bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of carbonic anhydrase and HIF-1α in Wilms tumours
Authors: Dungwa Josiah V , Hunt Linda P , Ramani Pramila
Published: September 2011

Background

Overexpression of carbonic anhydrase (CA IX) is associated with poor survival in several adult-type cancers but its expression is undocumented in Wilms tumour (WT), the most common tumour of the paediatric kidney.

Methods

CA9 expression was measured using polymerase chain reaction (PCR) in 13 WTs and matched-paired non-neoplastic kidneys (NKs). CA IX and hypoxia-inducible factor-1 α-subunit (HIF-1α) protein were quantified in 15 matched-paired WTs and NKs using enzyme-linked immunosorbent assays. CA IX and HIF-1α were localised by immunostaining tissue sections of 70 WTs (untreated WTs, n = 22; chemotherapy-treated WTs, n = 40; relapsed/metastatic WTs, n = 8). CA IX-positive untreated WTs (n = 14) were immunostained for vascular endothelial growth factor (VEGF), glucose transporter-1 (GLUT1) and CD31. Double staining for CA IX and CD31 was performed in WTs (n = 14).

Results

CA9 full length (FL) was significantly up-regulated in WTs compared to NKs (p = 0.009) by real-time PCR. Conventional PCR showed expression of alternative splice variant in all NKs and WTs but FL in WTs only. WTs showed a 2-fold increase in CA IX protein over NKs (p = 0.01). HIF-1α levels were up-regulated in WTs compared to NKs, although the difference was not statistically significant (p = 0.09). CA IX and HIF-1α immunolocalisation were observed in 63% and 93% of WTs, respectively. The median fraction of cells staining positively for CA IX and HIF-1α was 5% and 22%, respectively. There was no significant association between the expression of either CA IX or HIF-1α and clinicopathological variables in WTs resected following chemotherapy. VEGF and GLUT1 immunoreactivity was seen in 94% and 100% with the median fraction of 10% and 60% respectively. Co-expression and co-localisation of all four hypoxia markers was seen in 7/14 and 6/14 cases respectively. CA IX was seen in well vascularised areas as well as in the peri-necrotic areas.

Conclusions

Carbonic anhydrase 9 (mRNA and protein), and HIF-1α protein are overexpressed in a significant portion of WTs. No significant association was detected between the expression of either CA IX or HIF-1α and clinicopathological variables in WTs resected following chemotherapy. Cellular localisation studies in untreated WTs suggest that CA IX and HIF-1α are regulated by hypoxia and non-hypoxia mechanisms.
Metabolic engineering of the L-phenylalanine pathway in Escherichia coli for the production of S- or R-mandelic acid
Authors: Sun Zhoutong , Ning Yuanyuan , Liu Lixia , Liu Yingmiao , Sun Bingbing , Jiang Weihong , Yang Chen , Yang Sheng
Published: September 2011

Background

Mandelic acid (MA), an important component in pharmaceutical syntheses, is currently produced exclusively via petrochemical processes. Growing concerns over the environment and fossil energy costs have inspired a quest to develop alternative routes to MA using renewable resources. Herein we report the first direct route to optically pure MA from glucose via genetic modification of the L-phenylalanine pathway in E. coli.

Results

The introduction of hydroxymandelate synthase (HmaS) from Amycolatopsis orientalis into E. coli led to a yield of 0.092 g/L S-MA. By combined deletion of competing pathways, further optimization of S-MA production was achieved, and the yield reached 0.74 g/L within 24 h. To produce R-MA, hydroxymandelate oxidase (Hmo) from Streptomyces coelicolor and D-mandelate dehydrogenase (DMD) from Rhodotorula graminis were co-expressed in an S-MA-producing strain, and the resulting strain was capable of producing 0.68 g/L R-MA. Finally, phenylpyruvate feeding experiments suggest that HmaS is a potential bottleneck to further improvement in yields.

Conclusions

We have constructed E. coli strains that successfully accomplished the production of S- and R-MA directly from glucose. Our work provides the first example of the completely fermentative production of S- and R-MA from renewable feedstock.
Tuning the electronic transport properties of graphene through functionalisation with fluorine
Authors: Withers Freddie , Russo Saverio , Dubois Marc , Craciun Monica F
Published: September 2011

We demonstrate the possibility to tune the electronic transport properties of graphene mono-layers and multi-layers by functionalisation with fluorine. For mono-layer samples, with increasing the fluorine content, we observe a transition from electronic transport through Mott variable range hopping (VRH) in two dimensions to Efros-Shklovskii VRH. Multi-layer fluorinated graphene with high concentration of fluorine show two-dimensional Mott VRH transport, whereas CF0.28 multi-layer flakes exhibit thermally activated transport through near neighbour hopping. Our experimental findings demonstrate that the ability to control the degree of functionalisation of graphene is instrumental to engineer different electronic properties in graphene materials.
Ethnozoology in Brazil: current status and perspectives
Authors: Alves Rômulo RN , Souto Wedson MS
Published: September 2011

