bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citalopram for agitation in Alzheimer's disease: Design and methods
Authors: Drye Lea T. , Ismail Zahinoor , Porsteinsson Anton P. , Rosenberg Paul B. , Weintraub Daniel , Marano Christopher , Pelton Gregory , Frangakis Constantine , Rabins Peter V. , Munro Cynthia A. , Meinert Curtis L. , Devanand D.P. , Yesavage Jerome , Mintzer Jacobo E. , Schneider Lon S. , Pollock Bruce G. , Lyketsos Constantine G. ,   CitAD Research Group
Published: February 2012

AbstractBackgroundAgitation is one of the most common neuropsychiatric symptoms of Alzheimer's disease (AD), and is associated with serious adverse consequences for patients and caregivers. Evidence‐supported treatment options for agitation are limited. The citalopram for agitation in Alzheimer's disease (CitAD) study was designed to evaluate the potential of citalopram to ameliorate these symptoms.MethodsCitAD is a randomized, double‐masked, placebo‐controlled multicenter clinical trial, with two parallel treatment groups assigned in a 1:1 ratio and randomization stratified by clinical center. The study included eight recruiting clinical centers, a chair's office, and a coordinating center located in university settings in the United States and Canada. A total of 200 individuals having probable AD with clinically significant agitation and without major depression were recruited for this study. Patients were randomized to receive citalopram (target dose of 30 mg/d) or matching placebo. Caregivers of patients in both treatment groups received a structured psychosocial therapy. Agitation was compared between treatment groups using the NeuroBehavioral Rating Scale and the AD Cooperative Study‐ Clinical Global Impression of Change, which are the primary outcomes. Functional performance, cognition, caregiver distress, and rates of adverse and serious adverse events were also measured.ConclusionThe authors believe the design elements in CitAD are important features to be included in trials assessing the safety and efficacy of psychotropic medications for clinically significant agitation in AD.
Enticing for me but unfair to her: Can targeted pricing evoke socially conscious behavior?
Authors: Wang Yu , Krishna Aradhna 
Published: January 2012

AbstractPrior research shows that consumers stop purchasing from firms that treat them badly. In this research we show that consumers also resist firms that treat other consumers badly while favoring them. In three experiments, we demonstrate such social consciousness in the context of targeted pricing, where firms offer lower prices to new (versus old) customers. A significant proportion of consumers in our experiments give up money to resist the price‐discriminating firm, especially when the discrimination is more salient or is not justified. Further, perceived unfairness mediates the relationship between the salience and justification of the pricing practice and consumer resistance.
Stem cells in human normal endometrium and endometrial cancer cells: Characterization of side population cells
Authors: Kato Kiyoko 
Published: January 2012

AbstractRecently, adult stem cells have been identified in several mature tissues. The human endometrium is responsive to sex steroid hormone. It undergoes extraordinary growth in a cyclic manner and is shed and regenerated throughout a woman's lifetime. It has been proposed that the human endometrium may contain a population of stem cells, which are responsible for its remarkable regenerative ability. It is also suggested that stem‐like cells exist in cancer tissues. Stem‐like cell subpopulations, referred to as “side population” (SP) cells, have been identified in several tissues and tumors based on their ability to efflux the fluorescent dye Hoechst 33342. Recently, we isolated and characterized the SP cells in normal human endometrium and in an endometrial cancer (EC) cell line. Endometrial SP cells can function as progenitor cells. EC SP cells show the following: (1) reductions in the expression levels of differentiation markers; (2) long‐term repopulating properties; (3) self‐renewal capacity; (4) enhancement of migration and podia formation; (5) enhancement of tumorigenicity; and (6) bipotent developmental potential (tumor cells and stroma‐like cells), suggesting that these SP cells have cancer stem‐like cell features. We review the articles that show the presence of stem cells in normal endometrium and EC cells and demonstrate the results of our studies.
Mala Bizta Sochal Klu: underground, alternative and commercial in Havana hip hop
Authors: Baker Geoff 
Published: February 2012

