bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sedimentation in the floodplains of the Mekong Delta, Vietnam Part II: deposition and erosion
Authors: Hung Nguyen Nghia , Delgado José Miguel , Güntner Andreas , Merz Bruno , Bárdossy András , Apel Heiko 
Published: April 2013

AbstractDeposition and erosion play a key role in the determination of the sediment budget of a river basin, as well as for floodplain sedimentation. Floodplain sedimentation, in turn, is a relevant factor for the design of flood protection measures, productivity of agro‐ecosystems, and for ecological rehabilitation plans. In the Mekong Delta, erosion and deposition are important factors for geomorphological processes like the compensation of deltaic subsidence as well as for agricultural productivity. Floodplain deposition is also counteracting the increasing climate change induced hazard by sea level rise in the delta. Despite this importance, a sediment database of the Mekong Delta is lacking, and the knowledge about erosion and deposition processes is limited. In the Vietnamese part of the Delta, the annually flooded natural floodplains have been replaced by a dense system of channels, dikes, paddy fields, and aquaculture ponds, resulting in floodplain compartments protected by ring dikes. The agricultural productivity depends on the sediment and associated nutrient input to the floodplains by the annual floods. However, no quantitative information regarding their sediment trapping efficiency has been reported yet. The present study investigates deposition and erosion based on intensive field measurements in three consecutive years (2008, 2009, and 2010). Optical backscatter sensors are used in combination with sediment traps for interpreting deposition and erosion processes in different locations. In our study area, the mean calculated deposition rate is 6.86 kg/m2 (≈ 6 mm/year). The key parameters for calculating erosion and deposition are estimated, i.e. the critical bed shear stress for deposition and erosion and the surface constant erosion rate. The bulk of the floodplain sediment deposition is found to occur during the initial stage of floodplain inundation. This finding has direct implications on the operation of sluice gates in order to optimize sediment input and distribution in the floodplains. Copyright © 2013 John Wiley & Sons, Ltd.
Protein‐Protein Interaction Modeling and Inhibition: The TAU Bioinfo3D Perspective
Authors: Wolfson Haim J. 
Published: April 2013

AbstractProtein‐protein interactions are central to cell function. In order to fully understand these interactions, one has to elucidate the three‐dimensional structures of the underlying complexes. While experimental methods have advanced significantly in the last decade, there are still few structures of protein complexes in the Protein Data Bank. Reliable computational techniques are required to fill in this gap. Better understanding of protein‐protein interactions has also opened a large number of potential targets for the pharmaceutical industry, which previously viewed these interactions as “undruggable”. In this review, we focus on the algorithms developed by the Tel Aviv University Structural Bioinformatics (Bioinfo3D) Lab to model protein‐protein interactions, and on a preliminary attempt to search for peptide inhibitors for these interactions. All the algorithms presented are among the fastest available today and can be accessed via the group web server.
ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function
Authors: Celniker Gershon , Nimrod Guy , Ashkenazy Haim , Glaser Fabian , Martz Eric , Mayrose Itay , Pupko Tal , Ben‐Tal Nir 
Published: April 2013

AbstractMany mutations disappear from the population because they impair protein function and/or stability. Thus, amino acid positions that are essential for proper function evolve more slowly than others, or in other words, the slow evolutionary rate of a position reflects its importance. ConSurf (http://consurf.tau.ac.il), reviewed in this manuscript, exploits this to reveal key amino acid positions that are important for maintaining the native conformation(s) of the protein and its function, be it binding, catalysis, transport, etc. Given the sequence or 3D structure of the query protein as input, a search for similar sequences is conducted and the sequences are aligned. The multiple sequence alignment is subsequently used to calculate the evolutionary rates of each amino acid site, using Bayesian or maximum‐likelihood algorithms. Both algorithms take into account the evolutionary relationships between the sequences, reflected in phylogenetic trees, to alleviate problems due to uneven (biased) sampling in sequence space. This is particularly important when the number of sequences is low. The ConSurf‐DB, a new release of which is presented here, provides precalculated ConSurf conservation analysis of nearly all available structures in the Protein DataBank (PDB). The usefulness of ConSurf for the study of individual proteins and mutations, as well as a range of large‐scale, genome‐wide applications, is reviewed.
The Effects of Mutations on Protein Function: A Comparative Study of Three Databases of Mutations in Humans
Authors: Azia Ariel , Uversky Vladimir N. , Horovitz Amnon , Unger Ron 
Published: April 2013

