bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary footprint of coevolving positions in genes
Authors: Dib Linda , Silvestro Daniele , Salamin Nicolas
Published: January 2014

Motivation: The analysis of molecular coevolution provides information on the potential functional and structural implication of positions along DNA sequences, and several methods are available to identify coevolving positions using probabilistic or combinatorial approaches. The specific nucleotide or amino acid profile associated with the coevolution process is, however, not estimated, but only known profiles, such as the Watson–Crick constraint, are usually considered a priori in current measures of coevolution.

Results: Here, we propose a new probabilistic model, Coev, to identify coevolving positions and their associated profile in DNA sequences while incorporating the underlying phylogenetic relationships. The process of coevolution is modeled by a 16 × 16 instantaneous rate matrix that includes rates of transition as well as a profile of coevolution. We used simulated, empirical and illustrative data to evaluate our model and to compare it with a model of ‘independent’ evolution using Akaike Information Criterion. We showed that the Coev model is able to discriminate between coevolving and non-coevolving positions and provides better specificity and specificity than other available approaches. We further demonstrate that the identification of the profile of coevolution can shed new light on the process of dependent substitution during lineage evolution.

Availability:  http://www2.unil.ch/phylo/bioinformatics/coev

Contact:  nicolas.salamin@unil.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
Authors: Gatto Laurent , Breckels Lisa M. , Wieczorek Samuel , Burger Thomas , Lilley Kathryn S.
Published: January 2014

Motivation: Experimental spatial proteomics, i.e. the high-throughput assignment of proteins to sub-cellular compartments based on quantitative proteomics data, promises to shed new light on many biological processes given adequate computational tools.

Results: Here we present pRoloc, a complete infrastructure to support and guide the sound analysis of quantitative mass-spectrometry-based spatial proteomics data. It provides functionality for unsupervised and supervised machine learning for data exploration and protein classification and novelty detection to identify new putative sub-cellular clusters. The software builds upon existing infrastructure for data management and data processing.

Availability:  pRoloc is implemented in the R language and available under an open-source license from the Bioconductor project (http://www.bioconductor.org/). A vignette with a complete tutorial describing data import/export and analysis is included in the package. Test data is available in the companion package pRolocdata.

Contact:  lg390@cam.ac.uk
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation
Authors: Stecher Glen , Liu Li , Sanderford Maxwell , Peterson Daniel , Tamura Koichiro , Kumar Sudhir
Published: January 2014

Summary: Computational diagnosis of amino acid variants in the human exome is the first step in assessing the disruptive impacts of non-synonymous single nucleotide variants (nsSNVs) on human health and disease. The Molecular Evolutionary Genetics Analysis software with mutational diagnosis (MEGA-MD) is a suite of tools developed to forecast the deleteriousness of nsSNVs using multiple methods and to explore nsSNVs in the context of the variability permitted in the long-term evolution of the affected position. In its graphical interface for use on desktops, it enables interactive computational diagnosis and evolutionary exploration of nsSNVs. As a web service, MEGA-MD is suitable for diagnosing variants on an exome scale. The MEGA-MD suite intends to serve the needs for conducting low- and high-throughput analysis of nsSNVs in diverse applications.

Availability:  www.megasoftware.net/mega-md and www.mypeg.info

Contact:  s.kumar@asu.edu
Environmental and fishery-driven dynamics of the common octopus (Octopus vulgaris) based on time-series analyses from leeward Algarve, southern Portugal
Authors: Sonderblohm Carlos P. , Pereira João , Erzini Karim
Published: January 2014

Dynamic factor analysis was used to explore monthly landings per unit effort (LPUE) series of Octopus vulgaris and environmental variables recorded in the southwest Iberian Peninsula, south Portugal. Despite the large fluctuations in the octopus abundance series, results showed a strong aggregation pattern for the last 3 months of the year, possibly related to the input of new recruits to the fishery. The calculated common trend for the 12 months time-series presented significant correlations with autumn rainfall of the previous year (lag − 1), particularly for the October, November, and December series. Other important correlations were found for the Western Mediterranean Oscillation index (lag − 1), Ekman transport, summer river run-off (lag − 1), horizontal and vertical component of windstress, among others. The main trend describes a moderate steady increase in LPUE during the last 10 years, suggesting that octopus abundance has increased from 1990 to 2010. The strong correlations of the monthly octopus LPUE series, together with the annual life cycle, suggest that after environmentally controlled recruitment, population dynamics is largely fishery driven, resulting in strong seasonality in the landings.
A framework for mapping small-scale coastal fisheries using fishers' knowledge
Authors: Léopold Marc , Guillemot Nicolas , Rocklin Delphine , Chen Cheryl
Published: January 2014

