bluuebunny/crossref_metadata_2025_split huggingface dataset:
A methodology for ontology update in the semantic grid environment
Authors: Flahive Andrew , Taniar David , Rahayu Wenny , Apduhan Bernady O. 
Published: May 2012

SummaryOntology as a formal representation of a domain knowledge has played an important role in a distributed environment whereby semantic interoperability is a major factor. In this paper, we particularly focus on a distributed ontology framework that utilizes Semantic Grid resources. The semantic representation in a machine‐understandable format (i.e., an ontology) is the backbone that enables interoperability between different user nodes in a semantic grid environment. However, the domain knowledge represented within an ontology is not static. From time to time, its concepts, properties and relationships need to be replaced or updated. Although many existing work have been focusing on how to utilize an ontology to support interoperability within a distributed environment, they often assume a rather static ontology. This paper focuses on formalizing and validating the process of ontology update, whereby sections of one ontology O2 are replaced by a subset extracted from another ontology O1. In the first phase, a subset S1 is extracted from ontology O1. Then in the second phase, the concepts in ontology O2 are replaced by S1. At the end of the process, the resulting ontology O2 must still be a valid ontology. A semantic completeness checking also needs to be conducted so that the updated ontology O2 is complete. A case study based on the Unified Medical Language System ontology from the medical informatics domain is presented. We use a semantic grid environment to build a framework for reusing, extracting and updating an ontology using a SOA. These allow the subset extracted from one ontology, to replace sections of another ontology, using shared resources in the semantic grid environment. A prototype of the framework is built using Web Services and a complexity evaluation measure is presented. The results of several simulations show ontology update in the semantic grid is a viable solution and can be further optimized. Copyright © 2012 John Wiley & Sons, Ltd.
Automatic segmentation of cell nuclei in Feulgen‐stained histological sections of prostate cancer and quantitative evaluation of segmentation results
Authors: Nielsen Birgitte , Albregtsen Fritz , Danielsen Håvard E. 
Published: May 2012

AbstractDigital image analysis of cell nuclei is useful to obtain quantitative information for the diagnosis and prognosis of cancer. However, the lack of a reliable automatic nuclear segmentation is a limiting factor for high‐throughput nuclear image analysis. We have developed a method for automatic segmentation of nuclei in Feulgen‐stained histological sections of prostate cancer. A local adaptive thresholding with an object perimeter gradient verification step detected the nuclei and was combined with an active contour model that featured an optimized initialization and worked within a restricted region to improve convergence of the segmentation of each nucleus. The method was tested on 30 randomly selected image frames from three cases, comparing the results from the automatic algorithm to a manual delineation of 924 nuclei. The automatic method segmented a few more nuclei compared to the manual method, and about 73% of the manually segmented nuclei were also segmented by the automatic method. For each nucleus segmented both manually and automatically, the accuracy (i.e., agreement with manual delineation) was estimated. The mean segmentation sensitivity/specificity were 95%/96%. The results from the automatic method were not significantly different from the ground truth provided by manual segmentation. This opens the possibility for large‐scale nuclear analysis based on automatic segmentation of nuclei in Feulgen‐stained histological sections. © 2012 International Society for Advancement of Cytometry
Fluorescence in situ hybridization of three oncogenes on a leiomyoma
Authors: Faruqi Shamim Ahmad , Saquib Mohammad , Harsch Christopher , Noumoff Joel S. 
Published: May 2012

AbstractUsing fluorescence in situ hybridization technique, expression of three oncogenes, C‐myc, RARa, and cyclin‐D was tested on a uterine leiomyoma. C‐myc and RARa were amplified in approximately 30% and 90% of the cells, respectively. Numerous small signals of C‐myc were indicative of the presence of double minutes. Amplification of RARa is being reported for the first time in a leiomyoma. Cyclin‐D was normal in diploid cells while it was highly amplified in polyploid cells. Low levels of amplified C‐myc and cyclin‐D cells seem to be the reason for this tumor to be benign, while RARa could not be effective without the association of some other gene such as PML. Information presented here are significant toward developing new curative strategies such as gene‐specific drugs and molecular manipulation to stop the activity of cancer gene. Further study may elucidate that how fibroids grow and maintain their rare benign nature. Microsc. Res. Tech. 75:1147–1149, 2012. © 2012 Wiley Periodicals, Inc.
Microvascular patterns in the blubber of shallow and deep diving odontocetes
Authors: McClelland Sara J. , Gay Mark , Pabst D. Ann , Dillaman Richard , Westgate Andrew J. , Koopman Heather N. 
Published: May 2012

