bluuebunny/crossref_metadata_2025 huggingface dataset:
Fourfold symmetric anisotropic magnetoresistance based on magnetocrystalline anisotropy and antiphase boundaries in reactive sputtered epitaxial Fe3O4 films
Authors: Li P. , Jiang E. Y. , Bai H. L.
Published: March 2010

The fourfold symmetric anisotropic magnetoresistance (AMR) at high fields in epitaxial Fe3O4 films, which is incompatible with the traditional twofold symmetry, was found to be independent with the current direction but associated with their magnetocrystalline anisotropy. (001)-, (110)-, and (112)-oriented Fe3O4 films show fourfold symmetry in AMR while twofold symmetry appears for (111)-oriented Fe3O4 films. The cubic magnetocrystalline anisotropy field superimposed onto the external magnetic field modifies the alignment of the spins near antiphase boundaries, leading to the oscillating scattering rate for the transport electrons across antiphase boundaries and thus the corresponding fourfold symmetry in AMR.
Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations
Authors: Reilly Anthony M. , Habershon Scott , Morrison Carole A. , Rankin David W. H.
Published: March 2010

Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.
Fabrication and characterization of an induced GaAs single hole transistor
Authors: Klochan O. , Chen J. C. H. , Micolich A. P. , Hamilton A. R. , Muraki K. , Hirayama Y.
Published: March 2010

We have fabricated and characterized a single hole transistor in an undoped AlGaAs-GaAs heterostructure. Our device consists of a p-type quantum dot, populated using an electric field rather than modulation doping. Low temperature transport measurements reveal periodic conductance oscillations due to Coulomb blockade. We find that the low frequency charge noise is comparable to that in modulation-doped GaAs single electron transistors (SETs), and an order of magnitude better than in silicon SETs.
An efficient, simple, and precise way to map strain with nanometer resolution in semiconductor devices
Authors: Koch Christoph T. , Özdöl V. Burak , van Aken Peter A.
Published: March 2010

We report on the development of the dark-field inline electron holography technique and its application to map strain in technologically relevant structures, using as an example the strain-engineered gate channel in a 45 nm metal-oxide semiconductor field-effect transistor structure. We show that this technique combines a large field of view of several micrometers with high precision (better than 0.01%), high spatial resolution (better than 1 nm), and very loose experimental requirements not possible with any other technique currently available.
Solution-processed bulk heterojunction photovoltaic devices based on poly(2-methoxy,5-octoxy)-1,4-phenylenevinylene-multiwalled carbon nanotubes/PbSe quantum dots bilayer
Authors: Feng Yiyu , Yun Daqin , Zhang Xuequan , Feng Wei
Published: March 2010

A solution-processed bulk heterojuction photovoltaic cell was fabricated based on poly[(2-methoxy,5-octoxy)-1,4-phenylenevinylene](MOPPV)-multiwalled carbon nanotubes (MWNT)/spherical PbSe quantum dots bilayer. Surface morphology shows the interpenetrating network of well-dispersed MWNT in MOPPV matrix. Blueshifted band in absorption and photoluminescence spectra indicate the strong electron interaction between MWNT and MOPPV. A marked twofold increase in short-circuit current (1.71 mA/cm2) and power-conversion efficiency (0.40%) of ITO/MOPPV-MWNT:phenyl-C61-butyric acid methyl ester (PCBM)/PbSe/Al devices was achieved compared with that without MWNT. Results indicate that the enhanced performance was contributed by high photocurrent due to efficient exciton dissociation, charge transfer, and mobility in MWNT pathway.
Effect of antiferromagnetic order on the dielectric properties of Bi2Fe4O9
Authors: Park Y. A. , Song K. M. , Lee K. D. , Won C. J. , Hur N.
Published: March 2010

We investigated the dielectric and magnetic properties of Bi2Fe4O9 single crystals. The dielectric anomalies observed at the magnetic transition temperature indicate that there is a strong coupling between the magnetic and dielectric properties. The anisotropic magnetic contribution of the dielectric constant is discussed in terms of the spin correlation function, ⟨Si⋅Sj⟩, below the antiferromagnetic transition at 240 K.
Optical anisotropies of Si grown on step-graded SiGe(110) layers
Authors: Balderas-Navarro R. E. , Lastras-Martínez L. F. , Arimoto K. , Castro-García R. , Villalobos-Aguilar O. , Lastras-Martínez A. , Nakagawa K. , Sawano K. , Shiraki Y. , Usami N. , Nakajima K.
Published: March 2010

Macroreflectance and microreflectance difference spectroscopies have been used to measure the strain induced optical anisotropies of semiconductor structures comprised of strained Si(110) thin films deposited on top of step-graded SiGe virtual substrates. The stress relaxation mechanism mainly occurs by the introduction of microtwin formation, whose fluctuation depends strongly on growth conditions. Correlations of such optical diagnostics with x-ray diffraction measurements and atomic force microscopy images, allow for the in situ study of the strain within both the top Si layer and the SiGe underneath with an spatial resolution of at least 5 μm.
Influence of Na on Cu(In,Ga)Se2 solar cells grown on polyimide substrates at low temperature: Impact on the Cu(In,Ga)Se2/Mo interface
Authors: Caballero R. , Kaufmann C. A. , Eisenbarth T. , Grimm A. , Lauermann I. , Unold T. , Klenk R. , Schock H. W.
Published: March 2010