AbstractSingle‐nucleotide mutations (SNPs) in protein‐coding regions of the human genome are a major factor in determining human variation in health and disease. Here, we analyze the amino acid changes and functional effects due to non‐synonymous SNPs. Three databases were used: (i) Variation – mutations found in the general human population; (ii) Cosmic – mutations found in cancer cells; and (iii) Pathogenic – a curated subset of mutations in Variation that are associated with diseases. The distributions of amino acid changes in these datasets were analyzed. It is shown that mutations in the Pathogenic dataset, in particular, tend to introduce order‐promoting residues. The effects of the mutations in these datasets were also studied using the program Polyphen‐2, which predicts the functional impact of non‐synonymous mutations. In order to evaluate the significance of these predicted effects, we compared them to those due to the same amino acid replacements introduced at other positions in the same proteins as a control. A mutation can be deleterious because the amino acid change is drastic (for example a change from hydrophobic residue to hydrophilic residue) or because of its location in the protein. We found that, on both counts, mutations in the Variation dataset tend to be less deleterious than randomly expected whereas mutations in the Pathogenic dataset tend to be more deleterious than their control mutations. The mutations in the Cosmic dataset are found to be more deleterious than those in its control set but less than those in Pathogenic.
JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia
Authors: Hanson Robert M. , Prilusky Jaime , Renjian Zhou , Nakane Takanori , Sussman Joel L. 
Published: April 2013

AbstractAlthough Java does not run on some handheld devices, e.g., iPads and iPhones, JavaScript does. The development of JSmol, a JavaScript‐only version of Jmol, is described, and its use in Proteopedia is demonstrated. A key aspect of JSmol is that it includes the full implementation of the entire set of Jmol functionalities, including file reading and writing, scripting, and rendering. The relative performances of Java‐based Jmol and JavaScript‐only JSmol are discussed. We can now confirm that the guiding principles of Java programming can be completely and relatively straightforwardly transformed directly into JavaScript, requiring no Java applet, and producing identical graphical results. JSmol is thus the first full‐featured molecular viewer, and the first ever viewer for proteins, which can be utilized with an internet browser on handheld devices lacking Java. Since the MediaWiki features of Proteopedia have been modified to optionally use JSmol, the wealth of crowd‐sourced content in Proteopedia is now directly available on such devices, without the need to download any additional applet.
Time‐Dependent Inhibition and Induction of Human Cytochrome P4503A4/5 by an Oral IAP Antagonist, LCL161, In Vitro and In Vivo in Healthy Subjects
Authors: Dhuria Shyeilla , Einolf Heidi , Mangold James , Sen Suman , Gu Helen , Wang Lai , Cameron Scott 
Published: April 2013

AbstractTumor cells can evade programmed cell death via up‐regulation of inhibitor of apoptosis proteins (IAPs). LCL161 is a small molecule oral IAP antagonist in development for use in combination with cytotoxic agents. The effect of LCL161 on CYP3A4/5 (CYP3A) activity was investigated in vitro and in a clinical study. Results in human liver microsomes indicated LCL161 inhibited CYP3A in a concentration‐ and time‐dependent manner (KI of 0.797 µM and kinact of 0.0803 min−1). LCL161 activated human PXR in a reporter gene assay and induced CYP3A4 mRNA up to ∼5‐fold in human hepatocytes. In healthy subjects, the dual inhibitor and inductive effects of a single dose of LCL161 were characterized using single midazolam doses, given before and at three time points after the LCL161 dose. Midazolam Cmax increased 3.22‐fold and AUC(0‐inf) increased 9.32‐fold when administered four hours after LCL161. Three days later, midazolam Cmax decreased by 27% and AUC(0‐inf) decreased by 30%. No drug interaction remained one week later. The strong CYP3A inhibition by LCL161 was accurately predicted using dynamic physiologically‐based pharmacokinetic (PBPK) modeling approaches in Simcyp. However, the observed induction effect after the LCL161 dose could not be modeled; suggesting direct enzyme induction by LCL161 was not the underlying mechanism.
Effect of silanization of titanium dioxide on photocatalytic decomposition of 2,4‐dinitropheonol under irradiation with artificial UV light and sunlight
Authors: Shiraishi Fumihide , Ueno Mariko , Chand Rumi , Shibata Yuichiro , Luitel Hom Nath 
Published: April 2013

