bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Design of Field Experiments With Survey Outcomes: A Framework for Selecting More Efficient, Robust, and Ethical Designs
Authors: Broockman David E. , Kalla Joshua L. , Sekhon Jasjeet S. 
Published: September 2017

There is increasing interest in experiments where outcomes are measured by surveys and treatments are delivered by a separate mechanism in the real world, such as by mailers, door-to-door canvasses, phone calls, or online ads. However, common designs for such experiments are often prohibitively expensive, vulnerable to bias, and raise ethical concerns. We show how four methodological practices currently uncommon in such experiments have previously undocumented complementarities that can dramatically relax these constraints when at least two are used in combination: (1) online surveys recruited from a defined sampling frame (2) with at least one baseline wave prior to treatment (3) with multiple items combined into an index to measure outcomes and, (4) when possible, a placebo control. We provide a general and extensible framework that allows researchers to determine the most efficient mix of these practices in diverse applications. Two studies then examine how these practices perform empirically. First, we examine the representativeness of online panel respondents recruited from a defined sampling frame and find that their representativeness compares favorably to phone panel respondents. Second, an original experiment successfully implements all four practices in the context of a door-to-door canvassing experiment. We conclude discussing potential extensions.
Indirect evidence of pathogen-associated altered oocyte production in queens of the invasive yellow crazy ant, Anoplolepis gracilipes, in Arnhem Land, Australia
Authors: Cooling M.D. , Hoffmann B.D. , Gruber M.A.M. , Lester P.J. 
Published: September 2017

AbstractAnoplolepis gracilipes is one of the six most widespread and pestiferous invasive ant species. Populations of this invader in Arnhem Land, Australia have been observed to decline, but the reasons behind these declines are not known. We investigated if there is evidence of a pathogen that could be responsible for killing ant queens or affecting their reproductive output. We measured queen number per nest, fecundity and fat content of queens from A. gracilipes populations in various stages of decline or expansion. We found no significant difference in any of these variables among populations. However, 23% of queens were found to have melanized nodules, a cellular immune response, in their ovaries and fat bodies. The melanized nodules found in dissected queens are highly likely to indicate the presence of pathogens or parasites capable of infecting A. gracilipes. Queens with nodules had significantly fewer oocytes in their ovaries, but nodule presence was not associated with low ant population abundances. Although the microorganism responsible for the nodules is as yet unidentified, this is the first evidence of the presence of a pathogenic microorganism in the invasive ant A. gracilipes that may be affecting reproduction.
The Thrace Basin and the Black Sea: the Eocene–Oligocene marine connection
Authors: OKAY ARAL I. , ÖZCAN ERCAN , HAKYEMEZ AYNUR , SIYAKO MUZAFFER , SUNAL GÜRSEL , KYLANDER-CLARK ANDREW R.C. 
Published: September 2017

AbstractThe Late Cretaceous – Recent West Black Sea Basin and the Eocene–Oligocene Thrace Basin are separated by the Strandja arch comprising metamorphic and magmatic rocks. Since Late Cretaceous time the Strandja arch formed a palaeo-high separating the two basins which accumulated clastic sediment of >9 km thickness. During late Eocene – early Oligocene time the marine connection between these basins existed through the Çatalca gap west of Istanbul. The Çatalca gap lies on the damage zone of a major Cretaceous strike-slip fault; it formed a 15 km wide marine gateway, where carbonate-rich sediments of thicknessc.350 m were deposited. The sequence consists of upper Eocene shallow marine limestones (SBZ18-20) overlain by upper Eocene – lower Oligocene (P16-P19 zones) pelagic marl with a rich fauna of planktonic foraminifera; the marls are intercalated with 31–32 Ma acidic tuff and calc-arenite beds. The Çatalca gap is bounded in the west by a major normal fault, which marks the eastern boundary of the Thrace Basin. Seismic reflection profiles, well data and zircon U–Pb ages indicate that the Thrace Basin sequence west of the fault is late Eocene – middle Oligocene (37–27 Ma) in age and that the fault has accommodated 2 km of subsidence. Although there was a marine connection between the West Black Sea and Thrace basins during late Eocene – early Oligocene time, no significant exchange of clastic sediment took place. Sedimentation in the Çatalca gap ended abruptly during early Oligocene time by uplift, and this eventually led to the paralic conditions in the Thrace Basin.
Targeting tumor multicellular aggregation through IGPR-1 inhibits colon cancer growth and improves chemotherapy
Authors: Woolf N , Pearson B E , Bondzie P A , Meyer R D , Lavaei M , Belkina A C , Chitalia V , Rahimi N 
Published: September 2017

