bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference
Authors: Cornish Adam , Guda Chittibabu
Published: October 2015

High-throughput sequencing, especially of exomes, is a popular diagnostic tool, but it is difficult to determine which tools are the best at analyzing this data. In this study, we use the NIST Genome in a Bottle results as a novel resource for validation of our exome analysis pipeline. We use six different aligners and five different variant callers to determine which pipeline, of the 30 total, performs the best on a human exome that was used to help generate the list of variants detected by the Genome in a Bottle Consortium. Of these 30 pipelines, we found that Novoalign in conjunction with GATK UnifiedGenotyper exhibited the highest sensitivity while maintaining a low number of false positives for SNVs. However, it is apparent that indels are still difficult for any pipeline to handle with none of the tools achieving an average sensitivity higher than 33% or a Positive Predictive Value (PPV) higher than 53%. Lastly, as expected, it was found that aligners can play as vital a role in variant detection as variant callers themselves.
Phase II Study of Personalized Peptide Vaccination with Both a Hepatitis C Virus-Derived Peptide and Peptides from Tumor-Associated Antigens for the Treatment of HCV-Positive Advanced Hepatocellular Carcinoma Patients
Authors: Yutani Shigeru , Ueshima Kazuomi , Abe Kazumichi , Ishiguro Atsushi , Eguchi Junichi , Matsueda Satoko , Komatsu Nobukazu , Shichijo Shigeki , Yamada Akira , Itoh Kyogo , Sasada Tetsuro , Kudo Masatoshi , Noguchi Masanori
Published: October 2015

Objective. To evaluate safety and immune responses of personalized peptide vaccination (PPV) for hepatitis C virus- (HCV-) positive advanced hepatocellular carcinoma (HCC).Patients and Methods. Patients diagnosed with HCV-positive advanced HCC were eligible for this study. A maximum of four HLA-matched peptides were selected based on the preexisting IgG responses specific to 32 different peptides, which consisted of a single HCV-derived peptide at core protein positions 35–44 (C-35) and 31 peptides derived from 15 different tumor-associated antigens (TAAs), followed by subcutaneous administration once per week for 8 weeks. Peptide-specific cytotoxic T lymphocyte (CTL) and IgG responses were measured before and after vaccination.Results. Forty-two patients were enrolled. Grade 3 injection site skin reaction was observed in 2 patients, but no other PPV-related severe adverse events were noted. Peptide-specific CTL responses before vaccination were observed in only 3 of 42 patients, but they became detectable in 23 of 36 patients tested after vaccination. Peptide-specific IgG responses were also boosted in 19 of 36 patients. Peptide-specific IgG1 responses to both C-35 and TAA-derived peptides could be potentially prognostic for overall survival.Conclusion. Further clinical study of PPV would be warranted for HCV-positive advanced HCC, based on the safety and strong immune induction.
Protective Effect ofArtemisia asiaticaExtract and Its Active Compound Eupatilin against Cisplatin-Induced Renal Damage
Authors: Park Jun Yeon , Lee Dahae , Jang Hyuk-Jai , Jang Dae Sik , Kwon Hak Cheol , Kim Ki Hyun , Kim Su-Nam , Hwang Gwi Seo , Kang Ki Sung , Eom Dae-Woon
Published: October 2015

The present study investigated the renoprotective effect of anArtemisia asiaticaextract and eupatilin in kidney epithelial (LLC-PK1) cells. Although cisplatin is effective against several cancers, its use is limited due to severe nephrotoxicity. Eupatilin is a flavonoid compound isolated from theArtemisiaplant and possesses antioxidant as well as potent anticancer properties. In the LLC-PK1 cellular model, the decline in cell viability induced by oxidative stress, such as that induced by cisplatin, was significantly and dose-dependently inhibited by theA. asiaticaextract and eupatilin. The increased protein expressions of phosphorylated JNK and p38 by cisplatin in cells were markedly reduced afterA. asiaticaextract or eupatilin cotreatment. The elevated expression of cleaved caspase-3 was significantly reduced byA. asiaticaextract and eupatilin, and the elevated percentage of apoptotic cells after cisplatin treatment in LLC-PK1 cells was markedly decreased by cotreatment withA. asiaticaextract or eupatilin. Taken together, these results suggest thatA. asiaticaextract and eupatilin could cure or prevent cisplatin-induced renal toxicity without any adverse effect; thus, it can be used in combination with cisplatin to prevent nephrotoxicity.
Almost Periodic Solution for an Epidemic Prey-Predator System with Impulsive Effects and Multiple Delays
Authors: Tian Baodan , Chen Ning , Qiu Yanhong
Published: October 2015

A nonautonomous epidemic prey-predator system with impulsive effects and multiple delays is considered; further, there is an epidemic disease in the predator. By the mean-value theorem of multiple variables, integral inequalities, differential inequalities, and other mathematical analysis skills, sufficient conditions which guarantee the permanence of the system are obtained. Furthermore, by constructing a series of Lyapunov functionals it is proved that there exists a unique uniformly asymptotically stable almost periodic solution of the system.
Carbon Fiber Composites of Pure Polypropylene and Maleated Polypropylene Blends Obtained from Injection and Compression Moulding
Authors: Pérez-Rocha D. , Morales-Cepeda A. B. , Navarro-Pardo F. , Lozano-Ramírez T. , LaFleur P. G.
Published: October 2015

