bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution
Authors: Zhu Sheng , Cao You-Zhi , Jiang Cong , Tan Bi-Yue , Wang Zhong , Feng Sisi , Zhang Liang , Su Xiao-Hua , Brejova Brona , Vinar Tomas , Xu Meng , Wang Ming-Xiu , Zhang Shou-Gong , Huang Min-Ren , Wu Rongling , Zhou Yan 
Published: August 2012

Abstract

Background
The fungus Marssonina brunnea is a causal pathogen of Marssonina leaf spot that devastates poplar plantations by defoliating susceptible trees before normal fall leaf drop.

Results
We sequence the genome of M. brunnea with a size of 52 Mb assembled into 89 scaffolds, representing the first sequenced Dermateaceae genome. By inoculating this fungus onto a poplar hybrid clone, we investigate how M. brunnea interacts and co-evolves with its host to colonize poplar leaves. While a handful of virulence genes in M. brunnea, mostly from the LysM family, are detected to up-regulate during infection, the poplar down-regulates its resistance genes, such as nucleotide binding site domains and leucine rich repeats, in response to infection. From 10,027 predicted proteins of M. brunnea in a comparison with those from poplar, we identify four poplar transferases that stimulate the host to resist M. brunnea. These transferas-encoding genes may have driven the co-evolution of M. brunnea and Populus during the process of infection and anti-infection.

Conclusions
Our results from the draft sequence of the M. brunnea genome provide evidence for genome-genome interactions that play an important role in poplar-pathogen co-evolution. This knowledge could help to design effective strategies for controlling Marssonina leaf spot in poplar.
A simple and inexpensive haemozoin-based colorimetric method to evaluate anti-malarial drug activity
Authors: Men Tran Thanh , Huy Nguyen Tien , Trang Dai Thi Xuan , Shuaibu Mohammed Nasir , Hirayama Kenji , Kamei Kaeko 
Published: August 2012

Abstract

Background
The spread of drug resistance in malaria parasites and the limited number of effective drugs for treatment indicates the need for new anti-malarial compounds. Current assays evaluating drugs against Plasmodium falciparum require expensive materials and equipment, thus limiting the search for new drugs, particularly in developing countries. This study describes an inexpensive procedure that is based on the advantage of a positive correlation between the haemozoin level of infected erythrocytes and parasite load.

Methods
The relationship between parasitaemia and the haemozoin level of infected erythrocytes was investigated after converting haemozoin into monomeric haem. The 50% inhibitory concentration (IC50) values of chloroquine, quinine, artemisinin, quinidine and clotrimazole against P. falciparum K1 and 9A strains were determined using the novel assay method.

Results
The haemozoin of parasites was extracted and converted into monomeric haem, allowing the use of a colorimeter to efficiently and rapidly measure the growth of the parasites. There was a strong and direct linear relationship between the absorbance of haem converted from haemozoin and the percentage of the parasite (R2 = 0.9929). Furthermore, the IC50 values of drugs were within the range of the values previously reported.

Conclusion
The haemozoin-based colorimetric assay can be considered as an alternative, simple, robust, inexpensive and convenient method, making it applicable in developing countries.
Transgene therapy for rat anti-Thy1.1 glomerulonephritis via mesangial cell vector with a polyethylenimine/decorin nanocomplex
Authors: Sun Jian-Yong , Sun Yu , Wu Hui-Juan , Zhang Hong-Xia , Zhao Zhong-Hua , Chen Qi , Zhang Zhi-Gang 
Published: August 2012

