bluuebunny/crossref_metadata_2025 huggingface dataset:
Innovative statistical interpretation of Shewanella oneidensis microbial fuel cells data
Authors: Babanova Sofia , Bretschger Orianna , Roy Jared , Cheung Andrea , Artyushkova Kateryna , Atanassov Plamen
Published: March 2014

Principal component analysis in combination with uncertainty of measurement results enables the predictive capability to optimize biology and engineering simultaneously.
Ionic tagged DABCO grafted on magnetic nanoparticles: a water-compatible catalyst for the aqueous aza-Michael addition of amines to α,β-unsaturated amides
Authors: Ying Anguo , Liu Shuo , Ni Yuxiang , Qiu Fangli , Xu Songlin , Tang Wenyuan
Published: March 2014

A water compatible DABCO grafted on magnetic nanoparticles with an ionic tag has been developed and used to catalyze the aza-Michael addition.
How does conformational flexibility influence key structural features involved in activation of anaplastic lymphoma kinase?
Authors: Karabencheva Tatyana G. , Lee Christian C. , Black Gary W. , Donev Rossen , Christov Christo Z.
Published: March 2014

Anaplastic Lymphoma Kinase (ALK) plays a major role in developing tumor processes and therefore has emerged as a validated therapeutic target.
A new route to dithia- and thiaoxacyclooctynes via Nicholas reaction
Authors: Hagendorn Tobias , Bräse Stefan
Published: March 2014

By using the Nicholas reaction we managed to design a concise synthesis that only uses three steps to build the eight-membered ring. It was also possible to functionalize said alkyne with a fluorophore.
Facile synthesis of PbTiO3 truncated octahedra via solid-state reaction and their application in low-temperature CO oxidation by loading Pt nanoparticles
Authors: Yin Simin , Zhu Yihan , Ren Zhaohui , Chao Chunying , Li Xiang , Wei Xiao , Shen Ge , Han Yu , Han Gaorong
Published: March 2014

Pt NPs have been investigated to selectively nucleate on the {111} facets of PbTiO3 truncated octahedra, exhibiting a remarkable low-temperature catalytic activity towards CO oxidation with a 100% conversion at ∼50 °C.
Nanostructured flexible Mg-modified LiMnPO4 matrix as high-rate cathode materials for Li-ion batteries
Authors: Lu Qi , Hutchings Gregory S. , Zhou Yang , Xin Huolin L. , Zheng Haimei , Jiao Feng
Published: March 2014

The LiMg0.05Mn0.95PO4 embeded carbon nano-matraix exhibts flexibity and high-performance as cathode lihitum battery materials.
Efficient dye-sensitized solar cells employing highly environmentally-friendly ubiquinone 10 based I2-free electrolyte inspired by photosynthesis
Authors: Yu Zhenhua , You Sujian , Wang Changlei , Bu Chenghao , Bai Sihang , Zhou Ziyao , Tai Qidong , Liu Wei , Guo Shishang , Zhao Xing-zhong
Published: March 2014

A highly environmentally-friendly ubiquinone 10 (UQ10) based I2-free electrolyte, which is inspired by photosynthesis, is employed in dye-sensitized solar cells (DSSCs) under 100 mW cm−2(AM 1.5G) illumination.
Antimicrobial activity of copper and copper(i) oxide thin films deposited via aerosol-assisted CVD
Authors: Hassan Iman A. , Parkin Ivan P. , Nair Sean P. , Carmalt Claire J.
Published: March 2014

High antimicrobial efficacy of Cu and Cu2O films, deposited via aerosol-assisted chemical vapour deposition, was observed against E. coli and S. aureus.
Using metal nanoparticles as a visual sensor for the discrimination of proteins
Authors: Liu Haiyan , Ma Lin , Xu Shenghao , Hua Wenhao , Ouyang Jin
Published: March 2014

The fluorescence of metal NPs is changed differently upon binding to a protein-in gel, forming a visual sensor for protein discrimination.
C/EBPβ (CCAAT/enhancer-binding protein β) mediates progesterone production through transcriptional regulation in co-operation with SF-1 (steroidogenic factor-1)
Authors: Mizutani Tetsuya , Ju Yunfeng , Imamichi Yoshitaka , Osaki Tsukasa , Yazawa Takashi , Kawabe Shinya , Ishikane Shin , Matsumura Takehiro , Kanno Masafumi , Kamiki Yasue , Kimura Kohei , Minamino Naoto , Miyamoto Kaoru
Published: March 2014

The transcription factor SF-1 (steroidogenic factor-1) is a master regulator of steroidogenesis. Previously, we have found that SF-1 induces the differentiation of mesenchymal stem cells into steroidogenic cells. To elucidate the molecular mechanisms of SF-1-mediated functions, we attempted to identify protein components of the SF-1 nuclear protein complex in differentiated cells. SF-1 immunoaffinity chromatography followed by MS/MS analysis was performed, and 24 proteins were identified. Among these proteins, we focused on C/EBPβ (CCAAT/enhancer-binding protein β), which is an essential transcription factor for ovulation and luteinization, as the transcriptional mechanisms of C/EBPβ working together with SF-1 are poorly understood. C/EBPβ knockdown attenuated cAMP-induced progesterone production in granulosa tumour-derived KGN cells by altering STAR (steroidogenic acute regulatory protein), CYP11A1 (cytochrome P450, family 11, subfamily A, polypeptide 1) and HSD3B2 (hydroxy-δ-5-steroid dehydrogenase, 3β- and steroid δ-isomerase 2) expression. EMSA and ChIP assays revealed novel C/EBPβ-binding sites in the upstream regions of the HSD3B2 and CYP11A1 genes. These interactions were enhanced by cAMP stimulation. Luciferase assays showed that C/EBPβ-responsive regions were found in each promoter and C/EBPβ is involved in the cAMP-induced transcriptional activity of these genes together with SF-1. These results indicate that C/EBPβ is an important mediator of progesterone production by working together with SF-1, especially under tropic hormone-stimulated conditions.
Structural and biochemical characterization of the KLHL3–WNK kinase interaction important in blood pressure regulation
Authors: Schumacher Frances-Rose , Sorrell Fiona J. , Alessi Dario R. , Bullock Alex N. , Kurz Thimo
Published: March 2014