AbstractThe terms underground, alternative and commercial are widely used in discussions of popular music scenes in Havana and around the world. In Cuba, the words alternative and underground are often used interchangeably, in critical as well as popular discourse. I propose a working definition of, and a distinction between, these terms in Havana, since to render them synonymous reduces their usefulness. The distinction between underground and commercial, in contrast, is widely seen as self-evident, by critics as well as by fans. However, a simplistic dichotomy glosses over the interpenetration of these terms, which are of limited use as analytical categories. This discussion of terminology is grounded in an analysis of the politics of style in Havana hip hop.
The promotional state ‘after neo-liberalism’: ideologies of governance and New Zealand's pop renaissance
Authors: Scott Michael , Craig David 
Published: February 2012

AbstractThis article responds to Frith and Cloonan's (2008) call for researchers considering the relationship between the state and popular music to analyse more closely the ideologies of governance that undergird music policy. Building on Cloonan's ‘promotional state’ and drawing on recent New Zealand experience, this paper shows how New Zealand's Labour government (1999–2008) developed policies to support the export of ‘Kiwi’ pop which requires a reconsideration of state music policy as interventions in the market. The work of the New Zealand Music Commission in generating and coordinating working partnerships with diverse music industry actors illustrates emerging forms of ‘after neo-liberal’ ideology and governance, wherein state-related actors and musicians each and together adapt to market arrangements through supply side, social inclusion and new institutional policy settings and modalities. This article offers points of comparison to types of ideological and governing/institutional formations we can expect to see emerging in promotional states elsewhere.
Shot-to-shot reproducibility in the emission of fast highly charged metal ions from a laser ion source
Authors: Krása J. , Velyhan A. , Margarone D. , Krouský E. , Láska L. , Jungwirth K. , Rohlena K. , Ullschmied J. , Parys P. , Ryć L. , Wołowski J. 
Published: February 2012

The generation of fast highly charged metal ions with the use of the sub-nanosecond Prague Asterix Laser System, operated at a fundamental wavelength of 1315 nm, is reported. Particular attention is paid to shot-to-shot reproducibility in the ion emission. Au and Pd targets were exposed to intensities up to 5 × 1016 W/cm2. Above the laser intensity threshold of ∼3 × 1014 W/cm2 the plasma is generated in a form of irregular bursts. The maximum energy of protons constituting the leading edge of the fastest burst reaches a value up to 1 MeV. The fast ions in the following bursts have energy gradually decreasing with the increasing burst number, namely, from a value of about 0.5 MeV/charge regardless of the atomic number and mass of the ionized species.
Low energy collisions of CN(X  2Σ+) with He in magnetic ﬁelds
Authors: Feng Eryin , Shao Xi , Yu Chunhua , Sun Chunyan , Huang Wuying 
Published: February 2012

A theoretical investigation of the He–CN(2Σ+) complex is presented. We perform ab initio calculations of the interaction potential energy surface and carry out accurate calculations of bound energy levels of the complex including the molecular fine structure. We find the potential has a shallow minimum and supports seven and nine bound levels in complex with 3He and 4He, respectively. Based on the potential the quantum scattering calculation is then implemented for elastic and inelastic cross sections of the magnetically trappable low-field-seeking state of CN(2Σ+) in collision with 3He atom. The cold collision properties and the influence of the external magnetic field as well as the effect of the uncertainty of interaction potential on the collisionally induced Zeeman relaxation are explored and discussed in detail. The ratios of elastic to inelastic cross sections are large over a wide range of collision energy, magnetic field, and scaling factor of the potential, suggesting helium buffer gas loading and cooling of CN in a magnetic trap is a good prospect.
At the request of the authors, this article is being retracted effective 18 May 2012.
Chado Controller: advanced annotation management with a community annotation system
Authors: Guignon Valentin , Droc Gaëtan , Alaux Michael , Baurens Franc-Christophe , Garsmeur Olivier , Poiron Claire , Carver Tim , Rouard Mathieu , Bocs Stéphanie 
Published: January 2012