There are still open questions regarding the nature of the positive effect of the presence of Na on the performance of Cu(In,Ga)Se2 based, chalcopyrite thin film solar cells, especially at low processing temperatures. Studying Cu(In,Ga)Se2 thin film devices fabricated from low-temperature coevaporated absorbers on polyimide substrates by admittance and J-V-T measurements, characteristic properties are identified for different amounts of Na present during the growth. A roll-over behavior can be directly correlated with the Na-content. X-ray photoelectron spectroscopy shows the development of a MoSe2 phase at the back contact of the device. Efficiencies of 15.1% with MgF2 antireflection coating are demonstrated.
Dominance, body size and internal relatedness influence male reproductive success in eastern grey kangaroos (Macropus giganteus)
Authors: Miller Emily J. , Eldridge Mark D. B. , Cooper Desmond W. , Herbert Catherine A.
Published: February 2010

Knowledge of the determinants of reproductive success is essential for understanding the adaptive significance of particular traits. The present study examined whether particular behavioural, morphological, physiological or genetic traits were correlated with male dominance and reproductive success using three semi-free-ranging captive populations (n = 98) of the eastern grey kangaroo (Macropus giganteus). The morphological traits measured included bodyweight, head, forearm, tail, pes and leg length, forearm and bicep circumference, and testis size. Blood samples were collected to determine serum testosterone concentrations. All individuals were typed for 10 microsatellite loci and paternity determined for each pouch young. To determine the influence of relatedness and genetic diversity on male reproductive success, internal relatedness, standardised heterozygosity and mean d2 were calculated. Dominant males sired a significantly higher proportion of offspring than smaller, lower-ranked males and had higher testosterone concentrations. Males that sired offspring were significantly heavier and had larger body size. Sires were significantly more heterozygous and genetically dissimilar to breeding females than non-sires. Despite the wealth of knowledge on the social organisation of kangaroos, this is the first study to assign parentage and male reproductive success using molecular evidence.
Inherent capacity of the pituitary gland to produce gonadotropins is not influenced by the number of ovarian follicles ≥3 mm in diameter in cattle
Authors: Mossa F. , Jimenez-Krassel F. , Walsh S. , Berry D. P. , Butler S. T. , Folger J. , Smith G. W. , Ireland J. L. H. , Lonergan P. , Ireland J. J. , Evans A. C. O.
Published: February 2010

We hypothesised that higher serum FSH concentrations in cattle with low v. high follicle numbers during follicular waves are caused by a different capacity of the pituitary gland to produce gonadotropins. Dairy cows with high (≥30; n = 5) and low (≤15; n = 5) follicle numbers were selected and serum concentrations of oestradiol and FSH during an oestrous cycle were measured. Cows were ovariectomised at oestrus and bled frequently up to 8 days after ovariectomy. After 33 days, cows were injected with gonadotropin-releasing hormone (GnRH) and bled intensively up to 8 h after GnRH injection. One day later, animals were injected with follicular fluid (FF) from bovine follicles and were bled intensively up to 2 days after the first injection. Serum concentrations of FSH and LH were measured. After 2 days, cows were killed and their pituitary glands collected. Prior to ovariectomy, serum oestradiol concentrations were similar between groups, whereas FSH concentrations were higher in cattle with low v. high numbers of follicles. No differences were detected in serum gonadotropin concentrations after ovariectomy, GnRH injection or FF challenge between groups. The results indicate that the inherent capacity of the pituitary gland to secrete gonadotropins does not differ between cattle with high v. low numbers of follicles during follicular waves.
Depletion of BIRC6 leads to retarded bovine early embryonic development and blastocyst formation in vitro
Authors: Salilew-Wondim Dessie , Hölker Micheal , Rings Franca , Phatsara Chirawath , Mohammadi-Sangcheshmeh Abdollah , Tholen Ernst , Schellander Karl , Tesfaye Dawit
Published: February 2010

Baculoviral inhibitors of apoptosis repeat-containing 6 (BIRC6) is believed to inhibit apoptosis by targeting key cell-death proteins. To understand its involvement during bovine preimplantation embryo development, two consecutive experiments were conducted by targeted knockdown of its mRNA and protein using RNA interference. In Experiment 1, the effect of BIRC6 knockdown during the early stages of preimplantation embryo development was assessed by injecting zygotes with long double-stranded RNA (ldsRNA) and short hairpin RNA (shRNA) against BIRC6 mRNA followed by in vitro culturing until 96 h post insemination (hpi). The results showed that in RNA-injected zygote groups, reduced levels of BIRC6 mRNA and protein were accompanied by an increase (P < 0.05) in the proportion of 2- and 4-cell and uncleaved embryos and a corresponding decrease (P < 0.05) in the number of 8-cell embryos. In Experiment 2, the effect of BIRC6 knockdown on blastocyst formation, blastocyst total cell number and the extent of apoptosis was investigated. Consequently, zygotes injected with ldsRNA and shRNA resulted in lower (P < 0.05) blastocyst formation and total blastocyst cell number. Moreover, the apoptotic cell ratio, CASPASE 3 and 7 activity, BAX to BCL-2 ratio and levels of SMAC and CASPASE 9 were higher in blastocysts derived from the ldsRNA and shRNA groups, suggesting increased apoptosis in those blastocysts. The results of this study reveal the importance of BIRC6 expression for embryo survival during bovine preimplantation embryo development. However, whether BIRC6 is essential for implantation and fetal development during bovine pregnancy needs further research.
The spermatozoa of the dasyurid marsupial, Sminthopsis crassicaudata, are highly susceptible to cold shock
Authors: Czarny N. A. , Rodger J. C.
Published: February 2010

