bluuebunny/crossref_metadata_2025 huggingface dataset:
MMFPh: a maximal motif finder for phosphoproteomics datasets
Authors: Wang Tuobin , Kettenbach Arminja N. , Gerber Scott A. , Bailey-Kellogg Chris
Published: April 2012

Motivation: Protein phosphorylation, driven by specific recognition of substrates by kinases and phosphatases, plays central roles in a variety of important cellular processes such as signaling and enzyme activation. Mass spectrometry enables the determination of phosphorylated peptides (and thereby proteins) in scenarios ranging from targeted in vitro studies to in vivo cell lysates under particular conditions. The characterization of commonalities among identified phosphopeptides provides insights into the specificities of the kinases involved in a study. Several algorithms have been developed to uncover linear motifs representing position-specific amino acid patterns in sets of phosphopeptides. To more fully capture the available information, reduce sensitivity to both parameter choices and natural experimental variation, and develop more precise characterizations of kinase specificities, it is necessary to determine all statistically significant motifs represented in a dataset.

Results: We have developed MMFPh (Maximal Motif Finder for Phosphoproteomics datasets), which extends the approach of the popular phosphorylation motif software Motif-X (Schwartz and Gygi, 2005) to identify all statistically significant motifs and return the maximal ones (those not subsumed by motifs with more fixed amino acids). In tests with both synthetic and experimental data, we show that MMFPh finds important motifs missed by the greedy approach of Motif-X, while also finding more motifs that are more characteristic of the dataset relative to the background proteome. Thus MMFPh is in some sense both more sensitive and more specific in characterizing the involved kinases. We also show that MMFPh compares favorably to other recent methods for finding phosphorylation motifs. Furthermore, MMFPh is less dependent on parameter choices. We support this powerful new approach with a web interface so that it may become a useful tool for studies of kinase specificity and phosphorylation site prediction.

Availability: A web server is at www.cs.dartmouth.edu/~cbk/

Contact:  cbk@cs.dartmouth.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Altered immunoregulatory profile during anti-tumour necrosis factor treatment of patients with inflammatory bowel disease
Authors: Grundström J , Linton L , Thunberg S , Forsslund H , Janczewska I , Befrits R , van Hage M , Gafvelin G , Eberhardson M
Published: April 2012

Inflammatory bowel disease (IBD) can be treated effectively by anti-tumour necrosis factor (TNF) therapy. We set out to investigate the unclear immunoregulatory mechanisms of the treatment. Thirty-four patients with IBD treated with anti-TNF were included. Lymphocytes from peripheral blood and intestinal biopsies were analysed by flow cytometry. Regulation of antigen-stimulated proliferation was analysed by blocking of interleukin (IL)-10, transforming growth factor (TGF)-β or depletion of CD25+ cells in peripheral blood mononuclear cell cultures. No changes in CD4+CD25+, CD25+TNF-RII+ or CD4+CD25+forkhead box protein 3 (FoxP3+) T cells could be observed in peripheral blood after, in comparison to before, 6 weeks of treatment. The suppressive ability of CD4+CD25+ cells did not change. There was an initial decrease of CD4+CD25+ cells in intestinal mucosa after 2 weeks of treatment, followed by an increase of these cells from weeks 2 to 6 of treatment (P < 0·05). This was accompanied by an increased percentage of CD69+ cells among these cells after 6 weeks of treatment compared to before treatment (P < 0·01). There was also an increase of mucosal T helper type1 cells from weeks 2 to 6 (P < 0·05). In addition, CD25+TNF-RII+ cells in the mucosa were decreased after 6 weeks of treatment compared to before treatment (P < 0·05). Before treatment, peripheral blood mononuclear cell baseline proliferation was increased when IL-10 was blocked (P < 0·01), but not after. In CD25+ cell-depleted cultures proliferation increased after treatment (P < 0·05). Our data indicate that anti-TNF treatment leads to an induction of effector T cells. Anti-TNF therapy has no significant impact on regulatory T cells in IBD, although the composition of regulatory T cell subsets may change during treatment.
Lenalidomide enhancement of human T cell functions in human immunodeficiency virus (HIV)-infected and HIV-negative CD4 T lymphocytopenic patients
Authors: Lim H , Kane L , Schwartz J B , Hesdorffer C S , Deeks S G , Greig N , Ferrucci L , Goetzl E J
Published: April 2012

