bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ranking billions of web pages using diodes
Authors: Kaul Rohit , Yun Yeogirl , Kim Seong-Gon 
Published: July 2009

Introduction

Because of the web's rapid growth and lack of central organization, Internet search engines play a vital role in assisting the users of the Web in retrieving relevant information out of the tens of billions of documents available. With millions of dollars of potential revenue at stake, commercial Web sites compete fiercely to be placed prominently within the first page returned by a search engine. As a result, search engine optimizers (SEOs) developed various forms of search engine spamming (or spamdexing) techniques to artificially inflate the rankings of Web pages. Link-based ranking algorithms, such as Google's PageRank, have been largely effective against most conventional spamming techniques.
However, PageRank has three fundamental flaws that, when exploited aggressively, can be proven to be its Achilles' heel: First, PageRank gives a minimum guaranteed score to every page on the Web; second, it rewards all incoming links as valid endorsements; and third, it imposes no penalty for making links to low-quality pages. SEOs can take advantage of these shortcomings to the extreme by employing an Artificial Web, a collection of an extremely large number of computer-generated Web pages containing many links to only a few target pages. Each page of the Artificial Web collects the minimum PageRank and feeds it back to the target pages. Although the individual endorsements are small, the flaws of PageRank make it possible for an Artificial Web to accumulate sizable PageRank values for the target pages. The SEOs can even download a substantial portion of the real Web and modify only the destinations of the hyperlinks, thus circumventing any detection algorithms based on the quality or the size of pages. As the size of an Artificial Web can be comparable to that of the real Web, SEOs can seriously compromise the objectivity of the results that PageRank provides. Although some statistical measures can be employed to identify specific attributes associated with an Artificial Web and filter them out of search results, it is far more desirable to develop a new ranking model that is free of such exploits to begin with.
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

AbstractThe 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

AbstractMigration 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

AbstractMadagascar 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.
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

AbstractSevere 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

AbstractPersons 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

Abstract

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

Abstract

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

AbstractBackgroundEnteropathogenicEscherichia 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.ResultsFive 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.ConclusionSome 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

Abstract

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

Abstract

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

Abstract

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.