bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance evaluation of precision nanopositioning devices caused by uncertainties due to tolerances using function approximation moment method
Authors: Huh J. S. , Kim K. H. , Kang D. W. , Gweon D. G. , Kwak B. M.
Published: January 2006

Precision nanopositioning is an important technology in industry and requires tight design specifications. Tolerances, although very small, are allocated in all dimensions of structures at devices and are understood as sources of performance variations. In this research, we aim to study detail influence of tolerances on various system response functions of a precision stage, especially parasitic motion and resonant frequencies. A function approximation moment method (FAMM) is developed and applied to study it. The variations are mathematically expressed as their statistical moments and the probabilities of satisfaction are obtained as a result of the FAMM. A finite element model of the target stage, which is nonmonolithic, is generated and verified with basic measurements. The possible initial deformation after assembly is found by the formulation of minimizing strain energy. With this model, the FAMM is used to estimate the statistical moments and probability density functions of the performance functions. The calculated results facilitate understanding of the characteristics of the stage in terms of probability. The inevitable mismatch, even under a small tolerance, is found to cause a large parasitic motion and should be considered in the design and manufacturing process.
First-principles calculations of structural and mechanical properties of Cu6Sn5
Authors: Lee N. T. S. , Tan V. B. C. , Lim K. M.
Published: January 2006

The elastic constants of polycrystalline Cu6Sn5—an intermetallic in lead-free alternatives of several material systems—are presented. The results are obtained by applying: (i) Reported crystallographic structure of monoclinic single crystal Cu6Sn5, (ii) structure optimization and determination of single crystal elastic constants from first principle calculations, and (iii) limit analysis of polycrystal stiffness based on single crystal properties. The agreement between the calculated Young’s modulus (120 GPa) and those from nanoindentation experiments (112–125 GPa), and the tight bounds on the predicted polycrystal values give a measure of confidence in other calculated properties for which experimental data are unavailable.
Ferromagnetic order in Ge1−xCrxTe
Authors: Fukuma Y. , Asada H. , Koyanagi T.
Published: January 2006

The ferromagnetic properties of IV-VI diluted magnetic semiconductor Ge1−xCrxTe films prepared by sputtering are investigated. The ferromagnetism such as the spontaneous magnetization and the Curie temperature is significantly affected by the stoichiometry, while the ferromagnetism of Ge1−xMnxTe films was hardly affected by the defects and depended strongly on the hole concentration [Y. Fukuma, H. Asada, N. Nishimura, and T. Koyanagui, J. Appl. Phys. 93, 4034 (2003)]. The difference could be ascribed to the interaction of the ferromagnetic order: short-range order such as a superexchange mechanism plays more an important role than long-range order such as a Ruderman-Kittel-Kasuya-Yosida mechanism in the ferromagnetism of the Ge1−xCrxTe films.
Measuring Multiple Deprivation at the Small-Area Level
Authors: Noble Michael , Wright Gemma , Smith George , Dibben Chris
Published: January 2006

Indices to measure deprivation at a small-area level have been used in the United Kingdom to target regeneration policy for over thirty years. The development of the Indices of Deprivation 2000 for England and comparable indices for Northern Ireland, Wales, and Scotland, involved a fundamental reappraisal and reconceptualisation of small-area level multiple deprivation and its measurement. Multiple deprivation is articulated as an accumulation of discrete dimensions or ‘domains’ of deprivation. This paper presents the key principles that were taken into consideration when constructing these four indices and the more recent English Indices of Deprivation 2004, and provides an account of the statistical techniques that were used to operationalise them.
Retail Restructuring and Consumer Choice 1. Long-Term Local Changes in Consumer Behaviour: Portsmouth, 1980–2002
Authors: Clarke Ian , Hallsworth Alan , Jackson Peter , de Kervenoael Ronan , del Aguila Rossana Perez , Kirkup Malcolm
Published: January 2006

Over the last two decades fundamental changes have taken place in the global supply and local structure of provision of British food retailing. Consumer lifestyles have also changed markedly. Despite some important studies of local interactions between new retail developments and consumers, we argue in this paper that there is a critical need to gauge the cumulative effects of these changes on consumer behaviour over longer periods. In this, the first of two papers, we present the main findings of a study of the effects of long-term retail change on consumers at the local level. We provide in this paper an overview of the changing geography of retail provision and patterns of consumption at the local level. We contextualise the Portsmouth study area as a locality that typifies national changes in retail provision and consumer lifestyles; outline the main findings of two large-scale surveys of food shopping behaviour carried out in 1980 and 2002; and reveal the impacts of retail restructuring on consumer behaviour. We focus in particular on choice between stores at the local level and end by problematising our understanding of how consumers experience choice, emphasising the need for qualitative research. This issue is then dealt with in our complementary second paper, which explores choice within stores and how this relates to the broader spatial context.
Sovereigns and Subjects: A Geopolitical History of Metropolitan Reform in the USA
Authors: Johnson Katherine M
Published: January 2006

