bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating a Product Donation Program: Challenges for Charitable Capacity
Authors: Gazley Beth , Abner Gordon 
Published: December 2013

AbstractThis article offers one of the first efforts at describing the impact of a national product donation program. Despite the importance of in‐kind giving to the corporate and charitable sectors, little research has explained how in‐kind gifts are used effectively once they leave the donor's hands. In this study we examine outcomes and impacts associated with a product donation program, including numbers served, a faith‐based mission, the ability to process product donations effectively, the extent of performance measurement, and the effect of program experience on continued participation. Data come from Good360's Framing Hope program, a partnership between The Home Depot stores and local charities across the United States. Our findings support the organizational capacity literature in suggesting that experience with this program only partly mitigates the challenges of participation and that success may be due to how central the program is to organizational objectives.
Democratic Values and Civic Engagement of Local Voluntary Associations
Authors: Lundåsen Susanne Wallman 
Published: December 2013

AbstractIn this study I investigate whether and to what extent local voluntary associations in Sweden maintain values of democratic governance. The study is based upon a survey of about 400 local voluntary associations within four local communities. The results show that a vast majority of these associations are supportive of member influence and governance through internal democracy. These values can also explain civic engagement of these local voluntary associations. The results indicate that if these values would change radically it would probably have an impact on civic engagement of these organizations, but at present the support remains solid.
Mechanism of pro‐tumorigenic effect of BMP‐6: Neovascularization involving tumor‐associated macrophages and IL‐1α
Authors: Kwon Seok Joo , Lee Geun Taek , Lee Jae‐Ho , Iwakura Yoichiro , Kim Wun‐Jae , Kim Isaac Yi 
Published: December 2013

AbstractINTRODUCTIONOverexpression of bone morphogenetic protein‐6 (BMP‐6) has been reported in human prostate cancer tissues. Previously we have demonstrated that BMP‐6 enhances prostate cancer growth in mice and not in tissue culture. Herein, we have investigated the mechanism of BMP‐6's pro‐tumorigenic effect in prostate cancer.METHODSTramp C2 murine and LNCaP human prostate cancer cell lines were co‐cultured with RAW 264.7 and THP‐1 cells, respectively. IL‐1α knockout mice were used to confirm the role of BMP‐6/IL‐1α loop in vivo. Lastly, conditional macrophage null mice cd11b‐DTR was used.RESULTSThe results demonstrated that BMP‐6 induced the expression of IL‐1α in macrophages via a cross‐talk between NF‐κB1 p50 and Smad1. When endothelial cells were treated with conditioned media harvested from macrophages incubated with BMP‐6, tube formation was detected. In the presence of IL‐1α neutralizing antibody, endothelial tube formation was blocked. In vivo, tumor growth and neovascularization decreased significantly when BMP‐6 was expressed in IL‐1α knockout and conditional macrophage‐null mice.CONCLUSIONSProstate cancer‐derived BMP‐6 stimulates tumor‐associated macrophages to produce IL‐1α through a crosstalk between Smad1 and NF‐κB1; IL‐1α, in turn, promotes angiogenesis and prostate cancer growth. Prostate 74:121–133, 2014. © 2013 Wiley Periodicals, Inc.
Protonation states of active‐site lysines of penicillin‐binding protein 6 from Escherichia coli and the mechanistic implications
Authors: Kumarasiri Malika , Zhang Weilie , Shi Qicun , Fisher Jed F. , Mobashery Shahriar 
Published: December 2013

