bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volcanism on Io: the Post-Galileo View, and a Comparison with Earth
Authors: Davies Ashley Gerard 
Published: March 2016

AbstractAt the end of the Galileo mission in September 2003, and approximately three years after the Cassini Jovian flyby, it is an appropriate time to reflect on the recent advances made in Io science. Data have been analyzed and volcanic processes have begun to be quantified. This paper reviews these advances from a purely volcano-logical perspective, looking at particular volcanos of interest, and comparing styles of ionian activity with those seen on Earth.
Characterization of the Zonal Wind Flow in the Upper Atmosphere of Titan with the VLT
Authors: Courtin Régis , Luz David , Gautier Daniel , Appourchaux Thierry , Lebreton Jean-Pierre , Ferri Francesca , Lara Luisa , Hourdin Frédéric , Kaufer Andreas 
Published: March 2016

AbstractWe report on recent efforts to characterize the zonal wind flow in the upper atmosphere of Titan from high resolution spectroscopic observations with the Very Large Telescope.
Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis
Authors: Chauhan Rinki , Ravi Janani , Datta Pratik , Chen Tianlong , Schnappinger Dirk , Bassler Kevin E. , Balázsi Gábor , Gennaro Maria Laura 
Published: March 2016

AbstractAccessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics.
Laboratory observations of slow earthquakes and the spectrum of tectonic fault slip modes
Authors: Leeman J. R. , Saffer D. M. , Scuderi M. M. , Marone C. 
Published: March 2016

AbstractSlow earthquakes represent an important conundrum in earthquake physics. While regular earthquakes are catastrophic events with rupture velocities governed by elastic wave speed, the processes that underlie slow fault slip phenomena, including recent discoveries of tremor, slow-slip and low-frequency earthquakes, are less understood. Theoretical models and sparse laboratory observations have provided insights, but the physics of slow fault rupture remain enigmatic. Here we report on laboratory observations that illuminate the mechanics of slow-slip phenomena. We show that a spectrum of slow-slip behaviours arises near the threshold between stable and unstable failure, and is governed by frictional dynamics via the interplay of fault frictional properties, effective normal stress and the elastic stiffness of the surrounding material. This generalizable frictional mechanism may act in concert with other hypothesized processes that damp dynamic ruptures, and is consistent with the broad range of geologic environments where slow earthquakes are observed.
Topological vacuum bubbles by anyon braiding
Authors: Han Cheolhee , Park Jinhong , Gefen Yuval , Sim H.-S. 
Published: March 2016

AbstractAccording to a basic rule of fermionic and bosonic many-body physics, known as the linked cluster theorem, physical observables are not affected by vacuum bubbles, which represent virtual particles created from vacuum and self-annihilating without interacting with real particles. Here we show that this conventional knowledge must be revised for anyons, quasiparticles that obey fractional exchange statistics intermediate between fermions and bosons. We find that a certain class of vacuum bubbles of Abelian anyons does affect physical observables. They represent virtually excited anyons that wind around real anyonic excitations. These topological bubbles result in a temperature-dependent phase shift of Fabry–Perot interference patterns in the fractional quantum Hall regime accessible in current experiments, thus providing a tool for direct and unambiguous observation of elusive fractional statistics.
Chirality of nanophotonic waveguide with embedded quantum emitter for unidirectional spin transfer
Authors: Coles R. J. , Price D. M. , Dixon J. E. , Royall B. , Clarke E. , Kok P. , Skolnick M. S. , Fox A. M. , Makhonin M. N. 
Published: March 2016

