bluuebunny/crossref_metadata_2025 huggingface dataset:
Electric-field control of phase separation and memory effect in Pr0.6Ca0.4MnO3/Pb(Mg1/3Nb2/3)0.7Ti0.3O3 heterostructures
Authors: Chen Q. P. , Yang J. J. , Zhao Y. G. , Zhang S. , Wang J. W. , Zhu M. H. , Yu Y. , Zhang X. Z. , Wang Zhu , Yang Bin , Xie D. , Ren T. L.
Published: April 2011

Heterostructures were fabricated by growing Pr0.6Ca0.4MnO3 (PCMO) films on Pb(Mg1/3Nb2/3)0.7Ti0.3O3 substrates. It was shown that the magnetizations of the samples can be tuned dramatically by electric fields via piezostrain and the effect is dominated by the change in phase separation. More interestingly, the electric-field control of magnetization is nonvolatile, manifesting a memory effect of strain. The results were discussed by considering the effect of electric-field-induced strain on the energy landscape of PCMO and the resultant change in phase separation. This work is helpful for exploring the evolution of phase separation with well-controlled strains and the magnetoelectric coupling effect.
Observation of spin wave modes depending on a tunable periodic magnetic field
Authors: Bai Lihui , Kohda Makoto , Nitta Junsaku
Published: April 2011

Excited spin waves in Ni0.8Fe0.2 strips are studied by detecting electrical signals with the use of a spin rectification effect. Through a meander control line, a periodic magnetic field is applied on the strips. Spin wave modes strongly depends on the periodic magnetic field. In a short period sample, we find spin wave coupling effect controlled by the periodic magnetic field, which can be used as a tunable spin wave filter.
A way to determine the permittivity of metallized surfaces at terahertz frequencies
Authors: Gerasimov V. V. , Knyazev B. A. , Nikitin A. K. , Zhizhin G. N.
Published: April 2011

A method for determining the dielectric permittivity of metal surfaces at terahertz (THz) frequencies has been suggested and tested. The method implies excitation of surface plasmons (SPs) on the sample surface and measurements of the SPs propagation length and field penetration depth in air. The technique was tested on evaporated gold with Novosibirsk free-electron laser at the wavelength of 130 μm. The method suggested paves the way for refractometry of metallized surfaces at THz frequencies.
Single quantum dot emission at telecom wavelengths from metamorphic InAs/InGaAs nanostructures grown on GaAs substrates
Authors: Seravalli L. , Trevisi G. , Frigeri P. , Rivas D. , Muñoz-Matutano G. , Suárez I. , Alén B. , Canet-Ferrer J. , Martínez-Pastor J. P.
Published: April 2011

We report on the growth by molecular beam epitaxy and the study by atomic force microscopy and photoluminescence of low density metamorphic InAs/InGaAs quantum dots. subcritical InAs coverages allow to obtain 108 cm−2 dot density and metamorphic InxGa1−xAs (x=0.15,0.30) confining layers result in emission wavelengths at 1.3 μm. We discuss optimal growth parameters and demonstrate single quantum dot emission up to 1350 nm at low temperatures, by distinguishing the main exciton complexes in these nanostructures. Reported results indicate that metamorphic quantum dots could be valuable candidates as single photon sources for long wavelength telecom windows.
The oxygen dimer in Si: Its relationship to the light-induced degradation of Si solar cells?
Authors: Murin L. I. , Tolkacheva E. A. , Markevich V. P. , Peaker A. R. , Hamilton B. , Monakhov E. , Svensson B. G. , Lindström J. L. , Santos P. , Coutinho J. , Carvalho A.
Published: May 2011

It is widely believed that the light induced degradation of crystalline silicon solar cells is due to the formation of a BsO2i recombination center created by the optically excited migration of the oxygen dimer (charge-state-driven motion). In this letter the concentration dependence of the neutral state of O2i on [Oi] in p- and n-type Cz–Si has been determined using infrared absorption. A systematic search for the absorption signature of the dimer in the doubly positively charged state has been unsuccessful. These data strongly suggest that charge-state-driven motion (Bourgoin–Corbett mechanism) of the oxygen dimer cannot occur in typical solar silicon and hence bring into question the accepted degradation mechanism.
Influence of anisotropic light-hole band structure on indirect tunneling in silicon
Authors: Chen Edward , Pan Dee-Son
Published: April 2011

In this letter, we have clarified the physics of indirect interband tunneling in silicon. By considering the detailed anisotropic light-hole band structure, the magnitude of the current densities shows J⟨110⟩≈J⟨111⟩≈10×J⟨100⟩ under the low electric field and J⟨110⟩≈J⟨111⟩≈3×J⟨100⟩ under the high electric field. The quantitative result is consistent with the recent experimental data. The study also indicates that the indirect tunneling current in strain silicon or Si1−xGex can be changed a lot by the highly anisotropic valence band structure.
Note: Flowing ion population from a resonance cavity source
Authors: Gayetsky Lisa E. , Lynch Kristina A.
Published: April 2011

