bluuebunny/crossref_metadata_2025 huggingface dataset:
Correction factors for saturation effects in white light and laser absorption spectroscopy for application to low pressure plasmas
Authors: Briefi S. , Wimmer C. , Fantz U.
Published: May 2012

In white light absorption spectroscopy, the broadening of the absorption signal due to the apparatus profile of the spectrometer may lead to an underestimation of the determined density as one measures an apparent optical depth. This is in particular true for high optical depth where saturation effects of the transmitted intensity occur. Provided that the line profile of the absorption line is known, the apparent optical depth effect can be accounted for by introducing a correction factor. The impact of the saturation and the approach of considering the effect are demonstrated for argon and indium lines in low pressure plasmas where correction factors of one order of magnitude or even higher are reached very easily. For the indium line, the hyperfine splitting has been taken into account. In laser absorption, the line profile is resolved. However, the weak but rather broad background emission of the laser diode can cause a saturation signal at the photo diode resulting also in an underestimation of the density obtained from the analysis. It is shown that this can be taken into account by fitting the theoretical line profile to the measured absorption signal which yields also a correction factor. The method is introduced and demonstrated at the example of the cesium resonance line including the hyperfine splitting. Typical correction factors around two are obtained for the cesium ground state density at conditions of a low pressure negative hydrogen ion source in which cesium is evaporated to enhance the negative ion production.
Electrical transport and optical model of GaAs-AlInP core-shell nanowires
Authors: Chia A. C. E. , Tirado M. , Li Y. , Zhao S. , Mi Z. , Comedi D. , LaPierre R. R.
Published: May 2012

GaAs nanowires were passivated by AlInP shells grown by the Au-assisted vapor-liquid-solid method in a gas source molecular beam epitaxy system. Transmission electron microscopy confirmed a core-shell GaAs-AlInP structure. Current-voltage measurements on ensemble nanowires indicated improved carrier transport properties in the passivated nanowires as compared to their unpassivated counterpart. Similarly, individual nanowires showed improved photoluminescence intensity upon passivation. A detailed model is presented to quantify the observed improvements in nanowire conduction and luminescence in terms of a reduction in surface charge trap density and surface recombination velocity upon passivation. The model includes the effects of high-level injection, bulk recombination, and surface recombination. The model can be used as a tool for assessing various passivation methods.
Effect of the multiple reflections of a light beam on the thermal wave field of a sample of finite thickness
Authors: Zambrano-Arjona M. A. , Ordonez-Miranda J. , Medina-Esquivel R. A. , Peñuñuri F. , Martinez P. , Alvarado-Gil J. J.
Published: May 2012

The thermal wave field in a sample of thickness L and optical absorption coefficient β is derived and analyzed, by considering the effects of the multiple reflections of a modulated light beam within the sample. By comparing the corresponding amplitude and phase spectra, in presence and absence of those reflections, it is shown that their effects are strongly determined by the product βL. When the thermal wave field is measured at the illuminated surface, those effects appear remarkably on the amplitude and phase in the thermally thin and thermally thick regimes, respectively, and for βL≲2. The deviation of the amplitude spectrum due to the multiple reflections of incident light beam can be as large as 25%. In contrast, when the thermal wave field is measured at the non-illuminated surface, the contribution of the multiple reflections shows up on both the amplitude and phase in the thermally thick regimes, and for βL≲5. These spectra exhibit deviations of about 20% from their corresponding values without the effects of the light reflections. The obtained results show that the accurate measurement of the thermal and/or optical properties of the sample material, based on the amplitude and phase spectra, requires the consideration of those multiple reflections, especially for the cases where βL≈1. The predictions of the proposed approach for the optical absorption coefficient are in reasonable agreement with the results obtained through an independent technique based on a spectrometer.
Reversibility in the inverse magnetocaloric effect in Mn3GaC studied by direct adiabatic temperature-change measurements
Authors: Çakιr Ö. , Acet M.
Published: May 2012

Thermal-hysteresis affects adversely the reversibility of the magnetocaloric effect around a first order magnetostructural transition. In Mn3GaC, a first order antiferromagnetic-ferromagnetic transition is accompanied by a volume-change and a 5 K thermal-hysteresis. We study the reversibility of the magnetocaloric effect in the transition region by direct adiabatic temperature-change measurements. The magnetic field is cycled between 0 and 3 T, and the temperature-change is observed. We find that the system exhibits a temperature-change of 3.1 K in the virgin state, and all subsequent cycling leads to a 2.8 K warming and cooling when the field is decreased and increased, respectively.
Anomalies of magnetic properties and magnetovolume effect in Cd1−xMnxGeAs2 at hydrostatic pressure
Authors: Mollaev A. Yu. , Kamilov I. K. , Arslanov R. K. , Arslanov T. R. , Zalibekov U. Z. , Novotortsev V. M. , Marenkin S. F. , Trukhan V. M.
Published: May 2012

We present the experimental results of the effect hydrostatic pressure up to P ≤ 7 GPa applied at the room temperatures in diluted magnetic semiconductor Cd1−xMnxGeAs2 (x = 0.06 − 0.3). We have found the pressure areas at which anomalies in magnetic properties were observed. Induced by hydrostatic pressure at P > 1.5 GPa magnetic phase transitions, interpreted as metamagnetic transition, were observed. The transitions from magnetic-ordered into magnetic disordered phases in region P > 4.1 GPa on the pressure dependences of relative volume compressibility were detected. We estimated the values of bulk modulus and volume magnetostriction. It is shown that high pressures significantly decrease the Curie temperature with values dTC/dP ≈ (−14.0 ÷ −6.8) K/GPa.
Cooperative interactions of BRAF
V600E
kinase and
CDKN2A
locus deficiency in pediatric malignant astrocytoma as a basis for rational therapy
Authors: Huillard Emmanuelle , Hashizume Rintaro , Phillips Joanna J. , Griveau Amélie , Ihrie Rebecca A. , Aoki Yasuyuki , Nicolaides Theodore , Perry Arie , Waldman Todd , McMahon Martin , Weiss William A. , Petritsch Claudia , James C. David , Rowitch David H.
Published: May 2012