A comparative study of the mechanical performance of PP and PP/PP-g-MAH blends reinforced with carbon fibre (CF) obtained by two different moulding techniques is presented. Three filler contents were used for fabricating the composites: 1, 3, and 5 pph (parts per hundred). The crystallisation behaviour of the composites was studied by differential scanning calorimetry. Morphological and structural features of these samples were observed by atomic field microscopy and Fourier-transform infrared spectroscopy, respectively. Mechanical properties of the injection and compression moulded composites were evaluated by means of tensile and impact resistance tests. The fracture surface of the impacted samples was observed by scanning electron microscopy. The processing method had a noticeable effect on the results obtained in these tests. Young’s modulus was enhanced up to 147% when adding 5 pph CF to a PP matrix when processed by compression moulding. Addition of PP-g-MAH and CF had a favourable effect on the tensile and impact strength properties in most samples; these composites showed improved performance as the filler content was increased.
Proteomic Changes of Tissue-Tolerable Plasma Treated Airway Epithelial Cells and Their Relation to Wound Healing
Authors: Lendeckel Derik , Eymann Christine , Emicke Philipp , Daeschlein Georg , Darm Katrin , O’Neil Serena , Beule Achim G. , von Woedtke Thomas , Völker Uwe , Weltmann Klaus-Dieter , Jünger Michael , Hosemann Werner , Scharf Christian
Published: October 2015

Background. The worldwide increasing number of patients suffering from nonhealing wounds requires the development of new safe strategies for wound repair. Recent studies suggest the possibility of nonthermal (cold) plasma application for the acceleration of wound closure.Methods. Anin vitrowound healing model with upper airway S9 epithelial cells was established to determine the macroscopically optimal dosage of tissue-tolerable plasma (TTP) for wound regeneration, while a 2D-difference gel electrophoresis (2D-DIGE) approach was used to quantify the proteomic changes in a hypothesis-free manner and to evaluate the balance of beneficial and adverse effects due to TTP application.Results. Plasma doses from 30 s up to 360 s were tested in relation to wound closure after 24 h, 48 h, 72 h, 96 h, and 120 h, in which lower doses (30, 60, and 120 s) resulted in dose-dependent improved wound healing rate compared to untreated cells. Thereby, the 120 s dose caused significantly the best wound healing properties after 96 and 120 h. The proteome analysis combined with IPA revealed that a lot of affected stress adaptation responses are linked to oxidative stress response emphasizing oxidative stress as a possible key event in the regeneration process of epithelial cells as well as in the adaptation to plasma exposure. Further cellular and molecular functions like proliferation and apoptosis were significantly up- or downregulated by all TTP treatments but mostly by the 120 s dose.Conclusions. For the first time, we were able to show plasma effects on cellular adaptation of upper airway epithelial S9 cells improving wound healing. This is of particular interest for plasma application, for example, in the surgery field of otorhinolaryngology or internal medicine.
Research on the Preparation and Mechanism of the Organic Montmorillonite and Its Application in Drilling Fluid
Authors: Wang Xiaolong , Liu Baolin , Yu Peizhi
Published: October 2015

The study focused on the relation of structure, property, and application of composite prepared by organic cation intercalated montmorillonite (Mt). Herein a new kind of green and steady ionic liquid, 1‐hexadecyl‐3‐methylimidazolium chloride monohydrate (C12mimCl), was chosen as the intercalated agent. This study used molecular dynamics (MD) modeling to examine the interlayer microstructures of montmorillonite intercalated with C12mimCl. The C12mimCl intercalation was relatively fast with a large rate constant. The process was affected by the initial concentration of the solution; the basal spacing increased to 2.08 nm after intercalation. The coordination of electrostatic interaction and hydrogen bonding expelled water molecules out of the clay gallery and bound the layer together, which led to the dehydration of clay. The intercalation of C12minCl into Mt interlayer space affected rheology of the system and improved various properties. This organic clay composite was environmentally friendly and could be used in drilling fluid system. These models provided insights into the prediction of synthesized organic cationic‐clay microstructure and guidelines for relevant engineering applications.
Phenotypes, Risk Factors, and Mechanisms of Adult‐Onset Asthma
Authors: Ilmarinen Pinja , Tuomisto Leena E. , Kankaanranta Hannu
Published: October 2015

Asthma is a heterogeneous disease with many phenotypes, and age at disease onset is an important factor in separating the phenotypes. Genetic factors, atopy, and early respiratory tract infections are well‐recognized factors predisposing to childhood‐onset asthma. Adult‐onset asthma is more often associated with obesity, smoking, depression, or other life‐style or environmental factors, even though genetic factors and respiratory tract infections may also play a role in adult‐onset disease. Adult‐onset asthma is characterized by absence of atopy and is often severe requiring treatment with high dose of inhaled and/or oral steroids. Variety of risk factors and nonatopic nature of adult‐onset disease suggest that variety of mechanisms is involved in the disease pathogenesis and that these mechanisms differ from the pathobiology of childhood‐onset asthma with prevailing Th2 airway inflammation. Recognition of the mechanisms and mediators that drive the adult‐onset disease helps to develop novel strategies for the treatment. The aim of this review was to summarize the current knowledge on the pathogenesis of adult‐onset asthma and to concentrate on the mechanisms and mediators involved in establishing adult‐onset asthma in response to specific risk factors. We also discuss the involvement of these mechanisms in the currently recognized phenotypes of adult‐onset asthma.
Effects of Dietary Supplementation of Oregano Essential Oil to Sows on Oxidative Stress Status, Lactation Feed Intake of Sows, and Piglet Performance
Authors: Tan Chengquan , Wei Hongkui , Sun Haiqing , Ao Jiangtao , Long Guang , Jiang Siwen , Peng Jian
Published: October 2015

