bluuebunny/crossref_metadata_2025 huggingface dataset:
Sperm Seen Competing
Authors: Carmichael Stephen W.
Published: August 2010

It is well known that females of some insects mate with more than one male before the ova are fertilized. The post-copulatory behavior of the sperm has been studied for decades, but until now there has not been a method to definitively determine the “ownership” of sperm within the female genital tract. In a very clever study, Mollie Manier, John Belote, Kirstin Berben, David Novikov, Will Stuart, and Scott Pitnick offer an answer to this dilemma .
NetNotes
Authors: Phillips Thomas E.
Published: August 2010

Selected postings from the Microscopy Listserver from May 1, 2010 to June 30, 2010. Complete listings and subscription information can be obtained at http://www.microscopy.com. Postings may have been edited to conserve space or for clarity.
Tomographic P wave velocity and vertical velocity gradient structure across the geothermal site Groß Schönebeck (NE German Basin): Relationship to lithology, salt tectonics, and thermal regime
Authors: Bauer K. , Moeck I. , Norden B. , Schulze A. , Weber M. , Wirth H.
Published: August 2010

Seismic wide‐angle data were collected along a 40‐km‐long profile centered at the geothermal research well GrSk 3/90 in the Northeast German Basin. Tomographic inversion of travel time data provided a velocity and a vertical velocity gradient model, indicative of Cenozoic to Pre‐Permian sediments. Wide‐angle reflections are modeled and interpreted as top Zechstein and top Pre‐Permian. Changes in velocity gradients are interpreted as the transition from mechanical to chemical compaction at 2–3 km depth, and localized salt structures are imaged, suggesting a previously unknown salt pillow in the southern part of the seismic profile. The Zechstein salt shows decreased velocities in the adjacent salt pillows compared to the salt lows, which is confirmed by sonic log data. This decrease in velocity could be explained by the mobilization of less dense salt, which moved and formed the salt pillows, whereas the denser salt remained in place at the salt lows. We interpret a narrow subvertical low‐velocity zone under the salt pillow at GrSk 3/90 as a fault in the deep Permian to Pre‐Permian. This WNW‐ESE trending fault influenced the location of the salt tectonics and led to the formation of a fault‐bounded graben in the Rotliegend sandstones with optimal mechanical conditions for geothermal production. Thermal modeling showed that salt pillows are related to chimney effects, a decrease in temperature, and increasing velocity. The assumed variations in salt lithology, density, and strain must thus be even higher to compensate for the temperature effect.
Assimilation of the dual‐polarization Doppler radar data for a convective storm with a warm‐rain radar forward operator
Authors: Li Xuanli , Mecikalski John R.
Published: August 2010

In this paper, a data assimilation scheme is built to utilize the dual‐polarization Doppler radar observations collected by the C band Advanced Radar for Meteorological and Operational Research and is tested with a case study for a mesoscale convective system (MCS) over northern Alabama in the afternoon of 15 March 2008. Three variables, horizontal reflectivity, differential reflectivity, and radial velocity are assimilated into the advanced research version of the Weather Research and Forecasting model. A warm rain radar operator is constructed to assimilate the horizontal reflectivity and differential reflectivity data with the three‐dimensional variational data assimilation (3DVAR) system. The main goals of this paper are to, first, demonstrate the improvements in short‐term forecasts of the moist convection when fields unique to the dual‐polarization radar are assimilated into a regional model and, second, to understand how these fields may best be integrated in a data assimilation system like 3DVAR to improve short‐term storm forecast. The results show that the horizontal reflectivity, differential reflectivity, and radial velocity data can be successfully assimilated using our data assimilation scheme. The assimilation of the horizontal reflectivity and radial velocity data has a significant positive impact on the reflectivity distribution of the MCS. An additional improvement (10%–20%) in the initial condition is found when the differential reflectivity data are further assimilated. Moreover, the improved initial condition leads to apparent improvement in short‐term forecast of the MCS. The best forecast is produced when both horizontal and differential reflectivity and radial velocity data are assimilated. This improvement can be attributed to the improved estimate of liquid water content by using the radar operator with combined information of both horizontal reflectivity and differential reflectivity. This study demonstrates the benefit of utilizing the observations from single dual‐polarization radar. With the forthcoming upgrade of the current U. S. “NEXRAD” radar system (set to begin in ∼2010), a dual‐polarization radar network will be available. Assimilating observations from the dual‐polarization Doppler radar network could be a potential technique to further improve the short‐term numerical forecasts of convective storms.
A new methodology for flood hazard assessment considering dike breaches
Authors: Vorogushyn S. , Merz B. , Lindenschmidt K.‐E. , Apel H.
Published: August 2010

