bluuebunny/crossref_metadata_2025 huggingface dataset:
The Development of an Efficient Test Automation and Sample Tracking System in a High-Throughput Veterinary Laboratory to Improve the Emergency Response to Outbreaks of Highly Infectious Disease in Great Britain
Authors: McGiven J. , Hendry L. , Brown D. , Gillard K. , Katiyar A. , Stack J. , Perrett L. , Rollins M. , Hughes S. , Ready R. , Kemp P. , Morris P. , Mawhinney I.
Published: March 2007

Serological surveillance testing for bovine brucellosis, Enzootic Bovine Leukosis, and Warble fly reaches approximately 1.7 million tests every year in the UK. An automated system was developed to improve the quality of data handling for all three surveys. The objectives were to make improvements in efficiency, sample tracking, and test reporting and to develop an epidemiological database. The developed system of bar-coded samples and test plates processed on automated equipment capable of scanning barcodes and transferring information across a computer network met the data objectives. Consolidating and automating the highly repetitive liquid-handling steps met the cost objectives. To reduce the impact of temporary bottlenecks in the system, a philosophy of ‘islands of automation’ was adopted to maximize the throughput. The creation of this system was driven largely by the need to have in place an effective emergency response capability to handle the serological needs of an outbreak of an acute and highly infectious veterinary disease such as Foot and Mouth Disease (FMD) in the UK.
Automation of Cell-Based and Noncell-Based Permeability Assays
Authors: Kellard Libby , Engelstein Marcy
Published: March 2007

Assays that predict passive absorption of orally administered drugs have become increasingly important in the early drug discovery process. A molecule must have the potential to be orally absorbed for the compound to be considered a potential lead candidate. High-throughput assays are needed to meet the increased demand for screening of permeability characteristics. Automation of both noncell-based and cell-based permeability assays is discussed in this paper. The methods use a variety of multiwell filter plates in either 24- or 96-well format. UV/Vis or LC/MS analysis is used to generate data for the automated assays and results are compared to samples prepared manually. Two noncell-based assays: Parallel Artificial Membrane Permeation Assay (Kansey, M.; Senner, F.; Gubernator, K. Physiochemical high throughput screening: parallel artificial membrane permeation assay in the description of passive absorption process. J. Med. Chem., 1998, 41, 1007–1010; Kansey, M.; Fische, H.; Kratzat, K.; Senner, F.; Wagner, B.; Parrilla, I. High-throughput artificial membrane permeability studies in early lead discovery and development. Pharmacokinet. Optim. Drug Res., 2001, XII, 448–464.) and Hexadecane Method (HDM) Permeability along with cell-based drug transport assays using Caco-2 and Madin-Darby canine Kidney (MDCK) have been successfully automated on a variety of liquid handlers.
Blotting Pattern Optimization of Contact-Based Microarray Spotting
Authors: Wake Masatetsu , Najmabadi Peyman , Goldenberg Andrew A.
Published: March 2007

Microarray analysis as a tool that provides the opportunity for simultaneous study of thousands of molecules has greatly contributed to research in many areas including functional genomics and proteomics, disease diagnosis and drug discovery. Pin-based spotting has been widely used in microarray fabrication. This paper investigates blotting procedure, that is, removing excess reagent from pins. A new optimum blotting pattern is proposed. Blotting constraints and parameters are identified and a new pattern, Beta program is proposed and compared with a patented and commonly used blotting pattern, Alpha program. A simulation program has been developed using LabVIEW to demonstrate and compare different blotting patterns. Based on the simulation results, the optimal blotting pattern in terms of speed of blotting operation and density of spots on a slide using different types of source microplates has been obtained. The optimum Beta program showed an increase of 11 times in the density of spots compared to the Alpha program. The Beta program is ready for implemention to improve the efficiency of blotting procedure.
Physical activity and cognitive health
Authors: Jedrziewski M. Kathryn , Lee Virginia M.-Y. , Trojanowski John Q.
Published: March 2007

Background

The industrialized nations are experiencing a demographic revolution caused by the continuing increase in longevity and the rapid rise in the percentage of the population older than 65 years. Interventions that promote healthy aging will continue to gain significance as efforts to delay disability and loss of function intensify.

Methods

Because physical activity has been implicated in promoting healthy aging, here we review a large body of research that examines physical activity and cognitive health. Specifically, we focus on the associations of physical activity with cognitive function and dementia, including prevention, delay, or slowing down of disease progression. Thus, we have prepared a descriptive review of the literature including various types of publications, prospective cohort, case‐control, clinical trial, and meta‐analysis articles published since 1999 in peer‐reviewed journals.

Results

On the basis of currently available data, we conclude that the relative risk of cognitive decline with aging might diminish in individuals who are physically active; however, this has not been definitively demonstrated thus far.

