bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistics and Dynamics of Aircraft Encounters of Turbulence over Greenland
Authors: Lane Todd P. , Doyle James D. , Sharman Robert D. , Shapiro Melvyn A. , Watson Campbell D. 
Published: February 2009

Abstract
Historical records of aviation turbulence encounters above Greenland are examined for the period from 2000 to 2006. These data identify an important flow regime that contributes to the occurrence of aircraft turbulence encounters, associated with the passage of surface cyclones that direct easterly or southeasterly flow over Greenland’s imposing terrain. The result of this incident flow is the generation of mountain waves that may become unstable through interactions with the background directional wind shear. It is shown that this regime accounted for approximately 40% of the significant turbulent events identified in the 7-yr database. In addition, two specific cases from the database are examined in more detail using a high-resolution mesoscale model. The model simulations highlight the important role of three-dimensional gravity wave–critical level interactions and demonstrate the utility of high-resolution forecasts in the prediction of such events.
A New Approach to Forecasting Typhoon Frequency over the Western North Pacific
Authors: Fan Ke , Wang Huijun 
Published: February 2009

Abstract
This paper presents a new approach for forecasting the typhoon frequency of the western North Pacific (WNP). The year-to-year increase or decrease in typhoon frequency is first forecasted to yield a net typhoon frequency prediction. Five key predictors for the year-to-year increment in the number of typhoons in the WNP have been identified, and a forecast model is established using a multilinear regression method based on data taken from 1965 to 2001. Using the forecast model, a hindcast of the typhoon frequency of the WNP during 2002–07 is made. The model exhibited a reasonably close fit for the period 1965–2007, including the larger anomalies in 1997 and 1998. It also accounted for the smaller variability of the typhoon frequency of the WNP during the validation period 2002–07 with an average root-mean-square error (RMSE) of 1.3 (2.85) during 2002–07 (1965–2001). The cross-validation test of the prediction model shows that the new approach and the prediction model demonstrate better prediction skill when compared to the models established based on typhoon frequency rather than the typhoon frequency increment. Thus, this new approach has the potential to improve the operational forecasting skill for typhoon frequency in the WNP.
The tyrosine phosphatase CD148 is an essential positive regulator of platelet activation and thrombosis
Authors: Senis Yotis A. , Tomlinson Michael G. , Ellison Stuart , Mazharian Alexandra , Lim Jenson , Zhao Yan , Kornerup Kristin N. , Auger Jocelyn M. , Thomas Steve G. , Dhanjal Tarvinder , Kalia Neena , Zhu Jing W. , Weiss Arthur , Watson Steve P. 
Published: February 2009

Abstract
Platelets play a fundamental role in hemostasis and thrombosis. They are also involved in pathologic conditions resulting from blocked blood vessels, including myocardial infarction and ischemic stroke. Platelet adhesion, activation, and aggregation at sites of vascular injury are regulated by a diverse repertoire of tyrosine kinase–linked and G protein–coupled receptors. Src family kinases (SFKs) play a central role in initiating and propagating signaling from several platelet surface receptors; however, the underlying mechanism of how SFK activity is regulated in platelets remains unclear. CD148 is the only receptor-like protein tyrosine phosphatase identified in platelets to date. In the present study, we show that mutant mice lacking CD148 exhibited a bleeding tendency and defective arterial thrombosis. Basal SFK activity was found to be markedly reduced in CD148-deficient platelets, resulting in a global hyporesponsiveness to agonists that signal through SFKs, including collagen and fibrinogen. G protein–coupled receptor responses to thrombin and other agonists were also marginally reduced. These results highlight CD148 as a global regulator of platelet activation and a novel antithrombotic drug target.
Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites
Authors: Shi Baochen , Guo Xiangqian , Wu Tao , Sheng Sitong , Wang Jie , Skogerbø Geir , Zhu Xiaopeng , Chen Runsheng 
Published: February 2009

Abstract

Background
A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I hypersensitive sites within the nuclear chromatin is a powerful and well-established method of identifying regulatory element candidates.