The experimental low energy plasma for hemispherical analyzers nominal testing thermal plasma facility of Dartmouth College uses a microwave plasma source which generates an ionosphere-like plasma through a two-step process. The plasma is initially generated inside a cylindrical, insulated, resonance cavity. This initial plasma must pass through a sheath in order to enter the main experimental region. This process imparts a significant flow velocity to the ions which has been neglected in previous analysis of this plasma source. We predict the flow energy of the ions to be between 12-15 eV depending on conservation laws and show agreement with experimental results.
A topological point defect regulates the evolution of extended defects in irradiated silicon
Authors: Park Hyoungki , Wilkins John W.
Published: April 2011

Clustering and annihilation of atomic-scale bond defects dominate nucleation and evolution of submicron-scale extended interstitial defects in irradiated silicon. Molecular dynamics simulations reveal the role of the bond defect in the thermal evolution of extended defects and identify the atomistic evolution paths. Accurate density functional theory calculations establish formation energies, activation barriers, and electronic structures of the bond defect and its clusters, and extended interstitial defects.
Magnetically aligned carbon nanotube in nanopaper enabled shape-memory nanocomposite for high speed electrical actuation
Authors: Lu Haibao , Gou Jihua , Leng Jinsong , Du Shanyi
Published: April 2011

A new shape-memory nanocomposite that exhibits rapid electrical actuation capabilities is fabricated by incorporating self-assembly multiwalled carbon nanotube (MWCNT) nanopaper and magnetic CNTs into a styrene-based shape-memory polymer (SMP). The MWCNT nanopaper was coated on the surface to give high electrical conductivity to SMP. Electromagnetic CNTs were blended with and, vertically aligned into the SMP resin upon a magnetic field, to facilitate the heat transfer from the nanopaper to the underlying SMP. This not only significantly enhances heat transfer but also gives high speed electrical actuation.
Structure and phase behavior of a confined nanodroplet composed of the flexible chain molecules
Authors: Kim Soon-Chul , Kim Eun-Young , Seong Baek-Seok
Published: April 2011

A polymer density functional theory has been employed for investigating the structure and phase behaviors of the chain polymer, which is modelled as the tangentially connected sphere chain with an attractive interaction, inside the nanosized pores. The excess free energy of the chain polymer has been approximated as the modified fundamental measure-theory for the hard spheres, the Wertheim's first-order perturbation for the chain connectivity, and the mean-field approximation for the van der Waals contribution. For the value of the chemical potential corresponding to a stable liquid phase in the bulk system and a metastable vapor phase, the flexible chain molecules undergo the liquid-vapor transition as the pore size is reduced; the vapor is the stable phase at small volume, whereas the liquid is the stable phase at large volume. The wide liquid-vapor coexistence curve, which explains the wide range of metastable liquid-vapor states, is observed at low temperature. The increase of temperature and decrease of pore size result in a narrowing of liquid-vapor coexistence curves. The increase of chain length leads to a shift of the liquid-vapor coexistence curve towards lower values of chemical potential. The coexistence curves for the confined phase diagram are contained within the corresponding bulk liquid-vapor coexistence curve. The equilibrium capillary phase transition occurs at a higher chemical potential than in the bulk phase.
Room temperature quantum cascade lasers with 27% wall plug efficiency
Authors: Bai Y. , Bandyopadhyay N. , Tsao S. , Slivken S. , Razeghi M.
Published: May 2011

Using the recently proposed shallow-well design, we demonstrate InP based quantum cascade lasers (QCLs) emitting around 4.9 μm with 27% and 21% wall plug efficiencies in room temperature (298 K) pulsed and continuous wave (cw) operations, respectively. The laser core consists of 40 QCL-stages. The highest cw efficiency is obtained from a buried-ridge device with a ridge width of 8 μm and a cavity length of 5 mm. The front and back facets are antireflection and high-reflection coated, respectively. The maximum single facet cw power at room temperature amounts to 5.1 W.
Origin of the efficiency enhancement in ferroelectric functionalized organic solar cells
Authors: Asadi Kamal , de Bruyn Paul , Blom Paul W. M. , de Leeuw Dago M.
Published: May 2011

We have investigated the efficiency enhancement of organic solar cells upon incorporation of a thin ferroelectric polymer layer. For non-Ohmic contacts the enhancement is due to an increased open circuit voltage, which is, however, independent of the ferroelectric polarization direction. Ferroelectricity cannot play a role due to depolarization and charge compensation. The same improvement is also obtained with a non-ferroelectric fluorinated polymer. The data unambiguously show that the improved efficiency is solely due to improvement of the cathode. The fluorinated polymer layer plays the role of LiF in an optimized solar cell.
Abnormal expression of uncoupling protein-2 correlates with CYP11A1 expression in polycystic ovary syndrome
Authors: Liu Yun , Jiang Hong , He Ling-Yun , Huang Wu-Jian , He Xiao-Yu , Xing Fu-Qi
Published: May 2011

