bluuebunny/crossref_metadata_2025_split huggingface dataset:
Femtosecond laser fabrication of high‐Q whispering gallery mode microresonators via two‐photon polymerization
Authors: Tomazio Nathália B. , Otuka Adriano J. G. , Almeida Gustavo F. B. , Roselló‐Mechó Xavier , Andrés Miguel V. , Mendonça Cleber R. 
Published: February 2017

ABSTRACTWhispering gallery mode microresonators have been triggering considerable advances in science due to their ability to confine light within small dielectric volumes, which makes them suitable for a wide range of applications. Lithographic approaches have been the dominant technique for fabricating microresonators; however, they restrict the choice of materials due to their multistep processing nature. As an alternative, they report the direct laser fabrication of acrylic based hollow microcylinder resonators, via two‐photon polymerization, with good structural integrity and sidewall roughness of 1.5 nm, which make them promising candidates for photonic applications in the near‐infrared. Such polymeric microresonators exhibit finesse close to 103 and a quality factor of 1
105, a performance achieved without any additional processing step, which would restrict the choices of materials to be incorporated into the polymeric resonator. This advantage thereby broadens the widespread use of the polymeric microresonators, making them an excellent platform for lasing and nonlinear optics studies in the near‐infrared. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017, 55, 569–574
Inferring structure in bipartite networks using the latent blockmodel and exact ICL
Authors: WYSE JASON , FRIEL NIAL , LATOUCHE PIERRE 
Published: February 2017

AbstractWe consider the task of simultaneous clustering of the two node sets involved in a bipartite network. The approach we adopt is based on use of the exact integrated complete likelihood for the latent blockmodel. Using this allows one to infer the number of clusters as well as cluster memberships using a greedy search. This gives a model-based clustering of the node sets. Experiments on simulated bipartite network data show that the greedy search approach is vastly more scalable than competing Markov chain Monte Carlo-based methods. Application to a number of real observed bipartite networks demonstrate the algorithms discussed.
Creating context for social influence processes in multiplex networks
Authors: OSTOIC J. ANTONIO RIVERO 
Published: February 2017

AbstractThis paper elaborates on two theories of social influence processes to multiplex network structures. First, cohesion influence is based on mutual communication made by different types of relations, and second comparison influence that is built on contrasting types of tie. While a system of bundles with a mutual character constitutes the setting for a multiplex network exposure measure within cohesion, comparison influence is defined algebraically through classes of actors in terms of a weakly balanced semiring structure that considers positive, negative, and also ambivalent types of tie. A case study with these approaches is made on an entrepreneurial community network with formal business relations, informal friendship ties, and perceived competition among the firms, and the methods are validated with the Sampson Monastery data set.
Local-global principles for Weil–Châtelet divisibility in positive characteristic
Authors: CREUTZ BRENDAN , VOLOCH JOSÉ FELIPE 
Published: February 2017

AbstractWe extend existing results characterizing Weil-Châtelet divisibility of locally trivial torsors over number fields to global fields of positive characteristic. Building on work of González-Avilés and Tan, we characterize when local-global divisibility holds in such contexts, providing examples showing that these results are optimal. We give an example of an elliptic curve over a global field of characteristic 2 containing a rational point which is locally divisible by 8, but is not divisible by 8 as well as examples showing that the analogous local-global principle for divisibility in the Weil-Châtelet group can also fail.
Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice
Authors: Janecka Magdalena , Marzi Sarah J. , Parsons Michael J. , Liu Lin , Paya-Cano Jose L. , Smith Rebecca G. , Fernandes Cathy , Schalkwyk Leonard C. 
Published: February 2017

