bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the resistance of microbial biofilms: Has proteomics been helpful?
Authors: Seneviratne C. Jayampath , Wang Yu , Jin Lijian , Wong Sarah S. W. , Herath Thanuja D. K. , Samaranayake Lakshman P. 
Published: January 2012

AbstractBiofilms are surface‐attached, matrix‐encased, structured microbial communities which display phenotypic features that are dramatically different from those of their free‐floating, or planktonic, counterparts. Biofilms seem to be the preferred mode of growth of microorganisms in nature, and at least 65% of all human infections are associated with biofilms. The most notable and clinically relevant property of biofilms is their greater resistance to antimicrobials compared with their planktonic counterparts. Although both bacterial and fungal biofilms display this phenotypic feature, the exact mechanisms underlying their increased drug resistance are yet to be determined. Advances in proteomics techniques during the past decade have facilitated in‐depth analysis of the possible mechanisms underpinning increased drug resistance in biofilms. These studies have demonstrated the ability of proteomics techniques to unravel new targets for combating microbial biofilms. In this review, we discuss the putative drug resistance mechanisms of microbial biofilms that have been uncovered by proteomics and critically evaluate the possible contribution of the new knowledge to future development in the field. We also summarize strategic uses of novel proteomics technologies in studies related to drug resistance mechanisms of microbial biofilms.
Combinatorial peptide ligand libraries for the analysis of low‐expression proteins: Validation for normal urine and definition of a first protein MAP
Authors: Santucci Laura , Candiano Giovanni , Bruschi Maurizio , D'Ambrosio Chiara , Petretto Andrea , Scaloni Andrea , Urbani Andrea , Righetti Pier G. , Ghiggeri Gian M. 
Published: January 2012

AbstractIn this review, we report the evolution on experimental conditions for the analysis of normal urine based on combinatorial peptide ligand library (CPLL) treatment and successive 2‐DE and 2‐DE/MS analysis. The main topics are (i) definition of the urine sample requirements, (ii) optimization of the urine/ligand ratio, (iii) essay conditions, (iv) en bloc elution. Overall, normal urine protein composition as studied by 2‐DE includes over 2600 spots. Relevant data on inter and intraessay reproducibility obtained by the analysis of different normal urines repeated several times are also here presented. We found a 73% reproducibility upon analysis of the same sample and 68% correspondence of protein composition among different normal urine samples. Based on the above results, we are completing the characterization with LC‐MS of 249 spots. The composition of normal urine proteins after CPLLs is finally shown with the indication of those spots which are currently under identification. This map will be completed in a near future; in the meantime this would represent the basic reference sample for newly developed studies on human diseases.
Probing protein stability and proteolytic resistance by loop scanning: A comprehensive mutational analysis
Authors: Ahmad Shoeb , Kumar Virender , Ramanand K. Bhanu , Rao N. Madhusudhana 
Published: January 2012

AbstractImprovement in protein thermostability was often found to be associated with increase in its proteolytic resistance as revealed by comparative studies of homologous proteins from extremophiles or mutational studies. Structural elements of protein responsible for this association are not firmly established although loops are implicated indirectly due to their structural role in protein stability. To get a better insight, a detailed study of protein wide mutants and their influence on stability and proteolytic resistance would be helpful. To generate such a data set, a model protein, Bacillus subtilis lipase was subjected to loop scanning site‐saturation mutagenesis on 86 positions spanning all loops including termini. Upon screening of ∼16,000 clones, 17 single mutants with improved thermostability were identified with increment in apparent melting temperature (Tmapp) by 1–6°C resulting in an increase in free energy of unfolding (ΔGunf) by 0.04–1.16 kcal/mol. Proteolytic resistance of all single mutants upon incubation with nonspecific protease, Subtilisin A, was determined. Upon comparison, post‐proteolysis residual activities as well as kinetics of proteolysis of mutants showed excellent correlation with ΔGunf, (r > 0.9), suggesting that proteolysis was strongly correlated with the global stability of this protein. This significant correlation in this set, with least possible sequence changes (single aa substitution), while covering >60% of protein surface strongly argues for the covariance of these two variables. Compared to studies from extremophiles, with large sequence heterogeneity, the observed correlation in such a narrow sequence space (ΔΔGunf = 1.57 kcal−1) justifies the robustness of this relation.
A novel amino acid substitution Ala‐122‐Tyr in ALS confers high‐level and broad resistance across ALS‐inhibiting herbicides
Authors: Han Heping , Yu Qin , Purba Edison , Li Mei , Walsh Michael , Friesen Shane , Powles Stephen B 
Published: January 2012

