bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of the RBM4-initiated splicing cascade on modulating the carcinogenic signature of colorectal cancer cells
Authors: Lin Jung-Chun , Lee Yuan-Chii , Liang Yu-Chih , Fann Yang C. , Johnson Kory R. , Lin Ying-Ju
Published: March 2017

A growing body of studies has demonstrated that dysregulated splicing profiles constitute pivotal mechanisms for carcinogenesis. In this study, we identified discriminative splicing profiles of colorectal cancer (CRC) cells compared to adjacent normal tissues using deep RNA-sequencing (RNA-seq). The RNA-seq results and cohort studies indicated a relatively high ratio of exon 4-excluded neuro-oncological ventral antigen 1 (Nova1−4) and intron 2-retained SRSF6 (SRSF6+intron 2) transcripts in CRC tissues and cell lines. Nova1 variants exhibited differential effects on eliminating SRSF6 expression in CRC cells by inducing SRSF6+intron 2 transcripts which were considered to be the putative target of alternative splicing-coupled nonsense-mediated decay mechanism. Moreover, the splicing profile of vascular endothelial growth factor (VEGF)165/VEGF165b transcripts was relevant to SRSF6 expression, which manipulates the progression of CRC calls. These results highlight the novel and hierarchical role of an alternative splicing cascade that is involved in the development of CRC.
Ultrasensitive colorimetric detection of circulating tumor DNA using hybridization chain reaction and the pivot of triplex DNA
Authors: Li Ruimin , Zou Li , Luo Yanwei , Zhang Manjun , Ling Liansheng
Published: March 2017

This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA. Nevertheless, in the absence of ctDNA, no HCR happens. Thus, no triplex DNA and G-Quadruplex structure is formed, producing a negligible background. The colorimetric sensing platform is successfully applied in complex biological environments such as human blood plasma for ctDNA detection, with a detection limit corresponding to 0.1 pM. This study unambiguously uses triplex DNA forming as the pivot to integrate nucleic acid amplification and DNAzymes for producing a highly sensitive signal with low background.
Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1-dependent processes
Authors: Rallis Charalampos , Townsend StJohn , Bähler Jürg
Published: March 2017

The Target of Rapamycin (TOR) signalling network plays important roles in aging and disease. The AMP-activated protein kinase (AMPK) and the Gsk3 kinase inhibit TOR during stress. We performed genetic interaction screens using synthetic genetic arrays (SGA) with gsk3 and amk2 as query mutants, the latter encoding the regulatory subunit of AMPK. We identified 69 negative and 82 positive common genetic interactors, with functions related to cellular growth and stress. The 120 gsk3-specific negative interactors included genes functioning in translation and ribosomes. The 215 amk2-specific negative interactors included genes functioning in chromatin silencing and DNA damage repair. Both amk2- and gsk3-specific interactors were enriched in phenotype categories related to abnormal cell size and shape. We also performed SGA screen with the amk2 gsk3 double mutant as a query. Mutants sensitive to 5-fluorouracil, an anticancer drug are under-represented within the 305 positive interactors specific for the amk2 gsk3 query. The triple-mutant SGA screen showed higher number of negative interactions than the double mutant SGA screens and uncovered additional genetic network information. These results reveal common and specialized roles of AMPK and Gsk3 in mediating TOR-dependent processes, indicating that AMPK and Gsk3 act in parallel to inhibit TOR function in fission yeast.
Mutagenesis and redox partners analysis of the P450 fatty acid decarboxylase OleTJE
Authors: Fang Bo , Xu Huifang , Liu Yi , Qi Fengxia , Zhang Wei , Chen Hui , Wang Cong , Wang Yilin , Yang Wenxia , Li Shengying
Published: March 2017

The cytochrome P450 enzyme OleTJE from Jeotgalicoccus sp. ATCC 8456 is capable of converting free long-chain fatty acids into α-alkenes via one-step oxidative decarboxylation in presence of H2O2 as cofactor or using redox partner systems. This enzyme has attracted much attention due to its intriguing but unclear catalytic mechanism and potential application in biofuel production. Here, we investigated the functionality of a select group of residues (Arg245, Cys365, His85, and Ile170) in the active site of OleTJE through extensive mutagenesis analysis. The key roles of these residues for catalytic activity and reaction type selectivity were identified. In addition, a range of heterologous redox partners were found to be able to efficiently support the decarboxylation activity of OleTJE. The best combination turned out to be SeFdx-6 (ferredoxin) from Synechococcus elongatus PCC 7942 and CgFdR-2 (ferredoxin reductase) from Corynebacterium glutamicum ATCC 13032, which gave the highest myristic acid conversion rate of 94.4%. Moreover, Michaelis-Menton kinetic parameters of OleTJE towards myristic acid were determined.
Myocardial oxidative damage is induced by cardiac Fas-dependent and mitochondria-dependent apoptotic pathways in human cocaine-related overdose
Authors: Turillazzi Emanuela , Cerretani Daniela , Cantatore Santina , Fiaschi Anna Ida , Frati Paola , Micheli Lucia , Neri Margherita , Cipolloni Luigi , Di Paolo Marco , Pinchi Enrica , Riezzo Irene , Santurro Alessandro , Vullo Annamaria , Fineschi Vittorio
Published: March 2017