AbstractScalable quantum technologies may be achieved by faithful conversion between matter qubits and photonic qubits in integrated circuit geometries. Within this context, quantum dots possess well-defined spin states (matter qubits), which couple efficiently to photons. By embedding them in nanophotonic waveguides, they provide a promising platform for quantum technology implementations. In this paper, we demonstrate that the naturally occurring electromagnetic field chirality that arises in nanobeam waveguides leads to unidirectional photon emission from quantum dot spin states, with resultant in-plane transfer of matter-qubit information. The chiral behaviour occurs despite the non-chiral geometry and material of the waveguides. Using dot registration techniques, we achieve a quantum emitter deterministically positioned at a chiral point and realize spin-path conversion by design. We further show that the chiral phenomena are much more tolerant to dot position than in standard photonic crystal waveguides, exhibit spin-path readout up to 95±5% and have potential to serve as the basis of spin-logic and network implementations.
Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing
Authors: Miyaoka Yuichiro , Berman Jennifer R. , Cooper Samantha B. , Mayerl Steven J. , Chan Amanda H. , Zhang Bin , Karlin-Neumann George A. , Conklin Bruce R. 
Published: March 2016

AbstractPrecise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR–based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator–like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology.
Inhibitory Effect of Sophorolipid on Candida albicans Biofilm Formation and Hyphal Growth
Authors: Haque Farazul , Alfatah Md. , Ganesan K. , Bhattacharyya Mani Shankar 
Published: March 2016

AbstractCandida albicans causes superficial and life-threatening systemic infections. These are difficult to treat often due to drug resistance, particularly because C. albicans biofilms are inherently resistant to most antifungals. Sophorolipid (SL), a glycolipid biosurfactant, has been shown to have antimicrobial and anticancer properties. In this study, we investigated the effect of SL on C. albicans biofilm formation and preformed biofilms. SL was found to inhibit C. albicans biofilm formation as well as reduce the viability of preformed biofilms. Moreover, SL, when used along with amphotericin B (AmB) or fluconazole (FLZ), was found to act synergistically against biofilm formation and preformed biofilms. Effect of SL on C. albicans biofilm formation was further visualized by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM), which revealed absence of hyphae, typical biofilm architecture and alteration in the morphology of biofilm cells. We also found that SL downregulates the expression of hypha specific genes HWP1, ALS1, ALS3, ECE1 and SAP4, which possibly explains the inhibitory effect of SL on hyphae and biofilm formation.
Transplantation of Defined Populations of Differentiated Human Neural Stem Cell Progeny
Authors: Fortin Jeff M. , Azari Hassan , Zheng Tong , Darioosh Roya P. , Schmoll Michael E. , Vedam-Mai Vinata , Deleyrolle Loic P. , Reynolds Brent A. 
Published: March 2016

AbstractMany neurological injuries are likely too extensive for the limited repair capacity of endogenous neural stem cells (NSCs). An alternative is to isolate NSCs from a donor and expand them in vitro as transplantation material. Numerous groups have already transplanted neural stem and precursor cells. A caveat to this approach is the undefined phenotypic distribution of the donor cells, which has three principle drawbacks: (1) Stem-like cells retain the capacity to proliferate in vivo. (2) There is little control over the cells’ terminal differentiation, e.g., a graft intended to replace neurons might choose a predominantly glial fate. (3) There is limited ability of researchers to alter the combination of cell types in pursuit of a precise treatment. We demonstrate a procedure for differentiating human neural precursor cells (hNPCs) in vitro, followed by isolation of the neuronal progeny. We transplanted undifferentiated hNPCs or a defined concentration of hNPC-derived neurons into mice, then compared these two groups with regard to their survival, proliferation and phenotypic fate. We present evidence suggesting that in vitro-differentiated-and-purified neurons survive as well in vivo as their undifferentiated progenitors and undergo less proliferation and less astrocytic differentiation. We also describe techniques for optimizing low-temperature cell preservation and portability.
Two host microRNAs influence WSSV replication via STAT gene regulation
Authors: Huang Ying , Wang Wen , Ren Qian 
Published: March 2016