Ancient connections between animals and human are seen in cultures throughout the world in multiple forms of interaction with the local fauna that form the core of Ethnozoology. Historically, ethnozoological publications grew out of studies undertaken in academic areas such as zoology, human ecology, sociology and anthropology - reflecting the interdisciplinary character of this discipline. The rich fauna and cultural diversity found in Brazil, with many different species of animals being used for an extremely wide diversity of purposes by Amerindian societies (as well as the descendents of the original European colonists and African slaves), presents an excellent backdrop for examining the relationships that exist between humans and other animals. This work presents a historical view of ethnozoological research in Brazil and examines its evolution, tendencies, and future perspectives. In summary, literature researches indicated that ethnozoology experienced significant advances in recent years in Brazil, although from a qualitative point of view improvement is still needed in terms of methodological procedures, taxonomic precision, and the use of quantitative techniques. A wide range of methodologies and theories are available in different areas of learning that can be put to good use in ethnozoological approaches if the right questions are asked. The challenges to studying ethnozoology in Brazil are not insignificant, and the tendencies described in the present study may aid in defining research strategies that will maintain the quantitative growth observed in the recent years but likewise foster needed qualitative improvements.
The presence of a lipoma in the Eustachian tube: a case report
Authors: Liu Zhuofu , Wang Dehui , Liu Quan
Published: September 2011

Introduction

The incidence of lipoma in the Eustachian tube is very rare, and to the best of our knowledge, has not been reported in the literature. Tumors that form in the cartilaginous portion of the Eustachian tube can be successfully removed by an endoscopic approach.

Case presentation

We report an incidentally-detected lipoma of the Eustachian tube in a 34-year-old Asian woman with a six-year history of persistent otitis media in her right ear. Our patient underwent surgery five years ago for the possibility of a choanal polyp, but her ear symptoms continued to be problematic following the surgery. Our patient was examined at our hospital, and computed tomography revealed a well-defined, hypodense, non-enhancing lesion involving the right Eustachian tube, measuring 1.6 × 2.4 cm. The mass was excised using an endoscopic approach, and was found to originate from the cartilaginous portion of the Eustachian tube. The tumor was sent for histopathologic evaluation. The postoperative course went smoothly, and our patient recovered during follow-up over the next five months.

Conclusion

Lipoma of the Eustachian tube is very rare compared with other tumors. Improved radiologic modalities aid the diagnosis of this benign tumor. Endoscopic removal of the tumor is possible and has helped in early recovery.
Lymphocyte-Depleted Classical Hodgkin's Lymphoma: A Comprehensive Analysis From the German Hodgkin Study Group
Authors: Klimm Beate , Franklin Jeremy , Stein Harald , Eichenauer Dennis A. , Haverkamp Heinz , Diehl Volker , Fuchs Michael , Borchmann Peter , Engert Andreas
Published: September 2011

Purpose

To investigate the clinical characteristics and treatment outcome of patients with lymphocyte-depleted classical Hodgkin's lymphoma (LDCHL) compared with other histologic subtypes of Hodgkin's lymphoma (HL).

Patients and Methods

From a total of 12,155 evaluable patients with biopsy-proven HL treated within the German Hodgkin Study Group trials HD4 to HD15, 10,019 patients underwent central expert pathology review. Eighty-four patients with LDCHL (< 1%) were identified and confirmed. The median follow-up time was 67 months.

Results

Patients with LDCHL, compared with patients with other histologic subtypes, presented more often with advanced disease (74% v 42%, respectively; P < .001) and “B” symptoms (76% v 41%, respectively; P < .001). Other risk factors were also more frequent in patients with LDCHL. Complete remission or unconfirmed complete remission was achieved in 82% of patients with LDCHL compared with 93% of patients with other HL subtypes (P < .001), and more patients with LDCHL had progressive disease. At 5 years, progression-free survival (PFS) and overall survival (OS) were significantly lower in patients with LDCHL compared with patients with other HL subtypes (PFS, 71% v 85%, respectively; P < .001; OS, 83% v 92%, respectively; P = .0018). However, when analyzing the subgroup of patients who underwent treatment with intensified or dose-dense bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone, patients with LDCHL (n = 39) had similar outcomes when compared with patients with other subtypes of HL (n = 3,564; P = .61).

Conclusion

LDCHL has a different pattern from other HL subtypes with more clinical risk factors at initial diagnosis and significantly poorer prognosis. Patients with LDCHL should be treated with modern dose-intense treatment strategies.
Inflows of Capital to Developing Countries in the 1990s
Authors: Calvo Guillermo A , Leiderman Leonardo , Reinhart Carmen M
Published: September 2011

Half a decade has passed since the resurgence of international capital flows to many developing countries and history has, once again, shown that foreign investment is prone to repeated booms and busts. Mexico's 1994 crisis is but a recent example that highlights the vulnerability of capital-importing countries to abrupt reversals; thus, an aim of policy is to reduce that vulnerability. This paper discusses the principal causes, facts, and policies that have characterized capital inflows to Asia and Latin America. In particular, the authors examine what policies have proved useful in protecting these economies from the vagaries of international capital flow.
Bias in the Consumer Price Index: What Is the Evidence?
Authors: Moulton Brent R
Published: September 2011

Recent research has suggested that the upward bias of the U.S. consumer price index may be significant, and correcting the biases would have important long-run effects on the federal budget deficit. The author describes the sampling procedures used in constructing the consumer price index, and gives simple examples of formula bias and quality adjustment. He then reviews the empirical evidence, attempting to show which biases are reliably estimated and which estimates of bias are based on extrapolation and guesswork. The author discusses possibilities for further research leading to potential improvements in the consumer price index.
Classroom Games: Information Cascades
Authors: Anderson Lisa R , Holt Charles A
Published: September 2011