The aim of this study is to analyse cardiac specimens from human cocaine-related overdose, to verify the hypothesis that cardiac toxicity by acute exposure to high dosage of cocaine could be mediated by unbalanced myocardial oxidative stress, and to evaluate the apoptotic response. To address these issues, biochemical and immunohistological markers of oxidative/nitrosative stress were evaluated. We found that i-NOS, NOX2 and nitrotyrosine expression were significantly higher in the hearts of subjects who had died from high doses of cocaine, compared to the control group. Increase of these markers was associated with a dramatic increase in 8-OHdG, another marker of oxidative stress. A high number of TUNEL-positive apoptotic myocells was observed in the study group compared to the control group. The immunoexpression of TNF-α was significantly higher in the cocaine group compared to the control group. Furthermore, we detected a significantly stronger immunoresponse to anti-SMAC/DIABLO in our study group compared to control cases. Both cardiac Fas-dependent and mitochondria-dependent apoptotic pathways appeared to be activated to a greater extent in the cocaine group than in the control group. Our results highlight the central role of oxidative stress in cocaine toxicity. High levels of NOS can promote the oxidation process and lead to apoptosis.
Pathologic Roles of Receptor-Associated Prorenin System in Idiopathic Epiretinal Membrane
Authors: Dong Yoko , Kanda Atsuhiro , Noda Kousuke , Saito Wataru , Ishida Susumu
Published: March 2017

Receptor-associated prorenin system (RAPS) refers to the pathogenic mechanism whereby prorenin binding to (pro)renin receptor [(P)RR] dually activates tissue renin-angiotensin system (RAS) and RAS-independent signaling via (P)RR. The aim of this study is to determine the association of RAPS with idiopathic epiretinal membrane (iERM). Reverse transcription-PCR indicated the expression of RAPS components, including (P)RR and Ang II type 1 receptor (AT1R), in iERM tissues and human Müller glial cell line. Double-labeling analyses demonstrated that (P)RR and AT1R were detected in cells positive for glial fibrillary acidic protein, a marker for glial cells, and co-localized with prorenin and angiotensinogen, respectively. Administration of prorenin to Müller glial cells enhanced mRNA expression of fibroblast growth factor 2, while Ang II application stimulated the expression of glial cell line-derived neurotrophic factor, nerve growth factor, and transforming growth factor-β1. These expression levels induced by prorenin or Ang II were reversed by (P)RR or AT1R blockade, respectively. Immunofluorescence revealed tissue co-localization of (P)RR and AT1R with the products of the upregulated genes in vitro. The present findings suggest the involvement of RAPS in the pathogenesis of iERM.
Revealing new insights into different phosphorus-starving responses between two maize (Zea mays) inbred lines by transcriptomic and proteomic studies
Authors: Jiang Huimin , Zhang Jianfeng , Han Zhuo , Yang Juncheng , Ge Cailin , Wu Qingyu
Published: March 2017

Phosphorus (P) is an essential plant nutrient, and deficiency of P is one of the most important factors restricting maize yield. Therefore, it is necessary to develop a more efficient program of P fertilization and breeding crop varieties with enhanced Pi uptake and use efficiency, which required understanding how plants respond to Pi starvation. To understand how maize plants adapt to P-deficiency stress, we screened 116 inbred lines in the field and identified two lines, DSY2 and DSY79 that were extreme low-P resistant and sensitive, respectively. We further conducted physiological, transcriptomic, and proteomic studies using the roots of DSY2 and DSY79 under normal or low-P conditions. The results showed that the low-P resistant line, DSY2 had larger root length, surface area and volume, higher root vitality, as well as acid phosphatase activity as compared with the low-P sensitive line, DSY79 under the low-P condition. The transcriptomic and proteomic results suggest that dramatic more genes were induced in DSY2, including the plant hormone signaling, acid phosphatase, and metabolite genes, as compared with DSY79 after being challenged by low-P stress. The new insights generated in this study will be useful toward the improvement of P-utilize efficiency in maize.
Major shifts at the range edge of marine forests: the combined effects of climate changes and limited dispersal
Authors: Assis J. , Berecibar E. , Claro B. , Alberto F. , Reed D. , Raimondi P. , Serrão E. A.
Published: March 2017

Global climate change is likely to constrain low latitude range edges across many taxa and habitats. Such is the case for NE Atlantic marine macroalgal forests, important ecosystems whose main structuring species is the annual kelpSaccorhiza polyschides. We coupled ecological niche modelling with simulations of potential dispersal and delayed development stages to infer the major forces shaping range edges and to predict their dynamics. Models indicated that the southern limit is set by high winter temperatures above the physiological tolerance of overwintering microscopic stages and reduced upwelling during recruitment. The best range predictions were achieved assuming low spatial dispersal (5 km) and delayed stages up to two years (temporal dispersal). Reconstructing distributions through time indicated losses of ~30% from 1986 to 2014, restrictingS. polyschidesto upwelling regions at the southern edge. Future predictions further restrict populations to a unique refugium in northwestern Iberia. Losses were dependent on the emissions scenario, with the most drastic one shifting ~38% of the current distribution by 2100. Such distributional changes might not be rescued by dispersal in space or time (as shown for the recent past) and are expected to drive major biodiversity loss and changes in ecosystem functioning.
Effects of silk fibroin in murine dry eye
Authors: Kim Chae Eun , Lee Ji Hyun , Yeon Yeung Kyu , Park Chan Hum , Yang JaeWook
Published: March 2017