Fifty-four multiparous large white sows were used to determine the effects of supplementing oregano essential oil (OEO) to the gestation and lactation diets on oxidative stress status, lactation feed intake, and their piglet performance. Two groups were fed diets with (OEO;n=28) or without (Control;n=26) supplemental 15 mg/kg OEO during gestation and lactation. The serum levels of reactive oxygen species (ROS) (P<0.05), 8-hydroxy-deoxyguanosine (8-OHdG) (P<0.05), and thiobarbituric acid reactive substances (TBARS) (P<0.05) were higher during gestation (days 90 and 109) and lactation (days 1 and 3) than in early gestation (day 10). Compared with the control group, the OEO diet significantly reduced sows’ serum concentrations of 8-OHdG (P<0.05) and TBARS (P<0.01) on day 1 of lactation. The OEO diet increased the sows’ counts of faecallactobacillus(P<0.001) while reducingEscherichia coli(P<0.001) andEnterococcus(P<0.001). In the third week of lactation the treatment tended to increase sow’s feed intake (P=0.07), which resulted in higher average daily gain (P<0.01) of piglets. Our results demonstrated that there is an increased systemic oxidative stress during late gestation and early lactation of sows. The OEO supplementation to sows’ diet improved performance of their piglets, which may be attributed to the reduced oxidative stress.
Middle Cerebral Artery Atherosclerotic Plaques in Recent Small Subcortical Infarction: A Three-Dimensional High-resolution MR Study
Authors: Zou Xiao-Dong , Chung Yiu-Cho , Zhang Lei , Han Ying , Yang Qi , Jia Jianping
Published: October 2015

Purpose. Conventional two-dimensional vessel wall imaging has been used to depict the middle cerebral artery (MCA) wall in patients with recent small subcortical infarctions (RSSIs). However, its clinical use has been limited by restricted spatial coverage, low signal-to-noise ratio (SNR), and long scan time. We used a novel three-dimensional high-resolution MR imaging (3D HR-MRI) technique to investigate the presence, locations, and contrast-enhanced patterns of MCA plaques and their relationship with RSSI.Methods. Nineteen consecutive patients with RSSI but no luminal stenosis on MR angiography were prospectively enrolled. 3D HR-MRI was performed using a T1w-SPACE sequence at 3.0 T. The presence, locations, and contrast-enhanced patterns of the MCA plaques on the ipsilateral and contralateral sides to the RSSI were analyzed.Results. Eighteen patients successfully completed the study. MCA atherosclerotic plaques occurred more frequently on the ipsilateral than the contralateral side to the RSSI (72.2% versus 33.3%,P=0.044). The occurrence of superiorly located plaques was significantly higher on the ipsilateral than the contralateral side of the MCA (66.7% versus 27.8%;P=0.044).Conclusions. Superiorly located plaques are closely associated with RSSI. 3D high-resolution vessel wall imaging may be a potential tool for etiologic assessment of ischemic stroke.
Laterality of Stance during Optic Flow Stimulation in Male and Female Young Adults
Authors: Persiani Michela , Piras Alessandro , Squatrito Salvatore , Raffi Milena
Published: October 2015

During self-motion, the spatial and temporal properties of the optic flow input directly influence the body sway. Men and women have anatomical and biomechanical differences that influence the postural control during visual stimulation. Given that recent findings suggest a peculiar role of each leg in the postural control of the two genders, we investigated whether the body sway during optic flow perturbances is lateralized and whether anteroposterior and mediolateral components of specific center of pressure (COP) parameters of the right and left legs differ, reexamining a previous experiment (Raffi et al. (2014)) performed with two, side-by-side, force plates. Experiments were performed on 24 right-handed and right-footed young subjects. We analyzed five measures related to the COP of each foot and global data: anteroposterior and mediolateral range of oscillation, anteroposterior and mediolateral COP velocity, and sway area. Results showed that men consistently had larger COP parameters than women. The values of the COP parameters were correlated between the two feet only in the mediolateral axis of women. These findings suggest that optic flow stimulation causes asymmetry in postural balance and different lateralization of postural controls in men and women.
Impact of Moderate Heat, Carvacrol, and Thymol Treatments on the Viability, Injury, and Stress Response ofListeria monocytogenes
Authors: Guevara L. , Antolinos V. , Palop A. , Periago P. M.
Published: October 2015

The microbial safety and stability of minimally processed foods are based on the application of combined preservative factors. Since microorganisms are able to develop adaptive networks to survive under conditions of stress, food safety may be affected, and therefore understanding of stress adaptive mechanisms plays a key role in designing safe food processing conditions. In the present study, the viability and the sublethal injury ofListeria monocytogenesexposed to moderate heat (55°C) and/or essential oil compounds (carvacrol and thymol, 0.3 mM) treatments were studied. Synergistic effects were obtained when combining mild heat (55°C) with one or both essential oil compounds, leading to inactivation kinetics values three to four times lower than when using heat alone. All the treatments applied caused some injury in the population. The injury levels ranged from around 20% of the surviving population under the mildest conditions to more than 99.99% under the most stringent conditions. Protein extracts of cells exposed to these treatments were analysed by two-dimensional gel electrophoresis. The results obtained revealed that stressed cells exhibited differential protein expression to control cells. The proteins upregulated under these stressing conditions were implicated, among other functions, in stress response, metabolism, and protein refolding.
Parametric Study on Dynamic Response of Fiber Reinforced Polymer Composite Bridges
Authors: Prachasaree Woraphot , Sangkaew Attapon , Limkatanyu Suchart , GangaRao Hota V. S.
Published: October 2015

