bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncertainties in North American Land Data Assimilation Systems over the Contiguous United States
Authors: Mo Kingtse C. , Chen Li-Chuan , Shukla Shraddhanand , Bohn Theodore J. , Lettenmaier Dennis P. 
Published: February 2012

Abstract
The Environmental Modeling Center (EMC) at the National Centers for Environmental Prediction (NCEP) and the University of Washington (UW) run parallel drought monitoring systems over the continental United States based on the North American Land Data Assimilation System (NLDAS). The NCEP system uses four land surface models (LSMs): Variable Infiltration Capacity (VIC), Noah, Mosaic, and Sacramento (SAC). The UW system uses VIC, SAC, Noah, and the Community Land Model (CLM). An assessment of differences in drought characteristics using both systems for the period 1979–2008 was performed. For soil moisture (SM) percentiles and runoff indices, differences are relatively small among different LSMs in the same system. However, the ensemble mean differences between the two systems are large over the western United States—in some cases exceeding 20% for SM and runoff percentile differences. These differences are most apparent after 2002 when the NCEP system transitioned to use the real-time North American Regional Reanalysis (NARR) and its precipitation gauge station data. (The UW system went into real-time operation in 2005.) Experiments were performed to address the sources of uncertainties. Comparison of simulations using the two systems with different model forcings indicates that the precipitation forcing differences are the primary source of the SM and runoff differences. While temperature, shortwave and longwave radiation, and wind speed forcing differences are also large after 2002, their contributions to SM and runoff differences are much smaller than precipitation.
An Extended Kalman Filter Framework for Polarimetric X-Band Weather Radar Data Processing
Authors: Schneebeli Marc , Berne Alexis 
Published: February 2012

Abstract
The different quantities measured by dual-polarization radar systems are closely linked to each other. An extended Kalman filter framework is proposed in order to make use of constraints on individual radar observables that are induced by these relations. This new approach simultaneously estimates the specific differential phase on propagation Kdp, the attenuation-corrected reflectivity at horizontal polarization Zh, and the attenuation-corrected differential reflectivity Zdr, as well as the differential phase shift on backscatter δhυ. In a simulation experiment it is found that Kdp and δhυ can be retrieved with higher accuracy and spatial resolution than existing estimators that solely rely on a smoothed measurement of the differential phase shift Ψdp. Attenuation-corrected Zh was retrieved with an accuracy similar to standard algorithms, but improvements were found for attenuation-corrected Zdr. In addition, the algorithm can be used for radar calibration by comparing the directly retrieved differential phase shift on propagation Φdp with the accumulated Kdp estimates. The extended Kalman filter estimation scheme was applied to data collected with an X-band polarimetric radar in the Swiss Alps in 2010. Radome attenuation appears to be significant (up to 5 dB) in moderate to intense rain events and hence needs to be corrected in order to have reliable quantitative precipitation estimates. Measurements corrected for radome and propagation attenuation were converted into rain-rate R with a newly developed relation between R, Kdp, and Zdr. The good agreement between rain-rate values inferred from ground observations and from the radar measurements confirms the reliability of the proposed radar processing technique.
WHOI SDSL Data-Link Project—Ethernet Telemetry through Sea Cables
Authors: Swartz Marshall , Torres Daniel J. , Liberatore Steve , Millard Robert 
Published: February 2012

AbstractA data telemetry technique for communicating over standard oceanographic sea cables that achieves a nearly 100-fold increase in bandwidth as compared to traditional systems has been recently developed and successfully used at sea on board two Research Vessel (R/V) Atlantis cruises with an 8.5-km, 0.322-in.-diameter three-conductor sea cable. The system uses commercially available modules to provide Ethernet connectivity through existing sea cables, linking serial and video underwater instrumentation to the shipboard user. The new method applies Synchronous Digital Subscriber Line (SDSL) communications technology to undersea applications, greatly increasing the opportunities to use scientific instrumentation from existing ships and sea cables at minimal cost and without modification.
Determinants of Firms’ Liquidation and Acquisition in the Indian Electronics Industry
Authors: Irfan Mohd 
Published: February 2012

