bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological assessment of the interface between tumor and neighboring tissues, by magnetic resonance imaging, before and after radiotherapy in patients with locally advanced rectal cancer
Authors: Torkzad M. R. , Suzuki C. , Tanaka S. , Palmer G. , Holm T. , Blomqvist L. 
Published: November 2008

Background: Magnetic resonance imaging (MRI) in rectal cancer is sometimes performed after radiotherapy (MRI 2) to evaluate tumor response and to choose alternative forms of surgery. The accuracy of MRI 2 in distinguishing tumor delineation might be difficult due to fibrosis. Purpose: To evaluate the morphological changes in the interface between the tumor and neighboring organs on MRI 2 performed after radiotherapy, and to assess the accuracies of MRI before and after radiotherapy compared to histopathology after surgery. Material and Methods: Sixteen patients with locally advanced primary rectal cancer, with MRI before and after radiotherapy, were retrospectively studied, concerning the interface between the tumor and neighboring structures. The accuracies of MRI before and after radiotherapy were compared based on histopathology as a reference. Results: The accuracies of both MRI before and after radiotherapy were moderate, with no additional value of MRI after radiotherapy compared to MRI before radiotherapy. The most predictive form of interface for involvement of a neighboring organ after radiotherapy was nodular growth of the tumor into a neighboring structure. Conclusion: The morphological assessment of pelvic MRI after preoperative radiotherapy does not provide any significant new information about tumor extent in patients with locally advanced rectal cancer.
Diagnostic pitfalls in postinterventional intraarterial magnetic resonance angiography after recanalization of femoropopliteal arterial occlusions
Authors: Huegli R. W. , Aschwanden M. , Kos S. , Rasmus M. , Jaeger K. , Jacob A. L. , Bilecen D. 
Published: November 2008

Background: Magnetic resonance (MR)-guided vascular interventions are of increasing interest, and, with the use of contrast-enhanced techniques, intraarterial contrast-enhanced MR angiography (ia-ce-MRA) competes with intraarterial digital subtraction angiography (ia-DSA) for the diagnostic evaluation of the infrainguinal vessel tree. Purpose: To assess the diagnostic value of ia-ce-MRA and high-resolution T1-weighted (hr-T1w) imaging compared to the gold-standard ia-DSA for residual stenosis and local dissections after femoropopliteal recanalization in patients with peripheral arterial occlusive disease (PAOD). Material and Methods: Eight patients with PAOD and short vessel occlusion of their femoropopliteal arteries underwent recanalization and balloon positioning under DSA. Patients were transferred to a short-bore MR scanner. Percutaneous transluminal angioplasty (PTA) was accomplished under MR fluoroscopy. Pre- and postinterventional ia-ce three-dimensional (3D) gradient-echo MRA with gadopentate dimeglumine was performed using the intraarterial introducer sheath. Maximum intensity projections (MIP) and multiplanar reconstructions (MPR) were calculated from the data set. High-resolution T1w images of the angioplasty region before and after dilatation were acquired. Control ia-DSA images were obtained. Results: The postinterventional angioplasty results for stenosis grading were comparable in ia-MRA and ia-DSA. Only two of five local dissections in ia-DSA were visualized with the ia-ce-MRA runs including MIPs and MPRs. To clearly depict dissection, hr-T1w images were needed. Conclusion: Grading of stenotic lesions with ia-ce-MRA after PTA is comparable to ia-DSA. Intraarterial ce-MRA with calculated MIPs and MPRs is only partially sufficient to visualize local dissections after PTA. High-resolution T1w images are required for precise diagnosis of dissections in magnetic resonance tomography.
Usefulness of diffusion-weighted imaging and dynamic contrast-enhanced magnetic resonance imaging in the diagnosis of prostate transition-zone cancer
Authors: Yoshizako T. , Wada A. , Hayashi T. , Uchida K. , Sumura M. , Uchida N. , Kitagaki H. , Igawa M. 
Published: November 2008