AbstractBACKGROUNDTiO2‐based heterogeneous photocatalysis is an effective way to degrade harmful refractory organic compounds. However, the rate of photocatalytic reaction is significantly decreased by film diffusion resistance and several other factors. To overcome this problem, TiO2 immobilized on a stainless steel screen is hydrophobically treated using a (γ‐aminopropyl) triethoxysilane–toluene solution and the performance of the silanized TiO2 for the photocatalytic decomposition of 2,4‐dinitrophenol (2,4‐DNP) is investigated.RESULTSThe reactant 2,4‐DNP is slowly decomposed when its aqueous solution is treated using an unsilanized TiO2 screen without mixing the solution, whereas the rate of decomposition is certainly increased by use of a silanized TiO2 screen, and further increased by mixing the solution. The use of sunlight as a UV light source provides a higher rate of decomposition than does the use of an artificial UV lamp. The rate of decomposition in a well‐mixed solution is less affected up to 1.5 cm in solution depth.CONCLUSIONSThe use of the TiO2 screen silanized with a 2% silane–toluene solution under liquid mixing decreases film diffusion resistance and facilitates rapid decomposition of 2,4‐DNP. The simultaneous use of sunlight as a UV light source and a wind‐powered propeller for liquid mixing is effective. © 2013 Society of Chemical Industry
Regional covariance patterns of gray matter alterations in Alzheimer's disease and its replicability evaluation
Authors: Guo Xiaojuan , Chen Kewei , Zhang Yumei , Wang Yan , Yao Li 
Published: April 2013

PurposeTo identify regional network covariance patterns of gray matter associated with Alzheimer's disease (AD) and to further evaluate its replicability and stability.Materials and MethodsThis study applied a multivariate analytic approach based on scaled subprofile modeling (SSM) to structural magnetic resonance imaging (MRI) data from 19 patients with AD and 19 healthy controls (HC). We further applied the derived covariance patterns to examine the replicability and stability of AD‐associated covariance patterns in an independent dataset (13 AD and 14 HC) acquired with a different scanner.ResultsThe AD‐associated covariance patterns identified from SSM combined principal components mainly involved the temporal lobe and parietal lobe. The expression of covariance patterns was significantly higher in AD patients than HC (t(36) = 5.84, P = 5.75E−7) and predicted the AD/HC group membership (84% sensitivity and 90% specificity). In replicability evaluation, the expression of the forward applied covariance patterns was still statistically significant and had acceptable discriminability (69% sensitivity and 71% specificity).ConclusionAD patients showed regional gray matter alterations in a reliable covariance manner. The results suggest that SSM has utility for characterizing covariant features, and therefore can assist with further understanding covariance patterns of gray matter in AD based on the view of the network. J. Magn. Reson. Imaging 2014;39:143–149. © 2013 Wiley Periodicals, Inc.
Robust selective signal suppression using binomial off‐resonant rectangular (BORR) pulses
Authors: Ye Yongquan , Hu Jiani , Haacke E. Mark 
Published: April 2013

PurposeTo study the selective signal suppression capability of a binomial off‐resonant rectangular (BORR) radiofrequency pulse method.Materials and MethodsThe BORR pulse consists of two consecutive rectangular pulses with a phase difference of π. The exact solution of the Bloch equations was used to simulate its frequency response. The BORR pulse was implemented in a gradient echo sequence and tested on phantoms, the knee, and the breast.ResultsThe frequency response of the BORR pulse acquired on the phantom confirmed the theory. Broad suppression bands ensured high suppression efficiency and robustness in both in vitro and in vivo scans compared with other saturation pulses.ConclusionThe BORR pulse method provides a simple, efficient, and robust selective signal suppression alternative for three‐dimensional short TR (repetition time) imaging. J. Magn. Reson. Imaging 2014;39:195–202. © 2013 Wiley Periodicals, Inc.
Retrospective evaluation of antibody index of human parvovirus B19 as a prognostic factor in patients with dilated and ischemic cardiomyopathy
Authors: Zedtwitz‐Liebenstein Konstantin , Robak Oliver , Burgmann Heinz , Frass Michael 
Published: April 2013

