bluuebunny/crossref_metadata_2025 huggingface dataset:
S-cone discrimination for stimuli with spatial and temporal chromatic contrast
Authors: CAO DINGCAI , ZELE ANDREW J. , SMITH VIVIANNE C. , POKORNY JOEL
Published: July 2008

In the natural environment, color discriminations are made within a rich context of spatial and temporal variation. In classical laboratory methods for studying chromatic discrimination, there is typically a border between the test and adapting fields that introduces a spatial chromatic contrast signal. Typically, the roles of spatial and temporal contrast on chromatic discrimination are not assessed in the laboratory approach. In this study, S-cone discrimination was measured using stimulus paradigms that controlled the level of spatio-temporal S-cone contrast between the tests and adapting fields. The results indicate that S-cone discrimination of chromaticity differences between a pedestal and adapting surround is equivalent for stimuli containing spatial, temporal or spatial-and-temporal chromatic contrast between the test field and the surround. For a stimulus condition that did not contain spatial or temporal contrast, the visual system adapted to the pedestal instead of the surround. The data are interpreted in terms of a model consistent with primate koniocellular pathway physiology. The paradigms provide an approach for studying the effects of spatial and temporal contrast on discrimination in natural scenes.
L- and M-Cone isolating ERGs: LED versus CRT stimulation
Authors: MURRAY I.J. , KREMERS J. , PARRY N.R.A.
Published: July 2008

Using double silent substitution, it is possible to generate L-cone and M-cone isolating electroretinograms (ERGs) on a CRT. A major limitation of the technique is that the depth of modulation of cone classes is limited by the restricted luminance of the phosphors and their spectral overlap. To address this problem we have ported the technique to a four-color LED Ganzfeld stimulus (Diagnosis ColorDome). This allows higher retinal illuminances, higher contrasts, and triple silent substitution. With careful control over the retinal area stimulated, we show that the same data can be recorded from both CRT and LED stimuli when luminance, size and cone contrast are kept constant. Importantly, the different temporal profiles of the two devices do not influence the ERG amplitude and phase plots. We present data over a much wider range of luminances (up to about 10000 trolands) and contrasts with the LED stimulator than previously reported with CRT screens. We conclude that the close resemblance between data obtained with an LED stimulator and with a CRT screen indicate that the differences have a purely physiological origin.
Chromatic discrimination losses in multiple sclerosis patients with and without optic neuritis using the Cambridge Colour Test
Authors: MOURA ANA LAURA DE ARAÚJO , TEIXEIRA ROSANI APARECIDA ANTUNES , OIWA NESTOR N. , COSTA MARCELO F. , FEITOSA-SANTANA CLAUDIA , CALLEGARO DAGOBERTO , HAMER RUSSELL D. , VENTURA DORA FIX
Published: July 2008

We assessed chromatic discrimination in multiple sclerosis (MS) patients both with (ON) and without (no ON) a history of optic neuritis using the Cambridge color test (CCT). Our goal was to determine the magnitude and chromatic axes of any color vision losses in both patient groups, and to evaluate age-related changes in chromatic discrimination in both patient groups compared to normals. Using the CCT, we measured chromatic discrimination along the protan, deutan and tritan axes in 35 patients with MS (17 ON eyes) and 74 age matched controls. Color thresholds for both patient groups were significantly higher than controls' along the protan and tritan axes (p < 0.001). In addition, the ON and no-ON groups differed significantly along all three-color axes (p < 0.001). MS patients presented a progressive color discrimination impairment with age (along the deutan and tritan axes) that was almost two times faster than controls, even in the absence of ON. These findings suggest that demyelinating diseases reduce sensitivity to color vision in both red-green and blue-yellow axes, implying impairment in both parvocellular and koniocellular visual pathways. The CCT is a useful tool to help characterize vision losses in MS, and the relationship between these losses and degree of optic nerve involvement.
Topography of the long- to middle-wavelength sensitive cone ratio in the human retina assessed with a wide-field color multifocal electroretinogram
Authors: KUCHENBECKER JAMES A. , SAHAY MANISHA , TAIT DIANE M. , NEITZ MAUREEN , NEITZ JAY
Published: July 2008

The topographical distribution of relative sensitivity to red and green lights across the retina was assayed using a custom-made wide-field color multifocal electroretinogram apparatus. There were increases in the relative sensitivity to red compared to green light in the periphery that correlate with observed increases in the relative amount of long (L) compared to middle (M) wavelength sensitive opsin mRNA. These results provide electrophysiological evidence that there is a dramatic increase in the ratio of L to M cones in the far periphery of the human retina. The central to far peripheral homogeneity in cone proportions has implications for understanding the developmental mechanisms that determine the identity of a cone as L or M and for understanding the circuitry for color vision in the peripheral retina.
Color and luminance increment thresholds in poor readers
Authors: DAIN STEPHEN J. , FLOYD RICHARD A. , ELLIOT ROBERT T.
Published: July 2008