Background: Conventional T2-weighted (T2-WI) magnetic resonance imaging (MRI) has poor sensitivity for prostate transition-zone (TZ) cancer detection. Purpose: To retrospectively evaluate the clinical value of diffusion-weighted MRI (DW-MRI) and dynamic contrast-enhanced MRI (DCE-MRI) in combination with T2-WI for the diagnosis of TZ cancer. Material and Methods: Twenty-six TZ cancers in 23 patients with at least one tumor (tumor size >10 mm) located predominantly in the TZ were included in the study. Sixteen peripheral-zone (PZ) cancers in 12 patients with PZ cancer but without TZ cancer (control group) were selected by step-section pathologic maps. All patients underwent MRI and radical prostatectomy. MRI was obtained by a 1.5T superconducting system with a phased-array coil. Imaging sequences were T2-WI with fat saturation (FST2-WI), DW-MRI (single-shot echoplanar image, b=0 and 1000 s/mm2, apparent diffusion coefficient [ADC] map findings), and DCE-MRI (3D fast spoiled gradient recalled [SPGR], contrast medium [0.2 mmol/kg], total injection time 5 s, image acquisition 30, 60, and 90 s). Sensitivity, specificity, accuracy, and positive predictive value (PPV) for the diagnosis of TZ cancer were evaluated in four protocols: A) FST2-WI alone, B) FST2-WI plus DW-MRI, C) FST2-WI plus DCE-MRI, D) FST2-WI plus DW-MRI plus DCE-MRI. Results: Sensitivity, specificity, accuracy, and PPV in protocol A (FST2-WI alone) were 61.5%, 68.8%, 64.3%, and 76.2%, respectively. FST2-WI plus DW-MRI (protocol B) improved the sensitivity, specificity, accuracy, and PPV. In FST2-WI plus DW-MRI plus DCE-MRI (protocol D), the number of true-negative lesions increased and false-positive lesions decreased, and the sensitivity, specificity, accuracy, and PPV were 69.2%, 93.8%, 78.6%, and 94.7%, respectively. There was a significant difference between protocols A and D ( P<0.05). Conclusion: Adding DW-MRI to FST2-WI in the diagnosis of prostate TZ cancer increased the diagnostic accuracy. The addition of DCE-MRI may be an option to improve the specificity and PPV of diagnosing TZ cancer with FST2-WI and DW-MRI.
GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes
Authors: Chen Wei , Liang Liming , Abecasis Gonçalo R. 
Published: November 2008

Abstract
Summary: We describe an interactive package that provides graphical overviews of the results of whole-genome association studies in datasets with rich multi-dimensional phenotypic information, such as global surveys of gene expression. Windows, Linux and Mac binaries are available from our website.
Availability: http://www.sph.umich.edu/csg/weich/software.html
Contact: weich@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Phylogenetic inference under recombination using Bayesian stochastic topology selection
Authors: Webb Alex , Hancock John M. , Holmes Chris C. 
Published: November 2008

Abstract
Motivation: Conventional phylogenetic analysis for characterizing the relatedness between taxa typically assumes that a single relationship exists between species at every site along the genome. This assumption fails to take into account recombination which is a fundamental process for generating diversity and can lead to spurious results. Recombination induces a localized phylogenetic structure which may vary along the genome. Here, we generalize a hidden Markov model (HMM) to infer changes in phylogeny along multiple sequence alignments while accounting for rate heterogeneity; the hidden states refer to the unobserved phylogenic topology underlying the relatedness at a genomic location. The dimensionality of the number of hidden states (topologies) and their structure are random (not known a priori) and are sampled using Markov chain Monte Carlo algorithms. The HMM structure allows us to analytically integrate out over all possible changepoints in topologies as well as all the unknown branch lengths.
Results: We demonstrate our approach on simulated data and also to the genome of a suspected HIV recombinant strain as well as to an investigation of recombination in the sequences of 15 laboratory mouse strains sequenced by Perlegen Sciences. Our findings indicate that our method allows us to distinguish between rate heterogeneity and variation in phylogeny caused by recombination without being restricted to 4-taxa data.
Availability: The method has been implemented in JAVA and is available, along with data studied here, from http://www.stats.ox.ac.uk/~webb.
Contact: cholmes@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
AmiGO: online access to ontology and annotation data
Authors: Carbon Seth , Ireland Amelia , Mungall Christopher J. , Shu ShengQiang , Marshall Brad , Lewis Suzanna ,   the AmiGO Hub,   the Web Presence Working Group
Published: November 2008

