bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lymphocyte to monocyte ratio and prognostic nutritional index predict survival outcomes of hepatitis B virus‐associated hepatocellular carcinoma patients after curative hepatectomy
Authors: Wu Si‐Jia , Lin Yi‐Xin , Ye Hui , Li Fu‐Yu , Xiong Xian‐Ze , Cheng Nan‐Sheng 
Published: May 2016

IntroductionLymphocytes are an integral part of lymphocyte to monocyte ratio (LMR) and prognostic nutritional index (PNI). Both LMR and PNI which reflect body's inflammatory and nutritional status can be obtained from routine blood and biochemical test conveniently. Little evidence concerning the prognostic value of LMR and PNI in hepatocellular carcinoma (HCC) patients has been published. This study aimed to investigate the prognostic value of LMR and PNI in hepatitis B virals (HBV)—associated HCC patients who underwent curative hepatectomy.MethodsBetween January 2008 and June 2013, 450 surgically treated HCC patients were retrospectively analyzed. Clinicopathological parameters, LMR and PNI were collected and compared. The multivariate analysis was performed to indentify independent prognostic factors. Overall survival (OS) and recurrence‐free survival (RFS) rates were also compared.ResultsTumor size, vascular invasion, alpha fetoprotein level, LMR and PNI were independent prognostic factors for OS. Tumor number, tumor size, vascular invasion, LMR and PNI were independent prognostic factors for RFS. Either a high LMR or PNI could predict favorable OS and RFS in surgically treated HCC patients and vice versa.ConclusionsBoth LMR and PNI were significant independent predictors that can predict survival outcomes in HBV‐associated HCC patients who received curative hepatectomy. J. Surg. Oncol. 2016;114:202–210. © 2016 Wiley Periodicals, Inc.
Spatial Gradients of Intensity and Persistence of Soil Water Repellency Under Different Forest Types in Central Mexico
Authors: Alanís Nancy , Hernández‐Madrigal Víctor M. , Cerdà Artemi , Muñoz‐Rojas Miriam , Zavala Lorena M. , Jordán Antonio 
Published: May 2016

AbstractOrganic residues release hydrophobic compounds to the soil that may induce soil water repellency (WR), which may inhibit infiltration and increase runoff and soil loss rates. Although there are many studies on soil WR through the world, very few investigations have been conducted in Mexican areas. This paper studies the natural background of soil WR in soils from central Mexico under representative forest types, analyzing the spatial distribution of soil WR in relation with tree canopy, vegetation cover and main soil chemical (pH, CaCO3, organic C content and exchangeable cations) and physical properties (texture). The water drop penetration time and the ethanol tests were used to assess persistence and intensity of soil WR, respectively. Although soil WR was not related with soil properties, it decreased strongly from soil below the canopy of conifers to soil below oaks. When different types of vegetation cover were considered, the proportion of water‐repellent soil increased following the sequence: bare soil < shrubs and herbaceous plants < shrubs < trees from fir, fir‐pine‐oak and pine‐oak forest. We found an inverse relation with distance to the tree trunks, contributing to create a patchy pattern of soil WR, with soils under the canopy of conifers showing the most severe WR levels. The spatial distribution of soil WR is also conditioned by microclimatic gradients, as persistence and intensity of soil WR were usually lower in shaded areas (upslope transects from the tree trunks), where soil moisture content is expected to be higher on average through the year. Copyright © 2016 John Wiley & Sons, Ltd.
Glass transition temperature of colloidal polystyrene dispersed in various liquids
Authors: Christie Dane , Zhang Chuan , Fu Jie , Koel Bruce , Priestley Rodney D. 
Published: May 2016