This paper describes how to set up a classroom exercise in which students see private signals and make public decisions in sequence. A pattern of conforming decisions in this context is called an information cascade. Once a cascade starts, it is rational for students to ignore their private signals and follow the pattern of previous decisions. This exercise provides an interactive framework that facilitates discussions of Bayes's rule, information, and social conformity.
In Honor of Lawrence H. Summers, Winner of the John Bates Clark Medal
Authors: Poterba James M
Published: September 2011

This paper summarizes the research contributions of Lawrence Summers, who was awarded the 1993 John Bates Clark Medal by the American Economic Association. It focuses on research in four subfields of economics: public finance, labor economies, financial economies, and macroeconomics. The paper describes the substantive importance and impact of Summers's research in each area, as well as the general research style and strategy that runs through his work.
High-sensitivity troponin assays in the evaluation of patients with acute chest pain in the emergency department
Authors: Christ Michael , Bertsch Thomas , Popp Steffen , Bahrmann Philipp , Heppner Hans-Jürgen , Müller Christian
Published: September 2011

Evaluating patients with acute chest pain presenting to the emergency department remains an ongoing challenge. The spectrum of etiologies in acute chest pain ranges from minor disease entities to life-threatening diseases, such as pulmonary embolism, acute aortic dissection or acute myocardial infarction (MI). The diagnosis of acute MI is usually made integrating the triad of patient history and clinical presentation, readings of 12-lead ECG and measurement of cardiac troponins (cTn). Introduction of high-sensitivity cTn assays substantially increases sensitivity to identify patients with acute MI even at the time of presentation to the emergency department at the cost of specificity. However, the proportion of patients presenting with cTn positive, non-vascular cardiac chest pain triples with the implementation of new sensitive cTn assays increasing the difficulty for the emergency physician to identify those patients who are at need for invasive diagnostics. The main objectives of this mini-review are 1) to discuss elements of disposition decision made by the emergency physician for the evaluation of chest pain patients, 2) to summarize recent advances in assay technology and relate these findings into the clinical context, and 3) to discuss possible consequences for the clinical work and suggest an algorithm for the clinical evaluation of chest pain patients in the emergency department.
Refiner bleaching in a peroxide-based ATMP process compared with conventional bleaching
Authors: Gorski Dmitri , Johansson Lars , Engstrand Per
Published: September 2011

The aim of this study was to compare refiner bleaching with conventional laboratory bleaching by means of hydrogen peroxide and magnesium hydroxide. Refiner bleaching in this study was a part of the ATMP (advanced thermo mechanical pulping) process, in which bleaching chemicals are added to the first stage refiner. Unbleached reference pulp which underwent similar mechanical treatment as refiner bleached pulp was used for laboratory bleaching. Bleaching efficiency was found to be almost equal for pilot scale refiner bleaching and conventional laboratory bleaching. A brightness increase of 10 ISO% was reached with addition of 26 kg t-1hydrogen peroxide leading to a final brightness of 66 ISO% using both methods. Slightly more COD (52 kg t-1compared with 46 kg t-1) was generated in refiner bleaching compared with conventional laboratory bleaching to equal brightness with the same chemicals added.
Source-Studies Approach to Michael Nyman’s Score for "The Draughtsman’s Contract"
Authors: Cooper David , Sapiro Ian
Published: September 2011

The composer Michael Nyman has donated a unique collection of his original sound materials and other documentation to the University of Leeds on long-term loan for scholarly investigation. There are more than 500 individual items in the archive, which includes film, television and concert music, as well as associated items of paperwork, and the films directed by Peter Greenaway feature strongly in the collection. Evidence for the underlying creative processes in film composition can be found within the source materials which include the source recordings and stereo mixdowns of cues, materials often disposed of by film and television companies after a film’s release or TV program's broadcast. This article questions the extent to which the surviving audio and supporting documentary materials reflect the development of the score and the relationships between Nyman’s music and Greenaway’s images as exemplified in the non-mainstream film "The Draughtsman’s Contract".
Robust Inversion of Time-domain Electromagnetic Data: Application to Unexploded Ordnance Discrimination
Authors: Beran Laurens , Billings Stephen , Oldenburg Doug
Published: September 2011

We invert time-domain electromagnetic data for the purpose of discriminating between buried unexploded ordnance (UXO) and non-hazardous metallic clutter. The observed secondary magnetic field radiated by a conductor is forward modeled as a linear combination of decaying, orthogonal dipoles. We show via a perturbation analysis that errors in the measurement of sensor position propagate to non-normal errors on the observed data. A least squares (L2) inversion assumes normal errors on the data, so non-normal errors have the potential to bias dipole parameter estimates. In contrast, robust norms are designed to downweight the effect of outlying (noisy) data and so can provide useful parameter estimates when there is a non-normal component to the noise.