Suppressed T cell functions in human immunodeficiency virus (HIV) infection were identified and corrected by lenalidomide in middle-aged HIV-infected patients. Chemotaxis of T cells from HIV-infected men (n = 6, mean 43 years) to sphingosine 1-phosphate (S1P) and CCL21 was significantly lower than that of HIV-negative men (n = 6, mean 41 years), and was enhanced significantly up to control levels by 100 and 1000 nM lenalidomide. Generation of interleukin (IL)-2, but not interferon (IFN)-γ, by T cells of middle-aged HIV-infected men was significantly lower than that for controls and was increased significantly by 10–1000 nM lenalidomide up to a maximum of more than 300%. CD4 and CD8 T cells isolated from healthy middle-aged men and reconstituted in vitro at a low CD4 : CD8 ratio typical of HIV infection had depressed chemotaxis to S1P, but not CCL21, and generation of IL-2, but not IFN-γ. Significant enhancement of chemotaxis to S1P and CCL21was induced by 100–1000 nM lenalidomide only for normal T cells at a low CD4 : CD8 ratio. T cells from HIV-negative middle-aged CD4 T lymphocytopenic patients (n = 3), with a CD4 : CD8 ratio as low as that of HIV-infected patients, had similarly diminished chemotaxis to S1P and CCL21, and depressed generation of IL-2, but not IFN-γ. Lenalidomide at 30–1000 nM significantly enhanced chemotaxis to S1P and IL-2 generation for T cells from HIV-negative CD4 T lymphocytopenic patients as from HIV-infected patients, with less effect on CCL21-elicited chemotaxis and none for IFN-γ generation. Defects in functions of T cells from middle-aged HIV-infected men are partially attributable to CD4 T lymphocytopenia and are corrected by lenalidomide.
Stability of tallgrass prairie during a 19‐year increase in growing season precipitation
Authors: Collins Scott L. , Koerner Sally E. , Plaut Jennifer A. , Okie Jordan G. , Brese Daniel , Calabrese Laura B. , Carvajal Alejandra , Evansen Ryan J. , Nonaka Etsuko
Published: April 2012

1. Precipitation is considered to be a key driver of ecosystem processes in mesic grasslands, and climate models predict changes in the amount and intensity of precipitation under future global change scenarios. Although most experimental rainfall studies decrease precipitation, seasonal rainfall is predicted to increase in the northern Great Plains under climate change.

2. We analysed changes in community composition and structure of upland and lowland native tallgrass prairie in central Kansas, USA, subjected to 19 years of irrigation designed to eliminate moisture stress throughout the growing season.

3. Irrigation had limited effects on species richness in both upland and lowland prairie. Total cover increased significantly and consistently with irrigation in drier uplands and in more mesic lowlands. Abundance of rhizomatous, tall, perennial species as well as C3forbs increased with irrigation.

4. The strongest response to irrigation came within the dominant functional type, C4perennial grasses.Panicum virgatumbecame the dominant species in irrigated lowlands, whereasAndropogon gerardiiremained the dominant species in irrigated uplands and in control plots. Overall, irrigation had less effect on community composition and structure than other known drivers of grassland structure and function.

5. In comparison with other studies, our results demonstrate that water addition has less of an impact than fire, grazing or nitrogen addition on composition and dynamics in this mesic grassland. The strongest response to long‐term irrigation occurredwithinthe dominant functional type: tall, perennial, rhizomatous, C4grasses. Thus, functional redundancy will buffer this ecosystem from potential increases in rainfall due to climate change. Finally, our results highlight the limited utility of qualitative functional traits to predict how this mesic grassland will respond to climate change.
HORMAD1‐dependent checkpoint/surveillance mechanism eliminates asynaptic oocytes
Authors: Kogo Hiroshi , Tsutsumi Makiko , Ohye Tamae , Inagaki Hidehito , Abe Takaya , Kurahashi Hiroki
Published: April 2012

Meiotic pachytene checkpoints monitor the failure of homologous recombination and synapsis to ensure faithful chromosome segregation during gamete formation. To date, the molecular basis of the mammalian pachytene checkpoints has remained largely unknown. We here report that mouse HORMAD1 is required for a meiotic prophase checkpoint that eliminates asynaptic oocytes. Hormad1‐deficient mice are infertile and show an extensive failure of homologous pairing and synapsis, consistent with the evolutionarily conserved function of meiotic HORMA domain proteins. Unexpectedly, Hormad1‐deficient ovaries contain a normal number of oocytes despite asynapsis and consequently produce aneuploid oocytes, indicating a checkpoint failure. By the analysis of Hormad1/Spo11 double mutants, the Hormad1 deficiency was found to abrogate the massive oocyte loss in the Spo11‐deficient ovary. The Hormad1 deficiency also causes the eventual loss of pseudo sex body in the Spo11‐deficient ovary and testis. These results suggest the involvement of HORMAD1 in the repressive chromatin domain formation that is proposed to be important in the meiotic prophase checkpoints. We also show the extensive phosphorylation of HORMAD1 in the Spo11‐deficient testis and ovary, suggesting an involvement of novel DNA damage–independent phosphorylation signaling in the surveillance mechanism. Our present results provide clues to HORMAD1‐dependent checkpoint in response to asynapsis in mammalian meiosis.
Study of correlation between maternal fatigue and uterine contraction pattern in the active phase of labour
Authors: Ebrahimzadeh Samira , Golmakani Nahid , Kabirian Maryam , Shakeri Mohhamad T
Published: April 2012

Aims and objectives.  To evaluate the correlation between maternal fatigue and uterine contraction pattern at the beginning of the active phase of labour.

Background.  Fatigue is one of the most common complaints in pregnant women that often continues until delivery. Maternal fatigue prolongs the labour process and increases the rate of cesarian section. Studies on the pattern of uterine contractions have shown that the length of the fall time is longer in prolonged labours than in normal deliveries.

Design.  A cross‐sectional study.

Methods.  This study was conducted on 100 primiparous women who were referred to Ommolbanin Hospital (Mashhad, Iran) in 2011. Maternal fatigue was assessed at the beginning of the active phase of labour. Then, the pattern of uterine contractions was monitored for 30 minutes by an external tocodynamometer. The F/R ratio was determined by measuring the time for a contraction to return to its baseline from its peak and the time for a contraction to rise to its peak. The data were analysed by chi‐square and anova tests.