ABSTRACTRecently, there has been significant interest in measuring the glass transition temperature (Tg) of thin polymer films floated atop liquid substrates. However, such films still have intrinsically asymmetric interfaces, that is, a free surface and a liquid–polymer interface. In an effort to analyze the influence of different liquids on the Tg of confined polymers in which there is no interfacial asymmetry, a colloidal suspension of polystyrene (PS) nanoparticles (NPs) was employed. The Tgs of PS NPs suspended in either glycerol or an ionic liquid were characterized using differential scanning calorimetry. Nanoparticles suspended in an ionic liquid showed an invariance of Tg with confinement, that is, decreasing diameter. In contrast, nanoparticles suspended in glycerol showed a slight decrease in Tg with confinement. The dependence of NP Tg on the nature of the surrounding liquid exhibited a positive correlation with the interfacial energy of the liquid–PS interface and no correlation with interfacial softness, as measured by viscosity. A comparison of the results with thin films supported by liquid or solid substrates revealed a nontrivial interplay between interfacial softness and interfacial interactions on the Tg of confined PS. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 1776–1783
The ribosome in action: Tuning of translational efficiency and protein folding
Authors: Rodnina Marina V. 
Published: May 2016

Marina V. Rodnina is the winner of the 2015 Hans Neurath Award.AbstractThe cellular proteome is shaped by the combined activities of the gene expression and quality control machineries. While transcription plays an undoubtedly important role, in recent years also translation emerged as a key step that defines the composition and quality of the proteome and the functional activity of proteins in the cell. Among the different post‐transcriptional control mechanisms, translation initiation and elongation provide multiple checkpoints that can affect translational efficiency. A multitude of specific signals in mRNAs can determine the frequency of translation initiation, choice of the open reading frame, global and local elongation velocities, and the folding of the emerging protein. In addition to specific signatures in the mRNAs, also variations in the global pools of translation components, including ribosomes, tRNAs, mRNAs, and translation factors can alter translational efficiencies. The cellular outcomes of phenomena such as mRNA codon bias are sometimes difficult to understand due to the staggering complexity of covariates that affect codon usage, translation, and protein folding. Here we summarize the experimental evidence on how the ribosome—together with the other components of the translational machinery—can alter translational efficiencies of mRNA at the initiation and elongation stages and how translation velocity affects protein folding. We seek to explain these findings in the context of mechanistic work on the ribosome. The results argue in favour of a new understanding of translation control as a hub that links mRNA homeostasis to production and quality control of proteins in the cell.
Robotic‐Assisted Pancreatic Resections
Authors: Boggi Ugo , Napoli Niccolò , Costa Francesca , Kauffmann Emanuele F. , Menonna Francesca , Iacopi Sara , Vistoli Fabio , Amorese Gabriella 
Published: May 2016

AbstractBackgroundRobotic assistance enhances surgical dexterity and could facilitate wider adoption of laparoscopy for pancreatic resections (PR).MethodsData were prospectively entered into a database and analyzed retrospectively to assess feasibility and safety of robotic‐assisted PR (RAPR). Additionally, robotic‐assisted pancreaticoduodenectomy (RAPD) was compared to a contemporary group of open pancreaticoduodenectomies (OPD).ResultsBetween October 2008 and October 2014, 200 consecutive patients underwent RAPR. Three procedures were converted to open surgery (1.5 %), despite 14 patients required associated vascular procedures. RAPD was performed in 83 patients (41.5 %), distal pancreatectomy in 83 (41.5 %), total pancreatectomy in 17 (8.5 %), tumor enucleation in 12 (6 %), and central pancreatectomy in 5 (2.5 %). Thirty‐day and 90‐day mortality rates were 0.5 and 1 %, respectively. Both deaths occurred after RAPD with vein resection. Complications occurred in 63.0 % of the patients (≥Clavien‐Dindo grade IIIb in 4 %). Median comprehensive complication index was 20.9 (0‐26.2). Incidence of grade B/C pancreatic fistula was 28.0 %. Reoperation was required in 14 patients (7.0 %). The risk of reoperation decreased after post‐operative day 20 (OR 0.072) (p = 0.0015). When compared to OPD, RAPD was associated with longer mean operative time (527.2 ± 166.1 vs. 425.3 ± 92.7; <0.0001) but had an equivalent safety profile. The median number of examined lymph nodes (37; 28.8–45.3 vs. 36; 28–52.8) and the rate of margin positivity in patients diagnosed with pancreatic cancer were also similar (12.5 vs. 45.5 %).ConclusionsRAPR, including RAPD, are safely feasible in selected patients. The results of RAPD in pancreatic cancer are encouraging but deserve further investigation.
Continuous adjoint-based error estimation and its application to adaptive discontinuous Galerkin method
Authors: Yue Huiqiang , Liu Tiegang , Shaydurov V. 
Published: May 2016

