bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis of a Sialic Acid Containing Complex‐Type N‐Glycan on a Solid Support
Authors: Tanaka Katsunori , Fujii Yohei , Tokimoto Hiroomi , Mori Yasutaka , Tanaka Shin‐ichi , Bao Guang‐ming , Siwu Eric R. O. , Nakayabu Aiko , Fukase Koichi 
Published: January 2009

AbstractOn solid ground: A new solid‐phase synthesis of N‐linked glycans featuring 1) highly stereoselective β‐mannosylation and microfluidic α‐sialylation and 2) efficient glycosylation of the N‐phenyltrifluoroacetimidate units on JandaJel resin is reported. Reagent concentration effects by a fluorous solvent are effectively applied, and the use of these methods results in the first synthesis of a sialic acid containing complex‐type N‐glycan on a solid support.magnified imageA new solid‐phase synthesis of N‐linked glycans featuring 1) highly stereoselective β‐mannosylation and microfluidic α‐sialylation and 2) efficient glycosylation of the N‐phenyltrifluoroacetimidate units on JandaJel resin is reported. Reagent concentration effects by a fluorous solvent are effectively applied, and the use of these methods results in the first synthesis of a sialic acid containing complex‐type N‐glycan on a solid support.
Framing of imprecise quantities: When are lower interval bounds preferred to upper bounds?
Authors: Halberg Anne‐Marie , Teigen Karl Halvor 
Published: January 2009

AbstractImprecisely known quantities (e.g., predictions) are often described in approximate terms as “more than X” or “less than Y” (e.g., “Ann will earn more than $50 000” or “less than $60 000”). Such phrases carry both quantitative and qualitative (pragmatic) information. Three studies are reported showing that lower limit estimates (more than, over, minimum) are generally more frequent, and considered more appropriate than upper limit estimates (less than, under, maximum) over a wide range of contexts. This is partly due to scalar properties of the number system, where lower numbers are attained before, and included in higher numbers, but not vice versa. As a result, upper limit statements are perceived as negations, and carry more specific information about the speaker's communicative concerns. Upper limit statements are preferred with amounts or quantities that can be perceived as small, whereas lower limit statements can be used both to indicate large quantities and as a default. Copyright © 2009 John Wiley & Sons, Ltd.
The need for the incorporation of phylogeny in the measurement of biological diversity, with special reference to ecosystem functioning research
Authors: King Ian 
Published: January 2009

AbstractDefining and measuring biodiversity is an important research area in biology, with very interesting theoretical and applied aspects. Numerous definitions have been proposed, and these definitions of biodiversity influence how it is measured. From the still commonly used measure of species diversity, through higher taxon diversity, molecular measures, ecological measures and indicator taxa, these measures have as their fundamental shortcoming the lack of an explicit consideration of the evolutionary context represented by phylogenies. Attempts have been made to incorporate phylogenetic considerations into measuring biodiversity, but more hypothesis‐driven research needs to be done. A specific case study is presented of how this added emphasis on phylogeny‐based biodiversity measurement can influence the way in which research is directed and hypotheses are generated. The elucidation of the relationship of biodiversity to ecosystem functioning is a very timely concern with the unarguable loss of biodiversity this planet is experiencing, whichever way biodiversity is measured.
The spectra of point mutations in vertebrate genomes
Authors: Albrecht‐Buehler Guenter 
Published: January 2009

AbstractIn spite of the importance of point mutations for evolution and human diseases, their natural spectrum of incidence in different species is not known. Here I propose to determine these spectra by comparing consecutive sequence periods in stretches of repetitive DNA. The article presents the analysis of more than 51,000 such point mutations identified by this approach in the genomes of human, chimpanzee, rat, mouse, pufferfish, zebrafish, and sea squirt. I propose to explain the observed spectra by auto‐mutagenic mechanisms of genome variation involving the inter‐conversions of nucleotides, single base‐pair inversions and their combinations.
The life and death of gene families
Authors: Demuth Jeffery P. , Hahn Matthew W. 
Published: January 2009

AbstractOne of the unique insights provided by the growing number of fully sequenced genomes is the pervasiveness of gene duplication and gene loss. Indeed, several metrics now suggest that rates of gene birth and death per gene are only 10–40% lower than nucleotide substitutions per site, and that per nucleotide, the consequent lineage‐specific expansion and contraction of gene families may play at least as large a role in adaptation as changes in orthologous sequences. While gene family evolution is pervasive, it may be especially important in our own evolution since it appears that the “revolving door” of gene duplication and loss has undergone multiple accelerations in the lineage leading to humans. In this paper, we review current understanding of gene family evolution including: methods for inferring copy number change, evidence for adaptive expansion and adaptive contraction of gene families, the origins of new families and deaths of previously established ones, and finally we conclude with a perspective on challenges and promising directions for future research.
RNA regulation of epigenetic processes
Authors: Mattick John S. , Amaral Paulo P. , Dinger Marcel E. , Mercer Tim R. , Mehler Mark F. 
Published: January 2009

