bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Integrated Display and Analysis Methodology for Multivariable Radar Data
Authors: Dolan Brenda A. , Rutledge Steven A. 
Published: August 2007

Abstract
Polarimetric Doppler radars provide valuable information about the kinematic and microphysical structure of storms. However, in-depth analysis using radar products, such as Doppler-derived wind vectors and hydrometeor identification, has been difficult to achieve in (near) real time, mainly because of the large volumes of data generated by these radars, lack of quick access to these data, and the challenge of applying quality-control measures in real time. This study focuses on modifying and automating several radar-analysis and quality-control algorithms currently used in postprocessing and merging the resulting data from several radars into an integrated analysis and display in (near) real time. Although the method was developed for a specific network of four Doppler radars: two Weather Surveillance Radar-1988 Doppler (WSR-88D) radars (KFTG and KCYS) and two Colorado State University (CSU) research radars [Pawnee and CSU–University of Chicago–Illinois State Water Survey (CSU–CHILL)], the software is easily adaptable to any radar platform or network of radars. The software includes code to synthesize radial velocities to obtain three-dimensional wind vectors and includes algorithms for automatic quality control of the raw polarimetric data, hydrometeor identification, and rainfall rate. The software was successfully tested during the summers of 2004 and 2005 at the CSU–CHILL radar facility, ingesting data from the four-radar network. The display software allows users the ability to view mosaics of reflectivity, wind vectors, and rain rates, to zoom in and out of radar features easily, to create vertical cross sections, to contour data, and to archive data in real time. Despite the lag time of approximately 10 min, the software proved invaluable for diagnosing areas of intense rainfall, hail, strong updrafts, and other features such as mesocyclones and convergence lines. A case study is presented to demonstrate the utility of the software.
The Behavior of Number Concentration Tendencies for the Continuous Collection Growth Equation Using One- and Two-Moment Bulk Parameterization Schemes
Authors: Straka Jerry M. , Kanak Katharine M. , Gilmore Matthew S. 
Published: August 2007

Abstract
This paper presents a mathematical explanation for the nonconservation of total number concentration Nt of hydrometeors for the continuous collection growth process, for which Nt physically should be conserved for selected one- and two-moment bulk parameterization schemes. Where possible, physical explanations are proposed. The assumption of a constant no in scheme A is physically inconsistent with the continuous collection growth process, as is the assumption of a constant Dn for scheme B. Scheme E also is nonconservative, but it seems this result is not because of a physically inconsistent specification; rather the solution scheme’s equations simply do not satisfy Nt conservation and Nt does not come into the derivation. Even scheme F, which perfectly conserves Nt, does not preserve the distribution shape in comparison with a bin model.
A Comparison of Continuous Soil Moisture Simulations Using Different Soil Hydraulic Parameterizations for a Site in Germany
Authors: Schädler Gerd 
Published: August 2007

AbstractContinuous time series of soil water content over a period of more than 9 months for a midlatitude sandy loam soil covered by grass are calculated with the Campbell and the van Genuchten soil hydraulic functions and the Clapp–Hornberger, Cosby et al., and Rawls–Brakensiek parameter sets. The results are compared with soil water content observed at several soil depths, and the water balance components are evaluated. The Campbell soil hydraulic functions are often used by meteorologists, whereas the van Genuchten functions are widespread among hydrologists. The simulations are performed with the “VEG3D” soil–vegetation model in stand-alone mode forced by on-site meteorological observations. The soil water content and meteorological observations were obtained within the Regional Climate Project (REKLIP) at a site in the Rhine valley in southern Germany with 10-min temporal resolution. Apart from the different soil hydraulic functions and parameter sets, the effects of different lower boundary conditions and initializations on the simulations are compared in terms of statistical quantities like mean error, bias, correlation coefficient, and least squares fit. Large differences between the various combinations are found. For the situation considered in this paper, the van Genuchten–Clapp–Hornberger, the Campbell–Cosby et al., and the van Genuchten–Rawls–Brakensiek combinations give the best overall agreement with the observations.
How collaborative is pair work? ESL tertiary students composing in pairs
Authors: Storch Neomy 
Published: August 2007