WNK1 [with no lysine (K)] and WNK4 regulate blood pressure by controlling the activity of ion co-transporters in the kidney. Groundbreaking work has revealed that the ubiquitylation and hence levels of WNK isoforms are controlled by a Cullin-RING E3 ubiquitin ligase complex (CRL3KLHL3) that utilizes CUL3 (Cullin3) and its substrate adaptor, KLHL3 (Kelch-like protein 3). Loss-of-function mutations in either CUL3 or KLHL3 cause the hereditary high blood pressure disease Gordon's syndrome by stabilizing WNK isoforms. KLHL3 binds to a highly conserved degron motif located within the C-terminal non-catalytic domain of WNK isoforms. This interaction is essential for ubiquitylation by CRL3KLHL3 and disease-causing mutations in WNK4 and KLHL3 exert their effects on blood pressure by disrupting this interaction. In the present study, we report on the crystal structure of the KLHL3 Kelch domain in complex with the WNK4 degron motif. This reveals an intricate web of interactions between conserved residues on the surface of the Kelch domain β-propeller and the WNK4 degron motif. Importantly, many of the disease-causing mutations inhibit binding by disrupting critical interface contacts. We also present the structure of the WNK4 degron motif in complex with KLHL2 that has also been reported to bind WNK4. This confirms that KLHL2 interacts with WNK kinases in a similar manner to KLHL3, but strikingly different to how another KLHL protein, KEAP1 (Kelch-like enoyl-CoA hydratase-associated protein 1), binds to its substrate NRF2 (nuclear factor-erythroid 2-related factor 2). The present study provides further insights into how Kelch-like adaptor proteins recognize their substrates and provides a structural basis for how mutations in WNK4 and KLHL3 lead to hypertension.
Higher Prevalence of Autoimmune Diseases and Longer Spells of Vertigo in Patients Affected With Familial Ménière's Disease: A Clinical Comparison of Familial and Sporadic Ménière's Disease
Authors: Hietikko Elina , Sorri Martti , Männikkö Minna , Kotimäki Jouko
Published: March 2014

Purpose

This study compared clinical features, predisposing factors, and concomitant diseases between sporadic and familial Ménière's disease (MD).

Method

Retrospective chart review and postal questionnaire were used. Participants were 250 definite patients with MD (sporadic,
n
=149; familial,
n
= 101) who fulfilled the American Academy of Otorhinolaryngology–Head and Neck Surgery (1995) criteria.

Results

On average, familial patients were affected 5.6 years earlier than sporadic patients, and they suffered from significantly longer spells of vertigo (
p
= .007). The prevalence of rheumatoid arthritis (
p
= .002) and other autoimmune diseases (
p
= .046) was higher among the familial patients, who also had more migraine (
p
= .036) and hearing impairment (
p
= .002) in their families.

Conclusion

The clinical features of familial and sporadic MD are very similar in general, but some differences do exist. Familial MD patients are affected earlier and suffer from longer spells of vertigo.

Supplemental Material

https://doi.org/10.23641/asha.14963505
Vocal Interaction Between Children With Down Syndrome and Their Parents
Authors: Thiemann-Bourque Kathy S. , Warren Steven F. , Brady Nancy , Gilkerson Jill , Richards Jeffrey A.
Published: March 2014

Purpose

The purpose of this study was to describe differences in parent input and child vocal behaviors of children with Down syndrome (DS) compared with typically developing (TD) children. The goals were to describe the language learning environments at distinctly different ages in early childhood.

Method

Nine children with DS and 9 age-matched TD children participated; 4 children in each group were ages 9–11 months, and 5 were between 25 and 54 months. Measures were derived from automated vocal analysis. A digital language processor measured the richness of the child's language environment, including number of adult words, conversational turns, and child vocalizations.

Results

Analyses indicated no significant differences in words spoken by parents of younger versus older children with DS and significantly more words spoken by parents of TD children than parents of children with DS. Differences between the DS and TD groups were observed in rates of all vocal behaviors, with no differences noted between the younger versus older children with DS, and the younger TD children did not vocalize significantly more than the younger DS children.