Results
Here, we report the first genome-wide analysis of DNase I hypersensitive sites (DHSs) in Caenorhabditis elegans. The data was obtained by hybridizing DNase I-treated and end-captured material from young adult worms to a high-resolution tiling microarray. The data show that C. elegans DHSs were significantly enriched within intergenic regions located 2 kb upstream and downstream of coding genes, and also that a considerable fraction of all DHSs mapped to intergenic positions distant to annotated coding genes. Annotated transcribed loci were generally depleted in DHSs relative to intergenic regions, but DHSs were nonetheless enriched in coding exons and UTRs, whereas introns were significantly depleted in DHSs. Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function. It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes.

Conclusion
We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.
Structural alterations in the seminiferous tubules of rats treated with immunosuppressor tacrolimus
Authors: Caneguim Breno H , Cerri Paulo S , Spolidório Luís C , Miraglia Sandra M , Sasso-Cerri Estela 
Published: February 2009

AbstractBackgroundTacrolimus (FK-506) is an immunosuppressant that binds to a specific immunophilin, resulting in the suppression of the cellular immune response during transplant rejection. Except for some alterations in the spermatozoa, testicular morphological alterations have not been described in rats treated with tacrolimus. In the present study, we purpose to evaluate if the treatment with tacrolimus at long term of follow-up interferes in the integrity of the seminiferous tubules.MethodsRats aging 42-day-old received daily subcutaneous injections of 1 mg/kg/day of tacrolimus during 30 (T-30) and 60 (T-60) days; the rats from control groups (C-30 and C-60) received saline solution. The left testes were fixed in 4% formaldehyde and embedded in glycol methacrylate for morphological and morphometric analyses while right testes were fixed in Bouin's liquid and embedded in paraffin for detection of cell death by the TUNEL method. The epithelial and total tubular areas as well as the stages of the seminiferous epithelium and the number of spermatocytes, spermatids and Sertoli cells (SC) per tubule were obtained.ResultsIn the treated groups, seminiferous tubules irregularly outlined showed disarranged cellular layers and loss of germ cells probably due to cell death, which was revealed by TUNEL method. In addition to germ cells, structural alterations in the SC and folding of the peritubular tissue were usually observed. The morphometric results revealed significant decrease in the number of SC, spermatocytes, spermatids and significant reduction in the epithelial and total tubular areas.ConclusionTacrolimus induces significant histopathological disorders in the seminiferous tubules, resulting in spermatogenic damage and reduction in the number of Sertoli cells. A careful evaluation of the peritubular components will be necessary to clarify if these alterations are related to the effect of FK-506 on the peritubular tissue.
Video-assisted thoracic surgery (VATS) as a safe alternative for the resection of pulmonary metastases: a retrospective cohort study
Authors: Carballo Marilee , Maish Mary S. , Jaroszewski Dawn E. , Holmes Carmack E. 
Published: February 2009

Abstract

Background
VATS has become a preferred method for benign surgical conditions, yet still remains controversial for malignancies. The purpose of this study was to review our results of pulmonary metastasectomies using both conventional open thoracotomy and VATS techniques.

Methods
This is a retrospective chart review of pulmonary metastasectomies performed from 1986 to 2006. The surgical approach used for the initial pulmonary metastasectomy was either open thoracotomy or VATS. Main outcomes were overall survival and recurrence free survival, evaluated using Kaplan Meier analysis. A non-inferiority margin was set at 0.2.

Results
A total of 280 surgical procedures were performed on 186 patients. From 171 eligible individuals, 135 patients were treated with thoracotomy (82 M, 53 F; median age 49 years), and 36 with VATS (18 M, 18 F; median age 58.5 years). Primary cancers were mainly: 81 sarcoma (47%), 26 colorectal adenocarcinoma (15%) and 22 renal cell carcinoma (13%). Median postoperative follow was 26.2 months. The conversion rate was 10.3% and there were no cases of pleural cavity seeding. The 5-year overall survival rates were 58.8% for thoracotomy and 69.6% for VATS, with median overall survival of 53.2 months and 30.1 months, respectively (p = 0.03). The estimated difference in 5-year overall survival was 10.8%. Second occurrences were noted in 59 thoracotomy and 10 VATS patients. The 5-year recurrence free survival rates were 51% in thoracotomy and 67% in VATS (p = 0.27), with median recurrence free survival of 24.8 months and 25.6 months, respectively.