Since the late 1970s research has suggested that marsupial spermatozoa did not suffer cold shock. We have re-examined cold shock to investigate problems with freezing of spermatozoa from a dasyurid marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata). Epididymal spermatozoa were rapidly cooled to 0.5°C in a pre-cooled tube held in an iced-water slurry. Upon re-warming all spermatozoa were immotile and the addition of 10% or 20% egg yolk to the sperm medium had no beneficial effect. Spermatozoa that were rapidly cooled to 4°C maintained only 2% motility when re-warmed but the addition of at least 10% egg yolk was beneficial and upon re-warming greater than 65% of the initial motility was maintained. In order to achieve motile spermatozoa at 0°C, controlled-rate cooling at 0.5°C min–1 was examined. In the absence of egg yolk there was a significant decline in the percentage of motile spermatozoa below 4°C. However, the inclusion of at least 10% egg yolk resulted in no loss of motility in spermatozoa cooled to 0°C. This is the first experimental study indicating that spermatozoa from a marsupial are highly susceptible to cold shock and that the impact of rapid chilling can be mitigated by the addition of 10% egg yolk. The ability to successfully cool the spermatozoa of S. crassicaudata to 0°C may have an important role in future studies examining dasyurid sperm cryopreservation.
Sperm morphology, motility and fertilisation capacity in the myobatrachid frog Crinia georgiana
Authors: Dziminski Martin A. , Roberts J. D. , Simmons Leigh W.
Published: February 2010

Sperm traits have been found to vary between individuals within populations in a variety of taxa. Sperm motility, morphometry and viability may be expected to have important effects on male fertility, although previous studies have found varying patterns, especially in external fertilisers. In the present study, we examined the effects of sperm swimming velocity, the proportion of motile spermatozoa, sperm head and tail length and the proportion of live spermatozoa on fertilisation success in the externally fertilising myobatrachid frog Crinia georgiana using IVF techniques and by controlling sperm numbers. We found no effect of any of the sperm traits we measured on IVF success. Neither did we find any relationship between sperm morphology and sperm performance. There was a negative relationship between sperm viability and male body size, which could be a function of age or an alternative tactic of differential investment in spermatozoa by smaller-sized males using sneak tactics in multiple matings. In contrast with most externally fertilising aquatic organisms, high rates of fertilisation appear to be achieved in C. georgiana with relatively low sperm swimming speeds.
RFD Award Lecture 2009.In vitro maturation of farm animal oocytes: a useful tool for investigating the mechanisms leading to full-term development
Authors: Gandolfi Fulvio , Brevini Tiziana A. L.
Published: February 2010

Due to logistical and economic reasons, assisted reproduction of domestic animals has been based mostly on the use of oocytes isolated from ovaries collected at the slaughterhouse. In order to propagate valuable or rare genetic material, perform somatic cell nuclear transfer or generate genetically modified animals, it is essential to obtain fully competent oocytes that will allow full-term development of the in vitro-produced embryos. Such a need makes clear the crucial role played by oocyte quality. In fact, it is easy to compromise the oocyte’s developmental potential but it is impossible to restore once it has been lost. Almost three decades after the first cow, sheep, goat, horse and pig in vitro-generated offspring were born, a large body of information has accumulated on the mechanisms regulating oocyte competence and on how the latter may be preserved during all the required manipulations. The amount of knowledge is far from complete and many laboratories are actively working to further expand it. In this review we will highlight the aspects of the ongoing research in which we have been actively involved.
Intrafollicular testosterone concentration and sex ratio in individually cultured bovine embryos
Authors: García-Herreros Manuel , Bermejo-Álvarez Pablo , Rizos Dimitrios , Gutiérrez-Adán Alfonso , Fahey Alan G. , Lonergan Patrick
Published: February 2010

