bluuebunny/crossref_metadata_2025 huggingface dataset:
Cloudy sounding and cloud‐top height retrieval from AIRS alone single field‐of‐view radiance measurements
Authors: Weisz Elisabeth , Li Jun , Li Jinlong , Zhou Daniel K. , Huang Hung‐Lung , Goldberg Mitchell D. , Yang Ping
Published: June 2007

High‐spectral resolution measurements from the Atmospheric Infrared Sounder (AIRS) onboard the EOS (Earth Observing System) Aqua satellite provide unique information about atmospheric state, surface and cloud properties. This paper presents an AIRS alone single field‐of‐view (SFOV) retrieval algorithm to simultaneously retrieve temperature, humidity and ozone profiles under all weather conditions, as well as cloud‐top pressure (CTP) under cloudy skies. For optically thick cloud conditions the above‐cloud soundings are derived, whereas for clear skies and optically thin cloud conditions the profiles are retrieved from 0.005 hPa down to the earth's surface. Initial validation has been conducted by using the operational MODIS (Moderate Resolution Imaging Spectroradiometer) product, ECMWF (European Centre for Medium‐Range Weather Forecasts) analysis fields and radiosonde observations (RAOBs). These inter‐comparisons clearly demonstrate the potential of this algorithm to process data from high‐spectral infrared (IR) sounder instruments.
Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
Authors: Haygood Ralph , Fedrigo Olivier , Hanson Brian , Yokoyama Ken-Daigoro , Wray Gregory
Published: June 2007

Surveys of protein-coding sequences for evidence of positive selection in humans and chimpanzees have flagged surprisingly few genes known to be involved in neural or nutritional processes, despite the pronounced differences between humans and chimpanzees in behavior, cognition, and diet. It may be that most such differences are due to changes in gene regulation rather than protein structure. Here, we present the first survey of promoter (5'-flanking) regions, which are rich in cis-regulatory sequences, for signatures of positive selection in humans. Our results indicate that positive selection has targeted the regulation of many genes known to be involved in neural development and function, both in the brain and elsewhere in the nervous system, and in nutrition, particularly glucose metabolism.
A critical role for CCL2 and CCL3 chemokines in the regulation of polymorphonuclear neutrophils recruitment during corneal infection in mice
Authors: Xue Mei‐Lang , Thakur Archana , Cole Nerida , Lloyd Andrew , Stapleton Fiona , Wakefield Denis , Willcox Mark D P
Published: June 2007

While the role of CC chemokines in mononuclear cell trafficking and activation has been well studied, the functional role of CC chemokines in the regulation of polymorphonuclear neutrophil (PMN) recruitment in vivo has not been widely examined. Bacterial infection of the cornea (keratitis) is a relatively common, sometimes sight‐threatening disease, which features acute inflammation with ulceration and PMN infiltration. Here, we demonstrate a critical role for the chemokines, CCL2 and CCL3, in the Pseudomonas aeruginosa‐induced model of corneal infection in BALB/c mice. Treatment of mice with anti‐CCL2 or anti‐CCL3 antibodies resulted in a significant reduction in severity of corneal damage and PMN infiltration at 1 and 7 days after infection compared to control antibody‐treated eyes, but did not significantly alter the rate of bacterial clearance from the cornea. Our findings provide strong evidence that CCL2 and CCL3 are critical regulators of PMN recruitment, and may lead to therapeutic strategies via targeting of the CC chemokines, CCL2 and CCL3, in the management of P. aeruginosa keratitis.
Reproductive success in a reintroduced population of a critically endangered shrub, Symonanthus bancroftii (Solanaceae)
Authors: Ye Qigang , Bunn Eric , Krauss Siegfried L. , Dixon Kingsley W.
Published: June 2007

Symonanthus bancroftii is a critically endangered dioecious shrub, with only one male and one female plant known in the wild. Micropropagated, clonal plants of the male and female parents were hand-pollinated. Seed was germinated in sterile culture and a subsequent daughter (F1) seedling was multiplied in vitro. Micropropagated plants of the original parents and daughter were reintroduced to a natural habitat site. We detail the first study of pollination biology and reproductive success in this extremely rare species. Floral morphology, flowering phenology, pollen viability, female receptivity and fruit set of reintroduced plants of S. bancroftii were investigated. Flower viability of S. bancroftii shows a 25-day maximum for male flowers, whereas non-pollinated female flowers remain viable for a maximum of 38 days (female parent) and 41 days (daughter), respectively. Flowering of reintroduced male and female plants overlaps from mid-June to early November. Pollen remained viable for at least 8 days after anther dehiscence. Maximum stigma longevity recorded was 28 days (female parent) and 39 days (daughter) and maximum ovule longevity varied from 13 days (female parent) to 28 days (daughter). The mean percentage of flowers setting fruit was 39 ± 13% for female parent plants and 48 ± 4% for daughter plants. Empirical reproductive success measures for male–daughter crosses generally exceeded those of the original parent crosses. The reproductive success of S. bancroftii so soon after reintroduction of plants is a positive sign indicating that rapid accumulation of a soil seedbank is feasible and is thus an important first step towards successful establishment of self-sustaining populations of this critically endangered species.
Myxomycetes of subantarctic Macquarie Island
Authors: Stephenson Steven L. , Laursen Gary A. , Seppelt Rodney D.
Published: June 2007

