bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observations of the Evolution of the Nocturnal and Convective Boundary Layers and the Structure of Open-Celled Convection on 14 June 2002
Authors: Bennett Lindsay J. , Weckwerth Tammy M. , Blyth Alan M. , Geerts Bart , Miao Qun , Richardson Yvette P. 
Published: February 2010

Abstract
The Boundary Layer Evolution (BLE) missions of the International H2O Project (IHOP_2002) were designed to provide comprehensive observations of the distribution of water vapor in the quiescent boundary layer and its evolution during the early morning. The case study discussed in this paper presents detailed observations of the development of the boundary layer from before sunrise through to the period of growth of the mature convective boundary layer (CBL) during the 14 June 2002 BLE mission. The large number of remote sensing platforms, including the multiple instruments collocated at the Homestead Profiling Site, provided a detailed set of measurements of the growth and structure of the CBL.
The observations describe the classic evolution of a daytime CBL, beginning with a shallow nocturnal boundary layer (NBL) below the remnants of the previous day’s mixed layer, or residual layer. The vertical distribution of humidity in these layers during the early morning was affected by advection of dry air and by gravity waves. About an hour after sunrise a CBL developed, and gradually deepened with time as it mixed out the NBL and residual layer. The growth of the top of the CBL was particularly well observed because of the strong vertical gradients in temperature, humidity, and aerosol concentration. As the CBL deepened and the average CBL wind speed decreased, the mode of convective organization evolved from horizontal convective rolls to open-celled convection. A unique set of detailed measurements of the structure of the open cells was obtained from multiple instruments including the Doppler-on-Wheels radar, the Mobile Integrated Profiling System wind profiler, and the Scanning Raman lidar. They showed the relationship between open cells, thermals, mantle echoes, and the CBL top.
Efficacy of the JAK2 inhibitor INCB16562 in a murine model of MPLW515L-induced thrombocytosis and myelofibrosis
Authors: Koppikar Priya , Abdel-Wahab Omar , Hedvat Cyrus , Marubayashi Sachie , Patel Jay , Goel Aviva , Kucine Nicole , Gardner Jeffrey R. , Combs Andrew P. , Vaddi Kris , Haley Patrick J. , Burn Timothy C. , Rupar Mark , Bromberg Jacqueline F. , Heaney Mark L. , de Stanchina Elisa , Fridman Jordan S. , Levine Ross L. 
Published: February 2010

AbstractThe discovery of JAK2 and MPL mutations in patients with myeloproliferative neoplasms (MPNs) provided important insight into the genetic basis of these disorders and led to the development of JAK2 kinase inhibitors for MPN therapy. Although recent studies have shown that JAK2 kinase inhibitors demonstrate efficacy in a JAK2V617F murine bone marrow transplantation model, the effects of JAK2 inhibitors on MPLW515L-mediated myeloproliferation have not been investigated. In this report, we describe the in vitro and in vivo effects of INCB16562, a small-molecule JAK2 inhibitor. INCB16562 inhibited proliferation and signaling in cell lines transformed by JAK2 and MPL mutations. Compared with vehicle treatment, INCB16562 treatment improved survival, normalized white blood cell counts and platelet counts, and markedly reduced extramedullary hematopoeisis and bone marrow fibrosis. We observed inhibition of STAT3 and STAT5 phosphorylation in vivo consistent with potent inhibition of JAK-STAT signaling. These data suggest JAK2 inhibitor therapy may be of value in the treatment of JAK2V617F-negative MPNs. However, we did not observe a decrease in the size of the malignant clone in the bone marrow of treated mice at the end of therapy, which suggests that JAK2 inhibitor therapy, by itself, was not curative in this MPN model.
Development of multilineage adult hematopoiesis in the zebrafish with a runx1 truncation mutation
Authors: Sood Raman , English Milton A. , Belele Christiane L. , Jin Hao , Bishop Kevin , Haskins Rebecca , McKinney Mary Cathleen , Chahal Jagman , Weinstein Brant M. , Wen Zilong , Liu P. Paul 
Published: February 2010