Results.  The results showed that there was a significant relationship between maternal fatigue and uterine contraction pattern. The F/R ratio was increased with increase in fatigue severity.

Conclusions.  Fatigue causes changes in the pattern of uterine contractions. The return time of a contraction from its peak to its baseline (fall) is increased with increase in fatigue severity.

Relevance to clinical practice.  Offering strategies to prevent tiredness and reduce the related fatigue complications.
Bypassing proximal health care facilities for acute care: a survey of patients in a Ghanaian Accident and Emergency Centre
Authors: Yaffee A. Q. , Whiteside L. K. , Oteng R. A. , Carter P. M. , Donkor P. , Rominski S. D. , Kruk M. E. , Cunningham R. M.
Published: April 2012

Objective  To characterise the population that presents to the Accident and Emergency Centre (AEC) at Komfo Anokye Teaching Hospital (KATH) and to identify risk factors associated with bypassing proximal care facilities.

Methods  A structured questionnaire was verbally administered to patients presenting to the AEC over 2 weeks. The questionnaire focused on the use of health care resources and characteristics of current illness or injury. Measures recorded include demographics, socioeconomic status, chief complaint, transportation and mobility, reasons for choosing KATH and health care service utilisation and cost.

Results  The total rate of bypassing proximal care was 33.9%. On multivariate analysis, factors positively associated with bypassing included age older than 38 years (OR: 2.18, P 0.04) and prior visits to facility (OR 2.88, P 0.01). Bypassers were less likely to be insured (OR 0.31, P 0.01), to be seeking care due to injury (OR 0.42, P 0.03) and to have previously sought care for the problem (OR 0.10, P < 0.001).

Conclusions  Patients who bypass facilities near them to seek care at an urban AEC in Ghana do so for a combination of reasons including familiarity with the facility, chief complaint and insurance status. Understanding bypassing behaviour is important for guiding health care utilisation policy decisions and streamlining cost‐effective, appropriate access to care for all patients.
Neuromodulation of Pelvic Visceral Pain: Review of the Literature and Case Series of Potential Novel Targets for Treatment
Authors: Hunter Corey , Davé Nimish , Diwan Sudhir , Deer Timothy
Published: April 2012

Chronic pelvic pain (CPP) is complex and often resistant to treatment. While the exact pathophysiology is unknown, the pain states resultant from conditions such as interstitial cystitis and the like yield patients with a presentation that bears a striking similarity to neuropathic syndromes that are known to respond to neuromodulation. While there has been past success using the sacral region as a target for spinal cord stimulation (SCS) to treat these patients, there remains to be a consensus on the optimal location for lead placement. In this article, the authors discuss the potential etiology of CPP, examine the current literature on lead placement for SCS as a method of treatment, as well as present several cases where novel lead placement was successfully employed.
Surfaces of Longing. Cosmopolitan Aspiration and Frustration in Egypt
Authors: SCHIELKE SAMULI
Published: April 2012

One of the most ambiguous outcomes of globalization has been the emergence of a large class of people who subscribe to global trends in religion, consumerism, nationalism, sports and popular culture, without having access to the mobility nor the symbolic capital that are associated with cosmopolitanism. This sense of aspiration is far from ephemeral. It is material, it has shape, surface, and form. This photo essay attempts to connect this sensual presence of images, and materials with the sense of longing and discontent involved in looking out to the world from the vantage point of underprivileged social milieus in Egypt.
Development of a Non-Invasive Dynamic Pulmonary Function Monitor
Authors: Sokoloff Michael D. , Bortner Larry , Panos Ralph J.
Published: April 2012

Characterizing the complexity of airflow limitation in diagnosing and assessing disease severity in asthma, COPD, cystic fibrosis, and other respiratory diseases can help guide clinicians toward the most appropriate treatments. Current technologies allow obstructive lung disease to be measured with about 5%−10% precision. A noninvasive dynamic pulmonary function monitor (DPFM) can quantify ventilation inhomogeneities, such as those originating in partially blocked or constricted small airways, with 1% precision if inert gas concentrations can be measured accurately and precisely over three to four decades of sensitivity. We have studied the precision and linearity of a commercially available mass spectrometer, sampling the gas exhaled by a mechanical lung analog, mimicking a multibreath inert gas washout measurement. The root mean square deviation of the inert gas concentration measured for each “breath,” compared to the expected value for a purely exponential decay, is found to be about 1.1% over three decades of concentration. The corresponding overall impairment, a specific measure of ventilation inhomogeneity, is found to be about 0.2%, which indicates that were inhomogeneities observed, the corresponding impairment could be measured with 1% precision.
A scaling transformation for classifier output based on likelihood ratio: Applications to a CAD workstation for diagnosis of breast cancer
Authors: Horsch Karla , Pesce Lorenzo L. , Giger Maryellen L. , Metz Charles E. , Jiang Yulei
Published: April 2012

Purpose:

The authors developed scaling methods that monotonically transform the output of one classifier to the “scale” of another. Such transformations affect the distribution of classifier output while leaving the ROC curve unchanged. In particular, they investigated transformations between radiologists and computer classifiers, with the goal of addressing the problem of comparing and interpreting case‐specific values of output from two classifiers.

