bluuebunny/crossref_metadata_2025 huggingface dataset:
Individual identification and sexual dimorphism in the endangered Balearic Midwife Toad, Alytes muletensis (Sanchíz and Adrover, 1981)
Authors: Pérez-Mellado Valentín , Pinya Samuel
Published: July 2009

The Majorcan Midwife Toad (Alytes muletensis) is and endemic and threatened species of the island of Mallorca which has been the subject of a large number of studies. However, there is a lack of information about the adult fraction of wild populations. Here we show the first step to increase the knowledge of adult Majorcan midwife toads, how to recognize them individually and how to distinguish between males and females. We tested with satisfactory results a photoidentification method that can be used to identify adults individually. In order to sex individuals in the wild we carry out a morphological study with fourteen variables building a discriminant function which allow us to sex all captured adults.
Spring migration distances of some Central European amphibian species
Authors: Kovar Roman , Brabec Marek , Bocek Radomir , Vita Radovan
Published: July 2009

Migration distances of eight species of amphibians were studied at 14 sites in the Czech Republic in the course of the 2007 spring migration season. Drift fences with pit-fall traps were installed at varying distances from the reproduction pond. No substitute breeding ponds were available nearby. 4423 m of drift fence was installed and data from a total of 4823 specimens were collected. The estimate 95th percentile migration distances for the newts Lissotriton vulgaris, Mesotriton alpestris and Triturus cristatus were between 105-866 m, and for the frogs Bombina bombina, Bufo bufo, Rana arvalis and R. temporaria estimates were between 170-2214 m. No adult individuals of R. ridibunda were caught out of water. With two exceptions in B. bufo there were no significant among-site differences in migration distances between L. vulgaris, T. cristatus and B. bufo. There were no significant between-sex differences in migration distances of L. vulgaris, M. alpestris, T. cristatus, B. bufo and R. arvalis. Thanks to a great number of various sites processed simultaneously and by the same methodology, presented data provide information on the overall distribution of migration distances in different habitats. The results could be used for the estimation of the extent of the influence on amphibian populations in cases of transection or other habitat degradation in the vicinity of their reproduction ponds.
Population densities and conservation assessments for three species of chameleons in the Toliara region of south-western Madagascar
Authors: Andriamandimbiarisoa Laza , Raxworthy Christopher , Karsten Kristopher , Fox Stanley
Published: July 2009

Madagascar is a high conservation priority. Rainforests receive most of the focus, but the dry deciduous and spiny forests of south-western Madagascar house many endemics, are under high deforestation pressure, and remain largely unprotected. Charismatic vertebrates, like chameleons, face a secondary threat: harvesting for the commercial pet trade. Six chameleons inhabit the arid southwest near Toliara: Furcifer antimena, F. belalandaensis, F. labordi, F. lateralis, F. oustaleti, and F. verrucosus. We measured population densities of three of those species. Furcifer verrucosus has a large distribution, was dense (97.7 ha–1; 95% CI = 60.2-158.6), and inhabited forests and anthropogenic habitats. Furcifer labordi was much less dense (30.8 ha–1; 13.4-70.9), has a restricted range, and has a unique life history that makes it susceptible to perturbations from deforestation or illegal harvesting. Furcifer antimena was the least dense (17.0 ha–1; 9.3-30.9) and has an even smaller distribution range. We lack density data for F. lateralis, but this species was abundant in anthropogenic habitats. Within their respective ranges, there are currently no protected areas for F. antimena and only few for F. labordi; these two species are far less abundant than the more widely spread F. verrucosus. We recommend that high conservation priority be focused on F. antimena and the southern populations of F. labordi due to their restricted distributions, susceptibility to extirpation, lower population densities, and lack of formal protection. Establishing protected areas in the Ranobe region and north of the Fiherenana River, in the Belalanda region, would help protect important populations of these vulnerable species.
Laser beam welding of dissimilar aluminium alloys of 2000 and 7000 series: Effect of post-welding thermal treatments on T joint strength
Authors: Badini C. , Pavese M. , Fino P. , Biamino S.
Published: July 2009

Two experimental aluminium alloys (belonging to 2000 and 7000 series respectively) were welded using the laser beam welding (LBW) technique and an Al–Si alloy as filler. Different combinations of pre- and post-welding thermal treatments were proposed. The change of strength during aging treatments was investigated by microhardness measurements carried out on the weld and on the regions of the alloys not affected by the LBW process. The microstructure of the welded specimens was studied by scanning electron microscopy and energy dispersive X-ray spectroscopy. The strength of the joints after different thermal treatments was checked by T pull tests. Different thermal treatments resulted in different final strengths of the joint.
Electromagnetic impact welding of Mg to Al sheets
Authors: Kore S. D. , Imbert J. , Worswick M. J. , Zhou Y.
Published: July 2009

Magnesium (Mg) and aluminium (Al) alloys have been lap welded using an electromagnetic impact welding technique. Metallographic examination of the welds has revealed sound and defect free interfaces. Complete metal continuity has been observed with a characteristic wavy interface. X-ray diffraction analysis has shown no intermetallic phases and suggested that this electromagnetic technique is a solid state welding process. All the shear strength samples welded with discharge energy of 6·7 kJ failed away from weld either in the plastically deformed zone or in the base metal. Optimum discharge energy has been determined as 6·7 kJ based on the shear strength results of the welds.
Effect of tool rotation rate on microstructure and mechanical properties of friction stir welded copper
Authors: Liu H. J. , Shen J. J. , Huang Y. X. , Kuang L. Y. , Liu C. , Li C.
Published: July 2009