AbstractAlthough the search for quantitative trait loci for behaviour remains a considerable challenge, the complicated genetic architecture of quantitative traits is beginning to be understood. The current project utilised heterogeneous stock (HS) male mice (n = 580) to investigate the genetic basis for brain weights, activity, anxiety and cognitive phenotypes. We identified 126 single nucleotide polymorphisms (SNPs) in genes involved in regulation of neurotransmitter systems, nerve growth/death and gene expression, and subsequently investigated their associations with changes in behaviour and/or brain weights in our sample. We found significant associations between four SNP-phenotype pairs, after controlling for multiple testing. Specificity protein 2 (Sp2,rs3708840), tryptophan hydroxylase 1 (Tph1,rs262731280) and serotonin receptor 3A (Htr3a,rs50670893) were associated with activity/anxiety behaviours, and microtubule-associated protein 2(Map2,rs13475902) was associated with cognitive performance. All these genes except forTph1were expressed in the brain above the array median, and remained significantly associated with relevant behaviours after controlling for the family structure. Additionally, we found evidence for a correlation betweenHtr3aexpression and activity. We discuss our findings in the light of the advantages and limitations of currently available mouse genetic tools, suggesting further directions for association studies in rodents.
Controlled doping by self-assembled dendrimer-like macromolecules
Authors: Wu Haigang , Guan Bin , Sun Yingri , Zhu Yiping , Dan Yaping 
Published: February 2017

AbstractDoping via self-assembled macromolecules might offer a solution for developing single atom electronics by precisely placing individual dopants at arbitrary location to meet the requirement for circuit design. Here we synthesize dendrimer-like polyglycerol macromolecules with each carrying one phosphorus atom in the core. The macromolecules are immobilized by the coupling reagent onto silicon surfaces that are pre-modified with a monolayer of undecylenic acid. Nuclear magnetic resonance (NMR) and X-ray photoelectron spectroscopy (XPS) are employed to characterize the synthesized macromolecules and the modified silicon surfaces, respectively. After rapid thermal annealing, the phosphorus atoms carried by the macromolecules diffuse into the silicon substrate, forming dopants at a concentration of 1017 cm−3. Low-temperature Hall effect measurements reveal that the ionization process is rather complicated. Unlike the widely reported simple ionization of phosphorus dopants, nitrogen and carbon are also involved in the electronic activities in the monolayer doped silicon.
Upregulation of MiR-205 transcriptionally suppresses SMAD4 and PTEN and contributes to human ovarian cancer progression
Authors: Li Juanni , Hu Kuan , Gong Guanghui , Zhu Ding , Wang Yixuan , Liu Hailing , Wu Xiaoying 
Published: February 2017

AbstractMicroRNAs (miRNAs) function as critical regulators of gene expression and their deregulation is associated with the development and progression of various cancers. This study aimed to investigate the biological role and mechanism of miR-205 in ovarian cancer (OC). MiR-205 was upregulated in OC tissues and cells in comparison to the controls. Meanwhile, overexpression of miR-205 was significantly associated with poor overall survival of OC patients. Functional study indicated that ectopic expression of miR-205 significantly promoted cell proliferation, migration, invasion and chemoresistance of OC cells. SMAD4 and PTEN were identified as direct targets of miR-205 using luciferase reporter assays, real-time PCR (qRT-PCR), and western blot. Most interestingly,in vivostudies indicated that miR-205 markedly promoted the growth and metastasis of tumors and the expression of miR-205 was also found to be inversely correlated with that of SMAD4 and PTEN in nude mice. Overall, we suggest that miR-205 functions as an oncogenic miRNA by directly binding to SMAD4 and PTEN, providing a novel target for the molecular treatment of ovarian cancer.
TDAG8 involved in initiating inflammatory hyperalgesia and establishing hyperalgesic priming in mice
Authors: Dai Shih-Ping , Huang Ya-Han , Chang Chung-Jen , Huang Yu-Fen , Hsieh Wei-Shan , Tabata Yasuhiko , Ishii Satoshii , Sun Wei-Hsin 
Published: February 2017