Conclusions

Parents of children with DS continue to provide consistent levels of input across the early language learning years; however, child vocal behaviors remain low after the age of 24 months, suggesting the need for additional and alternative intervention approaches.
Waveguide‐based combining S‐band high power microwaves
Authors: Zhang Qiang , Peng Shengren , Yuan Chengwei , Liu Lie
Published: March 2014

Incoherent power combining system is a promising technique for enhancing the output power level of narrow‐band high‐power microwave devices, and waveguide‐based combiner usually has the virtues of high transmission efficiency, proper bandwidth and high power‐handling capacity within a compact structure. A specific cross‐junction combiner is proposed for combining the S/S band microwave beams, and the detailed simulation and experimental results are presented. The investigations show that the combiner realises integration of GW level power combination and mode conversion from two microwave sources simultaneously.
Extension of robust three‐stage Kalman filter for state estimation during Mars entry
Authors: Wu Yunzhang , Fu Huimin , Xiao Qiang , Zhang Yongbo
Published: March 2014

In the context of unknown inputs (unknown dynamic biases) and unknown measurement systematic errors, this article studies the extension of robust three‐stage Kalman filter (ERThSKF) that satisfies high precision entry navigation filter requirements for Mars pinpoint landing mission. The imprecise dynamic model with uncertain parameters could produce unknown inputs. Using radiometric beacons and/or inertial measurement unit (IMU) as output observation during the Mars atmospheric entry phase, the measurement data from the radio range and/or IMU have unknown measurement systematic errors. To solve these problems, we made an ERThSKF to obtain the accurate state estimation of the uncertain non‐linear Mars system with unknown inputs and unknown measurement systematic errors which can be effectively estimated and compensated. Computer simulations show that the proposed navigation filter algorithm in this study can achieve high convergence speed and minor errors, which fulfils the need of future pinpoint Mars landing missions.
Debye scale turbulence within the electron diffusion layer during magnetic reconnection
Authors: Jara-Almonte J. , Daughton W. , Ji H.
Published: March 2014

During collisionless, anti-parallel magnetic reconnection, the electron diffusion layer is the region of both fieldline breaking and plasma mixing. Due to the in-plane electrostatic fields associated with collisionless reconnection, the inflowing plasmas are accelerated towards the X-line and form counter-streaming beams within the unmagnetized diffusion layer. This configuration is inherently unstable to in-plane electrostatic streaming instabilities provided that there is sufficient scale separation between the Debye length λD and the electron skin depth c/ωpe. This scale separation has hitherto not been well resolved in kinetic simulations. Using both 2D fully kinetic simulations and a simple linear model, we demonstrate that these in-plane streaming instabilities generate Debye scale turbulence within the electron diffusion layer at electron temperatures relevant to magnetic reconnection both in the magnetosphere and in laboratory experiments.
Mg2+ coordinating dynamics in Mg:ATP fueled motor proteins
Authors: Bojovschi A. , Liu Ming S. , Sadus Richard J.
Published: March 2014

The coordination of Mg2+ with the triphosphate group of adenosine triphosphate (ATP) in motor proteins is investigated using data mining and molecular dynamics. The possible coordination structures available from crystal data for actin, myosin, RNA polymerase, DNA polymerase, DNA helicase, and F1-ATPase are verified and investigated further by molecular dynamics. Coordination states are evaluated using structural analysis and quantified by radial distribution functions, coordination numbers, and pair interaction energy calculations. The results reveal a diverse range of both transitory and stable coordination arrangements between Mg2+ and ATP. The two most stable coordinating states occur when Mg2+ coordinates two or three oxygens from the triphosphate group of ATP. Evidence for five-site coordination is also reported involving water in addition to the triphosphate group. The stable states correspond to a pair interaction energy of either ∼−2750 kJ/mol or −3500 kJ/mol. The role of water molecules in the hydration shell surrounding Mg2+ is also reported.
Post magnetic field annealing effect on magnetic and structural properties of Co80Pt20 nanowires and nanotubes fabricated by electrochemical method
Authors: Ali S. S. , Javed K. , Shi D. W. , Tao L. L. , Jiang J. , Zhai G. J. , Han X. F.
Published: March 2014

Highly ordered Co80Pt20 nanowires (NWs) and nanotubes (NTs) have been synthesized by low cost DC electrochemical deposition method with constant stirring during the fabrication process in anodic aluminum oxide nano-templates with average pore diameter of about 200 nm. The structural and magnetic properties of nanostructures have been investigated before and after simple and magnetic field annealing. Magnetic field of 1 T has been applied during annealing process in the direction perpendicular to NWs and NTs axis. X-Ray Diffraction analysis shows face centered cubic (fcc) as the dominant phase for Co80Pt20 NWs and post annealing led to better crystallinity with retained fcc phase. Furthermore, magnetic properties, including saturation magnetization (Ms), squareness ratio (Mr/Ms), and coercivity (Hc), have been investigated as a function of annealing temperature by Vibrating Sample Magnetometer.
Permittivity and permeability of Zn(Fe)/ZnO nanocapsules and their microwave absorption in the 2–18 GHz range
Authors: Wang Z. H. , Jiang L. W. , Li D. , Jiang J. J. , Ma S. , Wang H. , Geng D. Y. , An J. , He J. , Liu W. , Zhang Z. D.
Published: March 2014

The permittivity and permeability of Zn or Zn(Fe) nanoparticles with core-shell structure were investigated for frequencies from 2 to 18 GHz. The particles contain oxides shell in the form of ZnO, while the core material is Zn or Zn(Fe). The resonance frequency in permittivity corresponds to the maximum microwave absorption in the Zn/ZnO nanocapsules, which is not shifted with changing the thickness of the absorbent. However, with doping Fe (about 40%) in Zn/ZnO nanocapsules, the position for the maximum microwave absorption is shifted to lower frequencies with increasing the thickness of the absorbent.
Optimization of exchange bias in Co2FeAl0.5Si0.5 Heusler alloy layers
Authors: Hirohata Atsufumi , Izumida Keisuke , Ishizawa Satoshi , Sagar James , Nakayama Tadachika
Published: March 2014