AbstractBlubber, a specialized form of subdermal adipose tissue, surrounds marine mammal bodies. Typically, adipose tissue is perfused by capillaries but information on blubber vascularization is lacking. This study's goals were to: 1) describe and compare the microvasculature (capillaries, microarterioles, and microvenules) of blubber across odontocete species; 2) compare microvasculature of blubber to adipose tissue; and 3) examine relationships between blubber's lipid composition and its microvasculature. Percent microvascularity, distribution, branching pattern, and diameter of microvessels were determined from images of histochemically stained blubber sections from shallow‐diving bottlenose dolphins (Tursiops truncatus), deeper‐diving pygmy sperm whales (Kogia breviceps), deep‐diving beaked whales (Mesoplodon densirostris; Ziphius cavirostris), and the subdermal adipose tissue of domestic pigs (Sus scrofa). Tursiops blubber showed significant stratification in percent microvascularity among the superficial, middle, and deep layers and had a significantly higher percent microvascularity than all other animals analyzed, in which the microvasculature was more uniformly distributed. The percent microvasculature of Kogia blubber was lower than that of Tursiops but higher than that of beaked whales and the subdermal adipose tissue of domestic pigs. Tursiops had the most microvascular branching. Microvessel diameter was relatively uniform in all species. There were no clear patterns associating microvascular and lipid characteristics. The microvascular characteristics of the superficial layer of blubber resembled the adipose tissue of terrestrial mammals, suggesting some conservation of microvascular patterns in mammalian adipose tissue. The middle and deep layers of blubber, particularly in Tursiops, showed the greatest departure from typical mammalian microvascular arrangement. Factors such as metabolics or thermoregulation may be influencing the microvasculature in these layers. © J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.
Modelling runoff in a Swiss glacierized catchment—part I: methodology and application in the Findelen basin under a long‐lasting stable climate
Authors: Uhlmann Bastienne , Jordan Frédéric , Beniston Martin 
Published: May 2012

AbstractThe complex topography of the Alps makes detailed hydrological modelling a real challenge. It is yet an essential task to improve the insight of hydrological processes in the context of intensification of renewable energy use and under the constraints of climate change. In this perspective and as a case study, the runoff of a small highly glacierized basin in the Swiss Alps—namely the Findelen catchment area—has been modelled with a hydrological model (Routing System 3.0; RS3.0). It is a conceptual model, based on object‐oriented programming and it computes snow‐melt, glaciers, infiltration and runoff processes. As input, it requires hourly air temperatures and precipitation, and the geomorphologic features of the catchment area and glacier. RS3.0 has proven to be very efficient in reproducing discharge. To evaluate the impacts of climate change on runoff—the final objective of the study addressed in a companion paper—a stochastic meteorological data generator has been developed to reproduce a sequence of air temperature and precipitation over more than one century. In this way, a continuous series of daily discharge values has been simulated by RS3.0 with the stochastic input data. This methodology has also enabled an assessment of the glacier response time to a stable climate. Indeed, if the climatic conditions of the standard reference period 1961‐1990 were to be preserved throughout the 21st century, the simulation shows that the watershed would be slow to adapt: the glaciers would be balanced with the atmospheric conditions and the water discharge would reach a lower stable value in more than 40 years. However, the glacierized area would lose only 3.5% of its surface. Copyright © 2012 Royal Meteorological Society
Downscaled GCM projections of winter and summer mass balance for Central European glaciers (2000–2100) from ensemble simulations with ECHAM5‐MPIOM
Authors: Springer Claudia , Matulla Christoph , Schöner Wolfgang , Steinacker Reinhold , Wagner Sebastian 
Published: May 2012