Defect free copper welds were achieved by friction stir welding (FSW) carried out at a constant welding speed of 100 mm min−1. The influence of tool rotation rate on microstructure, mechanical properties and fracture location was investigated. As the tool rotation rate increased, the grains of nugget zone grew significantly, the thermomechanically affected zone became indistinct and the grain size increased, but the effect of tool rotation rate on the grain size of heat affected zone was limited. Both ultimate tensile strength (UTS) and elongation increased first and then decreased with increasing rotation rate and the UTS achieved a highest value of 282 MPa at the rotation rate of 400 rev min−1 together with the welding speed of 100 mm min−1, which was on the level of the base metal. The fracture occurred at the cavity defect on the advancing side of the joint when the FSW was performed at a low tool rotation rate, while it occurred on the retreating side when the tool rotation rate was relatively high.
Development of decorative and corrosion resistant plasma electrolytic oxidation coatings on AM50 magnesium alloy
Authors: Bala Srinivasan P. , Liang J. , Blawert C. , Störmer M. , Dietzel W.
Published: July 2009

Plasma electrolytic oxidation of AM50 magnesium alloy was performed in alkaline phosphate electrolyte with and without the addition of titania sol. The coatings produced in the phosphate electrolyte were constituted with MgO and Mg3(PO4)2. The coatings obtained in the phosphate electrolyte with the addition of titania sol were blue in colour and contained additionally the TiO2 and Mg2TiO4 phases. The phosphate PEO coating provided a two order of magnitude improvement in corrosion resistance to the AM50 magnesium alloy as was shown by the potentiodynamic polarisation measurements. With differences in the physical appearance, microstructural morphology and phase composition, the coatings produced in titania sol containing electrolytes offered an improved corrosion resistance compared to the mere phosphate PEO coating.
Multipass scratch test behaviour of TiAlN thin film deposited on 316L stainless steel and Ti6Al4V alloy with dc biased and pulsed magnetron sputtering
Authors: Yıldız F. , Alsaran A. , Çelik A. , Efeoğlu İ.
Published: July 2009

In this study, TiAlN thin film was deposited with dc magnetron sputtering on 316L stainless steel and Ti6Al4V alloy which are widely used as hip joint implants. The adhesion behaviour of TiAlN thin films was investigated by multipass scratch tester. Multipass scratching with three progressive loads was performed on each sample. Observations of the scratch tests showed that there were three main failure events which were identified and labelled as Lc1, Lc2 and Lc3. Failure mechanisms were discussed according to SEM examinations of the scratch tracks. The TiAlN films with dense and homogeneous structure preferentially grew on the plane of (200) for 316L stainless steel and (111) for Ti6Al4V alloy. During the multipass scratch test, the friction coefficients were measured between 0·02 and 0·05. The best values for the friction coefficient were obtained from the films preferentially deposited on the plane of (111). After the scratch test, the thin film was damaged by mechanisms of chipping, flaking and spalling.
Low temperature plasma carbonitriding of ASTM F138 and ASTM F1586 biomedical stainless steels
Authors: Buhagiar J. , Dong H.
Published: July 2009

Low temperature carbonitriding has been reported to improve the wear resistance of engineering grade AISI 316 through the formation of a hybrid S phase, but little or no research work has been applied to medical grade austenitic stainless steels. In this study, the aforementioned hybrid S phase has been successfully implemented in the surface of two medical grade austenitic stainless steels, ASTM F138 and ASTM F1586, as well as on engineering grade AISI 316 for comparison. The wear behaviour of the plasma carbonitrided and the untreated samples was compared using reciprocating sliding wear tests in air, Ringer's solution and distilled water. Experimental results have demonstrated that low temperature plasma carbonitriding can effectively reduce the wear of these two medical grade materials independent of the testing conditions. Wear results from the reciprocating wear test have shown that for the ASTM F138 alloy an improvement over the untreated material of 450% (in air) and 100% (in Ringer's solution) was registered; for the ASTM F1586 stainless steel, the improvements over the untreated materials were 380% (in air) and 40% (in Ringer's solution). It is proposed that the improved performance of the treated samples can be attributed to a desired combination of the significantly improved hardness which provides a better support to the surface oxide layer and the retained good corrosion resistance.
Monitoring of plasma processing chamber using ion energy analyser and time series neural network
Authors: Kim B. , Kim S.
Published: July 2009

A new technique to monitor plasma processes is presented. An autocorrelated neural time series (A-NTS) network was used to model ion energy distribution (IED). The ion energy data were collected during a deposition of silicon nitride films in a SiH4–NH3 inductively coupled plasma. A backpropagation neural network was used to build IED model. Prediction performance of A-NTS model was evaluated as a function of training tolerance as well as a detection sensitivity. The A-NTS models demonstrated detection sensitivities high enough to detect plasma faults. Maximum sensitivity of A-NTS models obtained was more than 55% for all fault cases. Optimised A-NTS models yielded the prediction errors of 1·41 and 2·18% for 80 and 60% IED respectively. The presented technique can be applied to monitor any kinds of plasma faults and is expected effective particularly to those faults sensitive to ion bombardment variations.
Neutrophil elastase is severely down-regulated in severe congenital neutropenia independent of ELA2 or HAX1 mutations but dependent on LEF-1
Authors: Skokowa Julia , Fobiwe John Paul , Dan Lan , Thakur Basant Kumar , Welte Karl
Published: July 2009

