bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal evolution of boundary‐layer turbulence measured by aircraft during the AMMA 2006 Special Observation Period
Authors: Saïd F. , Canut G. , Durand P. , Lohou F. , Lothon M. 
Published: September 2009

AbstractDuring the African Monsoon Multidisciplinary Analysis (AMMA) field campaign, the ATR research aircraft made observations of fluxes and thermodynamics during three 15‐day periods, which allowed the seasonal evolution of the atmospheric boundary‐layer (ABL) characteristics to be monitored before and after the monsoon onset. As expected, temperature and humidity showed a contrast between dry warm conditions and moister cooler conditions from one period to the other. Most of the time, the wind blew from the west (northwesterly to southwesterly) in the ABL and from the east in the free troposphere. Following rainfall events occuring in July and August, surface sensible heat flux decreased and evaporation increased while the momentum flux remained large in the entire boundary layer, whatever the period. The aim of this paper is to characterize turbulence in terms of fluxes and length‐scales for ABLs that exhibit particular characteristics relative to (i) entrainment at the top, (ii) wind rotation at the interface between the monsoon and the Saharan air layer and (iii) seasonal variability. In spite of the poorer accuracy of the turbulent flux estimations at the top of the ABL, the flux profiles were observed to increase or decrease linearly with altitude which enabled accurate estimates of entrainment flux ratios. It was found that the moisture flux distribution in the ABL was governed by top‐down processes during the driest period and a mixture of top‐down and bottom‐up processes during the monsoon period. Significant differences in turbulence length‐scales were also highlighted. Copyright © 2009 Royal Meteorological Society
Nonequivalent Effects of Diverse LogP Algorithms in Three QSAR Studies
Authors: de Melo Eduardo Borges , Ferreira Márcia Miguel Castro 
Published: September 2009

AbstractDespite of the availability and facility of accessing several algorithms for calculation of LogP in QSA(P)R studies, articles typically do not describe the selection procedure for the method used. Therefore, three studies to verify the influence of different LogP algorithms on building QSAR models were performed. Two QSAR data sets from the literature (forty‐two tricyclic phtalimide inhibitors of HIV‐integrase and fourty‐six TIBO derivatives inhibitors of HIV‐reverse transcriptase) were used together with LogP calculated by thirteen algorithms, and several regression models were constructed and compared. A new QSAR study for 4,5‐dihydroxypyrimidine carboxamides inhibitors of HIV‐1 integrase was also performed. The explained and predicted variance, results from external validation, leave‐N‐out cross‐validation and y‐randomization test were analyzed for all models from the three data sets. Despite the same physicochemical meaning, LogP's calculated by distinct methods may show different levels of contribution to the model. This observation comes out from the comparison of validated models. These results indicate that the arbitrary choice of one specific algorithm for LogP calculation, as is usual in QSA(P)R studies , does not necessarily lead to the highest quality model for the analyzed data set.
Gaussian process modeling of large‐scale terrain
Authors: Vasudevan Shrihari , Ramos Fabio , Nettleton Eric , Durrant‐Whyte Hugh 
Published: September 2009

AbstractBuilding a model of large‐scale terrain that can adequately handle uncertainty and incompleteness in a statistically sound way is a challenging problem. This work proposes the use of Gaussian processes as models of large‐scale terrain. The proposed model naturally provides a multiresolution representation of space, incorporates and handles uncertainties aptly, and copes with incompleteness of sensory information. Gaussian process regression techniques are applied to estimate and interpolate (to fill gaps in occluded areas) elevation information across the field. The estimates obtained are the best linear unbiased estimates for the data under consideration. A single nonstationary (neural network) Gaussian process is shown to be powerful enough to model large and complex terrain, effectively handling issues relating to discontinuous data. A local approximation method based on a “moving window” methodology and implemented using k‐dimensional (KD)‐trees is also proposed. This enables the approach to handle extremely large data sets, thereby completely addressing its scalability issues. Experiments are performed on large‐scale data sets taken from real mining applications. These data sets include sparse mine planning data, which are representative of a global positioning system–based survey, as well as dense laser scanner data taken at different mine sites. Further, extensive statistical performance evaluation and benchmarking of the technique has been performed through cross‐validation experiments. They conclude that for dense and/or flat data, the proposed approach will perform very competitively with grid‐based approaches using standard interpolation techniques and triangulated irregular networks using triangle‐based interpolation techniques; for sparse and/or complex data, however, it would significantly outperform them. © 2009 Wiley Periodicals, Inc.
Bayesian inference for the stereotype regression model: Application to a case–control study of prostate cancer
Authors: Ahn Jaeil , Mukherjee Bhramar , Banerjee Mousumi , Cooney Kathleen A. 
Published: September 2009

