bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic studies with 3‐Oxo‐N‐[4‐(3‐oxo‐ 3‐phenylpropionylamino)‐phenyl]‐3‐phenylpropionamide
Authors: Abdelrazek Fathy M. , Sobhy Nehal A. , Metz Peter , Bazbouz Akram A. 
Published: January 2012

Abstract3‐Oxo‐N‐[4‐(3‐oxo‐3‐phenylpropionylamino)‐phenyl]‐3‐phenylpropionamide 1 and its derivative 2‐benzoyl‐N‐[4‐(2‐benzoyl‐3‐(dimethylamino‐acryloylamino)‐phenyl]‐3‐dimethylaminoacrylamide 12 are used for the synthesis of the hitherto not known bis‐heterocyclic amine and bis‐heterocyclic carboxamide derivatives. Plausible mechanisms are discussed for the formation of the new compounds. J. Heterocyclic Chem., (2012).
Locoregional MYCN‐amplified neuroblastoma
Authors: Morales La Madrid Andres , Volchenboum Samuel , Gastier‐Foster Julie M. , Pyatt Robert , Liu Don , Pytel Peter , Lavarino Cinzia , Rodriguez Eva , Cohn Susan L. 
Published: January 2012

AbstractMYCN‐amplification is strongly associated with other high‐risk prognostic factors and poor outcome in neuroblastoma. Infrequently, amplification of MYCN has been identified in localized tumors with favorable biologic features. Outcome for these children is difficult to predict and optimal treatment strategies remain unclear. We report a 5‐month‐old who presented with an MYCN‐amplified INSS stage 3, pelvic neuroblastoma. The tumor had favorable histology, hyperdiploidy, and lacked 1p36 and 11q23 aberrations. Although the patient met the criteria for high‐risk neuroblastoma, because of the discordant prognostic markers we elected to treat her according to an intermediate‐risk protocol. She remains event‐free more than 18 months. Pediatr Blood Cancer 2012;59:736–738. © 2011 Wiley Periodicals, Inc.
Acoustic emission testing of aboveground petroleum storage tanks: Risk assessment and lessons learned
Authors: Sánchez Martín , Cardenas Nicolas , Dominguez Veronica A. 
Published: December 2011

AbstractThis article discusses the in‐service inspection experience of aboveground storage tanks (AST) with the acoustic emission method (AE). The risk assessment is made according to the American Petroleum Institute (API) Publication 353. Weighting factors were developed to modify the risk of each AST after the AE floor inspection and conventional inspection for the shell and roof.Specific procedures are presented through the analysis of elastic waves generated in the tanks by external load. We have considered different noise sources with emphasis in sources caused by leakage of the product to comply with the Argentinian National Regulations in Leak Control. To validate the methodology, we have compared the proposed in‐service inspection and its weighting factors with the traditional inspection (e.g., with magnetic flux leakage).Finally, we have studied the signal interference which is cause from the cathodic protection system. This can lead to an incorrect analysis in the postprocessing. © 2012 American Institute of Chemical Engineers Process Saf Prog, 2012
Teens telling tales: How maternal and peer audiences support narrative identity development
Authors: McLean Kate C. , Jennings Lauren E. 
Published: December 2011

ABSTRACTPrior research has shown that parents help children to develop the requisite skills to construct an autobiographical self in past event conversations, yet research in adolescence is lacking. Further, friendships increase in importance during adolescence, and these new relationships may play a role in narrative identity development. The current study examined past event conversations between adolescents (n = 22; mean age = 13) and their friends, and adolescents and their mothers. Conversations were reliably coded for degree of personal meaning communicated and listener scaffolding behavior. Results showed that friends showed less frequent explicit scaffolding of narrative identity than mothers, although listener scaffolding behavior was associated with adolescent meaning‐making for both friends and mothers. Additional qualitative analysis of the conversations suggests that friends may be more engaged in scaffolding the self‐presentational aspects of narrative identity, as well as providing a safe arena for exploration away from mothers.
Puerto Rican adolescents’ disclosure and lying to parents about peer and risky activities: Associations with teens’ perceptions of Latino values
Authors: Villalobos Myriam , Smetana Judith G. 
Published: December 2011