The study aimed to investigate the effects of silk fibroin in a mouse model of dry eye. The experimental dry eye mouse model was developed using more than twelve-weeks-old NOD.B10.H2b mice exposing them to 30–40% ambient humidity and injecting them with scopolamine hydrobromide for 10 days. Tear production and corneal irregularity score were measured by the instillation of phosphate buffered saline or silk fibroin. Corneal detachment and conjunctival goblet cell density were observed by hematoxylin and eosin or periodic acid Schiff staining in the cornea or conjunctiva. The expression of inflammatory markers was detected by immunohistochemistry in the lacrimal gland. The silk group tear production was increased, and corneal smoothness was improved. The corneal epithelial cells and conjunctival goblet cells were recovered in the silk groups. The expression of inflammatory factors was inhibited in the lacrimal gland of the silk group. These results show that silk fibroin improved the cornea, conjunctiva, and lacrimal gland in the mouse model of dry eye. These findings suggest that silk fibroin has anti-inflammatory effects in the experimental models of dry eye.
Hydrogen bonds between methanol and the light liquid olefins 1-pentene and 1-hexene: from application to fundamental science
Authors: Zhang Zhaoxi , Xiao Tiancun , Al-Megren Hamid , Aldrees Saud A. , Al-Kinany Mohammad , Kuznetsov Vladimir L. , Kuznetsov Maxim L. , Edwards Peter P.
Published: March 2017

Hydrogen bonding is the critical component of a new, sustainable ‘Extractive Refining’ technology for reducing the olefin content of commercial FCC gasoline.
Synthesis and evaluation of a tag-free photoactive phospho-ceramide analogue-1 (PCERA-1) probe to study immunomodulation in macrophages
Authors: Dandela Rambabu , Mashiach Roi , Adepu Raju , Gregor Rachel , Athamna Muhammad , Zecharia Efrat , Ernst Orna , Zor Tsaffrir , Meijler Michael M.
Published: March 2017

Phospho-ceramide analogue-1 (PCERA-1), a synthetic analogue of ceramide-1-phosphate (C1P), has been previously shown to act as a potent modulator of macrophage activity and inflammation.
Investigation of the complexation of natZr(iv) and 89Zr(iv) by hydroxypyridinones for the development of chelators for PET imaging applications
Authors: Guérard F. , Beyler M. , Lee Y.-S. , Tripier R. , Gestin J.-F. , Brechbiel M. W.
Published: March 2017

Hydroxypyridinones were studied in their most simple form for the complexation of Zr(iv) which provides important data for the design of pre-organized chelators of this metal for nuclear imaging applications.
CO2-modified solvents for chromatographic separation
Authors: Yuan X. , Kim E. G. , Sanders C. A. , Richter B. E. , Cunningham M. F. , Jessop P. G. , Oleschuk R. D.
Published: March 2017

CO2modified mobile phases are used to adjust the retention factor of compounds on (primary, secondary and tertiary amine) functionalized columns.
Synthesis and self-assembly of a D3h symmetric polycyclic aromatic hydrocarbon into a rigid 2D honeycomb network
Authors: Zhang Liyan , Li Jinling , Qiu Shuhai , Huang Xiaobo , Zeng Zebing
Published: March 2017

C
3 symmetric hexa-peri-hexabenzocoronene carboxylic acid assembles into a rigid 2D honeycomb network at a solid–liquid interface.
Dendritic chitosan as a magnetic and biocompatible nanocarrier for the simultaneous delivery of doxorubicin and methotrexate to MCF-7 cell line
Authors: Rahimi Mahdi , Safa Kazem D. , Alizadeh Effat , Salehi Roya
Published: March 2017

A novel smart, biocompatible, and pH-responsive magnetic highly branched chitosan was synthesized efficiently for use in dual-anticancer drug delivery systems.
Effect of sample temperature, pH, and matrix on the percentage protein binding of protein-bound uraemic toxins
Authors: Deltombe Olivier , Dhondt Annemieke , Van Biesen Wim , Glorieux Griet , Eloot Sunny
Published: March 2017

While studying and trying to optimise dialysis clearances of protein-bound uraemic toxins (PBUTs), the percentage protein binding (% PB) may be an important parameter and can be calculated from measured free and total concentrations.
Tertiary amine self-catalyzed intramolecular Csp3–H functionalization with in situ generated allenes for the formation of 3-alkenyl indolines
Authors: Zhao Yulei , Xu Murong , Zheng Zhong , Yuan Yang , Li Yanzhong
Published: March 2017

Tandem Pd(0) catalyzed allenylation/tertiary amine self-catalyzed Csp3–H functionalization reaction for the synthesis of 3-alkenyl indolines.
Synthesis of yolk–shell mesoporous silica nanoparticles via a facile one-pot approach
Authors: Song Jing-Chuan , Xue Fei-Fei , Zhang Xing-Xing , Lu Zhong-Yuan , Sun Zhao-Yan
Published: March 2017

A simple and facile one-pot method is proposed for the fabrication of yolk–shell mesoporous silica particles for the first time and the particle size can be well controlled.
Luminescence and white-light emitting luminescent sensor of tetrafluoroterephthalate-lanthanide metal–organic frameworks
Authors: Han Yongqiang , Yan Pengfei , Sun Jingwen , An Guanghui , Yao Xu , Li Yuxin , Li Guangming
Published: March 2017

H2TFBDC lanthanide complexes emitting white light was synthesized and a luminescent sensor for the detection of benzaldehyde has been produced.
Design, structural diversity and properties of novel zwitterionic metal–organic frameworks
Authors: Aulakh Darpandeep , Nicoletta Anthony P. , Pyser Joshua B. , Varghese Juby R. , Wriedt Mario
Published: March 2017