Although malignant astrocytomas are a leading cause of cancer-related death in children, rational therapeutic strategies are lacking. We previously identified activating mutations of v-raf murine sarcoma viral oncogene homolog B1 (
BRAF
) (
BRAF

T1799A

encoding BRAF
V600E
) in association with homozygous cyclin-dependent kinase inhibitor 2A (
CDKN2A
, encoding
p14ARF
and
p16Ink4a
) deletions in pediatric infiltrative astrocytomas. Here we report that BRAF
V600E
expression in neural progenitors (NPs) is insufficient for tumorigenesis and increases NP cellular differentiation as well as apoptosis. In contrast, astrocytomas are readily generated from NPs with additional
Ink4a-Arf
deletion. The BRAF
V600E
inhibitor PLX4720 significantly increased survival of mice after intracranial transplant of genetically relevant murine or human astrocytoma cells. Moreover, combination therapy using PLX4720 plus the Cyclin-dependent kinase (CDK) 4/6-specific inhibitor PD0332991 further extended survival relative to either monotherapy. Our findings indicate a rational therapeutic strategy for treating a subset of pediatric astrocytomas with
BRAF

V600E

mutation and
CDKN2A
deficiency.
Sulfur isotope variability of oceanic DMSP generation and its contributions to marine biogenic sulfur emissions
Authors: Oduro Harry , Van Alstyne Kathryn L. , Farquhar James
Published: May 2012

Oceanic dimethylsulfoniopropionate (DMSP) is the precursor to dimethylsulfide (DMS), which plays a role in climate regulation through transformation to methanesulfonic acid (MSA) and non-seasalt sulfate (NSS-SO
4
2−
) aerosols. Here, we report measurements of the abundance and sulfur isotope compositions of DMSP from one phytoplankton species (
Prorocentrum minimum
) and five intertidal macroalgal species (
Ulva lactuca
,
Ulva linza, Ulvaria obscura, Ulva prolifera
, and
Polysiphonia hendryi
) in marine waters. We show that the sulfur isotope compositions (δ
34
S) of DMSP are depleted in
34
S relative to the source seawater sulfate by ∼1–3‰ and are correlated with the observed intracellular content of methionine, suggesting a link to metabolic pathways of methionine production. We suggest that this variability of δ
34
S is transferred to atmospheric geochemical products of DMSP degradation (DMS, MSA, and NSS-SO
4
2−
), carrying implications for the interpretation of variability in δ
34
S of MSA and NSS-SO
4
2−
that links them to changes in growth conditions and populations of DMSP producers rather than to the contributions of DMS and non-DMS sources.
Efficient genetic modification and germ-line transmission of primordial germ cells using piggyBac and Tol2 transposons
Authors: Macdonald Joni , Taylor Lorna , Sherman Adrian , Kawakami Koichi , Takahashi Yoshiko , Sang Helen M. , McGrew Michael J.
Published: May 2012

The derivation of germ-line competent avian primordial germ cells establishes a cell-based model system for the investigation of germ cell differentiation and the production of genetically modified animals. Current methods to modify primordial germ cells using DNA or retroviral vectors are inefficient and prone to epigenetic silencing. Here, we validate the use of transposable elements for the genetic manipulation of primordial germ cells. We demonstrate that chicken primordial germ cells can be modified in vitro using transposable elements. Both piggyBac and Tol2 transposons efficiently transpose primordial germ cells. Tol2 transposon integration sites were spread throughout both the macro- and microchromosomes of the chicken genome and were more prevalent in gene transcriptional units and intronic regions, consistent with transposon integrations observed in other species. We determined that the presence of insulator elements was not required for reporter gene expression from the integrated transposon. We further demonstrate that a gene-trap cassette carried in the Tol2 transposon can trap and mutate endogenous transcripts in primordial germ cells. Finally, we observed that modified primordial germ cells form functional gametes as demonstrated by the generation of transgenic offspring that correctly expressed a reporter gene carried in the transposon. Transposable elements are therefore efficient vectors for the genetic manipulation of primordial germ cells and the chicken genome.
Fe
2+
binds iron responsive element-RNA, selectively changing protein-binding affinities and regulating mRNA repression and activation
Authors: Ma Jia , Haldar Suranjana , Khan Mateen A. , Sharma Sohani Das , Merrick William C. , Theil Elizabeth C. , Goss Dixie J.
Published: May 2012