AbstractAdhesion to extracellular matrix (ECM) is crucially important for survival of normal epithelial cells as detachment from ECM triggers specific apoptosis known as anoikis. As tumor cells lose the requirement for anchorage to ECM, they rely on cell–cell adhesion ‘multicellular aggregation’ for survival. Multicellular aggregation of tumor cells also significantly determines the sensitivity of tumor cells to the cytotoxic effects of chemotherapeutics. In this report, we demonstrate that expression of immunoglobulin containing and proline-rich receptor-1 (IGPR-1) is upregulated in human primary colon cancer. Our study demonstrates that IGPR-1 promotes tumor multicellular aggregation, and interfering with its adhesive function inhibits multicellular aggregation and, increases cell death. IGPR-1 supports colon carcinoma tumor xenograft growth in mouse, and inhibiting its activity by shRNA or blocking antibody inhibits tumor growth. More importantly, IGPR-1 regulates sensitivity of tumor cells to the chemotherapeutic agent, doxorubicin/adriamycin by a mechanism that involves doxorubicin-induced AKT activation and phosphorylation of IGPR-1 at Ser220. Our findings offer novel insight into IGPR-1's role in colorectal tumor growth, tumor chemosensitivity, and as a possible novel anti-cancer target.
Structural investigation of nucleophosmin interaction with the tumor suppressor Fbw7γ
Authors: Di Matteo A , Franceschini M , Paiardini A , Grottesi A , Chiarella S , Rocchio S , Di Natale C , Marasco D , Vitagliano L , Travaglini-Allocatelli C , Federici L 
Published: September 2017

AbstractNucleophosmin (NPM1) is a multifunctional nucleolar protein implicated in ribogenesis, centrosome duplication, cell cycle control, regulation of DNA repair and apoptotic response to stress stimuli. The majority of these functions are played through the interactions with a variety of protein partners. NPM1 is frequently overexpressed in solid tumors of different histological origin. Furthermore NPM1 is the most frequently mutated protein in acute myeloid leukemia (AML) patients. Mutations map to the C-terminal domain and lead to the aberrant and stable localization of the protein in the cytoplasm of leukemic blasts. Among NPM1 protein partners, a pivotal role is played by the tumor suppressor Fbw7γ, an E3-ubiquitin ligase that degrades oncoproteins like c-MYC, cyclin E, Notch and c-jun. In AML with NPM1 mutations, Fbw7γ is degraded following its abnormal cytosolic delocalization by mutated NPM1. This mechanism also applies to other tumor suppressors and it has been suggested that it may play a key role in leukemogenesis. Here we analyse the interaction between NPM1 and Fbw7γ, by identifying the protein surfaces implicated in recognition and key aminoacids involved. Based on the results of computational methods, we propose a structural model for the interaction, which is substantiated by experimental findings on several site-directed mutants. We also extend the analysis to two other NPM1 partners (HIV Tat and CENP-W) and conclude that NPM1 uses the same molecular surface as a platform for recognizing different protein partners. We suggest that this region of NPM1 may be targeted for cancer treatment.
Large room temperature spin-to-charge conversion signals in a few-layer graphene/Pt lateral heterostructure
Authors: Yan Wenjing , Sagasta Edurne , Ribeiro Mário , Niimi Yasuhiro , Hueso Luis E. , Casanova Fèlix 
Published: September 2017

