bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas
Authors: Sun Yanwei , Wang Chunming , Wang Ning , Jiang Xiyuan , Mao Huizhu , Zhu Changxiang , Wen Fujiang , Wang Xianghua , Lu Zhijun , Yue Genhua , Xu Zengfu , Ye Jian 
Published: January 2017

AbstractSeed size is a major determinant of seed yield but few is known about the genetics controlling of seed size in plants. Phytohormones cytokinin and brassinosteroid were known to be involved in the regulation of herbaceous plant seed development. Here we identified a homolog of Auxin Response Factor 19 (JcARF19) from a woody plant Jatropha curcas and genetically demonstrated its functions in controlling seed size and seed yield. Through Virus Induced Gene Silencing (VIGS), we found that JcARF19 was a positive upstream modulator in auxin signaling and may control plant organ size in J. curcas. Importantly, transgenic overexpression of JcARF19 significantly increased seed size and seed yield in plants Arabidopsis thaliana and J. curcas, indicating the importance of auxin pathway in seed yield controlling in dicot plants. Transcripts analysis indicated that ectopic expression of JcARF19 in J. curcas upregulated auxin responsive genes encoding essential regulators in cell differentiation and cytoskeletal dynamics of seed development. Our data suggested the potential of improving seed traits by precisely engineering auxin signaling in woody perennial plants.
Fractional lattice charge transport
Authors: Flach Sergej , Khomeriki Ramaz 
Published: January 2017

AbstractWe consider the dynamics of noninteracting quantum particles on a square lattice in the presence of a magnetic flux α and a dc electric field E oriented along the lattice diagonal. In general, the adiabatic dynamics will be characterized by Bloch oscillations in the electrical field direction and dispersive ballistic transport in the perpendicular direction. For rational values of α and a corresponding discrete set of values of E(α) vanishing gaps in the spectrum induce a fractionalization of the charge in the perpendicular direction - while left movers are still performing dispersive ballistic transport, the complementary fraction of right movers is propagating in a dispersionless relativistic manner in the opposite direction. Generalizations and the possible probing of the effect with atomic Bose-Einstein condensates and photonic networks are discussed. Zak phase of respective band associated with gap closing regime has been computed and it is found converging to π/2 value.
Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose
Authors: Yuen Jonathan D. , Walper Scott A. , Melde Brian J. , Daniele Michael A. , Stenger David A. 
Published: January 2017

AbstractWe report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L−1.
Integration of Visual and Joint Information to Enable Linear Reaching Motions
Authors: Eberle Henry , Nasuto Slawomir J. , Hayashi Yoshikatsu 
Published: January 2017

AbstractA new dynamics-driven control law was developed for a robot arm, based on the feedback control law which uses the linear transformation directly from work space to joint space. This was validated using a simulation of a two-joint planar robot arm and an optimisation algorithm was used to find the optimum matrix to generate straight trajectories of the end-effector in the work space. We found that this linear matrix can be decomposed into the rotation matrix representing the orientation of the goal direction and the joint relation matrix ( MJRM) representing the joint response to errors in the Cartesian work space. The decomposition of the linear matrix indicates the separation of path planning in terms of the direction of the reaching motion and the synergies of joint coordination. Once the MJRM is numerically obtained, the feedfoward planning of reaching direction allows us to provide asymptotically stable, linear trajectories in the entire work space through rotational transformation, completely avoiding the use of inverse kinematics. Our dynamics-driven control law suggests an interesting framework for interpreting human reaching motion control alternative to the dominant inverse method based explanations, avoiding expensive computation of the inverse kinematics and the point-to-point control along the desired trajectories.
Transcriptional profiling of olfactory system development identifies distal antenna as a regulator of subset of neuronal fates
Authors: Barish Scott , Li Qingyun , Pan Jia W. , Soeder Charlie , Jones Corbin , Volkan Pelin C. 
Published: January 2017

AbstractDrosophila uses 50 different olfactory receptor neuron (ORN) classes that are clustered within distinct sensilla subtypes to decipher their chemical environment. Each sensilla subtype houses 1–4 ORN identities that arise through asymmetric divisions of a single sensory organ precursor (SOP). Despite a number of mutational studies investigating the regulation of ORN development, a majority of the transcriptional programs that lead to the different ORN classes in the developing olfactory system are unknown. Here we use transcriptional profiling across the time series of antennal development to identify novel transcriptional programs governing the differentiation of ORNs. We surveyed four critical developmental stages of the olfactory system: 3rd instar larval (prepatterning), 8 hours after puparium formation (APF, SOP selection), 40 hrs APF (neurogenesis), and adult antennae. We focused on the expression profiles of olfactory receptor genes and transcription factors—the two main classes of genes that regulate the sensory identity of ORNs. We identify distinct clusters of genes that have overlapping temporal expression profiles suggesting they have a key role during olfactory system development. We show that the expression of the transcription factor distal antenna (dan) is highly similar to other prepatterning factors and is required for the expression of a subset of ORs.
Model for large-area monolayer coverage of polystyrene nanospheres by spin coating
Authors: Chandramohan Abhishek , Sibirev Nikolai V. , Dubrovskii Vladimir G. , Petty Michael C. , Gallant Andrew J. , Zeze Dagou A. 
Published: January 2017