AbstractThe stereotype regression model for categorical outcomes, proposed by Anderson (J. Roy. Statist. Soc. B.1984;46:1–30) is nested between the baseline‐category logits and adjacent category logits model with proportional odds structure. The stereotype model is more parsimonious than the ordinary baseline‐category (or multinomial logistic) model due to a product representation of the log‐odds‐ratios in terms of a common parameter corresponding to each predictor and category‐specific scores. The model could be used for both ordered and unordered outcomes. For ordered outcomes, the stereotype model allows more flexibility than the popular proportional odds model in capturing highly subjective ordinal scaling which does not result from categorization of a single latent variable, but are inherently multi‐dimensional in nature. As pointed out by Greenland (Statist. Med.1994;13:1665–1677), an additional advantage of the stereotype model is that it provides unbiased and valid inference under outcome‐stratified sampling as in case–control studies. In addition, for matched case–control studies, the stereotype model is amenable to classical conditional likelihood principle, whereas there is no reduction due to sufficiency under the proportional odds model. In spite of these attractive features, the model has been applied less, as there are issues with maximum likelihood estimation and likelihood‐based testing approaches due to non‐linearity and lack of identifiability of the parameters. We present comprehensive Bayesian inference and model comparison procedure for this class of models as an alternative to the classical frequentist approach. We illustrate our methodology by analyzing data from The Flint Men's Health Study, a case–control study of prostate cancer in African‐American men aged 40–79 years. We use clinical staging of prostate cancer in terms of Tumors, Nodes and Metastasis as the categorical response of interest. Copyright © 2009 John Wiley & Sons, Ltd.
Understanding software maintenance and evolution by analyzing individual changes: a literature review
Authors: Benestad Hans Christian , Anda Bente , Arisholm Erik 
Published: September 2009

AbstractUnderstanding, managing and reducing costs and risks inherent in change are key challenges of software maintenance and evolution, addressed in empirical studies with many different research approaches. Change‐based studies analyze data that describes the individual changes made to software systems. This approach can be effective in order to discover cost and risk factors that are hidden at more aggregated levels. However, it is not trivial to derive appropriate measures of individual changes for specific measurement goals. The purpose of this review is to improve change‐based studies by (1) summarizing how attributes of changes have been measured to reach specific study goals and (2) describing current achievements and challenges, leading to a guide for future change‐based studies. Thirty‐four papers conformed to the inclusion criteria. Forty‐three attributes of changes were identified, and classified according to a conceptual model developed for the purpose of this classification. The goal of each study was to either characterize the evolution process, to assess causal factors of cost and risk, or to predict costs and risks. Effective accumulation of knowledge across change‐based studies requires precise definitions of attributes and measures of change. We recommend that new change‐based studies base such definitions on the proposed conceptual model. Copyright © 2009 John Wiley & Sons, Ltd.
Use of Z‐scores to select a fetal biometric reference curve
Authors: Sananes N. , Guigue V. , Kohler M. , Bouffet N. , Cancellier M. , Hornecker F. , Hunsinger M. C. , Kohler A. , Mager C. , Neumann M. , Schmerber E. , Tanghe M. , Nisand I. , Favre R. 
Published: September 2009