Iron increases synthesis rates of proteins encoded in iron-responsive element (IRE)-mRNAs; metabolic iron (“free,” “labile”) is Fe
2+
. The noncoding IRE-RNA structure, approximately 30 nt, folds into a stem loop to control synthesis of proteins in iron trafficking, cell cycling, and nervous system function. IRE-RNA riboregulators bind specifically to iron-regulatory proteins (IRP) proteins, inhibiting ribosome binding. Deletion of the IRE-RNA from an mRNA decreases both IRP binding and IRP-independent protein synthesis, indicating effects of other “factors.” Current models of IRE-mRNA regulation, emphasizing iron-dependent degradation/modification of IRP, lack answers about how iron increases IRE-RNA/IRP protein dissociation or how IRE-RNA, after IRP dissociation, influences protein synthesis rates. However, we observed Fe
2+
(anaerobic) or Mn
2+
selectively increase the IRE-RNA/IRP
K
D
. Here we show: (
i
) Fe
2+
binds to the IRE-RNA, altering its conformation (by 2-aminopurine fluorescence and ethidium bromide displacement); (
ii
) metal ions increase translation of IRE-mRNA in vitro; (
iii
) eukaryotic initiation factor (eIF)4F binds specifically with high affinity to IRE-RNA; (
iv
) Fe
2+
increased eIF4F/IRE-RNA binding, which outcompetes IRP binding; (
v
) exogenous eIF4F rescued metal-dependent IRE-RNA translation in eIF4F-depeleted extracts. The regulation by metabolic iron binding to IRE-RNA to decrease inhibitor protein (IRP) binding and increase activator protein (eIF4F) binding identifies IRE-RNA as a riboregulator.
Tuning the threshold voltage in electrolyte-gated organic field-effect transistors
Authors: Kergoat Loïg , Herlogsson Lars , Piro Benoit , Pham Minh Chau , Horowitz Gilles , Crispin Xavier , Berggren Magnus
Published: May 2012

Low-voltage organic field-effect transistors (OFETs) promise for low power consumption logic circuits. To enhance the efficiency of the logic circuits, the control of the threshold voltage of the transistors are based on is crucial. We report the systematic control of the threshold voltage of electrolyte-gated OFETs by using various gate metals. The influence of the work function of the metal is investigated in metal-electrolyte-organic semiconductor diodes and electrolyte-gated OFETs. A good correlation is found between the flat-band potential and the threshold voltage. The possibility to tune the threshold voltage over half the potential range applied and to obtain depletion-like (positive threshold voltage) and enhancement (negative threshold voltage) transistors is of great interest when integrating these transistors in logic circuits. The combination of a depletion-like and enhancement transistor leads to a clear improvement of the noise margins in depleted-load unipolar inverters.
Structure, function and inhibition of the two- and three-domain 4Fe-4S IspG proteins
Authors: Liu Yi-Liang , Guerra Francisco , Wang Ke , Wang Weixue , Li Jikun , Huang Cancan , Zhu Wei , Houlihan Kevin , Li Zhi , Zhang Yong , Nair Satish K. , Oldfield Eric
Published: May 2012

IspG is a 4Fe4S protein involved in isoprenoid biosynthesis. Most bacterial IspGs contain two domains: a TIM barrel (A) and a 4Fe4S domain (B), but in plants and malaria parasites, there is a large insert domain (A*) whose structure and function are unknown. We show that bacterial IspGs function in solution as (AB)
2
dimers and that mutations in either both A or both B domains block activity. Chimeras harboring an A-mutation in one chain and a B-mutation in the other have 50% of the activity seen in wild-type protein, because there is still one catalytically active AB domain. However, a plant IspG functions as an AA*B monomer. We propose, using computational modeling and electron microscopy, that the A* insert domain has a TIM barrel structure that interacts with the A domain. This structural arrangement enables the A and B domains to interact in a “cup and ball” manner during catalysis, just as in the bacterial systems. EPR/HYSCORE spectra of reaction intermediate, product, and inhibitor ligands bound to both two and three domain proteins are identical, indicating the same local electronic structure, and computational docking indicates these ligands bridge both A and B domains. Overall, the results are of broad general interest because they indicate the insert domain in three-domain IspGs is a second TIM barrel that plays a structural role and that the pattern of inhibition of both two and three domain proteins are the same, results that can be expected to be of use in drug design.
Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS
Authors: Nomura Takeshi , Cranfield Charles G. , Deplazes Evelyne , Owen Dylan M. , Macmillan Alex , Battle Andrew R. , Constantine Maryrose , Sokabe Masahiro , Martinac Boris
Published: May 2012

Mechanosensitive (MS) channels of small (MscS) and large (MscL) conductance are the major players in the protection of bacterial cells against hypoosmotic shock. Although a great deal is known about structure and function of these channels, much less is known about how membrane lipids may influence their mechanosensitivity and function. In this study, we use liposome coreconstitution to examine the effects of different types of lipids on MscS and MscL mechanosensitivity simultaneously using the patch-clamp technique and confocal microscopy. Fluorescence lifetime imaging (FLIM)-FRET microscopy demonstrated that coreconstitution of MscS and MscL led to clustering of these channels causing a significant increase in the MscS activation threshold. Furthermore, the MscL/MscS threshold ratio dramatically decreased in thinner compared with thicker bilayers and upon addition of cholesterol, known to affect the bilayer thickness, stiffness and pressure profile. In contrast, application of micromolar concentrations of lysophosphatidylcholine (LPC) led to an increase of the MscL/MscS threshold ratio. These data suggest that differences in hydrophobic mismatch and bilayer stiffness, change in transbilayer pressure profile, and close proximity of MscL and MscS affect the structural dynamics of both channels to a different extent. Our findings may have far-reaching implications for other types of ion channels and membrane proteins that, like MscL and MscS, may coexist in multiple molecular complexes and, consequently, have their activation characteristics significantly affected by changes in the lipid environment and their proximity to each other.
Ultrafast photodriven intramolecular electron transfer from an iridium-based water-oxidation catalyst to perylene diimide derivatives
Authors: Vagnini Michael T. , Smeigh Amanda L. , Blakemore James D. , Eaton Samuel W. , Schley Nathan D. , D’Souza Francis , Crabtree Robert H. , Brudvig Gary W. , Co Dick T. , Wasielewski Michael R.
Published: May 2012