Because of high strength and stiffness to low self-weight ratio and ease of field installation, fiber reinforced polymer (FRP) composite materials are gaining popularity as the materials of choice to replace deteriorated concrete bridge decks. FRP bridge deck systems with lower damping compared to conventional bridge decks can lead to higher amplitudes of vibration causing dynamically active bridge deck leading serviceability problems. The FRP bridge models with different bridge configurations and loading patterns were simulated using finite element method. The dynamic response results under varying FRP deck system parameters were discussed and compared with standard specifications of bridge deck designs under dynamic loads. In addition, the dynamic load allowance equation as a function of natural frequency, span length, and vehicle speed was proposed in this study. The proposed dynamic load allowance related to the first flexural frequency was presented herein. The upper and lower bounds’ limits were established to provide design guidance in selecting suitable dynamic load allowance for FRP bridge systems.
Surveillance of Food- and Smear-Transmitted Pathogens in European Soldiers with Diarrhea on Deployment in the Tropics: Experience from the European Union Training Mission (EUTM) Mali
Authors: Frickmann Hagen , Warnke Philipp , Frey Claudia , Schmidt Salvatore , Janke Christian , Erkens Kay , Schotte Ulrich , Köller Thomas , Maaßen Winfried , Podbielski Andreas , Binder Alfred , Hinz Rebecca , Queyriaux Benjamin , Wiemer Dorothea , Schwarz Norbert Georg , Hagen Ralf Matthias
Published: October 2015

Introduction. Since 2013, European soldiers have been deployed on the European Union Training Mission (EUTM) in Mali. From the beginning, diarrhea has been among the most “urgent” concerns. Diarrhea surveillance based on deployable real-time PCR equipment was conducted between December 2013 and August 2014.Material and Methods. In total, 53 stool samples were obtained from 51 soldiers with acute diarrhea. Multiplex PCR panels comprised enteroinvasive bacteria, diarrhea-associatedEscherichia coli(EPEC, ETEC, EAEC, and EIEC), enteropathogenic viruses, and protozoa. Noroviruses were characterized by sequencing. Cultural screening for Enterobacteriaceae with extended-spectrum beta-lactamases (ESBL) with subsequent repetitive sequence-based PCR (rep-PCR) typing was performed. Clinical information was assessed.Results. Positive PCR results for diarrhea-associated pathogens were detected in 43/53 samples, comprising EPEC (n=21), ETEC (n=19), EAEC (n=15), Norovirus (n=10),Shigellaspp./EIEC (n=6),Cryptosporidium parvum(n=3),Giardia duodenalis(n=2),Salmonellaspp. (n=1), Astrovirus (n=1), Rotavirus (n=1), and Sapovirus (n=1). ESBL-positive Enterobacteriaceae were grown from 13 out of 48 samples. Simultaneous infections with several enteropathogenic agents were observed in 23 instances. Symptoms were mild to moderate. There were hints of autochthonous transmission.Conclusions. Multiplex real-time PCR proved to be suitable for diarrhea surveillance on deployment. Etiological attribution is challenging in cases of detection of multiple pathogens.
Fracture and Delamination Assessment of Prestressed Composite Concrete for Use with Pipe Jacking Method
Authors: Gong Qing , Zhu Hehua , Yan Zhiguo , Huang Boqi , Zhang Yao , Dong Zeyu
Published: October 2015

Prestressed composite concrete pipe (PCCP) has been widely used in water-transmission line and has been proven with many advantages over pure concrete or steel pipes, such as high performance with relatively low cost for materials as well as simplified installation and construction process. Recent efforts have been made to enable the PCCP structure suitable for pipe jacking method so as to replace the conventional cut and cover method. In this way, the construction time, disturbance to nearby structures, and the cost can be greatly reduced. In this paper, we present the full-scale experimental and numerical studies of PCCP and the evaluation of fracture and delamination behaviour of the structure when it is used with pipe jacking construction method subjected to various jacking forces and ground conditions.
Cellular Nutrition in Complex Three-Dimensional Scaffolds: A Comparison between Experiments and Computer Simulations
Authors: Bergemann Claudia , Elter Patrick , Lange Regina , Weißmann Volker , Hansmann Harald , Klinkenberg Ernst-Dieter , Nebe Barbara
Published: October 2015

Studies on bone cell ingrowth into synthetic, porous three-dimensional (3D) implants showed difficulties arising from impaired cellular proliferation and differentiation in the core region of these scaffolds with increasing scaffold volumein vitro. Therefore, we developed anin vitroperfusion cell culture module, which allows the analysis of cells in the interior of scaffolds under different medium flow rates. For each flow rate the cell viability was measured and compared with results from computer simulations that predict the local oxygen supply and shear stress inside the scaffold based on the finite element method. We found that the local cell viability correlates with the local oxygen concentration and the local shear stress. On the one hand the oxygen supply of the cells in the core becomes optimal with a higher perfusion flow. On the other hand shear stress caused by high flow rates impedes cell vitality, especially at the surface of the scaffold. Our results demonstrate that both parameters must be considered to derive an optimal nutrient flow rate.
Optimal Design of FPGA Switch Matrix with Ion Mobility Based Nonvolatile ReRAM
Authors: Hai-yun Peng , Wen-gang Zhou
Published: October 2015