AbstractChronic pain, resulting from injury, arthritis, and cancer, is often accompanied by inflammation. High concentrations of protons found in inflamed tissues results in tissue acidosis, a major cause of pain and hyperalgesia. Acidosis signals may mediate a transition from acute to chronic hyperalgesia (hyperalgesic priming) via proton-sensing G-protein-coupled receptors (GPCRs). The expression of T-cell death-associated gene 8 (TDAG8), a proton-sensing GPCR, is increased during inflammatory hyperalgesia. Attenuating TDAG8 expression in the spinal cord inhibits bone cancer pain, but whether TDAG8 is involved in inflammatory hyperalgesia or hyperalgesic priming remains unclear. In this study, we used TDAG8-knockout or -knockdown to explore the role of TDAG8 in pain. Suppressed TDAG8 expression delayed the onset of inflammatory hyperalgesia and shortened hyperalgesic time in mice. In a dual acid-injection model (acid [pH 5.0] injected twice, 5 days apart), shRNA inhibition of TDAG8 shortened the duration of the second hyperalgesia. Similar results were found in TDAG8-deficient mice. The dual administration of TDAG8 agonist also confirmed that TDAG8 is involved in hyperalgsic priming. Accordingly, TDAG8 may mediate acidosis signals to initiate inflammatory hyperalgesia and establish hyperalgesic priming.
Multidimensional metrics of niche space for use with diverse analytical techniques
Authors: Bowes Rachel E. , Thorp James H. , Reuman Daniel C. 
Published: February 2017

AbstractMultidimensional data are integral to many community-ecological studies and come in various forms, such as stable isotopes, compound specific analyses (e.g., amino acids and fatty acids), and both biodiversity and life history traits. Scientists employing such data often lack standardized metrics to evaluate communities in niche space where more than 2 dimensions are involved. To alleviate this problem, we developed a graphing and analytical approach for use with more than two variables, based on previously established stable isotope bi-plot metrics. We introduce here our community metrics as R scripts. By extending the original metrics to multiple dimensions, we created n-dimensional plots and metrics to characterize any set of quantitative measurements of a community. We demonstrate the utility of these metrics using stable isotope data; however, the approaches are applicable to many types of data. The resulting metrics provide more and better information compared to traditional analytic frameworks. The approach can be applied in many branches of community ecology, and it offers accessible metrics to quantitatively analyze the structure of communities across ecosystems and through time.
Honeybee locomotion is impaired by Am-CaV3 low voltage-activated Ca2+ channel antagonist
Authors: Rousset M. , Collet C. , Cens T. , Bastin F. , Raymond V. , Massou I. , Menard C. , Thibaud J.-B. , Charreton M. , Vignes M. , Chahine M. , Sandoz J. C. , Charnet P. 
Published: February 2017

AbstractVoltage‐gated Ca2+ channels are key transducers of cellular excitability and participate in several crucial physiological responses. In vertebrates, 10 Ca2+ channel genes, grouped in 3 families (CaV1, CaV2 and CaV3), have been described and characterized. Insects possess only one member of each family. These genes have been isolated in a limited number of species and very few have been characterized although, in addition to their crucial role, they may represent a collateral target for neurotoxic insecticides. We have isolated the 3 genes coding for the 3 Ca2+ channels expressed in Apis mellifera. This work provides the first detailed characterization of the honeybee T-type CaV3 Ca2+ channel and demonstrates the low toxicity of inhibiting this channel. Comparing Ca2+ currents recorded in bee neurons and myocytes with Ca2+ currents recorded in Xenopus oocytes expressing the honeybee CaV3 gene suggests native expression in bee muscle cells only. High‐voltage activated Ca2+ channels could be recorded in the somata of different cultured bee neurons. These functional data were confirmed by in situ hybridization, immunolocalization and in vivo analysis of the effects of a CaV3 inhibitor. The biophysical and pharmacological characterization and the tissue distribution of CaV3 suggest a role in honeybee muscle function.
Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1
Authors: Michael Alicia K. , Fribourgh Jennifer L. , Chelliah Yogarany , Sandate Colby R. , Hura Greg L. , Schneidman-Duhovny Dina , Tripathi Sarvind M. , Takahashi Joseph S. , Partch Carrie L. 
Published: February 2017

SignificanceCircadian rhythms depend upon the precise coordination of protein interactions within the transcription–translation feedback loop of the molecular clock. Period (PER) and cryptochrome (CRY) rhythmically repress activity of the circadian transcription factor, CLOCK:BMAL1 (brain and muscle Arnt-like protein 1), to establish daily patterns of gene expression. CRY1 binds to CLOCK:BMAL1 with and without PER to inhibit CLOCK:BMAL1 activity. Here we show that CRY1 interacts with the CLOCK PAS-B domain to dock the transcription factor into the secondary pocket of CRY1. Studies of a CRY1:CLOCK:BMAL1 complex highlight critical interfaces for the direct regulation of CLOCK:BMAL1 by cryptochromes. A molecular understanding of the clock mechanism is fundamental for the development and application of therapies for circadian-related disorders.
Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme
Authors: Li Yini , Zhou Mengying , Hu Qi , Bai Xiao-chen , Huang Weiyun , Scheres Sjors H. W. , Shi Yigong 
Published: February 2017

