bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infrared study of synthetic peptide analogues of the calcium‐binding site III of troponin C: The role of helix F of an EF‐hand motif
Authors: Nara Masayuki , Morii Hisayuki , Tanokura Masaru 
Published: October 2012

AbstractThe EF‐hand motif (helix–loop–helix) is a Ca2+‐binding domain that is common among many intracellular Ca2+‐binding proteins. We applied Fourier‐transform infrared spectroscopy to study the synthetic peptide analogues of site III of rabbit skeletal muscle troponin C (helix E–loop–helix F). The 17‐residue peptides corresponding to loop–helix F (DRDADGYIDAEELAEIF), where one residue is substituted by the D‐type amino acid, were investigated to disturb the α‐helical conformation of helix F systematically. These D‐type‐substituted peptides showed no band at about 1555 cm−1 even in the Ca2+‐loaded state although the native peptide (L‐type only) showed a band at about 1555 cm−1 in the Ca2+‐loaded state, which is assigned to the side‐chain COO− group of Glu at the 12th position, serving as the ligand for Ca2+ in the bidentate coordination mode. Therefore, helix F is vital to the interaction between the Ca2+ and the side‐chain COO− group of Glu at the 12th position. Implications of the COO− antisymmetric stretch and the amide‐I′ of the synthetic peptide analogues of the Ca2+‐binding sites are discussed. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 342–347, 2013.
Camptothecin‐7‐yl‐methanthiole: Semisynthesis and Biological Evaluation
Authors: Christodoulou Michael S. , Zunino Franco , Zuco Valentina , Borrelli Stella , Comi Daniela , Fontana Gabriele , Martinelli Marisa , Lorens James B. , Evensen Lasse , Sironi Maurizio , Pieraccini Stefano , Dalla Via Lisa , Gia Ornella Maria , Passarella Daniele 
Published: October 2012

AbstractThe introduction of a methylenthiol group at position 7 of camptothecin was carried out in four steps. This preparation also yielded the corresponding disulfide, which behaves as a prodrug due to its reactivity with glutathione. Assessment of their antiproliferative activities, investigations of their mechanism of action, and molecular modeling analysis indicated that the 7‐modified camptothecin derivatives described herein maintain the biological activity and drug–target interactions of the parent compound.
Low‐Molecular‐Weight CXCR4 Ligands with Variable Spacers
Authors: Narumi Tetsuo , Aikawa Haruo , Tanaka Tomohiro , Hashimoto Chie , Ohashi Nami , Nomura Wataru , Kobayakawa Takuya , Takano Hikaru , Hirota Yuki , Murakami Tsutomu , Yamamoto Naoki , Tamamura Hirokazu 
Published: October 2012

AbstractLow‐molecular‐weight CXCR4 ligands based on known lead compounds including the 14‐mer peptide T140, the cyclic pentapeptide FC131, peptide mimetics, and dipicolylamine‐containing compounds were designed and synthesized. Three types of aromatic spacers, 1,4‐phenylenedimethanamine, naphthalene‐2,6‐diyldimethanamine, and [1,1′‐biphenyl]‐4,4′‐diyldimethanamine, were used to build four pharmacophore groups. As pharmacophore groups, 2‐pyridylmethyl and 1‐naphthylmethyl are present in all of the compounds, and several aromatic groups and a cationic group from 1‐propylguanidine and 1,1,3,3‐tetramethyl‐2‐propylguanidine were also used. Several compounds showed significant CXCR4 binding affinity, and zinc(II) complexation of bis(pyridin‐2‐ylmethyl)amine moieties resulted in a remarkable increase in CXCR4 binding affinity.
Numerical investigation of axonal cargo rerouting in a dendrite: A three kinetic state model
Authors: Kuznetsov A. V. 
Published: October 2012

SUMMARYThe purpose of this paper is to develop a three‐kinetic state model to investigate axonal cargo rerouting in a dendrite. It is assumed that axonal cargos are transported by kinesin motors; they can enter dendrites riding on plus‐end‐out microtubules (MTs). If this happens, cargos are rerouted by dissociating from these MTs and associating with minus‐end‐out MTs. The same kinesin motors then move axonal cargos out of the dendrite. The model predicts how far axonal cargos can penetrate into the dendrite, concentrations of various populations of axonal cargos, and cargo fluxes. Copyright © 2012 John Wiley & Sons, Ltd.
MyExperimentalScience, extending the ‘workflow’
Authors: Frey Jeremy G. , Milsted Andrew , Michaelides Danius , Roure David De 
Published: October 2012

