bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics ofBesnoitia besnoitiinfection in cattle
Authors: ÁLVAREZ-GARCÍA G. , GARCÍA-LUNAR P. , GUTIÉRREZ-EXPÓSITO D. , SHKAP V. , ORTEGA-MORA L. M. 
Published: May 2014

SUMMARYBovine besnoitiosis is caused by the cyst-forming apicomplexan parasiteBesnoitia besnoiti.This disease progresses in two sequential phases: a febrile acute phase with oedemas and respiratory disorders, and a chronic phase characterized by the presence of subcutaneous tissue cysts and skin lesions. Serious consequences of the infection are poor body condition, sterility in bulls and eventual death. The role of host/parasite-dependent factors, which play a major role in the pathogenesis of the disease, is not yet fully elucidated. Isolate/strain virulence, parasite stage, dose and the route of parasite inoculation were studied under different experimental conditions, which make it difficult to compare the results. Data on host-dependent factors obtained from naturally infected cattle showed that (i) the seroprevalence of infection is similar in both sexes; (ii) seropositivity increases with age; (iii) both beef and dairy cattle are susceptible to the infection; and (iv) the cell-mediated immune response is likely to play a major role because a T cell response has been observed around several tissue cysts. Whether colostral antibodies are protective and to what extent the humoral immune response might reflect the disease/protection status require further research. Thus, a well-established experimental bovine model could help to clarify these important questions. The dynamics ofB. besnoitiinfection in cattle and available knowledge on relevant factors in the pathogenesis of the infection are reviewed in the present work.
Melatonin enhances thein vitromaturation and developmental potential of bovine oocytes denuded of the cumulus oophorus
Authors: Zhao Xue-Ming , Min Jiang-Tao , Du Wei-Hua , Hao Hai-Sheng , Liu Yan , Qin Tong , Wang Dong , Zhu Hua-Bin 
Published: May 2014

SummaryThis study was designed to determine the effect of melatonin on thein vitromaturation (IVM) and developmental potential of bovine oocytes denuded of the cumulus oophorus (DOs). DOs were cultured alone (DOs) or with 10−9M melatonin (DOs + MT), cumulus–oocyte complexes (COCs) were cultured without melatonin as the control. After IVM, meiosis II (MII) rates of DOs, and reactive oxygen species (ROS) levels, apoptotic rates and parthenogenetic blastocyst rates of MII oocytes were determined. The relative expression of ATP synthase F0 Subunit 6 and 8 (ATP6andATP8), bone morphogenetic protein 15 (BMP-15) and growth differentiation factor 9 (GDF-9) mRNA in MII oocytes and IFN-tau (IFN-τ),Na+/K+-ATPase, catenin-beta like 1 (CTNNBL1) andAQP3mRNA in parthenogenetic blastocysts were quantified using real-time polymerase chain reaction (PCR). The results showed that: (1) melatonin significantly increased the MII rate of DOs (65.67 ± 3.59 % vs. 82.29 ± 3.92%;P <0.05), decreased the ROS level (4.83 ± 0.42 counts per second (c.p.s) vs. 3.78 ± 0.29 c.p.s;P <0.05) and apoptotic rate (36.99 ± 3.62 % vs. 21.88 ± 2.08 %;P <0.05) and moderated the reduction of relative mRNA levels ofATP6,ATP8,BMP-15andGDF-9caused by oocyte denudation; (2) melatonin significantly increased the developmental rate (24.17 ± 3.54 % vs. 35.26 ± 4.87%;P <0.05), and expression levels ofIFN-τ,Na+/K+-ATPase,CTNNBL1andAQP3mRNA of blastocyst. These results indicated that melatonin significantly improved the IVM quality of DOs, leading to an increased parthenogenetic blastocyst formation rate and quality.
The Rights of States, the Rule of Law, and Coercion: Reflections on Pauline Kleingeld's Kant and Cosmopolitanism
Authors: Bernstein Alyssa R. 
Published: May 2014