Macquarie Island is an oceanic island located 1000 km south-east of Tasmania. The island, which lies close to but north of the Antarctic Convergence, is the southernmost island in the world with a fairly complete cover of vegetation. However, the vascular flora is impoverished and consists of only 46 species. During the period of late January to late April of 1995, 412 field collections of myxomycetes, representing at least 22 species in 11 genera, were obtained during the course of an intensive survey of fungal biodiversity on Macquarie Island. Moist-chamber cultures prepared with various types of plant debris yielded only 14 collections, but this total included three additional species and two additional genera. All but four of the species we recorded from the island are new records for the South Polar Region. Most field collections were associated with Stilbocarpa polaris (Araliaceae) and Pleurophyllum hookeri (Asteraceae), the usual dominants in the herbfield communities that commonly occur on upper beach slopes and coastal terraces. Trichia verrucosa (80 collections), Diderma alpinum (78) and Craterium leucocephalum (59) were the most consistently abundant myxomycetes. Other species represented by ≥15 collections were Didymium cf. dubium, Collaria lurida, Lamproderma arcyrioides and Didymium macquariense. The latter is a species new to science that was described from material collected during the present study. All of the species of myxomycetes now known to occur on Macquarie Island are members of the Trichiales, Physarales, Stemonitales or Echinosteliales; no member of the Liceales or Ceratiomyxales was ever collected.
Male twins reduce fitness of female co-twins in humans
Authors: Lummaa Virpi , Pettay Jenni E. , Russell Andrew F.
Published: June 2007

In mammals, including humans, female fetuses that are exposed to testosterone from adjacent male fetuses
in utero
can have masculinized anatomy and behavior. However, the reproductive consequences of such prebirth sex-ratio effects for offspring and their implications for maternal fitness remain unexplored. Here we investigate the effects of being gestated with a male co-twin for daughter lifetime reproductive success, and the fitness consequences for mothers of producing mixed-sex twins in preindustrial (1734–1888) Finns. We show that daughters born with a male co-twin have reduced lifetime reproductive success compared to those born with a female co-twin. This reduction arises because such daughters have decreased probabilities of marrying as well as reduced fecundity. Mothers who produce opposite-sex twins consequently have fewer grandchildren (and hence lower fitness) than mothers who produce same-sex twins. Our results are unlikely to be a consequence of females born with male co-twins receiving less nutrition because such females do not have reduced survival and increases in food availability fail to improve their reproductive success. Nor are our results explained by after-birth social factors (females growing up with similarly aged brothers) because females born with a male co-twin have reduced success even when their co-twin dies shortly after birth and are raised as singletons after birth. Our findings suggest that hormonal interactions between opposite-sex fetuses known to influence female morphology and behavior can also have negative effects on daughter fecundity and, hence, maternal fitness, and bear significant implications for adaptive sex allocation in mammals.
ARF functions as a melanoma tumor suppressor by inducing p53-independent senescence
Authors: Ha Linan , Ichikawa Takeshi , Anver Miriam , Dickins Ross , Lowe Scott , Sharpless Norman E. , Krimpenfort Paul , DePinho Ronald A. , Bennett Dorothy C. , Sviderskaya Elena V. , Merlino Glenn
Published: June 2007

Inactivation of the p53 pathway represents the most common molecular defect of human cancer. But in the setting of melanoma, a highly aggressive and invariably fatal malignancy in its advanced disseminated form, mutation/deletion of p53 is relatively rare, whereas its positive regulator ARF is often lost. Here, we show that genetic deficiency in Arf but not p53 facilitates rapid development of melanoma in a genetically engineered mouse model. This difference is accounted for, at least in part, by the unanticipated observation that, unlike fibroblasts, senescence control in melanocytes is strongly regulated by Arf and not p53. Moreover, oncogenic NRAS collaborates with deficiency in Arf, but not p53, to fully transform melanocytes. Our data demonstrate that ARF and p53, although linked in a common pathway, suppress tumorigenesis through distinct, lineage-dependent mechanisms and suggest that ARF helps restrict melanoma progression by executing the oncogene-induced senescence program in benign nevi. Thus, therapeutics designed to restore wild-type p53 function may be insufficient to counter melanoma and other malignancies in which ARF holds p53-independent tumor suppressor activity.
Hydrogen bonding and Raman, IR, and 2D-IR spectroscopy of dilute HOD in liquid D
2
O
Authors: Auer B. , Kumar R. , Schmidt J. R. , Skinner J. L.
Published: June 2007

We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid D
2
O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid.
CD96 is a leukemic stem cell-specific marker in human acute myeloid leukemia
Authors: Hosen Naoki , Park Christopher Y. , Tatsumi Naoya , Oji Yusuke , Sugiyama Haruo , Gramatzki Martin , Krensky Alan M. , Weissman Irving L.
Published: June 2007

