bluuebunny/crossref_metadata_2025 huggingface dataset:
Observation and modeling of catchment‐scale solute transport in the hydrologic response: A tracer study
Authors: Botter G. , Peratoner F. , Putti M. , Zuliani A. , Zonta R. , Rinaldo A. , Marani M.
Published: May 2008

The coherent description of water flow and solute transport within heterogeneous hydrologic media (e.g., hillslopes or entire catchments) in response to external rainfall forcings represents a challenge in hydrological modeling. In this paper the mechanisms determining the mobilization and transport of solutes in soils through the paths of runoff formation are investigated by means of a tracer experiment conducted within an instrumented hillslope draining into a tributary of the Dese river basin (northeastern Italy). The response of the test catchment during a rainfall event occurred at the beginning of December 2006 has been analyzed by employing two different chemical tracers: nitrates from diffuse agricultural sources (NO3−) and lithium from a point injection (Li+). Rainfall depths, streamflows, and pressure heads within different soil horizons were also collected. The observed hydro‐chemical response of the Piovega Tre Comuni has been reproduced by a Mass Response Function solute transport model. Our results evidence the origins of the chromatographic effects seen in the system's response. In particular, the deep subsurface component of runoff is found to dominate the long‐term behavior of the hydrograph and proves responsible for exporting relatively large amounts of solutes from soil. Experimental evidences and modeling results also suggest that the behavior of the breakthrough curve in stream waters may be strongly affected by the persistence of the rainfall forcing and by the relative magnitude of the rainfall‐driven hydrologic contribution with respect to the background noise unrelated to soil moisture dynamics.
A DNA-based nanomechanical device with three robust states
Authors: Chakraborty Banani , Sha Ruojie , Seeman Nadrian C.
Published: May 2008

DNA has been used to build a variety of devices, ranging from those that are controlled by DNA structural transitions to those that are controlled by the addition of specific DNA strands. These sequence-dependent devices fulfill the promise of DNA in nanotechnology because a variety of devices in the same physical environment can be controlled individually. Many such devices have been reported, but most of them contain one or two structurally robust end states, in addition to a floppy intermediate or even a floppy end state. We describe a system in which three different structurally robust end states can be obtained, all resulting from the addition of different set strands to a single floppy intermediate. This system is an extension of the PX-JX
2
DNA device. The three states are related to each other by three different motions, a twofold rotation, a translation of ≈2.1–2.5 nm, and a twofold screw rotation, which combines these two motions. We demonstrate the transitions by gel electrophoresis, by fluorescence resonance energy transfer, and by atomic force microscopy. The control of this system by DNA strands opens the door to trinary logic and to systems containing
N
devices that are able to attain 3
N
structural states.
Sildenafil and cardiomyocyte-specific cGMP signaling prevent cardiomyopathic changes associated with dystrophin deficiency
Authors: Khairallah M. , Khairallah R. J. , Young M. E. , Allen B. G. , Gillis M. A. , Danialou G. , Deschepper C. F. , Petrof B. J. , Des Rosiers C.
Published: May 2008

We recently demonstrated early metabolic alterations in the dystrophin-deficient
mdx
heart that precede overt cardiomyopathy and may represent an early “subclinical” signature of a defective nitric oxide (NO)/cGMP pathway. In this study, we used genetic and pharmacological approaches to test the hypothesis that enhancing cGMP, downstream of NO formation, improves the contractile function, energy metabolism, and sarcolemmal integrity of the
mdx
heart. We first generated
mdx
mice overexpressing, in a cardiomyocyte-specific manner, guanylyl cyclase (GC) (
mdx
/GC
+/0
). When perfused
ex vivo
in the working mode, 12- and 20-week-old hearts maintained their contractile performance, as opposed to the severe deterioration observed in age-matched
mdx
hearts, which also displayed two to three times more lactate dehydrogenase release than
mdx
/GC
+/0
. At the metabolic level,
mdx
/GC
+/0
displayed a pattern of substrate selection for energy production that was similar to that of their
mdx
counterparts, but levels of citric acid cycle intermediates were significantly higher (36 ± 8%), suggesting improved mitochondrial function. Finally, the ability of dystrophin-deficient hearts to resist sarcolemmal damage induced
in vivo
by increasing the cardiac workload acutely with isoproterenol was enhanced by the presence of the transgene and even more so by inhibiting cGMP breakdown using the phosphodiesterase inhibitor sildenafil (44.4 ± 1.0% reduction in cardiomyocyte damage). Overall, these findings demonstrate that enhancing cGMP signaling, specifically downstream and independent of NO formation, in the dystrophin-deficient heart improves contractile performance, myocardial metabolic status, and sarcolemmal integrity and thus constitutes a potential clinical avenue for the treatment of the dystrophin-related cardiomyopathies.
Prediction of the tissue-specificity of selective estrogen receptor modulators by using a single biochemical method
Authors: Dai Susie Y. , Chalmers Michael J. , Bruning John , Bramlett Kelli S. , Osborne Harold E. , Montrose-Rafizadeh Chahrzad , Barr Robert J. , Wang Yong , Wang Minmin , Burris Thomas P. , Dodge Jeffrey A. , Griffin Patrick R.
Published: May 2008