Abstract
AmiGO is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium1; it can also be downloaded and installed to browse local ontologies and annotations.2 AmiGO is free open source software developed and maintained by the GO Consortium.
Availability: http://amigo.geneontology.org
Download: http://sourceforge.net/projects/geneontology/
Contact: sjcarbon@berkeleybop.org
NaCl-Induced Alternations of Cellular and Tissue Ion Fluxes in Roots of Salt-Resistant and Salt-Sensitive Poplar Species
Authors: Sun Jian , Chen Shaoliang , Dai Songxiang , Wang Ruigang , Li Niya , Shen Xin , Zhou Xiaoyang , Lu Cunfu , Zheng Xiaojiang , Hu Zanmin , Zhang Zengkai , Song Jin , Xu Yue 
Published: November 2008

AbstractUsing the scanning ion-selective electrode technique, fluxes of H+, Na+, and Cl− were investigated in roots and derived protoplasts of salt-tolerant Populus euphratica and salt-sensitive Populus popularis 35-44 (P. popularis). Compared to P. popularis, P. euphratica roots exhibited a higher capacity to extrude Na+ after a short-term exposure to 50 mm NaCl (24 h) and a long term in a saline environment of 100 mm NaCl (15 d). Root protoplasts, isolated from the long-term-stressed P. euphratica roots, had an enhanced Na+ efflux and a correspondingly increased H+ influx, especially at an acidic pH of 5.5. However, the NaCl-induced Na+/H+ exchange in root tissues and cells was inhibited by amiloride (a Na+/H+ antiporter inhibitor) or sodium orthovanadate (a plasma membrane H+-ATPase inhibitor). These results indicate that the Na+ extrusion in stressed P. euphratica roots is the result of an active Na+/H+ antiport across the plasma membrane. In comparison, the Na+/H+ antiport system in salt-stressed P. popularis roots was insufficient to exclude Na+ at both the tissue and cellular levels. Moreover, salt-treated P. euphratica roots retained a higher capacity for Cl− exclusion than P. popularis, especially during a long term in high salinity. The pattern of NaCl-induced fluxes of H+, Na+, and Cl− differs from that caused by isomotic mannitol in P. euphratica roots, suggesting that NaCl-induced alternations of root ion fluxes are mainly the result of ion-specific effects.
Alterations in the Endogenous Ascorbic Acid Content Affect Flowering Time in Arabidopsis
Authors: Kotchoni Simeon O. , Larrimore Katherine E. , Mukherjee Madhumati , Kempinski Chase F. , Barth Carina 
Published: November 2008