Methods:

Using both simulated and radiologists' rating data of breast imaging cases, the authors investigated a likelihood‐ratio‐scaling transformation, based on “matching” classifier likelihood ratios. For comparison, three other scaling transformations were investigated that were based on matching classifier true positive fraction, false positive fraction, or cumulative distribution function, respectively. The authors explored modifying the computer output to reflect the scale of the radiologist, as well as modifying the radiologist's ratings to reflect the scale of the computer. They also evaluated how dataset size affects the transformations.

Results:

When ROC curves of two classifiers differed substantially, the four transformations were found to be quite different. The likelihood‐ratio scaling transformation was found to vary widely from radiologist to radiologist. Similar results were found for the other transformations. Our simulations explored the effect of database sizes on the accuracy of the estimation of our scaling transformations.

Conclusions:

The likelihood‐ratio‐scaling transformation that the authors have developed and evaluated was shown to be capable of transforming computer and radiologist outputs to a common scale reliably, thereby allowing the comparison of the computer and radiologist outputs on the basis of a clinically relevant statistic.
LANTHANUM TITANATE NANOPARTICLES ER FLUIDS WITH HIGH PERFORMANCE
Authors: WANG DE , SHEN RONG , WEI SHIQIANG , LU KUNQUAN
Published: April 2012

A new type of electrorheological (ER) fluid consisting of lanthanum titanate (LTO) nanoparticles is developed. The ER fluids were prepared by suspending LTO powder in silicone oil and the particles were fabricated by wet chemical method. This ER fluid shows excellent ER properties: The static yield stress reaches over 150 kPa under 5 kV/mm with linear dependence on the applied DC electric field, and the current density is below 10 μA/cm2. In order to investigate the affect factor on the ER behavior, the LTO powder were heated under different temperatures. The ER performances of two particles treated under different temperatures were compared and the composition changes for those particles were analyzed with TG-FTIR technique. It was found that the static yield stress of the suspensions fell from over 150 kPa to about 40 kPa and the current densities decreased prominently as the rise of the heating temperature. TG-FTIR analysis indicated that polar groups remained in the particles such as alkyl group, hydroxyl group and carbonyl group etc., contribute to the ER effect significantly. The experimental results are helpful to understand the mechanism of the high ER effect and to synthesize better ER materials.
CONTROLLED SYNTHESIS OF THE ZnWO4 NANOSTRUCTURE AND STUDY OF THEIR STRUCTURAL AND OPTICAL PROPERTIES
Authors: HUNG NGUYEN MANH , HANG LAM THI , VAN KHANH NGUYEN , THAO DU THI XUAN , VAN MINH NGUYEN
Published: April 2012

We investigate the effects of calcination time and concentration of solution on the structure, as well as optical properties in ZnWO4 nanopowder prepared by hydrothermal method. The prepared powder were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman scattering, optical absorption and photoluminescent spectroscopy (PL). It is shown that the grain size and morphology of ZnWO4 nanopowder can be controlled by adjusting the reaction time as well as the concentration of the solution. The resultant sample is a pure phase of ZnWO4 without any impurities. The result showed that the optical property of ZnWO4 nanopowders depend on their grain size. The optical band gap becomes narrower as the reaction time or concentration of solution is increased. The improved PL properties of the ZnWO4 crystallites can be obtained with the optimal concentration of the solution.
GLOBAL DEVELOPMENT CYCLES: REDEFINING TECHNOLOGICAL INNOVATION CYCLES AND THEIR IMPACTS WITHIN A GLOBAL PERSPECTIVE
Authors: GALLIS MICHAEL , RALL EMILY LORANCE
Published: April 2012

In the past three decades, there has been a rise in neo-Schumpeterian approaches for understanding the role of innovation in technological development cycles. However, a literature review reveals two important factors are missing: first, an understanding of the role of the Global Network, defined as the connective network by which people, goods, and information move around the world, and second, a more holistic view of innovation cycles that is based on hierarchies of technologies and encompasses the influence of sociopolitical interactions and market integration worldwide. This paper presents a new conceptual framework for understanding the development of technology, taking these factors into account through the grouping of innovations into Global Development Cycles. With increasing globalization and radical technological development, the attempt to understand predictable, long-term pattern changes has never been more important if we are to effectively manage global development. The implications of this more comprehensive global perspective are discussed.
Directed synthesis of bi- and polynuclear clamshell-type phthalocyanines and their physico-chemical investigations
Authors: Tolbin Alexander Yu. , Pushkarev Victor E. , Shulishov Evgeny V. , Tomilova Larisa G.
Published: April 2012

Novel bi-, tri- and tetranuclear butyl- and tert-butyl-substituted clamshell-type phthalocyanines were synthesized starting from 2-hydroxyphthalocyanines with quantitative yields. The structures of the obtained compounds were characterized by a complex of NMR spectroscopy and mass spectrometry techniques. Applying electronic absorption spectroscopy (UV-vis) and density functional theory (DFT) showed the complicated conformation equilibria for the spacer-bonded macrocyclic compounds and led us to estimate their behavior dependent on the number and relative orientation of macrocycles.
NUMERICAL SIMULATION OF 2D LIQUID SLOSHING
Authors: CAI LI , ZHOU JUN , ZHOU FENGQI , XIE WENXIAN , NIE YUFENG
Published: April 2012