AbstractObjectiveFetal biometric data are a major part of prenatal ultrasound screening in the general population. The aim of this study was to analyze the effect of choice of reference curve on the quality of screening for growth abnormalities, using a statistical tool based on Z‐scores.MethodsThe biparietal diameter (BPD), head circumference (HC), abdominal circumference (AC) and femur length (FL) were measured in 9699 ultrasound scans during the second trimester (20–24 weeks of gestation) and 8100 scans during the third trimester (30–34 weeks of gestation). These biometric data were all transformed retrospectively into Z‐scores, calculated using five reference curves: those published by Snijders and Nicolaides (1994), Chitty et al. (1994), Kurmanavicius et al. (1999) and Salomon et al. (2006), and curves used at our ultrasound unit generated from a sample of the local population. The Z‐score distribution was compared with the expected normal distribution by calculation of the mean and SD, and using the Kolmogorov–Smirnov test. The sensitivity and specificity of each reference curve were calculated to determine the capacity of these curves to identify fetuses with measurements < 5th percentile or > 95th percentile for each parameter.ResultsMost of the distribution curves determined from the Z‐scores of the measurements taken differed significantly from a non‐skewed standard normal curve (mean of 0 and SD of 1). In our population, the Chitty reference curves gave the best results for identifying fetuses with abnormal (< 5th percentile or > 95th percentile) BPD (sensitivity, 100%; specificity, 97.24%), HC (sensitivity, 96.07%; specificity, 98.89%) and FL (sensitivity, 96.46%; specificity, 98.80%). The best reference for AC was the Salomon curve (sensitivity, 72.25%; specificity, 99.64%).ConclusionsChecking for good concordance between the study population and chosen reference data is a key initial step in quality control. Z‐scores are a simple tool for evaluating the performance of each reference curve for a given population in order to optimize the sensitivity and specificity of screening for fetal growth abnormalities. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
Molecular beacons and related probes for intracellular RNA imaging
Authors: Santangelo Philip J. 
Published: September 2009

AbstractAccurately imaging endogenous or non‐engineered RNA in live cells is not an easy task. Ideally, a probe and imaging strategy will have the following properties: (1) functional probes will be delivered to the desired cellular compartment, (2) they will achieve the correct level of affinity to bind target RNA efficiently but not inhibit their function, (3) be sensitive enough to allow for the accurate detection of the cellular RNA population, and (4) allow for the tracking of RNA through biogenesis, transport, translation, and degradation pathways. In this review, the capabilities of current nucleic acid‐based probes and strategies used to image native RNA are discussed and analyzed, and probe and strategy recommendations for new users are given. The review is concluded by addressing topics for future research, all in the hope of achieving the ideal RNA imaging probe and strategy. WIREs Nanomed Nanobiotechnol 2010 2 11–19This article is categorized under:

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Cytotoxicity Effects of Different Surfactant Molecules Conjugated to Carbon Nanotubes on Human Astrocytoma Cells
Authors: Dong Lifeng , Witkowski Colette M , Craig Michael M , Greenwade Molly M , Joseph Katherine L 
Published: September 2009

Abstract
Phase contrast and epifluorescence microscopy were utilized to monitor morphological changes in human astrocytoma cells during a time-course exposure to single-walled carbon nanotube (SWCNT) conjugates with different surfactants and to investigate sub-cellular distribution of the nanotube conjugates, respectively. Experimental results demonstrate that cytotoxicity of the nanotube/surfactant conjugates is related to the toxicity of surfactant molecules attached on the nanotube surfaces. Both sodium dodecyl sulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) are toxic to cells. Exposure to CNT/SDS conjugates (0.5 mg/mL) for less than 5 min caused changes in cell morphology resulting in a distinctly spherical shape compared to untreated cells. In contrast, sodium cholate (SC) and CNT/SC did not affect cell morphology, proliferation, or growth. These data indicate that SC is an environmentally friendly surfactant for the purification and dispersion of SWCNTs. Epifluorescence microscopy analysis of CNT/DNA conjugates revealed distribution in the cytoplasm of cells and did not show adverse effects on cell morphology, proliferation, or viability during a 72-h incubation. These observations suggest that the SWCNTs could be used as non-viral vectors for diagnostic and therapeutic molecules across the blood–brain barrier to the brain and the central nervous system.
Multi-axial correction system in the treatment of radial club hand
Authors: Bhat Suneel B. , Kamath Atul F. , Sehgal Kriti , Horn B. David , Hosalkar Harish S. 
Published: September 2009