A common teaching strategy in the language classroom is to assign students to work on a task in pairs or small groups. Research on group/pair has shown that such classroom organization promotes speaking practice and negotiations of meaning. However, most of the studies on pair work to date have focused on factors affecting the quantity of certain types of negotiation moves. Very few studies have investigated the nature of group or pair interactions; that is, whether they are collaborative or not. Moreover, very few studies have utilized tasks which require students to produce a written text in pairs. The study reported in this paper investigated the performance of three pairs of adult ESL students on a writing task assigned in class. The main source of data was transcripts of the pair talk. Other sources of data included the researcher’s observation notes and the written text the pairs produced. Data were analysed for salient features of student interactions and characteristics of collaborative pair work were identified. Results show that students working in pairs may not necessarily work in a collaborative manner, but where they do collaborate this may have an effect on task performance.
‘Why do you learn English?’ ‘Because the teacher is short.’ A study of Hungarian children’s foreign language learning motivation
Authors: Nikolov Marianne 
Published: August 2007

This article looks at the attitudes and motivation of Hungarian children between the ages of 6 and 14: why they think they study a foreign language, how they relate to school subjects and what classroom activities they like and dislike. The long-term study was conducted in the ethnographic tradition where the teacher, syllabus designer and researcher was the author, and the inquiry was prompted by classroom needs. Three groups of children were involved for eight years each during the years of 1977-85, 1985-93 and 1987-95 in Pécs, Hungary. The first part of the article considers the literature on motivation from the perspective of child foreign language learning, whereas the second part looks into how the findings of the Pécs study may contribute towards a better understanding of the effects of specific pedagogic procedures on motivation.
Bringing off-stage ‘noise’ to centre stage: a lesson in developing bilingual classroom discourse data
Authors: Pennington Martha C. 
Published: August 2007

A transcript of part of an English lesson conducted in a Hong Kong secondary school by an ethnic Chinese bilingual Cantonese-English teacher and his students is expanded and elaborated in stages to illustrate issues involved in developing bilingual classroom discourse data. The different transcripts of the same segment of classroom discourse demonstrate how the focus, the form and the level of transcription help to determine the analysis of the discourse and the view of it that can be derived by means of the investigative process. Through the elaboration of the transcript, it is shown how different interactants define their participation using the two available languages, English and Cantonese, within each of three frames of classroom interaction. In the segment of the lesson presented, which comprises a role-play activity, the teacher and two students participate in the lesson frame, where only English occurs. The teacher and other students participate in a lesson-support frame, where speech has a regulative function directed at keeping the lesson ‘on track’ and where English and Cantonese occur. These institutional frames may be exploited by speakers to convey implicit and explicit messages that encode different layers of meaning. Other students (but not the teacher) participate in a third, commentary frame, where they make evaluative comments in relation to the talk that is going on in the lesson frame and where most communication is in Cantonese. It is maintained that for the bilingual classroom discourse presented (and, by implication, for the larger context of discourse of which that segment is a part) a representation in terms of discourse frames provides a view of language use and participant interaction that aids further analysis and helps not only the researcher but also those to whom the data is presented to build a rich schema for understanding and interpreting the dynamics of that context. In particular, it makes it possible to observe how the main participants, the students, bend the institutional context to their own purposes.
Histone deacetylase–mediated transcriptional activation reduces proviral loads in HTLV-1–associated myelopathy/tropical spastic paraparesis patients
Authors: Lezin Agnès , Gillet Nicolas , Olindo Stéphane , Signaté Aïssatou , Grandvaux Nathalie , Verlaeten Olivier , Belrose Gildas , de Carvalho Bittencourt Marcelo , Hiscott John , Asquith Becca , Burny Arsène , Smadja Didier , Césaire Raymond , Willems Luc 
Published: August 2007

