bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data
Authors: Jang Ho , Hur Youngmi , Lee Hyunju 
Published: May 2016

AbstractDNA copy number alterations (CNAs) are the main genomic events that occur during the initiation and development of cancer. Distinguishing driver aberrant regions from passenger regions, which might contain candidate target genes for cancer therapies, is an important issue. Several methods for identifying cancer-driver genes from multiple cancer patients have been developed for single nucleotide polymorphism (SNP) arrays. However, for NGS data, methods for the SNP array cannot be directly applied because of different characteristics of NGS such as higher resolutions of data without predefined probes and incorrectly mapped reads to reference genomes. In this study, we developed a wavelet-based method for identification of focal genomic alterations for sequencing data (WIFA-Seq). We applied WIFA-Seq to whole genome sequencing data from glioblastoma multiforme, ovarian serous cystadenocarcinoma and lung adenocarcinoma, and identified focal genomic alterations, which contain candidate cancer-related genes as well as previously known cancer-driver genes.
Immobilization of Polyoxometalate in the Metal-Organic Framework rht-MOF-1: Towards a Highly Effective Heterogeneous Catalyst and Dye Scavenger
Authors: Sun Jing-Wen , Yan Peng-Fei , An Guang-Hui , Sha Jing-Quan , Li Guang-Ming , Yang Guo-Yu 
Published: May 2016

AbstractA series of three remarkable complexes [PMo12O40]@[Cu6O(TZI)3(H2O)9]4·OH·31H2O (H3TZI = 5-tetrazolylisophthalic acid; denoted as HLJU-1, HLJU = Heilongjiang University), [SiMo12O40]@[Cu6O(TZI)3(H2O)9]4·32H2O (denoted as HLJU-2) and [PW12O40]@[Cu6O(TZI)3(H2O)6]4·OH·31H2O (denoted as HLJU-3) have been isolated by using simple one-step solvothermal reaction of copper chloride, 5-tetrazolylisophthalic acid (H3TZI) and various Keggin-type polyoxometalates (POMs), respectively. Crystal analysis of HLJU 1−3 reveals that Keggin-type polyoxoanions have been fitted snuggly in the cages of rht-MOF-1 (MOF: metal−organic framework) with large cell volume in a range of 87968−88800 Å3 and large pore volume of about 68%. HLJU 1–3 exhibit unique catalytic selectivity and reactivity in the oxidation of alkylbenzene with environmental benign oxidant under mild condition in aqueous phase as well as the uptake capacity towards organic pollutants in aqueous solution.
Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils
Authors: Wild Birgit , Gentsch Norman , Čapek Petr , Diáková Kateřina , Alves Ricardo J. Eloy , Bárta Jiři , Gittel Antje , Hugelius Gustaf , Knoltsch Anna , Kuhry Peter , Lashchinskiy Nikolay , Mikutta Robert , Palmtag Juri , Schleper Christa , Schnecker Jörg , Shibistova Olga , Takriti Mounir , Torsvik Vigdis L. , Urich Tim , Watzka Margarete , Šantrůčková Hana , Guggenberger Georg , Richter Andreas 
Published: May 2016

AbstractArctic ecosystems are warming rapidly, which is expected to promote soil organic matter (SOM) decomposition. In addition to the direct warming effect, decomposition can also be indirectly stimulated via increased plant productivity and plant-soil C allocation and this so called “priming effect” might significantly alter the ecosystem C balance. In this study, we provide first mechanistic insights into the susceptibility of SOM decomposition in arctic permafrost soils to priming. By comparing 119 soils from four locations across the Siberian Arctic that cover all horizons of active layer and upper permafrost, we found that an increased availability of plant-derived organic C particularly stimulated decomposition in subsoil horizons where most of the arctic soil carbon is located. Considering the 1,035 Pg of arctic soil carbon, such an additional stimulation of decomposition beyond the direct temperature effect can accelerate net ecosystem C losses and amplify the positive feedback to global warming.
Proteome analysis for the global proteins in the jejunum tissues of enterotoxigenic Escherichia coli -infected piglets
Authors: Ren Wenkai , Yin Jie , Chen Shuai , Duan Jielin , Liu Gang , Li Tiejun , Li Nengzhang , Peng Yuanyi , Tan Bie , Yin Yulong 
Published: May 2016

