bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trading Cultures: Appellate Body Report on China–Audiovisuals (WT/DS363/AB/R, adopted 19 January 2010)
Authors: CONCONI PAOLA , PAUWELYN JOOST 
Published: March 2011

AbstractIn China–Audiovisuals, a series of Chinese restrictions on the importation and distribution of certain ‘cultural’ or ‘content’ goods and services were found to violate GATT, GATS, and China's Accession Protocol. This paper reviews the definition of what is a ‘good’ (is a ‘film’ a good or a service?) and the extent to which GATT Article XX exceptions can justify violations under WTO instruments other than the GATT itself. We argue that trade volumes are unlikely to significantly rise as a result of this ruling as it does not affect China's right to keep out foreign films and publications if China finds them objectionable. However, foreign producers of audiovisuals can now gain potentially large economic rents, by being able to export and distribute their products into the Chinese market. Finally, we discuss the issue of the protection of cultural goods and review the recent literature on trade and culture that has put forward economic arguments to justify, under some conditions, the protection of cultural goods.
United States – Continued Existence and Application of Zeroing Methodology: the end of Zeroing?
Authors: PRUSA THOMAS J. , VERMULST EDWIN 
Published: March 2011

AbstractThis is the eighth Appellate Body Report in which some aspect of zeroing was adjudicated. As in the prior cases, the AB again found the US practice inconsistent with several aspects of the Anti-Dumping Agreement. The novelty in this dispute was the EC attempt to broaden the concept of what constitutes an appealable measure. The EC challenged whether a WTO decision regarding zeroing could apply to subsequent proceedings that might modify duty levels and asked the AB to decide whether the United States' continued use of zeroing in the context of a given case was consistent with WTO obligations. The AB stated that in its attempt to bring an effective resolution to the zeroing issue, the EC is entitled to frame the subject of its challenge in such a way as to bring the ongoing use of the zeroing methodology in these cases, under the scrutiny of WTO dispute settlement. The AB then cautiously applied the new perspective to US zeroing practice.
Diversity and functional analysis of luxS genes in Vibrios from marine sponges Mycale laxissima and Ircinia strobilina
Authors: Zan Jindong , Fuqua Clay , Hill Russell T 
Published: March 2011

Abstract
Sponges harbor highly diverse and dense microbial communities, providing an environment in which bacterial signaling may be important. Quorum sensing (QS) is a cell density-dependent signaling process that bacteria employ to coordinate and regulate their gene expression. Previous studies have found that bacteria isolated from sponges are able to produce acyl-homoserine lactones (AHLs), an important class of QS molecules found in proteobacteria. Autoinducer-2 (AI-2) is a second class of QS molecule, and is considered to be an interspecies signal. However, AI-2 signaling has not been reported in sponge bacterial symbionts. In this study, degenerate primers were designed based on known Vibrio luxS sequences to amplify the luxS genes encoding AI-2 synthases of several Vibrio isolates from marine sponges Mycale laxissima and Ircinia strobilina. All the vibrios isolated from these two sponges had luxS genes and were able to produce signals with AI-2 activity as detected using a biological reporter. A novel group of luxS sequences was found, thus extending the known diversity of luxS genes. One isolate was chosen for further analysis of its luxS gene by expression of the gene in Escherichia coli DH5α and by characterization of the profile of AI-2 activity. This work provides the first information about luxS genes and AI-2 activity in sponge-associated bacterial communities.
Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing
Authors: Hong Pei-Ying , Wheeler Emily , Cann Isaac K O , Mackie Roderick I 
Published: March 2011

Abstract
Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species—the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value&gt;1E−9). In contrast, Ruminococcaceae were present at &gt;5-fold higher abundance in the LI than MI (P-value&gt;6E−14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356–896 OTUs) was &gt;2-fold higher than in the MI (112–567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that can effectively breakdown a wide variety of complex polysaccharides.
Mobile Technology and AAC Apps From an AAC Developer's Perspective
Authors: Hershberger Dave 
Published: March 2011

Abstract
Mobile computer technology has undergone profound changes over the past few years. It is important to appreciate the benefits and challenges of using mobile technology for AAC applications and to understand how various AAC stakeholders are affected by mobile devices and the corresponding changes in service delivery. This article will help us appreciate how our concept of an ‘AAC Solution’ may need to evolve to accommodate these new technologies.
The Evolution of Augmentative Communication and the Importance of Alternate Access
Authors: Chapple David 
Published: March 2011