AbstractEpigenetic modifications of chromatin may play a role in maintaining viral latency and thus persistence of the human T-lymphotropic virus type 1 (HTLV-1), which is responsible for HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP). A major determinant of disease progression is increased peripheral blood proviral load (PVL), possibly via the accumulation of infected cells in the central nervous system (CNS) creating a damaging inflammatory response. Current therapeutic approaches that focus on reducing either cell proliferation, viral replication, or tissue invasion are still unsatisfactory. Contrasting with these inhibitory strategies, we evaluated the efficacy of a novel approach aimed, paradoxically, at activating viral gene expression to expose virus-positive cells to the host immune response. We used valproate (VPA), a histone deacetylase inhibitor that has been used for decades as a chronic, safe treatment for epileptic disorders. Based on in vitro and in vivo data, we provide evidence that transient activation of the latent viral reservoir causes its collapse, a process that may alleviate the condition of HAM/TSP. This represents the first such approach to treating HAM/TSP, using gene activation therapy to tilt the host-pathogen balance in favor of an existing antiviral response. This trial is registered at http://clinicaltrials.gov/as no. NCT00519181.
Deletions within the HSV-tk transgene in long-lasting circulating gene-modified T cells infused with a hematopoietic graft
Authors: Deschamps Marina , Mercier-Lethondal Patricia , Certoux Jean Marie , Henry Carole , Lioure Bruno , Pagneux Céline , Cahn Jean Yves , Deconinck Eric , Robinet Eric , Tiberghien Pierre , Ferrand Christophe 
Published: August 2007

AbstractIn our previous phase 1/2 study aimed at controlling graft-versus-host disease, 12 patients received Herpes simplex virus thymidine kinase (HSV-tk+)/neomycin phosphotransferase (NeoR+)–expressing donor gene-modified T cells (GMCs) and underwent an HLA-identical sibling T-cell–depleted bone marrow transplantation (BMT). This study's objective was to follow up, to quantify, and to characterize persistently circulating GMCs more than 10 years after BMT. Circulating GMCs remain detectable in all 4 evaluable patients. However, NeoR- and HSV-tk–polymerase chain reaction (PCR) differently quantified in vivo counts, suggesting deletions within the HSV-tk gene. Further experiments, including a novel “transgene walking” PCR method, confirmed the presence of deletions. The deletions were unique, patient-specific, present in most circulating GMCs expressing NeoR, and shown to occur at time of GMC production. Unique patient-specific retroviral insertion sites (ISs) were found in all GMCs capable of in vitro expansion/cloning as well. These findings suggest a rare initial gene deletion event and an in vivo survival advantage of rare GMC clones resulting from an anti–HSV-tk immune response and/or ganciclovir treatment. In conclusion, we show that donor mature T cells infused with a T-cell–depleted graft persist in vivo for more than a decade. These cells, containing transgene deletions and subjected to significant in vivo selection, represent a small fraction of T cells infused at transplantation.
PARE: A tool for comparing protein abundance and mRNA expression data
Authors: Yu Eric Z , Burba Anne E Counterman , Gerstein Mark 
Published: August 2007

Abstract

Background
Techniques for measuring protein abundance are rapidly advancing and we are now in a situation where we anticipate many protein abundance data sets will be available in the near future. Since proteins are translated from mRNAs, their expression is expected to be related to their abundance, to some degree.

Results
We have developed a web tool, called PARE (Protein Abundance and mRNA Expression; http://proteomics.gersteinlab.org), to correlate these two quantities. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which are potentially worth further examination.

Conclusion
We anticipate PARE will facilitate comparative studies on mRNA and protein abundance by the proteomics community.
Comparison of quenching and extraction methodologies for metabolome analysis of Lactobacillus plantarum
Authors: Faijes Magda , Mars Astrid E , Smid Eddy J 
Published: August 2007

Abstract

Background
A reliable quenching and metabolite extraction method has been developed for Lactobacillus plantarum. The energy charge value was used as a critical indicator for fixation of metabolism.

