bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural genomics – expanding protein structural universe
Authors: Joachimiak Andrzej 
Published: November 2009

AbstractStructural Genomics has emerged as a multidisciplinary and international effort to expand the universe of protein folds by rapidly determining novel structures. This initiative takes advantage of the genome sequencing projects and technological advances in genomic analysis, molecular biology, proteomics, and structural biology. The international Structural Genomics efforts were initiated, in part, to achieve a more rapid understanding of sequence/structure relationships with the ultimate goal to make it feasible to predict an accurate 3D protein structure on the basis of sequence alone, and to elucidate novel biological function directly from primary genomic sequence. A number of Structural Genomics centers have been established to test and improve existing and develop new technologies. These centers developed the protein structure determination pipelines that include target selection, gene cloning and expression, protein and crystal production, structure determination, and structural and functional analysis. These pipelines are capable of determining hundreds of novel protein structures. Structural Genomics is rapidly expanding the universe of protein folds, creating new reagents, comprehensive libraries of expression clones, and databases for broad use. New high‐throughput technologies supported by robotics and automation in molecular biology, protein expression, purification, crystallization, and structure determination are being disseminated to the public and, therefore, contribute to the acceleration of new discoveries in biology. Ultimately, Structural Genomics will become a major component of and contributor to the next structural biology challenge – visualization of all major subcellular macromolecular assemblies of the cell.
Eukaryotic gene finding
Authors: Guigó Roderic 
Published: November 2009

Abstract
After the genome of an organism is sequenced and assembled, the first necessary step toward the understanding of its functional content is to locate all protein‐coding genes. Identification of genes is difficult in the eukaryotic genomes, because of the split nature of eukaryotic genes and because of the large intergenic spacers between adjacent genes. In this article, we will review how computational gene‐prediction programs address this difficulty, describing the basic components underlying most computational methods, and the strategies employed to integrate them.
Evolution of regulatory networks
Authors: Bornberg‐Bauer Erich , Veron Amelie 
Published: November 2009

AbstractGenetic regulation is intimately related to organismal development. Therefore, the understanding of genetic regulatory network evolution is also important for the understanding of organismal evolution.Recent advances in genomics, proteomics, and transcriptomics have provided means for comparative analysis of molecules and networks. The application of mathematical concepts such as graph analysis has helped us to analyze the data in more depth and quantify important properties of regulatory networks. The most basic element of regulatory networks is the transcription factor itself and its upstream and downstream regulatory regions. These elements arrange into motifs that have a recurrent topology across phyla. At the next higher level, motifs arrange into modules that comprise functionally and often evolutionary‐related transcription factors. These are controlled by some key regulators, probably the most ancestral proteins in such a family. As of current knowledge, the major driving forces in establishing networks with a certain topology are, apart from mutations, series of single‐gene duplication and domain rearrangements. A small set of anciently conserved DNA‐binding domains is frequently reused and their functions fine‐tuned by choice and alteration of secondary regulatory domains. Fewer general principles are known for both the structuring and the evolution of promoter regions since binding sites are sparse and fuzzy, and transcription activation is context dependent. Most recently, a controversial debate on neutral or selective evolution of expression levels has begun.
Experimental design
Authors: Dobbin Kevin K. , Simon Richard M. 
Published: November 2009

Abstract
Experimental design issues for dual‐label and single‐label microarray experiments are discussed, including identification of research objectives, avoidance of confounding, allotment of samples to arrays, and dyes in dual‐label experiments, dye bias, pooling RNA before labeling, and determination of the number of arrays required to achieve the study objectives.
CGH
data analysis
Authors: Margolin Adam A. , Greshock Joel , Weber Barbara L. 
Published: November 2009

Abstract
Array comparative genomic hybridization (aCGH) is an emerging technology for measuring genome‐wide DNA copy number. aCGH has been demonstrated as an effective tool in gene discovery and disease classification in cancer and other genetic disorders. This review describes recently employed analysis techniques for genomic copy number profiling using aCGH with a particular focus on how established gene expression array analysis techniques can be adapted for analysis of aCGH data. We intend this review to propose a framework to guide ongoing and future research in aCGH data analysis.
Relevance networks
Authors: Butte Atul J. 
Published: November 2009