This study focuses on development and application of a new modeling approach for a comprehensive flood hazard assessment along protected river reaches considering dike failures. The proposed Inundation Hazard Assessment Model (IHAM) represents a hybrid probabilistic‐deterministic model. It comprises three models that are coupled in a dynamic way: (1) 1D unsteady hydrodynamic model for river channel and floodplain between dikes; (2) probabilistic dike breach model which determines possible dike breach locations, breach widths and breach outflow discharges; and (3) 2D raster‐based inundation model for the dike‐protected floodplain areas. Due to the unsteady nature of the 1D and 2D models and runtime coupling, the interdependence between the hydraulic loads on dikes at various locations along the reach is explicitly considered. This ensures a more realistic representation of the fluvial system dynamics under extreme conditions compared to the steady approaches. The probabilistic dike breach model describes dike failures due to three failure mechanisms: overtopping, piping and slope instability caused by seepage flow through the dike core (micro‐instability). The 2D storage cell model computes various flood intensity indicators such as water depth, flow velocity, and inundation duration. IHAM is embedded in a Monte Carlo simulation in order to account for the natural variability of the input hydrograph form and the randomness of dike failures. Besides binary (wet/dry) inundation patterns, IHAM generates new probabilistic flood hazard maps for each intensity indicator and the associated uncertainty bounds. Furthermore, the novel probabilistic dike hazard maps indicate the failure probability of dikes for each considered breach mechanism.
A selective procedure for absolute paleointensity in lava flows
Authors: Valet Jean Pierre , Herrero‐Bervera Emilio , Carlut Julie , Kondopoulou Despina
Published: August 2010

We present a compilation of experiments of absolute paleointensity using double heating protocols on very recent lava flows from Hawaii, La Réunion, the Canary islands and Santorini. The existence of a sharp distribution of grain sizes carried by a single mineralogical phase always yielded successful determinations of paleointensity that deviate by less than 10% from the actual field value. Thus, a rapid decrease of at least 70% of the initial magnetization over a narrow range of temperatures prior to the Curie point combined with a unique mineralogical phase define an optimal situation for obtaining reliable estimates of absolute paleointensity. Consequently, we suggest that stepwise standard thermal demagnetization of companion specimens should be routinely performed prior to paleointensity experiments. Not only do these measurements provide important information about the characteristic magnetization, but they indicate which samples are appropriate for paleointensity experiments, which increases the success rate to almost 100%.
Why is longwave cloud feedback positive?
Authors: Zelinka Mark D. , Hartmann Dennis L.
Published: August 2010

Longwave cloud feedback is systematically positive and nearly the same magnitude across all global climate models used in the Intergovernmental Panel on Climate Change Fourth Assessment Report (AR4). Here it is shown that this robust positive longwave cloud feedback is caused in large part by the tendency for tropical high clouds to rise in such a way as to remain at nearly the same temperature as the climate warms. Furthermore, it is shown that such a cloud response to a warming climate is consistent with well‐known physics, specifically the requirement that, in equilibrium, tropospheric heating by convection can only be large in the altitude range where radiative cooling is efficient, following the fixed anvil temperature hypothesis of Hartmann and Larson (2002). Longwave cloud feedback computed assuming that high‐cloud temperature follows upper tropospheric convergence‐weighted temperature, which we refer to as proportionately higher anvil temperature, gives an excellent prediction of the longwave cloud feedback in the AR4 models. The ensemble‐mean feedback of 0.5 W m−2 K−1 is much larger than that calculated assuming clouds remain at fixed pressure, highlighting the large contribution from rising cloud tops to the robustly positive feedback. An important result of this study is that the convergence profile computed from clear‐sky energy and mass balance warms slightly as the climate warms, in proportion to the increase in stability, which results in a longwave cloud feedback that is slightly smaller than that calculated assuming clouds remain at fixed temperature.
Structure of the (0001) basal twin boundary in Bi2Te3
Authors: Medlin D. L. , Ramasse Q. M. , Spataru C. D. , Yang N. Y. C.
Published: August 2010

We investigate the structure of the (0001) basal twin boundary in Bi2Te3. Electron diffraction measurements show that this interface corresponds to a 180° rotation of the crystal about the [0001] axis, an alignment that reverses the stacking of the basal planes. The basal planes in the perfect Bi2Te3 structure are arranged in a repeating sequence of five-layer wide Te(1)–Bi–Te(2)–Bi–Te(1) packets. Thus, it is possible for the twin interface to be located at one of three distinct locations: at the Te(2) layer, the Bi layer, or the Te(1) layer. Using aberration-corrected high-angle annular dark field scanning transmission electron microscopy, we show that the twin boundary is terminated at the Te(1) layer, where the stacking forms a double-layer of Te. Our observations are consistent with ab initio calculations, which predict this twin termination to have the lowest interfacial energy of the three configurations we considered. Our calculations and observations also find a small expansion in the interplanar spacing at the interface.
Phenomenological study of irregular cellular automata based on Lyapunov exponents and Jacobians
Authors: Baetens Jan M. , De Baets Bernard
Published: August 2010

