bluuebunny/crossref_metadata_2025 huggingface dataset:
Life-Long Physical Activity Involvement and the Risk of Ischemic Stroke in Southern China
Authors: Lee Andy H. , Liang Wenbin
Published: January 2011

A case-control study was conducted in southern China to investigate the relationship between life-long physical activity involvement and the risk of ischemic stroke. Information on life-long physical activity exposure and other lifestyle characteristics was obtained from 374 incident stroke patients and 464 hospital-based controls using a validated and reliable questionnaire. Logistic regression analyses were performed to assess the association between life-long physical activity involvement and the ischemic stroke risk. The control subjects reported more involvement in physical activity over the life course than the stroke patients (). The risk of ischemic stroke was inversely associated with life-long physical activity exposure, with adjusted odds ratio 0.39 (95% confidence interval 0.25 to 0.59) for participants who had always been involved relative to those who have never been much involved. The dose-response relationship was also significant (). Therefore, being active life long should be encouraged to prevent this major chronic disease.
Origins of the Domestic Dog and the Rich Potential for Gene Mapping
Authors: Shearman Jeremy R. , Wilton Alan N.
Published: January 2011

The unique breeding structure of the domestic dog makes canine genetics a useful tool to further the understanding of inherited diseases and gene function. Answers to the questions of when and where the dog was domesticated from the wolf are uncertain, but how the modern diversity of dog breeds was developed is documented. Breed development has resulted in many genetically isolated populations which are segregating for different alleles for disease and morphological and behavioral traits. Many genetic tools are available for dog research allowing investigation into the genetic basis of these phenotypes. Research into causes of diseases in dogs is relevant to humans and other species; comparative genomics is being used to transfer genetic information to them, including some studies on morphological and behavioral phenotypes. Because of the unique breed structure and well-maintained pedigrees, dogs represent a model organism containing a wealth of genetic information.
Protein Kinase C‐Regulated Aβ Production and Clearance
Authors: Kim Taehyun , Hinton David J. , Choi Doo-Sup
Published: January 2011

Alzheimer’s disease (AD) is the most common form of dementia among the elderly population. AD, which is characterized as a disease of cognitive deficits, is mainly associated with an increase of amyloid β‐peptide (Aβ) in the brain. A growing body of recent studies suggests that protein kinase C (PKC) promotes the production of the secretory form of amyloid precursor protein (sAPPα) via the activation of α‐secretase activity, which reduces the accumulation of pathogenic Aβ levels in the brain. Moreover, activation of PKCα and mitogen‐activated protein kinase (MAPK) is known to increase sAPPα. A novel type of PKC, PKCε, activates the Aβ degrading activity of endothelin converting enzyme type 1 (ECE‐1), which might be mediated via the MAPK pathway as well. Furthermore, dysregulation of PKC‐MAPK signaling is known to increase Aβ levels in the brain, which results in AD phenotypes. Here, we discuss roles of PKC in Aβ production and clearance and its implication in AD.
Californian forest fire plumes over Southwestern British Columbia: lidar, sunphotometry, and mountaintop chemistry observations
Authors: McKendry I. , Strawbridge K. , Karumudi M. L. , O'Neill N. , Macdonald A. M. , Leaitch R. , Jaffe D. , Cottle P. , Sharma S. , Sheridan P. , Ogren J.
Published: January 2011

Abstract. Forest fires in Northern California and Oregon were responsible for two significant regional scale aerosol transport events observed in southern British Columbia during summer 2008. A combination of ground based (CORALNet) and satellite (CALIPSO) lidar, sunphotometry and high altitude chemistry observations permitted unprecedented characterization of forest fire plume height and mixing as well as description of optical properties and physicochemistry of the aerosol. In southwestern BC, lidar observations show the smoke to be mixed through a layer extending to 5–6 km a.g.l. where the aerosol was confined by an elevated inversion in both cases. Depolarization ratios for a trans-Pacific dust event (providing a basis for comparison) and the two smoke events were consistent with observations of dust and smoke events elsewhere and permit discrimination of aerosol events in the region. Based on sunphotometry, the Aerosol Optical Thicknesses (AOT) reached maxima of ~0.7 and ~0.4 for the two events respectively. Dubovik-retrieval values of reff, f during both the June/July and August events varied between about 0.13 and 0.15 μm and confirm the dominance of accumulation mode size particles in the forest fire plumes. Both Whistler Peak and Mount Bachelor Observatory data show that smoke events are accompanied by elevated CO and O3 concentrations as well as elevated K+/SO4 ratios. In addition to documenting the meteorology and physic-chemical characteristics of two regional scale biomass burning plumes, this study demonstrates the positive analytical synergies arising from the suite of measurements now in place in the Pacific Northwest, and complemented by satellite borne instruments.
Cloud macroscopic organization: order emerging from randomness
Authors: Yuan T.
Published: January 2011

