bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling of the metabolic transcriptome via single molecule molecular inversion probes
Authors: de Bitter Tessa , van de Water Carlijn , van den Heuvel Corina , Zeelen Carolien , Eijkelenboom Astrid , Tops Bastiaan , Oosterwijk Egbert , Kolev Dimitar , Mulders Peter , ter Laan Mark , van Lith Sanne , Leenders William 
Published: September 2017

AbstractCancer-specific metabolic alterations are of high interest as therapeutic targets. These alterations vary between tumor types, and to employ metabolic targeting to its fullest potential there is a need for robust methods that identify candidate targetable metabolic pathways in individual cancers. Currently, such methods include 13C-tracing studies and mass spectrometry/ magnetic resonance spectroscopic imaging. Due to high cost and complexity, such studies are restricted to a research setting. We here present the validation of a novel technique of metabolic profiling, based on multiplex targeted next generation sequencing of RNA with single molecule molecular inversion probes (smMIPs), designed to measure activity of and mutations in genes that encode metabolic enzymes. We here profiled an isogenic pair of cell lines, differing in expression of the Von Hippel Lindau protein, an important regulator of hypoxia-inducible genes. We show that smMIP-profiling provides relevant information on active metabolic pathways. Because smMIP-based targeted RNAseq is cost-effective and can be applied in a medium high-throughput setting (200 samples can be profiled simultaneously in one next generation sequencing run) it is a highly interesting approach for profiling of the activity of genes of interest, including those regulating metabolism, in a routine patient care setting.
Evaluation of Bleb Fluid After Baerveldt Glaucoma Implantation Using Magnetic Resonance Imaging
Authors: Iwasaki Kentaro , Kanamoto Masayuki , Takihara Yuji , Arimura Shogo , Takamura Yoshihiro , Kimura Hirohiko , Inatani Masaru 
Published: September 2017

AbstractWe evaluated bleb fluid images taken after Baerveldt glaucoma implantation. T2-weighted images of bleb fluid were scanned with 3 Tesla magnetic resonance imaging in 52 patients who had undergone tube-shunt surgery using the 350-mm2 endplate Baerveldt glaucoma implant; three-dimensional images were constructed from these images. Bleb fluid images were classified into either a layer of bleb fluid on either side of the endplate (double bleb layer group; n = 24) or one layer outside the endplate (single bleb layer group; n = 28). Despite there being no correlation between the bleb volume and the postoperative IOP (r = −0.080; P = 0.57), the double bleb layer group had significantly lower postoperative IOPs than the single bleb layer group (12.3 ± 3.8 mmHg vs. 14.7 ± 4.1 mmHg, respectively; P = 0.033). The single bleb layer was significantly related to higher numbers of prior intraocular surgeries (relative risk = 2.85; P = 0.0014). Formation of a layer of bleb fluid on either side of the endplate may have resulted in the lower postoperative IOPs after Baerveldt glaucoma implantation. Repeated intraocular surgery adversely affects formation of the double bleb layer.
Dual Roles of Two Isoforms of Autophagy-related Gene ATG10 in HCV-Subgenomic replicon Mediated Autophagy Flux and Innate Immunity
Authors: Zhao Qiong , Hu Zhan-Ying , Zhang Jing-Pu , Jiang Jian-Dong , Ma Yuan-yuan , Li Jian-rui , Peng Zong-gen , Chen Jin-hua 
Published: September 2017

AbstractAutophagy and immune response are two defense systems that human-body uses against viral infection. Previous studies documented that some viral mechanisms circumvented host immunity mechanisms and hijacked autophagy for its replication and survival. Here, we focus on interactions between autophagy mechanism and innate-immune-response in HCV-subgenomic replicon cells to find a mechanism linking the two pathways. We report distinct effects of two autophagy-related protein ATG10s on HCV-subgenomic replication. ATG10, a canonical long isoform in autophagy process, can facilitate HCV-subgenomic replicon amplification by promoting autophagosome formation and by combining with and detaining autophagosomes in cellular periphery, causing impaired autophagy flux. ATG10S, a non-canonical short isoform of ATG10 proteins, can activate expression of IL28A/B and immunity genes related to viral ds-RNA including ddx-58, tlr-3, tlr-7, irf-3 and irf-7, and promote autophagolysosome formation by directly combining and driving autophagosomes to perinuclear region where lysosomes gather, leading to lysosomal degradation of HCV-subgenomic replicon in HepG2 cells. ATG10S also can suppress infectious HCV virion replication in Huh7.5 cells. Another finding is that IL28A protein directly conjugates ATG10S and helps autophagosome docking to lysosomes. ATG10S might be a new host factor against HCV replication, and as a target for screening chemicals with new anti-virus mechanisms.
New model for predicting preterm delivery during the second trimester of pregnancy
Authors: Zhu Ya-zhi , Peng Guo-qin , Tian Gui-xiang , Qu Xue-ling , Xiao Shui-yuan 
Published: September 2017