Recent studies have suggested a relationship between bovine follicular fluid testosterone concentration and the likelihood of the oocyte being fertilised by an X- or Y-bearing spermatozoon; however, this theory has been challenged. To further test this hypothesis, follicles were dissected from the ovaries of slaughtered heifers, measured and carefully ruptured. The cumulus–oocyte complex (COC) was removed and the follicular fluid collected and testosterone concentration determined by radioimmunoassay. COCs were matured, fertilised and cultured in an individually identifiable manner; all cleaved embryos (2- to 4-cell stage, n = 164) had their sex determined by PCR. Testosterone concentrations were positively skewed. There was no significant difference between follicular fluid testosterone concentrations in male and female embryos (mean ± s.e.m. 51.5 ± 5.59 and 49.5 ± 7.42 ng mL–1, respectively). Linear, quadratic and cubic logistical regression showed that follicular testosterone concentration could not reliably predict the sex of the embryo with odds ratios of 1.001, 1.013 and 1.066, repectively, and coefficient of determination (R2) values of 0.0003, 0.0126 and 0.0567, respectively. Follicular size and testosterone concentration were not related (R2 = 0.087). Finally, follicular size had no influence on embryo sex determination (P = 0.70). In conclusion, under the conditions of the present study, the likelihood of an oocyte being fertilised by an X- or Y-bearing spermatozoon was not affected by the size of the follicle from which it was derived, nor by the testosterone concentration in the follicular fluid.
Aromatase gene expression in immature rat Sertoli cells: age-related changes in the FSH signalling pathway
Authors: Bouraïma-Lelong Hélène , Vanneste Marion , Delalande Christelle , Zanatta Leïla , Wolczynski Slawomir , Carreau Serge
Published: February 2010

Aromatase, the enzyme responsible for the transformation of androgens into oestrogens, is encoded by the cyp19 gene expressed in the testis. The aim of the present study was to analyse the evolution of aromatase gene expression under FSH control in rat Sertoli cells between 10 and 30 days post partum, corresponding to the end of the proliferative period of Sertoli cells, establishment of the blood–testis barrier and acquisition of the mature phenotype. The maximum stimulatory effect of FSH on aromatase gene expression was obtained in 20-day-old rat Sertoli cells, compared with cells from 10- and 30-day-old rats, in parallel with the differentiation of Sertoli cells. Using two effectors of the protein kinase A pathway (i.e. forskolin and dibutyryl-cAMP) revealed differential effects between cells from rats aged 20 and 30 days, implying the involvement of another signalling pathway. Experiments using the specific phosphatidylinositol 3-kinase (PI3-K) inhibitor LY294002 revealed that PI3-K is strongly involved in FSH-induced aromatase expression in Sertoli cells from both 20- and 30-day-old rats. In vivo, this decrease could be explained by a negative effect exerted by germ cells because, in coculture, aromatase gene expression in 20-day-old Sertoli cells is greatly diminished.
Immunodetection of inhibin in the human testis and epididymis during normal development and in non-tumoural testicular lesions
Authors: Nistal Manuel , González-Peramato Pilar , De Miguel Maria P.
Published: February 2010

Plasma concentrations of inhibin are correlated with spermatogenetic function. Inhibin is secreted mainly by the Sertoli and Leydig cells of the testis. In the human epididymis, the location and function of inhibin are contentious. Thus, the aim of the present study was to determine the location of inhibin in the human epididymis. Investigations were performed in samples with normal testicular function at different stages of development, as well as in samples in which testicular function or the testicular–epididymal connection were altered. In fetal, newborn and infant testes, Sertoli and Leydig cells stained positive for inhibin, whereas no such staining was detected in the epididymides. Inhibin was located in both the Sertoli and Leydig cells, as well as in the epididymis, in the apical pole of mainly secretory cells in the efferent ducts. This staining pattern was not correlated with the staining pattern for macrophages. The main duct of the epididymis was negative for inhibin staining. In ischaemic atrophic testes, the few tubules in which Sertoli cells were present stained positive for inhibin, whereas the epididymides stained negative. In paediatric cryptorchidism, Sertoli and Leydig cells stained positive for inhibin, whereas the epididymides were negative. In adult cryptorchidism, Sertoli and Leydig cells stained positive for inhibin, even in tubules containing Sertoli cells only. Interestingly, inhibin was absent from the efferent ducts. In three cases undergoing hormonal treatment prior to subsequent gender change, Sertoli and Leydig cells stained positive for inhibin. In contrast, the efferent ducts were negative or only faintly positive in cases of shorter hormonal treatment. In all cases studied, the presence of inhibin in the efferent ducts was associated with its production in the testis, suggesting that the epididymis is not responsible for the production of inhibin in men. The pattern of inhibin staining does not correlate with that of macrophages, suggesting that inhibin is not degraded in the human epididymis. The data suggest that, in humans, inhibin is secreted by Sertoli cells into the seminiferous tubules and then travels towards the efferent ducts, where it is reabsorbed into the bloodstream.
Effects of medium and hypothermic temperatures on preservation of isolated porcine testis cells
Authors: Yang Yanfei , Honaramooz Ali
Published: February 2010

