bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspects of designing and evaluating seasonal‐to‐interannual Arctic sea‐ice prediction systems
Authors: Hawkins Ed , Tietsche Steffen , Day Jonathan J. , Melia Nathanael , Haines Keith , Keeley Sarah
Published: July 2015

Using lessons from idealised predictability experiments, we discuss some issues and perspectives on the design of operational seasonal to inter‐annual Arctic sea‐ice prediction systems. We first review the opportunities to use a hierarchy of different types of experiment to learn about the predictability of Arctic climate. We also examine key issues for ensemble system design, such as measuring skill, the role of ensemble size and generation of ensemble members. When assessing the potential skill of a set of prediction experiments, using more than one metric is essential as different choices can significantly alter conclusions about the presence or lack of skill. We find that increasing both the number of hindcasts and ensemble size is important for reliably assessing the correlation and expected error in forecasts. For other metrics, such as dispersion, increasing ensemble size is most important. Probabilistic measures of skill can also provide useful information about the reliability of forecasts. In addition, various methods for generating the different ensemble members are tested. The range of techniques can produce surprisingly different ensemble spread characteristics. The lessons learnt should help inform the design of future operational prediction systems.
Augmented Half Normal Effects Plots in the Presence of a Few Error Degrees of Freedom
Authors: Grömping Ulrike
Published: July 2015

Fractional factorial 2‐level experiments are often conducted without any error degrees of freedom. In such cases, a half‐normal effects plot—also called Daniel plot according to its inventor Cuthbert Daniel—can be used for assessing effect significance. Half‐normal effects plots are often accompanied by a numeric method for assessing effect significance, most prominently Lenth's method. There are, however, also situations for which a few error degrees of freedom are available, for example, from a replicated center point run. For such cases, besides the obvious possibilities of either ignoring the few replicates (i.e., using half‐normal effects plot and Lenth's method, as if they were not there) or using analysis of variance with the replicates for estimating the error variance, several further proposals for assessing effect significance exist. This paper compares the published methods for significance testing, proposes an additional one (that might be very close to what JMP does) and advocates the use of an augmented half‐normal effects plot that shows error points and a null reference line along with the effects. It is argued that such a plot can be useful in a fully replicated experiment for assessing whether the replication process was of adequate quality. The method is available in the author's R package DoE.base. Copyright © 2015 John Wiley & Sons, Ltd.
A composite likelihood approach for estimating HIV prevalence in the presence of spatial variation
Authors: Wirth Kathleen E. , Agniel Denis , Barr Christopher D. , Austin Matthew D. , DeGruttola Victor
Published: July 2015

Since 1990, the World Health Organization has recommended HIV surveillance among pregnant women as an essential surveillance activity for countries with generalized HIV epidemics. Despite the widespread availability and potential usefulness of antenatal HIV surveillance, analyses of such data present important challenges. Within an individual clinic, the HIV status of its attendees may be correlated because of similarities in HIV risk among women close in age. Between‐clinic correlation may also arise as women often seek antenatal care at clinics located close to their home, and individuals living in nearby communities may share important characteristics or behaviours related to susceptibility. A general estimating equation‐based approach for spatially‐correlated, binary data such as that antenatal HIV surveillance based on a pairwise composite likelihood has been described. We present an extended version of this model that can accommodate penalized spline estimators and apply it to antenatal HIV surveillance data collected in 2011 in Botswana to estimate the effects of proximity to the ‘hotspot’ of the country's HIV epidemic and age on HIV prevalence. Finally, we compare the results with a logistic regression analysis, which ignores potential correlation of responses. Copyright © 2015 John Wiley & Sons, Ltd.
Statistical metrics for assessing the quality of wind power scenarios for stochastic unit commitment
Authors: Sari Didem , Lee Youngrok , Ryan Sarah , Woodruff David
Published: July 2015

In power systems with high penetration of wind generation, probabilistic scenarios are generated for use in stochastic formulations of day‐ahead unit commitment problems. To minimize the expected cost, the wind power scenarios should accurately represent the stochastic process for available wind power. We employ some statistical evaluation metrics to assess whether the scenario set possesses desirable properties that are expected to lead to a lower cost in stochastic unit commitment. A new mass transportation distance rank histogram is developed for assessing the reliability of unequally likely scenarios. Energy scores, rank histograms and Brier scores are applied to alternative sets of scenarios that are generated by two very different methods. The mass transportation distance rank histogram is best able to distinguish between sets of scenarios that are more or less calibrated according to their bias, variability and autocorrelation. Copyright © 2015 John Wiley & Sons, Ltd.
Fuzzy complexes: Specific binding without complete folding
Authors: Sharma Rashmi , Raduly Zsolt , Miskei Marton , Fuxreiter Monika
Published: July 2015

Specific molecular recognition is assumed to require a well‐defined set of contacts and devoid of conformational and interaction ambiguities. Growing experimental evidence demonstrates however, that structural multiplicity or dynamic disorder can be retained in protein complexes, termed as fuzziness. Fuzzy regions establish alternative contacts between specific partners usually via transient interactions. Nature often tailors the dynamic properties of these segments via post‐translational modifications or alternative splicing to fine‐tune affinity. Most experimentally characterized fuzzy complexes are involved in regulation of gene‐expression, signal transduction and cell‐cycle regulation. Fuzziness is also characteristic to viral protein complexes, cytoskeleton structure, and surprisingly in a few metabolic enzymes. A plausible role of fuzzy complexes in increasing half‐life of intrinsically disordered proteins is also discussed.
An Evaluation of Individually Delivered Secret Agent Society Social Skills Program for Children with High-Functioning Autism Spectrum Disorders: A Pilot Study
Authors: Tan Yunxi Lynette , Mazzucchelli Trevor G. , Beaumont Renae
Published: July 2015