AbstractIn this study, a new model for predicting preterm delivery (PD) was proposed. The primary model was constructed using ten selected variables, as previously defined in seventeen different studies. The ability of the model to predict PD was evaluated using the combined measurement from these variables. Therefore, a prospective investigation was performed by enrolling 130 pregnant patients whose gestational ages varied from 17+0 to 28+6 weeks. The patients underwent epidemiological surveys and ultrasonographic measurements of their cervixes, and cervicovaginal fluid and serum were collected during a routine speculum examination performed by the managing gynecologist. The results showed eight significant variables were included in the present analysis, and combination of the positive variables indicated an increased probability of PD in pregnant patients. The accuracy for predicting PD were as follows: one positive – 42.9%; two positives – 75.0%; three positives – 81.8% and four positives – 100.0%. In particular, the combination of ≥2× positives had the best predictive value, with a relatively high sensitivity (82.6%), specificity (88.1%) and accuracy rate (79.2%), and was considered the cut-off point for predicting PD. In conclusion, the new model provides a useful reference for evaluating the risk of PD in clinical cases.
Electrostatics of non-neutral biological microdomains
Authors: Cartailler J. , Schuss Z. , Holcman D. 
Published: September 2017

AbstractVoltage and charge distributions in cellular microdomains regulate communications, excitability, and signal transduction. We report here new electrical laws in a biological cell, which follow from a nonlinear electro-diffusion model. These newly discovered laws derive from the geometrical cell-membrane properties, such as membrane curvature, volume, and surface area. The electro-diffusion laws can now be used to predict and interpret voltage distribution in cellular microdomains such as synapses, dendritic spine, cilia and more.
Propolis envelope in Apis mellifera colonies supports honey bees against the pathogen, Paenibacillus larvae
Authors: Borba Renata S. , Spivak Marla 
Published: September 2017

AbstractHoney bees have immune defenses both as individuals and as a colony (e.g., individual and social immunity). One form of honey bee social immunity is the collection of antimicrobial plant resins and the deposition of the resins as a propolis envelope within the nest. In this study, we tested the effects of the propolis envelope as a natural defense against Paenibacillus larvae, the causative agent of American foulbrood (AFB) disease. Using colonies with and without a propolis envelope, we quantified: 1) the antimicrobial activity of larval food fed to 1–2 day old larvae; and 2) clinical signs of AFB. Our results show that the antimicrobial activity of larval food was significantly higher when challenged colonies had a propolis envelope compared to colonies without the envelope. In addition, colonies with a propolis envelope had significantly reduced levels of AFB clinical signs two months following challenge. Our results indicate that the propolis envelope serves as an antimicrobial layer around the colony that helps protect the brood from bacterial pathogen infection, resulting in a lower colony-level infection load.
Elastic properties of single-walled carbon nanotube thin film by nanoindentation test
Authors: Tang Xingling , El-Hami Abdelkhalak , El-Hami Khalil , EID Mohamed , Si Chaorun 
Published: September 2017

AbstractThis paper carries out a preliminary study for the elastic properties of single walled carbon nanotube (SWCNT) thin film. The SWCNT thin films (~250 nm) are prepared by a simple and cost effective method of spin-coating technology. Nanoindentation test with a Berkovich indenter is used to determine the hardness and elastic modulus of the SWCNT thin film. It is important to note that the elastic properties of SWCNT film are indirectly derived from the information of load and displacement of the indenter under certain assumptions, deviation of the ‘test value’ is inevitable. In this regard, uncertainty analysis is an effective process in guarantying the validity of the material properties. This paper carries out uncertainty estimation for the tested elastic properties of SWCNT film by nanoindentation. Experimental results and uncertainty analysis indicates that nanoindentation test could be an effective and reliable method in determine the elastic properties of SWCNT thin film. Moreover, the obtained values of hardness and elastic modulus can further benefit the design of SWCNT thin film based components.
Magnetoelectric oxide based stochastic spin device towards solving combinatorial optimization problems
Authors: Sharmin Saima , Shim Yong , Roy Kaushik 
Published: September 2017

AbstractSolving combinatorial optimization problems is challenging. Mapping onto the ground-state search problem of the Ising Hamiltonian is a promising approach in this field, where the components of the optimization set are modeled as artificial spin units. The search for a suitable physical system to realize these spin units is an active area of research. In this work, we have demonstrated a scheme to model the Ising Hamiltonian with multiferroic oxide/nanomagnet units. Although nanomagnet-based implementation has been shown before, we have utilized the magnetoelectric effect of the multiferroics to make voltagecontrolled spin units with less current flow in the network. Moreover, we have proposed a unique approach of configuring the coupling network of the system directly from the Ising Hamiltonian of a traveling salesman problem (TSP). We have developed a coupled micromagnetic simulation framework and solved TSPs of size 26-city and 15-city with an accuracy of 100% for the latter.
Identification of key metabolic changes during liver fibrosis progression in rats using a urine and serum metabolomics approach
Authors: Chang Hong , Meng Hong-yu , Liu Shu-min , Wang Yu , Yang Xiao-xu , Lu Fang , Wang Hong-yu 
Published: September 2017