When positional errors are modeled as independent Gaussian perturbations, we find that weighted least squares and robust inversions have comparable performance. Both inversion techniques estimate data uncertainties from observed data, and this has the effect of making the least squares inversion robust to outliers. However, when simulated errors are correlated, robust inversion with a bisquare norm provides a marked improvement over L2 inversion. Application of robust inversion to real data sets from Camp Sibert, Alabama produced an incremental improvement to the initial L2 inversion, identifying outlying ordnance items and improving discrimination performance.
Feasibility of UASB/trickling filter systems without final clarifiers for the treatment of domestic wastewater in small communities in Brazil
Authors: Chernicharo C. A. L. , Almeida P. G. S.
Published: September 2011

The paper analyses the concept and performance of different configurations of compact UASB/TF systems, without the final clarification stage, in relation to the removal of organic matter. The experiments were carried out in two sets of UASB/TF systems operating without secondary clarifiers, as follows: (i) four shallow (2.50 m height) TFs, each one filled with a different packing material; and (ii) two deep (4.20 m height) TFs, one filled with polyethylene corrugated sheets and the other with mixed polyethylene and sponge sheets. For the conditions tested (different packing material in shallow and deep TF), the UASB/TF systems had consistently complied (90 to 100% of the results) with the Brazilian discharge standards regarding to BOD, COD, and TSS parameters. The average BOD, COD and TSS effluent concentrations stayed below 40 mg BOD L−1, 100 mg COD L−1 and 50 mg TSS L−1, respectively. UASB/TF systems can constitute an attractive alternative for domestic wastewater treatment in small communities in developing countries, especially considering its operational simplicity and very low running costs.
Prevalence of Typhoid fever among the Children in a Semi Urban Area of Bangladesh
Authors: Rahman AKMM , Ahmad M , Begum RS , Hossain MZ , Hoque SA , Matin A , Yeasmin L , Manum MGS
Published: September 2011

Context: In Bangladesh, typhoid fever is a round the year problem which sometimes take epidemic proportions. The reason behind such occurrences are unsafe water supply, defective sewage system and unhygienic food handling practice. This study was designed to find out the prevalence of typhoid fever and related factors like sanitation facilities and food practice among the children of low income group people living in Kamrangir char and its adjacent areas in the semi urban Dhaka. Methodology: Data were collected from June 2009 to May 2010, from a sample of 96 patients with fever of more than seven days duration, who presented in the paediatric outpatient department of Dhaka Medical College Hospital, Dhaka. Detailed history, comprehensive physical examination and other relevant informations of the patients were recorded by following standard procedures. A raised anti O level with titre of >1:160 as well as other blood parameters were considered significant of having typhoid fever. Results: This study shows that 84(87.50%) patients had typhoid fever based on clinical examination and serological test results (widal test). It was observed that prevalence of enteric fever was high among the patients of school going age group (66.67%), habituated with unsafe drinking water (58.33%) and junk foods (72.92%). Statistical analysis showed that SSC level education in the parents who remain outside during the major part of the day for their livelihood had significant positive relationship with prevalence of typhoid fever. It was concluded that prevalence of typhoid fever was high among the children of school going age, who consume unsafe drinking water and food from outside source. Keywords: Typhoid fever; semi urban area; children. DOI: http://dx.doi.org/10.3329/jdmc.v20i1.8570 J Dhaka Med Coll. 2011; 20(1) :37-43
Distribution of ABO and Rh blood Groups Among Tribal Population of Sylhet, Bangladesh
Authors: Begum D , Amin MR , Khatun F , Ahmed SS , Sinha SK , Rahman MA
Published: September 2011

Context: Distribution of blood groups varies among ethnic groups throughout the world. Blood groups of tribals should be determined as they are ethnically different from the main population of Bangladesh. Materials and Methods: To observe the distribution pattern of ABO and Rh blood groups and to compare the groups among Manipuris (1434) and Khasias (204), this descriptive crosssectional study was conducted in the Department of Physiology, Dhaka Medical College, Dhaka, from July 2006 to June 2007. Manipuris were divided in Bishnupriya (658), Meitei (460) and Meitei-Pangan (316) according to their ethnic origin. Data were collected from Manipuri (12) and Khasia (2) localities selected by systematic random sampling. ABO and Rh blood groups of participants were determined by the antigen antibody agglutination test of slide method. Data from groups were compared by chi-square test with 95% confidence limit. Results: There are significant variations in the distribution of ABO (p<0.001) and Rh (p<0.001) blood groups among all study groups. Blood group A was more frequent among Meiteis (40%) and Meitei-Pangans (42.41%) whereas blood group O was more frequent in Bishnupriyas (47.72%) and Khasias (35.29%). In all tribal communities, AB blood group was least frequent. Rh positive participants (97.43%) were more than Rh negative (2.57%). In Khasias, no Rh negative group was found. Rh negativity was more in Bishnupriyas (4.9%) which was significantly higher than Meiteis (0.87%) and Meitei-Pangans. (1.94%) (X2=16.7; p<0.001). Conclusion: Distribution of ABO blood groups varies among the Manipuris and Khasias. Significant variation is also found in three groups of Manipuris and the distribution corresponds with the pattern of their ancestors. Key words: ABO blood group; Rh blood group; tribal population; Sylhet. DOI: http://dx.doi.org/10.3329/jdmc.v20i1.8581 J Dhaka Med Coll. 2011; 20(1) :44-50
Evaluation of Haematuria and Use of Phase Contrast Microscope: A Short Review
Authors: Sultana T , Sultana T , Rahman MQ , Ahmed ANN
Published: September 2011