AbstractThere is increasing evidence that dynamic changes to chromatin, chromosomes and nuclear architecture are regulated by RNA signalling. Although the precise molecular mechanisms are not well understood, they appear to involve the differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. A significant fraction of the genome‐wide transcription of non‐protein coding RNAs may be involved in this process, comprising a previously hidden layer of intermediary genetic information that underpins developmental ontogeny and the differences between species, ecotypes and individuals. It is also evident that RNA editing is a primary means by which hardwired genetic information in animals can be altered by environmental signals, especially in the brain, indicating a dynamic RNA‐mediated interplay between the transcriptome, the environment and the epigenome. Moreover, RNA‐directed regulatory processes may also transfer epigenetic information not only within cells but also between cells and organ systems, as well as across generations.
X‐chromosome upregulation and inactivation: two sides of the dosage compensation mechanism in mammals
Authors: Dementyeva Elena V. , Shevchenko Alexander I. , Zakian Suren M. 
Published: January 2009

AbstractMammals have a very complex, tightly controlled, and developmentally regulated process of dosage compensation. One form of the process equalizes expression of the X‐linked genes, present as a single copy in males (XY) and as two copies in females (XX), by inactivation of one of the two X‐chromosomes in females. The second form of the process leads to balanced expression between the X‐linked and autosomal genes by transcriptional upregulation of the active X in males and females. However, not all X‐linked genes are absolutely balanced. This review is focused on the recent advances in studying the dosage compensation phenomenon in mammals.
Beta‐catenin and axis formation in planarians
Authors: Meinhardt Hans 
Published: January 2009

AbstractIn three recent articles it was shown that β‐catenin is crucial for the establishment and the maintenance of the overall polarity and especially for the character ‘posterior’ in planarians. If the transcription of the β‐catenin gene was silenced by RNA interference, the overall polarity is lost, and in regenerating fragments a posterior blastema displays anterior characters by forming eyes and anterior ganglia. An attempt is made to integrate these new data, well‐known older observations, and observations from other regenerating systems into an outline of a model that will clarify our current understanding as well as highlight areas still to be developed.
A day of systems and synthetic biology for non‐experts
Authors: Moore Andrew 
Published: January 2009

AbstractFrom understanding ageing to the creation of artificial membrane‐bounded ‘organisms’, systems biology and synthetic biology are seen as the latest revolutions in the life sciences. They certainly represent a major change of gear, but paradigm shifts? This is open to debate, to say the least. For scientists they open up exciting ways of studying living systems, of formulating the ‘laws of life’, and the relationship between the origin of life, evolution and artificial biological systems. However, the ethical and societal considerations are probably indistinguishable from those of human genetics and genetically modified organisms. There are some tangible developments just around the corner for society, and as ever, our ability to understand the consequences of, and manage, our own progress lags far behind our technological abilities. Furthermore our educational systems are doing a bad job of preparing the next generation of scientists and non‐scientists.
Adsorption of peroxidase on Celite 545 directly from ammonium sulfate fractionated white radish (Raphanus sativus) proteins
Authors: Satar Rukhsana , Husain Qayyum 
Published: January 2009

AbstractThis paper demonstrates the direct immobilization of peroxidase from ammonium sulfate fractionated white radish proteins on an inorganic support, Celite 545. The adsorbed peroxidase was crosslinked by using glutaraldehyde. The activity yield for white radish peroxidase was adsorbed on Celite 545 was 70% and this activity was decreased and remained 60% of the initial activity after crosslinking by glutaraldehyde. The pH and temperature‐optima for both soluble and immobilized peroxidase was at pH 5.5 and 40°C. Immobilized peroxidase retained higher stability against heat and water‐miscible organic solvents. In the presence of 5.0 mM mercuric chloride, immobilized white radish peroxidase retained 41% of its initial activity while the free enzyme lost 93% activity. Soluble enzyme lost 61% of its initial activity while immobilized peroxidase retained 86% of the original activity when exposed to 0.02 mM sodium azide for 1 h. The Km values were 0.056 and 0.07 mM for free and immobilized enzyme, respectively. Immobilized white radish peroxidase exhibited lower Vmax as compared to the soluble enzyme. Immobilized peroxidase preparation showed better storage stability as compared to its soluble counterpart.
It takes two to flirt with a dimeric RNase
Authors: D'Alessio Giuseppe 
Published: January 2009