The effects of medium and hypothermic temperatures on testis cells were investigated to develop a strategy for their short-term preservation. Testes from 1-week-old piglets were enzymatically dissociated for cell isolation. In Experiment 1, testis cells were stored at either room (RT) or refrigeration (RG) temperature for 6 days in one of 13 different media. Live cell recovery was assayed daily using trypan blue exclusion. In Experiment 2, three media at RG were selected for immunocytochemical and in vitro culture studies. Live cell recovery was also assayed daily for 6 days using both trypan blue exclusion and a fluorochrome assay kit. For all media tested, significantly or numerically more live cells were maintained at RG than RT. On preservation Day 3 at RG (cell isolation day as Day 0), 20% FBS-Leibovitz resulted in the highest live cell recovery (89.5 ± 1.7%) and DPBS in the lowest (60.3 ± 1.9%). On Day 6 at RG, 20% FBS- Leibovitz also resulted in the best preservation efficiency with 80.9 ± 1.8% of Day 0 live cells recovered. There was no difference in live cell recovery detected by the two viability assays. After preservation, the proportion of gonocytes did not change, whereas that of Sertoli and peritubular cells increased and decreased, respectively. After 6 days of hypothermic preservation, testis cells showed similar culture potential to fresh cells. These results show that testis cells can be preserved for 6 days under hypothermic conditions with a live cell recovery of more than 80% and after-storage viability of 88%.
Evidence for a functional sidedness to the αβTCR
Authors: Kuhns Michael S. , Girvin Andrew T. , Klein Lawrence O. , Chen Rebecca , Jensen Kirk D.C. , Newell Evan W. , Huppa Johannes B. , Lillemeier Björn F. , Huse Morgan , Chien Yueh-hsiu , Garcia K. Christopher , Davis Mark M.
Published: March 2010

The T cell receptor (TCR) and associated CD3γε, δε, and ζζ signaling dimers allow T cells to discriminate between different antigens and respond accordingly, but our knowledge of how these parts fit and work together is incomplete. In this study, we provide additional evidence that the CD3 heterodimers congregate on one side of the TCR in both the αβ and γδTCR-CD3 complexes. We also report that the other side of the αβTCR mediates homotypic αβTCR interactions and signaling. Specifically, an erythropoietin receptor-based dimerization assay was used to show that, upon complex assembly, the CD3ε chains of two CD3 heterodimers are arranged side-by-side in both the αβ and γδTCR-CD3 complexes. This system was also used to show that αβTCRs can dimerize in the cell membrane and that mutating the unusual outer strands of the Cα domain impairs this dimerization. Finally, we present data showing that, for CD4 T cells, the mutations that impair αβTCR dimerization also alter ligand-induced calcium mobilization, TCR accumulation at the site of pMHC contact, and polarization toward the site of antigen contact. These data reveal a “functional-sidedness” to the αβTCR constant region, with dimerization occurring on the side of the TCR opposite from where the CD3 heterodimers are located.
Intact implicit learning in autism spectrum conditions
Authors: Brown Jamie , Aczel Balazs , Jiménez Luis , Kaufman Scott Barry , Grant Kate Plaisted
Published: March 2010

Individuals with autism spectrum condition (ASC) have diagnostic impairments in skills that are associated with an implicit acquisition; however, it is not clear whether ASC individuals show specific implicit learning deficits. We compared ASC and typically developing (TD) individuals matched for IQ on five learning tasks: four implicit learning tasks—contextual cueing, serial reaction time, artificial grammar learning, and probabilistic classification learning tasks—that used procedures expressly designed to minimize the use of explicit strategies, and one comparison explicit learning task, paired associates learning. We found implicit learning to be intact in ASC. Beyond no evidence of differences, there was evidence of statistical equivalence between the groups on all the implicit learning tasks. This was not a consequence of compensation by explicit learning ability or IQ. Furthermore, there was no evidence to relate implicit learning to ASC symptomatology. We conclude that implicit mechanisms are preserved in ASC and propose that it is disruption by other atypical processes that impact negatively on the development of skills associated with an implicit acquisition.
CPFP: a central proteomics facilities pipeline
Authors: Trudgian David C. , Thomas Benjamin , McGowan Simon J. , Kessler Benedikt M. , Salek Mogjiborahman , Acuto Oreste
Published: February 2010

Summary: The central proteomics facilities pipeline (CPFP) provides identification, validation, and quantitation of peptides and proteins from LC-MS/MS datasets through an easy to use web interface. It is the first analysis pipeline targeted specifically at the needs of proteomics core facilities, reducing the data analysis load on staff, and allowing facility clients to easily access and work with their data. Identification of peptides is performed using multiple search engines, their output combined and validated using state-of-the-art techniques for improved results. Cluster execution of jobs allows analysis capacity to be increased easily as demand grows.

Availability: Released under the Common Development and Distribution License at http://cpfp.sourceforge.net/. Demonstration available at https://cpfp-master.molbiol.ox.ac.uk/cpfp_demo

Contact:  dctrud@ccmp.ox.ac.uk
A min-cut algorithm for the consistency problem in multiple sequence alignment
Authors: Corel Eduardo , Pitschi Florian , Morgenstern Burkhard
Published: February 2010

Motivation: Multiple sequence alignments can be constructed on the basis of pairwise local sequence similarities. This approach is rather flexible and can combine the advantages of global and local alignment methods. The restriction to pairwise alignments as building blocks, however, can lead to misalignments since weak homologies may be missed if only pairs of sequences are compared.

Results: Herein, we propose a graph-theoretical approach to find local multiple sequence similarities. Starting with pairwise alignments produced by DIALIGN, we use a min-cut algorithm to find potential (partial) alignment columns that we use to construct a final multiple alignment. On real and simulated benchmark data, our approach consistently outperforms the standard version of DIALIGN where local pairwise alignments are greedily incorporated into a multiple alignment.