Here, we demonstrate that a single biochemical assay is able to predict the tissue-selective pharmacology of an array of selective estrogen receptor modulators (SERMs). We describe an approach to classify estrogen receptor (ER) modulators based on dynamics of the receptor-ligand complex as probed with hydrogen/deuterium exchange (HDX) mass spectrometry. Differential HDX mapping coupled with cluster and discriminate analysis effectively predicted tissue-selective function in most, but not all, cases tested. We demonstrate that analysis of dynamics of the receptor–ligand complex facilitates binning of ER modulators into distinct groups based on structural dynamics. Importantly, we were able to differentiate small structural changes within ER ligands of the same chemotype. In addition, HDX revealed differentially stabilized regions within the ligand-binding pocket that may contribute to the different pharmacology phenotypes of the compounds independent of helix 12 positioning. In summary, HDX provides a sensitive and rapid approach to classify modulators of the estrogen receptor that correlates with their pharmacological profile.
Expression of an estrogen receptor agonist in differentiating osteoblast cultures
Authors: McCarthy Thomas L. , Clough Mary E. , Gundberg Caren M. , Centrella Michael
Published: May 2008

Osteoblasts respond in direct and indirect ways to estrogens, and age-dependent changes in hormone levels and bone health can be limited by focused hormone replacement therapy. In this study, we report the release and isolation of an estrogen receptor agonist from osteoblast cultures. This entity reprises many aspects of estradiol activity in isolated osteoblasts, but differs from authentic estradiol by several biochemical and physical criteria. At levels that occur in conditioned medium from differentiating osteoblast cultures, the agonist directly drives gene expression through estrogen-sensitive response elements, activates the obligate osteoblast transcription factor Runx2, and potently enhances Smad-dependent gene expression in response to TGF-β, but exhibits relatively lesser suppressive effects on gene expression through C/EBP and AP-1-binding protein transcription factors. Estrogen receptor agonist activity is resistant to heating at 100°C and separable from the bulk of the remaining alcohol- and hexane-soluble molecules by C18 chromatography. MS and molecular fragmentation analyses predict a
M
r
of 415.2 to 437.2. Therefore, in addition to earlier studies showing that osteoblasts readily respond to and metabolize various sex steroid-like substrates, we find that they also generate a potent estrogen receptor agonist during differentiation
in vitro
. Changes in the availability of a molecule like this within bone may relate to differences in skeletal integrity with aging or metabolic disease.
Hyperpolarization-activated graded persistent activity in the prefrontal cortex
Authors: Winograd Milena , Destexhe Alain , Sanchez-Vives Maria V.
Published: May 2008

We describe a phenomenon of hyperpolarization-activated graded persistent activity (HAGPA) in prefrontal cortex neurons. Successive hyperpolarizing pulses induced increasingly higher rates of tonic firing that remained stable for tens of seconds, allowing the neuron to retain a memory of the previous history of stimulation. This phenomenon occurred at the cellular level and in the absence of neuromodulators. Neurons with HAGPA had a sag during hyperpolarization, and blocking h-current eliminated the sag and prevented HAGPA, suggesting that the activation of this hyperpolarization-activated cationic current was necessary for the occurrence of the phenomenon. A single-neuron biophysical model including h-current modulation by intracellular calcium was able to display HAGPA. This form of neuronal memory not only allows the transformation of inhibition into an increase of firing rate, but also endows neurons with a mechanism to compute the properties of successive inputs into persistent activity, thus solving a difficult computational problem.
Fecal transmission of AA amyloidosis in the cheetah contributes to high incidence of disease
Authors: Zhang Beiru , Une Yumi , Fu Xiaoying , Yan Jingmin , Ge FengXia , Yao Junjie , Sawashita Jinko , Mori Masayuki , Tomozawa Hiroshi , Kametani Fuyuki , Higuchi Keiichi
Published: May 2008

AA amyloidosis is one of the principal causes of morbidity and mortality in captive cheetahs (
Acinonyx jubatus
), which are in danger of extinction, but little is known about the underlying mechanisms. Given the transmissible characteristics of AA amyloidosis, transmission between captive cheetahs may be a possible mechanism involved in the high incidence of AA amyloidosis. In this study of animals with AA amyloidosis, we found that cheetah feces contained AA amyloid fibrils that were different from those of the liver with regard to molecular weight and shape and had greater transmissibility. The infectious activity of fecal AA amyloid fibrils was reduced or abolished by the protein denaturants 6 M guanidine·HCl and formic acid or by AA immunodepletion. Thus, we propose that feces are a vehicle of transmission that may accelerate AA amyloidosis in captive cheetah populations. These results provide a pathogenesis for AA amyloidosis and suggest possible measures for rescuing cheetahs from extinction.
Common SNP in
pre-miR-146a
decreases mature miR expression and predisposes to papillary thyroid carcinoma
Authors: Jazdzewski Krystian , Murray Elizabeth L. , Franssila Kaarle , Jarzab Barbara , Schoenberg Daniel R. , de la Chapelle Albert
Published: May 2008