Significance
As a prototypical initiator caspase, caspase-9 has been rigorously studied for 20 years. Although activation of the caspase-9 zymogen and catalytic activity of the mature caspase-9 both strictly depend on the Apaf-1 apoptosome, the underlying mechanism remains poorly understood. Previous mechanistic studies relied heavily on engineered caspase-9 in the absence of the Apaf-1 apoptosome. In this study, we tackle the problem through structure determination of the Apaf-1 apoptosome bound to caspase-9 and biochemical analysis of caspase-9 activity in the presence of the Apaf-1 apoptosome. The results demonstrate that the Apaf-1 apoptosome activates caspase-9 by two means: suppressing the inhibition mediated by the caspase recruitment domains (CARD) domain and stimulating the catalytic activity of the protease domain.
Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins
Authors: He Yi , Maisuradze Gia G. , Yin Yanping , Kachlishvili Khatuna , Rackovsky S. , Scheraga Harold A. 
Published: February 2017

Significance
We study a set of proteins that exhibit low sequence identity, but high structural homology and functional similarity. It is demonstrated that a physics-based sequence comparison tool, the property factor method, is able to detect differences between the sequences of these proteins that correlate with differences in their structures and dynamics. It is shown that these sequence differences are not detected in this challenging system by conventional alignment methods. This result suggests that a significant amount of the information encoded in protein sequences is not captured by evolutionarily motivated comparison methods.
Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression
Authors: Sripathy Smitha , Leko Vid , Adrianse Robin L. , Loe Taylor , Foss Eric J. , Dalrymple Emily , Lao Uyen , Gatbonton-Schwager Tonibelle , Carter Kelly T. , Payer Bernhard , Paddison Patrick J. , Grady William M. , Lee Jeannie T. , Bartolomei Marisa S. , Bedalov Antonio 
Published: February 2017

Significance
Rett syndrome is a neurodevelopmental disorder in girls who are heterozygous for a mutation in the X-linked gene MeCP2. Because cells in these individuals will be missing MeCP2 function only when the wild-type copy of the gene is on the inactive X, reactivation of the silenced copy of MeCP2 presents a potential therapeutic strategy. To identify genes that silence MeCP2 on the inactive X and that could therefore prove valuable as therapeutic targets, we carried out a screen for genes whose down-regulation reactivated a MeCP2 reporter on the inactive X. The 30 genes we have identified reveal a genetic circuitry required for maintenance of X-chromosome inactivation in differentiated cells and a large number of targets suitable for pharmacologic intervention.
ADP-ribosylhydrolase activity of Chikungunya virus macrodomain is critical for virus replication and virulence
Authors: McPherson Robert Lyle , Abraham Rachy , Sreekumar Easwaran , Ong Shao-En , Cheng Shang-Jung , Baxter Victoria K. , Kistemaker Hans A. V. , Filippov Dmitri V. , Griffin Diane E. , Leung Anthony K. L. 
Published: February 2017

Significance
Viral outbreaks can be sudden and result in devastating social and economic consequences. Chikungunya virus (CHIKV) outbreaks of rash, arthritis, and neurologic disease have occurred in Africa, Asia, Europe, and the Americas. There are no licensed vaccines to prevent or drugs to treat CHIKV infection, and the mechanisms of disease generation are poorly understood. Here, we identify a macrodomain-containing CHIKV protein with enzymatic ADP-ribosylhydrolase activity that is critical for virulence in mammals and define the substrate specificity of this enzyme. Given the conservation of viral macrodomains in all alphaviruses and coronaviruses, our study may guide the design of small molecule chemical compounds that block hydrolase activity for treatment of a range of virus infections.
Effect of decompression drying treatment on physical properties of solid foods
Authors: Morikawa Takuya , Takada Norihisa , Miura Makoto 
Published: February 2017

