bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic Performance of Ten Liver Function Models in Patients with Hepatocellular Carcinoma Undergoing Radiofrequency Ablation
Authors: Ho Shu-Yein , Liu Po-Hong , Hsu Chia-Yang , Chiou Yi-You , Su Chien-Wei , Lee Yun-Hsuan , Huang Yi-Hsiang , Lee Fa-Yauh , Hou Ming-Chih , Huo Teh-Ia 
Published: January 2018

AbstractLiver functional capacity is a crucial survival determinant for hepatocellular carcinoma (HCC). Noninvasive models were proposed to assess hepatic reserve, but their performance in outcome prediction is unclear. We aimed to investigate 10 currently used liver function models in HCC patients undergoing radiofrequency ablation (RFA). A total 499 HCC patients were prospectively identified. Homogeneity and corrected Akaike information criteria (AICc) were compared. Cox proportional hazards model was used to identify independent survival predictors. Significance survival differences were found across 10 noninvasive models (all p < 0.001) except for GUCI and APRI grade 2 vs 3, and King’s score grade 1 vs 2. Among these models, ALBI grade showed the highest homogeneity and lowest AICs value, indicating a better prognostic performance. Within Child-Turcotte-Pugh (CTP) score 5 group, significant survival difference was demonstrated between ALBI grade 1 and 2 (p < 0.001); for those with CTP score 6 or higher, only ALBI grade 2 and 3 showed survival difference (p < 0.001). Cox analysis disclosed that ALBI grade, tumor size and performance status were independent prognostic predictors. There was significant correlation between CTP score and other 9 models. We conclude that ALBI grade may serve as objective and feasible surrogate for prognostic prediction in HCC patients undergoing RFA.
Efficient isolation on Vero.DogSLAMtag cells and full genome characterization of Dolphin Morbillivirus (DMV) by next generation sequencing
Authors: Peletto Simone , Caruso Claudio , Cerutti Francesco , Modesto Paola , Biolatti Cristina , Pautasso Alessandra , Grattarola Carla , Giorda Federica , Mazzariol Sandro , Mignone Walter , Masoero Loretta , Casalone Cristina , Acutis Pier Luigi 
Published: January 2018

AbstractThe Dolphin Morbillivirus (DMV) genome from the first Mediterranean epidemic (1990-’92) is the only cetacean Morbillivirus that has been completely sequenced. Here, we report the first application of next generation sequencing (NGS) to morbillivirus infection of aquatic mammals. A viral isolate, representative of the 2006-’08 Mediterranean epidemic (DMV_IZSPLV_2008), efficiently grew on Vero.DogSLAMtag cells and was submitted to whole genome characterization by NGS. The final genome length was 15,673 nucleotides, covering 99.82% of the DMV reference genome. Comparison of DMV_IZSPLV_2008 and 1990-’92 DMV strain sequences revealed 157 nucleotide mutations and 47 amino acid changes. The sequence similarity was 98.7% at the full genome level. Whole-genome phylogeny suggested that the DMV strain circulating during the 2006-’08 epidemics emerged from the 1990-’92 DMV strain. Viral isolation is considered the “gold standard” for morbillivirus diagnostics but efficient propagation of infectious virus is difficult to achieve. The successful cell replication of this strain allowed performing NGS directly from the viral RNA, without prior PCR amplification. We therefore provide to the scientific community a second DMV genome, representative of another major outbreak. Interestingly, genome comparison revealed that the neglected L gene encompasses 74% of the genetic diversity and might serve as “hypervariable” target for strain characterization.
Biochemical and genetic characterization of a novel metallo-β-lactamase from marine bacterium Erythrobacter litoralis HTCC 2594
Authors: Jiang Xia-Wei , Cheng Hong , Huo Ying-Yi , Xu Lin , Wu Yue-Hong , Liu Wen-Hong , Tao Fang-Fang , Cui Xin-Jie , Zheng Bei-Wen 
Published: January 2018