In this paper, we present an extended ghost fluid method (GFM) for computations of liquid sloshing in incompressible multifluids consisting of inviscid and viscous regions. That is, the sloshing interface between inviscid and viscous fluids is tracked by the zero contour of a level set function and the appropriate sloshing interface conditions are captured by defining ghost fluids that have the velocities and pressure of the real fluid at each point while fixing the density and the kinematic viscosity of the other fluid. Meanwhile, a second order single-fluid solver, the central-weighted-essentially-nonoscillatory(CWENO)-type central-upwind scheme, is developed from our previous works. The high resolution and the nonoscillatory quality of the scheme can be verified by solving several numerical experiments. Nonlinear sloshing inside a pitching partially filled rectangular tank with/without baffles has been investigated.
MATHEMATICAL MODELING OF TUMOR CELL GROWTH AND IMMUNE SYSTEM INTERACTIONS
Authors: RIHAN FATHALLA A. , SAFAN MUNTASER , ABDEEN MOHAMED A. , ABDEL-RAHMAN DUAA H.
Published: April 2012

In this paper, we provide a family of ordinary and delay differential equations to describe the dynamics of tumor-growth and immunotherapy interactions. We explore the effects of adoptive cellular immunotherapy on the model and describe under what circumstances the tumor can be eliminated. The possibility of clearing the tumor, with a strategy, is based on two parameters in the model: the rate of influx of the effector cells, and the rate of influx of IL2. The critical tumor-growth rate, below which endemic tumor does not exist, has been found. One can use the model to make predictions about tumor-dormancy.
NUMERICAL INVESTIGATION OF THE RELEASE OF DRUG FROM A DRUG-DELIVERY DEVICE
Authors: GARSHASBI M. , GHARIBI H. KAMAL
Published: April 2012

In this study a mathematical model for the release of drug from porous, nonswelling transdermal drug-delivery devices to a perfect sink is considered. The drug is postulated to diffuse in both the solvent-filled pores and the body of the polymer. The limit in which the dissolution of drug is the dominant process is considered and a moving boundary problem governing drug release is derived. This model is solved numerically under some spacial conditions. Furthermore, another limit case in which the dissolution process is not so rapid is investigated and analytical and numerical solutions based on Fourier series solution and finite differences method are derived. Finally, the numerical and analytical solutions are compared to show the ability of the proposed numerical procedures.
PROTEIN TERTIARY STRUCTURE PREDICTION BASED ON MAIN CHAIN ANGLE USING A HYBRID BEES COLONY OPTIMIZATION ALGORITHM
Authors: MAHMOOD ZAKARIA N. , MAHMUDDIN MASSUDI , MAHMOOD MOHAMMED NOORALDEEN
Published: April 2012

Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on amino acid sequence but on the way the amino acid thread folds as well. This study provides a prototype system that able to predict a protein tertiary structure. Several methods are used to develop and evaluate the system to produce better accuracy in protein 3D structure prediction. The Bees Optimization algorithm which inspired from the honey bees food foraging method, is used in the searching phase. In this study, the experiment is conducted on short sequence proteins that have been used by the previous researches using well-known tools. The proposed approach shows a promising result.
THE EFFECTIVE CONNECTIVITY BETWEEN THE TWO PRIMARY MOTOR AREAS IN THE BRAIN DURING BILATERAL TAPPING OF HAND FINGERS
Authors: YUSOFF A. N. , HAMID K. A.
Published: April 2012

Dynamic causal modeling (DCM) was implemented on datasets obtained from an externally-triggered finger tapping functional MRI experiment performed by 5 male and female subjects. The objective was to model the effective connectivity between two significantly activated primary motor regions (M1). The left and right hemisphere M1s are found to be effectively and bidirectionally connected to each other. Both connections are modulated by the stimulus-free contextual input. These connectivities are however not gated (influenced) by any of the two M1s, ruling out the possibility of the non-linear behavior of connections between both M1s. A dynamic causal model was finally suggested.
Focal Therapy in the Management of Prostate Cancer: An Emerging Approach for Localized Prostate Cancer
Authors: Nomura Takeo , Mimata Hiromitsu
Published: April 2012

A widespread screening with prostate-specific antigen (PSA) has led increased diagnosis of localized prostate cancer along with a reduction in the proportion of advanced-stage disease at diagnosis. Over the past decade, interest in focal therapy as a less morbid option for the treatment of localized low-risk prostate cancer has recently been renewed due to downward stage migration. Focal therapy stands midway between active surveillance and radical treatments, combining minimal morbidity with cancer control. Several techniques of focal therapy have potential for isolated ablation of a tumor focus with sparing of uninvolved surround tissue demonstrating excellent short-term cancer control and a favorable patient’s quality of life. However, to date, tissue ablation has mostly used for near-whole prostate gland ablation without taking advantage of accompanying the technological capabilities. The available ablative technologies include cryotherapy, high-intensity focused ultrasound (HIFU), and vascular-targeted photodynamic therapy (VTP). Despite the interest in focal therapy, this technology has not yet been a well-established procedure nor provided sufficient data, because of the lack of randomized trial comparing the efficacy and morbidity of the standard treatment options. In this paper we briefly summarize the recent data regarding focal therapy for prostate cancer and these new therapeutic modalities.
CFD Simulation of Transonic Flow in High-Voltage Circuit Breaker
Authors: Ye Xiangyang , Dhotre Mahesh
Published: April 2012