Abstract
Polyethylenimine (PEI), a cationic polymer, is one of the most efficient non-viral vectors for transgene therapy. Decorin (DCN), a leucine-rich proteoglycan secreted by glomerular mesangial cells (MC), is a promising anti-fibrotic agent for the treatment of glomerulonephritis. In this study, we used PEI–DCN nanocomplexes with different N/P ratios to transfect MC in vitro and deliver the MC vector with PEI–DCN expressing into rat anti-Thy1.1 nephritis kidney tissue via injection into the left renal artery in vivo. The PEI–plasmid DNA complex at N/P 20 had the highest level of transfection efficiency and the lowest level of cytotoxicity in cultured MC. Following injection, the ex vivo gene was transferred successfully into the glomeruli of the rat anti-Thy1.1 nephritis model by the MC vector with the PEI–DCN complex. The exogenous MC with DCN expression was located mainly in the mesangium and the glomerular capillary. Over-expression of DCN in diseased glomeruli could result in the inhibition of collagen IV deposition and MC proliferation. The pathological changes of rat nephritis were alleviated following injection of the vector. These findings demonstrate that the DCN gene delivered by the PEI–DNA nanocomplex with the MC vector is a promising therapeutic method for the treatment of glomerulonephritis.
Comparative host protein interactions with HTLV-1 p30 and HTLV-2 p28: insights into difference in pathobiology of human retroviruses
Authors: Doueiri Rami , Anupam Rajaneesh , Kvaratskhelia Mamuka , Green Kari B , Lairmore Michael D , Green Patrick L 
Published: August 2012

Abstract

Background
Human T lymphotropic virus type-1 (HTLV-1) and type 2 (HTLV-2) are closely related human retroviruses, but have unique disease associations. HTLV-1 is the causative agent of an aggressive T-cell leukemia known as adult T-cell leukemia (ATL), HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP), and other inflammatory diseases. HTLV-2 infection has not been clearly associated with any disease condition. Although both viruses can transform T cells in vitro, the HTLV-1 provirus is mainly detected in CD4+ T cells whereas HTLV-2 is mainly detected in CD8+ T cells of infected individuals. HTLV-1 and HTLV-2 encode accessory proteins p30 and p28, respectively, which share partial amino acid homology and are required for viral persistence in vivo. The goal of this study was to identify host proteins interacting with p30 and p28 in order to understand their role in pathogenesis.

Results
Affinity-tag purification coupled with mass spectrometric (MS) analyses revealed 42 and 22 potential interacting cellular partners of p30 and p28, respectively. Of these, only three cellular proteins, protein arginine methyltransferase 5 (PRMT5), hnRNP K and 60 S ribosomal protein L8 were detected in both p30 and p28 fractions. To validate the proteomic results, four interacting proteins were selected for further analyses using immunoblot assays. In full agreement with the MS analysis two cellular proteins REGγ and NEAF-interacting protein 30 (NIP30) selectively interacted with p30 and not with p28; heterogeneous nuclear ribonucleoprotein H1 (hnRNP H1) bound to p28 and not to p30; and PRMT5 interacted with both p30 and p28. Further studies demonstrated that reduced levels of PRMT5 resulted in decreased HTLV-2 viral gene expression whereas the viral gene expression of HTLV-1 was unchanged.

Conclusion
The comparisons of p30 and p28 host protein interaction proteome showed striking differences with some degree of overlap. PRMT5, one of the host proteins that interacted with both p30 and p28 differentially affected HTLV-1 and HTLV-2 viral gene expression suggesting that PRMT5 is involved at different stages of HTLV-1 and HTLV-2 biology. These findings suggest that distinct host protein interaction profiles of p30 and p28 could, in part, be responsible for differences in HTLV-1 and HTLV-2 pathobiology. This study provides new avenues of investigation into mechanisms of viral infection, tropism and persistence.
Influence of Specimen Geometry on Sample Disturbance Observed in Oedometric Testing of Clay Shales
Authors: Powell J. Suzanne , Siemens Greg , Take W. Andy , Remenda Vicki 
Published: August 2012