AbstractThis study is based on the study from Matulla et al. (2009) where the glacier under estimation has been Peyto Glacier in Canada. The same methods have been used for five Austrian glaciers; projections of glacier mass balance are generated from ensembles of general circulation model (GCM) simulations by the use of direct statistical downscaling. Thereby, the general features of the atmospheric circulation over an expanded geographical region covering the European Alps are linked empirically to winter and summer mass balance records measured at five glaciers in Austria. The projections are taken from an ensemble of ECHAM5‐MPIOM simulations forced with the IPCC‐SRES scenarios A1B and B1. Results based on the statistical downscaling indicate decreasing balances for both winter and summer. These results suggest continued frontal recession and downwasting of the alpine glaciers in this region until 2100. For Jamtalferner, these suggestions reach reductions of about 1000 mm water equivalent in summer. Copyright © 2012 Royal Meteorological Society
Head and neck soft tissue sarcomas: Unique lack of significance of synchronous node metastases
Authors: Smith Valerie A. , Overton Lewis J. , Lentsch Eric J. 
Published: May 2012

AbstractBackgroundRegional lymph node metastasis (RLNM) has been identified as a poor prognostic indicator for patients with soft tissue sarcomas (STS) of the extremities and trunk. However, the effect of RLNM on survival in patients with STS of the head and neck (HN) has not previously been explored. Our objective was to analyze RLNM as a prognostic indicator in HN‐STS, and to compare this cohort to patients with STS of non‐head and neck regions (NHN‐STS).MethodsSTS patients were identified using the Surveillance, Epidemiology, and End Results database. Only patients without concurrent distant metastasis who underwent surgery and pathologic node staging were included. Patients were categorized based on tumor location: (1) HN‐STS and (2) NHN‐STS. Clinicopathologic data and disease‐specific survival (DSS) were compared between node‐negative and node‐positive patients in each group.ResultsWe identified 183 cases of node‐positive STS (25 HN‐STS, 158 NHN‐STS). In the HN‐STS group, pN1 status was not associated with any of the clinicopathologic factors that we analyzed. DSS was similar among pN0 and pN1 patients with HN‐STS (P = 0.59); however, in the NHN‐STS group, node‐positivity was significantly associated with disease‐specific mortality (P < 0.001).ConclusionsSynchronous RLNM may not affect DSS in patients HN‐STS. Node‐positive patients with HN‐STS appear to be unique from those with NHN‐STS. J. Surg. Oncol. 2012; 106:837–843. © 2012 Wiley Periodicals, Inc.
A new semi‐automated method for fetal volume measurements with three‐dimensional ultrasound: preliminary results
Authors: Smeets Nicol A. C. , Dvinskikh Natallia A. , Winkens Bjorn , Oei S. Guid 
Published: May 2012

ABSTRACTObjectiveComplications in pregnancy are suggested to be the result of intrauterine conditions in the first trimester of pregnancy. Three‐dimensional ultrasound volume measurements might give more information, compared with two‐dimensional measurements. Commonly available methods for volume measurements are not suited for daily practice. This is a report of preliminary results of a promising, more practical semi‐automated method for volume calculations with three‐dimensional ultrasound.MethodVolume datasets of 16 objects (10.2–41.5 cm3) were obtained. Euclidean shortening flow and Perona and Malik were used as image enhancement techniques. The image gradient was calculated. The points of interest were detected by the iso‐intensity and the edge‐detection technique. Volume measurements with Volume Computer‐aided AnaLysis (VOCAL) are used as a reference. A volume dataset of a first trimester fetus was acquired to test this method in vivo.ResultsThe mathematical calculations with iso‐intensity (Perona and Malik: average = −1.57 cm3, SD = 4.05; and Euclidean shortening flow: average = −1.38 cm3, SD = 2.47) showed results comparable with the VOCAL method (average = +1.28 cm3, SD = 2.07). We also succeeded in detecting all voxels in the whole contour of a 12‐week fetus.ConclusionMathematical volume calculations are possible with the semi‐automated method. We were able to apply this new method on a first trimester fetus. This new method is promising for future use in the daily practice. © 2012 John Wiley & Sons, Ltd.
Postmortem examination of human fetal hearts at or below 20 weeks' gestation: a comparison of high‐field MRI at 9.4 T with lower‐field MRI magnets and stereomicroscopic autopsy
Authors: Votino C. , Jani J. , Verhoye M. , Bessieres B. , Fierens Y. , Segers V. , Vorsselmans A. , Kang X. , Cos T. , Foulon W. , De Mey J. , Cannie M. 
Published: May 2012