Background Radial club hand is a well-recognized congenital malformation characterized by hypoplasia of bone and soft tissue on the radial aspect of the forearm and hand. The modalities of treatment have traditionally varied from stretching casts with soft-tissue procedures to the use of multiple corrective osteotomies. These osteotomies can be stabilized by a variety of methods, including external fixators that allow the possibility of gradual distraction with neohistiogenesis. This current study outlines the usage of one such device (multi-axial correction system [MAC]) in the management of deformity associated with severe radial club hand. Methods Three consecutive cases of unilateral or bilateral severe (Bayne type IV) congenital radial club hand were corrected using MAC fixation in the last 5 years. This is a retrospective review of all three cases. Data parameters included: patient demographics, presentation findings, degree of deformity, amount of correction/lengthening, length of procedure, length of treatment, and associated complications. The surgical technique is described in detail for the benefit of the readership. Results The three patients with severe congenital radial club hand had a total of four limb involvements that underwent correction using osteotomies and usage of the MAC device for external fixation. All three patients underwent successful correction of deformity with the restoration of alignment, lengthening of forearm for improvement of function, and stabilization of the wrist (mean duration, mean lengthening, mean time to consolidation). The MAC system was well tolerated in all patients and associated complications were limited. Conclusion The MAC fixator seems to be a good alternative modality of stabilization and correction for severe congenital radial club hand deformities. Its usage is fairly simple and it provides the ease of application of a mono-lateral fixator with far superior three-dimensional control, like the circular external fixator. We recommend that clinicians should add this modality to their armamentarium for the deformity correction of severe radial club hand and others in general.
Transgene Stacking and Coordinated Expression of Plant Defensins Confer Fungal Resistance in Rice
Authors: Jha Sanjay , Chattoo Bharat Bhushan 
Published: September 2009

Abstract
Transgenic rice with cleavable chimeric polyprotein and single-protein gene constructs placed under the control of single maize ubiquitin promoter were generated by Agrobacterium tumefaciens-mediated transformation. The polyprotein precursor consists of a leader peptide and two different antimicrobial proteins (AMPs), Dm-AMP1 and Rs-AFP2, from the seeds of Dahlia merckii and Raphanus sativus, respectively. These genes were linked by a 16 amino acid Ib-AMP linker peptide region isolated from the seeds of Impatiens balsamina. Average expression of Dm-AMP1 and Rs-AFP2 was 8.35 ± 0.56 and 8.1 ± 0.6 2 g/mg of total soluble proteins in the leaf extracts of transgenic plants. Plants transformed with polyprotein construct showed significantly improved disease resistance against Magnaporthe oryzae and Rhizoctonia solani by 90% and 79%, respectively, as compared to untransformed plants. The plants transformed with polyprotein construct were more resistant to M. oryzae compared to plants transformed with control single-gene constructs of Dm-AMP1 and Rs-AFP2. The chimeric polyprotein was cleaved and present in equimolar concentration in transgenic rice and the individual AMPs were secreted into the extracellular space. The results of in vitro, in planta, and microscopic analyses suggest that chimeric polyprotein expression has the potential to provide broad-spectrum disease resistance in rice.
Gene networks involved in apoptosis induced by hyperthermia in human lymphoma U937 cells
Authors: Furusawa Yukihiro , Tabuchi Yoshiaki , Takasaki Ichiro , Wada Shigehito , Ohtsuka Kenzo , Kondo Takashi 
Published: September 2009