AbstractCardiotropic viral infections are important causative factors in dilated cardiomyopathy. This retrospective study examined the antibody index for human parvovirus B19 in patients suffering from dilated or ischemic cardiomyopathy as a prognostic factor for stable left ventricular function. Blood specimens from 43 patients with the diagnosis of dilated or ischemic cardiomyopathy were analyzed for human parvovirus B19 by polymerase chain reaction (PCR) and enzyme immunoassay kit for qualitative determination of IgG and IgM antibodies. To exclude patients with acute myocarditis, only patients with onset of symptoms more than 4 months previously were included. Patients with dilated cardiomyopathy and a high antibody index showed a significantly better clinical outcome when compared to patients with a low IgG antibody index (8.5 ± 2.4 vs. 3.1 ± 2.6; P = 0.006). There was no significant difference in left ventricular ejection fraction between patients with a high antibody index and patients with a lower antibody index (P = 0.59). The presence of human parvovirus B19 antibodies is associated with protective immunity. A high antibody index seems to be a good prognostic factor for the disease correlating to a relatively stable left ventricular ejection fraction. J. Med. Virol. 85: 1111–1114, 2013. © 2013 Wiley Periodicals, Inc.
Hepatitis E virus infection in Latin America: A review
Authors: Echevarría J.M. , González J.E. , Lewis‐Ximenez L.L. , dos Santos D.R. Lopes , Munné M.S. , Pinto M.A. , Pujol F.H. , Rodríguez‐Lay L.A. 
Published: April 2013

AbstractData reported during recent years reveal the complex picture of the epidemiology of hepatitis E virus (HEV) infection in Latin America. Whereas in countries like Argentina and Brazil is almost identical to the characteristic of most countries from North America and Europe, HEV in the Caribbean and Mexico involves the water‐borne, non‐zoonotic viral genotypes responsible for epidemics in Asia and Africa. Nevertheless, Latin America has been considered a highly endemic region for hepatitis E in the scientific literature, a generalization that ignores the above complexity. In addition, reports from isolated Amerindian communities, which display well known, important and very specific epidemiological features for hepatitis B and D virus infections are neither taken into account when considering the epidemiology of hepatitis E in the region. This review updates compilation of the available information for the HEV infection, both among humans and other mammals, in Latin America, discusses the strengths and the weaknesses of our current knowledge, and identifies future areas of research. J. Med. Virol. 85: 1037–1045, 2013. © 2013 Wiley Periodicals, Inc.
Seroprevalence of Kaposi's sarcoma‐associated herpesvirus among men who have sex with men in Japan
Authors: Katano Harutaka , Yokomaku Yoshiyuki , Fukumoto Hitomi , Kanno Takayuki , Nakayama Tomoyuki , Shingae Akitomo , Sugiura Wataru , Ichikawa Seiichi , Yasuoka Akira 
Published: April 2013

AbstractKaposi's sarcoma‐associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma, causes malignancies frequently in patients with acquired immunodeficiency syndrome. In the United States and Europe, KSHV infection is common among men who have sex with men. However, the seroprevalence of KSHV among men who have sex with men in Japan is unknown. In the present study, the seroprevalence of KSHV was investigated among 230 men who have sex with men and 400 age‐ and area of residence‐matched men (controls) using a mixed‐antigen (KSHV‐encoded K8.1, open reading frame 59, 65, and 73 proteins) enzyme‐linked immunosorbent assay and an immunofluorescence assay. Among the Japanese men who have sex with men, serological assays revealed that 27 (11.7%) were seropositive for KSHV; 20 (5%) of the men in the control group were also KSHV seropositive. The seroprevalence of KSHV among men who have sex with men was significantly higher than in the control group (odds ratio = 2.52, 95% confidence intervals = 1.38–4.62, P = 0.0019, Chi‐square test). Infection with the human immunodeficiency virus, Treponema pallidum, or hepatitis B and C virus did not correlate with KSHV infection. Furthermore, the association of KSHV seropositivity with specific sexual activities was not statistically significant. In conclusion, a higher KSHV seroprevalence was found among Japanese men who have sex with men than among the controls, suggesting that the circulation of KSHV infection is more efficient among men who have sex with men in Japan than among men who do not engage in such sexual activities. J. Med. Virol. 85: 1046–1052, 2013. © 2013 Wiley Periodicals, Inc.
Molecular epidemiology of measles virus in Taiwan in 2010–2011: The common genotype changed from H1 to D9 and the first appearance of D4
Authors: Cheng Wen‐Yueh , Tung Hsiao‐Ping , Wang Hsiao‐Chi , Lee Li‐Li , Wu Ho‐Sheng , Liu Ming‐Tsan 
Published: April 2013

