular volume of the RET/PTC− and RET/PTC+ nodules was not significant. After 36 months of follow-up, the RET/PTC+ group (n = 16) reached a volume higher than the RET/PTC− group (n = 90) (5.04 ± 2.67 vs. 3.04 ± 2.26 ml; P = 0.0028). We calculated the monthly change of nodule volumes as a percentage of baseline. After a mean follow-up of 36.6 months, the monthly volume increase of nodules bearing a RET rearrangement was 4.3-fold that of nodules with wild-type RET (1.83 ± 1.2 vs. 0.43 ± 1.0% of baseline volume; P < 0.0001).

Conclusions:

Benign thyroid nodules bearing RET rearrangements grow more rapidly than those with wild-type RET. Searching for RET rearrangements in benign thyroid nodules might be useful to the clinician in choosing the more appropriate and timely therapeutic option.
Effect of Exenatide on Splanchnic and Peripheral Glucose Metabolism in Type 2 Diabetic Subjects
Authors: Cersosimo E. , Gastaldelli A. , Cervera A. , Wajcberg E. , Sriwijilkamol A. , Fernandez M. , Zuo P. , Petz R. , Triplitt C. , Musi N. , DeFronzo R. A.
Published: March 2011

Objective:

Our objective was to examine the mechanisms via which exenatide attenuates postprandial hyperglycemia in type 2 diabetes mellitus (T2DM).

Study Design:

Seventeen T2DM patients (44 yr; seven females, 10 males; body mass index = 33.6 kg/m2; glycosylated hemoglobin = 7.9%) received a mixed meal followed for 6 h with double-tracer technique ([1-14C]glucose orally; [3-3H]glucose iv) before and after 2 wk of exenatide. In protocol II (n = 5), but not in protocol I (n = 12), exenatide was given in the morning of the repeat meal. Total and oral glucose appearance rates (RaT and RaO, respectively), endogenous glucose production (EGP), splanchnic glucose uptake (75 g − RaO), and hepatic insulin resistance (basal EGP × fasting plasma insulin) were determined.

Results:

After 2 wk of exenatide (protocol I), fasting plasma glucose decreased (from 10.2 to 7.6 mm) and mean postmeal plasma glucose decreased (from 13.2 to 11.3 mm) (P < 0.05); fasting and meal-stimulated plasma insulin and glucagon did not change significantly. After exenatide, basal EGP decreased (from 13.9 to 10.8 μmol/kg · min, P < 0.05), and hepatic insulin resistance declined (both P < 0.05). RaO, gastric emptying (acetaminophen area under the curve), and splanchnic glucose uptake did not change. In protocol II (exenatide given before repeat meal), fasting plasma glucose decreased (from 11.1 to 8.9 mm) and mean postmeal plasma glucose decreased (from 14.2 to 10.1 mm) (P < 0.05); fasting and meal-stimulated plasma insulin and glucagon did not change significantly. After exenatide, basal EGP decreased (from 13.4 to 10.7 μmol/kg · min, P = 0.05). RaT and RaO decreased markedly from 0–180 min after meal ingestion, consistent with exenatide's action to delay gastric emptying.

Conclusions:

Exenatide improves 1) fasting hyperglycemia by reducing basal EGP and 2) postmeal hyperglycemia by reducing the appearance of oral glucose in the systemic circulation.
Fetal Thyroid Hormone Level at Birth Is Associated with Fetal Growth
Authors: Shields Beverley M. , Knight Beatrice A. , Hill Anita , Hattersley Andrew T. , Vaidya Bijay
Published: March 2011

Context:

Thyroid function is known to play an important role in fetal neurological development, but its role in regulating fetal growth is not well established. Overt maternal and fetal thyroid disorders are associated with reduced birth weight. We hypothesized that, even in the absence of overt thyroid dysfunction, maternal and fetal thyroid function influence fetal growth.

Aim:

In normal, healthy pregnancies, we aimed to assess whether fetal thyroid hormone at birth (as measured in cord blood) is associated with fetal growth. We also aimed to study whether fetal thyroid hormone at birth is associated with maternal thyroid hormone in the third trimester.