Results
Four different aqueous quenching solutions, all containing 60% of methanol, were compared for their efficiency. Only the solutions containing either 70 mM HEPES or 0.85% (w/v) ammonium carbonate (pH 5.5) caused less than 10% cell leakage and the energy charge of the quenched cells was high, indicating rapid inactivation of the metabolism.
The efficiency of extraction of intracellular metabolites from cell cultures depends on the extraction methods, and is expected to vary between micro-organisms. For L. plantarum, we have compared five different extraction methodologies based on (i) cold methanol, (ii) perchloric acid, (iii) boiling ethanol, (iv) chloroform/methanol (1:1) and (v) chloroform/water (1:1). Quantification of representative intracellular metabolites showed that the best extraction efficiencies were achieved with cold methanol, boiling ethanol and perchloric acid.

Conclusion
The ammonium carbonate solution was selected as the most suitable quenching buffer for metabolomics studies in L. plantarum because (i) leakage is minimal, (ii) the energy charge indicates good fixation of metabolism, and (iii) all components are easily removed during freeze-drying. A modified procedure based on cold methanol extraction combined good extractability with mild extraction conditions and high enzymatic inactivation. These features make the combination of these quenching and extraction protocols very suitable for metabolomics studies with L. plantarum.
Molecular portrait of cisplatin induced response in human testis cancer cell lines based on gene expression profiles
Authors: Duale Nur , Lindeman Birgitte , Komada Mitsuko , Olsen Ann-Karin , Andreassen Ashild , Soderlund Erik J , Brunborg Gunnar 
Published: August 2007

Abstract

Background
Testicular germ cell tumors (TGCTs) respond well to cisplatin-based chemotherapy and show a low incidence of acquired resistance compared to most somatic tumors. The reasons for these specific characteristics are not known in detail but seem to be multifactorial. We have studied gene expression profiles of testicular and colon cancer derived cell lines treated with cisplatin. The main goal of this study was to identify novel gene expression profiles with their functional categories and the biochemical pathways that are associated with TGCT cells' response to cisplatin.

Results
Genes that were differentially expressed between the TGCT cell lines vs the (somatic) HCT116 cell line, after cisplatin treatment, were identified using the significance analysis of microarrays (SAM) method. The response of TGCT cells was strikingly different from that of HCT116, and we identified 1794 genes that were differentially expressed. Functional classification of these genes showed that they participate in a variety of different and widely distributed functional categories and biochemical pathways. Database mining showed significant association of genes (n = 41) induced by cisplatin in our study, and genes previously reported to by expressed in differentiated TGCT cells. We identified 37 p53-responsive genes that were altered after cisplatin exposure. We also identified 40 target genes for two microRNAs, hsa-mir-372 and 373 that may interfere with p53 signaling in TGCTs. The tumor suppressor genes NEO1 and LATS2, and the estrogen receptor gene ESR1, all have binding sites for p53 and hsa-mir-372/373. NEO1 and LATS2 were down-regulated in TGCT cells following cisplatin exposure, while ESR1 was up-regulated in TGCT cells. Cisplatin-induced genes associated with terminal growth arrest through senescence were identified, indicating associations which were not previously described for TGCT cells.

Conclusion
By linking our gene expression data to publicly available databases and literature, we provide a global pattern of cisplatin induced cellular response that is specific for testicular cancer cell lines. We have identified cisplatin-responsive functional classes and pathways, such as the angiogenesis, Wnt, integrin, and cadherin signaling pathways. The identification of differentially expressed genes in this study may contribute to a better understanding of the unusual sensitivity of TGCT to some DNA-damaging agents.
The impact of operative approach on outcome of surgery for gastro-oesophageal tumours
Authors: Suttie Stuart A , Li Alan GK , Quinn Martha , Park Kenneth GM 
Published: August 2007

Abstract

Background
The choice of operation for tumours at or around the gastro-oesophageal junction remains controversial with little evidence to support one technique over another. This study examines the prevalence of margin involvement and nodal disease and their impact on outcome following three surgical approaches (Ivor Lewis, transhiatal and left thoraco-laparotomy) for these tumours.

