bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tornado Climatology of Finland
Authors: Rauhala Jenni , Brooks Harold E. , Schultz David M. 
Published: December 2011

Abstract
A tornado climatology for Finland is constructed from 1796 to 2007. The climatology consists of two datasets. A historical dataset (1796–1996) is largely constructed from newspaper archives and other historical archives and datasets, and a recent dataset (1997–2007) is largely constructed from eyewitness accounts sent to the Finnish Meteorological Institute and news reports. This article describes the process of collecting and evaluating possible tornado reports. Altogether, 298 Finnish tornado cases compose the climatology: 129 from the historical dataset and 169 from the recent dataset. An annual average of 14 tornado cases occur in Finland (1997–2007). A case with a significant tornado (F2 or stronger) occurs in our database on average every other year, composing 14% of all tornado cases. All documented tornadoes in Finland have occurred between April and November. As in the neighboring countries in northern Europe, July and August are the months with the maximum frequency of tornado cases, coincident with the highest lightning occurrence both over land and sea. Waterspouts tend to be favored later in the summer, peaking in August. The peak month for significant tornadoes is August. The diurnal peak for tornado cases is 1700–1859 local time.
GPIbα regulates platelet size by controlling the subcellular localization of filamin
Authors: Kanaji Taisuke , Ware Jerry , Okamura Takashi , Newman Peter J. 
Published: December 2011

AbstractInteraction between the cytoplasmic domain of GPIbα with its cytoskeletal binding partner, filamin, is a major determinant of platelet size, and deficiency of either protein results in macrothrombocytopenia. To clarify the mechanism by which GPIbα-filamin interactions regulate platelet production, we manipulated the expression levels of filamin and GPIb in cultured embryonic stem cells (ESCs) that were subsequently differentiated into platelets. Knocking down filamins A and B resulted in the production of ESC-derived proplatelets with abnormally large swellings and proplatelet shafts that generated giant platelets in culture. Large platelets could also be generated by overexpressing GPIbα in ESCs, or by overexpressing in vivo a transgene encoding a chimeric protein containing the cytoplasmic domain of GPIbα. To identify the mechanism by which the GPIb:filamin ratio regulates platelet size, we manipulated filamin and GPIbα levels in HEK293T cells and examined the effects of overexpressing either protein on their ability to traffic to the cell periphery. Accumulation of either protein within the endoplasmic reticulum resulted in trapping of the other. Taken together, these data demonstrate that coordinated expression of GPIbα and filamin is required for efficient trafficking of either protein to the cell surface, and for production of normal-sized platelets.
HMGA1 drives stem cell, inflammatory pathway, and cell cycle progression genes during lymphoid tumorigenesis
Authors: Schuldenfrei Andrew , Belton Amy , Kowalski Jeanne , Talbot C Conover , Di Cello Francescopaolo , Poh Weijie , Tsai Hua-Ling , Shah Sandeep N , Huso Tait H , Huso David L , Resar Linda MS 
Published: December 2011