AbstractEnterotoxigenic Escherichia coli (ETEC) is a common cause of diarrhea in humans and livestock. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) combined with multidimensional liquid chromatography (LC) and MS analysis was used for screening the differentially expressed proteins in piglet jejunum after ETEC infection. Totally 1,897 proteins were identified with quantitative information in piglet jejunum. We identified 92 differentially expressed proteins in ETEC-induced diarrhea, of which 30 were up regulated and 62 down regulated. Most of the differentially expressed proteins were involved in intestinal function of binding, metabolic process, catalytic activity and immune responses. The inhibition of intestinal immune responses in the jejunum in ETEC-induced diarrhea was also validated by immunobloting and RT-PCR. Our study is the first attempt to analyze the protein profile of ETEC-infected piglets by quantitative proteomics, and our findings could provide valuable information with respect to better understanding the host response to ETEC infection.
Pharmacokinetics and tolerability of NSC23925b, a novel P-glycoprotein inhibitor: preclinical study in mice and rats
Authors: Gao Yan , Shen Jacson K. , Choy Edwin , Zhang Zhan , Mankin Henry J. , Hornicek Francis J. , Duan Zhenfeng 
Published: May 2016

AbstractOverexpression of P-glycoprotein (Pgp) increases multidrug resistance (MDR) in cancer, which greatly impedes satisfactory clinical treatment and outcomes of cancer patients. Due to unknown pharmacokinetics, the use of Pgp inhibitors to overcome MDR in the clinical setting remains elusive despite promising in vitro results. The purpose of our current preclinical study is to investigate the pharmacokinetics and tolerability of NSC23925b, a novel and potent P-glycoprotein inhibitor, in rodents. Plasma pharmacokinetic studies of single-dose NSC23925b alone or in combination with paclitaxel or doxorubicin were conducted in male BALB/c mice and Sprague-Dawley rats. Additionally, inhibition of human cytochrome P450 (CYP450) by NSC23925b was examined in vitro. Finally, the maximum tolerated dose (MTD) of NSC23925b was determined. NSC23925b displayed favorable pharmacokinetic profiles after intraperitoneal/intravenous (I.P./I.V.) injection alone or combined with chemotherapeutic drugs. The plasma pharmacokinetic characteristics of the chemotherapy drugs were not affected when co-administered with NSC23925b. All the animals tolerated the I.P./I.V. administration of NSC23925b. Moreover, the enzymatic activity of human CYP450 was not inhibited by NSC23925b. Our results demonstrated that Pgp inhibitor NSC23925b exhibits encouraging preclinical pharmacokinetic characteristics and limited toxicity in vivo. NSC23925b has the potential to treat cancer patients with MDR in the future.
Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium
Authors: Pyne Michael E. , Bruder Mark R. , Moo-Young Murray , Chung Duane A. , Chou C. Perry 
Published: May 2016

AbstractApplication of CRISPR-Cas9 systems has revolutionized genome editing across all domains of life. Here we report implementation of the heterologous Type II CRISPR-Cas9 system in Clostridium pasteurianum for markerless genome editing. Since 74% of species harbor CRISPR-Cas loci in Clostridium, we also explored the prospect of co-opting host-encoded CRISPR-Cas machinery for genome editing. Motivation for this work was bolstered from the observation that plasmids expressing heterologous cas9 result in poor transformation of Clostridium. To address this barrier and establish proof-of-concept, we focus on characterization and exploitation of the C. pasteurianum Type I-B CRISPR-Cas system. In silico spacer analysis and in vivo interference assays revealed three protospacer adjacent motif (PAM) sequences required for site-specific nucleolytic attack. Introduction of a synthetic CRISPR array and cpaAIR gene deletion template yielded an editing efficiency of 100%. In contrast, the heterologous Type II CRISPR-Cas9 system generated only 25% of the total yield of edited cells, suggesting that native machinery provides a superior foundation for genome editing by precluding expression of cas9 in trans. To broaden our approach, we also identified putative PAM sequences in three key species of Clostridium. This is the first report of genome editing through harnessing native CRISPR-Cas machinery in Clostridium.
Screening of an anti-inflammatory peptide from Hydrophis cyanocinctus and analysis of its activities and mechanism in DSS-induced acute colitis
Authors: Zheng Zengjie , Jiang Hailong , Huang Yan , Wang Jie , Qiu Lei , Hu Zhenlin , Ma Xingyuan , Lu Yiming 
Published: May 2016