Photodriving the activity of water-oxidation catalysts is a critical step toward generating fuel from sunlight. The design of a system with optimal energetics and kinetics requires a mechanistic understanding of the single-electron transfer events in catalyst activation. To this end, we report here the synthesis and photophysical characterization of two covalently bound chromophore-catalyst electron transfer dyads, in which the dyes are derivatives of the strong photooxidant perylene-3,4:9,10-bis(dicarboximide) (PDI) and the molecular catalyst is the Cp
∗
Ir(ppy)Cl metal complex, where ppy = 2-phenylpyridine. Photoexcitation of the PDI in each dyad results in reduction of the chromophore to PDI
•-
in less than 10 ps, a process that outcompetes any generation of
3∗
PDI by spin-orbit-induced intersystem crossing. Biexponential charge recombination largely to the PDI-Ir(III) ground state is suggestive of multiple populations of the PDI
•-
-Ir(IV) ion-pair, whose relative abundance varies with solvent polarity. Electrochemical studies of the dyads show strong irreversible oxidation current similar to that seen for model catalysts, indicating that the catalytic integrity of the metal complex is maintained upon attachment to the high molecular weight photosensitizer.
αE-catenin is an autoinhibited molecule that coactivates vinculin
Authors: Choi Hee-Jung , Pokutta Sabine , Cadwell Gregory W. , Bobkov Andrey A. , Bankston Laurie A. , Liddington Robert C. , Weis William I.
Published: May 2012

αE-catenin, an essential component of the adherens junction, interacts with the classical cadherin–β-catenin complex and with F-actin, but its precise role is unknown. αE-catenin also binds to the F-actin-binding protein vinculin, which also appears to be important in junction assembly. Vinculin and αE-catenin are homologs that contain a series of helical bundle domains, D1–D5. We mapped the vinculin-binding site to a sequence in D3a comprising the central two helices of a four-helix bundle. The crystal structure of this peptide motif bound to vinculin D1 shows that the two helices adopt a parallel, colinear arrangement suggesting that the αE-catenin D3a bundle must unfold in order to bind vinculin. We show that αE-catenin D3 binds strongly to vinculin, whereas larger fragments and full-length αE-catenin bind approximately 1,000-fold more weakly. Thus, intramolecular interactions within αE-catenin inhibit binding to vinculin. The actin-binding activity of vinculin is inhibited by an intramolecular interaction between the head (D1–D4) and the actin-binding D5 tail. In the absence of F-actin, there is no detectable binding of αE-catenin D3 to full-length vinculin; however, αE-catenin D3 promotes binding of vinculin to F-actin whereas full-length αE-catenin does not. These findings support the combinatorial or “coincidence” model of activation in which binding of high-affinity proteins to the vinculin head and tail is required to shift the conformational equilibrium of vinculin from a closed, autoinhibited state to an open, stable F-actin-binding state. The data also imply that αE-catenin must be activated in order to bind to vinculin.
Hijacking a hydroxyethyl unit from a central metabolic ketose into a nonribosomal peptide assembly line
Authors: Peng Chao , Pu Jin-Yue , Song Li-Qiang , Jian Xiao-Hong , Tang Man-Cheng , Tang Gong-Li
Published: May 2012

Nonribosomal peptide synthetases (NRPSs) usually catalyze the biosynthesis of peptide natural products by sequential selection, activation, and condensation of amino acid precursors. It was reported that some fatty acids, α-ketoacids, and α-hydroxyacids originating from amino acid metabolism as well as polyketide-derived units can also be used by NRPS assembly lines as an alternative to amino acids. Ecteinascidin 743 (ET-743), naphthyridinomycin (NDM), and quinocarcin (QNC) are three important antitumor natural products belonging to the tetrahydroisoquinoline family. Although ET-743 has been approved as an anticancer drug, the origin of an identical two-carbon (C
2
) fragment among these three antibiotics has not been elucidated despite much effort in the biosynthetic research in the past 30 y. Here we report that two unexpected two-component transketolases (TKases), NapB/NapD in the NDM biosynthetic pathway and QncN/QncL in QNC biosynthesis, catalyze the transfer of a glycolaldehyde unit from ketose to the lipoyl group to yield the glycolicacyl lipoic acid intermediate and then transfer the C
2
unit to an acyl carrier protein (ACP) to form glycolicacyl-
S
-ACP as an extender unit for NRPS. Our results demonstrate a unique NRPS extender unit directly derived from ketose phosphates through (α,β-dihydroxyethyl)-thiamin diphosphate and a lipoyl group-tethered ester intermediate catalyzed by the TKase-ACP platform in the context of NDM and QNC biosynthesis, all of which also highlights the biosynthesis of ET-743. This hybrid system and precursor are distinct from the previously described universal modes involving the NRPS machinery. They exemplify an alternate strategy in hybrid NRPS biochemistry and enrich the diversity of precursors for NRPS combinatorial biosynthesis.
Impact of naval sonar signals on Atlantic herring (Clupea harengus) during summer feeding
Authors: Sivle Lise Doksæter , Kvadsheim Petter Helgevold , Ainslie Michael A. , Solow Andrew , Handegard Nils Olav , Nordlund Nina , Lam Frans-Peter A.
Published: May 2012