Why does metropolitan reform have such a poor track record in the United States as compared with other industrialized countries? The most common answer is the exceptional localism of US culture, which has embedded itself over the years in institutions that foster political fragmentation and sprawl. This paper, inspired by recent developments in Europe, offers an alternative explanation in the divided sovereignty of the US federal system. Sovereignty, a highly debated concept at the global level, remains a very real political hurdle at the local level because it constitutes the primary field of struggle for any claims for local self-government. The significance of divided sovereignty is the potential recourse that a second sovereign can offer to metropolitan reformers. A reframing of the issue from a constitutional perspective reveals a sharp contrast in the political conditions for metropolitan reform between Europe and the USA today: as sovereignty has moved up in Europe, secured by treaties that have shifted whole realms of authority and right to the European Union, it has been moving down in the USA, pushed by a generation of Republican presidents and an activist Supreme Court. It also highlights a political fault line that has been largely missing from theoretical and policy debates over metropolitan reform in the USA: the conflict between the big cities and their direct sovereign, the subnational states. In this paper I reconsider the troubled history of metropolitan reform in the United States from this constitutional perspective, situating efforts to achieve metropolitan self-governance in the context of the shifting division of sovereignty in the US federal system over the past seventy years.
Segmented Local Labor Markets in Postreform China: Gender Earnings Inequality in the Case of Two Towns in Zhejiang Province
Authors: Xu Wei , Tan Kok-Chiang , Wang Guixin
Published: January 2006

In this paper we aim to explore the segmentation structure of Chinese labor markets, especially gender-related segmentation, at a local level. Through a case-study approach, the discussion is centered on the multiple dualities of the local labor market determined by gender, place, migration, and the rural–urban divide. Although the empirical findings on gender differentiation in Chinese labor markets validate the conclusions of labor-market segmentation theory in general, they also point to the uniqueness of the segmentation processes of the Chinese labor market during the course of its economic transition since the reform. In this study we find that both place and space play an important role in configuring labor market segments, and the spatial construction of local labor markets is shaped greatly by the rural–urban social structure as defined by the household-registration system.
The Retreat of the Upper and Middle Classes to Gated Communities in the Poststructural Adjustment Era: The Case of Trinidad
Authors: Mycoo Michelle
Published: January 2006

The emergence of gated communities of the upper-income and middle-income classes can be directly traced to the failure of governments to close the growing divide between rich and poor and to solve the accompanying wave of crime and fear of violence. It is also a result of an abandonment of faith in governments' capacities to deliver and maintain infrastructure and civic services. State failure has influenced people's decisions to encircle their living space, defend it, and to service their needs autonomously like citizens of the ancient walled cities. The trend toward social exclusion and spatial segregation is characteristic of these modern ministates, which poses planning, policy, and administrative questions for decisionmakers. In this paper I first set out to understand the emergence of gated communities as a global phenomenon, but particularly in the Latin American and Caribbean context. Secondly, I seek to examine the retreat of the upper and middle classes to gated communities in the poststructural adjustment years, using Trinidad as a case study. Finally, I put forward conclusions and policy prescriptions of relevance to cities in addressing the emerging issues.
Evidence for a Role of Action in Colour Perception
Authors: Bompas Aline , O'Regan J Kevin
Published: January 2006

Action is not usually considered to play a role in colour perception. However, sensorimotor theories of perception (eg O'Regan and Noë, 2001 Behavior and Brain Science24 939–1011) suggest that, on the contrary, the transformations created by action in the sensory input are a necessary condition for all perception. In the case of colour vision, eye movements may explain how a retina with significant irregularities in resolution and cone arrangement (Roorda and Williams, 1999 Nature 397 520–522) could permit the perception of a richly coloured world (Clark and O'Regan, 2000 15th International Conference on Pattern Recognition volume 2: Pattern Recognition and Neural Networks pp 503–506; Skaff et al, 2002 16th International Conference on Pattern Recognition volume 2, pp 681–684). We provide evidence that perception of colour is modified when an artificial coupling is introduced linking eye movements and colour changes. After 40 min of wearing left-field-blue/right-field-yellow spectacles, observers' colour vision adapts so that, after removing the spectacles, white patches seem to become bluer when the eyes move rightwards and yellower when the eyes move leftwards. This induced dependence of colour perception on the direction of eye saccade is shown to be related to the amount of eye movements during exposure. This result, which cannot be explained either by retinal adaptation, or by a conditioned association between colour and side, constitutes first clear evidence for a role of eye movements in perceived colour and argues for the involvement in colour perception of neural mechanisms continuously tuned to sensorimotor contingencies.
Tactile Pattern Discrimination at Adjacent Locations along the Proximal — Distal Axis of the Index Finger
Authors: Horner David T
Published: January 2006