Abstract. Clouds play a central role in many aspects of the climate system and their forms and shapes are remarkably diverse. Appropriate representation of clouds in climate models is a major challenge because cloud processes span at least eight orders of magnitude in spatial scales. Here we show that there exists order in cloud size distribution of low-level clouds and it follows a power-law distribution with exponent γ close to 2. γ is insensitive to yearly variations in environmental conditions, but has regional variations and land-ocean contrasts. More importantly, we demonstrate this self-organizing behavior of clouds emerges naturally from a complex network model with simple, physical organizing principles: random clumping and merging. We also show clear-cloudy sky symmetry in terms of macroscopic organization because of similar fundamental underlying organizing principles. The order in the apparently complex cloud-clear field thus has its root in random simple interactions. Studying cloud organization with complex network models is an attractive new approach that has wide applications in climate science. This approach is fully complementary to deterministic models and the two approaches provide a powerful framework to meet the challenge of representing clouds in our climate models when working in tandem.
Role of sea surface temperature responses in simulation of the climatic effect of mineral dust aerosol
Authors: Yue X. , Liao H. , Wang H. J. , Li S. L. , Tang J. P.
Published: January 2011

Abstract. Mineral dust aerosol can be transported over the nearby oceans and influence the energy balance at the sea surface. The role of dust-induced sea surface temperature (SST) responses in simulations of the climatic effect of dust is examined by using a general circulation model with online simulation of mineral dust and a coupled mixed-layer ocean model. Both the longwave and shortwave radiative effects of mineral dust aerosol are considered in climate simulations. The SST responses are found to be very influential on simulated dust-induced climate change, especially when climate simulations consider the two-way dust-climate coupling to account for the feedbacks. With prescribed SSTs and dust concentrations, we obtain an increase of 0.02 K in the global and annual mean surface air temperature (SAT) in response to dust radiative effects. In contrast, when SSTs are allowed to respond to radiative forcing of dust in the presence of the dust cycle-climate interactions, we obtain a global and annual mean cooling of 0.09 K in SAT by dust. The extra cooling simulated with the SST responses can be attributed to the following two factors: (1) The negative net radiative forcing of dust at the surface reduces SST, which decreases latent heat fluxes and upward transport of water vapor, resulting in less warming in the atmosphere; (2) The positive feedback between SST responses and dust cycle. The dust-induced reductions in SST lead to reductions in precipitation (or wet deposition of dust) and hence increase the global burden of small dust particles. These small particles have strong scattering effects, which enhance the dust cooling at the surface and further reduce SSTs.
Application of SCIAMACHY and MOPITT CO total column measurements to evaluate model results over biomass burning regions and Eastern China
Authors: Liu C. , Beirle S. , Butler T. , Liu J. , Hoor P. , Jöckel P. , Penning de Vries M. , Pozzer A. , Frankenberg C. , Lawrence M. G. , Lelieveld J. , Platt U. , Wagner T.
Published: January 2011

Abstract. We developed a new CO vertical column density product from near IR observations of the SCIAMACHY instrument onboard ENVISAT. For the correction of a temporally and spatially variable offset of the CO vertical column densities we apply a normalisation procedure based on coincident MOPITT (version 4) observations over the oceans. The resulting normalised SCIAMACHY CO data are well suited for the investigation of the CO distribution over continents, where important emission sources are located. We use only SCIAMACHY observations for effective cloud fractions below 20%. Since the remaining effects of clouds can still be large (up to 100%), we applied a cloud correction scheme which explicitly considers the cloud fraction, cloud top height and surface albedo of individual observations. We compared our new SCIAMACHY CO data set, and also observations from the MOPITT instrument, to the results from three global atmospheric chemistry models (MATCH, EMAC at low and high resolution, and GEOS-Chem); the focus of this comparison is on regions with strong CO emissions (from biomass burning or anthropogenic sources). The comparison indicates that over most of these regions the seasonal cycle is generally captured well but the simulated CO vertical column densities are systematically smaller than those from the satellite observations, in particular with respect to SCIAMACHY observations. Because of the high sensitivity of the SCIAMACHY observations to the lowest part of the atmosphere, this indicates that especially close to the surface the model simulations systematically underestimate the true atmospheric CO concentrations, probably caused by an underestimation of CO emissions by current emission inventories. For some biomass burning regions, however, such as Central Africa in July–August, model results are also found to be higher than the satellite observations.
Sensitivity of Holocene atmospheric CO2and the modern carbon budget to early human land use: analyses with a process-based model
Authors: Stocker B. D. , Strassmann K. , Joos F.
Published: January 2011

Abstract. A Dynamic Global Vegetation model coupled to a simplified Earth system model is used to simulate the impact of anthropogenic land cover changes (ALCC) on Holocene atmospheric CO2 and the contemporary carbon cycle. The model results suggest that early agricultural activities cannot explain the mid to late Holocene CO2 rise of 20 ppm measured on ice cores and that proposed upward revisions of Holocene ALCC imply a smaller contemporary terrestrial carbon sink. A set of illustrative scenarios is applied to test the robustness of these conclusions and to address the large discrepancies between published ALCC reconstructions. Simulated changes in atmospheric CO2 due to ALCC are less than 1 ppm before 1000 AD and 30 ppm at 2004 AD when the HYDE 3.1 ALCC reconstruction is prescribed for the past 12 000 years. Cumulative emissions of 69 GtC at 1850 and 233 GtC at 2004 AD are comparable to earlier estimates. CO2 changes due to ALCC exceed the simulated natural interannual variability only after 1000 AD. To consider evidence that land area used per person was higher before than during early industrialisation, agricultural areas from HYDE 3.1 were increased by a factor of two prior to 1700 AD (scenario H2). For the H2 scenario, the contemporary terrestrial carbon sink required to close the atmospheric CO2 budget is reduced by 0.5 GtC yr−1. Simulated CO2 remains small even in scenarios where average land use per person is increased beyond the range of published estimates. Even extreme assumptions for preindustrial land conversion and high per-capita land use do not result in simulated CO2 emissions that are sufficient to explain the magnitude and the timing of the late Holocene CO2 increase.
Short term changes in methanol emission and pectin methylesterase activity are not directly affected by light in Lycopersicon esculentum
Authors: Oikawa P. Y. , Li L. , Timko M. P. , Mak J. E. , Lerdau M. T.
Published: January 2011

