bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation of Locally Derived Stem/Progenitor Cells From the Peri-Infarct Area That Do Not Migrate From the Lateral Ventricle After Cortical Stroke
Authors: Shimada Issei S. , Peterson Brittni M. , Spees Jeffrey L.
Published: July 2010

Background and Purpose—

Neurogenesis can arise from neural stem/progenitor cells of the subventricular zone after strokes involving both the cortex and striatum. However, it is controversial whether all types of stroke and strokes of different sizes activate neurogenesis from the subventricular zone niche. In contrast with cortical/striatal strokes, repair and remodeling after mild cortical strokes may involve to a greater extent local cortical stem/progenitor cells and cells from nonneurogenic niches.

Methods—

We compared stem/progenitor cell responses after focal cortical strokes produced by distal middle cerebral artery occlusion and cortical/striatal strokes produced by the intraluminal suture model. To label migrating neuroblasts from the subventricular zone, we injected DiI to the lateral ventricle after distal middle cerebral artery occlusion. By immunohistochemistry, we characterized cells expressing stem/progenitor cell markers in the peri-infarct area. We isolated cortical stem/progenitor cells from the peri-infarct area after distal middle cerebral artery occlusion and assayed their self-renewal and differentiation capacity.

Results—

In contrast with cortical/striatal strokes, focal cortical strokes did not induce neuroblast migration from the subventricular zone to the infarct zone after distal middle cerebral artery occlusion. By immunohistochemistry, we observed subpopulations of reactive astrocytes in the peri-infarct area that coexpressed radial glial cell markers such as Sox2, Nestin, and RC2. Clonal neural spheres isolated from the peri-infarct area after distal middle cerebral artery occlusion differentiated into neurons, astrocytes, oligodendrocytes, and smooth muscle cells. Notably, neural spheres isolated from the peri-infarct area also expressed RC2 before differentiation.

Conclusions—

Mild cortical strokes that do not penetrate the striatum activate local cortical stem/progenitor cells but do not induce neuroblast migration from the subventricular zone niche.
Neuroprotective Effect of Bax-Inhibiting Peptide on Neonatal Brain Injury
Authors: Wang Xiaoyang , Han Wei , Du Xiaonan , Zhu Changlian , Carlsson Ylva , Mallard Carina , Jacotot Etienne , Hagberg Henrik
Published: July 2010

Background and Purpose—

Mitochondria play a critical role in mediating cell death in both the adult and immature brain. The cyclophilin D mitochondrial membrane permeability transition pore is critical in adult ischemia, whereas in neonatal hypoxic–ischemic (HI) brain injury, mitochondrial permeabilization appears to be primarily Bax-dependent. The aim of this study was to evaluate the neuroprotective effect of a cell-penetrating Bax-inhibiting peptide (BIP) on neonatal mouse HI brain injury.

Methods—

BIP (5 μL, 5 mg/mL) or a BIP-negative control (5 μL, 5 mg/mL) was injected intracerebroventricularly immediately before HI in postnatal day 9 mice. Mice were euthanized at different time points after HI for evaluation of brain injury, Bax activation, release of proapoptotic proteins, and caspase activation. The trace fear conditioning and cylinder tests were performed for evaluation of the functional recovery after BIP treatment.

Results—

At 5 days after HI, there was a 41.2% reduction of brain injury in BIP-treated mice compared with BIP-negative control treated animals. Myelin basic protein and neurofilament quantification revealed that BIP reduced white matter injury. BIP treatment conferred improvement in both sensorimotor and memory functions at 7 weeks after HI. BIP protection was associated with a reduction of Bax activation, mitochondrial permeabilization, and downstream caspase activation.

Conclusions—

Bax inhibition provides neuroprotection and functional improvement in a neonatal mouse model of HI.
Psychometric Comparisons of 3 Functional Ambulation Measures for Patients With Stroke
Authors: Lin Jau-Hong , Hsu Miao-Ju , Hsu Hsin-Wen , Wu Hung-Chia , Hsieh Ching-Lin
Published: July 2010

Background and Purpose—

We compared the test–retest reliability, validity, and responsiveness of the Dynamic Gait Index, the 4-item Dynamic Gait Index, and the Functional Gait Assessment for assessment of walking in patients with stroke.