A discrimination task was used to examine how locations on the glabrous skin of the terminal and middle phalanges of the index finger affect the perceived shape of tactile patterns. On each trial, a pair of same-shape or different-shape patterns was presented successively on the distal half, on the proximal half, or on both halves of a phalanx. Observers responded “same” or “different” depending on the perceived pattern shape. Performance was compared between the two phalanges, with two different pattern sets. For patterns at separate locations, performance was uniformly poor. For patterns at the same location, performance was better on the distal halves than on the proximal halves of both phalanges for one pattern set but not for the other. Performance was best on the distal half of the terminal phalanx. The results are discussed in terms of the densities of innervation of first-order afferents.
Motion Perception in the Ageing Visual System: Minimum Motion, Motion Coherence, and Speed Discrimination Thresholds
Authors: Snowden Robert J , Kavanagh Emma
Published: January 2006

We aimed to address two issues: first, to describe how the perception of motion differs in elderly observers as compared to younger ones; and, second, to see if these changes in motion perception could be accounted for by the known changes in the ability of elderly observers to detect patterns (as indexed via contrast sensitivity). The lower threshold of motion, motion coherence, and speed discrimination were measured, alongside contrast sensitivity, in a group of thirty-two older (mean age 61.5 years) and thirty-two younger (mean age 23.2 years) subjects. The older observers showed losses in their ability to detect slow motions as indexed via the lower threshold of motion for random-dot patterns and for gratings of a range of spatial frequencies. They also were impaired on a test of motion coherence, but only for stimuli of a slow to medium speed, whereas faster speeds showed no decline with age. Finally, at all speeds tested the older observers required greater differences in speed in order to discriminate between patterns moving at different speeds. The pattern of losses on motion perception tasks was not predicted by the deficits of the older groups, such as loss of detection thresholds for high spatial and/or temporal frequencies. It is concluded that these hypotheses do not provide an adequate account of the data, and therefore that the losses occurring with age are complex and probably are a result of the loss of several types of cell.
Spatial-Frequency Thresholds for Object Categorisation at Basic and Subordinate Levels
Authors: Collin Charles A
Published: January 2006

In an attempt to understand how low-level visual information contributes to object categorisation, previous studies have examined the effects of spatially filtering images on object recognition at different levels of abstraction. Here, the quantitative thresholds for object categorisation at the basic and subordinate levels are determined by using a combination of the method of adjustment and a match-to-sample method. Participants were asked to adjust the cut-off of either a low-pass or high-pass filter applied to a target image until they reached the threshold at which they could match the target image to one of six simultaneously presented category names. This allowed more quantitative analysis of the spatial frequencies necessary for recognition than previous studies. Results indicate that a more central range of low spatial frequencies is necessary for subordinate categorisation than basic, though the difference is small, at about 0.25 octaves. Conversely, there was no effect of categorisation level on high-pass thresholds.
Lipid content of honey bee-collected pollen from south-east Australia
Authors: Somerville D. C.
Published: January 2006

The use of solvent extraction or petroleum spirits to extract lipids (fats) from 172 samples of honey bee-collected pollens provided a range of lipid contents from 0% for Eucalyptus macrorhyncha to 11.2% for Hypochoeris radicata. The mean for all 172 samples, representing 61 species, was 2.52%. The mean from 31 endemic species was 1.78%, whereas the mean for 30 exotic species was 4.13%. When pollens from 1 species, Echium plantagineum, were extensively surveyed, the lipid levels could be predictably estimated, falling within a range of 0.6 to 2.46% and a mean of 1.6%. A number of pollens from particular species consistently showed high levels of lipids, which were observed to be highly favoured by foraging honey bees. The pollens noted to be particularly attractive to foraging honey bees included Brassica napus (mean 7.1%), Sisymbrium officinale (mean 5.8%), Rapistrum rugosum (mean 6%) and Hypochoeris radicata (mean 7.2%).
Mesophaenocora polyova, gen. nov., sp. nov. from Uruguay and establishment of the new subfamily Mesophaenocorinae (Platyhelminthes : Rhabdocoela : Typhloplanidae)
Authors: Noreña Carolina , Brusa Francisco , Ponce de León Rodrigo , Damborenea Cristina
Published: January 2006

Mesophaenocora polyova is a new species discovered in temporary ponds in Uruguay. It has testicles and vitellaria in grape-like bunches, the genital atrium is V-shaped and differentiated into two regions (male and female) and the bursa copulatrix is absent. A seminal receptacle and ‘vesicula resorbiens’ are present. This combination of characters distinguishes Mesophaenocora from the other genera in the Typhloplanidae. A preliminary cladistic analysis of subfamily relationships places the new taxon in a high position in the tree. The new subfamily belongs to a clade within the subfamilies Mesostominae and Phaenocorinae, showing affinity between these three taxa. The erection of this new subfamily is supported by cladistic analysis.
Phylogenetic relationships of the Australian Leptophlebiidae (Ephemeroptera)
Authors: Christidis Faye
Published: January 2006

