bluuebunny/crossref_metadata_2025 huggingface dataset:
Sex-related differences in chromatic sensitivity
Authors: RODRÍGUEZ-CARMONA M. , SHARPE L.T. , HARLOW J.A. , BARBUR J.L.
Published: July 2008

Generally women are believed to be more discriminating than men in the use of color names and this is often taken to imply superior color vision. However, if both X-chromosome linked color deficient males (∼8%) and females (<1%) as well as heterozygote female carriers (∼15%) are excluded from comparisons, then differences between men and women in red-green (RG) color discrimination have been reported as not being significant (e.g., Pickford, 1944; Hood et al., 2006). We re-examined this question by assessing the performance of 150 males and 150 females on the color assessment and diagnosis (CAD) test (Rodriguez-Carmona et al., 2005). This is a sensitive test that yields small color detection thresholds. The test employs direction-specific, moving, chromatic stimuli embedded in a background of random, dynamic, luminance contrast noise. A four-alternative, forced-choice procedure is employed to measure the subject's thresholds for detection of color signals in 16 directions in color space, while ensuring that the subject cannot make use of any residual luminance contrast signals. In addition, we measured the Rayleigh anomaloscope matches in a subgroup of 111 males and 114 females. All the age-matched males (30.8 ± 9.7) and females (26.7 ± 8.8) had normal color vision as diagnosed by a battery of conventional color vision tests. Females with known color deficient relatives were excluded from the study. Comparisons between the male and female groups revealed no significant differences in anomaloscope midpoints (p = 0.709), but a significant difference in matching ranges (p = 0.040); females on average tended to have a larger mean range (4.11) than males (3.75). Females also had significantly higher CAD thresholds than males along the RG (p = 0.0004), but not along the yellow-blue (YB) discrimination axis. The differences between males and females in RG discrimination may be related to the heterozygosity in X-linked cone photo pigment expression common among females.
Color vision in children and the Lanthony New Color Test
Authors: LING BARBARA Y. , DAIN STEPHEN J.
Published: July 2008

Much is known about color vision in infants, adolescents, and adults, but very few studies report the changes, which occur in color perception of children in their early schooling years. There is also a shortage of suitable color vision tests for children. This study investigated the changes in color vision of school students between 5–12 years old using the Lanthony New Color Test (NCT). Subjects of all ages were able to complete a shortened form of this test adequately. The Vingrys and King-Smith (1988) method of panel test analysis and Adams and Rodic (1982) color confusion score were adapted to analyze their performance of the test. This study confirmed that there are changes in color perception occurring in this age group. Color perception abilities increased as a function of age and there was also an improvement in the performance on the NCT with age. This can be attributed to both cognitive development and changes occurring to the color vision system.
Cone visual pigments of monotremes: Filling the phylogenetic gap
Authors: WAKEFIELD MATTHEW J. , ANDERSON MARK , CHANG ELLEN , WEI KE-JUN , KAUL RAJINDER , GRAVES JENNIFER A. MARSHALL , GRÜTZNER FRANK , DEEB SAMIR S.
Published: July 2008

We have determined the sequence and genomic organization of the genes encoding the cone visual pigment of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus), and inferred their spectral properties and evolutionary pathways. We prepared platypus and echidna retinal RNA and used primers of the middle-wave-sensitive (MWS), long-wave-sensitive (LWS), and short-wave sensitive (SWS1) pigments corresponding to coding sequences that are highly conserved among mammals; to PCR amplify the corresponding pigment sequences. Amplification from the retinal RNA revealed the expression of LWS pigment mRNA that is homologous in sequence and spectral properties to the primate LWS visual pigments. However, we were unable to amplify the mammalian SWS1 pigment from these two species, indicating this gene was lost prior to the echidna-platypus divergence (∼21 MYA). Subsequently, when the platypus genome sequence became available, we found an LWS pigment gene in a conserved genomic arrangement that resembles the primate pigment, but, surprisingly we found an adjacent (∼20 kb) SWS2 pigment gene within this conserved genomic arrangement. We obtained the same result after sequencing the echidna genes. The encoded SWS2 pigment is predicted to have a wavelength of maximal absorption of about 440 nm, and is paralogous to SWS pigments typically found in reptiles, birds, and fish but not in mammals. This study suggests the locus control region (LCR) has played an important role in the conservation of photo receptor gene arrays and the control of their spatial and temporal expression in the retina in all mammals. In conclusion, a duplication event of an ancestral cone visual pigment gene, followed by sequence divergence and selection gave rise to the LWS and SWS2 visual pigments. So far, the echidna and platypus are the only mammals that share the gene structure of the LWS-SWS2 pigment gene complex with reptiles, birds and fishes.
Time course of rod influences on hue perception
Authors: BUCK STEVEN L. , THOMAS LAURA P. , CONNOR CASSANDRA R. , GREEN KATELYN B. , QUINTANA TZIRE
Published: July 2008