We have fabricated and investigated IrMn3/Co2FeAl0.5Si0.5 stacks to meet the criteria for future spintronic device applications which requires low-temperature crystallisation (<250 °C) and a large exchange bias Hex (>500 Oe). Such a system would form the pinned layer in spin-valve or tunnel junction applications. We have demonstrated that annealing at 300 °C which can achieve crystalline ordering in the Co2FeAl0.5Si0.5 layer giving ∼80% of the predicted saturation magnetisation. We have also induced an exchange bias of ∼240 Oe at the interface. These values are close to the above criteria and confirm the potential of using antiferromagnet/Heusler-alloy stacks in current Si-based processes.
Low temperature carrier redistribution dynamics in InGaN/GaN quantum wells
Authors: Badcock T. J. , Dawson P. , Davies M. J. , Kappers M. J. , Massabuau F. C.-P. , Oehler F. , Oliver R. A. , Humphreys C. J.
Published: March 2014

We have studied the carrier recombination dynamics in an InGaN/GaN multiple quantum well structure as a function of emission energy and excitation density between temperatures of 10 K and 100 K. Under relatively low levels of excitation, the photoluminescence (PL) intensity and decay time of emission on the high energy side of the luminescence spectrum decrease strongly between 10 K and 50 K. In contrast, for emission detected on the low energy side of the spectrum, the PL intensity and decay time increase over the same temperature range. These results are consistent with a thermally activated carrier redistribution process in which the (temperature dependent) average timescale for carrier transfer into or out of a localised state depends on the energy of the given state. Thus, the transfer time out of shallow, weakly localised states is considerably shorter than the arrival time into more deeply localised states. This picture is consistent with carriers hopping between localisation sites in an uncorrelated disorder potential where the density of localised states decreases with increasing localisation depth, e.g., a exponential or Gaussian distribution resulting from random alloy disorder. Under significantly higher levels of excitation, the increased occupation fraction of the localised states results in a greater average separation distance between unoccupied localised states, causing a suppression of the spectral and dynamic signatures of the hopping transfer of carriers.
Origin of spin-glass and exchange bias in La1∕3Sr2∕3FeO3−γ nanoparticles
Authors: da Silva R. B. , de Araújo J. H. , Soares J. M. , Machado F. L. A.
Published: March 2014

The structure and the magnetic properties of nanopowdered samples of La1∕3Sr2∕3FeO3−γ with average particles size d in the range of 67-367 nm prepared by a sol-gel method were investigated in detail. The samples were characterized by X-ray diffraction, scanning electron microscopy, specific heat, Mössbauer spectroscopy, ac susceptibility, and magnetization measurements. Exchange bias with vertical magnetization shift was found in all samples. Charge ordering and antiferromagnetism were observed close to 200 K for large particles (d ≥ 304 nm) samples, while for particles with intermediated and smaller values (d ≤ 156 nm) a cluster-glass like behaviour and a short range charge ordering were seen near 115 K and 200 K, respectively. The spin-glass like and exchange bias behaviour in nanopowdered samples of La1∕3Sr2∕3FeO3−γ are associated to compact Fe3+ antiferromagnetic (AF) clusters caused by an oxygen deficiency, which was found to be higher in the samples with the smallest average particles sizes. The effect of exchange bias and vertical magnetization shifts are explained by a simple model involving the interaction of one AF phase with a canted AF phase.
The stochastic model for ternary and quaternary alloys: Application of the Bernoulli relation to the phonon spectra of mixed crystals
Authors: Marchewka M. , Woźny M. , Polit J. , Kisiel A. , Robouch B. V. , Marcelli A. , Sheregii E. M.
Published: March 2014

To understand and interpret the experimental data on the phonon spectra of the solid solutions, it is necessary to describe mathematically the non-regular distribution of atoms in their lattices. It appears that such description is possible in case of the strongly stochastically homogenous distribution which requires a great number of atoms and very carefully mixed alloys. These conditions are generally fulfilled in case of high quality homogenous semiconductor solid solutions of the III–V and II–VI semiconductor compounds. In this case, we can use the Bernoulli relation describing probability of the occurrence of one n equivalent event which can be applied, to the probability of finding one from n configurations in the solid solution lattice. The results described in this paper for ternary HgCdTe and GaAsP as well as quaternary ZnCdHgTe can provide an affirmative answer to the question: whether stochastic geometry, e.g., the Bernoulli relation, is enough to describe the observed phonon spectra.
Intrinsic fluctuations of dust grain charge in multi-component plasmas
Authors: Shotorban B.
Published: March 2014

A master equation is formulated to model the states of the grain charge in a general multi-component plasma, where there are electrons and various kinds of positive or negative ions that are singly or multiply charged. A Fokker-Planck equation is developed from the master equation through the system-size expansion method. The Fokker-Planck equation has a Gaussian solution with a mean and variance governed by two initial-value differential equations involving the rates of the attachment of ions and electrons to the dust grain. Also, a Langevin equation and a discrete stochastic method are developed to model the time variation of the grain charge. Grain charging in a plasma containing electrons, protons, and alpha particles with Maxwellian distributions is considered as an example problem. The Gaussian solution is in very good agreement with the master equation solution numerically obtained for this problem.
Stamping single wall nanotubes for circuit quantum electrodynamics
Authors: Viennot J. J. , Palomo J. , Kontos T.
Published: March 2014

