bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-range movement of large mechanically interlocked DNA nanostructures
Authors: List Jonathan , Falgenhauer Elisabeth , Kopperger Enzo , Pardatscher Günther , Simmel Friedrich C. 
Published: August 2016

AbstractInterlocked molecules such as catenanes and rotaxanes, connected only via mechanical bonds have the ability to perform large-scale sliding and rotational movements, making them attractive components for the construction of artificial molecular machines and motors. We here demonstrate the realization of large, rigid rotaxane structures composed of DNA origami subunits. The structures can be easily modified to carry a molecular cargo or nanoparticles. By using multiple axle modules, rotaxane constructs are realized with axle lengths of up to 355 nm and a fuel/anti-fuel mechanism is employed to switch the rotaxanes between a mobile and a fixed state. We also create extended pseudo-rotaxanes, in which origami rings can slide along supramolecular DNA filaments over several hundreds of nanometres. The rings can be actively moved and tracked using atomic force microscopy.
EPG Recordings Reveal Differential Feeding Behaviors in Sogatella furcifera in Response to Plant Virus Infection and Transmission Success
Authors: Lei Wenbin , Li Pei , Han Yongqiang , Gong Shaolong , Yang Lang , Hou Maolin 
Published: August 2016

AbstractPlant viruses are primarily transmitted by insect vectors and virus infection may influence on the vectors’ feeding behaviors. Using an electrical penetration graph, we detected that infection with the Southern rice black-streaked dwarf virus (SRBSDV) in the white-backed planthopper (WBPH) and in rice plants both altered the vector’s feeding behavior. When viruliferous WBPH (carrying SRBSDV) were fed on uninfected plants, they spent more time in salivation and phloem sap ingestion than non-viruliferous insects. In comparison with uninfected plants, infected plants showed an arrestant effect on non-viruliferous WBPH for phloem sap ingestion. Differential feeding behaviors were also detected between the WBPH that inoculated or acquired SRBSDV and those that failed to. The WBPH that inoculated SRBSDV exhibited more probing bouts, salivation events and phloem sap ingestion events and longer salivation than those that failed to. The WBPH that acquired SRBSDV were quicker to reach phloem and spent more time in phloem sap ingestion than those that failed to. These behavior alterations in the vector may have adaptive advantages for SRBSDV transmission and spread success because greater salivation by viruliferous vectors on uninfected hosts will promote virus inoculation, whereas more sap ingestion by non-viruliferous vectors on infected hosts will promote virus acquisition.
Three-decade long fertilization-induced soil organic carbon sequestration depends on edaphic characteristics in six typical croplands
Authors: Liang Feng , Li Jianwei , Yang Xueyun , Huang Shaomin , Cai Zejiang , Gao Hongjun , Ma Junyong , Cui Xian , Xu Minggang 
Published: August 2016

AbstractFertilizations affect soil organic carbon (SOC) content but the relative influences of the edaphic and climate factors on SOC storage are rarely studied across wide spatiotemporal scales. This study synthesized long-term datasets of fertilization experiments in six typical Chinese croplands, and calculated annual C input from crops and manure amendments, changes in SOC storage (ΔSOC) and C sequestration efficiency (i.e. the percentage of soil C change per unit of C input, hereafter referred as CSE) in 0–20 cm soil over three decades. Three fertilization treatments include no fertilization (CK), chemical nitrogen, phosphorus and potassium fertilizers (NPK) and combined chemical fertilizers and manure (NPKM). Results showed significant fertilization effects on C input and ΔSOC (NPKM>NPK>CK), and significantly higher CSE in Qiyang at Hunan than Zhengzhou at Henan and Heihe at Heilongjiang. The variance partitioning analysis (VPA) showed more variance of CSE can be explained by edaphic factors (up to 39.7%) than other factors. Furthermore, soil available N content and pH were identified as the major soil properties explaining CSE variance. This study demonstrated key controls of soil fertility factors on SOC sequestration and informs the need to develop strategic soil management plan to promote soil carbon sequestration under long-term intensive fertilization.
Association of Gestational Hypertensive Disorders with Retinopathy of prematurity: A Systematic Review and Meta-analysis
Authors: Chan Priscilla Y. L. , Tang Shu-Min , Au Sunny C. L. , Rong Shi-Song , Lau Henry H. W. , Ko Simon T. C. , Ng Danny S. C. , Chen Li Jia , Yam Jason C. S. 
Published: August 2016