This study examines the determinants of firms’ liquidation and acquisition in the Indian electronics industry during the period 1990–2006. It is argued that liquidation and acquisition are alternative modes of exit. Therefore, these modes of exit might have different determinants. To explore this possibility, a multinomial logistic (MNL) regression model is estimated using cross-sectional data of 540 firms. We find that the effects of age, size, leverage, innovative competence and profitability are significant for the likelihood of liquidation. In contrast, the effect of profitability was found insignificant for the likelihood of acquisition. Moreover, the effects of size and leverage are dissimilar across the exit modes, that is, large firms are more likely to be liquidated but less likely to be acquired, and high leverage firms are more likely to be liquidated but less likely to be acquired. The findings of this study show that the determinants of liquidation and acquisition modes of exit are different in the Indian electronics industry. JEL Classification: C25, G33, G34, L63
Public Library Picture Collecting in Late Nineteenth-Century America
Authors: Brodherson David 
Published: February 2012

In the United States during the late nineteenth and early twentieth centuries, librarians and their newly established professional group, the American Library Association (ALA), considered one of their great triumphs the collection of pictures as a form of art and visual information. News of acquisition and management of every imaginable pictorial medium ranging from paintings to lithographs, engravings, etchings, photographs, and larger runs of photomechanical reproductions appeared in the new professional periodicals of ‘library economy’. This article concentrates on the achievements of public library picture collecting often reported in the new nineteenth-century journalism of ‘library economy’. We are largely unaware of the early writings about public library picture collecting; nevertheless, the issues addressed about picture collecting are part of the intellectual DNA of librarians, scholars, and readers managing information or reading periodicals today.
Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening
Authors: Pastore Chiara , Zenoni Sara , Tornielli Giovanni Battista , Allegro Gianluca , Dal Santo Silvia , Valentini Gabriele , Intrieri Cesare , Pezzotti Mario , Filippetti Ilaria 
Published: February 2012

AbstractBackgroundCluster thinning is an agronomic practice in which a proportion of berry clusters are removed from the vine to increase the source/sink ratio and improve the quality of the remaining berries. Until now no transcriptomic data have been reported describing the mechanisms that underlie the agronomic and biochemical effects of thinning.ResultsWe profiled the transcriptome ofVitis viniferacv. Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. Thinning increased the source/sink ratio from 0.6 to 1.2 m2leaf area per kg of berries and boosted the sugar and anthocyanin content at harvest. Extensive transcriptome remodeling was observed in thinned vines 2 weeks after thinning and at ripening. This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed.ConclusionCluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process.
NOV/CCN3 attenuates inflammatory pain through regulation of matrix metalloproteinases-2 and -9
Authors: Kular Lara , Rivat Cyril , Lelongt Brigitte , Calmel Claire , Laurent Maryvonne , Pohl Michel , Kitabgi Patrick , Melik-Parsadaniantz Stéphane , Martinerie Cécile 
Published: February 2012

Abstract

Background
Sustained neuroinflammation strongly contributes to the pathogenesis of pain. The clinical challenge of chronic pain relief led to the identification of molecules such as cytokines, chemokines and more recently matrix metalloproteinases (MMPs) as putative therapeutic targets. Evidence points to a founder member of the matricial CCN family, NOV/CCN3, as a modulator of these inflammatory mediators. We thus investigated the possible involvement of NOV in a preclinical model of persistent inflammatory pain.

Methods
We used the complete Freund's adjuvant (CFA)-induced model of persistent inflammatory pain and cultured primary sensory neurons for in vitro experiments. The mRNA expression of NOV and pro-inflammatory factors were measured with real-time quantitative PCR, CCL2 protein expression was assessed using ELISA, MMP-2 and -9 activities using zymography. The effect of drugs on tactile allodynia was evaluated by the von Frey test.