Although papillary thyroid carcinoma (PTC) displays strong heritability, no predisposing germ-line mutations have been found. We show that a common G/C polymorphism (rs2910164) within the pre-miR-146a sequence reduced the amount of pre- and mature miR-146a from the C allele 1.9- and 1.8-fold, respectively, compared with the G allele. This is matched by a similar decrease in the amount of each pre-miR generated from the corresponding pri-miR-146a in an
in vitro
processing reaction. The C allele also interfered with the binding of a nuclear factor to pre-miR-146a. The reduction in miR-146a led to less efficient inhibition of target genes involved in the Toll-like receptor and cytokine signaling pathway (TRAF6, IRAK1), and PTC1 (also known as CCDC6 or H4), a gene frequently rearranged with RET proto-oncogene in PTC. In an association study of 608 PTC patients and 901 controls, we found marked differences in genotype distribution of rs2910164 (
P
= 0.000002), the GC heterozygous state being associated with an increased risk of acquiring PTC (odds ratio = 1.62,
P
= 0.000007), and both homozygous states protective with odds ratio = 0.42 for the CC genotype (
P
= 0.003) and odds ratio = 0.69 for the GG genotype (
P
= 0.0006). Moreover, 4.7% of tumors had undergone somatic mutations of the SNP sequence. Thus, our data suggest that a common polymorphism in pre-miR-146a affects the miR expression, contributes to the genetic predisposition to PTC, and plays a role in the tumorigenesis through somatic mutation. Preliminary evidence suggests that these effects are mediated through target genes whose expression is affected by the SNP status.
The class III PI(3)K Vps34 promotes autophagy and endocytosis but not TOR signaling in Drosophila
Authors: Juhász Gábor , Hill Jahda H. , Yan Ying , Sass Miklós , Baehrecke Eric H. , Backer Jonathan M. , Neufeld Thomas P.
Published: May 2008

Degradation of cytoplasmic components by autophagy requires the class III phosphatidylinositol 3 (PI(3))–kinase Vps34, but the mechanisms by which this kinase and its lipid product PI(3) phosphate (PI(3)P) promote autophagy are unclear. In mammalian cells, Vps34, with the proautophagic tumor suppressors Beclin1/Atg6, Bif-1, and UVRAG, forms a multiprotein complex that initiates autophagosome formation. Distinct Vps34 complexes also regulate endocytic processes that are critical for late-stage autophagosome-lysosome fusion. In contrast, Vps34 may also transduce activating nutrient signals to mammalian target of rapamycin (TOR), a negative regulator of autophagy. To determine potential in vivo functions of Vps34, we generated mutations in the single Drosophila melanogaster Vps34 orthologue, causing cell-autonomous disruption of autophagosome/autolysosome formation in larval fat body cells. Endocytosis is also disrupted in Vps34−/− animals, but we demonstrate that this does not account for their autophagy defect. Unexpectedly, TOR signaling is unaffected in Vps34 mutants, indicating that Vps34 does not act upstream of TOR in this system. Instead, we show that TOR/Atg1 signaling regulates the starvation-induced recruitment of PI(3)P to nascent autophagosomes. Our results suggest that Vps34 is regulated by TOR-dependent nutrient signals directly at sites of autophagosome formation.
Proteasomal degradation restricts the nuclear lifespan of AID
Authors: Aoufouchi Said , Faili Ahmad , Zober Carole , D'Orlando Orietta , Weller Sandra , Weill Jean-Claude , Reynaud Claude-Agnès
Published: May 2008

Activation-induced cytidine deaminase (AID) initiates all postrearrangement processes that diversify the immunoglobulin repertoire by specific deamination of cytidines at the immunoglobulin (Ig) locus. As uncontrolled expression of AID is potentially mutagenic, different types of regulation, particularly nucleocytoplasmic shuttling, restrict the likelihood of AID–deoxyribonucleic acid encounters. We studied additional mechanisms of regulation affecting the stability of the AID protein. No modulation of protein accumulation according to the cell cycle was observed in a Burkitt's lymphoma cell line. In contrast, the half-life of AID was markedly reduced in the nucleus, and this destabilization was accompanied by a polyubiquitination that was revealed in the presence of proteasome inhibitors. The same compartment-specific degradation was observed in activated mouse B cells, and also in a non–B cell line. No specific lysine residues could be linked to this degradation, so it remains unclear whether polyubiquitination proceeds through several alternatives sites or through the protein N terminus. The nuclear-restricted form of AID displayed enhanced mutagenicity at both Ig and non-Ig loci, most notably at TP53, suggesting that modulation of nuclear AID content through proteasomal degradation may represent another level of control of AID activity.
Breaking tolerance to the natural human liver autoantigen cytochrome P450 2D6 by virus infection
Authors: Holdener Martin , Hintermann Edith , Bayer Monika , Rhode Antje , Rodrigo Evelyn , Hintereder Gudrun , Johnson Eric F. , Gonzalez Frank J. , Pfeilschifter Josef , Manns Michael P. , Herrath Matthias von G. , Christen Urs
Published: May 2008