Abstract
Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl.
Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc
The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form
Contact: valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)
Authors: Schwalb Björn , Schulz Daniel , Sun Mai , Zacher Benedikt , Dümcke Sebastian , Martin Dietmar E. , Cramer Patrick , Tresch Achim 
Published: January 2012

Abstract
Summary: Standard transcriptomics measures total cellular RNA levels. Our understanding of gene regulation would be greatly improved if we could measure RNA synthesis and decay rates on a genome-wide level. To that end, the Dynamic Transcriptome Analysis (DTA) method has been developed. DTA combines metabolic RNA labeling with standard transcriptomics to measure RNA synthesis and decay rates in a precise and non-perturbing manner. Here, we present the open source R/Bioconductor software package DTA. It implements all required bioinformatics steps that allow the accurate absolute quantification and comparison of RNA turnover.
Availability: DTA is part of R/Bioconductor. To download and install DTA refer to http://bioconductor.org/packages/2.10/bioc/html/DTA.html
Contact: schwalb@lmb.uni-muenchen.de
A new approach to bias correction in RNA-Seq
Authors: Jones Daniel C. , Ruzzo Walter L. , Peng Xinxia , Katze Michael G. 
Published: January 2012

Abstract
Motivation: Quantification of sequence abundance in RNA-Seq experiments is often conflated by protocol-specific sequence bias. The exact sources of the bias are unknown, but may be influenced by polymerase chain reaction amplification, or differing primer affinities and mixtures, for example. The result is decreased accuracy in many applications, such as de novo gene annotation and transcript quantification.
Results: We present a new method to measure and correct for these influences using a simple graphical model. Our model does not rely on existing gene annotations, and model selection is performed automatically making it applicable with few assumptions. We evaluate our method on several datasets, and by multiple criteria, demonstrating that it effectively decreases bias and increases uniformity. Additionally, we provide theoretical and empirical results showing that the method is unlikely to have any effect on unbiased data, suggesting it can be applied with little risk of spurious adjustment.
Availability: The method is implemented in the seqbias R/Bioconductor package, available freely under the LGPL license from http://bioconductor.org
Contact: dcjones@cs.washington.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Transcriptome Analysis and Comparison Explorer—T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms
Authors: Philipp E. E. R. , Kraemer L. , Mountfort D. , Schilhabel M. , Schreiber S. , Rosenstiel P. 
Published: January 2012

Abstract
Motivation: Next generation sequencing (NGS) technologies allow a rapid and cost-effective compilation of large RNA sequence datasets in model and non-model organisms. However, the storage and analysis of transcriptome information from different NGS platforms is still a significant bottleneck, leading to a delay in data dissemination and subsequent biological understanding. Especially database interfaces with transcriptome analysis modules going beyond mere read counts are missing. Here, we present the Transcriptome Analysis and Comparison Explorer (T-ACE), a tool designed for the organization and analysis of large sequence datasets, and especially suited for transcriptome projects of non-model organisms with little or no a priori sequence information. T-ACE offers a TCL-based interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information belonging to single sequences or contigs, such as annotation or read coverage, is linked to the respective sequence and immediately accessible. Sequences and assigned information can be searched via keyword- or BLAST-search. Additionally, T-ACE provides within and between transcriptome analysis modules on the level of expression, GO terms, KEGG pathways and protein domains. Results are visualized and can be easily exported for external analysis. We developed T-ACE for laboratory environments, which have only a limited amount of bioinformatics support, and for collaborative projects in which different partners work on the same dataset from different locations or platforms (Windows/Linux/MacOS). For laboratories with some experience in bioinformatics and programming, the low complexity of the database structure and open-source code provides a framework that can be customized according to the different needs of the user and transcriptome project.
Contact: e.philipp@ikmb.uni-kiel.de; l.kraemer@ikmb.uni_kiel.de; p.rosenstiel@mucosa.de
Supplementary information: Supplementary data are available at Bioinformatics online.
A co-module approach for elucidating drug–disease associations and revealing their molecular basis
Authors: Zhao Shiwen , Li Shao 
Published: January 2012