Stimulation of dark-adapted rods can shift the hues associated with specific wavelengths throughout the spectrum: Rods exert a green bias (strengthen green relative to red) at longer wavelengths and a blue bias (strengthen blue relative to yellow) at short-to-middle wavelengths. A third rod influence at shorter wavelengths is more complicated because it has been shown to reverse direction with change of stimulus duration. Thus, for 30-ms stimuli, rods exert a green bias like that observed at longer wavelengths. However, for 1-s stimuli, rods exert a red bias that is observed nowhere else in the spectrum. We examined the latency (time course) of rod hue biases by measuring the shifts of the three spectral unique hues under dark-adapted versus bleached (cone plateau) conditions. The rod green bias at unique yellow (mean 10 nm) and, in contrast to some prior studies, the rod blue bias at unique green (mean 21 nm) were not systematically affected by test stimulus duration. A quick rod green bias (mean 5 nm) was shown at unique blue for two of three observers but was dominated by a slower rod red bias (mean 11 nm) after 30–50 ms of rod stimulation. These opposing rod influences may reflect competing effects of rod signals on ML-cone and S-cone pathways.
Nucleotide polymorphisms upstream of the X-chromosome opsin gene array tune L:M cone ratio
Authors: GUNTHER KAREN L. , NEITZ JAY , NEITZ MAUREEN
Published: July 2008

In support of the long-held idea that cone ratio is genetically determined by variation linked to the X-chromosome opsin gene locus, the present study identified nucleotide differences in DNA segments containing regulatory regions of the L and M opsin genes that are associated with significant differences in the relative number of L versus M cones. Specific haplotypes (combinations of genetic differences) were identified that correlated with high versus low L:M cone ratio. These findings are consistent with the biological principle that DNA sequence variations affect binding affinities for protein components of complexes that influence the relative probability that an L versus M opsin gene will be silenced during development, and in turn, produce variation in the proportion of L to M cones.
Color vision in the black howler monkey (Alouatta caraya)
Authors: ARAÚJO ANTÔNIO C. , DIDONET JULIA J. , ARAÚJO CAROLINA S. , SALETTI PATRÍCIA G. , BORGES TÂNIA R.J. , PESSOA VALDIR F.
Published: July 2008

Electrophysiological and molecular genetic studies have shown that howler monkeys (Alouatta) are unique among all studied platyrrhines: they have the potential to display trichromatic color vision among males and females. This study examined the color discrimination abilities of four howler monkeys (Alouatta caraya) through a series of tasks involving a behavioral paradigm of discrimination learning. The animals were maintained and housed as a group in the Zoological Gardens of Brasília and were tested in their own home cages. Stimuli consisting of pairs of Munsell color chips were presented in random brightness values to assure that discriminations were based on color rather than brightness cues. All the animals (three males, one female) successfully discriminated all the stimulus pairs, including those that would be expected to be difficult for a dichromatic monkey. These results are consistent with the earlier predictions suggesting that howler monkeys are routinely trichromatic.
Dissimilarity of yellow-blue surfaces under neutral light sources differing in intensity: Separate contributions of light intensity and chroma
Authors: TOKUNAGA RUMI , LOGVINENKO ALEXANDER D. , MALONEY LAURENCE T.
Published: July 2008

Observers viewed two side-by-side arrays each of which contained three yellow Munsell papers, three blue, and one neutral Munsell. Each array was illuminated uniformly and independently of the other. The neutral light source intensities were 1380, 125, or 20 lux. All six possible combinations of light intensities were set as illumination conditions. On each trial, observers were asked to rate the dissimilarity between each chip in one array and each chip in the other by using a 30-point scale. Each pair of surfaces in each illumination condition was judged five times. We analyzed this data using non-metric multi-dimensional scaling to determine how light intensity and surface chroma contributed to dissimilarity and how they interacted. Dissimilarities were captured by a three-dimensional configuration in which one dimension corresponded to differences in light intensity.
The color of night: Surface color categorization by color defective observers under dim illuminations
Authors: POKORNY JOEL , LUTZE MARGARET , CAO DINGCAI , ZELE ANDREW J.
Published: July 2008

People with normal trichromatic color vision experience variegated hue percepts under dim illuminations where only rod photoreceptors mediate vision. Here, hue perceptions were determined for persons with congenital color vision deficiencies over a wide range of light levels, including very low light levels where rods alone mediate vision. Deuteranomalous trichromats, deuteranopes and protanopes served as observers. The appearances of 24 paper color samples from the OSA Uniform Color Scales were gauged under successively dimmer illuminations from 10 to 0.0003 Lux (1.0 to −3.5 log Lux). Triads of samples were chosen representing each of eight basic color categories; “red,” “pink,” “orange,” “yellow,” “green,” “blue,” “purple,” and “gray.” Samples within each triad varied in lightness. Observers sorted samples into groups that they could categorize with specific color names. Above −0.5 log Lux, the dichromatic and anomalous trichromatic observers sorted the samples into the original representative color groups, with some exceptions. At light levels where rods alone mediate vision, the color names assigned by the deuteranomalous trichromats were similar to the color names used by color normals; higher scotopic reflectance samples were classified as blue-green-grey and lower reflectance samples as red-orange. Color names reported by the dichromats at the dimmest light levels had extensive overlap in their sample scotopic lightness distributions. Dichromats did not assign scotopic color names based on the sample scotopic lightness, as did deuteranomalous trichromats and colour-normals. We reasoned that the reduction in color gamut that a dichromat experiences at photopic light levels leads to a limited association of rod color perception with objects differing in scotopic reflectance.
Longitudinal evaluation of expression of virally delivered transgenes in gerbil cone photoreceptors
Authors: MAUCK MATTHEW C. , MANCUSO KATHERINE , KUCHENBECKER JAMES A. , CONNOR THOMAS B. , HAUSWIRTH WILLIAM W. , NEITZ JAY , NEITZ MAUREEN
Published: July 2008