Abstract
There has been a significant amount of research investigating the relationship between sample disturbance and laboratory test results in soft soils. As a result of this research, the general rule adopted is that using larger specimens results in less sample disturbance. When testing these larger specimens in the laboratory, the results are more representative of in situ behavior of the materials. In contrast, there has been relatively little corresponding research performed on hard soils whose behavior typically lies on the boundary between rock and soil. Extensive unloading in hard soils, from sampling, results in large suctions (negative pore pressures) and the formation of fractures that are uncharacteristic of the material in its natural state. This poses the question of whether the use of small specimens would produce more reliable laboratory results. This paper investigates the following two hypotheses within the context of oedometric testing: (1) testing smaller diameter specimens will produce results more representative of the in situ behavior of the material, and (2) an aspect ratio of 2.5 may reduce disturbance to the specimen during preparation are tested. The results of this testing program, including the intact material properties, and a characterization of the compression behaviour of clay shale from the Bearpaw Formation is also presented herein. Results show that a reduced specimen size, when working with a hard clay shale, minimizes the effect of disturbance and produces results that are the most representative of the intact material. Decreased specimen size also aids in determining preconsolidation pressure by not only reducing the disturbance to the sample resulting from unloading, but also by enabling these high stresses to be achieved in conventional testing equipment. Two criteria from the literature were used to assess disturbance within the oedometer specimens. Overall, the methods provide a good baseline of assessing disturbance, however, there is less gradation to the quality of a specimen in a hard soil. Parameters Cc and σ′p were sensitive to sample disturbance, however, other parameters such as cv and K were less dramatically affected by disturbance. Therefore, care must be taken when assessing the compression of a hard soil as failing to achieve sufficiently higher stresses and the presence of disturbed specimens may lead to misleading Cc and σ′p values.
Testing Methane-Hydrate-Saturated Soil Using a Line Dissociation Apparatus
Authors: Falser S. , Palmer A. C. , Tan T. S. , Loh M. 
Published: August 2012

AbstractThe combination of energy source and geohazardous potential of natural gas hydrate has raised the need to understand the processes related to hydrate dissociation within the sediment. In this article, several existing methane hydrate dissociation apparatuses are listed and their sample size capabilities given. A new design for line dissociation tests by combined electrical heating and pressure reduction from a miniature wellbore is presented. The 180-mm-diameter × 225-mm-length hydrate-bearing soil samples can be tested over a wide range of near in situ conditions, with pore pressures of up to 15 MPa, temperatures as low as −5°C and a maximum effective stress of 5.5 MPa. During testing, the pore pressure, local temperature changes, vertical strain, the extracted gas and water volumes, and radial density changes are measured. The devices used are shown and described in detail. The sample formation steps by the water excess method are described, and the dissociation behaviour of a typical 40 % hydrate-saturated sand sample during local heating and pressure reduction are illustrated.
Performance Evaluation of SBS Modified Asphalt with Different Anti-aging Additives
Authors: Feng Zhengang , Xu Song , Sun Yubin , Yu Jianying 
Published: August 2012

Abstract
The effects of three different types of anti-aging additives (bumetrizole, octabenzone, and tinuvin770) on the physical and rheological properties of styrene butadiene styrene (SBS) modified asphalt were investigated by means of conventional physical properties tests and dynamic shear rheometer (DSR) tests. In order to evaluate the aging properties of different anti-aging additive/SBS modified asphalts, the thin film oven test and ultraviolet (UV) radiation test were performed, and different aging parameters were compared. The results show that the penetration, ductility, and softening point are increased, whereas the viscosity is decreased, with the addition of different anti-aging additives. The DSR analysis indicates that anti-aging additives can enhance the elastic behavior and improve the thermal stability of SBS modified asphalt. Improvement in the thermal-oxidative aging properties of SBS modified asphalt can be achieved with the three different anti-aging additives, but the UV aging properties of anti-aging additive/SBS modified asphalts are dependent on the type of anti-aging additive. Of the three different anti-aging additives, tinuvin770 improves both the thermal- and the photo-oxidative aging resistance of SBS modified asphalt significantly.
Nonlinear Response Characterization of Bituminous Mortar
Authors: Woldekidan M. F. , Huurman M. , Mo L. T. 
Published: August 2012