Permanent cure of acute myeloid leukemia (AML) by chemotherapy alone remains elusive for most patients because of the inability to effectively eradicate leukemic stem cells (LSCs), the self-renewing component of the leukemia. To develop therapies that effectively target LSC, one potential strategy is to identify cell surface markers that can distinguish LSC from normal hematopoietic stem cells (HSCs). In this study, we employ a signal sequence trap strategy to isolate cell surface molecules expressed on human AML-LSC and find that CD96, which is a member of the Ig gene superfamily, is a promising candidate as an LSC-specific antigen. FACS analysis demonstrates that CD96 is expressed on the majority of CD34+CD38−AML cells in many cases (74.0 ± 25.3% in 19 of 29 cases), whereas only a few (4.9 ± 1.6%) cells in the normal HSC-enriched population (Lin−CD34+CD38−CD90+) expressed CD96 weakly. To examine whether CD96+AML cells are enriched for LSC activity, we separated AML cells into CD96+and CD96−fractions and transplanted them into irradiated newborn Rag2−/−γc−/−mice. In four of five samples, only CD96+cells showed significant levels of engraftment in bone marrow of the recipient mice. These results demonstrate that CD96 is a cell surface marker present on many AML-LSC and may serve as an LSC-specific therapeutic target.
Distinct brain networks for adaptive and stable task control in humans
Authors: Dosenbach Nico U. F. , Fair Damien A. , Miezin Francis M. , Cohen Alexander L. , Wenger Kristin K. , Dosenbach Ronny A. T. , Fox Michael D. , Snyder Abraham Z. , Vincent Justin L. , Raichle Marcus E. , Schlaggar Bradley L. , Petersen Steven E.
Published: June 2007

Control regions in the brain are thought to provide signals that configure the brain's moment-to-moment information processing. Previously, we identified regions that carried signals related to task-control initiation, maintenance, and adjustment. Here we characterize the interactions of these regions by applying graph theory to resting state functional connectivity MRI data. In contrast to previous, more unitary models of control, this approach suggests the presence of two distinct task-control networks. A frontoparietal network included the dorsolateral prefrontal cortex and intraparietal sulcus. This network emphasized start-cue and error-related activity and may initiate and adapt control on a trial-by-trial basis. The second network included dorsal anterior cingulate/medial superior frontal cortex, anterior insula/frontal operculum, and anterior prefrontal cortex. Among other signals, these regions showed activity sustained across the entire task epoch, suggesting that this network may control goal-directed behavior through the stable maintenance of task sets. These two independent networks appear to operate on different time scales and affect downstream processing via dissociable mechanisms.
Toward a unifying model of malaria-induced channel activity
Authors: Bouyer Guillaume , Egée Stéphane , Thomas Serge L. Y.
Published: June 2007

Infection of RBC by the malaria parasite
Plasmodium falciparum
activates, at the trophozoite stage, a membrane current 100- to 150-fold larger than in uninfected RBC. This current is carried by small anion channels initially described in supraphysiological ion concentrations (1.115 M Cl
−
) and named plasmodial surface anion channels (PSAC), suggesting their plasmodial origin. Our results obtained with physiological ion concentrations (0.145 M Cl
−
) support the notion that the parasite-induced channels represent enhanced activity versions of anion channels already present in uninfected RBCs. Among them, an 18-pS inwardly rectifying anion channel (IRC) and a 4- to 5-pS small conductance anion channel (SCC) were present in most single-channel recordings of infected membranes. The aim of this study was to clarify disparities in the reported electrophysiological data and to investigate possible technical reasons why these discrepancies have arisen. We demonstrate that PSAC is the supraphysiological correlate of the SCC and is inhibited by Zn
2+
, suggesting that it is a ClC-2 channel. We show that in physiological solutions 80% of the membrane conductance in infected cells can be accounted for by IRC and 20% can be accounted for by SCC whereas in supraphysiological conditions the membrane conductance is almost exclusively carried by SCC (PSAC) because the IRC is functionally turned off.
Interaction of a plant virus-encoded protein with the major nucleolar protein fibrillarin is required for systemic virus infection
Authors: Kim Sang Hyon , MacFarlane Stuart , Kalinina Natalia O. , Rakitina Daria V. , Ryabov Eugene V. , Gillespie Trudi , Haupt Sophie , Brown John W. S. , Taliansky Michael
Published: June 2007