ABSTRACTThe protonation states of the two active‐site lysines (Lys69 and Lys235) of PBP 6 of Escherichia coli were explored to understand the active site chemistry of this enzyme. Each lysine was individually mutated to cysteine, and the resultant two mutant proteins were purified to homogeneity. Each protein was denatured, and its cysteine was chemically modified to produce an S‐aminoethylated cysteine (γ‐thialysine) residue. Following renaturation, the evaluation of the kinetics of the dd‐carboxypeptidase activity of PBP 6 as a function of pH was found consistent with one lysine in its free‐base (Lys69) and the other in the protonated state (Lys235) for optimal catalysis. The experimental estimates for their pKa values were compared with the pKa values calculated computationally, using molecular‐dynamics simulations and a thermodynamic cycle. Study of the γ‐thialysine69 showed that lysine at position 69 influenced the basic limb of catalysis, consistent with the fact that the two lysine side chains are in proximity to each other in the active site. Based on these observations, a reaction sequence for PBP 6 is proposed, wherein protonated Lys235 serves as the electrostatic substrate anchor and Lys69 as the conduit for protons in the course of the acylation and deacylation half‐reactions. Proteins 2014; 82:1348–1358. © 2013 Wiley Periodicals, Inc.
Thicknesses of individual layers of artery wall indicate increased cardiovascular risk in severe pre‐eclampsia
Authors: Akhter T. , Larsson M. , Wikström A. K. , Naessen T. 
Published: December 2013

ABSTRACTObjectiveTo assess whether thicknesses of the intima and media in the common carotid artery (CCA) and the intima/media ratio (I/M) indicate an increased cardiovascular risk in non‐pregnant women with a history of previous severe pre‐eclampsia.MethodsThicknesses of the CCA intima and media layers were measured using non‐invasive high‐frequency (22 MHz) ultrasound in 42 women with a history of severe pre‐eclampsia and 44 women with previous normal pregnancy.ResultsWomen with a history of severe pre‐eclampsia had a thicker CCA intima and a higher I/M than had women with previous normal pregnancy, also after adjustment for mean arterial pressure, body mass index and CCA intima–media thickness (IMT) (all P < 0.0001). CCA‐IMT did not differ significantly between groups. In receiver–operating characteristics curve analysis, intima thickness and I/M clearly discriminated between women with and those without previous pre‐eclampsia (area under the receiver–operating characteristics curve (AUC), 0.98 and 0.93), whereas CCA‐IMT did not (AUC, 0.52).ConclusionsCCA individual intima and media thicknesses as well as I/M, but not CCA‐IMT, reflect the known increased long-term cardiovascular risk of pre‐eclampsia. Estimation of individual CCA layers using high‐frequency ultrasound appears preferable to measuring CCA‐IMT for investigating arterial effects and the increased cardiovascular risk in women with a history of severe pre‐eclampsia. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.
B‐flow ultrasound facilitates visualization of contrast medium during hysterosalpingo‐contrast sonography
Authors: Sladkevicius P. , Zannoni L. , Valentin L. 
Published: December 2013

ABSTRACTObjectiveTo assess if B‐flow ultrasound improves visualization of flow of contrast medium in the Fallopian tubes during hysterosalpingo‐contrast sonography (HyCoSy) compared with grayscale ultrasound.MethodsThis prospective observational study included 160 women referred for HyCoSy as part of infertility work‐up between January 2011 and September 2012. In each woman, at the same session, HyCoSy was performed first using saline with air and then using Sonovue®, and for each contrast medium, grayscale ultrasound was first used and then B‐flow ultrasound was used. Flow of contrast was observed in three parts of each tube: intramural, middle and distal.ResultsIn 129 (81%) women, flow of Sonovue was observed in the intramural part of both tubes and in the pouch of Douglas when using grayscale ultrasound. In these women, flow of Sonovue was seen in the middle part of 70% of the 258 tubes when using grayscale ultrasound and in 93% when using B‐flow ultrasound; and in the distal part in 81% when using grayscale ultrasound and in 98% when using B‐flow ultrasound. When using air and saline, flow was seen in the intramural part of 90% and 93% of the tubes, in the middle part in 54% and 72%, and in the distal part in 66% and 90%, using grayscale ultrasound and B‐flow ultrasound, respectively.ConclusionB‐flow ultrasound facilitates detection of flow of contrast in the middle and distal parts of the tubes at HyCoSy, especially when a mixture of saline and air is used as contrast medium. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd
Global disorders of consciousness
Authors: Bayne Tim , Hohwy Jakob 
Published: December 2013