Delivery of foreign opsin genes to cone photoreceptors using recombinant adeno-associated virus (rAAV) is a potential tool for studying the basic mechanisms underlying cone based vision and for treating vision disorders. We used an in vivo retinal imaging system to monitor, over time, expression of virally-delivered genes targeted to cone photoreceptors in the Mongolian gerbil (Meriones unguiculatus). Gerbils have a well-developed photopic visual system, with 11–14% of their photoreceptors being cones. We used replication deficient serotype 5 rAAV to deliver a gene for green fluorescent protein (GFP). In an effort to direct expression of the gene specifically to either S or M cones, the transgene was under the control of either the human X-chromosome opsin gene regulatory elements, i.e., an enhancer termed the locus control region (LCR) and L promoter, or the human S-opsin promoter. Longitudinal fluorescence images reveal that gene expression is first detectable about 14 days post-injection, reaches a peak after about 3 months, and is observed more than a year post-injection if the initial viral concentration is sufficiently high. The regulatory elements are able to direct expression to a subpopulation of cones while excluding expression in rods and non-photoreceptor retinal cells. When the same viral constructs are used to deliver a human long-wavelength opsin gene to gerbil cones, stimulation of the introduced human photopigment with long-wavelength light produces robust cone responses.
A computer-controlled color vision test for children based on the Cambridge Colour Test
Authors: GOULART PAULO R. K. , BANDEIRA MARCIO L. , TSUBOTA DANIELA , OIWA NESTOR N. , COSTA MARCELO F. , VENTURA DORA F.
Published: July 2008

The present study aimed at providing conditions for the assessment of color discrimination in children using a modified version of the Cambridge Colour Test (CCT, Cambridge Research Systems Ltd., Rochester, UK). Since the task of indicating the gap of the Landolt C used in that test proved counterintuitive and/or difficult for young children to understand, we changed the target stimulus to a patch of color approximately the size of the Landolt C gap (about 7° of visual angle at 50 cm from the monitor). The modifications were performed for the CCT Trivector test which measures color discrimination for the protan, deutan and tritan confusion lines. Experiment 1 sought to evaluate the correspondence between the CCT and the child-friendly adaptation with adult subjects (n= 29) with normal color vision. Results showed good agreement between the two test versions. Experiment 2 tested the child-friendly software with children 2 to 7 years old (n= 25) using operant training techniques for establishing and maintaining the subjects' performance. Color discrimination thresholds were progressively lower as age increased within the age range tested (2 to 30 years old), and the data—including those obtained for children—fell within the range of thresholds previously obtained for adults with the CCT. The protan and deutan thresholds were consistently lower than tritan thresholds, a pattern repeatedly observed in adults tested with the CCT. The results demonstrate that the test is fit for assessment of color discrimination in young children and may be a useful tool for the establishment of color vision thresholds during development.
Poorer color discrimination by females when tested with pseudoisochromatic plates containing vanishing designs on neutral backgrounds
Authors: BARAAS RIGMOR C.
Published: July 2008

It might be expected that normal trichromatic females would perform as well as normal trichromatic males of the same age when tested with standard clinical color-vision tests that use pseudoisochromatic vanishing designs on neutral gray backgrounds such as the Hardy-Rand-Rittler (HRR) pseudoisochromatic plates and the Neitz Test of Color Vision (NTCV). Here 2966 children aged 6–13 years from four municipalities in Norway were tested in their school classrooms with the NTCV. Children who made errors on the test were retested. 187 males and 152 females made one or more errors on retest, and each was tested individually on the Richmond HRR Fourth Edition. 8% of the males were defined as color deficient when a double criterion for failing was applied, that is, one or more errors on the NTCV and two or more errors on the HRR. The calculated frequency of color-deficient females (homozygotes) for the same criterion is 0.42%. By contrast, 3% of females failed the criterion that gave a stable population of color-deficient males. This result is considered in relation to reports of female carriers of color-vision deficiency having problems with the Ishihara test and of females having poorer color discrimination than males.
The phenomenal dissociation between coloration and object-hole effects in the watercolor illusion
Authors: TANCA MARIA , PINNA BAINGIO
Published: July 2008