High-functioning children with autism spectrum disorders display social skill deficits that can have a debilitating impact on their daily lives. The Secret Agent Society (SAS) program has been shown to be effective in improving the social skills of these children when delivered in a group setting. This pilot study evaluated whether individually delivered SAS would yield similar outcomes. Three participants were recruited for the 9-week intervention. Measures of social competence were administered at four points: pretest 1, pretest 2, post-intervention, and 6-week follow-up. Participants showed significant improvement in half of the measures assessing social competence. On a third of these measures, two participants demonstrated improvements to within the range of their typically developing peers. Follow-up results suggested that improvements were maintained at 6 weeks’ post-intervention. Limitations of this study and directions for future research are discussed.
Investigation of a leptospirosis outbreak in triathlon participants, Réunion Island, 2013
Authors: PAGÈS F. , LARRIEU S. , SIMOES J. , LENABAT P. , KURTKOWIAK B. , GUERNIER V. , LE MINTER G. , LAGADEC E. , GOMARD Y. , MICHAULT A. , JAFFAR-BANDJEE M. C. , DELLAGI K. , PICARDEAU M. , TORTOSA P. , FILLEUL L.
Published: July 2015

We report herein the investigation of a leptospirosis outbreak occurring in triathlon competitors on Réunion Island, Indian Ocean. All participants were contacted by phone or email and answered a questionnaire. Detection and molecular characterization of pathogenicLeptospirawas conducted in inpatients and in rodents trapped at the vicinity of the event. Of the 160 athletes competing, 101 (63·1%) agreed to participate in the study. Leptospirosis was biologically confirmed for 9/10 suspected cases either by real-time PCR or serological tests (MAT or ELISA). The total attack rate, children's attack rate, swimmers’ attack rate, and the attack rate in adult swimmers were respectively estimated at 8·1% [95% confidence interval (CI) 4·3–14·7], 0%, 12·7% (95% CI 6·8–22·4) and 23·1% (95% CI 12·6–33·8). Leptospirosis cases reported significantly more wounds [risk ratio (RR) 4·5, 95% CI 1·6–13], wore complete neoprene suits less often (RR 4·3, 95% CI 1·3–14·5) and were most frequently unlicensed (RR 6·6, 95% CI 2·9–14·8). The epidemiological investigation supported that some measures such as the use of neoprene suits proved efficient in protecting swimmers against infection. PCR detection in rats revealed highLeptospirainfection rates. Partial sequencing of the 16S gene and serology on both human and animal samples strongly suggests that rats were the main contaminators and were likely at the origin of the infection in humans.
How and when plume zonation appeared during the 132 Myr evolution of the Tristan Hotspot
Authors: Hoernle Kaj , Rohde Joana , Hauff Folkmar , Garbe-Schönberg Dieter , Homrighausen Stephan , Werner Reinhard , Morgan Jason P.
Published: July 2015

Increasingly, spatial geochemical zonation, present as geographically distinct, subparallel trends, is observed along hotspot tracks, such as Hawaii and the Galapagos. The origin of this zonation is currently unclear. Recently zonation was found along the last ∼70 Myr of the Tristan-Gough hotspot track. Here we present new Sr–Nd–Pb–Hf isotope data from the older parts of this hotspot track (Walvis Ridge and Rio Grande Rise) and re-evaluate published data from the Etendeka and Parana flood basalts erupted at the initiation of the hotspot track. We show that only the enriched Gough, but not the less-enriched Tristan, component is present in the earlier (70–132 Ma) history of the hotspot. Here we present a model that can explain the temporal evolution and origin of plume zonation for both the Tristan-Gough and Hawaiian hotspots, two end member types of zoned plumes, through processes taking place in the plume sources at the base of the lower mantle.
Prediction of drug-induced nephrotoxicity and injury mechanisms with human induced pluripotent stem cell-derived cells and machine learning methods
Authors: Kandasamy Karthikeyan , Chuah Jacqueline Kai Chin , Su Ran , Huang Peng , Eng Kim Guan , Xiong Sijing , Li Yao , Chia Chun Siang , Loo Lit-Hsin , Zink Daniele
Published: July 2015

The renal proximal tubule is a main target for drug-induced toxicity. The prediction of proximal tubular toxicity during drug development remains difficult. Any in vitro methods based on induced pluripotent stem cell-derived renal cells had not been developed, so far. Here, we developed a rapid 1-step protocol for the differentiation of human induced pluripotent stem cells (hiPSC) into proximal tubular-like cells. These proximal tubular-like cells had a purity of >90% after 8 days of differentiation and could be directly applied for compound screening. The nephrotoxicity prediction performance of the cells was determined by evaluating their responses to 30 compounds. The results were automatically determined using a machine learning algorithm called random forest. In this way, proximal tubular toxicity in humans could be predicted with 99.8% training accuracy and 87.0% test accuracy. Further, we studied the underlying mechanisms of injury and drug-induced cellular pathways in these hiPSC-derived renal cells and the results were in agreement with human and animal data. Our methods will enable the development of personalized or disease-specific hiPSC-based renal in vitro models for compound screening and nephrotoxicity prediction.
Spontaneous Regeneration of Human Photoreceptor Outer Segments
Authors: Horton Jonathan C. , Parker Alicia B. , Botelho James V. , Duncan Jacque L.
Published: July 2015