Abstract
An adaptive mesh refinement algorithm based on a continuous adjoint approach is developed. Both the primal equation and the adjoint equation are approximated with the discontinuous Galerkin (DG) method. The proposed adaptive algorithm is used in compressible Euler equations. Numerical tests are made to show the superiority of the proposed adaptive algorithm.
Allele-specific silencing of EEC p63 mutant R304W restores p63 transcriptional activity
Authors: Novelli F , Lena A M , Panatta E , Nasser W , Shalom-Feuerstein R , Candi E , Melino G 
Published: May 2016

AbstractEEC (ectrodactily-ectodermal dysplasia and cleft lip/palate) syndrome is a rare genetic disease, autosomal dominant inherited. It is part of the ectodermal dysplasia disorders caused by heterozygous mutations inTP63gene. EEC patients present limb malformations, orofacial clefting, skin and skin’s appendages defects, ocular abnormalities. The transcription factor p63, encoded byTP63, is a master gene for the commitment of ectodermal-derived tissues, being expressed in the apical ectodermal ridge is critical for vertebrate limb formation and, at a later stage, for skin and skin’s appendages development. The ΔNp63αisoform is predominantly expressed in epithelial cells and it is indispensable for preserving the self-renewal capacity of adult stem cells and to engage specific epithelial differentiation programs. Small interfering RNA (siRNA) offers a potential therapy approach for EEC patients by selectively silencing the mutant allele. Here, using a systemic screening based on a dual-luciferase reported gene assay, we have successfully identified specific siRNAs for repressing the EEC-causing p63 mutant, R304W. Upon siRNA treatment, we were able to restore ΔNp63-WT allele transcriptional function in induced pluripotent stem cells that were derived from EEC patient biopsy. This study demonstrates that siRNAs approach is promising and, may pave the way for curing/delaying major symptoms, such as cornea degeneration and skin erosions in young EEC patients.
Knockdown of linc-UFC1 suppresses proliferation and induces apoptosis of colorectal cancer
Authors: Yu T , Shan T-D , Li J-Y , Huang C-Z , Wang S-Y , Ouyang H , Lu X-J , Xu J-H , Zhong W , Chen Q-K 
Published: May 2016

AbstractLong intergenic noncoding RNAs (lincRNAs) have important roles in biological functions, molecular mechanisms and prognostic values in colorectal cancer (CRC). In this context, the roles of linc-UFC1 remain to be elucidated. In this study, linc-UFC1 was overexpressed in CRC patient tissues and positively correlated with tumor grade, N stage and M stage. Inhibition of linc-UFC1 resulted in cell proliferation inhibition and G1 cell cycle arrest, which was mediated by cyclin D1, CDK4, Rb and phosphorylated Rb. In addition, inhibition of linc-UFC1 induced cell apoptosis through the intrinsic apoptosis signaling pathway, as evidenced by the activation of caspase-9 and caspase-3. An investigation of the signaling pathway revealed that the effects on proliferation and apoptosis following linc-UFC1 knockdown were mediated by suppression of β-catenin and activation of phosphorylated P38. Furthermore, the P38 inhibitor SB203580 could attenuate the apoptotic effect achieved by linc-UFC1 knockdown, confirming the involvement of P38 signaling in the induced apoptosis. Taken together, linc-UFC1 might have a critical role in pro-proliferation and anti-apoptosis in CRC by regulating the cell cycle, intrinsic apoptosis, and β-catenin and P38 signaling. Thus, linc-UFC1 could be a potential therapeutic target and novel molecular biomarker for CRC.
Upregulated long non-coding RNA AGAP2-AS1 represses LATS2 and KLF2 expression through interacting with EZH2 and LSD1 in non-small-cell lung cancer cells
Authors: Li W , Sun M , Zang C , Ma P , He J , Zhang M , Huang Z , Ding Y , Shu Y 
Published: May 2016