Polycystic ovary syndrome (PCOS) may result from hypersensitivity to insulin, which is negatively regulated by uncoupling protein (UCP)-2. Because cholesterol side-chain cleavage enzyme (CYP11A1) is closely linked to PCOS, the expression of UCP-2 and CYP11A1 in ovarian tissues from PCOS patients was examined in the present study. Twelve PCOS patients with hyperandrogenaemia who underwent laparoscopic ovarian wedge resection and 12 age-matched control patients who underwent contralateral ovarian biopsy were enrolled in the study. UCP-2 expression in early stage (primordial, primary and secondary) and late stage (sinus and mature) follicles was examined using immunohistochemistry, whereas UCP-2 and CYP11A1 mRNA and protein levels in ovarian tissue were determined using quantitative reverse transcription–polymerase chain reaction and western blot analyses, respectively. UCP-2 expression increased significantly with follicular development in both control and PCOS tissue, with expression in early stage follicles from PCOS patients significantly greater than that in controls. In addition, both UCP-2 and CYP11A1mRNA and protein levels, mean fasting blood glucose concentrations and fasting serum insulin levels were significantly higher in PCOS patients compared with the control group. Finally, a significant correlation between UCP-2 and CYP11A1 expression was found in PCOS but not control patients. In conclusion, in PCOS patients, there was a correlation between UCP-2 and CYP11A1 expression, which was significantly higher than in the control group. These changes in UCP-2 and CYP11A1 expression may mediate follicle development in PCOS.
Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors
Authors: Goldfeld Dahlia A. , Zhu Kai , Beuming Thijs , Friesner Richard A.
Published: May 2011

We present results of the restoration of all crystallographically available intra- and extracellular loops of four G-protein-coupled receptors (GPCRs): bovine rhodopsin (bRh), the turkey β-1 adrenergic receptor (β1Ar), and the human β-2 adrenergic (β2Ar) and A2A adenosine (A2Ar) receptors. We use our Protein Local Optimization Program (PLOP), which samples conformational space from first principles to build sets of loop candidates and then discriminates between them using our physics-based, all-atom energy function with implicit solvent. We also discuss a new kind of explicit membrane calculation developed for GPCR loops that interact, either in the native structure or in low-energy false-positive structures, with the membrane, and thus exist in a multiphase environment not previously incorporated in PLOP. Our results demonstrate a significant advance over previous work reported in the literature, and of particular note we are able to accurately restore the extremely long second extracellular loop (ECL2), which is also key for GPCR ligand binding. In the case of β2Ar, accurate ECL2 restoration required seeding a small helix into the loop in the appropriate region, based on alignment with the β1Ar ECL2 loop, and then running loop reconstruction simulations with and without the seeded helix present; simulations containing the helix attain significantly lower total energies than those without the helix, and have rmsds close to the native structure. For β1Ar, the same protocol was used, except the alignment was done to β2Ar. These results represent an encouraging start for the more difficult problem of accurate loop refinement for GPCR homology modeling.
Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly
Authors: Cho Suhyung , Hoang Amy , Sinha Rahul , Zhong Xiang-Yang , Fu Xiang-Dong , Krainer Adrian R. , Ghosh Gourisankar
Published: May 2011

It has been widely accepted that the early spliceosome assembly begins with U1 small nuclear ribonucleoprotein (U1 snRNP) binding to the 5′ splice site (5′SS), which is assisted by the Ser/Arg (SR)-rich proteins in mammalian cells. In this process, the RS domain of SR proteins is thought to directly interact with the RS motif of U1-70K, which is subject to regulation by RS domain phosphorylation. Here we report that the early spliceosome assembly event is mediated by the RNA recognition domains (RRM) of serine/arginine-rich splicing factor 1 (SRSF1), which bridges the RRM of U1-70K to pre-mRNA by using the surface opposite to the RNA binding site. Specific mutation in the RRM of SRSF1 that disrupted the RRM–RRM interaction also inhibits the formation of spliceosomal E complex and splicing. We further demonstrate that the hypo-phosphorylated RS domain of SRSF1 interacts with its own RRM, thus competing with U1-70K binding, whereas the hyper-phosphorylated RS domain permits the formation of a ternary complex containing ESE, an SR protein, and U1 snRNP. Therefore, phosphorylation of the RS domain in SRSF1 appears to induce a key molecular switch from intra- to intermolecular interactions, suggesting a plausible mechanism for the documented requirement for the phosphorylation/dephosphorylation cycle during pre-mRNA splicing.
Continuous neurogenesis in the adult forebrain is required for innate olfactory responses
Authors: Sakamoto Masayuki , Imayoshi Itaru , Ohtsuka Toshiyuki , Yamaguchi Masahiro , Mori Kensaku , Kageyama Ryoichiro
Published: May 2011

Although the functional significance of adult neurogenesis in hippocampal-dependent learning and memory has been well documented, the role of such neurogenesis in olfactory activity is rather obscure. To understand the significance of adult neurogenesis in olfactory functions, we genetically ablated newly born neurons by using tamoxifen-treated Nestin-CreER
T2
;neuron-specific enolase-diphtheria toxin fragment A (NSE-DTA) mice. In these mice, tamoxifen-inducible Cre recombinase allows the NSE (
Eno2
) gene to drive DTA expression in differentiating neurons, leading to the efficient ablation of newly born neurons in the forebrain. These mutant mice were capable of discriminating odors as competently as control mice. Strikingly, although control and mutant mice frequently showed freezing behaviors to a fox scent, a predator odor, mutant mice approached this odor when they were conditioned to associate the odor with a reward, whereas control mice did not approach the odor. Furthermore, although mutant males and females showed normal social recognition behaviors to other mice of a different sex, mutant males displayed deficits in male–male aggression and male sexual behaviors toward females, whereas mutant females displayed deficits in fertility and nurturing, indicating that sex-specific activities, which are known to depend on olfaction, are impaired. These results suggest that continuous neurogenesis is required for predator avoidance and sex-specific responses that are olfaction dependent and innately programmed.
T-cell immunoglobulin and mucin domain 1 (TIM-1) is a receptor for
Zaire Ebolavirus
and
Lake Victoria Marburgvirus
Authors: Kondratowicz Andrew S. , Lennemann Nicholas J. , Sinn Patrick L. , Davey Robert A. , Hunt Catherine L. , Moller-Tank Sven , Meyerholz David K. , Rennert Paul , Mullins Robert F. , Brindley Melinda , Sandersfeld Lindsay M. , Quinn Kathrina , Weller Melodie , McCray Paul B. , Chiorini John , Maury Wendy
Published: May 2011