In recent decades there has been a great deal of interest in global disorders of consciousness, such as the vegetative state, the minimally conscious state, and epileptic absence seizures. Global disorders of consciousness pose significant challenges to consciousness science in that the ordinary pretheoretical criteria for the ascription of consciousness are not easily applied in such contexts, and it is often unclear what kinds of conscious states—if any—patients are in. At the same time, global disorders of consciousness also promise to reveal a great deal about the nature of consciousness and the relationship between consciousness and cognitive and behavioral control. WIREs Cogn Sci 2014, 5:129–138. doi: 10.1002/wcs.1270This article is categorized under:

Philosophy > Consciousness
Document visualization: an overview of current research
Authors: Gan Qihong , Zhu Min , Li Mingzhao , Liang Ting , Cao Yu , Zhou Baoyao 
Published: December 2013

As the number of sources and quantity of document information explodes, efficient and intuitive visualization tools are desperately needed to assist users in understanding the contents and features of a document, while discovering hidden information. This overview introduces fundamental concepts of and designs for document visualization, a number of representative methods in the field, and challenges as well as promising directions of future development. The focus is on explaining the rationale and characteristics of representative document visualization methods for each category. A discussion of the limitations of our classification and a comparison of reviewed methods are presented at the end. This overview also aims to point out theoretical and practical challenges in document visualization. WIREs Comput Stat 2014, 6:19–36. doi: 10.1002/wics.1285This article is categorized under:

Algorithms and Computational Methods > Computer Graphics
Statistical Learning and Exploratory Methods of the Data Sciences > Text Mining
Examining missing data mechanisms via homogeneity of parameters, homogeneity of distributions, and multivariate normality
Authors: Jamshidian Mortaza , Yuan Ke‐Hai 
Published: December 2013

This paper reviews various methods of identifying missing data mechanisms. The three well‐known mechanisms of missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR) are considered. A number of tests deem rejection of homogeneity of means and/or covariances (HMC) among observed data patterns as a means to reject MCAR. Utility of these tests as well as their shortcomings are discussed. In particular, examples of MAR and MNAR data with homogeneous means and covariances between their observed data patterns are provided for which tests of HMC fail to reject MCAR. More generally, tests of homogeneity of parameter estimates between various subsets of data are reviewed and their utility as tests of MCAR and MAR (in special cases) is pointed out. Since many tests of MCAR assume multinormality, methods to assess this assumption in the context of incomplete data are reviewed. Tests of homogeneity of distributions among observed data patterns for MCAR are also considered. A new nonparametric test of this type is proposed on the basis of pairwise comparison of marginal distributions. Finally, methods of examining missing data mechanism based on sensitivity analysis including methods that model missing data mechanism based on logistic, probit, and latent variable regression models, as well as methods that do not require modeling of missing data mechanism are reviewed. The paper concludes with some practical comments about the validity and utility of tests of missing data mechanism. WIREs Comput Stat 2014, 6:56–73. doi: 10.1002/wics.1287This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Applications of Computational Statistics > Psychometrics
Investigation into the effects of prenatal alcohol exposure on postnatal spine development and expression of synaptophysin and PSD95 in rat hippocampus
Authors: Elibol‐Can Birsen , Kilic Ertugrul , Yuruker Sinan , Jakubowska‐Dogru Ewa 
Published: December 2013