Abstract. Plants are an important source of atmospheric methanol (MeOH), the second most abundant organic gas after methane. Factors regulating phytogenic MeOH production are not well constrained in current MeOH emission models. Previous studies have indicated that light may have a direct influence on MeOH production. As light is known to regulate cell wall expansion, it was predicted that light would stimulate MeOH production through the pectin methylesterase (PME) pathway. MeOH emissions normalized for stomatal conductance (gs) did not, however, increase with light over short time scales (20–30 min). After experimentally controlling for gs and temperature, no light activation of PME activity or MeOH emission was observed. The results clearly demonstrate that light does not directly influence short-term changes in MeOH production and emission. Our data suggest that substrate limitation may be important in regulating MeOH production over short time scales. Future investigation of the long-term impacts of light on MeOH production may increase understanding of MeOH emission dynamics at the seasonal time scale.
Drought-associated changes in climate and their relevance for ecosystem experiments and models
Authors: De Boeck H. J. , Verbeeck H.
Published: January 2011

Abstract. Drought periods can have important impacts on plant productivity and ecosystem functioning, but climatic conditions other than the lack of precipitation during droughts have never been quantified and have therefore not been considered explicitly in both experimental and modeling studies. Here, we identify which climatic characteristics deviate from normal during droughts and how these deviations could affect plant responses. Analysis of 609 years of daily data from nine Western European meteorological datasets reveals that droughts in the studied region are consistently associated with more sunshine (+45%), increased mean (+1.6 °C) and maximum (+2.8 °C) air temperatures and vapour pressure deficits that were 51% higher than under normal conditions. These deviations from normal increase significantly as droughts progress. Using the process-model ORCHIDEE, we simulated droughts consistent with the results of the dataset analysis and compared water and carbon exchange of three different vegetation types during such natural droughts and droughts in which only the precipitation was affected. The comparison revealed contrasting responses: carbon loss was higher under natural drought in grasslands, while increased carbon uptake was found especially in decidious forests. This difference was attributed to better access to water reserves in forest ecosystems which prevented drought stress. This demonstrates that the warmer and sunnier conditions naturally associated with droughts can either improve growth or aggravate drought-related stress, depending on water reserves. As the impacts of including or excluding climatic parameters that correlate with drought are substantial, we propose that both experimental and modeling efforts should take into account other environmental factors than merely precipitation.
Estimating strategies for multiparameter Multivariate Extreme Value copulas
Authors: Salvadori G. , De Michele C.
Published: January 2011

Abstract. Multivariate Extreme Value models are a fundamental tool in order to assess potentially dangerous events. Exploiting recent theoretical developments in the theory of Copulas, new multiparameter models can be easily constructed. In this paper we suggest several strategies in order to estimate the parameters of the selected copula, according to different criteria: these may use a single station approach, or a cluster strategy, or exploit all the pair-wise relationships between the available gauge stations. An application to flood data is also illustrated and discussed.
Effective roughness modelling as a tool for soil moisture retrieval from C- and L-band SAR
Authors: Lievens H. , Verhoest N. E. C. , De Keyser E. , Vernieuwe H. , Matgen P. , Álvarez-Mozos J. , De Baets B.
Published: January 2011

Abstract. Soil moisture retrieval from Synthetic Aperture Radar (SAR) using state-of-the-art back\\-scatter models is not fully operational at present, mainly due to difficulties involved in the parameterisation of soil surface roughness. Recently, increasing interest has been drawn to the use of calibrated or effective roughness parameters, as they circumvent issues known to the parameterisation of field-measured roughness. This paper analyses effective roughness parameters derived from C- and L-band SAR observations over a large number of agricultural seedbed sites in Europe. It shows that param\\-eters may largely differ between SAR acquisitions, as they are related to the observed backscatter coefficients and variations in the local incidence angle. Therefore, a statistical model is developed that allows for estimating effective roughness parameters from microwave backscatter observations. Subsequently, these parameters can be propagated through the Integral Equation Model (IEM) for soil moisture retrieval. It is shown that fairly accurate soil moisture results are obtained both at C- and L-band, with an RMSE ranging between 4 vol% and 6.5 vol%.
Analyses of relationship between Loess Plateau erosion and sunspots based on wavelet transform
Authors: Gao P. , Mu X.-M. , Li R. , Wang F.
Published: January 2011

