bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining the appropriate exchange-correlation functional for time-dependent density functional theory studies of charge-transfer excitations in organic dyes
Authors: Dev Pratibha , Agrawal Saurabh , English Niall J.
Published: June 2012

UV-Vis spectra are calculated using time-dependent density functional theory for several organic dyes – 4-(N, N-dimethylamino) benzonitrile, alizarin, squaraine, polyene-linker dyes, oligothiophene-containing coumarin dyes (NKX series) and triphenylamine-donor dyes. Most of these dyes (except, for the first two) or their derivatives are considered to be promising organic dyes for dye-sensitized solar cells. An accurate description of the photophysics of such dyes is imperative for understanding and creating better dyes. To this end, we studied the dyes within several approximations to the exchange-correlation functional. The chosen functionals – PBE, M06L, B3LYP, M06, CAM-B3LYP, and wB97 – represent the various classes of approximations that are currently being used to study material properties. From amongst the six approximations studied here, CAM-B3LYP outperformed the others in its description of charge-transfer excitations in most (though, not all) of the dyes. This study shows why it is difficult to choose a particular functional a priori, especially when starting out with a new dye for solar cell application. A possible way to judge the fitness of an approximation is used in this work and it is shown to provide a good quantitative guideline for subsequent research in this field.
Synchrotron-based ultrafast x-ray diffraction at high repetition rates
Authors: Navirian H. , Shayduk R. , Leitenberger W. , Goldshteyn J. , Gaal P. , Bargheer M.
Published: June 2012

We present a setup for ultrafast x-ray diffraction (UXRD) based at the storage ring BESSY II, in particular, a pump laser that excites the sample using 250 fs laser-pulses at repetition rates ranging from 208 kHz to 1.25 MHz. We discuss issues connected to the high heat-load and spatio-temporal alignment strategies in the context of a UXRD experiment at high repetition rates. The spatial overlap between laser pump and x-ray probe pulse is obtained with 10 μm precision and transient lattice changes can be recorded with an accuracy of δa/a0 = 10−6. We also compare time-resolved x-ray diffraction signals from a laser excited LSMO/STO superlattice with phonon dynamics simulations. From the analysis we determine the x-ray pulse duration to 120 ps in standard operation mode and below 10 ps in low-α mode.
Synchronization of high speed framing camera and intense electron-beam accelerator
Authors: Cheng Xin-Bing , Liu Jin-Liang , Hong Zhi-Qiang , Qian Bao-Liang
Published: June 2012

A new trigger program is proposed to realize the synchronization of high speed framing camera (HSFC) and intense electron-beam accelerator (IEBA). The trigger program which include light signal acquisition radiated from main switch of IEBA and signal processing circuit could provide a trigger signal with rise time of 17 ns and amplitude of about 5 V. First, the light signal was collected by an avalanche photodiode (APD) module, and the delay time between the output voltage of APD and load voltage of IEBA was tested, it was about 35 ns. Subsequently, the output voltage of APD was processed further by the signal processing circuit to obtain the trigger signal. At last, by combining the trigger program with an IEBA, the trigger program operated stably, and a delay time of 30 ns between the trigger signal of HSFC and output voltage of IEBA was obtained. Meanwhile, when surface flashover occurred at the high density polyethylene sample, the delay time between the trigger signal of HSFC and flashover current was up to 150 ns, which satisfied the need of synchronization of HSFC and IEBA. So the experiment results proved that the trigger program could compensate the time (called compensated time) of the trigger signal processing time and the inherent delay time of the HSFC.
High pressure study of molecular dynamics of protic ionic liquid lidocaine hydrochloride
Authors: Swiety-Pospiech A. , Wojnarowska Z. , Pionteck J. , Pawlus S. , Grzybowski A. , Hensel-Bielowka S. , Grzybowska K. , Szulc A. , Paluch M.
Published: June 2012

In this paper, we investigate the effect of pressure on the molecular dynamics of protic ionic liquid lidocaine hydrochloride, a commonly used pharmaceutical, by means of dielectric spectroscopy and pressure-temperature-volume methods. We observed that near Tg the pressure dependence of conductivity relaxation times reveals a peculiar behavior, which can be treated as a manifestation of decoupling between ion migration and structural relaxation times. Moreover, we discuss the validity of thermodynamic scaling in lidocaine HCl. We also employed the temperature-volume Avramov model to determine the value of pressure coefficient of glass transition temperature, dTg/dP|P = 0.1. Finally, we investigate the role of thermal and density fluctuations in controlling of molecular dynamics of the examined compound.
Hyper-resistivity and electron thermal conductivity due to destroyed magnetic surfaces in axisymmetric plasma equilibria
Authors: Weening R. H.
Published: June 2012