Results
NOV was expressed in neurons of both dorsal root ganglia (DRG) and dorsal horn of the spinal cord (DHSC). After intraplantar CFA injection, NOV levels were transiently and persistently down-regulated in the DRG and DHSC, respectively, occurring at the maintenance phase of pain (15 days). NOV-reduced expression was restored after treatment of CFA rats with dexamethasone. In vitro, results based on cultured DRG neurons showed that siRNA-mediated inhibition of NOV enhanced IL-1β- and TNF-α-induced MMP-2, MMP-9 and CCL2 expression whereas NOV addition inhibited TNF-α-induced MMP-9 expression through β1 integrin engagement. In vivo, the intrathecal delivery of MMP-9 inhibitor attenuated mechanical allodynia of CFA rats. Importantly, intrathecal administration of NOV siRNA specifically led to an up-regulation of MMP-9 in the DRG and MMP-2 in the DHSC concomitant with increased mechanical allodynia. Finally, NOV intrathecal treatment specifically abolished the induction of MMP-9 in the DRG and, MMP-9 and MMP-2 in the DHSC of CFA rats. This inhibitory effect on MMP is associated with reduced mechanical allodynia.

Conclusions
This study identifies NOV as a new actor against inflammatory pain through regulation of MMPs thus uncovering NOV as an attractive candidate for therapeutic improvement in pain relief.
Sequence analysis of Epstein-Barr virus EBNA-2 gene coding amino acid 148-487 in nasopharyngeal and gastric carcinomas
Authors: Wang Xinying , Wang Yun , Wu Guocai , Chao Yan , Sun Zhifu , Luo Bing 
Published: February 2012

AbstractBackgroundThe Epstein-Barr virus (EBV) nuclear antigen 2 (EBNA-2) plays a key role in the B-cell growth transformation by initiating and maintaining the proliferation of infected B-cell upon EBV infection in vitro. Most studies about EBNA-2 have focused on its functions yet little is known for its intertypic polymorphisms.ResultsCoding region for amino acid (aa) 148-487 of the EBNA-2 gene was sequenced in 25 EBV-associated gastric carcinomas (EBVaGCs), 56 nasopharyngeal carcinomas (NPCs) and 32 throat washings (TWs) from healthy donors in Northern China. Three variations (g48991t, c48998a, t49613a) were detected in all of the samples (113/113, 100%). EBNA-2 could be classified into four distinct subtypes: E2-A, E2-B, E2-C and E2-D based on the deletion status of three aa (294Q, 357K and 358G). Subtypes E2-A and E2-C were detected in 56/113 (49.6%), 38/113 (33.6%) samples, respectively. E2-A was observed more in EBVaGCs samples and subtype E2-D was only detected in the NPC samples. Variation analysis in EBNA-2 functional domains: the TAD residue (I438L) and the NLS residues (E476G, P484H and I486T) were only detected in NPC samples which located in the carboxyl terminus of EBNA-2 gene.ConclusionsThe subtypes E2-A and E2-C were the dominant genotypes of the EBNA-2 gene in Northern China. The subtype E2-D may be associated with the tumorigenesis of NPC. The NPC isolates were prone harbor to more mutations than the other two groups in the functional domains.
A rice transient assay system identifies a novel domain in NRR required for interaction with NH1/OsNPR1 and inhibition of NH1-mediated transcriptional activation
Authors: Chern Mawsheng , Bai Wei , Sze-To Wing Hoi , Canlas Patrick E , Bartley Laura E , Ronald Pamela C 
Published: February 2012

Abstract

Background
Arabidopsis NPR1 is a master regulator of systemic acquired resistance. NPR1 binds to TGA transcription factors and functions as a transcriptional co-activator. In rice, NH1/OsNPR1 functions to enhance innate immunity. NRR disrupts NH1 function, when over-expressed.