AbstractReversibility of hepatic fibrosis is an intrinsic response to chronic injury, and with on-going damage, fibrosis can progress to its end-stage consequence, cirrhosis. Non-invasive and reliable biomarkers for early detection of liver fibrosis are needed. Based on the CCl4-induced liver fibrosis rat model, urinary and serum metabolic profiling performed by LC-QTOF-MS associated with histological progression were utilized to identify liver fibrosis-specific potential biomarkers for early prediction and to reveal significant fibrotic pathways and their dynamic changes in different stages of liver fibrosis. Finally, nine differential metabolites in urine and ten in serum were selected and identified involving the most relevant metabolic pathways. Perturbations of tryptophan, valine, leucine, isoleucine, and citrate (TCA) cycle metabolites, along with sphingolipid and glycerophospholipid metabolites, occurred from the onset of liver fibrosis. Furthermore, dysregulation of valine and bile acid biosynthesis metabolites occurred in the intermediate and advanced stages. More importantly, among these metabolites, urinary kynurenic acid, 5-hydroxyindoleacetyl glycine, 4-(2-amino-3-hydroxyphenyl)-2,4-dioxobutanoic acid and serum sphinganine, sphingomyelin,﻿ L-leucine, L-tryptophan, and LysoPC(17:0) changed at all time points and may serve as potential early biomarkers for the diagnosis of hepatic fibrosis and as therapeutic targets. Overall, this work evaluates the potential of these metabolites for the early detection of liver fibrosis.
Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars
Authors: Chaturvedi Samridhi , Rego Alexandre , Lucas Lauren K. , Gompert Zachariah 
Published: September 2017

AbstractMicrobes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.
Interrogation of γ-tubulin alleles using high-resolution fitness measurements reveals a distinct cytoplasmic function in spindle alignment
Authors: Shulist Kristian , Yen Eric , Kaitna Susanne , Leary Allen , Decterov Alexandra , Gupta Debarun , Vogel Jackie 
Published: September 2017

Abstractγ-Tubulin has a well-established role in nucleating the assembly of microtubules, yet how phosphorylation regulates its activity remains unclear. Here, we use a time-resolved, fitness-based SGA approach to compare two γ-tubulin alleles, and find that the genetic interaction profile of γtub-Y362E is enriched in spindle positioning and cell polarity genes relative to that of γtub-Y445D, which is enriched in genes involved in spindle assembly and stability. In γtub-Y362E cells, we find a defect in spindle alignment and an increase in the number of astral microtubules at both spindle poles. Our results suggest that the γtub-Y362E allele is a separation-of-function mutation that reveals a role for γ-tubulin phospho-regulation in spindle alignment. We propose that phosphorylation of the evolutionarily conserved Y362 residue of budding yeast γ-tubulin contributes to regulating the number of astral microtubules associated with spindle poles, and promoting efficient pre-anaphase spindle alignment.
Diffusion kurtosis imaging evaluating epithelial–mesenchymal transition in colorectal carcinoma xenografts model: a preliminary study
Authors: Liu Huanhuan , Shen Wenbin , Zhang Caiyuan , Cui Yanfen , Li Jinning , Zhang Tingting , Chen Weibo , Wang Dengbin 
Published: September 2017

AbstractEpithelial-mesenchymal transition (EMT) plays an important role in aggravating invasiveness and metastatic behavior of colorectal cancer (CRC). Identification of EMT is important for structuring treatment strategy, but has not yet been studied by using noninvasive imaging modality. Diffusion kurtosis imaging (DKI) is an advanced diffusion weighted model that could reflect tissue microstructural changes in vivo. In this study, EMT was induced in CRC cells (HCT116) by overexpressing Snail1 gene. We aimed to investigate the value of DKI in identifying EMT in CRC and decipher the correlations between DKI-derived parameters and EMT biomarker E-cadherin and cell proliferative index Ki-67 expression. Our results revealed that HCT116/Snail1 cells presented changes consistent with EMT resulting in significant increase in migration and invasion capacities. DKI could identify CRC with EMT, in which the DKI-derived parameter diffusivity was significantly lower, and kurtosis was significantly higher than those in the CRC/Control. Diffusivity was negatively and kurtosis was positively correlated with Ki-67 expression, whereas diffusivity was positively and kurtosis was negatively correlated with E-cadherin expression. Therefore, our study concluded that DKI can identify EMT in CRC xenograft tumors. EMT-contained CRC tumors with high Ki-67 and low E-cadherin expression were vulnerable to have lower diffusivity and higher kurtosis coefficients.
The role of metronomic capecitabine for treatment of recurrent hepatocellular carcinoma after liver transplantation
Authors: Ravaioli Matteo , Cucchetti Alessandro , Pinna Antonio Daniele , De Pace Vanessa , Neri Flavia , Barbera Maria Aurelia , Maroni Lorenzo , Frega Giorgio , Palloni Andrea , De Lorenzo Stefania , Ripoli Maria Cristina , Pantaleo Maria Abbondanza , Cescon Matteo , Del Gaudio Massimo , Brandi Giovanni 
Published: September 2017