In order to model the effects of small-scale current-driven magnetic fluctuations in a mean-field theoretical description of a large-scale plasma magnetic field B(x,t), a space and time dependent hyper-resistivity Λ(x,t) can be incorporated into the Ohm’s law for the parallel electric field E⋅B. Using Boozer coordinates, a theoretical method is presented that allows for a determination of the hyper-resistivity Λ(ψ) functional dependence on the toroidal magnetic flux ψ for arbitrary experimental steady-state Grad-Shafranov axisymmetric plasma equilibria, if values are given for the parallel plasma resistivity η(ψ) and the local distribution of any auxiliary plasma current. Heat transport in regions of plasma magnetic surfaces destroyed by resistive tearing modes can then be modeled by an electron thermal conductivity ke(ψ)=(ɛ02me/e2)Λ(ψ), where e and me are the electron charge and mass, respectively, while ɛ0 is the permittivity of free space. An important result obtained for axisymmetric plasma equilibria is that the ψψ−component of the metric tensor of Boozer coordinates is given by the relation gψψ(ψ)≡∇ψ⋅∇ψ=[μ0G(ψ)][μ0I(ψ)]/ι(ψ), with μ0 the permeability of free space, G(ψ) the poloidal current outside a magnetic surface, I(ψ) the toroidal current inside a magnetic surface, and ι(ψ) the rotational transform.
Calculation of impurity poloidal rotation from measured poloidal asymmetries in the toroidal rotation of a tokamak plasma
Authors: Chrystal C. , Burrell K. H. , Grierson B. A. , Groebner R. J. , Kaplan D. H.
Published: June 2012

To improve poloidal rotation measurement capabilities on the DIII-D tokamak, new chords for the charge exchange recombination spectroscopy (CER) diagnostic have been installed. CER is a common method for measuring impurity rotation in tokamak plasmas. These new chords make measurements on the high-field side of the plasma. They are designed so that they can measure toroidal rotation without the need for the calculation of atomic physics corrections. Asymmetry between toroidal rotation on the high- and low-field sides of the plasma is used to calculate poloidal rotation. Results for the main impurity in the plasma are shown and compared with a neoclassical calculation of poloidal rotation.
Epitaxial GaN films by hyperthermal ion-beam nitridation of Ga droplets
Authors: Gerlach J. W. , Ivanov T. , Neumann L. , Höche Th. , Hirsch D. , Rauschenbach B.
Published: June 2012

Epitaxial GaN film formation on bare 6H-SiC(0001) substrates via the process of transformation of Ga droplets into a thin GaN film by applying hyperthermal nitrogen ions is investigated. Pre-deposited Ga atoms in well defined amounts form large droplets on the substrate surface which are subsequently nitridated at a substrate temperature of 630 °C by a low-energy nitrogen ion beam from a constricted glow-discharge ion source. The Ga deposition and ion-beam nitridation process steps are monitored in situ by reflection high-energy electron diffraction. Ex situ characterization by x-ray diffraction and reflectivity techniques, Rutherford backscattering spectrometry, and electron microscopy shows that the thickness of the resulting GaN films depends on the various amounts of pre-deposited gallium. The films are epitaxial to the substrate, exhibit a mosaic like, smooth surface topography and consist of coalesced large domains of low defect density. Possible transport mechanisms of reactive nitrogen species during hyperthermal nitridation are discussed and the formation of GaN films by an ion-beam assisted process is explained.
Light-soaking issue in polymer solar cells: Photoinduced energy level alignment at the sol-gel processed metal oxide and indium tin oxide interface
Authors: Kim Junghwan , Kim Geunjin , Choi Youna , Lee Jongjin , Heum Park Sung , Lee Kwanghee
Published: June 2012

We report the origin of the strong UV-irradiation dependence, generally known as a “light-soaking” process, in inverted polymer solar cells (I-PSCs) using the interface of an sol-gel processed titanium sub-oxide (TiOx) and indium tin oxide (ITO) cathode. When I-PSCs incorporating TiOx as an electron-selecting layer were fabricated, the as-prepared devices exhibited an anomalous J-V curve with a kink shape, resulting in an extremely low efficiency. However, the kink shape disappeared after white light irradiation for considerable duration, after which the device parameters recovered the normal values expected for this class of devices. By using electrochemical impedance spectroscopy and by measuring the contact potential difference and transient photoconductivity of the TiOx layer, we found that the light-soaking process in I-PSCs originates from the photoinduced “rearrangement of the Fermi levels” at the sol-gel processed TiOx and ITO cathode interface together with trap sites existing in the TiOx layer. Based on our data, we optimized I-PSC devices with a high fill factor (FF) of ∼70%.
Low threshold amplified spontaneous emission from dye-doped DNA biopolymer
Authors: Hung Yu-Chueh , Su Che-Hsuan , Huang Hsien-Wen
Published: June 2012

In this study, we investigate the amplified spontaneous emission (ASE) properties and conduct a comparative study for two kinds of dye-doped deoxyribonucleic acid (DNA) biopolymers. The system consists of optical films made of DNA modified by two types of surfactants and doped with a common laser dye rhodamine 6G (Rh6G). The ASE properties of the optical films were characterized by a pulsed Nd:YAG laser. The results show that low threshold of DNA biopolymer can be achieved by the employment of suitable surfactant in the system, resulting from an efficient energy transfer process. Coupled with the fluorescence enhancement exhibited in DNA, this effect can further advance biopolymers toward highly efficient media for lasing applications and organic solid-state lasers.
Analyzing photo-induced interfacial charging in IZO/pentacene/C60/bathocuproine/Al organic solar cells by electric-field-induced optical second-harmonic generation measurement
Authors: Chen Xiangyu , Taguchi Dai , Manaka Takaaki , Iwamoto Mitsumasa
Published: June 2012