ABSTRACTDisclosure and lying to mothers and fathers about different activities, as defined within social domain theory, were examined as a function of Latino family values in 109 Puerto Rican lower socioeconomic status middle adolescents (M = 15.58 years, SD = 1.18) living in the United States. Questionnaires revealed that teens sometimes disclosed to parents about their risky prudential (unhealthy or unsafe) and peer activities. Lying was infrequent, although greater for risky than for peer issues. In general, path analyses demonstrated that teens’ greater adherence to Latino family values and trust in parents were associated with more disclosure and less lying to mothers. However, these findings were moderated by the type of issue considered and perceptions of parents’ Latino family values.
Mycobacterium massilienseoutbreak after intramuscular injection, South Korea
Authors: KIM H. J. , CHO Y. , LEE S. , KOOK Y. , LEE D. , LEE J. , PARK B. J. 
Published: January 2012

SUMMARYWe conducted an epidemic investigation to discover the route of transmission and the host factors of an outbreak of post-injection abscesses. Of the 2984 patients who visited a single clinic, 77 cases were identified and 208 age- and sex-matched controls were selected for analysis. Injected medicationsper sewere not found to be responsible, and a deviation from safe injection practice suggested the likelihood of diluent contamination. Therefore the injected medications were classified according to whether there was a need for a diluent, and two medications showed a statistically significant association, i.e. injection with pheniramine [adjusted odds ratios (aOR) 5·93, 95% confidence interval (CI) 2·97–11·87] and ribostamycin (aOR 47·95, 95% CI 11·08–207·53). However, when considered concurrently, pheniramine lost statistical significance (aOR 8·71, 95% CI 0·44–171·61) suggesting that normal saline was the causative agent of this outbreak. Epidemiological evidence strongly suggested that this post-injection outbreak was caused by saline contaminated withMycobacterium massiliensewithout direct microbiological evidence.
Taking the Temperature: Implications for Adoption of Election Day Registration, State-Level Voter Turnout, and Life Expectancy
Authors: Wuffle A , Brians Craig Leonard , Coulter Kristine 
Published: January 2012

AbstractWe consider the neglected importance of temperature as an explanatory variable. We show that: (1) colder states have turnout that is high relative to the national average; (2) the coldest states in the United States were more likely to adopt Election Day Registration (EDR) than other states, and very hot states never did so; and (3) those who live in colder states live longer.
Thermostatic Voting: Presidential Elections in Light of New Policy Data
Authors: Bølstad Jørgen 
Published: January 2012

AbstractExisting studies imply a model of “thermostatic voting”—a phenomenon characterized by negative feedback from government policy to election outcomes, suggesting that a party's success in setting policy diminishes its electoral prospects. This phenomenon could give politicians an incentive to constrain the fulfillment of public demands, which would conflict with the notion of electoral accountability, which also forms part of the theoretical framework in question. This article addresses this paradox and provides new data that expand an existing time series of American policy liberalism. Employing the new data, the article identifies thermostatic voting in American presidential elections, but in light of the analysis, certain empirical features are also identified that reduce the possible incentive to withhold promised policy changes.
Improving AFM Images with Harmonic Interference by Spectral Analysis
Authors: Kiwilszo Marek , Zieliński Artur , Smulko Janusz , Darowicki Kazimierz 
Published: January 2012

AbstractAtomic force microscopy (AFM) is one of the most sensitive tools for nanoscale imaging. As such, it is very sensitive to external noise sources that can affect the quality of collected data. The intensity of the disturbance depends on the noise source and the mode of operation. In some cases, the internal noise from commercial AFM controllers can be significant and difficult to remove. Thus, a new method based on spectrum analysis of the scanned images is proposed to reduce harmonic disturbances. The proposal is a post-processing method and can be applied at any time after measurements. This article includes a few methods of harmonic cancellation (e.g., median filtering, wavelet denoising, Savitzky-Golay smoothing) and compares their effectiveness. The proposed method, based on Fourier transform of the scanned images, was more productive than the other methods mentioned before. The presented data were achieved for images of conductive layers taken in a contact AFM mode.
Specificity of Training in the Lingual Musculature
Authors: Clark Heather M. 
Published: January 2012

Purpose
Training specificity for a number of exercise parameters has been demonstrated for the limb musculature. The current study is a Phase I exploration of training specificity in the lingual musculature.

Method
Twenty-five healthy participants were assigned to 1 of 5 training conditions. Four groups completed 4 weeks of lingual exercise targeting strength, endurance, power, or speed; a control group did not exercise. Performance measures of strength, endurance, power, and speed were obtained before and after training.