Conclusion
In cases of pulmonary metastases, VATS is an acceptable alternative that is both safe and efficacious. Non-inferiority analysis of 5-year overall survival demonstrates that VATS is equivalent to thoracotomy. VATS patients also have a longer recurrence free survival. Based on our experience, it is permissible to use VATS resection in these circumstances: small tumor, fewer nodules, single lesion, age ≤ 53, unilateral, tumor size amenable to wedge resection, and non-recurrent disease.
Cost-utility analysis of palivizumab in Italy: results from a simulation model in the prophylaxis of respiratory syncytial virus infection (RSV) among high-risk preterm infants
Authors: Chirico Gaetano , Ravasio Roberto , Sbarigia Urbano 
Published: February 2009

Abstract

Introduction
The aim of this study was to assess the cost-utility of palivizumab versus no prophylaxis in the prevention of respiratory syncytial virus infection among high-risk preterm infants.

Methods
We used and adapted a pre-existent model in which two cohorts of patients received palivizumab or no prophylaxis. The patients were followed for their expected lifetimes. The economic evaluation was conducted from the perspective of the Italian National Health Service. We considered Life-Years Gained (LYGs), Quality-Adjusted Life-Years (QALYs) and direct medical costs (pharmacological treatment, hospitalization, recurrences for wheezing, etc.). LYGs and QALYs were based on the results of a double blind cohort study with prospective follow-up and direct medical costs were based on Italian treatment patterns. Benefits and costs were discounted at 3%. Costs were assessed in 2007 Euros. Sensitivity and threshold analysis on key clinical and economic parameters were performed.

Result
For the two cohorts, the expected life-years (per patient) with palivizumab versus no prophylaxis were 29.842 and 29.754 years, respectively. Quality-adjusted life years (per patient) with palivizumab were 29.202, and for no prophylaxis were 29.043. The expected cost (per patient) was € 6,244.20 with palivizumab and € 4,867.70 with no prophylaxis. We calculated for palivizumab versus no prophylaxis the incremental cost per LYG and per QALY gained. It was € 15,568.65 and € 8,676.74, respectively.

Conclusion
This study suggests that, compared with no prophylaxis, palivizumab is cost-effective in the prevention of respiratory syncytial virus infection among high risk preterm infants.
High frequency of BRCA1, but not CHEK2 or NBS1 (NBN), founder mutations in Russian ovarian cancer patients
Authors: Suspitsin Evgeny N , Sherina Nathalia Yu , Ponomariova Daria N , Sokolenko Anna P , Iyevleva Aglaya G , Gorodnova Tatyana V , Zaitseva Olga A , Yatsuk Olga S , Togo Alexandr V , Tkachenko Nathalia N , Shiyanov Grigory A , Lobeiko Oksana S , Krylova Nadezhda Yu , Matsko Dmitry E , Maximov Sergey Ya , Urmancheyeva Adel F , Porhanova Nathalia V , Imyanitov Evgeny N 
Published: February 2009

Abstract

Background
A significant portion of ovarian cancer (OC) cases is caused by germ-line mutations in BRCA1 or BRCA2 genes. BRCA testing is cheap in populations with founder effect and therefore recommended for all patients with OC diagnosis. Recurrent mutations constitute the vast majority of BRCA defects in Russia, however their impact in OC morbidity has not been yet systematically studied. Furthermore, Russian population is characterized by a relatively high frequency of CHEK2 and NBS1 (NBN) heterozygotes, but it remains unclear whether these two genes contribute to the OC risk.

Methods
The study included 354 OC patients from 2 distinct, geographically remote regions (290 from North-Western Russia (St.-Petersburg) and 64 from the south of the country (Krasnodar)). DNA samples were tested by allele-specific PCR for the presence of 8 founder mutations (BRCA1 5382insC, BRCA1 4153delA, BRCA1 185delAG, BRCA1 300T>G, BRCA2 6174delT, CHEK2 1100delC, CHEK2 IVS2+1G>A, NBS1 657del5). In addition, literature data on the occurrence of BRCA1, BRCA2, CHEK2 and NBS1 mutations in non-selected ovarian cancer patients were reviewed.

Results
BRCA1 5382insC allele was detected in 28/290 (9.7%) OC cases from the North-West and 11/64 (17.2%) OC patients from the South of Russia. In addition, 4 BRCA1 185delAG, 2 BRCA1 4153delA, 1 BRCA2 6174delT, 2 CHEK2 1100delC and 1 NBS1 657del5 mutation were detected. 1 patient from Krasnodar was heterozygous for both BRCA1 5382insC and NBS1 657del5 variants.