There are high demands for research of new device with greater accessing speed and stability to replace the current SRAM storage cell. The resistive random access memory (ReRAM) is a metal oxide which is based on nonvolatile memory device possessing the characteristics of high read/write speed, high storage density, low power, low cost, very small cell, being nonvolatile, and unlimited writing endurance. The device has extreme short erasing time and the stored charge cannot be destroyed after power-off. Therefore, the ReRAM device is a significant storage device for many applications in the next generation. In this paper, we first explored the mechanism of the ReRAM device based on ion mobility model and then applied this device to optimize the design of FPGA switching matrix. The results show that it is beneficial to enhance the FPGA performance to replace traditional SRAM cells with ReRAM cells for the switching matrix.
Quality Assessment of Ojeok-San, a Traditional Herbal Formula, Using High-Performance Liquid Chromatography Combined with Chemometric Analysis
Authors: Kim Jung-Hoon , Seo Chang-Seob , Kim Seong-Sil , Shin Hyeun-Kyoo
Published: October 2015

Ojeok-san (OJS) is a traditional herbal formula consisting of 17 herbal medicines that has been used to treat various disorders. In this study, quantitative analytical methods were developed using high-performance liquid chromatography equipped with a photodiode array detector to determine 19 marker compounds in OJS preparations, which was then combined with chemometric analysis. The method developed was validated in terms of its precision and accuracy. The intra- and interday precision of the marker compounds were <3.0% of the relative standard deviation (RSD) and the recovery of the marker compounds was 92.74%–104.16% with RSD values <3.0%. The results of our quantitative analysis show that the quantities of the 19 marker compounds varied between a laboratory water extract and commercial OJS granules. The chemometric analysis used, principal component analysis (PCA) and hierarchical clustering analysis (HCA), also showed that the OJS water extract produced using a laboratory method clearly differed from the commercial OJS granules; therefore, an equalized production process is required for quality control of OJS preparations. Our results suggest that the HPLC analytical methods developed are suitable for the quantification and quality assessment of OJS preparations when combined with chemometric analysis involving PCA and HCA.
Functionalised Au Coated Iron Oxide Nanocomposites Based Reusable Immunosensor for AFB1 Detection
Authors: Chauhan Ruchika , Basu T.
Published: October 2015

A reusable sandwiched electrochemical piezoelectric immunosensor has been developed for aflatoxin B1 (AFB1) detection using gold coated iron oxide core‐shell (Au‐Fe3O4) nanostructure. The monoclonal anti‐aflatoxin antibody (aAFB1) was immobilized on self‐assembled monolayer of 4‐aminothiophenol on gold coated quartz crystal to fabricate immunoelectrode (BSA/aAFB1/4‐ATP/Au). In addition, secondary rabbit‐immunoglobulin antibodies (r‐IgGs) functionalized with Au‐Fe3O4 NPs via cysteamine (r‐IgG‐Cys‐Au‐Fe3O4) were allowed to interact with AFB1. Both competitive and noncompetitive strategies were employed and a competition between coated AFB1 and free AFB1 was carried out. The competitive mode shows higher linear range (0.05 to 5 ng mL−1) than the noncompetitive one (0.5 to 5 ng mL−1), high sensitivity 335.7 µA ng−1 mL cm−2, and LOD 0.07 ng mL−1. The fabricated immunosensor has been tested using cereal samples spiked with different concentrations of AFB1. The developed competitive immunoelectrode displays good reproducibility, and storage stability and regenerated with negligible loss in activity through removal of the r‐IgG‐Cys‐Au‐Fe3O4 conjugate using a strong external magnet.
PPCM: Combing Multiple Classifiers to Improve Protein-Protein Interaction Prediction
Authors: Yao Jianzhuang , Guo Hong , Yang Xiaohan
Published: October 2015

Determining protein-protein interaction (PPI) in biological systems is of considerable importance, and prediction of PPI has become a popular research area. Although different classifiers have been developed for PPI prediction, no single classifier seems to be able to predict PPI with high confidence. We postulated that by combining individual classifiers the accuracy of PPI prediction could be improved. We developed a method called protein-protein interaction prediction classifiers merger (PPCM), and this method combines output from two PPI prediction tools, GO2PPI and Phyloprof, using Random Forests algorithm. The performance of PPCM was tested by area under the curve (AUC) using an assembled Gold Standard database that contains both positive and negative PPI pairs. Our AUC test showed that PPCM significantly improved the PPI prediction accuracy over the corresponding individual classifiers. We found that additional classifiers incorporated into PPCM could lead to further improvement in the PPI prediction accuracy. Furthermore, cross species PPCM could achieve competitive and even better prediction accuracy compared to the single species PPCM. This study established a robust pipeline for PPI prediction by integrating multiple classifiers using Random Forests algorithm. This pipeline will be useful for predicting PPI in nonmodel species.
Developing a Powerful and Resilient Smart Body Sensor Network through Hypercube Interconnection
Authors: Almogren Ahmad S.
Published: October 2015

With recent advances in wireless sensor networks and embedded computing technologies, body sensor networks (BSNs) have become practically feasible. BSNs consist of a number of sensor nodes located and deployed over the human body. These sensors continuously gather vital sign data of the body area to be used in various intelligent systems in smart environments. This paper presents an intelligent design of the body sensor network based on virtual hypercube structure backbone termed as Smart BodyNet. The main purpose of the Smart BodyNet is to provide resilience for the BSN operation and reduce power consumption. Various experiments were carried out to show the performance of the Smart BodyNet design as compared to the state-of-the-art approaches.
Neural Network Control-Based Drive Design of Servomotor and Its Application to Automatic Guided Vehicle
Authors: Wang Ming-Shyan , Chen Seng-Chi , Chuang Po-Hsiang , Wu Shih-Yu , Hsu Fu-Shung
Published: October 2015