By using electric-field-induced optical second-harmonic generation (EFISHG) measurement, we investigated interfacial carrier behavior in organic solar cells (OSCs) with a blocking layer of bathocuproine (BCP). Results evidently showed that the Maxwell-Wagner type excess charges accumulate on both pentacene/C60 and C60/BCP interfaces. Meanwhile, the introduction of BCP layer enhances photocarrier generation in the OSCs and results in the increase of the conductivity of the pentacene and C60 layers, which significantly suppresses the charge accumulation on the pentacene/C60 interface. The role of the BCP blocking layer was discussed with taking into account the dielectric nature of the active organic OSC layer on the basis of the Maxwell-Wagner effect model.
Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59
Authors: Khersonsky Olga , Kiss Gert , Röthlisberger Daniela , Dym Orly , Albeck Shira , Houk Kendall N. , Baker David , Tawfik Dan S.
Published: June 2012

Computational design is a test of our understanding of enzyme catalysis and a means of engineering novel, tailor-made enzymes. While the de novo computational design of catalytically efficient enzymes remains a challenge, designed enzymes may comprise unique starting points for further optimization by directed evolution. Directed evolution of two computationally designed Kemp eliminases, KE07 and KE70, led to low to moderately efficient enzymes (
k
cat
/
K
m
values of ≤ 5 × 10
4
 M
-1
s
-1
). Here we describe the optimization of a third design, KE59. Although KE59 was the most catalytically efficient Kemp eliminase from this design series (by
k
cat
/
K
m
, and by catalyzing the elimination of nonactivated benzisoxazoles), its impaired stability prevented its evolutionary optimization. To boost KE59’s evolvability, stabilizing consensus mutations were included in the libraries throughout the directed evolution process. The libraries were also screened with less activated substrates. Sixteen rounds of mutation and selection led to > 2,000-fold increase in catalytic efficiency, mainly via higher
k
cat
values. The best KE59 variants exhibited
k
cat
/
K
m
values up to 0.6 × 10
6
 M
-1
s
-1
, and
k
cat
/
k
uncat
values of ≤ 10
7
almost regardless of substrate reactivity. Biochemical, structural, and molecular dynamics (MD) simulation studies provided insights regarding the optimization of KE59. Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies.
Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle
Authors: Barnes Jonathan C. , Fahrenbach Albert C. , Dyar Scott M. , Frasconi Marco , Giesener Marc A. , Zhu Zhixue , Liu Zhichang , Hartlieb Karel J. , Carmieli Ranaan , Wasielewski Michael R. , Stoddart J. Fraser
Published: June 2012

The kinetics and thermodynamics of intramolecular electron transfer (IET) can be subjected to redox control in a bistable [2]rotaxane comprised of a dumbbell component containing an electron-rich 1,5-dioxynaphthalene (DNP) unit and an electron-poor phenylene-bridged bipyridinium (P-BIPY2+) unit and a cyclobis (paraquat-p-phenylene) (CBPQT4+) ring component. The [2]rotaxane exists in the ground-state co-conformation (GSCC) wherein the CBPQT4+ring encircles the DNP unit. Reduction of the CBPQT4+leads to the CBPQT2(•+)diradical dication while the P-BIPY2+unit is reduced to its P-BIPY•+radical cation. A radical-state co-conformation (RSCC) results from movement of the CBPQT2(•+)ring along the dumbbell to surround the P-BIPY•+unit. This shuttling event induces IET to occur between the pyridinium redox centers of the P-BIPY•+unit, a property which is absent between these redox centers in the free dumbbell and in the 1∶1 complex formed between the CBPQT2(•+)ring and the radical cation of methyl-phenylene-viologen (MPV•+). Using electron paramagnetic resonance (EPR) spectroscopy, the process of IET was investigated by monitoring the line broadening at varying temperatures and determining the rate constant (kET = 1.33 × 107 s-1) and activation energy (ΔG‡ = 1.01 kcal mol-1) for electron transfer. These values were compared to the corresponding values predicted, using the optical absorption spectra and Marcus–Hush theory.
Enhancing dissociative chemisorption of H
2
O on Cu(111) via vibrational excitation
Authors: Jiang Bin , Ren Xuefeng , Xie Daiqian , Guo Hua
Published: June 2012

The dissociative chemisorption of water is an important step in many heterogeneous catalytic processes. Here, the mode selectivity of this process was examined quantum mechanically on a realistic potential energy surface determined by fitting planewave density functional calculations spanning a large configuration space. The quantum dynamics of the surface reaction were characterized by a six-dimensional model including all important internal coordinates of H
2
O and its distance to the surface. It was found that excitations in all three vibrational modes are capable of enhancing reactivity more effectively than increasing translational energy, consistent with the “late” transition state in the reaction path.
Statistical model-based testing to evaluate the recurrence of genomic aberrations
Authors: Niida Atushi , Imoto Seiya , Shimamura Teppei , Miyano Satoru
Published: June 2012