Autoimmune liver diseases, such as autoimmune hepatitis (AIH) and primary biliary cirrhosis, often have severe consequences for the patient. Because of a lack of appropriate animal models, not much is known about their potential viral etiology. Infection by liver-tropic viruses is one possibility for the breakdown of self-tolerance. Therefore, we infected mice with adenovirus Ad5 expressing human cytochrome P450 2D6 (Ad-2D6). Ad-2D6–infected mice developed persistent autoimmune liver disease, apparent by cellular infiltration, hepatic fibrosis, “fused” liver lobules, and necrosis. Similar to type 2 AIH patients, Ad-2D6–infected mice generated type 1 liver kidney microsomal–like antibodies recognizing the immunodominant epitope WDPAQPPRD of cytochrome P450 2D6 (CYP2D6). Interestingly, Ad-2D6–infected wild-type FVB/N mice displayed exacerbated liver damage when compared with transgenic mice expressing the identical human CYP2D6 protein in the liver, indicating the presence of a stronger immunological tolerance in CYP2D6 mice. We demonstrate for the first time that infection with a virus expressing a natural human autoantigen breaks tolerance, resulting in a chronic form of severe, autoimmune liver damage. Our novel model system should be instrumental for studying mechanisms involved in the initiation, propagation, and precipitation of virus-induced autoimmune liver diseases.
Development and characterization of IL-21–producing CD4+ T cells
Authors: Suto Akira , Kashiwakuma Daisuke , Kagami Shin-ichiro , Hirose Koichi , Watanabe Norihiko , Yokote Kotaro , Saito Yasushi , Nakayama Toshinori , Grusby Michael J. , Iwamoto Itsuo , Nakajima Hiroshi
Published: May 2008

It has recently been shown that interleukin (IL)-21 is produced by Th17 cells, functions as an autocrine growth factor for Th17 cells, and plays critical roles in autoimmune diseases. In this study, we investigated the differentiation and characteristics of IL-21–producing CD4+ T cells by intracellular staining. Unexpectedly, we found that under Th17-polarizing conditions, the majority of IL-21–producing CD4+ T cells did not produce IL-17A and -17F. We also found that IL-6 and -21 potently induced the development of IL-21–producing CD4+ T cells without the induction of IL-4, IFN-γ, IL-17A, or IL-17F production. On the other hand, TGF-β inhibited IL-6– and IL-21–induced development of IL-21–producing CD4+ T cells. IL-2 enhanced the development of IL-21–producing CD4+ T cells under Th17-polarizing conditions. Finally, IL-21–producing CD4+ T cells exhibited a stable phenotype of IL-21 production in the presence of IL-6, but retained the potential to produce IL-4 under Th2-polarizing conditions and IL-17A under Th17-polarizing conditions. These results suggest that IL-21–producing CD4+ T cells exhibit distinct characteristics from Th17 cells and develop preferentially in an IL-6–rich environment devoid of TGF-β, and that IL-21 functions as an autocrine growth factor for IL-21–producing CD4+ T cells.
Control of hematopoietic stem cell quiescence by the E3 ubiquitin ligase Fbw7
Authors: Thompson Benjamin J. , Jankovic Vladimir , Gao Jie , Buonamici Silvia , Vest Alan , Lee Jennifer May , Zavadil Jiri , Nimer Stephen D. , Aifantis Iannis
Published: May 2008

Ubiquitination is a posttranslational mechanism that controls diverse cellular processes. We focus here on the ubiquitin ligase Fbw7, a recently identified hematopoietic tumor suppressor that can target for degradation several important oncogenes, including Notch1, c-Myc, and cyclin E. We have generated conditional Fbw7 knockout animals and inactivated the gene in hematopoietic stem cells (HSCs), progenitors, and their differentiated progeny. Deletion of Fbw7 specifically and rapidly affects hematopoiesis in a cell-autonomous manner. Fbw7−/− HSCs show defective maintenance of quiescence, leading to impaired self-renewal and a severe loss of competitive repopulating capacity. Furthermore, Fbw7−/− progenitors are unable to colonize the thymus, leading to a profound depletion of T cell progenitors. Deletion of Fbw7 in bone marrow (BM) stem cells and progenitors leads to the stabilization of c-Myc, a transcription factor previously implicated in HSC self-renewal. On the other hand, neither Notch1 nor cyclin E is visibly stabilized in the BM of Fbw7-deficient mice. Gene expression studies of Fbw7−/− HSCs and hematopoietic progenitors indicate that Fbw7 regulates, through the regulation of HSC cycle entry, the transcriptional “signature” that is associated with the quiescent, self-renewing HSC phenotype.
Outbreak of Postoperative Endophthalmitis in a Thai Tertiary Care Center
Authors: Apisarnthanarak Anucha , Jirajariyavej Supanee , Thongphubeth Kanokporn , Yuekyen Chananart , Warren David K. , Fraser Victoria J.
Published: May 2008

We performed a study with a 1:3 ratio of case patients (n = 11) to control patients (n = 33) to evaluate risk factors for postoperative endophthalmitis in a Thai tertiary care center. Multivariate analysis revealed that diabetes mellitus and surgeon A were associated risk factors. Preoperative diabetes mellitus control and the improvement of infection control practices led to the termination of the outbreak.
Inverse Correlation Between Level of Professional Education and Rate of Handwashing Compliance in a Teaching Hospital
Authors: Duggan Joan M. , Hensley Sandra , Khuder Sadik , Papadimos Thomas J. , Jacobs Lloyd
Published: May 2008

Objective.