Severe congenital neutropenia (CN) is a heterogeneous disorder of myelopoiesis which follows an autosomal dominant or autosomal recessive pattern of inheritance. Genetic analyses indicate mutations in the ELA2 gene in most patients. We have identified LEF-1 as a decisive transcription factor in granulopoiesis controlling proliferation and granulocytic differentiation by direct activation of its target gene, C/EBPα. In patients with CN, the expression of LEF-1 and C/EBPα was abrogated in myeloid progenitors leading to maturation arrest of granulopoiesis. In the present study we demonstrated that ELA2 mRNA expression in myeloid progenitors and plasma protein levels of neutrophil elastase (NE) were markedly reduced in patients with CN harboring mutations in either ELA2 or HAX-1 genes. The ELA2 gene promoter is positively regulated by the direct binding of LEF-1 or C/EBPα, documenting the role of LEF1 in the diminished ELA2 expression. We found that transduction of hematopoietic cells with LEF-1 cDNA resulted in the up-regulation of ELA2/NE synthesis, whereas inhibition of LEF-1 by shRNA led to a marked reduction in the levels of ELA2/NE. LEF-1 rescue of CD34+ cells isolated from 2 patients with CN resulted in granulocytic differentiation of the cells which was in line with increased levels of functionally active ELA2/NE.
The Duffy-null state is associated with a survival advantage in leukopenic HIV-infected persons of African ancestry
Authors: Kulkarni Hemant , Marconi Vincent C. , He Weijing , Landrum Michael L. , Okulicz Jason F. , Delmar Judith , Kazandjian Dickran , Castiblanco John , Ahuja Seema S. , Wright Edwina J. , Weiss Robin A. , Clark Robert A. , Dolan Matthew J. , Ahuja Sunil K.
Published: July 2009

Persons of African ancestry, on average, have lower white blood cell (WBC) counts than those of European descent (ethnic leukopenia), but whether this impacts negatively on HIV-1 disease course remains unknown. Here, in a large natural history cohort of HIV-infected subjects, we show that, although leukopenia (< 4000 WBC/mm3 during infection) was associated with an accelerated HIV disease course, this effect was more prominent in leukopenic subjects of European than African ancestry. The African-specific −46C/C genotype of Duffy Antigen Receptor for Chemokines (DARC) confers the malaria-resisting, Duffy-null phenotype, and we found that the recently described association of this genotype with ethnic leukopenia extends to HIV-infected African Americans (AAs). The association of Duffy-null status with HIV disease course differed according to WBC but not CD4+ T-cell counts, such that leukopenic but not nonleukopenic HIV+ AAs with DARC −46C/C had a survival advantage compared with all Duffy-positive subjects. This survival advantage became increasingly pronounced in those with progressively lower WBC counts. These data highlight that the interaction between DARC genotype and the cellular milieu defined by WBC counts may influence HIV disease course, and this may provide a partial explanation of why ethnic leukopenia remains benign in HIV-infected AAs, despite immunodeficiency.
Information management for high content live cell imaging
Authors: Jameson Daniel , Turner David A , Ankers John , Kennedy Stephnie , Ryan Sheila , Swainston Neil , Griffiths Tony , Spiller David G , Oliver Stephen G , White Michael RH , Kell Douglas B , Paton Norman W
Published: July 2009

Background

High content live cell imaging experiments are able to track the cellular localisation of labelled proteins in multiple live cells over a time course. Experiments using high content live cell imaging will generate multiple large datasets that are often stored in an ad-hoc manner. This hinders identification of previously gathered data that may be relevant to current analyses. Whilst solutions exist for managing image data, they are primarily concerned with storage and retrieval of the images themselves and not the data derived from the images. There is therefore a requirement for an information management solution that facilitates the indexing of experimental metadata and results of high content live cell imaging experiments.

Results

We have designed and implemented a data model and information management solution for the data gathered through high content live cell imaging experiments. Many of the experiments to be stored measure the translocation of fluorescently labelled proteins from cytoplasm to nucleus in individual cells. The functionality of this database has been enhanced by the addition of an algorithm that automatically annotates results of these experiments with the timings of translocations and periods of any oscillatory translocations as they are uploaded to the repository. Testing has shown the algorithm to perform well with a variety of previously unseen data.

Conclusion

Our repository is a fully functional example of how high throughput imaging data may be effectively indexed and managed to address the requirements of end users. By implementing the automated analysis of experimental results, we have provided a clear impetus for individuals to ensure that their data forms part of that which is stored in the repository. Although focused on imaging, the solution provided is sufficiently generic to be applied to other functional proteomics and genomics experiments. The software is available from: fhttp://code.google.com/p/livecellim/
MLVA-16 typing of 295 marine mammal Brucella isolates from different animal and geographic origins identifies 7 major groups within Brucella ceti and Brucella pinnipedialis
Authors: Maquart Marianne , Le Flèche Philippe , Foster Geoffrey , Tryland Morten , Ramisse Françoise , Djønne Berit , Al Dahouk Sascha , Jacques Isabelle , Neubauer Heinrich , Walravens Karl , Godfroid Jacques , Cloeckaert Axel , Vergnaud Gilles
Published: July 2009

Background

Since 1994, Brucella strains have been isolated from a wide range of marine mammals. They are currently recognized as two new Brucella species, B. pinnipedialis for the pinniped isolates and B. ceti for the cetacean isolates in agreement with host preference and specific phenotypic and molecular markers. In order to investigate the genetic relationships within the marine mammal Brucella isolates and with reference to terrestrial mammal Brucella isolates, we applied in this study the Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) approach. A previously published assay comprising 16 loci (MLVA-16) that has been shown to be highly relevant and efficient for typing and clustering Brucella strains from animal and human origin was used.