Sivle, L. D., Kvadsheim, P. H., Ainslie, M. A., Solow, A., Handegard, N. O. Nordlund, N., and Lam, F-P. A. 2012. Impact of naval sonar signals on Atlantic herring (Clupea harengus) during summer feeding. – ICES Journal of Marine Science, 69: 1078–1085. Naval anti-submarine sonars produce intense sounds within the hearing range of Atlantic herring (Clupea harengus). In this study, schools of Atlantic herring were exposed to sonar signals of 1–2 kHz (low-frequency active sonar, LFAS) and 6–7 kHz (mid-frequency active sonar, MFAS) and playbacks of killer whale feeding sounds during their summer feeding migration in the Norwegian Sea. The fish schools neither significantly dived nor changed their packing density in response to the LFAS and MFAS transmissions received by the fish at estimated sound pressure levels (SPLs; RMS) up to 176 and 157 dB re 1 μPa and estimated cumulative sound exposure levels up to 181 and 162 dB re 1 μPa² s, respectively. In contrast, killer whale feeding sounds induced diving responses at received SPLs at ∼150 dB re 1 μPa. Herring behaviour was studied by using a 116-kHz hull mounted fishery sonar. This seems a promising method for studying the behaviour of free-ranging fish in situations in which other methods are difficult to use, such as migrating schools and fish close to the surface.
Polarization-analyzed small-angle neutron scattering. I. Polarized data reduction usingPol-Corr
Authors: Krycka Kathryn , Chen Wangchun , Borchers Julie , Maranville Brian , Watson Shannon
Published: May 2012

Pol-Corris a free computer program that corrects for the neutron polarization inefficiencies that are characteristic of polarization-analyzed small-angle neutron scattering experiments, namely those inefficiencies associated with a static neutron polarizer, a neutron spin flipper, beam depolarization and a time-varying neutron spin analyzer. The software is designed to interface directly with small-angle neutron scattering data acquired at the NIST Center for Neutron Research, but the algorithms are generally applicable and can be readily adapted for other data formats. The explicit neutron measurements required to characterize each polarizing element are derived, and these become the input parameters forPol-Corr.
TheP–V–Tequation of state of D2O ice VI determined by neutron powder diffraction in the range 0 <P< 2.6 GPa and 120 <T< 330 K, and the isothermal equation of state of D2O ice VII from 2 to 7 GPa at room temperature
Authors: Fortes A. D. , Wood I. G. , Tucker M. G. , Marshall W. G.
Published: May 2012

Neutron powder diffraction data have been collected from deuterated ice VI (space groupP42/nmc,Z= 10) at 76 state points in its field of thermodynamic stability above 150 K (approximately 0.6 <P< 2.1 GPa) and in a region of metastable persistence below 150 K (0 <P< 2.6 GPa). The refined unit-cell parameters and unit-cell volume have been fitted with six-parameter functions based upon a Murnaghan equation of state (EoS), with simple polynomial expressions to describe the temperature dependence of the volume (or axis length) and the bulk modulus (or axial incompressibility). ThisP–V–TEoS is compared with earlier empirically derived and computationally obtained equations of state, and with the elastic properties determined by ultrasonic or Brillouin scattering methods. It is found that D2O ice VI is ∼5% stiffer (i.e.it has a larger bulk modulus,K, at a givenPandT) than H2O ice VI, in agreement with unpublishedcij/ρ data for D2O ice VI provided by the Shimizu Laboratory, Gifu University, Japan (S. Sasaki, personal communication). This difference is due entirely to a greater incompressibility parallel to theaaxis than for the protonated isotopologue; the incompressibilities of thecaxis for both H2O and D2O ice VI are very similar. TheP–V–TEoS is used to estimate the volume change and enthalpy of melting. Additional data on the isothermal compression of ices II and V at 240 K (0.2–0.4 and 0.4–0.7 GPa, respectively), and of ice VII at 295–300 K (2–7 GPa), are also reported and compared with earlier literature data.
A Bayesian approach for denoising one-dimensional data
Authors: Hogg III Charles R. , Mullen Katharine , Levin Igor
Published: May 2012

A Bayesian technique to correct for Poisson noise in one-dimensional data, such as X-ray/neutron scattering curves, is presented. This `denoising' method calculates a probability for any given curve to be the true underlying signal and generates the curves having the highest probabilities. Gaussian processes with a nonstationary squared-exponential covariance function are used to obtain smooth curves without needing to assume a particular functional form. Two benchmark denoising methods, adaptive weights smoothing and wavelet shrinkage, formed a basis for comparison. All three methods were tested on different types of X-ray scattering data. Besides producing quantitative uncertainty estimates, which the benchmarks lacked, the Bayesian technique met or exceeded their fidelity to the true signal, as measured by mean-square residuals. A free software implementation of the methods described in this paper has been developed.
EDMA: a computer program for topological analysis of discrete electron densities
Authors: Palatinus Lukáš , Prathapa Siriyara Jagannatha , van Smaalen Sander
Published: May 2012

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.
Pair distribution function analysis of molecular compounds: significance and modeling approach discussed using the example ofp-terphenyl
Authors: Rademacher Nadine , Daemen Luke L. , Chronister Eric L. , Proffen Thomas
Published: May 2012

Modeling the pair distribution function (PDF) of molecular compounds is a challenging task because intra- and intermolecular interactions lead to very different features in the PDF. This article discusses the different peak shapes in PDFs of molecular compounds in detail. Moreover, the common methods to calculate PDFs from structural models are summarized and evaluated with respect to molecular systems and an approach to calculate PDFs from molecular crystals more accurately is introduced.p-Terphenyl was chosen as a test compound. It adopts a crystal structure with disordered features and short-range order. The short-range order was previously investigated by analyzing single-crystal diffuse scattering and it was also extracted from experimental PDFs during this study.
PROSPERO: online prediction of crystallographic success from experimental results and sequence
Authors: Zucker Frank H. , Kim Hae Young , Merritt Ethan A.
Published: May 2012