Methods:

In 616 healthy mother-child pairs, TSH, free T4 (FT4), and free T3 (FT3) were measured in mothers at 28 wk gestation and in umbilical cord blood at birth. Birth weight, length, head circumference, and tricep and bicep skinfold thicknesses were measured on the babies.

Results:

Cord FT4 was associated with birth weight (r = 0.25; P < 0.001), length (r = 0.17; P < 0.001), and sum of skinfolds (r = 0.19; P < 0.001). There were no associations between birth measurements and either cord TSH or cord FT3. Maternal FT4 and cord FT4 were correlated (r = 0.14; P = 0.0004), and there were weaker negative associations between maternal TSH and cord FT4 (r = −0.08; P = 0.04) and FT3 (r = −0.10; P = 0.01).

Conclusion:

Associations between cord FT4 and birth size suggest that fetal thyroid function may be important in regulating fetal growth, both of skeletal size and fat. The correlation between third-trimester maternal FT4 and cord FT4 supports the belief that maternal T4 crosses the placenta even in late gestation.
Traditional male circumcision-related fatalities in the Mthatha area of South Africa
Authors: Meel B L
Published: March 2011

Traditional male circumcision is still widely practised by the Xhosa population throughout South Africa. Male circumcision is carried out mainly during summer and winter seasons. This is a retrospective record review of the male circumcision-related fatalities at Mthatha General Hospital during 2005 and 2006. The purpose of this study is to highlight the problem of circumcision-related deaths in the Mthatha area of South Africa. Twenty-five deaths related to traditional circumcisions were recorded over the period. The common causes of deaths were septicaemia (9 patients; 36%), pneumonia (5; 20%), dehydration (3; 12%), assault (3; 12%), thromboembolism (2; 8%), gangrene (2; 8%) and congestive heart failure (1; 4%). All fatalities were among black Africans with a median age of 17.56 (SD = 2.56) years. In seven deaths (28%) the young men came from the Libode District. The youngest victim was 12 years old. Most of the deaths (13; 52%) occurred in July 2006. The mortality associated with traditional male circumcision in the Mthatha area of South Africa is alarming.
Investigation on the Effects of Depth-to-Span Ratio of Tensegrity Flat Grids on Their Seismic Behavior
Authors: Valipour Masoud , Sadeghi Arjang
Published: March 2011

Tensegrity state is a stable self-equilibrated state of a spatial system that contains a non-continuous set of compressive elements (struts) inside a continuous set of self-tensioned elements (cables).

At the present study, the seismic behavior of double layer flat tensegrity grids consisted of quadrangular tensegrity prisms, have been investigated by carrying out nonlinear full transient time-history dynamic analysis. In order to determine the effects of depth-to-span ratio on seismic behavior of flat tensegrity grids, several non-linear time history analyses have been performed by ANSYS finite element program. Three 1/10, 1/12 & 1/15 grid depth-to-span ratios have been considered for investigation. Then the effects of depth-to-span ratio on seismic behavior of tensegrity flat grids have been determined. It is shown that these systems are sensitive and vulnerable against seismic excitations.

Based on the obtained results, some design recommendations have been presented regarding to the seismic behavior of these systems.
Parametric Structural Design and beyond
Authors: Rolvink Anke , van de Straat Roel , Coenders Jeroen
Published: March 2011

In order to directly make insightful which implications follow from structural design changes and to be able to adapt a structural design quickly to geometrical design changes made by the architect, the structural engineer may embed a parametric and associative design approach in the structural design process. This approach focuses on parametric modelling and the development of parametric tools which serve specific needs in the structural design process, allowing designers for instance to quickly communicate and discuss alternatives or to inform design team members of structural results of changing design parameters.

