bluuebunny/crossref_metadata_2025 huggingface dataset:
Variant profiling of evolving prokaryotic populations
Authors: Zojer Markus , Schuster Lisa N. , Schulz Frederik , Pfundner Alexander , Horn Matthias , Rattei Thomas
Published: February 2017

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at.
Plasmonics of 2D Nanomaterials: Properties and Applications
Authors: Li Yu , Li Ziwei , Chi Cheng , Shan Hangyong , Zheng Liheng , Fang Zheyu
Published: February 2017

Plasmonics has developed for decades in the field of condensed matter physics and optics. Based on the classical Maxwell theory, collective excitations exhibit profound light‐matter interaction properties beyond classical physics in lots of material systems. With the development of nanofabrication and characterization technology, ultra‐thin two‐dimensional (2D) nanomaterials attract tremendous interest and show exceptional plasmonic properties. Here, we elaborate the advanced optical properties of 2D materials especially graphene and monolayer molybdenum disulfide (MoS2), review the plasmonic properties of graphene, and discuss the coupling effect in hybrid 2D nanomaterials. Then, the plasmonic tuning methods of 2D nanomaterials are presented from theoretical models to experimental investigations. Furthermore, we reveal the potential applications in photocatalysis, photovoltaics and photodetections, based on the development of 2D nanomaterials, we make a prospect for the future theoretical physics and practical applications.
Growth characteristics and endocrine abnormalities in 22q11.2 deletion syndrome
Authors: Levy‐Shraga Yael , Gothelf Doron , Goichberg Zohar , Katz Uriel , Somech Raz , Pinhas‐Hamiel Orit , Modan‐Moses Dalit
Published: February 2017

22q11.2 deletion syndrome (22q11.2DS) has a wide range of clinical features including endocrine abnormalities. We aimed to characterize growth patterns, hypoparathyroidism, and thyroid dysfunction of individuals with 22q11.2DS. Anthropometric and laboratory measurements were obtained from the charts of 48 individuals (males=28, 8.0±6.8 visits/participant) followed at a national 22q11.2DS clinic between 2009 and 2016. Age at diagnosis was 4.3±4.9 years and age at last evaluation 11.2±7.2 years. Median height‐SDS was negative at all ages. Height‐SDS at last visit was correlated to the midparental height‐SDS (r=0.52 P=0.002). Yet, participants did not reach their target height, with a difference of 1.06±1.07 SD (P <0.0001). Height‐SDS at last visit of participants with a heart defect was lower compared to participants with a normal heart (−1.5±1.4 vs. −0.6±0.8, P=0.036), with lower height‐SDS in the subgroup of participants with severe heart defects (−2.1±1.6, P=0.009). Mean IGF1‐SDS was low (−0.99±1.68) but was not correlated with height‐SDS. Thirteen patients (27%) had hypoparathyroidism: 10 presented during infancy and 3 during adolescence. Five patients (10.4%, female=4) had thyroid abnormalities. In conclusions, individuals with 22q11.2 DS have a distinct growth pattern consisting of growth restriction at all ages, resulting in final adult height in the low‐normal range. Hypoparathyroidism is common and may present during the neonatal period as well as later in life. Thyroid abnormalities may present during childhood, adolescence, or adulthood.
Influence of structure properties on protein–protein interactions—QSAR modeling of changes in diffusion coefficients
Authors: Bauer Katharina Christin , Hämmerling Frank , Kittelmann Jörg , Dürr Cathrin , Görlich Fabian , Hubbuch Jürgen
Published: February 2017

Information about protein–protein interactions provides valuable knowledge about the phase behavior of protein solutions during the biopharmaceutical production process. Up to date it is possible to capture their overall impact by an experimentally determined potential of mean force. For the description of this potential, the second virial coefficient , the diffusion interaction parameter , the storage modulus , or the diffusion coefficient is applied. In silico methods do not only have the potential to predict these parameters, but also to provide deeper understanding of the molecular origin of the protein–protein interactions by correlating the data to the protein's three‐dimensional structure. This methodology furthermore allows a lower sample consumption and less experimental effort. Of all in silico methods, QSAR modeling, which correlates the properties of the molecule's structure with the experimental behavior, seems to be particularly suitable for this purpose. To verify this, the study reported here dealt with the determination of a QSAR model for the diffusion coefficient of proteins. This model consisted of diffusion coefficients for six different model proteins at various pH values and NaCl concentrations. The generated QSAR model showed a good correlation between experimental and predicted data with a coefficient of determination  = 0.9 and a good predictability for an external test set with  = 0.91. The information about the properties affecting protein–protein interactions present in solution was in agreement with experiment and theory. Furthermore, the model was able to give a more detailed picture of the protein properties influencing the diffusion coefficient and the acting protein–protein interactions. Biotechnol. Bioeng. 2017;114: 821–831. © 2016 Wiley Periodicals, Inc.
Immunotherapy against metastatic bladder cancer by combined administration of granulocyte macrophage‐colony stimulating factor and interleukin‐2 surface modified MB49 bladder cancer stem cells vaccine
Authors: Wang Chun‐yan , Hua Rui , Liu Li , Zhan Xiaomin , Chen Simei , Quan Song , Chu Qing‐jun , Zhu Yong‐tong
Published: February 2017