Abstract
Over the past 20 years, there have been many advances in the computer industry as well as in augmentative and alternative communication (AAC) devices. Computers are becoming more compact and have multiple purposes, such as the iPhone, which is a cell phone, mp3 player, and an Internet browser. AAC devices also have evolved to become multi-purpose devices; the most sophisticated devices have functionality similar to the iPhone and iPod. Recently, the idea of having the iPhone and iPad as a communication device was initiated with the development of language applications specifically for this format. It might be true that this idea could become the future of AAC devices; however, there are major access issues to overcome before the idea is a reality. This article will chronicle advancements in AAC devices, specifically on access methods, throughout the years, towards the transition to handheld devices. The newest technologies hold much promise with both features and affordability factors being highly attractive. Yet, these technologies must be made to incorporate alternate access if they are to meet their fullest potential as AAC tools.
AAC Evaluations and New Mobile Technologies: Asking and Answering the Right Questions
Authors: McBride Debby 
Published: March 2011

Abstract
The latest mobile technology options have heightened the interest in AAC today. Due to the ease of access and the availability of this technology, there are considerably more device choices available for persons with complex communication needs (CCN). There is an opportunity to build upon the enthusiasm surrounding these new mobile technologies by including all stakeholders in the AAC evaluation process. The clinician needs to ensure the use of sound AAC evaluation principles and procedures and prioritize the individual needs of the communicator. Recommendations about the use of an AAC high-tech device should flow from the evaluation and feature-matching process. The purpose of this paper is to suggest new ways to revisit the basics of a comprehensive AAC evaluation in order to better ensure that individuals who use AAC are being provided with the tools and features they need.
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Authors: Blom Jochen , Jakobi Tobias , Doppmeier Daniel , Jaenicke Sebastian , Kalinowski Jörn , Stoye Jens , Goesmann Alexander 
Published: March 2011

Abstract
Motivation: The introduction of next-generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short reads to reference sequences a standard application in modern bioinformatics. Short-read alignment is needed for reference based re-sequencing of complete genomes as well as for gene expression analysis based on transcriptome sequencing. Several approaches were developed during the last years allowing for a fast alignment of short sequences to a given template. Methods available to date use heuristic techniques to gain a speedup of the alignments, thereby missing possible alignment positions. Furthermore, most approaches return only one best hit for every query sequence, thus losing the potentially valuable information of alternative alignment positions with identical scores.
Results: We developed SARUMAN (Semiglobal Alignment of short Reads Using CUDA and NeedleMAN-Wunsch), a mapping approach that returns all possible alignment positions of a read in a reference sequence under a given error threshold, together with one optimal alignment for each of these positions. Alignments are computed in parallel on graphics hardware, facilitating an considerable speedup of this normally time-consuming step. Combining our filter algorithm with CUDA-accelerated alignments, we were able to align reads to microbial genomes in time comparable or even faster than all published approaches, while still providing an exact, complete and optimal result. At the same time, SARUMAN runs on every standard Linux PC with a CUDA-compatible graphics accelerator.
Availability: http://www.cebitec.uni-bielefeld.de/brf/saruman/saruman.html.
Contact: jblom@cebitec.uni-bielefeld.de
Supplementary information: Supplementary data are available at Bioinformatics online.
A novel network-based method for measuring the functional relationship between gene sets
Authors: Wang Qianghu , Sun Jie , Zhou Meng , Yang Haixiu , Li Yan , Li Xiang , Lv Sali , Li Xia , Li Yixue 
Published: March 2011

Abstract
Motivation: In the functional genomic era, a large number of gene sets have been identified via high-throughput genomic and proteomic technologies. These gene sets of interest are often related to the same or similar disorders or phenotypes, and are commonly presented as differentially expressed gene lists, co-expressed gene modules, protein complexes or signaling pathways. However, biologists are still faced by the challenge of comparing gene sets and interpreting the functional relationships between gene sets into an understanding of the underlying biological mechanisms.
Results: We introduce a novel network-based method, designated corrected cumulative rank score (CCRS), which analyzes the functional communication and physical interaction between genes, and presents an easy-to-use web-based toolkit called GsNetCom to quantify the functional relationship between two gene sets. To evaluate the performance of our method in assessing the functional similarity between two gene sets, we analyzed the functional coherence of complexes in functional catalog and identified protein complexes in the same functional catalog. The results suggested that CCRS can offer a significant advance in addressing the functional relationship between different gene sets compared with several other available tools or algorithms with similar functionality. We also conducted the case study based on our method, and succeeded in prioritizing candidate leukemia-associated protein complexes and expanding the prioritization and analysis of cancer-related complexes to other cancer types. In addition, GsNetCom provides a new insight into the communication between gene modules, such as exploring gene sets from the perspective of well-annotated protein complexes.
Availability and Implementation: GsNetCom is a freely available web accessible toolkit at http://bioinfo.hrbmu.edu.cn/GsNetCom.
Contact: lixia@hrbmu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Inference of transcriptional regulatory network by bootstrapping patterns
Authors: Wang Hei-Chia , Chen Yi-HSiu , Kao Hung-Yu , Tsai Shaw-Jenq 
Published: March 2011