AbstractPauline Kleingeld argues that according to Kant it would be wrong to coerce a state into an international federation, due to the wrongness of paternalism. Although I agree that Kant opposes the waging of war as a means to peace, I disagree with Kleingeld's account of the reasons why he would oppose coercing a state into a federation. Since she does not address the broader question of the permissibility of interstate coercion, she does not properly address the narrower question of whether coercion to compel a state to join a federation can be permissible. I revise and supplement her arguments.
Serum-dependent processing of late apoptotic cells for enhanced efferocytosis
Authors: Liang Y Y , Arnold T , Michlmayr A , Rainprecht D , Perticevic B , Spittler A , Oehler R 
Published: May 2014

AbstractBinding of the serum protein complement component C1q to the surface of dying cells facilitates their clearance by phagocytes in a process termed efferocytosis. Here, we investigate during which phase of apoptotic cell death progression C1q binding takes place. Purified C1q was found to bind to all dying cells and, albeit weaker, also to viable cells. The presence of serum abrogated completely the binding to viable cells. In addition, C1q binding to dying cells was limited to a specific subpopulation of late apoptotic/secondary necrotic cells. Co-culturing serum-treated apoptotic cells with human monocytes revealed a much higher phagocytosis of C1q-positive than of C1q-negative late apoptotic/secondary necrotic cells. But this phagocytosis-promoting activity could not be observed with purified C1q. Serum-treated C1q-positive late apoptotic/secondary necrotic cells exhibited a similar volume, a similar degraded protein composition, but a much lower DNA content in comparison with the remaining late apoptotic/secondary necrotic cells. This was mediated by a serum-bound nuclease activity that could be abrogated by G-actin, which is a specific inhibitor of serum DNase I. These results show that serum factors are involved in the prevention of C1q binding to viable cells and in the processing of late apoptotic/secondary necrotic cells promoting cell death progression toward apoptotic bodies. This process leads to the exposure of C1q-binding structures and facilitates efferocytosis.
Extortion subdues human players but is finally punished in the prisoner’s dilemma
Authors: Hilbe Christian , Röhl Torsten , Milinski Manfred 
Published: May 2014

AbstractExtortion is the practice of obtaining advantages through explicit forces and threats. Recently, it was demonstrated that even the repeated prisoner’s dilemma, one of the key models to explain mutual cooperation, allows for implicit forms of extortion. According to the theory, extortioners demand and receive an excessive share of any surplus, which allows them to outperform any adapting co-player. To explore the performance of such strategies against humans, we have designed an economic experiment in which participants were matched either with an extortioner or with a generous co-player. Although extortioners succeeded against each of their human opponents, extortion resulted in lower payoffs than generosity. Human subjects showed a strong concern for fairness: they punished extortion by refusing to fully cooperate, thereby reducing their own, and even more so, the extortioner’s gains. Thus, the prospects of extorting others in social relationships seem limited; in the long run, generosity is more profitable.
Imaging atomic-level random walk of a point defect in graphene
Authors: Kotakoski Jani , Mangler Clemens , Meyer Jannik C. 
Published: May 2014

AbstractDeviations from the perfect atomic arrangements in crystals play an important role in affecting their properties. Similarly, diffusion of such deviations is behind many microstructural changes in solids. However, observation of point defect diffusion is hindered both by the difficulties related to direct imaging of non-periodic structures and by the timescales involved in the diffusion process. Here, instead of imaging thermal diffusion, we stimulate and follow the migration of a divacancy through graphene lattice using a scanning transmission electron microscope operated at 60 kV. The beam-activated process happens on a timescale that allows us to capture a significant part of the structural transformations and trajectory of the defect. The low voltage combined with ultra-high vacuum conditions ensure that the defect remains stable over long image sequences, which allows us for the first time to directly follow the diffusion of a point defect in a crystalline material.
High-Precision Distribution of Highly Stable Optical Pulse Trains with 8.8 × 10−19 instability
Authors: Ning B. , Zhang S. Y. , Hou D. , Wu J. T. , Li Z. B. , Zhao J. Y. 
Published: May 2014