Motivation: In cancer genomes, chromosomal regions harboring cancer genes are often subjected to genomic aberrations like copy number alteration and loss of heterozygosity. Given this, finding recurrent genomic aberrations is considered an apt approach for screening cancer genes. Although several permutation-based tests have been proposed for this purpose, none of them are designed to find recurrent aberrations from the genomic dataset without paired normal sample controls. Their application to unpaired genomic data may lead to false discoveries, because they retrieve pseudo-aberrations that exist in normal genomes as polymorphisms.

Results: We develop a new parametric method named parametric aberration recurrence test (PART) to test for the recurrence of genomic aberrations. The introduction of Poisson-binomial statistics allow us to compute small P-values more efficiently and precisely than the previously proposed permutation-based approach. Moreover, we extended PART to cover unpaired data (PART-up) so that there is a statistical basis for analyzing unpaired genomic data. PART-up uses information from unpaired normal sample controls to remove pseudo-aberrations in unpaired genomic data. Using PART-up, we successfully predict recurrent genomic aberrations in cancer cell line samples whose paired normal sample controls are unavailable. This article thus proposes a powerful statistical framework for the identification of driver aberrations, which would be applicable to ever-increasing amounts of cancer genomic data seen in the era of next generation sequencing.

Availability: Our implementations of PART and PART-up are available from http://www.hgc.jp/~niiyan/PART/manual.html.

Contact:  aniida@ims.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
GenomeRing: alignment visualization based on SuperGenome coordinates
Authors: Herbig A. , Jäger G. , Battke F. , Nieselt K.
Published: June 2012

Motivation: The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

Results: Here, we present two complementary approaches to tackle this problem. First, we propose the SuperGenome concept for the computation of a common coordinate system for all genomes in a multiple alignment. This coordinate system allows for the consistent placement of genome annotations in the presence of insertions, deletions and rearrangements. Second, we present the GenomeRing visualization that, based on the SuperGenome, creates an interactive overview visualization of the multiple genome alignment in a circular layout. We demonstrate our methods by applying them to an alignment of Campylobacter jejuni strains for the discovery of genomic islands as well as to an alignment of Helicobacter pylori, which we visualize in combination with gene expression data.

Availability: GenomeRing and example data is available at http://it.inf.uni-tuebingen.de/software/genomering/

Contact:  kay.nieselt@uni-tuebingen.de
On the pursuit of the brain network for proto-syntactic learning in non-human primates: conceptual issues and neurobiological hypotheses
Authors: Petkov Christopher I. , Wilson Benjamin
Published: June 2012

Songbirds have become impressive neurobiological models for aspects of human verbal communication because they learn to sequence their song elements, analogous, in some ways, to how humans learn to produce spoken sequences with syntactic structure. However, mammals such as non-human primates are considered to be at best limited-vocal learners and not able to sequence their vocalizations, although some of these animals can learn certain ‘artificial grammar’ sequences. Thus, conceptual issues have slowed the progress in exploring potential neurobiological homologues to language-related processes in species that are taxonomically closely related to humans. We consider some of the conceptual issues impeding a pursuit of, as we define them, ‘proto-syntactic’ capabilities and their neuronal substrates in non-human animals. We also discuss ways to better bridge comparative behavioural and neurobiological data between humans and other animals. Finally, we propose guiding neurobiological hypotheses with which we aim to facilitate the future testing of the level of correspondence between the human brain network for syntactic-learning and related neurobiological networks present in other primates. Insights from the study of non-human primates and other mammals are likely to complement those being obtained in birds to further our knowledge of the human language-related network at the cellular level.
An approach to separating the levels of hierarchical structure building in language and mathematics
Authors: Makuuchi Michiru , Bahlmann Jörg , Friederici Angela D.
Published: June 2012

We aimed to dissociate two levels of hierarchical structure building in language and mathematics, namely ‘first-level’ (the build-up of hierarchical structure with externally given elements) and ‘second-level’ (the build-up of hierarchical structure with internally represented elements produced by first-level processes). Using functional magnetic resonance imaging, we investigated these processes in three domains: sentence comprehension, arithmetic calculation (using Reverse Polish notation, which gives two operands followed by an operator) and a working memory control task. All tasks required the build-up of hierarchical structures at the first- and second-level, resulting in a similar computational hierarchy across language and mathematics, as well as in a working memory control task. Using a novel method that estimates the difference in the integration cost for conditions of different trial durations, we found an anterior-to-posterior functional organization in the prefrontal cortex, according to the level of hierarchy. Common to all domains, the ventral premotor cortex (PMv) supports first-level hierarchy building, while the dorsal pars opercularis (POd) subserves second-level hierarchy building, with lower activation for language compared with the other two tasks. These results suggest that the POd and the PMv support domain-general mechanisms for hierarchical structure building, with the POd being uniquely efficient for language.
Gaetbulibacter lutimaris sp. nov., isolated from a tidal flat sediment
Authors: Yoon Jung-Hoon , Lee Soo-Young , Oh Tae-Kwang
Published: June 2012