SUMMARYScience, especially experimental science, has always depended on the careful capture of plans, actions, raw and processed data and conclusions. With scientific research now so inextricably dependent on computers, the use of an electronic laboratory notebook (ELN) is almost essential. The meticulous notebooks of Michael Faraday and other scientists of his era remain as role models for the recording that is necessary, but they cannot provide the essential support for discussion, sharing, collaboration and formal verification. A blog (a contraction of Web log) can form the basis for implementing an electronic notebook but does not suffice to meet all the needs of an ELN. This paper describes the LabTrove ELN, which is blog based but provides numerous additional features, such as version control, security policies and a flexible metadata scheme, and facilities for interchanging objects with other systems. The MyExperimentalScience project links LabTrove with myExperiment, a repository for workflows in a collaborative environment, thereby making LabTrove templates available for discovery and reuse. Collaboration, sharing and reuse are essential for scientific progress, which depends on individual scientists building on the results already produced by others. Open‐source ELNs such as LabTrove are ideal vehicles to support the growth of Open Notebook Science. Copyright © 2012 John Wiley & Sons, Ltd.
Comparison of two flow‐based imaging methods to measure individual red blood cell area and volume
Authors: Tomaiuolo Giovanna , Rossi Domenico , Caserta Sergio , Cesarelli Mario , Guido Stefano 
Published: October 2012

AbstractThe red blood cells (RBCs) population is characterized by a high heterogeneity in membrane area, cellular volume, and mechanical properties, mainly due to the variety of mechanical and chemical stresses that a red cell undergoes in its entire life span. Here, we provide the first simultaneous area and volume measurements of RBCs flowing in microcapillaries, by using high‐speed video microscopy imaging and quantitative data processing based on image analysis techniques. Both confined and unbounded flow conditions (depending on the relative size of RBCs and microcapillary diameter) are investigated. The results are compared with micropipette experiments from the literature and data from Coulter counter routine clinical blood tests. Good agreement is found for RBC volume, especially in the case of confined flow conditions. Surface area measurements, which are lacking in the routine clinical test, are of special interest being a potential diagnostic parameter of altered cell deformability and aggregability. Overall, our results provide a novel flow methodology suitable for high‐throughput measurements of RBC geometrical parameters, allowing one to overcome the limits of classical static methods, such as micropipette aspiration, which are not suitable for handling a large number of cells. © 2012 International Society for Advancement of Cytometry
Histone H5—chromatin interactions in situ are strongly modulated by H5 C‐terminal phosphorylation
Authors: Kostova Nora N. , Srebreva Ljuba , Markov Dimiter V. , Sarg Bettina , Lindner Herbert H. , Rundquist Ingemar 
Published: October 2012

AbstractWe used linker histone‐depleted normal human fibroblast nuclei as templates to study how phosphorylation affects histone H5 binding to chromatin in situ. Permeabilized cells were treated with 0.7 M NaCl to extract the native linker histones. Histone H5 was purified from chicken erythrocytes and phosphorylated in vitro by recombinant cdk5/p35 kinase. High performance capillary electrophoresis (HPCE) showed that the phosphorylated protein contained a mixture of multiply phosphorylated forms. Control experiments, using mass spectrometry, revealed that up to five SPXK motifs in the C terminus were phosphorylated, but also that about 10% of the protein contained one phosphoserine in the N‐terminus. Reconstitution of H1‐depleted fibroblast nuclei with nonphosphorylated or phosphorylated H5 was performed at physiological ionic strength. The bound H5 was then extracted using NaCl concentrations in the range of 0.15 to 0.7 M. The release of the H5 molecules was monitored by DAPI staining and image cytofluorometry. Our results show that H5 phosphorylation substantially reduced its affinity for chromatin in situ, which support previous observations indicating that C‐terminal phosphorylation may be essential for the biological functions of linker histones. © 2012 International Society for Advancement of Cytometry
On the impact of temperature on path selection for wireless ad‐hoc sensor networks
Authors: Tseng Chih‐Cheng , Wang Hwang‐Cheng , Kuo Fang‐Chang , Ting Kuo‐Chang , Xie Bing‐En 
Published: October 2012