AbstractEthanol is known as a potent teratogen responsible for the fetal alcohol syndrome characterized by cognitive deficits especially pronounced in juveniles but ameliorating in adults. Since the mechanisms of these deficits and following partial recovery are not fully elucidated, the aim of the present study was to investigate the process of synaptogenesis in the hippocampus over the first two months of life in control and fetal‐alcohol rats. Ethanol was delivered to the pregnant dams by intragastric intubation throughout 7–21 gestation days at the daily dose of 6 g/kg generating a mean blood alcohol level of 246.6 ± 40.9 mg/dl on gestation day 20. The spine densities as well as the expression of pre‐ and postsynaptic proteins, synaptophysin (SYP) and PSD‐95 protein, were evaluated for three distinct hippocampal regions: CA1, CA2+3, and DG and four postnatal days: PD1, PD10, PD30 and PD60, independently. Our results confirmed an intensive synaptogenesis within the brain spurt period (first 10 postnatal days), however, the temporal pattern of changes in the SYP and PSD‐95 expression was different. The ethanol exposure during half of the 1st and the whole 2nd human trimester equivalent resulted in an overall trend toward lower values of synaptic indices at PD1 with a fast recovery from these deficits observed already at PD10. At PD30, around the age when the most pronounced behavioral deficits have been previously reported in juvenile fetal‐alcohol subjects, no significant changes were found in either the hippocampal levels of synaptic proteins or in the spine density in principal hippocampal neurons.
Developing novel blood‐based biomarkers for Alzheimer's disease
Authors: Snyder Heather M. , Carrillo Maria C. , Grodstein Francine , Henriksen Kim , Jeromin Andreas , Lovestone Simon , Mielke Michelle M. , O'Bryant Sid , Sarasa Manual , Sj⊘gren Magnus , Soares Holly , Teeling Jessica , Trushina Eugenia , Ward Malcolm , West Tim , Bain Lisa J. , Shineman Diana W. , Weiner Michael , Fillit Howard M. 
Published: December 2013

AbstractAlzheimer's disease is the public health crisis of the 21st century. There is a clear need for a widely available, inexpensive and reliable method to diagnosis Alzheimer's disease in the earliest stages, track disease progression, and accelerate clinical development of new therapeutics. One avenue of research being explored is blood based biomarkers. In April 2012, the Alzheimer's Association and the Alzheimer's Drug Discovery Foundation convened top scientists from around the world to discuss the state of blood based biomarker development. This manuscript summarizes the meeting and the resultant discussion, including potential next steps to move this area of research forward.
Zur deutschen Adaptation der Neuropsychological Assessment Battery (NAB)
Authors: Buczylowska Dorota , Bornschlegl Mona , Daseking Monika , Jäncke Lutz , Petermann Franz 
Published: December 2013

Standardisierte Testverfahren bilden einen wichtigen Bestandteil neuropsychologischer Diagnostik. Im deutschsprachigen Raum besteht ein großer Bedarf für eine einheitlich normierte neuropsychologische Testbatterie. Die Neuropsychological Assessment Battery (NAB) ist ein in den USA entwickeltes Verfahren zur Beurteilung der neuropsychologischen Funktionen bei Erwachsenen (Alter 18 – 97 Jahre). Die NAB besteht aus zwei äquivalenten Parallelformen, die jeweils in sechs Module untergliedert sind: Screening, Aufmerksamkeit, Sprache, Gedächtnis, Wahrnehmung und Exekutive Funktionen. Das Verfahren ermöglicht eine umfangreiche, psychometrisch fundierte und ökologisch valide Diagnostik. Die NAB wird im Hinblick auf die Entstehungsgeschichte, psychometrische Güte und bisherige Rezeption präsentiert. Die Autorengruppe arbeitet zurzeit an der deutschen Adaptation und Normierung der NAB.
Observation of glass-like low-temperature anomalies in the acoustic properties of nanostructured metals
Authors: Natsik V. D. , Vatazhuk E. N. , Pal-Val P. P. , Pal-Val L. N. , Moskalenko V. A. 
Published: December 2013

The values and temperature dependences of the dynamic Young's modulus E(T) of two metals (Ti, Zr) in crystalline (CR) and nanostructured (NS) states are measured by the composite vibrator method at a frequency of ω = 5·105 s−1 over temperatures of 2–20 K. The transition from CR (coarse grained polycrystals) to NS (ultra-fine grained polycrystals) is induced by severe plastic deformation (SPD). The transition of the metals into the NS state is found to be accompanied by a softening of the modulus by a few percent and by the appearance of a distinctive feature in the ENS(T) curves: a transition from a logarithmic to a power-law dependence with increasing temperature at a crossover temperature Tc ≈ 6–8 K, a behavior typical of the elastic moduli of glasses. Structural distortions in the NS state with atomic disorder properties (a glass subsystem or “phase”) are interpreted in terms of dislocation concepts because of the accumulation of high densities of dislocations in metals with random configurations of the dislocation lines induced by SPD. In an appendix the dynamic properties of the dislocation lines fragments are compared, and an analogy established, with the dynamics of quasi-local excitations in glasses (so-called two-level tunnel systems and harmonic oscillators), which are invoked in the theory of glasses to describe their low-temperature properties.
Optical and carrier transport properties of graphene oxide based crystalline-Si/organic Schottky junction solar cells
Authors: Khatri I. , Tang Z. , Hiate T. , Liu Q. , Ishikawa R. , Ueno K. , Shirai H. 
Published: December 2013