AbstractThe management of recurrent hepatocellular carcinoma untreatable with surgical options is based on systemic therapy with sorafenib. Due to the high rates of adverse events connected to the therapy with sorafenib, metronomic capecitabine seems a promising strategy for these patients. We analyzed the data of 38 patients with hepatocellular carcinoma recurrent after liver transplantation performed at our center. We compared the outcome of 17 patients receiving metronomic capecitabine versus 20 patients experiencing best supportive care and versus the data of the literature about treatment with sorafenib. In the group treated with metronomic capecitabine we observed an increased survival after tumor recurrence at the univariate and multivariate analysis compared to the group of best supportive care (median 22 months vs. 7 months, p < 0.01). Data from the literature on the use of sorafenib showed outcomes like our study group, with similar patient and tumoral features. The episodes of acute rejection and the tumor stage at the recurrence showed a correlation with patient survival at the univariate analysis. The metronomic capecitabine for hepatocellular cancer recurrent after liver transplantation seems effective without important adverse events and comparable results to sorafenib.
Microwave properties of the single-layer periodic structure composites composed of ethylene-vinyl acetate and polycrystalline iron fibers
Authors: Guo Zhibo , Huang Hailong , Xie Ding , Xia Hui 
Published: September 2017

AbstractA single-layer microwave absorbing structure composed of the ethylene-vinyl acetate (EVA) powders and polycrystalline iron fibers (PIFs) with thickness of 2 mm, which has a periodic array of circular hole, is designed and fabricated using the mechanical method. We show that the reflection loss (RL) can be easily adjusted by changing the geometric parameters. The maximum RL is 18.7 dB at 15 GHz, and the effective absorption bandwidth of 1.7 GHz for the diameter of circular hole is 10 mm, and enhanced to be 23.7 dB at 15.1 GHz with the corresponding bandwidth of 7.2 GHz when the diameter decreases to 5 mm. The measured absorption of the composite is in good accordance with the simulation results. Furthermore, the possible absorption mechanism of the composite has been discussed. Our results illustrate that the integration of frequency selective surface (FSS) with traditional PIFs can achieve a wide frequency range of a strong absorption.
Large manipulative experiments revealed variations of insect abundance and trophic levels in response to the cumulative effects of sheep grazing
Authors: Ma Jingchuan , Huang Xunbing , Qin Xinghu , Ding Yong , Hong Jun , Du Guilin , Li Xinyi , Gao Wenyuan , Zhang Zhuoran , Wang Guangjun , Wang Ning , Zhang Zehua 
Published: September 2017

AbstractLivestock grazing can affect insects by altering habitat quality; however, the effects of grazing years and intensities on insect abundance and trophic level during manipulative sheep grazing are not well understood. Therefore, we investigated these effects in a large manipulative experiment from 2014 to 2016 in the eastern Eurasian steppe, China. Insect abundance decreased as sheep grazing intensities increased, with a significant cumulative effect occurring during grazing years. The largest families, Acrididae and Cicadellidae, were susceptible to sheep grazing, but Formicidae was tolerant. Trophic primary and secondary consumer insects were negatively impacted by increased grazing intensities, while secondary consumers were limited by the decreased primary consumers. Poor vegetation conditions caused by heavy sheep grazing were detrimental to the existence of Acrididae, Cicadellidae, primary and secondary consumer insects, but were beneficial to Formicidae. This study revealed variations in insect abundance and trophic level in response to continuous sheep grazing in steppe grasslands. Overall, our results indicate that continuous years of heavy- and over- sheep grazing should be eliminated. Moreover, our findings highlight the importance of more flexible sheep grazing management and will be useful for developing guidelines to optimize livestock production while maintaining species diversity and ecosystem health.
Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches
Authors: Qian Xiaoqin , Hou Jiayi , Wang Zheng , Ye Yi , Lang Min , Gao Tianzhen , Liu Jing , Hou Yiping 
Published: September 2017

AbstractThere is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term ‘NGS+’ for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.