bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal management of diaphragmatic rhabdomyosarcoma presenting with fetal hydrops
Authors: Reitter A. , Peters J. , Wittekindt B. , Buxmann H. , Geka F. , Rolle U. , Schlößer R. , Louwen F. 
Published: October 2011

AbstractFetal malignant tumors are rare. We present a case of intrauterine diagnosis of a diaphragmatic tumor presenting with fetal hydrops at 32 weeks' gestation. The sonographic findings were bilateral pleural effusion, ascites and skin edema. A large right‐sided diaphragmatic tumor was identified. Owing to the findings on ultrasound and magnetic resonance imaging a solid malignant tumor was suspected. The pleural effusions were drained and malignant cells identified. Because of rapid tumor progression Cesarean section was performed and a hydropic female newborn was delivered at 34 + 0 weeks' gestation. There was no sign of metastatic disease. Postnatally tumor biopsy revealed an alveolar rhabdomyosarcoma. Therapy included chemotherapy and secondary surgical intervention. After a good primary response with complete remission after 6 months, the rhabdomyosarcoma relapsed at 12 months with cerebral metastasis. The prognosis was poor. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Preoperative diagnosis of metastatic ovarian cancer is related to origin of primary tumor
Authors: Guerriero S. , Alcazar J. L. , Pascual M. A. , Ajossa S. , Olartecoechea B. , Hereter L. 
Published: October 2011

AbstractObjectiveTo describe the gray‐scale and color Doppler ultrasound features as well as some clinical and biochemical features of metastatic ovarian tumors according to the origin of the primary tumor in a large study population,MethodsThis was a retrospective analysis of 116 masses in 92 patients (mean age, 51 years) evaluated and treated at three European university centers for a metastatic tumor in the ovary. All patients had undergone transvaginal color Doppler ultrasound according to a standardized protocol prior to surgery and tumor removal. Ultrasound features analyzed were bilaterality, tumor volume, morphologic gray‐scale appearance and color score. CA 125 was also recorded.ResultsPrimary tumor histological diagnosis was as follows: colon‐sigmoid (n = 32), stomach (n = 28), breast (n = 20), uterus (n = 17), lymphoma (n = 4), liver‐pancreas‐biliary tract (n = 4) and miscellaneous (n = 11). There were no differences in age, menopausal status or CA 125 values according to origin of primary tumor. Bilaterality was significantly more frequent in stomach metastases (56%) in comparison with colon‐sigmoid and liver‐pancreas‐biliary tract metastases (18.5% and 0%, respectively, P < 0.05). Median tumor volume was significantly lower in breast metastases (33.5 mL) compared with other metastases (P < 0.05) except stomach metastases and metastatic tumors from the miscellaneous group. Ovarian metastases from breast cancers were significantly more frequently solid in comparison to stomach, colorectal and uterine cancer metastases (95.0% vs. 60.8%, 46.8% and 70.6%, respectively, P < 0.05), and tended to appear moderately or highly vascularized. There were no differences in color score among all groups, although the percentage of masses with abundant color was high (50–82%).ConclusionsOvarian metastases derived from breast cancers tend to be small, solid and vascularized; they seem to be the only ovarian metastases whose primary tumor origin can be suspected by ultrasonography preoperatively. Color score does not seem to help suspect the origin of the primary tumor. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.
Clusters in dense-inertial granular flows
Authors: Campbell Charles S. 
Published: October 2011