Phylogenetic relationships among the Australian Leptophlebiidae genera and selected genera from South America and New Zealand were investigated using a cladistic analysis of 43 morphological characters. The outcomes of this analysis were largely consistent with the higher-level relationships previously proposed by Pescador and Peters (1980). The monophyly of the Meridialaris lineage (comprising Austrophlebioides, Tillyardophlebia, Kirrara, ‘WT sp. 1’ and ‘WT sp. 2’ from Australia, Meridialaris from South America and Deleatidium and Atalophlebioides from New Zealand) was strongly supported, as was the monophyly of the Nousia lineage (Nyungara, Nousia and Koorrnonga). However, Australian genera assigned to the Hapsiphlebia lineage (Atalophlebia, Kalbaybaria, Ulmerophlebia, Jappa and Atalomicria) did not form a monophlyletic group. There was support for a sister-group relationship between the Dactylophlebia and Meridialaris lineages, and for the placement of Garinjuga (Penaphlebia lineage) as the sister-group to a large clade comprising genera of the Nousia, Dactylophlebia and Meridialaris lineages. The phylogenetic analysis provided some clarification of the affinities of Neboissophlebia, Bibulmena, Loamaggalangta and Kaninga. These genera appear to belong to lineages not recognised previously among the Gondwanan Leptophlebiidae.
Determining reproductive parameters for population assessments of chondrichthyan species with asynchronous ovulation and parturition: piked spurdog (Squalus megalops) as a case study
Authors: Braccini J. Matías , Gillanders Bronwyn M. , Walker Terence I.
Published: January 2006

Population assessments of chondrichthyan species require several key parameters of their reproductive biology, which were estimated for Squalus megalops (Macleay, 1881). Length-at-maturity differed depending on the criterion adopted for defining maturity. In the case of males, length-at-maturity was smallest when condition of seminal vesicles was adopted as a maturity criterion. For females, length-at-maturity was smallest when the largest follicle diameter >3 mm was adopted as the criterion for maturity; this was appropriate only as an indicator of the onset of maturity. Mature males are capable of mating throughout the year. Females have a continuous asynchronous reproductive cycle. The sex ratio of embryos is 1 : 1 and litter size and near-term embryo length increase with maternal length. Females have an ovarian cycle and gestation period of two years. This was reflected in the differences found between the maturity and maternity ogives. Although all females are mature at 600 mm, only 50% of them contribute to annual recruitment each year. Hence, for chondrichthyan species with reproductive cycles of two, three or more years, if maturity ogives are used in population assessments instead of maternity ogives, the models will overestimate recruitment rates.
Automated acoustic tracking of aquatic animals: scales, design and deployment of listening station arrays
Authors: Heupel M. R. , Semmens J. M. , Hobday A. J.
Published: January 2006

The recent introduction of low-cost, moored data-logging acoustic receivers has provided opportunities for tracking marine organisms over small (hundreds of metres) and large scales (hundreds of kilometres). Acoustic receivers have been deployed in many different environments to examine specific hypotheses regarding the movement of aquatic species. This technology provides many advantages for studying aquatic animal movement patterns, but also has limitations and provides unique difficulties for users. Study design, applications, advantages and limitations are discussed with examples from past and current studies. Data management and analysis techniques are in their infancy and few standardised techniques exist. Complications with data management and potential data analysis techniques are discussed. Examples from the literature are utilised wherever possible to provide useful references.
Cellular identification of water gustatory receptor neurons and their central projection pattern in
Drosophila
Authors: Inoshita Tsuyoshi , Tanimura Teiichi
Published: January 2006

Water perception is important for insects, because they are particularly vulnerable to water loss because their body size is small. In
Drosophila
, gustatory receptor neurons are located at the base of the taste sensilla on the labellum, tarsi, and wing margins. One of the gustatory receptor neurons in typical sensilla is known to respond to water. To reveal the neural mechanisms of water perception in
Drosophila
, it is necessary to identify water receptor neurons and their projection patterns. We used a Gal4 enhancer trap strain in which GAL4 is expressed in a single gustatory receptor neuron in each sensillum on the labellum. We investigated the function of these neurons by expressing the upstream activating sequence transgenes,
shibire
ts1
, tetanus toxin light chain, or diphtheria toxin A chain. Results from the proboscis extension reflex test and electrophysiological recordings indicated that the GAL4-expressing neurons respond to water. We show here that the water receptor neurons project to a specific region in the subesophageal ganglion, thus revealing the water taste sensory map in
Drosophila
.
IA-2β, but not IA-2, is induced by ghrelin and inhibits glucose-stimulated insulin secretion
Authors: Doi Asako , Shono Takeshi , Nishi Masahiro , Furuta Hiroto , Sasaki Hideyuki , Nanjo Kishio
Published: January 2006