AbstractThe high-precision distribution of optical pulse trains via fibre links has had a considerable impact in many fields. In most published work, the accuracy is still fundamentally limited by unavoidable noise sources, such as thermal and shot noise from conventional photodiodes and thermal noise from mixers. Here, we demonstrate a new high-precision timing distribution system that uses a highly precise phase detector to obviously reduce the effect of these limitations. Instead of using photodiodes and microwave mixers, we use several fibre Sagnac-loop-based optical-microwave phase detectors (OM-PDs) to achieve optical-electrical conversion and phase measurements, thereby suppressing the sources of noise and achieving ultra-high accuracy. The results of a distribution experiment using a 10-km fibre link indicate that our system exhibits a residual instability of 2.0 × 10−15 at1 s and8.8 × 10−19 at 40,000 s and an integrated timing jitter as low as 3.8 fs in a bandwidth of 1 Hz to 100 kHz. This low instability and timing jitter make it possible for our system to be used in the distribution of optical-clock signals or in applications that require extremely accurate frequency/time synchronisation.
Discovery of InsP6-kinases as InsP6-dephosphorylating enzymes provides a new mechanism of cytosolic InsP6 degradation driven by the cellular ATP/ADP ratio
Authors: Wundenberg Torsten , Grabinski Nicole , Lin Hongying , Mayr Georg W. 
Published: May 2014

InsP6 (inositol hexakisphosphate), the most abundant inositol phosphate in metazoa, is pyrophosphorylated to InsP7 [5PP-InsP5 (diphosphoinositol pentakisphosphate)] by cytosolic and nuclear IP6Ks (InsP6 kinases) and to 1PP-InsP5 by another InsP6/InsP7 kinase family. MINPP1 (multiple inositol-polyphosphate phosphatase 1), the only known InsP6 phosphatase, is localized in the ER (endoplasmic reticulum) and lysosome lumina. A mechanism of cytosolic InsP6 dephosphorylation has remained enigmatic so far. In the present study, we demonstrated that IP6Ks change their kinase activity towards InsP6 at a decreasing ATP/ADP ratio to an ADP phosphotransferase activity and dephosphorylate InsP6. Enantio-selective analysis revealed that Ins(2,3,4,5,6)P5 is the main InsP5 product of the IP6K reaction, whereas the exclusive product of MINPP1 activity is the enantiomer Ins(1,2,4,5,6)P5. Whereas lentiviral RNAi-based depletion of MINPP1 at falling cellular ATP/ADP ratios had no significant impact on Ins(2,3,4,5,6)P5 production, the use of the selective IP6K inhibitor TNP [N2-(m-trifluorobenzyl),N6-(p-nitrobenzyl)purine] abolished the production of this enatiomer in different types of cells. Furthermore, by analysis of rat tissue and human blood samples all (main and minor) dephosphorylation products of InsP6 were detected in vivo. In summary, we identified IP6Ks as novel nuclear and cytosolic InsP6- (and InsP5-) dephosphorylating enzymes whose activity is sensitively driven by a decrease in the cellular ATP/ADP ratio, thus suggesting a role for IP6Ks as cellular adenylate energy ‘sensors’.
Assessing flexibility requirements in power systems
Authors: Dvorkin Yury , Kirschen Daniel S. , Ortega‐Vazquez Miguel A. 
Published: May 2014

This study proposes a methodology to assess the effect of wind power production on the flexibility requirements of a power system. First, the study describes the probabilistic characteristics of the intra‐hour net load variability and demonstrates that they are best captured by non‐parametric statistics. Then, this non‐parametric approach is used to determine simultaneously the hourly flexibility requirements at a given probability level for large and small, continuous and discrete disturbances. This approach allocates the required flexibility among primary, secondary and tertiary regulation intervals. The usefulness of this method is then illustrated using actual 1 min resolution net load data, which has been clustered to take advantage of seasonal and daily differences in flexibility requirements.
Indium nitride humidity sensing devices with microwave resonant property
Authors: Yang Chih Chin 
Published: May 2014