Originally, cellular automata (CA) have been defined upon regular tessellations of the n-dimensional Euclidean space, while CA on irregular tessellations have received only little attention from the scientific community, notwithstanding serious shortcomings are associated with the former manner of subdividing Rn. In this paper we present a profound phenomenological study of two-state, two-dimensional irregular CA from a dynamical systems viewpoint. We opted to exploit properly defined quantitative measures instead of resorting to qualitative methods for discriminating between behavioral classes. As such, we employ Lyapunov exponents, measuring the divergence rate of close trajectories in phase space, and Jacobians, formulated using Boolean derivatives and expressing the sensitivity of a cellular automaton to its inputs. Both are stated for two-state CA on irregular tessellations, enabling us to characterize these discrete dynamical systems, and advancing us to propose a classification scheme for this CA family. In addition, a relationship between these quantitative measures is established in extension of the insights already developed for the classical CA paradigm. Finally, we discuss the repercussions on the CA dynamics that arise when the geometric variability of the spatial entities is taken into account during the CA simulation.
Combined effect of Debye plasma environment and external electric field on hydrogen atom
Authors: Paul S. , Ho Y. K.
Published: August 2010

We consider weakly coupled plasmas, characterized by Debye–Huckel model potential, and an external electric field along z-axis. Due to plasma environment the energy levels of atom are shifted up, bound states are merged to continuum. For external electric field the excited energy levels also split up; degenerate energy eigenvalues become nondegenerate. In the presence of external electric field, energy levels are shifted up and down, except ground state. The ground state energy value is shifted only down. Therefore, it is very interesting to study the combined effect of plasmas and external electric field on a simple atom (hydrogen). To calculate the energy levels and the corresponding states, we expand the wave function in terms of linear combination of the basis functions. The basis is generated by hydrogenic wave functions. Here, we estimate various plasma surroundings and electric field strengths. We observe converged results for the basis size 45, with angular momentum states up to eight.
Hysteresis effects in the magnetic-field-induced reverse martensitic transition in magnetic shape-memory alloys
Authors: Krenke Thorsten , Aksoy Seda , Duman Eyüp , Acet Mehmet , Moya Xavier , Mañosa Lluís , Planes Antoni
Published: August 2010

We study the mechanism of magnetic-field-induced reverse martensitic transformations by considering the field-induced temperature-shifts in the thermal hysteresis loop of the magnetization and critical fields determined from magnetization isotherms. We consider first the temperature-shifts in a symmetric thermal hysteresis loop and extend the discussion to the case of the Heusler-based Ni50Mn34In16 magnetically superelastic alloy having a nonsymmetric thermal hysteresis loop. We obtain two different temperature-behaviors for the critical field depending on whether the initial measurement temperature lies on the forward or on the reverse transformation path of the thermal hysteresis.
Alchemical derivatives of reaction energetics
Authors: Sheppard Daniel , Henkelman Graeme , von Lilienfeld O. Anatole
Published: August 2010

Based on molecular grand canonical ensemble density functional theory, we present a theoretical description of how reaction barriers and enthalpies change as atoms in the system are subjected to alchemical transformations, from one element into another. The change in the energy barrier for the umbrella inversion of ammonia is calculated along an alchemical path in which the molecule is transformed into water, and the change in the enthalpy of protonation for methane is calculated as the molecule is transformed into a neon atom via ammonia, water, and hydrogen fluoride. Alchemical derivatives are calculated analytically from the electrostatic potential in the unperturbed system, and compared to numerical derivatives calculated with finite difference interpolation of the pseudopotentials for the atoms being transformed. Good agreement is found between the analytical and numerical derivatives. Alchemical derivatives are also shown to be predictive for integer changes in atomic numbers for oxygen binding to a 79 atom palladium nanoparticle, illustrating their potential use in gradient-based optimization algorithms for the rational design of catalysts.
Diversity-induced resonance on weighted scale-free networks
Authors: Wu Liang , Zhu Shiqun , Luo Xiaoqin
Published: August 2010

The diversity-induced resonance in weighted scale-free networks is investigated numerically and analytically. The couplings are weighted according to node degree. It is found that self-organized phase shifts occur between large-degree and small-degree nodes, although there is no time delay in coupling terms. Such spontaneous phase shifts are relevant to the improvement of signal resonance amplification. This finding may help to better understand how the collective behavior of individual units promotes the response of the whole system to external signals.
Ga
2
Te
3
phase change material for low-power phase change memory application
Authors: Zhu Hao , Yin Jiang , Xia Yidong , Liu Zhiguo
Published: August 2010