Collecting spatial information on fisheries catch and effort is essential to understanding the spatial processes of exploited population dynamics and to manage heterogeneously distributed resources and uses. The use of fishers' knowledge through geographical information systems (GISs) is increasingly considered as a promising source of local information on small-scale coastal fisheries. In this paper we describe the first framework for mapping entire small-scale coastal fisheries using fishers' knowledge on catch size and fishing effort. Four mangrove and coral reef fisheries targeting invertebrates or finfish in New Caledonia (southwest Pacific) were mapped following a five-step framework: (i) stratified random sampling of regular fishers; (ii) collection of fishers' knowledge of fishing areas, fishing effort, and catch size through map-based interviews; (iii) data integration into a spatial geodatabase; (iv) statistical extrapolation of fisher data to the fishery scale; and (v) mapping of catch, effort, and catch per unit effort (CPUE) for each fishery using a GIS overlay procedure. We found evidence that fishers' knowledge supplied precise and accurate quantitative and spatial information on catch size, fishing effort and CPUE for entire fisheries. Fisheries maps captured the fine-scale spatial distribution of fishing activities in a variety of ways according to target taxa, gear type, and home ports. Applications include area-based marine conservation planning and fishery monitoring, management, and governance. This integrated framework can be generalized to a large range of data-poor coastal and inland small-scale fisheries.
Transcriptional repressor NIR interacts with the p53-inhibiting ubiquitin ligase MDM2
Authors: Heyne Kristina , Förster Juliane , Schüle Roland , Roemer Klaus
Published: January 2014

NIR (novel INHAT repressor) can bind to p53 at promoters and inhibit p53-mediated gene transactivation by blocking histone acetylation carried out by p300/CBP. Like NIR, the E3 ubiquitin ligase MDM2 can also bind and inhibit p53 at promoters. Here, we present data indicating that NIR, which shuttles between the nucleolus and nucleoplasm, not only binds to p53 but also directly to MDM2, in part via the central acidic and zinc finger domain of MDM2 that is also contacted by several other nucleolus-based MDM2/p53-regulating proteins. Like some of these, NIR was able to inhibit the ubiquitination of MDM2 and stabilize MDM2; however, unlike these nucleolus-based MDM2 regulators, NIR did not inhibit MDM2 to activate p53. Rather, NIR cooperated with MDM2 to repress p53-induced transactivation. This cooperative repression may at least in part involve p300/CBP. We show that NIR can block the acetylation of p53 and MDM2. Non-acetylated p53 has been documented previously to more readily associate with inhibitory MDM2. NIR may thus help to sustain the inhibitory p53:MDM2 complex, and we present evidence suggesting that all three proteins can indeed form a ternary complex. In sum, our findings suggest that NIR can support MDM2 to suppress p53 as a transcriptional activator.
An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments
Authors: Duitama Jorge , Quintero Juan Camilo , Cruz Daniel Felipe , Quintero Constanza , Hubmann Georg , Foulquié-Moreno Maria R. , Verstrepen Kevin J. , Thevelein Johan M. , Tohme Joe
Published: January 2014

Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.
Heat Shock Protein 72 Expressing Stress in Sepsis: Unbridgeable Gap between Animal and Human Studies—A Hypothetical “Comparative” Study
Authors: Briassoulis George , Briassouli Efrossini , Fitrolaki Diana-Michaela , Plati Ioanna , Apostolou Kleovoulos , Tavladaki Theonymfi , Spanaki Anna-Maria
Published: January 2014

Heat shock protein 72 (Hsp72) exhibits a protective role during times of increased risk of pathogenic challenge and/or tissue damage. The aim of the study was to ascertain Hsp72 protective effect differences between animal and human studies in sepsis using a hypothetical “comparative study” model. Forty-one in vivo (56.1%), in vitro (17.1%), or combined (26.8%) animal and 14 in vivo (2) or in vitro (12) human Hsp72 studies (P<0.0001) were enrolled in the analysis. Of the 14 human studies, 50% showed a protective Hsp72 effect compared to 95.8% protection shown in septic animal studies (P<0.0001). Only human studies reported Hsp72-associated mortality (21.4%) or infection (7.1%) or reported results (14.3%) to be nonprotective (P<0.001). In animal models, any Hsp72 induction method tried increased intracellular Hsp72 (100%), compared to 57.1% of human studies (P<0.02), reduced proinflammatory cytokines (28/29), and enhanced survival (18/18). Animal studies show a clear Hsp72 protective effect in sepsis. Human studies are inconclusive, showing either protection or a possible relation to mortality and infections. This might be due to the fact that using evermore purified target cell populations in animal models, a lot of clinical information regarding the net response that occurs in sepsis is missing.
Optimizing Maxillary Aesthetics of a Severe Compromised Tooth through Orthodontic Movement and Dental Implants
Authors: de Molon Rafael Scaf , de Avila Erica Dorigatti , Cirelli Joni Augusto , Cardoso Mauricio de Almeida , Capelozza-Filho Leopoldino , Borelli Barros Luiz Antonio
Published: January 2014

Treatment of severe compromised tooth in the maxillary anterior area still poses great challenge to the clinicians. Several treatment modalities have been proposed to restore the function and aesthetics in teeth with advanced periodontal disease. The present study aims to report a case of traumatic injury of a left-maxillary central incisor with ridge preservation, orthodontic movement, and implant therapy. A 45-year-old woman underwent the proposed treatment for her left central incisor: basic periodontal therapy, xenogenous bone graft, and guided bone regeneration (GBR). Six months after the graft procedure, orthodontic movement by means of alignment and leveling was made and a coronal displacement of the gingival margin and vertical bone apposition could be observed after 13 months of active movement. Afterwards, a dental implant was placed followed by a connective tissue graft and immediate provisionalization of the crown. In conclusion, orthodontic movement was effective to improve the gingival tissue and alveolar bone prior to implant placement favoring the aesthetic results. Six years postoperatively, the results revealed height and width alveolar bone gain indicating that the treatment proposed was able to restore all the functional and aesthetic parameters.
Silencing Sexually Transmitted Infections: Topical siRNA-Based Interventions for the Prevention of HIV and HSV
Authors: Wheeler Lee Adam
Published: January 2014