Conclusions

Further research is needed to determine conclusively the effects of physical activity on cognitive function and dementia and to elucidate the basis for this linkage.
Subjective memory complaints, education, and risk of Alzheimer's disease
Authors: van Oijen Marieke , de Jong Frank Jan , Hofman Albert , Koudstaal Peter J. , Breteler Monique M. B.
Published: March 2007

Background

Subjective memory complaints are common in the elderly. Although memory complaints are associated with an increased risk of Alzheimer's disease in persons with cognitive impairment as well as in persons with normal cognition, they are commonly considered of less importance than objective cognitive measures. We hypothesized that the clinical relevance of subjective memory complaints might vary with educational background.

Methods

The study was performed within the Rotterdam Study, a prospective population‐based cohort study among 7983 persons 55 years and older. Subjective memory complaints and level of education were assessed in the baseline interview (1990 to 1993). During a mean follow‐up of 9.0 years we identified 568 incident Alzheimer's disease patients. We estimated the association between subjective memory complaints and risk of dementia by means of Cox proportional hazard models.

Results

The association between subjective memory complaints and risk of Alzheimer's disease varied across levels of education. The risk of Alzheimer's disease associated with subjective memory complaints was higher in highly educated persons (age‐ and sex‐adjusted hazard ratio, 2.33; 95% confidence interval [CI], 1.00–5.49) than in persons with a low education (age‐ and sex‐adjusted hazard ratio, 1.53; 95% CI, 1.15–2.05) (P value for interaction, .02). In highly educated persons without objective cognitive impairment (Mini‐Mental State Examination score, 29 or 30) the risk of Alzheimer's disease was highest (age‐ and sex‐adjusted hazard ratio, 2.98; 95% CI, 1.76–5.02).

Conclusions

Especially in persons with a high level of education who still perform well on formal cognitive tests, subjective memory complaints might be an important first sign of imminent Alzheimer's disease.
Multilobular tumour of bone of the thoracic wall in a cat
Authors: Rossetti Enrica , Bertolini Giovanna , Zotti Alessandro
Published: March 2007

Multilobular tumour of bone is a rare neoplasm of the skull in middle-aged, medium-to-large breed dogs even if a few cases have also been described in cats and one horse. The aim of the present paper is to show both the computed-tomography features and the pathological findings of the above neoplasm affecting the thoracic wall of a cat. To the best of the authors' knowledge, such anomalous tumour localisation has never been reported and imaged in feline medicine.
Lowland rainforest response to hydrological changes during the last 1500 years in Gabon, Western Equatorial Africa
Authors: Ngomanda Alfred , Jolly Dominique , Bentaleb Ilhem , Chepstow-Lusty Alex , Makaya M'voubou , Maley Jean , Fontugne Michel , Oslisly Richard , Rabenkogo Nicaise
Published: March 2007

Pollen and δ13CTOM data obtained from two contrasting lake sequences (Lakes Kamalété and Nguène), located 200 km apart in the lowland rainforest of Gabon, provide complementary local and regional 1500-yr records of high resolution (15–30 yr) vegetation change. A combination of aquatic, semi-aquatic and terrestrial pollen showed in both records that the tropical rainforest increased during periods of high rainfall and decreased during drought intervals. The strong fluctuations of water balance at decadal scale during the “Medieval Warm Period” (∼ 1100–800 cal yr BP) coincided with a noticeable increase in shade-intolerant taxa, indicating recurring rainforest canopy disturbance. The δ13CTOM signal showed high-amplitude variations in both records, which positively correlates with the rainforest dynamics and local vegetation changes. The similar trends in both the pollen and the δ13CTOM signals between these sites demonstrate the regional broadly synchronous timing of shifting hydrological conditions. The largely positive co-variation between strong fluctuations of hydrological conditions and changes in rainforest structure and composition indicate that regional climatic change is probably the driving force for major rainforest dynamics in Gabon. Any significant anthropogenic impact on vegetation has not been clearly identified, and this issue still needs to be resolved independently by obtaining detailed archeological records across the interval 1400–800 BP, which currently seem to be extremely rare or not easily available.
800-yr-long records of annual air temperature and precipitation over southern Siberia inferred from Teletskoye Lake sediments
Authors: Kalugin Ivan , Daryin Andrei , Smolyaninova Lyubov , Andreev Andrei , Diekmann Bernhard , Khlystov Oleg
Published: March 2007

A unique 800-yr-long record of annual temperatures and precipitation over the south of western Siberia has been reconstructed from the bottom sediments of Teletskoye Lake, Altai Mountains using an X-ray fluorescence scanner (XRF) providing 0.1-mm resolution timeseries of elemental composition and X-ray density (XRD). Br content appears to be broadly correlative with mean annual temperature variations because of changes in catchment vegetation productivity. Sr/Rb ratio reflects the proportion of the unweathered terrestrial fraction. XRD appears to reflect water yield regime and sediment flux. Sedimentation is rather continuous because annual clastic supply and deposited mass are the same. The artificial neural networks method was applied to convert annual sedimentary time-series of XRD, Br content, and Sr/Rb ratio to annual records of temperature and precipitation using a transfer function. Comparison of these reconstructed Siberian records with the annual record of air temperature for the Northern Hemisphere shows similar trends in climatic variability over the past 800 yr. Estimated harmonic oscillations of temperature and precipitation values for both historical and reconstructed periods reveal subdecadal cyclicity.
Stratigraphy and environmental reconstruction at the middle Wisconsinan Gilman Canyon formation type locality, Buzzard's Roost, southwestern Nebraska, USA
Authors: Johnson William C. , Willey Karen L. , Mason Joseph A. , May David W.
Published: March 2007