The nucleolus and specific nucleolar proteins are involved in the life cycles of some plant and animal viruses, but the functions of these proteins and of nucleolar trafficking in virus infections are largely unknown. The ORF3 protein of the plant virus, groundnut rosette virus (an umbravirus), has been shown to cycle through the nucleus, passing through Cajal bodies to the nucleolus and then exiting back into the cytoplasm. This journey is absolutely required for the formation of viral ribonucleoprotein particles (RNPs) that, themselves, are essential for the spread of the virus to noninoculated leaves of the shoot tip. Here, we show that these processes rely on the interaction of the ORF3 protein with fibrillarin, a major nucleolar protein. Silencing of the fibrillarin gene prevents long-distance movement of groundnut rosette virus but does not affect viral replication or cell-to-cell movement. Repressing fibrillarin production also localizes the ORF3 protein to multiple Cajal body-like aggregates that fail to fuse with the nucleolus. Umbraviral ORF3 protein and fibrillarin interact
in vitro
and, when mixed with umbravirus RNA, form an RNP complex. This complex has a filamentous structure with some regular helical features, resembling the RNP complex formed
in vivo
during umbravirus infection. The filaments formed
in vitro
are infectious when inoculated to plants, and their infectivity is resistant to RNase. These results demonstrate previously undescribed functions for fibrillarin as an essential component of translocatable viral RNPs and may have implications for other plant and animal viruses that interact with the nucleolus.
CD8− DCs induce IL-12–independent Th1 differentiation through Delta 4 Notch-like ligand in response to bacterial LPS
Authors: Skokos Dimitris , Nussenzweig Michel C.
Published: June 2007

Toll-like receptor (TLR) ligation is believed to skew T cell responses toward T helper (Th)1 differentiation by inducing interleukin (IL)-12 secretion by CD8+ dendritic cells (DCs). However, TLR-dependent Th1 responses occur in the absence of IL-12. To determine how DCs induce Th1 differentiation in the absence of IL-12, we examined the response of IL-12–deficient DCs to bacterial lipopolysaccharide (LPS). We find that LPS activates MyD88-dependent Delta 4 Notch-like ligand expression by CD8− DCs, and that these cells direct Th1 differentiation by an IL-12–independent and Notch-dependent mechanism in vitro and in vivo. Thus, activation of the two DC subsets by TLR4 leads to Th1 responses by two distinct MyD88-dependent pathways.
MK2 controls the level of negative feedback in the NF-κB pathway and is essential for vascular permeability and airway inflammation
Authors: Gorska Magdalena M. , Liang Qiaoling , Stafford Susan J. , Goplen Nicolas , Dharajiya Nilesh , Guo Lei , Sur Sanjiv , Gaestel Matthias , Alam Rafeul
Published: June 2007

We demonstrate that mitogen-activated protein kinase–activated kinase-2 (MK2) is essential for localized Th2-type inflammation and development of experimental asthma. MK2 deficiency does not affect systemic Th2 immunity, but reduces endothelial permeability, as well as adhesion molecule and chemokine expression. NF-κB regulates transcription of adhesion molecules and chemokines. We show that MK2 and its substrate HSP27 are essential for sustained NF-κB activation. MK2 and HSP27 prevent nuclear retention of p38 by sequestering it in the cytosol. As a result, MK2 precludes excessive phosphorylation of MSK1. By reducing MSK1 activity, MK2 prevents p65 NF-κB hyperphosphorylation and excessive IκBα transcription. IκBα mediates nuclear export of p65. By reducing IκBα level, MK2 prevents premature export of NF-κB from the nucleus. Thus, the MK2–HSP27 pathway regulates the NF-κB transcriptional output by switching the activation pattern from high level, but short lasting, to moderate-level, but long lasting. This pattern of activation is essential for many NF-κB–regulated genes and development of inflammation. Thus, the MK2–HSP27 pathway is an excellent target for therapeutic control of localized inflammatory diseases.
How the rich get richer
Authors: Rossner Mike , Mellman Ira
Published: June 2007

HHMI will bestow monetary rewards on a commercial publisher in return for the type of public access already provided by many nonprofit publishers.
Nestling immune response to phytohaemagglutinin is not heritable in collared flycatchers
Authors: Pitala Natalia , Gustafsson Lars , Sendecka Joanna , Brommer Jon E
Published: June 2007

The response to intradermally injected phytohaemagglutinin (PHA-response) is a commonly used quantification of avian immunocompetence (the ability to resist pathogens). Parasite-mediated sexual selection requires heritable immunocompetence, but evidence for heritability of PHA-response in birds largely stems from full-sib comparisons. Using an animal model approach, we quantified the narrow-sense heritability of PHA-response in 1626 collared flycatcher (
Ficedula albicollis
) nestlings from 332 families, most of which were cross-fostered. Nestling PHA-response was not significantly heritable (
h
2
=0.06±0.10), but was subject to non-heritable nest-of-origin effects (10% of variation). Our findings illustrate that full-sib comparisons of immunological measures may lead to an inflated estimate of heritability and also reveal a limited role of nestling PHA-response for sexual selection in this population.
Kin recognition in an annual plant
Authors: Dudley Susan A , File Amanda L
Published: June 2007

Kin recognition is important in animal social systems. However, though plants often compete with kin, there has been as yet no direct evidence that plants recognize kin in competitive interactions. Here we show in the annual plantCakile edentula, allocation to roots increased when groups of strangers shared a common pot, but not when groups of siblings shared a pot. Our results demonstrate that plants can discriminate kin in competitive interactions and indicate that the root interactions may provide the cue for kin recognition. Because greater root allocation is argued to increase below-ground competitive ability, the results are consistent with kin selection.
Stochasticity and heterogeneity in host–vector models
Authors: Lloyd Alun L , Zhang Ji , Root A.Morgan
Published: June 2007

