bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xrcc2 Modulates Spontaneous and Radiation-Induced Tumorigenesis in Apcmin/+ Mice
Authors: Haines Jackie W. , Coster Margaret R. , Adam Julie , Cheeseman Michael , Ainsbury Elizabeth A. , Thacker John , Bouffler Simon D. 
Published: July 2010

Abstract
XRCC2 has an important role in repair of DNA damage by homologous recombination. Adult Apcmin/+ (min, multiple intestinal neoplasia) mice, wild-type or heterozygous for Xrcc2 deficiency, were sham-irradiated or 2-Gy X-irradiated. Spontaneous mammary and intestinal tumor incidences are lower in Apcmin/+ Xrcc2+/− mice than in Apcmin/+ Xrcc2+/+ mice (mammary tumors: 14% and 38%, respectively, χ2 P = 0.03; intestinal adenomas in mice reaching full life span: 108.6 and 130.1, respectively, t-test P = 0.005). Following irradiation, the increase in mammary tumors was greatest in female mice heterozygous for Xrcc2 (7.25 ± 0.50-fold in Apcmin/+ Xrcc2+/− mice compared with 2.57 ± 0.35-fold in Apcmin/+ Xrcc2+/+ mice; t-test P &lt; 0.001). The increase in intestinal tumor multiplicity following irradiation was significantly greater in Apcmin/+ Xrcc2+/− mice (Apcmin/+ Xrcc2+/−, 4.14 ± 0.05-fold, versus Apcmin/+ Xrcc2+/+, 3.30 ± 0.05-fold; t-test P &lt; 0.001). Loss of heterozygosity of all chromosome 18 markers was greater in intestinal tumors from Apcmin/+ Xrcc2+/− mice than in tumors from Apcmin/+ Xrcc2+/+ mice. These findings indicate that Xrcc2 haploinsufficiency reduces spontaneous tumor incidence on an Apcmin/+ background but increases the tumorigenic response to radiation. Mol Cancer Res; 8(9); 1227–33. ©2010 AACR.
The Numismatic Finds from the Qumran Plateau Excavations 2004‐2006, and 2008 Seasons
Authors: Price Randall , Farhi Yoav 
Published: July 2010

AbstractThis article contains the preliminary report of nine coins, ranging from the second century b.c.e. to the fourth century c.e., that were found during the 2004‐2006 and 2008 seasons of the 2002‐2008 excavations at the Qumran Plateau, carried out under the direction of Dr. Randall Price of Liberty University with the assistance of Israeli archaeologists Dr. Oren Gutfeld and Yakov Kalman.
Simplicius on the Theaetetus (In Physica 17,38-18,23 Diels)
Authors: Menn Stephen 
Published: July 2010

AbstractAristotle in Physics I,1 says some strange-sounding things about how we come to know wholes and parts, universals and particulars. In explicating these, Simplicius distinguishes an initial rough cognition of a thing as a whole, an intermediate “cognition according to the definition and through the elements,” and a final cognition of how the thing’s many elements are united: only this last is πιστήμη. Simplicius refers to the Theaetetus for the point about what is needed for πιστήμη and the ways that cognition according to the definition and through the elements falls short. By unpacking this reference I try to reconstruct Simplicius’ reading of “Socrates’ Dream,” its place in the Theaetetus’ larger argument, and its harmony with other Platonic and Aristotelian texts. But this reconstruction depends on undoing some catastrophic emendations in Diels’s text of Simplicius. Diels’s emendations arise from his assumptions about definitions and elements, in Socrates’ Dream and elsewhere, and rethinking the Simplicius passage may help us rethink those assumptions.
Short Note
Authors: Briffard Colette 
Published: July 2010

AbstractThe aim of this short note is to demonstrate that the emphasis on Moses’ Levitical ancestry in the beginning of his birth account (Ex 2:1) reminds the tablets containing Sargon’s birth account. However, Ex 2:1 also contains ideas that take the opposite view of Sargon’s auto-proclamation and his destiny as a conqueror.
Im Dickicht der Pentateuchforschung: Ein Plädoyer für die umstrittene Neuere Urkundenhypothese
Authors: Schmidt Ludwig 
Published: July 2010