Photoreceptors are damaged in many common eye diseases, such as macular degeneration, retinal detachment and retinitis pigmentosa. The development of methods to promote the repair or replacement of affected photoreceptors is a major goal of vision research. In this context, it would be useful to know whether photoreceptors are capable of undergoing some degree of spontaneous regeneration after injury. We report a subject who lost retinal function in a wide zone around the optic disc, giving rise to massive enlargement of the physiological blind spot. Imaging with an adaptive optics scanning laser ophthalmoscope (AOSLO) showed depletion of cone outer segments in the affected retina. A year later visual function had improved, with shrinkage of the enlarged blind spot. AOSLO imaging showed repopulation of cone outer segments, although their density remained below normal. There was a one-to-one match between sites of formerly missing outer segments and new outer segments that had appeared over the course of the year’s recovery. This correspondence provided direct morphological evidence that damaged cones are capable, under some circumstances, of generating new outer segments.
VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants
Authors: Nagpal Gandharva , Gupta Sudheer , Chaudhary Kumardeep , Kumar Dhanda Sandeep , Prakash Satya , Raghava Gajendra P. S.
Published: July 2015

Immunomodulatory oligodeoxynucleotides (IMODNs) are the short DNA sequences that activate the innate immune system via toll-like receptor 9. These sequences predominantly contain unmethylated CpG motifs. In this work, we describe VaccineDA (Vaccine DNA adjuvants), a web-based resource developed to design IMODN-based vaccine adjuvants. We collected and analyzed 2193 experimentally validated IMODNs obtained from the literature. Certain types of nucleotides (e.g., T, GT, TC, TT, CGT, TCG, TTT) are dominant in IMODNs. Based on these observations, we developed support vector machine-based models to predict IMODNs using various compositions. The developed models achieved the maximum Matthews Correlation Coefficient (MCC) of 0.75 with an accuracy of 87.57% using the pentanucleotide composition. The integration of motif information further improved the performance of our model from the MCC of 0.75 to 0.77. Similarly, models were developed to predict palindromic IMODNs and attained a maximum MCC of 0.84 with the accuracy of 91.94%. These models were evaluated using a five-fold cross-validation technique as well as validated on an independent dataset. The models developed in this study were integrated into VaccineDA to provide a wide range of services that facilitate the design of DNA-based vaccine adjuvants (http://crdd.osdd.net/raghava/vaccineda/).
Laser-scanning cytometry can quantify human adipocyte browning and proves effectiveness of irisin
Authors: Kristóf Endre , Doan-Xuan Quang-Minh , Bai Péter , Bacso Zsolt , Fésüs László
Published: July 2015

Laser-scanning cytometry is presented as a tool allowing population scale analysis ofex vivohuman brown adipogenic differentiation. It combines texture analysis and detection of Ucp1 protein content in single brown adipocytes of mixed cell populations with gene expression pattern and functional characteristics of browning. Using this method we could validate mouse data in human samples demonstrating the effectiveness of irisin to induce “beige” differentiation of subcutaneous white adipocytes.
Proteomic analysis reveals that COP9 signalosome complex subunit 7A (CSN7A) is essential for the phase transition of migratory locust
Authors: Tong Xi-Wen , Chen Bing , Huang Li-Hua , Feng Qi-Li , Kang Le
Published: July 2015

The migratory locust displays a reversible, density-dependent transition between the two phases of gregaria and solitaria. This phenomenon is a typical kind of behavior plasticity. Here, we report that COP9 signalosome complex subunit 7A (CSN7A) is involved in the regulation of locust phase transition. Firstly, 90 proteins were identified to express differentially between the two phases by quantitative proteomic analysis. Gregaria revealed higher levels in proteins related to structure formation, melanism and energy metabolism, whereas solitaria had more abundant proteins related to digestion, absorption and chemical sensing. Subsequently, ten proteins including CSN7A were found to reveal differential mRNA expression profiles between the two phases. The CSN7A had higher mRNA level in the gregaria as compared with the solitaria and the mRNA amount in the gregaria decreased remarkably during the 32 h-isolation. However, the mRNA level in the solitaria kept constant during the crowding rearing. Finally and importantly, RNA interference of CSN7A in gregaria resulted in obvious phase transition towards solitaria within 24 h. It suggests that CSN7A plays an essential role in the transition of gregaria towards solitaria in the migratory locust. To our knowledge, it’s the first time to report the role of CSN in behavior plasticity of animals.
Anti-CD antibody microarray for human leukocyte morphology examination allows analyzing rare cell populations and suggesting preliminary diagnosis in leukemia
Authors: Khvastunova Alina N. , Kuznetsova Sofya A. , Al-Radi Liubov S. , Vylegzhanina Alexandra V. , Zakirova Anna O. , Fedyanina Olga S. , Filatov Alexander V. , Vorobjev Ivan A. , Ataullakhanov Fazly
Published: July 2015