Methods
A retrospective analysis was conducted of patients undergoing surgery for distal oesophageal and gastro-oesophageal junction tumours by a single surgeon over ten years. Comparisons were undertaken in terms of tumour clearance, nodal yield, postoperative morbidity, mortality, and median survival. All patients were followed up until death or the end of the data collection (mean follow up 33.2 months).

Results
A total of 104 patients were operated on of which 102 underwent resection (98%). Median age was 64.1 yrs (range 32.1–79.4) with 77 males and 25 females. Procedures included 29 Ivor Lewis, 31 transhiatal and 42 left-thoraco-laparotomies. Postoperative mortality was 2.9% and median survival 23 months. Margin involvement was 24.1% (two distal, one proximal and 17 circumferential margins). Operative approach had no significant effect on nodal clearance, margin involvement, postoperative mortality or morbidity and survival. Lymph node positive disease had a significantly worse median survival of 15.8 months compared to 39.7 months for node negative (p = 0.007), irrespective of approach.

Conclusion
Surgical approach had no effect on postoperative mortality, circumferential tumour, nodal clearance or survival. This suggests that the choice of operative approach for tumours at the gastro-oesophageal junction may be based on the individual patient and tumour location rather than surgical dogma.
Genomic and proteomic profiling II: Comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars
Authors: Luo Xiaoping , Pan Qun , Liu Li , Chegini Nasser 
Published: August 2007

Abstract

Background
Leiomyoma have often been compared to keloids because of their fibrotic characteristic and higher rate of occurrence among African Americans as compared to other ethnic groups. To evaluate such a correlation at molecular level this study comparatively analyzed leiomyomas with keloids, surgical scars and peritoneal adhesions to identify genes that are either commonly and/or individually distinguish these fibrotic disorders despite differences in the nature of their development and growth.

Methods
Microarray gene expression profiling and realtime PCR.

Results
The analysis identified 3 to 12% of the genes on the arrays as differentially expressed among these tissues based on P ranking at greater than or equal to 0.005 followed by 2-fold cutoff change selection. Of these genes about 400 genes were identified as differentially expressed in leiomyomas as compared to keloids/incisional scars, and 85 genes as compared to peritoneal adhesions (greater than or equal to 0.01). Functional analysis indicated that the majority of these genes serve as regulators of cell growth (cell cycle/apoptosis), tissue turnover, transcription factors and signal transduction. Of these genes the expression of E2F1, RUNX3, EGR3, TBPIP, ECM-2, ESM1, THBS1, GAS1, ADAM17, CST6, FBLN5, and COL18A was confirmed in these tissues using quantitative realtime PCR based on low-density arrays.

Conclusion
the results indicated that the molecular feature of leiomyomas is comparable but may be under different tissue-specific regulatory control to those of keloids and differ at the levels rather than tissue-specific expression of selected number of genes functionally regulating cell growth and apoptosis, inflammation, angiogenesis and tissue turnover.
Initial community perspectives on the Health Service Extension Programme in Welkait, Ethiopia
Authors: Negusse Haile , McAuliffe Eilish , MacLachlan Malcolm 
Published: August 2007

Abstract

Background
The Health Service Extension Programme (HSEP) is an innovative approach to addressing the shortfall in health human resources in Ethiopia. It has developed a new cadre of Health Extension Workers (HEWs), who are charged with providing the health and hygiene promotion and some treatment services, which together constitute the bedrock of Ethiopia's community health system.

Methods
This study seeks to explore the experience of the HSEP from the perspective of the community who received the service. A random sample of 60 female heads-of-household in a remote area of Tigray participated in a structured interview survey.

Results
Although Health Extension Workers (HEWs) had visited them less frequently than planned, participants generally found the programme to be helpful. Despite this, their basic health knowledge was still quite poor regarding the major communicable diseases and their vectors. Participants felt the new HESP represented an improvement on previous health provision. HEWs were preferred over Traditional Birth Attendants for assistance with labour

Conclusion
While the introduction of HEWs has been a positive experience for women living at the study site, the frequency of visits, extent of effectively imparted health knowledge and affects of HEWs on other health providers needs to be further explored.