AbstractNanosphere lithography, an inexpensive and high throughput technique capable of producing nanostructure (below 100 nm feature size) arrays, relies on the formation of a monolayer of self-assembled nanospheres, followed by custom-etching to produce nanometre size features on large-area substrates. A theoretical model underpinning the self-ordering process by centrifugation is proposed to describe the interplay between the spin speed and solution concentration. The model describes the deposition of a dense and uniform monolayer by the implicit contribution of gravity, centrifugal force and surface tension, which can be accounted for using only the spin speed and the solid/liquid volume ratio. We demonstrate that the spin recipe for the monolayer formation can be represented as a pathway on a 2D phase plane. The model accounts for the ratio of polystyrene nanospheres (300 nm), water, methanol and surfactant in the solution, crucial for large area uniform and periodic monolayer deposition. The monolayer is exploited to create arrays of nanoscale features using ‘short’ or ‘extended’ reactive ion etching to produce 30–60 nm (diameter) nanodots or 100–200 nm (diameter) nanoholes over the entire substrate, respectively. The nanostructures were subsequently utilized to create master stamps for nanoimprint lithography.
Polarization conversion in plasmonic nanoantennas for metasurfaces using structural asymmetry and mode hybridization
Authors: Wiecha Peter R. , Black Leo-Jay , Wang Yudong , Paillard Vincent , Girard Christian , Muskens Otto L. , Arbouet Arnaud 
Published: January 2017

AbstractPolarization control using single plasmonic nanoantennas is of interest for subwavelength optical components in nano-optical circuits and metasurfaces. Here, we investigate the role of two mechanisms for polarization conversion by plasmonic antennas: Structural asymmetry and plasmon hybridization through strong coupling. As a model system we investigate L-shaped antennas consisting of two orthogonal nanorods which lengths and coupling strength can be independently controlled. An analytical model based on field susceptibilities is developed to extract key parameters and to address the influence of antenna morphology and excitation wavelength on polarization conversion efficiency and scattering intensities. Optical spectroscopy experiments performed on individual antennas, further supported by electrodynamical simulations based on the Green Dyadic Method, confirm the trends extracted from the analytical model. Mode hybridization and structural asymmetry allow address-ing different input polarizations and wavelengths, providing additional degrees of freedom for agile polarization conversion in nanophotonic devices.
Coordinated cell motility is regulated by a combination of LKB1 farnesylation and kinase activity
Authors: Wilkinson S. , Hou Y. , Zoine J. T. , Saltz J. , Zhang C. , Chen Z. , Cooper L. A. D. , Marcus A. I. 
Published: January 2017

AbstractCell motility requires the precise coordination of cell polarization, lamellipodia formation, adhesion, and force generation. LKB1 is a multi-functional serine/threonine kinase that associates with actin at the cellular leading edge of motile cells and suppresses FAK. We sought to understand how LKB1 coordinates these multiple events by systematically dissecting LKB1 protein domain function in combination with live cell imaging and computational approaches. We show that LKB1-actin colocalization is dependent upon LKB1 farnesylation leading to RhoA-ROCK-mediated stress fiber formation, but membrane dynamics is reliant on LKB1 kinase activity. We propose that LKB1 kinase activity controls membrane dynamics through FAK since loss of LKB1 kinase activity results in morphologically defective nascent adhesion sites. In contrast, defective farnesylation mislocalizes nascent adhesion sites, suggesting that LKB1 farnesylation serves as a targeting mechanism for properly localizing adhesion sites during cell motility. Together, we propose a model where coordination of LKB1 farnesylation and kinase activity serve as a multi-step mechanism to coordinate cell motility during migration.
Time-resolved neutron scattering provides new insight into protein substrate processing by a AAA+ unfoldase
Authors: Ibrahim Ziad , Martel Anne , Moulin Martine , Kim Henry S. , Härtlein Michael , Franzetti Bruno , Gabel Frank 
Published: January 2017