We describe a method for leukocyte sorting by a microarray of anti-cluster-of-differentiation (anti-CD) antibodies and for preparation of the bound cells for morphological or cytochemical examination. The procedure results in a “sorted” smear with cells positive for certain surface antigens localised in predefined areas. The morphology and cytochemistry of the microarray-captured normal and neoplastic peripheral blood mononuclear cells are identical to the same characteristics in a smear. The microarray permits to determine the proportions of cells positive for the CD antigens on the microarray panel with high correlation with flow cytometry. Using the anti-CD microarray we show that normal granular lymphocytes and lymphocytes with radial segmentation of the nuclei are positive for CD3, CD8, CD16 or CD56 but not for CD4 or CD19. We also show that the described technique permits to obtain a pure leukemic cell population or to separate two leukemic cell populations on different antibody spots and to study their morphology or cytochemistry directly on the microarray. In cases of leukemias/lymphomas when circulating neoplastic cells are morphologically distinct, preliminary diagnosis can be suggested from full analysis of cell morphology, cytochemistry and their binding pattern on the microarray.
Passively mode-locked fiber laser by a cell-type WS2 nanosheets saturable absorber
Authors: Yan Peiguang , Liu Aijiang , Chen Yushan , Wang JinZhang , Ruan Shuangchen , Chen Hao , Ding Jinfei
Published: July 2015

A cell-type saturable absorber has been demonstrated by filling the single mode photonic crystal fiber (SMPCF) with tungsten disulfide (WS2) nanosheets. The modulation depth, saturable intensity and non-saturable loss of this SA are measured to be 3.53%, 159 MW/cm2 and 23.2%, respectively. Based on this SA, a passively mode-locked EDF laser has been achieved with pulse duration of 808 fs and repetition rate of 19.57 MHz and signal-noise-ratio (SNR) of 60.5 dB. Our results demonstrate that the cell-type WS2 nanosheets SA can serve as a good candidate for short-pulse mode locker.
Calcium ion-induced formation of β-sheet/-turn structure leading to alteration of osteogenic activity of bone morphogenetic protein-2
Authors: Zhang Wenjing , He Hongyan , Tian Yu , Gan Qi , Zhang Jing , Yuan Yuan , Liu Changsheng
Published: July 2015

Preserving bioactivity of bone morphogenetic protein 2 (BMP-2) still remains a challenge in protein-based therapy. It is not known how Ca2+ released from extracellular matrix or existing in physiological environment influences bioactivity in situ till now. Here, effects of extracellular Ca2+ on conformation and osteogenic bioactivity of recombinant human BMP-2 (rhBMP-2) were investigated systematically. In vitro results indicated that Ca2+ could bind rhBMP-2 rapidly and had no obvious effect on cell behaviors. Low concentration of Ca2+ (0.18 mM) enhanced rhBMP-2-induced osteogenic differentiation, while high Ca2+ concentration (>1.80 mM) exerted negative effect. In vivo ectopic bone formation exhibited similar trend. Further studies by circular dichroism spectroscopy, fluorescence spectroscopy, together with cell culture experiments revealed at low concentration, weak interaction of Ca2+ and rhBMP-2 slightly increased β-sheet/-turn content and facilitated recognition of BMP-2 and BMPRIA. But, high Ca2+ concentration (>1.8 mM) induced formation of Ca-rhBMP-2 complex and markedly increased content of β-sheet/-turn, which led to inhibition binding of rhBMP-2 and BMPRIA and thus suppression of downstream Smad1/5/8, ERK1/2 and p38 mitogen-associated protein kinase signaling pathways. Our work suggests osteogenic bioactivity of BMP-2 can be adjusted via extracellular Ca2+, which should provide guide and assist for development of BMP-2-based materials for bone regeneration.
Graphene-based nanoprobes for molecular diagnostics
Authors: Chen Shixing , Li Fuwu , Fan Chunhai , Song Shiping
Published: July 2015

This review focuses on the construction of graphene-based nanoprobes and their use for the detection of various bioactive molecules in molecular diagnostics.
Silver nanoparticles anchored on nitrogen-doped graphene as a novel electrochemical biosensing platform with enhanced sensitivity for aptamer-based pesticide assay
Authors: Jiang Ding , Du Xiaojiao , Liu Qian , Zhou Lei , Dai Liming , Qian Jing , Wang Kun
Published: July 2015

Silver nanoparticle decorated nitrogen-doped graphene was designed as a novel electrochemical biosensing platform with enhanced sensitivity for aptamer-based pesticide assay.
Reactive atmospheric pressure plasma for highly efficient removal of structure-directing agents from zeolite thin films
Authors: Chien H.-T. , Chen M.-C. , Huang P.-S. , Lai J.-Y. , Hsu C.-C. , Kang D.-Y.
Published: July 2015

We present a plasma-based technique for rapid removal of SDA from as-synthesized zeolite films.
Raman spectroscopy for detecting supported planar lipid bilayers composed of ganglioside-GM1/sphingomyelin/cholesterol in the presence of amyloid-β
Authors: Hu Zhiping , Wang Xiaoli , Wang Weirong , Zhang Zhenlong , Gao Huiping , Mao Yanli
Published: July 2015

The molecular vibrations of GM1/SM/Chol SPBs and the conformational transformation of Aβ(1–40) on GM1/SM/Chol SPBs are analyzed by Raman spectroscopy.
Plutonium partitioning in water–granite and water–α-FeOOH systems: from a viewpoint of a three-phase system
Authors: Lin Jianfeng , Dang Haijun , Xie Jinchuan , Zhou Guoqing , Li Mei , Zhang Jihong
Published: July 2015