A high-voltage circuit breaker is an indispensable piece of equipment in the electric transmission and distribution systems. Transonic flow typically occurs inside breaking chamber during the current interruption, which determines the insulating characteristics of gas. Therefore, accurate compressible flow simulations are required to improve the prediction of the breakdown voltages in various test duties of high-voltage circuit breakers. In this work, investigation of the impact of the solvers on the prediction capability of the breakdown voltages in capacitive switching is presented. For this purpose, a number of compressible nozzle flow validation cases have been presented. The investigation is then further extended for a real high-voltage circuit breaker geometry. The correlation between the flow prediction accuracy and the breakdown voltage prediction capability is identified.
A Case of Typical Carcinoid of the Larynx
Authors: Sato Shintaro , Kuratomi Yuichiro , Yamasaki Fumio , Inokuchi Akira
Published: April 2012

We report herein a rare case of typical carcinoid occurring primarily in the epiglottis. The patient was a 70-year-old man. On initial examination, a polypoid lesion with irregular surface near the center right-hand side of the laryngeal surface of the epiglottis was observed, and a biopsy was performed. Pathological examination of the specimen suggested the possibility of adenocarcinoma. Surgical excision was performed by means of laryngomicrosurgery. A Weerda-type laryngoscope was used to open the larynx, supplemented by rigid nasal sinus surgery endoscopes, and the right-hand half of the epiglottis were excised was ensured using a CO2laser. Postoperative pathological diagnosis was negative for adenocarcinoma and squamous cell cancer; typical carcinoid was diagnosed according to the World Health Organization criteria. Aspiration occurred postoperatively, swallowing training was therefore provided, and the patient was discharged from hospital 2 months after surgery when he was able to eat normally. As of 4 years after surgery, the patient remains under follow-up observation by means of PET-CT and neck, thoracic, and abdominal CT administered at appropriate intervals, but no findings indicating obvious recurrence or metastasis have been observed, and the patient displays good swallowing function.
Deposition and Characterization of CVD-Grown Ge-Sb Thin Film Device for Phase-Change Memory Application
Authors: Huang C. C. , Gholipour B. , Knight K. , Ou J. Y. , Hewak D. W.
Published: April 2012

Germanium antimony (Ge-Sb) thin films with tuneable compositions have been fabricated on SiO2/Si, borosilicate glass, and quartz glass substrates by chemical vapour deposition (CVD). Deposition takes place at atmospheric pressure using metal chloride precursors at reaction temperatures between 750 and 875°C. The compositions and structures of these thin films have been characterized by micro-Raman, scanning electron microscope (SEM) with energy dispersive X-ray analysis (EDX) and X-ray diffraction (XRD) techniques. A prototype Ge-Sb thin film phase-change memory device has been fabricated and reversible threshold and phase-change switching demonstrated electrically, with a threshold voltage of 2.2–2.5 V. These CVD-grown Ge-Sb films show promise for applications such as phase-change memory and optical, electronic, and plasmonic switching.
Mouse Tissues that Undergo Neoplastic Progression after K-Ras Activation Are Distinguished by Nuclear Translocation of phospho-Erk1/2 and Robust Tumor Suppressor Responses
Authors: Parikh Neha , Shuck Ryan L. , Nguyen Thuy-Ai , Herron Alan , Donehower Lawrence A.
Published: April 2012

Mutation of K-Ras is a frequent oncogenic event in human cancers, particularly cancers of lungs, pancreas, and colon. It remains unclear why some tissues are more susceptible to Ras-induced transformation than others. Here, we globally activated a mutant oncogenic K-Ras allele (K-RasG12D) in mice and examined the tissue-specific effects of this activation on cancer pathobiology, Ras signaling, tumor suppressor, DNA damage, and inflammatory responses. Within 5 to 6 weeks of oncogenic Ras activation, mice develop oral and gastric papillomas, lung adenomas, and hematopoietic hyperproliferation and turn moribund. The oral, gastric, and lung premalignant lesions display activated extracellular signal–regulated kinases (Erk)1/2 and NF-κB signaling as well as activated tumor suppressor and DNA damage responses. Other organs such as pancreas, liver, and small intestine do not exhibit neoplastic progression within 6 weeks following K-RasG12D activation and do not show a potent tumor suppressor response. Even though robust Erk1/2 signaling is activated in all the tissues examined, the pErk1/2 distribution remains largely cytoplasmic in K-RasG12D–refractory tissues (pancreas, liver, and intestines) as opposed to a predominantly nuclear localization in K-RasG12D–induced neoplasms of lung, oral, and gastric mucosa. The downstream targets of Ras signaling, pElk-1 and c-Myc, are elevated in K-RasG12D–induced neoplastic lesions but not in K-RasG12D–refractory tissues. We propose that oncogenic K-Ras–refractory tissues delay oncogenic progression by spatially limiting the efficacy of Ras/Raf/Erk1/2 signaling, whereas K-Ras–responsive tissues exhibit activated Ras/Raf/Erk1/2 signaling, rapidly form premalignant tumors, and activate potent antitumor responses that effectively prevent further malignant progression. Mol Cancer Res; 10(6); 845–55. ©2012 AACR.
Reversible Minimal Change Nephrotic Syndrome and Glomerular IgA Deposition Associated with Nonparenteral Heroin Abuse: A Case Report
Authors: Turgutalp Kenan , Kiykim Ahmet , Karabulut Umit , Gursoy Didar , Gurses Iclal
Published: April 2012