Abstract
Motivation: Transcriptional regulatory networks, which consist of linkages between transcription factors (TF) and target genes (TGene), control the expression of a genome and play important roles in all aspects of an organism's life cycle. Accurate prediction of transcriptional regulatory networks is critical in providing useful information for biologists to determine what to do next. Currently, there is a substantial amount of fragmented gene regulation information described in the medical literature. However, current related text analysis methods designed to identify protein–protein interactions are not entirely suitable for finding transcriptional regulatory networks.
Result: In this article, we propose an automatic regulatory network inference method that uses bootstrapping of description patterns to predict the relationship between a TF and its TGenes. The proposed method differs from other regulatory network generators in that it makes use of both positive and negative patterns for different vector combinations in a sentence. Moreover, the positive pattern learning process can be fully automatic. Furthermore, patterns for active and passive voice sentences are learned separately. The experiments use 609 HIF-1 expert-tagged articles from PubMed as the gold standard. The results show that the proposed method can automatically generate a predicted regulatory network for a transcription factor. Our system achieves an F-measure of 72.60%.
Availability: The software, training/test datasets and learned patterns are available at http://140.116.99.138/∼hcw0901/PubMedSearch.php
Contact: seantsai@mail.ncku.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Development and Validation of the Questionnaire of Satisfaction with Perioperative Anesthetic Care for General and Regional Anesthesia in Taiwanese Patients
Authors: Mui Wui-Chiu , Chang Chia-Ming , Cheng Kong-Fah , Lee Tak-Yu , Ng Kwok-On , Tsao Kao-Rong , Hwang Fang-Ming 
Published: March 2011

Background
To fulfill the increasing demand of service quality improvement in recent years, it is imperative to develop a proper instrument to evaluate patient satisfaction with perioperative anesthetic care for many institutes in Taiwan.

Methods
We used a six-factor 32-item pilot questionnaire developed in our previous study as our starting point in this study. Exploratory factor analysis of the pilot questionnaire for factor structure generation was performed in general anesthesia patients (group 1, n = 320) and resulted in the generation of the Patient Satisfaction with Perioperative Anesthetic Care questionnaire (PSPACq). Confirmatory factor analysis of the PSPACq in general anesthesia (group 2, n = 565) and regional anesthesia (group 3, n = 225) patients was performed for validation and cross-validation of the PSPACq model, respectively. The confounding variables and the patient loyalty effects on PSPACq scores were analyzed to evaluate the nomological validity of the PSPACq.

Result
Exploratory factor analysis of the pilot questionnaire in group 1 resulted in the development of the PSPACq (a seven-factor 30-item model). The standardized coefficients and indexes for the assessment of fit of the PSPACq model in group 2 (validation) and group 3 (cross-validation) patients revealed a well-fitting model. The results of the loyalty scores and confounding variables support the nomological validity of the PSPACq.

Conclusions
A valid and reliable questionnaire (PSPACq) with Taiwanese culture characteristics was developed and is suitable for testing of patient satisfaction with perioperative anesthesia care for patients receiving general or regional anesthesia for their surgery.
Integration of Auxin and Salt Signals by the NAC Transcription Factor NTM2 during Seed Germination in Arabidopsis
Authors: Park Jungmin , Kim Youn-Sung , Kim Sang-Gyu , Jung Jae-Hoon , Woo Je-Chang , Park Chung-Mo 
Published: March 2011