We report on a dry transfer technique for single wall carbon nanotube devices, which allows to embed them in high finesse microwave cavity. We demonstrate the ground state charge readout and a quality factor of about 3000 down to the single photon regime. This technique allows to make devices such as double quantum dots, which could be instrumental for achieving the strong spin photon coupling. It can easily be extended to generic carbon nanotube based microwave devices.
Temperature, pressure, and size dependence of Pd-H interaction in size selected Pd-Ag and Pd-Cu alloy nanoparticles: In-situ X-ray diffraction studies
Authors: Sengar Saurabh K. , Mehta B. R. , Kulriya P. K.
Published: March 2014

In this study, in-situ X-ray diffraction has been carried out to investigate the effect of temperature and pressure on hydrogen induced lattice parameter variation in size selected Pd-Ag and Pd-Cu alloy nanoparticles. The nanoparticles of three different mobility equivalent diameters (20, 40, and 60 nm) having a narrow size distribution were prepared by gas phase synthesis method. In the present range of temperature (350 K to 250 K) and pressure (10−4 to 100 millibars), no α (H/Pd ≤ 0.03) ↔ β (H/Pd ≥ 0.54) phase transition is observed. At temperature higher than 300 °C or pressure lower than 25 millibars, there is a large difference in the rate at which lattice constant varies as a function of pressure and temperature. Further, the lattice variation with temperature and pressure is also observed to depend upon the nanoparticle size. At lower temperature or higher pressure, size of the nanoparticle seems to be relatively less important. These results are explained on the basis of the relative dominance of physical absorption and diffusion of H in Pd alloy nanoparticles at different temperature and pressure. In the present study, absence of α ↔ β phase transition points towards the advantage of using Pd-alloy nanoparticles in applications requiring long term and repeated hydrogen cycling.
Nanowire photonic crystal waveguides for single-atom trapping and strong light-matter interactions
Authors: Yu S.-P. , Hood J. D. , Muniz J. A. , Martin M. J. , Norte Richard , Hung C.-L. , Meenehan Seán M. , Cohen Justin D. , Painter Oskar , Kimble H. J.
Published: March 2014

We present a comprehensive study of dispersion-engineered nanowire photonic crystal waveguides suitable for experiments in quantum optics and atomic physics with optically trapped atoms. Detailed design methodology and specifications are provided, as are the processing steps used to create silicon nitride waveguides of low optical loss in the near-IR. Measurements of the waveguide optical properties and power-handling capability are also presented.
Combining wavelet and linear-regression methods to model the effect of available forage on daily grazing and lying activity of mature Bos indicus cows during summer months
Authors: Gadberry M. S. , Whitworth W. , Montgomery G.
Published: March 2014

Cattle exhibit a circadian rhythm of grazing and lying behaviour. Understanding how available forage (FA) interrupts this rhythm and at what time or spans of time throughout the day could be beneficial in understanding grazing dynamics. Predictable changes in activity using FA would also permit changes in activity to indicate when forage supply is approaching a threshold for optimal herd productivity. The objective of the present study was to utilise wavelet techniques to evaluate the changes in herd-level lying, grazing and standing or walking behaviour in response to varying levels of FA. This objective was accomplished by (1) applying the discrete Haar wavelet transformation to lying and grazing activity, (2) examining the relationship of the transformation coefficients with FA, and (3) developing coefficient-prediction equations to model the relationship between the coefficient and FA. Data for the study were established by monitoring the grazing behaviour of up to three cattle herds, during June, July and August of Years 2010, 2011 and 2012. The minimal FA studied was 12.8 kg DM/100 kg bodyweight and maximum FA was 56.5 kg DM/100 kg bodyweight. Lying and grazing activity were significantly (P < 0.05) correlated with a single-wavelet coefficient and these occurred at different scales (timespans). Linear models to predict coefficients were constructed for correlations of P < 0.05. The coefficient for lying was predicted as 0.011944 × FA – 0.641426 (r2 = 0.31), and the coefficient for grazing was predicted as 0.009547 × FA – 0.847766 (r2 = 0.21). On the basis of location of the predicted coefficients within the wavelet pyramid, from 0600 hours to 0900 hours, lying activity increased as FA increased; however, from 1000 hours to 1300 hours, lying activity decreased as FA increased. Lying activity converged during the timespan from 1400 hours to 2100 hours. Prior to 1300 hours, fewer cattle were predicted grazing as FA decreased. Following 1300 hours, the proportion of cattle grazing increased as FA decreased. In conclusion, the use of wavelet techniques in combination with linear regression provided a mechanism to study the magnitude of changes in herd grazing and lying activities at different scales of time throughout the day due to varying quantities of FA. However, the slope coefficient of the linear models to estimate the wavelet coefficients that were significantly correlated with FA resulted in modest changes in estimated activity. Therefore, utilising time-of-day-related changes in activity may not be a practical mechanism to delineate modest forage shortages.
Breeding forages in Florida for resistance to nematodes
Authors: Quesenberry Kenneth , Munoz Patricio , Blount Ann , Kenworthy Kevin , Crow William
Published: March 2014