Methods—

Forty-five outpatients participating in the validity and responsiveness study were tested using the 3 walking measures as well as the 10-m walk test, Barthel Index, and Postural Assessment Scale for Stroke Patients. We tested them during the first week, then again after 2 months and 5 months of therapy. Another 48 chronic patients completed the 3 measures twice, 1 week apart, in the test–retest reliability study.

Results—

Thirty-five participants completed 3 time-point assessments. The Functional Gait Assessment showed the least floor and ceiling effects, indicating it has the best discriminative ability for patients with stroke with high walking function. We found the 3 measures were highly correlated with each other, indicating excellent concurrent validity, and all measures at the first week of therapy were moderately to highly correlated with the Barthel Index scores at 5 months, indicating good predictive validity. Responsiveness of the 3 measures was moderate during a 5-month period, and all showed good test–retest reliability. The minimal detectable changes between tests indicate acceptable random error.

Conclusions—

All 3 measures showed sufficient validity, responsiveness, and reliability for assessment of walking function in patients with stroke undergoing rehabilitation, but the Functional Gait Assessment is recommended for its psychometric properties.
The Numismatic Finds from the Qumran Plateau Excavations 2004‐2006, and 2008 Seasons
Authors: Price Randall , Farhi Yoav
Published: July 2010

This 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

Aristotle 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

The 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

Recent 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

The 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

Three 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

The 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

The 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

Analyses 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

Significant 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

Previous 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

Four 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.
Effect of heat treatment on small scale fragmentation of aluminium alloy
Authors: Edwards M. R. , Deal C.
Published: July 2010

Small scale explosions, using a detonator, of 7075 aluminium alloy cylinders, 15–100 mm outside diameter, were carried out to investigate the effects of heat treatment on fragmentation. This was the finest for the strongest as received alloy and coarsest for the softest overaged alloy. This effect was similar to that seen in investigations of the fragmentation of steel. Cylinders of 50 and 100 mm in diameter did not fragment but plastically deformed with maximum deformation at the cylinder bottom. Fragmentation of 33 and 42 mm diameter cylinders produced long fragments typical of the break-up of thick walled cylinders. At smaller diameters, break-up gave fragments of several shapes, finer fragments being largely associated with the smallest diameter cylinders and the highest strength alloys. Results followed those seen in large scale studies of cylinder break-up and suggest the possibility of using small scale fragmentation experiments in the investigation of the effects of composition, heat treatment and processing on natural fragmentation.
Influence of initial gap on weld expulsion in resistance spot welding of dual phase steel
Authors: Shen J. , Zhang Y. S. , Lai X. M.
Published: July 2010

The weld expulsion is prone to occur and severely affects the nugget quality when the initial gap between dual phase (DP) steel sheets exist in resistance spot welding (RSW). To investigate the effect of initial gap on weld expulsion, a finite element model was developed to analyse the weld nugget formation process with different initial gaps for DP steels. An estimation method of expulsion occurrence based on the ratio of the nugget radius Rn and the contact radius Rc between sheets was proposed to get the critical initial gap without expulsion. The simulation and experimental results showed that the weld expulsion would not happen until the gap spacing reaches the critical value. The critical initial gap of DP steel is much smaller than that of low carbon steel. For both DP steel and low carbon steel, the critical initial gap would increase with the thickening of the steel sheet.
Optimisation of process parameters in friction stir welding based on residual stress analysis: A feasibility study
Authors: Tutum C. C. , Hattel J. H.
Published: July 2010

The present paper considers the optimisation of process parameters in friction stir welding (FSW). More specifically, the choices of rotational speed and traverse welding speed have been investigated using genetic algorithms. The welding process is simulated in a transient, two-dimensional sequentially coupled thermomechanical model in ANSYS. This model is then used in an optimisation case where the two objectives are the minimisation of the peak residual stresses and the maximisation of the welding speed. The results indicate that the objectives for the considered case are conflicting, and this is presented as a Pareto optimal front. Moreover, a higher welding speed for a fixed rotational speed results, in general, in slightly higher stress levels in the tension zone, whereas a higher rotational speed for a fixed welding speed yields somewhat lower peak residual stress, however, a wider tension zone, leading to a substantially higher residual tensile force.
Cooling rate in 800 to 500°C range from dimensional analysis
Authors: Arora A. , Roy G. G. , DebRoy T.
Published: July 2010