AbstractRecent research has mostly argued against the traditional claim that the Pentateuch contains the documents of the Yahwist, the Elohist and the priestly writer (the new documentary hypothesis). After a survey of recent theories (I) the essay argues for the validity of this hypothesis (II). The priestly document is an own source and ends with the death of Moses (Dtn 34:1a*, 7-9). Furthermore it is demonstrated that there existed a yahwistic pre-priestly narrative structure from Gen 12 to Num 24 which originated in the time of Solomon. Against recent theories the Patriarchs were first literarily connected with the exodus by this Yahwist, and not by an exilic Yahwist or by P. The existence of the Elohist from the northern kingdom around 760 is proven by various arguments. Finally, the essay ends with remarks on the redactions of the (exilic) Jehowist and the pentateuchal redactor.
Cucurbita super caput ionae Translation and Theology in the Old Latin Tradition
Authors: Bazzana Giovanni B. 
Published: July 2010

AbstractThe present paper aims at examining one passage in the Old Latin and Vulgate translations of the Book of Jonah, where Jerome inserted a controversial change by translating the Hebrew qyqywn with the Latin haedera instead of the usual cucurbita. The reasons for this variation are neither immediately evident nor directly stated by the translator, but an analysis of iconographical documents will show that Jerome wanted to exclude the possibility of a millenarian interpretation, which, after the conversion of Constantine, he had to deem heretic.
The Non-Eternal Dynastic Promises of Jehu of Israel and Esarhaddon of Assyria
Authors: Lamb David T. 
Published: July 2010

AbstractThree Israelite kings receive promises of a dynasty continuing indefinitely (David, Solomon and Jeroboam I), but Jehu of Israel is the only ruler in the Hebrew Bible with a non-eternal dynastic promise. While many Assyrian rulers claim divine election and speak of “eternal” dynasties, the dynastic promise of Esarhaddon is unusual because of its modest nature. The dynastic promises of Jehu and Esarhaddon are therefore unique within their ANE context because of their lack of hyperbolic language, guaranteeing only four or two generations of continuity. Since both rulers assume the throne in the midst of a political crisis their reigns would have been reasonable times for promises legitimizing their dynasties. A comparison of these two oracles will not only allow the interesting parallels between the two promises to be clearly seen, but also reveal the crucial role that non-eternal dynastic oracles can play in establishing royal legitimacy.
A Place in the Dust: Text, Topography and a Toponymic Note on Micah 1:10-12a
Authors: Suriano Matthew J. 
Published: July 2010

AbstractThe poetry of Micah’s oracle of doom (Mic 1:8-16) combines two undeniable motifs, the motif of the lament and that of geography. The latter motif is not well understood due to the obscurity of the place names found in vv. 10a-12b. A careful study of the oracle’s geographical context, however, will lead to a more precise understanding of the topography of vv. 10-12b and serve as the basis for the identification of one of the more enigmatic place names, Beth-le-aphrah (v. 10b), with the archaeological site of Tell el-‘Areini.
Constantinople and the End Time: The Ottoman Conquest as a Portent of the Last Hour
Authors: Şahin Kaya 
Published: July 2010

AbstractThe Muslim conquest of Constantinople was seen in various apocalyptic traditions as one of the portents of the end. An Ottoman mystic, Ahmed Bî-cân, gave voice to these apocalyptic fears and expectations soon after the Ottoman conquest in 1453 CE. His apocalyptic narrative, expressed in the Turkish vernacular, placed the Ottoman enterprise within the final tribulations and hailed the sultan, Mehmed II, as an apocalyptic warrior. This endorsement heralded the emergence of a new imperial ideology in the sixteenth century: Ottoman history became an important component of universal history, while Ottoman sultans were attributed cosmic responsibilities and messianic abilities.
Identifiability, Genomics and UK Data Protection Law
Authors: Curren Liam , Kaye Jane , Boddington Paula , Melham Karen , Hawkins Naomi , Gowans Heather , Kanellopoulou Nadja 
Published: July 2010