Abstract. Loess Plateau is one of the worst soil erosion regions in the world, which may resulted from various factors such as precipitation, land cover and land use, soil, vegetation, human intervention, as well as solar activities. The purpose of this study is to find the relationship between soil erosion and sunspot activity on the Loess Plateau, through analyses of the sunspot relative number and the long-term sediment discharge series in Longmen station in the Yellow River based on the Morlet wavelet method. In this paper, annual sediment discharge series from 1919–2008 in Longmen station and the sunspot relative number were decomposed with Complex Morlet wavelet. The results of real part, modulus and the second power of modulus showed an obvious periodic variability in sediment discharge, with 25–40 years, about 10 years, and less than 10 years scales. There are six centers of energy. From the wavelet variance, 6, 12, and 35 years periods were detected within 50-year scale, and the 35-year period is the most significant one. Similar analyses were conducted for the sunspot relative number during the same period of 1919–2008. The sunspot series showed an 11-year periodic variation, and two energy center. Then, the correlation analyses for 11-year scale were computed. From a long-term period (1919–2008) view, there is no significant correlation between the sediment discharge and the sunspot relative number; however, it is evident that the correlations exist in short-term periods. The results also indicate that the relationships between solar activities and the erosion of the Loess Plateau are complicated.
Amoeba
Authors: Anderson O Roger , Rogerson Andrew
Published: January 2011

Amoebae are single‐celled eukaryotic microorganisms that move by cytoplasmic streaming and possess characteristic surface projections of the cell known as pseudopodia. They are categorised among the heterotrophic protozoa and are grouped with photosynthetic protozoa and algae in an eclectic group, the protists. Modern molecular genetic research has begun to clarify the evolutionary relationships among the amoeboid protists leading to a more natural classification system. The focus here is on the naked amoebae (formerly known as gymnamoebae) that are included in the taxonomic group Amoebozoa. They are important as members of microbial communities where they are significant links in the foodwebs, promote purification of water in the natural environment and waste water treatment plants and contribute to the fertility of aquatic and terrestrial environments. Only a few are known to be human pathogens or carriers of pathogens, including the pathogenic bacterium causing Legionnaires disease.

Key Concepts:

Amoebae, though considered to be primitive unicellular organisms, have a highly complex cellular organisation and exhibit diverse behaviour.

Amoeboid protists, a group of pseudopod‐bearing unicellular organisms, are an eclectic group of phylogenetically diverse organisms that have adapted a similar amoeboid morphology through convergent evolution.

Naked amoebae lack a substantial surface coat or layer that distinguishes them from the testate amoebae, enclosed by an external test or tectum with one or more openings where the pseudopodia emerge.

Amoebae prey on a wide variety of other unicellular organisms, including bacteria and protists, though the smaller amoebae are almost exclusively bacterial predators.

Free‐living amoebae are significant members of aquatic and terrestrial communities where they serve as links at the base of the food web, promote remineralisation of nutrients through predation on bacteria and help to clarify waste water supply by removing bacteria and promoting the degradation of suspended waste particles.
Fruit Structure and Diversity
Authors: Ferrandiz Cristina
Published: January 2011

Fruits are produced by flowers after pollination and fertilisation and derive mainly from the pistil of the flower. Fruits have a major economical importance, constituting the most valuable part of the crop production of the world. Fruits provide seeds with protection and mechanisms for dispersal and, thus, represent a key evolutionary innovation of the Angiosperms, enabling the offspring to travel and colonise new areas. Fruits may be dry or fleshy, dehiscent or indehiscent, and are adapted in a great variety of ways for the dispersal of seeds. Our knowledge on the genetics of fruit development has improved substantially in the past few years, mainly through studies of the dehiscence process in

Arabidopsis thaliana

and of the ripening process in tomato.

Key Concepts:

Fruits serve two main purposes: protect the developing seeds and ensure seed dispersal.

Fruits represent a major evolutionary innovation, key for Angiosperm success.

Fruit morphological and functional diversity reflect adaptations to different agents that are used for dispersal.
Laveran, Charles Louis Alphonse
Authors: Osborne Michael A
Published: January 2011

Charles Louis Alphonse Laveran was a French army physician. His 1880 discovery of the malaria parasite and other contributions to medical parasitology merited the 1907 Nobel Prize in Physiology or Medicine. He also worked on sleeping sickness, Leishmaniasis and other parasitic human and animal diseases.

Key Concepts:

The parasite of malaria was discovered in 1880.

Malaria was an important disease in Europe and the Mediterranean Basin.
Interference Reflection Microscopy
Authors: Weber Igor
Published: January 2011

Interference reflection microscopy (IRM) utilises interference of light reflected from closely apposed surfaces to provide an image containing information about the separation of those surfaces. In cell biology, IRM is used to image structures at the base of adherent cells and to measure cell–substratum distances, as well as to investigate mechanisms of cell–substratum adhesion. IRM is also used to study topology and dynamics of biomimetic systems such as vesicles, supported membranes and other multilayered structures. Basic IRM optical configuration is relatively easy to set up, and image analysis can provide information about interfacial distances with nanometer precision and millisecond time resolution. IRM can be readily combined with other microscopic techniques, and with force transducing devices such as optical tweezers, micropipettes and microcantilevers. New advancements in the field include dual‐wavelength IRM and fluctuation contrast IRM.