AbstractElectrical generation and detection of pure spin currents without the need of magnetic materials are key elements for the realization of full electrically controlled spintronic devices. In this framework, achieving a large spin-to-charge conversion signal is crucial, as considerable outputs are needed for plausible applications. Unfortunately, the values obtained so far have been rather low. Here we exploit the spin Hall effect by using Pt, a non-magnetic metal with strong spin-orbit coupling, to generate and detect pure spin currents in a few-layer graphene channel. Furthermore, the outstanding properties of graphene, with long-distance spin transport and higher electrical resistivity than metals, allow us to achieve in our graphene/Pt lateral heterostructures the largest spin-to-charge output voltage at room temperature reported so far in the literature. Our approach opens up exciting opportunities towards the implementation of spin-orbit-based logic circuits and all electrical control of spin information without magnetic field.
Squirming motion of baby skyrmions in nematic fluids
Authors: Ackerman Paul J. , Boyle Timothy , Smalyukh Ivan I. 
Published: September 2017

AbstractSkyrmions are topologically protected continuous field configurations that cannot be smoothly transformed to a uniform state. They behave like particles and give origins to the field of skyrmionics that promises racetrack memory and other technological applications. Unraveling the non-equilibrium behavior of such topological solitons is a challenge. We realize skyrmions in a chiral liquid crystal and, using numerical modeling and polarized video microscopy, demonstrate electrically driven squirming motion. We reveal the intricate details of non-equilibrium topology-preserving textural changes driving this behavior. Direction of the skyrmion’s motion is robustly controlled in a plane orthogonal to the applied field and can be reversed by varying frequency. Our findings may spur a paradigm of soliton dynamics in soft matter, with a rich interplay between topology, chirality, and orientational viscoelasticity.
Total synthesis of avenaol
Authors: Yasui Motohiro , Ota Rina , Tsukano Chihiro , Takemoto Yoshiji 
Published: September 2017

AbstractAvenaol, isolated from the allelopathic plant black oat, was the first C20 germination stimulant related to strigolactones. Structurally, it consisted of a bicyclo[4.1.0]heptanone skeleton containing a cyclopropane ring bearing three main chains projecting in the same direction (i.e. all-cis-substituted cyclopropane). Herein, we report the total synthesis of avenaol using a robust strategy involving the formation of an all-cis-substituted cyclopropane via an alkylidenecyclopropane. The key factors in the success of this total synthesis include the Rh-catalysed intramolecular cyclopropanation of an allene, an Ir-catalysed stereoselective double-bond isomerisation, and the differentiation of two hydroxymethyl groups via the regioselective formation and oxidation of a tetrahydropyran based on the reactivity of a cyclopropyl group. This strategy effectively avoids the undesired ring opening of the cyclopropane ring and the formation of a caged structure. Furthermore, this study confirms the proposed structure of avenaol, including its unique all-cis-substituted cyclopropane moiety.
A replication study of genetic risk loci for ischemic stroke in a Dutch population: a case-control study
Authors: Hauer Allard J. , Pulit Sara L. , van den Berg Leonard H. , de Bakker Paul I. W. , Veldink Jan H. , Ruigrok Ynte M. ,   Dutch Parelsnoer Institute-Cerebrovascular accident (CVA) Study Group, Klijn Catharina J. M. , Algra Ale , van Dijk Ewoud J. , Koudstaal Peter J. , Luijckx Gert-Jan , Nederkoorn Paul J. , van Oostenbrugge Robert J. , Visser Marieke C. , Wermer Marieke J. , Kappelle L. Jaap 
Published: September 2017

AbstractWe aimed to replicate reported associations of 10 SNPs at eight distinct loci with overall ischemic stroke (IS) and its subtypes in an independent cohort of Dutch IS patients. We included 1,375 IS patients enrolled in a prospective multicenter hospital-based cohort in the Netherlands, and 1,533 population-level controls of Dutch descent. We tested these SNPs for association with overall IS and its subtypes (large artery atherosclerosis, small vessel disease and cardioembolic stroke (CE), as classified by TOAST) using an additive multivariable logistic regression model, adjusting for age and sex. We obtained odds ratios (OR) with 95% confidence intervals (95% CI) for the risk allele of each SNP analyzed and exact p-values by permutation. We confirmed the association at 4q25 (PITX2) (OR 1.43; 95% CI, 1.13–1.81, p = 0.029) and 16q22 (ZFHX3) (OR 1.62; 95% CI, 1.26–2.07, p = 0.001) as risk loci for CE. Locus 16q22 was also associated with overall IS (OR 1.24; 95% CI, 1.08–1.42, p = 0.016). Other loci previously associated with IS and/or its subtypes were not confirmed. In conclusion, we validated two loci (4q25, 16q22) associated with CE. In addition, our study may suggest that the association of locus 16q22 may not be limited to CE, but also includes overall IS.
Isomers Identification of 2-hydroxyglutarate acid disodium salt (2HG) by Terahertz Time-domain Spectroscopy
Authors: Chen Wanqing , Peng Yan , Jiang Xiankai , Zhao Jiayu , Zhao Hongwei , Zhu Yiming 
Published: September 2017