Forage legumes and grasses provide the basis for the worldwide ruminant animal livestock industry, and most of these forages come from perennial pasture plants. As animal agriculture has intensified, pest pressures on perennial forages often also become more prevalent. Among these pest plant parasitic nematodes, especially root-knot nematodes (RKN) (Meloidogyne spp.) have been shown to be major forage crop pests. In this paper, we summarise research from the University of Florida related to development of methods for screening germplasm for RKN responses, results from germplasm evaluations across a range of forage legume and grass species, and progress from breeding and selection research including studies of the genetic basis of resistance. We then present prospects for continued genetic improvement in RKN resistance using conventional and modern molecular methods.
PDF and cAMP enhance PER stability in
Drosophila
clock neurons
Authors: Li Yue , Guo Fang , Shen James , Rosbash Michael
Published: March 2014

Significance

This work describes an advance in the understanding of how the important circadian neuropeptide PDF contributes to the function of the molecular clock in
Drosophila
neurons. The famous
per

S

allele of
period
significantly improves the rhythmicity of flies missing PDF. The
per

S

gene product degrades rapidly, suggesting that PDF-mediated cAMP affects PER stability. Indeed, increasing cAMP levels and cAMP-mediated protein kinase A (PKA) activity stabilizes PER, in tissue culture cells and in circadian neurons. PDF addition to fly brains in vitro has a similar effect. Our observations taken together indicate that PDF contributes to clock neuron function by activating PKA, stabilizing PER, and thereby slowing the pace of clock neurons that respond to PDF.
Doing Arithmetic by Hand: Hand Movements during Exact Arithmetic Reveal Systematic, Dynamic Spatial Processing
Authors: Marghetis Tyler , Núñez Rafael , Bergen Benjamin K.
Published: March 2014

Mathematics requires precise inferences about abstract objects inaccessible to perception. How is this possible? One proposal is that mathematical reasoning, while concerned with entirely abstract objects, nevertheless relies on neural resources specialized for interacting with the world—in other words, mathematics may be grounded in spatial or sensorimotor systems. Mental arithmetic, for instance, could involve shifts in spatial attention along a mental “number-line”, the product of cultural artefacts and practices that systematically spatialize number and arithmetic. Here, we investigate this hypothesized spatial processing during exact, symbolic arithmetic (e.g., 4 + 3 = 7). Participants added and subtracted single-digit numbers and selected the exact solution from responses in the top corners of a computer monitor. While they made their selections using a computer mouse, we recorded the movement of their hand as indexed by the streaming x, y coordinates of the computer mouse cursor. As predicted, hand movements during addition and subtraction were systematically deflected toward the right and the left, respectively, as if calculation involved simultaneously simulating motion along a left-to-right mental number-line. This spatial–arithmetical bias, moreover, was distinct from—but correlated with—individuals’ spatial–numerical biases (i.e., spatial–numerical association of response codes, SNARC, effect). These results are the first evidence that exact, symbolic arithmetic prompts systematic spatial processing associated with mental calculation. We discuss the possibility that mathematical calculation relies, in part, on an integrated system of spatial processes.
Interpreting the projective hierarchy in expansions of the real line
Authors: Hieronymi Philipp , Tychonievich Michael
Published: March 2014

We give a criterion when an expansion of the ordered set of real numbers defines the image of

(

R

,
+
,
⋅
,

N

)

(\mathbb {R},+,\cdot ,\mathbb {N})

under a semialgebraic injection. In particular, we show that for a non-quadratic irrational number

α
\alpha

, the expansion of the ordered

Q

(
α
)

\mathbb {Q}(\alpha )

-vector space of real numbers by

N

\mathbb {N}

defines multiplication on

R

\mathbb {R}

.
Divergence-conforming HDG methods for Stokes flows
Authors: Cockburn Bernardo , Sayas Francisco-Javier
Published: March 2014

In this paper, we show that by sending the normal stabilization function to infinity in the hybridizable discontinuous Galerkin methods previously proposed in [Comput. Methods Appl. Mech. Engrg. 199 (2010), 582–597], for Stokes flows, a new class of divergence-conforming methods is obtained which maintains the convergence properties of the original methods. Thus, all the components of the approximate solution, which use polynomial spaces of degree

k
k

, converge with the optimal order of

k
+
1

k+1

in

L
2

L^2

for any

k
≥
0

k \ge 0

. Moreover, the postprocessed velocity approximation is also divergence-conforming, exactly divergence-free and converges with order

k
+
2

k+2

for

k
≥
1

k\ge 1

and with order

1
1

for

k
=
0

k=0

. The novelty of the analysis is that it proceeds by taking the limit when the normal stabilization goes to infinity in the error estimates recently obtained in [Math. Comp., 80 (2011) 723–760].
Nucleophosmin modulates stability, activity, and nucleolar accumulation of base excision repair proteins
Authors: Poletto Mattia , Lirussi Lisa , Wilson David M. , Tell Gianluca
Published: March 2014