AbstractBACKGROUND: Wild radish, a problem weed worldwide, is a severe dicotyledonous weed in crops. In Australia, sustained reliance on ALS‐inhibiting herbicides to control this species has led to the evolution of many resistant populations endowed by any of several ALS mutations. The molecular basis of ALS‐inhibiting herbicide resistance in a novel resistant population was studied.RESULTS: ALS gene sequencing revealed a previously unreported substitution of Tyr for Ala at amino acid position 122 in resistant individuals of a wild radish population (WARR30). A purified subpopulation individually homozygous for the Ala‐122‐Tyr mutation was generated and characterised in terms of its response to the different chemical classes of ALS‐inhibiting herbicides. Whole‐plant dose‐response studies showed that the purified subpopulation was highly resistant to chlorsulfuron, metosulam and imazamox, with LD50 or GR50 R/S ratio of > 1024, > 512 and > 137 respectively. The resistance to imazypyr was found to be relatively moderate (but still substantial), with LD50 and GR50 R/S ratios of > 16 and > 7.8 respectively. In vitro ALS activity assays showed that Ala‐122‐Tyr ALS was highly resistant to all tested ALS‐inhibiting herbicides.CONCLUSION: The molecular basis of ALS‐inhibiting herbicide resistance in wild radish population WARR30 was identified to be due to an Ala‐122‐Tyr mutation in the ALS gene. This is the first report of an amino acid substitution at Ala‐122 in the plant ALS that confers high‐level and broad‐spectrum resistance to ALS‐inhibiting herbicides, a remarkable contrast to the known mutation Ala‐122‐Thr endowing resistance to imidazolinone herbicide. Copyright © 2012 Society of Chemical Industry
Determination of dislocation densities in InN
Authors: Ardali Sukru , Tiras Engin , Gunes Mustafa , Balkan Naci , Ajagunna Adebowale Olufunso , Iliopoulos Eleftherios , Georgakilas Alexandros 
Published: January 2012

AbstractThe magneto‐transport measurements, carried out at magnetic fields up to 11 T and in the temperature range between 1.8 K and 300 K, are used to investigate the scattering mechanisms in GaN/InN/AlN double heterojunctions. Theoretical modeling is based on a variational approach to solving Boltzmann transport equation. It is found that dislocation scattering is the dominant scattering mechanisms at low temperatures because of the large lattice mismatch with the substrate and hence the high density of dislocations in these material systems. Nevertheless, InN epilayers are characterized by a high background carrier density, probably associated with unwanted impurities. Therefore, we also included in our calculations the ionized impurity scattering. However, the effect of ionized impurity scattering as well as the acoustic phonon scattering, remote‐ background‐ionized impurity scattering, and interface roughness scattering on electron mobility are much smaller than that of dislocation scattering. The dislocation densities, in samples with InN thicknesses of 0.4, 0.6 and 0.8 µm, are then determined from the best fit to the experimental data for the low‐temperature transport mobility (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of the properties of In‐related alloys by AFM
Authors: Minj Albert , Cavalcoli Daniela , Cavallini Anna 
Published: January 2012