AbstractSnake has been used for centuries as a traditional Chinese medicine, especially for therapeutic treatment for inflammatory diseases; however, its mechanisms of action and active constituents remain controversial. In our study, a tumor necrosis factor receptor 1 (TNFR1) selective binding peptide, Hydrostatin-SN1 (H-SN1), which was screened from a Hydrophis cyanocinctus venom gland T7 phage display library, was shown to exhibit significant anti-inflammatory activity in vitro and in vivo. As a TNFR1 antagonist, it reduced cytotoxicity mediated by TNF-α in L929 fibroblasts and effectively inhibited the combination between TNF-α with TNFR1 in surface plasmon resonance analysis. H-SN1 was also shown to suppress TNFR1–associated signaling pathways as it minimized TNF-α-induced NF-кB and MAPK activation in HEK293 embryonic kidney and HT29 adenocarcinoma cell lines. We next determined the effect of H-SN1 in vivo using a murine model of acute colitis induced by dextran sodium sulfate, demonstrating that H-SN1 lowered the clinical parameters of acute colitis including the disease activity index and histologic scores. H-SN1 also inhibited TNF/TNFR1 downstream targets at both mRNA and protein levels. These results indicate that H-SN1 might represent a suitable candidate for use in the treatment of TNF-α-associated inflammatory diseases such as inflammatory bowel diseases.
Semi-automatic recognition of marine debris on beaches
Authors: Ge Zhenpeng , Shi Huahong , Mei Xuefei , Dai Zhijun , Li Daoji 
Published: May 2016

AbstractAn increasing amount of anthropogenic marine debris is pervading the earth’s environmental systems, resulting in an enormous threat to living organisms. Additionally, the large amount of marine debris around the world has been investigated mostly through tedious manual methods. Therefore, we propose the use of a new technique, light detection and ranging (LIDAR), for the semi-automatic recognition of marine debris on a beach because of its substantially more efficient role in comparison with other more laborious methods. Our results revealed that LIDAR should be used for the classification of marine debris into plastic, paper, cloth and metal. Additionally, we reconstructed a 3-dimensional model of different types of debris on a beach with a high validity of debris revivification using LIDAR-based individual separation. These findings demonstrate that the availability of this new technique enables detailed observations to be made of debris on a large beach that was previously not possible. It is strongly suggested that LIDAR could be implemented as an appropriate monitoring tool for marine debris by global researchers and governments.
Inflammation in Complicated Pregnancy and Its Outcome
Authors: Kalagiri Ram , Carder Timothy , Choudhury Saiara , Vora Niraj , Ballard Amie , Govande Vinayak , Drever Nathan , Beeram Madhava , Uddin M. 
Published: May 2016

Background Normal pregnancy relies on a careful balance between immune tolerance and suppression. It is known that strict regulation of maternal immune function, in addition to components of inflammation, is paramount to successful pregnancy, and any imbalance between proinflammatory and anti-inflammatory cytokines and chemokines can lead to aberrant inflammation, often seen in complicated pregnancies. Inflammation in complicated pregnancies is directly associated with increased mortality and morbidity of the mother and offspring. Aberrant inflammatory reactions in complicated pregnancies often lead to adverse outcomes, such as spontaneous abortion, preterm labor, intrauterine growth restriction, and fetal demise. The role of inflammation in different stages of normal pregnancy is reviewed, compared, and contrasted with aberrant inflammation in complicated pregnancies. The complications addressed are preterm labor, pregnancy loss, infection, preeclampsia, maternal obesity, gestational diabetes mellitus, autoimmune diseases, and inflammatory bowel disease.
Aim This article examines the role of various inflammatory factors contributing to aberrant inflammation in complicated pregnancies. By understanding the aberrant inflammatory process in complicated pregnancies, novel diagnostic tools and therapeutic interventions for modulating it appropriately can be identified.
1.4.3 Hydrolysis of Amides
Authors: Hall M. , Faber K. , Tasnádi G. 
Published: May 2016