Abstract
Motivation: Understanding how drugs and diseases are associated in the molecular level is of critical importance to unveil disease mechanisms and treatments. Until recently, few studies attempt end to discover important gene modules shared by both drugs and diseases.
Results: Here, we propose a novel presentation of drug–gene–disease relationship, a ‘co-module’, which is characterized by closely related drugs, diseases and genes. We first define a network-based gene closeness profile to relate drug to disease. Then, we develop a Bayesian partition method to identify drug–gene–disease co-modules underlying the gene closeness data. Genes share similar notable patterns with respect not only to the drugs but also the diseases within a co-module. Simulations show that our method, comCIPHER, achieves a better performance compared with a popular co-module detection method, PPA. We apply comCIPHER to a set consisting of 723 drugs, 275 diseases and 1442 genes and demonstrate that our co-module approach is able to identify new drug–disease associations and highlight their molecular basis. Disease co-morbidity emerges as well. Three co-modules are further illustrated in which new drug applications, including the anti-cancer metastasis activity of an anti-asthma drug Pranlukast, and a cardiovascular stress-testing agent Arbutamine for obesity, as well as potential side-effects, e.g. hypotension for Triamterene, are computationally identified.
Availability: The compiled version of comCIPHER can be found at http://bioinfo.au.tsinghua.edu.cn/comCIPHER/. The 86 co-modules can be downloaded from http://bioinfo.au.tsinghua.edu.cn/comCIPHER/Co_Module_Results.zip.
Contact: shaoli@mail.tsinghua.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction
Authors: Westesson Oscar , Barquist Lars , Holmes Ian 
Published: January 2012

Abstract
Summary: We describe handalign, a software package for Bayesian reconstruction of phylogenetic history. The underlying model of sequence evolution describes indels and substitutions. Alignments, trees and model parameters are all treated as jointly dependent random variables and sampled via Metropolis–Hastings Markov chain Monte Carlo (MCMC), enabling systematic statistical parameter inference and hypothesis testing. handalign implements several different MCMC proposal kernels, allows sampling from arbitrary target distributions via Hastings ratios, and uses standard file formats for trees, alignments and models.
Availability and Implementation: Installation and usage instructions are at http://biowiki.org/HandAlign
Contact: ihh@berkeley.edu
Supplementary information:Supplementary material is available at Bioinformatics online.
SOAP3: ultra-fast GPU-based parallel alignment tool for short reads
Authors: Liu Chi-Man , Wong Thomas , Wu Edward , Luo Ruibang , Yiu Siu-Ming , Li Yingrui , Wang Bingqiang , Yu Chang , Chu Xiaowen , Zhao Kaiyong , Li Ruiqiang , Lam Tak-Wah 
Published: January 2012

Abstract
Summary: SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU. When tested with millions of Illumina Hiseq 2000 length-100 bp reads, SOAP3 takes &lt; 30 s to align a million read pairs onto the human reference genome and is at least 7.5 and 20 times faster than BWA and Bowtie, respectively. For aligning reads with up to four mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.
Availability: SOAP3 is available at: http://www.cs.hku.hk/2bwt-tools/soap3; http://soap.genomics.org.cn/soap3.html.
Contact: liruiqiang@gmail.com, twlam@cs.hku.hk
First Report of a Ceratobasidium sp. Causing Root Rot on Canola in Washington State
Authors: Schroeder K. L. , Paulitz T. C. 
Published: February 2012