Ga 2 Te 3 films show a higher crystallization temperature, wider band gap, better data retention ability (keeping the amorphous state at 112 °C for ten years), and higher room-temperature resistivity of the crystalline state as compared with Ge2Sb2Te5. Ga2Te3 phase change memory cells with an effective diameter of 1 μm also show fast switching speed. The set operation was done by a 400 ns-2.4 V pulse, and the reset operation was done by a 30 ns-5.5 V pulse. The dynamic switching ratio between the OFF and ON states is over than 103.
Adaptor protein is essential for insect cytokine signaling in hemocytes
Authors: Oda Yasunori , Matsumoto Hitoshi , Kurakake Maiko , Ochiai Masanori , Ohnishi Atsushi , Hayakawa Yoichi
Published: August 2010

Growth-blocking peptide (GBP) is an insect cytokine that stimulates a class of immune cells called plasmatocytes to adhere to one another and to foreign surfaces. Although extensive structure-activity studies have been performed on the GBP and its mutants in Lepidoptera
Pseudaletia separata
, the signaling pathway of GBP-dependent activation of plasmatocytes remains unknown. We identified an adaptor protein (P77) with a molecular mass of 77 kDa containing SH2/SH3 domain binding motifs and an immunoreceptor tyrosine-based activation motif (ITAM)–like domain in the cytoplasmic region of the C terminus. Although P77 showed no capacity for direct binding with GBP, its cytoplasmic tyrosine residues were specifically phosphorylated within seconds after GBP was added to a plasmatocyte suspension. Tyrosine phosphorylation of P77 also was observed when hemocytes were incubated with
Enterobactor cloacae
or
Micrococcus luteus,
but this phosphorylation was found to be induced by GBP released from hemocytes stimulated by the pathogens. Tyrosine phosphorylation of the integrin β subunit also was detected in plasmatocytes stimulated by GBP. Double-stranded RNAs targeting
P77
not only decreased GBP-dependent tyrosine phosphorylation of the integrin β subunit, but also abolished GBP-induced spreading of plasmatocytes on foreign surfaces.
P77
RNAi larvae also showed significantly higher mortality than control larvae after infection with
Serratia marcescens
, indicating that P77 is essential for GBP to mediate a normal innate cellular immunity in insects. These results demonstrate that GBP signaling in plasmatocytes requires the adaptor protein P77, and that active P77-assisted tyrosine phosphorylation of integrins is critical for the activation of plasmatocytes.
The apical-basal cell polarity determinant Crumbs regulates Hippo signaling in
Drosophila
Authors: Chen Chiao-Lin , Gajewski Kathleen M. , Hamaratoglu Fisun , Bossuyt Wouter , Sansores-Garcia Leticia , Tao Chunyao , Halder Georg
Published: August 2010

Defects in apical-basal cell polarity and abnormal expression of cell polarity determinants are often associated with cancer in vertebrates. In
Drosophila
, abnormal expression of apical-basal determinants can cause neoplastic phenotypes, including loss of cell polarity and overproliferation. However, the pathways through which apical-basal polarity determinants affect growth are poorly understood. Here, we investigated the mechanism by which the apical determinant Crumbs (Crb) affects growth in
Drosophila
imaginal discs. Overexpression of Crb causes severe overproliferation, and we found that loss of Crb similarly results in overgrowth of imaginal discs. Crb gain and loss of function caused defects in Hippo signaling, a key signaling pathway that controls tissue growth in
Drosophila
and mammals. Manipulation of Crb levels caused the up-regulation of Hippo target genes, genetically interacted with known Hippo pathway components, and required Yorkie, a transcriptional coactivator that acts downstream in the Hippo pathway, for target gene induction and overgrowth. Interestingly, Crb regulates growth and cell polarity through different motifs in its intracellular domain. A juxtamembrane FERM domain-binding motif is responsible for growth regulation and induction of Hippo target gene expression, whereas Crb uses a PDZ-binding motif to form a complex with other polarity factors. The Hippo pathway component Expanded, an apically localized adaptor protein, is mislocalized in both
crb
mutant cells and Crb overexpressing tissues, whereas the other Hippo pathway components, Fat and Merlin, are unaffected. Taken together, our data show that Crb regulates growth through Hippo signaling, and thus identify Crb as a previously undescribed upstream input into the Hippo pathway.
In planta
changes in protein phosphorylation induced by the plant hormone abscisic acid
Authors: Kline Kelli G. , Barrett-Wilt Gregory A. , Sussman Michael R.
Published: August 2010