AbstractMOCVD grown Al1‐xInxN/AlN/GaN heterostructures have been characterized by atomic force microscopy(AFM) in semi‐contact and conductive mode. The surface of In‐related alloys consist of grain‐like structures indicating step flow and 3D‐growth with TDs of density equal to ∼108/cm2, the origin of which is mostly attributed to lattice mismatch between GaN and sapphire. These TDs with screw or mixed components terminate at the surface of overgrown layers as V‐defects, which are six‐facetted inverted pyramidal structures. Strain relaxation mechanism, formation of cracks and its propagation to the surface of the samples have been also investigated. With phase‐imaging (in semi‐contact AFM), we have traced sites of indium segregation in the V‐defects, surface‐relaxation and crack propagation in In‐related alloys. These sites in V‐defects and cracks were found to be highly conductive by current‐AFM either due to the presence of In‐segregation or due to lowering of potential barrier as a consequence of strain‐relaxation. They may be the possible dominant cause of leakage current in Schottky diodes. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Inhomogeneous electron distribution in InN nanowires: Influence on the optical properties
Authors: Molina‐Sánchez A. , Segura‐Ruiz J. , Garro N. , García‐Cristóbal A. , Cantarero A. , Iikawa F. , Denker C. , Malindretos J. , Rizzi A. 
Published: January 2012

AbstractIn this work, we study theoretically and experimentally the influence of the surface electron accumulation on the optical properties of InN nanowires. For this purpose, the photoluminescence and photoluminescence excitation spectra have been measured for a set of self‐assembled InN NWs grown under different conditions. The photoluminescence excitation experimental lineshapes have been reproduced by a self‐consistent calculation of the absorption in a cylindrical InN nanowires. With the self‐consistent model we can explore how the optical absorption depends on nanowires radius and doping concentration. Our model solves the Schrödinger equation for a cylindrical nanowire of infinite length, assuming a parabolic conduction band. The columnar geometry introduces effects in both the electron density and in the self‐consistent conduction band profile, with no equivalence in planar layer. On the other hand, the differences in the photoluminescence excitation spectra are related to the inhomogeneous electron distribution inside the nanowires, caused by a bulk donor concentration and a two‐dimensional density of ionized surface states. For nanowire radii larger than 30 nm, such concentrations modify the absorption edge and the lineshape, respectively, and can be determined from the comparison with the experimental data (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbothermal Reduction of Iron Ore Applying Microwave Energy
Authors: Renato de Castro Edmilson , Breda Mourão Marcelo , Jermolovicius Luiz Alberto , Takano Cyro , Thomaz Senise José 
Published: January 2012

AbstractThis paper presents the results of a study on carbothermal reduction of iron ore made under the microwave field in equipment specially developed for this purpose. The equipment allows the control of radiated and reflected microwave power, and therefore measures the microwave energy actually applied to the load in the reduction process. It also allows performing energy balances and determining the reaction rate with high levels of confidence by simultaneously measuring temperature and mass of the material upon reduction with high reproducibility. We used a microwave generator of 2.45 GHz with variable power up to 3000 W. Self‐reducing pellets under argon atmosphere, containing iron ore and petroleum coke, with 3.5 g of mass and 15 mm of diameter were declined. We obtained the kinetic curves of reduction of iron ore and of energy consumption to the process in the maximum electric field, in the maximum magnetic field and at different values of power/mass. The data allow analyzing how the microwave energy was actually consumed in the reduction of ore.
An Intercomparison Study of Analytical Methods for the Determination of Magnesium in Low Alloy Steel
Authors: Recknagel Sebastian , Richter Silke , Reinholdsson Fredrik , Pettersson Jean , Gustavsson Ingemar 
Published: January 2012

AbstractIn an intercomparison study three low alloy steel materials were analyzed on their content of the trace element Mg, and five different analytical techniques were used, namely spark‐OES, inductively coupled plasma optical emission spectrometry (ICP‐OES), inductively coupled plasma time of flight mass spectrometry (ICP‐TOFMS), inductively coupled plasma quadrupole mass spectrometry (ICP‐QMS), and glow discharge mass spectrometry (GD‐MS). Solid steel discs were used for analysis with spark‐OES and GD‐MS. For the analyses with ICP‐OES, ICP‐TOFMS, and ICP‐QMS steel chips were wet‐digested in aqua regia, and the wet‐digestion was performed either in polypropylene tubes placed in a heating block or in Teflon pressure vessels using a microwave assisted system. The Mg concentrations obtained for the three steel materials were: 2.0, 2.8, and 10.3 µg g−1, respectively, and the spread in results was acceptable, giving RSD values in the range of 20–30%.
Experimental Investigation on Optimal Carbon/Hydrogen Ratio for Developing Iron Bath Reactor with H2–C Mixture Reduction
Authors: Bo Zhang , Jie Guo , Huaiwei Zhang , Jiajun Mao , Qiuju Li , Dongyan Wang , Xin Hong 
Published: January 2012