For centuries physicians have been using urine as one of the non-invasive means for assessing diseases. Haematuria is a frequently encountered abnormality in clinical practice. Haematuria may have either a glomerular or a non-glomerular origin. The morphological study of urinary red cells by Phase-Contrast Microscopy (PCM) is a useful diagnostic marker for glomerular bleeding, if correctly interpreted and used. Today, urinalysis and in particular identification of red cells morphology by Phase-Contrast Microscopy has been a widely accepted technique for determining the site of haematuria. A short review on haematuria and Phase-Contrast Microscopy are presented here for updating knowledge and academic interest. Key words: Phase-contrast microscope; Haematuria; Dysmorphic red cell. DOI: http://dx.doi.org/10.3329/jdmc.v20i1.8584 J Dhaka Med Coll. 2011; 20(1) :63-67
It was a Supraclinoid Stenosis Rather Than Extracranial Carotid Stenosis
Authors: Chowdhury RN , Rahman KM , Khan SU , Sarker RN , Nabi S , Siddiqui MR , Mohammad QD
Published: September 2011

Carotid stenosis, both intracranial and extracranial is a significant risk factor for transient ischaemic attack and ischaemic stroke. Significant carotid stenosis increases the risk of artery to artery embolization. Duplex Ultrasound (USD) is a screening test for identification and grading of carotid stenosis. USD is less sensitive and specific than cerebral Digital Subtraction Angiogram (DSA) for evaluation of carotid stenosis. USD might underestimate or overestimate degree of carotid stenosis. Here a case is presented where USD found bilateral significant extracranial carotid stenosis, whereas DSA reported no right common carotid artery and left common carotid artery bifurcation stenosis rather there was significant 70% supraclinoid right internal carotid artery stenosis. Key words: Carotid stenosis; Supraclinoid stenosis; Duplex ultrasound examination; Digital subtraction angiogram DOI: http://dx.doi.org/10.3329/jdmc.v20i1.8586 J Dhaka Med Coll. 2011; 20(1) :75-77
Exit Strategy
Authors: Gottschalk P.
Published: September 2011

Outsourcing contracts do not last forever. And sooner or later, the client has to think of “where to go by the end of this contract?” and “how to get there?” Resources are necessary no matter if the decision is renegotiating with current supplier, changing supplier, or bringing IT home. Sometimes, unexpected events occur, and these needs require resources as well.
Cooperation Design System Based on Mobile-C Agent Platform
Authors: Yu Bo , Zhang Zi Xian , Feng Yi Xiong , Diago Luis Ariel , Hagiwara Ichiro
Published: September 2011

Over the past decades, Distributed Systems (DS) have been adopted for industrial applications to improve the system efficiency because distributed architecture has advantages in resource utilization, fault toleration .etc. Multi-Agent System (MAS) arises from combination of the theories of artificial intelligence and distributed systems. One character of MAS is their self-organization, so how to implement an effective mechanism for self-organization of agents is important to a MAS system, this paper describes the design and implementation of a Mobile-C based agent management system, in which Mobile-C was adopted as the implementation platform, and this paper also described an agent-based cooperative design application using this system to manage all the agents involved.
Researches on Design and Implementations of Two 2-Bit Predictors
Authors: Zhang Long , Tao Fang , Xiang Jin Feng
Published: September 2011

High-performance superscalar processors, which can be used in building base-stations of cell phones and cloud-based web servers, rely heavily on aggressive branch predictors to avoid stalls no matter the branch is taken or not. Dynamic branch predictor which is based on the historical records of the previously executed branches always outputs good performance. Two-bit predictor discussed in this paper is one of the most popular ones that always practically employed. This paper demonstrates two implementations of two-bit predictors. Using BTB to process solo conditional branches is the first one, which is normally used. Other categories of branch instructions may results in several bubbles as the penalty. While the other implementation employs BTB dealing with all kinds of branch instructions, generating target addresses without any delay cycle. Simulation results show that the second implementation has much better performance than the former one. It decreases the mis-prediction rate from 12.26% to 11.48%, and also has much higher prediction accuracy on indirect jumps. With these results, we have our predictor re-designed accordingly and implemented successfully in superscalar processors.
Local Refinement for Graph Partitioning Based on Level Structure
Authors: Yao Lu , Wang Zheng Hua , Cao Wei , Li Zong Zhe
Published: September 2011

Graph partitioning is a fundamental problem in several scientific and engineering applications. In this paper, we propose a heuristic local refinement algorithm for graph partitioning, which seeks to improve the quality of separators by reducing the width of the level structure. The experiments reported in this paper show that the use of our local refinement algorithm results in a considerable improvement in the quality of partitions over conventional graph partitioning scheme based on level structure.
Study on the Algorithm for Real-Time Interpolation of NURBS Curve
Authors: Hui Ji Zhuang , Ma Yan , Liu Ze Feng
Published: September 2011

In order to meet the needs of high speed and high precision computerized numerical control machining, a calculation based on the control of contour error and feeding acceleration for the real-time interpolation of Non-uniform rational B-spline (NURBS) curves was presented in this paper. On the premise of meeting the error requirement, machine can process parts with the highest feeding speed to achieve interpolation precision and interpolation speed optimization, and improve processing quality and efficiency.
Research on Hiding Technology of Web Malicious Code
Authors: Zhang Deng Yin , Wang Zhen Xing , Zhao Xiao Qiang
Published: September 2011