Abscisic acid (ABA) is a hormone that controls seed dormancy and germination as well as the overall plant response to important environmental stresses such as drought. Recent studies have demonstrated that the ABA-bound receptor binds to and inhibits a class of protein phosphatases. To identify more broadly the phosphoproteins affected by this hormone in vivo, we used
14
N/
15
N metabolic labeling to perform a quantitative untargeted mass spectrometric analysis of the
Arabidopsis thaliana
phosphoproteome following ABA treatment. We found that 50 different phosphopeptides had their phosphorylation state significantly altered by ABA over a treatment period lasting 5–30 min. Among these changes were increases in phosphorylation of subfamily 2 SNF1-related kinases and ABA-responsive basic leucine zipper transcription factors implicated in ABA signaling by previous in vitro studies. Furthermore, four members of the aquaporin family showed decreased phosphorylation at a carboxy-terminal serine which is predicted to cause closure of the water-transporting aquaporin gate, consistent with ABA's role in ameliorating the effect of drought. Finally, more than 20 proteins not previously known to be involved with ABA were found to have significantly altered phosphorylation levels. Many of these changes are phosphorylation decreases, indicating that an expanded model of ABA signaling, beyond simple phosphatase inhibition, may be necessary. This quantitative proteomics dataset provides a more comprehensive, albeit incomplete, view both of the protein targets whose biochemical activities are likely to be controlled by ABA and of the nature of the emerging phosphorylation and dephosphorylation cascades triggered by this hormone.
Rap1b facilitates NK cell functions via IQGAP1-mediated signalosomes
Authors: Awasthi Aradhana , Samarakoon Asanga , Chu Haiyan , Kamalakannan Rajasekaran , Quilliam Lawrence A. , Chrzanowska-Wodnicka Magdalena , White Gilbert C. , Malarkannan Subramaniam
Published: August 2010

Rap1 GTPases control immune synapse formation and signaling in lymphocytes. However, the precise molecular mechanism by which Rap1 regulates natural killer (NK) cell activation is not known. Using Rap1a or Rap1b knockout mice, we identify Rap1b as the major isoform in NK cells. Its absence significantly impaired LFA1 polarization, spreading, and microtubule organizing center (MTOC) formation in NK cells. Neither Rap1 isoform was essential for NK cytotoxicity. However, absence of Rap1b impaired NKG2D, Ly49D, and NCR1-mediated cytokine and chemokine production. Upon activation, Rap1b colocalized with the scaffolding protein IQGAP1. This interaction facilitated sequential phosphorylation of B-Raf, C-Raf, and ERK1/2 and helped IQGAP1 to form a large signalosome in the perinuclear region. These results reveal a previously unrecognized role for Rap1b in NK cell signaling and effector functions.
Improving performances of suboptimal greedy iterative biclustering heuristics via localization
Authors: Erten Cesim , Sözdinler Melih
Published: August 2010

Motivation: Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. Even the simplest versions of the problem are computationally hard. Most of the proposed solutions therefore employ greedy iterative heuristics that locally optimize a suitably assigned scoring function.

Methods: We provide a fast and simple pre-processing algorithm called localization that reorders the rows and columns of the input data matrix in such a way as to group correlated entries in small local neighborhoods within the matrix. The proposed localization algorithm takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. In order to evaluate the effectivenesss of the localization pre-processing algorithm, we focus on three representative greedy iterative heuristic methods. We show how the localization pre-processing can be incorporated into each representative algorithm to improve biclustering performance. Furthermore, we propose a simple biclustering algorithm, Random Extraction After Localization (REAL) that randomly extracts submatrices from the localization pre-processed data matrix, eliminates those with low similarity scores, and provides the rest as correlated structures representing biclusters.

Results: We compare the proposed localization pre-processing with another pre-processing alternative, non-negative matrix factorization. We show that our fast and simple localization procedure provides similar or even better results than the computationally heavy matrix factorization pre-processing with regards to H-value tests. We next demonstrate that the performances of the three representative greedy iterative heuristic methods improve with localization pre-processing when biological correlations in the form of functional enrichment and PPI verification constitute the main performance criteria. The fact that the random extraction method based on localization REAL performs better than the representative greedy heuristic methods under same criteria also confirms the effectiveness of the suggested pre-processing method.

Availability:  Supplementary material including code implementations in LEDA C++ library, experimental data, and the results are available at http://code.google.com/p/biclustering/

Contacts:  cesim@khas.edu.tr; melihsozdinler@boun.edu.tr

Supplementary information:  Supplementary data are available at Bioinformatics online.
A discriminatory function for prediction of protein–DNA interactions based on alpha shape modeling
Authors: Zhou Weiqiang , Yan Hong
Published: August 2010

Motivation: Protein–DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein–DNA complex are becoming available, the surface characteristics of the complex become an important research topic.

Result: In our work, we apply an alpha shape model to represent the surface structure of the protein–DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein–DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of −8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of −7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein–DNA interactions.

Availability: The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm

Contact:  kenandzhou@hotmail.com
OpenStructure: a flexible software framework for computational structural biology
Authors: Biasini Marco , Mariani Valerio , Haas Jürgen , Scheuber Stefan , Schenk Andreas D. , Schwede Torsten , Philippsen Ansgar
Published: August 2010

Motivation: Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure—demonstrating its value for the development of next-generation structural biology algorithms.