The glycoproteins (GP) of enveloped viruses facilitate entry into the host cell by interacting with specific cellular receptors. Despite extensive study, a cellular receptor for the deadly filoviruses
Ebolavirus
and
Marburgvirus
has yet to be identified and characterized. Here, we show that T-cell Ig and mucin domain 1 (TIM-1) binds to the receptor binding domain of the Zaire Ebola virus (EBOV) glycoprotein, and ectopic TIM-1 expression in poorly permissive cells enhances EBOV infection by 10- to 30-fold. Conversely, reduction of cell-surface expression of TIM-1 by RNAi decreased infection of highly permissive Vero cells. TIM-1 expression within the human body is broader than previously appreciated, with expression on mucosal epithelia from the trachea, cornea, and conjunctiva—tissues believed to be important during in vivo transmission of filoviruses. Recognition that TIM-1 serves as a receptor for filoviruses on these mucosal epithelial surfaces provides a mechanistic understanding of routes of entry into the human body via inhalation of aerosol particles or hand-to-eye contact. ARD5, a monoclonal antibody against the IgV domain of TIM-1, blocked EBOV binding and infection, suggesting that antibodies or small molecules directed against this cellular receptor may provide effective filovirus antivirals.
Contemporaneous and recent radiations of the world's major succulent plant lineages
Authors: Arakaki Mónica , Christin Pascal-Antoine , Nyffeler Reto , Lendel Anita , Eggli Urs , Ogburn R. Matthew , Spriggs Elizabeth , Moore Michael J. , Edwards Erika J.
Published: May 2011

The cacti are one of the most celebrated radiations of succulent plants. There has been much speculation about their age, but progress in dating cactus origins has been hindered by the lack of fossil data for cacti or their close relatives. Using a hybrid phylogenomic approach, we estimated that the cactus lineage diverged from its closest relatives ≈35 million years ago (Ma). However, major diversification events in cacti were more recent, with most species-rich clades originating in the late Miocene, ≈10–5 Ma. Diversification rates of several cactus lineages rival other estimates of extremely rapid speciation in plants. Major cactus radiations were contemporaneous with those of South African ice plants and North American agaves, revealing a simultaneous diversification of several of the world's major succulent plant lineages across multiple continents. This short geological time period also harbored the majority of origins of C
4
photosynthesis and the global rise of C
4
grasslands. A global expansion of arid environments during this time could have provided new ecological opportunity for both succulent and C
4
plant syndromes. Alternatively, recent work has identified a substantial decline in atmospheric CO
2
≈15–8 Ma, which would have strongly favored C
4
evolution and expansion of C
4
-dominated grasslands. Lowered atmospheric CO
2
would also substantially exacerbate plant water stress in marginally arid environments, providing preadapted succulent plants with a sharp advantage in a broader set of ecological conditions and promoting their rapid diversification across the landscape.
Influenza virus aerosol exposure and analytical system for ferrets
Authors: Gustin Kortney M. , Belser Jessica A. , Wadford Debra A. , Pearce Melissa B. , Katz Jacqueline M. , Tumpey Terrence M. , Maines Taronna R.
Published: May 2011

Understanding the transmission ability of newly emerging influenza viruses is central to the development of public health preparedness and prevention strategies. Animals are used to model influenza virus infection and transmission, but the routinely used intranasal inoculation of a liquid virus suspension does not reflect natural infection. We report the development of an inoculation method that delivers an influenza virus aerosol inoculum to ferrets and the characterization of size distribution and viable virus present in aerosols shed from infected ferrets during normal breathing and sneezing. By comparing virus deposition, infectivity, virulence, and transmissibility among animals inoculated intranasally or by aerosols with a human (H3N2) or avian (H5N1) influenza virus, we demonstrate that aerosol inoculations more closely resemble a natural, airborne influenza virus infection and that viable virus is measurable in droplets and droplet nuclei exhaled by infected ferrets. These methods will provide improved risk assessment of emerging influenza viruses that pose a threat to public health.
Transcription cofactors TRIM24, TRIM28, and TRIM33 associate to form regulatory complexes that suppress murine hepatocellular carcinoma
Authors: Herquel Benjamin , Ouararhni Khalid , Khetchoumian Konstantin , Ignat Mihaela , Teletin Marius , Mark Manuel , Béchade Guillaume , Van Dorsselaer Alain , Sanglier-Cianférani Sarah , Hamiche Ali , Cammas Florence , Davidson Irwin , Losson Régine
Published: April 2011