Structure and properties of steel welds are affected by their cooling rates in the 800 to 500°C range. The available cooling rate correlations are based mostly on heat conduction equation that ignores convective heat transfer and are inaccurate or empirical in nature and valid only for a limited range of welding conditions. Numerical heat and fluid flow models can accurately calculate cooling rates, but they are not widely available. In the present paper, the authors propose and test a generalised correlation for cooling rate developed through dimensional analysis, valid for a wide range of welding processes, operating parameters and material properties.
Weld metal phase transformation of as welded 6Mo superaustenitic stainless steel after cross-weld fatigue
Authors: Wu C.-C. , Chen C.-Y. , Wang S.-H. , Yang J.-R. , Fang J.
Published: July 2010

The cyclic plastic deformation of the weldment of superaustenitic stainless steel with 6% molybdenum (UNS S31254) demonstrates that the strain rate does not affect the strength, but affects the ductility significantly. The response of tensile peak stress versus number of cycles for the weldment shows the cyclic hardening followed by the cyclic softening. A secondary hardening that appears at 1·5% strain amplitude is related to the strain induced martensite formation. The dislocations piled-up at the δ-ferrite grain boundary due to the essential rigid property of ferrite have a higher content of chromium and molybdenum. With a high fatigue strain rate, the austenite matrix of the weld metal exhibits persistent slip bands after fatigue at 0·6% strain amplitude and evolves to dislocation cell structures at 1·5% strain amplitude. The martensite band or the martensite sheath is formed at 1·5% strain, depending on the magnitude of the strain rate.
Effect of isothermal aging on room temperature impression creep of lead free Sn–9Zn and Sn–8Zn–3Bi solders
Authors: Mahmudi R. , Geranmayeh A. R. , Noori H. , Khanbareh H. , Jahangiri N.
Published: July 2010

The influence of isothermal aging on the creep behaviour of Sn–9Zn and Sn–8Zn–3Bi solder alloys was studied by impression testing. The tests were carried out under constant impression stress in the range from 90 to 230 MPa at room temperature. Aging affected the microstructure and, thus, the creep behaviour of the materials. The binary Sn–9Zn alloy, with an as cast microstructure characterised by an almost uniform distribution of fine Zn precipitates, was much more creep resistant than the aged condition containing a more sparse precipitate in a softer matrix. In the ternary Sn–8Zn–3Bi alloy, however, isothermal aging enhanced Bi precipitation with almost no change in the distribution and density of Zn particles, the result being an improved creep resistance of the aged material. Irrespective of the processing condition, Sn–8Zn–3Bi showed much lower steady state creep rates than the Sn–9Zn due to both precipitation and a solid solutioning effect of Bi in the Sn matrix. The stress exponents of the as cast and aged conditions were found to be respectively 8·5 and 7·7 for Sn–9Zn and 9·8 and 7·8 for Sn–8Zn–3Bi. These values are in agreement with those determined by room temperature conventional creep testing of the same materials reported in the literature.
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

The 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

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

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

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

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/.
Microarray Analysis of Response of Salmonella during Infection of HLA-B27- Transfected Human Macrophage-Like U937 Cells
Authors: Ge Shichao , Danino Vittoria , He Qiushui , Hinton Jay CD , Granfors Kaisa
Published: July 2010

Background

Human leukocyte antigen (HLA)-B27 is strongly associated with the development of reactive arthritis (ReA) in humans after salmonellosis. Human monocytic U937 cells transfected with HLA-B27 are less able to eliminate intracellularSalmonella entericaserovar Enteritidis than those transfected with control HLA antigens (e.g. HLA-A2). To investigate further the mechanisms by which HLA-B27-transfected cells allow increased replication of these bacteria, a DNA-based microarray was used for comparative genomic analysis ofS. Enteritidis grown in HLA-B27- or HLA-A2-transfected cells. The microarray consisted of 5080 oligonucleotides from different serovars ofSalmonellaincludingS. Enteritidis PT4-specific genes. Bacterial RNA was isolated from the infected HLA-B27- or HLA-A2-transfected cells, reverse-transcribed to cDNA, and hybridized with the oligonucleotides on the microarrays. Some microarray results were confirmed by RT-PCR.

