bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Study of the Impacts of Vertical Diffusion on the Structure and Intensity of the Tropical Cyclones Using the High-Resolution HWRF System
Authors: Gopalakrishnan Sundararaman G. , Marks Frank , Zhang Jun A. , Zhang Xuejin , Bao Jian-Wen , Tallapragada Vijay 
Published: August 2012

AbstractThe Hurricane Weather Research and Forecasting (HWRF) system was used in an idealized framework to gain a fundamental understanding of the variability in tropical cyclone (TC) structure and intensity prediction that may arise due to vertical diffusion. The modeling system uses the Medium-Range Forecast parameterization scheme. Flight-level data collected by a NOAA WP-3D research aircraft during the eyewall penetration of category 5 Hurricane Hugo (1989) at an altitude of about 450–500 m and Hurricane Allen (1980) were used as the basis to best match the modeled eddy diffusivities with wind speed. While reduction of the eddy diffusivity to a quarter of its original value produced the best match with the observations, such a reduction revealed a significant decrease in the height of the inflow layer as well which, in turn, drastically affected the size and intensity changes in the modeled TC. The cross-isobaric flow (inflow) was observed to be stronger with the decrease in the inflow depth. Stronger inflow not only increased the spin of the storm, enhancing the generalized Coriolis term in the equations of motion for tangential velocity, but also resulted in enhanced equivalent potential temperature in the boundary layer, a stronger and warmer core, and, subsequently, a stronger storm. More importantly, rapid acceleration of the inflow not only produced a stronger outflow at the top of the inflow layer, more consistent with observations, but also a smaller inner core that was less than half the size of the original.
Warm Conveyor Belts in Idealized Moist Baroclinic Wave Simulations
Authors: Schemm Sebastian , Wernli Heini , Papritz Lukas 
Published: August 2012

AbstractThis idealized modeling study of moist baroclinic waves addresses the formation of moist ascending airstreams, so-called warm conveyor belts (WCBs), their characteristics, and their significance for the downstream flow evolution. Baroclinic wave simulations are performed on the f plane, growing from a finite-amplitude upper-level potential vorticity (PV) perturbation on a zonally uniform jet stream. This nonmodal approach allows for dispersive upstream and downstream development and for studying WCBs in the primary cyclone and the downstream cyclone. A saturation adjustment scheme is used as the only difference between the dry and moist simulations, which are systematically compared using a cyclone-tracking algorithm, with an eddy kinetic energy budget analysis, and from a PV perspective. Using trajectories and a selection criterion of maximum ascent, forward- and rearward-sloping WCBs in the moist simulation are identified. No WCB is identified in the dry simulation. Forward-sloping WCBs originate in the warm sector, move into the frontal fracture region, and ascend over the bent-back front, where maximum latent heating occurs in this simulation. The outflow of these WCBs is located at altitudes with prevailing zonal winds; they hence flow anticyclonically (“forward”) into the downstream ridge. In case of a slightly weaker ascent, WCBs curve cyclonically (“rearward”) above the cyclone center. A detailed analysis of the PV evolution along the WCBs reveals PV production in the lower troposphere and destruction in the upper troposphere. Consequently, WCBs transport low-PV air into their outflow region, which contributes to the formation of distinct negative PV anomalies. They, in turn, affect the downstream flow and enhance downstream cyclogenesis.
Climatology and Meteorological Evolution of Major Wildfire Events over the Northeast United States
Authors: Pollina Joseph B. , Colle Brian A. , Charney Joseph J. 
Published: August 2012

Abstract
This study presents a spatial and temporal climatology of major wildfire events, defined as &gt;100 acres burned (&gt;40.47 ha, where 1 ha = 2.47 acre), in the northeast United States from 1999 to 2009 and the meteorological conditions associated with these events. The northeast United States is divided into two regions: region 1 is centered over the higher terrain of the northeast United States and region 2 is primarily over the coastal plain. About 59% of all wildfire events in these two regions occur in April and May, with ~76% in region 1 and ~53% in region 2. There is large interannual variability in wildfire frequency, with some years having 4–5 times more fire events than other years. The synoptic flow patterns associated with northeast United States wildfires are classified using the North American Regional Reanalysis. The most common synoptic pattern for region 1 is a surface high pressure system centered over the northern Appalachians, which occurred in approximately 46% of all events. For region 2, the prehigh anticyclone type extending from southeast Canada and the Great Lakes to the northeast United States is the most common pattern, occurring in about 46% of all events. A trajectory analysis highlights the influence of large-scale subsidence and decreasing relative humidity during the events, with the prehigh pattern showing the strongest subsidence and downslope drying in the lee of the Appalachians.
Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1expression in mouse limb buds
Authors: Zuniga Aimée , Laurent Frédéric , Lopez-Rios Javier , Klasen Christian , Matt Nicolas , Zeller Rolf 
Published: August 2012

Abstract
Background
Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1) is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1) locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds.