From a viewpoint of a three-phase system, the mobile colloidal species play the most important role in Pu migration in the underground water–granite system.
Base-promoted synthesis of dibenzoxazepinamines and quinazolinimines under metal-free conditions
Authors: Feng Jian-Bo , Wu Xiao-Feng
Published: July 2015

An interesting base-promoted protocol for the synthesis of dibenzo[b,f][1,4]oxazepin-11-amines and quinazolinimines has been developed. Starting from commercially available 2-fluorobenzonitriles, 2-aminophenols and 2-aminoethanol, good to excellent yields of the corresponding heterocycles can be achieved.
Viscosity measurement based on the tapping-induced free vibration of sessile droplets using MEMS-based piezoresistive cantilevers
Authors: Nguyen Thanh-Vinh , Nguyen Minh-Dung , Takahashi Hidetoshi , Matsumoto Kiyoshi , Shimoyama Isao
Published: July 2015

We propose a MEMS-based cantilever array to estimate the viscosity of small droplets based on their tapping-induced vibration.
Are fancy acidic or neutral ligands really needed for synergism in ionic liquids? A comparative study of lanthanoid extraction in CHCl3 and an ionic liquid
Authors: Atanassova Maria , Kurteva Vanya , Lubenov Lubomir , Varbanov Sabi , Billard Isabelle
Published: July 2015

Five lanthanoid ions were extracted with 3-methyl-1-phenyl-4-(4-phenylbenzoyl)-pyrazol-5-one in combination with calix[4]arene as a synergistic agent using CHCl3 or 1-butyl-3-methylimidazolium-bis(trifluoromethanesulfonyl)imide as solvent.
Rh(iii)-catalyzed cyclization reaction of azoles with alkynes: efficient synthesis of azole-fused-pyridines
Authors: Chen Xuebing , Wu Youzhi , Xu Jinyi , Yao Hequan , Lin Aijun , Huang Yue
Published: July 2015

A Rh(iii)-catalyzed cyclization of azoles with alkynes has been developed to construct azole-fused-pyridines in good to excellent yields.
Silicon nanowires-based fluorescent sensor for in situ detection of hydrogen sulfide in extracellular environment
Authors: Wang Huimin , Mu Lixuan , She Guangwei , Shi Wensheng
Published: July 2015

Based on a Si nanowire array, a fluorescent sensor for H2S was realized and successfully used for real time and in situ imaging of the changes in extracellular H2S of live cells.
Microstructure and charge carrier dynamics in Dy substituted phase stabilized cubic Bi2O3
Authors: Bandyopadhyay Swagata , Dutta Abhigyan
Published: July 2015

Structural conversion of Bi2O3from monoclinic to cubic phase due to doping of Dy.
UV photocatalytic activity of Au@ZnO core–shell nanostructure with enhanced UV emission
Authors: Jiang Tingting , Qin Xueying , Sun Ye , Yu Miao
Published: July 2015

Au@ZnO core–shell nanostructures with increased ultraviolet photoluminescence emissions present remarkably enhanced ultraviolet photocatalytic properties, based on bidirectional electron transfer between Au and ZnO.
Fluorescent magnetic nanosensors for Zn2+ and CN− in aqueous solution prepared from adamantane-modified fluorescein and β-cyclodextrin-modified Fe3O4@SiO2via host–guest interactions
Authors: Li Qiang , Zhang Yue , Jin Yang , Yang Qingbiao , Du Jianshi , Li Yaoxian
Published: July 2015

A novel multifunctional fluorescent chemosensor has been constructed with a highly selective “off–on” behavior, recoverability and recyclability.
Design, synthesis and thermal behaviour of a series of well-defined clickable and triggerable sulfonate polymers
Authors: Kolomanska Joanna , Johnston Priscilla , Gregori Alberto , Fraga Domínguez Isabel , Egelhaaf Hans-Joachim , Perrier Sébastien , Rivaton Agnès , Dagron-Lartigau Christine , Topham Paul D.
Published: July 2015

In the printing industry, the exploitation of triggerable materials that can have their surface properties altered on application of a post-deposition external stimulus has been crucial for the production of robust layers and patterns.
Electronic transport properties of in-plane heterostructures constructed by MoS2 and WS2 nanoribbons
Authors: Zhou Yi , Dong Jichen , Li Hui
Published: July 2015

A new and simple kind of in-plane heterostructure is constructed by MoS2 nanoribbons (MoS2NRs) and WS2 nanoribbons (WS2NRs) arranged both perpendicularly and in parallel.
Learning beyond the classroom: using text messages to measure general chemistry students' study habits
Authors: Ye Li , Oueini Razanne , Dickerson Austin P. , Lewis Scott E.
Published: July 2015

This study used a series of text message inquiries sent to General Chemistry students asking: “Have you studied for General Chemistry I in the past 48 hours? If so, how did you study?” This method for collecting data is novel to chemistry education research so the first research goals were to investigate the feasibility of the technique and the evidence for validity of the data collected. The results showed that text messages provide ample data on students' study habits though initial participant recruitment may pose a challenge. This study also explored evidence for validity and found that the percent of students reporting studying peaked with each exam date matching the expected trend (content validity) and participants in the study had only small departures from the population of students at the setting (generalizable validity). Second, students' study habits were characterized using cluster analysis finding three clusters: students that knowingly do not study, students who describe mandatory course components as studying and students who study in addition to the mandatory course components. These student groups were compared on a common exam in the course with the last group out-performing those who knowingly do not study. Finally, student study habits were charted across the semester and show signs of adapting, possibly as a result of course expectations or course content.
The effect of cross-linking on the molecular dynamics of the segmental and β Johari–Goldstein processes in polyvinylpyrrolidone-based copolymers
Authors: Redondo-Foj Belén , Sanchis María Jesús , Ortiz-Serna Pilar , Carsí Marta , García José Miguel , García Félix Clemente
Published: July 2015