Abstract
Relevance networks offer a method for constructing networks of similarity between genes, with the principal advantages being the ability to (1) include features of more than one data type (i.e., clinical, expression, and phenotypic data in the same analysis), (2) represent multiple connections between genes (e.g., a transcription factor may be responsible for regulating the expression of multiple other genes), and (3) capture negative as well as positive correlations (e.g., those from tumor‐suppressing genes). Java‐based software is available to construct relevance networks.
Analysis and prediction of membrane protein structure
Authors: Eyre Tina A. , Partridge Linda , Thornton Janet M. 
Published: November 2009

Abstract
Despite the importance of membrane proteins, relatively little is known even now about their structures because of the practical difficulties associated with the crystallization of these proteins. While we can identify transmembrane helices and predict their topology with high accuracy, we do not fully understand the forces that drive the packing of these helices in 3D. Recently, however, more membrane protein structures have become available and several computational studies have analyzed them. This chapter describes the results of these analyses and their implications for the prediction of 3D structural models for membrane proteins.
Ab initio
structure prediction
Authors: Baker David , Taylor William R. 
Published: November 2009

Abstract
The prediction of a folded protein structure from just its amino acid sequence (ab initio prediction) has been an outstanding problem in theoretical molecular biology for many years. Attempts based purely on physicochemical principles have had little success (except for short peptides), and a variety of approaches have been developed on the basis of the incorporation of known protein features to overcome this limitation. The most successful of these are based on building proteins from short fragments, and the performance of the ROSETTA program, which uses this method, is described.
Protein structure comparison
Authors: Holm Liisa 
Published: November 2009

Abstract
Automatic methods of protein structure comparison allow similarities to be found between proteins that cannot be seen using just sequence data. This allows distant evolutionary relationships to be proposed and can help elucidate the function of a protein. The all‐against‐all comparison of known protein structures has allowed the structure of “fold‐space” to be mapped, from broad general trends to specific clusters of proteins that have the same evolutionary origins. Collections can be found in databases accessible through the Internet. There are many practical methods for structure comparison using a variety of algorithms and similarity measures. There is no absolutely correct approach and the choice of method must be matched to the aspect of structure being investigated.
Asbestos
Authors: Jolicoeur Carmel R. , Alary Jean‐Francois , Sokov Asta 
Published: November 2009

Abstract

Geology and Fiber Morphology

Crystal Structure of Asbestos Fibers

Properties of Asbestos Fibers

Analytical Methods and Identification of Asbestos Fibers

Fiber Classification and Standard Testing Methods

Industrial Applications

Alternative Industrial Fibers and Materials

Health and Safety
Food Toxicants, Naturally Occurring
Authors: Hoskins Fred H. 
Published: November 2009

Abstract

Toxic Proteins, Peptides, Amides, and Amino Acids

Phytoalexins

Oligosaccharides

Oxalates, Phytates, and Other Chelates

Vasoactive and Psychoactive Amines and Alkaloids

Antinutrients

Vitamin Toxicity

Essential Minerals and Heavy Trace Elements

Cyanogenic Glycosides

Nitrates, Nitrites, and Nitrosamines

Sodium Chloride

Toxins

Legislation and Regulatory Considerations
Information Retrieval
Authors: Barcelon‐Yang Cynthia S. , Brownlee Evelyn L. , Calhoun Emmett D. , Caputo Bruno A. , Cumbo Charles C. , Daniszewski Joseph P. , Eckel Douglas A. , Glaspey Kenneth H. , Green‐Kocher Darlyn C. , Gruber Marianne B. , Isselmann Margaret M. , Johns Thomas C. , King Alicia P. , Krentz David M. , Kvalnes Fluorence H. , Minikiewicz Luray M. , Nazer Behrooz , Parsons Angela K.G. , Perrotto Carol R. , Ratliff Rita D. , Sikes Jeanette C. , Webster Amie H. 
Published: November 2009

Abstract

On‐Line Database Resources

Chemical Information and Search Methods and Services

Patent Information and Search Methods/Services

Environmental and Safety Information and Search Methods and Services

On‐Line Search Aids

Optical Disk‐Based Information and Document Image Systems

Private Bibliographic and Text Databases
Molecular and Supermolecular Electronics
Authors: Roberts Gareth 
Published: November 2009