Nucleophosmin (NPM1) is a multifunctional protein that controls cell growth and genome stability via a mechanism that involves nucleolar–cytoplasmic shuttling. It is clear that NPM1 also contributes to the DNA damage response, yet its exact function is poorly understood. We recently linked NPM1 expression to the functional activation of the major abasic endonuclease in mammalian base excision repair (BER), apurinic/apyrimidinic endonuclease 1 (APE1). Here we unveil a novel role for NPM1 as a modulator of the whole BER pathway by 1) controlling BER protein levels, 2) regulating total BER capacity, and 3) modulating the nucleolar localization of several BER enzymes. We find that cell treatment with the genotoxin cisplatin leads to concurrent relocalization of NPM1 and BER components from nucleoli to the nucleoplasm, and cellular experiments targeting APE1 suggest a role for the redistribution of nucleolar BER factors in determining cisplatin toxicity. Finally, based on the use of APE1 as a representative protein of the BER pathway, our data suggest a function for BER proteins in the regulation of ribogenesis.
Capitalized Costs of Habitat Conservation Easements
Authors: Lawley Chad , Towe Charles
Published: March 2014

Perpetual conservation easements permanently remove the option to convert existing habitat to more intensive agricultural production. If existing habitat is at threat of conversion, removing the option to convert will reduce land values. In this article, we estimate the land value discount resulting from perpetual habitat conservation easements by using propensity score matching. We find that on the average eased parcel, land values fall by approximately $86 per acre for every acre of eased habitat. On average, our results suggest that landowners have been adequately compensated and conservation agencies have successfully secured habitat at risk of conversion.
Optimal metabolic route search based on atom mappings
Authors: Latendresse Mario , Krummenacker Markus , Karp Peter D.
Published: March 2014

Motivation: A key computational problem in metabolic engineering is finding efficient metabolic routes from a source to a target compound in genome-scale reaction networks, potentially considering the addition of new reactions. Efficiency can be based on many factors, such as route lengths, atoms conserved and the number of new reactions, and the new enzymes to catalyze them, added to the route. Fast algorithms are needed to systematically search these large genome-scale reaction networks.

Results: We present the algorithm used in the new RouteSearch tool within the Pathway Tools software. This algorithm is based on a general Branch-and-Bound search and involves constructing a network of atom mappings to facilitate efficient searching. As far as we know, it is the first published algorithm that finds guaranteed optimal routes where atom conservation is part of the optimality criteria. RouteSearch includes a graphical user interface that speeds user understanding of its search results. We evaluated the algorithm on five example metabolic-engineering problems from the literature; for one problem the published solution was equivalent to the optimal route found by RouteSearch; for the remaining four problems, RouteSearch found the published solution as one of its best-scored solutions. These problems were each solved in less than 5 s of computational time.

Availability and implementation: RouteSearch is accessible at BioCyc.org by using the menu command RouteSearch and by downloading Pathway Tools. Pathway Tools software is freely available to academic users, and for a fee to commercial users. Download from: http://biocyc.org/download.shtml .

Contact:  mario.latendresse@sri.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
KAnalyze: a fast versatile pipelined K-mer toolkit
Authors: Audano Peter , Vannberg Fredrik
Published: March 2014

Motivation : Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language.

Results : As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes.

Availability and implementation : KAnalyze is available on SourceForge:

https://sourceforge.net/projects/kanalyze/

Contact:  fredrik.vannberg@biology.gatech.edu

Supplementary information : Supplementary data are available at Bioinformatics online.
Measuring Transparency
Authors: Hollyer James R. , Rosendorff B. Peter , Vreeland James Raymond
Published: March 2014

Transparency is often viewed as crucial to government accountability, but its measurement remains elusive. This concept encompasses many dimensions, which have distinct effects. In this article, we focus on a specific dimension of transparency: governments' collection and dissemination of aggregate data. We construct a measure of this aspect of transparency, using an item response model that treats transparency as a latent predictor of the reporting of data to the World Bank's World Development Indicators. The resultant index covers 125 countries from 1980 to 2010. Unlike some alternatives (e.g., Freedom House), our measure—the HRV index—is based on objective criteria rather than subjective expert judgments. Unlike newspaper circulation numbers, HRV reflects the dissemination of credible content—in that it has survived the World Bank's quality control assessment. In a validation exercise, we find that our measure outperforms newspaper circulation as a predictor of Law and Order and Bureaucratic Quality as measured by the ICRG, particularly in autocracies. It performs as well as newspaper circulation in predicting corruption. These findings suggest that data dissemination is a distinct, and politically relevant, form of transparency.
Cardiac Arrest during Hospitalization for Delivery in the United States, 1998–2011
Authors: Mhyre Jill M. , Tsen Lawrence C. , Einav Sharon , Kuklina Elena V. , Leffert Lisa R. , Bateman Brian T.
Published: March 2014

Background:

The objective of this analysis was to evaluate the frequency, distribution of potential etiologies, and survival rates of maternal cardiopulmonary arrest during the hospitalization for delivery in the United States.

Methods:

By using data from the Nationwide Inpatient Sample during the years 1998 through 2011, the authors obtained weighted estimates of the number of U.S. hospitalizations for delivery complicated by maternal cardiac arrest. Clinical and demographic risk factors, potential etiologies, and outcomes were identified and compared in women with and without cardiac arrest. The authors tested for temporal trends in the occurrence and survival associated with maternal arrest.

Results:

Cardiac arrest complicated 1 in 12,000 or 8.5 per 100,000 hospitalizations for delivery (99% CI, 7.7 to 9.3 per 100,000). The most common potential etiologies of arrest included hemorrhage, heart failure, amniotic fluid embolism, and sepsis. Among patients with cardiac arrest, 58.9% of patients (99% CI, 54.8 to 63.0%) survived to hospital discharge.