The global impact of sexually transmitted infections (STIs) is significant. The sexual transmission of viruses such as herpes simplex virus type-2 (HSV-2) and the human immunodeficiency virus type-1 (HIV-1), has been especially difficult to control. To date, no effective vaccines have been developed to prevent the transmission of these STIs. Although antiretroviral drugs have been remarkably successful in treating the symptoms associated with these viral infections, the feasibility of their widespread use for prevention purposes may be more limited. Microbicides might provide an attractive alternative option to reduce their spread. In particular, topically applied small inhibitory RNAs (siRNAs) have been shown to not only block transmission of viral STIs to mucosal tissues bothin vitroandin vivo, but also confer durable knockdown of target gene expression, thereby circumventing the need to apply a microbicide around the time of sexual encounter, when compliance is mostly difficult. Despite numerous clinical trials currently testing the efficacy of siRNA-based therapeutics, they have yet to be approved for use in the treatment of viral STIs. While several obstacles to their successful implementation in the clinic still exist, promising preclinical studies suggest that siRNAs are a viable modality for the future prevention and treatment of HSV and HIV.
Viability Discrimination of a Class of Control Systems on a Nonsmooth Region
Authors: Zhao Na , Lv Jianfeng , Yang Jinlin , Liu Xinzhi
Published: January 2014

The viability problem is an important field of study in control theory; the corresponding research has profound significance in both theory and practice. In this paper, we consider the viability for both an affine nonlinear hybrid system and a hybrid differential inclusion on a region with subdifferentiable boundary. Based on the nonsmooth analysis theory, we obtain a method to verify the viability condition at a point, when the boundary function of the region is subdifferentiable and its subdifferential is convex hull of many finite points.
Fatigue Durability Analysis of Collecting Rapping System in Electrostatic Precipitators under Impact Loading
Authors: Neyestanak Ali Akbar Lotfi , Adib Nazari Saeed , Imam Ali , Aghanajafi Cyrus
Published: January 2014

Due to the importance of collecting rapping system in electrostatic precipitators (ESP) and controlling the relevant damage under impact loading, fatigue durability of this system is analyzed in the present study based on the numerical and experimental results considering fatigue damage growth and vibration acceleration in the collecting system because of the successive impact of rapping hammers. By microscopic examination of the fracture surface of rapping hammer, beach marks obviously show typical fatigue failure in the rapping hammer arm. In addition, the microscopic examination of the cross section of the collecting plates indicates the corrosion voids which cause crack and eventually fatigue failure. The finite element method is applied to determine both the stress and concentration positions of dynamic stress on the rapping system under impact loading. The paper results can be utilized in system optimization and new material selection for the system by evaluating rapping system durability.
Structured P2P Overlay of Mobile Brokers for Realizing Publish/Subscribe Communication in VANET
Authors: Pandey Tulika , Garg Deepak , Gore Manoj Madhava
Published: January 2014

Publish/subscribe communication paradigm provides asynchrony and decoupling, making it an elegant alternative for designing applications in distributed and dynamic environment such as vehicular ad hoc networks (VANETs). In this paradigm, the broker is the most important component that decouples other two components, namely, publisher and subscriber. Previous research efforts have either utilized the deployment of distributed brokers on stationary road side info-stations or have assigned the role of broker to any moving vehicle on ad hoc basis. In one approach, lots of preinstalled infrastructures are needed whereas, in another, the quality of service is not guaranteed due to unpredictable moving and stopping patterns of vehicles. In this paper, we present the architecture of distributed mobile brokers which are dynamically reconfigurable in the form of structured P2P overlay and act as rendezvous points for matching publications and subscriptions. We have taken city buses in urban settings to act as mobile brokers whereas other vehicles are considered to be in role of publishers and subscribers. These mobile brokers also assist in locating a vehicle for successful and timely transfer of notifications. We have performed an extensive simulation study to compare our approach with previously proposed approaches. Simulation results establish the applicability of our approach.
On the Existence of Solutions for the Critical Fractional Laplacian Equation inℝN
Authors: Shen Zifei , Gao Fashun
Published: January 2014

We study existence of solutions for the fractional Laplacian equation-Δsu+Vxu=u2*s-2u+fx, uinℝN,u∈Hs(RN), with critical exponent2*s=2N/(N-2s),N>2s,s∈0, 1, whereVx≥0has a potential well andf:ℝN×ℝ→ℝis a lower order perturbation of the critical poweru2*s-2u. By employing the variational method, we prove the existence of nontrivial solutions for the equation.
Cyclosporine and Herbal Supplement Interactions
Authors: Colombo D. , Lunardon L. , Bellia G.
Published: January 2014