AbstractWe present a combination of small-angle neutron scattering, deuterium labelling and contrast variation, temperature activation and fluorescence spectroscopy as a novel approach to obtain time-resolved, structural data individually from macromolecular complexes and their substrates during active biochemical reactions. The approach allowed us to monitor the mechanical unfolding of a green fluorescent protein model substrate by the archaeal AAA+ PAN unfoldase on the sub-minute time scale. Concomitant with the unfolding of its substrate, the PAN complex underwent an energy-dependent transition from a relaxed to a contracted conformation, followed by a slower expansion to its initial state at the end of the reaction. The results support a model in which AAA ATPases unfold their substrates in a reversible power stroke mechanism involving several subunits and demonstrate the general utility of this time-resolved approach for studying the structural molecular kinetics of multiple protein remodelling complexes and their substrates on the sub-minute time scale.
Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus
Authors: Fernández Lucía , González Silvia , Campelo Ana Belén , Martínez Beatriz , Rodríguez Ana , García Pilar 
Published: January 2017

AbstractAn important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.
The role of configurational disorder on plastic and dynamic deformation in Cu64Zr36 metallic glasses: A molecular dynamics analysis
Authors: Feng S. D. , Chan K. C. , Chen S. H. , Zhao L. , Liu R. P. 
Published: January 2017

AbstractThe varying degrees of configurational disorder in metallic glasses are investigated quantitatively by molecular dynamics studies. A parameter, the quasi-nearest atom, is used to characterize the configurational disorder in metallic glasses. Our observations suggest configurational disorder play a role in structural heterogeneity, plasticity and dynamic relaxations in metallic glasses. The broad configurational disorder regions distribution is the indicator of abundant potential deformation units and relaxations. Plastic flow, as well as relaxation, is believed to start at configurational disorder regions. The width of the shear bands and dynamic relaxations can then be regulated by the degree of configurational disorder regions in metallic glasses.
Determining arterial wave transit time from a single aortic pressure pulse in rats: vascular impulse response analysis
Authors: Chang Ru-Wen , Chang Chun-Yi , Lai Liang-Chuan , Wu Ming-Shiou , Young Tai-Horng , Chen Yih-Sharng , Wang Chih-Hsien , Chang Kuo-Chu 
Published: January 2017

AbstractArterial wave transit time (τw) in the lower body circulation is an effective biomarker of cardiovascular risk that substantially affects systolic workload imposed on the heart. This study evaluated a method for determining τw from the vascular impulse response on the basis of the measured aortic pressure and an assumed triangular flow (Qtri). The base of the unknown Qtri was constructed with a duration set equal to ejection time. The timing of the peak triangle was derived using a fourth-order derivative of the pressure waveform. Values of τws obtained using Qtri were compared with those obtained from the measure aortic flow wave (Qm). Healthy rats (n = 27), rats with chronic kidney disease (CKD; n = 22), and rats with type 1 (n = 22) or type 2 (n = 11) diabetes were analyzed. The cardiovascular conditions in the CKD rats and both diabetic groups were characterized by a decrease in τws. The following significant relation was observed (P < 0.0001): τwtriQ = −1.5709 + 1.0604 × τwmQ (r2 = 0.9641). Our finding indicates that aortic impulse response can be an effective method for the estimation of arterial τw by using a single pressure recording together with the assumed Qtri.
Differential effects of phytotherapic preparations in the hSOD1 Drosophila melanogaster model of ALS
Authors: De Rose Francescaelena , Marotta Roberto , Talani Giuseppe , Catelani Tiziano , Solari Paolo , Poddighe Simone , Borghero Giuseppe , Marrosu Francesco , Sanna Enrico , Kasture Sanjay , Acquas Elio , Liscia Anna 
Published: January 2017

AbstractThe present study was aimed at characterizing the effects of Withania somnifera (Wse) and Mucuna pruriens (Mpe) on a Drosophila melanogaster model for Amyotrophic Lateral Sclerosis (ALS). In particular, the effects of Wse and Mpe were assessed following feeding the flies selectively overexpressing the wild human copper, zinc-superoxide dismutase (hSOD1-gain-of-function) in Drosophila motoneurons. Although ALS-hSOD1 mutants showed no impairment in life span, with respect to GAL4 controls, the results revealed impairment of climbing behaviour, muscle electrophysiological parameters (latency and amplitude of ePSPs) as well as thoracic ganglia mitochondrial functions. Interestingly, Wse treatment significantly increased lifespan of hSDO1 while Mpe had not effect. Conversely, both Wse and Mpe significantly rescued climbing impairment, and also latency and amplitude of ePSPs as well as failure responses to high frequency DLM stimulation. Finally, mitochondrial alterations were any more present in Wse- but not in Mpe-treated hSOD1 mutants. Hence, given the role of inflammation in the development of ALS, the high translational impact of the model, the known anti-inflammatory properties of these extracts, and the viability of their clinical use, these results suggest that the application of Wse and Mpe might represent a valuable pharmacological strategy to counteract the progression of ALS and related symptoms.
Challenges Faced in Translating the Benefits of Surfactant Replacement Therapy to a Resource-Limited Setting
Authors: Hamilton N. , Trotman Helen 
Published: January 2017