AbstractThis study used a decompression drying instrument to investigate the effects of a drying treatment on the physical properties of solid foods. Commercial tofu was used as a model food and was treated at different temperature and pressure conditions in a drying chamber. Overall, high temperatures resulted in better drying. Additionally, pressure in the chamber influenced the drying conditions of samples. Differences in physical properties, such as food texture, shrinkage, and color were observed among some samples, even with similar moisture content. This was caused by differences in moisture distribution in the food, which seems to have manifested as a thin, dried film on the surfaces of samples. It caused inefficient drying and changes in physical properties. Control of the drying conditions (i.e. pressure and heat supply) has relations with not only physical properties, but also the drying efficiency of solid foods.
Estimating year-class strength of Icelandic summer-spawning herring on the basis of two survey methods
Authors: Gudmundsdottir Asta , Oskarsson Gudmundur J. , Sveinbjörnsson Sveinn 
Published: February 2017

Abstract
Gudmundsdottir, A., Oskarsson, G. J., and Sveinbjörnsson, S. 2007. Estimating year-class strength of Icelandic summer-spawning herring on the basis of two survey methods. – ICES Journal of Marine Science, 64: 1182–1190. Recruitment indices at age 1 and 2 were constructed for Icelandic summer-spawning herring using data from two inherently different survey methods on their nursery areas for the years 1988–2003. The surveys were a shrimp, bottom-trawl survey and a herring acoustic survey. Indices were compared with the year-class strength at age 2 derived from an assessment model (AMCI) used for the stock. A juvenile index at age 1 from the acoustic survey and at age 2 from the shrimp-trawl survey correlated significantly with the modelled recruitment, although only marginally with each other. One index was not considered markedly better than the other, and both have shortcomings even if the acoustic survey is believed better than the trawl survey for quantifying juvenile herring. The recruitment index at age 1 derived from the acoustic survey can be improved as an indicator of recruitment if that survey were to be extended to cover the nursery areas off western and southeastern Iceland, and the same areas covered each year.
Using computational theory to constrain statistical models of neural data
Authors: Linderman Scott W. , Gershman Samuel J. 
Published: February 2017

AbstractComputational neuroscience is, to first order, dominated by two approaches: the “bottom-up” approach, which searches for statistical patterns in large-scale neural recordings, and the “top-down” approach, which begins with a theory of computation and considers plausible neural implementations. While this division is not clear-cut, we argue that these approaches should be much more intimately linked. From a Bayesian perspective, computational theories provide constrained prior distributions on neural data—albeit highly sophisticated ones. By connecting theory to observation via a probabilistic model, we provide the link necessary to test, evaluate, and revise our theories in a data-driven and statistically rigorous fashion. This review highlights examples of this theory-driven pipeline for neural data analysis in recent literature and illustrates it with a worked example based on the temporal difference learning model of dopamine.
Field manipulations of resources mediate the transition from intraspecific competition to facilitation
Authors: Svanfeldt Karin , Monro Keyne , Marshall Dustin J. 
Published: February 2017

Summary

Population density affects individual performance, though its effects are often mixed. For sessile species, increases in population density typically reduce performance. Still, cases of positive density‐dependence do occur in sessile systems and demand explanation. The stress gradient hypothesis (SGH) predicts that under stressful conditions, positive effects of facilitation may outweigh the negative effects of competition.
While some elements of the SGH are well studied, its potential to explain intraspecific facilitation has received little attention. Further, there have been questions regarding whether the SGH holds if the stressor is a resource. Most studies of interactions between the environment and intraspecific facilitation have relied on natural environmental gradients; manipulative studies are much rarer.
To test the effects of intraspecific density and resources, we manipulated resource availability over natural population densities for the marine bryozoan Watersipora subtorquata.
We found negative effects of density on colony performance in low resource environments, but mainly positive density‐dependence in high resource environments. By adding resources, competition effects were reduced and the positive effects of facilitation were revealed.
Our results suggest that resource availability mediates the relative strength of competition and facilitation in our system. We also suggest that intraspecific facilitation is more common than may be appreciated and that environmental variation may mediate the balance between negative and positive density‐dependence.