The paper presents multiple projects within these categories of parametric approaches. They are concentrated on design and analysis with the goal of presenting practical examples of these approaches in structural design which were integrated in the full design process in order to benefit from the qualities of a multi-disciplinary parametric and associative design process.
Acoustic Performance as a Design Driver: Sound Simulation and Parametric Modeling Using SmartGeometry
Authors: Peters Brady
Published: March 2011

Acoustic performance is an inevitable part of architectural design. Our sonic experience is modified by the geometry and material choices of the designer. Acoustic performance must be understood both on the level of material performance and also at the level of the entire composition. With new parametric and scripting tools performance driven design is possible. Parametric design and scripting tools can be used to explore not only singular objectives, but gradient conditions. Acoustic performance is often thought of in terms of singular performance criteria. This research suggested acoustic design can be understood in terms of gradients and multiple performance parameters. Simulation and modeling techniques for computational acoustic prediction now allow architects to more fully engage with the phenomenon of sound and digital models can be studied to produce data, visualizations, animations, and auralizations of acoustic performance.

SmartGeometry has promoted design methods and educational potentials of a performance-driven approach to architectural design through parametric modeling and scripting. The SmartGeometry workshops have provided links between engineering and architecture, analysis and design; they have provided parametric and scripting tools that can provide both a common platform, links between platforms, but importantly an intellectual platform where these ideas can mix. These workshops and conferences have inspired two projects that both used acoustic performance as a design driver. The Smithsonian Institution Courtyard Enclosure and the Manufacturing Parametric Acoustic Surfaces (MPAS) installation at SmartGeometry 2010 are presented as examples of projects that used sound simulation parametric modeling to create acoustically performance driven architecture.
Collaborative Design and Live Interaction with Parametric Models Using UbiMash
Authors: Salim Flora Dilys , Mulder Hugo , Jaworski Przemyslaw , Ransom James Willems , Cutellic Pierre , Iseki Takehiko , Leo Stefan Di , Köm Yelta
Published: March 2011

Due to the complexity of parametric modeling, it has been the task of only a handful of experts in the design team to develop, build and modify parametric models. The complexity of parametric models increases exponentially with the number of design aspects it incorporates. The ambiguity of parametric models towards the modeled design intent explains that modifying the model is often isolated as an individual exercise. Developments in physical and ubiquitous computing, however, allow for collaboration and interaction with parametric models in other ways. Communication, coordination, and interaction between parametric models and the physical and social environment are the context of this paper. The paper describes some of the projects that were outcomes of the SmartGeometry 2010 workshops. These projects are dealing with mass collaboration using Twitter, tangible interfaces, parametric design and construction coordination and geometrical interpretation of datasets.
Single and multi angle nephelometric approach to the study of coag-flocculation of coal effluent medium using Brachystegia eurycoma coagulant (BEC)
Authors: Menkiti M. , Onukwuli O.
Published: March 2011

Coag-flocculation behavior of Brachystegia eurycoma coagulant (BEC) in respect of pH variation in coal washery effluent has been investigated at room temperature using various dosages of unblended BEC. Coag-flocculation parameters such as order of reaction α, rate constant (K and Ks), coagulation period, τ1/2 e.t.c were determined. Turbidity measurement was employed using the single angle nephelometric method while BEC processing was based on work reported by Adebowale and Adebowale. Maximum parameter values are recorded at K of 6.6667×10-3m3/kg.s; dosage of (0.2 and 0.4kg/m3), pH2 and τ1/2 of 1.7293s while the minimum values are recorded at 5.00×10-4m3/kg.s, dosage of 0.3kg/m3, pH 6 and τ1/2 of 23.0572s. Minimum value of coag-flocculation efficiency is >98%; thus establishing BEC as a potential effective coag-flocculant. Parameters obtained lie within the range of previous works and confirm that the theory of perikinetics holds for coag-flocculation of the coal washery effluent using BEC at the experimental conditions.
Does the Attentional Focus Adopted by Swimmers Affect Their Performance?
Authors: Stoate Isabelle , Wulf Gabriele
Published: March 2011