Abstract
Seed germination is regulated through elaborately interacting signaling networks that integrate diverse environmental cues into hormonal signaling pathways. Roles of gibberellic acid and abscisic acid in germination have been studied extensively using Arabidopsis (Arabidopsis thaliana) mutants having alterations in seed germination. Auxin has also been implicated in seed germination. However, how auxin influences germination is largely unknown. Here, we demonstrate that auxin is linked via the IAA30 gene with a salt signaling cascade mediated by the NAM-ATAF1/2-CUC2 transcription factor NTM2/Arabidopsis NAC domain-containing protein 69 (for NAC with Transmembrane Motif1) during seed germination. Germination of the NTM2-deficient ntm2-1 mutant seeds exhibited enhanced resistance to high salinity. However, the salt resistance disappeared in the ntm2-1 mutant overexpressing the IAA30 gene, which was induced by salt in a NTM2-dependent manner. Auxin exhibited no discernible effects on germination under normal growth conditions. Under high salinity, however, whereas exogenous application of auxin further suppressed the germination of control seeds, the auxin effects were reduced in the ntm2-1 mutant. Consistent with the inhibitory effects of auxin on germination, germination of YUCCA 3-overexpressing plants containing elevated levels of active auxin was more severely influenced by salt. These observations indicate that auxin delays seed germination under high salinity through cross talk with the NTM2-mediated salt signaling in Arabidopsis.
Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake
Authors: Chen Y. , Gondro C. , Quinn K. , Herd R. M. , Parnell P. F. , Vanselow B. 
Published: March 2011

SummaryFeed efficiency is an economically important trait in beef production. It can be measured as residual feed intake. This is the difference between actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. DNA‐based marker‐assisted selection would help beef breeders to accelerate genetic improvement for feed efficiency by reducing the generation interval and would obviate the high cost of measuring residual feed intake. Although numbers of quantitative trait loci and candidate genes have been identified with the advance of molecular genetics, our understanding of the physiological mechanisms and the nature of genes underlying residual feed intake is limited. The aim of the study was to use global gene expression profiling by microarray to identify genes that are differentially expressed in cattle, using lines genetically selected for low and high residual feed intake, and to uncover candidate genes for residual feed intake. A long‐oligo microarray with 24 000 probes was used to profile the liver transcriptome of 44 cattle selected for high or low residual feed intake. One hundred and sixty‐one unique genes were identified as being differentially expressed between animals with high and low residual feed intake. These genes were involved in seven gene networks affecting cellular growth and proliferation, cellular assembly and organization, cell signalling, drug metabolism, protein synthesis, lipid metabolism, and carbohydrate metabolism. Analysis of functional data using a transcriptional approach allows a better understanding of the underlying biological processes involved in residual feed intake and also allows the identification of candidate genes for marker‐assisted selection.
Does β‐adrenoceptor blocker therapy improve cancer survival? Findings from a population‐based retrospective cohort study
Authors: Shah Sunil M. , Carey Iain M. , Owen Christopher G. , Harris Tess , DeWilde Stephen , Cook Derek G. 
Published: March 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • In vitro studies suggest that β‐adrenoceptor blocker therapy inhibits cancer cell proliferation and migration leading to their consideration as novel therapeutic agents for cancer.• While trials in humans have suggested β‐adrenoceptor blockers have no effect on cancer incidence, their effect on cancer survival has not been studied.• Recent limited evidence in breast cancer patients suggests that β‐adrenoceptor blockers may improve cancer‐specific survival. WHAT THIS STUDY ADDS • This study is the first to examine cancer survival in patients receiving β‐adrenoceptor blockers across a range of common cancers in a large population‐based sample.• For common tumour sites, including lung, breast and colon, there was no evidence that β‐adrenoceptor blocker treatment modified overall survival but poorer survival was seen in patients with prostate and pancreatic cancer.• Our findings do not support development of clinical trials on β‐adrenoceptor blocker therapy for cancer without further evidence of a beneficial effect in humans.AIMS To examine the effect of β‐adrenoceptor blocker treatment on cancer survival.METHODS In a UK primary care database, we compared patients with a new cancer diagnosis receiving β‐adrenoceptor blockers regularly (n= 1406) with patients receiving other antihypertensive medication (n= 2056).RESULTS Compared with cancer patients receiving other antihypertensive medication, patients receiving β‐adrenoceptor blocker therapy experienced slightly poorer survival (HR = 1.18, 95% CI 1.04, 1.33 for all β‐adrenoceptor blockers; HR = 1.21, 95% CI 0.94, 1.55 for non‐selective β‐adrenoceptor blockers). This poorer overall survival was explained by patients with pancreatic and prostate cancer with no evidence of an effect on survival for patients with lung, breast or colorectal cancer. Analysis in a cancer‐free matched parallel cohort did not suggest selection bias masked a beneficial effect.CONCLUSION Our study does not support the hypothesis that β‐adrenoceptor blockers improve survival for common cancers.