Demographic stochasticity and heterogeneity in transmission of infection can affect the dynamics of host–vector disease systems in important ways. We discuss the use of analytic techniques to assess the impact of demographic stochasticity in both well-mixed and heterogeneous settings. Disease invasion probabilities can be calculated using branching process methodology. We review the use of this theory for host–vector infections and examine its use in the face of heterogeneous transmission. Situations in which there is a marked asymmetry in transmission between host and vector are seen to be of particular interest. For endemic infections, stochasticity leads to variation in prevalence about the endemic level. If these fluctuations are large enough, disease extinction can occur via endemic fade-out. We develop moment equations that quantify the impact of stochasticity, providing insight into the likelihood of stochastic extinction. We frame our discussion in terms of the simple Ross malaria model, but discuss extensions to more realistic host–vector models.
Gyroid cuticular structures in butterfly wing scales: biological photonic crystals
Authors: Michielsen K , Stavenga D.G
Published: June 2007

We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostrisandTeinopalpus imperialis) and lycaenids (Callophrys rubi,Cyanophrys remus,Mitoura gryneusandCallophrys dumetorum). Using published scanning and transmission electron microscopy (TEM) images, analytical modelling and computer-generated TEM micrographs, we find that the three-dimensional cuticular structures can be modelled by gyroid structures with various filling fractions and lattice parameters. We give a brief discussion of the formation of cubic gyroid membranes from the smooth endoplasmic reticulum in the scale's cell, which dry and harden to leave the cuticular structure behind when the cell dies. The scales ofC. rubiare a potentially attractive biotemplate for producing three-dimensional optical photonic crystals since for these scales the cuticle-filling fraction is nearly optimal for obtaining the largest photonic band gap in a gyroid structure.
A new self-healing epoxy with tungsten (VI) chloride catalyst
Authors: Kamphaus Jason M , Rule Joseph D , Moore Jeffrey S , Sottos Nancy R , White Scott R
Published: June 2007

Using self-healing materials in commercial applications requires healing chemistry that is cost-effective, widely available and tolerant of moderate temperature excursions. We investigate the use of tungsten (VI) chloride as a catalyst precursor for the ring-opening metathesis polymerization of
exo-
dicyclopentadiene (
exo
-DCPD) in self-healing applications as a means to achieve these goals. The environmental stability of WCl
6
using three different delivery methods was evaluated and the associated healing performance was assessed following fracture toughness recovery protocols. Both as-received and recrystallized forms of the WCl
6
resulted in nearly complete fracture recovery in self-activated tests, where healing agent is manually injected into the crack plane, at 12 wt% WCl
6
loading.
In situ
healing using 15 wt% microcapsules of the
exo
-DCPD produced healing efficiencies of approximately 20%.
Frictional and elastic energy in gecko adhesive detachment
Authors: Gravish Nick , Wilkinson Matt , Autumn Kellar
Published: June 2007

Geckos use millions of adhesive setae on their toes to climb vertical surfaces at speeds of over 1 m s
−1
. Climbing presents a significant challenge for an adhesive since it requires both strong attachment and easy, rapid removal. Conventional pressure-sensitive adhesives are either strong and difficult to remove (e.g. duct tape) or weak and easy to remove (e.g. sticky notes). We discovered that the energy required to detach adhering tokay gecko setae (
W
d
) is modulated by the angle (
θ
) of a linear path of detachment. Gecko setae resist detachment when dragged towards the animal during detachment (
θ
=30°) requiring
W
d
=5.0±0.86 (s.e.) J m
−2
to detach, largely due to frictional losses. This external frictional loss is analogous to viscous internal frictional losses during detachment of pressure-sensitive adhesives. We found that, remarkably, setae possess a built-in release mechanism. Setae acted as springs when loaded in tension during attachment and returned elastic energy when detached along the optimal path (
θ
=130°), resulting in
W
d
=−0.8±0.12 J m
−2
. The release of elastic energy from the setal shaft probably causes spontaneous release, suggesting that curved shafts may enable easy detachment in natural, and synthetic, gecko adhesives.
Engineering functional protein interfaces for immunologically modified field effect transistor (ImmunoFET) by molecular genetic means
Authors: Eteshola Edward , Keener Matthew T , Elias Mark , Shapiro John , Brillson Leonard J , Bhushan Bharat , Lee Stephen Craig
Published: June 2007