Cyclosporine (CyA) is a well-known immunosuppressant with a narrow therapeutic window. Its bioavailability is affected by many other traditional drugs and herbal extracts. Cytochrome P-450 isoenzymes CYP3A4 and CYP3A5 and protein P-glycoprotein (P-gp) are involved in CyA bioavailability. Interactions of CyA with herbal extracts are not well known, but, given their increased concomitant use, it is important to know which extracts, many of which are commonly self-prescribed, can affect CyA blood concentrations. Decreased CyA blood concentration has been shown with St John’s wort in case reports and, in vivo animal studies, with ginger, liquorice, scutellariae radix, and quercetin. Increased CyA concentration has been reported in patients with grapefruit juice, chamomile, or berberine, and with cannabidiol or resveratrol in animal studies. Effects ofEchinaceaandSerenoa repenson CyA levels have not been shown consistently, but concomitant use should be avoided. Although findings from animal studies cannot be directly translated into humans, avoiding concomitant use of herbal extracts is prudent until human clinical studies have ruled out any possible interaction. Clinicians should interview their patients carefully about their use of herbal supplements before CyA administration, and those receiving CyA should be warned about possible interactions between herbal preparations and CyA.
Bedside Percutaneous Tracheostomy versus Open Surgical Tracheostomy in Non-ICU Patients
Authors: Brotfain Evgeni , Koyfman Leonid , Frenkel Amit , Semyonov Michael , Peiser Jochanan G. , Hayun-Maman Hagit , Boyko Matthew , Gruenbaum Shaun E. , Zlotnik Alexander , Klein Moti
Published: January 2014

Percutaneous bedside tracheostomy (PBT) is a one of the common and safe procedures in intensive care units through the world. In the present paper we published our clinical experience with a performance of PBTs in the regular ward by intensive care physicians’ team. We found it safe and similar outcome in comparison to open surgical tracheostomy method in operation room by ENT team. The performance of PBT in the regular ward showed potential economic advantages in saving medical staff and operating room resources.
Antimicrobial Activity of Thin Solid Films of Silver Doped Hydroxyapatite Prepared by Sol-Gel Method
Authors: Iconaru Simona Liliana , Chapon Patrick , Le Coustumer Philippe , Predoi Daniela
Published: January 2014

In this work, the preparation and characterization of silver doped hydroxyapatite thin films were reported and their antimicrobial activity was characterized. Silver doped hydroxyapatite (Ag:HAp) thin films coatings substrate was prepared on commercially pure Si disks by sol-gel method. The silver doped hydroxyapatite thin films were characterized by various techniques such as Scanning electron microscopy (SEM) with energy Dispersive X-ray attachment (X-EDS), Fourier transform infrared spectroscopy (FT-IR), and glow discharge optical emission spectroscopy (GDOES). These techniques have permitted the structural and chemical characterisation of the silver doped hydroxyapatite thin films. The antimicrobial effect of the Ag:HAp thin films onEscherichia coliandStaphylococcus aureusbacteria was then investigated. This is the first study on the antimicrobial effect of Ag:HAp thin films obtained by sol-gel method. The results of this study have shown that the Ag:HAp thin films withxAg=0.5are effective againstE. coliandS. aureusafter 24 h.
Area Efficient Implementation of MTI Processing Module on a Reconfigurable Platform
Authors: Yousuf Munaza , Aziz Arshad , Mahmud Riaz
Published: January 2014

This paper presents an area efficient Field Programmable Gate Array (FPGA) based digital design of a processing module for MTI radar. Signal contaminated with noise and clutter is modelled to test the efficacy of the design algorithms. For flexibility of design and to achieve optimized results, we have combined the high-level utility of MATLAB with the flexibility and optimization on FPGA for this implementation. Two- and three-pulse cancellers are chosen for design due to its simplicity in both concept and implementation. The results obtained are efficient in terms of enhanced throughput per Slice (TPA) of 1.146, that is, occupying fewer area resources on hardware while achieving optimized speed. The outcomes show that this design of MTI radar processor has many advantages, such as high processing precision, strong processing ability, real time, and low cost. All these advantages greatly contribute to the design requirements and make it appropriate for the application of high-speed signal processing.
Using Targeted Virotherapy to Treat a Resistant Ewing Sarcoma Model: From the Bedside to the Bench and Back
Authors: Abdelbary Hesham , Brown Christopher W. , Werier Joel , Bell John
Published: January 2014

Metastatic Ewing sarcoma (EWS) is often resistant to current multimodal chemotherapeutic regimens. Oncolytic virus therapy (OV) is a novel therapeutic platform whereby viruses can selectively infect as well as replicate in and kill tumor cells, while sparing normal tissues. The purpose of this study is to investigate the efficacy of the biotherapeutic oncolytic agent, vesicular stomatitis virus (VSVΔM51), to kill EWS cells that are resistant to conventional therapy. Our hypothesis is that systemic delivery of VSVΔM51 can demonstrate tumor-specific killing of resistant EWS cells, as well as a significant decrease of tumor burden in EWS bearing mice.Methods. A biopsy sample was obtained from a patient with metastatic EWS and was used to establish a novel EWS cell line.In vitroassays evaluated the oncolytic effect of vesicular stomatitis virus (VSVΔM51) on this cell line. EWS xenograft mice model bearing either lung or subcutaneous tumors was established to evaluate the antitumor specific oncolytic effect of VSVΔM51 after local and systemic delivery.Results. The established EWS cell line shared similar molecular and genetic traits to the patient’s original tumor specimen. VSVΔM51 effectively infected and killed EWS cellsin vitro. In vivo,VSVΔM51 selectively infected and killed EWS and led to significant delay in tumor growth.Conclusion. This study has been designed to implement a translational link between the bedside and the bench, where a specific challenging clinical scenario guided this basic science research. This research demonstrated that a sarcoma, which is resistant to current conventional standard therapies, is still susceptible to an alternative therapeutic platform, such as OV. Adding OV to the armamentarium of sarcoma treatment can enhance the future therapeutic approach towards these cancer patients.
L-Arginine Supplementation in Type II Diabetic Rats Preserves Renal Function and Improves Insulin Sensitivity by Altering the Nitric Oxide Pathway
Authors: Claybaugh Taylor , Decker Sarah , McCall Kelly , Slyvka Yuriy , Steimle Jerrod , Wood Aaron , Schaefer Megan , Thuma Jean , Inman Sharon
Published: January 2014