SUMMARYTo lengthen the lifetime of the routing paths in wireless ad‐hoc sensor networks, some of the routing algorithms take the utilization of battery of mobile nodes into account. However, the utilization of a battery is decided not only by its output voltage but also by its temperature. To the best of our knowledge, all of the proposed algorithms do not take this temperature effect into account so far. Hence, it results in selecting improper routes. In this article, we will propose a three‐step systematic method that considers the temperature of a mobile node's battery to calculate the battery's utilization. Simulation results show that the battery's temperature is critical to the lifetime of ad‐doc sensor networks if we let the method be applied to the power‐aware source routing (PSR) algorithm and maximum path lifetime routing (MPLR) algorithm. Copyright © 2012 John Wiley & Sons, Ltd.
Application of High‐Throughput Sequencing in Medicinal Plant Transcriptome Studies
Authors: Hao Da‐Cheng , Chen Shi‐Lin , Xiao Pei‐Gen , Liu Ming 
Published: October 2012

Abstract

Preclinical Research

Two alternative approaches to medicinal plant transcriptome analysis, RNA sequencing (RNA‐seq) and digital gene expression (DGE), are sequence based and have become increasingly popular due to rapid developments in high‐throughput sequencing technologies. Among the high‐throughput sequencing techniques, the 454 pyrosequencing and Illumina sequencing platforms are the first to be commercially available and established and thus widely used in various fields of medicinal plant transcriptome research. Metabolic pathway analysis of medicinal plants and molecular marker mining for molecular breeding can be facilitated and accelerated by RNA‐seq. DGE provides novel insights into biochemical mechanisms in medicinal plants. This review illustrates the potential of high‐throughput sequencing in drug discovery, drug development, and large‐scale production of plant natural products, and envisions its future development and applications in medicinal plant transcriptome studies.
Exploring the Mysteries of Traditional Chinese Medicine Systematically by Expression Microarrays
Authors: Cheng Feng 
Published: October 2012

Abstract

Preclinical Research

Traditional Chinese medicine often clashes with contemporary medicine because its principles and concepts are difficult to understand to scientists with a background in contemporary medicine. Therefore, more proof and explanation of traditional Chinese medicine at the molecular level are necessary. Expression microarrays, among the most important genomics techniques in modern systems biology, can simultaneously detect the expression levels of thousands of genes and identify related gene networks in biological systems. They may connect gene expression at the microlevel and system information at the macrolevel together. Expression microarrays may create building blocks to bridge traditional Chinese medicine and contemporary medicine. They may not only identify the action (or toxicological) mechanism or active ingredients of Chinese herbal medicine but also reveal the molecular mechanism of traditional Chinese medicine theories. The following is a brief overview of some applications of expression microarrays for traditional Chinese medicine studies.
The Current Status of Metabolomics in Drug Discovery and Development
Authors: Robertson Donald G. , Reily Michael D. 
Published: October 2012

Abstract

Preclinical Research

Metabolomics technology has been part of pharmaceutical discovery and development for over a decade and a half. Like many new technologies embraced by the industry, metabolomics gained early and wide acceptance as a novel tool for the rapid elucidation of mechanisms and biomarkers in preclinical discovery only to fall victim to overhype and overpromise. While many dedicated metabolomic groups have disappeared from industry, the academic world has embraced the technology and important new advances have been made such that the technology is beginning to reemerge in the industrial setting. Advances in instrumentation and data analyses have led the way in this resurgence followed by important new clinical applications. The technology has come a long way in the last decade, and we can anticipate an even more exciting ride in the next.
Omics‐Based Systems Vaccinology for Vaccine Target Identification
Authors: He Yongqun 
Published: October 2012