The attachment and interactions of analyte receptor biomolecules at solid–liquid interfaces are critical to development of hybrid biological–synthetic sensor devices across all size regimes. We use protein engineering approaches to engineer the sensing interface of biochemically modified field effect transistor sensors (BioFET). To date, we have deposited analyte receptor proteins on FET sensing channels by direct adsorption, used self-assembled monolayers to tether receptor proteins to planar FET SiO
2
sensing gates and demonstrated interface biochemical function and electrical function of the corresponding sensors. We have also used phage display to identify short peptides that recognize thermally grown SiO
2
. Our interest in these peptides is as affinity domains that can be inserted as translational fusions into receptor proteins (antibody fragments or other molecules) to drive oriented interaction with FET sensing surfaces. We have also identified single-chain fragment variables (scFvs, antibody fragments) that recognize an analyte of interest as potential sensor receptors. In addition, we have developed a protein engineering technology (scanning circular permutagenesis) that allows us to alter protein topography to manipulate the position of functional domains of the protein relative to the BioFET sensing surface.
An optimization structure for frictional plasticity
Authors: Chandler H.W , Sands C.M
Published: June 2007

A theoretical framework of rigid plasticity is presented that is based on optimization and includes frictional dissipation. It has been used in this paper as a foundation for existing and modified models of granular materials consisting of rigid granules. It has the major advantage that it enables yield criteria to be created numerically, which is particularly useful when analytical expressions cannot be found. This framework is constructed by first postulating: (i) a dissipation function that can depend on the current components of stress, but is always homogeneous of degree one and positive definite, (ii) a volume constraint function that is also homogeneous of degree one, and (iii) a balance of the rate of doing work and the rate at which energy needs to be dissipated. A mathematical process similar to the construction of a dual norm in convex analysis then leads to: a flow rule; a single natural representation of the yield surface; and a useful constitutive inequality involving the components of stress and strain rate.

Dissipation functions appropriate for the Drucker–Prager and Matsuoka–Nakai yield surfaces are investigated when a simple dilation rule is the volume constraint. These include a case where an explicit expression for the yield function is not found and, instead, the yield function is found numerically. Such numerical yield functions have been checked graphically against carefully constructed envelopes and found to be consistent with them.
Quantum phase transitions without thermodynamic limits
Authors: Brody Dorje C , Hook Daniel W , Hughston Lane P
Published: June 2007

A new microcanonical equilibrium state is introduced for quantum systems with finite-dimensional state spaces. Equilibrium is characterized by a uniform distribution on a level surface of the expectation value of the Hamiltonian. The distinguishing feature of the proposed equilibrium state is that the corresponding density of states is a continuous function of the energy, and hence thermodynamic functions are well defined for finite quantum systems. The density of states, however, is not in general an analytic function. It is demonstrated that generic quantum systems therefore exhibit second-order phase transitions at finite temperatures.
Song repertoire size varies with HVC volume and is indicative of male quality in song sparrows (Melospiza melodia)
Authors: Pfaff Jeremy A , Zanette Liana , MacDougall-Shackleton Scott A , MacDougall-Shackleton Elizabeth A
Published: June 2007

Complex birdsong is a classic example of a sexually selected ornamental trait. In many species, females prefer males with large song repertoires, possibly because repertoire size is limited by the size of song control nuclei which reflect developmental success. We investigated whether song repertoire size was indicative of brain area and male quality in song sparrows (Melospiza melodia) by determining if repertoire size was related to the volume of song control nucleus HVC, as well as several morphological, immunological and genetic indices of quality. We found that males with large repertoires had larger HVCs and were in better body condition. They also had lower heterophil to lymphocyte ratios, indicating less physiological stress and a robust immune system as measured by the number of lymphocytes per red blood cell. Song repertoire size also tended to increase with neutral-locus genetic diversity, as assessed by meand2, but was not related to internal relatedness. Our results suggest several mechanisms that might explain the finding of a recent study that song sparrows with large song repertoires have higher lifetime fitness.
Courtship and genetic quality: asymmetric males show their best side
Authors: Gross Mart R , Suk Ho Young , Robertson Cory T
Published: June 2007

Fluctuating asymmetry (FA), the small random deviations from perfect morphological symmetry that result during development, is ubiquitous throughout the animal kingdom. In many species, FA seems to play a role in mate choice, perhaps because it signals an individual's genetic quality and health. However, the relationship between an individual's FA and behaviour is generally unknown: what do more asymmetric individuals do about their own asymmetry? We now show for the first time that individuals respond behaviourally to their own morphological FA in what appears to be an adaptive manner. During courtship, male guppies exhibiting high FA in ornamental colour, bias their displays towards their more colourful body side, thus potentially increasing their attractiveness by exaggerating the quantity of their orange signal. This appears to be a strictly behavioural male response to cues provided by females, as it does not occur when males court a non-reactive model female. Whether inferior males realize any mating advantage remains uncertain, but our study clearly demonstrates a behavioural response to random morphological asymmetries that appears to be adaptive. We propose that the tendency to show or otherwise use a ‘best side’ is common in nature, with implications for sexual signalling and the evolution of more pronounced asymmetries.
Turning the other cheek: the viewpoint dependence of facial expression after-effects
Authors: Benton Christopher P , Etchells Peter J , Porter Gillian , Clark Andrew P , Penton-Voak Ian S , Nikolov Stavri G
Published: June 2007