The middle Wisconsinan Gilman Canyon Formation at the Buzzard's Roost type locality in southwestern Nebraska was investigated to document the stratigraphy and to reconstruct the environmental and climate record. The Gilman Canyon Formation was subdivided into three loess units and three soils, with radiocarbon ages constraining it between about 40 ka and 25 ka. Stable carbon isotope ratios, magnetic susceptibility, and carbon content were used to define and characterize soils within both the Gilman Canyon Formation and underlying Illinoian Loveland Loess. At the height of soil development within the Gilman Canyon Formation, climate was supporting C4-dominated grassland, with July temperatures equal to or exceeding those of today. Soil-forming intervals within the Loveland Loess, including the Sangamon Soil, also exhibited relative increases in C4 biomass. Climate, as recorded in the Gilman Canyon Formation, is corroborated by regional proxy data. The formation accumulated during MIS 3, and concurrent soil formation coincided with a summer insolation maximum.
Climatic controls of Holocene fire patterns in southern South America
Authors: Whitlock Cathy , Moreno Patricio I. , Bartlein Patrick
Published: March 2007

Holocene fire–climate–vegetation linkages are mostly understood at individual sites by comparing charcoal and pollen records with other paleoenvironmental proxy and model simulations. This scale of reconstruction often obscures detection of large-scale patterns in past fire activity that are related to changes in regional climate and vegetation. A network of 31 charcoal records from southern South America was examined to assess fire history along a transect from subtropic to subantarctic biomes. The charcoal data indicate that fire activity was greater than present at ca. 12,000 cal yr BP and increased further and was widespread at 9500 cal yr BP. Fire activity decreased and became more spatially variable by 6000 cal yr BP, and this trend continued to present. Atmospheric circulation anomalies during recent high-fire years show a southward shift in westerlies, and paleoclimate model simulations and data syntheses suggest that such conditions may have prevailed for millennia in the early Holocene when the pole-to-equator temperature gradients were weaker and annual temperatures were higher than present, in response to orbital-time-scale insolation changes.
Higher education study in later life: what is the point?
Authors: JAMIESON ANNE
Published: March 2007

This article reports a study of older people in higher education, their socio-economic characteristics and the motivations and reported benefits of their studies. Whilst research on older learners is growing, particularly the benefits of the learning process itself, little is known about those who engage in higher education study. The findings are reported of a survey of graduates from the two UK higher education institutions that specialise in part-time study provision. The study population is distinctive in two respects: their participation in the accreditation process and that they complete with a formal qualification. It is shown that, whilst a sizable proportion of the middle-aged and older students are well-off and well educated, there is also considerable heterogeneity and that many are making up for opportunities lost earlier in life. A substantial proportion of the ‘middle-aged’ graduates still saw qualifications as a pathway to enhanced employment opportunities, whereas the older graduates placed more weight on wider benefits. The qualification was seen as an important aspect of their chosen study. Using the responses to qualitative interviews, the article explores the role of the qualification in the lives of the older graduates, and illustrates how this particular kind of study is an element of their strategies to manage the transition from work to retirement, and to make life in retirement more meaningful.
Chemical Caspase Inhibitors Enhance Cell Culture Viabilities and Protein Titer
Authors: Arden Nilou , Ahn Shin‐hyung , Vaz Wayne , Rhodes Malcolm , Hancock Christina , Abitorabi M. Abi , Betenbaugh Michael J.
Published: March 2007

Mammalian cell cultures are integral to the production of therapeutic and diagnostic proteins. A common problem encountered in culturing these cell lines, however, is a loss in viability at later stages of the cell culture process. In this study the effects of three newly synthesized chemical caspase inhibitors were investigated for their capacity to inhibit cell death. Findings show that these protease inhibitors were successful in prolonging cellular viabilities among anchorage‐dependent CHO‐K1 and HEK‐293 cells lines. Cells treated with one inhibitor, 7312, performed as well or better when compared with the commercially known caspase inhibitor, zVAD.fmk. Suspension CHO cells producing an IgG were used to investigate the capacity of 7312 to improve protein production. Treatment of cells with 7312 increased integrated cell densities by 33% with treated cells having a higher maximum cell density and higher viability. As a result, monoclonal antibody titers increased by 20% and higher in spinner flask experiments. Increasing productivity in mammalian cell cultures has key implications for the pharmaceutical and biotechnology sectors, which are presently focused on developing methods to enhance cell performance in bioreactor environments.
Volcanic hybrid earthquakes that are brittle‐failure events
Authors: Harrington Rebecca M. , Brodsky Emily E.
Published: March 2007