Results

294 marine mammal Brucella strains collected in European waters from 173 animals and a human isolate from New Zealand presumably from marine origin were investigated by MLVA-16. Marine mammal Brucella isolates were shown to be different from the recognized terrestrial mammal Brucella species and biovars and corresponded to 3 major related groups, one specific of the B. ceti strains, one of the B. pinnipedialis strains and the last composed of the human isolate. In the B. ceti group, 3 subclusters were identified, distinguishing a cluster of dolphin, minke whale and porpoise isolates and two clusters mostly composed of dolphin isolates. These results were in accordance with published analyses using other phenotypic or molecular approaches, or different panels of VNTR loci. The B. pinnipedialis group could be similarly subdivided in 3 subclusters, one composed exclusively of isolates from hooded seals (Cystophora cristata) and the two others comprising other seal species isolates.

Conclusion

The clustering analysis of a large collection of marine mammal Brucella isolates from European waters significantly strengthens the current view of the population structure of these two species, and their relative position with respect to the rest of the Brucella genus. MLVA-16 is confirmed as being a rapid, highly discriminatory and reproducible method to classify Brucella strains including the marine mammal isolates. The Brucella2009 MLVA-16 genotyping database available at http://mlva.u-psud.fr/ is providing a detailed coverage of all 9 currently recognized Brucella species.
Invasiveness as a putative additional virulence mechanism of some atypical Enteropathogenic Escherichia colistrains with different uncommon intimin types
Authors: Yamamoto Denise , Hernandes Rodrigo T , Blanco Miguel , Greune Lilo , Schmidt M Alexander , Carneiro Sylvia M , Dahbi Ghizlane , Blanco Jesús E , Mora Azucena , Blanco Jorge , Gomes Tânia AT
Published: July 2009

Background

EnteropathogenicEscherichia coli(EPEC) produce attaching/effacing (A/E) lesions on eukaryotic cells mediated by the outer membrane adhesin intimin. EPEC are sub-grouped into typical (tEPEC) and atypical (aEPEC). We have recently demonstrated that aEPEC strain 1551-2 (serotype O non-typable, non-motile) invades HeLa cells by a process dependent on the expression of intimin sub-type omicron. In this study, we evaluated whether aEPEC strains expressing other intimin sub-types are also invasive using the quantitative gentamicin protection assay. We also evaluated whether aEPEC invade differentiated intestinal T84 cells.

Results

Five of six strains invaded HeLa and T84 cells in a range of 13.3%–20.9% and 5.8%–17.8%, respectively, of the total cell-associated bacteria. The strains studied were significantly more invasive than prototype tEPEC strain E2348/69 (1.4% and 0.5% in HeLa and T84 cells, respectively). Invasiveness was confirmed by transmission electron microscopy. We also showed that invasion of HeLa cells by aEPEC 1551-2 depended on actin filaments, but not on microtubules. In addition, disruption of tight junctions enhanced its invasion efficiency in T84 cells, suggesting preferential invasion via a non-differentiated surface.

Conclusion

Some aEPEC strains may invade intestinal cellsin vitrowith varying efficiencies and independently of the intimin sub-type.
Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies
Authors: Bacchetti De Gregoris Tristano , Borra Marco , Biffali Elio , Bekel Thomas , Burgess J Grant , Kirby Richard R , Clare Anthony S
Published: July 2009

Background

Balanus amphitrite is a barnacle commonly used in biofouling research. Although many aspects of its biology have been elucidated, the lack of genetic information is impeding a molecular understanding of its life cycle. As part of a wider multidisciplinary approach to reveal the biogenic cues influencing barnacle settlement and metamorphosis, we have sequenced and annotated the first cDNA library for B. amphitrite. We also present a systematic validation of potential reference genes for normalization of quantitative real-time PCR (qRT-PCR) data obtained from different developmental stages of this animal.

Results

We generated a cDNA library containing expressed sequence tags (ESTs) from adult B. amphitrite. A total of 609 unique sequences (comprising 79 assembled clusters and 530 singlets) were derived from 905 reliable unidirectionally sequenced ESTs. Bioinformatics tools such as BLAST, HMMer and InterPro were employed to allow functional annotation of the ESTs. Based on these analyses, we selected 11 genes to study their ability to normalize qRT-PCR data. Total RNA extracted from 7 developmental stages was reverse transcribed and the expression stability of the selected genes was compared using geNorm, BestKeeper and NormFinder. These software programs produced highly comparable results, with the most stable gene being mt-cyb, while tuba, tubb and cp1 were clearly unsuitable for data normalization.