To evaluate educational level as a contributing factor in handwashing compliance.

Design.

Observation of hand washing opportunities was performed for approximately 12 weeks before an announced Joint Commission on Accreditation of Healthcare Organizations (JCAHO) visit and for approximately 10 weeks after the visit. Trained observers recorded the date, time, and location of the observation; the type of healthcare worker or hospital employee observed; and the type of hand hygiene opportunity observed.

Setting.

University of Toledo Medical Center, a 319-bed teaching hospital.

Results.

A total of 2,373 observations were performed. The rate of hand washing compliance among nurses was 91.3% overall. Medical attending physicians had the lowest observed rate of compliance (72.4%; P < .001). Nurses showed statistically significant improvement in their rate of hand hygiene compliance after the JCAHO visit (P = .001), but no improvement was seen for attending physicians (P = .117). The compliance rate in the surgical intensive care unit was more than 90%, greater than that in other hospital units (P = .001). Statistically, the compliance rate was better during the first part of the week (Monday, Tuesday, and Wednesday) than during the latter part of the week (Thursday and Friday) (P = .002), and the compliance rate was better during the 3 PM-1 1 PM shift, compared with the 7 AM-3 PM shift (P < .001). When evaluated by logistic regression analysis, non-physician healthcare worker status and observation after the JCAHO accreditation visit were associated with an increased rate of hand hygiene compliance.

Conclusion.

An inverse correlation existed between the level of professional educational and the rate of compliance. Future research initiatives may need to address the different motivating factors for hand hygiene among nurses and physicians to increase compliance.
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
Authors: Viklund Håkan , Elofsson Arne
Published: May 2008

Motivation: As α-helical transmembrane proteins constitute roughly 25% of a typical genome and are vital parts of many essential biological processes, structural knowledge of these proteins is necessary for increasing our understanding of such processes. Because structural knowledge of transmembrane proteins is difficult to attain experimentally, improved methods for prediction of structural features of these proteins are important.

Results: OCTOPUS, a new method for predicting transmembrane protein topology is presented and benchmarked using a dataset of 124 sequences with known structures. Using a novel combination of hidden Markov models and artificial neural networks, OCTOPUS predicts the correct topology for 94% of the sequences. In particular, OCTOPUS is the first topology predictor to fully integrate modeling of reentrant/membrane-dipping regions and transmembrane hairpins in the topological grammar.

Availability: OCTOPUS is available as a web server at http://octopus.cbr.su.se.

Contact:  arne@bioinfo.se

Supplementary information:  Supplementary data are available at Bioinformatics online.
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
Authors: Wehe André , Bansal Mukul S. , Burleigh J. Gordon , Eulenstein Oliver
Published: May 2008

Summary: DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++.

Availability: DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Contact:  oeulenst@cs.iastate.edu
Sir Herbert Charles Pereira. 12 May 1913 — 19 December 2004
Authors: McCulloch J. S. G.
Published: May 2008

Sir Charles Pereira's professional life was dedicated to research in agriculture and forestry to improve life in developing countries, mainly in the tropics; this was achieved through an enhanced understanding and management of the vital water resources.
Phasing of dragonfly wings can improve aerodynamic efficiency by removing swirl
Authors: Usherwood James R , Lehmann Fritz-Olaf
Published: May 2008

Dragonflies are dramatic, successful aerial predators, notable for their flight agility and endurance. Further, they are highly capable of low-speed, hovering and even backwards flight. While insects have repeatedly modified or reduced one pair of wings, or mechanically coupled their fore and hind wings, dragonflies and damselflies have maintained their distinctive, independently controllable, four-winged form for over 300 Myr. Despite efforts at understanding the implications of flapping flight with two pairs of wings, previous studies have generally painted a rather disappointing picture: interaction between fore and hind wings reduces the lift compared with two pairs of wings operating in isolation. Here, we demonstrate with a mechanical model dragonfly that, despite presenting no advantage in terms of lift, flying with two pairs of wings can be highly effective at improving aerodynamic efficiency. This is achieved by recovering energy from the wake wasted as swirl in a manner analogous to coaxial contra-rotating helicopter rotors. With the appropriate fore–hind wing phasing, aerodynamic power requirements can be reduced up to 22 per cent compared with a single pair of wings, indicating one advantage of four-winged flying that may apply to both dragonflies and, in the future, biomimetic micro air vehicles.
Detection of mortality clusters associated with highly pathogenic avian influenza in poultry: a theoretical analysis
Authors: Savill Nicholas J , St. Rose Suzanne G , Woolhouse Mark E.J
Published: May 2008