Volcanoes generate a variety of pre‐eruptive low‐frequency seismic signals. Hybrid earthquakes comprise a class of these signals having high‐frequency onsets followed by low‐frequency ringing. They are used empirically to predict eruptions, but their ambiguous physical origin limits their diagnostic use. The short‐duration, near‐field hybrid seismograms associated with the 2004 Mount St. Helens eruption indicate that much of the prolonged signal is due to path rather than resonating fluids. We show using seismic source spectra that the hybrids have a corner frequency/seismic moment relationship that scales consistently with brittle‐failure. The unusually low frequency of these earthquakes can result from low rupture velocities combined with strong path effects due to their shallow sources. This new application of near‐field instrumentation provides the first seismological evidence for brittle‐failure as a major process in dome building, and suggests that hybrids should not be used as direct indicators of fluids.
Optical properties of shallow tropical cumuli derived from ARM ground‐based remote sensing
Authors: McFarlane S. A. , Grabowski W. W.
Published: March 2007

This paper presents results from ground‐based remote sensing of optical properties of shallow convective clouds over the Nauru ARM site using the technique developed by McFarlane et al. (2002). Herein, the results of a pilot study are presented with analysis of about six months of cloud data. The effective radius re shows large spatial variability, with the frequency of occurrence relatively narrow near the cloud base, and gradually widening aloft. Available column data for LWC and re allow derivation of the pdf of the optical thickness τ. The pdf shows that clouds with τ in the range 5 to 10 are most frequent, but there is a long tail with clouds up to τ = 100. These results are discussed in the context of traditional observations of cloud microstructure using an instrumented aircraft.
Effect of zonally asymmetric ozone on stratospheric temperature and planetary wave propagation
Authors: Gabriel Axel , Peters Dieter , Kirchner Ingo , Graf Hans‐F.
Published: March 2007

For northern winter hemisphere, decadal means of zonally asymmetric stratospheric ozone are derived from ECMWF Reanalysis (ERA‐40) and included in the GCM MAECHAM5 to investigate their effects on temperature and planetary wave propagation in the middle atmosphere. The stratospheric ozone of ERA‐40 shows a strong decadal increase in wave one structure with amplitudes of 10% of zonal mean ozone during the 1990s. The model calculations reveal that the related radiation perturbations induce significant temperature changes increasing with height (−4 K at 50 hPa and −8 K at 0.1 hPa) due to an increase in amplitude and a shift in phase of stratospheric wave one. Also, we found an induced shift of up‐ and eastward directed stationary wave trains from the eastern to the western hemisphere. The results illustrate the important influence of ozone‐dynamics interaction, and suggest that the decadal changes in zonally asymmetric ozone may have contributed largely to observed stratospheric temperature trends.
The corneal response to infection with Staphylococcus aureus in the absence of interleukin‐4
Authors: Cole Nerida , Hume Emma B , Khan Shamila , Garthwaite Linda , Schubert Tracey , Reeve Vivienne , Willcox Mark D P
Published: March 2007

Interleukin‐4 (IL‐4) has previously been implicated in a protective response to Staphylococcus aureus corneal infection. Consequently, the specific role of IL‐4 during S. aureus corneal infection was investigated using IL‐4 gene knockout mice. The eyes of IL‐4−/− mice and wild‐type mice were challenged topically with S. aureus and examined at 24 h post‐infection. Keratitis was examined clinically and histologically. Bacterial and polymorphonuclear leucocytes (PMN) numbers were enumerated and cytokine and chemokine levels determined by enzyme‐linked immunosorbent assay. Exogenous IL‐4 was administered to both IL‐4−/− and wild‐type mice and clinical parameters were determined. A lack of IL‐4 resulted in a significant increase in clinical scores, pathology, bacterial load and neutrophil numbers. The absence of IL‐4 also resulted in an upregulation of interferon (IFN)‐γ and a downregulation of IL‐6, IL‐10 and the chemokines KC and macrophage inflammatory protein‐2. Administration of exogenous IL‐4 to IL‐4−/− mice was protective but time‐dependent. This study highlights the protective role of IL‐4 during S. aureus infection and emphasizes the balance between IL‐4 and IFN‐γ in achieving bacterial control and maintaining the integrity of the cornea. This information may lead to the development of novel therapeutic strategies potentially improving the prognosis for infection of this unique avascular site.
Noncatastrophic and catastrophic vacuum breakdowns of carbon nanotube film under direct current conditions
Authors: Liang X. H. , Deng S. Z. , Xu N. S. , Chen Jun , Huang N. Y. , She J. C.
Published: March 2007

The degradation and damage of carbon nanotube (CNT) films caused by field emission were investigated by carefully studying the effect of emission current density of different levels on the CNT film. It is found that the behavior of the vacuum breakdown of a CNT film is very different from a metal cathode. A critical emission current density may be identified, 500A∕m2, for example, for our present samples, below which the evaporation of CNT tips and breaking at defect sites of a group of CNTs of long length are the major causes of damage to the CNT film. When the emission current density is higher than the critical value, microarcing gives rise to significant catastrophic damage to the CNT film. A theoretical model proposed early for CNT vacuum breakdown was adapted to explain the present findings, which assumes thermal runaway as an initiating mechanism for CNT vacuum breakdown, taking into account the important role of Joule heating.
Restricted open-shell Kohn-Sham theory: Simulation of the pyrrole photodissociation
Authors: Frank Irmgard , Damianos Konstantina
Published: March 2007