AbstractMicroRNAs (miRNAs) have important roles in post-transcriptional regulation of gene expression. During viral infection, viruses utilize hosts to enhance their replication by altering cellular miRNAs. The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway plays crucial roles in the antiviral responses. In this study, two miRNAs (miR-9041 and miR-9850) from Macrobrachium rosenbergii were found to promote white spot syndrome virus (WSSV) replication. The up-regulation of miR-9041 or miR-9850 suppresses STAT expression in the gills of M. rosenbergii, which subsequently down-regulates the expression of its downstream dynamin (Dnm) genes: Dnm1, Dnm2, and Dnm3. Knockdown of miR-9041 and miR-9850 restricts WSSV replication by up-regulating STAT and Dnm gene expression. The silencing of STAT, Dnm1, Dnm2, or Dnm3 led to an increase of the number of WSSV copies in shrimp. The injection of recombinant Dnm1, Dnm2, or Dnm3 proteins could inhibit WSSV replication in vivo. Overall, our research indicates the roles of host miRNAs in the enhancement of WSSV replication by regulating the host JAK/STAT pathway.
Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7
Authors: Zanphorlin Leticia Maria , de Giuseppe Priscila Oliveira , Honorato Rodrigo Vargas , Tonoli Celisa Caldana Costa , Fattori Juliana , Crespim Elaine , de Oliveira Paulo Sergio Lopes , Ruller Roberto , Murakami Mario Tyago 
Published: March 2016

AbstractPsychrophilic enzymes evolved from a plethora of structural scaffolds via multiple molecular pathways. Elucidating their adaptive strategies is instrumental to understand how life can thrive in cold ecosystems and to tailor enzymes for biotechnological applications at low temperatures. In this work, we used X-ray crystallography,in solutionstudies and molecular dynamics simulations to reveal the structural basis for cold adaptation of the GH1 β-glucosidase fromExiguobacterium antarcticumB7. We discovered that the selective pressure of low temperatures favored mutations that redesigned the protein surface, reduced the number of salt bridges, exposed more hydrophobic regions to the solvent and gave rise to a tetrameric arrangement not found in mesophilic and thermophilic homologues. As a result, some solvent-exposed regions became more flexible in the cold-adapted tetramer, likely contributing to enhance enzymatic activity at cold environments. The tetramer stabilizes the native conformation of the enzyme, leading to a 10-fold higher activity compared to the disassembled monomers. According to phylogenetic analysis, diverse adaptive strategies to cold environments emerged in the GH1 family, being tetramerization an alternative, not a rule. These findings reveal a novel strategy for enzyme cold adaptation and provide a framework for the semi-rational engineering of β-glucosidases aiming at cold industrial processes.
The transfer of titanium dioxide nanoparticles from the host plant to butterfly larvae through a food chain
Authors: Kubo-Irie Miyoko , Yokoyama Masaaki , Shinkai Yusuke , Niki Rikio , Takeda Ken , Irie Masaru 
Published: March 2016

AbstractThis study aimed to examine the transfer of nanoparticles within a terrestrial food chain. Oviposited eggs of the swallowtail butterfly (Atrophaneura alcinous) were hatched on the leaves of the host plant (Aristolochia debilis) and the root stock and root hairs were submerged in a suspension of 10 μg/ml titanium dioxide nanoparticles (TiO2-NPs) in a 100 ml bottle. The presence of TiO2-NPs in the veins of the leaves was confirmed by X-ray analytical microscopy (X-ray AM). The hatched 1st instar larvae fed on the leaves to moult into 2nd instar larvae. Small agglomerates of TiO2-NPs less than 150 nm in diameter were identified in the vascular tissue of the exposed plant, the midgut and the excreta of the larvae by transmission electron microscopy. The image of Ti elemental mapping by X-ray AM was analysed with the quantitative spatial information mapping (QSIM) technique. The results demonstrated that TiO2-NPs were transferred from the plant to the larvae and they were disseminated throughout the environment via larval excreta.
Sex reversal assessments reveal different vulnerability to endocrine disruption between deeply diverged anuran lineages
Authors: Tamschick Stephanie , Rozenblut-Kościsty Beata , Ogielska Maria , Lehmann Andreas , Lymberakis Petros , Hoffmann Frauke , Lutz Ilka , Kloas Werner , Stöck Matthias 
Published: March 2016