We investigated the graphene oxide (GO) based n-type crystalline silicon (c-Si)/conductive poly(ethylene dioxythiophene):poly(styrenesulfonate)(PEDOT:PSS) Schottky junction devices with optical characterization and carrier transport measurement techniques. The optical transmittance in the UV region decreased markedly for the films with increasing the concentration of GO whereas it increased markedly in the visible-infrared regions. Spectroscopic ellipsometry revealed that the ordinary and extraordinary index of refraction increased with increasing the concentration of GO. The hole mobility also increased from 1.14 for pristine film to 1.85 cm2/V s for the 12–15 wt. % GO modified film with no significant increases of carrier concentration. The highest conductivity was found for a 15 wt. % GO modified PEDOT:PSS film: the c-Si/PEDOT:PSS:GO device using this sample exhibited a relatively high power conversion efficiency of 11.04%. In addition, the insertion of a 2–3 nm-thick GO thin layer at the c-Si/PEDOT:PSS interface suppressed the carrier recombination efficiency of dark electron and photo-generated hole at the anode, resulting in the increased photovoltaic performance. This study indicates that the GO can be good candidates for hole transporting layer of c-Si/PEDOT:PSS Schottky junction solar cell.
This article is being retracted effective 18 December 2014.
Reversing Property Rights: Practice‐Based Approaches for Controlling Agricultural Nonpoint‐source Water Pollution When Emissions Aggregate Nonlinearly
Authors: Rabotyagov Sergey S. , Valcu Adriana M. , Kling Catherine L. 
Published: December 2013

AbstractNonpoint‐source water pollution remains a major issue despite decades of research and sizable conservation programs. We suggest that by taking advantage of contemporary modeling and optimization approaches, good approximations to physical relationships can be constructed so that even in the presence of unobservable field emissions and nonlinear fate and transport relationships, standard economic tools of command‐and‐control requirements, performance standards, and trading can be implemented. The Boone River Watershed in the U.S. state of Iowa is used for empirical demonstration. Although the approach can be used to construct voluntary conservation policies, the described policies involve imposing requirements on agricultural polluters rather than relying on voluntary actions alone.
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
Authors: Winterhalter Charles , Widera Paweł , Krasnogor Natalio 
Published: December 2013

Abstract
Summary: JEPETTO (Java Enrichment of Pathways Extended To TOpology) is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis. The plugin integrates information from three separate web servers we published previously, specializing in enrichment analysis, pathways expansion and topological matching. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. We demonstrate the utility of the JEPETTO plugin on a set of misregulated genes associated with Alzheimer’s disease.
Availability: Source code and binaries are freely available for download at http://apps.cytoscape.org/apps/jepetto, implemented in Java and multi-platform. Installable directly via Cytoscape plugin manager. Released under the GNU General Public Licence.
Contact: jepetto.plugin@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
Authors: Zerbino Daniel R. , Johnson Nathan , Juettemann Thomas , Wilder Steven P. , Flicek Paul 
Published: December 2013

Abstract
Motivation: Using high-throughput sequencing, researchers are now generating hundreds of whole-genome assays to measure various features such as transcription factor binding, histone marks, DNA methylation or RNA transcription. Displaying so much data generally leads to a confusing accumulation of plots. We describe here a multithreaded library that computes statistics on large numbers of datasets (Wiggle, BigWig, Bed, BigBed and BAM), generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.
Availability and Implementation: The code is freely available under Apache 2.0 license at www.github.com/Ensembl/Wiggletools
Contact: zerbino@ebi.ac.uk or flicek@ebi.ac.uk