The authors study the photodissociation reactions of pyrrole and N-methylpyrrole using first-principles molecular dynamics. The first excited state is described with restricted open-shell Kohn-Sham theory. They find a small barrier in the excited state potential energy surface. The possibility of energy redistribution near the Franck-Condon region leads to two different reaction channels in on-the-fly simulations on a single diabatic potential energy surface. The results are discussed in comparison with previous ab initio calculations and with experiments.
Ultraviolet photolysis of adenine: Dissociation via the π1σ* state
Authors: Nix Michael G. D. , Devine Adam L. , Cronin Bríd , Ashfold Michael N. R.
Published: March 2007

High resolution total kinetic energy release (TKER) spectra of the H atom fragments resulting from photodissociation of jet-cooled adenine molecules at 17 wavelengths in the range 280>λphot>214nm are reported. TKER spectra obtained at λphot>233nm display broad, isotropic profiles that peak at low TKER (∼1800cm−1) and are largely insensitive to the choice of excitation wavelength. The bulk of these products is attributed to unintended multiphoton dissociation processes. TKER spectra recorded at λphot⩽233nm display additional fast structure, which is attributed to N9–H bond fission on the π1σ* potential energy surface (PES). Analysis of the kinetic energies and recoil anisotropies of the H atoms responsible for the fast structure suggests excitation to two π1π* excited states (the La1 and Bb1 states) at λphot∼230nm, both of which dissociate to yield H atoms together with ground state adeninyl fragments by radiationless transfer through conical intersections with the π1σ* PES. Parallels with the photochemistry exhibited by other, smaller heteroaromatics (pyrrole, imidazole, phenol, etc.) are highlighted, as are inconsistencies between the present conclusions and those reached in two other recent studies of excited state adenine molecules.
Complex dynamics in a cross-catalytic self-replication mechanism
Authors: Beutel Kathleen M. , Peacock-López Enrique
Published: March 2007

The authors consider a minimal cross-catalytic self-replicating system of only two cross-catalytic templates that mimics the R3C ligase ribozyme system of Dong-Eu and Joyce [Chem. Biol. 11, 1505 (2004)]. This system displays considerably more complex dynamics than its self-replicating counterpart. In particular, the authors discuss the Poincaré-Andronov-Hopf bifurcation, canard transitions, excitability, and hysteresis that yield birhythmicity between simple and complex oscillations.
Improved organic semiconductor lasers based on a mixed-order distributed feedback resonator design
Authors: Karnutsch C. , Pflumm C. , Heliotis G. , deMello J. C. , Bradley D. D. C. , Wang J. , Weimann T. , Haug V. , Gärtner C. , Lemmer U.
Published: March 2007

The authors present organic semiconductor distributed feedback lasers based on thin films of the conjugated polymer poly[9,9-dioctylfluorene-co-9,9-di(4-methoxy-phenyl)fluorene] and employing an improved resonator design. In order to combine the advantages of first- and second-order distributed feedback resonators, the authors utilize a mixed-order grating design: A second-order Bragg scattering region that provides efficient vertical outcoupling of the laser radiation is surrounded by first-order scattering regions that give rise to strong feedback. By optimizing the film thickness to obtain laser oscillation at the polymer maximum gain wavelength, a very low laser threshold of 45pJ∕pulse (≈36nJ∕cm2) was realized with this resonator concept.
The activation of alkyl cyanides using a rhodiumtrispyrazolylborate complex
Authors: Vetter Andrew J. , Rieth Ryan D. , Jones William D.
Published: March 2007

The photochemical reaction of Tp′Rh(L)(η
2
-PhN=L) [Tp′ = tris-(3,5-dimethyl pyrazolyl)borate, L = CNCH
2
CMe
3
] to form the coordinatively unsaturated reactive fragment, [Tp′Rh(L)], in the presence of alkylnitriles has been studied. The [Tp′Rh(L)] complex has been shown to selectively activate the primary C

H terminus of acetonitrile, propionitrile, butyronitrile, and valeronitrile. The resulting hydrides showed uncharacteristic stability in the presence of C
6
D
6
and their rates of reductive elimination were monitored by
1
H NMR spectroscopy. Competition reactions permit the establishment of the relative stabilities of the activation products.
Rab27b regulates number and secretion of platelet dense granules
Authors: Tolmachova Tanya , Åbrink Magnus , Futter Clare E. , Authi Kalwant S. , Seabra Miguel C.
Published: March 2007