The hypotheses of a visual basis to reading disabilities in some children have centered around deficits in the visual processes displaying more transient reponses to stimuli although hyperactivity in the visual processes displaying sustained reponses to stimuli has also been proposed as a mechanism. In addition, there is clear evidence that colored lenses and/or colored overlays and/or colored backgrounds can influence performance in reading and/or may assist in providing comfortable vision for reading and, as a consequence, the ability to maintain reading for longer. As a consequence, it is surprising that the color vision of poor readers is relatively little studied. We assessed luminance increment thresholds and equi-luminous red-green and blue-yellow increment thresholds using a computer based test in central vision and at 10° nasally employing the paradigm pioneered by King-Smith. We examined 35 poor readers (based on the Neale Analysis of Reading) and compared their performance with 35 normal readers matched for age and IQ. Poor readers produced similar luminance contrast thresholds for both foveal and peripheral presentation compared with normals. Similarly, chromatic contrast discrimination for the red/green stimuli was the same in normal and poor readers. However, poor readers had significantly lower thresholds/higher sensitivity for the blue/yellow stimuli, for both foveal and peripheral presentation, compared with normal readers. This hypersensitivity in blue-yellow discrimination may point to why colored lenses and overlays are often found to be effective in assisting many poor readers.
Distinguishing L from M photopigment coding sequences by hybridization to novel locked nucleic acid (LNA) oligonucleotide probes
Authors: PETTAN-BREWER CHRISTINA , FU LI , DEEB SAMIR S.
Published: July 2008

Many attempts have been made over the years to distinguish human and primate L (long-wavelength sensitive) from M (middle-wavelength sensitive) cone photoreceptors using either immunohistochemistry orin situhybridization. These attempts have been unsuccessful due to the very high degree of identity between the sequences of the L and M proteins and encoding mRNAs. The recent development of chemically modified oligonucleotide probes, referred to as locked nucleic acid (LNA) probes, has shown that they hybridize with much greater affinity and specificity to the target nucleic acid. This has greatly increased the potential for differentiating L from M cones byin situhybridization. We have designed LNA oligonucleotide probes that are complementary to either the L or M coding sequences located in exon 5 of theMacaca nemestrinaL and M pigment genes. We have shown that the LNA-M and LNA-L probes hybridize specifically to their respective target nucleic acid sequencesin vitro. This result strongly suggests that these probes would be instrumental in rapidly distinguishing L from M cone in the entire retina, and in defining the cone mosaic during development and in adults.
A study of unusual Rayleigh matches in deutan deficiency
Authors: BARBUR J.L. , RODRIGUEZ-CARMONA M. , HARLOW J.A. , MANCUSO K. , NEITZ J. , NEITZ M.
Published: July 2008

Rayleigh match data were modeled with the aim of explaining the locations of match midpoints and matching ranges, both in normal trichromats and in subjects with congenital color deficiency. Model parameters included the wavelength of peak sensitivity of cone photopigments, the effective photopigment optical density, and the noise amplitude in the red-green color channel. In order to avoid the suprathreshold, perceptual effects of extreme L:M cone ratios on color vision, selective post-receptoral amplification of cone signals is needed. The associated noise is also amplified and this causes corresponding changes in red-green threshold sensitivity. We propose that the noise amplitude and hence the size of the matching range in normal trichromats relates to the known inter-subject variation in the relative numbers of L and M cones. If this hypothesis can be shown to account for the extremes of the red-green matching range measured in normal trichromats, it is of interest to establish the extent to which it also predicts the unexpected, small matching ranges that are observed in some subjects with red-green color deficiency. A subset of subjects with deutan deficiency that exhibited less common Nagel matches were selected for genetic analysis of their cone pigment genes in order to confirm the type of deficiency, and to predict the corresponding peak wavelength separation (δλmax) of their two, long-wavelength cone pigments. The Rayleigh match model predicted accurately the midpoint and the range for the spectral differences specified by the genes. The prediction also required plausible selection of effective optical density of the cone pigments and noise. The noise needed varied, but the estimates were confined to lie within the limits established from the matching ranges measured in normal trichromats. The model predicts correctly the small matching ranges measured in some deuteranomalous subjects, principally accounted for by a low estimate of noise level in the red-green channel. The model also predicts the “normal” matches made by some subjects that rely on two hybrid genes and therefore exhibit red-green thresholds outside the normal range, typical of mild deuteranomaly.
The number of discernible colors perceived by dichromats in natural scenes and the effects of colored lenses
Authors: LINHARES JOÃO M.M. , PINTO PAULO D. , NASCIMENTO SÉRGIO M.C.
Published: July 2008