AbstractAscorbic acid (AA) protects plants against abiotic stress. Previous studies suggested that this antioxidant is also involved in the control of flowering. To decipher how AA influences flowering time, we studied the four AA-deficient Arabidopsis (Arabidopsis thaliana) mutants vtc1-1, vtc2-1, vtc3-1, and vtc4-1 when grown under short and long days. These mutants flowered and senesced before the wild type irrespective of the photoperiod, a response that cannot simply be attributed to slightly elevated oxidative stress in the mutants. Transcript profiling of various flowering pathway genes revealed a correlation of altered mRNA levels and flowering time. For example, circadian clock and photoperiodic pathway genes were significantly higher in the vtc mutants than in the wild type under both short and long days, a result that is consistent with the early-flowering phenotype of the mutants. In contrast, when the AA content was artificially increased, flowering was delayed, which correlated with lower mRNA levels of circadian clock and photoperiodic pathway genes compared with plants treated with water. Similar observations were made for the autonomous pathway. Genetic analyses demonstrated that various photoperiodic and autonomous pathway mutants are epistatic to the vtc1-1 mutant. In conclusion, our transcript and genetic analyses suggest that AA acts upstream of the photoperiodic and autonomous pathways.
HAB1–SWI3B Interaction Reveals a Link between Abscisic Acid Signaling and Putative SWI/SNF Chromatin-Remodeling Complexes in Arabidopsis
Authors: Saez Angela , Rodrigues Americo , Santiago Julia , Rubio Silvia , Rodriguez Pedro L. 
Published: November 2008

Abstract
Abscisic acid (ABA) has an important role for plant growth, development, and stress adaptation. HYPERSENSITIVE TO ABA1 (HAB1) is a protein phosphatase type 2C that plays a key role as a negative regulator of ABA signaling; however, the molecular details of HAB1 action in this process are not known. A two-hybrid screen revealed that SWI3B, an Arabidopsis thaliana homolog of the yeast SWI3 subunit of SWI/SNF chromatin-remodeling complexes, is a prevalent interacting partner of HAB1. The interaction mapped to the N-terminal half of SWI3B and required an intact protein phosphatase catalytic domain. Bimolecular fluorescence complementation and coimmunoprecipitation assays confirmed the interaction of HAB1 and SWI3B in the nucleus of plant cells. swi3b mutants showed a reduced sensitivity to ABA-mediated inhibition of seed germination and growth and reduced expression of the ABA-responsive genes RAB18 and RD29B. Chromatin immunoprecipitation experiments showed that the presence of HAB1 in the vicinity of RD29B and RAB18 promoters was abolished by ABA, which suggests a direct involvement of HAB1 in the regulation of ABA-induced transcription. Additionally, our results uncover SWI3B as a novel positive regulator of ABA signaling and suggest that HAB1 modulates ABA response through the regulation of a putative SWI/SNF chromatin-remodeling complex.
Today's UK professional association library and information service
Authors: Jean Madden Maryna 
Published: November 2008

PurposeThis paper aims to present an overview of the current library and information service in UK professional associations. Challenges in the sector are identified and some of the best information services are examined in order to construct useful models for best practice.Design/methodology/approachA mixed method approach is used: literature review, sources‐based research, content analysis of web sites, statistical analysis, and open‐ended interviews. A total of 50 web sites of professional associations were analysed and 13 association representatives were interviewed. Models of best practice in professional association library and information services are proposed.FindingsThe professional associations with the best web site information provision often have excellent in‐house libraries and a growth in membership between 1999 and 2007. Challenges include: attracting and retaining members through the information services, sufficient marketing and promotion of information services, generating or attracting enough funds, keeping information up‐to‐date, creating benchmarks and standards, and developing information policies and strategy.Practical implicationsThe proposed models can be used by professional association library information services to improve their service delivery.Originality/valueThe study contributes to the under‐researched area of library and information services of UK professional associations. The paper outlines original models for building information strategy and best practice.
Evidence‐based practice, healthcare delivery and information management
Authors: Isetta Marco 
Published: November 2008

PurposeThe evidence‐based practice (EBP) model appears to have established itself as the principal change driver and discourse for the healthcare sector. This study sets out to identify the emergence of the term EBP in the professional literature to establish an empirical foundation for discussion. The understanding of and relevance to healthcare practitioners in a large South West London hospital are assessed and their views related to the perspective of library and information professionals to assess implications for practice.Design/methodology/approachAn extensive literature search was carried out and the data generated used to produce a growth curve for the literature. A survey of health care professionals using e‐mail and follow‐up interviews was undertaken at the case hospital.FindingsBetween 1998 and 2004 the number of papers appearing to discuss the theme increased four‐fold. The first recorded reference was in 1991. The EBP model had strong official and political support in the field. On the user sample there is evidence of resistance to the orthodoxy.Practical implicationsThe EBP model – variously adopted by several healthcare agencies – has placed information management at the centre of the care process. In spite of this, there are few definite implications for the role of library and information professionals, since the world of information and the UK NHS itself are continually in a state of flux, and the current EBP dominance may neither strengthen nor safeguard it.Originality/valueThe bibliometric study provides a baseline. The study of healthcare professionals is a case study to add to knowledge of practice.
Promotion, speculation and their outcome
Authors: Williams David M. , Armstrong John 
Published: November 2008