The watercolor illusion is a color spreading effect at long-range diffusing from a thin colored contour juxtaposed to a chromatic one of higher contrast and a object-hole effect across a large area (Pinna, 1987; Pinna et al., 2001, 2003; Pinna & Reeves, 2006). The watercolored figure appears evenly colored by an opaque light veil of chromatic tint (coloration effect), with a clear surface color property spreading from the lighter contour. At the same time, the watercolored figure manifests a strong figure-ground organization and a solid figural appearance comparable to a bas-relief illuminated from the top (object-hole effect). It appears similar to a rounded surface segregated in depth, which extends out from the flat surface. The complementary region appears as a hole or empty space. The phenomenal properties of coloration and object-hole effects raise some questions. Can the two effects be considered relatively independent? Under what conditions can a possible dissociation occur? How does the dissociation of one effect, say the coloration, influence the object-hole effect and vice versa? To answer these questions two new effects related to the watercolor illusion were psychophysically studied: (1) the “uneven watercolor,” based on a modified watercolor figure without volumetric and three-dimensional properties but with a strong coloration effect and (2) the “watercolor surface capture,” where oblique lines within a watercolor figure appear bulging, curved in depth and segregated from those that are perceived as placed in the background or perceived through holes. The results of two experiments suggest that the coloration effect can be dissociated from the object-hole one. These results are discussed in the light of a simple summation hypothesis of the underlying effects composing the whole figurality. This hypothesis can suggest further investigation both in the phenomenal and in the neurophysiological domain.
Guest Editors' Foreword: Proceedings of the 19th Biennial Symposium of the International Colour Vision Society. Held July 2007 Belém, Brazil
Authors: Silveira Luiz Carlos de Lima , Smithson Hannah , Ventura Dora Fix , Lee Barry B.
Published: July 2008

The 19th Symposium of the International Colour Vision Society (ICVS) was held in Belém, Brazil in July 2007. This was the first time that the Society has met in Latin America. The Amazonian region was a unique location for this inauguration due both to its situation close to a vast, largely unexplored region of nature, and resources—an inspiring challenge for scientific study—and to the quality of the vision research developing in the region.
Initial Fluvial Response to the Removal of Oregon's Marmot Dam
Authors: Major Jon J. , Spicer Kurt R. , Rhode Abagail , O'Connor Jim E. , Bragg Heather M. , Tanner Dwight Q. , Anderson Chauncey W. , Wallick J. Rose , Grant Gordon E.
Published: July 2008

A temporary, 14‐meter‐high earthen cofferdam standing in place of Marmot Dam was breached on 19 October 2007, allowing the 80‐ kilometer‐long Sandy River to flow freely from Mount Hood, Oreg., to the Columbia River for the first time in nearly 100 years. Marmot Dam is one of the largest dams in the western United States (in terms of height and volume of stored sediment) to have been removed in the past 40 years, and its removal exposed approximately 730,000 cubic meters of stored sand and gravel to erosion and transport by the newly energetic mountain river. At the time, its breach represented the greatest release of sediment from any U.S. dam removal. (The March 2008 breaching of Montana's Milltown Dam exposed about 5–10 times as much sediment to potential erosion.)
Survey of Geoscience Departments Finds Shared Goals and Challenges
Authors: Richardson Randall M. , Ormand Carol J.
Published: July 2008

Results of an online survey of a broad variety of geoscience departments at Canadian and U.S. colleges and universities have indicated a striking degree of common perspective across institution types. In the survey, which was sent to 900 institutions and completed by 364 respondents (for a response rate of nearly 40%), respondents noted that three of the most important measures of a successful department were effective curricula; recruitment of students, staff, and faculty; and building partnerships within and outside of their institutions.
Climate change and the tropopause
Authors: Showstack Randy
Published: July 2008

The Stratosphere‐Troposphere Analyses of Regional Transport (START08) project, which continued through June, is helping researchers improve computer models of global climate in preparation for the next report by the Intergovernmental Panel on Climate Change. The project, based at the National Center for Atmospheric Research (NCAR) in Boulder, Colo., has focused on the tropopause and deploys the U.S. National Science Foundation/NCAR Gulfstream‐V airplane (also known as the High‐Performance Instrumented Airborne Platform for Environmental Research (HIAPER)) to take air samples.
A late Quaternary climate reconstruction based on borehole heat flux data, borehole temperature data, and the instrumental record
Authors: Huang S. P. , Pollack H. N. , Shen P.‐Y.
Published: July 2008

We present a suite of new 20,000 year reconstructions that integrate three types of geothermal information: a global database of terrestrial heat flux measurements, another database of temperature versus depth observations, and the 20th century instrumental record of temperature, all referenced to the 1961–1990 mean of the instrumental record. These reconstructions show the warming from the last glacial maximum, the occurrence of a mid‐Holocene warm episode, a Medieval Warm Period (MWP), a Little Ice Age (LIA), and the rapid warming of the 20th century. The reconstructions show the temperatures of the mid‐Holocene warm episode some 1–2 K above the reference level, the maximum of the MWP at or slightly below the reference level, the minimum of the LIA about 1 K below the reference level, and end‐of‐20th century temperatures about 0.5 K above the reference level.
SuperDARN observations of daytime MSTIDs in the auroral and mid‐latitudes: Possibility of long‐distance propagation
Authors: Ishida T. , Hosokawa K. , Shibata T. , Suzuki S. , Nishitani N. , Ogawa T.
Published: July 2008