The number of discernible colors perceived by normal trichromats when viewing natural scenes can be estimated by analyzing idealized color volumes or hyperspectral data obtained from actual scenes. The purpose of the present work was to estimate the relative impairment in chromatic diversity experienced by dichromats when viewing natural scenes and to investigate the effects of colored lenses. The estimates were obtained computationally from the analysis of hyperspectral images of natural scenes and using a quantitative model of dichromats' vision. The color volume corresponding to each scene was represented in CIELAB color space and segmented into cubes of unitary side. For normal trichromats, the number of discernible colors was estimated by counting the number of non-empty cubes. For dichromats, an algorithm simulating for normal observers the appearance of the scenes for dichromats was used, and the number of discernible colors was then counted as for normal trichromats. The effects of colored lenses were estimated by prior filtering the spectral radiance from the scenes with the spectral transmittance function of the lenses. It was found that in dichromatic vision the number of discernible colors was about 7% of normal trichromatic vision. With some colored lenses considerable improvements in chromatic diversity were obtained for trichromats; for dichromats, however, only modest improvements could be obtained with efficiency levels dependent on the combination of scene, lens and type of deficiency.
European diet and public health: The continuing challenge
Authors: Luzzi Anna Ferro , James W P T
Published: July 2008

There has been a dramatic improvement in the health of European children and adults since 1900. These improvements were remarkable in the first half of the century, with a progressive fall in the death of children and pregnant women and substantial increases in life expectancy. This century's early health changes were not the result of the provision of medical services, the discovery of drugs and antibiotics, or even the increasing capacity to immunise children against an ever greater range of infectious diseases. They resulted from improvements in the diet, in the housing, occupational and social conditions of workers and their families. Since World War II, with modern living conditions, the general year-around availability of a huge variety of foods, expanding immunisation and improving health care through the health services, with modern therapeutic techniques and new drugs, life expectancy continues to increase in many European countries. These are great public health achievements which should not be overlooked by policy makers and indeed the public.
Characterization and validation of methane products from the Atmospheric Infrared Sounder (AIRS)
Authors: Xiong Xiaozhen , Barnet Chris , Maddy Eric , Sweeney Colm , Liu Xingpin , Zhou Lihang , Goldberg Mitch
Published: July 2008

This paper presents the characterization and validation of retrievals of atmospheric methane (CH4) vertical profiles by the Atmospheric Infrared Sounder (AIRS) on the EOS/Aqua platform. AIRS channels near 7.6 μm are used for CH4 retrieval, and they are most sensitive to the middle to upper troposphere, i.e., about 200–300 hPa in the tropics and 400–500 hPa in the polar region. The atmospheric temperature‐humidity profiles, surface skin temperature, and emissivity required to derive CH4 are obtained from retrievals using separate AIRS channels and the Advanced Microwave Sounding Unit (AMSU). Comparison of AIRS retrieved profiles with some in situ aircraft CH4 profiles implied that the forward model used in the AIRS retrieval system V4.0 required a 2% increase in methane absorption coefficients for strong absorption channels, and this bias adjustment was implemented in the AIRS retrieval system V5.0. As a new operational product in V5.0, AIRS CH4 were validated using in situ aircraft observations at 22 sites of the NOAA Earth System Research Laboratory, Global Monitoring Division (NOAA/ESRL/GMD), ranging from the Arctic to the tropical South Pacific Ocean, but their altitudes are usually above 300 hPa. The results show the bias of the retrieved CH4 profiles for this version is −1.4∼0.1% and its RMS difference is about 0.5–1.6%, depending on altitude. These validation comparisons provide critical assessment of the retrieval algorithm and will continue using more in situ observations together with future improvement to the retrieval algorithm. AIRS CH4 products include not only the CH4 profile but also the information content. As examples, the products of AIRS CH4 in August 2004 and the difference of CH4 in May and September 2004 are shown. From these results a few features are evident: (1) a large AIRS CH4 plume southwest of the Tibetan plateau that may be associated with deep convection during the Asian summer monsoon; (2) high mixing ratios of AIRS CH4 in southeastern Asia and in the high northern hemisphere in the summer; and (3) the increase of AIRS CH4 from May to September in the high northern hemisphere that is likely linked with wetland emission but needs more study. Further analysis of these data and its comparison with model data will be addressed in a separate paper.
Quantification of subsurface heat storage in a GCM simulation
Authors: MacDougall Andrew H. , González‐Rouco J. Fidel , Stevens M. Bruce , Beltrami Hugo
Published: July 2008