AbstractMultiple anthropogenic stressors cause worldwide amphibian declines. Among several poorly investigated causes is global pollution of aquatic ecosystems with endocrine disrupting compounds (EDCs). These substances interfere with the endocrine system and can affect the sexual development of vertebrates including amphibians. We test the susceptibility to an environmentally relevant contraceptive, the artificial estrogen 17α-ethinylestradiol (EE2), simultaneously in three deeply divergent systematic anuran families, a model-species,Xenopus laevis(Pipidae) and two non-models,Hyla arborea(Hylidae) andBufo viridis(Bufonidae). Our new approach combines synchronized tadpole exposure to three EE2-concentrations (50, 500, 5,000 ng/L) in a flow-through-system and pioneers genetic and histological sexing of metamorphs in non-model anurans for EDC-studies. This novel methodology reveals striking quantitative differences in genetic-male-to-phenotypic-female sex reversal in non-model vs. model species. Our findings qualify molecular sexing in EDC-analyses as requirement to identify sex reversals and state-of-the-art approaches as mandatory to detect species-specific vulnerabilities to EDCs in amphibians.
Redox proteins of hydroxylating bacterial dioxygenases establish a regulatory cascade that prevents gratuitous induction of tetralin biodegradation genes
Authors: Ledesma-García Laura , Sánchez-Azqueta Ana , Medina Milagros , Reyes-Ramírez Francisca , Santero Eduardo 
Published: March 2016

AbstractBacterial dioxygenase systems are multicomponent enzymes that catalyze the initial degradation of many environmentally hazardous compounds. In Sphingopyxis granuli strain TFA tetralin dioxygenase hydroxylates tetralin, an organic contaminant. It consists of a ferredoxin reductase (ThnA4), a ferredoxin (ThnA3) and a oxygenase (ThnA1/ThnA2), forming a NAD(P)H–ThnA4–ThnA3–ThnA1/ThnA2 electron transport chain. ThnA3 has also a regulatory function since it prevents expression of tetralin degradation genes (thn) in the presence of non-metabolizable substrates of the catabolic pathway. This role is of physiological relevance since avoids gratuitous and wasteful production of catabolic enzymes. Our hypothesis for thn regulation implies that ThnA3 exerts its action by diverting electrons towards the regulator ThnY, an iron-sulfur flavoprotein that together with the transcriptional activator ThnR is necessary for thn gene expression. Here we analyze electron transfer among ThnA4, ThnA3 and ThnY by using stopped-flow spectrophotometry and determination of midpoint reduction potentials. Our results indicate that when accumulated in its reduced form ThnA3 is able to fully reduce ThnY. In addition, we have reproduced in vitro the regulatory circuit in the proposed physiological direction, NAD(P)H–ThnA4–ThnA3–ThnY. ThnA3 represents an unprecedented way of communication between a catabolic pathway and its regulatory system to prevent gratuitous induction.
Non‐linear resistance training reduces inflammatory biomarkers in persons living with HIV: A randomized controlled trial
Authors: Zanetti Hugo Ribeiro , da Cruz Lucas Gonçalves , Lourenço Camilo Luís Monteiro , Neves Fernando de Freitas , Silva‐Vergara Mário Leon , Mendes Edmar Lacerda 
Published: March 2016