In modern network confrontation, it is very important to improve the viability of web malicious code. According to the generation and propagation characteristics, we propose the web malicious code hidden solutions which are based on deformation and encryption. Combining with MS09002 vulnerabilities we give an application example of web Trojan hidden. Test results show that the proposed integrated solution has the better capacity of avoiding virus killing and the stronger hidden performance. The significant improvement of viability of web malicious code is very important of application.
Multiple Coronary Artery Thrombosis in 5,10-Methylenetetrahydrofolate Reductase Gene Mutation
Authors: Campanile Alfonso , Sozzi Fabiola B. , Danzi Gian Battista
Published: September 2011

A 42-year-old man presented at our attention with chest pain. His cardiac risk factors were smoking habit and family history of coronary artery disease. At the ECG, a mild ST-segment elevation in the inferior leads was shown. A normal left ventricular function was demonstrated at the echocardiography. An emergency coronary angiography was performed, and an extensive thrombosis of the right coronary artery and midleft anterior descending coronary artery was visualized. A primary angioplasty with thrombus aspiration and direct stenting of both sites followed. Biochemical analysis revealed a high plasma homocysteine level with a homozygotic anomaly of the 5,10-methylenetetrahydrofolate reductase. Currently, a nine-month followup negative for cardiac events is recorded.
Quantification of pore-size spectrums by solute breakthrough curves
Authors: Erşahin S.
Published: September 2011

Abstract. Breakthrough of conservative tracers may be used to quantify pore-size spectrum and pore-water velocity distributions in a porous medium. In this study, a theory was proposed to calculate pore-water velocity and corresponding pore-size spectrum in porous media, and its application was demonstrated. Miscible displacement tests of chloride were conducted with sand columns (5 cm id and 5 cm length), repacked with washed sand with a particle size of 2–1, 1–0.45, 0.45–0.325 and <0.325 mm in diameter. The resulting breakthrough curves were divided into approximately 20 segments, and for each segment, a concentration of Cl in an out-flowing effluent was used with corresponding effluent volume and travel time to calculate corresponding pore water velocity (v) and pore-radius. Mean v (vb) calculated for a column was approximated by geometric averaging the calculated v-values for the BTC. To validate the developed model, laboratory measured and approximated values of vb were compared. The correlation analysis conducted between measured and approximated vb resulted in a correlation coefficient of r = 0.89 (P < 0.01). The results revealed that size distribution of effective pores could be quite different even in replicates of small sand columns, which are highly similar in particle-size and total porosity.
Genotypic tropism of antiretroviral‐treated patients with drug resistant HIV‐1
Authors: Parczewski Milosz , Leszczyszyn‐Pynka Magdalena , Urbanska Anna , Bander Dorota , Boron‐Kaczmarska Anna
Published: September 2011

CCR5 inhibitors remain an attractive antiretroviral treatment option for HIV‐infected patients; however, tropism testing should be utilized prior their introduction. This study analyzed genotypic HIV‐1 tropisms in patients with evidence of genotypic drug resistance to antiretroviral therapies in Northwest Poland. V3 loop sequences were analyzed from plasma samples obtained from patients presenting with virologic treatment failure while on combined antiretroviral treatment and with evidence of genotypic drug resistance. Genotypic X4 and R5 tropisms were identified using the geno2pheno algorithm with a false positive rate threshold set at 10%. Clinical data for all patients examined was collected, in addition to determining the CCR5 Δ32 genotype and calculating the genotypic susceptibility score (GSS). Virologic treatment failure and the presence of drug resistant mutations were observed in 37/450 (8.4%) patients on cART (combination antiretroviral therapy) with successful tropism analysis carried out on 35 (95%) cases. In 22 (62.9%) and 13 (37.1%) cases the R5 and X4 tropisms were predicted, respectively. An association between viral X4 tropism and the M41L (P = 0.04) resistance mutation and R5 tropism and the K103N (P = 0.07) resistance mutation were observed. GSS values were lower in the group with NRTI (P = 0.01) and NNRTI resistance (P = 0.048). In the majority of the drug resistant patients, R5 tropic viruses were found. As genotypic tropism testing is easy to carry out and interpret, its use in clinical practice would be highly useful in determining the use of appropriate drug therapies. J. Med. Virol. 83:1869–1875, 2011. © 2011 Wiley‐Liss, Inc.
Adherence, therapeutic intensity, and the number of dispensed drugs
Authors: Hovstadius Bo , Petersson Göran
Published: September 2011

Purpose

To estimate non‐adherence in relation to the therapeutic intensity (TI) and the number of dispensed drugs per individual and study whether the TI can be used as an estimator of non‐adherence with an increasing number of drugs.

Methods

The study comprised an individual‐based register of all dispensed outpatient prescriptions in Sweden in 2006, including 6.2 million individuals. The applied definition of drug was the chemical entity or substance comprising the fifth level in the World Health Organisation's Anatomic, Therapeutic, Chemical classification. The defined daily dosage per individual during 12 months was applied as an indicator of the TI.

Results

We found a positive linear relation between the TI and the increasing number of dispensed drugs per individual, both for men and women. We found a slightly diminishing TI with an increasing number of drugs only for the age groups above 70 years, at a level above 13 drugs per individual.