Conclusion

The collection of B. amphitrite ESTs and their annotation has been made publically available representing an important resource for both basic and applied research on this species. We developed a qRT-PCR assay to determine the most reliable reference genes. Transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, although other genes also performed well and could prove useful to normalize gene expression studies.
c-MycERTAM transgene silencing in a genetically modified human neural stem cell line implanted into MCAo rodent brain
Authors: Stevanato Lara , Corteling Randolph L , Stroemer Paul , Hope Andrew , Heward Julie , Miljan Erik A , Sinden John D
Published: July 2009

Background

The human neural stem cell line CTX0E03 was developed for the cell based treatment of chronic stroke disability. Derived from fetal cortical brain tissue, CTX0E03 is a clonal cell line that contains a single copy of the c-mycERTAM transgene delivered by retroviral infection. Under the conditional regulation by 4-hydroxytamoxifen (4-OHT), c-mycERTAM enabled large-scale stable banking of the CTX0E03 cells. In this study, we investigated the fate of this transgene following growth arrest (EGF, bFGF and 4-OHT withdrawal) in vitro and following intracerebral implantation into a mid-cerebral artery occluded (MCAo) rat brain. In vitro, 4-weeks after removing growth factors and 4-OHT from the culture medium, c-mycERTAM transgene transcription is reduced by ~75%. Furthermore, immunocytochemistry and western blotting demonstrated a concurrent decrease in the c-MycERTAM protein. To examine the transcription of the transgene in vivo, CTX0E03 cells (450,000) were implanted 4-weeks post MCAo lesion and analysed for human cell survival and c-mycERTAM transcription by qPCR and qRT-PCR, respectively.

Results

The results show that CTX0E03 cells were present in all grafted animal brains ranging from 6.3% to 39.8% of the total cells injected. Prior to implantation, the CTX0E03 cell suspension contained 215.7 (SEM = 13.2) copies of the c-mycERTAM transcript per cell. After implantation the c-mycERTAM transcript copy number per CTX0E03 cell had reduced to 6.9 (SEM = 3.4) at 1-week and 7.7 (SEM = 2.5) at 4-weeks. Bisulfite genomic DNA sequencing of the in vivo samples confirmed c-mycERTAM silencing occurred through methylation of the transgene promoter sequence.

Conclusion

In conclusion the results confirm that CTX0E03 cells downregulated c-mycERTAM transgene expression both in vitro following EGF, bFGF and 4-OHT withdrawal and in vivo following implantation in MCAo rat brain. The silencing of the c-mycERTAM transgene in vivo provides an additional safety feature of CTX0E03 cells for potential clinical application.
GLUT1 gene is a potential hypoxic marker in colorectal cancer patients
Authors: Chung Fu-Yen , Huang Ming-Yii , Yeh Ching-Sheng , Chang Hui-Jen , Cheng Tian-Lu , Yen Li-Chen , Wang Jaw-Yuan , Lin Shiu-Ru
Published: July 2009

Background

Tumor hypoxia is an important factor related to tumor resistance to radiotherapy and chemotherapy. This study investigated molecules synthesized in colorectal cancer cells during hypoxia to explore the possibility of developing molecular probes capable of detecting cell death and/or the efficiency of radiotherapy and chemotherapy.

Methods

At first, we incubated two human colorectal adenocarcinoma cell lines SW480 (UICC stage II) and SW620 (UICC stage III) cells in hypoxic (≤2% O2, 93% N2, and 5% CO2) and normoxic conditions (20% O2, 75% N2, and 5% CO2) for 24 h and 48 h. The relative expression ratio of GLUT1 mRNA in hypoxic conditions was analyzed by RT-PCR. Ten cancerous tissues collected from human colorectal cancer patients were examined. HIF-1α and HIF-2α levels were measured to indicate the degree of hypoxia, and gene expression under hypoxic conditions was determined. As a comparison, HIF-1α, HIF-2α, and GLUT1 levels were measured in the peripheral blood of 100 CRC patients.

Results

Hypoxia-induced lactate was found to be elevated 3.24- to 3.36-fold in SW480 cells, and 3.06- to 3.17-fold in SW620 cells. The increased relative expression ratio of GLUT1 mRNA, under hypoxic conditions was higher in SW620 cells (1.39- to 1.72-fold elevation) than in SW480 cells (1.24- to 1.66-fold elevation). HIF-1α and HIF-2α levels were elevated and GLUT1 genes were significantly overexpressed in CRC tissue specimens. The elevated ratio of GLUT1 was higher in stage III and IV CRC tissue specimens than in the stage I and II (2.97–4.73 versus 1.44–2.11). GLUT1 mRNA was also increased in the peripheral blood of stage II and III CRC patients as compared to stage I patients, suggesting that GLUT1 may serve as a hypoxic indicator in CRC patients.

Conclusion

In conclusion, this study demonstrated that GLUT1 has the potential to be employed as a molecular marker to indicate the degree of hypoxia experienced by tumors circulating in the blood of cancer patients.
Mortality attributable to excess adiposity in England and Wales in 2003 and 2015: explorations with a spreadsheet implementation of the Comparative Risk Assessment methodology
Authors: Kelly Christopher , Pashayan Nora , Munisamy Sreetharan , Powles John W
Published: July 2009

Background

Our aim was to estimate the burden of fatal disease attributable to excess adiposity in England and Wales in 2003 and 2015 and to explore the sensitivity of the estimates to the assumptions and methods used.