The propagation parameters of daytime medium‐scale traveling ionospheric disturbances (MSTIDs) are investigated for the first time using near‐simultaneous SuperDARN radar data obtained at auroral and middle latitudes. The observations suggest that MSTIDs can propagate from auroral to mid‐latitudes with persistent propagation parameters if the dominant propagation direction is approximately equatorward. However, statistical analysis implies that a portion of MSTIDs with higher horizontal phase velocity are unable to reach the mid‐latitude due to enhanced dissipation and the reduction of the ion‐drag effect.
Nitrate and nitrite in Australian leafy vegetables
Authors: Parks S. E. , Huett D. O. , Campbell L. C. , Spohr L. J.
Published: July 2008

A market survey of Australian leafy vegetables and a winter and spring experiment with Swiss chard were conducted to examine nitrate and nitrite levels in leaves. The relationship between growth response to nitrogen (N) supply and light level and accumulation of N in leaves was of particular interest. The survey that included 7 types of lettuce and endive (Asteraceae), 6 leafy Asian vegetables (Brassicaceae), and Swiss chard and spinach (Amaranthaceae) showed that fresh leafy vegetables available during a 6-month period on the Australian market can range in nitrate-N from 12 to 1400 mg/kg fresh weight and nitrite-N from 0 to 37.5 mg/kg. Some samples exceeded the limits for nitrate and nitrite based on international food safety standards. The response of Swiss chard to N supply and light was investigated. The accumulation of nitrate in Swiss chard was primarily influenced by increasing N supply and not by light level. Light conditions for all treatments in both the winter and spring experiments exceeded the critical level (~200 μmol/m2.s) required to increase leaf nitrate. Growth and leaf nitrate concentration were higher for spring, associated with average minimum to maximum temperatures of 18–39°C, compared with 14–28°C for winter. Treatment effects on nitrite-N in Swiss chard could not be determined because nitrite was only detected in one-third of plants. The importance of N supply in affecting nitrate accumulation in vegetables is highlighted by the Swiss chard experiments. It confirmed that nitrate accumulation occurs at optimal to supra-optimal nitrate supply, emphasising for growers the undesirable effect of excessive fertiliser use.
A comprehensive assay for targeted multiplex amplification of human DNA sequences
Authors: Krishnakumar Sujatha , Zheng Jianbiao , Wilhelmy Julie , Faham Malek , Mindrinos Michael , Davis Ronald
Published: July 2008

We developed a robust and reproducible methodology to amplify human sequences in parallel for use in downstream multiplexed sequence analyses. We call the methodology SMART (Spacer Multiplex Amplification Reaction), and it is based, in part, on padlock probe technology. As a proof of principle, we used SMART technology to simultaneously amplify 485 human exons ranging from 100 to 500 bp from human genomic DNA. In multiple repetitions, >90% of the targets were successfully amplified with a high degree of uniformity, with 70% of targets falling within a 10-fold range and all products falling within a 100-fold range of each other in abundance. We used long padlock probes (LPPs) >300 bases in length for the assay, and the increased length of these probes allowed for the capture of human sequences up to 500 bp in length, which is optimal for capturing most human exons. To engineer the LPPs, we developed a method that generates ssDNA molecules with precise ends, using an appropriately designed dsDNA template. The template has appropriate restriction sites engineered into it that can be digested to generate nucleotide overhangs that are suitable for lambda exonuclease digestion, producing a single-stranded probe from dsDNA. The SMART technology is flexible and can be easily adapted to multiplex tens of thousands of target sequences in a single reaction.
ERPs studies of cognitive processing during sleep
Authors: Ibáñez Agustín M. , Martín René San , Hurtado Esteban , López Vladimir
Published: July 2008

In the last few decades, several works on cognitive processing during sleep have emerged. The study of cognitive processing with event related potentials (ERPs) during sleep is a topic of great interest, since ERPs allow the study of stimulation with passive paradigms (without conscious response or behavioural response), opening multiple research possibilities during different sleep phases. We review ERPs modulated by cognitive processes during sleep: N1, Mismatch Negativity (MMN), P2, P3, N400‐like, N300–N550, among others. The review shows that there are different cognitive discriminations during sleep related to the frequency, intensity, duration, saliency, novelty, proportion of appearance, meaning, and even sentential integration of stimuli. The fascinating results of cognitive processing during sleep imply serious challenges for cognitive models. The studies of ERPs, together with techniques of neuroimaging, have demonstrated the existence of cognitive processing during sleep. A fundamental question to be considered is if these cognitive phenomena are similar to processing that occurs during wakefulness. Based on this question we discussed the existence of possible mechanisms associated with sleep, as well as the specific cognitive and neurophysiologic differences of wakefulness and sleep. Much knowledge is still required to even understand the conjunction of dramatic changes in cerebral dynamics and the occurrence of cognitive processes. We propose some insights based on ERPs research for further construction of theoretical models for integrating both cognitive processing and specific brain sleep dynamics.
The DEAD-Box RNA Helicase DDX3 Associates with Export Messenger Ribonucleoproteins as well asTip-associated Protein and Participates in Translational Control
Authors: Lai Ming-Chih , Lee Yan-Hwa Wu , Tarn Woan-Yuh
Published: July 2008