The Rab27 GTPase subfamily consists of two closely related homologs, Rab27a and Rab27b. Rab27a has been shown previously to regulate organelle movement and regulated exocytosis in a wide variety of secretory cells. However, the role of the more restrictedly expressed Rab27b remains unclear. Here we describe the creation of
Rab27b
knockout (KO) strain that was subsequently crossed with the naturally occurring
Rab27a
KO line,
ashen
, to produce double KO (
Rab27a
ash/ash
Rab27b
−/−
) mice.
Rab27b
KO (and double KO) exhibit significant hemorrhagic disease in contrast to
ashen
mice.
In vitro
assays demonstrated impaired aggregation with collagen and U46619 and reduced secretion of dense granules in both
Rab27b
and double KO strains. Additionally, we detected a 50% reduction in the number of dense granules per platelet and diminished platelet serotonin content, possibly due to a dense granule packaging defect into proplatelets during megakaryocyte maturation. The presence of Rab27a partially compensated for the secretory defect but not the reduced granule number. The morphology and function of platelet α-granules were unaffected. Our data suggest that Rab27b is a key regulator of dense granule secretion in platelets and thus a candidate gene for δ-storage pool deficiency in humans.
Meiotic recombination-related DNA synthesis and its implications for cross-over and non-cross-over recombinant formation
Authors: Terasawa Masahiro , Ogawa Hideyuki , Tsukamoto Yasumasa , Shinohara Miki , Shirahige Katsuhiko , Kleckner Nancy , Ogawa Tomoko
Published: March 2007

Meiotic recombination-related DNA synthesis (MRDS) was analyzed in
Saccharomyces cerevisiae
by specifically timed incorporation of thymidine analogs into chromosomes. Lengths and positions of incorporation tracts were determined relative to a known recombination hot spot along DNA, as was the timing and localization of incorporation relative to forming and formed synaptonemal complex in spread chromosomes. Distinct patterns could be specifically associated with the majority cross-over and non-cross-over recombination processes. The results obtained provide direct evidence for key aspects of current consensus recombination models, provide information regarding temporal and spatial relationships between non-cross-over formation and the synaptonemal complex, and raise the possibility that removal of RecA homolog Rad51 plays a key role in regulating onset of MRDS. Finally, classical observations on MRDS in
Drosophila
, mouse, and lily are readily mapped onto the findings presented here, providing further evidence for a broadly conserved meiotic recombination process.
Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy
Authors: Prabhat Prashant , Gan Zhuo , Chao Jerry , Ram Sripad , Vaccaro Carlos , Gibbons Steven , Ober Raimund J. , Ward E. Sally
Published: March 2007

The intracellular events on the recycling pathway that lead from sorting endosomes to exocytosis at the plasma membrane are central to cellular function. However, despite intensive study, these processes are poorly characterized in spatial and dynamic terms. The primary reason for this is that, to date, it has not been possible to visualize rapidly moving intracellular compartments in three dimensions in cells. Here, we use a recently developed imaging setup in which multiple planes can be simultaneously imaged within the cell in conjunction with visualization of the plasma membrane plane by using total internal reflection fluorescence microscopy. This has allowed us to track and characterize intracellular events on the recycling pathway that lead to exocytosis of the MHC Class I-related receptor, FcRn. We observe both direct delivery of tubular and vesicular transport containers (TCs) from sorting endosomes to exocytic sites at the plasma membrane, and indirect pathways in which TCs that are not in proximity to sorting endosomes undergo exocytosis. TCs can also interact with different sorting endosomes before exocytosis. Our data provide insight into the intracellular events that precede exocytic fusion.
Discovery and analysis of the first endogenous lentivirus
Authors: Katzourakis Aris , Tristem Michael , Pybus Oliver G. , Gifford Robert J.
Published: March 2007

The lentiviruses are associated with a wide range of chronic diseases in mammals. These include immunodeficiencies (such as HIV/AIDS in humans), malignancies, and lymphatic and neurological disorders in primates, felids, and a variety of wild and domesticated ungulates. Evolutionary analyses of the genomic sequences of modern-day lentiviruses have suggested a relatively recent date for their emergence, but the failure to identify any endogenous, vertically transmitted examples has meant that their longer term evolutionary history and origin remain unknown. Here we report the discovery and characterization of retroviral sequences belonging to a new lentiviral subgroup from the European rabbit (
Oryctolagus cuniculus
). These viruses, the first endogenous examples described, are >7 million years old and thus provide the first evidence for an ancient origin of the lentiviruses. Despite being ancient, this subgroup contains many of the features found in present-day lentiviruses, such as the presence of
tat and
rev genes, thus also indicating an ancient origin for the complex regulation of lentivirus gene expression. Although the virus we describe is defective, reconstruction of an infectious progenitor could provide novel insights into lentivirus biology and host interactions.
Transformation of human mesenchymal stem cells increases their dependency on oxidative phosphorylation for energy production
Authors: Funes Juan M. , Quintero Marisol , Henderson Stephen , Martinez Dolores , Qureshi Uzma , Westwood Claire , Clements Mark O. , Bourboulia Dimitra , Pedley R. Barbara , Moncada Salvador , Boshoff Chris
Published: March 2007