Shallow bottom boundary conditions (BBCs) in the soil components of general circulation models (GCMs) impose artificial limits on subsurface heat storage. To assess this problem we estimate the subsurface heat content from two future climate simulations and compare to that obtained from an offline soil model (FDLSM) driven by GCM skin temperatures. FDLSM is then used as an offline substitute for the subsurface of the GCM ECHO‐G. With a 600‐m BBC and driven by ECHO‐G future temperatures, the FDLSM subsurface absorbs 6.2 (7.5) times more heat than the ECHO‐G soil model (10 m deep) under the Intergovernmental Panel on Climate Change (IPCC) A2 (B2) emission scenario. This suggests that shallow BBCs in GCM simulations may underestimate the heat stored in the subsurface, particularly for northern high latitudes. This effect could be relevant in assessing the energy balance and climate change in the next century.
Serum profiling and biomarker discovery of rat mammary tumors using mass-coded abundance tags (MCAT)
Authors: Rowell Craig , Puckett Glen , Raorty Kevin , Kirk Marion , Wilson Landon , Wang Sam , Carpenter Mark , Lamartiniere Coral
Published: July 2008

Advances in Mass-spectrometry techniques allow for the rapid processing and evaluation of complex biological mixtures such as blood/serum. These samples represent a protein rich environment as well as a sentinel monitoring system of the entire organism. The central tenet of these studies is that changes in the microenvironment of a tissue, brought about by a disease process, will lead to sufficient changes in the protein and peptide pattern of the serum, such that the differences can be accurately detected and correctly associated with a particular disease state. Using mass-spectrometry approaches we have developed techniques that allow us to compare samples from tumor-free and tumor present serum samples simultaneously to find biomarkers that indicate the presence of cancer. To examine potentially important but less abundant proteins, ultrafiltration (UF) was used to eliminate the more abundant proteins and combine this with the non-isotopic peptide tags (S-methylthioacetimidate and S-methyl thiopropionimidate) described by Beardsley and Reilley (J. Proteome Res. 2: 15-21, 2003) to differentiate our samples. Use of these mass-coded abundance tags (MCAT) allows for simultaneous evaluation of serum samples from tumor present, and tumor free animals. Using an oa time-of-flight mass-spectrometer (Q-tof) with electrospray ionization we produce high quality spectrums to screen for peptides that have only one tag. Specificity of tagging increases the likelihood that the peptide resulted from a protein unique to either the control or conditioned state. Using the ms/ms function of the Q-tof we sequence the peptide and identify the parent protein. Specifically, our lab is using UF, MCAT and the Q-tof to evaluate rat models of chemically-induced tumors. By using animal models we overcome much of the variability that may exist in human serum samples due to differences in gender, diet and cancer initiation. We have shown that these systems allow for the identification of both small molecules such as Alpha S1 casein precursor (24 kDa) as well as proteins greater than the MCO such as Fibrinogen alpha/alpha E precursor and Coagulation factor 2 (86 and 70 kDa, respectively). With positive sequence identification we can now evaluate the tumors themselves to determine if the proteins are over-expressed in the tumor vs. normal tissues. Using this method of “bottom-up” analysis provides information on the nature and composition of our samples to more rapidly identify those proteins that are unique to the tumor state of the animals.
Genotypic variation for drought stress response traits in soybean. II. Inter-relations between epidermal conductance, osmotic potential, relative water content, and plant survival
Authors: James A. T. , Lawn R. J. , Cooper M.
Published: July 2008

As part of a project exploring the potential for using leaf physiological traits to improve drought tolerance in soybean, studies were conducted to explore whether epidermal conductance (ge), osmotic potential (π), and relative water content (RWC) influenced turgor maintenance and ultimately the survival of droughted plants. In a glasshouse study, plants of 8 soybean genotypes that showed different expression of the traits were grown in well watered soil-filled beds for 21 days and then exposed to terminal water deficit stress. The trends in each trait were then monitored periodically until plant death. Genotypic differences were observed in the rate of decline in RWC as the soil dried, in the temporal patterns of change in ge and π, in the duration of survival after watering ceased, and in the critical relative water content (RWCC) at which plants died. In general, ge became smaller and π became more negative as RWC declined and plants acclimated to the increasing stress. Genotypic differences in ge remained broadly consistent as RWC declined. In contrast, the genotypic rankings for π in stressed plants were poorly correlated with those for well watered plants, indicating differential genotypic capacity for osmotic adjustment (OA) in response to stress. Survival times among genotypes after stress commenced ranged from 27 to 41 days, while RWCC ranged from 49% down to 41%. The differences in survival time among the genotypes were able to be explained by genotypic differences in the rate of decline in RWC and in the RWCC, using a multiple linear regression relationship (R
2 = 0.94**). In turn, genotypic differences in the rate of decline in RWC were positively correlated (r = 0.75*) with ge at 70% RWC, and with OA over the drying period (r = 0.98**). In a second study in a controlled environment facility, leaf area retention at 90% soil water extraction was greatest in the one genotype that combined low ge, high OA, and low RWCC. Overall, the responses from the two studies were consistent with the hypothesis that turgor maintenance and ultimately leaf and plant survival of different genotypes during advanced stages of drought stress are enhanced by low ge, high OA capacity, and low RWCC.
Genotypic variation for drought stress response traits in soybean. III. Broad-sense heritability of epidermal conductance, osmotic potential, and relative water content
Authors: James A. T. , Lawn R. J. , Cooper M.
Published: July 2008