Rhizoctonia root rot occurs commonly on canola (Brassica napus L.) in Washington State. Recently, isolates of an additional pathogen were found to be involved in this disease complex. Isolates of an AG-I-like Ceratobasidium sp. were collected from roots and root zone soil in central Washington near Ritzville. Identity of selected isolates was verified by sequencing the internal transcribed spacer (ITS) region of the rDNA (GenBank Accession Nos. JQ247570, JQ247571, and JQ247572), with a 90 to 93% identity to AG-I. All isolates also amplified with AG-I-like specific primers (1). Six isolates were included in pathogenicity assays conducted in the greenhouse. There were five replicates of three plants for each treatment and the experiment was conducted twice. Pasteurized soil was infested with ground oat inoculum (1%) and placed into containers (3.8 × 21 cm). Infested soils were seeded with canola, chickpea (Cicer arietinum L.), lentil (Lens culinaris Medik.), pea (Pisum sativum L.), barley (Hordeum vulgare L.), or wheat (Triticum aestivum L.). After 3 weeks of incubation at 15°C, the plants were destructively harvested. The emergence of canola was consistently reduced in soil infested with a Ceratobasidium sp., with reductions of 0 to 23% (average 11%). There was no postemergence damping-off, a symptom commonly associated with AG-2-1 (2). Plant height and top dry weights were significantly reduced for canola seeded into infested soil. Heights of plants growing in infested soil was reduced by 25 to 53% (average 42%) and top dry weight was reduced by 37 to 81% (average 61%) compared with the noninfested control. The legume hosts tested in this study were also affected by this Ceratobasidium sp., but to a lesser extent. Compared with the noninfested controls, there was evidence of preemergence damping-off in chickpea (0 to 27%, average 13%) and pea plants were consistently stunted (5 to 23%, average 12%). Chickpea and pea plants grown in infested soil also had reduced top dry weights of 9 to 28% (average 17%) and 13 to 35% (average 21%), respectively. The roots of all infected hosts had a characteristic brown discoloration with tapered, rotted root tips (spear tips). There was no reduction in emergence or plant height of wheat and barley; there was inconsistent reduction in dry weight of these plants. To our knowledge, this is the first report of a Ceratobasidium sp. causing disease on canola in Washington State. References: (1) P. A. Okubara et al. Phytopathology 98:837, 2008. (2) T. C. Paulitz et al. Plant Dis. 90:829, 2006.
PoppyAPETALA1/FRUITFULLOrthologs Control Flowering Time, Branching, Perianth Identity, and Fruit Development
Authors: Pabón-Mora Natalia , Ambrose Barbara A. , Litt Amy 
Published: January 2012

AbstractSeveral MADS box gene lineages involved in flower development have undergone duplications that correlate with the diversification of large groups of flowering plants. In the APETALA1 gene lineage, a major duplication coincides with the origin of the core eudicots, resulting in the euFUL and the euAP1 clades. Arabidopsis FRUITFULL (FUL) and APETALA1 (AP1) function redundantly in specifying floral meristem identity but function independently in sepal and petal identity (AP1) and in proper fruit development and determinacy (FUL). Many of these functions are largely conserved in other core eudicot euAP1 and euFUL genes, but notably, the role of APETALA1 as an “A-function” (sepal and petal identity) gene is thought to be Brassicaceae specific. Understanding how functional divergence of the core eudicot duplicates occurred requires a careful examination of the function of preduplication (FUL-like) genes. Using virus-induced gene silencing, we show that FUL-like genes in opium poppy (Papaver somniferum) and California poppy (Eschscholzia californica) function in axillary meristem growth and in floral meristem and sepal identity and that they also play a key role in fruit development. Interestingly, in opium poppy, these genes also control flowering time and petal identity, suggesting that AP1/FUL homologs might have been independently recruited in petal identity. Because the FUL-like gene functional repertoire encompasses all roles previously described for the core eudicot euAP1 and euFUL genes, we postulate subfunctionalization as the functional outcome after the major AP1/FUL gene lineage duplication event.