Abstract
Runx1 is required for the emergence of hematopoietic stem cells (HSCs) from hemogenic endothelium during embryogenesis. However, its role in the generation and maintenance of HSCs during adult hematopoiesis remains uncertain. Here, we present analysis of a zebrafish mutant line carrying a truncation mutation, W84X, in runx1. The runx1W84X/W84X embryos showed blockage in the initiation of definitive hematopoiesis, but some embryos were able to recover from a larval “bloodless” phase and develop to fertile adults with multilineage hematopoiesis. Using cd41–green fluorescent protein transgenic zebrafish and lineage tracing, we demonstrated that the runx1W84X/W84X embryos developed cd41+ HSCs in the aorta-gonad-mesonephros region, which later migrated to the kidney, the site of adult hematopoiesis. Overall, our data suggest that in zebrafish adult HSCs can be formed without an intact runx1.
Cigarette smoke enhances β-defensin 2 expression in rat airwaysvianuclear factor-κB activation
Authors: Chen L. , Sun B-B. , Wang T. , Wang X. , Li J-Q. , Wang H-X. , Zhang S-F. , Liu D-S. , Liu L. , Xu D. , Ou X-M. , Chen Y-J. , Yang T. , Zhou H. , Wen F-Q. 
Published: February 2010

β-defensin 2 (BD-2), an antimicrobial peptide, participates in airway defence. Cigarette smoke (CS) is a major risk factor for the development of chronic obstructive pulmonary disease. This study mainly aims to investigate the effect of CS on rat BD-2 (rBD-2) expression in rat airways.Rats were exposed to CS and treated with caffeic acid phenethyl ester (CAPE), a nuclear factor (NF)-κB inhibitor, or astragaloside IV (AS-IV), an active ingredient ofAstragalus mongholicus. Besides the analysis of bronchoalveolar lavage fluid (BALF) and histological changes after CS exposure, rBD-2 expression was investigated with immunohistochemistry, reverse transcription PCR and ELISA. Total glutathione and nitric oxide (NO) levels in rat lungs were also detected.CS exposure markedly increased rBD-2 immunoreactivity, as well as rBD-2 mRNA and protein levels in rat airways, which were inhibited by CAPE treatment. Moreover, associated airway inflammation induced by CS was demonstrated by histological changes, increased cell counts and pro-inflammatory cytokines in BALF, and NF-κB activation and high levels of total glutathione and NO, which were all reversed by AS-IV in a dose-dependent fashion.In conclusion, CS exposure induces rBD-2 expression in rat airwaysviaa NF-κB-dependent pathway, and AS-IV attenuates CS-induced airway inflammation due to its anti-inflammatory and antioxidant properties, at least partly through NF-κB inactivation.
Application of a prediction model for work-related sensitisation in bakery workers
Authors: Meijer E. , Suarthana E. , Rooijackers J. , Grobbee D.E. , Jacobs J.H. , Meijster T. , de Monchy J.G.R. , van Otterloo E. , van Rooy F.G.B.G.J. , Spithoven J.J.G. , Zaat V.A.C. , Heederik D.J.J. 
Published: February 2010

Identification of work-related allergy, particularly work-related asthma, in a (nationwide) medical surveillance programme among bakery workers requires an effective and efficient strategy.Bakers at high risk of having work-related allergy were indentified by use of a questionnaire-based prediction model for work-related sensitisation. The questionnaire was applied among 5,325 participating bakers. Sequential diagnostic investigations were performed only in those with an elevated risk. Performance of the model was evaluated in 674 randomly selected bakers who participated in the medical surveillance programme and the validation study. Clinical investigations were evaluated in the first 73 bakers referred at high risk.Overall 90% of bakers at risk of having asthma could be identified. Individuals at low risk showed 0.3–3.8% work-related respiratory symptoms, medication use or absenteeism. Predicting flour sensitisation by a simple questionnaire and score chart seems more effective at detecting work-related allergy than serology testing followed by clinical investigation in all immunoglobulin E class II-positive individuals.This prediction based stratification procedure appeared effective in detecting work-related allergy among bakers and can accurately be used for periodic examination, especially in small enterprises where delivery of adequate care is difficult. This approach may contribute to cost reduction.
BMP-2 functions independently of SHH signaling and triggers cell condensation and apoptosis in regenerating axolotl limbs
Authors: Guimond Jean-Charles , Lévesque Mathieu , Michaud Pierre-Luc , Berdugo Jérémie , Finnson Kenneth , Philip Anie , Roy Stéphane 
Published: February 2010