AbstractIn the dense-inertial regime of granular flow, the stresses scale inertially, but the flow is dominated by clusters of particles. This paper describes observations of cluster development in this regime. Clusters were seen to form for both elastic and inelastic reasons: elastic when the shear rate pushes the particles together faster than the contacts can elastically disperse them, and inelastic as large energy dissipation leads to cluster formation. Furthermore, large particle surface friction leads to cluster formation both for structural reasons, because it generates stronger clusters, and for energetic reasons, as friction dissipates energy. However, the most intriguing result of this work is that clusters appear to have little effect on the rheology of the dense inertial regime, which suggests that one can model the dense inertial regime with entirely collisional hard sphere models, and not have to worry about the complexities of modelling clusters. But at the same time it presents a physical puzzle, as one would normally expect the rheology to be strongly dependent on microstructural features such as clusters, particularly as they present an elastic pathway for internal momentum transport. There is no completely satisfying explanation for why the clusters can be ignored, but two possibilities suggest themselves. Because the clusters are short-lived, it is possible that they do not survive long enough to make a significant contribution to the momentum transport. And it is also possible for the granular temperature that governs transport between clusters to act as a rate-limiting bottleneck that is in overall control of the momentum transport rate.
MAKING A LIVELIHOOD IN (AND BEYOND) THE AFRICAN CITY: THE EXPERIENCE OF ZIMBABWE
Authors: Potts Deborah 
Published: October 2011

ABSTRACTThe formal labour markets and economies of many cities in sub-Saharan Africa have been very weak for decades and this has led to significant adaptations in the nature of the livelihoods of most urban households. The lack of formal and reasonably paid jobs has also had a strong impact on population growth in cities, although this is often not recognized. This article reviews some of these trends and illustrates them with case study material from Harare, Zimbabwe. There, many urban residents have increasingly struggled to get by and their perceptions of the city and their future within it show a strong negative trend. Links to rural areas and the possibility of making livelihoods there in the future have become more important. These adaptations build on the long history of rural–urban linkages in sub-Saharan Africa but contemporary practices, including patterns of circular migration, are influenced by the harsh realities of African urban economies. The decisions and future plans of some migrants may not, therefore, fit with their aspirations – and the degree and nature of this mismatch are influenced by factors such as gender, age and position in the urban household, and links to rural areas. It is suggested that it helps to analyse the consequent migration patterns in terms of a framework in which migrants’ decisions to stay in the city or leave it are conceptualized as either willing or reluctant.
SEEING AND BEING SEEN: POLITICS, ART AND THE EVERYDAY IN OMAR BADSHA'S DURBAN PHOTOGRAPHY, 1960s–1980s
Authors: Hayes Patricia 
Published: October 2011

ABSTRACTThere is an assumption that the photographic iconography of the South African struggle against apartheid is universally known and familiar. It is however dominated by certain tropes and categories that obscure the many complexities and nuances of its origins, its practitioners and its effects. This article focuses on one photographer, Omar Badsha, and explores his own narrations about city and family life in the Indian Ocean port city of Durban, and the artistic and political trajectories in which he was embedded that gave rise to his own photographic work and the organization of other photographers into the collective known as Afrapix. Badsha grew up in ‘the imperial ghetto’ of Grey Street in Durban within a rich legacy of radical political and cultural debate, becoming an artist and later a trade union organizer. It is the imperatives of the latter work that pushed him into photography as a medium of literacy. Many of his own photographs started as a personal visual diary when he re-explored the spaces of his childhood as an adult, and in the process became increasingly sensitized to the parallels between political and religious ritual. In particular he was fascinated by the dynamics between the leaders and the led, and the techniques and theatricalities of the different genres of mobilization. His work and the multiple forces and influences at play suggest that there were (and are) plural and competing aesthetic regimes during (and after) apartheid that are little recognized, mostly due to a deeply entrenched (and ongoing) separation between the domains of aesthetics and politics in South Africa and elsewhere outside the African continent.
ERM for insurance companies – adding the investor's point of view
Authors: Hitchcox A. N. , Klumpes P. J. M. , McGaughey K. W. , Smith A. D. , Taverner N. H. 
Published: October 2011

AbstractA major outcome of ERM activities in insurance companies has been the bringing together of all of the key risks in the company, to be managed collectively in a holistic fashion. The authors of this paper believe that an ERM framework also needs to look beyond the company, and have regard to the risk management needs of investors, from the point of view of the contribution of the insurance company to the overall risk and reward of their total investment portfolios. To meet these needs, the ERM framework needs to provide sufficient information on topics such as systematic risk, potential correlations of earnings from future new business with macroeconomic trends, other risks to franchise value, and sources of model risk within the company. The paper does not provide solutions for the issues described above; but limits itself to describing and discussing the direction for some important new initiatives in ERM activities.
Galaxies on Sub-Galactic Scales
Authors: Jerjen Helmut 
Published: October 2011