AbstractRecently, long non-coding RNAs (lncRNAs) are identified as new crucial regulators of diverse cellular processes, including cell proliferation, differentiation and cancer cells metastasis. Accumulating evidence has revealed that aberrant lncRNA expression plays important roles in carcinogenesis and tumor progression. However, the expression pattern and biological function of lncRNAs in non-small-cell lung cancer (NSCLC) remain largely unknown. In this study, we performed comprehensive analysis of lncRNA expression in human NSCLC samples by using microarray data from Gene Expression Omnibus. After validation in a cohort of 80 pairs of NSCLC tissues, we identified a differentially expressed novel oncogenic lncRNA termed as AGAP2-AS1. The AGAP2-AS1 expression level was significantly upregulated in NSCLC tissues and negatively correlated with poor prognostic outcomes in patients. In vitro loss- and gain-of-function assays revealed that AGAP2-AS1 knockdown inhibited cell proliferation, migration and invasion, and induced cell apoptosis. In vivo assays also confirmed the ability of AGAP2-AS1 to promote tumor growth. Furthermore, mechanistic investigation showed that AGAP2-AS1 could bind with enhancer of zeste homolog 2 and lysine (K)-specific demethylase 1A, and recruit them to KLF2 and LATS2 promoter regions to repress their transcription. Taken together, our findings indicate that AGAP2-AS1 may act as an oncogene by repressing tumor-suppressor LATS2 and KLF2 transcription. By clarifying the AGAP2-AS1 mechanisms underlying NSCLC development and progression, these findings might promote the development of novel therapeutic strategies for this disease.
Implementation of dispersion-free slow acoustic wave propagation and phase engineering with helical-structured metamaterials
Authors: Zhu Xuefeng , Li Kun , Zhang Peng , Zhu Jie , Zhang Jintao , Tian Chao , Liu Shengchun 
Published: May 2016

AbstractThe ability to slow down wave propagation in materials has attracted significant research interest. A successful solution will give rise to manageable enhanced wave–matter interaction, freewheeling phase engineering and spatial compression of wave signals. The existing methods are typically associated with constructing dispersive materials or structures with local resonators, thus resulting in unavoidable distortion of waveforms. Here we show that, with helical-structured acoustic metamaterials, it is now possible to implement dispersion-free sound deceleration. The helical-structured metamaterials present a non-dispersive high effective refractive index that is tunable through adjusting the helicity of structures, while the wavefront revolution plays a dominant role in reducing the group velocity. Finally, we numerically and experimentally demonstrate that the helical-structured metamaterials with designed inhomogeneous unit cells can turn a normally incident plane wave into a self-accelerating beam on the prescribed parabolic trajectory. The helical-structured metamaterials will have profound impact to applications in explorations of slow wave physics.
Independent modulations of the transmission amplitudes and phases by using Huygens metasurfaces
Authors: Wan Xiang , Jia Sheng Li , Cui Tie Jun , Zhao Yong Jiu 
Published: May 2016

AbstractWe propose ultrathin Huygens metasurfaces to control transmission amplitudes and phases of electromagnetic waves independently, in which each unit cell is comprised of an electric dipole and a magnetic dipole. By altering the electric and magnetic responses of unit cells, arbitrary complex transmission coefficients with modulus values smaller than 0.85 are obtained. Two Huygens metasurfaces capable of controlling the diffraction orders are designed and fabricated by modulating the distributions of the complex transmission coefficients. More complicated functions such as holographic imaging can also be accomplished by using the proposed Huygens metasurfaces.
LAMP Detection Assays for Boxwood Blight Pathogens: A Comparative Genomics Approach
Authors: Malapi-Wight Martha , Demers Jill E. , Veltri Daniel , Marra Robert E. , Crouch Jo Anne 
Published: May 2016

AbstractRapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. This comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.
The synergy between the insect-inspired claws and adhesive pads increases the attachment ability on various rough surfaces
Authors: Song Yi , Dai Zhendong , Wang Zhouyi , Ji Aihong , Gorb Stanislav N. 
Published: May 2016