AbstractAnalyses of individuals’ genomes — their entire DNA sequence — have increased knowledge about the links between genetics and disease. Anticipated advances in ‘next generation’ DNA-sequencing techniques will see the routine research use of whole genomes, rather than distinct parts, within the next few years. The scientific benefits of genomic research are, however, accompanied by legal and ethical concerns. Despite the assumption that genetic research data can and will be rendered anonymous, participants’ identities can sometimes be elucidated, which could cause data protection legislation to apply. We undertake a timely reappraisal of these laws — particularly new penalties — and identifiability in genomic research.
Moving on: From Enterprise policy to Innovation Policy in the Western Balkans
Authors: Roper Stephen 
Published: July 2010

AbstractSignificant progress has been made in recent years in the development of enterprise policy in the Western Balkans. Issues remain, however, in the support provided for innovative enterprises. In this paper we use data from the 2005 Business Environment and Enterprise Performance Survey to identify the determinants of innovation in locally-owned firms in the Western Balkans and compare these to the other CEEE countries and the CIS. Based on an econometric examination of the innovation production function in each area we observe marked differences in the determinants of innovation. First, in the Western Balkan countries (WBCs) R&D and higher-level skills have little impact on firms' innovation outputs, a result which contrasts strongly with results for the CEEE, CIS and other more developed economies. Second, we find no evidence of innovation benefits from urban locations in innovation in the WBCs or that public support is having any positive effect on innovation outcomes. Again, this experience is at odds with evidence from other regions. Third, innovation outputs in the WBCs are being negatively influenced by aspects of the business environment. These results suggest a need for an active and rather interventionist innovation policy in the WBCs to address these system failures. A range of policy options are developed.
Integration Mechanisms for Heading Perception
Authors: Vaina Lucia , Calabro Finnegan , Sikoglu Elif , Beardsley Scott 
Published: July 2010

AbstractPrevious studies of heading perception suggest that human observers employ spatiotemporal pooling to accommodate noise in optic flow stimuli. Here, we investigated how spatial and temporal integration mechanisms are used for judgments of heading through a psychophysical experiment involving three different types of noise. Furthermore, we developed two ideal observer models to study the components of the spatial information used by observers when performing the heading task. In the psychophysical experiment, we applied three types of direction noise to optic flow stimuli to differentiate the involvement of spatial and temporal integration mechanisms. The results indicate that temporal integration mechanisms play a role in heading perception, though their contribution is weaker than that of the spatial integration mechanisms. To elucidate how observers process spatial information to extract heading from a noisy optic flow field, we compared psychophysical performance in response to random-walk direction noise with that of two ideal observer models (IOMs). One model relied on 2D screen-projected flow information (2D-IOM), while the other used environmental, i.e., 3D, flow information (3D-IOM). The results suggest that human observers compensate for the loss of information during the 2D retinal projection of the visual scene for modest amounts of noise. This suggests the likelihood of a 3D reconstruction during heading perception, which breaks down under extreme levels of noise.
Detecting Sudden Changes in Dynamic Rotation Displays
Authors: Thiel Rachael , Petersik J. Timothy 
Published: July 2010

AbstractFour experiments and controls were run in order to determine the ability of the visual system to detect slight changes in three-dimensional (3D) rotating stimuli in comparison to two-dimensional (2D) controls. A small number of observers (between 5 and 8) viewed computerized displays of pixel-defined transparent rotating spheres or circular patches of pixels drifting linearly in opposite directions. Halfway through the circuit of rotation a letter was briefly displayed and the rotation continued with some change introduced. Our results showed that for horizontal shifts of the stimulus on the X-axis, changes in the axis of rotation, and additions/deletions of pixels, observers were better at detecting the changes associated with 3D motion than 2D motion. There was no good 2D control for approaching and receding stimuli, but on the basis of other results it was concluded that 3D movement had no advantage. It is suggested that rotation in 3D is more readily monitored by the visual system than simultaneous 2D motions in opposite directions.
IκB kinase overcomes PI3K/Akt and ERK/MAPK to control FOXO3a activity in acute myeloid leukemia
Authors: Chapuis Nicolas , Park Sophie , Leotoing Laurent , Tamburini Jerome , Verdier Frederique , Bardet Valerie , Green Alexa S. , Willems Lise , Agou Fabrice , Ifrah Norbert , Dreyfus François , Bismuth Georges , Baud Veronique , Lacombe Catherine , Mayeux Patrick , Bouscary Didier 
Published: July 2010