AbstractThis chapter describes the enzymatic hydrolysis of amide substrates. The main target compounds are amino acids, obtained via the kinetic resolution of amino acid amides and N-acylated amino acids using aminopeptidases, amidases, and aminoacylases. In addition, methods leading to enantiopure carboxylic acids and amines as well as lactamase-catalyzed processes are presented.
Improved electroluminescence of quantum dot light-emitting diodes enabled by a partial ligand exchange with benzenethiol
Authors: Kim Daekyoung , Fu Yan , Kim Jungwoo , Lee Ki-heon , Kim Hyoungsub , Yang Heesun , Chae Heeyeop 
Published: May 2016

Abstract
In this study, benzenethiol ligands were applied to the surface of CdSe@ZnS core@shell quantum dots (QDs) and their effect on the performance of quantum dot light-emitting diodes (QD-LEDs) was investigated. Conventional long-chained oleic acid (OA) and trioctylphosphine (TOP) capping ligands were partially replaced by short-chained benzenethiol ligands in order to increase the stability of QDs during purification and also improve the electroluminescence performance of QD-LEDs. The quantum yield of the QD solution was increased from 41% to 84% by the benzenethiol ligand exchange. The mobility of the QD films with benzenethiol ligands approximately doubled to 2.42 × 10−5 cm2 V−1 s−1 from 1.19 × 10−5 cm2 V−1 s−1 compared to the device consisting of OA/TOP-capped QDs, and an approximately 1.8-fold improvement was achieved over QD-LEDs fabricated with bezenethiol ligand-exchanged QDs with respect to the maximum luminance and current efficiency. The turn-on voltage decreased by about −0.6 V through shifting the energy level of the QDs with benzenethiol ligands compared to conventional OA and TOP ligands.
Skin-electrode impedance measurement during ECG acquisition: method’s validation
Authors: Casal Leonardo , Mura Guillermo La 
Published: May 2016

Abstract
Skm-electrode impedance measurement can provide valuable information prior. dunng and post electrocardiographic (ECG) or electroencephalographs (EEG) acquisitions. In this work we validate a method for skm-electrode impedance measurement using test circuits with known resistance and capacitor values, at different frequencies for injected excitation current. Finally the method is successfully used for impedance measurement during ECG acquisition on a subject usmg 125 Hz and 6 nA square wave excitation signal at instrumentation amplifier mput. The method can be used for many electrodes configuration.
Video-analysis Interface for Angular Joint Measurement
Authors: Mondani M , Ghersi I , Miralles M T 
Published: May 2016

Abstract
Real-time quantification of joint articular movement is instrumental in the comprehensive assessment of significant biomechanical gestures. The development of an interface, based on an automatic algorithm for 3D-motion analysis, is presented in this work. The graphical interface uses open-source libraries for video processing, and its use is intuitive. The proposed method is low-cost, of acceptable precision (|εθ| < 1°), and minimally invasive. It allows to obtain angular movement of joints in different planes, synchronized with the video of the gesture, as well as to make comparisons and calculate parameters of interest from the acquired angular kinematics.
Executive Compensation Incentives Contingent on Long-Term Accounting Performance
Authors: Li Zhi , Wang Lingling 
Published: May 2016

Abstract
The percentage of S&P 500 firms using multiyear accounting-based performance (MAP) incentives for CEOs increased from 16.5% in 1996 to 43.3% in 2008. The use and design of MAP incentives depend on the signal quality of accounting versus stock performance, shareholder horizons, strategic imperatives, and board independence. After the technology bubble, option expensing, and the publicity of option backdating, firms increasingly use stock-based MAP plans to replace options, resulting in changes in pay structure, but not in pay level. While firms respond to the evolving contracting environment, they consider firm characteristics and shareholder preferences and do not blindly follow the trend.
Received September 20, 2013; accepted November 20, 2015 by Editor David Denis.
Key indexes choosing approach of complex equipment’s development cost based on grey incidence cluster model
Authors: Xie Naiming , Hu Chuanzhen , Yin Songming 
Published: May 2016

Purpose
– The purpose of this paper is to establish a combined model for selecting key indexes of complex equipment, and then improve the cost forecasting precision of the model. The problem how to choose the key elements of complex products has always been concerned on many fields, such as cost assessment, investment decision making, etc.