Nuclear export of mRNA is tightly linked to transcription, nuclear mRNA processing, and subsequent maturation in the cytoplasm. Tip-associated protein (TAP) is the major nuclear mRNA export receptor, and it acts coordinately with various factors involved in mRNA expression. We screened for protein factors that associate with TAP and identified several candidates, including RNA helicase DDX3. We demonstrate that DDX3 directly interacts with TAP and that its association with TAP as well as mRNA ribonucleoprotein complexes may occur in the nucleus. Depletion of TAP resulted in nuclear accumulation of DDX3, suggesting that DDX3 is, at least in part, exported along with messenger ribonucleoproteins to the cytoplasm via the TAP-mediated pathway. Moreover, the observation that DDX3 localizes transiently in cytoplasmic stress granules under cell stress conditions suggests a role for DDX3 in translational control. Indeed, DDX3 associates with translation initiation complexes. However, DDX3 is probably not critical for general mRNA translation but may instead promote efficient translation of mRNAs containing a long or structured 5′ untranslated region. Given that the DDX3 RNA helicase activity is essential for its involvement in translation, we suggest that DDX3 facilitates translation by resolving secondary structures of the 5′-untranslated region in mRNAs during ribosome scanning.
ChemmineR: a compound mining framework for R
Authors: Cao Yiqun , Charisi Anna , Cheng Li-Chang , Jiang Tao , Girke Thomas
Published: July 2008

Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popularstatistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions.

Results: We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services.

Availability:  ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer

Contact:  thomas.girke@ucr.edu
Coherent coupling of feedback loops: a design principle of cell signaling networks
Authors: Kwon Yung-Keun , Cho Kwang-Hyun
Published: July 2008

Motivation:It is widely accepted that cell signaling networks have been evolved to be robust against perturbations. To investigate the topological characteristics resulting in such robustness, we have examined large-scale signaling networks and found that a number of feedback loops are present mostly in coupled structures. In particular, the coupling was made in a coherent way implying that same types of feedback loops are interlinked together.

Results: We have investigated the role of such coherently coupled feedback loops through extensive Boolean network simulations and found that a high proportion of coherent couplings can enhance the robustness of a network against its state perturbations. Moreover, we found that the robustness achieved by coherently coupled feedback loops can be kept evolutionarily stable. All these results imply that the coherent coupling of feedback loops might be a design principle of cell signaling networks devised to achieve the robustness.

Contact:  ckh@kaist.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Extant mammal body masses suggest punctuated equilibrium
Authors: Mattila Tiina M , Bokma Folmer
Published: July 2008

Is gradual microevolutionary change within species simultaneously the source of macroevolutionary differentiation between species? Since its first publication, Darwin's original idea that phenotypic differences between species develop gradually over time, as the accumulation of small selection-induced changes in successive generations has been challenged by palaeontologists claiming that, instead, new species quickly acquire their phenotypes to remain virtually unchanged until going extinct again. This controversy, widely known as the ‘punctuated equilibrium’ debate, remained unresolved, largely owing to the difficulty of distinguishing biological species from fossil remains. We analysed body masses of 2143 existing mammal species on a phylogeny comprising 4510 (i.e. nearly all) extant species to estimate rates of gradual (anagenetic) and speciational (cladogenetic) evolution. Our Bayesian estimates from mammals as well as separate sub-clades such as primates and carnivores suggest that gradual evolution is responsible for only a small part of body size variation between mammal species.
Parasitic mites as part-time bodyguards of a host wasp
Authors: Okabe Kimiko , Makino Shun'ichi
Published: July 2008

Some bees and wasps that host mites have peculiar pocket-like structures called acarinaria. These have long been considered as morphological adaptations to securely transfer beneficial mites into nests, and thus are thought to be the product of a mutualistic relationship. However, there has been little compelling evidence to support this hypothesis. We demonstrated that the parasitic miteEnsliniella parasitica, which uses acarinaria, increases the reproductive success of its host waspAllodynerus delphinalisby protecting it from parasitoid wasps. Every time the parasitoidMelittobia acastaaccessed a prepupal or pupal wasp host cell, adult mites attacked it, continuously clinging to it and possibly piercing the intersegmental membrane of the parasitoid with their chelicerae. Subsequent mortality of the parasitoid depended on the number of attacking mites: an average of six mites led to a 70% chance of mortality, and 10 mites led to a 100% chance of mortality. In this way, parent mites protect the food source (juvenile wasps) for themselves and ultimately for their offspring. We propose that wasps evolved acarinaria to maintain this protective guarding behaviour.
Neuronal Diversity and Temporal Dynamics: The Unity of Hippocampal Circuit Operations
Authors: Klausberger Thomas , Somogyi Peter
Published: July 2008