Results
We have established a rice transient protoplast assay to demonstrate that NH1 is a transcriptional co-activator and that NRR represses NH1-mediated activation. We identified three NRR homologues (RH1, RH2, and RH3). RH1 and RH3, but not RH2, also effectively repress NH1-mediated transcriptional activation. NRR, RH1, RH2, and RH3 share sequence similarity in a region beyond the previously identified NPR1-interacting domain. This region is required for strong interaction with NH1. A double point mutation, W66A/F70A, in this novel NH1-interacting domain severely reduces interaction with NH1. Mutation W66A/F70A also greatly reduces the ability of NRR to repress NH1-mediated activation. RH2 carries a deviation (amino acids AV) in this region as compared to consensus sequences (amino acids ED) among NRR, RH1, and RH3. A substitution (AV to ED) in RH2 results in strong binding of mutant RH2ED to NH1 and effective repression of NH1-mediated activation.

Conclusions
The protoplast-based transient system can be used to dissect protein domains associated with their functions. Our results demonstrate that the ability of NRR and its homologues to repress NH1-mediated transcriptional activation is tightly correlated with their ability to bind to NH1. Furthermore, a sequence is identified as a novel NH1-interacting domain. Importantly, this novel sequence is widely present in plant species, from cereals to castor bean plants, to poplar trees, to Arabidopsis, indicating its significance in plants.
Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genes
Authors: Lotta Luca A , Wang Mark , Yu Jin , Martinelli Ida , Yu Fuli , Passamonti Serena M , Consonni Dario , Pappalardo Emanuela , Menegatti Marzia , Scherer Steven E , Lewis Lora L , Akbar Humeira , Wu Yuanqing , Bainbridge Matthew N , Muzny Donna M , Mannucci Pier M , Gibbs Richard A , Peyvandi Flora 
Published: February 2012

AbstractBackgroundNext-generation DNA sequencing is opening new avenues for genetic association studies in common diseases that, like deep vein thrombosis (DVT), have a strong genetic predisposition still largely unexplained by currently identified risk variants. In order to develop sequencing and analytical pipelines for the application of next-generation sequencing to complex diseases, we conducted a pilot study sequencing the coding area of 186 hemostatic/proinflammatory genes in 10 Italian cases of idiopathic DVT and 12 healthy controls.ResultsA molecular-barcoding strategy was used to multiplex DNA target capture and sequencing, while retaining individual sequence information. Genomic libraries with barcode sequence-tags were pooled (in pools of 8 or 16 samples) and enriched for target DNA sequences. Sequencing was performed on ABI SOLiD-4 platforms. We produced > 12 gigabases of raw sequence data to sequence at high coverage (average: 42X) the 700-kilobase target area in 22 individuals. A total of 1876 high-quality genetic variants were identified (1778 single nucleotide substitutions and 98 insertions/deletions). Annotation on databases of genetic variation and human disease mutations revealed several novel, potentially deleterious mutations. We tested 576 common variants in a case-control association analysis, carrying the top-5 associations over to replication in up to 719 DVT cases and 719 controls. We also conducted an analysis of the burden of nonsynonymous variants in coagulation factor and anticoagulant genes. We found an excess of rare missense mutations in anticoagulant genes in DVT cases compared to controls and an association for a missense polymorphism ofFGA(rs6050; p = 1.9 × 10-5, OR 1.45; 95% CI, 1.22-1.72; after replication in > 1400 individuals).ConclusionsWe implemented a barcode-based strategy to efficiently multiplex sequencing of hundreds of candidate genes in several individuals. In the relatively small dataset of our pilot study we were able to identify bona fide associations with DVT. Our study illustrates the potential of next-generation sequencing for the discovery of genetic variation predisposing to complex diseases.
An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish
Authors: Reading Benjamin J , Chapman Robert W , Schaff Jennifer E , Scholl Elizabeth H , Opperman Charles H , Sullivan Craig V 
Published: February 2012

Abstract

Background
The striped bass and its relatives (genus Morone) are important fisheries and aquaculture species native to estuaries and rivers of the Atlantic coast and Gulf of Mexico in North America. To open avenues of gene expression research on reproduction and breeding of striped bass, we generated a collection of expressed sequence tags (ESTs) from a complementary DNA (cDNA) library representative of their ovarian transcriptome.