An increased dependency on glycolysis for ATP production is considered to be a hallmark of tumor cells. Whether this increase in glycolytic activity is due mainly to inherent metabolic alterations or to the hypoxic microenvironment remains controversial. Here we have transformed human adult mesenchymal stem cells (MSC) using genetic alterations as described for differentiated cells. Our data suggest that MSC require disruption of the same pathways as have been shown for differentiated cells to confer a fully transformed phenotype. Furthermore, we found that MSC are more glycolytic than primary human fibroblasts and, in contrast to differentiated cells, do not depend on increased aerobic glycolysis for ATP production during transformation. These data indicate that aerobic glycolysis (the Warburg effect) is not an intrinsic component of the transformation of adult stem cells, and that oncogenic adaptation to bioenergetic requirements, in some circumstances, may also rely on increases in oxidative phosphorylation. We did find, however, a reversible increase in the transcription of glycolytic enzymes in tumors generated by transformed MSC, indicating this is a secondary phenomenon resulting from adaptation of the tumor to its microenvironment.
Cranial muscle defects of Pitx2 mutants result from specification defects in the first branchial arch
Authors: Shih Hung Ping , Gross Michael K. , Kioussi Chrissa
Published: March 2007

Pitx2 expression is observed during all states of the myogenic progression in embryonic muscle anlagen and persists in adult muscle. Pitx2 mutant mice form all but a few muscle anlagen. Loss or degeneration in muscle anlagen could generally be attributed to the loss of a muscle attachment site induced by some other aspect of the Pitx2 phenotype. Muscles derived from the first branchial arch were absent, whereas muscles derived from the second branchial arch were merely distorted in Pitx2 mutants at midgestation. Pitx2 was expressed well before, and was required for, initiation of the myogenic progression in the first, but not second, branchial arch mesoderm. Pitx2 was also required for expression of premyoblast specification markers Tbx1, Tcf21, and Msc in the first, but not second, branchial arch. First, but not second, arch mesoderm of Pitx2 mutants failed to enlarge after embryonic day 9.5, well before the onset of the myogenic progression. Thus, Pitx2 contributes to specification of first, but not second, arch mesoderm. The jaw of Pitx2 mutants was vestigial by midgestation, but significant size reductions were observed as early as embryonic day 10.5. The diminutive first branchial arch of mutants could not be explained by loss of mesoderm alone, suggesting that Pitx2 contributes to the earliest specification of jaw itself.
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets
Authors: Davey Robert , Savva George , Dicks Jo , Roberts Ian N.
Published: March 2007

MPP is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposon-based insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software.

Availability: MPP source code, executables and online help are available at http://cbr.jic.ac.uk/dicks/software/

Contact:  robert.davey@bbsrc.ac.uk
Improved centroids estimation for the nearest shrunken centroid classifier
Authors: Wang Sijian , Zhu Ji
Published: March 2007

Motivation: The nearest shrunken centroid (NSC) method has been successfully applied in many DNA-microarray classification problems. The NSC uses ‘shrunken’ centroids as prototypes for each class and identifies subsets of genes that best characterize each class. Classification is then made to the nearest (shrunken) centroid. The NSC is very easy to implement and very easy to interpret, however, it has drawbacks.

Results: We show that the NSC method can be interpreted in the framework of LASSO regression. Based on that, we consider two new methods, adaptive L∞-norm penalized NSC (ALP-NSC) and adaptive hierarchically penalized NSC (AHP-NSC), with two different penalty functions for microarray classification, which improve over the NSC. Unlike the L1-norm penalty used in LASSO, the penalty terms that we consider make use of the fact that parameters belonging to one gene should be treated as a natural group. Numerical results indicate that the two new methods tend to remove irrelevant genes more effectively and provide better classification results than the L1-norm approach.

Availability: R code for the ALP-NSC and the AHP-NSC algorithms are available from authors upon request.

Contact:  jizhu@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Semantic Web Service provision: a realistic framework for Bioinformatics programmers
Authors: Gordon Paul M.K. , Trinh Quang , Sensen Christoph W.
Published: March 2007

Summary: Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework (‘MobyServlet’) that very simply allows an existing Java application to conform to the MOBY-S semantic Web Services protocol. Using an existing Java program for codon-pair bias determination as an example, we enumerate the steps required for MOBY-S compliance. With minimal programming effort, such a deployment has the advantages of: (1) wider exposure to the user community by automatic inclusion in all MOBY-S client programs and (2) automatic interoperability with other MOBY-S services for input and output. Complex on-line analysis will become easier for biologists as more developers adopt MOBY-S.

Availability: The framework and documentation are freely available from the Java developer's section of http://www.biomoby.org/.

Contact:  gordonp@ucalgary.ca
POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties
Authors: Tung Chun-Wei , Ho Shinn-Ying
Published: March 2007

Motivation: Both modeling of antigen-processing pathway including major histocompatibility complex (MHC) binding and immunogenicity prediction of those MHC-binding peptides are essential to develop a computer-aided system of peptide-based vaccine design that is one goal of immunoinformatics. Numerous studies have dealt with modeling the immunogenic pathway but not the intractable problem of immunogenicity prediction due to complex effects of many intrinsic and extrinsic factors. Moderate affinity of the MHC–peptide complex is essential to induce immune responses, but the relationship between the affinity and peptide immunogenicity is too weak to use for predicting immunogenicity. This study focuses on mining informative physicochemical properties from known experimental immunogenicity data to understand immune responses and predict immunogenicity of MHC-binding peptides accurately.