An effective microstructure indium nitride (InN) humidity sensing (INHUSE) device has been developed after InN compound was appropriately annealed with nitrogen source compensation. An X‐ray diffraction spectrum of the as‐synthesised structure shows one strong peak at 30.5° corresponding to the (0002) atomic plane of the InN hexagonal compound. The InN compound of p‐type is exhibited to reach an average Hall coefficient of 2.270 × 107 m2/C, which can be conjugated with the n‐type substrate to construct the p–n sensing device with a resonant tunnelling property. The Raman spectrum reveals the longitudinal optical phonon mode A1(LO) (polar mode), transverse optical phonon mode A1(TO) (polar mode) and transverse optical phonon mode E1(TO) of the InN‐based INHUSE device in 582, 437 and 473 cm−1, respectively. The negative differential resistance effect of the INHUSE device with an excellent peak current density in 13.2 kA/cm2 and an outstanding peak to valley current ratio of about 3.36 is exhibited. Experimental moisture examination of the INHUSE device from RH30 to 90% in accordance with the calculation of the microwave resonant property up to GHz is completed. The linear region of relative humidity measurement is from RH40 to 70% in resistance value, reached as the measured resistance value at about 31 Ω. The sensitivity of the INHUSE device is about 50 kHz/RH% for the self‐resonant frequency and 2.5 MHz/RH% for the resistive cutoff frequency.
Evaluating the utility of dynamical downscaling in agricultural impacts projections
Authors: Glotter Michael , Elliott Joshua , McInerney David , Best Neil , Foster Ian , Moyer Elisabeth J. 
Published: May 2014

SignificanceOne of the largest concerns about future climate change is its potential effect on food supply. Crop yield projections require climate inputs at higher resolution than typical for global climate models, and the computationally expensive technique of dynamical downscaling is widely used for this translation. We simulate maize yield in the United States to test whether current dynamical downscaling methods add value over simpler downscaling approaches. Our results suggest that they do not. Addressing large-scale systematic biases in climate output may be a higher priority for understanding future climate change impacts.
Ribosomal protein–Mdm2–p53 pathway coordinates nutrient stress with lipid metabolism by regulating MCD and promoting fatty acid oxidation
Authors: Liu Yong , He Yizhou , Jin Aiwen , Tikunov Andrey P. , Zhou Lishi , Tollini Laura A. , Leslie Patrick , Kim Tae-Hyung , Li Lei O. , Coleman Rosalind A. , Gu Zhennan , Chen Yong Q. , Macdonald Jeffrey M. , Graves Lee M. , Zhang Yanping 
Published: May 2014

SignificanceAlthough progress has been made in the characterization of p53 in regulating metabolism, very little is known about the signaling pathways involved in this regulation in response to stress in vivo. Here we show thatp53controls hepatic fatty acid oxidation in mice in response to fasting. Disruption of ribosome protein (RP)-mouse double minute (Mdm)2 binding inMdm2C305Fmice results in fasting-induced hepatosteatosis. A full-dosage ofp53and an intact RP-Mdm2-p53 pathway are required for the induction of malonyl coA decarboxylase (MCD), a critical regulator of fatty acid oxidation. Thus, the RP-Mdm2-p53 pathway functions as a key regulator of hepatic lipid homeostasis in response to nutrient deprivation stress, a function that has implications in organismal survival and tumor suppression.
Regulation of photosystem I light harvesting by zeaxanthin
Authors: Ballottari Matteo , Alcocer Marcelo J. P. , D’Andrea Cosimo , Viola Daniele , Ahn Tae Kyu , Petrozza Annamaria , Polli Dario , Fleming Graham R. , Cerullo Giulio , Bassi Roberto 
Published: May 2014

SignificanceChloroplasts are particularly prone to photooxidative damage, and carotenoids play a key role in photoprotection. Under excess light conditions, plants accumulate a carotenoid, zeaxanthin, involved in multiple photoprotection events. Although the function of zeaxanthin in photosystem II (PSII) has been investigated thoroughly, its role in photosystem I (PSI) had not been identified. In this work we report a zeaxanthin-dependent regulation of PSI functional antenna size inArabidopsis thaliana. We identified a zeaxanthin-dependent quenching process coupled to improved photostability of PSI, as measured in isolated complexes and leaves. We show that, similar to its action in PSII, zeaxanthin binding to components of PSI leads to the formation of carotenoid radical cations, quenching a fraction of the excitation energy absorbed.
An Automated Algorithm to Preselect Patients to Be Assessed Individually in Point Prevalence Surveys for Hospital-Acquired Infections in Surgery
Authors: Streefkerk Roel H. R. A. , Moorman Peter W. , Parlevliet Gerard A. , van der Hoeven Conrad , Verbrugh Henri A. , Vos Margreet C. , Verkooijen Roel P. 
Published: May 2014