In previous studies, it has been shown that the granulocyte macrophage‐colony stimulating factor (GM‐CSF) or interleukin‐2 (IL‐2) surface modified MB49 bladder cancer stem cells (MCSCs) vaccine could induce a specific antitumor immunity and against bladder cancer in mice model respectively. However, whether combined administration of GM‐CSF and IL‐2 could produce specific immune responses to cancer stem cells (CSCs) was uncertain. MCSCs were established and characterized. GM‐CSF and IL‐2 MCSCs vaccines were prepared and bioactivity was evaluated. The therapeutic, protective, specific, and memorial immune response animal experiments were designed. Tumor‐specific cytotoxic T lymphocytes assay, enzyme linked immunosorbent assay, flow cytometry assay were performed to indentify whether vaccine caused an antitumor immunity. Streptavidin (SA)‐GM‐CSF and SA‐IL‐2 MCSCs vaccines were prepared successfully. Such vaccines inhibited the volume of tumor and prolonged the survival of the mice in animal experiments. The express of IgG or IFN‐c, the portion of dendritic cells, CD8+ and CD4+ T cells were highest in the combined vaccines group than the SA‐GM‐CSF vaccine group, the SA‐IL‐2 vaccine group, the MCSCs group and the PBS group. The combined of GM‐CSF and IL‐2 vaccines could induce better antitumor immunity than a vaccine alone.
Pyranochromones from Dictyoloma vandellianum A. Juss and Their Cytotoxic Evaluation
Authors: Alves Iura M. , Abreu Lucas S. , Costa Cinara O. S. , Le Hyaric Mireille , Guedes Maria Lenise S. , Soares Milena B. P. , Bezerra Daniel P. , Velozo Eudes S.
Published: February 2017

One new chromone 3,3‐dimethylallylspatheliachromene methyl ether (1), as well as five known chromones, 6‐(3‐methylbut‐2‐enyl) allopteroxylin methyl ether (2), 6‐(3‐methylbut‐2‐enyl) allopteroxylin (3), 3,3‐dimethylallylspatheliachromene (4), 5‐O‐methylcneorumchromone K (5) and spatheliabischromene (6), two alkaloids, 8‐methoxy‐N‐methylflindersine (7) and 8‐methoxyflindersine (8), and two limonoids, limonin diosphenol (9) and rutaevin (10), were isolated from Dictyoloma vandellianum A. Juss (Rutaceae). Cytotoxic activities towards tumor cell lines B16‐F10, HepG2, K562 and HL60 and non‐tumor cells PBMC were evaluated for compounds 1 – 6. Compound 1 was the most active showing IC50 values ranging from 6.26 to 14.82 μg/ml in B16‐F10 and K562 cell lines, respectively, and presented IC50 value of 11.65 μg/ml in PBMC cell line.
Carbonic Anhydrase and Urease Inhibitory Potential of Various Plant Phenolics Using in vitro and in silico Methods
Authors: Rauf Abdur , Raza Muslim , Saleem Muhammad , Ozgen Ufuk , Karaoglan Esen Sezen , Renda Gulin , Palaska Erhan , Orhan Ilkay Erdogan
Published: February 2017

Plant phenolics are known to display many pharmacological activities. In the current study, eight phenolic compounds, e.g., luteolin 5‐O‐β‐glucoside (1), methyl rosmarinate (2), apigenin (3), vicenin 2 (4), lithospermic acid (5), soyasaponin II (6), rubiadin 3‐O‐β‐primeveroside (7), and 4‐(β‐d‐glucopyranosyloxy)benzyl 3,4‐dihydroxybenzoate (8), isolated from various plant species were tested at 0.2 mm against carbonic anhydrase‐II (CA‐II) and urease using microtiter assays. Urease inhibition rate for compounds 1 – 8 ranged between 5.0 – 41.7%, while only compounds 1, 2, and 4 showed a considerable inhibition over 50% against CA‐II with the IC50 values of 73.5 ± 1.05, 39.5 ± 1.14, and 104.5 ± 2.50 μm, respectively, where IC50 of the reference (acetazolamide) was 21.0 ± 0.12 μm. In silico experiments were also performed through two docking softwares (Autodock Vina and i‐GEMDOCK) in order to find out interactions between the compounds and CA‐II. Actually, compounds 6 (30.0%) and 7 (42.0%) possessed a better binding capability toward the active site of CA‐II. According to our results obtained in this study, among the phenolic compounds screened, particularly 1, 2, and 4 appear to be the promising inhibitors of CA‐II and may be further investigated as possible leads for diuretic, anti‐glaucoma, and antiepileptic agents.
Heparanase 1 involvement in prostate physiopathology
Authors: Barbosa Guilherme O. , Cervigne Nilva K. , Carvalho Hernandes F. , Augusto Taize M.
Published: February 2017

The prostate is a compound exocrine gland of the male reproductive tract universally present in mammals. It is highly responsive to androgen and can be committed by a variety of pathological complications as prostatitis, benign, and malignant proliferative changes, which may be intensified by aging. Prostate intensively turnover its extracellular matrix (ECM) either at homeostasis or disease which includes a dynamically change of glycosaminoglycan composition during the life of an individual. Among the different enzymes playing a role in such changes, heparanase‐1 is responsible for cleaving heparan sulfate (HS) at a limited number of sites, clearly involved in tissue remodeling. Its activity has been strongly implicated in cell invasion associated with cancer metastasis, a consequence of the structural modification that loosens the ECM barrier. In the present review we focuses in some aspects of the prostate physiology and diseases, particular prostate cancer, evidencing how the HPSE‐1 activity encompasses the relationship of both processes.
Unexpected Activity for Glycerol Electro‐Oxidation of Nanostructured Pd−Pt and Pd−Pt−Ru Catalysts
Authors: Garcia Amanda Cristina , Morais Claudia , Napporn Teko. W. , Kokoh K. Boniface , Tremiliosi‐Filho Germano
Published: February 2017