AbstractMetallo-β-lactamases (MBLs) are a group of enzymes that can inactivate most commonly used β-lactam-based antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an urgent threat to public health as evidenced by its success in rapidly disseminating worldwide since its first discovery. Here we report the biochemical and genetic characteristics of a novel MBL, ElBla2, from the marine bacterium Erythrobacter litoralis HTCC 2594. This enzyme has a higher amino acid sequence similarity to NDM-1 (56%) than any previously reported MBL. Enzymatic assays and secondary structure alignment also confirmed the high similarity between these two enzymes. Whole genome comparison of four Erythrobacter species showed that genes located upstream and downstream of elbla2 were highly conserved, which may indicate that elbla2 was lost during evolution. Furthermore, we predicted two prophages, 13 genomic islands and 25 open reading frames related to insertion sequences in the genome of E. litoralis HTCC 2594. However, unlike NDM-1, the chromosome encoded ElBla2 did not locate in or near these mobile genetic elements, indicating that it cannot transfer between strains. Finally, following our phylogenetic analysis, we suggest a reclassification of E. litoralis HTCC 2594 as a novel species: Erythrobacter sp. HTCC 2594.
Foxo1 Promotes Th9 Cell Differentiation and Airway Allergy
Authors: Buttrick Thomas S. , Wang Wei , Yung Christina , Trieu Kenneth G. , Patel Kruti , Khoury Samia J. , Ai Xingbin , Elyaman Wassim 
Published: January 2018

AbstractT helper 9 (Th9) cells are effector CD4+ T cells that are characterized by the production of interleukin-9 (IL-9) and have been associated with allergic responses. Here, we found that the expression of the transcription factor forkhead box O1 (Foxo1) was induced in Th9 and Foxo1 plays a crucial role in the differentiation of Th9 cells. Pharmacological inhibition of Foxo1 or genetic disruption of Foxo1 in CD4+ T cells caused a reduction in IL-9 expression while upregulating IL-17A and IFNγ production. Furthermore, chromatin immunoprecipitation (ChIP) followed by luciferase assays revealed direct binding of Foxo1 to both the Il9 and Irf4 promoters and induces their transactivation. Lastly, adoptive transfer of Th9 cells into lungs induced asthma-like symptoms that were ameliorated by Foxo1 inhibitor, AS1842856. Together, our findings demonstrate a novel regulator of Th9 cells with a direct implication in allergic inflammation.
Integrated miRNA-mRNA spatial signature for oral squamous cell carcinoma: a prospective profiling study of Narrow Band Imaging guided resection
Authors: Farah Camile S. , Fox Simon A. , Dalley Andrew J. 
Published: January 2018

AbstractOral squamous cell carcinoma (OSCC) is a common malignancy for which there is poor prognosis and limited therapeutic options. The objective was to identify mRNA targets of dysregulated miRNAs in OSCC using integrated analysis and understand molecular abnormality in surgical margins. We used biopsies along the spatial axis from normal tissue defined by narrow band imaging (NBI) through conventional white light (WL) margins to tumour from 18 patients undergoing surgical resection for OSCC. Overall 119 miRNA and 4794 mRNA were differentially expressed along the adjacent normal tissue to tumour axis. Analysis of miRNA profiles demonstrated the NBI margins were molecularly distinct from both the tumour and WL margin. Integrated analysis identified 193 miRNA-mRNA interactions correlated to the spatial axis of NBI-WL-T. We used cross-validation analysis to derive a spatial interactome signature of OSCC comprising 100 putative miRNA-mRNA interactions between 40 miRNA and 96 mRNA. Bioinformatic analysis suggests that miRNA dysregulation in OSCC may contribute to activation of the oncostatin M, BDNF and TGF-β pathways. Our data demonstrates that surgical margins defined by NBI leave less potentially malignant residual tissue. The miRNA-mRNA interactome provides insight into dysregulated miRNA signalling in OSCC and supports molecular definition of tumour margins.
Coupled‐inductor‐inverse high step‐up converter
Authors: Li Fei , Yao Yu , Wang Zhi , Liu Hongchen 
Published: January 2018

This study presents a novel high conversion gain converter with a tightly coupled‐inductor‐inverse for distributed generation system, where high conversion gain is regularly required. The new converter utilises coupled‐inductor‐inverse network for high conversion gain applications that is not presently comparable with the existing coupled inductor‐based high conversion gain converters. The new converter has a unique feature that the voltage gain is lifted by reducing the turns ratio of the coupled inductor. Subsequently, the diode–capacitor circuit is introduced to primarily recycle the leakage energy, and secondly help to boost the output voltage. This study depicts the main waveforms of the proposed converter and the relevant derivation of the operation principle. The theoretical analysis is verified by the experimental waveforms based on a prototype circuit rated 400 W output power.
Characterization of gamma field in the JSI TRIGA reactor
Authors: Ambrožič Klemen , Radulović Vladimir , Snoj Luka , Gruel Adrien , Guillou Mael Le , Blaise Patrick , Destouches Christophe , Barbot Loïc 
Published: January 2018