AbstractThe FOXO transcription factors are involved in multiple signaling pathways and have tumor-suppressor functions. In acute myeloid leukemia (AML), deregulation of oncogenic kinases, including Akt, extra-signal–regulated kinase, or IκB kinase, is frequently observed, which may potentially inactivate FOXO activity. We therefore investigated the mechanism underlying the regulation of FOXO3a, the only FOXO protein constantly expressed in AML blast cells. We show that in both primary AML samples and in a MV4-11/FOXO3a-GFP cell line, FOXO3a is in a constant inactive state due to its cytoplasmic localization, and that neither PI3K/Akt nor extra-signal–regulated kinase–specific inhibition resulted in its nuclear translocation. In contrast, the anti-Nemo peptide that specifically inhibits IKK activity was found to induce FOXO3a nuclear localization in leukemic cells. Furthermore, an IKK-insensitive FOXO3a protein mutated at S644 translocated into the nucleus and activated the transcription of the Fas-L and p21Cip1 genes. This, in turn, inhibited leukemic cell proliferation and induced apoptosis. These results thus indicate that IKK activity maintains FOXO3a in the cytoplasm and establishes an important role of FOXO3a inactivation in the proliferation and survival of AML cells. The restoration of FOXO3a activity by interacting with its subcellular distribution may thus represent a new attractive therapeutic strategy for AML.
Contributions of TRAIL-mediated megakaryocyte apoptosis to impaired megakaryocyte and platelet production in immune thrombocytopenia
Authors: Yang Lei , Wang Lin , Zhao Chun-hong , Zhu Xiao-juan , Hou Yu , Jun Peng , Hou Ming 
Published: July 2010

Abstract
Recent in vitro studies provide evidence for autoantibody-induced suppression of megakaryocytopoiesis and show a reduction in megakaryocyte production and maturation in the presence of immune thrombocytopenia (ITP) plasma. Here, we present CD34+ cells from healthy umbilical cord blood mononuclear cells cultured in medium containing thrombopoietin, stem cell factor, interleukin-3, and 10% plasma from either ITP patients or healthy subjects. The quantity, quality, and apoptosis of megakaryocytes were measured. We observed that most ITP plasma boosted megakaryocyte quantity but impaired quality, resulting in significantly less polyploidy cells (N ≥ 4) and platelet release. In these megakaryocytes, we found a lower percentage of cell apoptosis, a lower expression of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), and a higher expression of Bcl-xL. Furthermore, there was a decrease of sTRAIL in ITP plasma and in cell culture supernatants of this group compared with the control group. Our findings suggest that decreased apoptosis of megakaryocytes also contributes to in vitro dysmegakaryocytopoiesis and reduced platelet production. The abnormal expression of sTRAIL in plasma and TRAIL and Bcl-xL in megakaryocytes may play a role in the pathogenesis of impaired megakaryocyte apoptosis in ITP.
KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes
Authors: Heinen Stephanie , Thielen Bernhard , Schomburg Dietmar 
Published: July 2010

Abstract

Background
The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed.

Description
Here we present a text mining algorithm for the extraction of kinetic information such as KM, Ki, kcat etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (KM, Ki, kcat, kcat/KM, Vmax, IC50, S0.5, Kd, Ka, t1/2, pI, nH, specific activity, Vmax/KM) from about 17 million PubMed abstracts and combine them with other data in the abstract.
A manual verification of approx. 1,000 randomly chosen results yielded a recall between 51% and 84% and a precision ranging from 55% to 96%, depending of the category searched.
The results were stored in a database and are available as "KID the KInetic Database" via the internet.