Abstract2-Hydroxyglutaric acid disodium salt (2HG) is a unique biomarker existing in glioma, which can be used for recognizing cancer development stage and identifying the boundary between the ordinary tissue and cancer tissue. However, the most efficient detection method for 2HG now is Magnetic Resonance Spectroscopy (MRS), whose testing time is at least twenty minutes and the variability of 2HG (continuous synthesis and decomposition) determines it cannot be used as the real-time image in medical surgery. In this paper, by using the Terahertz Time-domain Spectroscopy (THz-TDS) System, we investigate the vibration spectra of 2HG isomers and further distinguish their physical properties by using Density Functional Theory. The differences between isomers are mainly attributed to the proton transfer inside the carbon chain. These results indicate that terahertz technology can identify the isomers of 2HG accurate and fast, which has important significance for the further investigation of glioma and clinical surgery.
FLT1 and transcriptome-wide polyadenylation site (PAS) analysis in preeclampsia
Authors: Ashar-Patel Ami , Kaymaz Yasin , Rajakumar Augustine , Bailey Jeffrey A. , Karumanchi S. Ananth , Moore Melissa J. 
Published: September 2017

AbstractMaternal symptoms of preeclampsia (PE) are primarily driven by excess anti-angiogenic factors originating from the placenta. Chief among these are soluble Flt1 proteins (sFlt1s) produced from alternatively polyadenylated mRNA isoforms. Here we used polyadenylation site sequencing (PAS-Seq) of RNA from normal and PE human placentae to interrogate transcriptome-wide gene expression and alternative polyadenylation signatures associated with early-onset PE (EO-PE; symptom onset < 34 weeks) and late-onset PE (LO-PE; symptom onset > 34 weeks) cohorts. While we observed no general shift in alternative polyadenylation associated with PE, the EO-PE and LO-PE cohorts do exhibit gene expression profiles distinct from both each other and from normal placentae. The only two genes upregulated across all transcriptome-wide PE analyses to date (microarray, RNA-Seq and PAS-Seq) are NRIP1 (RIP140), a transcriptional co-regulator linked to metabolic syndromes associated with obesity, and Flt1. Consistent with sFlt1 overproduction being a significant driver of clinical symptoms, placental Flt1 mRNA levels strongly correlate with maternal blood pressure. For Flt1, just three mRNA isoforms account for > 94% of all transcripts, with increased transcription of the entire locus driving Flt1 upregulation in both EO-PE and LO-PE. These three isoforms thus represent potential targets for therapeutic RNA interference (RNAi) in both early and late presentations.
Clustering of conformational IgE epitopes on the major dog allergen Can f 1
Authors: Curin Mirela , Weber Milena , Hofer Gerhard , Apostolovic Danijela , Keller Walter , Reininger Renate , Swoboda Ines , Spitzauer Susanne , Focke-Tejkl Margit , van Hage Marianne , Valenta Rudolf 
Published: September 2017

AbstractImmunoglobulin E (IgE)-associated allergy affects more than 25% of the population. Can f 1 is the major dog allergen associated with respiratory symptoms but the epitopes recognized by allergic patients IgE on Can f 1 are unknown. To characterize IgE epitopes of Can f 1 recognized by dog allergic patients, six overlapping peptides spanning the Can f 1 sequence were synthesized. In direct IgE epitope mapping experiments peptides were analyzed for IgE reactivity by dot blot and Enzyme-linked immunosorbent assay (ELISA) with sera from dog allergic patients. For indirect epitope-mapping, rabbits were immunized with the peptides to generate specific IgG antibodies which were used to inhibit allergic patients’ IgE binding to Can f 1. IgE binding sites were visualized on a model of the Can f 1 three-dimensional structure. We found that Can f 1 does not contain any relevant sequential IgE epitopes. However, IgE inhibition experiments with anti-peptide specific IgGs showed that Can f 1 N- and C-terminal portion assembled a major conformational binding site. In conclusion, our study is the first to identify the major IgE epitope-containing area of the dog allergen Can f 1. This finding is important for the development of allergen-specific treatment strategies.
Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs
Authors: Drag Markus , Skinkyté-Juskiené Ruta , Do Duy N. , Kogelman Lisette J. A. , Kadarmideen Haja N. 
Published: September 2017