TRIM24 (TIF1α), TRIM28 (TIF1β), and TRIM33 (TIF1γ) are three related cofactors belonging to the tripartite motif superfamily that interact with distinct transcription factors. TRIM24 interacts with the liganded retinoic acid (RA) receptor to repress its transcriptional activity. Germ line inactivation of TRIM24 in mice deregulates RA-signaling in hepatocytes leading to the development of hepatocellular carcinoma (HCC). Here we show that TRIM24 can be purified as at least two macromolecular complexes comprising either TRIM33 or TRIM33 and TRIM28. Somatic hepatocyte-specific inactivation of TRIM24, TRIM28, or TRIM33 all promote HCC in a cell-autonomous manner in mice. Moreover, HCC formation upon TRIM24 inactivation is strongly potentiated by further loss of TRIM33. These results demonstrate that the TIF1-related subfamily of TRIM proteins interact both physically and functionally to modulate HCC formation in mice.
Stimulus-dependent EEG activity reflects internal updating of tactile working memory in humans
Authors: Spitzer Bernhard , Blankenburg Felix
Published: May 2011

Despite recent advances in uncovering the neural signature of tactile working memory processing in animals and humans, the representation of internally modified somatosensory working memory content has not been studied so far. Here, recording EEG in human participants (n= 25) performing a modified delayed match-to-sample task allowed us to disambiguate internally driven memory processing from encoding-related delay activity. After presentation of two distinct vibrotactile frequencies to different index fingers, a visual cue indicated which of the two previous stimuli had to be maintained in working memory throughout a retention interval for subsequent frequency discrimination against a probe stimulus. During cued stimulus maintenance, α activity (8–13 Hz) over early somatosensory cortices was lateralized according to the cued tactile stimulus, even though the location of the stimuli was task irrelevant. The task-relevant memory content, in contrast, was found to be represented in right prefrontal cortex. The key finding was that the visually presented instructions triggered systematic modulations of prefrontal β-band activity (20–25 Hz), which selectively reflected the to-be-maintained frequency of the cued tactile vibration. The results expand previous evidence for parametric representations of vibrotactile frequency in the prefrontal cortex and corroborate a central role of dynamic β-band synchronization during active processing of an analog stimulus quantity in human working memory. In particular, our findings suggest that such processing supports not only sustained maintenance but also purposeful modification and updating of the task-relevant working memory contents.
A PL-manifold of nonnegative curvature homeomorphic to 𝑆²×𝑆² is a direct metric product
Authors: Orshanskiy Sergey
Published: May 2011

Let

M
4

M^4

be a PL-manifold of nonnegative curvature that is homeomorphic to a product of two spheres,

S
2

×

S
2

S^2 \times S^2

. We prove that

M
M

is a direct metric product of two spheres endowed with some polyhedral metrics. In other words,

M
M

is a direct metric product of the surfaces of two convex polyhedra in

R

3

\mathbb {R}^3

.

The classical H. Hopf hypothesis states: for any Riemannian metric on

S
2

×

S
2

S^2 \times S^2

of nonnegative sectional curvature the curvature cannot be strictly positive at all points. The result of this paper can be viewed as a PL-version of Hopf’s hypothesis. It confirms the remark of M. Gromov that the condition of nonnegative curvature in the PL-case appears to be stronger than nonnegative sectional curvature of Riemannian manifolds and analogous to the condition of a nonnegative curvature operator.
Distribution of residues in approximate subgroups of 𝔽_{𝕡}*
Authors: Hegyvári Norbert , Hennecart François
Published: May 2011

We extend a result due to Bourgain on the uniform distribution of residues by proving that subsets of the type

f
(
I
)
⋅
H

f(I)\cdot H

are equidistributed (as

p
p

tends to infinity), where

f
f

is a polynomial,

I
I

is an interval of

F

p

\mathbb {F}_p

and

H
H

is an approximate subgroup of

F

p
∗

\mathbb {F}_p^*

with size larger than polylogarithmic in

p
p

.
parmigene—a parallel R package for mutual information estimation and gene network reconstruction
Authors: Sales Gabriele , Romualdi Chiara
Published: April 2011

Motivation: Inferring large transcriptional networks using mutual information has been shown to be effective in several experimental setup. Unfortunately, this approach has two main drawbacks: (i) several mutual information estimators are prone to biases and (ii) available software still has large computational costs when processing thousand of genes.

Results: Here, we present parmigene (PARallel Mutual Information estimation for GEne NEtwork reconstruction), an R package that tries to fill the above gaps. It implements a mutual information estimator based on k-nearest neighbor distances that is minimally biased with respect to the other methods and uses a parallel computing paradigm to reconstruct gene regulatory networks. We test parmigene on in silico and real data. We show that parmigene gives more precise results than existing softwares with strikingly less computational costs.

Availability and Implementation: The parmigene package is available on the CRAN network at http://cran.r-project.org/web/packages/.