Abstract

Background
Axolotls have the unique ability, among vertebrates, to perfectly regenerate complex body parts, such as limbs, after amputation. In addition, axolotls pattern developing and regenerating autopods from the anterior to posterior axis instead of posterior to anterior like all tetrapods studied to date. Sonic hedgehog is important in establishing this anterior-posterior axis of limbs in all tetrapods including axolotls. Interestingly, its expression is conserved (to the posterior side of limb buds and blastemas) in axolotl limbs as in other tetrapods. It has been suggested that BMP-2 may be the secondary mediator of sonic hedgehog, although there is mounting evidence to the contrary in mice. Since BMP-2 expression is on the anterior portion of developing and regenerating limbs prior to digit patterning, opposite to the expression of sonic hedgehog, we examined whether BMP-2 expression was dependent on sonic hedgehog signaling and whether it affects patterning of the autopod during regeneration.

Results
The expression of BMP-2 and SOX-9 in developing and regenerating axolotl limbs corresponded to the first digits forming in the anterior portion of the autopods. The inhibition of sonic hedgehog signaling with cyclopamine caused hypomorphic limbs (during development and regeneration) but did not affect the expression of BMP-2 and SOX-9. Overexpression of BMP-2 in regenerating limbs caused a loss of digits. Overexpression of Noggin (BMP inhibitor) in regenerating limbs also resulted in a loss of digits. Histological analysis indicated that the loss due to BMP-2 overexpression was the result of increased cell condensation and apoptosis while the loss caused by Noggin was due to a decrease in cell division.

Conclusion
The expression of BMP-2 and its target SOX-9 was independent of sonic hedgehog signaling in developing and regenerating limbs. Their expression correlated with chondrogenesis and the appearance of skeletal elements has described in other tetrapods. Overexpression of BMP-2 did not cause the formation of extra digits, which is consistent with the hypothesis that it is not the secondary signal of sonic hedgehog. However, it did cause the formation of hypomorphic limbs as a result of increased cellular condensation and apoptosis. Taken together, these results suggest that BMP-2 does not have a direct role in patterning regenerating limbs but may be important to trigger condensation prior to ossification and to mediate apoptosis.
Erratum to: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
Authors: Mica Erica , Piccolo Viviana , Delledonne Massimo , Ferrarini Alberto , Pezzotti Mario , Casati Cesare , Del Fabbro Cristian , Valle Giorgio , Policriti Alberto , Morgante Michele , Pesole Graziano , Pè M Enrico , Horner David S 
Published: February 2010

Abstract
The version of this article published in BMC Genomics 2009, 10: 558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted by these unreliable data. In this full-length correction, new data replace those found to be unreliable, leading to a more straightforward interpretation without altering the principle conclusions of the study. Table 1 and associated methods have been corrected, Figure 1 deleted, supplementary file 1 added, and modifications made to the sections "Deep sequencing of small RNAs from grapevine leaf tissue" and "Microarray analysis of miRNA expression". The editors and authors regret the inconvenience caused to readers by premature publication of the original paper.

Background

MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families.

Results

Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts.

Conclusions

Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.
Polymorphisms in O-methyltransferase genes are associated with stover cell wall digestibility in European maize (Zea maysL.)
Authors: Brenner Everton A , Zein Imad , Chen Yongsheng , Andersen Jeppe R , Wenzel Gerhard , Ouzunova Milena , Eder Joachim , Darnhofer Birte , Frei Uschi , Barrière Yves , Lübberstedt Thomas 
Published: February 2010

Abstract

Background
OMT (O-methyltransferase) genes are involved in lignin biosynthesis, which relates to stover cell wall digestibility. Reduced lignin content is an important determinant of both forage quality and ethanol conversion efficiency of maize stover.