Conclusions
The presented algorithm delivers a considerable amount of information and therefore may aid to accelerate the research and the automated analysis required for today's systems biology approaches. The database obtained by analysing PubMed abstracts may be a valuable help in the field of chemical and biological kinetics. It is completely based upon text mining and therefore complements manually curated databases.
The database is available at http://kid.tu-bs.de. The source code of the algorithm is provided under the GNU General Public Licence and available on request from the author.
Full-length cDNA sequences from Rhesus monkey placenta tissue: analysis and utility for comparative mapping
Authors: Kim Dae-Soo , Huh Jae-Won , Kim Young-Hyun , Park Sang-Je , Lee Sang-Rae , Chang Kyu-Tae 
Published: July 2010

Abstract

Background
Rhesus monkeys (Macaca mulatta) are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (Macaca
fascicularis), and to humans, sharing a last common ancestor from about 25 million years ago. Although rhesus monkeys have been studied extensively under field and laboratory conditions, research has been limited by the lack of genetic resources. The present study generated placenta full-length cDNA libraries, characterized the resulting expressed sequence tags, and described their utility for comparative mapping with human RefSeq mRNA transcripts.

Results
From rhesus monkey placenta full-length cDNA libraries, 2000 full-length cDNA sequences were determined and 1835 rhesus placenta cDNA sequences longer than 100 bp were collected. These sequences were annotated based on homology to human genes. Homology search against human RefSeq mRNAs revealed that our collection included the sequences of 1462 putative rhesus monkey genes. Moreover, we identified 207 genes containing exon alterations in the coding region and the untranslated region of rhesus monkey transcripts, despite the highly conserved structure of the coding regions. Approximately 10% (187) of all full-length cDNA sequences did not represent any public human RefSeq mRNAs. Intriguingly, two rhesus monkey specific exons derived from the transposable elements of AluYRa2 (SINE family) and MER11B (LTR family) were also identified.

Conclusion
The 1835 rhesus monkey placenta full-length cDNA sequences described here could expand genomic resources and information of rhesus monkeys. This increased genomic information will greatly contribute to the development of evolutionary biology and biomedical research.
YeastWeb: a workset-centric web resource for gene family analysis in yeast
Authors: Chu Yanhui , Yuan Xiaohuan , Guo Yanqin , Zhang Yufei , Wu Yan , Liu Haifeng , Wu Dan , Bao Haihua , Guan Lixin , Jin Xiudong 
Published: July 2010

Abstract

Background
Currently, a number of yeast genomes with different physiological features have been sequenced and annotated, which provides invaluable information to investigate yeast genetics, evolutionary mechanism, structure and function of gene families.

Description
YeastWeb is a novel database created to provide access to gene families derived from the available yeast genomes by assigning the genes into putative families. It has many useful features that complement existing databases, such as SGD, CYGD and Génolevures: 1) Detailed computational annotation was conducted with each entry with InterProScan, EMBOSS and functional/pathway databases, such as GO, COG and KEGG; 2) A well established user-friendly environment was created to allow users to retrieve the annotated genes and gene families using functional classification browser, keyword search or similarity-based search; 3) Workset offers users many powerful functions to manage the retrieved data efficiently, associate the individual items easily and save the intermediate results conveniently; 4) A series of comparative genomics and molecular evolution analysis tools are neatly implemented to allow users to view multiple sequence alignments and phylogenetic tree of gene families. At present, YeastWeb holds the gene families clustered from various MCL inflation values from a total of 13 available yeast genomes.

Conclusions
Given the great interest in yeast research, YeastWeb has the potential to become a useful resource for the scientific community of yeast biologists and related researchers investigating the evolutionary relationship of yeast gene families. YeastWeb is available at http://centre.bioinformatics.zj.cn/Yeast/.