Rat studies demonstrated that type II diabetes mellitus (T2DM) decreases both the production and bioavailability of nitric oxide (NO). L-arginine (LA) provides the precursor for the production of NO. We hypothesized that LA dietary supplementation will preserve NO production via endothelial nitric oxide synthase (eNOS) causing renal microvascular vasodilation and increased glomerular blood flow and thus increasing glomerular filtration rate (GFR). This would impede the formation of reactive oxygen species which contributes to cell damage and death. LA supplementation preserved GFR in the treated diabetic rats compared to untreated diabetic rats. We provide evidence that this effect may be due to increased levels of eNOS and urinary cyclic guanosine monophosphate, which leads to renal microvascular vasodilation. Plasma nitrotyrosine was decreased in the LA treated rats; however, plasma nitrite levels remained unaffected as expected. Marked improvements in glucose tolerance were also observed in the LA treated diabetic rats. These results demonstrate that LA supplementation preserves NO activity and may delay the onset of insulin resistance and renal dysfunction during hyperglycemic stress. These results suggest the importance of the NO pathway in consequent renal dysfunction and in the development of insulin resistance in diabetic rats.
RNAi-Mediated Knockdown of IKK1 in Transgenic Mice Using a Transgenic Construct Containing the Human H1 Promoter
Authors: Moreno-Maldonado Rodolfo , Murillas Rodolfo , Navarro Manuel , Page Angustias , Suarez-Cabrera Cristian , Alameda Josefa P. , Bravo Ana , Casanova M. Llanos , Ramirez Angel
Published: January 2014

Inhibition of gene expression through siRNAs is a tool increasingly used for the study of gene function in model systems, including transgenic mice. To achieve perdurable effects, the stable expression of siRNAs by an integrated transgenic construct is necessary. For transgenic siRNA expression, promoters transcribed by either RNApol II or III (such as U6 or H1 promoters) can be used. Relatively large amounts of small RNAs synthesis are achieved when using RNApol III promoters, which can be advantageous in knockdown experiments. To study the feasibility of H1 promoter-driven RNAi-expressing constructs for protein knockdown in transgenic mice, we chose IKK1 as the target gene. Our results indicate that constructs containing the H1 promoter are sensitive to the presence of prokaryotic sequences and to transgene position effects, similar to RNApol II promoters-driven constructs. We observed variable expression levels of transgenic siRNA among different tissues and animals and a reduction of up to 80% in IKK1 expression. Furthermore, IKK1 knockdown led to hair follicle alterations. In summary, we show that constructs directed by the H1 promoter can be used for knockdown of genes of interest in different organs and for the generation of animal models complementary to knockout and overexpression models.
A Downlink and Uplink Alignment Scheme for Power Saving in IEEE 802.16 Protocol
Authors: Chen Jenhui , Tarn Woei-Hwa , Lee Jiann-Der
Published: January 2014

This study shows the problem of power saving mechanism (PSM) that sleep intervals of uplink (UL) connections do not synchronize with sleep intervals of downlink (DL) connections. That is, the energy of a mobile station (MS) is notreallysaved if the DL connections are in the sleep mode while the UL connections are in normal mode, and vice versa. To avoid the asynchronism of power saving (PS) between UL and DL connections, we invent a mechanism of DL connections regulating UL connections, calledDL and UL Alignment(DUAL) scheme, to improve the energy efficiency for PS. Considering that the buffer size of MS is limited, DUAL uses the mean packet arrival rate of ULλuand a relatively safe threshold of buffer sizeQTas the parameters to estimate the maximum allowable waiting time to align the UL with the DL connections. To analyze the performance of DUAL, a system model of PS is proposed to evaluate the performance of DUAL under different conditions. The correctness of performance analysis of DUAL is validated by using simulation with realistic parameters. Numerical experiments show that DUAL improves the energy conservation significantly when UL traffic is greater than DL traffic.
Occurrence ofBordetellaInfection in Pigs in Northern India
Authors: Kumar Sandeep , Singh Bhoj R. , Bhardwaj Monika , Singh Vidya
Published: January 2014