PurposeOffering an empirical study of the rush to promote a new technology of its time, which is a significant phenomenon in its own right, the paper's purpose is to offer a reminder that new technologies often generate speculative and unstable business conditions.Design/methodology/approachThe paper uses Henry English'sA Complete View of the Joint Stock Companies Formed during the Years 1824 and 1825to identify companies (n=70), and follows up cases with record and archive study.FindingsThe development of steamship services was an important push of transportation and communication technology. The establishment of steam shipping services in coastal waters and near country trade is an analogy of later technologies such as the telegraph, telephone and latterly computer‐mediated digital communication over the internet with global reach. Unlike the canal and railway manias the outcome was minimal.Practical implicationsAs in the Dotcom boom of the early 2000s the study highlights the dangers of speculative business ventures (over‐ambitious promotion and fraud) which lacked a strong link to markets, the pull of significant demand and were weak in terms of business acumen and organization.Originality/valueAs a piece of original business historical research it is not only the findings which are of value, but the paper represents an exemplar of the continued use of archival and record material and information resources to support scholarly activity. Historians of today who wish to study the emerging digital economy may yet encounter problems in an ability to draw on bodies of contemporary evidence. The current issues of digital archiving and digital curation are only just beginning to be appreciated.
A new emerging trend? Cross border trade union mergers
Authors: Gennard John 
Published: November 2008

PurposeThe purpose of this editorial is to examine moves towards cross border trade union mergers.Design/methodology/approachThis editorial outlines the reasons why trade unions see the need to act outside their nation state boundaries.FindingsIn the globalised economy if trade unions are to defend and advance the living standards of their members they cannot confine their activities to their national labour markets. Currently, trade unions attempt to do this via multi‐lateral link ups via Global Trade Union Federations and by developing links with their sister unions in other countries. A new mechanism is now being developed by trade unions to counter balance the economic strength of multi‐nationals, namely cross border trade union mergers.Originality/valueThe editorial offers insights into the reasons for, and gives examples, for the emerging trend of the movement towards cross border trade union mergers.
Trends in information categories on costume and textile collection web sites
Authors: Saiki Diana , Robbins Audrey 
Published: November 2008

PurposeThe purpose of this research is to assess trends in information categories featured on costume and textile collection web sites, and to assess differences in the online capabilities of these features between 1997 and 2006.Design/methodology/approachThe instrument was a content analysis of costume and textile collection web sites developed from a study completed in 1997. The previous study identified information categories which included hyperlinks to other sites, events calendars and forms to arrange visits, FAQs, online tours, and discussion group links. Information about education programs, contacting staff, volunteering, membership, and museum purchases was also noted. Data were collected from the 60 web sites used in the original study.FindingsThe findings revealed that costume and textile museums were using web sites to stimulate interest in visiting the physical museum. A picture of the artifact does not show all the specific features of an actual costume and textile, and thus the audience needs to actually visit the museum in order to learn about costume and textiles. A comparison of the 1997 and 2006 data revealed an increase in the frequency of features with higher levels of interaction capabilities.Research limitations/implicationsThe research was limited to observing web sites and web site information categories documented in the original study.Originality/valueThe paper identifies the information categories that costume and textile museums find most useful to fulfill audience needs and describes trends in the use of information on web sites which can serve as a guideline in developing museum web sites.