AbstractThe basic idea of H2–C mixture reduction reflects advantages of hydrogen for fast reaction and low heat absorption in smelting reduction reactor, where hydrogen is used as main reducing agent and carbon as main heat generator on purpose to cut down total energy consumption and CO2 emission. This article aimed at the experimental investigation of optimal carbon/hydrogen ratio, a key parameter of iron oxide reduction with mixture reductive agents of carbon and hydrogen. Experiments were carried out using a pure Al2O3 crucible which was placed in a tubular furnace for high temperature. Two investigation methods were adopted, one was injecting acetylene/hydrogen mixture reducing gas into molten iron oxides and another was blowing hydrogen into iron bath during continuous feeding fine ore mixing solid carbon dust. Parameters such as apparent de‐oxidation rate and utilization ratio of reductive agents were calculated from content analysis of exhaust gas after dust removing and drying. In experiments highest total de‐oxidation rate and satisfied apparent utilization ratio of hydrogen were obtained under conditions with temperatures of 1823 K and carbon/hydrogen ratio in region from 0.5:1 to 2:1.
The Novel Function of OCT4B Isoform-265 in Genotoxic Stress
Authors: Gao Yuan , Wei Jianshu , Han Jin , Wang Xia , Su Guannan , Zhao Yannan , Chen Bing , Xiao Zhifeng , Cao Jiani , Dai Jianwu 
Published: January 2012

Abstract
OCT4 is a key transcription factor in maintaining the pluripotency and self-renewal of embryonic stem cells (ESCs). Human OCT4 gene can generate three mRNA isoforms (OCT4A, OCT4B, and OCT4B1) by alternative splicing and four protein isoforms (OCT4A, OCT4B-265, OCT4B-190, and OCT4B-164) by alternative splicing or alternative translation initiation. OCT4A is a transcription factor responsible for the stemness of ESCs, while the function of OCT4B protein isoforms is still not clear. We have previously reported that OCT4B-190 functioned in cell stress response. Here, we present another product of OCT4 gene, OCT4B-265, which is upregulated under genotoxic stress in stem cells, and it may function in stress response through p53 signaling pathway. This work gives an insight into the novel function of OCT4B protein isoforms and helps us to understand the complex expression patterns and biological functions of OCT4 gene.
Disclosure of potential conflicts of interest is found at the end of this article.
Large‐scale science education intervention research we can use
Authors: Penuel William R. , Fishman Barry J. 
Published: January 2012

AbstractThis article develops an argument that the type of intervention research most useful for improving science teaching and learning and leading to scalable interventions includes both research to develop and gather evidence of the efficacy of innovations and a different kind of research,design‐based implementation research(DBIR). DBIR in education focuses on what is required to bring interventions and knowledge about learning to all students, wherever they might engage in science learning. This research focuses on implementation, both in the development and initial testing of interventions and in the scaling up process. In contrast to traditional intervention research that focuses principally on one level of educational systems, DBIR designs and tests interventions that cross levels and settings of learning, with the aim of investigating and improving the effective implementation of interventions. The article concludes by outlining four areas of DBIR that may improve the likelihood that new standards for science education will achieve their intended purpose of establishing an effective, equitable, and coherent system of opportunities for science learning in the United States. © 2012 Wiley Periodicals, Inc. J Res Sci Teach 49: 281–304, 2012
Large‐scale interventions in science education: The road to utopia?
Authors: Marx Ronald W. 
Published: January 2012