Results
Variation in genomic sequences coding for COMT, CCoAOMT1, and CCoAOMT2 was analyzed in relation to stover cell wall digestibility for a panel of 40 European forage maize inbred lines, and re-analyzed for a panel of 34 lines from a published French study. Different methodologies for association analysis were performed and compared. Across association methodologies, a total number of 25, 12, 1, 6 COMT polymorphic sites were significantly associated with DNDF, OMD, NDF, and WSC, respectively. Association analysis for CCoAOMT1 and CCoAOMT2 identified substantially fewer polymorphic sites (3 and 2, respectively) associated with the investigated traits. Our re-analysis on the 34 lines from a published French dataset identified 14 polymorphic sites significantly associated with cell wall digestibility, two of them were consistent with our study. Promising polymorphisms putatively causally associated with variability of cell wall digestibility were inferred from the total number of significantly associated SNPs/Indels.

Conclusions
Several polymorphic sites for three O-methyltransferase loci were associated with stover cell wall digestibility. All three tested genes seem to be involved in controlling DNDF, in particular COMT. Thus, considerable variation among Bm3 wildtype alleles can be exploited for improving cell-wall digestibility. Target sites for functional markers were identified enabling development of efficient marker-based selection strategies.
Orphan receptor GPR110, an oncogene overexpressed in lung and prostate cancer
Authors: Lum Amy M , Wang Bruce B , Beck-Engeser Gabriele B , Li Lauri , Channa Namitha , Wabl Matthias 
Published: February 2010

Abstract

Background
GPR110 is an orphan G protein-coupled receptor--a receptor without a known ligand, a known signaling pathway, or a known function. Despite the lack of information, one can assume that orphan receptors have important biological roles. In a retroviral insertion mutagenesis screen in the mouse, we identified GPR110 as an oncogene. This prompted us to study the potential isoforms that can be gleaned from known GPR110 transcripts, and the expression of these isoforms in normal and transformed human tissues.

Methods
Various epitope-tagged isoforms of GPR110 were expressed in cell lines and assayed by western blotting to determine cleavage, surface localization, and secretion patterns. GPR110 transcript and protein levels were measured in lung and prostate cancer cell lines and clinical samples, respectively, by quantitative PCR and immunohistochemistry.

Results
We found four potential splice variants of GPR110. Of these variants, we confirmed three as being expressed as proteins on the cell surface. Isoform 1 is the canonical form, with a molecular mass of about 100 kD. Isoforms 2 and 3 are truncated products of isoform 1, and are 25 and 23 kD, respectively. These truncated isoforms lack the seven-span transmembrane domain characteristic of GPR proteins and thus are not likely to be membrane anchored; indeed, isoform 2 can be secreted. Compared with the median gene expression of ~200 selected genes, GPR110 expression was low in most tissues. However, it had higher than average gene expression in normal kidney tissue and in prostate tissues originating from older donors. Although identified as an oncogene in murine T lymphomas, GPR110 is greatly overexpressed in human lung and prostate cancers. As detected by immunohistochemistry, GPR110 was overexpressed in 20 of 27 (74%) lung adenocarcinoma tissue cores and in 17 of 29 (59%) prostate adenocarcinoma tissue cores. Additionally, staining with a GPR110 antibody enabled us to differentiate between benign prostate hyperplasia and potential incipient malignancy.