Key Concepts:

Interference reflection microscopy measures the distance between close surfaces.

Cell adhesion areas such as focal contacts can be mapped by IRM.

IRM provides vertical resolution in the nanometer range.

Dual‐wavelength IRM removes ambiguity in measurements of vertical distances up to 800 nm.

IRM can determine amplitudes of local membrane fluctuations.
History of Ecology
Authors: Jax Kurt
Published: January 2011

Although there have been ‘ecological’ ideas and investigations over many centuries, the history of ecology as a self‐conscious science started only in the last decades of the nineteenth century. Originating from different roots, especially natural history and physiology, it soon developed into different specialities, such as animal and plant ecology, which at first developed at least partly independently from each other. Nevertheless, already from the first half of the twentieth century on, there have been attempts to arrive at unifying theories, an important culmination of which can be seen in the rise of ecosystems ecology. In the wake of an emerging awareness for environmental problems in the 1960s, ecology also became perceived by a broader public. This led to increasing demands on the science and also changed the work and subjects of ecologists to include much more application‐driven and interdisciplinary research.

Key Concepts:

Ecology has always been a hybrid science, building both on natural history and on physiology.

The different traditions of ecology have developed partly independently during the first decades of ecology as a ‘self‐conscious ecology’.

Only since the 1960s and 1970s ecology became a field also known and valued outside smaller academic circles.

Ecology is basically a biological science, must not be confused with ‘environmental thinking’.
GAS

5
Gene
Authors: Hirose Tetsuro
Published: January 2011

GAS5

(growth arrest‐specific 5) is a nonprotein‐coding small nucleolar
ribonucleic acid
(snoRNA) host gene. Ten box C/D snoRNAs are encoded within the 11 introns of the human

GAS5

gene, whereas the spliced exons have little protein‐coding potential.

GAS5

has been classified as a member of the 5′ oligopyrimidine tract (5′ TOP) gene family. It is ubiquitously expressed, but the spliced

GAS5

transcript is rapidly degraded in proliferating cells. Growth‐dependent translation mediated by the 5′ TOP sequence present at its 5′‐terminus determines the level of the

GAS5

spliced transcript by a mechanism of translation‐linked RNA degradation. The spliced

GAS5

transcript plays a critical role in arresting cell growth and inducing apoptosis. The decreased expression of

GAS5

in breast cancer suggests that

GAS5

acts as a tumour suppressor. The spliced

GAS5

transcript suppresses steroid‐responsive transcription by direct association of the several steroid receptors and acts as a molecular decoy.

Key Concepts:

GAS5
is a nonprotein‐coding small nucleolar RNA host gene.

A translation‐linked mRNA decay pathway controls growth arrest‐specific accumulation of
GAS5
by way of its 5′‐terminal oligopyrimidine tract (5′ TOP).

GAS5
functions to arrest cell growth and to induce apoptosis.

GAS5
binds to steroid hormone receptors through its 3′‐terminal stem‐loop structure to suppress steroid‐responsive transcription.
Schizophrenia and 22q11.2 Deletion Syndrome
Authors: Sundram Frederick , Murphy Kieran C
Published: January 2011

22q11.2 deletion syndrome (22q11.2DS), also known as velocardiofacial syndrome, is the most frequent known interstitial deletion found in humans. It is associated with high rates of psychiatric disorder and, in particular, schizophrenia (approximately 30%) and schizophrenia‐spectrum disorders. The 22q11.2 region is rich in genes coding for brain development, and consequently, deletion of 22q11.2 provides a useful neurodevelopmental model for understanding the evolution of psychotic disorders in both 22q11.2DS and the nondeleted general population. 22q11.2DS is also associated with significant structural and functional neuroanatomical abnormalities, which underlie the high rates of psychosis seen in affected individuals. Further research is currently underway to determine the cognitive, genetic and neuroanatomical correlates of psychosis seen in the disorder.

Key Concepts:

22q11.2DS provides for a genetic and neurodevelopmental model for understanding psychotic disorder seen not only with the syndrome but can also be extrapolated to the general nondeleted population.

Although 22q11.2DS is associated with marked phenotypic variability, psychiatric disorder and, in particular, schizophrenia‐spectrum disorders occur in approximately 30% of deleted individuals.

Schizophrenia‐spectrum disorders arise as prodromal or subthreshold psychotic symptoms during childhood and adolescence followed by subsequent expression during adulthood where it is largely indistinguishable from the psychosis seen in the nondeleted population.

Apart from being the monozygotic co‐twin of a proband with psychosis or being the offspring of parents with schizophrenia, 22q11.2 deletion is the highest known risk factor for the development of schizophrenia.
Image Analysis Tools in Proteomics
Authors: Dowsey Andrew W , English Jane A , Lisacek Frederique , Morris Jeffrey S , Yang Guang‐Zhong , Dunn Michael J
Published: January 2011

Image analysis tools have matured into a number of established commercial packages and freely available programs that underpin research in expression proteomics. With respect to the available tools, we describe the challenges and methods for image analysis in two‐dimensional gel electrophoresis and the emerging high‐throughput ‘shotgun’ proteomics platform of liquid chromatography coupled to mass spectrometry. Two workflows can be identified: the established pipeline of spot detection followed by spot matching, and the new alternative pipeline of image alignment followed by consensus spot detection. In practice, image analysis is often viewed as a major bottleneck in proteomics, and we will further touch on emerging research that aims to statistically model and integrate data earlier in the pipeline to minimise manual interaction and therefore the subjective bias and restrictions that it brings.