Rapid detection of infectious disease outbreaks is often crucial for their effective control. One example is highly pathogenic avian influenza (HPAI) such as H5N1 in commercial poultry flocks. There are no quantitative data, however, on how quickly the effects of HPAI infection in poultry flocks can be detected. Here, we study, using an individual-based mathematical model, time to detection in chicken flocks. Detection is triggered when mortality, food or water intake or egg production in layers pass recommended thresholds suggested from the experience of past HPAI outbreaks. We suggest a new threshold for caged flocks—the cage mortality detection threshold—as a more sensitive threshold than current ones. Time to detection is shown to depend nonlinearly on
R
0
and is particularly sensitive for
R
0
<10. It also depends logarithmically on flock size and number of birds per cage. We also examine how many false alarms occur in uninfected flocks when we vary detection thresholds owing to background mortality. The false alarm rate is shown to be sensitive to detection thresholds, dependent on flock size and background mortality and independent of the length of the production cycle. We suggest that current detection thresholds appear sufficient to rapidly detect the effects of a high
R
0
HPAI strain such as H7N7 over a wide range of flock sizes. Time to detection of the effects of a low
R
0
HPAI strain such as H5N1 can be significantly improved, particularly for large flocks, by lowering detection thresholds, and this can be accomplished without causing excessive false alarms in uninfected flocks. The results are discussed in terms of optimizing the design of disease surveillance programmes in general.
On annular self-similar solutions in resistive magnetogasdynamics
Authors: Lock R.M , Mestel A.J
Published: May 2008

We consider the implosion of a hollow cylinder of ideal gas with non-zero electrical resistivity. It is shown that there exist self-similar solutions that collapse in a finite time for a range of power-law dependences of the resistivity on the plasma temperature,
η
∼
T

δ

. In contrast to the earlier work with zero resistivity, all field variables are finite up to the instant of collapse and the compression is homogeneous. A solution in closed form is found for constant diffusivity,
δ
=0. It is shown that
δ
→0 is a singular limit with the density and sound speed adjusting over a layer of thickness |
δ
|
1/2
at the inner boundary.
Dynamics of a truss structure and its moving-oscillator exciter with separation and impact–reattachment
Authors: Baeza Luis , Ouyang Huajiang
Published: May 2008

The dynamic response of a stationary structure excited by a moving structure is studied in this paper. The stationary structure is in the form of a truss made of a number of rigidly connected Timoshenko beams, while the moving structure consists of two masses linked by a spring and a dashpot (oscillator). To facilitate the mathematical model of the moving-load dynamics of the whole system, the frequencies and modes of the stationary structure are first obtained by the finite-element method and then they are cast in an analytical form within each element through the element shape functions. This is a distinct advantage of this paper. Each component beam of the stationary structure is meshed with an adaptable number of Timoshenko beam elements to allow efficient modelling of the vibration of the structure for a wide range of travelling speeds of the moving oscillator. During the horizontal travel and vertical vibration of the oscillator, it may separate from the vibrating stationary structure and subsequently may reattach to the stationary structure with impact. These two phenomena have been studied in only a few papers for simple moving-load problems in the past and have never been studied for the present problem. It is found through simulated examples that the dynamic response at high speeds can be several times higher than the relevant static response, and separation and reattachment with impact produce a noticeable difference in the dynamic response. Multiple separation and impact events are possible at high speeds. It is also interesting to observe that separation may occur at high subcritical speeds and impact at various values of the coefficient of restitution has mild local influence on the dynamic response after reattachment.
Dislocation pile-ups in Fe at high temperature
Authors: Fitzgerald S.P , Dudarev S.L
Published: May 2008

Dislocation ‘pile-ups’ occur in crystals when a number of similar dislocations, gliding in a common slip plane, are driven by an applied stress towards an obstacle that they cannot overcome. In contrast to dislocation walls, pile-ups give rise to a long-range stress field, and their properties strongly influence the plastic behaviour of the crystal as a whole. In this paper, we apply the analytic model of a pile-up (due to Eshelby, Frank and Nabarro) to a cubic crystal. Full anisotropic elasticity is used, and the model is extended to predict the plastic displacement generated by a dislocation source during the formation of a pile-up. The results are applied to Fe close to the temperature of the α–γ phase transition, where the inclusion of anisotropy leads to a strikingly different prediction from that of the isotropic approximation.
The Coolidge effect, individual recognition and selection for distinctive cuticular signatures in a burying beetle
Authors: Steiger Sandra , Franz Ragna , Eggert Anne-Katrin , Müller Josef K
Published: May 2008