Bordetella bronchisepticainfection causing atrophic rhinitis in pigs is reported from almost all countries. In the present study, occurrence ofBordetellainfection in apparently healthy pigs was determined in 392 pigs sampled to collect 358 serum samples and 316 nasal swabs from Northern India by conventional bacterioscopy, detection of antigen with multiplex polymerase chain reaction (mPCR), and detection of antibodies with microagglutination test (MAT) and enzyme linked immune-sorbent assay (ELISA).Bordetella bronchisepticacould be isolated from six (1.92%) nasal swabs. Although isolates varied significantly in their antimicrobial sensitivity, they had similar plasmid profile. The genus specific and species specific amplicons were detected from 8.2% and 4.4% nasal swabs using mPCR withalcgene (genus specific) andflagene andfim2 gene (species specific) primers, respectively. Observations revealed that there may be other bordetellae infecting pigs because about 50% of the samples positive using mPCR for genus specific amplicons failed to confirm presence ofB. bronchiseptica. Of the pig sera tested with MAT and ELISA forBordetellaantibodies, 67.6% and 86.3% samples, respectively, were positive. For antigen detection mPCR was more sensitive than conventional bacterioscopy while for detection of antibodies neither of the two tests (MAT and ELISA) had specificity in relation to antigen detection. Study indicated high prevalence of infection in swine herds in Northern India.
Gastrointestinal Helminth Parasites Community of Fish Species in a Niger Delta Tidal Creek, Nigeria
Authors: Ogbeibu Anthony Ekata , Okaka Christopher Ehighaukho , Oribhabor Blessing Julius
Published: January 2014

A pool of fish species in a Niger Delta tidal creek, Buguma Creek, Nigeria, collected monthly from November 2004 to June 2006, at flood tides, were examined for gastrointestinal helminth parasites. The fish species were caught with hooks and lines and cast nets. Only nematode parasites were encountered in the study. Of the 1,149 fish specimens examined, 213 (representing 18.5%) were infected with various nematodes parasites.Dasyatis margaritahad the highest prevalence rate of 66.7% (2 infected out of 3 examined), followed byPseudotolithus(Pseudotolithus)senegalensiswith a prevalence of 41.7% (10 infected out of 24), while the least infected wereArius gigasandPomadasys jubeliniwith prevalence of 3.8% and 1.4%, respectively. No infection was recorded inElops lacerta,Gobiussp.,Lutjanus agennes,L. goreensis,Argyrosomus regius,Sphyraena guachancho,S. sphyraena,Cynoglossus senegalensis,Sarotherodon melanotheron,Tilapia guineensis,Liza falcipinnis,Mugil cephalus, andM. curema. The nematode parasites,Capillaria zederi, andAplectana hamatospiculahad the highest prevalence of 33.3% inD. margarita.Laurotravassoxyurissp. also had the same prevalence inTrichiurus lepturus.Goezia sigalasihad the second highest prevalence of 12.5% inP.(Fonticulus)elongatuswhich had the highest number examined, due to its high dominance in the water.
Contralateral Ear Occlusion for Improving the Reliability of Otoacoustic Emission Screening Tests
Authors: Papsin Emily , Harrison Adrienne L. , Carraro Mattia , Harrison Robert V.
Published: January 2014

Newborn hearing screening is an established healthcare standard in many countries and testing is feasible using otoacoustic emission (OAE) recording. It is well documented that OAEs can be suppressed by acoustic stimulation of the ear contralateral to the test ear. In clinical otoacoustic emission testing carried out in a sound attenuating booth, ambient noise levels are low such that the efferent system is not activated. However in newborn hearing screening, OAEs are often recorded in hospital or clinic environments, where ambient noise levels can be 60–70 dB SPL. Thus, results in the test ear can be influenced by ambient noise stimulating the opposite ear. Surprisingly, in hearing screening protocols there are no recommendations for avoiding contralateral suppression, that is, protecting the opposite ear from noise by blocking the ear canal. In the present study we have compared transient evoked and distortion product OAEs measured with and without contralateral ear plugging, in environmental settings with ambient noise levels <25 dB SPL, 45 dB SPL, and 55 dB SPL. We found out that without contralateral ear occlusion, ambient noise levels above 55 dB SPL can significantly attenuate OAE signals. We strongly suggest contralateral ear occlusion in OAE based hearing screening in noisy environments.
Design, Synthesis, andIn VitroKinetics Study of Atenolol Prodrugs for the Use in Aqueous Formulations
Authors: Karaman Rafik , Qtait Alaa , Dajani Khulod Khayyat , Abu Lafi Saleh
Published: January 2014

Based on DFT, MP2, and the density functional from Truhlar group (hybrid GGA: MPW1k) calculations for an acid-catalyzed hydrolysis of nine Kirby’s N-alkylmaleamic acids and two atenolol prodrugs were designed. The calculations demonstrated that the amide bond cleavage is due to intramolecular nucleophilic catalysis by the adjacent carboxylic acid group and the rate-limiting step is determined based on the nature of the amine leaving group. In addition, a linear correlation of the calculated and experimental rate values has drawn credible basis for designing atenolol prodrugs that are bitterless, are stable in neutral aqueous solutions, and have the potential to release the parent drug in a sustained release manner. For example, based on the calculated B3LYP/6-31 G (d,p) rates, the predictedt1/2(a time needed for 50% of the prodrug to be converted into drug) values for atenolol prodrugs ProD 1-ProD 2 at pH 2 were 65.3 hours (6.3 hours as calculated by GGA: MPW1K) and 11.8 minutes, respectively.In vitrokinetic study of atenolol prodrug ProD 1 demonstrated that thet1/2was largely affected by the pH of the medium. The determinedt1/2values in 1N HCl, buffer pH 2, and buffer pH 5 were 2.53, 3.82, and 133 hours, respectively.
Designing Lead Optimisation of MMP-12 Inhibitors
Authors: Borrotti Matteo , De March Davide , Slanzi Debora , Poli Irene
Published: January 2014