Availability: Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org.

Contact:  torsten.schwede@unibas.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Relation between Latitude and Breeding Seasons in Birds
Authors: Baker. John R.
Published: August 2010

As one goes north from the temperate latitudes one finds a general tendency for the egg‐laying seasons of birds of all kinds to start later and later at the rate of some 20 or 30 days per 10o of latitude.

 As one goes south from the temperate latitudes into the northern tropical and equatorial zones one finds a general tendency for the Accipitres, Coraciiformes, and, to a less extent, the Passeres, to start their egg‐laying earlier and earlier.

 The Charadriiformes, Gralise, Herodiones, and Anseres behave differently. In the northern hemisphere they tend to breed later in the tropical and equatorial zones than in the subtropical and temperate.

 There is a general tendency for birds in the tropics to reach the height of their main breeding seasons somewhat before the sun passes overhead. Two breeding seasons in the year are therefore quite common, but birds which breed only once select either the northward (Accipitres, etc.) or southward (Grallae, etc.) swing of the sun.

 The main proximate causes of the breeding seasons of birds in nature are thought to be temperature and length of day in the boreal and temperate zones, and rain and/or intensity of insolation near the equator. The time of arrival from migration is often an important factor.

 Much egg‐laying occurs when days are getting shorter, and indeed it often proceeds rapidly while they are decreasing in length and only between 11 and 12 hours long.

 There is, however, little egg‐laying when the day is shorter than 11 hours, and almost none when it is less than 10.

 Under natural conditions birds exhibit no tendency to start breeding everywhere when the days reach a certain length nor when, they are becoming longer particularly quickly.
Cranial Development of Galeichthys felis*
Authors: Bamford T. W.
Published: August 2010

Stages of Galeichthys felis between 8 and 50 mm. were examined. The skull is platybasic, with indications of a pila antotica, and without a sign of a trigeminofacialis chamber or a previously functional myodome. The myodomal spaces are discussed. The occipital cross commissure is rudimentary and misplaced medially, and the anterior pit line relation is identical with that of Amia and reminiscent of Palaeoniscids.

The so‐called “internal carotid” is really the efferent pseudobranchial artery and it passes through the trabecula in development. The internal carotid is absent in all stages examined. The pseudobranch is genuine pseudobranch, Pituitary veins are present.

The hyomandibular fuses with the palatoquadrate. The relations of the viith nerve to the hyomandibular articulation are peculiar, and a thin strip of cartilage inserted into the hyomandibular articulation is described. A tabular, endopterygoid and pre‐articular have been recognized, and the identity of the post‐temporal definitely established. The following bones are shown to be the result of fusion:
Labyrinthodonts from South Africa
Authors: Parrington F. R.
Published: August 2010

A revision of the neorhachitomous labyrinthodont Lydekkerina huxleyi (Lydekker) has been made to correct details of the dermal bones in the region of the nares and the proportions of the basicranial region, and to add to the recorded accounts of the palate.

The stapes of Lydekkerina is shown to have a clearly defined point of attachment for a cartilaginous connection to the quadrate; an anteroventral accessory process from the head, which is supported by the parafenestral crista of the pterygoid; and an additional anterodorsal accessory process.

A new labyrinthodont, Limnoiketes paludinatans, is described. It is believed to be closely related to the main stem of the group between Rhinesuchus and the Triassic capitosaurs. The type is believed to be an immature animal.

The abrupt change in the South African Karroo fauna which took place at the start of the Trias is discussed. It is believed to have been due to a swamping of the geosyncline in which the Beaufort rocks were deposited because the only large forms which survived through the Lystrosaurus zone were aquatic or semi‐aquatic. This conclusion implies that the larger members of the fauna at least were confined to the basin of deposition. It is pointed out that, from quite independent evidence, Bystrow has deduced a contemporaneous change from a relatively dry to a humid climate in the region of the Russian platform.
A new fish of the genus Clarias Gronov. from Lake Nyasa, with notes on the distribution of the Clariidae and other catfishes in the lake.
Authors: Jackson P. B. N. , Trewavas E.
Published: August 2010

Summary

A new species of Clarias, C. foveolatus nov., from deep water in Lake Nyasa, is described and figured. Other new clariids occur, probably constituting with the known endemic forms a species‐flock of about eight species.

Researches indicate that a distinction should be drawn between those fishes which inhabit Lake Nyasa and those which occur in adjoining rivers and swamps, but seldom or never in the open lake. Of the seven species of Clarias listed from Lake Nyasa three scarcely occur in the lake proper, one more sparingly than has previously been supposed, and the three species which occur most abundantly are all endemic.
STUDIES ON THE LIFE‐HISTORY AND ECOLOGY OF THE TREMATODE GENUS RENICOLA COHN, 1904*
Authors: WRIGHT C. A.
Published: August 2010

A review of the morphological criteria on which the species of Renicola are separated is given and an analysis of the value of these criteria is made, Three new host records for the genus Renicola are given and the worms found are described. The pathology of the infected bird's kidney is discussed.