Design/methodology/approach
– Using Grey System Theory to establish a cost estimation model of complicated equipment is more reasonable under the few data and poor information. Therefore, this paper constructs cost index’s system of complex equipment, and then quantitative and qualitative analysis methods are utilized to calculate the grey entropy between the characteristic parameter and the behavior parameters. Further, establish the grey relational clustering matrix of the behavior sequences by using the grey relative incidence analysis. Finally, the authors select key indicators according to the grey degree.

Findings
– The experiment demonstrates that the cost key parameters of complex equipment can be successfully screened out by the proposed approach, and the cost estimation accuracy of complicated products is improved.

Practical implications
– The method proposed in this paper could be utilized to solve some practical problems, particularly the selection of cost critical parameters for complex products with few samples and poor information. Taking the cost key indexes of civil aircraft as an example, the results verified the validity of the GICM model.

Originality/value
– In this paper, the authors develop the method of GICM model. Taking the data of civil aircraft as an example, the authors screen the key indicators of complex products successfully, and improve the prediction accuracy of the GM (1, N) model by using the selected parameters, which provides a reference for some firms.
The study on key influencing factors of mergers and acquisitions performance based on China state-owned listed enterprises
Authors: Zhao Xi , Qu Haitao , Huang Yimin 
Published: May 2016

Purpose
– The purpose of this paper is to analyze the key influencing factors which affect the performance of M
&
A and the key influencing factors by establishing grey relational sequence model. The results can not only perfect the current existing theoretical system, but also provide theoretical guide for M
&
A practice.

Design/methodology/approach
– First of all, this paper analyzes the M
&
A performance through the literature reviews, and then establishes the grey model about M
&
A performance from three influencing factors: profitability, operational and development capacity to analyze its key influencing factors which affect M
&
A performance. Furthermore, the key factors influencing of M
&
A performance are analyzed, the results can be obtained through the analysis of the grey relative degree based on six years’ data of state-owned enterprises.

Findings
– In this paper, some results can be found that ownership restriction and executive compensation can significantly affect corporate profitability and operation ability. M
&
A and institutional investors can be affected greater from the perspective of development ability and profitability. In general, enterprise scale has little affect on the performance after M
&
A.

Practical implications
– With the sustainable development of economic globalization, M
&
A has become an important strategy for the rapid growth of the enterprise, enlargement market and brand effect. But the performance after M
&
A in most enterprises does not improve. As the pillar of the national economy, state-owned enterprises have an important impact on China’s economic development and urgently need to be reformed.

Originality/value
– This paper analyzes the key factors through establishing grey relative sequence model to analyze the correlation of M
&
A performance and influencing factors, and finds key influencing factors which affect the performance of M
&
A. The conclusion can provide policy guidance for the improvement of M
&
A performance in the future.
Positive risk-taking: from rhetoric to reality
Authors: Morgan Steve , Andrews Nick 
Published: May 2016

Purpose– For health and social care services to become truly person-centred requires a fundamentally positive mindset from professionals and care workers, and a willingness to take some risks. The purpose of this paper is to explore how this will apply to delivering dementia services, where almost all of the initial impressions are of deficits, disability and disadvantage.Design/methodology/approach– The co-authors combine their knowledge and experience of supporting and developing staff working in dementia services. The concept of positive risk-taking is explored within the legislative framework of the Mental Capacity Act 2005, Safeguarding and the Care Act 2014.Findings– Practitioners face a range of challenges when it comes to supporting people living with dementia to take risks through exercising personal choices and making their own decisions. However, the concept of positive risk-taking applies equally to people living with dementia who have or who lack mental capacity in relation to their decision making.Originality/value– This paper places positive risk-taking within a context of strengths-based, values-based and relationship-based working. Practical tips are offered for putting positive risk-taking into practice.