The design of new molecules with desired properties is in general a very difficult problem, involving heavy experimentation with high investment of resources and possible negative impact on the environment. The standard approach consists of iteration among formulation, synthesis, and testing cycles, which is a very long and laborious process. In this paper we address the so-called lead optimisation process by developing a new strategy to design experiments and modelling data, namely, the evolutionary model-based design for optimisation (EDO). This approach is developed on a very small set of experimental points, which change in relation to the response of the experimentation according to the principle of evolution and insights gained through statistical models. This new procedure is validated on a data set provided as test environment by Pickett et al. (2011), and the results are analysed and compared to the genetic algorithm optimisation (GAO) as a benchmark. The very good performance of the EDO approach is shown in its capacity to uncover the optimum value using a very limited set of experimental points, avoiding unnecessary experimentation.
Removal of EOG Artifacts from EEG Recordings Using Stationary Subspace Analysis
Authors: Zeng Hong , Song Aiguo
Published: January 2014

An effective approach is proposed in this paper to remove ocular artifacts from the raw EEG recording. The proposed approach first conducts the blind source separation on the raw EEG recording by the stationary subspace analysis (SSA) algorithm. Unlike the classic blind source separation algorithms, SSA is explicitly tailored to the understanding of distribution changes, where both the mean and the covariance matrix are taken into account. In addition, neither independency nor uncorrelation is required among the sources by SSA. Thereby, it can concentrate artifacts in fewer components than the representative blind source separation methods. Next, the components that are determined to be related to the ocular artifacts are projected back to be subtracted from EEG signals, producing the clean EEG data eventually. The experimental results on both the artificially contaminated EEG data and real EEG data have demonstrated the effectiveness of the proposed method, in particular for the cases where limited number of electrodes are used for the recording, as well as when the artifact contaminated signal is highly nonstationary and the underlying sources cannot be assumed to be independent or uncorrelated.
Rapid Spontaneous Resolution of Fibromatosis Colli in a 3-Week-Old Girl
Authors: Adamoli Paolo , Pavone Piero , Falsaperla Raffaele , Longo Roberta , Vitaliti Giovanna , Andaloro Claudio , Agostino Serra , Cocuzza Salvatore
Published: January 2014

Fibromatosis colli is an uncommon benign, congenital fibrous tumor or pseudotumor of the sternocleidomastoid muscle that manifests in infancy. In some of these patients tightening of the muscle results in torticollis. We report the case of a 3-week-old child, who presented with a neck mass localized in the left side with reduced mobility of the head. The diagnosis of fibromatosis colli was raised by ultrasound sonography. The mass regressed spontaneously within 3 months without surgical or physical treatment.
The Boundedness of Intrinsic Square Functions on the Weighted Herz Spaces
Authors: Wang Hua
Published: January 2014

We will obtain the strong type and weak type estimates of intrinsic square functions including the Lusin area integral, Littlewood-Paley𝒢-function, and𝒢λ*-function on the weighted Herz spacesK˙qα,p(w1,w2)(Kqα,p(w1,w2))with general weights.
Towards the Automated Analysis and Database Development of Defibrillator Data from Cardiac Arrest
Authors: Eftestøl Trygve , Sherman Lawrence D.
Published: January 2014

Background.During resuscitation of cardiac arrest victims a variety of information in electronic format is recorded as part of the documentation of the patient care contact and in order to be provided for case review for quality improvement. Such review requires considerable effort and resources. There is also the problem of interobserver effects.Objective.We show that it is possible to efficiently analyze resuscitation episodes automatically using a minimal set of the available information.Methods and Results.A minimal set of variables is defined which describe therapeutic events (compression sequences and defibrillations) and corresponding patient response events (annotated rhythm transitions). From this a state sequence representation of the resuscitation episode is constructed and an algorithm is developed for reasoning with this representation and extract review variables automatically. As a case study, the method is applied to the data abstraction process used in the King County EMS. The automatically generated variables are compared to the original ones with accuracies≥90%for 18 variables and≥85%for the remaining four variables.Conclusions.It is possible to use the information present in the CPR process data recorded by the AED along with rhythm and chest compression annotations to automate the episode review.
Optimal Manoeuvres of Underactuated Linear Mechanical Systems: The Case of Controlling Gantry Crane Operations
Authors: Woods S. , Szyszkowski W.
Published: January 2014

A method of solving optimal manoeuvre control of linear underactuated mechanical systems is presented. The nonintegrable constraints present in such systems are handled by adding dummy actuators and then by applying Lagrange multipliers to reduce their action to zero. The open- and closed-loop control schemes can be analyzed. The method, referred to as the constrained modal space optimal control (CMSOC), is illustrated in the examples of gantry crane operations.
A Real Representation Method for Solving Yakubovich-j-Conjugate Quaternion Matrix Equation
Authors: Song Caiqin , Feng Jun-e , Wang Xiaodong , Zhao Jianli
Published: January 2014