AbstractMeasles has been controlled effectively in some countries because of high coverage rates with an effective vaccine. However, measles outbreaks still occasionally occur in areas with high vaccine coverage as a result of imported transmission. To identify the sources of measles infection and to determine whether measles cases are part of a single outbreak or due to multiple importations, measles virus (MV) genotyping is required and plays an important role in MV elimination. In Taiwan, genotype H1 of MV was detected most frequently before 2009. From 2006 to 2011, 47 of 48 genotype H1 cases were associated with the imported cases, indicating that genotype H1 was not an endemic genotype in Taiwan after 2006. The distribution of the other genotypes (D3, D4, D5, D8, D9, and G3) detected during 2006–2011 varied by year. Taiwan has a pattern of measles genotypes that is consistent with the elimination of MV and with the absence of endemic genotypes. In this study, the genotypes of 40 cases of MV detected during 2010–2011 were investigated and analyzed. In 2010, the most common genotype changed from H1 (3/40) to D9 (35/40). In 2011, genotype H1 was not detected, and genotype D4 first appeared and was imported from Europe. The dynamic change of detected genotypes of MV in Taiwan is influenced by the activity of a measles control program in WHO regions. This study emphasizes that global synchronous elimination is important for an individual country or area to maintain free from MV. J. Med. Virol. 85: 1095–1099, 2013. © 2013 Wiley Periodicals, Inc.
Preparation of Poly(N‐Vinylcaprolactam) (NVCL) and Statistical Copolymers of NVCL with Variable Cloud Point Temperature by Using A Trithiocarbonate RAFT Agent
Authors: Ponce‐Vargas Sandra M. , Cortez‐Lemus Norma A. , Licea‐Claveríe Angel 
Published: April 2013

AbstractPreparation of PNVCL controlling its molecular weight and maintaining low dispersities by using a trithiocarbonate RAFT agent was achieved. Typical RAFT kinetics were not observed, nevertheless the prepared polymers were reactivated to grow a second hydrophobic poly(hexyl acrylate) block. A series of statistical copolymers of NVCL with N‐vinyl pyrrolidone, n‐hexyl acrylate, methacrylic acid, 2‐(diethylamino)ethyl methacrylate and 2‐(methacryloyloxy)benzoic acid with controlled dispersity were also prepared. By this copolymerization method the cloud point temperature of PNVCL was varied from 27 °C to 42 °C depending on comonomer type, content and pH of the aqueous solution.
Kinetic Modeling of 1,3‐Diene Polymerization Using a Neodymium‐Based Catalytic System: A New Approach for Calculating the Molecular Weight Distribution
Authors: Herrera‐Ordonez Jorge , Leon Ramón Diaz‐de , de Santiago‐Rodriguez Yair A. 
Published: April 2013

AbstractSummary: A new lumping‐based approach for calculating the molecular weight distribution (MWD) in polymerization systems is proposed. In order to illustrate its applicability the proposed methodology is used for modelling the kinetics of a 1,3‐diene polymerization using a binary neodymium‐based catalytic system. The model is capable of reproducing experimental data after fitting for the evolution of molecular weight and polydispersity. The results of this preliminary simulation are used as a guide to design kinetics experiments that may lead to improve the kinetic model and to deepen the knowledge of the system under study.
Polymerization of 1,3‐Butadiene with Several Catalytic Systems Based on Neodymium or Lithium in Presence of Ionic Liquids
Authors: de León Ramón Díaz , Córdova María Teresa Alonso , Medrano Francisco Javier Enríquez , Elizondo José Díaz , Camacho Odilia Pérez , Quiroz Aldo Romo , Céspedes Rosa Idalia Narro , Facio Adali Castañeda 
Published: April 2013

AbstractSummary: The anionic and Ziegler‐Natta polymerizations of 1,3‐butadiene initiated with n‐BuLi and NdV/TIBA/DEAC respectively were carried out in presence of ionic liquids and cyclohexane as solvent in both cases. Polybutadienes obtained were characterized by SEC, NMR and DSC techniques and results were compared with polybutadienes synthesized under similar conditions but in absence of ionic liquids. In all cases, the presence of ionic liquids caused a decrease in the reaction exothermal and also a diminution in the molecular weight distribution. The ionic liquids increased the microstructure cis‐1,4 in both kind of polymerizations, and promotes a shift towards lower temperatures in the glass‐transition temperature.