The study examined effects of attentional focus on swim speed in expert swimmers. In previous studies, an external focus directed at the movement effect has been shown to enhance automaticity, relative to an internal focus directed at the body movements (or no particular focus). The swimmers in the present study were given focus instructions related to the arm stroke in crawl swimming. All participants swam 3 lengths of a 25-yard pool, once under each of 3 conditions. In the external focus condition, they were instructed to focus on “pushing the water back”, in the internal focus conditions they were asked to focus on “pulling your hands back”, and in the control condition they were not given instructions. Swim times were similar in the control and external focus conditions, but they were significantly slower with an internal focus. Furthermore, questionnaire results revealed that most swimmers focused on the overall outcome (e.g., speed) in the control condition, whereas others indicated that they focused on specific body parts. Post-hoc analyses demonstrated that those in the latter group had slower swim times in the control condition than those with a focus on the outcome. Overall, the results provide converging evidence that a body-related, internal focus hampers performance. Moreover, when movements are already controlled automatically at a high skill level (and the focus is on the outcome), external focus instructions may be superfluous.
On Accelerating Image Display for WAP Based on EBCOT
Authors: Yang Wen-Jun
Published: March 2011

At present, because of the diversity of mobile devices and low bandwidth network, traditional internet application can not work efficiently on mobile devices. For example, it is very slow to download images from internet to a mobile phone. In order to overcome this problem, we propose a new method to design a wap application gateway based on embedded block coding with optimal truncation (EBCOT), which can modify images adaptively according to different types of mobile phones. Therefore we can quickly browse images with a mobile phone even in a low-bandwidth network.
Characteristics Optimization of the DPSS in the GridFTP Environment
Authors: Feng Xinhuan , Jia Qilong , Yang Xiaoqian , Tang Ningjiu
Published: March 2011

GridFTP's advantages over the traditional model for FTP and Distributed Parallel Storage System (DPSS) set the system's foundational role in the gird environment, while GridFTP's drawbacks establish unsatisfied communications with various file system servers on the networks. A model entitled Object Processing System (OPS) was proposed to optimize the transmission capabilities to lessen excessive turnover of GridFTP Network Transmission based on DPSS. Based on the OPS model, the transmission system can get the ability for parallel data processing more smoothly and 3–5% increase on the transmission speed in some special situations.
Sustainable Bird Based Tourism in India's Remote North-East Frontier
Authors: Mohan Dhananjai , Athreya Ramana
Published: March 2011

Arunachal Pradesh is the most biodiverse Indian state situated in its north-east with the second highest breeding bird diversity in the world. Despite this, the area did not exist in bird-based tourism map till as late as a few years back owing to remoteness and lack of proper infrastructure and documentation. An innovative community based ecotourism initiative started in 2006, has catapulted one of the protected areas, namely Eagle-nest Wildlife Sanctuary of this state to one of the top birding destination of the world in a very short time. After a thorough documentation of the birdlife of the area by a qualified researchers' team, basic infrastructure was created through grants from external donors. Today the high quality low volume bird based ecotourism is completely managed by local Bugun tribal community and provides employment to few locals besides contributing to Bugun community welfare funds in a sustainable manner without any external support. The community today takes pride in the activity and also ensures that the forests are well preserved. The innovative aspect of the initiative is a complete management by the community with no support from the Government, making it truly sustainable.
U.S. Cities Get Serious About Sustainability
Authors: Attinger Steve
Published: March 2011

In a time of global climate change, thousands of cities across the United States are taking action to become more sustainable by forging alliances, collaborating on innovative projects, and developing programs to reduce greenhouse gas (GHG) emissions. In spite of significant challenges, such as decreased revenues, reduced organizational capacity, or lack of a formalized long-term sustainability vision, U.S. cities in many cases are leading the charge in the governmental arena. Due to a city's inherent ability to influence people's actions through leading by example, city sustainability efforts are already having a substantial impact in the areas of natural resource conservation and social equity. This article examines how a number of cities in the San Francisco Bay Area are heeding the call to action by reducing their carbon footprints, conserving precious natural resources, and creating more livable, sustainable cities for current and future generations to enjoy.
STAT3 controls matrix metalloproteinase-1 expression in colon carcinoma cells by both direct and AP-1-mediated interaction with the MMP-1 promoter
Authors: Zugowski Constance , Lieder Franziska , Müller Annekatrin , Gasch Josephine , Corvinus Florian M. , Moriggl Richard , Friedrich Karlheinz
Published: March 2011