Anionic and flexible viologen derivates are explored as ligands for the synthesis of new zwitterionic metal–organic frameworks.
Frustrated Lewis pair behavior of a neutral scandium complex
Authors: Chang Kejian , Xu Xin
Published: March 2017

A neutral scandium complex featuring a Sc/P combination underwent typical FLP-type addition reactions to yield Sc/Rh heterobimetallic and scandium phosphazine complexes, respectively.
Correction: New tetranuclear manganese clusters with [MnII3MnIII] and [MnII2MnIII2] metallic cores exhibiting low and high spin ground state
Authors: Sobocińska M. , Antkowiak M. , Wojciechowski M. , Kamieniarz G. , Utko J. , Lis T.
Published: March 2017

Correction for ‘New tetranuclear manganese clusters with [MnII3MnIII] and [MnII2MnIII2] metallic cores exhibiting low and high spin ground state’ by M. Sobocińska et al., Dalton Trans., 2016, 45, 7303–7311.
A hybrid of carbon dots with 4-chloro-7-nitro-2,1,3-benzoxadiazole for selective detection of p-phenylenediamine
Authors: Wang Wen-Jing , Xia Jun-Mei , Hai Xin , Chen Ming-Li , Wang Jian-Hua
Published: March 2017

A hybrid of carbon dots with 4-chloro-7-nitro-2,1,3-benzoxadiazole facilitates selective and sensitive detection of p-phenylenediamine.
Long-chain α–ω diols from renewable fatty acids via tandem olefin metathesis–ester hydrogenation
Authors: Gonzalez-de-Castro Angela , Cosimi Elena , Aguila Mae Joanne B. , Gajewski Piotr , Schmitkamp Mike , de Vries Johannes G. , Lefort Laurent
Published: March 2017

Long chain α–ω diols were readily accessed from renewable fatty acid methyl esters following an orthogonal tandem self-metathesis–ester hydrogenation protocol.
Tandem cyclisation of vinyl radicals: a sustainable approach to indolines utilizing visible-light photoredox catalysis
Authors: Pagire Santosh K. , Reiser Oliver
Published: March 2017

2,3-Disubstituted indoles can be efficiently synthesised at room temperature from readily available benzylated ortho-amino-α-bromocinnamates by a photoredox catalysed tandem radical 1,6-H-translocation-cyclisation strategy, advancing previous protocols that called for overstoichiometric use of Bu3SnH/AIBN and reflux temperatures.
Design of a Cu(i)/C-doped boron nitride electrocatalyst for efficient conversion of CO2into acetic acid
Authors: Sun Xiaofu , Zhu Qinggong , Kang Xinchen , Liu Huizhen , Qian Qingli , Ma Jun , Zhang Zhaofu , Yang Guanying , Han Buxing
Published: March 2017

Cu(i) complex/BN-Cxcomposites exhibited high performance for electrochemical reduction of CO2to acetic acid in a [Emim]BF4-LiI-water electrolyte.
Synthesis, X-ray structure and electrochemical properties of hybrid binuclear metallophthalocyaninate-capped tris-pyridineoximates
Authors: Dudkin Semyon V. , Belov Alexander S. , Nelyubina Yulia V. , Savchuk Anastasia V. , Pavlov Alexander A. , Novikov Valentin V. , Voloshin Yan Z.
Published: March 2017

New antimony-capped iron and nickel(ii) tris-pyridineoximates easily underwent transmetallation with zirconium and hafnium(iv) phthalocyaninates giving metallophthalocyaninato-cross-linked complexes.
Facile synthesis and chiral recognition of block and star copolymers containing stereoregular helical poly(phenyl isocyanide) and polyethylene glycol blocks
Authors: Liu Na , Ma Cui-Hong , Sun Rui-Wen , Huang Jian , Li Chonglong , Wu Zong-Quan
Published: March 2017

A new Pd(ii) initiator bearing an alkyne headgroup was designed and synthesized.
Seawater operating bio-photovoltaic cells coupling semiconductor photoanodes and enzymatic biocathodes
Authors: Zhang Lingling , Álvarez-Martos Isabel , Vakurov Alexander , Ferapontova Elena E.
Published: March 2017

Clean and sustainable production of electricity from sunlight and seawater is possible by H2O/O2 recycling in bio-photovoltaic cells comprising semiconductor photoanodes and an enzymatic biocathode.
A Systematic Review of Isometric Lingual Strength-Training Programs in Adults With and Without Dysphagia
Authors: McKenna Victoria S. , Zhang Bin , Haines Morgan B. , Kelchner Lisa N.
Published: March 2017

Purpose

This systematic review summarizes the effects of isometric lingual strength training on lingual strength and swallow function in adult populations. Furthermore, it evaluates the designs of the reviewed studies and identifies areas of future research in isometric lingual strength training for dysphagia remediation.

Method

A comprehensive literature search of 3 databases and additional backward citation search identified 10 studies for inclusion in the review. The review reports and discusses the isometric-exercise intervention protocols, pre- and postintervention lingual-pressure data (maximum peak pressures and lingual-palatal pressures during swallowing), and oropharyngeal swallowing measures such as penetration-aspiration scales, oropharyngeal residue and duration, lingual volumes, and quality-of-life assessments.

Results

Studies reported gains in maximum peak lingual pressures following isometric lingual strength training for both healthy adults and select groups of individuals with dysphagia. However, due to the variability in study designs, it remains unclear whether strength gains generalize to swallow function.