The broad-sense heritability of 3 traits related to leaf survival in severely stressed plants was studied in several hybrid soybean populations. The 3 traits were epidermal conductance (ge), osmotic potential (π), and relative water content (RWC). The populations were generated by hybridising unrelated parental genotypes previously shown to differ in the 3 traits. ge (mm/s) was measured on well watered plants from 10 populations involving all combinations of 5 parental lines, grown in soil-filled beds in the glasshouse. π (MPa) and RWC (%) were measured on severely stressed plants of 3 populations involving all combinations of 3 different parents, growing into a terminal water deficit under a rainout shelter in the field. Broad-sense heritability for ge was significantly different from zero (P < 0.05) in all 10 populations and ranged from 60% to 93%. Heritability estimates for π70 (the tissue osmotic potential at 70% RWC) ranged from 33% to 71%. Only two estimates were statistically significant (P < 0.05) because of large standard errors and the fact that parental differences were smaller than previously observed. Broad-sense heritability for RWC of severely stressed plants ranged from 40% to 74%, and was statistically significant (P < 0.05) for 2 of the 3 populations. For all 3 traits, F2 progeny distributions were consistent with quantitative inheritance with a high degree of additive gene action. It was concluded that capacity exists to breed varieties with low ge, low π70, and high RWC in stressed plants. However, in the case of osmotic potential, genotypes with lower π70 combined with greater precision of measurement would be needed than proved possible in these studies. Further, specific strategies would be needed to select for the critical RWC, the minimal RWC at which leaf tissues die and which provides a measure of tissue dehydration tolerance. More research is also needed to characterise the dynamic relations between ge, π, and RWC in influencing leaf survival in soybean, before they could be confidently used in a breeding program to improve drought tolerance.
Design and testing of an automatic irrigation controller for fruit tree orchards, based on sap flow measurements
Authors: Fernández J. E. , Romero R. , Montaño J. C. , Diaz-Espejo A. , Muriel J. L. , Cuevas M. V. , Moreno F. , Girón I. F. , Palomo M. J.
Published: July 2008

We designed and tested an automatic irrigation control system for fruit tree orchards, designated CRP. At the end of each day, the device calculates the irrigation dose (ID) from sap flow readings in the trunk of trees irrigated to replenish the crop water needs, relative to similar measurements made in over-irrigated trees. It then acts on the pump and electrovalve to supply an ID sufficient to keep the soil close to its field capacity during the irrigation period. Remote control of the system is possible from any computer or Smartphone connected to the Internet. We tested the CRP in an olive orchard in southern Spain. The device was robust and able to filter and amplify the output voltages of the heat-pulse velocity probes and to calculate reliable sap flow data. It calculated and supplied daily irrigation amounts to the orchard according to the specified irrigation protocol. The remote control facility proved to be useful for getting real-time information both on the CRP behaviour and the applied IDs, and for changing parameters of the irrigation protocol. For our conditions, olive trees with big root systems growing in a soil with a remarkable water-holding capacity, the approach mentioned above for calculating ID had not enough resolution to replace the daily crop water consumption. The device, however, was able to react when the soil water content fell below the threshold for soil water deficit. The threshold value was identified with simultaneous measurements of stem water potential in the instrumented trees. Our results suggest a change in the irrigation protocol that will allow the CRP to apply a recovery irrigation whenever that threshold is reached, making the device suitable for applying a deficit irrigation strategy in the orchard.
Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition
Authors: Maiti Atanu , Morgan Michael T. , Pozharski Edwin , Drohat Alexander C.
Published: June 2008

Cytosine methylation at CpG dinucleotides produces m
5
CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m
5
C deamination yields mutagenic G·T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G·T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G·C pair. hTDG is inactive against normal A·T pairs, and is most effective for G·T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG
cat
) in complex with abasic DNA, at 2.8 Å resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG
cat
can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted
in vivo
, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.
Short article: Forgotten but not gone: Context effects on recognition do not require explicit memory for context
Authors: Levy Daniel A. , Rabinyan Elinor , Vakil Eli
Published: July 2008