In this pilot study, we evaluate an algorithm that uses predictive clinical and laboratory parameters to differentiate between patients with hospital-acquired infection (HAI) and patients without HAI. Seventy-four percent of the studied population of surgical patients could be reliably (negative predictive value of 98%) excluded from detailed assessment by the infection control practitioner.Infect Control Hosp Epidemiol 2014;35(7):886-887
Evaluation of an Algorithm for Electronic Surveillance of Hospital-Acquired Infections Yielding Serial Weekly Point Prevalence Scores
Authors: Streefkerk Roel H. R. A. , Borsboom Gerard J. J. M. , van der Hoeven Conrad P. , Vos Margreet C. , Verkooijen Roel P. , Verbrugh Henri A. 
Published: May 2014

Surveillance of hospital-acquired infections can be approximated by repeated surveys that are performed in a standardized, cost-effective manner. We developed an integrated software system for serial electronic hospital-wide point prevalence surveys using algorithms that proved highly sensitive and specific over a 5-year period in a large university medical center.Infect Control Hosp Epidemiol 2014;35(7):888–890
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers
Authors: Jiang Peng , Meyer Susanne , Hou Zhonggang , Propson Nicholas E. , Soh H. Tom , Thomson James A. , Stewart Ron 
Published: May 2014

Abstract
Summary: Aptamers are ‘synthetic antibodies’ that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro , rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a M eta-motif-based statistical framework and pipeline to P redict the Bind ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis.
Availability and implementation : MPBind software and documents are available at http://www.morgridge.net/MPBind.html . The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/ .
Contact : RStewart@morgridge.org
Supplementary information : Supplementary data are available at Bioinformatics online.
MoDPepInt: an interactive web server for prediction of modular domain–peptide interactions
Authors: Kundu Kousik , Mann Martin , Costa Fabrizio , Backofen Rolf 
Published: May 2014

Abstract
Summary : MoDPepInt (Modular Domain Peptide Interaction) is a new easy-to-use web server for the prediction of binding partners for modular protein domains. Currently, we offer models for SH2, SH3 and PDZ domains via the tools SH2PepInt, SH3PepInt and PDZPepInt, respectively. More specifically, our server offers predictions for 51 SH2 human domains and 69 SH3 human domains via single domain models, and predictions for 226 PDZ domains across several species, via 43 multidomain models. All models are based on support vector machines with different kernel functions ranging from polynomial, to Gaussian, to advanced graph kernels. In this way, we model non-linear interactions between amino acid residues. Results were validated on manually curated datasets achieving competitive performance against various state-of-the-art approaches.
Availability and implementation: The MoDPepInt server is available under the URL http://modpepint.informatik.uni-freiburg.de/
Contact : backofen@informatik.uni-freiburg.de
Supplementary information : Supplementary data are available at Bioinformatics online.
Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection
Authors: Conley Christopher J. , Smith Rob , Torgrip Ralf J. O. , Taylor Ryan M. , Tautenhahn Ralf , Prince John T. 
Published: May 2014

Abstract
Motivation: Isotope trace (IT) detection is a fundamental step for liquid or gas chromatography mass spectrometry (XC-MS) data analysis that faces a multitude of technical challenges on complex samples. The Kalman filter (KF) application to IT detection addresses some of these challenges; it discriminates closely eluting ITs in the m/z dimension, flexibly handles heteroscedastic m/z variances and does not bin the m/z axis. Yet, the behavior of this KF application has not been fully characterized, as no cost-free open-source implementation exists and incomplete evaluation standards for IT detection persist.
Results: Massifquant is an open-source solution for KF IT detection that has been subjected to novel and rigorous methods of performance evaluation. The presented evaluation with accompanying annotations and optimization guide sets a new standard for comparative IT detection. Compared with centWave, matchedFilter and MZMine2—alternative IT detection engines—Massifquant detected more true ITs in a real LC-MS complex sample, especially low-intensity ITs. It also offers competitive specificity and equally effective quantitation accuracy.
Availability and implementation: Massifquant is integrated into XCMS with GPL license ≥ 2.0 and hosted by Bioconductor: http://bioconductor.org . Annotation data are archived at http://hdl.lib.byu.edu/1877/3232 . Parameter optimization code and documentation is hosted at https://github.com/topherconley/optimize-it .
Contact: cjconley@ucdavis.edu or jtprince@chem.byu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.