Research reactors such as the “Jožzef Stefan” Institute TRIGA reactor have primarily been designed for experimentation and sample irradiation with neutrons. However recent developments in incorporating additional instrumentation for nuclear power plant support and with novel high flux material testing reactor designs, γ field characterization has become of great interest for the characterization of the changes in operational parameters of electronic devices and for the evaluation of γ heating of MTR’s structural materials in a representative reactor Γ spectrum.
In this paper, we present ongoing work on γ field characterization both experimentally, by performing γ field measurements, and by simulations, using Monte Carlo particle transport codes in conjunction with R2S methodology for delayed γ field characterization.
Development of a new bench for puncturing of irradiated fuel rods in STAR hot laboratory
Authors: Petitprez B. , Silvestre P. , Valenza P. , Boulore A. , David T. 
Published: January 2018

A new device for puncturing of irradiated fuel rods in commercial power plants has been designed by Fuel Research Department of CEA Cadarache in order to provide experimental data of high precision on fuel pins with various designs. It will replace the current set-up that has been used since 1998 in hot cell 2 of STAR facility with more than 200 rod puncturing experiments. Based on this consistent experimental feedback, the heavy-duty technique of rod perforation by clad punching has been preserved for the new bench. The method of double expansion of rod gases is also retained since it allows upgrading the confidence interval of volumetric results obtained from rod puncturing. Furthermore, many evolutions have been introduced in the new design in order to improve its reliability, to make the maintenance easier by remote handling and to reduce experimental uncertainties.
Tightness components have been studied with Sealing Laboratory Maestral at Pierrelatte so as to make them able to work under mixed pressure conditions (from vacuum at 10-5 mbar up to pressure at 50 bars) and to lengthen their lifetime under permanent gamma irradiation in hot cell. Bench ergonomics has been optimized to make its operating by remote handling easier and to secure the critical phases of a puncturing experiment. A high pressure gas line equipped with high precision pressure sensors out of cell can be connected to the bench in cell for calibration purposes. Uncertainty analyses using Monte Carlo calculations have been performed in order to optimize capacity of the different volumes of the apparatus according to volumetric characteristics of the rod to be punctured. At last this device is composed of independent modules which allow puncturing fuel pins out of different geometries (PWR, BWR, VVER).
After leak tests of the device and remote handling simulation in a mock-up cell, several punctures of calibrated specimens have been performed in 2016. The bench will be implemented soon in hot cell 2 of STAR facility for final qualification tests. PWR rod punctures are already planned for 2018.
Temporal Imaging CeBr3 Compton Camera: A New Concept for Nuclear Decommissioning and Nuclear Waste Management
Authors: Iltis A. , Snoussi H. , Magalhaes L. Rodrigues de , Hmissi M.Z. , Zafiarifety C. Tata , Tadonkeng G. Zeufack , Morel C. 
Published: January 2018

During nuclear decommissioning or waste management operations, a camera that could make an image of the contamination field and identify and quantify the contaminants would be a great progress. Compton cameras have been proposed, but their limited efficiency for high energy gamma rays and their cost have severely limited their application. Our objective is to promote a Compton camera for the energy range (200 keV – 2 MeV) that uses fast scintillating crystals and a new concept for locating scintillation event: Temporal Imaging.
Temporal Imaging uses monolithic plates of fast scintillators and measures photons time of arrival distribution in order to locate each gamma ray with a high precision in space (X,Y,Z), time (T) and energy (E). This provides a native estimation of the depth of interaction (Z) of every detected gamma ray. This also allows a time correction for the propagation time of scintillation photons inside the crystal, therefore resulting in excellent time resolution. The high temporal resolution of the system makes it possible to veto quite efficiently background by using narrow time coincidence (< 300 ps). It is also possible to reconstruct the direction of propagation of the photons inside the detector using timing constraints. The sensitivity of our system is better than 1 nSv/h in a 60 s acquisition with a 22Na source.
The project TEMPORAL is funded by the ANDRA/PAI under the grant No. RTSCNADAA160019.
Nuclear Fuel Assay through analysis of Uranium L-shell by Hybrid L-edge/XRF Densitometer using a Surrogate Material
Authors: Park Seunghoon , Joung Sungyeop , Park Jerry 
Published: January 2018