Aberrant activation of STAT3 in colorectal carcinoma (CRC) tissue is correlated with elevated expression of matrix metalloproteinase-1 (MMP-1). We analyzed transcriptional regulation of the human MMP-1 promoter in CRC cells by tyrosine phosphorylated (pY-) STAT3. One of six putative STAT binding elements within a 4.3 kb MMP-1 trancriptional promoter fragment showed a particular high affinity for STAT3in vitro. However, the most profound regulatory influence on MMP-1 promoter activity resides in a proximal region relative to the transcriptional start, bearing a pair of putative binding sites for STAT3 and AP-1. Mutational analysis of the combined STAT3/AP-1 recognition element revealed that the integrity of the STAT3 binding site is necessary, but not sufficient for both DNA interaction and transcriptional regulation by activated STAT3. Instead, the adjacent AP-1 site was essential for pY-STAT3-mediated transcription on the MMP-1 promoter. DNA-protein binding assays provided strong evidence for complex formation of STAT3 and c-Jun governed by protein-protein contacts. We observed striking coincidence for concerted aberrant activation of both STAT3 and AP-1 in human colon cancer specimens. This finding supports the notion that the combination of inappropriate STAT3 and AP-1 activities drives elevated MMP-1 expression and tissue invasion in colorectal cancer and is of clinical relevance.
A case of consistent discrepancies between urine and blood human chorionic gonadotropin measurements
Authors: Albersen Arjan , Kemper-Proper Evelien , Thelen Marc H.M. , Kianmanesh Rad Noush A. , Hoedemaeker Robert F. , Boesten Lianne S.M.
Published: March 2011

Background: Our laboratory was confronted with two successive urine samples from a single patient which tested positive for human chorionic gonadotropin (hCG) when tested with both qualitative and quantitative assays, combined with no detectable hCG in corresponding plasma samples.

Methods: Serial dilution and recovery experiments were performed in order to investigate the presence of interfering substances or a high-dose hook effect. The ovarian cysts that were removed from this patient were immunohistochemically stained using polyclonal anti-human hCG antibodies. Furthermore, a urine sample was sent to the USA hCG Reference Service for hCG variant analysis.

Results: Dilution and recovery experiments in urine and plasma samples were unremarkable. The biopsy stained negative for human hCG and free β-subunit. hCG isoform analysis in the urine sample revealed that approximately 87.5% of the immunoreactive hCG lacked the β-subunit C-terminal peptide (CTP).

Conclusions: We report a rare case in which two successive urine samples test positive for hCG whereas in corresponding plasma samples hCG is undetectable. The majority of the total hCG contained a degraded form of β-subunit that lacks the CTP. This hCG variant, possibly of pituitary origin, is thought to have an extreme fast clearance rate possibly explaining the discordance between the hCG results in urine and plasma samples.
The Use of Topography as an Indicator of Ground Water Flow Direction and Its Implications for Due Diligence
Authors: Blauvelt Robert P. , Fullmer David
Published: March 2011

Topography often is used as a quick and preliminary method to identify local and regional ground water flow patterns within the upper-most saturated interval. This approach usually is applied in designing shallow monitoring networks at properties or in areas where little to no site specific hydrogeologic data are available. Perhaps the most problematic application of this method is in due diligence. Critical business decisions regularly are made based on potential environmental impacts from surrounding parcels using topographic presumptions about upgradient or downgradient ground water flow directions. However, what most practitioners fail to realize is that topography is a reliable predictor of ground water flow only under a fairly narrow range of physiographic conditions. To assist in determining when topography should be used to evaluate ground water flow direction within the upper-most saturated interval, we have developed an evaluation matrix that allows the investigator, who may have only modest hydrogeologic training, to rapidly identify when topography can be appropriately and reliably used to determine shallow ground water flow directions. Limitations on the use of the matrix are provided as well as suggestions for obtaining site specific data that allow for a more definitive understanding of shallow ground water flow without the need for intrusive field work.
Bankruptcy Law and Entrepreneurship
Authors: Primo David M. , Green Wm Scott
Published: March 2011