The cross-linking effect on the molecular dynamics of vinylpyrrolidone (VP)/butyl acrylate (BA) copolymers is reflected in the α process, but more significantly in the β Johari–Goldstein (JG) relaxation.
Electro-capillary effects in capillary filling dynamics of electrorheological fluids
Authors: Dhar Jayabrata , Ghosh Uddipta , Chakraborty Suman
Published: July 2015

The flow of electrorheological fluids is characterized by an apparent increase in viscosity manifested by the yield stress property of the fluid, which is a function of the applied electric field and the concentration of the suspended solute phase within the dielectric medium.
Pt/porous nanorods of ceria as efficient high temperature catalysts with remarkable catalytic stability for carbon dioxide reforming of methane
Authors: Zhang Zhiyun , Li Jing , Gao Wei , Ma Yuanyuan , Qu Yongquan
Published: July 2015

Pt/porous nanorods of CeO2 with a large surface area, a high oxygen storage capacity and a remarkable thermal stability exhibit high catalytic activity and stability for the carbon dioxide reforming of methane reaction at 800 °C.
Cyano-substitution on the end-capping group: facile access toward asymmetrical squaraine showing strong dipole–dipole interactions as a high performance small molecular organic solar cells material
Authors: Yang Daobin , Jiao Yan , Yang Lin , Chen Yao , Mizoi Satoshi , Huang Yan , Pu Xuemei , Lu Zhiyun , Sasabe Hisahiro , Kido Junji
Published: July 2015

Cyano-substituted asymmetrical squaraines for organic solar cells with a high PCE was synthesized.
A trimetallic V–Co–Fe oxide nanoparticle as an efficient and stable electrocatalyst for oxygen evolution reaction
Authors: Gao Taotao , Jin Zhaoyu , Liao Mei , Xiao Jinlan , Yuan Hongyan , Xiao Dan
Published: July 2015

Hydrothermally synthesized V–Co–Fe oxide nanoparticles are reported as a highly active and stable electrocatalyst for the oxygen evolution reaction.
The solid solution series Tl(V1−xCrx)5Se8: crystal structure, magnetic and thermoelectric properties
Authors: Maier Stefan , Lefèvre Robin , Lin Xinsong , Nunna Raghavendra , Berthebaud David , Hèbert Sylvie , Mar Arthur , Gascoin Franck
Published: July 2015

The crystal structure of single crystalline members of the solid solution series Tl(V1−xCrx)5Se8 (x = 0–1 and Δx = 0.2) was determined and the magnetic and thermoelectric properties of bulk TlV5Se8 were investigated.
Employing dual scaling mode for adaptive hill climbing method on buck converter
Authors: Tan Chin Yew , Rahim Nasrudin Abd , Selvaraj Jeyraj
Published: July 2015

For adaptive hill climbing method, variable stepping is achieved by sizing the change of power over the change of voltage (dPPV/dVPV) and change of power over change of D (dPPV/dD) to appropriate step size using a properly tuned scaling factor. However, the photovoltaic (PV) power versus voltage curve has two different slopes which are the left‐hand side of the maximum power point (MPP), and right‐hand side of MPP (ROM). The fine‐tuned scaling factor for the left‐hand side PV slope has good performance at left‐hand side of MPP (LOM) but can cause overshoot when system operates at the ROM; while scaling factor properly tuned for the right‐hand side PV slope has good performance at ROM but slow voltage response when the system operates at LOM. Dual scaling factor technique is proposed to achieve good performance at LOM and ROM. Besides that, the drawback of implementing hill climbing method on buck converter is discussed, where using constant step size, the hill climbing method has small voltage response at point far from MPP but large voltage response at point near MPP. Based on the results obtained from a lab‐scale prototype, it is proven that the proposed method is simple and effective.
Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens
Authors: Chaikuad Apirat , Knapp Stefan , von Delft Frank
Published: July 2015

The quest for an optimal limited set of effective crystallization conditions remains a challenge in macromolecular crystallography, an issue that is complicated by the large number of chemicals which have been deemed to be suitable for promoting crystal growth. The lack of rational approaches towards the selection of successful chemical space and representative combinations has led to significant overlapping conditions, which are currently present in a multitude of commercially available crystallization screens. Here, an alternative approach to the sampling of widely used PEG precipitants is suggested through the use of PEG smears, which are mixtures of different PEGs with a requirement of either neutral or cooperatively positive effects of each component on crystal growth. Four newly defined smears were classified by molecular-weight groups and enabled the preservation of specific properties related to different polymer sizes. These smears not only allowed a wide coverage of properties of these polymers, but also reduced PEG variables, enabling greater sampling of other parameters such as buffers and additives. The efficiency of the smear-based screens was evaluated on more than 220 diverse recombinant human proteins, which overall revealed a good initial crystallization success rate of nearly 50%. In addition, in several cases successful crystallizations were only obtained using PEG smears, while various commercial screens failed to yield crystals. The defined smears therefore offer an alternative approach towards PEG sampling, which will benefit the design of crystallization screens sampling a wide chemical space of this key precipitant.
Structural basis ofDeerpox virus-mediated inhibition of apoptosis
Authors: Burton Denis R. , Caria Sofia , Marshall Bevan , Barry Michele , Kvansakul Marc
Published: July 2015

Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that theDeerpox virusinhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteinsviatwo conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.
Structural and adhesive properties of the long polar fimbriae protein LpfD from adherent-invasiveEscherichia coli
Authors: Coppens Fanny , Iyyathurai Jegan , Ruer Ségolène , Fioravanti Antonella , Taganna Joemar , Vereecke Lars , De Greve Henri , Remaut Han
Published: July 2015

Crohn's disease (CD) is an inflammatory bowel disease characterized by an exaggerated immune response to commensal microbiota in the intestines of patients. Metagenomic studies have identified specific bacterial species and strains with increased prevalence in CD patients, amongst which is the adherent-invasiveEscherichia coli(AIEC) strain LF82. AIEC strains express long polar fimbriae (LPF), which are known to target Peyer's patches in a mouse CD model. Here, the recombinant production of a soluble, self-complemented construct of the LpfD protein ofE. coliLF82 is reported and it is demonstrated that it forms the adhesive tip subunit of LPF. The LpfD crystal reveals an N-terminal adhesin domain and a C-terminal pilin domain that connects the adhesin to the minor pilus subunit LpfE. Surface topology and sequence conservation in the adhesin domain hint at a putative receptor-binding pocket as found in theKlebsiella pneumoniaeMrkD andE. coliF17-G (GafD) adhesins. Immunohistostaining of murine intestinal tissue sections revealed that LpfD specifically binds to the intestinal mucosa and submucosa. LpfD binding was found to be resistant to treatment withO- orN-glycosidases, but was lost in collagenase-treated tissue sections, indicating the possible involvement of an intestinal matrix-associated protein as the LpfD receptor. LpfD strongly adhered to isolated fibronectin in anin vitroassay, and showed lower levels of binding to collagen V and laminin and no binding to collagens I, III and IV.
Structural evidence for asymmetric ligand binding to transthyretin
Authors: Cianci Michele , Folli Claudia , Zonta Francesco , Florio Paola , Berni Rodolfo , Zanotti Giuseppe
Published: July 2015

Human transthyretin (TTR) represents a notable example of an amyloidogenic protein, and several compounds that are able to stabilize its native state have been proposed as effective drugs in the therapy of TTR amyloidosis. The two thyroxine (T4) binding sites present in the TTR tetramer display negative binding cooperativity. Here, structures of TTR in complex with three natural polyphenols (pterostilbene, quercetin and apigenin) have been determined, in which this asymmetry manifests itself as the presence of a main binding site with clear ligand occupancy and related electron density and a second minor site with a much lower ligand occupancy. The results of an analysis of the structural differences between the two binding sites are consistent with such a binding asymmetry. The different ability of TTR ligands to saturate the two T4 binding sites of the tetrameric protein can be ascribed to the different affinity of ligands for the weaker binding site. In comparison, the high-affinity ligand tafamidis, co-crystallized under the same experimental conditions, was able to fully saturate the two T4 binding sites. This asymmetry is characterized by the presence of small but significant differences in the conformation of the cavity of the two binding sites. Molecular-dynamics simulations suggest the presence of even larger differences in solution. Competition binding assays carried out in solution revealed the presence of a preferential binding site in TTR for the polyphenols pterostilbene and quercetin that was different from the preferential binding site for T4. The TTR binding asymmetry could possibly be exploited for the therapy of TTR amyloidosis by using a cocktail of two drugs, each of which exhibits preferential binding for a distinct binding site, thus favouring saturation of the tetrameric protein and consequently its stabilization.
A new micro-furnace for in situ high-temperature single-crystal X-ray diffraction measurements
Authors: Alvaro M. , Angel R. J. , Marciano C. , Milani S. , Scandolo L. , Mazzucchelli M. L. , Zaffiro G. , Rustioni G. , Briccola M. , Domeneghetti M. C. , Nestola F.
Published: July 2015

A new micro-furnace equipped with an H-shaped resistance heater has been developed to conduct in situ single-crystal X-ray diffraction experiments at high temperature. The compact design of the furnace does not restrict access to reciprocal space out to 2θ = 60°. Therefore, unit-cell parameters and intensity data can be determined to a resolution of 0.71 Å with Mo radiation. The combined use of mineral phases with well characterized lattice expansion (e.g. pure Si and SiO2 quartz) and a small-diameter (0.025 mm) K-type thermocouple allowed accurate temperature calibration from room temperature to about 1273 K and consequent evaluation of thermal gradients and stability. The new furnace design allows temperatures up to about 1273 K to be reached with a thermal stability better than ±5 K even at the highest temperatures. Measurements of the lattice thermal expansion of pure silicon (Si), pure synthetic grossular garnet (Ca3Al2Si3O12) and quartz (SiO2) are presented to demonstrate the performance of the device. Its main advantages and limitations and important considerations for using it to perform high-temperature diffraction measurements are discussed.
Xtal-xplore-R: a graphical tool for exploring the residual function involved in crystal structure determination
Authors: Simons Jan Marten , Roth Georg
Published: July 2015