Contact:  chiara.romualdi@unipd.it

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
Authors: Kiryu Hisanori , Terai Goro , Imamura Osamu , Yoneyama Hiroyuki , Suzuki Kenji , Asai Kiyoshi
Published: April 2011

Motivation: The importance of RNA sequence analysis has been increasing since the discovery of various types of non-coding RNAs transcribed in animal cells. Conventional RNA sequence analyses have mainly focused on structured regions, which are stabilized by the stacking energies acting on adjacent base pairs. On the other hand, recent findings regarding the mechanisms of small interfering RNAs (siRNAs) and transcription regulation by microRNAs (miRNAs) indicate the importance of analyzing accessible regions where no base pairs exist. So far, relatively few studies have investigated the nature of such regions.

Results: We have conducted a detailed investigation of accessibilities around the target sites of siRNAs and miRNAs. We have exhaustively calculated the correlations between the accessibilities around the target sites and the repression levels of the corresponding mRNAs. We have computed the accessibilities with an originally developed software package, called ‘Raccess’, which computes the accessibility of all the segments of a fixed length for a given RNA sequence when the maximal distance between base pairs is limited to a fixed size W. We show that the computed accessibilities are relatively insensitive to the choice of the maximal span W. We have found that the efficacy of siRNAs depends strongly on the accessibility of the very 3′-end of their binding sites, which might reflect a target site recognition mechanism in the RNA-induced silencing complex. We also show that the efficacy of miRNAs has a similar dependence on the accessibilities, but some miRNAs also show positive correlations between the efficacy and the accessibilities in broad regions downstream of their putative binding sites, which might imply that the downstream regions of the target sites are bound by other proteins that allow the miRNAs to implement their functions. We have also investigated the off-target effects of an siRNA as a potential RNAi therapeutic. We show that the off-target effects of the siRNA have similar correlations to the miRNA repression, indicating that they are caused by the same mechanism.

Availability: The C++ source code of the Raccess software is available at http://www.ncrna.org/software/Raccess/ The microarray data on the measurements of the siRNA off-target effects are also available at the same site.

Contact:  kiryu-h@k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Xanthomonas campestris Diffusible Factor Is 3-Hydroxybenzoic Acid and Is Associated with Xanthomonadin Biosynthesis, Cell Viability, Antioxidant Activity, and Systemic Invasion
Authors: He Ya-Wen , Wu Ji'en , Zhou Lian , Yang Fan , He Yong-Qiang , Jiang Bo-Le , Bai Linquan , Xu Yuquan , Deng Zixin , Tang Ji-Liang , Zhang Lian-Hui
Published: May 2011

Xanthomonas campestris pv. campestris produces a membrane-bound yellow pigment called xanthomonadin. A diffusible factor (DF) has been reported to regulate xanthomonadin biosynthesis. In this study, DF was purified from bacterial culture supernatants using a combination of solvent extraction, flash chromatography, and high-performance liquid chromatography. Mass spectrometry and nuclear magnetic resonance analyses resolved the DF chemical structure as 3-hydroxybenzoic acid (3-HBA), which was further confirmed by synthetic 3-HBA. Significantly, bioassay and in silico analysis suggest that DF production is widely conserved in a range of bacterial species. Analysis of DF derivatives established the hydroxyl group and its position as the key structural features for the role of DF in xanthomonadin biosynthesis. In addition, we showed that DF is also associated with bacterial survival, H2O2 resistance, and systemic invasion. Furthermore, evidence was also presented that DF and diffusible signaling factor have overlapping functions in modulation of bacterial survival, H2O2 resistance, and virulence. Utilization of different mechanisms to modulate similar virulence traits may provide X. campestris pv. campestris with plasticity in response to various environmental cues.
Jeotgalibacillus soli sp. nov., a Gram-stain-positive bacterium isolated from soil
Authors: Cunha Sofia , Tiago Igor , Paiva Gabriel , Nobre Fernanda , da Costa Milton S. , Veríssimo António
Published: April 2011

A Gram-staining-positive, motile, rod-shaped, spore-forming bacterium, designated P9T, was isolated from soil in Portugal. This organism was aerobic and catalase- and oxidase-positive. It had an optimum growth temperature of about 35 °C and an optimum growth pH of about 8.0–8.5, and grew in medium with 0–9 % (w/v) NaCl. The cell-wall peptidoglycan was of the A1α type, with l-lysine as the diagnostic diamino acid. The major respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C15 : 0 (45.4 %), iso-C15 : 0 (22.0 %) and anteiso-C17 : 0 (11.2 %). The genomic DNA G+C content was about 39.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain P9T was most closely related to Jeotgalibacillus campisalis DSM 18983T (96.8 %) and Jeotgalibacillus
marinus DSM 1297T (96.5 %). These two recognized species formed a coherent cluster with strain P9T that was supported by a bootstrap value of 99 %. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, strain P9T ( = DSM 23228T = LMG 25523T) represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus soli sp. nov. is proposed.
RNA-sequence analysis of human B-cells
Authors: Toung Jonathan M. , Morley Michael , Li Mingyao , Cheung Vivian G.
Published: May 2011