In the cerebral cortex, diverse types of neurons form intricate circuits and cooperate in time for the processing and storage of information. Recent advances reveal a spatiotemporal division of labor in cortical circuits, as exemplified in the CA1 hippocampal area. In particular, distinct GABAergic (γ-aminobutyric acid–releasing) cell types subdivide the surface of pyramidal cells and act in discrete time windows, either on the same or on different subcellular compartments. They also interact with glutamatergic pyramidal cell inputs in a domain-specific manner and support synaptic temporal dynamics, network oscillations, selection of cell assemblies, and the implementation of brain states. The spatiotemporal specializations in cortical circuits reveal that cellular diversity and temporal dynamics coemerged during evolution, providing a basis for cognitive behavior.
Self-Sorted, Aligned Nanotube Networks for Thin-Film Transistors
Authors: LeMieux Melburne C. , Roberts Mark , Barman Soumendra , Jin Yong Wan , Kim Jong Min , Bao Zhenan
Published: July 2008

To find use in electronics, single-walled carbon nanotubes need to be efficiently separated by electronic type and aligned to ensure optimal and reproducible electronic properties. We report the fabrication of single-walled carbon nanotube (SWNT) network field-effect transistors, deposited from solution, possessing controllable topology and an on/off ratio as high as 900,000. The spin-assisted alignment and density of the SWNTs are tuned by different surfaces that effectively vary the degree of interaction with surface functionalities in the device channel. This leads to a self-sorted SWNT network in which nanotube chirality separation and simultaneous control of density and alignment occur in one step during device fabrication. Micro-Raman experiments corroborate device results as a function of surface chemistry, indicating enrichment of the specific SWNT electronic type absorbed onto the modified dielectric.
Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops
Authors: Tsai Tony Yu-Chen , Choi Yoon Sup , Ma Wenzhe , Pomerening Joseph R. , Tang Chao , Ferrell James E.
Published: July 2008

A simple negative feedback loop of interacting genes or proteins has the potential to generate sustained oscillations. However, many biological oscillators also have a positive feedback loop, raising the question of what advantages the extra loop imparts. Through computational studies, we show that it is generally difficult to adjust a negative feedback oscillator's frequency without compromising its amplitude, whereas with positive-plus-negative feedback, one can achieve a widely tunable frequency and near-constant amplitude. This tunability makes the latter design suitable for biological rhythms like heartbeats and cell cycles that need to provide a constant output over a range of frequencies. Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant.
Finite Scale of Spatial Representation in the Hippocampus
Authors: Kjelstrup Kirsten Brun , Solstad Trygve , Brun Vegard Heimly , Hafting Torkel , Leutgeb Stefan , Witter Menno P. , Moser Edvard I. , Moser May-Britt
Published: July 2008

To determine how spatial scale is represented in the pyramidal cell population of the hippocampus, we recorded neural activity at multiple longitudinal levels of this brain area while rats ran back and forth on an 18-meter-long linear track. CA3 cells had well-defined place fields at all levels. The scale of representation increased almost linearly from <1 meter at the dorsal pole to ∼10 meters at the ventral pole. The results suggest that the place-cell map includes the entire hippocampus and that environments are represented in the hippocampus at a topographically graded but finite continuum of scales.
Large and Rapid Melt-Induced Velocity Changes in the Ablation Zone of the Greenland Ice Sheet
Authors: van de Wal R. S. W. , Boot W. , van den Broeke M. R. , Smeets C. J. P. P. , Reijmer C. H. , Donker J. J. A. , Oerlemans J.
Published: July 2008

Continuous Global Positioning System observations reveal rapid and large ice velocity fluctuations in the western ablation zone of the Greenland Ice Sheet. Within days, ice velocity reacts to increased meltwater production and increases by a factor of 4. Such a response is much stronger and much faster than previously reported. Over a longer period of 17 years, annual ice velocities have decreased slightly, which suggests that the englacial hydraulic system adjusts constantly to the variable meltwater input, which results in a more or less constant ice flux over the years. The positive-feedback mechanism between melt rate and ice velocity appears to be a seasonal process that may have only a limited effect on the response of the ice sheet to climate warming over the next decades.
Volcanism on Mercury: Evidence from the First MESSENGER Flyby
Authors: Head James W. , Murchie Scott L. , Prockter Louise M. , Robinson Mark S. , Solomon Sean C. , Strom Robert G. , Chapman Clark R. , Watters Thomas R. , McClintock William E. , Blewett David T. , Gillis-Davis Jeffrey J.
Published: July 2008