Context effects on recognition memory provide an important indirect assay of associative learning and source memory. Neuropsychological studies have indicated that such context effects may obtain even if the contexts themselves are not remembered—for example, in individuals impaired on direct tests of memory for contextual information. In contrast, a recent study indicated that the effects of temporal context reinstatement on visual recognition obtain only when the contextual information itself was explicitly recollected. Here we report that the effects of reinstatement of spatial-simultaneous context on visual object recognition memory obtain irrespective of whether those context stimuli are explicitly recognized. We suggest that spatial-simultaneous context effects might be based on ensemble unitization of target and context stimuli at encoding, whereas temporal context effects may require recollective processes.
Capture of AT-rich Chromatin by ELYS Recruits POM121 and NDC1 to Initiate Nuclear Pore Assembly
Authors: Rasala Beth A. , Ramos Corinne , Harel Amnon , Forbes Douglass J.
Published: July 2008

Assembly of the nuclear pore, gateway to the genome, from its component subunits is a complex process. In higher eukaryotes, nuclear pore assembly begins with the binding of ELYS/MEL-28 to chromatin and recruitment of the large critical Nup107-160 pore subunit. The choreography of steps that follow is largely speculative. Here, we set out to molecularly define early steps in nuclear pore assembly, beginning with chromatin binding. Point mutation analysis indicates that pore assembly is exquisitely sensitive to the change of only two amino acids in the AT-hook motif of ELYS. The dependence on AT-rich chromatin for ELYS binding is borne out by the use of two DNA-binding antibiotics. AT-binding Distamycin A largely blocks nuclear pore assembly, whereas GC-binding Chromomycin A3does not. Next, we find that recruitment of vesicles containing the key integral membrane pore proteins POM121 and NDC1 to the forming nucleus is dependent on chromatin-bound ELYS/Nup107-160 complex, whereas recruitment of gp210 vesicles is not. Indeed, we reveal an interaction between the cytoplasmic domain of POM121 and the Nup107-160 complex. Our data thus suggest an order for nuclear pore assembly of 1) AT-rich chromatin sites, 2) ELYS, 3) the Nup107-160 complex, and 4) POM121- and NDC1-containing membrane vesicles and/or sheets, followed by (5) assembly of the bulk of the remaining soluble pore subunits.
ZO-1- and ZO-2-Dependent Integration of Myosin-2 to Epithelial Zonula Adherens
Authors: Yamazaki Yuji , Umeda Kazuaki , Wada Masami , Nada Shigeyuki , Okada Masato , Tsukita Shoichiro , Tsukita Sachiko
Published: July 2008

For the zonula adherens (ZA) to be established by linear arrangement of adherens junctions (AJs) in epithelial sheet cells, critical for the epithelial cell sheet formation and intercellular barrier function, myosin-2 is supposedly integrated into the ZA with the result of overlapping localization of E-cadherin/actin/myosin-2. Here, we immunofluorescently showed that myosin-2 failed to be integrated into the ZA in cultured epithelial-type ZO1(ko)/2(kd) Eph4 cells lacking ZO-1 and -2 (zonula occludens-1 and -2) by knockout and knockdown, respectively. Instead, a linearized but fragmented arrangement of AJs was formed in the way that it was positive for E-cadherin/actin, but negative for myosin-2 (designated prezonula-AJ). Transfection of full-length ZO-1 or ZO-2, or ZO-1 lacking its PDZ (PSD-95/discs large/zonula occludens-1)-1/2 domains (but not one lacking PDZ-1/2/3) into ZO1(ko)/2(kd) Eph4 cells restored the junctional integration of myosin-2 with prezonula-AJ to establish the ZA. Transfection of dominant-active RhoA or Rho-kinase (ROCK), as well as administration of lysophosphatidic acid or Y27632, which activates RhoA or inhibits ROCK, respectively, suggested that RhoA regulated the junctional integration of myosin-2 into ZA in a manner such that ROCK played a necessary but not-sufficient role. Fluorescence resonance energy transfer analyses revealed that spatiotemporal Rho-activation occurred in a ZO-1/2–dependent way to establish ZA from primordial forms in epithelial cells.
RACK1 Regulates Directional Cell Migration by Acting on Gβγ at the Interface with Its Effectors PLCβ and PI3Kγ
Authors: Chen Songhai , Lin Fang , Shin Myung Eun , Wang Fei , Shen Lixin , Hamm Heidi E.
Published: July 2008