How do we visually encode facial expressions? Is this done by viewpoint-dependent mechanisms representing facial expressions as two-dimensional templates or do we build more complex viewpoint independent three-dimensional representations? Recent facial adaptation techniques offer a powerful way to address these questions. Prolonged viewing of a stimulus (
adaptation
) changes the perception of subsequently viewed stimuli (an
after-effect
). Adaptation to a particular attribute is believed to target those neural mechanisms encoding that attribute. We gathered images of facial expressions taken simultaneously from five different viewpoints evenly spread from the three-quarter leftward to the three-quarter rightward facing view. We measured the strength of expression after-effects as a function of the difference between adaptation and test viewpoints. Our data show that, although there is a decrease in after-effect over test viewpoint, there remains a substantial after-effect when adapt and test are at differing three-quarter views. We take these results to indicate that neural systems encoding facial expressions contain a mixture of viewpoint-dependent and viewpoint-independent elements. This accords with evidence from single cell recording studies in macaque and is consonant with a view in which viewpoint-independent expression encoding arises from a combination of view-dependent expression-sensitive responses.
Habitat-dependent call divergence in the common cuckoo: is it a potential signal for assortative mating?
Authors: Fuisz Tibor I , de Kort Selvino R
Published: June 2007

The common cuckoo (Cuculus canorus) is an obligate brood parasite that mimics the eggs of its hosts. The host-specific egg pattern is thought to be inherited matrilinearly, creating female-only host-specific races. Males are thought not to be adapted to their host and they maintain the species by mating arbitrarily with respect to host specialization of females. However, recent results suggest that male cuckoos may also show host-specific adaptations and these may require assortative mating with respect to host. The calls males produce on the breeding grounds could provide a potential mechanism for assortative mating. We tested whether male cuckoo calls differ more between nearby populations that parasitize different hosts than between distant populations that parasitize the same host. We recorded the calls of geographically distant pairs of populations in Hungary, with each pair consisting of a forest population and a nearby reed bed population. Each habitat is characterized by one main host species for the common cuckoo. Our results show that calls of distant cuckoo populations from the same habitat type are more similar to each other than they are to those of nearby populations from a different habitat. These results suggest that cuckoo calls differ sufficiently to allow recognition of habitat-specific individuals.
Mimicry on the edge: why do mimics vary in resemblance to their model in different parts of their geographical range?
Authors: Harper George R , Pfennig David W
Published: June 2007

Batesian mimics—benign species that predators avoid because they resemble a dangerous species—often vary geographically in resemblance to their model. Such geographical variation in mimic–model resemblance may reflect geographical variation in model abundance. Natural selection should favour even poor mimics where their model is common, but only good mimics where their model is rare. We tested these predictions in a snake-mimicry complex where the geographical range of the mimic extends beyond that of its model. Mimics on the edge of their model's range (where the model was rare) resembled the model more closely than did mimics in the centre of their model's range (where the model was common). When free-ranging natural predators on the edge of the model's range were given a choice of attacking replicas of good or poor mimics, they avoided only good mimics. By contrast, those in the centre of the model's range attacked good and poor mimics equally frequently. Generally, although poor mimics may persist in areas where their model is common, only the best mimics should occur in areas where their model is rare. Thus, counter-intuitively, the best mimics may occur on the edge of their model's range.
Natal habitat-biased dispersal in the Siberian flying squirrel
Authors: Selonen Vesa , Hanski Ilpo K , Desrochers André
Published: June 2007

Theoretically, dispersers should target the habitat where prospects for fitness will be highest. Aiming for a habitat similar to the natal area (natal habitat-biased dispersal) has been hypothesized as a probable rule of thumb for dispersers, but has received very little empirical support to date. We investigated similarities between natal and post-dispersal settlement sites with radio-collared Siberian flying squirrels (Pteromys volansL.). Juveniles born in small patches and raised in nests close to patch edge settled in small patches and used nests close to edges after dispersal. In addition, post-dispersal use of dreys (versus cavities) was similar to that observed in natal sites. However, the quality of settlement habitat was unrelated to the quality of the natal site, which suggests that natal experience on average-quality habitats may not lead to ecological traps for flying squirrels. This study provides evidence that habitat selection at the landscape scale is influenced by habitat of natal area.
Evidence for the existence of a robust pattern of prey selection in food webs
Authors: Stouffer Daniel B , Camacho Juan , Jiang Wenxin , Nunes Amaral Luís A
Published: June 2007

Food webs aim to provide a thorough representation of the trophic interactions found in an ecosystem. The complexity of empirical food webs, however, is leading many ecologists to focus dynamic ecosystem studies on smaller microcosm or mesocosm studies based upon community modules, which comprise three to five species and the interactions likely to have ecological relevance. We provide here a structural counterpart to community modules. We investigate food-web ‘motifs’ which are
n
-species connected subgraphs found within the food web. Remarkably, we find that the over- and under-representation of three-species motifs in empirical food webs can be understood through comparison to a static food-web model, the niche model. Our result conclusively demonstrates that predation upon species with some ‘characteristic’ niche value is the prey selection mechanism consistent with the structural properties of empirical food webs.
Obligate symbiont involved in pest status of host insect
Authors: Hosokawa Takahiro , Kikuchi Yoshitomo , Shimada Masakazu , Fukatsu Takema
Published: June 2007