Conclusion

Although isometric lingual strength training is a promising intervention for oropharyngeal dysphagia, the current literature is too variable to confidently report specific therapeutic benefits. Future investigations should target homogenous patient populations and use randomized controlled trials to determine the efficacy of this treatment for individuals with dysphagia.
Synthesis of Multisubstituted 1,4-Dihydrobenzoxazin-2-ones through a One-Pot Nucleophilic N-Alkylation/C-Alkylation of Cyclic α-Imino Esters
Authors: De Munck Lode , Vila Carlos , Pons Carolina , Pedro José
Published: March 2017

A nucleophilic N-alkylation of 2-oxobenzoxazine-2-carboxylates with organozinc reagents with good selectivities and in moderate to good yields is described. Moreover, the synthesis of multisubstituted 1,4-dihydrobenzoxazine-2-ones bearing a tetrasubstituted carbon atom via a one-pot N-alkylation/C-alkylation reactions is reported.
Risk factors for inadequate bowel preparation: a validated predictive score
Authors: Gimeno-García Antonio , Baute Jose , Hernandez Goretti , Morales Dalia , Gonzalez-Pérez Carmen , Nicolás-Pérez David , Alarcon-Fernández Onofre , Jiménez Alejandro , Hernandez-Guerra Manuel , Romero Rafael , Alonso Inmaculada , Gonzalez Yanira , Adrian Zaida , Carrillo Marta , Ramos Laura , Quintero Enrique
Published: March 2017

Background and study aim Inadequate bowel cleansing negatively affects the efficiency of colonoscopy in routine clinical practice. The aim of this study was to design and validate a predictive model for inadequate bowel cleanliness.

Patients and methods The model was built from 667 consecutive outpatients (development cohort) who were prospectively scheduled for colonoscopy between June and September 2014. The validation cohort included 409 outpatients who underwent colonoscopy between October and December 2014. Cleansing was evaluated using the Boston Bowel Preparation Scale (BBPS). Bowel preparation was administered on the same day as the examination.

Results In the development cohort, BBPS was adequate in 541 patients (81.1 %). At multivariate analysis, antidepressants (odds ratio [OR] 4.25, 95 % confidence interval [CI] 1.91 – 9.47), co-morbidity (OR 3.35, 95 %CI 2.16 – 5.18), constipation (OR 2.09, 95 %CI 1.29 – 3.40), and abdominal/pelvic surgery (OR 1.60, 95 %CI 1.03 – 2.47) were independent predictors for inadequate cleansing. The model built with these variables showed an area under the curve of 0.72 in the development cohort and 0.70 in the validation cohort. A cutoff of 1.225 predicted inadequate bowel preparation with a sensitivity, specificity, positive predictive value, and negative predictive value of 60.3 % (95 %CI 51.6 – 68.4), 75.4 % (95 %CI 71.6 – 78.9), 36.4 % (95 %CI 30.1 – 43.1), and 89.1 % (95 %CI 85.9 – 91.6) in the development cohort, and 50.0 % (95 %CI 38.1 – 61.9), 80.0 % (95 %CI 75.3 – 84.2), 35.7 % (95 %CI 26.4 – 45.6), and 87.9 % (95 %CI 83.7 – 91.3) in the validation cohort.

Conclusion A simple score may assist the clinician in predicting which patients are at high risk of inadequate bowel cleanliness. This may guide changes in bowel preparation strategy accordingly.
Measurement and modeling of plasma parameters in reactive high-power impulse magnetron sputtering of Ti in Ar/O2 mixtures
Authors: Čada M. , Lundin D. , Hubička Z.
Published: March 2017

A reactive high-power impulse magnetron sputtering (HiPIMS) process using a titanium target in a mixture of Ar/O2 has been investigated for different modes of operation including pure argon, metallic, transition, and compound mode. The trends and changes in the plasma density ne and the effective electron temperature Teff, have been measured by the time-resolved Langmuir probe technique. The same experimental process conditions have also been studied using a recently developed reactive ionization region model (R-IRM), making it possible to compare the acquired experimental results with the model results. It was found that trends in the plasma density and mean electron energy as measured by the Langmuir probe are in good agreement with the results obtained from the R-IRM model for different pulse discharge current densities. The effective electron temperature generally increases with an increasing oxygen flow rate. It is likely due to a reduction of sputtered Ti, due to compound formation on the target, which forces the discharge to increase the electron energy to increase the ionization rate of the process gas (Ar/O2) to maintain a high HiPIMS discharge current. Small variations in the plasma density were detected between the middle part of the plasma pulse as compared to the end of the plasma pulse, when transitioning from the metal mode to the poisoned mode. It is found that the time-evolution of the electron density is rather well correlated with the discharge current waveform. On the other hand, the mean electron energy did not change significantly between the middle and the end of the plasma pulse. For the lower pulse discharge current, both the model and experimental data have shown a slight increase in the plasma density with increasing O2 mass flow rate.
Enhanced oxidation of TiO2 films prepared by high power impulse magnetron sputtering running in metallic mode
Authors: Stranak V. , Kratochvil J. , Olejnicek J. , Ksirova P. , Sezemsky P. , Cada M. , Hubicka Z.
Published: March 2017

A method is introduced that allows suppressing unwanted effects of target poisoning during reactive high-power impulse magnetron sputtering (R-HiPIMS) employed for deposition of oxide films. The method, based on higher reactivity of excited/activated oxygen species, is studied and demonstrated on TiO2 films deposited in R-HiPIMS discharge running very close to the metallic mode with a high deposition rate. An external source of energetic plasma that activates oxygen gas, delivered to the vicinity of the substrate, is combined with conventional R-HiPIMS of the Ti target. The activated oxygen species enable reducing the total flow rate, which simultaneously results in suppression of the target poisoning effect. On the other hand, sufficient oxidation and growth of transparent crystalline TiO2 films were observed.
The 3-cycle weighted spectral distribution in evolving community-based networks
Authors: Jiao Bo , Wu Xiaoqun
Published: March 2017