Conclusion
Our work suggests a role for GPR110 in tumor physiology and supports it as a potential therapeutic candidate and disease marker for both lung and prostate cancer.
Non-rigid registration of breast surfaces using the laplace and diffusion equations
Authors: Ong Rowena E , Ou Jao J , Miga Michael I 
Published: February 2010

Abstract
A semi-automated, non-rigid breast surface registration method is presented that involves solving the Laplace or diffusion equations over undeformed and deformed breast surfaces. The resulting potential energy fields and isocontours are used to establish surface correspondence. This novel surface-based method, which does not require intensity images, anatomical landmarks, or fiducials, is compared to a gold standard of thin-plate spline (TPS) interpolation. Realistic finite element simulations of breast compression and further testing against a tissue-mimicking phantom demonstrate that this method is capable of registering surfaces experiencing 6 - 36 mm compression to within a mean error of 0.5 - 5.7 mm.
Smart density: a more accurate method of measuring rural residential density for health-related research
Authors: Owens Peter M , Titus-Ernstoff Linda , Gibson Lucinda , Beach Michael L , Beauregard Sandy , Dalton Madeline A 
Published: February 2010

Abstract

Background
Studies involving the built environment have typically relied on US Census data to measure residential density. However, census geographic units are often unsuited to health-related research, especially in rural areas where development is clustered and discontinuous.

Objective
We evaluated the accuracy of both standard census methods and alternative GIS-based methods to measure rural density.

Methods
We compared residential density (units/acre) in 335 Vermont school neighborhoods using conventional census geographic units (tract, block group and block) with two GIS buffer measures: a 1-kilometer (km) circle around the school and a 1-km circle intersected with a 100-meter (m) road-network buffer. The accuracy of each method was validated against the actual residential density for each neighborhood based on the Vermont e911 database, which provides an exact geo-location for all residential structures in the state.

Results
Standard census measures underestimate residential density in rural areas. In addition, the degree of error is inconsistent so even the relative rank of neighborhood densities varies across census measures. Census measures explain only 61% to 66% of the variation in actual residential density. In contrast, GIS buffer measures explain approximately 90% of the variation. Combining a 1-km circle with a road-network buffer provides the closest approximation of actual residential density.

Conclusion
Residential density based on census units can mask clusters of development in rural areas and distort associations between residential density and health-related behaviors and outcomes. GIS-defined buffers, including a 1-km circle and a road-network buffer, can be used in conjunction with census data to obtain a more accurate measure of residential density.
Exploring the validity of estimating EQ-5D and SF-6D utility values from the health assessment questionnaire in patients with inflammatory arthritis
Authors: Harrison Mark J , Lunt Mark , Verstappen Suzanne MM , Watson Kath D , Bansback Nick J , Symmons Deborah PM 
Published: February 2010

AbstractBackgroundUtility scores are used to estimate Quality Adjusted Life Years (QALYs), applied in determining the cost-effectiveness of health care interventions. In studies where no preference based measures are collected, indirect methods have been developed to estimate utilities from clinical instruments. The aim of this study was to evaluate a published method of estimating the EuroQol-5D (EQ-5D) and Short Form-6D (SF-6D) (preference based) utility scores from the Health Assessment Questionnaire (HAQ) in patients with inflammatory arthritis.MethodsData were used from 3 cohorts of patients with: early inflammatory arthritis (<10 weeks duration); established (>5 years duration) stable rheumatoid arthritis (RA); and RA being treated with anti-TNF therapy. Patients completed the EQ-5D, SF-6D and HAQ at baseline and a follow-up assessment. EQ-5D and SF-6D scores were predicted from the HAQ using a published method. Differences between predicted and observed EQ-5D and SF-6D scores were assessed using the paired t-test and linear regression.ResultsPredicted utility scores were generally higher than observed scores (range of differences: EQ-5D 0.01 - 0.06; SF-6D 0.05 - 0.10). Change between predicted values of the EQ-5D and SF-6D corresponded well with observed change in patients with established RA. Change in predicted SF-6D scores was, however, less than half of that in observed values (p < 0.001) in patients with more active disease. Predicted EQ-5D scores underestimated change in cohorts of patients with more active disease.ConclusionPredicted utility scores overestimated baseline values but underestimated change. Predicting utility values from the HAQ will therefore likely underestimate the QALYs of interventions, particularly for patients with active disease. We recommend the inclusion of at least one preference based measure in future clinical studies.