Availability: The prototype is freely available under GNU Public Licence from E.C.

Contact:  ecorel@gwdg.de
Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules
Authors: Chou Wei-Yao , Chou Wei-I , Pai Tun-Wen , Lin Shu-Chuan , Jiang Ting-Ying , Tang Chuan-Yi , Chang Margaret Dah-Tsyr
Published: February 2010

Motivation: Carbohydrate-binding modules (CBMs) share similar secondary and tertiary topology, but their primary sequence identity is low. Computational identification of ligand-binding residues allows biologists to better understand the protein–carbohydrate binding mechanism. In general, functional characterization can be alternatively solved by alignment-based manners. As alignment accuracy based on conventional methods is often sensitive to sequence identity, low sequence identity among query sequences makes it difficult to precisely locate small portions of relevant features. Therefore, we propose a feature-incorporated alignment (FIA) to flexibly align conserved signatures in CBMs. Then, an FIA-based target-template prediction model was further implemented to identify functional ligand-binding residues.

Results:  Arabidopsis thaliana CBM45 and CBM53 were used to validate the FIA-based prediction model. The predicted ligand-binding residues residing on the surface in the hypothetical structures were verified to be ligand-binding residues. In the absence of 3D structural information, FIA demonstrated significant improvement in the estimation of sequence similarity and identity for a total of 808 sequences from 11 different CBM families as compared with six leading tools by Friedman rank test.

Contact:  dtchang@life.nthu.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Post hocpower estimation in large-scale multiple testing problems
Authors: Zehetmayer Sonja , Posch Martin
Published: February 2010

Background: The statistical power or multiple Type II error rate in large-scale multiple testing problems as, for example, in gene expression microarray experiments, depends on typically unknown parameters and is therefore difficult to assess a priori. However, it has been suggested to estimate the multiple Type II error rate post hoc, based on the observed data.

Methods: We consider a class of post hoc estimators that are functions of the estimated proportion of true null hypotheses among all hypotheses. Numerous estimators for this proportion have been proposed and we investigate the statistical properties of the derived multiple Type II error rate estimators in an extensive simulation study.

Results: The performance of the estimators in terms of the mean squared error depends sensitively on the distributional scenario. Estimators based on empirical distributions of the null hypotheses are superior in the presence of strongly correlated test statistics.

Availability: R-code to compute all considered estimators based on P-values and supplementary material is available on the authors web page http://statistics.msi.meduniwien.ac.at/index.php?page=pageszfnr

Contact:  martin.posch@meduniwien.ac.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
High quality SNP calling using Illumina data at shallow coverage
Authors: Malhis Nawar , Jones Steven J. M.
Published: February 2010

Motivation: Detection of single nucleotide polymorphisms (SNPs) has been a major application in processing second generation sequencing (SGS) data. In principle, SNPs are called on single base differences between a reference genome and a sequence generated from SGS short reads of a sample genome. However, this exercise is far from trivial; several parameters related to sequencing quality, and/or reference genome properties, play essential effect on the accuracy of called SNPs especially at shallow coverage data. In this work, we present Slider II, an alignment and SNP calling approach that demonstrates improved algorithmic approaches enabling larger number of called SNPs with lower false positive rate. In addition to the regular alignment and SNP calling, as an optional feature, Slider II is capable of utilizing information about known SNPs of a target genome, as priors, in the alignment and SNPs calling to enhance it's capability of detecting these known SNPs and novel SNPs and mutations in their vicinity.

Contact:  nmalhis@bcgsc.ca

Supplementary information and availability:  Supplementary data are available at Bioinformatics online and at http://www.bcgsc.ca/platform/bioinfo/software/SliderII
Prolonged Remission of a Demyelinating Neuropathy in a Patient With Lymphoma and Sjögren's Syndrome After Rituximab Therapy
Authors: Botez Stephan A , Herrmann David N
Published: February 2010

Chronic acquired demyelinating polyneuropathies may be refractory to conventional therapy including corticosteroids, plasma exchange, and intravenous immunoglobulin (Ig) or require long-term immunotherapy to maintain remission. Use of alternative approaches such as Rituximab, an anti-CD20 antibody, in the treatment of demyelinating polyneuropathy, unrelated to IgM gammopathy and myelin-associated glycoprotein antibodies, has been the subject of only a few case reports. We report the case of a 79-year-old woman with a distal acquired demyelinating polyneuropathy in the context of Sjögren's syndrome, IgG paraproteinemia, and occult lymphoma who has had an excellent and durable response to Rituximab therapy.
Muscle-Eye-Brain Disease
Authors: Shenoy Anant M , Markowitz Jennifer A , Bonnemann Carsten G , Krishnamoorthy Kalpathy , Bossler Aaron D , Tseng Brian S
Published: February 2010