AbstractBoar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. Differential expression analysis revealed substantial changes with log-transformed fold changes of liver and testis from −3.39 to 2.96 and −7.51 to 3.53, respectively. Co-expression network analysis revealed one module with a correlation of −0.27 in liver and three modules with correlations of 0.31, −0.44 and −0.49 in testis. Differential expression and co-expression analysis revealed candidate biomarkers with varying biological functions: phase I (COQ3,COX6C,CYP2J2,CYP2B6,ACOX2) and phase II metabolism (GSTO1,GSR,FMO3) of skatole and androstenone in liver to steroidgenesis (HSD17B7,HSD17B8,CYP27A1), regulation of steroidgenesis (STARD10,CYB5R3) and GnRH signalling (MAPK3,MAP2K2,MAP3K2) in testis. Overrepresented pathways included “Ribosome”, “Protein export” and “Oxidative phosphorylation” in liver and “Steroid hormone biosynthesis” and “Gap junction” in testis. Future work should evaluate the biomarkers in large populations to ensure their usefulness in genomic selection programs.
Physiological and transcriptome analysis of heteromorphic leaves and hydrophilic roots in response to soil drying in desert Populus euphratica
Authors: Iqbal Arshad , Wang Tianxiang , Wu Guodong , Tang Wensi , Zhu Chen , Wang Dapeng , Li Yi , Wang Huafang 
Published: September 2017

AbstractPopulus euphraticaOlivier, which has been considered as a tree model for the study of higher plant response to abiotic stresses, survive in the desert ecosystem characterized by extreme drought stress. To survive in the harsh environmental condition the plant species have developed some plasticity such as the development of heteromorphic leaves and well-developed roots system. We investigated the physiological and molecular mechanisms enabling this species to cope with severe stress caused by drought. The heterophylly, evolved from linear to toothed-ovate shape, showed the significant difference in cuticle thickness, stomata densities, and sizes. Physiological parameters, SOD, POD, PPO, CAT activity, free proline, soluble protein and MDA contents fluctuated in response to soil drying. Gene expression profile of roots monitored at control and 4 moisture gradients regimes showed the up-regulation of 124, 130, 126 and 162 and down-regulation of 138, 251, 314, 168 DEGs, respectively. Xyloglucan endotransglucosylase/ hydrolase gene (XET) up-regulated at different moisture gradients, was cloned and expressed in tobacco. TheXETpromoter sequence harbors the drought signaling responsivecis-elements. The promoter expression activity varies in different organs. Over-expression and knocked down transgenic tobacco plant analysis confirmed the role ofXETgene in roots growth and drought resistance.
Higher-order spin and charge dynamics in a quantum dot-lead hybrid system
Authors: Otsuka Tomohiro , Nakajima Takashi , Delbecq Matthieu R. , Amaha Shinichi , Yoneda Jun , Takeda Kenta , Allison Giles , Stano Peter , Noiri Akito , Ito Takumi , Loss Daniel , Ludwig Arne , Wieck Andreas D. , Tarucha Seigo 
Published: September 2017

AbstractUnderstanding the dynamics of open quantum systems is important and challenging in basic physics and applications for quantum devices and quantum computing. Semiconductor quantum dots offer a good platform to explore the physics of open quantum systems because we can tune parameters including the coupling to the environment or leads. Here, we apply the fast single-shot measurement techniques from spin qubit experiments to explore the spin and charge dynamics due to tunnel coupling to a lead in a quantum dot-lead hybrid system. We experimentally observe both spin and charge time evolution via first- and second-order tunneling processes, and reveal the dynamics of the spin-flip through the intermediate state. These results enable and stimulate the exploration of spin dynamics in dot-lead hybrid systems, and may offer useful resources for spin manipulation and simulation of open quantum systems.