An automatic guided vehicle (AGV) is extensively used for productions in a flexible manufacture system with high efficiency and high flexibility. A servomotor-based AGV is designed and implemented in this paper. In order to steer the AGV to go along a predefined path with corner or arc, the conventional proportional-integral-derivative (PID) control is used in the system. However, it is difficult to tune PID gains at various conditions. As a result, the neural network (NN) control is considered to assist the PID control for gain tuning. The experimental results are first provided to verify the correctness of the neural network plus PID control for 400 W-motor control system. Secondly, the AGV includes two sets of the designed motor systems and CAN BUS transmission so that it can move along the straight line and curve paths shown in the taped videos.
An IMRT/VMAT Technique for Nonsmall Cell Lung Cancer
Authors: Zhao Nan , Yang Ruijie , Wang Junjie , Zhang Xile , Li Jinna
Published: October 2015

The study is to investigate a Hybrid IMRT/VMAT technique which combines intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) for the treatment of nonsmall cell lung cancer (NSCLC). Two partial arcs VMAT, 5-field IMRT, and hybrid plans were created for 15 patients with NSCLC. The hybrid plans were combination of 2 partial arcs VMAT and 5-field IMRT. The dose distribution of planning target volume (PTV) and organs at risk (OARs) for hybrid technique was compared with IMRT and VMAT. The monitor units (MUs) and treatment delivery time were also evaluated. Hybrid technique significantly improved the target conformity and homogeneity compared with IMRT and VMAT. The mean delivery time of IMRT, VMAT, and hybrid plans was 280 s, 114 s, and 327 s, respectively. The mean MUs needed for IMRT, VMAT, and hybrid plans were 933, 512, and 737, respectively. Hybrid technique reducedV5,V10,V30, and MLD of normal lung compared with VMAT and spared the OARs better with fewer MUs with the cost of a little higherV5,V10, and mean lung dose (MLD) of normal lung compared with IMRT. Hybrid IMRT/VMAT can be a viable radiotherapy technique with better plan quality.
Influence of Malondialdehyde and Matrix Metalloproteinase‐9 on Progression of Carotid Atherosclerosis in Chronic Renal Disease with Cardiometabolic Syndrome
Authors: Rašić Senija , Rebić Damir , Hasić Sabaheta , Rašić Ismar , Delić Šarac Marina
Published: October 2015

Objective was to assess whether the concentration of malondialdehyde (MDA) as a marker of lipid peroxidation and serum concentration of matrix metalloproteinase‐9 (MMP‐9) are involved in the process of atherosclerosis in chronic kidney disease (CKD) patients nondialysis‐dependent and those on peritoneal dialysis (PD), both with signs of cardiometabolic syndrome (CMS). Thirty CKD and 22 PD patients were included in a study. All observed patients were divided into three subgroups depending on the degree of atherosclerotic changes in the carotid arteries (CA). Severity of atherosclerotic changes in the CA was evaluated by ultrasonography. We confirmed significantly lower level of serum MDA throughout all the stages of atherosclerosis in PD patients compared with observed CKD patients (P < 0.05) and increased serum concentration of MDA and MMP‐9 with the progression of severity atherosclerotic changes in both groups of patients. The multiple regression analysis revealed that MDA and MMP‐9 are significant predictors of changes in IMT‐CA CKD patients (P < 0.05) and plaque score on CA in these patients (P < 0.05). The results suggest that MDA and MMP‐9 could be mediators of CKD‐related vascular remodeling in CMS.
Explicit Formulas for Meixner Polynomials
Authors: Kruchinin Dmitry V. , Shablya Yuriy V.
Published: October 2015

Using notions of composita and composition of generating functions, we show an easy way to obtain explicit formulas for some current polynomials. Particularly, we consider the Meixner polynomials of the first and second kinds.
Friends or Foes: Matrix Metalloproteinases and Their Multifaceted Roles in Neurodegenerative Diseases
Authors: Brkic Marjana , Balusu Sriram , Libert Claude , Vandenbroucke Roosmarijn E.
Published: October 2015

Neurodegeneration is a chronic progressive loss of neuronal cells leading to deterioration of central nervous system (CNS) functionality. It has been shown that neuroinflammation precedes neurodegeneration in various neurodegenerative diseases. Matrix metalloproteinases (MMPs), a protein family of zinc‐containing endopeptidases, are essential in (neuro)inflammation and might be involved in neurodegeneration. Although MMPs are indispensable for physiological development and functioning of the organism, they are often referred to as double‐edged swords due to their ability to also inflict substantial damage in various pathological conditions. MMP activity is strictly controlled, and its dysregulation leads to a variety of pathologies. Investigation of their potential use as therapeutic targets requires a better understanding of their contributions to the development of neurodegenerative diseases. Here, we review MMPs and their roles in neurodegenerative diseases: Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), and multiple sclerosis (MS). We also discuss MMP inhibition as a possible therapeutic strategy to treat neurodegenerative diseases.
Laboratory Investigation of Fatigue Characteristics of Asphalt Mixtures with Steel Slag Aggregates
Authors: Ziari Hassan , Nowbakht Shams , Rezaei Sajad , Mahboob Arash
Published: October 2015