Objective: To report for the first time a case of reversible minimal change nephrotic syndrome with immunoglobulin A (IgA) deposition associated with heroin. Clinical Presentation and Intervention: A 29-year-old male heroin abuser who developed nephrotic syndrome was admitted to our clinic. Renal biopsy revealed minimal change disease with IgA deposition. Because spontaneous complete remission was observed after cessation of heroin, a diagnosis of minimal change nephrotic syndrome with IgA deposition associated with heroin abuse was considered. Conclusion: This case showed minimal change nephrotic syndrome with IgA deposition that had a benign clinical course.
Circulating Women as Objects of Trade in Malay Historical Texts
Authors: Hashim Ruzy Suliza , Tahir Ungku Maimunah Mohd , Jalaluddin Nor Hashimah , Mohamad Zulkarnaen
Published: April 2012

Abstract

In this paper, we shall discuss ‘circulating women’ as objects of trade based on the corpus of three historical texts such as The Malay Annals (Sejarah Melayu) and Misa Melayu Perak. Barbara Andaya (2006:104) has cogently argued that “Southeast Asia is an attractive laboratory to investigate women’s economic roles” especially in the early modern period. By focusing on issues related to marriage and slave trade, we look specifically at the movements of women in the chronicles. Whether they were consorts, concubines and maids-in-waiting in the Malay courts, the traffic of women showed an intricate web of social exchange where symmetrical and asymmetrical reciprocity took place in various political situations of the day. By showing these exchanges, we unveil an aspect of women and trade in early modern Southeast Asia where women were involved in boosting male prestige and power, political hierarchy, social identity and legitimacy.
Investigating the Mechanisms of Diurnal Rainfall Variability Using a Regional Climate Model
Authors: Evans Jason P. , Westra Seth
Published: April 2012

This study investigates the ability of a regional climate model (RCM) to simulate the diurnal cycle of precipitation over southeast Australia, to provide a basis for understanding the mechanisms that drive diurnal variability. When compared with 195 observation gauges, the RCM tends to simulate too many occurrences and too little intensity for precipitation events at the 3-hourly time scale. However, the overall precipitation amounts are well simulated and the diurnal variability in occurrences and intensities are generally well reproduced, particularly in spring and summer. In terms of precipitation amounts, the RCM overestimated the diurnal cycle during the warmer months but was reasonably accurate during winter. The timing of the maxima and minima was found to match the observed timings well. The spatial pattern of diurnal variability in the Weather Research and Forecasting model outputs was remarkably similar to the observed record, capturing many features of regional variability. The RCM diurnal cycle was dominated by the convective (subgrid scale) precipitation. In the RCM the diurnal cycle of convective precipitation over land corresponds well to atmospheric instability and thermally triggered convection over large areas, and also to the large-scale moisture convergence at 700 hPa along the east coast, with the strongest diurnal cycles present where these three mechanisms are in phase.
A foundation for universal T-cell based immunotherapy: T cells engineered to express a CD19-specific chimeric-antigen-receptor and eliminate expression of endogenous TCR
Authors: Torikai Hiroki , Reik Andreas , Liu Pei-Qi , Zhou Yuanyue , Zhang Ling , Maiti Sourindra , Huls Helen , Miller Jeffrey C. , Kebriaei Partow , Rabinovitch Brian , Lee Dean A. , Champlin Richard E. , Bonini Chiara , Naldini Luigi , Rebar Edward J. , Gregory Philip D. , Holmes Michael C. , Cooper Laurence J. N.
Published: April 2012

Clinical-grade T cells are genetically modified ex vivo to express a chimeric antigen receptor (CAR) to redirect specificity to a tumor associated antigen (TAA) thereby conferring antitumor activity in vivo. T cells expressing a CD19-specific CAR recognize B-cell malignancies in multiple recipients independent of major histocompatibility complex (MHC) because the specificity domains are cloned from the variable chains of a CD19 monoclonal antibody. We now report a major step toward eliminating the need to generate patient-specific T cells by generating universal allogeneic TAA-specific T cells from one donor that might be administered to multiple recipients. This was achieved by genetically editing CD19-specific CAR+ T cells to eliminate expression of the endogenous αβ T-cell receptor (TCR) to prevent a graft-versus-host response without compromising CAR-dependent effector functions. Genetically modified T cells were generated using the Sleeping Beauty system to stably introduce the CD19-specific CAR with subsequent permanent deletion of α or β TCR chains with designer zinc finger nucleases. We show that these engineered T cells display the expected property of having redirected specificity for CD19 without responding to TCR stimulation. CAR+TCRneg T cells of this type may potentially have efficacy as an off-the-shelf therapy for investigational treatment of B-lineage malignancies.
Statistical limit superior and limit inferior in intuitionistic fuzzy normed spaces
Authors: Alghamdi Mohammad Ali , Alotaibi Abdullah , Danish Lohani Qutubuddin Mohammad , Mursaleen Mohammad
Published: April 2012

Recently, the concepts of statistical convergence, ideal convergence and lacunary statistical convergence have been studied in intuitionistic fuzzy normed spaces. In this article, we study the concepts of statistical limit superior and statistical limit inferior in intuitionistic fuzzy normed spaces. We also give an example to compute these points in intuitionistic fuzzy normed spaces.