Abstract
In mesomechanics performance studies of porous asphalt concrete (PA), one of the crucial component materials influencing the raveling performance of the mixture is bituminous mortar. In relation fatigue performance, the viscoelastic response of the mortar for loads corresponding to the magnitude and frequency of the truck loading is important. In this paper, the mechanical response of a bituminous mortar material is investigated at various shear stress levels and loading frequencies. A dynamic shear rheometer setup with a specimen geometry specially developed for mortar testing is utilized. The mortar, which consists of bitumen, filler, and fine fractions of sand, is produced with a composition similar to that of a standard PA mixture. The tests were conducted at various temperatures in the frequency domain. The results show that the selected mortar test setup produces results with good repeatability. The results of high shear measurements show the presence of nonlinear behavior at shear stress levels in the range of 10 kPa for temperatures of 30°C and above. At temperatures of 0°C and below, the mortar exhibits linear viscoelastic behavior at shear stress levels of up to 1 MPa. The observed nonlinear viscoelastic behavior is described using Schapery nonlinear theory. The paper discusses the testing methods and the interpretation and description of results with the nonlinear theory. It also discusses the implications of the results for mechanistic based PA performance models.
Isolated Voids in Amorphous Silicon and Related Materials Measured by Effusion of Implanted Helium
Authors: Beyer W. , Hilgers W. , Lennartz D. , Pennartz F. , Prunici P. 
Published: August 2012

ABSTRACTEffusion measurements of hydrogen and implanted helium are reported for (undoped) amorphous and crystalline Si:H and related materials. Effusion of helium observed at temperatures > 600°C is attributed to isolated voids present in the material from the preparation process. While rather high void densities are detected for amorphous silicon films prepared by such deposition techniques like vacuum evaporation or sputtering, much smaller densities are found for plasma grown hydrogenated amorphous silicon (a-Si:H). For device-grade a-Si:H, the density of cavities which can trap helium is estimated to be about 2x1018/cm3at most, suggesting that crystalline silicon type divacancies are not the major hydrogen incorporation site.
Intermetallic Formation in PZT for MEMS Structures
Authors: Sharma Kanu priya , Oseroff Thomas , Lunardi Leda 
Published: August 2012

ABSTRACTCrack free lead zirconate titanate (PZT) films for piezoelectric based MEMS devices have been prepared by a multiple coating sol gel process on platinized silicon (100) substrates. Rapid thermal annealing and Conventional furnace annealing were used for densification and crystallization of the amorphous PZT films. Scanning electron microscopy (SEM), Transmission electron microscopy (TEM) and Atomic force microscopy (AFM) were used to observe surface film morphology and grain growth. The phase content of the films was analyzed using X-ray diffraction. The role of intermetallics formed during the heat treatment in the growth of different orientations has also been observed. Film aging critical for device performance has been observed and methods to revert aging effects have been examined and discussed.
Estimation of Expected Life-Years Saved From Successful Prevention of End-Stage Renal Disease in Elderly Patients With Diabetes
Authors: Yang Deng-Chi , Lee Lukas Jyuhn-Hsiarn , Hsu Chih-Cheng , Chang Yu-Yin , Wang Ming-Cheng , Lin Wei-Hung , Chang Chia-Ming , Wang Jung-Der 
Published: August 2012

OBJECTIVE
Because of the increasing incidence and prevalence of diabetes as a leading cause of end-stage renal disease (ESRD) in the aging population, we estimated the expected life-years (LYs) saved from successful prevention of ESRD in elderly patients with diabetes.

RESEARCH DESIGN AND METHODS
We conducted a population-based cohort study using the National Health Insurance Research Database. We identified all incidences of ESRD in the individuals &gt;65 years of age who were receiving maintenance hemodialysis (N = 24,243) from the registry files of catastrophic illnesses in Taiwan from 1 July 1997 to 31 December 2005. We then retrospectively searched the database to determine whether there had been a diagnosis of diabetes in these cases. After the exclusion of individuals with malignancy (n = 3,423), we extrapolated the survival rates through the end of 2006 using the Monte Carlo method. Using the data of preventable ESRD cases due to diabetes and expected years of life lost (EYLL) in each age stratum, we further estimated the expected LYs saved from successful prevention of ESRD in elderly patients with diabetes.

RESULTS
The estimated average EYLL was 10.6–5.8 and 12.3–7.3 years for diabetic males and females, respectively, aged 65–79 years. In total, 5,430.1 LYs and 10,177 LYs could be saved by the successful prevention of ESRD in male and female elderly patients with diabetes, respectively, in a single year.