Ruthenium‐modified palladium/platinum bimetallic materials were synthesized at nanoscale by using the formic acid method. This soft and surfactant‐less chemical approach led to a trimetallic catalyst (Pd25Pt25Ru50/C) that displayed excellent ability toward glycerol oxidation and also a favorable capacity for CO oxidation, as a probing molecule. In the case of glycerol, the main oxidation peak shifted remarkably from 500 mV towards lower electrode potentials. From cyclic voltammetry combined with in situ infrared spectroscopy experiments, our findings provided evidence of weakly adsorbed carbonaceous species on the trimetallic electrode, probably owing to the ligand effect.
Conditions of microvessel occlusion for blood coagulation in flow
Authors: Bouchnita A. , Galochkina T. , Kurbatova P. , Nony P. , Volpert V.
Published: February 2017

Vessel occlusion is a perturbation of blood flow inside a blood vessel because of the fibrin clot formation. As a result, blood circulation in the vessel can be slowed down or even stopped. This can provoke the risk of cardiovascular events. In order to explore this phenomenon, we used a previously developed mathematical model of blood clotting to describe the concentrations of blood factors with a reaction‐diffusion system of equations. The Navier‐Stokes equations were used to model blood flow, and we treated the clot as a porous medium. We identify the conditions of partial or complete occlusion in a small vessel depending on various physical and physiological parameters. In particular, we were interested in the conditions on blood flow and diameter of the wounded area. The existence of a critical flow velocity separating the regimes of partial and complete occlusion was demonstrated through the mathematical investigation of a simplified model of thrombin wave propagation in Poiseuille flow. We observed different regimes of vessel occlusion depending on the model parameters both for the numerical simulations and in the theoretical study. Then, we compared the rate of clot growth in flow obtained in the simulations with experimental data. Both of them showed the existence of different regimes of clot growth depending on the velocity of blood flow.
Compactness of Alexandrov‐Nirenberg Surfaces
Authors: Han Qing , Hong Jiaxing , Huang Genggeng
Published: February 2017

We study a class of compact surfaces in ℝ3 introduced by Alexandrov and generalized by Nirenberg and prove a compactness result under suitable assumptions on induced metrics and Gauss curvatures.© 2017 Wiley Periodicals, Inc.
Generation of Singlet Oxygen by Persistent Luminescent Nanoparticle–Photosensitizer Conjugates: A Proof of Principle for Photodynamic Therapy without Light
Authors: Ozdemir Tugba , Lu Yu‐Chen , Kolemen Safacan , Tanriverdi‐Ecik Esra , Akkaya Engin U.
Published: February 2017

The broader application of photodynamic therapy as a treatment procedure for cancer is hampered by the limited penetration of light through mammalian tissues. Since the photosensitized generation of cytotoxic singlet oxygen requires effective excitation of the tumor‐localized photosensitizer, photodynamic action can only be guaranteed for the first few millimeters of the irradiated tissues. In this work, we demonstrated that the phenomenon of persistent luminescence, that is, delayed emission from certain metal‐ion excited states (with crystal defects acting as energy traps), can provide an alternative excitation possibility. Thus, persistent luminescent nanoparticles functionalized by FRET‐matching Bodipy sensitizers (FRET=Förster resonance energy transfer) were excited in situ before administration into a cell culture or an organism. It was found that this system continues to produce singlet oxygen regardless of their location and without any need for continuous photonic excitation.
Monitoring active species in an atmospheric pressure dielectric‐barrier discharge: Observation of the Herman‐infrared system
Authors: Annušová Adriana , Čermák Peter , Rakovský Jozef , Martišovitš Viktor , Veis Pavel
Published: February 2017

An electronic and spectroscopic study of dielectric‐barrier discharge transition from the Townsend to the filamentary mode is presented. The discharge is generated under pure nitrogen flow at atmospheric pressure in a reactor with parallel configuration of cylindrical electrodes covered with Al2O3 dielectrics, applying a frequency of 4.85 kHz. The goal of the study was to find optimal conditions for observation of the Herman‐infrared (HIR) transition (C” → A') in a perspective to develop and test a ro‐vibrational model for this quintet band. We have focused on finding the maximum emissivity of the HIR transition in the homogeneous discharge regime as it offers a more suitable source for calibrating the HIR model. Besides the capability of generating a spatially homogeneous type of radiation, our discharge design also allowed the observation of HIR without detectable interference from the first positive system of nitrogen which is not common for atmospheric pressure discharges. In the study, a time‐resolved observation of the NOγ system, the second positive and the HIR nitrogen systems were performed and their emissivities analysed as a function of the discharge period and power. The optimum for the observation of the HIR system was found at 2.94 W (power density of 6 W/cm3), corresponding to the Townsend discharge just before its transition to the filamentary one.
A Study on Cell Body Model for Highly Integrated Circuits
Authors: OKUYAMA ATSUSHI , SAEKI KATSUTOSHI , SEKINE YOSHIFUMI
Published: February 2017