AbstractThe purpose of this study is to analyse the effect of 12 weeks of non‐linear resistance training (NLRT) on anthropometry, muscle strength and inflammatory biomarkers in persons infected with human immunodeficiency virus (PIHIV). Thirty previously sedentary PIHIVs were randomized into the NLRT (n = 15) and control (CON, n = 15) groups. NLRT group were submitted to 12 weeks of training, whereas the CON group maintained their daily habits. At baseline and after 12 weeks, both groups underwent anthropometric evaluations and blood sampling for the analysis of inflammatory biomarkers. Analysis of covariance using preintervention values as covariate was performed to determine the effects of exercise on anthropometry, muscle strength, cytokines levels and T cells. Significance was set at p < 0.05. After 12 weeks of intervention, there was a decrease in subcutaneous body fat (p < .0001), neck, abdomen and waist circumferences (p < .05), waist‐to‐hip ratio (p = .009), blood levels of interleukin (IL)‐1β (p = .029), IL‐6 (p = .005), IL‐8 (p = .010), and tumour necrosis factor (TNF)‐α (p = .001) and an increase in muscle strength (p < .0001), IL‐10 levels (p = .030) and CD4+ (p = .004) and CD8+ (p < .0001) counts in the NLRT compared to CON group. Twelve weeks of NLRT promoted positive changes in the body fat, body circumferences, muscular strength and inflammatory profile in PIHIV.
Impacts of large-scale restoration efforts on black bear habitat use in Canyon de Chelly National Monument, Arizona, United States
Authors: Tredick Catherine A. , Kelly Marcella J. , Vaughan Michael R. 
Published: March 2016

Abstract
Impacts of large-scale changes in habitat due to human development, invasive species, and climate change are important considerations for wildlife management. Likewise, as efforts increase to recover and restore human-altered landscapes, indirect consequences on nontarget components of the restored ecosystem also must be considered. Currently, efforts are underway to eradicate nonnative Russian olive (Elaeagnus angustifolia) and tamarisk (Tamarix spp.) in Canyon de Chelly National Monument (CACH), United States, yet impacts to native wildlife, including the American black bear (Ursus americanus), which relies on these species for escape cover and foraging habitat, are not fully understood. Further, these efforts have the potential to impact sociopolitical aspects of the ecosystem, namely human–bear interactions (e.g., raiding of crops and livestock). We used occupancy modeling to evaluate black bear foraging ecology and habitat use in CACH to better understand how bears are using native and nonnative habitat resources and how restoration efforts may impact bears and human–bear interactions. We found that black bears rely heavily on Russian olive for food and that habitat use is driven by both native and nonnative (i.e., Russian olive) food resources; thus, restoration of native habitat in CACH may have negative impacts on bears through loss of a primary nonnative food source and escape cover. Furthermore, bear–human interactions may temporarily increase in the short term as bears adjust to this loss. Evaluating habitat use in an occupancy modeling framework provides an effective means for gauging nontarget impacts of restoration efforts on wildlife species, an essential step in effective wildlife management.
Reflections on the so-called value-free ideal
Authors: Tsui Anne 
Published: March 2016

Purpose– Value-free science is an ideal that is neither possible nor desirable, especially for social sciences. The subject of social sciences is individuals and groups; hence social, moral, ethical, or political values are inherent and unavoidable in all steps of the scientific process. Further, the authority of science requires the scientist to be responsible experts in ensuring the reliability of knowledge and in assessing the risks in applying the research findings in social policies and practices. The purpose of this essay is to discuss the role of values in business school research.Design/methodology/approach– The author explains the two primary types of values relevant for science: epistemic – norms and standards to ensure good science – and social – criteria not relevant for discovering the truth of knowledge but may influence decisions related to science especially in evaluating the cost of wrongful conclusions from the research evidence. Based on an analysis of published criticisms of business school research and the author’s own analysis, the author describes how business school research is infused with social and political values, undermining the objectivity and quality of science by business scientists.Findings– The author endorses the idea of responsible science – science that recognizes the mutual dependence between science and society, and that aims to satisfy both epistemic and social values. The author offers a modest proposal to encourage transformation of business school research to meet both rigor (valid and reliable knowledge) and relevance (useful for practice) – the hallmark of responsible science.Research limitations/implications– The ideas in this essay have implications for further work on identifying the relevant epistemic and social values to guide business school research.Originality/value– The idea of responsible science can potentially transform business school’s research to become both scientifically rigorous and societally relevant.