The species of cercariae of the “Rhodometopa” group found during the present work are listed and two new species are described. Some general observations on the anatomy of these cercariae are made. The miracidia of Renicola sp. from Puffinus puffinus are described. The development of the sporocysts of the “Rhodometopa” group of cercariae is described and a new interpretation of the structure of the body‐wall of these sporocysts is presented. Observations on the emergence of cercariae from infected snails are described, also observations on the behaviour of these cercariae. Experimental infection of Turritella communis with the eggs of Renicola sp. is described and the results are discussed.

A new host for the metacercariae of the “Rhodometopa”‘ group (Clupea sprattus) is recorded. Two types of metacercarial cysts are described. The infection rate in sprats is discussed. Attempts to bring about excystation by means of in vitro digests are described, also unsuccessful attempts to produce experimental infection of Renicola spp. in birds. The connection between the sprat as an intermediate host and the high infection rate of Renicola sp. in Puffinus puffinus is discussed.
ON THE LIFE HISTORY OF TRICHOCERA SALTATOR (HARRIS) (DIPTERA, TRICHOCERIDAE)
Authors: LAURENCE B. R.
Published: August 2010

A species of Trichocera lives in the larval stage in cow pats, the larvae feeding on the dung.

Although the definition of some of the species of Trichocera is difficult it is believed that the species associated with the cow dung is Trichocera saltator (Harris). Variation of the adult morphology is discussed.

The larval stages feed and grow in the coldest months of the year, between October and February, despite the habitat often being completely frozen during frosts.

The larvae enter a diapause in March and adults do not emerge until September or later.

The length of life of the adult in the laboratory in the winter is from five to fifty‐nine days.

The adults appear to be most active at night.

Different species of Trichocera in Britain may have different life histories.
ILLUMINATION AND ITS EFFECT ON THE SETTLEMENT OF BARNACLE CYPRIDS*
Authors: DANIEL A.
Published: August 2010

For every 100 cyprids of B. amphitrite which attached during night time, between 230 and 530 cyprids attached during the day. They avoided attachment under direct sunlight, however, suggesting that they preferred diffuse light. Cyprids of B. tintinnabulum showed a more marked preference for diffuse light and settled in greater numbers during dusk and daybreak, rather than about noon. In contrast, larvae of C. stellatus settled most abundantly in direct sunlight.

Artificial illumination at night encouraged the settlement of all three species. B. amphitrite settled most at an intensity of five foot candles. B. tintinnabulum settled more at 0.5 than at one or more foot candles. C. stellatus settled more at 35 foot candles than at lesser illuminations. These preferences probably play an important part in leading the larvae to the different habitats favoured by each species.
THE SYSTEMATIC POSITION OF BROWNEICHTH YS ORNATUS WOODWARD (PISCES, ACTINOPTERGII)
Authors: GRIFFITH J. , Foxon G.E.H.
Published: August 2010

The unique holotype of Browneichthys ornatus Woodward has been reexamined. Illustrations of the specimen are published for the first time, and, although it has not been possible to add considerably to the text of the original account, a short redescription is included. The systematic position of Browneichthys ornatus is discussed. It is concluded that this species should not be retained in the family Saurichthyidae and its transfer to the family Coccolepidae is proposed.
Aphid‐hunting wasps: a field study of Passaloecus
Authors: CORBET SARAH A. , BACKHOUSE M.
Published: August 2010

Three species of pemphredonine wasps, Passaloecus insignis, P.gracilis and P.corniger, were observed nesting in disused beetle holes in pine boards. The species differed from one another in the size, height above ground and aspect of the holes selected as nest sites.

P.insignis and P.gracilis stocked their nests with aphids of several species, but P.corniger females stole paralysed aphids from nests stocked by P.insignis, P.gracilis or by conspecifics, sometimes breaking open the outer door of a nest to do so.

The outer doors of the nests were of pine resin; P.corniger and P.insignis added pellets of other material to the surface. P.corniger females revisited their nests after sealing the outer door and behaved as if scent‐marking them, perhaps conferring protection against robbery by conspecifics.

Adult male wasps probably fed on honeydew. They appeared early and seemed to have a flying season of only a few days, whereas females probably lived and flew for about eight weeks after emergence.

The behaviour of nest‐stocking female wasps is considered in relation to the temperature of their microhabitats.

The possible use of pemphredonine wasps for the biological control of aphids or thrips in glasshouses is discussed.
A comparison, by sweep sampling, of the arthropod fauna of secondary vegetation in Michigan, England and Costa Rica
Authors: JANZEN DANIEL H. , POND CAROLINE M.
Published: August 2010

Six 800‐sweep samples of English and Michigan (“old field”) secondary vegetation arthropods are compared with Costa Rican samples taken in the same way.