A number of recent studies on neural networks (NNs) have been conducted with the purpose of applying engineering to the brain function. One approach which focuses on the dynamics of the living organism, various Artificial Neural Networks (ANNs) has been proposed. However, the NN of a living body is very large in scale. Therefore, when we analyze the dynamics using the hardware NN model, the number of devices and the circuit size should be smaller. In this paper, we aim to reduce the area of a cell body model, and look into the cell body model made up of only NMOS. As a result, it is clearly shown that the packaging density of the proposed model can reduce the size of a traditional model by more than half.
Context‐dependent individual behavioral consistency in Daphnia
Authors: Heuschele Jan , Ekvall Mikael T. , Bianco Giuseppe , Hylander Samuel , Hansson Lars‐Anders
Published: February 2017

The understanding of consistent individual differences in behavior, often termed “personality,” for adapting and coping with threats and novel environmental conditions has advanced considerably during the last decade. However, advancements are almost exclusively associated with higher‐order animals, whereas studies focusing on smaller aquatic organisms are still rare. Here, we show individual differences in the swimming behavior of Daphnia magna, a clonal freshwater invertebrate, before, during, and after being exposed to a lethal threat, ultraviolet radiation (UVR). We show consistency in swimming velocity among both mothers and daughters of D. magna in a neutral environment, whereas this pattern breaks down when exposed to UVR. Our study also, for the first time, illustrates how the ontogenetic development in swimming and refuge‐seeking behavior of young individuals eventually approaches that of adults. Overall, we show that aquatic invertebrates are far from being identical robots, but instead they show considerable individual differences in behavior that can be attributed to both ontogenetic development and individual consistency. Our study also demonstrates, for the first time, that behavioral consistency and repeatability, that is, something resembling “personality,” is context and state dependent in this zooplankter taxa.
Accuracy of a Classical Test Theory–Based Procedure for Estimating the Reliability of a Multistage Test
Authors: Kim Sooyeon , Livingston Samuel A.
Published: February 2017

The purpose of this simulation study was to assess the accuracy of a classical test theory (CTT)–based procedure for estimating the alternate‐forms reliability of scores on a multistage test (MST) having 3 stages. We generated item difficulty and discrimination parameters for 10 parallel, nonoverlapping forms of the complete 3‐stage test and ability parameters for a population of 30,000 simulated test takers. Using these parameters to generate item responses, we ran each of the 30,000 simulated test takers through each of the 10 simulated forms of the 3‐stage test and computed the correlation of the scores on each pair of simulated test forms. We then computed the CTT estimate of the reliability, in the full population of 30,000 simulated test takers, of the total scaled scores resulting from the multistage testing procedure. We computed the estimate separately from the simulated responses to each of the 10 simulated forms of the 3‐stage test. The reliability estimates from each simulated form of the MST differed by less than .005 from the average of the correlations between scores on that form and on the other 9 simulated forms of the MST.
Fat tails and spurious estimation of consumption‐based asset pricing models
Authors: Toda Alexis Akira , Walsh Kieran James
Published: February 2017

The standard generalized method of moments (GMM) estimation of Euler equations in heterogeneous‐agent consumption‐based asset pricing models is inconsistent under fat tails because the GMM criterion is asymptotically random. To illustrate this, we generate asset returns and consumption data from an incomplete‐market dynamic general equilibrium model that is analytically solvable and exhibits power laws in consumption. Monte Carlo experiments suggest that the standard GMM estimation is inconsistent and susceptible to Type II errors (incorrect nonrejection of false models). Estimating an overidentified model by dividing agents into age cohorts appears to mitigate Type I and II errors.
Fkbp10 Deletion in Osteoblasts Leads to Qualitative Defects in Bone
Authors: Lietman Caressa D , Lim Joohyun , Grafe Ingo , Chen Yuqing , Ding Hao , Bi Xiaohong , Ambrose Catherine G , Fratzl‐Zelman Nadja , Roschger Paul , Klaushofer Klaus , Wagermaier Wolfgang , Schmidt Ingo , Fratzl Peter , Rai Jyoti , Weis MaryAnn , Eyre David , Keene Douglas R , Krakow Deborah , Lee Brendan H
Published: February 2017

Osteogenesis imperfecta (OI), also known as brittle bone disease, displays a spectrum of clinical severity from mild (OI type I) to severe early lethality (OI type II), with clinical features including low bone mass, fractures, and deformities. Mutations in the FK506 Binding Protein 10 (FKBP10), gene encoding the 65‐kDa protein FKBP65, cause a recessive form of OI and Bruck syndrome, the latter being characterized by joint contractures in addition to low bone mass. We previously showed that Fkbp10 expression is limited to bone, tendon, and ligaments in postnatal tissues. Furthermore, in both patients and Fkbp10 knockout mice, collagen telopeptide hydroxylysine crosslinking is dramatically reduced. To further characterize the bone specific contributions of Fkbp10, we conditionally ablated FKBP65 in Fkbp10fl/fl mice (Mus musculus; C57BL/6) using the osteoblast‐specific Col1a1 2.3‐kb Cre recombinase. Using μCT, histomorphometry and quantitative backscattered electron imaging, we found minimal alterations in the quantity of bone and no differences in the degree of bone matrix mineralization in this model. However, mass spectroscopy (MS) of bone collagen demonstrated a decrease in mature, hydroxylysine‐aldehyde crosslinking. Furthermore, bone of mutant mice exhibits a reduction in mineral‐to‐matrix ratio and in crystal size as shown by Raman spectroscopy and small‐angle X‐ray scattering, respectively. Importantly, abnormalities in bone quality were associated with impaired bone biomechanical strength in mutant femurs compared with those of wild‐type littermates. Taken together, these data suggest that the altered collagen crosslinking through Fkbp10 ablation in osteoblasts primarily leads to a qualitative defect in the skeleton. © 2017 American Society for Bone and Mineral Research.
Proteomics Applications in Dental Derived Stem Cells
Authors: Li Jie , Tian Weidong , Song Jinlin
Published: February 2017