Methods

A spreadsheet implementation of the World Health Organization's (WHO) Comparative Risk Assessment (CRA) methodology for continuously distributed exposures was used. For our base case, adiposity-related risks were assumed to be minimal with a mean (SD) BMI of 21 (1) Kg m-2. All cause mortality risks for 2015 were taken from the Government Actuary and alternative compositions by cause derived. Disease-specific relative risks by BMI were taken from the CRA project and varied in sensitivity analyses.

Results

Under base case methods and assumptions for 2003, approximately 41,000 deaths and a loss of 1.05 years of life expectancy were attributed to excess adiposity. Seventy-seven percent of all diabetic deaths, 23% of all ischaemic heart disease deaths and 14% of all cerebrovascular disease deaths were attributed to excess adiposity. Predictions for 2015 were found to be more sensitive to assumptions about the future course of mortality risks for diabetes than to variation in the assumed trend in BMI. On less favourable assumptions the attributable loss of life expectancy in 2015 would rise modestly to 1.28 years.

Conclusion

Excess adiposity appears to contribute materially but modestly to mortality risks in England and Wales and this contribution is likely to increase in the future. Uncertainty centres on future trends of associated diseases, especially diabetes. The robustness of these estimates is limited by the lack of control for correlated risks by stratification and by the empirical uncertainty surrounding the effects of prolonged excess adiposity beginning in adolescence.
Plasma carotenoids, retinol, and tocopherols and postmenopausal breast cancer risk in the Multiethnic Cohort Study: a nested case-control study
Authors: Epplein Meira , Shvetsov Yurii B , Wilkens Lynne R , Franke Adrian A , Cooney Robert V , Le Marchand Loïc , Henderson Brian E , Kolonel Laurence N , Goodman Marc T
Published: July 2009

Introduction

Assessments by the handful of prospective studies of the association of serum antioxidants and breast cancer risk have yielded inconsistent results. This multiethnic nested case-control study sought to examine the association of plasma carotenoids, retinol, and tocopherols with postmenopausal breast cancer risk.

Methods

From the biospecimen subcohort of the Multiethnic Cohort Study, 286 incident postmenopausal breast cancer cases were matched to 535 controls on age, sex, ethnicity, study location (Hawaii or California), smoking status, date/time of collection and hours of fasting. We measured prediagnostic circulating levels of individual carotenoids, retinol, and tocopherols. Conditional logistic regression was used to compute odds ratios and 95% confidence intervals.

Results

Women with breast cancer tended to have lower levels of plasma carotenoids and tocopherols than matched controls, but the differences were not large or statistically significant and the trends were not monotonic. No association was seen with retinol. A sensitivity analysis excluding cases diagnosed within 1 year after blood draw did not alter the findings.

Conclusions

The lack of significant associations in this multiethnic population is consistent with previously observed results from less racially-diverse cohorts and serves as further evidence against a causal link between plasma micronutrient concentrations and postmenopausal breast cancer risk.
Development of a Green Building Decision Support Tool: A Collaborative Process
Authors: Ewing Ben , Baker Erin
Published: July 2009

In this paper, we discuss a collaborative process for developing a decision tool to support decisions around investment in green energy technologies. Our tool was developed specifically for the Hitchcock Center for the Environment, a local environmental education organization, and the development process began as an undergraduate student service learning project. Building on the student projects, we developed an Excel-based tool that allows users to select various combinations of technologies and instantly see the financial, environmental, and educational impacts of their choice. Given our initial parameters and the preferences of the Hitchcock Center staff, the optimal configuration included installing a biomass heating system and a composting toilet, but avoiding investment in other green technologies, yielding an annualized preference-adjusted cost of $5,252.58. Sensitivity analysis indicated that the optimal choice was not sensitive to environmental valuations, and only slightly sensitive to educational values. All participants in the process found the concept and practice of value elicitation to be useful and illuminating.
Incentives for Retailer Forecasting: Rebates vs. Returns
Authors: Taylor Terry A. , Xiao Wenqiang
Published: July 2009

This paper studies a manufacturer that sells to a newsvendor retailer who can improve the quality of her demand information by exerting costly forecasting effort. In such a setting, contracts play two roles: providing incentives to influence the retailer's forecasting decision and eliciting information obtained by forecasting to inform production decisions. We focus on two forms of contracts that are widely used in such settings and are mirror images of one another: a rebates contract, which compensates the retailer for the units she sells to end consumers, and a returns contract, which compensates the retailer for the units that are unsold. We characterize the optimal rebates contracts and returns contracts. Under rebates, the retailer, manufacturer, and total system may benefit from the retailer having inferior forecasting technology; this never occurs under returns. Although one might conjecture that returns would be inferior because its provision of “insurance” would discourage the retailer from forecasting, we show that returns are superior.
On the Relative Performance of Linear vs. Piecewise-Linear-Threshold Intertemporal Incentives
Authors: Chen Joseph Y. , Miller Bruce L.
Published: July 2009