AbstractBackgroundAlthough thehigh mobility group A1(HMGA1) gene is widely overexpressed in diverse cancers and portends a poor prognosis in some tumors, the molecular mechanisms that mediate its role in transformation have remained elusive.HMGA1functions as a potent oncogene in cultured cells and induces aggressive lymphoid tumors in transgenic mice. Because HMGA1 chromatin remodeling proteins regulate transcription,HMGA1is thought to drive malignant transformation by modulating expression of specific genes. Genome-wide studies to define HMGA1 transcriptional networks during tumorigenesis, however, are lacking. To define the HMGA1 transcriptome, we analyzed gene expression profiles in lymphoid cells fromHMGA1atransgenic mice at different stages in tumorigenesis.ResultsRNA from lymphoid samples at 2 months (before tumors develop) and 12 months (after tumors are well-established) was screened for differential expression of > 20,000 unique genes by microarray analysis (Affymetrix) using a parametric and nonparametric approach. Differential expression was confirmed by quantitative RT-PCR in a subset of genes. Differentially expressed genes were analyzed for cellular pathways and functions using Ingenuity Pathway Analysis. Early in tumorigenesis, HMGA1 induced inflammatory pathways with NFkappaB identified as a major node. In established tumors, HMGA1 induced pathways involved in cell cycle progression, cell-mediated immune response, and cancer. At both stages in tumorigenesis, HMGA1 induced pathways involved in cellular development, hematopoiesis, and hematologic development. Gene set enrichment analysis showed that stem cell and immature T cell genes are enriched in the established tumors. To determine if these results are relevant to human tumors, we knocked-down HMGA1 in human T-cell leukemia cells and identified a subset of genes dysregulated in both the transgenic and human lymphoid tumors.ConclusionsWe found thatHMGA1induces inflammatory pathways early in lymphoid tumorigenesis and pathways involved in stem cells, cell cycle progression, and cancer in established tumors.HMGA1also dyregulates genes and pathways involved in stem cells, cellular development and hematopoiesis at both early and late stages of tumorigenesis. These results provide insight intoHMGA1function during tumor development and point to cellular pathways that could serve as therapeutic targets in lymphoid and other human cancers with aberrantHMGA1expression.
Genetic architecture of gene expression in ovine skeletal muscle
Authors: Kogelman Lisette JA , Byrne Keren , Vuocolo Tony , Watson-Haigh Nathan S , Kadarmideen Haja N , Kijas James W , Oddy Hutton V , Gardner Graham E , Gondro Cedric , Tellam Ross L 
Published: December 2011

Abstract

Background
In livestock populations the genetic contribution to muscling is intensively monitored in the progeny of industry sires and used as a tool in selective breeding programs. The genes and pathways conferring this genetic merit are largely undefined. Genetic variation within a population has potential, amongst other mechanisms, to alter gene expression via cis- or trans-acting mechanisms in a manner that impacts the functional activities of specific pathways that contribute to muscling traits. By integrating sire-based genetic merit information for a muscling trait with progeny-based gene expression data we directly tested the hypothesis that there is genetic structure in the gene expression program in ovine skeletal muscle.

Results
The genetic performance of six sires for a well defined muscling trait, longissimus lumborum muscle depth, was measured using extensive progeny testing and expressed as an Estimated Breeding Value by comparison with contemporary sires. Microarray gene expression data were obtained for longissimus lumborum samples taken from forty progeny of the six sires (4-8 progeny/sire). Initial unsupervised hierarchical clustering analysis revealed strong genetic architecture to the gene expression data, which also discriminated the sire-based Estimated Breeding Value for the trait. An integrated systems biology approach was then used to identify the major functional pathways contributing to the genetics of enhanced muscling by using both Estimated Breeding Value weighted gene co-expression network analysis and a differential gene co-expression network analysis. The modules of genes revealed by these analyses were enriched for a number of functional terms summarised as muscle sarcomere organisation and development, protein catabolism (proteosome), RNA processing, mitochondrial function and transcriptional regulation.

Conclusions
This study has revealed strong genetic structure in the gene expression program within ovine longissimus lumborum muscle. The balance between muscle protein synthesis, at the levels of both transcription and translation control, and protein catabolism mediated by regulated proteolysis is likely to be the primary determinant of the genetic merit for the muscling trait in this sheep population. There is also evidence that high genetic merit for muscling is associated with a fibre type shift toward fast glycolytic fibres. This study provides insight into mechanisms, presumably subject to strong artificial selection, that underpin enhanced muscling in sheep populations.
Can the risk of secondary cancer induction after breast conserving therapy be reduced using intraoperative radiotherapy (IORT) with low-energy x-rays?
Authors: Aziz Muhammad Hammad , Schneider Frank , Clausen Sven , Blank Elena , Herskind Carsten , Afzal Muhammad , Wenz Frederik 
Published: December 2011

Abstract

Background
Radiation induced secondary cancers are a rare but severe late effect after breast conserving therapy. Intraoperative radiotherapy (IORT) is increasingly used during breast conserving surgery. The purpose of this analysis was to estimate secondary cancer risks after IORT compared to other modalities of breast radiotherapy (APBI - accelerated partial breast irradiation, EBRT - external beam radiotherapy).