AbstractTo attach reliably on various inclined rough surfaces, many insects have evolved both claws and adhesive pads on their feet. However, the interaction between these organs still remains unclear. Here we designed an artificial attachment device, which mimics the structure and function of claws and adhesive pads and tested it on stiff spheres of different dimensions. The results show that the attachment forces of claws decrease with an increase of the sphere radius. The forces may become very strong, when the sphere radius is smaller or comparable to the claw radius, because of the frictional self-lock. On the other hand, adhesive pads generate considerable adhesion on large sphere diameter due to large contact areas. The synergy effect between the claws and adhesive pads leads to much stronger attachment forces, if compared to the action of claw or adhesive pads independently (or even to the sum of both). The results carried out by our insect-inspired artificial attachment device clearly demonstrate why biological evolution employed two attachment organs working in concert. The results may greatly inspire the robot design, to obtain reliable attachment forces on various substrates.
An Atypical System for Studying Epithelial-Mesenchymal Transition in Hepatocellular Carcinoma
Authors: Vedagiri Dhiviya , Lashkari Hiren Vasantrai , Mangani Abubakar Siddiq , Kumar Jerald Mahesh , Jose Jedy , Thatipalli Avinash Raj , Harshan Krishnan Harinivas 
Published: May 2016

AbstractIntrahepatic and extrahepatic metastases are frequently detected in hepatocellular carcinoma (HCC). Epithelial-mesenchymal transition (EMT) is believed to drive metastasis. There are not many well-established model systems to study EMT in HCC. Here we identified an atypical EMT while characterizing a population of mesenchymal cells in Huh7.5 hepatoma cell cultures. Cells with distinct morphology appeared during geneticin treatment of Huh7.5 cultures. Molecular characterization of geneticin resistant Huh7.5M cells confirmed EMT. Huh7.5M cells expressed cancer stem cell markers. p38MAPK and ERK1/2 were substantially activated in Huh7.5M cells. Their Inhibition elevated E-Cadherin expression with concerted suppression of Vimentin and anchorage independent growth in Huh7.5M cells. TGFβ could not induce EMT in Huh7.5 cultures, but enriched mesenchymal populations, similar to geneticin. Huh7.5M cells formed more aggressive solid tumors, primarily comprising cells with epithelial morphology, in nude mice. Canonical EMT-TFs did not participate in this atypical EMT, indicating that the established canonical EMT-TFs do not drive every EMT and there is a dire need to identify additional factors. The system that we characterized is a unique model to study EMT, MET and biphasic TGFβ signaling in HCC and offers considerable potential to facilitate more insightful studies on deeper questions in tumor metastasis.
Persistence of Plasmodium falciparum parasitemia after artemisinin combination therapy: evidence from a randomized trial in Uganda
Authors: Chang Hsiao-Han , Meibalan Elamaran , Zelin Justin , Daniels Rachel , Eziefula Alice C. , Meyer Evan C. , Tadesse Fitsum , Grignard Lynn , Joice Regina C. , Drakeley Chris , Wirth Dyann F. , Volkman Sarah K. , Buckee Caroline , Bousema Teun , Marti Matthias 
Published: May 2016

AbstractArtemisinin resistance is rapidly spreading in Southeast Asia. The efficacy of artemisinin-combination therapy (ACT) continues to be excellent across Africa. We performed parasite transcriptional profiling and genotyping on samples from an antimalarial treatment trial in Uganda. We used qRT-PCR and genotyping to characterize residual circulating parasite populations after treatment with either ACT or ACT-primaquine. Transcripts suggestive of circulating ring stage parasites were present after treatment at a prevalence of >25% until at least 14 days post initiation of treatment. Greater than 98% of all ring stage parasites were cleared within the first 3 days, but subsequently persisted at low concentrations until day 14 after treatment. Genotyping demonstrated a significant decrease in multiplicity of infection within the first 2 days in both ACT and ACT-primaquine arms. However, multiple clone infections persisted until day 14 post treatment. Our data suggest the presence of genetically diverse persisting parasite populations after ACT treatment. Although we did not demonstrate clinical treatment failures after ACT and the viability and transmissibility of persisting ring stage parasites remain to be shown, these findings are of relevance for the interpretation of parasite clearance transmission dynamics and for monitoring drug effects in Plasmodium falciparum parasites.