Ghrelin is a newly discovered peptide and an endogenous ligand for growth hormone (GH) secretagogue (GHS) receptor. It has been shown to possess various central and peripheral effects, including GH secretion, food intake, and gastric and cardiac effects. Ghrelin and the GHS receptor are expressed also in pancreatic islets. We have identified several ghrelin-induced genes by PCR-select subtraction methods, among which is a β-cell autoantigen for type 1 diabetes, IA-2β. Administration of ghrelin increased IA-2β mRNA in mouse brain, pancreas, and insulinoma cell lines (MIN6 and βTC3). However, the expression of IA-2, another structurally related β-cell autoantigen, was not induced by ghrelin. Administration of ghrelin or overexpression of IA-2β, but not overexpression of IA-2, inhibited glucose-stimulated insulin secretion in MIN6 insulinoma cells and, moreover, inhibition of IA-2β expression by the RNA interference technique ameliorated ghrelin's inhibitory effects on glucose-stimulated insulin secretion. These findings strongly suggest that inhibitory effects of ghrelin on glucose-stimulated insulin secretion are at least partly due to increased expression of IA-2β induced by ghrelin. Our data demonstrate the link among ghrelin, IA-2β, and glucose-stimulated insulin secretion.
Recent behavioral history modifies coupling between cell activity and
Arc
gene transcription in hippocampal CA1 neurons
Authors: Guzowski John F. , Miyashita Teiko , Chawla Monica K. , Sanderson Jennifer , Maes Levi I. , Houston Frank P. , Lipa Peter , McNaughton Bruce L. , Worley Paul F. , Barnes Carol A.
Published: January 2006

The ability of neurons to alter their transcriptional programs in response to synaptic input is of fundamental importance to the neuroplastic mechanisms underlying learning and memory. Because of technical limitations of conventional gene detection methods, the current view of activity-dependent neural transcription derives from experiments in which neurons are assumed quiescent until a signaling stimulus is given. The present study was designed to move beyond this static model by examining how earlier episodes of neural activity influence transcription of the immediate–early gene
Arc
. Using a sensitive FISH method that detects primary transcript at genomic alleles, the proportion of hippocampal CA1 neurons that activate transcription of
Arc
RNA was constant at ≈40% in response to both a single novel exploration session and daily sessions repeated over 9 days. This proportion is similar to the percentage of active neurons defined electrophysiologically. However, this close correspondence was disrupted in rats exposed briefly, but repeatedly, to the same environment within a single day.
Arc
transcription in CA1 neurons declined dramatically after as few as four 5-min sessions, despite stable electrophysiological activity during all sessions. Additional experiments indicate that the decrement in
Arc
transcription occurred at the cellular, rather than synaptic level, and was not simply linked to habituation to novelty. Thus, the neural genomic response is governed by recent, but not remote, cell firing history in the behaving animal. This state-dependence of neuronal transcriptional coupling provides a mechanism of metaplasticity and may regulate capacity for synaptic modification in neural networks.
Variations in the association of papillomavirus E2 proteins with mitotic chromosomes
Authors: Oliveira Jaquelline G. , Colf Leremy A. , McBride Alison A.
Published: January 2006

The E2 protein segregates episomal bovine papillomavirus (BPV) genomes to daughter cells by tethering them to mitotic chromosomes, thus ensuring equal distribution and retention of viral DNA. To date, only the BPV1 E2 protein has been shown to bind to mitotic chromosomes. We assessed the localization of 13 different animal and human E2 proteins from seven papillomavirus genera, and we show that most of them are stably bound to chromosomes throughout mitosis. Furthermore, in contrast to the random association of BPV1 E2 with mitotic chromosomes, several of these proteins appear to bind to more specific regions of mitotic chromosomes. Using human papillomavirus (HPV) type 8 E2, we show that this region is adjacent to centromeres/kinetochores. Therefore, E2 proteins from both HPV and animal papillomavirus bind to mitotic chromosomes, and there are variations in the specificity of this binding. Only the α-papillomavirus E2 proteins do not stably associate with mitotic chromatin throughout mitosis. These proteins closely associate with prophase chromosomes and bind to chromosomes in telophase but not in metaphase. However, extraction of mitotic cells before fixation results in α-E2 proteins binding to the pericentromeric region of metaphase chromosomes, as observed for HPV8 E2. We postulate that this is the authentic target of these E2 proteins but that additional factors or a specialized cellular environment is required to stabilize this association. Thus, E2-mediated tethering of viral genomes to mitotic chromosomes is a common strategy of papillomaviruses, but different viruses have evolved different variations of this theme.
A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios
Authors: Sahoo Sanghamitra , Singh Anamika , Himabindu G. , Banerjee Jheelam , Sitalaximi T. , Gaikwad Sonali , Trivedi R. , Endicott Phillip , Kivisild Toomas , Metspalu Mait , Villems Richard , Kashyap V. K.
Published: January 2006

Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations share a common late Pleistocene maternal ancestry in India, some studies of the Y-chromosome markers have suggested a recent, substantial incursion from Central or West Eurasia. To investigate the origin of paternal lineages of Indian populations, 936 Y chromosomes, representing 32 tribal and 45 caste groups from all four major linguistic groups of India, were analyzed for 38 single-nucleotide polymorphic markers. Phylogeography of the major Y-chromosomal haplogroups in India, genetic distance, and admixture analyses all indicate that the recent external contribution to Dravidian- and Hindi-speaking caste groups has been low. The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family. The dyadic Y-chromosome composition of Tibeto-Burman speakers of India, however, can be attributed to a recent demographic process, which appears to have absorbed and overlain populations who previously spoke Austro-Asiatic languages.
An auxin-driven polarized transport model for phyllotaxis
Authors: Jönsson Henrik , Heisler Marcus G. , Shapiro Bruce E. , Meyerowitz Elliot M. , Mjolsness Eric
Published: January 2006

Recent studies show that plant organ positioning may be mediated by localized concentrations of the plant hormone auxin. Auxin patterning in the shoot apical meristem is in turn brought about by the subcellular polar distribution of the putative auxin efflux mediator, PIN1. However, the question of what signals determine PIN1 polarization and how this gives rise to regular patterns of auxin concentration remains unknown. Here we address these questions by using mathematical modeling combined with confocal imaging. We propose a model that is based on the assumption that auxin influences the polarization of its own efflux within the meristem epidermis. We show that such a model is sufficient to create regular spatial patterns of auxin concentration on systems with static and dynamic cellular connectivities, the latter governed by a mechanical model. We also optimize parameter values for the PIN1 dynamics by using a detailed auxin transport model, for which parameter values are taken from experimental estimates, together with a template consisting of cell and wall compartments as well as PIN1 concentrations quantitatively extracted from confocal data. The model shows how polarized transport can drive the formation of regular patterns.
Consistent simulations of multiple proxy responses to an abrupt climate change event
Authors: LeGrande A. N. , Schmidt G. A. , Shindell D. T. , Field C. V. , Miller R. L. , Koch D. M. , Faluvegi G. , Hoffmann G.
Published: January 2006

Isotope, aerosol, and methane records document an abrupt cooling event across the Northern Hemisphere at 8.2 kiloyears before present (kyr), while separate geologic lines of evidence document the catastrophic drainage of the glacial Lakes Agassiz and Ojibway into the Hudson Bay at approximately the same time. This melt water pulse may have been the catalyst for a decrease in North Atlantic Deep Water formation and subsequent cooling around the Northern Hemisphere. However, lack of direct evidence for ocean cooling has lead to speculation that this abrupt event was purely local to Greenland and called into question this proposed mechanism. We simulate the response to this melt water pulse using a coupled general circulation model that explicitly tracks water isotopes and with atmosphere-only experiments that calculate changes in atmospheric aerosol deposition (specifically
10
Be and dust) and wetland methane emissions. The simulations produce a short period of significantly diminished North Atlantic Deep Water and are able to quantitatively match paleoclimate observations, including the lack of isotopic signal in the North Atlantic. This direct comparison with multiple proxy records provides compelling evidence that changes in ocean circulation played a major role in this abrupt climate change event.
Dissociation of face-selective cortical responses by attention
Authors: Furey Maura L. , Tanskanen Topi , Beauchamp Michael S. , Avikainen Sari , Uutela Kimmo , Hari Riitta , Haxby James V.
Published: January 2006

We studied attentional modulation of cortical processing of faces and houses with functional MRI and magnetoencephalography (MEG). MEG detected an early, transient face-selective response. Directing attention to houses in “double-exposure” pictures of superimposed faces and houses strongly suppressed the characteristic, face-selective functional MRI response in the fusiform gyrus. By contrast, attention had no effect on the M170, the early, face-selective response detected with MEG. Late (>190 ms) category-related MEG responses elicited by faces and houses, however, were strongly modulated by attention. These results indicate that hemodynamic and electrophysiological measures of face-selective cortical processing complement each other. The hemodynamic signals reflect primarily late responses that can be modulated by feedback connections. By contrast, the early, face-specific M170 that was not modulated by attention likely reflects a rapid, feed-forward phase of face-selective processing.
Early auditory experience generates long-lasting memories that may subserve vocal learning in songbirds
Authors: Phan Mimi L. , Pytte Carolyn L. , Vicario David S.
Published: January 2006