Migration of cells up the chemoattractant gradients is mediated by the binding of chemoattractants to G protein–coupled receptors and activation of a network of coordinated excitatory and inhibitory signals. Although the excitatory process has been well studied, the molecular nature of the inhibitory signals remains largely elusive. Here we report that the receptor for activated C kinase 1 (RACK1), a novel binding protein of heterotrimeric G protein βγ (Gβγ) subunits, acts as a negative regulator of directed cell migration. After chemoattractant-induced polarization of Jurkat and neutrophil-like differentiated HL60 (dHL60) cells, RACK1 interacts with Gβγ and is recruited to the leading edge. Down-regulation of RACK1 dramatically enhances chemotaxis of cells, whereas overexpression of RACK1 or a fragment of RACK1 that retains Gβγ-binding capacity inhibits cell migration. Further studies reveal that RACK1 does not modulate cell migration through binding to other known interacting proteins such as PKCβ and Src. Rather, RACK1 selectively inhibits Gβγ-stimulated phosphatidylinositol 3-kinase γ (PI3Kγ) and phospholipase C (PLC) β activity, due to the competitive binding of RACK1, PI3Kγ, and PLCβ to Gβγ. Taken together, these findings provide a novel mechanism of regulating cell migration, i.e., RACK1-mediated interference with Gβγ-dependent activation of key effectors critical for chemotaxis.
Biological features of the Lophius piscatorius catch in Scottish waters
Authors: Laurenson Chevonne H. , Dobby Helen , McLay H. Anne , Leslie Beth
Published: July 2008

Laurenson, C. H., Dobby, H., McLay, H. A., and Leslie, B. 2008. Biological features of the Lophius piscatorius catch in Scottish waters. – ICES Journal of Marine Science, 65: 1281–1290. Here, data on 50 265 Lophius piscatorius sampled between 1998 and 2006 on board commercial fishing vessels during observer trips and chartered surveys at Shetland, west of Scotland, and Rockall are analysed. In each area, length differed significantly with depth (p < 0.001), there was an increase in modal size with increasing depth down to 450 m, and large fish dominated hauls in deeper water. The sex ratio of all data combined was 0.88 females:1 male, but it varied by area, depth, and season, with males greatly outnumbering females in deep water west of Scotland during the first quarter of the year. The proportion at length that were female differed significantly with depth, and the highest proportions of mature fish were in deep water at Rockall and west of Scotland. L50% maturities, for all data combined, were 102.4 cm for females and 58.3 cm for males.
Functional group diversity of bee pollinators increases crop yield
Authors: Hoehn Patrick , Tscharntke Teja , Tylianakis Jason M , Steffan-Dewenter Ingolf
Published: July 2008

Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkinCucurbita moschataDuch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees.
Training volunteers for the elderly in Israel
Authors: Vitner Gad , Shalom Vera , Yodfat Avital
Published: June 2008

Purpose

The purpose of this paper is to present a comprehensive training program for volunteers for the elderly in Israel, which has been operated under the National Insurance Institute of the State of Israel.

Design/methodology/approach

The paper considers the need and values of training elderly volunteers to support the elderly in the community. The methodology of training is presented, starting with the first program of a new volunteer and continue with an advanced consultant course. The methodology of maintaining and continuous improvement of the training programs are also discussed.

Findings

Each year, about 500 volunteers participate in a 64 hours (four weekly hours for 16 weeks) new volunteer course, and about 50 volunteers participate in the consultant course. In addition, all active volunteers (about 4,000) participate in regular training groups, every alternate week for two hours.

Originality/value

The paper introduces a unique training methodology and training programs for elderly volunteers to support the elderly in the community. A continuous improvement methodology is discussed to ensure training effectiveness.
Virtual reference, Second Life and traditional library enquiry services
Authors: Joint Nicholas
Published: June 2008

Purpose

The purpose of this paper is to examine recent thinking about reference services and library use of virtual reference (VR) software, in order to put into context the value of advanced social networking technologies such as Second Life to libraries and their users.

Design/methodology/approach

A brief review of the main developments in the recent history of VR, combined with a comparison of the relevant features in common between generic VR packages and Second Life.

Findings

That the key weaknesses of established VR services are also found in Second Life, but that these weaknesses should be readily overcome as technical advances are made and librarians clarify to software providers the type of functionality they require from their services.

Research limitations/implications

The need for a higher level of complex authentication functionality, as necessitated when combining digital library subscription services with interactive virtual library environments, is outlined and defined. This is a fertile area for service provider research and development.

Practical implications

The practical benefits of VR and Second Life services to libraries will be limited until the authentication issues summarised in this paper are addressed.