A Gram-stain-negative, aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, D1-y4T, was isolated from a tidal flat sediment of the South Sea in South Korea and subjected to a polyphasic study. Strain D1-y4T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain D1-y4T belonged to the genus

Gaetbulibacter

, joining the type strain of Gaetbulibacter marinus, with which it exhibited 97.8 % similarity. Sequence similarities to

Gaetbulibacter saemankumensis

SMK-12T and

Gaetbulibacter aestuarii

KYW382T were 96.5 and 96.2 %, respectively. Strain D1-y4T contained MK-6 as the predominant menaquionone and iso-C15 : 0, iso-C15 : 1 G and anteiso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain D1-y4T was 34.6 mol% and its mean DNA–DNA relatedness value with G. marinus KCTC 23046T was 7 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain D1-y4T is distinguishable from the three recognized

Gaetbulibacter

species. On the basis of the data presented here, strain D1-y4T is considered to represent a novel species of the genus

Gaetbulibacter

, for which the name Gaetbulibacter lutimaris sp. nov. is proposed. The type strain is D1-y4T ( = KCTC 23716T  = CCUG 61504T).
Sphingomonas

starnbergensis sp. nov., isolated from a prealpine freshwater lake
Authors: Chen Hong , Jogler Mareike , Tindall Brian J. , Klenk Hans-Peter , Rohde Manfred , Busse Hans-Jürgen , Overmann Jörg
Published: June 2012

A novel type of freshwater bacterium was isolated from the prealpine mesotrophic Starnberger See (Bavaria, southern Germany). Cells of strain 382T were Gram-negative and rod-shaped, motile and creamy-white. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew at pH values of 6–9 (optimum, pH 7) and temperatures of 10–37 °C (optimum, 28 °C). The genomic G+C content of strain 382T was 64.1 mol%. Based on 16S rRNA gene sequence analyses, strain 382T belongs to the family

Sphingomonadaceae

and clusters within the genus

Sphingomonas

.

Sphingomonas histidinilytica

UM 2T and

Sphingomonas wittichii

DSM 6014T were the closest relatives, as indicated by the highest 16S rRNA gene sequence similarities (97.1 % and 96.8 %, respectively).

Sphingomonas paucimobilis

DSM 1098T (the type species of the genus

Sphingomonas

) exhibited 95.3 % sequence similarity. This affiliation of strain 382T to the genus

Sphingomonas

is confirmed by the presence of Q-10 as the major respiratory quinone, two sphingoglycolipids, C14 : 0 2-OH as the major 2-hydroxy fatty acid and sym-homospermidine as the major polyamine. The main cellular fatty acids of strain 382T were C18 : 1ω7c (39 %), C16 : 1ω7c (21 %), C16 : 0 (10 %) and C14 : 0 2-OH (10 %). Based on the phylogenetic distance from other species of the genus

Sphingomonas

and its unusually high C16 : 1ω7c content, strain 382T represents a novel species of the genus

Sphingomonas

, for which the name

Sphingomonas

starnbergensis is proposed. The type strain is 382T ( = DSM 25077T  = LMG 26763T).
Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
Authors: Hogart Amber , Lichtenberg Jens , Ajay Subramanian S. , Anderson Stacie ,   NIH Intramural Sequencing Center, Margulies Elliott H. , Bodine David M.
Published: June 2012

DNA methylation is an essential epigenetic mark that is required for normal development. Knockout of the DNA methyltransferase enzymes in the mouse hematopoietic compartment reveals that methylation is critical for hematopoietic differentiation. To better understand the role of DNA methylation in hematopoiesis, we characterized genome-wide DNA methylation in primary mouse hematopoietic stem cells (HSCs), common myeloid progenitors (CMPs), and erythroblasts (ERYs). Methyl binding domain protein 2 (MBD) enrichment of DNA followed by massively parallel sequencing (MBD-seq) was used to map genome-wide DNA methylation. Globally, DNA methylation was most abundant in HSCs, with a 40% reduction in CMPs, and a 67% reduction in ERYs. Only 3% of peaks arise during differentiation, demonstrating a genome-wide decline in DNA methylation during erythroid development. Analysis of genomic features revealed that 98% of promoter CpG islands are hypomethylated, while 20%–25% of non-promoter CpG islands are methylated. Proximal promoter sequences of expressed genes are hypomethylated in all cell types, while gene body methylation positively correlates with gene expression in HSCs and CMPs. Elevated genome-wide DNA methylation in HSCs and the positive association between methylation and gene expression demonstrates that DNA methylation is a mark of cellular plasticity in HSCs. Using de novo motif discovery, we identified overrepresented transcription factor consensus binding motifs in methylated sequences. Motifs for several ETS transcription factors, including GABPA and ELF1, are overrepresented in methylated regions. Our genome-wide survey demonstrates that DNA methylation is markedly altered during myeloid differentiation and identifies critical regions of the genome and transcription factor programs that contribute to hematopoiesis.
Dynamic transitions in RNA polymerase II density profiles during transcription termination
Authors: Grosso Ana Rita , de Almeida Sérgio Fernandes , Braga José , Carmo-Fonseca Maria
Published: June 2012

Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3′-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for “metagene” analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3′-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3′-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3′-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.
Untangling diffraction intensity: modulation enhanced diffraction on ZrO2powder
Authors: van Beek Wouter , Emerich Hermann , Urakawa Atsushi , Palin Luca , Milanesio Marco , Caliandro Rocco , Viterbo Davide , Chernyshov Dmitry
Published: June 2012

This paper describes a new method for extracting the individual contributions to the diffracted intensity of subsets of atoms in the crystal structure. The periodic perturbation of the scattering process, required for untangling the scattered intensity, is provided by altering the resonant contributions. The theory of modulation enhanced diffraction (MED) is briefly recalled in the context of resonant scattering. A periodic variation in the atomic form factor has been achieved by changing the X-ray energy in such a way that the MED theory holds. Simulated results and experimental data are presented, together with necessary corrections. Two data analysis schemes are presented, both illustrating the advantages and drawbacks of the novel modulation technique.
Reduction of radiation damage and other benefits of short wavelengths for macromolecular crystallography data collection
Authors: Fourme Roger , Honkimäki Veijo , Girard Eric , Medjoubi Kadda , Dhaussy Anne-Claire , Kahn Richard
Published: June 2012

Circumventing radiation damage remains a major problem for X-ray macromolecular crystallography. Analysis of diffraction data collected from normal-sized cryocooled lysozyme crystals shows that the dose required to collect a data set of prescribed resolution and signal-to-noise ratio, assuming an ideally efficient detector, decreases with increasing photon energy in the investigated 6.5–33 keV range. For example, the data collection efficiency is increased by a factor of ∼8 from 8 to 33 keV. Monte Carlo simulations on lysozyme crystals in the range 5–80 keV, taking into account electron escape from samples of different size, also show a positive effect of high energy (albeit less pronounced than in experiments), especially for micrometre-sized samples, and suggest that the optimum energy range is ∼24–41 keV, depending on crystal size. The importance of counting pixel detectors with a good efficiency at high energy is underlined. Macromolecular crystallography beamlines should be modified, or purposely designed, in order to benefit from higher-energy radiation through reduction of global radiation damage, better data accuracy and extension of phasing by anomalous dispersion.
From patterns to space groups and the eigensymmetry of crystallographic orbits: a reinterpretation of some symmetry diagrams in IUCr Teaching Pamphlet No. 14
Authors: Suescun Leopoldo , Nespolo Massimo
Published: June 2012

The space group of a crystal pattern is the intersection group of the eigensymmetries of the crystallographic orbits corresponding to the occupied Wyckoff positions. Polar space groups without symmetry elements with glide or screw components smaller than 1/2 do not contain characteristic orbits and cannot be realized in patterns (structures) made by only one crystallographic type of object (atom). The space-group diagram of the general orbit for this type of group has an eigensymmetry that corresponds to a special orbit in a centrosymmetric supergroup of the generating group. This fact is often overlooked, as shown in the proposed solution for Plates (i)–(vi) of IUCr Teaching Pamphlet No. 14, and an alternative interpretation is given.
Shifts in soil organic carbon for plantation and pasture establishment in native forests and grasslands of South America
Authors: Eclesia Roxana P. , Jobbagy Esteban G. , Jackson Robert B. , Biganzoli Fernando , Piñeiro Gervasio
Published: June 2012

The replacement of native vegetation by pastures or tree plantations is increasing worldwide. Contradictory effects of these land use transitions on the direction of changes in soil organic carbon (SOC) stocks, quality, and vertical distribution have been reported, which could be explained by the characteristics of the new or prior vegetation, time since vegetation replacement, and environmental conditions. We used a series of paired‐field experiments and a literature synthesis to evaluate how these factors affectSOCcontents in transitions between tree‐ and grass‐dominated (grazed) ecosystems in South America. Both our field and literature approaches showed thatSOCchanges (0–20 cm of depth) were independent of the initial native vegetation (forest, grassland, or savanna) but strongly dependent on the characteristics of the new vegetation (tree plantations or pastures), its age, and precipitation. Pasture establishment increasedSOCcontents across all our precipitation gradient and C gains were greater as pastures aged. In contrast, tree plantations increasedSOCstocks in arid sites but decreased them in humid ones. However,SOClosses in humid sites were counterbalanced by the effect of plantation age, as plantations increased theirSOCstocks as plantations aged. A multiple regression model including age and precipitation explained more than 50% (p < 0.01) ofSOCchanges observed after sowing pastures or planting trees. The only clear shift observed in the vertical distribution ofSOCoccurred when pastures replaced native forests, withSOCgains in the surface soil but losses at greater depths. The changes inSOCstocks occurred mainly in the silt+clay soil size fraction (MAOM), whileSOCstocks in labile (POM) fraction remained relatively constant. Our results can be considered in designing strategies to increaseSOCstorage and soil fertility and highlight the importance of precipitation, soil depth, and age in determiningSOCchanges across a range of environments and land‐use transitions.
Do nitrogen fertilizers stimulate or inhibit methane emissions from rice fields?
Authors: Banger Kamaljit , Tian Hanqin , Lu Chaoqun
Published: June 2012