Results

When gene expression was compared betweenSalmonellagrown in HLA-B27 cells and in HLA-A2 cells, 118 of the 4610S. Enteritidis-related genes differed in expression at 8 h after infection, but no significant difference was detectable at 2 h after infection. These differentially expressed genes are mainly involved inSalmonellavirulence, DNA replication, energy conversion and metabolism, and uptake and metabolism of nutrient substances, etc. The difference suggests HLA-B27-dependent modulation ofSalmonellagene expression, resulting in increasedSalmonellareplication in HLA-B27-positive cells. Among the up-regulated genes were those located inSalmonellapathogenicity island (SPI)-2, which play a central role in intracellular survival and replication ofSalmonella.

Conclusions

This is the first report to show the regulation ofSalmonellagene expression by HLA-B27 during infection of host cells. This regulation probably leads to increasedSalmonellasurvival and replication in HLA-B27-positive cells. SPI-2 genes seem to contribute significantly to the increased replication.
Robustness analysis of culturing perturbations on Escherichia coli colony biofilm beta-lactam and aminoglycoside antibiotic tolerance
Authors: Zuroff Trevor R , Bernstein Hans , Lloyd-Randolfi Jenna , Jimenez-Taracido Lourdes , Stewart Philip S , Carlson Ross P
Published: July 2010

Background

Biofilms are ubiquitous. For instance, the majority of medical infections are thought to involve biofilms. However even after decades of investigation, the in vivo efficacy of many antimicrobial strategies is still debated suggesting there is a need for better understanding of biofilm antimicrobial tolerances. The current study's goal is to characterize the robustness of biofilm antibiotic tolerance to medically and industrially relevant culturing perturbations. By definition, robust systems will return similar, predictable responses when perturbed while non-robust systems will return very different and potentially unpredictable responses. The predictability of an antibiotic tolerance response is essential to developing, testing, and employing antimicrobial strategies.

Results

The antibiotic tolerance of Escherichia coli colony biofilms was tested against beta-lactam and aminoglycoside class antibiotics. Control scenario tolerances were compared to tolerances under culturing perturbations including 1) different nutritional environments 2) different temperatures 3) interruption of cellular quorum sensing and 4) different biofilm culture ages. Here, antibiotic tolerance was defined in terms of culturable biofilm cells recovered after a twenty four hour antibiotic treatment.

Colony biofilm antibiotic tolerances were not robust to perturbations. Altering basic culturing parameters like nutritional environment or temperature resulted in very different, non-intuitive antibiotic tolerance responses. Some minor perturbations like increasing the glucose concentration from 0.1 to 1 g/L caused a ten million fold difference in culturable cells over a twenty four hour antibiotic treatment.

Conclusions

The current study presents a basis for robustness analysis of biofilm antibiotic tolerance. Biofilm antibiotic tolerance can vary in unpredictable manners based on modest changes in culturing conditions. Common antimicrobial testing methods, which only consider a single culturing condition, are not desirable since slight culturing variations can lead to very different outcomes. The presented data suggest it is essential to test antimicrobial strategies over a range of culturing perturbations relevant to the targeted application. In addition, the highly dynamic antibiotic tolerance responses observed here may explain why some current antimicrobial strategies occasionally fail.
Identification of viral infections in the prostate and evaluation of their association with cancer
Authors: Martinez-Fierro Margarita L , Leach Robin J , Gomez-Guerra Lauro S , Garza-Guajardo Raquel , Johnson-Pais Teresa , Beuten Joke , Morales-Rodriguez Idelma B , Hernandez-Ordoñez Mario A , Calderon-Cardenas German , Ortiz-Lopez Rocio , Rivas-Estilla Ana M , Ancer-Rodriguez Jesus , Rojas-Martinez Augusto
Published: July 2010

Background

Several viruses with known oncogenic potential infect prostate tissue, among these are the polyomaviruses BKV, JCV, and SV40; human papillomaviruses (HPVs), and human cytomegalovirus (HCMV) infections. Recently, the Xenotropic Murine Leukemia Virus-related gammaretrovirus (XMRV) was identified in prostate tissue with a high prevalence observed in prostate cancer (PC) patients homozygous for the glutamine variant of the RNASEL protein (462Q/Q). Association studies with the R462Q allele and non-XMRV viruses have not been reported. We assessed associations between prostate cancer, prostate viral infections, and the RNASEL 462Q allele in Mexican cancer patients and controls.