Abstract

Preclinical Research

Omics technologies include genomics, transcriptomics, proteomics, metabolomics, and immunomics. These technologies have been used in vaccine research, which can be summarized using the term “vaccinomics.” These omics technologies combined with advanced bioinformatics analysis form the core of “systems vaccinology.” Omics technologies provide powerful methods in vaccine target identification. The genomics‐based reverse vaccinology starts with predicting vaccine protein candidates through in silico bioinformatics analysis of genome sequences. The VIOLIN Vaxign vaccine design program (http://www.violinet.org/vaxign) is the first web‐based vaccine target prediction software based on the reverse vaccinology strategy. Systematic transcriptomics and proteomics analyses facilitate rational vaccine target identification by detesting genome‐wide gene expression profiles. Immunomics is the study of the set of antigens recognized by host immune systems and has also been used for efficient vaccine target prediction. With the large amount of omics data available, it is necessary to integrate various vaccine data using ontologies, including the Gene Ontology (GO) and Vaccine Ontology (VO), for more efficient vaccine target prediction and assessment. All these omics technologies combined with advanced bioinformatics analysis methods for a systems biology‐based vaccine target prediction strategy. This article reviews the various omics technologies and how they can be used in vaccine target identification.
Hydraulic redistribution of soil water in Populus euphratica Oliv. in a central Asian desert riparian forest
Authors: Hao Xing‐Ming , Chen Ya‐Ning , Guo Bin , Ma Jian‐Xing 
Published: October 2012

ABSTRACTHydraulic redistribution has been widely confirmed to occur in the arid and semi‐arid ecosystems. However, no research has documented the existence of such a water use/sharing mechanism in the desert riparian forests of the lower reaches of the Tarim River. The current study continuously monitored the sap velocity of roots, micro‐meteorological factors and volumetric soil water content at different soil depths and different distances from the trunk to verify whether Populus euphratica Oliv., the dominant species of the riparian forest, has a hydraulic redistribution mechanism and to document its influence factors and ecological effects. We also sampled the stable isotope δ18O in both soil and plant samples. On the basis of this data, the magnitude of hydraulic redistribution, its driving factors and ecological effects were estimated statistically. The results demonstrate that P. euphratica possesses clear hydraulic lift properties, and the effect of hydraulic lift was distinct at depths of 60–120 cm in the soil within a distance of 4 m from the trunk. This soil moisture spatial variation was attributed to the spatial distribution of the root system. Furthermore, hydraulic lift can improve soil moisture, providing approximately 10–20% of daily water used in the upper soil layers (0–120 cm). By increasing the availability of water in the upper soil water, hydraulic lift can facilitate the existence of some herb species in the Populus community. For the first time, we have estimated the extent of hydraulic redistribution in these ecosystems, and the data indicate that hydraulic lift is an important process in the desert riparian forests in the extremely arid regions of Central Asia. Copyright © 2012 John Wiley & Sons, Ltd.
Molecular Palladium Precursors for Pd0 Nanoparticle Preparation by Microwave Irradiation: Synthesis, Structural Characterization and Catalytic Activity
Authors: Heinrich Frank , Keßler Michael T. , Dohmen Stephan , Singh Mrityunjay , Prechtl Martin H. G. , Mathur Sanjay 
Published: October 2012

AbstractTwo new palladium complexes [Pd(MEA)2Cl2] (1) and [Pd(MEA)2Br2] (2) [MEA = (2‐methoxyethyl)amine] were synthesized by the reaction of 2 equiv. of MEA with PdCl2 or [(cod)PdBr2] (cod = cycloocta‐1,5‐diene), respectively. Single‐crystal X‐ray diffraction analysis of 1 and 2 revealed the formation of square‐planar trans complexes with palladium coordinated by chloride/bromide ions and N‐atoms of MEA bonded in a monodentate fashion. Given their molecular form and solubility, 1 and 2 act as intractable precursors to Pd nanoparticles by microwave‐assisted synthesis. The influence of the reaction temperature, irradiation time and surfactant (PVP) concentration on the size (5–40 nm) of the resulting particles was studied by DLS (hydrodynamic diameter) and TEM analyses (particle size). The growth mechanism of the nanoparticles depended on the type of halide ligand. Powder X‐ray diffractometry confirmed the formation of elemental Pd particles that were embedded in carbonized wood to examine their potential as a catalyst. The catalytic activity of these nanoscale particles was evaluated in carbon–carbon cross‐coupling reactions by using Heck, Suzuki and Sonogashira reactions as benchmark models. The investigations included recycling experiments that resulted in total turnover numbers of 4321 (Heck), 6173 (Sonogashira) and 8223 (Suzuki).
Facile Synthesis of MIL‐68(In) Films with Controllable Morphology
Authors: Liu Jia , Zhang Feng , Zou Xiaoqin , Zhou Shuyuan , Li Lina , Sun Fuxing , Qiu Shilun 
Published: October 2012