The origin of plains on Mercury, whether by volcanic flooding or impact ejecta ponding, has been controversial since the Mariner 10 flybys (1974–75). High-resolution images (down to 150 meters per pixel) obtained during the first MESSENGER flyby show evidence for volcanic vents around the Caloris basin inner margin and demonstrate that plains were emplaced sequentially inside and adjacent to numerous large impact craters, to thicknesses in excess of several kilometers. Radial graben and a floor-fractured crater may indicate intrusive activity. These observations, coupled with additional evidence from color images and impact crater size-frequency distributions, support a volcanic origin for several regions of plains and substantiate the important role of volcanism in the geological history of Mercury.
Geology of the Caloris Basin, Mercury: A View from MESSENGER
Authors: Murchie Scott L. , Watters Thomas R. , Robinson Mark S. , Head James W. , Strom Robert G. , Chapman Clark R. , Solomon Sean C. , McClintock William E. , Prockter Louise M. , Domingue Deborah L. , Blewett David T.
Published: July 2008

The Caloris basin, the youngest known large impact basin on Mercury, is revealed in MESSENGER images to be modified by volcanism and deformation in a manner distinct from that of lunar impact basins. The morphology and spatial distribution of basin materials themselves closely match lunar counterparts. Evidence for a volcanic origin of the basin's interior plains includes embayed craters on the basin floor and diffuse deposits surrounding rimless depressions interpreted to be of pyroclastic origin. Unlike lunar maria, the volcanic plains in Caloris are higher in albedo than surrounding basin materials and lack spectral evidence for ferrous iron-bearing silicates. Tectonic landforms, contractional wrinkle ridges and extensional troughs, have distributions and age relations different from their counterparts in and around lunar basins, indicating a different stress history.
Relativistic Spin Precession in the Double Pulsar
Authors: Breton Rene P. , Kaspi Victoria M. , Kramer Michael , McLaughlin Maura A. , Lyutikov Maxim , Ransom Scott M. , Stairs Ingrid H. , Ferdman Robert D. , Camilo Fernando , Possenti Andrea
Published: July 2008

The double pulsar PSR J0737–3039A/B consists of two neutron stars in a highly relativistic orbit that displays a roughly 30-second eclipse when pulsar A passes behind pulsar B. Describing this eclipse of pulsar A as due to absorption occurring in the magnetosphere of pulsar B, we successfully used a simple geometric model to characterize the observed changing eclipse morphology and to measure the relativistic precession of pulsar B's spin axis around the total orbital angular momentum. This provides a test of general relativity and alternative theories of gravity in the strong-field regime. Our measured relativistic spin precession rate of

\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(4.77{^\circ}_{-0{^\circ}.65}^{+0{^\circ}.66}\) \end{document}

per year (68% confidence level) is consistent with that predicted by general relativity within an uncertainty of 13%.
Characterization of Step-Edge Barriers in Organic Thin-Film Growth
Authors: Hlawacek Gregor , Puschnig Peter , Frank Paul , Winkler Adolf , Ambrosch-Draxl Claudia , Teichert Christian
Published: July 2008

Detailed understanding of growth mechanisms in organic thin-film deposition is crucial for tailoring growth morphologies, which in turn determine the physical properties of the resulting films. For growth of the rodlike molecule
para
-sexiphenyl, the evolution of terraced mounds is observed by atomic force microscopy. Using methods established in inorganic epitaxy, we demonstrate the existence of an additional barrier (0.67 electron volt) for step-edge crossing—the Ehrlich-Schwoebel barrier. This result was confirmed by transition state theory, which revealed a bending of the molecule at the step edge. A gradual reduction of this barrier in the first layers led to an almost layer-by-layer growth during early deposition stage. The reported phenomena are a direct consequence of the complexity of the molecular building blocks versus atomic systems.
Impaired Gamma Interferon Response to
Mycobacterium vaccae
Antigens in Patients with Cavitary Pulmonary Tuberculosis
Authors: Rodríguez-Güell Elisabeth , Agustí Gemma , Corominas Mercè , Luquin Marina , Julián Esther
Published: July 2008

The ability of tuberculosis patients to recognize
Mycobacterium vaccae
-specific antigens before starting chemotherapy and according to disease severity was analyzed. We report that the
M. vaccae
cell wall skeleton fraction triggers more enhanced cytokine production than the whole bacterium. Moreover, a tendency was observed for a lower gamma interferon/interleukin-10 ratio in patients with cavitary disease induced by
M. vaccae
antigens.
Vancomycin Heteroresistance in Bloodstream Isolates of
Staphylococcus capitis
Authors: D'mello Danaë , Daley Andrew J. , Rahman Muhammad Shihab , Qu Yue , Garland Suzanne , Pearce Christopher , Deighton Margaret A.
Published: July 2008

Nine
Staphylococcus capitis
isolates from blood cultures of newborns were examined for resistance to vancomycin. MICs were within the susceptible range, but population profiling revealed a resistant subpopulation. Only isolates with the largest subpopulation were identified as heteroresistant to vancomycin by Etest. This finding may have therapeutic implications.