Assay of L-series of nuclear material solution is useful for determination of amount of nuclear materials and ratio of minor actinide in the materials. The hybrid system of energy dispersive X-ray absorption edge spectrometry, i.e. L-edge densitometry, and X-ray fluorescence spectrometry is one of the analysis methods. The hybrid L-edge/XRF densitometer can be a promising candidate for a portable and compact equipment due to advantage of using low energy X-ray beams without heavy shielding systems and liquid nitrogen cooling compared to hybrid K-edge/XRF densitometer.
A prototype of the equipment was evaluated for feasibility of the nuclear material assay using a surrogate material (lead) to avoid radiation effects from nuclear materials. The uncertainty of L-edge and XRF characteristics of the sample material and volume effects was discussed in the article.
Risks of Preterm Premature Rupture of Membranes and Preterm Birth Post Fetoscopy Based on Location of Trocar Insertion Site
Authors: Chon Andrew , Korst Lisa , Llanes Arlyn , Kontopoulos Eftichia , Quintero Ruben , Chmait Ramen 
Published: January 2018

Objective The objective of this study was to assess whether the location of the trocar insertion site for laser treatment of twin-twin transfusion syndrome was associated with preterm-premature rupture of membranes (PPROM) and preterm birth (PTB).
Study Design In this study trocar location was documented in the operating room. Lower uterine segment (LUS) location was defined as any insertion <10 cm vertically from the pubic symphysis. Lateral location was defined as ≥5 cm horizontally from the midline. Patient characteristics were tested against three outcomes: PPROM ≤ 21 days postoperative, PTB < 28 weeks, and PTB < 32 weeks. For each outcome, multiple logistic models were fitted to examine the effect of trocar location, controlling for potential risk factors.
Results A total of 743 patients were studied. Patients with LUS location were twice as likely as those with a more superior location to have PPROM ≤ 21 days (OR = 2.33, 1.12–4.83, p = 0.0236). Patients with both a LUS and Lateral location were over six times more likely to have PPROM ≤ 21 days (OR = 6.66, 2.36–18.78, p = 0.0003). Trocar insertion site was not associated with PTB.
Conclusion We found that trocar insertion in the LUS, particularly the lateral LUS, was associated with an increased risk of PPROM.
Food functionality research as a new national project in special reference to improvement of cognitive and locomotive abilities
Authors: Abe Keiko , Misaka Takumi 
Published: January 2018

Abstract
In Japan, where a super-aging society is realized, we are most concerned about healthy longevity, which would ascertain the wellness of people by improving their quality of life (QOL). In 2014, the Cabinet Office proposed a strategic innovation promotion programme, launching a national project for the development of the agricultural-forestry-fisheries food products with new functionalities for the next generation. In addition to focusing on a conventional prevention of lifestyle-associated metabolic syndromes, the project targets the scientific evidence of the activation of brain cognitive ability and the improvement of bodily locomotive function. The project also involves the analysis of the foods-sports interrelation of chronic importance, and the development of devices for the verification of QOL-associated maintenance of homeostasis. In this review, we provide an overview of these studies, with special reference to cognition as a case of the gut-brain axis which the author is particularly interested in.
Developing a framework for assessing the impact of geothermal development phases on ecosystem services
Authors: Semedi Jarot M. , Willemen Louise , Nurlambang Triarko , van der Meer Freek , Koestoer Raldi H. 
Published: January 2018