At present, the existence of a variety of dental derived stem cells has been documented. These cells displayed promising clinical application potential not only for teeth and its surrounding tissue regeneration, but also for other tissues, such as nerve and bone regeneration. Proteomics is an unbiased, global informatics tool that provides information on all protein expression levels as well as post‐translational modification in cells or tissues and is applicable to dental derived stem cells research. Over the last decade, considerable progress has been made to study the global proteome, secrotome, and membrane proteome of dental derived stem cells. Here, we present an overview of the proteomics studies in the context of stem cell research. Particular attention is given to dental derived stem cell types as well as current challenges and opportunities. J. Cell. Physiol. 232: 1602–1610, 2017. © 2016 Wiley Periodicals, Inc.
Optimal conditions of acid‐catalysed steam explosion pretreatment of banana lignocellulosic biomass for fermentable sugar production
Authors: Guerrero Ana Belén , Ballesteros Ignacio , Ballesteros Mercedes
Published: February 2017

BACKGROUND

Banana is one of the most cultivated fruit crops around the world. After its harvest, it generates large amounts of agricultural wastes. The objective of this study was to optimise the operational conditions of steam explosion pretreatment of the two main banana lignocellulosic residues, rachis and pseudostem, in order to achieve high overall sugar yields.

RESULTS

A response surface statistical model (22 + star points with triplicate at central point) was used for the optimisation, considering the enzymatic hydrolysis yield and the overall yield of glucose and xylose as main criteria. The optimal conditions of steam explosion pretreatment for pseudostem were established at 177 °C, 5 min and 2.2% H2SO4 (v/v), presenting a high overall glucose yield of 91.0%. For rachis, the optimal conditions were 198 °C, 5 min and 1.5% H2SO4 (v/v) with an overall glucose yield of 87.1%.

CONCLUSION

Optimal conditions for steam explosion pretreatment of agricultural banana wastes were determined. An acid‐catalysed pretreatment was needed due to the low presence of acetyl groups in both feedstocks. After rachis pretreatment, extractives, soluble ashes and hemicellulose were solubilised causing an enrichment of cellulose in the insoluble fraction. However, due to the high amount of starch in pseudostem, a significant amount of glucose was recovered in the liquid fraction. © 2017 Society of Chemical Industry
Performance enhancement and optimization of photocatalytic cyanide degradation in aqueous solution using Zn (II) and Fe (III) oxides as nanostructure supported on activated carbon
Authors: Eskandari Parisa , Farhadian Mehrdad , SolaimanyNazar Ali Reza
Published: February 2017

BACKGROUND

Cyanide is a toxic compound used in gold mining, steel, electroplating and chemical industries. In this research, different mole ratios of Fe3+/ZnO supported on powder activated carbon (PAC) in the presence of H2O2 under UV irradiation were used to degrade cyanide contamination. The photocatalyst was characterized by XRD, XRF, FESEM, TEM and BET and response surface methodology was applied to assess the individual and interaction effects of several operating factors on cyanide degradation efficiency and to determine the optimization conditions.

RESULTS

The results indicated that the average particle size of catalyst ranged from 20 to 60 nm. pH had the largest effect on response and there was interaction between initial cyanide concentration and pH. Decreasing the initial cyanide concentration and pH, while increasing the catalyst dosage, hydrogen peroxide concentration and irradiation time improved the cyanide degradation efficiency. The experimental result of cyanide degradation efficiency under optimum conditions ([CN]− = 250 mg L−1, photocatalyst = 1.4 g L−1, irradiation time = 180 min, pH=10, mole ratio of Fe3+/ZnO=6% and [H2O2] = 300 mg L−1) was about 98%. Photocatalytic activity was maintained even after seven successive cycles.

CONCLUSION

The synthesized reusable high activity nanostructure photocatalyst can be considered an applicable and environmentally friendly catalyst for the decontamination of cyanide‐polluted water. © 2017 Society of Chemical Industry
Spiro[4H–pyran‐3,3′‐oxindoles] Derived from 9,10‐dihydroacridine
Authors: Alipour Mousa , Baradarani Mehdi M. , Joule John A.
Published: February 2017

Reaction 6H‐pyrrolo[3,2,1‐de]acridine‐1,2‐dione (7) with cyclic 1,3‐dicarbonyl compounds in the presence of malononitrile or ethyl cyanoacetate generates spiro[4H‐pyran‐3,3′‐oxindoles] 8.
Effect of repetition time on metabolite quantification in the human brain in 1H MR spectroscopy at 3 tesla
Authors: Knight‐Scott Jack , Brennan Patricia , Palasis Susan , Zhong Xiaodong
Published: February 2017

Purpose

To examine the effects of repetition time (TR) on metabolite concentration measurements in the human brain in 1H magnetic resonance spectroscopy at 3 Tesla (T).