Key Concepts:

Precise quantification and differential analysis of protein expression is reliant on semiautomated image analysis tools.

Liquid chromatography/mass spectrometry (LC/MS) datasets can be processed in a similar manner to 2‐D gel electrophoresis (2‐DE) by conversion to images with the mass to charge ratio on one axis and retention time on the other.

The conventional image analysis workflow involves detection of protein/peptide spots on each dataset followed by matching of corresponding spots between each dataset and a designated reference.

An alternative workflow has emerged, which warps the images into alignment before determining a consensus spot detection on the set of images as a whole.

It is important for all researchers to understand the differing unique challenges for analysis tools posed by 2‐DE and LC/MS, such as varying operating conditions, artefacts and contaminants.

LC/MS analyses also include peptide deisotoping and charge state estimation steps, plus computation of normalised retention times for improved peptide identification.

Sound statistical treatment of the results is key, including the use of the false discovery rate correction for overcoming the multiple hypothesis problem.

With existing approaches, errors at each stage propagate and amplify as the pipeline progresses; therefore, emerging techniques are aiming to provide an integrated consensus analysis that borrows strength across the image set.

Consensus pinnacle detection and image‐based alignment and deconvolution are novel methods that can provide automated, reliable and robust quantification.

Functional data analysis presents a new statistical paradigm for image‐based differential detection able to compensate for multiple experimental factors and discover protein regulation in comigrated regions missed by spot‐centric approaches.
Family‐based Association Test (
FBAT
)
Authors: Laird Nan M
Published: January 2011

Statistical tests of association are commonly used to confirm or exclude a relationship between disease and selected genes. Tests which are based on data from unrelated individuals are very popular, but can be biased if the sample contains individuals with different genetic ancestries. Family‐based Association tests avoid the problem of bias due to mixed ancestry by using within family comparisons. Many different family designs are possible, the most popular using parents and offspring, but others use just sibships. Dichotomous, measured and time‐to‐onset phenotypes can be accommodated. FBATs are generally less powerful than tests based on a sample of unrelated individuals, but special settings exist, for example testing for rare variants with affected offspring and their parents, where the family design has a power advantage.

Key Concepts:

Genetic tests based on population samples can be biased due to differing genetic ancestries.

Association designs using family members can avoid bias by using within family comparison.

The simplest family test is the TDT which uses affected offspring and their parents.

FBAT refers to a class of tests for family designs that can accommodate any type of genetic model, any phenotype and any family configuration, e.g. parents and their offspring, sibships or even general pedigrees.

In general, FBAT's are less powerful than their population‐based counter‐parts, and they generally also require more genotyping, but in some circumstances, e.g. for rare variants and in testing for gene–environment interactions, they can be more powerful.
Deciphering the Evolution of the Mitochondrial Genetic Code in Arthropods
Authors: Abascal Federico , Patricio Mateus , Zardoya Rafael , Posada David
Published: January 2011

Inside arthropod's mitochondria the AGG codon is translated differently by distinct species. In some species, AGG is translated as lysine (Lys), whereas in others the typical mitochondrial genetic code of invertebrates operates, and AGG is translated as serine (Ser). There are also arthropods that, instead of translating AGG as Lys or Ser, simply make no use of this codon. The reassignment of the translation of the AGG codon from Ser to Lys has never been observed outside this taxonomic group. The molecular basis of this reassignment lies on point mutations at the anticodons of tRNA (transfer
ribonucleic acid
)–Ser and tRNA–Lys. Decodification of the AGG codon by the tRNA–Lys (with a CUU anticodon) requires a unique wobble pairing at the second position. The low affinity between the AGG codon and the CUU anticodon most likely explains why tRNA–Ser dominates over tRNA–Lys when both are able to recognise AGG. Ancestral character state reconstruction suggests that the arthropod‐specific genetic code variant (AGG=Lys) possibly was already present in the ancestor of arthropods, having reverted to the invertebrate character state (AGG=Ser) multiple times in different arthropod lineages.

Key Concepts:

The genetic code provides a translation table between the DNA and protein alphabets.

A standard genetic code shared by all life domains exists, but there are many variants.

Alternative genetic codes are frequently found in metazoan mitochondrial genomes, probably due to their small size and lack of several tRNAs.

Arthropods encompass a unique variant in which the AGG codon is translated as lysine, instead of serine, which is the standard meaning of AGG in invertebrates.

Some arthropods make no use of the AGG codon.

Several events of codon reassignment and reversions have occurred in parallel along the arthropod lineages.