This work presents Xtal-xplore-R, a tool dedicated to the visualization of two-dimensional cuts through the multidimensional crystallographic residual function. It imports arbitrary crystal structures, generates artificial diffraction data, and calculates and investigates the residual function in parameter space. The program serves two major purposes. Firstly, it is part of a more general project dealing with structure determination via global optimization techniques. In this context, the tool is being used to systematically analyse characteristic universal features of the target function (residual function) which can be used to develop appropriate problem-specific heuristic optimization algorithms. Secondly, Xtal-xplore-R is intended as a didactic tool to visualize how changes in atom parameters affect the residual function and can be used to demonstrate manual structure optimization for simple crystal structures.
On the design and experimental realization of a multislit-based very small angle neutron scattering instrument at the European Spallation Source
Authors: Abbas Sohrab , Désert Sylvain , Brûlet Annie , Thevenot Vincent , Permingeat Patrice , Lavie Pascal , Jestin Jacques
Published: July 2015

This article reports the design of a versatile multislit-based very small angle neutron scattering (VSANS) instrument working either as a dedicated instrument or as an add-on for any small-angle neutron scattering machine like the proposed SANS instrument, SKADI, at the future European Spallation Source. The use of multiple slits as a VSANS collimator for the time-of-flight techniques has been validated using McStas simulations. Various instrument configurations to achieve different minimum wavevector transfers in scattering experiments are proposed. The flexibility of the multislit VSANS instrument concept is demonstrated by showing the possibility of instrument length scaling for the first time, allowing access to varying minimum wavevector transfers with the same multislit setup. These options can provide smooth access to minimum wavevector transfers lower than ∼4 × 10−5 Å−1 and an overlapping of wavevector coverage with normal SANS mode, e.g. with the SKADI wavevector range of 10−3–1.1 Å−1. Such an angularly well defined and intense neutron beam will allow faster SANS studies of objects larger than 1 µm. Calculations have also been carried out for a radial collimator as an alternative to the multislit collimator setup. This extends the SANS Q range by an order of magnitude to 1 × 10−4 Å−1 with much simpler alignment. The multislit idea has been realized experimentally by building a prototype at Laboratoire Leon Brillouin, Saclay, with cross-talk-free geometry. Feasibility studies were carried out by making VSANS measurements with single- and multislit collimators, and the results are compared with multiple-pinhole geometry using classical SANS analysis tools.
Structure of human collapsin response mediator protein 1: a possible role of its C-terminal tail
Authors: Liu Szu-Heng , Huang Shih-Fang , Hsu Yuan-Ling , Pan Szu-Hua , Chen Yen-Ju , Lin Yi-Hung
Published: July 2015

Collapsin response mediator protein 1 (CRMP-1) is the first identified member of the CRMP family and is crucial for both the mediation of neuronal differentiation and in suppressing the invasion of lung cancer. The crystal structure of full-length human CRMP-1 was determined at a resolution of 3 Å. Human CRMP-1 comprises a tetrameric assembly; its overall structure is similar to that of mouse CRMP-1, but the measured electron density of the C-terminal residues 488–496 show a randomly coiled link that connects the protomers to each other, within which residues 497–572 are proteolytically susceptiblein vivo. Deletion of residues 472–572 by thrombinin vitronot only releases a randomly coiled tail but also transduces observable structural changes of CRMP-1, as revealed by analytical size-exclusive chromatography and circular dichroism spectra. These results indicate a possible alternative role in CRMP dynamics and function.
Structure of recombinant prolidase fromThermococcus sibiricusin space groupP21221
Authors: Timofeev Vladimir , Slutskaya Elvira , Gorbacheva Marina , Boyko Konstantin , Rakitina Tatiana , Korzhenevskiy Dmitry , Lipkin Alexey , Popov Vladimir
Published: July 2015

The crystal structure of recombinant prolidase fromThermococcus sibiricuswas determined by X-ray diffraction at a resolution of 2.6 Å and was found to contain a tetramer in the asymmetric unit. A protein crystal grown in microgravity using the counter-diffusion method was used for X-ray studies. The crystal belonged to space groupP21221, with unit-cell parametersa= 97.60,b= 123.72,c= 136.52 Å, α = β = γ = 90°. The structure was refined to anRcrystof 22.1% and anRfreeof 29.6%. The structure revealed flexible folding of the N-terminal domain of the protein as well as high variability in the positions of the bound metal ions. The coordinates of the resulting model were deposited in the Protein Data Bank as entry 4rgz.
Crystallographic studies of the extracytoplasmic function σ factor σJfromMycobacterium tuberculosis
Authors: Goutam Kapil , Gupta Arvind Kumar , Gopal Balasubramanian
Published: July 2015

Mycobacterium tuberculosishas multiple σ factors which enable the bacterium to reprogram its transcriptional machinery under diverse environmental conditions. σJ, an extracytoplasmic function σ factor, is upregulated in late stationary phase cultures and during human macrophage infection. σJgoverns the cellular response to hydrogen peroxide-mediated oxidative stress. σJdiffers from other canonical σ factors owing to the presence of a SnoaL_2 domain at the C-terminus. σJcrystals belonged to the tetragonal space groupI422, with unit-cell parametersa=b= 133.85,c= 75.08 Å. Diffraction data were collected to 2.16 Å resolution on the BM14 beamline at the European Synchrotron Radiation Facility (ESRF).