CONCLUSIONS
The LYs saved by successful prevention of ESRD in elderly patients with diabetes in a single year are substantial and deserve special attention, especially in elderly females.
Damage progression from impact in layered glass modeled with peridynamics
Authors: Bobaru Florin , Ha Youn , Hu Wenke 
Published: August 2012

Abstract
Dynamic fracture in brittle materials has been difficult to model and predict. Interfaces, such as those present in multi-layered glass systems, further complicate this problem. In this paper we use a simplified peridynamic model of a multi-layer glass system to simulate damage evolution under impact with a high-velocity projectile. The simulation results are compared with results from recently published experiments. Many of the damage morphologies reported in the experiments are captured by the peridynamic results. Some finer details seen in experiments and not replicated by the computational model due to limitations in available computational resources that limited the spatial resolution of the model, and to the simple contact conditions between the layers instead of the polyurethane bonding used in the experiments. The peridynamic model uncovers a fascinating time-evolution of damage and the dynamic interaction between the stress waves, propagating cracks, interfaces, and bending deformations, in three-dimensions.
Novel Nucleoside Analogue Fnc is Effective against Both Wild-Type and Lamivudine-Resistant HBV Clinical Isolates
Authors: Zhou Yubing , Zhang Yan , Yang Xiaoang , Zhao Jing , Zheng Liyun , Sun Changyu , Jiang Jinhua , Yang Qinghua , Wang Qingduan , Chang Junbiao 
Published: August 2012

Background HBV infection causes major public health problems worldwide. The clinical limitation of current antiviral drugs for HBV, such as lamivudine, is causing rapid emergence of drug-resistant viral strains during prolonged antiviral therapy. Therefore, new antiviral drugs are urgently needed to prevent or delay the selection of drug-resistant HBV mutants. A novel cytidine analogue, FNC (2′-deoxy-2′-β-fluoro-4′-azidocytidine), was recently shown to strongly inhibit human HBV and duck HBV (DHBV) replication in vitro and in vivo, respectively. The present study was designed to evaluate the in vitro antiviral activity of FNC against clinical wild-type and lamivudine-resistant HBV isolates in transiently transfected cells. Methods HBV DNA was extracted from serum samples collected both before lamivudine therapy and at the time of viral breakthrough and was amplified by PCR. The amplicon was cloned into a novel expression vector, pHY106, which can initiate the intracellular HBV replication cycle after cell transfection. Following transfection of the cloned amplicon into HepG2 cells, a drug susceptibility assay was performed. Quantitative real-time PCR was used for determining the amount of intracellular HBV DNA, and the effective concentration required to reduce HBV replication by 50% (EC50) was calculated. Results FNC inhibited the replication of both wild-type and lamivudine-resistant HBV clinical isolates in a dose-dependent manner, with mean ±sd EC50 values of 0.12 ±0.01 μM and 0.27 ±0.01 μM, respectively. Conclusions FNC is a potential antiviral agent against both wild-type and lamivudine-resistant HBV clinical isolates, and therefore deserves further evaluation for the treatment of HBV infection.
The genetic population structure of lotic and lentic mayflies of theBaetis vernusgroup (Ephemeroptera: Baetidae)
Authors: Drotz Marcus K. , Savolainen Eino , Saura Anssi , Ståhls Gunilla 
Published: August 2012

AbstractNymphs of lotic mayflies live in environments that are expected to give rise to different degrees of population structuring. Here we investigate two taxa adapted to different lifestyles.Baetis macaniKimmins (Ephemeroptera: Baetidae) lives in flowing water; brooks that may periodically dry out in the summer or freeze to the bottom in winter.Baetis jaerviiSavolainen is mostly found in sedge belts along the shores of lakes. Most insects living in flowing water show low levels of among-population genetic differentiation within and among catchments. Levels of differentiation in the lotic species are therefore assumed to be lower than in lenticB. jaervii. Here we test this hypothesis. Mitochondrial DNA and allele frequencies of nuclear genes were used to detect population structure in specimens originating from an extensive area from northern Finland. The genetic differentiation among populations of the loticB. macaniis more than twice the corresponding value for the lenticB. jaervii(FST0.33 versus 0.15, while the meanFSTbetween species was 0.33 and significant). The result is congruent within the cytochrome c oxidase subunit I gene (COI) partial gene frequencies. We argue that the significant genetic population structure, which only was found in the loticB. macani, is differentiated as a consequence to the unpredictable environment as contrasted to the stable environment in standing bodies of water.