Methods

130 subjects (55 prostate cancer cases and 75 controls) were enrolled in the study. DNA and RNA isolated from prostate tissues were screened for the presence of viral genomes. Genotyping of the RNASEL R462Q variant was performed by Taqman method.

Results

R/R, R/Q, and Q/Q frequencies for R462Q were 0.62, 0.38, and 0.0 for PC cases and 0.69, 0.24, and 0.07 for controls, respectively. HPV sequences were detected in 11 (20.0%) cases and 4 (5.3%) controls. XMRV and HCMV infections were detected in one and six control samples, respectively. The risk of PC was significantly increased (Odds Ratio = 3.98; 95% CI: 1.17-13.56, p = 0.027) by infection of the prostatic tissue with HPV. BKV, JCV, and SV40 sequences were not detected in any of the tissue samples examined.

Conclusions

We report a positive association between PC and HPV infection. The 462Q/Q RNASEL genotype was not represented in our PC cases; thus, its interaction with prostate viral infections and cancer could not be evaluated.
Synergistic effect of stromelysin-1 (matrix metalloproteinase-3) promoter (-1171 5A->6A) polymorphism in oral submucous fibrosis and head and neck lesions
Authors: Chaudhary Ajay K , Singh Mamta , Bharti Alok C , Singh Mangal , Shukla Shirish , Singh Atul K , Mehrotra Ravi
Published: July 2010

Background

Matrix metalloproteinases (MMPs) are enzymes that degrade all the components of extra cellular matrix and collagen. Various types of MMPs are known to be expressed and activated in patients with oral submucous fibrosis (OSMF) as well as head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to asses the association of the single nucleotide polymorphism (SNP) adenosine insertion/deletion polymorphism (-1171 5A->6A) in the MMP-3 promoter region in these lesions.

Methods

MMP-3 SNP was genotyped by polymerase chain reaction-restriction fragment polymorphism (PCR-RFLP) analysis in a case control study consisting of 362 participants; 101 cases of OSMF, 135 of HNSCC and 126 controls, compared for age, sex and habits. ROC distribution was plotted to assess the contributions of genetic variation in MMP-3 genotypes with relation to age.

Results

Analysis of MMP 3 (-1171 5A->6A) polymorphism revealed the frequency of 5A allele in OSMF, HNSCC and controls to be 0.15, 0.13 and 0.07, respectively. A significant difference was found in 5A genotype frequency between OSMF (5A genotype frequency = 0.15, p = 0.01, OR = 2.26, 95% CI = 1.22-4.20) and in controls (5A genotype frequency 0.07) as well as HNSCC (5A genotype frequency 0.13, p = 0.03,95%CI = 1.06-3.51) and controls (5A genotype frequency = 0.07) In this study, 5A genotype had greater than two fold risk for developing OSMF (OR = 2.26) and nearly the same in case of HNSCC (OR = 1.94) as compared to controls. In patients with OSMF as well as HNSCC, the ROC analysis between the MMP-3 genotype and age, 6A/6A allele was found to be significant in patients both over and under 45 years of age; while the 5A/5A carrier alleles showed an association only in patients less than 45 years of age.

Conclusions

This study concluded that the expression of MMP-3 genotype associated with the 5A alleles, it may have an important role in the susceptibility of the patients to develop OSMF and HNSCC.
A cross-sectional survey to evaluate knowledge, attitudes and practices (KAP) regarding seasonal influenza vaccination among European travellers to resource-limited destinations
Authors: Pfeil Alena , Mütsch Margot , Hatz Christoph , Szucs Thomas D
Published: July 2010

Background

Influenza is one of the most common vaccine-preventable diseases in travellers. By performing two cross-sectional questionnaire surveys during winter 2009 and winter 2010 among European travellers to resource-limited destinations, we aimed to investigate knowledge, attitudes and practices (KAP) regarding seasonal influenza vaccination.