One of the main organizing principles in real-world networks is that of network communities, where sets of nodes organize into densely linked clusters. Many of these community-based networks evolve over time, that is, we need some size-independent metrics to capture the connection relationships embedded in these clusters. One of these metrics is the average clustering coefficient, which represents the triangle relationships between all nodes of networks. However, the vast majority of network communities is composed of low-degree nodes. Thus, we should further investigate other size-independent metrics to subtly measure the triangle relationships between low-degree nodes. In this paper, we study the 3-cycle weighted spectral distribution (WSD) defined as the weighted sum of the normalized Laplacian spectral distribution with a scaling factor n, where n is the network size (i.e., the node number). Using some diachronic community-based network models and real-world networks, we demonstrate that the ratio of the 3-cycle WSD to the network size is asymptotically independent of the network size and strictly represents the triangle relationships between low-degree nodes. Additionally, we find that the ratio is a good indicator of the average clustering coefficient in evolving community-based systems.
Comparison of forecasting methods for vertical axis wind turbine applications in an urban/suburban area
Authors: Nguyen Lam , Metzger Meredith
Published: March 2017

Wind forecasting plays an important role in the economic benefit and system reliability of wind turbine power generation. The goal of the present study is to investigate different forecasting methods that can be used to improve the amount of energy captured by a small-scale vertical axis wind turbine (VAWT) operating in a gusty wind environment typical of an urban/suburban area. Four forecasting methods are studied in the present research: Persistence Method, Modified Persistence Method, Autoregressive Moving Average (ARMA) model, and Weather Research and Forecasting (WRF) model. The forecasting models are used to predict the wind conditions and optimal rotational speed of VAWTs located in Oklahoma City for data collected in 2009. In all cases, a constant rotational speed controller was used with a forecasting horizon of 1 day. The results indicate that a 5% increase in accuracy of the wind forecast could increase the total amount of energy captured by the VAWT by as much as 13%. The results also indicate that the use of a tuned speed adjustment factor (AF) in the modified persistence method improves the overall performance of the VAWT by as much as 6% compared to the persistence method. The value of AF was found to be site-independent and linearly proportional to the annual average wind speed. For the ARMA model, there exists an optimal amount of training data and forecasting horizon that results in minimal error when the forecasting data are compared to the actual data. For each of the sites investigated, the modified persistence method appears to slightly outperform the persistence, ARMA, and WRF models. In all cases, the forecasting models allow the VAWT to capture approximately 78%–85% of the optimal amount of energy that could be generated assuming the actual wind data were known in advance. The economic viability of the VAWT is also examined by comparing the Levelized Cost of Energy (LCOE) for the VAWT with the national electricity unit price. The LCOE of the system is competitive with the national electricity unit price at the sites where the annual average wind speed is 4.3 m/s or greater.
Investigation of plasma spokes in reactive high power impulse magnetron sputtering discharge
Authors: Hecimovic A. , Corbella C. , Maszl C. , Breilmann W. , von Keudell A.
Published: March 2017

Spokes, localised ionisation zones, are commonly observed in magnetron sputtering plasmas, appearing either with a triangular shape or with a diffuse shape, exhibiting self-organisation patterns. In this paper, we investigate the spoke properties (shape and emission) in a high power impulse magnetron sputtering (HiPIMS) discharge when reactive gas (N2 or O2) is added to the Ar gas, for three target materials; Al, Cr, and Ti. Peak discharge current and total pressure were kept constant, and the discharge voltage and mass flow ratios of Ar and the reactive gas were adjusted. The variation of the discharge voltage is used as an indication of a change of the secondary electron yield. The optical emission spectroscopy data demonstrate that by addition of reactive gas, the HiPIMS plasma exhibits a transition from a metal dominated plasma to the plasma dominated by Ar ions and, at high reactive gas partial pressures, to the plasma dominated by reactive gas ions. For all investigated materials, the spoke shape changed to the diffuse spoke shape in the poisoned mode. The change from the metal to the reactive gas dominated plasma and increase in the secondary electron production observed as the decrease of the discharge voltage corroborate our model of the spoke, where the diffuse spoke appears when the plasma is dominated by species capable of generating secondary electrons from the target. Behaviour of the discharge voltage and maximum plasma emission is strongly dependant on the target/reactive gas combination and does not fully match the behaviour observed in DC magnetron sputtering.
Increased efficiency in pn-junction PbS QD solar cells via NaHS treatment of the p-type layer
Authors: Speirs Mark J. , Balazs Daniel M. , Dirin Dmitry N. , Kovalenko Maksym V. , Loi Maria Antonietta
Published: March 2017

Lead sulfide quantum dot (PbS QD) solar cell efficiencies have improved rapidly over the past years due in large part to intelligent band alignment considerations. A pn-junction can be formed by connecting PbS layers with contrasting ligands. However, the resulting doping concentrations are typically low and cannot be effectively controlled. Here, we present a method of chemically p-doping films of thiol capped PbS QDs. P-n junction solar cells with increased doping in the p-type layer show improved short circuit current and fill factor, leading to an improvement in the power conversion efficiency from 7.1% to 7.6%. By examining Schottky diodes, field effect transistors, and the absorption spectra of treated and untreated PbS QDs, we show that the improved efficiency is due to the increased doping concentration in the thiol capped QD layer and to denser packing of the PbS QD film.
Photonic spin Hall effect by the spin-orbit interaction in a metasurface with elliptical nano-structures
Authors: Wang Ying-Hua , Jin Ren-Chao , Li Jia-Qi , Zhong Fan , Liu Hui , Kim Inki , Jo Yongjoon , Rho Junsuk , Dong Zheng-Gao
Published: March 2017