The growth of diffracting crystals from purified proteins is often a major bottleneck in determining structures of biological and medical interest. ThePROSPEROweb server, http://skuld.bmsc.washington.edu/prospero, is intended both to provide a means of organizing the potentially large numbers of experimental characterizations measured from such proteins, and to provide useful guidance for structural biologists who have succeeded in purifying their target protein but have reached an impasse in the difficult and poorly understood process of turning purified protein into well diffracting crystals. These researchers need to decide which of many possible rescue options are worth pursuing, given finite resources. This choice is even more crucial when attempting to solve high-priority but relatively difficult structures of eukaryotic proteins. The site currently uses theHyGX1predictor, which was trained and validated on protein samples from pathogenic protozoa (eukaryotes) using results from six types of experiment.PROSPEROallows users to store, analyze and display multiple results for each sample, to group samples into projects, and to share results and predictions with collaborators.
Li3Al(MoO4)3, a lyonsite molybdate
Authors: Bugaris Daniel E. , Loye Hans-Conrad zur
Published: May 2012

Trilithium aluminium trimolybdate(VI), Li3Al(MoO4)3, has been grown as single crystals from α-Al2O3and MoO3in an Li2MoO4flux at 998 K. This compound is an example of the well known lyonsite structure type, the general formula of which can be written asA16B12O48. Because this structure can accomodate cationic mixing as well as cationic vacancies, a wide range of chemical compositions can adopt this structure type. This has led to instances in the literature where membership in the lyonsite family has been overlooked when assigning the structure type to novel compounds. In the title compound, there are two octahedral sites with substitutional disorder between Li+and Al3+, as well as a trigonal prismatic site fully occupied by Li+. The (Li,Al)O6octahedra and LiO6trigonal prisms are linked to form hexagonal tunnels along the [100] axis. These polyhedra are connected by isolated MoO4tetrahedra. Infinite chains of face-sharing (Li,Al)O6octahedra extend through the centers of the tunnels. A mixed Li/Al site, an Li, an Mo, and two O atoms are located on mirror planes.
2-[({2-[(2-Hydroxy-5-methoxybenzylidene)amino]ethyl}imino)methyl]-4-methoxyphenol
Authors: Ourari Ali , Baameur Lotfi , Bouacida Sofiane , Ouari Kamel
Published: May 2012

The asymmetric unit of the title compound, C18H20N2O4, contains one-half molecule with an inversion center located at the centroid of the molecule. In the crystal, molecules are linked by C—H...π interactions, forming layers parallel to (101). An intramolecular O—H...N hydrogen bond also occurs.
4-[(1RS,5RS,7SR)-5-Methyl-2,4-dioxo-3,6-diazabicyclo[3.2.1]octan-7-yl]benzonitrile
Authors: Kudryavtsev Konstantin V. , Churakov Andrei V.
Published: May 2012

In the title compound, C14H13N3O2, the relative stereochemistry of the three stereogenic C atoms has been determined. In the crystal, N—H...O hydrogen bonds link the molecules into chains of inversion dimers running along the b axis.
Bis(acetato-κ2
O,O′)(4,4′-dimethyl-2,2′-bipyridine-κ2
N,N′)copper(II) monohydrate
Authors: Kaewthong Aphiwat , Sukwattanasinitt Mongkol , Muangsin Nongnuj
Published: May 2012

In the title compound, [Cu(C2H3O2)2(C12H12N2)2]·H2O, the CuII atom exhibits a distorted octahedral coordination geometry, defined by two N atoms from one 4,4′-dimethyl-2,2′-bipyridine ligand and four O atoms from two acetate ligands. In the crystal, O—H...O hydrogen bonds are observed between the coordinated carboxylate O atoms and the solvent water molecule.
2,5,7-Trimethyl-3-(4-methylphenylsulfonyl)-1-benzofuran
Authors: Choi Hong Dae , Seo Pil Ja , Lee Uk
Published: May 2012

In the title compound, C18H18O3S, the 4-methylphenyl ring makes a dihedral angle of 86.35 (3)° with the mean plane [mean deviation = 0.006 (1) Å] of the benzofuran fragment. In the crystal, molecules are linked by weak C—H...O and C—H...π interactions. The crystal structure also exhibits weak π–π interactions between the furan and benzene rings of neighbouring benzofuran systems [centroid–centroid distance = 3.685 (2), interplanar distance = 3.572 (2) and slippage = 0.906 (2) Å].
N-(4-Fluorophenyl)-2,2-dimethylpropanamide
Authors: Fang Zheng , Zhang Feng , Zou Bao-hua , Guo Kai
Published: May 2012

The crystal packing in the title compound, C11H14FNO, features N—H...O hydrogen bonds, resulting in chains of molecules running parallel to the c axis. The dihedral angle between the ring and the amide group is 39.1 (3)°.
4-Chloro-2-[(2,6-diisopropylphenyl)iminomethyl]phenol
Authors: Balamurugan P. , Kanmani Raja K. , Easwaramoorthy D. , Chakkaravarthi G. , Rajagopal G.
Published: May 2012

The asymmetric unit of the title compound, C19H22ClNO, contains two independent molecules in which the dihedral angles between the aromatic rings are 76.45 (9) and 74.69 (9)°. An intramolecular O—H...N hydrogen bond occurs in each molecule. The crystal structure features weak C—H...π interactions.
1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1-yl)ethanol
Authors: Kesternich Victor , Nelson-González Ronald , Pérez-Fehrmann Marcia , Cárdenas Alejandro , Brito Iván
Published: May 2012