Aim To determine the challenges, if any, in translating the benefits of surfactant replacement therapy (SRT) to a resource-limited setting.
Method This was a retrospective descriptive study comparing the outcome of 75 cases who received surfactant and 69 controls who did not at the University Hospital of the West Indies during the period 2001 to 2011. Descriptive analyses were performed. Statistical significance was taken at the level p < 0.05.
Results Only 13% of neonates with respiratory distress syndrome received surfactant therapy. The median time of surfactant administration was 16.5 hours (interquartile range: 6–37 hours). The mean ± standard deviation time between repeat doses was 19.1 ± 14 hours. There was no difference in mortality between cases (67%) and controls (59%) (p = 0.32). However, the cases who survived were less mature (28.3 ± 2 weeks) and less clinically stable (CRIB II [Clinical Risk Index for Babies] score: 8.2 ± 3) than their controls who survived (30.0 ± 2 weeks; CRIB II score: 6.0 ± 3) (p = 0.01). There was no difference in mean gestational age or CRIB II scores between nonsurviving cases and controls. A high incidence of sepsis, pneumothoraces, and pulmonary hemorrhage was noted in both cases and controls.
Conclusion SRT did not improve the overall outcome in preterm neonates treated with RDS. Challenges encountered in optimizing SRT included affordability and accessibility of surfactant, supportive equipment, and supportive therapies, as well as a high incidence of complications related to prematurity.
“Excellence R Us”: university research and the fetishisation of excellence
Authors: Moore Samuel , Neylon Cameron , Paul Eve Martin , Paul O’Donnell Daniel , Pattinson Damian 
Published: January 2017

AbstractThe rhetoric of “excellence” is pervasive across the academy. It is used to refer to research outputs as well as researchers, theory and education, individuals and organizations, from art history to zoology. But does “excellence” actually mean anything? Does this pervasive narrative of “excellence” do any good? Drawing on a range of sources we interrogate “excellence” as a concept and find that it has no intrinsic meaning in academia. Rather it functions as a linguistic interchange mechanism. To investigate whether this linguistic function is useful we examine how the rhetoric of excellence combines with narratives of scarcity and competition to show that the hyper-competition that arises from the performance of “excellence” is completely at odds with the qualities of good research. We trace the roots of issues in reproducibility, fraud, and homophily to this rhetoric. But we also show that this rhetoric is an internal, and not primarily an external, imposition. We conclude by proposing an alternative rhetoric based on soundness and capacity-building. In the final analysis, it turns out that that “excellence” is not excellent. Used in its current unqualified form it is a pernicious and dangerous rhetoric that undermines the very foundations of good research and scholarship. This article is published as part of a collection on the future of research assessment.
The ethics of intergenerational relationships
Authors: Thompson Janna 
Published: January 2017

AbstractAccording to the relational approach we have obligations to members of future generations not because of their interests or properties but because, and only because, they are our descendants or successors. Common accounts of relational duties do not explain how we can have obligations to people who do not yet exist. In this defence of the relational approach I examine three sources of intergenerational obligations: the concern of parents for their children, including their future children; the desire of community members to pass on a heritage to their descendants; and the relationship of citizens in an intergenerational polity.
Characterization and production of multifunctional cationic peptides derived from rice proteins
Authors: Taniguchi Masayuki , Ochiai Akihito 
Published: January 2017

Abstract
Food proteins have been identified as a source of bioactive peptides. These peptides are inactive within the sequence of the parent protein and must be released during gastrointestinal digestion, fermentation, or food processing. Of bioactive peptides, multifunctional cationic peptides are more useful than other peptides that have specific activity in promotion of health and/or the treatment of diseases. We have identified and characterized cationic peptides from rice enzymes and proteins that possess multiple functions, including antimicrobial, endotoxin-neutralizing, arginine gingipain-inhibitory, and/or angiogenic activities. In particular, we have elucidated the contribution of cationic amino acids (arginine and lysine) in the peptides to their bioactivities. Further, we have discussed the critical parameters, particularly proteinase preparations and fractionation or purification, in the enzymatic hydrolysis process for producing bioactive peptides from food proteins. Using an ampholyte-free isoelectric focusing (autofocusing) technique as a tool for fractionation, we successfully prepared fractions containing cationic peptides with multiple functions.