A term female infant was evaluated for global developmental delay, hypotonia, hyporeflexia, diffuse weakness including facial muscles, and visual impairment with optic nerve hypoplasia. In the absence of family history or perinatal concerns, an extensive investigation was performed, including lab studies, muscle biopsy, brain MRI and focused genetic testing. This revealed elevated serum CK, a structurally abnormal brain, and a dystrophic-appearing muscle biopsy with evidence of a glycosylation defect in the alpha-dystroglycan complex. Of the 6 known related genes, testing of the POMGnT1 gene showed three heterozygous missense mutations. Thus her history, examination, biopsy specimen, imaging, laboratory, and genetic studies are all consistent with the diagnosis of Muscle-Eye-Brain (MEB) disease. MEB is one of an emerging spectrum of congenital disorders that involve both central and peripheral nervous systems, described further in this case report.
Contralateral Cranial Polyneuropathy Due to Perineural Invasion by a Cutaneous Squamous Cell Carcinoma
Authors: Sundaram Arun N E , Simmons Zachary , Towfighi Javad , Sheehan Jonas , Reichwein Raymond
Published: February 2010

Cutaneous malignancies may spread to underlying nerves, a process known as perineural invasion (PNI). We report a patient who was found to have PNI presenting as a cranial polyneuropathy on the contralateral side of the face many years after the resection of a squamous cell carcinoma. All diagnostic testing was unrevealing until nerve biopsy was performed. This emphasizes the long asymptomatic period between treatment of a cutaneous malignancy and detection of PNI, and the development of PNI at a site distant from the original malignancy. Biopsy of a clinically involved nerve may permit diagnosis of PNI when other studies are normal.
Sensory Neuronopathy With Ro Antibodies: Response to Combination Immunosuppression
Authors: Hussain Aamir , Scelsa Stephen N
Published: February 2010

The objective of this study was to describe a case of sensory neuronopathy syndrome (SNS) with Ro antibodies who had nearly complete functional recovery with combination immunosuppression. Plasma exchange, azathioprine, and hydroxychloroquine were used in combination. The gait ataxia, kinesthetic sensation, and sensory response amplitudes showed considerable recovery with excellent functional outcomes. Prompt combined therapy with azathioprine and hydroxychloroquine is a promising therapy for patients with sensory neuronopathy syndrome and Ro antibodies.
An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria
Authors: Gaget Virginie , Gribaldo Simonetta , Tandeau de Marsac Nicole
Published: February 2010

The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA,nif,cpcandrpoC1genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (βsubunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6–44 aa) and sequence, and form part of what appears to be a longer signature sequence (43–81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.
Gordonia neofelifaecis sp. nov., a cholesterol side-chain-cleaving actinomycete isolated from the faeces of Neofelis nebulosa
Authors: Liu Yuchang , Ge Fanglan , Chen Guiying , Li Wei , Ma Pingmei , Zhang Guangxiang , Zeng Lihua
Published: February 2010

A cholesterol side-chain-cleaving bacterial strain, AD-6T, was isolated from fresh faeces of a clouded leopard (Neofelis nebulosa) and was studied using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that the novel strain formed a distinct subline within the genusGordonia, its closest neighbours being the type strains ofGordonia cholesterolivorans,Gordonia sihwensisandGordonia hydrophobica, with sequence similarity values of 98.2, 97.8 and 97.6 %, respectively. ThegyrBgene sequence of strain AD-6Texhibited similarities of 77–91 % with those of the type strains of recognized species of the genusGordonia, being most similar to the type strains ofG.sihwensis,G. hydrophobicaandGordonia hirsuta(91, 87 and 84 % similarity, respectively). The results of whole-cell fatty acid analyses and DNA–DNA relatedness data readily distinguished the new isolate from its nearest neighbours. Strain AD-6Tis therefore considered to represent a novel species of the genusGordonia, for which the nameGordonia neofelifaecissp. nov. is proposed. The type strain is AD-6T(=NRRL B-59395T=CCTCC AB-209144T).
Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant
Authors: Zhang Yu-Qin , Chen Jie , Liu Hong-Yu , Zhang Yue-Qin , Li Wen-Jun , Yu Li-Yan
Published: February 2010

A novel actinobacterial strain, designated CPCC 201356T, was isolated from a rhizosphere soil sample of the medicinal plantAstragalus membranaceusand subjected to a polyphasic taxonomic analysis. Good growth occurred at 20–32 °C, at pH 7.0–7.5 and with 0–1 % (w/v) NaCl. Colonies on R2A and ISP 2 agar were light red to red, round and lacked aerial mycelium; cells adhered to the agar. The peptidoglycan containedmeso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H4) and MK-9. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0and C17 : 1ω8c. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CPCC 201356Tbelonged to the familyGeodermatophilaceaeand consistently formed a distinct sub-branch withGeodermatophilus obscurusDSM 43160T. The organism showed 16S rRNA gene sequence similarity of 97.7 % withG. obscurusDSM 43160T. DNA–DNA hybridization between strain CPCC 201356TandG. obscurusDSM 43160Twas 17.4 %. On the basis of evidence from this polyphasic taxonomic study, a novel species,Geodermatophilus rubersp. nov., is proposed; the type strain is CPCC 201356T(=DSM 45317T=CCM 7619T).
A molecular dissociation between cued and contextual appetitive learning
Authors: Kheirbek Mazen A. , Beeler Jeff A. , Chi Wanhao , Ishikawa Yoshihiro , Zhuang Xiaoxi
Published: February 2010