Results
Three highly conserved regions (HMCO1-3) were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9 kb region located ~70 kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1), is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1 genomic landscape locate to the DNAse I hypersensitive sites identified in this genomic region by the ENCODE consortium.

Conclusions
This study establishes that distant cis-regulatory regions scattered through a larger genomic landscape control the highly dynamic expression of Grem1, which is key to normal progression of mouse limb bud development.
Genetic map of Triticum turgidumbased on a hexaploid wheat population without genetic recombination for D genome
Authors: Zhang Li , Luo Jiang-Tao , Hao Ming , Zhang Lian-Quan , Yuan Zhong-Wei , Yan Ze-Hong , Liu Ya-Xi , Zhang Bo , Liu Bao-Long , Liu Chun-Ji , Zhang Huai-Gang , Zheng You-Liang , Liu Deng-Cai 
Published: August 2012

Abstract

Background
A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population.

Results
Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B.

Conclusions
A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Authors: Guimarães Patricia M , Brasileiro Ana CM , Morgante Carolina V , Martins Andressa CQ , Pappas Georgios , Silva Orzenil B , Togawa Roberto , Leal-Bertioli Soraya CM , Araujo Ana CG , Moretzsohn Marcio C , Bertioli David J 
Published: August 2012

Abstract

Background
Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development.

Results
Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton
,
and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR.

Conclusions
This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Insights into the genome structure and copy-number variation of Eimeria tenella
Authors: Lim Lik-Sin , Tay Yea-Ling , Alias Halimah , Wan Kiew-Lian , Dear Paul H 
Published: August 2012

AbstractBackgroundEimeriais a genus of parasites in the same phylum (Apicomplexa) as human parasites such asToxoplasma,Cryptosporidiumand the malaria parasitePlasmodium.As an apicomplexan whose life-cycle involves a single host,Eimeriais a convenient model for understanding this group of organisms. Although the genomes of the Apicomplexa are diverse, that ofEimeriais unique in being composed of large alternating blocks of sequence with very different characteristics - an arrangement seen in no other organism. This arrangement has impeded efforts to fully sequence the genome ofEimeria, which remains the last of the major apicomplexans to be fully analyzed. In order to increase the value of the genome sequence data and aid in the effort to gain a better understanding of theEimeria tenellagenome, we constructed a whole genome map for the parasite.ResultsA total of 1245 contigs representing 70.0% of the whole genome assembly sequences (Wellcome Trust Sanger Institute) were selected and subjected to marker selection. Subsequently, 2482 HAPPY markers were developed and typed. Of these, 795 were considered as usable markers, and utilized in the construction of a HAPPY map. Markers developed from chromosomally-assigned genes were then integrated into the HAPPY map and this aided the assignment of a number of linkage groups to their respective chromosomes. BAC-end sequences and contigs from whole genome sequencing were also integrated to improve and validate the HAPPY map. This resulted in an integrated HAPPY map consisting of 60 linkage groups that covers approximately half of the estimated 60 Mb genome. Further analysis suggests that the segmental organization first seen in Chromosome 1 is present throughout the genome, with repeat-poor (P) regions alternating with repeat-rich (R) regions. Evidence of copy-number variation between strains was also uncovered.ConclusionsThis paper describes the application of a whole genome mapping method to improve the assembly of the genome ofE. tenellafrom shotgun data, and to help reveal its overall structure. A preliminary assessment of copy-number variation (extra or missing copies of genomic segments) between strains ofE. tenellawas also carried out. The emerging picture is of a very unusual genome architecture displaying inter-strain copy-number variation. We suggest that these features may be related to the known ability of this parasite to rapidly develop drug resistance.
Transcriptional profiling of gastric epithelial cells infected with wild type or arginase-deficient Helicobacter pylori
Authors: Kim Songhee H , Sierra Rosa A , McGee David J , Zabaleta Jovanny 
Published: August 2012

Abstract

Background

Helicobacter pylori causes acute and chronic gastric inflammation induced by proinflammatory cytokines and chemokines secreted by cells of the gastric mucosa, including gastric epithelial cells. Previous studies have demonstrated that the bacterial arginase, RocF, is involved in inhibiting T cell proliferation and CD3ζ expression, suggesting that arginase could be involved in a more general dampening of the immune response, perhaps by down-regulation of certain pro-inflammatory mediators.

Results
Global transcriptome analysis was performed on AGS gastric epithelial cells infected for 16 hours with a wild type Helicobacter pylori strain 26695, an arginase mutant (rocF-) or a rocF

+
complemented strain. H. pylori infection triggered altered host gene expression in genes involved in cell movement, death/growth/proliferation, and cellular function and maintenance. While the wild type strain stimulates host inflammatory pathways, the rocF- mutant induced significantly more expression of IL-8. The results of the microarray were verified using real-time PCR, and the differential levels of protein expression were confirmed by ELISA and Bioplex analysis. MIP-1B was also significantly secreted by AGS cells after H. pylori rocF- mutant infection, as determined by Bioplex. Even though not explored in this manuscript, the impact that the results presented here may have on the development of gastritis, warrant further research to understand the underlying mechanisms of the relationship between H. pylori RocF and IL-8 induction.

