bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChemInform Abstract: A Novel and Facile Synthesis of Barbatusol Methyl Ether.
Authors: WANG X. , CUI Y. , PAN X. , CHEN Y. 
Published: August 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: A Radical Prototype to Steroids: Synthesis of d,l‐5α‐D‐ Homoandrostane‐4α‐methyl‐3,17a‐dione.
Authors: ZORETIC P. A. , CHEN Z. , ZHANG Y. , RIBEIRO A. A. 
Published: August 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Synthesis and Antibacterial Activity of 1‐β‐Methylcarbapenems ( VIII) Having a 1,3‐Diazabicyclo(3.3.0)octan‐4‐one Moiety
Authors: NAM K. H. , OH C.‐H. , CHO J. K. , KIM H. J. , LEE K.‐S. , CHO J.‐H. 
Published: August 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Catalytic Dimerization of Alkyl Acrylates
Authors: TEMBE G. L. , BANDYOPADHYAY A. R. , GANESHPURE P. A. , SATISH S. 
Published: August 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: The Chemistry of C‐Sulfonyldithioformates
Authors: YASSIN S. M. 
Published: August 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Overview of Modern Magnetism
Authors: COEY J. M. D. 
Published: August 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A pediatric phase I trial and pharmacokinetic study of ispinesib: A Children's Oncology Group phase I consortium study
Authors: Souid Abdul‐Kader , Dubowy Ronald L. , Ingle Ashish M. , Conlan Maureen G. , Sun Junfeng , Blaney Susan M. , Adamson Peter C. 
Published: August 2010

AbstractPurposeTo determine the maximum‐tolerated dose, dose‐limiting toxicities, and pharmacokinetics of the kinesin spindle protein inhibitor ispinesib in pediatric patients with recurrent or refractory solid tumors.Subjects and MethodsIspinesib was administered as 1‐hr intravenous infusion weekly × 3, every 28 days. Cohorts of 3–6 patients were enrolled at 5, 7, 9, and 12 mg/m2/dose. Serial plasma samples for pharmacokinetic analyses were obtained after the first dose.ResultsTwenty‐four (13 females) patients with a median (range) age of 10 years (1–19) were enrolled in the study. At the 12 mg/m2 dose level dose‐limiting neutropenia occurred in 2/6 patients and hyperbilirubinemia in 1/6 patients, while at the 9 mg/m2 dose level 1/6 patients had dose‐limiting neutropenia. There were no objective responses, but three patients (diagnoses of anaplastic astrocytoma, alveolar soft part sarcoma, and ependymoblastoma) had stable disease for 4–7 courses. There was substantial interpatient variation in drug disposition. The median (range) terminal elimination half‐life was 16 (8–44) hr and the plasma drug clearance was 5 (1–14) L/hr/m2.ConclusionsThe maximum tolerated and recommended phase II dose for ispinesib administered weekly × 3 every 28 days for children with solid tumors is 9 mg/m2/dose. Plans for a phase II trial in select pediatric solid tumors are in development. Pediatr Blood Cancer. 2010;55:1323–1328. © 2010 Wiley‐Liss, Inc.
Race‐specific transition patterns among alcohol use classes in adolescent girls
Authors: Dauber Sarah E. , Paulson James F. , Leiferman Jenn A. 
Published: August 2010

ABSTRACTWe used data from the National Longitudinal Study of Adolescent Health to examine transitions among alcohol use classes in 2225 White and African American adolescent girls, and race differences in predictors of transition into and out of problematic drinking classes. Latent class analysis confirmed four classes for White girls and three for AA girls, defined in a previous study. Latent transition analysis revealed more stable abstainers and decreasing alcohol use among AA girls, and more increasing alcohol use among White girls, though stable abstainers were the largest group in both races. Increasing use was predicted by delinquency, academic misbehavior, substance use, and peer support for White girls, and by older age and delinquency for AA girls. Decreasing use was predicted by older age and depressive symptoms for White girls, and by family relationship quality and substance use for AA girls. Study limitations and implications of findings are discussed.
Madonna or Don McLean? The effect of order of exposure on relative liking
Authors: Pandelaere Mario , Millet Kobe , Van den Bergh Bram 
Published: August 2010