The origin of specific insect genotypes that enable efficient use of agricultural plants is an important subject not only in applied fields like pest control and management but also in basic disciplines like evolutionary biology. Conventionally, it has been presupposed that such pest-related ecological traits are attributed to genes encoded in the insect genomes. Here, however, we report that pest status of an insect is principally determined by symbiont genotype rather than by insect genotype. A pest stinkbug species,Megacopta punctatissima, performed well on crop legumes, while a closely related non-pest species,Megacopta cribraria, suffered low egg hatch rate on the plants. When their obligate gut symbiotic bacteria were experimentally exchanged between the species, their performance on the crop legumes was, strikingly, completely reversed: the pest species suffered low egg hatch rate, whereas the non-pest species restored normal egg hatch rate and showed good performance. The low egg hatch rates were attributed to nymphal mortality before or upon hatching, which were associated with the symbiont from the non-pest stinkbug irrespective of the host insect species. Our finding sheds new light on the evolutionary origin of insect pests, potentially leading to novel approaches to pest control and management.
Efficient estimation and ensemble generation in climate modelling
Authors: Annan J.D , Hargreaves J.C
Published: June 2007

In this paper, we review progress towards efficiently estimating parameters in climate models. Since the general problem is inherently intractable, a range of approximations and heuristic methods have been proposed. Simple Monte Carlo sampling methods, although easy to implement and very flexible, are rather inefficient, making implementation possible only in the very simplest models. More sophisticated methods based on random walks and gradient-descent methods can provide more efficient solutions, but it is often unclear how to extract probabilistic information from such methods and the computational costs are still generally too high for their application to state-of-the-art general circulation models (GCMs). The ensemble Kalman filter is an efficient Monte Carlo approximation which is optimal for linear problems, but we show here how its accuracy can degrade in nonlinear applications. Methods based on particle filtering may provide a solution to this problem but have yet to be studied in any detail in the realm of climate models. Statistical emulators show great promise for future research and their computational speed would eliminate much of the need for efficient sampling techniques. However, emulation of a full GCM has yet to be achieved and the construction of such represents a substantial computational task in itself.
Probabilistic climate change predictions applying Bayesian model averaging
Authors: Min Seung-Ki , Simonis Daniel , Hense Andreas
Published: June 2007

This study explores the sensitivity of probabilistic predictions of the twenty-first century surface air temperature (SAT) changes to different multi-model averaging methods using available simulations from the Intergovernmental Panel on Climate Change fourth assessment report. A way of observationally constrained prediction is provided by training multi-model simulations for the second half of the twentieth century with respect to long-term components. The Bayesian model averaging (BMA) produces weighted probability density functions (PDFs) and we compare two methods of estimating weighting factors: Bayes factor and expectation–maximization algorithm. It is shown that Bayesian-weighted PDFs for the global mean SAT changes are characterized by multi-modal structures from the middle of the twenty-first century onward, which are not clearly seen in arithmetic ensemble mean (AEM). This occurs because BMA tends to select a few high-skilled models and down-weight the others. Additionally, Bayesian results exhibit larger means and broader PDFs in the global mean predictions than the unweighted AEM. Multi-modality is more pronounced in the continental analysis using 30-year mean (2070–2099) SATs while there is only a little effect of Bayesian weighting on the 5–95% range. These results indicate that this approach to observationally constrained probabilistic predictions can be highly sensitive to the method of training, particularly for the later half of the twenty-first century, and that a more comprehensive approach combining different regions and/or variables is required.
Ensemble climate predictions using climate models and observational constraints
Authors: Stott Peter A , Forest Chris E
Published: June 2007

Two different approaches are described for constraining climate predictions based on observations of past climate change. The first uses large ensembles of simulations from computationally efficient models and the second uses small ensembles from state-of-the-art coupled ocean–atmosphere general circulation models. Each approach is described and the advantages of each are discussed. When compared, the two approaches are shown to give consistent ranges for future temperature changes. The consistency of these results, when obtained using independent techniques, demonstrates that past observed climate changes provide robust constraints on probable future climate changes. Such probabilistic predictions are useful for communities seeking to adapt to future change as well as providing important information for devising strategies for mitigating climate change.
The use of the multi-model ensemble in probabilistic climate projections
Authors: Tebaldi Claudia , Knutti Reto
Published: June 2007

Recent coordinated efforts, in which numerous climate models have been run for a common set of experiments, have produced large datasets of projections of future climate for various scenarios. Those multi-model ensembles sample initial condition, parameter as well as structural uncertainties in the model design, and they have prompted a variety of approaches to quantify uncertainty in future climate in a probabilistic way. This paper outlines the motivation for using multi-model ensembles, reviews the methodologies published so far and compares their results for regional temperature projections. The challenges in interpreting multi-model results, caused by the lack of verification of climate projections, the problem of model dependence, bias and tuning as well as the difficulty in making sense of an ‘ensemble of opportunity’, are discussed in detail.