Abstract
The 2014 Indonesian National Energy Policy has set a target to provide national primary energy usage reached 2.500 kWh per capita in the year 2025 and reached 7.000 kWh in the year 2050. The National Energy Policy state that the development of energy should consider the balance of energy economic values, energy supply security, and the conservation of the environment. This has led to the prioritization of renewable energy sources. Geothermal energy a renewable energy source that produces low carbon emissions and is widely available in Indonesia due to the country’s location in the “volcanic arc”. The development of geothermal energy faces several problems related to its potential locations in Indonesia. The potential sites for geothermal energy are mostly located in the volcanic landscapes that have a high hazard risk and are often designated protected areas. Local community low knowledge of geothermal use also a challenge for geothermal development where sometimes strong local culture stand in the way. Each phase of geothermal energy development (exploration, construction, operation and maintenance, and decommissioning) will have an impact on the landscape and everyone living in it. Meanwhile, natural and other human-induced drivers will keep landscapes and environments changing. This conference paper addresses the development of an integrated assessment to spatially measure the impact of geothermal energy development phases on ecosystem services. Listing the effects on the ecosystem services induced by each geothermal development phases and estimating the spatial impact using Geographic Information System (GIS) will result in an overview on where and how much each geothermal development phase affects the ecosystem and how this information could be included to improve national spatial planning.
I Will Give You My Vote but Not My Money: Preferences for Public versus Private Action in Addressing Social Issues
Authors: Norwood Franklin Bailey , Tonsor Glynn , Lusk Jayson L 
Published: January 2018

AbstractThis study explores the extent to which individuals will support public action but, in its absence, will not commit their own voluntary efforts. An internet survey was administered to over 3,500 individuals with hypothetical scenarios in which they could donate their own money toward a cause and/or support government action. When asked to choose between public or private action, most chose a combination of the two, suggesting that public and private partnerships are the preferred vehicle for solutions to social problems. Close to 20% indicated they would vote for laws to confront an issue but not contribute their own private donations.
Microarray is an efficient tool for circRNA profiling
Authors: Li Shasha , Teng Shuaishuai , Xu Junquan , Su Guannan , Zhang Yu , Zhao Jianqing , Zhang Suwei , Wang Haiyan , Qin Wenyan , Lu Zhi John , Guo Yong , Zhu Qianyong , Wang Dong 
Published: January 2018

Abstract
Circular RNAs (circRNAs) are emerging as a new class of endogenous and regulatory noncoding RNAs in latest years. With the widespread application of RNA sequencing (RNA-seq) technology and bioinformatics prediction, large numbers of circRNAs have been identified. However, at present, we lack a comprehensive characterization of all these circRNAs in interested samples. In this study, we integrated 87 935 circRNAs sequences that cover most of circRNAs identified till now represented in circBase to design microarray probes targeting back-splice site of each circRNA to profile expression of those circRNAs. By comparing the circRNA detection efficiency of RNA-seq with this circRNA microarray, we revealed that microarray is more efficient than RNA-seq for circRNA profiling. Then, we found ∼80 000 circRNAs were expressed in cervical tumors and matched normal tissues, and ∼25 000 of them were differently expressed. Notably, many of these circRNAs detected by this microarray can be validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) or RNA-seq. Strikingly, as many as ∼18 000 circRNAs could be robustly detected in cell-free plasma samples, and the expression of ∼2700 of them differed after surgery for tumor removal. Our findings provided a comprehensive and genome-wide characterization of circRNAs in paired normal tissues and tumors and plasma samples from multiple individuals. In addition, we also provide a rich resource with 41 microarray data sets and 10 RNA-seq data sets and strong evidences for circRNA expression in cervical cancer. In conclusion, circRNAs could be efficiently profiled by circRNA microarray to target their reported back-splice sites in interested samples.
PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling
Authors: Na Joong Chae , Lee Jong-Chan , Rhee Je-Keun , Shin Soo-Yong 
Published: January 2018

Abstract

Motivation
Single-individual haplotyping (SIH) is critical in genomic association studies and genetic diseases analysis. However, most genomic analysis studies do not perform haplotype-phasing analysis due to its complexity. Several computational methods have been developed to solve the SIH problem, but these approaches have not generated sufficiently reliable haplotypes.

Results
Here, we propose a novel SIH algorithm, called PEATH (Probabilistic Evolutionary Algorithm with Toggling for Haplotyping), to achieve more accurate and reliable haplotyping. The proposed PEATH method was compared to the most recent algorithms in terms of the phased length, N50 length, switch error rate and minimum error correction. The PEATH algorithm consistently provides the best phase and N50 lengths, as long as possible, given datasets. In addition, verification of the simulation data demonstrated that the PEATH method outperforms other methods on high noisy data. Additionally, the experimental results of a real dataset confirmed that the PEATH method achieved comparable or better accuracy.

Availability and implementation
Source code of PEATH is available at https://github.com/jcna99/PEATH.

Supplementary information
Supplementary data are available at Bioinformatics online.