We explore the link between bankruptcy laws and entrepreneurship in the U.S states. Using two measures of entrepreneurship capturing alternative conceptions of this phenomenon, we find that bankruptcy laws more favorable to debtors lead to increased levels of self-employment in some cases, though the effect is non-monotonic in the level of assets protected by the law. Counter to the conventional wisdom, however, more generous laws are linked to lower levels of “innovative” entrepreneurship. The paper concludes by suggesting why developing more refined measures of entrepreneurship is necessary to better understand the impact of public policies on this most vital of human activities.
Laminar convective heat transfer for in-plane spiral coils of noncircular cross sections ducts: A computational fluid dynamics study
Authors: Kurnia Jundika , Sasmito Agus , Mujumdar Arun
Published: March 2011

The objective of this study was to carry out a parametric study of laminar
flow and heat transfer characteristics of coils made of tubes of several
different cross-sections e.g. square, rectangular, half-circle, rectangular
and trapezoidal. For the purpose of ease of comparison, numerical experiments
were carried out base on a square-tube Reynolds number of 1000 and a fixed
fluid flow rate while length of the tube used to make coils of different
diameter and pitch was held constant. A figure of merit was defined to
compare the heat transfer performance of different geometry coils;
essentially it is defined as total heat transferred from the wall to the
surroundings per unit pumping power required. Simulations were carried out
for the case of constant wall temperature as well as constant heat flux. In
order to allow reasonable comparison between the two different boundary
conditions - constant wall temperature and constant wall heat flux - are
tested; the uniform heat flux boundary condition was computed by averaging
the heat transferred per unit area of the tube for the corresponding constant
wall temperature case. Results are presented and discussed in the light of
the geometric effects which have a significant effect on heat transfer
performance of coils.
Rectified ethanol production cost analysis
Authors: Budimir Nikola , Jaric Marko , Jacimovic Branislav , Genic Srbislav , Jacimovic Nikola
Published: March 2011

This paper deals with the impact of the most important factors of the total
production costs in bioethanol production. The most influential factors are:
total investment costs, price of raw materials (price of biomass, enzymes,
yeast), and energy costs. Taking into account these factors, a procedure for
estimation total production costs was establish. In order to gain insight
into the relationship of production and selling price of bioethanol, price of
bioethanol for some countries of the European Union and the United States are
given.
An improved computational method for non isothermal resin transfer moulding simulation
Authors: Saad Aouatif , Echchelh Adil , Hattabi Mohammed , El Ganaoui
Published: March 2011

The optimization in the simulation time of non-isothermal filling process
without losing effectiveness remains a challenge in the resin transfer
moulding process simulation. We are interested in this work on developing an
improved computational approach based on finite element method coupled with
control volume approach. Simulations can predict the position of the front of
resin flow, pressure and temperature distribution at each time step. Our
optimization approach is first based on the modification of conventional
control volume/finite element method, then on the adaptation of the iterative
algorithm of conjugate gradient to Compressed Sparse Row (CSR) storage
scheme. The approach has been validated by comparison with available results.
The proposed method yielded smoother flow fronts and reduced the error in the
pressure and temperature pattern that plagued the conventional fixed grid
methods. The solution accuracy was considerably higher than that of the
conventional method since we could proceed in the mesh refinement without a
significant increase in the computation time. Various thermal engineering
situations can be simulated by using the developed code.
Influence of upstream flow characteristics on the reattachment phenomenon in shallow cavities
Authors: Madi Arous , Mataoui Amina , Bouahmed Zahia
Published: March 2011

The influence of the upstream flow characteristics on the behavior of the
flow over a shallow cavity and on the reattachment phenomenon is examined in
this paper. Accordingly, a comparison of the cavity?s flow structure is
performed for two different upstream flows: the wall jet flow and the
boundary layer flow. The wall jet possesses a particular structure with two
regions: an inner layer analogous to that of a boundary layer and an outer
layer similar to that of a free jet; this layer is an additional source of
turbulence production in addition to that of the inner shear layer. The
present study interested to the effect of this external layer on the shallow
cavity?s flow. The numerical approach is based on the low Reynolds
stress-omega turbulence model. Fluent 6.3 and the pre-processor Gambit 2.3
are used for the computation. The numerical results indicate that the flow
structure is very sensitive to the upstream flow?s characteristics. Indeed,
for the same Reynolds number and the same boundary layer thickness at the
cavity leading edge, the cavity flow structure in a wall jet upstream flow
case differs considerably from that of a boundary layer upstream flow. The
most important finding is the earlier reattachment process in the wall jet
inflow case, where an important reduction of the reattachment length is
observed compared to that of a cavity under a boundary layer flow.
Rhythmic Diurnal Gene Expression in Human Adipose Tissue From Individuals Who Are Lean, Overweight, and Type 2 Diabetic
Authors: Otway Daniella T. , Mäntele Simone , Bretschneider Silvia , Wright John , Trayhurn Paul , Skene Debra J. , Robertson M. Denise , Johnston Jonathan D.
Published: March 2011