AbstractWhile many studies have shown that exposure frequency affects consumer attitudes and preferences, the current paper provides evidence that exposure order also does so. Three studies show that people like stimuli to which they are first exposed better than later encountered, similar stimuli. Controlling for exposure frequency and duration, individuals prefer the version of a song they heard first to a version they heard later and images they saw first to mirror images they saw later. In addition, our results suggest that perceived originality contributes to the preference for a first encountered stimulus. Our results are discussed in relation to research on order effects in sequential rating formats.
Nutritional Factors That Influence Change in Bone Density and Stress Fracture Risk Among Young Female Cross‐Country Runners
Authors: Nieves Jeri W. , Melsop Kathryn , Curtis Meredith , Kelsey Jennifer L. , Bachrach Laura K. , Greendale Gail , Sowers Mary Fran , Sainani Kristin L. 
Published: August 2010

ObjectiveTo identify nutrients, foods, and dietary patterns associated with stress fracture risk and changes in bone density among young female distance runners.Design and SettingTwo‐year, prospective cohort study. Observational data were collected in the course of a multicenter randomized trial of the effect of oral contraceptives on bone health.ParticipantsOne hundred and twenty‐five female competitive distance runners ages 18‐26 years.Assessment of Risk FactorsDietary variables were assessed with a food frequency questionnaire.Main Outcome MeasurementsBone mineral density and content (BMD/BMC) of the spine, hip, and total body were measured annually by dual x‐ray absorptiometry (DEXA). Stress fractures were recorded on monthly calendars, and had to be confirmed by radiograph, bone scan, or magnetic resonance imaging.ResultsSeventeen participants had at least one stress fracture during follow‐up. Higher intakes of calcium, skim milk, and dairy products were associated with lower rates of stress fracture. Each additional cup of skim milk consumed per day was associated with a 62% reduction in stress fracture incidence (P < .05); and a dietary pattern of high dairy and low fat intake was associated with a 68% reduction (P < .05). Higher intakes of skim milk, dairy foods, calcium, animal protein, and potassium were associated with significant (P < .05) gains in whole‐body BMD and BMC. Higher intakes of calcium, vitamin D, skim milk, dairy foods, potassium, and a dietary pattern of high dairy and low fat were associated with significant gains in hip BMD.ConclusionsIn young female runners, low‐fat dairy products and the major nutrients in milk (calcium, vitamin D, and protein) were associated with greater bone gains and a lower stress fracture rate. Potassium intake was also associated with greater gains in hip and whole‐body BMD.
A cell-based simulation software for multi-cellular systems
Authors: Hoehme Stefan , Drasdo Dirk 
Published: August 2010

Abstract
CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multi-cellular systems in 2D and 3D. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. The software includes many modules specifically tailored to support the simulation and analysis of virtual tissues including real-time 3D visualization and VRML 2.0 support. All cell and environment parameters can be independently varied which facilitates species specific simulations and allows for detailed analyses of growth dynamics and links between cellular and multi-cellular phenotypes.
Availability: CellSys is freely available for non-commercial use at http://msysbio.com/software/cellsys. The current version of CellSys permits the simulation of growing monolayer cultures and avascular tumor spheroids in liquid environment. Further functionality will be made available ongoing with published papers.
Contact: hoehme@izbi.uni-leipzig.de; dirk.drasdo@inria.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Search and clustering orders of magnitude faster than BLAST
Authors: Edgar Robert C. 
Published: August 2010

Abstract
Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.
Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch
Contact: robert@drive5.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Text mining meets workflow: linking U-Compare with Taverna
Authors: Kano Yoshinobu , Dobson Paul , Nakanishi Mio , Tsujii Jun'ichi , Ananiadou Sophia 
Published: August 2010

Abstract
Summary: Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare to Taverna, a generic workflow system, to expose text mining functionality to the bioinformatics community.
Availability: http://u-compare.org/taverna.html, http://u-compare.org
Contact: kano@is.s.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
Authors: Lachmann Alexander , Xu Huilei , Krishnan Jayanth , Berger Seth I. , Mazloom Amin R. , Ma'ayan Avi 
Published: August 2010