Results
Although statistically significant group effects were not detected, specificity was observed with respect to effect size for the performance variables of strength, endurance, and power. Further evidence of specificity was provided by the finding that training isotonic endurance did not increase performance on an isometric endurance task. Speed training did not improve performance on any of the outcome measures, nor did speed increase following training with any of the exercises.

Conclusions
The findings provide initial evidence that training specificity may be observed in the lingual musculature. The reported effect sizes can inform future studies examining the benefit of training muscle functions underlying speech and swallowing.
Micro-chemical synthesis of molecular probes on an electronic microfluidic device
Authors: Keng Pei Yuin , Chen Supin , Ding Huijiang , Sadeghi Saman , Shah Gaurav J. , Dooraghi Alex , Phelps Michael E. , Satyamurthy Nagichettiar , Chatziioannou Arion F. , Kim Chang-Jin “CJ” , van Dam R. Michael 
Published: December 2011

We have developed an all-electronic digital microfluidic device for microscale chemical synthesis in organic solvents, operated by electrowetting-on-dielectric (EWOD). As an example of the principles, we demonstrate the multistep synthesis of [
18
F]FDG, the most common radiotracer for positron emission tomography (PET), with high and reliable radio-fluorination efficiency of [
18
F]FTAG (88 ± 7%,
n
= 11) and quantitative hydrolysis to [
18
F]FDG (> 95%,
n
= 11). We furthermore show that batches of purified [
18
F]FDG can successfully be used for PET imaging in mice and that they pass typical quality control requirements for human use (including radiochemical purity, residual solvents, Kryptofix, chemical purity, and pH). We report statistical repeatability of the radiosynthesis rather than best-case results, demonstrating the robustness of the EWOD microfluidic platform. Exhibiting high compatibility with organic solvents and the ability to carry out sophisticated actuation and sensing of reaction droplets, EWOD is a unique platform for performing diverse microscale chemical syntheses in small volumes, including multistep processes with intermediate solvent-exchange steps.
SNPdbe: constructing an nsSNP functional impacts database
Authors: Schaefer Christian , Meier Alice , Rost Burkhard , Bromberg Yana 
Published: January 2012

Abstract
Summary: Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe—SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from &gt;2600 organisms; ‘human’ being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs.
Availability: http://www.rostlab.org/services/snpdbe
Contact: schaefer@rostlab.org; snpdbe@rostlab.org
VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer
Authors: Teer Jamie K. , Green Eric D. , Mullikin James C. , Biesecker Leslie G. 
Published: January 2012

Abstract
Summary: VarSifter is a graphical software tool for desktop computers that allows investigators of varying computational skills to easily and quickly sort, filter, and sift through sequence variation data. A variety of filters and a custom query framework allow filtering based on any combination of sample and annotation information. By simplifying visualization and analyses of exome-scale sequence variation data, this program will help bring the power and promise of massively-parallel DNA sequencing to a broader group of researchers.
Availability and Implementation: VarSifter is written in Java, and is freely available in source and binary versions, along with a User Guide, at http://research.nhgri.nih.gov/software/VarSifter/.
Contact: mullikin@mail.nih.gov
Supplementary Information: Additional figures and methods available online at the journal's website.
Approximating the set of local minima in partial RNA folding landscapes
Authors: Sahoo S. , Albrecht A.A. 
Published: January 2012

Abstract
Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).
Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2Dνlnν), where n is the sequence length, ν is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.
Contact: a.albrecht@qub.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments
Authors: Sokol Serguei , Millard Pierre , Portais Jean-Charles 
Published: January 2012

Abstract
Motivation: The problem of stationary metabolic flux analysis based on isotope labelling experiments first appeared in the early 1950s and was basically solved in early 2000s. Several algorithms and software packages are available for this problem. However, the generic stochastic algorithms (simulated annealing or evolution algorithms) currently used in these software require a lot of time to achieve acceptable precision. For deterministic algorithms, a common drawback is the lack of convergence stability for ill-conditioned systems or when started from a random point.
Results: In this article, we present a new deterministic algorithm with significantly increased numerical stability and accuracy of flux estimation compared with commonly used algorithms. It requires relatively short CPU time (from several seconds to several minutes with a standard PC architecture) to estimate fluxes in the central carbon metabolism network of Escherichia coli.
Availability: The software package influx_s implementing this algorithm is distributed under an OpenSource licence at http://metasys.insa-toulouse.fr/software/influx/
Contact: jean-charles.portais@insa-toulouse.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure
Authors: Koes David Ryan , Camacho Carlos J. 
Published: January 2012