The translation of the AGG codon as lysine implies an exceptional wobble pairing with the CUU anticodon at the second position (G::U).
l‐carnitine: Structure and Function
Authors: Demarquoy Jean
Published: January 2011

l‐carnitine is found in nearly all living cells.l‐carnitine present in human body can be either provided by a biosynthetic pathway or by food. Carnitine plays a major role in lipid and energy metabolism. In the human body, the primary role ofl‐carnitine is to shuttle long‐chain fatty acids into the mitochondria where they are used to produce energy.l‐carnitine is also involved in the peroxisomal oxidative metabolism and serves as a cofactor for various enzymatic reactions. Several reports suggest thatl‐carnitine may act as an anti‐oxidant agent and limit the deleterious effects of free radicals. Many studies have estimated the role and the potential effectiveness ofl‐carnitine in various physiological and pathophysiological states such as physical exercise, heart disease, aging, weight management and brain function. A deficiency inl‐carnitine has marked effects on the function of skeletal muscle, heart and nervous cells.

Key Concepts:

Carnitine is a cofactor for many enzymatic reactions.

Carnitine regulates various physiological functions.

Carnitine may limit ROS attack.
Photochemical Transformations Involving Copper Porphyrins and Phthalocyanines
Authors: Sergeeva Natalia N. , Senge Mathias O.
Published: January 2011

Introduction

Basic Photochemistry of Porphyrins and Phthalocyanines

Electron Transfer Systems and Photochemical Reactions

Photoinduced Electron Transfer in Applied Photochemistry

Green Chemistry of Copper‐Based Dyes: Photodegradation, Stabilization and Photocatalysis

Photobiochemistry

Acknowledgements
Copper(
I
) Hydride Reagents and Catalysts
Authors: Riant Olivier
Published: January 2011

Introduction

Preparation and Characterization of Copper Hydride Complexes and Catalysts

S
tryker's Reagent as a Chemoselective Reducing Agent

Catalytic Hydrosilylation of α,β‐Unsaturated Substrates

Catalytic Hydrosilylation of Ketones and Imines

Catalytic Domino Reactions

Hydrocupration of Alkynes
Copper‐Mediated Cross‐Coupling Reactions
Authors: Penn Liza , Gelman Dmitri
Published: January 2011

General Introduction

Carbon–Heteroatom Bond‐Forming Reactions

Carbon–Carbon Bond Forming Reactions
Fluorinated Organocopper Reagents
Authors: Davis Charles R. , Burton Donald J.
Published: January 2011

Introduction

Fluoroalkenylcopper Reagents

Difluorovinylcopper Reagents

Perfluoroallylcopper Reagents

Perfluoroalkynylcopper Reagents

Carboalkoxydifluoromethylenecopper Reagents

Dialkoxyphosphinylfluoromethylcopper Reagent

Dialkoxyphosphinyldifluoromethylcopper Reagents

Perfluorobenzylcopper Reagent

Perfluoroalkylcopper Reagents

Pentafluorophenylcopper Reagent

2,3,5,6‐Tetrafluoropyridylcopper Reagents
Porous alumina through protein foaming–consolidation method: effect of dispersant concentration on the physical properties
Authors: Fadli Ahmad , Sopyan Iis , Mel Maizirwan , Ahmad Zuraida
Published: January 2011

The influence of dispersant concentration on the physical properties of porous alumina ceramics formed by the protein foaming–consolidation method has been studied. Slurries of alumina powders, yolk, and dispersant were prepared by rigorously stirring the mixture for 3 h with an alumina‐to‐yolk ratio of 1:1 in weight and dispersant concentration of 0.01–0.05 wt.%. The resulting slip was poured into cylindrical shaped molds and followed by foaming and consolidation through drying at 180 °C for 1 h. The dried green bodies of the samples were then burned to remove the pore‐creating agent at 600 °C for 1 h, followed by sintering at 1550 °C for 2 h. The density of sintered alumina ceramics could be controlled by varying the dispersant concentration of the slurry. Measurement of the average pore size distribution showed that macropores of the sintered alumina porous bodies increased with decreasing density and were found in the range of 54.4 ± 12 to 424.5 ± 25 µm. The compressive strength was 4.6 ± 0.8 MPa at 54.5% porosity and it decreased significantly to 0.8 ± 0.1 MPa at 71.8% porosity. A shrinkage of 29.3 ± 2.7% was observed for the sample prepared using the slurry without dispersant and it increased to 35.8 ± 0.9% when the dispersant of 0.03% was added. Copyright © 2011 Curtin University of Technology and John Wiley & Sons, Ltd.
Antimicrobial Activity of a New Combination System of Benzimidazole and Various Azoles
Authors: Özkay Yusuf , Tunalı Yağmur , Karaca Hülya , Işıkdağ İlhan
Published: January 2011

In the present study a new series of benzimidazole derivatives bearing various (benz)azolylthio moieties were synthesized so as to investigate their antimicrobial activity. Structures of the target compounds (5a–5i) were confirmed by their IR, 1H‐NMR, ES‐MS spectral data, and elemental analyses. The synthesized compounds (5a–5i) exhibited poor activity against bacterial strains. On the other hand, antifungal activity of the compounds against Candida species was very significant. Brine‐Shrimp lethality assay was performed for determination of toxicity of the compounds. Compounds 5a, 5c, and 5d were evaluated as non‐toxic in addition to their attractive antifungal activity. However, the other compounds (5b, e–i) in the series showed toxicity to different extents.
Synthesis and Structure‐Activity Relationships of A Novel Class of Dithiocarbamic Acid Esters as Anticancer Agent
Authors: Hou Xueling , Ge Zemei , Wang Tingmin , Guo Wei , Wu Jun , Cui Jingrong , Lai Chingsan , Li Runtao
Published: January 2011