In the title compound, C10H9F2N3O, the dihedral angle between the mean planes of the triazole and benzene rings is 20.6 (2)°. In the crystal, molecules are linked by strong O—H... N hydrogen bonds into chains with graph-set notation C(9) along [100]. Weak C—H...N and C—H...F interactions are also observed.
(S)-Alanine–(S)-2-phenoxypropionic acid (1/1)
Authors: Amimoto Kiichi , Nishioka Yuma
Published: May 2012

In the title co-crystal, C3H7NO2·C9H10O3, the (S)-alanine molecule exists in the zwitterionic form stabilized by two pairs of N+—H...O− hydrogen bonds and an electrostatic interaction between the ammonium center and the carboxylate anion, forming a sheet along the ab plane. The carboxyl group of the (S)-2-phenoxypropionic acid molecule is connected to the top and bottom of the sheet via N+—H...O=C and O—H...O− [R
2
2(7) graph set] hydrogen bonds, giving an (S,S)-homochiral layer, in which both methyl groups of (S)-alanine and the phenyl rings of (S)-2-phenoxypropionic acid are oriented in the same direction along the b axis.
2-Aminocyclohexan-1-aminium thiocyanate
Authors: Salem Halima F. , Hasbullah Siti Aishah , Yamin Bohari M.
Published: May 2012

The title compound, C6H15N2
+·NCS−, was obtained unexpectedly from the reaction mixture of benzoyl chloride, ammonium thiocyanate and cyclohexane-1,2-diamine. The cyclohexane ring adopts a chair conformation. In the crystal, N—H...S and N—H...N interactions involving the thiocyanate anion and both the amine and the aminium N atoms link the molecules, forming two-dimensional networks parallel to (001).
9-(2-Bromophenoxycarbonyl)-10-methylacridinium trifluoromethanesulfonate
Authors: Trzybiński Damian , Sieradzan Andrzej , Krzymiński Karol , Błażejowski Jerzy
Published: May 2012

In the crystal structure of the title compound, C21H15BrNO2
+·CF3SO3
−, adjacent cations are linked through C—Br...π and π–π contacts [centroid–centroid distance = 3.744 (2) Å], and neighbouring cations and anions via C—H...O, C—F...π and S—O...π interactions. The acridine and benzene ring systems are oriented at a dihedral angle of 18.7 (1)°. The carboxy group is twisted at an angle of 69.3 (1)° relative to the acridine skeleton. The mean planes of adjacent acridine moieties are either parallel or inclined at an angle of 27.8 (1)° in the lattice.
Ethyl 2-[4-(4-chlorobenzoyl)phenoxy]-2-methylpropanoate
Authors: Yang Zhao , Wang Zhi-Xiang
Published: May 2012

In the title compound, C19H19ClO4, the dihedral angle between the mean planes of the benzene rings is 126.8 (1)°. Weak C—H...O interactions are observed.
3-Benzyl-7-(2,4-dichlorophenyl)-4H-1,3,4-thiadiazolo[2,3-c][1,2,4]triazin-4-one
Authors: Fun Hoong-Kun , Arshad Suhana , Sarojini B. K. , Imran U. A. , Krishna B.G.
Published: May 2012

In the title compound, C17H10Cl2N4OS, the phenyl ring and the H atoms attached to the adjacent C atom are disordered over two positions, with refined site occupancies of 0.509 (8) and 0.491 (8). The planar 4H-1,3,4-thiadiazolo[2,3-c][1,2,4]triazine ring system [maximum deviation = 0.048 (3) Å] forms dihedral angles of 76.9 (5), 74.9 (5) and 9.88 (12)°, respectively, with the major and minor parts of the disordered phenyl ring and with the dichloro-substituted benzene ring. In the crystal, pairs of C—H...O hydrogen bonds link the molecules, forming inversion dimers with an R
2
2(18) graph-set motif. A short S...N contact of 2.801 (3) Å is observed between the dimers.
Bis[hexaamminecobalt(III)] pentachloride nitrate
Authors: Wu Qihui , Du Chunyu , Lv Yang , Chen Guoliang , Pan Qinhe
Published: May 2012

The title compound, [Co(NH3)6]2Cl5(NO3), was obtained under hydrothermal conditions. The asymmetric unit contains three Co3+ ions, one lying on an inversion center and the other two located at 2/m positions. All Co3+ ions are six-coordinated by NH3 molecules, forming [Co(NH3)6]3+ octahedra, with Co—N distances in the range 1.945 (4)–1.967 (3) Å. The nitrate N atom and one of the O atoms lie at a mirror plane. Among the Cl− anions, one lies in a general position, one on a twofold axis and two on a mirror plane. N—H...O and N—H...Cl hydrogen bonds link the cations and anions into a three-dimensional network.
(E)-1-[4-(3-Bromopropoxy)phenyl]-2-p-tolyldiazene
Authors: Yu Zhen-Xiang , Li Bao
Published: May 2012

In the title molecule, C16H17BrN2O, the benzene rings, bridged by a diazene fragment, form a dihedral angle of 6.3 (2)°. The crystal packing exhibits relatively short Br...Br contacts of 3.6989 (14) Å.
A novel role for the non‐catalytic intracellular domain of Neprilysins in muscle physiology
Authors: Panz Mareike , Vitos‐Faleato Jessica , Jendretzki Arne , Heinisch Jürgen J. , Paululat Achim , Meyer Heiko
Published: May 2012

Background information

Neprilysins (Neps) are membrane‐bound M13 endopeptidases responsible for the activation and/or inactivation of peptide signalling events on cell surfaces. By hydrolysing their respective substrates, mammalian Neps are crucial to the metabolism of numerous bioactive peptides, especially in the nervous, immune, cardiovascular and inflammatory systems. On the basis of their involvement in essential physiological processes, proteins of the Nep family constitute putative therapeutic agents as well as targets in different diseases, including Alzheimer's disease.