In both humans and songbirds, infants learn vocalizations by imitating the sounds of adult tutors with whom they interact during an early sensitive period. Vocal learning occurs in few animal taxa; similarities in the imitation process between humans and songbirds make the songbird a unique system in which vocal learning mechanisms can be studied at the neurobiological level. One theory of vocal learning proposes that early auditory experience generates auditory memories that subsequently guide vocal imitation. We now present a combination of behavioral and neurophysiological results, obtained in a songbird, that support this theory. We show that neurons in a forebrain auditory area of adult male zebra finches are selectively tuned to the song of a tutor heard early in development. Furthermore, the strength of this selectivity shows a striking correlation with the fidelity of vocal imitation, suggesting that this auditory memory may have served as the model for song learning.
Epigenetic regulation of the tumor suppressor gene
TCF21
on 6q23-q24 in lung and head and neck cancer
Authors: Smith Laura T. , Lin Mauting , Brena Romulo M. , Lang James C. , Schuller David E. , Otterson Gregory A. , Morrison Carl D. , Smiraglia Dominic J. , Plass Christoph
Published: January 2006

The identification of tumor suppressor genes has classically depended on their localization within recurrent regions of loss of heterozygosity. According to Knudson's two-hit hypothesis, the remaining allele is lost, either genetically or, more recently identified, through epigenetic events. To date, retrospective analyses have determined promoter methylation as a common alternative alteration in cancer cells to silence cancer-related genes. Here we report an application of restriction landmark genomic scanning that allows for DNA methylation profiling along a region of recurrent loss of heterozygosity at chromosome 6q23-q24. This approach resulted in the identification of a tumor suppressor gene,
TCF21
, which is frequently lost in human malignancies. We demonstrate that
TCF21
is expressed in normal lung airway epithelial cells and aberrantly methylated and silenced in the majority of head and neck squamous cell carcinomas and non-small-cell lung cancers analyzed.
TCF21
is known to regulate mesenchymal cell transition into epithelial cells, a property that has been shown to be deficient in carcinomas. We further demonstrate that exogenous expression of
TCF21
in cells that have silenced the endogenous
TCF21
locus resulted in a reduction of tumor properties
in vitro
and
in vivo
.
A neurocomputational hypothesis for nicotine addiction
Authors: Gutkin Boris S. , Dehaene Stanislas , Changeux Jean-Pierre
Published: January 2006

We present a hypothetical neurocomputational model that combines a set of neural circuits at the molecular, cellular, and system levels and accounts for several neurobiological and behavioral processes leading to nicotine addiction. We propose that combining changes in the nicotinic receptor response, expressed by mesolimbic dopaminergic neurons, with dopamine-gated learning in action-selection circuits, suffices to capture the acquisition of nicotine addiction. We show that an opponent process enhanced by persistent nicotine-taking renders self-administration rigid and habitual by inhibiting the learning process, resulting in long-term impairments in the absence of the drug. The model implies distinct thresholds on the dosage and duration for the acquisition and persistence of nicotine addiction. Our hypothesis unites a number of prevalent ideas on nicotine action into a coherent formal network for further understanding of compulsive drug addiction.
High biological species diversity in the arctic flora
Authors: Grundt Hanne Hegre , Kjølner Siri , Borgen Liv , Rieseberg Loren H. , Brochmann Christian
Published: January 2006

The arctic flora is considered to be impoverished, but estimates of species diversity are based on morphological assessments, which may not provide accurate counts of biological species. Here we report on crossing relationships within three diploid circumpolar plant species in the genus
Draba
(Brassicaceae). Although 99% of parental individuals were fully fertile, the fertility of intraspecific crosses was surprisingly low. Hybrids from crosses within populations were mostly fertile (63%), but only 8% of the hybrids from crosses within and among geographic regions (Alaska, Greenland, Svalbard, and Norway) were fertile. The frequent occurrence of intraspecific crossing barriers is not accompanied by significant morphological or ecological differentiation, indicating that numerous cryptic biological species have arisen within each taxonomic species despite their recent (Pleistocene) origin.
The tumor suppressor menin regulates hematopoiesis and myeloid transformation by influencing Hox gene expression
Authors: Chen Ya-Xiong , Yan Jizhou , Keeshan Karen , Tubbs Anthony T. , Wang Haoren , Silva Albert , Brown Eric J. , Hess Jay L. , Pear Warren S. , Hua Xianxin
Published: January 2006

Menin is the product of the tumor suppressor gene
Men1
that is mutated in the inherited tumor syndrome multiple endocrine neoplasia type 1 (MEN1). Menin has been shown to interact with SET-1 domain-containing histone 3 lysine 4 (H3K4) methyltransferases including mixed lineage leukemia proteins to regulate homeobox (
Hox
) gene expression
in vitro
. Using conditional
Men1
knockout mice, we have investigated the requirement for menin in hematopoiesis and myeloid transformation.
Men1
excision causes reduction of Hoxa9 expression, colony formation by hematopoietic progenitors, and the peripheral white blood cell count. Menin directly activates Hoxa9 expression, at least in part, by binding to the
Hoxa9
locus, facilitating methylation of H3K4, and recruiting the methylated H3K4 binding protein chd1 to the locus. Consistent with signaling downstream of menin, ectopic expression of both Hoxa9 and Meis1 rescues colony formation defects in
Men1
-excised bone marrow. Moreover,
Men1
excision also suppresses proliferation of leukemogenic mixed lineage leukemia-AF9 fusion-protein-transformed myeloid cells and
Hoxa9
expression. These studies uncover an important role for menin in both normal hematopoiesis and myeloid transformation and provide a mechanistic understanding of menin's function in these processes that may be used for therapy.
Caspase recruitment domain protein 6 is a microtubule-interacting protein that positively modulates NF-κB activation
Authors: Dufner Almut , Pownall Scott , Mak Tak W.
Published: January 2006