Methods
Computer-tomography scans of an anthropomorphic phantom were acquired with an INTRABEAM IORT applicator (diameter 4 cm) in the outer quadrant of the breast and transferred via DICOM to the treatment planning system. Ipsilateral breast, contralateral breast, ipsilateral lung, contralateral lung, spine and heart were contoured. An INTRABEAM source (50 kV) was defined with the tip of the drift tube at the center of the spherical applicator. A dose of 20 Gy at 0 mm depth from the applicator surface was prescribed for IORT and 34 Gy (5 days × 2 × 3.4 Gy) at 10 mm depth for APBI. For EBRT a total dose of 50 Gy in 2 Gy fractions was planned using two tangential fields with wedges. The mean and maximal doses, DVHs and volumes receiving more than 0.1 Gy and 4 Gy of organs at risk (OAR) were calculated and compared. The life time risk for secondary cancers was estimated according to NCRP report 116.

Results
IORT delivered the lowest maximal doses to contralateral breast (< 0.3 Gy), ipsilateral (1.8 Gy) and contralateral lung (< 0.3 Gy), heart (1 Gy) and spine (< 0.3 Gy). In comparison, maximal doses for APBI were 2-5 times higher. EBRT delivered a maximal dose of 10.4 Gy to the contralateral breast and 53 Gy to the ipsilateral lung. OAR volumes receiving more than 4 Gy were 0% for IORT, < 2% for APBI and up to 10% for EBRT (ipsilateral lung). The estimated risk for secondary cancer in the respective OAR is considerably lower after IORT and/or APBI as compared to EBRT.

Conclusions
The calculations for maximal doses and volumes of OAR suggest that the risk of secondary cancer induction after IORT is lower than compared to APBI and EBRT.
Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network
Authors: Wang Jin , Haubrock Martin , Cao Kun-Ming , Hua Xu , Zhang Chen-Yu , Wingender Edgar , Li Jie 
Published: December 2011

AbstractBackgroundMicroRNA (miRNA) is a class of small RNAs of ~22nt which play essential roles in many crucial biological processes and numerous human diseases at post-transcriptional level of gene expression. It has been revealed that miRNA genes tend to be clustered, and the miRNAs organized into one cluster are usually transcribed coordinately. This implies a coordinated regulation mode exerted by clustered miRNAs. However, how the clustered miRNAs coordinate their regulations on large scale gene expression is still unclear.ResultsWe constructed the miRNA-transcription factor regulatory network that contains the interactions between transcription factors (TFs), miRNAs and non-TF protein-coding genes, and made a genome-wide study on the regulatory coordination of clustered miRNAs. We found that there are two types of miRNA clusters, i.e. homo-clusters that contain miRNAs of the same family and hetero-clusters that contain miRNAs of various families. In general, the homo-clustered as well as the hetero-clustered miRNAs both exhibit coordinated regulation since the miRNAs belonging to one cluster tend to be involved in the same network module, which performs a relatively isolated biological function. However, the homo-clustered miRNAs show a direct regulatory coordination that is realized by one-step regulation (i.e. the direct regulation of the coordinated targets), whereas the hetero-clustered miRNAs show an indirect regulatory coordination that is realized by a regulation comprising at least three steps (e.g. the regulation on the coordinated targets by a miRNA through a sequential action of two TFs). The direct and indirect regulation target different categories of genes, the former predominantly regulating genes involved in emergent responses, the latter targeting genes that imply long-term effects.ConclusionThe genomic clustering of miRNAs is closely related to the coordinated regulation in the gene regulatory network. The pattern of regulatory coordination is dependent on the composition of the miRNA cluster. The homo-clustered miRNAs mainly coordinate their regulation rapidly, while the hetero-clustered miRNAs exert control with a delay. The diverse pattern of regulatory coordination suggests distinct roles of the homo-clustered and the hetero-clustered miRNAs in biological processes.
Epidemiology and outcome of cardiac arrests reported in the lay-press: an observational study
Authors: Field Richard A , Soar Jasmeet , Nolan Jerry P , Perkins Gavin D 
Published: December 2011