Results

We here demonstrate that overexpression of Neprilysin 4 (Nep4) in Drosophila melanogaster leads to a severe muscle degeneration phenotype. This phenotype is observed for overexpression of full‐length Nep4 in somatic muscles and is accompanied by severely impaired movement of larvae and lethality in late larval development. On the contrary, down‐regulation of expression caused only the latter two effects. By expressing several mutated and truncated forms of Nep4 in transgenic animals, we show that the intracellular domain is responsible for the observed phenotypes while catalytic activity of the enzyme was apparently dispensable. A yeast two‐hybrid screen identified a yet uncharacterised carbohydrate kinase as a first interaction partner of the intracellular domain of Nep4.

Conclusions

These data demonstrate that the physiological significance of Nep4 is not limited to its function as an active peptidase but that the enzyme's intracellular N‐terminus is affecting muscle integrity, independent of the protein's enzymatic activity. To our knowledge, this is the first report of an intracellular Nep domain being involved in muscle integrity.
BClI polymorphism of the glucocorticoid receptor gene is associated with increased obesity, impaired glucose metabolism and dyslipidaemia in patients with Addison's disease
Authors: Giordano Roberta , Marzotti Stefania , Berardelli Rita , Karamouzis Ioannis , Brozzetti Annalisa , D'Angelo Valentina , Mengozzi Giulio , Mandrile Giorgia , Giachino Daniela , Migliaretti Giuseppe , Bini Vittorio , Falorni Alberto , Ghigo Ezio , Arvat Emanuela
Published: May 2012

Object

Although glucocorticoids are essential for health, several studies have shown that glucocorticoids replacement in Addison's disease might be involved in anthropometric and metabolic impairment, with increased cardiovascular risk, namely if conventional doses are used. As the effects of glucocorticoids are mediated by the glucocorticoid receptor, encoded by NR3C1 gene, different polymorphisms in the NR3C1 gene have been linked to altered glucocorticoid sensitivity in general population as well as in patients with obesity or metabolic syndrome.

Design

We investigated the impact of glucocorticoid receptor gene polymorphisms, including the BclI, N363S and ER22/23EK variants, on anthropometric parameters (BMI and waist circumference), metabolic profile (HOMA, OGTT and serum lipids) and ACTH levels in 50 patients with Addison's disease (34 women and 16 men, age 20–82 year) under glucocorticoids replacement.

Results

Neither N363S nor ER22/23EK variants were significantly associated with anthropometric, metabolic or hormonal parameters, while patients carrying the homozygous BclI polymorphism GG (n = 4) showed higher (P < 0·05) BMI, waist circumference, HOMA and 2‐h glucose levels after OGTT, as well as total cholesterol and triglycerides than those with wild‐type genotype CC (n = 28) or heterozygous CG (n = 18). The totality of GG patients was connoted by abdominal adiposity, impaired glucose tolerance/diabetes mellitus or dyslipidaemia, while a lower percentage of CC or CG patients showed some anthropometric and metabolic alterations.

Conclusion

These results suggest that BclI polymorphism may influence the sensitivity to glucocorticoids in patients with Addison's disease and may contribute, along with other factors, to the increase in central adiposity, impaired glucose metabolism and dyslipidaemia.
ACTH‐secreting pituitary microadenomas are associated with a higher prevalence of central hypothyroidism compared to other microadenoma types
Authors: Mathioudakis Nestoras , Thapa Sritika , Wand Gary S. , Salvatori Roberto
Published: May 2012

Context

Unlike pituitary macroadenomas, microadenomas (micros) are not commonly associated with hypopituitarism. In clinical practice, we have observed that patients with ACTH‐secreting micros have a higher than expected prevalence of central hypothyroidism (HT), and we speculated that this effect might be because of glucocorticoid‐induced suppression of the hypothalamic–pituitary–thyroid axis.

Objective

To determine whether there is a difference in the prevalence of central HT among ACTH micros compared to other types of microadenoma, and if so, to investigate whether this is directly related to the degree of hypercortisolism.

Design, setting and patients

Retrospective study of 149 newly diagnosed patients with pituitary micros: 34 ACTH‐secreting, 72 prolactin‐secreting (PRLomas) and 43 clinically nonfunctioning adenomas (NFAs).

Main outcomes measures

Prevalence of central HT, correlation between normalized free T4 or TSH vs normalized urinary free cortisol (UFC) or salivary cortisol.

Results

The prevalence of central HT was significantly higher in the ACTH compared to the non‐ACTH adenomas: 18% (ACTH), 1% (PRL) and 0% (NFAs). The mean normalized free T4 was lower in the ACTH micros compared to the non‐ACTH micros (1·29 ± 0·06 vs 1·50 ± 0·23, P = 0·0001). There was no correlation between the degree of hypercortisolism, as reflected by 24‐h urine free cortisol and salivary cortisol, and free T4 or TSH levels among the ACTH adenomas. Similarly, there were no differences in mean UFC or salivary cortisol between ACTH adenomas with and without central HT. Following transsphenoidal adenomectomy, central HT recovered in three of six patients with ACTH micros.

Conclusions

These findings suggest that patients with ACTH‐secreting microadenomas should always, at a minimum, undergo testing for central HT. However, given the potential for recovery of thyroid function following cure of Cushing disease, we recommend withholding thyroid hormone replacement until after pituitary surgery.