AbstractHistorical Review of Langmuir‐Blodgett FilmsThe Chemistry and Preparation of Langmuir FilmsLangmuir‐Blodgett Film DepositionApplications of Langmuir‐Blodgett FilmsModel System in Basic ResearchPromising Applied Research AreasConclusionsAuthor's AcknowledgmentsEditor's Acknowledgments
Optical Fiber Systems
Authors:   Lucent Technologies
Published: November 2009

AbstractFiber‐Optic Systems in PerspectiveTypes of Optical FibersCharacteristics Affecting Optical Fiber PerformanceGlass ProcessingImprovements in LasersLight‐Emitting Diode for TelecommunicationsErbium‐doped Fibers for AmplificationOptical Fibers in AircraftFiber Optics in BiomedicineFiber Optic Communications in BotanyFiber Optics in the Private NetworkFiber Optics in Industrial Instrumentation and NetworksOptical Fiber Terminology
Preliminary Staining of Bacteria: Negative Stain
Authors: Moyes Rita B. , Reynolds Jackie , Breakwell Donald P. 
Published: November 2009

AbstractNegative staining is one of the many staining techniques that can be employed for viewing of bacterial cell morphology and size. The advantages of the negative stain include the use of only one stain and the absence of heat fixation of the sample. Negative staining employs the use of an acidic stain and, due to repulsion between the negative charges of the stain and the bacterial surface, the dye will not penetrate the cell. In negative staining, the results yield a clear cell with a dark background. Curr. Protoc. Microbiol. 15:A.3F.1‐A.3F.5. © 2009 by John Wiley & Sons, Inc.
Differential Staining of Bacteria: Capsule Stain
Authors: Breakwell Donald P. , Moyes Rita B. , Reynolds Jackie 
Published: November 2009

AbstractBacterial capsules are composed of high‐molecular‐weight polysaccharides and/or polypeptides, and are associated with virulence and biofilm formation. Unfortunately, capsules do not stain well with crystal violet, methylene blue, or other simple stains. This unit describes two methods of capsule staining. The first is a wet‐mount method using india ink; the capsule is visualized as a refractile zone surrounding a cell. The second is a direct‐staining dry‐mount method that precipitates copper sulfate and leaves the capsule as a pale blue zone. Both methods are easily performed within ∼5 min. Curr. Protoc. Microbiol. 15:A.3I.1‐A.3I.4. © 2009 by John Wiley & Sons, Inc.
Agricultural tractor overturn deaths: Assessment of trends and risk factors
Authors: Myers John R. , Hendricks Kitty J. 
Published: November 2009

AbstractBackgroundTractor overturn deaths have been recognized as a public health concern for decades. Studies have reported on the hazards associated with tractor overturns, but none have reported on trends in tractor overturn fatality rates in the United States (US).MethodsTractor overturn fatality data from the Bureau of Labor Statistics Census of Fatal Occupational Injuries were used in Poisson regression models to: identify risk factors associated with overturn fatalities; examine trends in tractor overturn fatality rates between 1992 and 2007; and assess trends in overturn fatality rates for specific risk factors.ResultsCharacteristics found to be associated with tractor overturn fatality rates were age, type of farm, region, and the victim's relationship to the farm (P < 0.0001). Older age groups, crop farms, farms in the Midwest and Northeast, and family workers all had higher fatal tractor overturn risks. Overall, tractor overturn fatality rates declined 28.5% between 1992 and 2007. Significant decreases in tractor overturn fatality rates were found for the Northeast and South regions, hired workers, crop farms, and in every age group except those less than 25 years of age.ConclusionsTractor overturn fatality rates decreased between 1992 and 2007. These decreases were not consistent between different categories of the agricultural workforce or regions of the US. Changes in tractor overturn fatality rates may be partially explained by increases in the prevalence of ROPS on farm tractors in the US. ROPS promotion programs are needed to reduce tractor overturn fatalities, especially among those subpopulations at highest risk. Am. J. Ind. Med. Published 2009 Wiley‐Liss, Inc.
Industrial systems biology
Authors: Otero José Manuel , Nielsen Jens 
Published: November 2009