Conclusions:

Approximately 1 in 12,000 hospitalizations for delivery is complicated by cardiac arrest, most frequently due to hemorrhage, heart failure, amniotic fluid embolism, or sepsis. Survival depends on the underlying etiology of arrest.
Role of Vitamin D in Children With Hepatosteatosis
Authors: Yildiz Ismail , Erol Oguz B. , Toprak Sadik , Cantez Mustafa S. , Omer Beyhan , Kilic Ayse , Oguz Fatma , Uysalol Metin , Yekeler Ensar , Unuvar Emin
Published: March 2014

Background:

The increasing incidence of obesity in children is a significant risk factor for nonalcoholic fatty liver disease and obesity‐associated morbidity. Vitamin D has a major role in bone mineral metabolism and has antimicrobial, antioxidant properties. In this study we aimed to investigate the role of vitamin D in children with obesity with hepatosteatosis.

Methods:

A total of 101 children with obesity were included in this study. Hepatosteatosis was diagnosed and graded using ultrasonography. Serum levels of 25‐hydroxyvitamin D (25‐(OH) vitamin D), calcium, phosphate, alkaline phosphatase, and parathormone were tested. Two‐sided t test and Pearson χ2 tests were used for the relation between vitamin D and hepatosteatosis.

Results:

In our study group, 45.5% were girls (n = 46) and the mean age was 11.5 ± 2.8 years (range 3–17 years). Hepatosteatosis was identified in 58 children (57.4%). The diagnosis of grade 1 and grade 2 hepatosteatosis was made in 41 (40.6%) and 17 (16.8%) children, respectively. Median serum 25‐(OH) vitamin D levels in children without hepatosteatosis was 16.4 ng/mL (interquartile range 12.4–24.8 ng/mL), whereas children with grade 1 and grade 2 hepatosteatosis had 25‐(OH) vitamin D levels of 14.2 ng/mL (interquartile range 9.5–21.2 ng/mL) and 11.5 ng/mL (interquartile range 7.5–16.7 ng/mL), respectively (P = 0.005). There was a positive correlation between insulin resistance and the grade of hepatosteatosis (P = 0.03).

Conclusions:

Serum vitamin D levels in children with obesity with hepatosteatosis are significantly lower than vitamin D levels in children with obesity without hepatosteatosis. In this observational study we only refer to the association of vitamin D deficiency/insufficiency with hepatosteatosis.
Prospective Assessment of Inpatient Boxed Warning Prescriber Adherence
Authors: Kloet Megan A. , Lohr Brian R. , Smithburger Pamela L. , Seybert Amy L. , Kane-Gill Sandra L.
Published: March 2014

Objective

To evaluate medication boxed warning nonadherence in the inpatient setting.

Methods

This was a prospective cohort quality improvement project approved by our institution’s Total Quality Council. General medicine and ICU patients 18 years and older were included if they were cared for by a prescriber-led multidisciplinary team that included a pharmacist. Patients were evaluated for medication orders with an actionable boxed warning; if boxed warning nonadherence occurred, the physician’s reason was determined. Patients with boxed warning nonadherence were monitored for adverse drug reactions until discharge.

Results

A total of 393 patients (224 general medicine and 169 ICU) were evaluated for nonadherence to 149 actionable boxed warnings. There were 293 drugs (175 general medicine and 118 ICU) with boxed warnings prescribed, and more than 50% of these were medications restarted from home. A total of 23 boxed warning nonadherences occurred in general medicine patients, and NSAIDs accounted for 81% of these events. ICU patients experienced 11 boxed warning nonadherences, with nearly 54% from anti-infectives and immunosuppressants. Antipsychotics were the most commonly ordered boxed warning medication class in ICU patients. Reasons for nonadherence included knowledge deficit and an acceptable risk-to-benefit ratio. Two adverse drug reactions occurred from boxed warning nonadherences, both because of a drug-drug interaction.

Conclusions

Boxed warning nonadherence is a concern in the inpatient setting, specifically with NSAID use in general medicine patients and antipsychotic use in ICU patients. More than half of boxed warning nonadherence occurred in medications restarted from home, which emphasizes the need for medication evaluation during transitions of care.
Many ways to stay in the game: individual variability maintains high biodiversity in planktonic microorganisms
Authors: Menden-Deuer Susanne , Rowlett Julie
Published: March 2014

In apparent contradiction to competition theory, the number of known, coexisting plankton species far exceeds their explicable biodiversity—a discrepancy termed theParadox of the Plankton.We introduce a new game-theoretic model for competing microorganisms in which one player consists of all organisms of one species. The stable points for the population dynamics in our model, known as strategic behaviour distributions (SBDs), are probability distributions of behaviours across all organisms which imply a stable population of the species as a whole. We find that intra-specific variability is the key characteristic that ultimately allows coexistence because the outcomes of competitions between individuals with variable competitive abilities are unpredictable. Our simulations based on the theoretical model show that up to 100 species can coexist for at least 10 000 generations, and that even small population sizes or species with inferior competitive ability can survive when there is intra-specific variability. In nature, this variability can be observed as niche differentiation, variability in environmental and ecological factors, and variability of individual behaviours or physiology. Therefore, previous specific explanations of the paradox are consistent with and provide specific examples of our suggestion that individual variability is the mechanism which solves the paradox.