RNA-sequencing (RNA-seq) allows quantitative measurement of expression levels of genes and their transcripts. In this study, we sequenced complementary DNA fragments of cultured human B-cells and obtained 879 million 50-bp reads comprising 44 Gb of sequence. The results allowed us to study the gene expression profile of B-cells and to determine experimental parameters for sequencing-based expression studies. We identified 20,766 genes and 67,453 of their alternatively spliced transcripts. More than 90% of the genes with multiple exons are alternatively spliced; for most genes, one isoform is predominantly expressed. We found that while chromosomes differ in gene density, the percentage of transcribed genes in each chromosome is less variable. In addition, genes involved in related biological processes are expressed at more similar levels than genes with different functions. Besides characterizing gene expression, we also used the data to investigate the effect of sequencing depth on gene expression measurements. While 100 million reads are sufficient to detect most expressed genes and transcripts, about 500 million reads are needed to measure accurately their expression levels. We provide examples in which deep sequencing is needed to determine the relative abundance of genes and their isoforms. With data from 20 individuals and about 40 million sequence reads per sample, we uncovered only 21 alternatively spliced, multi-exon genes that are not in databases; this result suggests that at this sequence coverage, we can detect most of the known genes. Results from this project are available on the UCSC Genome Browser to allow readers to study the expression and structure of genes in human B-cells.
DNA Free Energy-Based Promoter Prediction and Comparative Analysis of Arabidopsis and Rice Genomes
Authors: Morey Czuee , Mookherjee Sushmita , Rajasekaran Ganesan , Bansal Manju
Published: April 2011

The cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) on the basis of free energy of DNA melting. For protein-coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice, respectively. For noncoding RNA genes, the program gives recall and precision of 94% and 75% for Arabidopsis and 95% and 90% for rice, respectively. Moreover, 96% of the false-positive predictions were located in noncoding regions of primary transcripts, out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.
Early Transcriptional Defense Responses in Arabidopsis Cell Suspension Culture under High-Light Conditions
Authors: González-Pérez Sergio , Gutiérrez Jorge , García-García Francisco , Osuna Daniel , Dopazo Joaquín , Lorenzo Óscar , Revuelta José L. , Arellano Juan B.
Published: April 2011

The early transcriptional defense responses and reactive oxygen species (ROS) production in Arabidopsis (Arabidopsis thaliana) cell suspension culture (ACSC), containing functional chloroplasts, were examined at high light (HL). The transcriptional analysis revealed that most of the ROS markers identified among the 449 transcripts with significant differential expression were transcripts specifically up-regulated by singlet oxygen (1O2). On the contrary, minimal correlation was established with transcripts specifically up-regulated by superoxide radical or hydrogen peroxide. The transcriptional analysis was supported by fluorescence microscopy experiments. The incubation of ACSC with the 1O2 sensor green reagent and 2′,7′-dichlorofluorescein diacetate showed that the 30-min-HL-treated cultures emitted fluorescence that corresponded with the production of 1O2 but not of hydrogen peroxide. Furthermore, the in vivo photodamage of the D1 protein of photosystem II indicated that the photogeneration of 1O2 took place within the photosystem II reaction center. Functional enrichment analyses identified transcripts that are key components of the ROS signaling transduction pathway in plants as well as others encoding transcription factors that regulate both ROS scavenging and water deficit stress. A meta-analysis examining the transcriptional profiles of mutants and hormone treatments in Arabidopsis showed a high correlation between ACSC at HL and the fluorescent mutant family of Arabidopsis, a producer of 1O2 in plastids. Intriguingly, a high correlation was also observed with ABA deficient1 and more axillary growth4, two mutants with defects in the biosynthesis pathways of two key (apo)carotenoid-derived plant hormones (i.e. abscisic acid and strigolactones, respectively). ACSC has proven to be a valuable system for studying early transcriptional responses to HL stress.
Male broad‐nosed pipefish Syngnathus typhle do not locate females by smell
Authors: Lindqvist C. , Sundin J. , Berglund A. , Rosenqvist G.
Published: May 2011

Broad‐nosed pipefish Syngnathus typhle were used to investigate whether males used scent in their search for mates. When the males in an experiment had access to olfactory cues only, they did not locate females better than they located males. Thus, S. typhle, was less successful in mate search when visual cues were absent.
Growth hormone is positively associated with surrogate markers of bone turnover during puberty
Authors: Russell Melissa , Breggia Anne , Mendes Nara , Klibanski Anne , Misra Madhusmita
Published: April 2011

Background  Puberty is characterized by increases in growth hormone (GH) and insulin‐like growth factor‐1 (IGF‐1) and the pubertal growth spurt. Bone formation and resorption also increase, consistent with increased bone metabolism.

Objective  To determine the relationship between pubertal bone metabolism, GH and IGF‐1. We hypothesized that bone turnover peaks at the time of greatest pubertal GH secretion.

Design and Subjects  Subjects included 86 girls and boys, 9–17 years‐old (BMI 10th–90th percentiles). Because higher endogenous GH secretion is associated with a higher nadir following oral glucose, we used the GH nadir following a 2‐h OGTT as indicative of GH status. Fasting serum IGF‐1, aminoterminal propeptide of type 1 procollagen (P1NP) and carboxy‐terminal collagen crosslinks (CTX) were obtained. Subjects were grouped per expected timing of peak growth. Group 1: Tanner 1 girls and Tanner 1–2 boys (period preceding peak growth), Group 2: Tanner 2–3 girls and Tanner 3–4 boys (period of peak growth) and Group 3: Tanner 4–5 girls and Tanner 5 boys (period following peak growth).