This paper employs numerical simulations to compare the relative performance of linear contracts with piecewise-linear-threshold contracts in the case where the agent chooses actions over time. These contracts are restricted to be functions of the ending value of aggregate output. We find strong evidence that only linear contracts need be considered in comparison with piecewise-linear-threshold contracts in the situation where cumulative output is only updated periodically and the agent's utility function is exponential. This finding holds even when there are only two periods and hence one change of action by the agent. However, we find that the best piecewise-linear-threshold contract is significantly superior to the best linear contract when the agent has a power utility function. These numerical simulations also call into question the use of a cap when the agent's compensation is based on the ending value of aggregate output and the agent's effort takes place over time.
Children's conceptions of mental illness: A naïve theory approach
Authors: Fox Claudine , Buchanan‐Barrow Eithne , Barrett Martyn
Published: July 2009

This paper reports two studies that investigated children's conceptions of mental illness using a naïve theory approach, drawing upon a conceptual framework for analysing illness representations which distinguishes between the identity, causes, consequences, curability, and timeline of an illness. The studies utilized semi‐structured interviewing and card selection tasks to assess 6‐ to 11‐year‐old children's conceptions of the causes and consequences (Study 1) and the curability and timeline (Study 2) of different mental and physical illnesses/ailments. The studies revealed that, at all ages, the children held coherent causal–explanatory ideas about the causes, consequences, curability, and timeline of both mental and physical illnesses/ailments. However, while younger children tended to rely on their knowledge of common physical illnesses when thinking about mental illnesses, providing contagion and contamination explanations of cause, older children demonstrated differences in their thinking about mental and physical illnesses. No substantial gender differences were found in the children's thinking. It is argued that children hold coherent conceptions of mental illness at all ages, but that mental illness only emerges as an ontologically distinct conceptual domain by the end of middle childhood.
What We Do Not Know: Perspectives on Wall-Window Combinations and Performance Assurance We Have yet to Address
Authors: Mathis R. Christopher , Johnson Steve
Published: July 2009

Collaborative efforts over several years resulted in the development of ASTM E2112, “Standard Practice for the Installation of Exterior Windows, Doors and Skylights”. Individuals from the window, sealant, and air barrier industries were involved in the development of the standard. Development of the standard was driven by a desire to reduce water leakage attributed to window installation practices, particularly in residential and light commercial construction. A consensus document addressing the installation of fenestration units in residential and light commercial construction was believed to be needed. While many believe that the development of ASTM E2112 has helped to reduce the prevalence of leaking installations, the Standard, even in its most updated form (ASTM E2112-07), still has significant limitations. This paper addresses some of the limitations of the Standard and is intended to provoke the further development and documentation of installation techniques for a wide array of wall-window combinations that are not yet addressed in ASTM E2112.
Sediment Trend Analysis in Support of Unexploded Explosive Ordnance Risk Assessment
Authors: McLaren Patrick , Braid Matthew
Published: July 2009

For 48 years (1952–2000) the south half of Lac Saint-Pierre, a widening of the St. Lawrence River between Montreal and Quebec, was used as an experimental firing range. Some 500,000 shells were fired into the lake, of which about 8000 are thought to contain energetic material. Approximately 2000 projectiles are considered as unexploded explosive ordnance (UXO). Furthermore, the lake itself is potentially the recipient of other contaminants associated with industrial wastes and agricultural runoff. The Canadian Department of National Defence, in order to research appropriate clearance approaches programs, instigated a large sediment transport study (sediment trend analysis or STA) to determine both sediment and contaminant sources and sinks and to assess the possible environmental consequences of various clearance options. STA is an empirical technique whereby patterns of sediment transport and dynamic behavior are derived from relative changes in grain-size distributions. About 1000 samples were collected at 500 m spacing encompassing the entire firing range. The lake bottom contained a complex number of sediment types ranging from “ancient” late glacial deposits, recent mud and sand, and a variety of mixtures. The STA identified the significance of the late glacial deposits as the dominant source for the sediments contained in the lake. The latter showed complex patterns of transport that originated from the ancient sediments and terminated on well-sorted sand. The findings demonstrated that anthropogenic contaminants were unlikely to be deposited in the lake sediments, or if they were, self-cleaning by natural processes would likely be rapid. Furthermore, trace metals were strongly associated with the ancient sediments evidently originating from an underlying anaerobic black shale formation. The STA provides an important framework to understand the chemistry of the sediments and their dynamics and helps to define the context within which the UXO clearance and environmental remediation options can be developed.
DFG Research Training Group “Algorithmic Synthesis of Reactive and Discrete-Continuous Systems (AlgoSyn)”DFG-Graduiertenkolleg “Algorithmische Synthese reaktiver und diskret-kontinuierlicher Systeme (AlgoSyn)”
Authors: Thomas Wolfgang , Bollue Kai , Gückel Dominique , Quiros Gustavo , Slaats Michaela , Ummels Michael
Published: July 2009

While methods of software validation and verification are by now well established, the approach of automatic synthesis of software (and hardware) is as yet only developed in quite rudimentary form. Algorithmic program synthesis is possible in restricted scenarios, in particular in reactive multi-agent systems with low data complexity and in control systems. Central issues are the establishment of system models that support algorithmic solutions, the combination of discrete and continuous parameters (in hybrid systems), and the exploration of applications. The aim of the Research Training Group AlgoSyn is to unify the expertise from computer science, mathematics, and four engineering disciplines (processor architectures, automatic control, process control engineering, train traffic systems), in order to push forward the desired integration of methods.
Dublettenerkennung unter Berücksichtigung von DatenabhängigkeitenDuplicate Detection Exploiting Data Relationships
Authors: Herschel Melanie
Published: July 2009