The metasurface with elliptical nano-structures containing doubly degenerate geometrical charge is designed to investigate the enhanced spin-orbit optical interactions, numerically as well as experimentally. It is found that localized surface plasmon (LSP) resonance with orbital angular momentum (i.e., rotating SP vortex mode carrying extrinsic orbital angular momentum) can be induced under linearly polarized illumination. On the contrary, the LSP resonance without orbital angular momentum is formed under circularly polarized illumination. Moreover, based on the different LSP modes as results of spin-orbit interaction with alternative geometrical charge, directional propagations of surface plasmon polariton in two orthogonal trajectories depending on spin states of the incident light are presented with experimental demonstration, a phenomenon called photonic spin Hall effect.
High electrical resistivity Nd-Fe-B die-upset magnet doped with eutectic DyF3–LiF salt mixture
Authors: Kim K. M. , Kim J. Y. , Kwon H. W. , Kim D. H. , Lee J. G. , Yu J. H.
Published: March 2017

Nd-Fe-B-type die-upset magnet with high electrical resistivity was prepared by doping of eutectic DyF3–LiF salt mixture. Mixture of melt-spun Nd-Fe-B flakes (MQU-F: Nd13.6Fe73.6Co6.6Ga0.6B5.6) and eutectic binary (DyF3–LiF) salt (25 mol% DyF3 – 75 mol% LiF) was hot-pressed and then die-upset. By adding the eutectic salt mixture (> 4 wt%), electrical resistivity of the die-upset magnet was enhanced to over 400 μΩ.cm compared to 190 μΩ.cm of the un-doped magnet. Remarkable enhancement of the electrical resistivity was attributed to homogeneous and continuous coverage of the interface between flakes by the easily melted eutectic salt dielectric mixture. It was revealed that active substitution of the Nd atoms in neighboring flakes by the Dy atoms from the added (DyF3–LiF) salt mixture had occurred during such a quick thermal processing of hot-pressing and die-upsetting. This Dy substitution led to coercivity enhancement in the die-upset magnet doped with the eutectic (DyF3–LiF) salt mixture. Coercivity and remanence of the die-upset magnet doped with (DyF3–LiF) salt mixture was as good as those of the DyF3-doped magnet.
High levels of population differentiation in two New Caledonian Scaevola species (Goodeniaceae) and its implications for conservation prioritisation and restoration
Authors: Wulff Adrien S. , Hollingsworth Peter M. , Piquet Marie , Ahrends Antje , L'Huillier Laurent , Fogliani Bruno
Published: March 2017

Population genetic structure was studied in two Scaevola (Goodeniaceae) species across their ranges in New Caledonia. Scaevola montana is locally common and distributed primarily on ultramafic substrates, and is used for ecological restoration of mining sites. Scaevola coccinea is a narrow endemic restricted to ultramafic soils in a single valley, where intensive mining activity occurs. We compared levels of diversity and differentiation in the two species using nuclear microsatellites, so as to understand the spatial scale at which populations become isolated. We also measured environmental distances among sites as a crude proxy to estimate where adaptive differentiation may occur. Populations of S. montana were sampled over a total distance of ~500 km. In contrast, the total range of S. coccinea is 12 × 6 km. Greater allelic diversity and gene diversity was detected within populations of S. montana than S. coccinea. Both species show high levels of population differentiation (S. montana FʹST = 0.437; S. coccinea FʹST = 0.54). The marked population structure in S. coccinea despite the close proximity of the sampled populations is associated with its pollination by territorial birds and no observed seed-dispersal agents, compared with the greater vagility of insect pollination and bird dispersal of S. montana. In S. coccinea, given the high levels of differentiation, we highlight the importance of each individual population for the conservation of intra-specific biodiversity in this species. In S. montana, we used a combination of the genetic data and environmental characteristics of each of the sample sites to outline general guidelines on seed sources for restoration programs.
A Combined Experimental and Theoretical Study on the Reaction Mechanism and Molecular Structure of 4-(Diphenylamino)-3-iodo-2(5H)-furanone
Authors: Song Xiumei , Xue Fuling , Feng Zongcai , Wang Yun , Wang Zhaoyang , Xi Yanli
Published: March 2017

The simultaneous α-iodination and Nβ-arylation mechanism of 5-alkyloxy-4-phenylamino-2(5H)-furanone by (diacetoxyiodo)benzene was investigated by means of density functional theory (DFT) with B3LYP/6-31G*//LANL2DZ, selecting 4-(diphenylamino)-5-methyloxy-3-iodo-2(5H)-furanone as the calculation model. In addition, the effect of solvent on the reaction pathway was investigated using the Polarisable Continuum Model (PCM). Good agreement was found between the computational and the experimental results. Furthermore, single crystals of 4-(diphenylamino)-5-ethoxy-3-iodo-2(5H)-furanone were grown by slow evaporation technique. The molecular structure analysis was performed by single crystal X-ray analysis and theoretical calculations using a semi-empirical quantum chemical method and DFT/B3LYP methods with a LANL2DZ as basis set.
Crowdsourcing and online collaborative translations
Authors: Jiménez-Crespo Miguel A.
Published: March 2017