Results: This study proposes a computational method to mine a feature set of informative physicochemical properties from MHC class I binding peptides to design a support vector machine (SVM) based system (named POPI) for the prediction of peptide immunogenicity. High performance of POPI arises mainly from an inheritable bi-objective genetic algorithm, which aims to automatically determine the best number m out of 531 physicochemical properties, identify these m properties and tune SVM parameters simultaneously. The dataset consisting of 428 human MHC class I binding peptides belonging to four classes of immunogenicity was established from MHCPEP, a database of MHC-binding peptides (Brusic et al., 1998). POPI, utilizing the m = 23 selected properties, performs well with the accuracy of 64.72% using leave-one-out cross-validation, compared with two sequence alignment-based prediction methods ALIGN (54.91%) and PSI-BLAST (53.23%). POPI is the first computational system for prediction of peptide immunogenicity based on physicochemical properties.

Availability: A web server for prediction of peptide immunogenicity (POPI) and the used dataset of MHC class I binding peptides (PEPMHCI) are available at http://iclab.life.nctu.edu.tw/POPI

Contact:  syho@mail.nctu.edu.tw
GoSh: a web-based database for goat and sheep EST sequences
Authors: Caprera Andrea , Lazzari Barbara , Stella Alessandra , Merelli Ivan , Caetano Alexandre R. , Mariani Paola
Published: March 2007

Summary: The GoSh database is a collection of 58 990 Capra hircus and Ovis aries expressed sequence tags. A perl pipeline was prepared to process sequences, and data were collected in a MySQL database. A PHP-based web interface allows browsing and querying the database. Putative single nucleotide polymorphism (SNP) detection, as well as search to repeats were performed, and links to external related resources were provided. Sequences were annotated against three different databases and an algorithm was implemented to create statistics of the distribution of retrieved homologous ontologies in the Gene Ontology categories. The GoSh database is a repository of data and links related to goat and sheep expressed genes.

Availability: The GoSh database is available at http://www.itb.cnr.it/gosh/

Contact:  andrea.caprera@tecnoparco.org
Ngila: global pairwise alignments with logarithmic and affine gap costs
Authors: Cartwright Reed A.
Published: March 2007

Summary: Ngila is an application that will find the best alignment of a pair of sequences using log-affine gap costs, which are the most biologically realistic gap costs.

Availability: Portable source code for Ngila can be downloaded from its development website, http://scit.us/projects/ngila/. It compiles on most operating systems.

Contact: racartwr@ncsu.edu or reed@scit.us

Supplementary information: Appendices
Unsupervised segmentation of continuous genomic data
Authors: Day Nathan , Hemmaplardh Andrew , Thurman Robert E. , Stamatoyannopoulos John A. , Noble William S.
Published: March 2007

Summary: The advent of high-density, high-volume genomic data has created the need for tools to summarize large datasets at multiple scales. HMMSeg is a command-line utility for the scale-specific segmentation of continuous genomic data using hidden Markov models (HMMs). Scale specificity is achieved by an optional wavelet-based smoothing operation. HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data.

Availability: http://noble.gs.washington.edu/proj/hmmseg

Contact: rthurman@u.washington.edu
IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform
Authors: Schultze Joachim L. , Eggle Daniela
Published: March 2007

Summary: IlluminaGUI is a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform. All key components of a microarray experiment, including quality control, normalization, inference and classification methods are provided in a ‘point and click’ approach. IlluminaGUI is implemented as a R package based on the R-Tcl/Tk interface and is available for platforms on which R runs including Windows, Mac and Unix-type machines.

Availability:  http://IlluminaGUI.dnsalias.org

Contact: joachim.schultze@uk-koeln.de
Quantitating tissue specificity of human genes to facilitate biomarker discovery
Authors: Vasmatzis George , Klee Eric W. , Kube Dagmar M. , Therneau Terry M. , Kosari Farhad
Published: March 2007

We describe a method to identify candidate cancer biomarkers by analyzing numeric approximations of tissue specificity of human genes. These approximations were calculated by analyzing predicted tissue expression distributions of genes derived from mapping expressed sequence tags (ESTs) to the human genome sequence using a binary indexing algorithm. Tissue-specificity values facilitated high-throughput analysis of the human genes and enabled the identification of genes highly specific to different tissues. Tissue expression distributions for several genes were compared to estimates obtained from other public gene expression datasets and experimentally validated using quantitative RT-PCR on RNA isolated from several human tissues. Our results demonstrate that most human genes (∼98%) are expressed in many tissues (low specificity), and only a small number of genes possess very specific tissue expression profiles. These genes comprise a rich dataset from which novel therapeutic targets and novel diagnostic serum biomarkers may be selected.

Contact: vasm@mayo.edu

Supplementary information: Supplementary data are available at Bioinformatics online.