There are many steel-manufacturing factories in Iran. All of their byproducts, steel slag, are dumped randomly in open areas, causing many environmentally hazardous problems. This research is intended to study the effectiveness of using steel slag aggregate (SSA) in improving the engineering properties, especially fatigue life of Asphalt Concrete (AC) produced with steel slag. The research started by evaluating the physical properties of the steel slag aggregate. Then the 13 types of mixes which contain steel slag in portion of fine aggregates or in portion of coarse aggregates or in all portions of aggregates were tested. The effectiveness of the SSA was judged by the improvement in Marshall stability, indirect tensile strength, resilient modulus, and fatigue life of the AC samples. It was found that replacing the 50% of the limestone coarse or fine aggregate by SSA improved the mechanical properties of the AC mixes.
Anorectal Malformation: Paediatric Problem Presenting in Adult
Authors: Chavan Rahulkumar N. , Chikkala Bhargav , Das Cinjini , Biswas Somak , Sarkar Diptendra Kumar , Pandey Sushil Kumar
Published: October 2015

This is a case report of 22-year-old girl admitted with abdominal distension, vomiting, and chronic constipation since birth. Abdomen was distended, and perineal examination revealed imperforate anus with vestibular fistula (ARM). So far worldwide very few cases have been reported about anorectal malformation presenting in adulthood, and thus extremely little data is available in the literature about an ideal management of anorectal malformation in adults. In our case in the treatment instead of conventional procedure of posterior sagittal anorectoplasty (PSARP) anal transposition was done and till two years after the definitive treatment during follow-up patient has been doing well with Kelly’s score of six. Our experience suggests that anal transposition provides satisfactory outcome in adults presenting late with anorectal malformation.
Effect of Laryngeal Squamous Cell Carcinoma Tissue Implantation on the Chick Embryo Chorioallantoic Membrane: Morphometric Measurements and Vascularity
Authors: Uloza Virgilijus , Kuzminienė Alina , Šalomskaitė-Davalgienė Sonata , Palubinskienė Jolita , Balnytė Ingrida , Ulozienė Ingrida , Šaferis Viktoras , Valančiūtė Angelija
Published: October 2015

Background. The aim of this study was to develop chick embryo chorioallantoic membrane (CAM) model of laryngeal squamous cell carcinoma (LSCC) and to evaluate the morphological and morphometric characteristics and angiogenic features of it.Methods. Fresh LSCC tissue samples obtained from 6 patients were implanted onto 15 chick embryo CAMs. Morphological, morphometric, and angiogenic changes in the CAM and chorionic epithelium were evaluated up to 4 days after the tumor implantation. Immunohistochemical analysis (34βE12, CD31, and Ki67 staining) was performed to detect cytokeratins and tumor endothelial cells and to evaluate the proliferative capacity of the tumor before and after implantation on the CAM.Results. The implanted LSCC tissue samples survived on the CAM in all the experiments and retained the essential morphologic characteristics and proliferative capacity of the original tumor. Implants induced thickening of both the CAM (103–417%,p=0.0001) and the chorionic epithelium (70–140%,p=0.0001) and increase in number of blood vessels (75–148%,p=0.0001) in the CAM.Conclusions. This study clarifies that chick embryo CAM is a relevant assay for implanting LSCC tissue and provides the first morphological and morphometric characterization of the LSCC CAM model that opens new perspectives to study this disease.
Clinical Trial of Human Fetal Brain-Derived Neural Stem/Progenitor Cell Transplantation in Patients with Traumatic Cervical Spinal Cord Injury
Authors: Shin Ji Cheol , Kim Keung Nyun , Yoo Jeehyun , Kim Il-Sun , Yun Seokhwan , Lee Hyejin , Jung Kwangsoo , Hwang Kyujin , Kim Miri , Lee Il-Shin , Shin Jeong Eun , Park Kook In
Published: October 2015

In a phase I/IIa open-label and nonrandomized controlled clinical trial, we sought to assess the safety and neurological effects of human neural stem/progenitor cells (hNSPCs) transplanted into the injured cord after traumatic cervical spinal cord injury (SCI). Of 19 treated subjects, 17 were sensorimotor complete and 2 were motor complete and sensory incomplete. hNSPCs derived from the fetal telencephalon were grown as neurospheres and transplanted into the cord. In the control group, who did not receive cell implantation but were otherwise closely matched with the transplantation group, 15 patients with traumatic cervical SCI were included. At 1 year after cell transplantation, there was no evidence of cord damage, syrinx or tumor formation, neurological deterioration, and exacerbating neuropathic pain or spasticity. The American Spinal Injury Association Impairment Scale (AIS) grade improved in 5 of 19 transplanted patients, 2 (A → C), 1 (A → B), and 2 (B → D), whereas only one patient in the control group showed improvement (A → B). Improvements included increased motor scores, recovery of motor levels, and responses to electrophysiological studies in the transplantation group. Therefore, the transplantation of hNSPCs into cervical SCI is safe and well-tolerated and is of modest neurological benefit up to 1 year after transplants. This trial is registered with Clinical Research Information Service (CRIS), Registration Number:KCT0000879.
A Model-Driven Approach for Wearable Systems Developments
Authors: Ruiz-Zafra Angel , Noguera Manuel , Benghazi Kawtar , Ochoa Sergio F.
Published: October 2015

This paper proposes a model-driven approach for developing high-level software interfaces that allow developers to interact with wearable devices easily. These components hide the heterogeneity of the devices interfaces and provide developers with a simple and homogeneous way to interoperate with these digital peripherals. The use of this approach also allows reducing risks and development efforts.
The Role of Reactive Oxygen Species in Myelofibrosis and Related Neoplasms
Authors: Bjørn Mads Emil , Hasselbalch Hans Carl
Published: October 2015