Based on a novel lead compound 4‐methylpiperazine‐1‐carbodithioic acid 3‐cyano‐3,3‐diphenylpropyl ester1, the systematic structural modification was carried out. All the synthesized compounds were evaluated for theirin‐vitroanticancer activities on four to six different cell lines at three different concentrations. Most of the tested compounds could selectively inhibit the growth of HL‐60 and Bel‐7402 cell lines at a medium concentration. Four compounds (3f,3g,3n, and5) were selected for the IC50test, and the results revealed that three compounds (3g,3n, and5) showed almost the same or a slightly weaker activity than compound1against HL‐60, and three compounds (3f,3g, and3n) showed >2‐fold higher potency than compound1against Bel‐7402. Thein‐vivoefficacy of3n · HClwas evaluated with transplanted hepatocyte carcinoma 22 as anin‐vivotest model. It was found that3n · HClcould inhibit significantly the growth of tumor, and that this effect was dose‐dependent. Meanwhile, the compound3n · HClshowed low toxicity compared with compound1 · HClas evidenced by the little body‐weight loss. These results confirmed that compound3n · HClis more potent than the lead compound1 · HCl. Preliminary structure–activity relationships indicated that: a) Both nitrile group and the cyclic amine containing at least two nitrogens were indispensable moieties to keep the activity; b) substitution of the piperazine ring is unfavorable for the improvement of activity; c) the suitable linker joining the piperazinyl dithiocarboxyl and diphenylacetonitril group should be ethylene; d) a non‐coplanar arrangement of the two benzene rings appears to be essential for activity.
Spatial abilities of expert clinical anatomists: Comparison of abilities between novices, intermediates, and experts in anatomy
Authors: Fernandez Ruth , Dror Itiel E. , Smith Claire
Published: January 2011

Spatial ability has been found to be a good predictor of success in learning anatomy. However, little research has explored whether spatial ability can be improved through anatomy education and experience. This study had two aims: (1) to determine if spatial ability is a learned or inherent facet in learning anatomy and (2) to ascertain if there is any difference in spatial ability between experts and novices in anatomy. Fifty participants were indentified: 10 controls, 10 novices, 10 intermediates, and 20 experts. Participants completed four computerized spatial ability tasks, a visual mental rotation task, categorical spatial judgment task, metric spatial task, and an image‐scanning task. The findings revealed that experts (P = 0.007) and intermediates (P = 0.016) were better in the metric spatial task than novices in terms of making more correct spatial judgments. Experts (P = 0.033), intermediates (P = 0.003), and novices (P = 0.004) were better in the categorical spatial task than controls in terms of speed of responses. These results suggest that certain spatial cognitive abilities are especially important and characteristic of work needed in clinical anatomy, and that education and experience contribute to further development of these abilities. Anat Sci Educ. © 2011 American Association of Anatomists.
An identification method for MIMO continuous‐time systems via iterative learning control concepts
Authors: Sakai Fumitoshi , Sugie Toshiharu
Published: January 2011

This paper presents an identification method based on an iterative learning control (ILC) concept for the multivariable continuous‐time system. For this purpose a projection type ILC, which updates the input in an appropriate parameter space, is extended to the case of multivariable systems. The robustness against measurement noise is achieved through both projection of continuous‐time I/O signals onto a finite dimensional space and noise tolerant learning algorithms. Finally, a numerical example is given to demonstrate how the parameter estimation can be achieved through the proposed identification method in the presence of heavy measurement noises.

Copyright © 2010 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society
A study of upper troposphere and lower stratosphere water vapor above the Tibetan Plateau using AIRS and MLS data
Authors: Tian Wenshou , Tian Hongying , Dhomse Sandip , Feng Wuhu
Published: January 2011

We use water vapor data from Atmospheric Infrared Sounder (AIRS) and Aura Microwave Limb Sounder (MLS) combined with meteorological data from ECMWF Interim (ERA‐Interim) reanalysis, to study some aspects of stratosphere–troposphere exchange (STE) near the Tibetan Plateau. Apart from a distinctive region of high water vapor in the lower stratosphere (LS) in summer near the southern Tibetan Plateau (between 30°N and 35°N), the water vapor in the upper troposphere and lower stratosphere (UTLS) adjacent to the northern Tibetan Plateau (40°N–45°N) is found to be relatively higher than the surrounding regions of the same latitude in March and April. This relatively high water vapor in the northern Tibetan Plateau UTLS is proposed to be associated with approaching cold surges from the north and forced lifting of air by high orography. Another interesting feature detected in this study is the region of low water vapor values on the order of 5–7 ppmv, that is more pronounced from May to September at around 200 hPa and located at 30°N–40°N western Tibetan Plateau. This low water vapor region is found to be related to an anticyclone developed at the western Tibetan Plateau which causes sinking of dry air from the stratosphere resulting lower water vapor values in the upper troposphere. Copyright © 2011 Royal Meteorological Society