Proteins containing a caspase recruitment domain (CARD) play pivotal roles in signal transduction leading to apoptosis and NF-κB activation and inflammation. Here we identify and characterize human and mouse CARD protein 6 (CARD6), CARD-containing proteins of unique structure. CARD6 associates with microtubules and interacts with receptor-interacting protein (RIP)-like interacting caspase-like apoptosis regulatory protein kinase (RICK), a CARD-containing member of the RIP family of protein kinases. These kinases are involved in multiple NF-κB signaling pathways important for innate and adaptive immune responses. Surprisingly, the CARDs of CARD6 and RICK were not required for their interaction; instead, mutational analysis revealed that the CARD of CARD6 negatively controls the association of these molecules. CARD6 also binds to RIP1, a RIP kinase homologue that lacks a CARD but contains a C-terminal death domain. Coexpression of RICK targets CARD6 to aggresomes via a mechanism that requires the CARD of RICK. Importantly, CARD6 expression has a synergistic effect on NF-κB activation induced by several independent signal transduction pathways. In summary, our results indicate that CARD6 is a regulator of NF-κB activation that modulates the functions of RIP kinase family members.
DNA barcodes distinguish species of tropical Lepidoptera
Authors: Hajibabaei Mehrdad , Janzen Daniel H. , Burns John M. , Hallwachs Winnie , Hebert Paul D. N.
Published: January 2006

Although central to much biological research, the identification of species is often difficult. The use of DNA barcodes, short DNA sequences from a standardized region of the genome, has recently been proposed as a tool to facilitate species identification and discovery. However, the effectiveness of DNA barcoding for identifying specimens in species-rich tropical biotas is unknown. Here we show that cytochrome
c
oxidase I DNA barcodes effectively discriminate among species in three Lepidoptera families from Area de Conservación Guanacaste in northwestern Costa Rica. We found that 97.9% of the 521 species recognized by prior taxonomic work possess distinctive cytochrome
c
oxidase I barcodes and that the few instances of interspecific sequence overlap involve very similar species. We also found two or more barcode clusters within each of 13 supposedly single species. Covariation between these clusters and morphological and/or ecological traits indicates overlooked species complexes. If these results are general, DNA barcoding will significantly aid species identification and discovery in tropical settings.
Nonequilibrium steady states in a vibrated-rod monolayer: tetratic, nematic, and smectic
correlations
Authors: Narayan Vijay , Menon Narayanan , Ramaswamy Sriram
Published: January 2006

We study experimentally the nonequilibrium phase behaviour of a horizontal monolayer of
macroscopic rods. The motion of the rods in two dimensions is driven by vibrations in the
vertical direction. In addition to varying packing fraction and aspect ratio as
in most studies on hard-particle systems, we take advantage of our ability to
vary the precise shape of these macroscopic particles to investigate the effect of
shape on their nonequilibrium steady states. We find that the shape plays an
important role in determining the nature of the orientational ordering at high packing
fraction. Cylindrical particles show substantial tetratic correlations over a range
of aspect ratios where spherocylinders have previously been shown to undergo
transitions between isotropic and nematic phases. Particles that are thinner at
the ends (rolling pins or bails) show nematic ordering over the same range of
aspect ratios, with a well established nematic phase at large aspect ratio and
a defect-ridden nematic state with large-scale swirling motion at small aspect
ratios. Finally, long-grain, basmati rice, whose geometry is intermediate between
the two shapes above, shows phases with strong indications of smectic order.
Multiple association analysis via simulated annealing (MASSA)
Authors: Pérez-Enciso M.
Published: January 2006

Summary: Genome-wide association studies are now technically feasible and likely to become a fundamental tool in unraveling the ultimate genetic basis of complex traits. However, new statistical and computational methods need to be developed to extract the maximum information in a realistic computing time. Here we propose a new method for multiple association analysis via simulated annealing that allows for epistasis and any number of markers. It consists of finding the model with lowest Bayesian information criterion using simulated annealing. The data are described by means of a mixed model and new alternative models are proposed using a set of rules, e.g. new sites can be added (or deleted), or new epistatic interactions can be included between existing genetic factors. The method is illustrated with simulated and real data.

Availability: An executable version of the program (MASSA) running under the Linux OS is freely available, together with documentation, at

Contact:  miguel.perez@uab.es