AbstractIn my long RNase‐life‐time I have had the fortune to entertain with Lelio Mazzarella what I have called special interactions, which not only advanced my knowledge of proteins but also gave pleasure, as one obtains by reading a beautiful book, an inspiring poem, or watching a very good movie. In this article, I recall the more than 30‐year long story of these interactions in which “it took two,” a structural biologist with his coworkers and a biochemist with his coworkers, to flirt with an unusual, dimeric RNase. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 989–994, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Molecular dynamics (MD) simulations of VIP and PACAP27
Authors: Corcho Francesc J. , Mokoena Paul , Bisetty Krishna , Perez Juan J. 
Published: January 2009

AbstractVasoactive intestinal peptide (VIP) and pituitary adenylate cyclase‐activating polypeptide‐27 (PACAP27) are members of the secretin‐glucagon family containing 28 and 27 residues, respectively. NMR spectroscopy studies suggest that the N‐terminus exhibit consecutive β‐turns whereas the central and C‐terminal parts of the VIP molecule have been characterized as being two α‐helices. In contrast, similar studies carried out on PACAP suggest that the shortest active peptide segment PACAP27 in the presence of trifluoroethanol (TFE) exhibits a disordered N‐terminal domain followed by a α‐helix expanding residues 9–26 with a discontinuity between residues 20 and 21. In the present study, a series of MD trajectories of VIP and PACAP27 were carried out using two different implicit models of the solvent: the Generalized Born that use an effective Born radii described by Onufriev, Bashford, and Case (GBOBC) and the Hawkins, Cramer, and Truhlar approximation (GBHCT) and two different force fields: AMBER ff99 and a modified version of the latter described by Sorin and Pande (Biophys J 2005, 88, 2472‐2493), ff99SP. Comparison of the structures obtained from the MD trajectories and those derived from the NMR studies in the literature indicates that the GBOBCmethod is more efficient in the exploration of the conformational space and presents a higher agreement with the experimental structure of VIP and PACAP27 in TFE. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 391–400, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Maltreated children's understanding of and emotional reactions to dependency court involvement
Authors: Quas Jodi A. , Wallin Allison R. , Horwitz Briana , Davis Elizabeth , Lyon Thomas D. 
Published: January 2009

AbstractLittle is known about the extent to which maltreated children understand what is happening during their participation in court proceedings, despite large numbers of children coming into contact with the legal system as victims of maltreatment. In the present study, maltreated 4‐ to 15‐year‐olds were interviewed about their understanding of dependency court on the day of their scheduled court visit. Their feelings about attending their hearings were also assessed, and after their hearing, their understanding of the decisions was examined. Age‐related improvements in children's understanding emerged. Also, children who were more knowledgeable about the legal system were less distressed about attending their hearings, as were younger children who had been in the system a longer time. Finally, a majority of children lacked full or accurate understanding of what actually happened during their hearings. Findings have implications for children's participation in legal proceedings and the development of interventions to facilitate children's legal understanding. Copyright © 2009 John Wiley & Sons, Ltd.
Violent offenses associated with co‐occurring substance use and mental health problems: Evidence from CJDATS
Authors: Sacks Stanley , Cleland Charles M. , Melnick Gerald , Flynn Patrick M. , Knight Kevin , Friedmann Peter D. , Prendergast Michael L. , Coen Carrie 
Published: January 2009

AbstractThe present study examines the relationship between substance use, mental health problems, and violence in a sample of offenders released from prison and referred to substance abuse treatment programs. Data from 34 sites (n = 1,349) in a federally funded cooperative, the Criminal Justice Drug Abuse Treatment Studies (CJDATS), were analyzed. Among parolees referred to substance abuse treatment, self‐reports for the six‐month period before the arrest resulting in their incarceration revealed frequent problems with both substance use and mental health. For most offenders with substance use problems, the quantity of alcohol consumed and the frequency of drug use were associated with a greater probability of self‐reported violence. Mental health problems were not indicative of increases in violent behavior, with the exception of antisocial personality problems, which were associated with violence. The paper emphasizes the importance of providing substance abuse treatment in relation to violent behavior among offenders with mental health problems being discharged to the community. Copyright © 2009 John Wiley & Sons, Ltd.
The Structural Diversity of Acidic Lipopeptide Antibiotics
Authors: Strieker Matthias , Marahiel Mohamed A. 
Published: January 2009