Objective The aims of this study were to evaluate the frequency with which cardiac arrests are reported in newspapers, assess the level of detail reported and ascertain whether this coverage gives a realistic portrayal of cardiac arrest outcomes to the lay-reader. Design Observational study. Setting All UK newspaper articles published between 1 January 2010 and 30 June 2010. Participants Articles containing the words ‘cardiac arrest’, ‘CPR’ or ‘resuscitation’ were screen for eligibility. Any articles not involving reference to a real cardiac arrest were excluded. Main outcome measures Data relating to patient demographics, arrest characteristics, treatment (CPR and defibrillation) and survival using the Utstein template were extracted. The results were then compared with cardiac arrest statistics from epidemiological studies. Results Six hundred and forty-eight articles were reviewed, 203 of which referred to individual cardiac arrest events; 22 events occurred in-hospital and 181 occurred out-of-hospital. In the out-of-hospital cardiac arrest (OHCA) group 32 (17.7%) were reported to survive to hospital discharge, almost all with good neurological outcome. The median age group was 31–45-year-olds, 52 (28.7%) were women and 40 were children. Seventy-five percent of victims received bystander CPR with 13 being attended to by lay-responders using AEDs, eight of which presented with a shockable rhythm of which six made a full recovery. Conclusion Survival to hospital discharge rate among newspaper reports was double that of complete epidemiological studies of OHCAs in urban environments. Newspapers may give readers an over-optimistic portrayal of cardiac arrest survival and neurological outcome following successful resuscitation.
Extranodal Marginal Zone Lymphoma of Mucosa-Associated Lymphoid Tissue With Amyloid Deposition
Authors: Ryan Russell J.H. , Sloan J. Mark , Collins A. Bernard , Mansouri Jaleh , Raje Noopur S. , Zukerberg Lawrence R. , Ferry Judith A. 
Published: December 2011

Abstract
Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) lymphoma is a mature B-cell neoplasm that typically follows an indolent clinical course. Amyloid deposition associated with MALT lymphoma is uncommon. We describe the clinical and pathologic features of 20 cases of MALT lymphoma and associated amyloid deposition across diverse primary sites. Frozen section immunofluorescence performed on 4 cases suggests that these deposits are a localized form of AL amyloid.
Clinical follow-up was available for 15 patients. Amyloid deposits distant from the initial site occurred in 5 cases, always at sites also involved by the underlying lymphoma. No definitive evidence of systemic amyloidosis affecting the heart, kidneys, or liver was present in any patient. Given the generally indolent clinical behavior of MALT lymphomas with associated amyloid, we do not recommend extensive follow-up testing for systemic amyloidosis or more aggressive therapy than would be indicated for other MALT lymphomas of similar clinical stage.
Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing
Authors: Bowen Margot E , Henke Katrin , Siegfried Kellee R , Warman Matthew L , Harris Matthew P 
Published: December 2011

AbstractThe generation and analysis of mutants in zebrafish has been instrumental in defining the genetic regulation of vertebrate development, physiology, and disease. However, identifying the genetic changes that underlie mutant phenotypes remains a significant bottleneck in the analysis of mutants. Whole-genome sequencing has recently emerged as a fast and efficient approach for identifying mutations in nonvertebrate model organisms. However, this approach has not been applied to zebrafish due to the complicating factors of having a large genome and lack of fully inbred lines. Here we provide a method for efficiently mapping and detecting mutations in zebrafish using these new parallel sequencing technologies. This method utilizes an extensive reference SNP database to define regions of homozygosity-by-descent by low coverage, whole-genome sequencing of pooled DNA from only a limited number of mutant F2 fish. With this approach we mapped each of the five different zebrafish mutants we sequenced and identified likely causative nonsense mutations in two and candidate mutations in the remainder. Furthermore, we provide evidence that one of the identified mutations, a nonsense mutation in bmp1a, underlies the welded mutant phenotype.
Experiments and Analysis of Multiscale Viscous Fingering during Forced Imbibition
Authors: Sharma Jyotsna , Inwood1 S. B , Kovscek A. R. 
Published: December 2011