AbstractObjectivesTo compare the diagnostic usefulness of high‐field with low‐field magnetic resonance imaging (MRI) and stereomicroscopic autopsy for examination of the heart in fetuses at or under 20 weeks' gestation.MethodsPrior to invasive stereomicroscopic autopsy, MRI scans at 9.4, 3.0 and 1.5 T were performed on 24 fetuses between 11 and 20 weeks' gestation, including 10 fetuses with cardiac abnormalities. The ability to visualize different heart structures was evaluated according to the different field strength MRI magnets used and gestational age at examination.ResultsOn 1.5‐ and 3.0‐T MRI, only the heart situs and four‐chamber view could be visualized consistently (in 75% or more of cases) when the fetus was beyond 16 weeks' gestation, but other heart structures could not be visualized for fetuses at any gestational age. In contrast, using high‐field MRI at 9.4 T, the heart situs, four‐chamber view and the outflow tracts could be visualized in all fetuses irrespective of gestational age. Using high‐field MRI, the sensitivity for detecting an abnormality of the four‐chamber view was 66.7% (95% CI, 30.1–92.1%) with a specificity of 80.0% (95% CI, 51.9–95.4%). For abnormalities of the outflow tracts, sensitivity was 75.0% (95% CI, 20.3–95.9%) and specificity 100.0% (95% CI, 83.3–100.0%). Eight fetuses out of 10 with congenital heart disease (CHD) were classified as having major CHD. High‐field MRI at 9.4 T was able to identify seven out of the eight cases of major CHD.ConclusionHigh‐field MRI at 9.4 T seems to be an acceptable alternative approach to invasive stereomicroscopic autopsy for fetuses with CHD at or below 20 weeks' gestation. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Climate change regional review: Poland
Authors: Kundzewicz Zbigniew W. , Matczak Piotr 
Published: May 2012

AbstractPoland is a country where a climate change warming signal can be detected in temperature, but observed changes in other variables, and especially in precipitation, are complex. Temperature projections indicate further warming, but models do not agree as to seasonal distribution of changes in precipitation. This article reviews evidence for climate change and its impacts in Poland, in the context of observations and projections. It also reviews various aspects of climate change mitigation policy in the country whose energy supply is more coal‐dominated than any other country. This is one reason why climate change mitigation efforts are modest and climate policy largely passive. The dramatic decline of industrial production involving a rapid decline in CO2 emissions during 1989–1992 was the crucial element of the Poland's position in the negotiations of international agreements. The European Union (EU) accession in 2004 tied Poland to EU climate policy. This cautious approach is largely in harmony with public attitudes. Poles are aware of climate change, but it is not considered as a priority issue and public opinion is divided about the issues of mitigation. Adaptation to climate change impacts in Poland is driven by the fact that observed impacts are not very large and there is no persuasive attribution of these impacts to greenhouse gas emissions. Reactive adaptation to climate change is preferred over anticipatory adaptation. There are several ‘special care’ areas in Poland in terms of adaptation: the mountains; the coastal zone of the Baltic Sea; and the river valleys. WIREs Clim Change 2012 doi: 10.1002/wcc.175This article is categorized under:

Trans‐Disciplinary Perspectives > National Reviews
Sex and the circuitry: progress toward a systems‐level understanding of vertebrate sex determination
Authors: Munger Steven C. , Capel Blanche 
Published: May 2012