Crowdsourcing and online collaborative translations have emerged in the last decade to the forefront of Translation Studies as one of the most dynamic and unpredictable phenomena that has attracted a growing number of researchers. The popularity of this set of varied translational processes holds the potential to reframe existing translation theories, redefine a number of tenets in the discipline, advance research in the so-called “technological turn” and impact public perceptions on translation. This book provides an interdisciplinary analysis of these phenomena from a descriptive and critical perspective, delving into industry approaches and fostering inter and intra disciplinary connections between areas in which the impact is the greatest, such as cognitive translatology, translation technologies, quality and translation evaluation, sociological approaches, text-linguistic approaches, audiovisual translation or translation pedagogy. This book is of special interest to translation researchers, translation students, industry experts or anyone with an interest on how crowdsourcing and online collaborative translations relate to past, present and future research and theorizations in Translation Studies.
Chapter 10. Sensitivity of maternal gesture to interlocutor and context
Authors: Zammit Maria , Schafer Graham
Published: March 2017

Child-directed communication may be systematically modified either because (1) it scaffolds language learning (the ‘Facilitative Strategy Hypothesis’) or (2) as a consequence of the semantic simplicity of interactions with children (the ‘Interactional Artefact Hypothesis’). To compare these hypotheses, we compared maternal gestural production in dialogue with adults and children. We also examined the sensitivity of gestural production to children’s concurrent linguistic level. Twenty-nine mothers and their 16–24-month-olds were video-recorded during a free play session, and during picture and word description tasks. In interaction with children, maternal gestural repertoires were limited, typically comprising concrete deictic and representational gestures; abstract emphatic gestures were rare. Maternal gesture and children’s current vocabulary were positively correlated. Thus, maternal gestural modification appears to scaffold word learning, supporting the Facilitative Strategy Hypothesis.
Chapter 20. Microgenesis of gestures during mental rotation tasks recapitulates ontogenesis
Authors: Chu Mingyuan , Kita Sotaro
Published: March 2017

People spontaneously produce gestures when they solve problems or explain their solutions to a problem. In this chapter, we will review and discuss evidence on the role of representational gestures in problem solving. The focus will be on our recent experiments (Chu & Kita, 2008), in which we used Shepard-Metzler type of mental rotation tasks to investigate how spontaneous gestures revealed the development of problem solving strategy over the course of the experiment and what role gesture played in the development process. We found that when solving novel problems regarding the physical world, adults go through similar symbolic distancing (Werner & Kaplan, 1963) and internalization (Piaget, 1968) processes as those that occur during young children’s cognitive development and gesture facilitates such processes.
Chapter 24. Gestures in overlap
Authors: Mondada Lorenza , Oloff Florence
Published: March 2017

This paper aims at contributing to the analysis of overlaps in turns-at-talk from both a sequential and a multimodal perspective. Overlaps have been studied within Conversation Analysis by focusing mainly on verbal and vocal resources; taking into account multimodal resources such as gesture, bodily posture, and gaze contributes to a better understanding of participants’ orientations to the sequential organization of overlapping talk and their management of speakership.First, we introduce the way in which overlaps have been studied in Conversation Analysis, mainly by Jefferson (1973, 1983, 2004) and Schegloff (2000); then we propose possible implications of their multimodal analysis. In order to demonstrate that speakers systematically orient to the overlap onset and resolution we analyze the multimodal conduct of overlapped speakers. Findings show methodical variations in trajectories of overlap resolution: speakers’ gestures in overlap display themselves as maintaining or withdrawing their turn, thereby exhibiting the speakership achieved and negotiated during overlap.
Reduction of self-heating effect in (Ga)ZnO thin film transistor
Authors: Amuthasurabi M , Chandradass J , Park Seong-Ju , Jesu Martin Leenus
Published: March 2017

RF magnetron sputtering technique was employed to fabricate gallium zinc oxide ((Ga)ZnO) semiconductor thin film transistor (TFT) at 100°C. X-ray diffraction and Scanning electron microscopy were used to identify the structure and morphology of (Ga)ZnO layer. Self-heating effect was very much reduced when compared with output characteristics of a TFT fabricated using undoped zinc oxide. The low deposition and processing temperatures make (Ga)ZnO-TFTs very promising for the flexible electronics.
rMATS-DVR: rMATS discovery of differential variants in RNA
Authors: Wang Jinkai , Pan Yang , Shen Shihao , Lin Lan , Xing Yi
Published: March 2017

Motivation

RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli.

Results

We have developed rMATS-DVR, a convenient and user-friendly software program to streamline the discovery of DVRs between two RNA-seq sample groups with replicates. rMATS-DVR combines a stringent GATK-based pipeline for calling SNVs including SNPs and RNA editing events in RNA-seq reads, with our rigorous rMATS statistical model for identifying differential isoform ratios using RNA-seq sequence count data with replicates. We applied rMATS-DVR to RNA-seq data of the human chronic myeloid leukemia cell line K562 in response to shRNA knockdown of the RNA editing enzyme ADAR1. rMATS-DVR discovered 1372 significant DVRs between knockdown and control. These DVRs encompassed known SNPs and RNA editing sites as well as novel SNVs, with the majority of DVRs corresponding to known RNA editing sites repressed after ADAR1 knockdown.

Availability and Implementation

rMATS-DVR is at https://github.com/Xinglab/rMATS-DVR.

Supplementary information

Supplementary data are available at Bioinformatics online.