AbstractThe chemical industry is currently undergoing a dramatic change driven by demand for developing more sustainable processes for the production of fuels, chemicals, and materials. In biotechnological processes different microorganisms can be exploited, and the large diversity of metabolic reactions represents a rich repository for the design of chemical conversion processes that lead to efficient production of desirable products. However, often microorganisms that produce a desirable product, either naturally or because they have been engineered through insertion of heterologous pathways, have low yields and productivities, and in order to establish an economically viable process it is necessary to improve the performance of the microorganism. Here metabolic engineering is the enabling technology. Through metabolic engineering the metabolic landscape of the microorganism is engineered such that there is an efficient conversion of the raw material, typically glucose, to the product of interest. This process may involve both insertion of new enzymes activities, deletion of existing enzyme activities, but often also deregulation of existing regulatory structures operating in the cell. In order to rapidly identify the optimal metabolic engineering strategy the industry is to an increasing extent looking into the use of tools from systems biology. This involves both x‐ome technologies such as transcriptome, proteome, metabolome, and fluxome analysis, and advanced mathematical modeling tools such as genome‐scale metabolic modeling. Here we look into the history of these different techniques and review how they find application in industrial biotechnology, which will lead to what we here define as industrial systems biology. Biotechnol. Bioeng. 2010; 105: 439–460. © 2009 Wiley Periodicals, Inc.
Public involvement in social and political participation processes: A gender perspective
Authors: De Piccoli Norma , Rollero Chiara 
Published: November 2009

AbstractOne interesting perspective from which to investigate participation processes is that of gender (Angelique & Culley, 2007). The disparity between male and female participation is evident, in particular when dealing with politics. The research reported here examines any differences between men and women in three different groups: non‐participants (N = 201), social participants (N = 167) and political participants (N = 184). Two specific aspects were considered: (a) the perception of sociopolitical control, that is leadership competence and policy control, and (b) the perception of costs and benefits derived from participation. In focusing on such perceptions, if any difference could be evidenced, we aimed to investigate if this difference was determined by gender, by the type of participation or by the interaction of gender and participation. Data show that leadership competence and policy control were both influenced by the type of participation. An interaction effect of gender and type of commitment for policy control was observed and gender had a direct effect on leadership competence. These results suggest that the gender gap seems to be connected more to the context than to effective gender characteristics. Other data on the perception of costs and benefits are discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Fine Tuning of Metallaborane Geometries: Chemistry of Metallaboranes of Early Transition Metals Derived from Metal Halides and Monoborane Reagents
Authors: Bose Shubhankar Kumar , Geetharani K. , Ramkumar V. , Mobin Shaikh M. , Ghosh Sundargopal 
Published: November 2009

AbstractReaction of [CpnMCl4−x] (M=V: n=x=2; M=Nb: n=1, x=0) or [Cp*TaCl4] (Cp=η5‐C5H5, Cp*=η5‐C5Me5), with [LiBH4⋅thf] at −70 °C followed by thermolysis at 85 °C in the presence of [BH3⋅thf] yielded the hydrogen‐rich metallaboranes [(CpM)2(B2H6)2] (1: M=V; 2: M=Nb) and [(Cp*Ta)2(B2H6)2] (3) in modest to high yields. Complexes 1 and 3 are the first structurally characterized compounds with a metal–metal bond bridged by two hexahydroborate (B2H6) groups forming a symmetrical complex. Addition of [BH3⋅thf] to 3 results in formation of a metallaborane [(Cp*Ta)2B4H8(μ‐BH4)] (4) containing a tetrahydroborate ligand, [BH4]−, bound exo to the bicapped tetrahedral cage [(Cp*Ta)2B4H8] by two Ta‐H‐B bridge bonds. The interesting structural feature of 4 is the coordination of the bridging tetrahydroborate group, which has two BH bonds coordinated to the tantalum atoms. All these new metallaboranes have been characterized by mass, 1H, 11B, and 13C NMR spectroscopy and elemental analysis and the structural types were established unequivocally by crystallographic analysis of 1–4.
P‐Chiral Ferrocenephospholanes: Synthesis, Reactivity, Metal Complex Chemistry and Application in the Asymmetric Hydrogenation of Olefins
Authors: Gschwend Björn , Pugin Benoît , Bertogg Andreas , Pfaltz Andreas 
Published: November 2009