Conclusions

The linear relationship between the TI and the increasing number of dispensed drugs per individual provides poor support for using decreasing TI as an estimator of non‐adherence. The low rate of cost‐related non‐adherence in Sweden might contribute to explaining the linear relationship. Copyright © 2011 John Wiley & Sons, Ltd.
Starch re‐crystallization kinetics as a function of various cations
Authors: Beck Margit , Jekle Mario , Becker Thomas
Published: September 2011

Starch retrogradation is the main cause of quality deterioration in starch‐containing foods during storage. The current work investigates the effect of different cations on the retrogradation of corn starch and the potential of reducing starch retrogradation with the aim of preparing products with an extended shelf life. To gelatinize the starch, starch–water suspensions containing various chloride salts (LiCl, NaCl, KCl, MgCl2, CaCl2, and NH4Cl) were heated in a DSC, stored up to 504 h at 8°C, and reheated again. Analysis of gelatinization behavior for each salt type indicates a relationship to the aW‐value of the starch–water system. The degree of re‐crystallization was calculated using the Avrami equation, and indicates that the starch re‐crystallization rate (k) is significantly (p < 0.01) reduced with the addition of a cation, unlike the reference (starch–water systems without salt). Further, bivalent cations such as Ca2+, Mg2+ decreased the starch re‐crystallization rate (k) more than univalent cations (Li+, NH, Na+, and K+). This result may be based on the theory that high cations with higher charge densities show greater hydration, and, therefore, lower aW‐values, than cations with lower charge densities. The results illustrate important results for predicting starch quality change when using sodium replacements.
MicroRNAs regulatory networks in myeloid lineage development and differentiation: regulators of the regulators
Authors: El Gazzar Mohamed , McCall Charles E
Published: September 2011

MicroRNAs (miRNAs) are abundant small molecules of ∼22 nucleotides that reprogram gene expression by targeting mRNA degradation and translation disruption. An emerging concept implicates miRNA coupling with transcription factors in myeloid‐based development of dendritic cells, monocytes and granulocytes, as well as function as mature cells and contributors to host defense and inflammation. Here, we review this new and important interactive circuitry and how it contributes to reprogramming cell phenotypic responses associated with mature immune competency.
SBRML Interoperability
Authors: Bergmann Frank
Published: September 2011

This presentation summarizes an initial meeting of SED-ML and SBRML editors in order to facilitate reuse and sharing of components of each language.
SBML Team facilities & software
Authors: Bergmann Frank , Keating Sarah
Published: September 2011

This presentation provides a brief overview of the new SBML online validator and the updates in the SBML Tool Matrix. This presentation ends with an update on the new version of the SBML Toolbox.
SBML Editor’s Report: Principles for Package Development
Authors: Smith Lucian
Published: September 2011

In the last six months, the SBML Editors have developed several principles to guide the development of SBML Level 3 packages. An update on what those principles are, and some controversies that have arisen as a result.
Update: MIRIAM Registry and SBO
Authors: Juty Nick
Published: September 2011

We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We also describe current status and planned improvements to this system, as well as providing an update on the Systems Biology ontology since the last COMBINE meeting in Edinburgh (2010).
Rapid copy number expansion and recent recruitment of domains in S‐receptor kinase‐like genes contribute to the origin of self‐incompatibility
Authors: Zhang Xiaohui , Wang Long , Yuan Yang , Tian Dacheng , Yang Sihai
Published: September 2011

More than half of flowering plants have a sophisticated mechanism for self‐pollen rejection, named self‐incompatibility. In the Brassicaceae family, the recognition specificity of a self‐incompatibility system is achieved by the interaction of the stigmatic S‐receptor kinase and its ligand S‐locus cysteine‐rich protein, which are encoded by two tightly linked polymorphic genes. During the last two decades, many studies have explored their functions, although their origin and evolutionary history have still not been elucidated clearly. In the present study, an extensive survey in nine whole‐genome sequenced plants, including one moss, one fern and seven flowering plants, was conducted to clarify these issues. The data obtained showed that S_locus_glycop domain‐related genes, which are land plant specific, have an ancient origin that can be traced back to early land plants and also have a significantly expansion in flowering plants. In the four predominant domain architectures (Types I to IV) of these proteins, Type III genes had absolute predominance and appeared to be raw materials for diversification of the S_locus_glycop domain‐related genes by frequent domain re‐organizations. S‐receptor kinase‐like sequences (Type IV) might have originated from Type III genes by domain gains, and S‐locus glycoprotein‐like sequences (Type I) might have arisen by partial duplication of its linked S‐receptor kinase genes. Although similar topologies were detected in S‐receptor kinase and S‐locus cysteine‐rich protein trees, their physical linkage were found only in Brassicaceae, suggesting that the strong linkage disequilibrium and their co‐evolution may be a key factor for the origin and maintenance of the S‐receptor kinase‐based self‐incompatibility system in Brassicaceae.
Antibiofilm Effects of Azithromycin and Erythromycin on Porphyromonas gingivalis
Authors: Maezono H. , Noiri Y. , Asahi Y. , Yamaguchi M. , Yamamoto R. , Izutani N. , Azakami H. , Ebisu S.
Published: September 2011