Conclusion
Founder BRCA1 mutations, especially BRCA1 5382insC variant, are responsible for substantial share of OC morbidity in Russia, therefore DNA testing has to be considered for every OC patient of Russian origin. Taken together with literature data, this study does not support the contribution of CHEK2 in OC risk, while the role of NBS1 heterozygosity may require further clarification.
Protein kinase D1 regulates matrix metalloproteinase expression and inhibits breast cancer cell invasion
Authors: Eiseler Tim , Döppler Heike , Yan Irene K , Goodison Steve , Storz Peter 
Published: February 2009

Abstract
Introduction
The biological and molecular events that regulate the invasiveness of breast tumour cells need to be further revealed to develop effective therapies that stop breast cancer from expanding and metastasising.

Methods
Human tissue samples of invasive breast cancer and normal breast, as well as breast cancer cell lines, were evaluated for protein kinase D (PKD) expression, to test if altered expression could serve as a marker for invasive breast cancer. We further utilised specific PKD1-shRNA and a system to inducibly-express PKD1 to analyse the role of PKD1 in the invasive behaviour of breast cancer cell lines in two-dimensional (2D) and three-dimensional (3D) culture. Invasive behaviour in breast cancer cell lines has been linked to matrix metalloproteinases (MMPs), so we also determined if PKD1 regulates the expression and activity of these enzymes.

Results
We found that the serine/threonine kinase, PKD1, is highly expressed in ductal epithelial cells of normal human breast tissue, but is reduced in its expression in more than 95% of all analysed samples of human invasive breast tumours. Additionally, PKD1 is not expressed in highly invasive breast cancer cell lines, whereas non-invasive or very low-invasive breast cancer cell lines express PKD1. Our results further implicate that in MDA-MB-231 cells PKD1 expression is blocked by epigenetic silencing via DNA methylation. The re-expression of constitutively-active PKD1 in MDA-MB-231 cells drastically reduced their ability to invade in 2D and 3D cell culture. Moreover, MCF-7 cells acquired the ability to invade in 2D and 3D cell culture when PKD1 expression was knocked-down by shRNA. PKD1 also regulated the expression of breast cancer cell MMPs, MMP-2, MMP-7, MMP-9, MMP-10, MMP-11, MMP-13, MMP-14 and MMP-15, providing a potential mechanism for PKD1 mediation of the invasive phenotype.

Conclusions
Our results identify decreased expression of the PKD1 as a marker for invasive breast cancer. They further suggest that the loss of PKD1 expression increases the malignant potential of breast cancer cells. This may be due to the function of PKD1 as a negative regulator of MMP expression. Our data suggest re-expression of PKD1 as a potential therapeutic strategy.
SEPALLATA3: the 'glue' for MADS box transcription factor complex formation
Authors: Immink Richard GH , Tonaco Isabella AN , de Folter Stefan , Shchennikova Anna , van Dijk Aalt DJ , Busscher-Lange Jacqueline , Borst Jan W , Angenent Gerco C 
Published: February 2009

Abstract
Background
Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and are thought to assemble into multimeric complexes. In this study a large-scale yeast three-hybrid screen is utilized to provide insight into the higher-order complex formation capacity of the Arabidopsis MADS box family. SEPALLATA3 (SEP3) has been shown to mediate complex formation and, therefore, special attention is paid to this factor in this study.

Results
In total, 106 multimeric complexes were identified; in more than half of these at least one SEP protein was present. Besides the known complexes involved in determining floral organ identity, various complexes consisting of combinations of proteins known to play a role in floral organ identity specification, and flowering time determination were discovered. The capacity to form this latter type of complex suggests that homeotic factors play essential roles in down-regulation of the MADS box genes involved in floral timing in the flower via negative auto-regulatory loops. Furthermore, various novel complexes were identified that may be important for the direct regulation of the floral transition process. A subsequent detailed analysis of the APETALA3, PISTILLATA, and SEP3 proteins in living plant cells suggests the formation of a multimeric complex in vivo.