Parasitic Hymenoptera and spiders accounted for a larger proportion of the arthropod fauna in the mid‐latitude than the tropical samples.

In one English field, the seasonal change in insect numbers was 88% of that recorded over all the seasonal and elevational changes examined in Costa Rica. Furthermore, the difference in the total dry weights of the arthropod fauna between December and July was similar to the difference found between the wet and dry seasons in tropical secondary vegetation (also similar to the difference between day and night values during the dry season).

Aphids and Psyllidae were far more abundant in the English site than in the Costa Rican mainland sites.

In mid‐summer, the English field had far more arthropods in it than did any of the tropical sites sampled.
The fate of an internal parasitoid, Nemeritis canescens, in a variety of insects
Authors: SALT GEORGE
Published: August 2010

The fate of Nemeritis canescens has been studied in 36 species or, counting different stages, in 51 kinds of insects, in order to discover the causes of its success or failure in each.

The parasitoid was able to develop to the adult stage in 14 of the species studied.

A defence reaction of the host, cellular encapsulation, was by far the most frequent cause of the death of canescens in species in which it could not develop.

Deposition of melanin over its mouth probably caused the death of canescens in two species; in other species the role of melanisation was subordinate to encapsulation.

Very few species, if any, were unsuitable as food; larvae of the parasitoid ingested and assimilated the blood of a wide variety of insects.

Some individuals of a few species were unsuitable as a habitat for the parasitoid larva.

The survival of canescens in suitable hosts is discussed with reference to the means by which this parasitoid resists defence reactions.

Attention is drawn to incidental results of the research: (i) a state of diapause in some hosts was transmitted to first‐instar larvae of canescens and delayed their development; (ii) evidence was found that the teratocytes formed by braconid parasitoids function as a means of preventing cellular defence reactions, that they act by attrition of the host, and that they protect a larva of canescens present in the same host; (iii) observations concerning the behaviour of adult canescens in attacking some species, and the survival of supernumerary larvae after competing for the host, are mentioned.
The influence of climate on melanism in the Two‐Spot ladybird, Adalia bipunctata, in central Italy
Authors: SCALI V. , CREED E. R.
Published: August 2010

The frequency of black forms of the Two‐Spot ladybird, Adalia bipunctata, progressively decreases with increasing altitude, inland from Viareggio and Pisa; it increases again, though not to the same extent, to the north east of the Apennines.

Probably temperature is an important selective agent, though air pollution may also have some effect.
A preliminary study of insect abundance on West Island, Aldabra Atoll, Indian Ocean
Authors: FRITH DAWN W.
Published: August 2010

Heath and Rothamsted light traps and a Johnson‐Taylor suction trap were used to sample flying insects on Aldabra Atoll.

The present study extended over two wet seasons. The pattern of relative monthly insect activity resembled the rainfall pattern. Catches were greatest during the months when there was a sudden marked increase in precipitation.

Lepidoptera dominated light trap catches and Diptera suction trap catches, the total monthly insect numbers therefore reflecting the abundance of these two orders. Hemiptera, Coleoptera and Hymenoptera were also common.

Predominant families were represented by only a few or even only one dominant species. These species were present throughout the study period although their monthly totals varied considerably, different species dominating the catches during different months.

The composition and size of catches in the three light traps was affected by the type of light source and surrounding vegetation.

A comprehensive list of families and selected common species is given with their relative monthly abundance in the light traps.

Suction trap catches were segregated on an hourly basis to give a broad indication of insect flight periodicity.
Bite force measurement in children with primary dentition
Authors: Mountain Gary , Wood David , Toumba Jack
Published: August 2010

Objectives

To determine the magnitude of the biting forces in young children aged 3–6 years in the primary dentition and analyse the potential effects of caries and malocclusion on maximum bite force.

Methods

Children aged 3–6 years of age attending primary schools within a major city in the UK were recruited to participate in this study. The magnitude of the bite force in Newtons (N) was measured bilaterally corresponding with the 1st and 2nd primary molars and central incisors using a new specifically designed single tooth bite force gauge.

Results

Two‐hundred and five children were included in the study. The prevalence of dental caries and malocclusion was found to be 30.4% and 17.1% respectively. The levels of bite force recorded showed comparatively wide intra‐ and inter‐individual variation with the maximum of the three bite force measurements ranging from 12.61 (N) to 353.64 (N) (M = 196.60, SD = 69.77).

Conclusion

Bite forces of young children show comparatively wide intra‐ and inter‐individual variation with some similarities with those found in the limited number of previous primary dentition studies undertaken elsewhere. The results will serve to provide key reference values for use both in paediatric dental clinical practice and wider research community.