AbstractThe Sloan Digital Sky Survey has been immensely successful in detecting new Milky Way satellite galaxies over the past seven years. It was instrumental in finding examples of the least luminous galaxies we know in the Universe, uncovering apparent inconsistencies between cold dark matter theory and dwarf galaxy properties, providing first evidence for a possible lower mass limit for dark matter halos in visible galaxies, and reopening the discussion about the building block scenario for the Milky Way halo. Nonetheless, these results are still drawn only from a relatively small number of galaxies distributed over an area covering about 29% of the sky, which leaves us currently with more questions than answers. The study of these extreme stellar systems is a multi-parameter problem: ages, metallicities, star formation histories, dark matter contents, population fractions and spatial distributions must be determined. Progress in the field is discussed and attention drawn to some of the limitations that currently hamper our ability to fully understand the phenomenon of the ‘ultra-faint dwarf galaxy’. In this context, the Stromlo Milky Way Satellite Survey represents a new initiative to systematically search and scrutinize optically elusive Milky Way satellite galaxies in the Southern hemisphere. In doing so, the program aims at investigating some of the challenging questions in stellar evolution, galaxy formation and near-field cosmology.
The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus
Authors: ElHefnawi Mahmoud , Hassan Nafisa , Kamar Mona , Siam Rania , Remoli Anna Lisa , El-Azab Iman , AlAidy Osama , Marsili Giulia , Sgarbanti Marco 
Published: October 2011

Abstract
Motivation: There is an urgent need for new medications to combat influenza pandemics.
Methods: Using the genome analysis of the influenza A virus performed previously, we designed and performed a combinatorial exhaustive systematic methodology for optimal design of universal therapeutic small interfering RNA molecules (siRNAs) targeting all diverse influenza A viral strains. The rationale was to integrate the factors for highly efficient design in a pipeline of analysis performed on possible influenza-targeting siRNAs. This analysis selects specific siRNAs that has the ability to target highly conserved, accessible and biologically significant regions. This would require minimal dosage and side effects.
Results and Discussion: First, &gt;6000 possible siRNAs were designed. Successive filtration followed where a novel method for siRNA scoring filtration layers was implemented. This method excluded siRNAs below the 90% experimental inhibition mapped scores using the intersection of 12 different scoring algorithms. Further filtration of siRNAs is done by eliminating those with off-targets in the human genome and those with undesirable properties and selecting siRNA targeting highly probable single-stranded regions. Finally, the optimal properties of the siRNA were ensured through selection of those targeting 100% conserved, biologically functional short motifs. Validation of a predicted active (sh114) and a predicted inactive (sh113) (that was filtered out in Stage 8) silencer of the NS1 gene showed significant inhibition of the NS1 gene for sh114, with negligible decrease for sh113 which failed target accessibility. This demonstrated the fertility of this methodology.
Contact: mahef@aucegypt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
Authors: Zhang Jin , Wu Yufeng 
Published: October 2011

Abstract
Motivation: Structural variation (SV), such as deletion, is an important type of genetic variation and may be associated with diseases. While there are many existing methods for detecting SVs, finding deletions is still challenging with low-coverage short sequence reads. Existing deletion finding methods for sequence reads either use the so-called split reads mapping for detecting deletions with exact breakpoints, or rely on discordant insert sizes to estimate approximate positions of deletions. Neither is completely satisfactory with low-coverage sequence reads.
Results: We present SVseq, an efficient two-stage approach, which combines the split reads mapping and discordant insert size analysis. The first stage is split reads mapping based on the Burrows–Wheeler transform (BWT), which finds candidate deletions. Our split reads mapping method allows mismatches and small indels, thus deletions near other small variations can be discovered and reads with sequencing errors can be utilized. The second stage filters the false positives by analyzing discordant insert sizes. SVseq is more accurate than an alternative approach when applying on simulated data and empirical data, and is also much faster.
Availability: The program SVseq can be downloaded at http://www.engr.uconn.edu/~jiz08001/
Contact: jinzhang@engr.uconn.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
BioTextQuest: a web-based biomedical text mining suite for concept discovery
Authors: Papanikolaou Nikolas , Pafilis Evangelos , Nikolaou Stavros , Ouzounis Christos A. , Iliopoulos Ioannis , Promponas Vasilis J. 
Published: October 2011