Materials and Methods

Spectra were acquired from the posterior cingulate of five healthy adults at repetition times of 1.5 s, 3.0 s, 4.0 s, 6.0 s, and 8.0 s on a 3T MRI system. Relaxation data were also acquired for the water signal in the voxel of interest to separate tissue water and cerebrospinal fluid signal contributions. All data were quantified relative to total creatine and relative to the tissue water signal.

Results

On average, the variance for absolute metabolite concentrations was smaller than that of ratio concentrations (P = 0.003). Metabolite ratio concentrations calculated from a short TR of 1.5 s significantly differed (P < 0.05) from their “true” ratios, i.e., ratios corrected for T1‐weighting. In comparison, absolute metabolite concentrations exhibited significant differences (P < 0.05) up to a 4‐s TR.

Conclusion

To minimize potential TR‐dependent concentration differences at 3T, a minimum TR of 2.5 s is suggested for ratio concentration measurements, and a 5‐s TR for absolute concentrations. When possible, preference should be to perform absolute concentration measurements.

Level of Evidence: 2

J. Magn. Reson. Imaging 2017;45:710–721.
Liver imaging reporting and data system v2014 categorization of hepatocellular carcinoma on gadoxetic acid‐enhanced MRI: Comparison with multiphasic multidetector computed tomography
Authors: Joo Ijin , Lee Jeong Min , Lee Dong Ho , Ahn Su Joa , Lee Eun Sun , Han Joon Koo
Published: February 2017

Purpose

To investigate the Liver Imaging Reporting and Data System (LI‐RADS) v2014 categorization of hepatocellular carcinomas (HCCs) on gadoxetic acid‐enhanced magnetic resonance imaging (Gd‐EOB‐MRI) in comparison with multiphasic multidetector computed tomography (MDCT).

Materials and Methods

Our Institutional Review Board approved this retrospective study and waived the requirement for informed consent. We included 182 high‐risk patients with 216 pathologically confirmed HCCs who underwent both Gd‐EOB‐MRI at 1.5 or 3T and multiphasic MDCT. Two independent radiologists assessed the presence or absence of major HCC features and assigned LI‐RADS categories before and after considering ancillary features on both MRI and MDCT. Finally, sensitivities of LR‐5/5v and frequencies of major HCC features were compared between MRI and MDCT using the McNemar test.

Results

Sensitivities of LR‐5/5v were not significantly different between MRI and MDCT (63.4% [137/216] vs. 64.4% [139/216], P = 0.831; 60.6% [131/216] vs. 60.6% [131/216], P = 0.868, for reviewers 1 and 2, respectively). Among major HCC features seen on consensus review, washout and capsule appearance were less frequently observed on MRI than on MDCT (69.0% [149/216] vs. 87.0% [188/216], P < 0.001 and 17.1% [37/216] vs. 31.5% [68/216], P < 0.001), while no significant differences were found for arterial hyperenhancement (88.9% [192/216] vs. 84.7% [183/216], P = 0.081). Ancillary features led to category changes in 18.1% (39/216) of nodules on MRI (all, LR‐3 to LR‐4), while no changes were seen on MDCT.

Conclusion

Using LI‐RADS, Gd‐EOB‐MRI showed comparable sensitivity to multiphasic MDCT for the diagnosis of HCCs, and ancillary features of MRI frequently led to the upgrade of nodules from LR‐3 to LR‐4.

Level of Evidence: 3

J. Magn. Reson. Imaging 2017;45:731–740.
Prognostic impact of complications after resection of early stage hepatocellular carcinoma
Authors: Margonis Georgios Antonios , Sasaki Kazunari , Andreatos Nikolaos , Nishioka Yujiro , Sugawara Toshitaka , Amini Neda , Buettner Stefan , Hashimoto Masaji , Shindoh Junichi , Pawlik Timothy M.
Published: February 2017

BACKGROUND

Resection is the most effective treatment for HCC. However, postoperative morbidity is common and its impact on long‐term oncological outcome remains unclear.

METHODS

Long‐term outcomes of 774 patients who underwent curative resection for early stage HCC at Johns Hopkins Hospital and Toranomon Hospital were investigated after stratifying by the development of postoperative overall and infectious complications.

RESULTS

A minor or major postoperative complication developed in 281 and 65 patients, respectively, while postoperative mortality was 1.3% (n = 10). The 5‐year cumulative recurrence and overall survival(OS) rates were 57.2% and 76.4%, respectively. Overall postoperative complications independently predicted worse OS in multivariable analysis (HR = 1.42, P = 0.021). Complication severity did not correlate with OS (P > 0.05). While infectious complications were not independent predictors of OS, the combination of blood transfusion and infectious complications led to significantly worse OS (66.3% vs. 44.9%, P = 0.008). Postoperative complications also correlated with increased recurrence risk, but only in patients with non‐cirrhotic parenchyma (55.0% vs. 47.7%, P = 0.035) or non‐viral hepatitis (55.6% vs. 44.4%, P = 0.002).