Results
Sequences of a total of 230,151 ESTs (51,259,448 bp) were acquired by Roche 454 pyrosequencing of cDNA pooled from ovarian tissues obtained at all stages of oocyte growth, at ovulation (eggs), and during preovulatory atresia. Quality filtering of ESTs allowed assembly of 11,208 high-quality contigs ≥ 100 bp, including 2,984 contigs 500 bp or longer (average length 895 bp). Blastx comparisons revealed 5,482 gene orthologues (E-value < 10-3), of which 4,120 (36.7% of total contigs) were annotated with Gene Ontology terms (E-value < 10-6). There were 5,726 remaining unknown unique sequences (51.1% of total contigs). All of the high-quality EST sequences are available in the National Center for Biotechnology Information (NCBI) Short Read Archive (GenBank: SRX007394). Informative contigs were considered to be abundant if they were assembled from groups of ESTs comprising ≥ 0.15% of the total short read sequences (≥ 345 reads/contig). Approximately 52.5% of these abundant contigs were predicted to have predominant ovary expression through digital differential display in silico comparisons to zebrafish (Danio rerio) UniGene orthologues. Over 1,300 Gene Ontology terms from Biological Process classes of Reproduction, Reproductive process, and Developmental process were assigned to this collection of annotated contigs.

Conclusions
This first large reference sequence database available for the ecologically and economically important temperate basses (genus Morone) provides a foundation for gene expression studies in these species. The predicted predominance of ovary gene expression and assignment of directly relevant Gene Ontology classes suggests a powerful utility of this dataset for analysis of ovarian gene expression related to fundamental questions of oogenesis. Additionally, a high definition Agilent 60-mer oligo ovary 'UniClone' microarray with 8 × 15,000 probe format has been designed based on this striped bass transcriptome (eArray Group: Striper Group, Design ID: 029004).
Seismic imaging of the water-column deep layer associated with the Deepwater Horizon oil spill
Authors: Hildebrand John A. , Armi Laurence , Henkart Paul C. 
Published: February 2012

The submerged hydrocarbon layer at a depth of approximately 1100–1200 m in the water column near the Deepwater Horizon well site was associated with a temperature anomaly that was imaged by seismic reflection data collected two days before and one day after the well shut-in. Conventional multichannel seismic reflection profiling data were processed to enhance water-column reflections by filtering out low-frequency energy and applying higher gain than typically used for imaging subsurface geology. The deep layer reflectivity, within a few km of the well site, has an impedance less than seawater by about a factor of approximately [Formula: see text], or equivalently, a negative sound-velocity step of about [Formula: see text]. Water-column profile data collected at the same time as the seismic data show a comparable sound velocity and temperature decrease associated with the deep layer. Mixing of less dense hydrocarbons entrains cold seawater, resulting in a temperature anomaly within the deep layer at the level of neutral buoyancy. This temperature contrast explains the negative sound-velocity anomaly associated with the deep reflector. Because of the small hydrocarbon concentration in the deep layer, their contribution to the seismic velocity anomaly is too small to be significant. The high horizontal resolution (3 m) of the seismic image reveals a layer with patchiness of several hundred meters lateral extent.
Efficacy and safety of endovenous foam sclerotherapy: meta-analysis for treatment of venous disorders
Authors: Rathbun S , Norris A , Stoner J 
Published: February 2012

Aim Endovenous foam sclerotherapy (EFS) is used widely throughout the USA for the treatment of venous disorders. The purpose of the quantitative meta-analysis was to systematically and comprehensively evaluate the literature to provide accurate estimates of safety and efficacy outcomes for this procedure. Methods A comprehensive electronic search of published literature in several databases was performed using a wide variety of MESH headings. In addition, meeting abstracts and bibliographies of selected references were reviewed for eligible papers. Two reviewers abstracted selected treatment-related data. Results Of 684 identified manuscripts and abstracts reviewed, 104 papers were abstracted and analysed. More than 50% were published between 2004 and 2008. EFS was found to be effective with similar vein occlusion rates to laser therapy, but less effective than surgery. In addition, major adverse effects were rare. Conclusions EFS is a safe and effective therapy for the treatment of venous disorders.