Conclusions
Overall, these results provide strong indications that higher-order complex formation is a general and essential molecular mechanism for plant MADS box protein functioning and attribute a pivotal role to the SEP3 'glue' protein in mediating multimerization.
NOD2/CARD15 on bone marrow CD34+ hematopoietic cells mediates induction of cytokines and cell differentiation
Authors: Sioud Mouldy , Fløisand Yngvar 
Published: February 2009

AbstractHuman bone marrow (BM) hematopoietic cells were found recently to express functional TLRs and TLR signaling-induced cytokine production and cell differentiation. Here, we have asked whether signals other than those from TLRs could instruct BM CD34+ cells to produce cytokines and differentiate by uncovering the role of nucleotide oligomerization domain (Nod)-like receptor (NLR) family members, NOD1 and NOD2. We show that NOD2 is expressed by freshly isolated human BM CD34+ cells, whereas the expression of its close homologue NOD1 is very weak. Stimulation of the cells by the muramyl dipeptide (MDP), but not its inactive D–D enantiomer, is sufficient to trigger the expression of TNF-α, GM-CSF, CD11c, CD14, CD206, and the transcription factor PU.1, which is indispensable for cell differentiation toward the myeloid lineage. MDP differentiated CD11c+ cell subset-activated T cells in MLR. Furthermore, NOD2 stimulation enhanced the CD34+ response to TLR ligands (e.g., LPS, palmitoyl-3-cysteine-serine-lysine-4) and increased intracellular α-defensin protein levels. Although the best-known function of NLRs involves mature cells, our data highlight for the first time the functionality of these receptors in human BM CD34+ hematopoietic cells.
CBR Strength (Puncture) of Geosynthetics
Authors: Murphy VP , Koerner RM 
Published: February 2009

Abstract
While there exist many types of mechanical tests for use on geosynthetics, most seem to be more suitable for one type of system or another. This paper focuses on a test which may have widespread applicability to assess the strength of all types of geosynthetics. It is the forcing of a 50-mm (2.0-in.) diameter plunger through a horizontally fixed geosynthetic of 150-mm (6.0-in.) diameter. Such dimensions are common to the California bearing ratio (CBR) test apparatus used in assessing soil strength for road subgrades. In actuality, the test is not a puncture test, but is an axisymmetric strength test and should be considered as such. The unsupported geosynthetic is indeed in a state of tension. The stress conditions are well defined, which allow for stress and strain to be calculated and compared to the actual value as obtained in a plane strain (wide width) tension test.
This approach has been followed in this study wherein a wide range of geosynthetics (geotextiles, geomembranes, geonets, and geocomposites) have been tested for CBR (puncture) strength and then calculations performed to determine stress and strain. These calculated values were then compared to those obtained in wide width tests. Results are interesting in that the average values of percent variation between wide width tensile strength and CBR calculated tensile strength for those geosynthetics tested are as follows: (1) geotextiles ±12%, (2) geomembranes ±33%, (3) geonets ±17%, and (4) geocomposites ±10%. It is felt that this type of test (which is basically an index test) is helpful in a number of situations, not the least of which is in assessing strength changes before and after exposure of various geosynthetic materials to chemical or biological incubation.
Determination of the Plastic Limit of a Soil by Means of a Rolling Device
Authors: Bobrowski LJ , Griekspoor DM 
Published: February 2009

Abstract
A rolling device was developed in order to obtain plastic limits in a more expeditious and uniform fashion. The device enables the operator to perform the test on four to five specimens simultaneously. It also dictates that the very strict specification for rolling the soil threads into diameters of 3.2 ± 0.5 mm (0.125 ± 0.020 in.) is met. It removes all subjectivity from the plastic limit determination by governing the diameter of the threads as well as removing any error that may be introduced due to the uniqueness of the human hand. The design and operation of the device are detailed in this paper.
Time-Temperature Superposition in Mechanical Durability Testing of Polyethylene Geomembranes
Authors: Lord AE , Hsuan YG , Koerner RM 
Published: February 2009

Abstract
The mechanical durability of polyethylene geomembranes is considered in this technical note. Polyethylene plastic pipe research has shown that there are universal factors for shifting high-temperature failure (short time) data to low temperatures (long time). Data presented here indicate that these same shift factors may also apply to geomembranes. Crack growth rate studies are proposed as a supplement to the currently used notched constant tensile load tests.