AbstractTo define the molecular mechanisms that mediate hyperthermia‐induced apoptosis, we performed microarray and computational gene expression analyses. U937 cells, a human myelomonocytic lymphoma cell line, were treated with hyperthermia at 42 °C for 90 min and cultured at 37 °C. Apoptotic cells (∼15%) were seen 6 h after hyperthermic treatment, and elevated expression of heat shock proteins (HSPs) including Hsp27, Hsp40, and Hsp70 was detected, following the activation of heat shock factor‐1. Of the 54,675 probe sets analyzed, 1334 were upregulated and 4214 were downregulated by >2.0‐fold in the cells treated with hyperthermia. A non‐hierarchical gene clustering algorithm, K‐means clustering, demonstrated 10 gene clusters. The gene network U1 or U2 that was obtained from up‐regulated genes in cluster I or IX contained HSPA1B, DNAJB1, HSPH1, and TXN or PML, LYN, and DUSP1, and were mainly associated with cellular compromise, and cellular function and maintenance or death, and cancer, respectively. In the decreased gene cluster II, the gene network D1 including CCNE1 and CEBPE was associated with the cell cycle and cellular growth and proliferation. These findings will provide a basis for understanding the detailed molecular mechanisms of apoptosis induced by hyperthermia at 42 °C in cells.
Effects of colchicine or demecolcine on cytoplasmic protrusions and assisted enucleation of golden hamster oocytes
Authors: Wang Lingyan , Jiang Han , Su Li , Tang Bo , Li Dexue , Li Ziyi 
Published: September 2009

AbstractTo establish experimental protocols for cloning golden hamsters, optimal concentrations of colchicine and demecolcine were determined for inducing cytoplasmic protrusion (containing chromosomes) and assisting enucleation of their oocytes. Denuded oocytes at different ages were treated with 2.5–10 μg/ml of colchicine for 1–4 h or 0.02–0.6 μg/ml of demecolcine for 15–60 min. Cytoplasmic protrusions of oocytes were removed with a micromanipulation pipette. The results show that: 1) at 13.5–18 h post‐hCG injection, ∼90% of oocytes treated for with 10 μg/ml of colchicine formed cytoplasmic protrusions, and in some oocytes enucleation occurred; 2) when treated with 0.4 μg/ml of demecolcine for 1 h, cytoplasmic protrusions 13.5–18 h post‐hCG treatment were present in almost all oocytes; 3) after the protrusions induced by either treatment had been removed, the assisted enucleation rate was >80%, whereas it was ∼32% with blind enucleation.
Genistein induces G2/M cell cycle arrest and apoptosis of human ovarian cancer cells via activation of DNA damage checkpoint pathways
Authors: Ouyang Gaoliang , Yao Luming , Ruan Kai , Song Gang , Mao Yubin , Bao Shideng 
Published: September 2009

AbstractGenistein is a major isoflavonoid in dietary soybean, commonly consumed in Asia. Genistein exerts inhibitory effects on the proliferation of various cancer cells and plays an important role in cancer prevention. However, the molecular and cellular mechanisms of genistein on human ovarian cancer cells are still little known. We show that exposure of human ovarian cancer HO‐8910 cells to genistein induces DNA damage, and triggers G2/M phase arrest and apoptosis. Furthermore, we also found that checkpoint proteins ATM and ATR are phosphorylated and activated in the cells treated with genistein. It is also shown that genistein increases the phosphorylation and activation of Chk1 and Chk2, which results in the phosphorylation and inactivation of phosphatases Cdc25C and Cdc25A, and thereby the phosphorylation and inactivation of Cdc2 which arrests cells in G2/M phase. Moreover, genistein enhances the phosphorylation and activation of p53, while decreases the ratio of Bcl‐2/Bax and Bcl‐xL/Bax and the level of phosphorylated Akt, which result in cells undergoing apoptosis. These results demonstrate that genistein‐activated ATM‐Chk2‐Cdc25 and ATR‐Chk1‐Cdc25 DNA damage checkpoint pathways can arrest ovarian cancer cells in G2/M phase, and induce apoptosis while the cellular DNA damage is too serious to be repaired. Thus, the antiproliferative, DNA damage‐inducing and pro‐apoptotic activities of genistein are probably responsible for its genotoxic effects on human ovarian cancer HO‐8910 cells.