Originality/value

The paper attempts to enlarge the literature on Second Life by discussing this recent innovation in terms of the broader historical context against which such digital library services have evolved. In particular, it points out the ironic similarity between digital reference environments and declining traditional reference services, which both are disadvantaged by their “distance” from core, authenticated digital library content.
Graduate development, discursive resources and the employment relationship at BAE Systems
Authors: Jenner Shirley
Published: June 2008

Purpose

The purpose of this paper is to examine the evolution of an employee opinion survey and to evaluate its impact on the graduate training programme and associated employment relationships.

Design/methodology/approach

The paper provides a detailed, longitudinal case study of one large‐scale UK organisation. The approach recognises that discursive resources have a material existence in the sense that they are embodied in the social practices of individuals and the institutions and organisations within which these social practices take place. Drawing on qualitative and quantitative data, the paper demonstrates how the design, delivery and evaluation of the graduate programme formed a learning nexus between management, graduates and other stakeholders.

Findings

The case study highlights the contested nature of organisational life, particularly in relation to matters of control and autonomy. However, improved graduate opinion survey ratings over time suggest that the evolving surveillance offered by internal research has been successful in achieving changed management behaviours. The case study has shown how graduate training, development and career management are best understood as discursive practices. Shared understandings about the nature of work are constructed though a communications nexus of key stakeholders.

Originality/value

The main contribution of this paper is to highlight the pivotal role of the corporate training programme and associated communications in the development of shared understandings of the nature of the employment relationship.
Case study: developing graduate engineers at Kentz Engineers & Constructors
Authors: O'Donnell Hugh , Karallis Takis , Sandelands Eric , Cassin James , O'Neill Donal
Published: June 2008

Purpose

The aim of this paper is to outline the approach and process in place within Kentz Engineers & Constructors to develop graduate engineers on an international basis.

Design/methodology/approach

The approach adopted is that of a case study which describes activities and processes within the organization and the rationale behind them, supported by appropriate material. The case study is based upon threads of experiences within the organization over an extended period of some years.

Findings

Findings include the need to facilitate experiential learning and provide mentoring within a socialization as well as developmental process.

Research limitations/implications

This is a case study focusing on the experiences and practices of one organization. It does not represent an empirical study. However, it contains insights that may be of practical value within businesses and other organizations seeking to develop graduate engineers, or, more broadly, seeking to manage the transition of new workers.

Originality/value

This paper illustrates the approach of one international organization to the development of graduate engineers within the construction industry.
A medical robot kinematics design approach based on knowledge management
Authors: Smith‐Guerin Natalie , Nouaille Laurence , Vieyres Pierre , Poisson Gerard
Published: June 2008

Purpose

The purpose of this paper is to present a methodology for medical robot kinematics design developed using a knowledge‐management approach.

Design/methodology/approach

A classification of medical robots is proposed based on their kinematic characteristics and 76 robot specifications were collected in a catalogue. Then, having drawn a generic specifications sheet, rules were proposed to choose a structure from these specifications.

Findings

Findings are situated at several levels: the catalogue, the classification of robots with respect to their kinematic characteristics, a generic and specific specifications sheet, and an organigram to choose the most relevant structure from the specifications.

Research limitations/implications

This structural synthesis represents a preliminary step in the design of medical robots which will be completed by an additional dimensional synthesis.

Originality/value

This work offers a new methodology for medical robots design distinct from what is usually done for medical or industrial robots design using intuition, expertise and non‐formal knowledge.
An exploratory study on quality costs in Turkish manufacturing companies
Authors: Uyar Ali
Published: June 2008

Purpose

The purpose of this study is to investigate the extent to which Turkish manufacturing companies implement a cost of quality (COQ) system, to evaluate how company performance has changed after COQ system implementation, and to identify the objectives behind COQ measuring and reporting.

Design/methodology/approach

The methodology of the study was a postal questionnaire survey. The survey was conducted with the top 500 industrial enterprises in Turkey specified by the Istanbul Chamber of Industry (ICI) for the year 2005. These firms are selected and ranked by ICI according to production‐based sales.

Findings

The findings indicated that almost half (49.5 percent) of responding firms currently implement a COQ system. After COQ system implementation, the following remarkable changes were observed in business operations of the responding companies: customer complaints decreased; rework and scrap decreased; warranty expenditures decreased; failure costs decreased; and sales volume increased. The most important three objectives behind COQ measuring and reporting are: overall quality improvement; setting cost reduction targets and measuring progress; and improving control of quality activities.

Research limitations/implications

The sample is restricted to the top 500 industrial enterprises in Turkey. As the data in this study were collected from manufacturing companies, the findings should not be generalized to other sectors.

Originality/value

The paper provides the general practices and perceptions of the largest Turkish manufacturing companies on quality costs.