Dublettenerkennung befasst sich mit dem Problem, verschiedene Datenbankrepräsentationen des gleichen Objekts zu identifizieren. Bisherige Algorithmen zur Dublettenerkennung ignorieren den Kontext, in dem sich die Daten befinden. Dabei enthält dieser oftmals weitere nützliche Daten, die das Ergebnis positiv beeinflussen können. In diesem Beitrag stellen wir Algorithmen zur Dublettenerkennung vor, die Beziehungen innerhalb der Daten ausnutzen.
Bayesian Quantitative Trait Locus Mapping Based on Reconstruction of Recent Genetic Histories
Authors: Gasbarra Dario , Pirinen Matti , Sillanpää Mikko J , Arjas Elja
Published: July 2009

We assume that quantitative measurements on a considered trait and unphased genotype data at certain marker loci are available on a sample of individuals from a background population. Our goal is to map quantitative trait loci by using a Bayesian model that performs, and makes use of, probabilistic reconstructions of the recent unobserved genealogical history (a pedigree and a gene flow at the marker loci) of the sampled individuals. This work extends variance component-based linkage analysis to settings where the unobserved pedigrees are considered as latent variables. In addition to the measured trait values and unphased genotype data at the marker loci, the method requires as an input estimates of the population allele frequencies and of a marker map, as well as some parameters related to the population size and the mating behavior. Given such data, the posterior distribution of the trait parameters (the number, the locations, and the relative variance contributions of the trait loci) is studied by using the reversible-jump Markov chain Monte Carlo methodology. We also introduce two shortcuts related to the trait parameters that allow us to do analytic integration, instead of stochastic sampling, in some parts of the algorithm. The method is tested on two simulated data sets. Comparisons with traditional variance component linkage analysis and association analysis demonstrate the benefits of our approach in a gene mapping context.
Distinctive Responses to Nitrogen Starvation in the Dominant Active Mutants of the Fission Yeast Rheb GTPase
Authors: Murai Tomoka , Nakase Yukiko , Fukuda Keiko , Chikashige Yuji , Tsutsumi Chihiro , Hiraoka Yasushi , Matsumoto Tomohiro
Published: July 2009

Rheb, a Ras-like small GTPase conserved from human to yeast, controls Tor kinase and plays a central role in the regulation of cell growth depending on extracellular conditions. Rhb1 (a fission yeast homolog of Rheb) regulates amino acid uptake as well as response to nitrogen starvation. In this study, we generated two mutants, rhb1-DA4 and rhb1-DA8, and characterized them genetically. The V17A mutation within the G1 box defined for the Ras-like GTPases was responsible for rhb1-DA4 and Q52R I76F within the switch II domain for rhb1-DA8. In fission yeast, two events—the induction of the meiosis-initiating gene mei2+ and cell division without cell growth—are a typical response to nitrogen starvation. Under nitrogen-rich conditions, Rheb stimulates Tor kinase, which, in turn, suppresses the response to nitrogen starvation. While amino acid uptake was prevented by both rhb1-DA4 and rhb1-DA8 in a dominant fashion, the response to nitrogen starvation was prevented only by rhb1-DA4. rhb1-DA8 thereby allowed genetic dissection of the Rheb-dependent signaling cascade. We postulate that the signaling cascade may branch below Rhb1 or Tor2 and regulate the amino acid uptake and response to nitrogen starvation independently.
Utility of Hepatic Transaminases to Recognize Abuse in Children
Authors: Lindberg Daniel , Makoroff Kathi , Harper Nancy , Laskey Antoinette , Bechtel Kirsten , Deye Katherine , Shapiro Robert ,   for the ULTRA Investigators
Published: July 2009

OBJECTIVE: Although experts recommend routine screening of hepatic transaminases (aspartate aminotransferase [AST] and alanine aminotransferase [ALT]) in cases of potential child physical abuse, this practice is highly variable. Our objective was to determine the sensitivity and specificity of routine transaminase testing in young children who underwent consultation for physical abuse.

PATIENTS AND METHODS: This was a prospective, multicenter, observational study of all children younger than 60 months referred for subspecialty evaluation of possible physical abuse. The child abuse team at each center recommended screening transaminases routinely as standard of care for all cases with a reasonable concern for physical abuse. Sensitivity and specificity for transaminases and clinical examination findings to detect identified abdominal injuries were determined, and receiver operating characteristic analysis was undertaken.

RESULTS: Of 1676 consultations, 1272 (76%) patients underwent transaminase testing, and 54 (3.2% [95% confidence interval: 2.4–4.2]) had identified abdominal injuries. Area under the curve for the highest level of either transaminase was 0.85. Using a threshold level of 80 IU/L for either AST or ALT yielded a sensitivity of 77% and a specificity of 82% (positive likelihood ratio: 4.3; negative likelihood ratio: 0.3). Of injuries with elevated transaminase levels, 14 (26%) were clinically occult, lacking abdominal bruising, tenderness, and distention. Several clinical findings used to predict abdominal injury had high specificity but low sensitivity.

CONCLUSIONS: In the population of children with concern for physical abuse, abdominal injury is an important cause of morbidity and mortality, but it is not so common as to warrant universal imaging. Abdominal imaging should be considered for potentially abused children when either the AST or ALT level is >80 IU/L or with abdominal bruising, distention, or tenderness.