In appetitive Pavlovian learning, animals learn to associate discrete cues or environmental contexts with rewarding outcomes, and these cues and/or contexts can potentiate an ongoing instrumental response for reward. Although anatomical substrates underlying cued and contextual learning have been proposed, it remains unknown whether specific molecular signaling pathways within the striatum underlie one form of learning or the other. Here, we show that while the striatum-enriched isoform of adenylyl cyclase (AC5) is required for cued appetitive Pavlovian learning, it is not required for contextual appetitive learning. Mice lacking AC5 (AC5KO) could not learn an appetitive Pavlovian learning task in which a discrete signal light predicted reward delivery, yet they could form associations between context and either natural or drug reward, which could in turn elicit Pavlovian approach behavior. However, unlike wild-type (WT) mice, AC5KO mice could not use these Pavlovian conditioned stimuli to potentiate ongoing instrumental behavior in a Pavlovian-to-instrumental transfer paradigm. These data suggest that AC5 is specifically required for learning associations between discrete cues and outcomes in which the temporal relationship between conditioned stimulus (CS) and unconditioned stimulus (US) is essential, while alternative signaling mechanisms may underlie the formation of associations between context and reward. In addition, loss of AC5 compromises the ability of both contextual and discrete cues to modulate instrumental behavior.
Arabidopsis RNA-Dependent RNA Polymerases and Dicer-Like Proteins in Antiviral Defense and Small Interfering RNA Biogenesis during Turnip Mosaic Virus Infection
Authors: Garcia-Ruiz Hernan , Takeda Atsushi , Chapman Elisabeth J. , Sullivan Christopher M. , Fahlgren Noah , Brempelis Katherine J. , Carrington James C.
Published: February 2010

Plants respond to virus infections by activation of RNA-based silencing, which limits infection at both the single-cell and system levels. Viruses encode RNA silencing suppressor proteins that interfere with this response. Wild-type Arabidopsis thaliana is immune to silencing suppressor (HC-Pro)-deficient Turnip mosaic virus, but immunity was lost in the absence of DICER-LIKE proteins DCL4 and DCL2. Systematic analysis of susceptibility and small RNA formation in Arabidopsis mutants lacking combinations of RNA-dependent RNA polymerase (RDR) and DCL proteins revealed that the vast majority of virus-derived small interfering RNAs (siRNAs) were dependent on DCL4 and RDR1, although full antiviral defense also required DCL2 and RDR6. Among the DCLs, DCL4 was sufficient for antiviral silencing in inoculated leaves, but DCL2 and DCL4 were both involved in silencing in systemic tissues (inflorescences). Basal levels of antiviral RNA silencing and siRNA biogenesis were detected in mutants lacking RDR1, RDR2, and RDR6, indicating an alternate route to form double-stranded RNA that does not depend on the three previously characterized RDR proteins.
The augmented subjective risk management process
Authors: Emblemsvåg Jan
Published: February 2010

Purpose

This paper aims to present an augmented subjective risk management process that can partially solve the problem of inconsistent results in qualitative risk management. Note that “subjective” in this context is to separate this risk management process from the purely statistical risk management processes often associated with finance.

Design/methodology/approach

The approach has been developed by logically approaching the problem of inconsistency and, based on experience and literature review, conceptually designing a solution.

Findings

The presented approach seems workable and indeed an improvement over standard qualitative approaches given reasonable skillful implementation.

Research limitations/implications

The approach has not yet been tested in real life, which must be undertaken in the future.

Practical implications

The presented approach will expand the subjective risk management process to include information management and to some extent knowledge management and thus add some more activities to the practice of risk management.

Originality/value

The paper presents an approach that so far seems useful in improving the consistency of subjective risk management. Also, it may be a valuable point of departure for further research.
Corporate environmental and financial performance: a multivariate approach
Authors: Moneva José M. , Ortas Eduardo
Published: February 2010

Purpose

The aim of this paper is to evaluate the significance of the link between corporate environmental and financial performance in order to show managers how an adequate management of environmental factors could contribute to the financial success of the firm.

Design/methodology/approach

The paper analyses the environmental and financial performance of a sample of 230 European companies. Under the stakeholder approach, the commitment to environmental performance is analysed and linked with the firms' financial improvement. The paper proposes a partial least squares model (PLS) for measuring corporate environmental and financial performance that seems to be the first time which has been applied in the field.

Findings

The results support the idea that enterprises which obtained higher rates of environmental performance show better financial performance levels in the future.

Research limitations/implications

The lack of a long series of environmental performance data for organisations is an obstacle for a broader analysis. This research shows the usefulness of the multivariate modelling for analysing the environmental and financial performance of businesses.

Practical implications

In practice, this research may show managers the need of taking into account the environmental management factors when configuring the strategic policy of the firm and how environmental management can impact to the financial success of the firms.

Originality/value

The use of PLS modelling for measuring environmental and financial performance theoretical concepts and considering a sample of European companies for the empirical analysis.