AbstractMetal–organic framework MIL‐68(In) films on silicon substrates have been fabricated successfully by a secondary growth method. The spherical colloidal seeds are 80 nm in size. The morphologies of the crystals in the film could be obtained by controlling the synthetic conditions. The organic base, which is an important factor that influences the crystal morphology, was focused upon. Crystal evolution is discussed and a possible growth mechanism is proposed based on observations made by means of SEM and XRD.
Eating Disorders, Substance Use Disorders, and Impulsiveness among Disordered Gamblers in a Community Sample
Authors: von Ranson Kristin M. , Wallace Laurel M. , Holub Alice , Hodgins David C. 
Published: October 2012

AbstractDisordered gambling and many eating disorders (EDs) involve recurrent loss of impulse control. We examined rates of specific EDs, ED psychopathology, substance use disorders, and their interrelationships with impulsiveness among community members with disordered gambling. Community‐recruited adults with pathological (n = 95) or problem (n = 9) gambling (N = 104; 51% female) completed structured interviews and questionnaires. We observed high rates of substance dependence, lifetime EDs, and current ED psychopathology; 20.8% of women (vs 1.9% of men) had a DSM‐IV ED, and 37.8% (vs 3.9%) had an ED according to proposed DSM‐5 criteria. Although disordered gambling severity was not associated with ED diagnosis or severity of ED psychopathology, greater disordered gambling severity and an ED diagnosis were both associated with increased impulsiveness. These findings suggest that impulsiveness might constitute a common personality characteristic that underlies disordered gambling and EDs. Copyright © 2012 John Wiley & Sons, Ltd and Eating Disorders Association.
Clusters of Personality Disorder Cognitions in the Eating Disorders
Authors: Waller Glenn , Ormonde Lisa , Kuteyi Yemi 
Published: October 2012

AbstractThis study examined whether comorbid personality disorder pathology in the eating disorders clusters into broader patterns, and whether those clusters have clinical validity in terms of levels of eating pathology and axis 1 comorbidity. The sample consisted of 214 eating‐disordered women who completed measures of personality disorder cognitions, eating pathology and axis 1 pathology at assessment. Three clusters of eating disorder patients emerged—low levels of personality pathology overall, high levels of cognitions underpinning anxiety‐based personality pathology, and high levels of all of the dimensions of personality pathology. These groups were validated by differences in levels of eating cognitions and axis 1 pathology. Personality disorder cognitions are clinically relevant to the eating disorders, but they might best be understood as broader sets of cognitions (‘anxiety‐centred’ and ‘general’), rather than in terms of individual personality disorder comorbidity or existing DSM personality disorder clusters. Copyright © 2012 John Wiley & Sons, Ltd and Eating Disorders Association.
Natural gas—Environmental impact: Air‐quality impacts from natural gas extraction and combustion
Authors: Shaw Stephanie 
Published: October 2012

AbstractThe Electric Power Research Institute (EPRI) performed a review of air‐quality issues related to natural gas extraction and combustion in 2011–12. This review focused on both traditional (e.g., particulate matter [PM], volatile organic compounds [VOCs]) and emerging air pollutants (e.g., ultrafine particle number) that are being considered in air‐quality management processes. This fact sheet summarizes the major topics and conclusions from this review.
Electric regulation: The future of solar is bright, right?
Authors: Bowden Nicholas S. 
Published: October 2012

AbstractIn 2011, the megawatts of photovoltaic (PV) capacity installed in the United States were double the capacity installed in 2010, according to the Interstate Renewable Energy Council's US Solar Market Trends 2011.1 The total number of megawatts of PV installed in 2011 reached 1,845 megawatts. These investments are fueled in large part by, besides the sun, government incentives. There are a plethora of incentives out there for solar PV installations, but arguably the best incentive program expired at the end of 2011, the inconspicuously deemed 1603 Program.2 To date, the 1603 Program has awarded approximately $13 billion to renewable energy installations.
Imidazol(in)ium‐2‐Carboxylates as Efficient Precursors to N‐Heterocyclic Carbene Complexes of Copper and Silver
Authors: Olszewski Tomasz K. , Jaskólska Dagmara E. 
Published: October 2012

ABSTRACTCopper and silver N‐heterocyclic carbene (NHC) complexes were prepared through a simple, base‐free protocol involving the decomposition of corresponding imidazol(in)ium‐2‐carboxylates under thermolytic conditions and a subsequent reaction of the in situ generated carbenes with copper(I) or silver(I) chloride, respectively. The desired NHC metal complexes were isolated with good yields after simple crystallization.