AbstractResisting resistance: Acidic lipopeptide antibiotics are very effective in fighting multidrug‐resistant Gram‐positive bacteria, including methicillin‐resistant Staphylococcus aureus and vancomycin‐resistant enterococci. The structural diversity of these lipopeptides, including daptomycin, which is already in clinical use, is depicted in this review. Engineering approaches to yield novel lipopeptides and tailoring events facilitating structural variety are presented.magnified imageAcidic lipopeptide antibiotics are a new class of potent antibiotics, which includes daptomycin, A54145, calcium‐dependent antibiotics (CDAs), friulimicins/amphomycins, laspartomycin/glycinocins and others. The importance of this novel class is exemplified by the success story of the clinically approved daptomycin, which is used for the treatment of skin infections and bacteremia caused by multidrug‐resistant bacteria, including methicillin‐resistant Staphylococcus aureus and vancomycin‐resistant enterococci. The potency of acidic lipopeptides is inherent in their chemical structure. The nonribosomally synthesized peptide cores consist of eleven to 13 amino acids, which are rigidified by the formation of a ten‐membered ring. An N‐terminal fatty acid, which facilitates insertion into the lipid bilayer of bacterial membranes, completes the structure. All these antibiotics contain multiple nonproteinogenic amino acids as well as different lipid tails; this yields remarkable structural diversity. This review summarizes the observed structural variety through a detailed description of the composition of the acidic lipopeptides. Furthermore, engineering approaches towards novel lipopeptides are presented. Recent discoveries in the field of tailoring enzymes, which enable structural plurality mainly by amino and fatty acid precursor biosynthesis, are highlighted.
Residual Dipolar Couplings in Short Peptidic Foldamers: Combined Analyses of Backbone and Side‐Chain Conformations and Evaluation of Structure Coordinates of Rigid Unnatural Amino Acids
Authors: Schmid Markus B. , Fleischmann Matthias , D'Elia Valerio , Reiser Oliver , Gronwald Wolfram , Gschwind Ruth M. 
Published: January 2009

AbstractA flexible tool for rigid systems. Residual dipolar couplings (RDCs) have proven to be valuable NMR structural parameters that provide insights into the backbone conformations of short linear peptidic foldamers, as illustrated here. This study demonstrates that RDCs at natural abundance can provide essential structural information even in the case of short linear peptides with unnatural amino acids. In addition, they allow for the detection of proline side‐chain conformations and are used as a quality check for the parameterizations of rigid unnatural amino acids.magnified image
Automated left ventricular delineation in X‐ray angiograms: A validation study
Authors: Oost Elco , Oemrawsingh Pranobe , Reiber Johan H. , Lelieveldt Boudewijn 
Published: January 2009

AbstractObjectives:Recently an automated analysis approach for left ventricular (LV) X‐ray angiographic studies was proposed. This particular study aims to assess the clinical potential of this approach.Background:Over the past 30 years much research has been carried out to develop a technique with automated contour detection of the LV outline in the end‐diastolic (ED) and end‐systolic (ES) phases. Very few have made it into clinical practice. Our latest approach is based on innovative model‐based image processing techniques.Methods:Two expert cardiologists analyzed 30 patient studies both by contouring the LV manually and by using the proposed automated methodology. In the latter procedure the experts were allowed to edit the automatically generated contours manually. The manual, automatic, and edited automatic contours were compared, focusing on accuracy, workflow efficiency, and inter‐ and intra‐observer variabilities.Results:No significant differences between the automatically derived and manual LV volumes were observed. The average patient study analysis time was reduced by 26%, from 4.2 to 3.1 min. When editing was required, 19% of the ED and 25% of the ES contour length needed manual correction. Furthermore, a reduction in inter‐observer variability of 12.4% was observed.Conclusions:Using the proposed automated methodology for X‐ray LV angiographic study analysis, a considerable reduction in required analysis time and manual effort is achieved. Because the acquired results are of clinically acceptable quality and the inter‐ and intra‐observer variabilities are reduced, this automated approach has the potential to optimize the analysis workflow for LV X‐ray angiography in clinical practice. © 2009 Wiley‐Liss, Inc.
The Effect of a Complexed Lithium Cation on a Norcarane‐Based Radical Clock
Authors: Jäger Christof M. , Hennemann Matthias , Clark Timothy 
Published: January 2009

AbstractMaking radical clocks run faster: Complexation of the 2‐norcaranyl radical to the “naked” lithium cation lowers the barrier to the “radical‐clock” rearrangement (see picture). However, model calculations on the mechanism of the hydroxylation of norcarane with cytochrome P450 suggest that no such electrostatic catalysis can be expected at the active site of the enzyme.magnified imageDensity‐functional theory (DFT) and ab initio calculations have been used to investigate the effect of a complexed lithium cation on the radical‐clock rearrangement of the 2‐norcaranyl radical to the 3‐cyclohexenylmethyl radical. As found earlier for ring‐closing radical clocks, complexation with a metal ion leads to a significant lowering of the barrier to rearrangement. DFT calculations on a model for the norcaranyl clock in cytochrome P450 confirm the two‐state reactivity proposal of Shaik et al. and indicate that the porphyrin exerts little or no electrostatic effect on the rearrangement barrier.