In rice cultivation, there are controversial reports on net impacts of nitrogen (N) fertilizers on methane (CH
4) emissions. Nitrogen fertilizers increase crop growth as well as alter CH
4 producing (Methanogens) and consuming (Methanotrophs) microbes, and thereby produce complex effects on CH
4 emissions. Objectives of this study were to determine net impact of N fertilizers on CH
4 emissions and to identify their underlying mechanisms in the rice soils. Database was obtained from 33 published papers that contained CH
4 emissions observations from N fertilizer (28–406 kg N ha−1) treatment and its control. Results have indicated that N fertilizers increased CH
4 emissions in 98 of 155 data pairs in rice soils. Response of CH
4 emissions per kg N fertilizer was significantly (P < 0.05) greater at < 140 kg N ha−1 than > 140 kg N ha−1 indicating that substrate switch from CH
4 to ammonia by Methanotrophs may not be a dominant mechanism for increased CH
4 emissions. On the contrary, decreased CH
4 emission in intermittent drainage by N fertilizers has suggested the stimulation of Methanotrophs in rice soils. Effects of N fertilizer stimulated Methanotrophs in reducing CH
4 emissions were modified by the continuous flood irrigation due to limitation of oxygen to Methanotrophs. Greater response of CH
4 emissions per kg N fertilizer in urea than ammonia sulfate probably indicated the interference of sulfate in the CH
4 production process. Overall, response of CH
4 emissions to N fertilizers was correlated with N‐induced crop yield (r = +0.39; P < 0.01), probably due to increased carbon substrates for Methanogens. Using CH
4 emission observations, this meta‐analysis has identified dominant microbial processes that control net effects of N fertilizers on CH
4 emissions in rice soils. Finally, we have provided a conceptual model that included microbial processes and controlling factors to predict effects of N fertilizers on CH
4 emissions in rice soils.
Validating the personal health records adoption model using a modified e‐Delphi
Authors: Logue Melanie D. , Effken Judith A.
Published: June 2012

logue m.d. & effken j.a. (2013) Validating the personal health records adoption model using a modified e‐Delphi. Journal of Advanced Nursing69(3), 685–696. doi: 10.1111/j.1365‐2648.2012.06056.x

Aim.  To report the results of a preliminary test of validity of a proposed theoretical framework of electronic personal health record adoption by older adults.

Background.  Personal health records can assist older adults in managing or co‐managing their chronic health conditions. Although there is interest by this population, their adoption of this technology has been slow. Without a comprehensive understanding of the reasons for this phenomenon, facilitating adoption will be difficult. Therefore, we developed a theoretical framework of adoption barriers and facilitators.

Design.  Survey.

Methods.  A modified e‐Delphi methodology was used to validate the framework by obtaining consensus from a panel of experts in related healthcare fields. These data were collected over 3 months in 2010. Of 16 expert panellists, 13 completed Round 1, 12 completed Rounds 2 and 3, and 9 completed Round 4. Central tendencies and percent agreement were computed to establish consensus.

Findings.  The e‐Delphi resulted in expert consensus on the concepts, variables, and empirical indicators that were retained in (or added to) the framework to describe barriers and/or facilitators to older adults’ adoption of personal health records for self‐management of chronic disease.

Conclusion.  The validated model will be used as the basis for developing an instrument to identify barriers and facilitators to personal health records adoption and use by older adults with chronic disease. With better understanding of the factors that influence personal health record adoption in this population, more effective strategies may be developed to increase adoption and thus improve chronic disease management.
Behavioural and electrophysiological responses of females of two species of tabanid to volatiles in urine of different mammals
Authors: BALDACCHINO F. , CADIER J. , PORCIANI A. , BUATOIS B. , DORMONT L. , JAY‐ROBERT P.
Published: June 2012

Urine volatiles from different ungulates (cows, horses and sheep) were tested as bait for tabanids in southeastern France using Nzi traps during the early summer of 2011.Tabanus bromiusLinnaeus, 1758 andAtylotus quadrifarius(Loew, 1874) (both: Diptera: Tabanidae) were the most captured species, respectively representing 57% and 41% of all tabanids collected (all of which were female). Horse urine significantly increased catches ofT. bromius(1.6‐fold) andA. quadrifarius(3.5‐fold), and sheep urine significantly increased catches ofA. quadrifarius(2.5‐fold). In parallel, an electroantennogram (EAG) study was conducted for the first time on these two species, in which EAGs were recorded using 1‐octen‐3‐ol and extracts of the same urine samples used in the field. ForT. bromius, the EAG response to 1‐octen‐3‐ol increased quasi‐sigmoidally with dose, with a maximum response at ≥100 µg on filter paper. For both species of tabanid, cow and horse urine elicited larger EAGs than did sheep urine. The behavioural implications in host‐seeking and feeding habits are discussed.
Estimating survival rates after ovarian cancer among women tested for BRCA1 and BRCA2 mutations
Authors: Narod SA , Moody JRK , Rosen B , Fan I , Risch A , Sun P , McLaughlin JR
Published: June 2012