CONCLUSIONS

Post‐operative morbidity independently predicted poor OS following hepatectomy for early stage HCC. A similar effect on recurrence was noted only in patients with favorable etiopathologic factors. Finally, the combination of peri‐operative transfusion and subsequent infectious complications was associated with a synergistic negative effect on prognosis.
Responses of Vegetation Activity to Drought in Northern China
Authors: Hua Ting , Wang Xunming , Zhang Caixia , Lang Lili , Li Hui
Published: February 2017

With the third‐generation normalized difference vegetation index and a multiple‐timescale drought index [standardized precipitation and evapotranspiration index (SPEI)], the relationships between vegetation activity in the growing season and drought occurrences during various seasons and at different timescales were investigated in northern China. Although poorly understood previously, knowledge of these relationships is crucial for climate, vegetation and hydrological studies. Our results show that over the past three decades, vegetation activity during the growing season was significantly correlated (p < 0⋅05) with drought occurrences over 78⋅5% of northern China and highly significantly correlated (p < 0⋅001) in semi‐arid regions. In addition, there were spatially variable responses of vegetation activity to the seasonality of drought events across northern China. When drought events occurred in pre‐season in the northern part of Inner Mongolia and Heilongjiang, parts of Shaanxi and Shanxi, and the western part of Xinjiang, they appear to have impacted vegetation activity, as indicated by the short and medium timescales of the drought indices (SPEI‐3 and SPEI‐6, with 3 and 6 months of accumulation, respectively). In the eastern part of Inner Mongolia, eastern part of Gansu and Qinghai, and southern parts of Ningxia, droughts during the growing season played a key role in vegetation growth, as recorded by the drought indices at all four timescales (SPEI‐3, SPEI‐6, SPEI‐12 and SPEI‐24). In addition, we also observed spatial variations in the responses of vegetation activity to droughts in northern China. Copyright © 2017 John Wiley & Sons, Ltd.
Can an injured nerve be used as a donor nerve for distal nerve transfer?—An experimental study in rats
Authors: Tzou Chieh Han , Lu Chuieng‐Yi Johnny , Chang Tommy Nai‐Jen , Chuang David Chwei‐Chin
Published: February 2017

Background

Distal nerve transfer has proven efficacy. The purpose of this study was to investigate if an injured nerve can be used as a donor nerve for transfer, and to determine the threshold of injury.

Materials and Methods

Rat's left ulnar‐nerves in the axilla with different degrees of injury were selected as the donor nerves for transfer, and the musculocutaneous‐nerves the target nerves for being re‐innervated. Six rats each served as positive and negative controls: Group A, intact ulnar‐nerve transfer; and Group E, the ulnar‐nerve was cut but no transfer. Ten rats each were assigned to Group B to Group D with 25%, 50%, and 75% transected ulnar‐nerve, respectively and all were transferred to the musculocutaneous‐nerve. After a 12‐week recovery period, outcomes were evaluated.

Results

Biceps muscle weight measurements showed all experimental groups—D 0.28 ± 0.02 g/72%, C 0.28 ± 0.03 g/73%, B 0.29 ± 0.04 g/74%, and A 0.29 ± 0.04 g/80%—were lighter than group H 0.36 ± 0.04 g, which were all statistically significant (P < 0.001). Muscle tetanus contraction force measurements were the lowest in group D35 ± 8.6 g/69%. Groups C and B measured 41 ± 8.5 g/75% and 40 ± 2.2 g/77% and group A 41 ± 9.4 g/95%, respectively. Group H showed muscle contraction force of 52 ± 7.2 g, which was statistically significant when compared to experimental groups (P < 0.05–0.001). EMG measurements of the biceps muscles showed: group D was 3.6 ± 0.7 mV/69%, group C was 3.6 ± 0.6 mV/75%, and group B was 4.2 mV ± 0.7/81%. Group H was5.1 ± 0.7 mV and statistically significant different when compared with experimental groups (P < 0.05–0.001).Axon counts of healthy ulnar‐nerve (Group H) were 1849 ± 362. Axon counts of the injured ulnar‐nerve were in group B 1447 ± 579/78%, group C 1051 ± 367/57% and group D 567 ± 230/31%.

Conclusion

The donor nerve should be healthy in order to provide optimal result. A big nerve (e.g., ulnar nerve) but injured with at least 75% axon spared is still potentially effective for transfer. In contrast, a small nerve (e.g., intercostal nerve) once injured with 75%axon spared would be considered a suboptimal donor nerve.
Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation
Authors: Zhang Yan‐Jun , Ding Jing‐Na , Zhong Hui , Han Ju‐Guang
Published: February 2017

Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double‐stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA‐binding activity, and impairs VP35‐mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all‐atom molecular dynamics (MD) simulation and binding energy calculation. R312A/R322A double mutations results in a completely different binding site and orientation upon the structure analyses. The calculated binding free energy results reveal that R312A, R322A, and K339A single mutations decrease the binding free energies by 17.82, 13.18, and 13.68 kcal mol−1, respectively. The binding energy decomposition indicates that the strong binding affinity of the key residues is mainly due to the contributions of electrostatic interactions in the gas phase, where come from the positively charged side chain and the negatively charged dsRNA backbone. R312A, R322A, and K339A single mutations have no significant effect on VP35 IID conformation, but the mutations influence the contributions of electrostatic interactions in the gas phase. The calculated results reveal that end‐cap residues which mainly contribute VDW interactions can recognize and capture dsRNA blunt ends, and the central basic residues (R312, R322, and K339) which mainly contribute favorable electrostatic interactions with dsRNA backbone can fix dsRNA binding site and orientation. Proteins 2017; 85:1008–1023. © 2017 Wiley Periodicals, Inc.
An Approach for Reliability Demonstration Test Based on Power‐Law Growth Model
Authors: Xu J. Y. , Yu D. , Xie M. , Hu Q. P.
Published: February 2017