AbstractMotivation: Protein–protein interactions (PPIs) are a promising, but challenging target for pharmaceutical intervention. One approach for addressing these difficult targets is the rational design of small-molecule inhibitors that mimic the chemical and physical properties of small clusters of key residues at the protein–protein interface. The identification of appropriate clusters of interface residues provides starting points for inhibitor design and supports an overall assessment of the susceptibility of PPIs to small-molecule inhibition.Results: We extract Small-Molecule Inhibitor Starting Points (SMISPs) from protein-ligand and protein–protein complexes in the Protein Data Bank (PDB). These SMISPs are used to train two distinct classifiers, a support vector machine and an easy to interpret exhaustive rule classifier. Both classifiers achieve better than 70% leave-one-complex-out cross-validation accuracy and correctly predict SMISPs of known PPI inhibitors not in the training set. A PDB-wide analysis suggests that nearly half of all PPIs may be susceptible to small-molecule inhibition.Availability: http://pocketquery.csb.pitt.edu.Contact: dkoes@pitt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Modeling community-wide molecular networks of multicellular systems
Authors: Komurov Kakajan 
Published: January 2012

Abstract
Motivation: Multicellular systems, such as tissues, are composed of different cell types that form a heterogeneous community. Behavior of these systems is determined by complex regulatory networks within (intracellular networks) and between (intercellular networks) cells. Increasingly more studies are applying genome-wide experimental approaches to delineate the contributions of individual cell types (e.g. stromal, epithelial, vascular cells) to collective behavior of heterogeneous cell communities (e.g. tumors). Although many computational methods have been developed for analyses of intracellular networks based on genome-scale data, these efforts have not been extended toward analyzing genomic data from heterogeneous cell communities.
Results: Here, we propose a network-based approach for analyses of genome-scale data from multiple cell types to extract community-wide molecular networks comprised of intra- and intercellular interactions. Intercellular interactions in this model can be physical interactions between proteins or indirect interactions mediated by secreted metabolites of neighboring cells. Applying this method on data from a recent study on xenograft mouse models of human lung adenocarcinoma, we uncover an extensive network of intra- and intercellular interactions involved in the acquired resistance to angiogenesis inhibitors.
Contact: kakajan.komurov@cchmc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
Authors: DeJongh Matthew , Bockstege Benjamin , Frybarger Paul , Hazekamp Nicholas , Kammeraad Joshua , McGeehan Travis 
Published: January 2012

Abstract
Summary: CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizations are useful for understanding organism-specific biochemistry and for highlighting the results of flux variability analysis experiments.
Availability and Implementation: Freely available for download on the web at http://sourceforge.net/projects/cytoseed/. Implemented in Java SE 6 and supported on all platforms that support Cytoscape.
Contact: dejongh@hope.edu
Supplementary information: Installation instructions, a tutorial, and full-size figures are available at http://www.cs.hope.edu/cytoseed/.
SHORT GRAIN1 Decreases Organ Elongation and Brassinosteroid Response in Rice
Authors: Nakagawa Hitoshi , Tanaka Atsunori , Tanabata Takanari , Ohtake Miki , Fujioka Shozo , Nakamura Hidemitsu , Ichikawa Hiroaki , Mori Masaki 
Published: December 2011

Abstract
We identified a short-grain mutant (Short grain1 (Sg1) Dominant) via phenotypic screening of 13,000 rice (Oryza sativa) activation-tagged lines. The causative gene, SG1, encodes a protein with unknown function that is preferentially expressed in roots and developing panicles. Overexpression of SG1 in rice produced a phenotype with short grains and dwarfing reminiscent of brassinosteroid (BR)-deficient mutants, with wide, dark-green, and erect leaves. However, the endogenous BR level in the SG1 overexpressor (SG1:OX) plants was comparable to the wild type. SG1:OX plants were insensitive to brassinolide in the lamina inclination assay. Therefore, SG1 appears to decrease responses to BRs. Despite shorter organs in the SG1:OX plants, their cell size was not decreased in the SG1:OX plants. Therefore, SG1 decreases organ elongation by decreasing cell proliferation. In contrast to the SG1:OX plants, RNA interference knockdown plants that down-regulated SG1 and a related gene, SG1-LIKE PROTEIN1, had longer grains and internodes in rachis branches than in the wild type. Taken together, these results suggest that SG1 decreases responses to BRs and elongation of organs such as seeds and the internodes of rachis branches through decreased cellular proliferation.