Abstract
Motivation: Experiments such as ChIP-chip, ChIP-seq, ChIP-PET and DamID (the four methods referred herein as ChIP-X) are used to profile the binding of transcription factors to DNA at a genome-wide scale. Such experiments provide hundreds to thousands of potential binding sites for a given transcription factor in proximity to gene coding regions.
Results: In order to integrate data from such studies and utilize it for further biological discovery, we collected interactions from such experiments to construct a mammalian ChIP-X database. The database contains 189 933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31 932 target genes. We used the database to analyze mRNA expression data where we perform gene-list enrichment analysis using the ChIP-X database as the prior biological knowledge gene-list library. The system is delivered as a web-based interactive application called ChIP Enrichment Analysis (ChEA). With ChEA, users can input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The ChEA database allowed us to reconstruct an initial network of transcription factors connected based on shared overlapping targets and binding site proximity. To demonstrate the utility of ChEA we present three case studies. We show how by combining the Connectivity Map (CMAP) with ChEA, we can rank pairs of compounds to be used to target specific transcription factor activity in cancer cells.
Availability: The ChEA software and ChIP-X database is freely available online at: http://amp.pharm.mssm.edu/lib/chea.jsp
Contact: avi.maayan@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Increased Activity of the Vacuolar Monosaccharide Transporter TMT1 Alters Cellular Sugar Partitioning, Sugar Signaling, and Seed Yield in Arabidopsis
Authors: Wingenter Karina , Schulz Alexander , Wormit Alexandra , Wic Stefan , Trentmann Oliver , Hoermiller Imke I. , Heyer Arnd G. , Marten Irene , Hedrich Rainer , Neuhaus H. Ekkehard 
Published: August 2010

Abstract
The extent to which vacuolar sugar transport activity affects molecular, cellular, and developmental processes in Arabidopsis (Arabidopsis thaliana) is unknown. Electrophysiological analysis revealed that overexpression of the tonoplast monosaccharide transporter TMT1 in a tmt1-2::tDNA mutant led to increased proton-coupled monosaccharide import into isolated mesophyll vacuoles in comparison with wild-type vacuoles. TMT1 overexpressor mutants grew faster than wild-type plants on soil and in high-glucose (Glc)-containing liquid medium. These effects were correlated with increased vacuolar monosaccharide compartmentation, as revealed by nonaqueous fractionation and by chlorophyllab-binding protein1 and nitrate reductase1 gene expression studies. Soil-grown TMT1 overexpressor plants respired less Glc than wild-type plants and only about half the amount of Glc respired by tmt1-2::tDNA mutants. In sum, these data show that TMT activity in wild-type plants limits vacuolar monosaccharide loading. Remarkably, TMT1 overexpressor mutants produced larger seeds and greater total seed yield, which was associated with increased lipid and protein content. These changes in seed properties were correlated with slightly decreased nocturnal CO2 release and increased sugar export rates from detached source leaves. The SUC2 gene, which codes for a sucrose transporter that may be critical for phloem loading in leaves, has been identified as Glc repressed. Thus, the observation that SUC2 mRNA increased slightly in TMT1 overexpressor leaves, characterized by lowered cytosolic Glc levels than wild-type leaves, provided further evidence of a stimulated source capacity. In summary, increased TMT activity in Arabidopsis induced modified subcellular sugar compartmentation, altered cellular sugar sensing, affected assimilate allocation, increased the biomass of Arabidopsis seeds, and accelerated early plant development.
Rapid Assessment of Gene Function in the Circadian Clock Using Artificial MicroRNA in Arabidopsis Mesophyll Protoplasts
Authors: Kim Jeongsik , Somers David E. 
Published: August 2010

Abstract
Rapid assessment of the effect of reduced levels of gene products is often a bottleneck in determining how to proceed with an interesting gene candidate. Additionally, gene families with closely related members can confound determination of the role of even a single one of the group. We describe here an in vivo method to rapidly determine gene function using transient expression of artificial microRNAs (amiRNAs) in Arabidopsis (Arabidopsis thaliana) mesophyll protoplasts. We use a luciferase-based reporter of circadian clock activity to optimize and validate this system. Protoplasts transiently cotransfected with promoter-luciferase and gene-specific amiRNA plasmids sustain free-running rhythms of bioluminescence for more than 6 d. Using both amiRNA plasmids available through the Arabidopsis Biological Resource Center, as well as custom design of constructs using the Weigel amiRNA design algorithm, we show that transient knockdown of known clock genes recapitulates the same circadian phenotypes reported in the literature for loss-of-function mutant plants. We additionally show that amiRNA designed to knock down expression of the casein kinase II β-subunit gene family lengthens period, consistent with previous reports of a short period in casein kinase II β-subunit overexpressors. Our results demonstrate that this system can facilitate a much more rapid analysis of gene function by obviating the need to initially establish stably transformed transgenics to assess the phenotype of gene knockdowns. This approach will be useful in a wide range of plant disciplines when an endogenous cell-based phenotype is observable or can be devised, as done here using a luciferase reporter.
The Type IIArabidopsisFormin14 Interacts with Microtubules and Microfilaments to Regulate Cell Division
Authors: Li Yanhua , Shen Yuan , Cai Chao , Zhong Chenchun , Zhu Lei , Yuan Ming , Ren Haiyun 
Published: August 2010