AMS Subject Classification (2000): 40A05; 40D25; 11B05; 60H10; 60B99; 26A03.
Cardiac tamponade related to a coronary injury by a pericardial calcification: an unusual complication
Authors: Cypierre Anne , Pesteil Francis , Cassat Claude , Parraf François , Bellier Rémy , Ursulet Lionel , Eveno Claire , Vignon Philippe , François Bruno
Published: April 2012

Background

Cardiac tamponade is a rare but severe complication of pericardial effusion with a poor prognosis. Prompt diagnosis using transthoracic echocardiography allows guiding initial therapeutic management. Although etiologies are numerous, cardiac tamponade is more often due to a hemopericardium. Rarely, a coronary injury may result in such a hemopericardium with cardiac tamponade. Coronary artery aneurysm are the main etiologies but blunt, open chest trauma or complication of endovascular procedures have also been described.

Case presentation

A 83-year-old hypertensive man presented for dizziness and hypotension. The patient had oliguria and mottled skin. Transthoracic echocardiography disclosed a circumferential pericardial effusion with a compressed right atrium, confirmed by contrast-enhanced thoracic CT scan. A pig-tail catheter allowed to withdraw 500 mL of blood, resulting in a transient improvement of hemodynamics. Rapidly, recurrent hypotension prompted a reoperation. An active bleeding was identified at the level of the retroventricular coronary artery. The pericardium was thickened with several "sharping" calcified plaques in the vicinity of the bleeding areas. On day 2, vasopressors were stopped and the patient was successfully extubated. Final diagnosis was a spontaneous cardiac tamponade secondary to a coronary artery injury attributed to a "sharping"calcified pericardial plaque.

Conclusion

Cardiac tamponade secondary to the development of a hemopericardium may develop as the result of a myocardial and coronary artery injury induced by a calcified pericardial plaque.
Using record linkage to monitor equity and variation in screening programmes
Authors: O’Reilly Dermot , Kinnear Heather , Rosato Michael , Mairs Adrian , Hall Clare
Published: April 2012

Background

Ecological or survey based methods to investigate screening uptake rates are fraught with many limitations which can be circumvented by record linkage between Census and health services datasets using variations in breast screening attendance as an exemplar. The aim of this current study is to identify the demographic, socio-economic factors associated with uptake of breast screening.

Methods

Record linkage study: combining 2001 Census data within the Northern Ireland Longitudinal Study (NILS) with data relating to validated breast screening histories from the National Breast Screening System. A cohort was identified of 37,059 women aged 48-64 at the Census who were invited for routine breast screening in the three years following the Census. All cohort attributes were as recorded on the Census form.

Results

The record linkage methodology enabled the records of almost 40,000 of those invited for screening to be analysed at an individual level, exceeding the largest published survey by a factor of ten. This produced a more robust analysis and demonstrated (in fully adjusted models) the lower uptake amongst non-married women and those in the lowest social class (OR 0.74; 95%CI 0.66, 0.82), factors that had not been reported earlier in the UK. In addition, with the availability of both individual and area information it was possible to show that the much lower screening uptake in urban areas is not due to differences in population composition suggesting unrecognised organisational problems.

Conclusions

Linkage of screening data to Census-based longitudinal studies is an efficient and powerful way to increase the evidence base on sources of variation in screening uptake within the UK.
Prognostic significance of MyD88 expression by human epithelial ovarian carcinoma cells
Authors: Zhu Yi , Huang Jian-Ming , Zhang Guo-Nan , Zha Xiao , Deng Bi-Fang
Published: April 2012

Background

MyD88 is an adaptor protein for TLR-4 signaling known to mediate paclitaxel resistance in epithelial ovarian carcinoma (EOC). This study examined the clinical significance of MyD88 expression in EOC.

Methods

MyD88 and TLR-4 expression were examined by immunocytochemistry in 109 specimens of ovarian tissues, comprising EOC (N = 83), borderline tumors (N = 9), benign cysts (N = 9) and normal ovarian tissue (N = 8), and clinical data collected by a retrospective chart review. The correlations between MyD88 expression and clinicopathological factors and outcomes were analyzed.

Results

TLR-4 expression was detected frequently in all the ovarian tissues. Distinct MyD88 expression was showed in EOC (64 of 83, 77.1 %), in borderline tumors (5 of 9, 55.6 %) and in benign cysts (3 of 9, 33.3 %), and normal ovarian tissue showed no MyD88 expression. Positive MyD88 expression significantly correlated with shorter disease-free and overall survival for EOC (P < 0.0001 and P = 0.0031), and high MyD88 expression was significantly correlated with tumor metastasis (P = 0.0012) for EOC. Univariate and multivariate analyses revealed that MyD88 expression was an independent prognostic factor for disease-free survival and overall survival for EOC.

Conclusion

Our data indicate that MyD88 expression is a significantly poor prognostic factor for EOC. A better understanding of the role of MyD88 expression in disease progression and outcome may be helpful for development of novel chemotherapies for patients with EOC.