Reliability demonstration test (RDT) is a critical and necessary step before the acceptance of an industrial system. Generally, a RDT focuses on designing a test plan through which one can judge whether the system reliability indices meet specific requirements. There are many established RDT plans, but few have incorporated the reliability growth aspects of the corresponding products. In this paper, we examine a comprehensive test plan that involves information concerning the reliability growth stage. An approach for RDT under the assumption of the power‐law model is proposed. It combines data related to the growth stage with those pertaining to the test stage of the product to reduce the cost of the test. Through simulation studies and numerical examples, we illustrate the characteristics of the test plan and significant reduction in test costs through our approach. Copyright © 2017 John Wiley & Sons, Ltd.
Concise analysis of current text automation and watermarking approaches
Authors: Alkawaz Mohammed Hazim , Sulong Ghazali , Saba Tanzila , Almazyad Abdulaziz S. , Rehman Amjad
Published: February 2017

With ceaseless utilization of web and other online advances, it has turned out to be amazingly simple to imitate, discuss, and convey digital material. Subsequently, confirmation and copyright assurance issues have been emerged. Text is the most widely used media of communication on the web as compared with images and videos. The significant part of books, daily papers, websites, commercial, research papers, reports, and numerous different archives are just the plain text. Therefore, copyrights protection of plain text is a critical issue that could not be accepted at all. This paper presents a concise analysis on information hiding techniques and their consequences. Various watermarking systems properties are highlighted along with different types of attacks and their possible defenses. Additionally, the current applications for text document watermarking and the reasons for the problems of text document watermarking are described. Finally, attacks characteristics are discussed including types of attacks, volumes, and nature on text. Current watermarking approaches are reviewed in depth, and consequently, their advantages and weaknesses are highlighted. Copyright © 2017 John Wiley & Sons, Ltd.
Quaking Is a Key Regulator of Endothelial Cell Differentiation, Neovascularization, and Angiogenesis
Authors: Cochrane Amy , Kelaini Sophia , Tsifaki Marianna , Bojdo James , Vilà-González Marta , Drehmer Daiana , Caines Rachel , Magee Corey , Eleftheriadou Magdalini , Hu Yanhua , Grieve David , Stitt Alan W. , Zeng Lingfang , Xu Qingbo , Margariti Andriana
Published: February 2017

The capability to derive endothelial cell (ECs) from induced pluripotent stem cells (iPSCs) holds huge therapeutic potential for cardiovascular disease. This study elucidates the precise role of the RNA-binding protein Quaking isoform 5 (QKI-5) during EC differentiation from both mouse and human iPSCs (hiPSCs) and dissects how RNA-binding proteins can improve differentiation efficiency toward cell therapy for important vascular diseases. iPSCs represent an attractive cellular approach for regenerative medicine today as they can be used to generate patient-specific therapeutic cells toward autologous cell therapy. In this study, using the model of iPSCs differentiation toward ECs, the QKI-5 was found to be an important regulator of STAT3 stabilization and vascular endothelial growth factor receptor 2 (VEGFR2) activation during the EC differentiation process. QKI-5 was induced during EC differentiation, resulting in stabilization of STAT3 expression and modulation of VEGFR2 transcriptional activation as well as VEGF secretion through direct binding to the 3′ UTR of STAT3. Importantly, mouse iPS-ECs overexpressing QKI-5 significantly improved angiogenesis and neovascularization and blood flow recovery in experimental hind limb ischemia. Notably, hiPSCs overexpressing QKI-5, induced angiogenesis on Matrigel plug assays in vivo only 7 days after subcutaneous injection in SCID mice. These results highlight a clear functional benefit of QKI-5 in neovascularization, blood flow recovery, and angiogenesis. Thus, they provide support to the growing consensus that elucidation of the molecular mechanisms underlying EC differentiation will ultimately advance stem cell regenerative therapy and eventually make the treatment of cardiovascular disease a reality. The RNA binding protein QKI-5 is induced during EC differentiation from iPSCs. RNA binding protein QKI-5 was induced during EC differentiation in parallel with the EC marker CD144. Immunofluorescence staining showing that QKI-5 is localized in the nucleus and stained in parallel with CD144 in differentiated ECs (scale bar = 50 µm).
Concise Review: Increasing the Validity of Cerebrovascular Disease Models and Experimental Methods for Translational Stem Cell Research
Authors: Boltze Johannes , Nitzsche Franziska , Jolkkonen Jukka , Weise Gesa , Pösel Claudia , Nitzsche Björn , Wagner Daniel-Christoph
Published: February 2017

Interspecies differences, anatomical and physiological aspects, as wells as simplified study designs contribute to an overestimation of treatment effects and limit the transferability of experimental results into clinical applications. Confounders of cell therapies for cerebrovascular disorders (CVD) include common CVD comorbidities, frequent medications potentially affecting endogenous and transplanted stem cells, as well as age- and immune-system–related effects. All those can contribute to a substantial modeling bias, ultimately limiting the prospective quality of preclinical research programs regarding the clinical value of a particular cell therapy. In this review, we discuss the nature and impact of most relevant confounders. We provide suggestions on how they can be considered to enhance the validity of CVD models in stem cell research. Acknowledging substantial and sometimes surprising effects of housing conditions, chronobiology, and intersex differences will further augment the translational value of animal models. We finally discuss options for the implementation of high-quality functional and imaging readout protocols. Altogether, this might help to gain a more holistic picture about the therapeutic impact of a particular cell therapy for CVD, but also on potential side and off-site effects of the intervention.