AbstractFormins have long been known to regulate microfilaments but have also recently been shown to associate with microtubules. In this study, Arabidopsis thaliana FORMIN14 (AFH14), a type II formin, was found to regulate both microtubule and microfilament arrays. AFH14 expressed in BY-2 cells was shown to decorate preprophase bands, spindles, and phragmoplasts and to induce coalignment of microtubules with microfilaments. These effects perturbed the process of cell division. Localization of AFH14 to microtubule-based structures was confirmed in Arabidopsis suspension cells. Knockdown of AFH14 in mitotic cells altered interactions between microtubules and microfilaments, resulting in the formation of an abnormal mitotic apparatus. In Arabidopsis afh14 T-DNA insertion mutants, microtubule arrays displayed abnormalities during the meiosis-associated process of microspore formation, which corresponded to altered phenotypes during tetrad formation. In vitro biochemical experiments showed that AFH14 bound directly to either microtubules or microfilaments and that the FH2 domain was essential for cytoskeleton binding and bundling. However, in the presence of both microtubules and microfilaments, AFH14 promoted interactions between microtubules and microfilaments. These results demonstrate that AFH14 is a unique plant formin that functions as a linking protein between microtubules and microfilaments and thus plays important roles in the process of plant cell division.
Financial barriers to the adoption of anaerobic digestion on US livestock operations
Authors: Gloy Brent A. , Dressler Jonathan B. 
Published: August 2010

PurposeAnaerobic digestion (AD) of livestock waste is a potential source of renewable energy and can reduce the methane emissions associated with livestock waste storage. Because AD is capital intensive, lenders will play a key role in the adoption of this technology. The purpose of this paper is to describe some of the barriers that currently make lenders reluctant to finance AD systems and provide recommendations for public policies that would reduce these barriers, making financing more available and encouraging farmers to adopt digester systems.Design/methodology/approachThis paper describes some of the barriers that currently make lenders reluctant to finance AD systems and makes recommendations for public policies that would reduce these barriers, thus making finance available.FindingsAD systems face a number of financial barriers which make lenders reluctant to finance them. Many of these barriers can be overcome by adopting policies and programs designed to improve the understanding of the financial situation associated with AD adoption and establishing markets that reward livestock operations for achieving the benefits associated with AD installation. Some of the more important potential solutions include developing mechanisms to collect and analyze data associated with AD system economics and developing markets that reward livestock operations for producing the non‐market outputs of renewable energy and methane emission reductions.Originality/valueThe ability to attract financing is a key barrier to the widespread adoption of anaerobic digester systems. This paper describes these challenges and identifies solutions which would reduce these barriers and lead to greater adoption of AD on the US livestock operations.
On the systemic nature of weather risk
Authors: Xu Wei , Filler Guenther , Odening Martin , Okhrin Ostap 
Published: August 2010

PurposeThe purpose of this paper is to assess the losses of weather‐related insurance at different regional levels. The possibility of spatial diversification of insurance is explored by estimating the joint occurrence on unfavorable weather conditions in different locations, looking particularly at the tail behavior of the loss distribution.Design/methodology/approachJoint weather‐related losses are estimated using copulas. Copulas avoid the direct estimation of multivariate distributions but allow for much greater flexibility in modeling the dependence structure of weather risks compared with simple correlation coefficients.FindingsResults indicate that indemnity payments based on temperature as well as on cumulative rainfall show strong stochastic dependence even at a large regional scale. Thus the possibility to reduce risk exposure by increasing the trading area of insurance is limited.Research limitations/implicationsThe empirical findings are limited by a rather weak database. In that case the estimation of high‐dimensional copulas leads to large estimation errors.Practical implicationsThe paper includes implications for the quantification of systemic weather risk which is important for the rate making of crop insurance and reinsurance.Originality/valueThis paper's results highlight how important the choice of the statistical approach is when modeling the dependence structure of weather risks.