Methods

Questionnaires were distributed in the waiting room to the visitors of the University of Zurich Centre for Travel' Health (CTH) in January and February 2009 and January 2010 prior to travel health counselling (CTH09 and CTH10). Questions included demographic data, travel-related characteristics and KAP regarding influenza vaccination. Data were analysed by using SPSS® version 14.0 for Windows. Differences in proportions were compared using the Chi-square test and the significance level was set at p ≤ 0.05. Predictors for seasonal and pandemic influenza vaccination were determined by multiple logistic regression analyses.

Results

With a response rate of 96.6%, 906 individuals were enrolled and 868 (92.5%) provided complete data. Seasonal influenza vaccination coverage was 13.7% (n = 119). Only 43 (14.2%) participants were vaccinated against pandemic influenza A/H1N1, mostly having received both vaccines simultaneously, the seasonal and pandemic one. Job-related purposes (44, 37%), age > 64 yrs (25, 21%) and recommendations of the family physician (27, 22.7%) were the most often reported reasons for being vaccinated. In the multiple logistic regression analyses of the pooled data increasing age (OR = 1.03, 95% CI 1.01 - 1.04), a business trip (OR = 0.39, 95% CI 0.17 - 0.92) and seasonal influenza vaccination in the previous winter seasons (OR = 12.91, 95% CI 8.09 - 20.58) were independent predictors for seasonal influenza vaccination in 2009 or 2010.

Influenza vaccination recommended by the family doctor (327, 37.7%), travel to regions with known high risk of influenza (305, 35.1%), and influenza vaccination required for job purposes (233, 26.8%) were most frequently mentioned to consider influenza vaccination.

Conclusions

Risk perception and vaccination coverage concerning seasonal and pandemic influenza was very poor among travellers to resource-limited destinations when compared to traditional at-risk groups. Previous access to influenza vaccination substantially facilitated vaccinations in the subsequent year. Information strategies about influenza should be intensified and include health professionals, e.g. family physicians, travel medicine practitioners and business enterprises.
End-of-life care in Germany: Study design, methods and first results of the EPACS study (Establishment of Hospice and Palliative Care Services in Germany)
Authors: Escobar Pinzón Luis Carlos , Münster Eva , Fischbeck Sabine , Unrath Michael , Claus Matthias , Martini Tanja , Weber Martin
Published: July 2010

Background

In order to tackle the deficits in the provision of palliative home care, profound structural changes in the outpatient sector were introduced by law in Germany in 2007. The EPACS study was carried out (Research Accompanying the Establishment of Hospice and Palliative Care Services in Rhineland-Palatinate, Germany) to document the quality of inpatient and outpatient end-of-life care in Rhineland-Palatinate, Germany, before the implementation of these changes. With this article we focus on the study design and methods of the EPACS-Study. We further report first results regarding several aspects of outpatient end-of-life care.

Methods

The cross-sectional survey was based on a random sample of 5000 inhabitants of Rhineland-Palatinate that had died from May 25 until August 24 of the year 2008. Relatives of these randomly drawn deceased persons were interviewed by means of a written survey.

Results

The overall response proportion considering only those questionnaires that actually were delivered (n = 3833) was 36.0%. Factors influencing participation were age, sex, and marital status. 355 (25.8%) deceased persons had used professional home care in the four weeks prior to their death, but only very few persons had used a specialised palliative home care service (n = 30; 8.5%). There was a clear gap between the need for specialised outpatient care and the actual utilisation of these services.

Conclusions

Satisfaction with professional home care was relatively high, but physicians were rated less favourable than nurses. There were deficits especially with respect to physicians' communicative and supportive skills. Further analyses are necessary to provide more detailed information about quality of care in different care settings and for distinct groups. Predictors of good care, as well as obstacles to it, must be further investigated. In the long run, a follow-up survey must be conducted to compare quality of home care before and after the structural changes in Germany.