Conclusions
We conclude that H. pylori arginase modulates multiple host signaling and metabolic pathways of infected gastric epithelial cells. Arginase may play a critical role in anti-inflammatory host responses that could contribute to the ability of H. pylori to establish chronic infections.
Medication documentation in a primary care network serving North Carolina medicaid patients: results of a cross-sectional chart review
Authors: Olson Matthew D , Tong Gretchen L , Steiner Beat D , Viera Anthony J , Ashkin Evan , Newton Warren P 
Published: August 2012

Abstract

Background
Medical records that do not accurately reflect the patient’s current medication list are an open invitation to errors and may compromise patient safety.

Methods
This cross-sectional study compares primary care provider (PCP) medication lists and pharmacy claims for 100 patients seen in 8 primary care practices and examines the association of congruence with demographic, clinical, and practice characteristics. Medication list congruence was measured as agreement of pharmacy claims with the entire PCP chart, including current medication list, visit notes, and correspondence sections.

Results
Congruence between pharmacy claims and the PCP chart was 65%. Congruence was associated with large chronic disease burden, frequent PCP visits, group practice, and patient age ≥45 years.

Conclusion
Agreement of medication lists between the PCP chart and pharmacy records is low. Medication documentation was more accurate among patients who have more chronic conditions, those who have frequent PCP visits, those whose practice has multiple providers, and those at least 45 years of age. Improved congruence among patients with multiple chronic conditions and in group practices may reflect more frequent visits and reviews by providers.
Interferon regulatory factor 4 binding protein is a novel p53 target gene and suppresses cisplatin-induced apoptosis of breast cancer cells
Authors: Yang Mingzhen , Yuan Fang , Li Peng , Chen Zhongjiao , Chen An , Li Shuhui , Hu Chuanmin 
Published: August 2012

Abstract

Background
Our previous work demonstrated that ectopic expression of interferon regulatory factor 4 binding protein (IBP) was correlated with the malignant behaviour of human breast cancer cells. The mechanisms controlling differential expression of IBP in breast cancer still remain unknown.

Results
To investigate the mechanism of IBP dysregulation in breast cancer, we identified IBP was a novel p53 target gene. IBP expression was negatively regulated by wild-type p53 and was p53 dependently suppressed by DNA damage agent cisplatin. Furthermore, high levels of IBP were found to decrease cisplatin-induced growth suppression and apoptotic cell death, which was associated with decreased p53 activity and imbalanced Bcl-2 family member expression.

Conclusions
IBP is a novel p53 target gene which suppresses cisplatin-mediated apoptosis of breast cancer cells via negative feedback regulation of the p53 signalling pathway, suggesting IBP may serve as a target for pharmacologic intervention of breast cancer resistant to cisplatin therapy.
Genotype-phenotype associations in neurofibromatosis type 1 (NF1): an increased risk of tumor complications in patients with NF1splice-site mutations?
Authors: Alkindy Adila , Chuzhanova Nadia , Kini Usha , Cooper David N , Upadhyaya Meena 
Published: August 2012

AbstractNeurofibromatosis type 1 (NF1) is a complex neurocutaneous disorder with an increased susceptibility to develop both benign and malignant tumors but with a wide spectrum of inter and intrafamilial clinical variability. The establishment of genotype-phenotype associations in NF1 is potentially useful for targeted therapeutic intervention but has generally been unsuccessful, apart from small subsets of molecularly defined patients. The objective of this study was to evaluate the clinical phenotype associated with the specific types ofNF1mutation in a retrospectively recorded clinical dataset comprising 149NF1mutation-known individuals from unrelated families. Each patient was assessed for ten NF1-related clinical features, including the number of café-au-lait spots, cutaneous and subcutaneous neurofibromas and the presence/absence of intertriginous skin freckling, Lisch nodules, plexiform and spinal neurofibromas, optic gliomas, other neoplasms (in particular CNS gliomas, malignant peripheral nerve sheath tumors (MPNSTs), juvenile myelomonocytic leukemia, rhabdomyosarcoma, phaechromocytoma, gastrointestinal stromal tumors, juvenile xanthogranuloma, and lipoma) and evidence of learning difficulties. Gender and age at examination were also recorded. Patients were subcategorized according to their associatedNF1germ line mutations: frame shift deletions (52), splice-site mutations (23), nonsense mutations (36), missense mutations (32) and other types of mutation (6). A significant association was apparent between possession of a splice-site mutation and the presence of brain gliomas and MPNSTs (p = 0.006). If confirmed, these findings are likely to be clinically important since up to a third of NF1 patients harbor splice-site mutations. A significant influence of gender was also observed on the number of subcutaneous neurofibromas (females,p = 0.009) and preschool learning difficulties (females,p = 0.022).