AbstractIn vertebrates, the gonad arises as a bipotential primordium that can differentiate as a testis or ovary. Cells are initially primed to adopt either fate by balanced antagonistic signaling pathways and transcription networks. Sexual fate is determined by activating the testis or ovarian pathway and repressing the alternative pathway. A complex, dynamic transcription network underlies this process, as approximately half the genome is being transcribed during this period, and many genes are expressed in a sexually dimorphic manner. This network is highly plastic; however, multiple lines of evidence suggest that many elements of the pathway converge on the stabilization or disruption of Sox9 expression. The single gene mutational approach has led to the identification of ∼30 additional genes involved in vertebrate sex determination. However, >50% of human disorders of sexual development (DSDs) are not explained by any of these genes, suggesting many critical elements of the system await discovery. Emerging technologies and genetic resources enable the investigation of the sex determination network on a global scale in the context of a variable genetic background or environmental influences. Using these new tools we can investigate how cells establish a bipotential state that is poised to adopt either sexual fate, and how they integrate multiple signaling and transcriptional inputs to drive a cell fate decision. Elucidating the genetic architecture underlying sex determination in model systems can lead to the identification of conserved modules correlated with phenotypic outcomes, and critical pressure points in the network that predict genes involved in DSDs in humans. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1172This article is categorized under:

Biological Mechanisms > Cell Fates
Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models
The Laboratory‐Clinician Team: A Professional Call to Action to Improve Communication and Collaboration for Optimal Patient Care in Chromosomal Microarray Testing
Authors: Wain Karen E. , Riggs Erin , Hanson Karen , Savage Melissa , Riethmaier Darlene , Muirhead Andrea , Mitchell Elyse , Packard Bethanny Smith , Faucett W. Andrew 
Published: May 2012

AbstractThe International Standards for Cytogenomic Arrays (ISCA) Consortium is a worldwide collaborative effort dedicated to optimizing patient care by improving the quality of chromosomal microarray testing. The primary effort of the ISCA Consortium has been the development of a database of copy number variants (CNVs) identified during the course of clinical microarray testing. This database is a powerful resource for clinicians, laboratories, and researchers, and can be utilized for a variety of applications, such as facilitating standardized interpretations of certain CNVs across laboratories or providing phenotypic information for counseling purposes when published data is sparse. A recognized limitation to the clinical utility of this database, however, is the quality of clinical information available for each patient. Clinical genetic counselors are uniquely suited to facilitate the communication of this information to the laboratory by virtue of their existing clinical responsibilities, case management skills, and appreciation of the evolving nature of scientific knowledge. We intend to highlight the critical role that genetic counselors play in ensuring optimal patient care through contributing to the clinical utility of the ISCA Consortium's database, as well as the quality of individual patient microarray reports provided by contributing laboratories. Current tools, paper and electronic forms, created to maximize this collaboration are shared. In addition to making a professional commitment to providing complete clinical information, genetic counselors are invited to become ISCA members and to become involved in the discussions and initiatives within the Consortium.
Abnormal brain function of the rat neonate in a prenatal 5‐bromo‐2′‐deoxyuridine (BrdU)‐induced developmental disorder model
Authors: Ogawa Tetsuo , Kuwagata Makiko , Muneoka Katsumasa , Wakai Chizu , Senuma Mika , Kubo Hiroko , Shioda Seiji 
Published: May 2012

AbstractNeonatal brain function was investigated in a prenatal BrdU‐induced developmental disorder model, which has been reported to exhibit behavioral abnormalities such as locomotor hyperactivity, impaired learning and memory, and lower anxiety in offspring. After 1 h home cage deprivation we observed an increase in the number of c‐Fos (neuronal activity marker) immunoreactive cells in several brain regions of the olfactory and stress‐related areas in normal neonates at 11 days. Next, pregnant rats were exposed to 50 mg/kg of BrdU from gestation days 9–15, and their offspring at 11 days were home‐cage deprived. Compared to vehicle control, the number of c‐Fos immunoreactive cells in BrdU group was found to be decreased in the piriform cortex and locus coeruleus, which are known to play an important role in neonatal learning and memory. We also analyzed Pearson product–moment correlation coefficient of the number of c‐Fos immunoreactive cells, focusing on the piriform cortex and locus coeruleus versus numerous other brain areas (11 areas including amygdala). Numerous significant correlations were observed in the vehicle control group, however, correlations of the locus coeruleus disappeared in the BrdU group. By observing c‐Fos immunoreactivity after home cage deprivation our study uncovers abnormal brain functions as early as postnatal day 11 in this disorder model. Based on these results, we propose a new histological approach for functional characterization of developmental disorder models.