Results  GH peaked at mid‐puberty (Group 2) and IGF‐1 in late puberty (Group 3). P1NP and CTX were highest in mid‐puberty compared with early and late puberty (P = 0·0009 and 0·006 in girls and P = 0·005 and 0·04 in boys). GH, but not IGF‐1, correlated with P1NP (r = 0·46 in both genders, P ≤ 0·008) and CTX (r = 0·37 and 0·38, P = 0·04 and 0·02 in girls and boys, respectively). Similarly, on regression modelling, GH (but not IGF‐1) predicted both bone turnover markers in both genders.

Conclusion  GH is strongly associated with pubertal bone metabolism, independent of systemic IGF‐1 in girls and boys.
Assessment of quality of fruits using impedance spectroscopy
Authors: Rehman Mahfoozur , Abu Izneid Basem A.J.A. , Abdullah Mohd Zaid , Arshad Mohd Rizal
Published: May 2011

This study deals with the development of a nondestructive impedance spectroscopic technique that may assess the conditions of the fruits to pluck them with the help of robotic arms. Preliminary investigations are made with the help of two‐terminal probe and an accurate LCR meter. The bulk impedance of mango has been measured to characterise raw and ripe fruits. Effective resistance and effective capacitance vs. frequency characteristics have been determined. The bulk effective resistances, of the ripe fruits, are found to be more than those of the raw fruits, in the frequency range of 1–6 kHz. In the same frequency range, effective capacitances of the raw fruits are found more than those of the ripe fruits. In the light of the data obtained, it can be said that the effective resistance may be used to differentiate between raw and ripe fruits in the frequency range of 1–6 kHz.
Perceived health and risk of undernutrition: a comparison of different nutritional screening results in older patients
Authors: Söderhamn Ulrika , Flateland Sylvi , Jessen Liss , Söderhamn Olle
Published: May 2011

Aims and objectives. To compare screening results using different nutritional screening instruments with respect to nutritional risk and associations with perceived health and health‐related issues in a group of older hospital patients.

Background. The association between lower perceived health and nutritional risk in older people is widely known. It is advised to use a screening instrument to identify nutritional at‐risk patients.

Design. A cross‐sectional study design was used.

Methods. One hundred and fifty‐eight older patients, in three medical hospital wards in two hospitals in southern Norway, were interviewed using a questionnaire containing questions about background variables, perceived health and health‐related issues and the nutritional screening instruments Nutritional Form for the Elderly and Mini Nutritional Assessment (including Mini Nutritional Assessment‐Short Form). Data were also collected regarding the screening instrument Nutrition Risk Screening 2002. All data were analysed using statistical methods.

Results. Many patients were at nutritional risk independent of instrument used. Nutrition Risk Screening 2002 identified fewer nutritional at‐risk patients than the other instruments did. Perceived ill health was significantly associated with nutritional risk using instruments specifically designed for older people. Feeling satisfied with life and lower risk of undernutrition were two important predictors for perceived good health.

Conclusions. Nutritional Form for the Elderly, Mini Nutritional Assessment and Mini Nutritional Assessment‐Short Form could identify approximately the same number of nutritional at‐risk patients. Being at nutritional risk had a negative impact on older patients’ perceived health.

Relevance for practice. Corresponding nutritional screening results can be obtained using either Nutritional Form for the Elderly or Mini Nutritional Assessment, as well as Mini Nutritional Assessment‐Short Form. Instruments designed for older people should be used to screen older patients. Factors associated with nutritional risk can aid nurses in becoming aware of nutritional at‐risk patients. Preventing undernutrition is important for overall health enhancement.
Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La
Authors: CASSONE BRYAN J. , MOLLOY MATTHEW J. , CHENG CHANGDE , TAN JOHN C. , HAHN MATTHEW W. , BESANSKY NORA J.
Published: May 2011

The African malaria mosquito Anopheles gambiae is polymorphic for chromosomal inversion 2La, whose frequency strongly correlates with degree of aridity across environmental gradients. Recent physiological studies have associated 2La with resistance to desiccation in adults and thermal stress in larvae, consistent with its proposed role in aridity tolerance. However, the genetic basis of these traits remains unknown. To identify genes that could be involved in the differential response to thermal stress, we compared global gene expression profiles of heat‐hardened 2La or 2L+a larvae at three time points, for up to eight hours following exposure to the heat stress. Treatment and control time series, replicated four times, revealed a common and massive induction of a core set of heat‐shock genes regardless of 2La orientation. However, clear differences between the 2La and 2L+a arrangements emerged at the earliest (0.25 h) time point, in the intensity and nature of the stress response. Overall, 2La was associated with the more aggressive response: larger numbers of genes were heat responsive and up‐regulated. Transcriptionally induced genes were enriched for functions related to ubiquitin‐proteasomal degradation, chaperoning and energy metabolism. The more muted transcriptional response of 2L+a was largely repressive, including genes involved in proteolysis and energy metabolism. These results may help explain the maintenance of the 2La inversion polymorphism in An. gambiae, as the survival benefits offered by high thermal sensitivity in harsh climates could be offset by the metabolic costs of such a drastic response in more equable climates.