The ability to recognize individuals is an important aspect of social interactions, but it can also be useful to avoid repeated matings with the same individual. The Coolidge effect is the progressive decline in a male's propensity to mate with the same female combined with a heightened sexual interest in new females. Although males that recognize previous partners and show a preference for novel females should have a selective advantage as they can distribute sperm evenly among the females they encounter, there are few invertebrate examples of the Coolidge effect. Here we present evidence for this effect in the burying beetle
Nicrophorus vespilloides
and examine the mechanism underlying the discrimination between familiar and novel mates. Burying beetles feed and reproduce on vertebrate carcasses, where they regularly encounter conspecifics. Males showed greater sexual interest in novel females (virgin or mated) than in females they had inseminated before. The application of identical cuticular extracts allowed us to experimentally create females with similar odours, and male responses to such females demonstrated that they use female cuticular patterns for discrimination. The chemical analysis of the cuticular profile revealed greater inter-individual variation in female than in male cuticular patterns, which might be due to greater selection on females to signal their individual identity.
Sex and space destabilize intransitive competition within and between species
Authors: Vellend Mark , Litrico Isabelle
Published: May 2008

Organisms ranging from bacteria and corals to plants and vertebrates can form intransitive competitive networks, in which coexistence can be maintained because no one species or genotype is superior to all others. However, in the simplest case with three competing types, the long-term outcome may not be so clear if two of the three represent the ends of a continuous heritable trait distribution within one species, as has been recently demonstrated empirically in a short-term experiment with plants. Using simulation models of this scenario, results with asexual reproduction confirm previous studies which showed that local interactions promote coexistence. However, with sexual reproduction, genetic variance is reduced because selection fluctuates between favouring the two extremes during population cycles, while sex continually produces intermediates. Sex thus slows the response to selection when it is the strongest and therefore slows the recovery from extreme abundances, creating larger abundance fluctuations. Local interactions do not stabilize dynamics with sex because the resultant spatial patches of one species are genetically heterogeneous, such that particular phenotypes do not benefit from spatial refuges. In sharp contrast to previous models suggesting that sex or local interactions stabilize population dynamics, here sex and local interactions destabilize dynamics and increase extinction risk.
Recent advances in reproductive neuroendocrinology: a role for RFamide peptides in seasonal reproduction?
Authors: Greives Timothy J , Kriegsfeld Lance J , Bentley George E , Tsutsui Kazuyoshi , Demas Gregory E
Published: May 2008

Most temperate-zone species use photoperiod to coordinate breeding and ensure that offspring are born during favourable conditions. Although photoperiodic influences on the reproductive axis have been well characterized, the precise mechanisms by which photoperiodic information and other seasonal cues are integrated to regulate reproductive function remain less well specified. Two recently discovered neuropeptides, kisspeptin and gonadotropin-inhibitory hormone, have pronounced opposing influences on reproductive function. This paper will review recent evidence for a role of these peptides in seasonal reproduction and propose a theoretical framework by which these novel regulatory peptides may serve to regulate seasonal breeding. Understanding the mechanisms regulating appropriate changes in reproductive status will serve to advance a wide range of life science disciplines.
Multiple ancient origins of neoteny in Lycidae (Coleoptera): consequences for ecology and macroevolution
Authors: Bocak Ladislav , Bocakova Milada , Hunt Toby , Vogler Alfried P
Published: May 2008

Neoteny, the maintenance of larval features in sexually mature adults, is a radical way of generating evolutionary novelty through shifts in relative timing of developmental programmes. While controlled by the environment in facultative neotenics, retention of larval features is obligatory in many species of Lycidae (net-winged beetles). They are studied here as an example of how developmental shifts and ecology interact to produce macroevolutionary impacts. We conducted a phylogenetic analysis of Lycidae based on DNA sequences from nuclear (18S and 28S rRNA) and mitochondrial (rrnL,cox1,cobandnad5) genes from a representative set of lineages (73 species), including 17 neotenic taxa. Major changes of basal relationships compared with those implied in the current classification generally supported three independent origins of neotenics in Lycidae. The southeast Asian Lyropaeinae and Ateliinae were in basal positions indicating evolutionary antiquity, also confirmed by molecular clock estimates, unlike the neotropical leptolycines nested within Calopterini and presumably much younger. neotenics exhibit typical K-selected traits including slow development, large body size, high investment in offspring and low dispersal. This correlated with low species richness and restricted ranges of neotenic lineages compared with their sisters. Yet, these factors did not impede the evolutionary persistence of affected lineages, even without reversals to fully metamorphosed forms, contradicting earlier suggestions of recent evolution from dispersive non-neotenics.
Protein crystals can be incommensurately modulated
Authors: Lovelace Jeffrey J. , Murphy Cameron R. , Daniels Lee , Narayan Kartik , Schutt Clarence E. , Lindberg Uno , Svensson Christer , Borgstahl Gloria E. O.
Published: May 2008