Abstract
Immiscible displacement of one fluid by another in porous media has practical applications where viscous oil is produced by water injection. A greater understanding of the flow patterns that evolve during such unstable displacements yields insights to improve predictive capability and increase oil recovery. Immiscible multiphase displacement exhibits a wide range of behaviors depending on the relative magnitude of viscous, capillary, and gravity forces. Using flow visualization images from forced imbibition experiments carried out in etched-silicon micromodels, we show that the conventional Darcy-type modeling of fluid flux is not predictive under unstable, immiscible, imbibition conditions at the scale of interest. When a less viscous fluid displaces a more viscous fluid at low capillary numbers, the displacement patterns show fractal, self-similar characteristics arising from viscous instabilities as well as local capillary control of interface movement. We show that such complex displacement patterns are modeled using statistical theories. We derive a scaling model to describe quantitatively the functional forms for saturation, fractional flow, and capillary dispersion profiles using the self-similarity characteristics inherent in the displacement patterns. For the specific range of flow rates (Nc~10−7) and oil to water viscosity ratios (M~8-400) considered in our experiments, both capillary and viscous forces are important and the displacement shows features similar to the invasion-percolation regime in the presence of a viscous gradient. Results show that functional relations of the scaling model are in considerable agreement with our experimental data.
Keywords: imbibition, nonequilibrium effects, viscous instabilities, multiphase flow
ESP installation in Very High Gas Environment (GOR 500 m3/m3), Using Multi Vane Pump and Tail-Pipe in PDO
Authors: Jedda Jamel , Al Houqani Said , Wardi Said 
Published: December 2011

Abstract
Running ESP in gassy environment was always a big challenge causing frequent pump gas lock and ESP motor to overheat due lack of sufficient fluid to cool it and eventually shorten ESP run life.
ESP was found to be the most suitable Artificial Lift method for WELL-01 as per the conducted Artificial Lift modelling. However, any selected ESP system has to have the capability to handle high Gas Oil Ratio (GOR), which was estimated around 500 m3/m3. After exploring all available technologies for handling high GOR in the market, decision was made to use the Centurion Multi Vane Pump (MVP) stage which was presented as the latest solution for gas handling. MVP integrates the three principles of Gas handling to a level of 90% of free gas at the pump intake:
- Balancing holes mitigate the pressure difference and thrust loading. If gas forms because of low pressure area, it can easily escape through those holes. - It has a split vane design. As a general rule when dealing with gas, the more homogenous the fluid, the better. The split vane design allows turbulent mixing to occur, which favourable for flow capacities to carry the gas without becoming stagnant. - The steep discharge angle of the MVP transmits a greater amount of Kinetic energy to the liquid, increasing lift at lower flow rates
In addition to that and for more precautionary measures, ESP installed in 5.5" shroud cross-overed to 2 7/8" tail-pipe in order to produce from below perforations to minimize the risk of gas entry to the pump. The total concept (MVP + Gas separator + tailpipe) worked well as the system last for almost three years after installation with a permanent annulus pressure of 38 bar.
WELL- 01 was meant to assess the reservoir potential and is the first high GOR (200‒500 m3/m3) well completed with an ESP system capable to handle such level of GOR.
Effects of Rapid Gas Decompression on Swellable Rubber and Common Oilfield Rubber Compounds
Authors: Young Dustin , Sevre Alf K. , Smith Peter E. , al-Madlouh Mohammed , Gjelstad Geir 
Published: December 2011

Abstract
Rubber or elastomeric seals are flexible polymers used in a variety of applications in many industries, and as polymer technology has advanced, they have become more widely used in oilfield equipment. One significant problem, however, has concerned the fact that they can be damaged during a rapid decrease of pressure after being exposed to environments containing gas. This phenomenon is known as explosive decompression (ED) or rapid gas decompression (RGD).
RGD damage can be manifested as splits, cracks, or bubbles in the seals (depending on the rubber type), length of exposure to the gas, and the rate of pressure decrease. Damage caused to a seal by RGD can range in severity from a slight weakening of the physical properties of the rubber to a catastrophic failure of the integrity of the seal. RGD can be caused by both surface operations and downhole conditions and can result in failure of the equipment in which the seals are used.
This paper discusses tests performed on various elastomeric samples, including swellable rubber, to determine the effects that RGD will have on the seals under varying conditions. The tests exposed each sample to a range of pressure drops and gas exposure times. The samples were analyzed after each test for physical changes and signs of RGD damage. The purpose of mapping the effects of RGD on multiple samples and the various conditions to which the seals were subjected was to 1) develop a better understanding of the conditions leading to RGD damage, and 2), to identify operations at risk for causing RGD damage to elastomeric seals. The testing and results are discussed in this paper.