A new approach is presented for obtaining the solutions to Yakubovich-j-conjugate quaternion matrix equationX−AX^B=CYbased on the real representation of a quaternion matrix. Compared to the existing results, there are no requirements on the coefficient matrixA. The closed form solution is established and the equivalent form of solution is given for this Yakubovich-j-conjugate quaternion matrix equation. Moreover, the existence of solution to complex conjugate matrix equationX−AX¯B=CYis also characterized and the solution is derived in an explicit form by means of real representation of a complex matrix. Actually, Yakubovich-conjugate matrix equation over complex field is a special case of Yakubovich-j-conjugate quaternion matrix equationX−AX^B=CY. Numerical example shows the effectiveness of the proposed results.
Improving Light Outcoupling Efficiency for OLEDs with Microlens Array Fabricated on Transparent Substrate
Authors: Wang Jun , Li Weizhi , Wang Chong
Published: January 2014

Low light outcoupling efficiency restricts the wide application of organic light‐emitting diodes in solid state light market although the internal quantum efficiency of the device could reach near to 100%. In order to improve the output efficiency, different kinds of microlens array on the substrate emission surface were designed and simulated using light tracing method. Simulation results indicate that the microlens array on the substrate could efficiently improve the light output efficiency and an enhancement of 1.8 could be obtained with optimized microlens structure design. The microlens array with semicircle shape using polymer material was fabricated on glass substrate by a facile approach. Finally, the organic device with microlens array substrate was manufactured and the light output of the device with surface microlens structure could increase to 1.64 times comparing with the device without microlens.
Angiotensin-Converting Enzyme Gene Insertion/Deletion Polymorphism and Small Vessel Cerebral Stroke in Indian Population
Authors: Prabhakar Puttachandra , De Tanima , Nagaraja Dindagur , Christopher Rita
Published: January 2014

Background. Hypertension is an established risk factor for small-vessel cerebral stroke and the renin-angiotensin system plays an important role in the maintenance of blood pressure. We aimed at evaluating the contribution of the angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism to the risk of small-vessel stroke in south Indian population.Materials and Methods. We investigated 128 patients diagnosed with small-vessel stroke and 236 age, and gender-matched healthy controls.ACEI/D polymorphism was detected by polymerase chain reaction.Results. Hypertension was significantly more prevalent in the patient group and was associated with 6-fold increase in risk for stroke.ACEgenotypes were in Hardy-Weinberg equilibrium in both patients and controls. Prevalence of DD, ID, and II genotypes in cases (34.4%, 43.7%, and 28%) did not differ significantly from controls (31.8%, 43.2%, and 25%). The polymorphism was not associated with small-vessel stroke (OR: 1.34; 95% CI: 0.52–1.55). However, diastolic blood pressure was associated with theACEI/D genotypes in the patients. (DD;90.2±14.2>ID;86.2±11.9>II;82.3±7.8 mm Hg,  P=0.047).Conclusion. Our study showed that hypertension, but notACEI/D polymorphism, increased the risk of small-vessel stroke.
Sufficient Descent Conjugate Gradient Methods for Solving Convex Constrained Nonlinear Monotone Equations
Authors: Liu San-Yang , Huang Yuan-Yuan , Jiao Hong-Wei
Published: January 2014

Two unified frameworks of some sufficient descent conjugate gradient methods are considered. Combined with the hyperplane projection method of Solodov and Svaiter, they are extended to solve convex constrained nonlinear monotone equations. Their global convergence is proven under some mild conditions. Numerical results illustrate that these methods are efficient and can be applied to solve large-scale nonsmooth equations.
Systemic Oxidative Stress and Conversion to Dementia of Elderly Patients with Mild Cognitive Impairment
Authors: Cervellati Carlo , Romani Arianna , Seripa Davide , Cremonini Eleonora , Bosi Cristina , Magon Stefania , Bergamini Carlo M. , Valacchi Giuseppe , Pilotto Alberto , Zuliani Giovanni
Published: January 2014

Mild cognitive impairment (MCI) is regarded as a prodromal phase of late onset Alzheimer’s disease (LOAD). It has been proposed that oxidative stress (OxS) might be implicated in the pathogenesis of LOAD. The aim of this study was to investigate whether a redox imbalance measured as serum level of hydroperoxides (i.e., by-products of lipid peroxidation) and/or serum antioxidant capacity might be predictive of the clinical progression of MCI to LOAD. The levels of these two markers were measured in 111 patients with MCI (follow-up:2.0 ± 0.6years), 105 patients with LOAD, and 118 nondemented healthy controls. Multivariate analysis adjusted for potential confounding factors, including age, gender, smoking, and comorbidities, showed a significant increase (P<0.05) in baseline levels of OxS in MCI and LOAD as compared to cognitive healthy controls. No differences in either of OxS markers were found by comparing MCI patients who converted (n = 29) or not converted (n = 82) to LOAD. Overall, these results suggest that systemic OxS might be a precocious feature of MCI and LOAD. However, the role of OxS as an early prognostic marker of progression to LOAD needs further investigations.