Abstract
Summary: BioTextQuest combines automated discovery of significant terms in article clusters with structured knowledge annotation, via Named Entity Recognition services, offering interactive user-friendly visualization. A tag-cloud-based illustration of terms labeling each document cluster are semantically annotated according to the biological entity, and a list of document titles enable users to simultaneously compare terms and documents of each cluster, facilitating concept association and hypothesis generation. BioTextQuest allows customization of analysis parameters, e.g. clustering/stemming algorithms, exclusion of documents/significant terms, to better match the biological question addressed.
Availability: http://biotextquest.biol.ucy.ac.cy
Contact: vprobon@ucy.ac.cy; iliopj@med.uoc.gr
Supplementary Information: Supplementary data are available at Bioinformatics online.
Pico-inplace-inversions between human and chimpanzee
Authors: Hou Minmei , Yao Ping , Antonou Angela , Johns Mitrick A. 
Published: October 2011

Abstract
Motivation: There have been several studies on the micro-inversions between human and chimpanzee, but there are large discrepancies among their results. Furthermore, all of them rely on alignment procedures or existing alignment results to identify inversions. However, the core alignment procedures do not take very small inversions into consideration. Therefore, their analyses cannot find inversions that are too small to be detected by a classic aligner. We call such inversions pico-inversions.
Results: We re-analyzed human–chimpanzee alignment from the UCSC Genome Browser for micro-inplace-inversions and screened for pico-inplace-inversions using a likelihood ratio test. We report that the quantity of inplace-inversions between human and chimpanzee is substantially greater than what had previously been discovered. We also present the software tool PicoInversionMiner to detect pico-inplace-inversions between closely related species.
Availability: Software tools, scripts and result data are available at http://faculty.cs.niu.edu/~hou/PicoInversion.html.
Contact: mhou@cs.niu.edu
FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis
Authors: Kumar Sudhir , Konikoff Charlotte , Van Emden Bernard , Busick Christopher , Davis Kailah T. , Ji Shuiwang , Wu Lin-Wei , Ramos Hector , Brody Thomas , Panchanathan Sethuraman , Ye Jieping , Karr Timothy L. , Gerold Kristyn , McCutchan Michael , Newfeld Stuart J. 
Published: October 2011

Abstract
Summary: Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.
Availability: http://www.flyexpress.net
Contact: s.kumar@asu.edu
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
Authors: Althammer Sonja , González-Vallinas Juan , Ballaré Cecilia , Beato Miguel , Eyras Eduardo 
Published: October 2011

Abstract
Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing.
Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics.
Availability: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy
Contact: eduardo.eyras@upf.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
Authors: Blakes Jonathan , Twycross Jamie , Romero−Campero Francisco Jose , Krasnogor Natalio 
Published: October 2011

Abstract
Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking.
Availability: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3.
Contact: Natalio.Krasnogor@nottingham.ac.uk
Automatic generation of protein structure cartoons with Pro-origami
Authors: Stivala Alex , Wybrow Michael , Wirth Anthony , Whisstock James C. , Stuckey Peter J. 
Published: October 2011

Abstract
Summary: Protein topology diagrams are 2D representations of protein structure that are particularly useful in understanding and analysing complex protein folds. Generating such diagrams presents a major problem in graph drawing, with automatic approaches often resulting in errors or uninterpretable results. Here we apply a breakthrough in diagram layout to protein topology cartoons, providing clear, accurate, interactive and editable diagrams, which are also an interface to a structural search method.
Availability: Pro-origami is available via a web server at http://munk.csse.unimelb.edu.au/pro-origami
Contact: a.stivala@pgrad.unimelb.edu.au; pjs@csse.unimelb.edu.au