Several studies have reported that women with ovarian cancer and a BRCA1 or BRCA2 mutations have better survival than women with ovarian cancer and no mutation. Potential reasons for this include possible differences in histologic subtype, stage, grade and response to chemotherapy, but some of the difference in survival may be due to systematic bias, i.e. a difference in survival rates for women who do and who do not undergo genetic testing. We estimated the survival rate in 1423 ovarian cancer patients from Ontario who had genetic testing and compared this with the survival rate for all 3367 ovarian cancer patients from the province from whom the tested sample was derived. Tested women had a 10‐year survival of 54.5%, compared to 35.8% for all patients in the province. We evaluated the extent to which three different methods of adjustment eliminated the observed difference. The adjusted rates for the tested cohort were closer to the provincial average, but each adjustment method resulted in a modest over‐estimate of 10‐year survival, ranging from 6.1% to 10.0%. The mortality advantage for tested women was due, in part, to a lower than expected mortality rate of tested women in the period following genetic testing.
A Plating‐PCR Technique for Detection and Quantification of the Biological Control Agent Agrobacterium vitis Strain E26 in Soil under Controlled Conditions
Authors: Bi Zhen , Li Jinyun , Guo Yanbin , Zheng Hui , Hu Bin , Wang Jianhui , Wang Huimin
Published: June 2012

Agrobacterium vitis strain E26 is a promising biocontrol agent of grapevine crown gall, an economically important disease of grape worldwide. In this report, we developed a Plating‐PCR method that allows specific detection and quantification of E26 by combining classical microbiological techniques with molecular tools. Random amplified polymorphic DNA fingerprints were used to differentiate E26 from other A. vitis strains. A differentially amplified fragment from E26 was sequenced and characterized as a sequence characterized amplified region (SCAR) marker. Two primer pairs were then designed and evaluated for their specificity against E26. One of the two SCAR primer pairs, 740F/R, was further selected for specific detection of strain E26. A plating assay coupled to PCR with the SCAR primers 740F/R allowed the assessment of population dynamics of E26 in non‐sterile grape rhizosphere soil under controlled conditions.
The Oviduct: Functional Genomic and Proteomic Approach
Authors: Mondéjar I , Acuña OS , Izquierdo‐Rico MJ , Coy P , Avilés M
Published: June 2012

Contents

The mammalian oviduct is an anatomical part of the female reproductive tract, which plays several important roles in the events related to fertilization and embryo development. This review examines and compares several studies related to the proteomic and transcriptomic profile of the oviduct in different domestic animals. This information could be important for clarifying the role of oviductal factors in different events regulating fertilization and early embryo development, as well as for improving synthetic media forin vitromaturation/in vitrofertilization/embryo culture techniques (IVM/IVF/EC).
Influence of Cool Storage before Freezing on the Quality of Frozen–Thawed Semen Samples in Dogs
Authors: Santana M , Batista M , Alamo D , González F , Niño T , Cabrera F , Gracia A
Published: June 2012

Contents

The aim of this study was to determinate the semen quality of frozen–thawed samples that were chilled for up to 2 days before freezing. The ejaculates (n = 18) from six dogs were collected, pooled and divided into six aliquots. The first aliquot (C, control) was frozen in liquid nitrogen using a conventional protocol to reach a final concentration of 100 × 106 spermatozoa/ml, 20% egg yolk and 5% glycerol. The remaining five aliquots were diluted with a chilled extender (Tris‐glucose and 20% egg yolk) and cooled at 4°C as follows: R1, the semen was cooled for 1 h; R6, the semen was cooled for 6 h; R12, the semen was cooled for 12 h; R24, the semen was cooled for 24 h and R48, the semen was cooled for 48 h. After the chilling period, a second extender was added (Tris‐glucose, 20% egg yolk, 10% glycerol and Equex at 1%) to reach a final composition similar to aliquot C, and then, the semen samples (R1, R6, R12, R24 and R48) were frozen in liquid nitrogen. The post‐thaw sperm quality was assessed in 30 straws from each experimental group. After freezing–thawing, the total sperm motility (approximately 60–70%) in the semen chilled for up to 48 h did not show any differences from the samples frozen by the conventional cryopreservation method (63.2%). No significant differences were detected in the percentages of abnormal sperm cells among the fresh semen, the control group and the frozen samples after the different cooling times. Finally, the post‐thaw percentages of damaged acrosomes showed a very uniform distribution, with mean values ranging between 7% and 10.5%. The results clearly demonstrated that cooling the semen up to 48 h before freezing did not produce a decrease in the semen quality when was compared with semen frozen by a traditional procedure.