Reactive oxygen species (ROS) have been implicated in a wide variety of disorders ranging between traumatic, infectious, inflammatory, and malignant diseases. ROS are involved in inflammation‐induced oxidative damage to cellular components including regulatory proteins and DNA. Furthermore, ROS have a major role in carcinogenesis and disease progression in the myeloproliferative neoplasms (MPNs), where the malignant clone itself produces excess of ROS thereby creating a vicious self‐perpetuating circle in which ROS activate proinflammatory pathways (NF‐κB) which in turn create more ROS. Targeting ROS may be a therapeutic option, which could possibly prevent genomic instability and ultimately myelofibrotic and leukemic transformation. In regard to the potent efficacy of the ROS‐scavenger N‐acetyl‐cysteine (NAC) in decreasing ROS levels, it is intriguing to consider if NAC treatment might benefit patients with MPN. The encouraging results from studies in cystic fibrosis, systemic lupus erythematosus, and chronic obstructive pulmonary disease warrant such studies. In addition, the antioxidative potential of the widely used agents, interferon‐alpha2, statins, and JAK inhibitors, should be investigated as well. A combinatorial approach using old agents with anticancer properties together with novel JAK1/2 inhibitors may open a new era for patients with MPNs, the outlook not only being “minimal residual disease” and potential cure but also a marked improvement in inflammation‐mediated comorbidities.
A Novel Iterative Method for Polar Decomposition and Matrix Sign Function
Authors: Soleymani F. , Stanimirović Predrag S. , Stojanović Igor
Published: October 2015

We define and investigate a globally convergent iterative method possessing sixth order of convergence which is intended to calculate the polar decomposition and the matrix sign function. Some analysis of stability and computational complexity are brought forward. The behaviors of the proposed algorithms are illustrated by numerical experiments.
Cable Tension Preslack Method Construction Simulation and Engineering Application for a Prestressed Suspended Dome
Authors: Liu Xuechun , Zhang Ailin , Fu Wanlin
Published: October 2015

To solve the shortage of traditional construction simulation methods for suspended dome structures, based on friction elements, node coupling technology, and local cooling, the cable tension preslack method is proposed in this paper, which is suitable for the whole process construction simulation of a suspended dome. This method was used to simulate the construction process of a large-span suspended dome case study. The effects on the simulation results of location deviation of joints, construction temperature, construction temporary supports, and friction of the cable-support joints were analyzed. The cable tension preslack method was demonstrated by comparing the data from the construction simulation with measured results, providing the control cable tension and the control standards for construction acceptance. The analysis demonstrated that the position deviation of the joint has little effect on the control value; the construction temperature and the friction of the cable-support joint significantly affect the control cable tension. The construction temperature, the temporary construction supports, and the friction of the cable-support joints all affect the internal force and deflection in the tensioned state but do not significantly affect the structural bearing characteristics at the load state. The forces should be primarily controlled in tensioned construction, while the deflections are controlled secondarily.
Numerical Simulation Analysis of Unfilled and Filled Reinforced Polypropylene on Thin-Walled Parts Formed Using the Injection-Moulding Process
Authors: Azaman M. D. , Sapuan S. M. , Sulaiman S. , Zainudin E. S. , Khalina A.
Published: October 2015

Thin-walled moulding technology has attracted increasing attention, particularly in electronic packing applications. The injection moulding of shallow, thin-walled parts with a thickness of 0.7 mm was performed using three types of materials from polypropylene, PP (PP, PP + 50 wt% wood composite, and PP + 10 wt% glass fibre composite). The highest deflection resulting from PP + 50 wt% wood does not occur in the critical area of the thin-walled part compared with PP + 10 wt% glass fibre. In addition, the results revealed that the warpage at the midpoint of the part surface injected using PP + 50 wt% wood is 0.04 mm lower than the value of 0.08 mm obtained when injected using PP + 10 wt% glass fibre. The warpage was hypothesised to result from the residual stress caused by nonuniform volumetric shrinkages formed during the solidification phase.
Physicochemical Characteristics and Composition of Three Morphotypes ofCyperus esculentusTubers and Tuber Oils
Authors: Bado Souleymane , Bazongo Patrice , Son Gouyahali , Kyaw Moe Thida , Forster Brian Peter , Nielen Stephan , Lykke Anne Mette , Ouédraogo Amadé , Bassolé Imaël Henri Nestor
Published: October 2015

Tuber characteristics and nutrient composition of three morphotypes ofCyperus esculentustubers and tuber oils were determined. The mean value for length and width of the tuber and one thousand dried tuber weights ranged from 0.98 to 1.31 cm, 0.90 to 1.19 cm, and 598 to 1044 g, respectively. Tubers displayed high level of starch (30.54–33.21 g 100 g−1), lipid (24.91–28.94 g 100 g−1), and sucrose (17.98–20.39 g 100 g−1). The yellow tubers had significantly higher content in lipid compared to black ones. Levels of ascorbic acid, tocopherol, andβ-carotene of the three morphotypes differed significantly. Yellow ones (morphotypes 1 and 2) were the richest in tocopherol and the poorest inβ-carotene. Saturated fatty acid content of morphotype 2 was significantly lower than that of morphotypes 1 and 3. Morphotype 3 had the significantly lowest PUFA content compared to morphotypes 1 and 2. Morphotype 1 was found to be richer in Ca, Cu, and Mn contents. Al, Mg, P, S, and Si were most abundant in morphotype 2. Morphotype 3 had the highest content of Cl, K, and Zn.