OBJECTIVE

Previous animal studies suggest a functional relationship between metabolism, type 2 diabetes, and the amplitude of daily rhythms in white adipose tissue (WAT). However, data interpretation is confounded by differences in genetic background and diet or limited sampling points. We have taken the novel approach of analyzing serial human WAT biopsies across a 24-h cycle in controlled laboratory conditions.

RESEARCH DESIGN AND METHODS

Lean (n = 8), overweight/obese (n = 11), or overweight/obese type 2 diabetic (n = 8) volunteers followed a strict sleep–wake and dietary regimen for 1 week prior to the laboratory study. They were then maintained in controlled light–dark conditions in a semirecumbent posture and fed hourly during wake periods. Subcutaneous WAT biopsies were collected every 6 h over 24 h, and gene expression was measured by quantitative PCR.

RESULTS

Lean individuals exhibited significant (P < 0.05) temporal changes of core clock (PER1, PER2, PER3, CRY2, BMAL1, and DBP) and metabolic (REVERBα, RIP140, and PGC1α) genes. The BMAL1 rhythm was in approximate antiphase with the other clock genes. It is noteworthy that there was no significant effect (P > 0.05) of increased body weight or type 2 diabetes on rhythmic gene expression.

CONCLUSIONS

The robust nature of these rhythms and their relative phasing indicate that WAT now can be considered as a peripheral tissue suitable for the study of in vivo human rhythms. Comparison of data between subject groups clearly indicates that obesity and type 2 diabetes are not related to the amplitude of rhythmic WAT gene expression in humans maintained under controlled conditions.
Diabetes and the Risk of Developing Parkinson’s Disease in Denmark
Authors: Schernhammer Eva , Hansen Johnni , Rugbjerg Kathrine , Wermuth Lene , Ritz Beate
Published: March 2011

OBJECTIVE

Insulin contributes to normal brain function. Previous studies have suggested associations between midlife diabetes and neurodegenerative diseases, including Parkinson’s disease. Using Danish population registers, we investigated whether a history of diabetes or the use of antidiabetes drugs was associated with Parkinson’s disease.

RESEARCH DESIGN AND METHODS

From the nationwide Danish Hospital Register hospital records, we identified 1,931 patients with a first-time diagnosis of Parkinson’s disease between 2001 and 2006. We randomly selected 9,651 population control subjects from the Central Population Registry and density matched them by birth year and sex. Pharmacy records comprising all antidiabetes and anti-Parkinson drug prescriptions in Denmark were available. Odds ratios (ORs) were estimated by logistic regression models.

RESULTS

Having diabetes, as defined by one or more hospitalizations and/or outpatient visits for the condition, was associated with a 36% increased risk of developing Parkinson’s disease (OR 1.36 [95% CI 1.08–1.71]). Similarly, diabetes defined by the use of any antidiabetes medications was associated with a 35% increased Parkinson’s disease risk (1.35 [1.10–1.65]). When diabetes was defined as the use of oral antidiabetes medications, effect estimates were stronger in women (2.92 [1.34–6.36]), whereas when diabetes was defined as any antidiabetes drug prescription, patients with early-onset Parkinson’s disease were at highest risk (i.e., Parkinson’s disease diagnosed before the age of 60 years; 3.07 [1.65–5.70]).

CONCLUSIONS

We found that a diagnosis of, or treatment received for, diabetes was significantly associated with an increased risk of developing Parkinson’s disease, especially younger-onset Parkinson’s disease. Our results suggest a common pathophysiologic pathway between the two diseases. Future studies should take age at Parkinson’s disease onset into account.