Antibiotic resistance of biofilm-grown bacteria contributes to chronic infections, such as marginal and periapical periodontitis, which are strongly associated with
Porphyromonas gingivalis
. Concurrent azithromycin (AZM) administration and mechanical debridement improve the clinical parameters of periodontal tissue
in situ
. We examined the
in vitro
efficacy of AZM against
P. gingivalis
biofilms. The susceptibilities of adherent
P. gingivalis
strains 381, HW24D1, 6/26, and W83 to AZM, erythromycin (ERY), ampicillin (AMP), ofloxacin (OFX), and gentamicin (GEN) were investigated using a static model. The optical densities of adherent
P. gingivalis
cells were significantly decreased by using AZM and ERY at sub-MIC levels compared with those of the controls in all the strains tested, except for the effect of ERY on strain W83. AMP and OFX inhibited
P. gingivalis
adherent cells at levels over their MICs, and GEN showed no inhibition in the static model. The effects of AZM and ERY against biofilm cells were investigated using a flow cell model. The ATP levels of
P. gingivalis
biofilms were significantly decreased by AZM at concentrations below the sub-MICs; however, ERY was not effective for inhibition of
P. gingivalis
biofilm cells at their sub-MICs. Furthermore, decreased density of
P. gingivalis
biofilms was observed three-dimensionally with sub-MIC AZM, using confocal laser scanning microscopy. These findings suggest that AZM is effective against
P. gingivalis
biofilms at sub-MIC levels and could have future clinical application for oral biofilm infections, such as chronic marginal and periapical periodontitis.
Draft Genome Sequence of Lactobacillus malefermentans KCTC 3548
Authors: Kim Dong-Wook , Choi Sang-Haeng , Kang Aram , Nam Seong-Hyeuk , Kim Dae-Soo , Kim Ryong Nam , Kim Aeri , Park Hong-Seog
Published: September 2011

We announce the draft genome sequence of the type strain
Lactobacillus malefermentans
KCTC 3548 (2,003,922 bp, with a G+C content of 41.1%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of beer; the genome consists of 172 large contigs (>100 bp in size). All of the contigs were assembled by using Newbler Assembler 2.3 (454 Life Science).
COMPOSITE HIGGS TO TWO PHOTONS AND GLUONS
Authors: HAPOLA TUOMAS , SANNINO FRANCESCO
Published: September 2011

We introduce a simple framework to estimate the composite Higgs boson coupling to two-photon in technicolor extensions of the standard model. The same framework allows us to predict the composite Higgs to two-gluon process. We compare the decay rates with the standard model ones and show that the corrections are typically of order one. We suggest, therefore, that the two-photon decay process can be used to disentangle a light composite Higgs from the standard model one. We also show that the Tevatron results for the gluon–gluon fusion production of the Higgs either exclude the techniquarks to carry color charges to the 95% confidence level, if the composite Higgs is light, or that the latter must be heavier than around 200 GeV.
CONTROLLING THE ROTATIONAL DYNAMICS OF THE MOLECULAR ORIENTATION BY TWO TIME-DELAYED LASER PULSES
Authors: XU SHUWU , HUANG YUNXIA , JI XIANMING
Published: September 2011

We show that the Raman transition probability can be manipulated by the relative time delay, the intensity ratio and the carrier-envelope phase between two time-delayed dual-color laser pulses. Our results indicate that when the second laser pulse is applied at half of the molecular rotational period, the contributions of the odd and the even rotational states are different. However, the two contributions are the same when the relative time delay is a full molecular rotational period. Time-dependent molecular orientation signals and their corresponding Fourier transforms validate the results.
Trajectory anonymity in publishing personal mobility data
Authors: Bonchi Francesco , Lakshmanan Laks V.S. , Wang Hui (Wendy)
Published: September 2011

Recent years have witnessed pervasive use of location-aware devices such as GSM mobile phones, GPS-enabled PDAs, location sensors, and active RFID tags. The use of these devices generates a huge collection of spatio-temporal data, variously called moving object data, trajectory data, or moblity data. These data can be used for various data analysis purposes such as city traffic control, mobility management, urban planning, and location-based service advertisements. Clearly, the spatio-temporal data so collected may help an attacker to discover personal and sensitive information like user habits, social customs, religious and sexual preferences of individuals. Consequently, it raises serious concerns about privacy. Simply replacing users' real identifiers (name, SSN, etc.) with pseudonyms is insufficient to guarantee anonymity. The problem is that due to the existence of quasi-identifiers, i.e., spatio-temporal data points that can be linked to external information to re-identify individuals, the attacker may be able to trace the anonymous spatio-temporal data back to individuals.

In this survey, we discuss recent advancement on anonymity preserving data publishing of moving object databases in an off-line fashion. We first introduce several anonymity models, then we describe in detail some of the proposed techniques to enforce trajectory anonymity, discussing their merits and limitations. We conclude by identifying challenging open problems that need attention.
From Gesture to Form: The Evolution of Expressive Freehand Spatial Interfaces
Authors: Keefe Daniel F.
Published: September 2011

This paper presents a series of insights from an ongoing investigation into refining custom spatial computer interfaces and graphical primitives for suggesting 3D form in immersive digital spaces. Technical innovations utilizing 3D gesture capture, force feedback, and stereoscopic presentation are described through reference to specific free-form digital sculptures created with the CavePainting and Drawing on Air interfaces. The role of the human hand in digital art practice and the potential of interfaces that tightly couple freehand movements with geometric algorithms are discussed.