For a normal periodic crystal, the X-ray diffraction pattern can be described by an orientation matrix and a set of three integers that indicate the reciprocal lattice points. Those integers determine the spacing along the reciprocal lattice directions. In aperiodic crystals, the diffraction pattern is modulated and the standard periodic main reflections are surrounded by satellite reflections. The successful indexing and refinement of the main unit cell andqvector usingTWINSOLVE, developed by Svensson [(2003). Lund University, Sweden], are reported here for an incommensurately modulated, aperiodic crystal of a profilin:actin complex. The indexing showed that the modulation is along thebdirection in the crystal, which corresponds to an `actin ribbon' formed by the crystal lattice. Interestingly, the transition to the aperiodic state was shown to be reversible and the diffraction pattern returned to the periodic state during data collection. It is likely that the protein underwent a conformational change that affected the neighbouring profilin:actin molecules in such a way as to produce the observed modulation in the diffraction pattern. Future work will aim to trap the incommensurately modulated crystal state, for example using cryocooling or chemical crosslinking, thus allowing complete X-ray data to be collected.
Size-broadening anisotropy in whole powder pattern fitting. Application to zinc oxide and interpretation of the apparent crystallites in terms of physical models
Authors: Popa N. C. , Balzar D.
Published: May 2008

A new anisotropic size-broadening model based on a spherical-harmonics representation allowing determination of both volume- and area-averaged apparent crystallites and convenient for implementation into Rietveld programs is described. The model effectiveness is demonstrated on a ZnO powder pattern exhibiting strongly anisotropic size broadening and pronounced super-Lorentzian peak shapes. Moreover, it is shown how the apparent crystallites can be interpreted in terms of physical models by using ellipsoidal and cylindrical crystallites with lognormal size distributions. This interpretation is critically assessed and it is argued that both simplified physical models anda prioricomplementary information (obtained by transmission electron microscopy, for instance) are often needed to avoid unstable and non-unique solutions.
Different models for the polar nanodomain structure of PZN and other relaxor ferroelectrics
Authors: Welberry T. R. , Goossens D. J.
Published: May 2008

Computer simulations have been carried out to test the recently proposed model for the nanodomain structure of relaxor ferroelectrics such as lead zinc niobate (PZN). In this recent model it was supposed that the polar nanodomains are three-dimensional, that the observed diffuse rods of scattering originate from the boundaries between domains and that the Pb displacements may be directed along \langle {100} \rangle, \langle {111} \rangle or \langle {110} \rangle. This is in marked contrast to a previously published model, which described the polar domains as thin plates with Pb displacements confined to the \langle {110} \rangle directions within the essentially two-dimensional domains. The present results confirm that \langle {100} \rangle and \langle {111} \rangle types of Pb displacement are viable possibilities, but the number of domain boundaries required to produce sufficiently strong diffuse rods of scattering means that individual domains cannot be described as three-dimensional and must still be relatively thin. The current work has been carried out with no direct involvement of theB-site cation ordering, which many workers assume is necessary to understand the formation of the polar nanodomains. While it may be true that theB-site cation distribution could provide an underlying perturbation field that might ultimately limit the extent of any polar domain, it is certainly not necessary to produce the observed scattering effects.
The Heterangiums of the British Coal Measures
Authors: Scott D H
Published: May 2008

The characters of the various species described have been given above (pp. 65, 73, 89, 91). The more general results may be summed up as follows:— The three British Coal-Measure species, Heterangium shorense, H. tiliœoides, and H. Lomaxii, agree in their more important characters and only differ in details. The fourth species, H. minimum, is of a different type.The three species first named may conveniently be grouped in a provisional subgenus, Polyangium, characterized by the leaf-trace, starting from the stele as two distinct bundles, which further divide on their outward course, the number of bundles in the petiole ranging from four to eight.In addition to the polydesniic structure, these three species further agree in the sharp delimitation of the primary peripheral xylem-strands, with the consequent differentiation of large interfascicular principal rays, and in the approach to exarchy iu the peripheral strands and leaf-trace bundles, the primary centrifugal xylem being comparatively little developed.It is probable that, besides H. shorense, H. tiliœoides, and H. Lomaxii, the four species described by Renault, from the Upper Coal Measures of Autun (H. punctatum*, H. Renaultii*, H. Duchartrei*, and H. bibractense) are referable to the subgenus Polyangium.The Lower Carboniferous species H. Grievii may be taken us the type of another subgenus, Eu-heterangium, characterized by the leaf-trace consisting of a single bundle only, where it leaves the stele, this bundle either remaining undivided on its outward course or dividing into two strands only. One Duleagate species, H. minimum, falls under this subgenus, as do also four of the Ostrau species described by Dr. Kubart, namely H. alatum, H. polystichum, H. Sehusteri, and H. Stunt. The peripheral xylem-strands are, on the whole, less distinct in Eu-heterangium than in Polyangium, but the degree of their differentiation varies in the different species. The xylemstrands may either be “ceutrally mesarch” or show a tendency towards exarchy. A third subgenus may be required for the Lyginopteroid species, such as H. Andrei, discovered by Dr. Kubart.The polydesinic species of Heterangium (Polyangium) show an interesting analogy with Medulioseæ and with the protostelic Calamopityeæ. There is, however, no sufficient evidence of any direct phylogenetic relation to either group. With Rhetinangium there is no special affinity, for, while this genus appears to have much in common with Heterangium, its leaf-trace is complex and not multiple, thus presenting only a remote analogy with that of the polydesmic Heterangiums. Megaloxylon is altogether more remote.