AbstractThis article provides commentary on the five articles in this issue on large‐scale interventions in science education for diverse student groups in varied educational settings. Using these articles as a point of departure, I discuss three challenges to science education research and practice. The first concerns the changed meaning of science education reform over the past two decades. The science education research and development community must be aware of the shifting policy and public awareness context of their work and react accordingly if it wishes for its work to make a difference in the lives of teachers and students. The second addresses the importance of teacher professional development and the role that well‐designed and internally valid research plays in developing knowledge in this area. The third discusses the chaotic and contradictory nature of educational policy in this country and argues that our field needs to align our research work with the ways in which real and impactful decisions are made about education in general and science education in particular. © 2012 Wiley Periodicals, Inc. J Res Sci Teach 49: 420–427, 2012
The virtual liver: a multidisciplinary, multilevel challenge for systems biology
Authors: Holzhütter Hermann‐Georg , Drasdo Dirk , Preusser Tobias , Lippert Jörg , Henney Adriano M. 
Published: January 2012

AbstractThe liver is the central metabolic organ in human physiology, with functions that are fundamentally important to the detoxification of xenobiotics (drugs), the maintenance of homeostasis of numerous blood metabolites, and the production of mediators of the acute phase response. Liver toxicity, whether actual or implied is the reason for the failure of a significant proportion of many promising novel medicines that consequently never reach the market, and diseases such as atherosclerosis, diabetes, and fatty liver diseases, that are a major burden on current health resources, are directly linked to functional and structural disorders of the liver. This article presents the concepts and approaches underpinning one of the most exciting and ambitious modeling projects in the field of systems biology and systems medicine. This major multidisciplinary research program is aimed at developing a whole‐organ model of the human liver, representing its central physiological functions under normal and pathological conditions The model will be composed of a larger battery of interconnected submodels representing liver anatomy and physiology, integrating processes across hierarchical levels in space, time, and structural organization. In this article, we outline the general architecture of the liver model and present first step taken to reach this ambitious goal. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1158This article is categorized under:

Models of Systems Properties and Processes > Cellular Models
Models of Systems Properties and Processes > Mechanistic Models
Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models
Translational, Genomic, and Systems Medicine > Translational Medicine
Reverse‐engineering human regulatory networks
Authors: Lefebvre Celine , Rieckhof Gabrielle , Califano Andrea 
Published: January 2012

AbstractThe explosion of genomic, transcriptomic, proteomic, metabolomic, and other omics data is challenging the research community to develop rational models for their organization and interpretation to generate novel biological knowledge. The development and use of gene regulatory networks to mechanistically interpret this data is an important development in molecular biology, usually captured under the banner of systems biology. As a result, the repertoire of methods for the reconstruction of comprehensive and cell‐context‐specific maps of regulatory interactions, or interactomes, has also exploded in the past few years. In this review, we focus on Network Biology and more specifically on methods for reverse engineering transcriptional, post‐transcriptional, and post‐translational human interaction networks and show how their interrogation is starting to impact our understanding of cellular pathophysiology and one's ability to predict cellular phenotypes from genome‐wide molecular observations. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1159This article is categorized under:

Analytical and Computational Methods > Analytical Methods
Biological Mechanisms > Regulatory Biology
Überwinde deinen inneren Schweinehund‘‘ - Analyse von Zugangswegen zur Motivierung bewegungsinaktiver Älterer
Authors: Allmer Henning , Allmer Marietta , Euskirchen Julian , Froboese Ingo , Wallmann Birgit , Walter Tina , Walschek Reimund 
Published: January 2012

Einleitung
Der gesundheitliche Nutzen der Bewegungs- und Sportaktivität für Ältere ist unbestritten. Da die Bewegungs- und Sportaktivität bei Älteren gering ausgeprägt ist, profitiert der überwiegende Teil der älteren Bevölkerung nicht vom gesundheitlichen Nutzen der Bewegungs- und Sportaktivität. Um bewegungs- und sportinaktive Ältere zu motivieren, wurde eine vergleichende Analyse der Effektivität verschiedener Zugangswege vorgenommen. Als effektiv erwiesen sich zielgruppenspezifische Zugangswege.