AbstractStarting from (R)‐N,N‐dimethyl‐1‐ferrocenylethylamine, a diastereoselective ortho‐lithiation procedure and a stereoconvergent intramolecular hydrophosphination gave access to P‐chiral ferrocenephospholanes. These mono‐ or bidentate ligands were converted to the corresponding rhodium and iridium complexes, including a chiral version of Crabtree’s catalyst, and tested in the asymmetric hydrogenation of functionalized and unfunctionalized olefins. A significant reactivity difference between the rhodium‐1,5‐cyclooctadiene and the rhodium‐norbornadiene complex was observed during catalyst activation.
Fine‐needle aspiration biopsy as an initial diagnostic modality in a clinically unsuspected case of invasive maxillary fungal sinusitis: A case report
Authors: Singh Neha , Siddaraju Neelaiah , Kumar Surendra , Muniraj Femela , Bakshi Satvinder , Gopalakrishnan Suryanarayanan 
Published: November 2009

AbstractCases of invasive fungal lesions involving the paranasal sinuses are generally diagnosed either on histologic examination or on fungal culture. Here, we report a case of invasive fungal sinusitis diagnosed primarily by a fine‐needle aspiration biopsy (FNAB).Our patient was a 36‐year‐old male who presented with a history of slowly progressive, painless swelling over the left cheek. The only positive clinical finding was a bony hard swelling in the left maxillary region, which was clinically interpreted as “fibrous dysplasia.” A computed tomographic (CT) examination of the paranasal sinuses showed a soft tissue attenuation lesion involving the bilateral maxillae, with the destruction of multiple bones and involvement of multiple sinuses and the bilateral orbits. FNAB of the maxillary swelling showed several giant cells, many of them exhibiting ingested organisms with a morphologic resemblance to the Aspergillus species of fungi. Strikingly, no significant inflammatory cells were seen on cytologic smears. Unfortunately, owing to a lack of initial clinical suspicion, as well as the patient's loss to further follow‐up, a culture/histopathologic examination could not be carried out.This case is presented chiefly to highlight the clinical utility of a simple FNAB procedure, as an initial diagnostic modality in cases of fungal sinusitis, which can masquerade clinically as a neoplastic lesion. In addition, if radiologic findings are also available at the time of cytologic examination, a pretherapeutic comment on the invasive nature of the lesion can also be made. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
Osteoclast‐rich undifferentiated carcinoma of the urinary tract: Cytologic findings and literature review
Authors: Castelino‐Prabhu Shobha , Ali Syed Z. 
Published: November 2009

AbstractThe association of urothelial carcinoma with osteoclast‐like giant cells is an exceptionally rare event. To our knowledge, there are no published reports of the cytopathologic characteristics of osteoclast‐rich undifferentiated carcinoma of the urinary tract. We report herein, the case of a 63‐year‐old man who was evaluated at The Johns Hopkins Hospital for gross hematuria of 4 months duration. Urinary cytology displayed high‐grade malignant cells with scattered osteoclast‐like giant cells in a background of acute inflammation and abundant red blood cells. Subsequently, a transurethral tumor resection was performed, which revealed infiltrating undifferentiated carcinoma with osteoclast‐like giant cells. The rarity of this neoplasm and its resemblance to other giant cell‐rich processes may pose diagnostic difficulties. A review of the important differential diagnoses is also presented. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
Ring‐Opening Reactions of Aziridines Fused to a Conformationally Locked Tetrahydropyran Ring
Authors: Karban Jindřich , Kroutil Jiří , Buděšínský Miloš , Sýkora Jan , Císařová Ivana 
Published: November 2009

Abstract1,6‐Anhydro‐2,3,4‐trideoxy‐2,3‐(tosylepimino)‐β‐D‐hexopyranoses 1 and 2 underwent aziridine ring‐opening reactions with halides and other heteroatom‐centered nucleophiles. Ribo‐epimine 1 provided trans‐diaxial and cis products. The lyxo‐epimine 2 gave trans‐diaxial and trans‐diequatorial products, depending upon the reaction conditions (acid cleavage versus base cleavage) and the nucleophile (hard nucleophiles versus soft ones). These results have been rationalized by assuming that both SN2 and borderline SN2 cleavage mechanisms are operative. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)