AbstractThe role of gestational hypertensive disorders, which includes both pre-eclampsia and gestational hypertension, in the development of retinopathy of prematurity (ROP) has been controversial. Therefore, this systematic review and meta-analysis is to evaluate the association between gestational hypertensive disoders and ROP. Eligible studies published up to June 5, 2016 were identified from MEDLINE and EMBASE that evaluated the association between the two conditions. Totally 1142 published records were retrieved for screening, 925 of them eligible for detailed evaluation. Finally 19 studies involving 45281 infants with 5388 cases of ROP met our criteria for meta-analysis. Gestational hypertensive disorders were not associated with ROP (unadjusted OR: 0.89; P = 0.38; adjusted OR: 1.35; P = 0.18). Subgroup analyses also revealed no significant association between ROP with pre-eclampsia (unadjusted OR: 0.85; P = 0.29; adjusted OR:1.29; P = 0.28) or with gestational hypertension (unadjusted OR: 1.10; P = 0.39; adjusted OR: 1.25; P = 0.60) separately. Sensitivity analysis indicated our results were robust. We concluded no significant association between gestational hypertensive disorders and ROP. More large scale well-conducted prospective cohorts on the topic are needed.
Novel super-resolution capable mitochondrial probe, MitoRed AIE, enables assessment of real-time molecular mitochondrial dynamics
Authors: Lo Camden Yeung-Wah , Chen Sijie , Creed Sarah Jayne , Kang Miaomiao , Zhao Na , Tang Ben Zhong , Elgass Kirstin Diana 
Published: August 2016

AbstractMitochondria and mitochondrial dynamics play vital roles in health and disease. With the intricate nanometer-scale structure and rapid dynamics of mitochondria, super-resolution microscopy techniques possess great un-tapped potential to significantly contribute to understanding mitochondrial biology and kinetics. Here we present a novel mitochondrial probe (MitoRed AIE) suitable for live mitochondrial dynamics imaging and single particle tracking (SPT), together with a multi-dimensional data analysis approach to assess local mitochondrial (membrane) fluidity. The MitoRed AIE probe localizes primarily to mitochondrial membranes, with 95 ms fluorophore on-time delivering 106 photons/ms, characteristics which we exploit to demonstrate live cell 100 fps 3D time-lapse tracking of mitochondria. Combining our experimental and analytical approaches, we uncover mitochondrial dynamics at unprecedented time scales. This approach opens up a new regime into high spatio-temporal resolution dynamics in many areas of mitochondrial biology.
Quasisolitons in self-diffusive excitable systems, or Why asymmetric diffusivity obeys the Second Law
Authors: Biktashev V. N. , Tsyganov M. A. 
Published: August 2016

AbstractSolitons, defined as nonlinear waves which can reflect from boundaries or transmit through each other, are found in conservative, fully integrable systems. Similar phenomena, dubbed quasi-solitons, have been observed also in dissipative, “excitable” systems, either at finely tuned parameters (near a bifurcation) or in systems with cross-diffusion. Here we demonstrate that quasi-solitons can be robustly observed in excitable systems with excitable kinetics and with self-diffusion only. This includes quasi-solitons of fixed shape (like KdV solitons) or envelope quasi-solitons (like NLS solitons). This can happen in systems with more than two components, and can be explained by effective cross-diffusion, which emerges via adiabatic elimination of a fast but diffusing component. We describe here a reduction procedure can be used for the search of complicated wave regimes in multi-component, stiff systems by studying simplified, soft systems.
Seabird acoustic communication at sea: a new perspective using bio-logging devices
Authors: Thiebault Andréa , Pistorius Pierre , Mullers Ralf , Tremblay Yann 
Published: August 2016

AbstractMost seabirds are very noisy at their breeding colonies, when aggregated in high densities. Calls are used for individual recognition and also emitted during agonistic interactions. When at sea, many seabirds aggregate over patchily distributed resources and may benefit from foraging in groups. Because these aggregations are so common, it raises the question of whether seabirds use acoustic communication when foraging at sea? We deployed video-cameras with built in microphones on 36 Cape gannets (Morus capensis) during the breeding season of 2010–2011 at Bird Island (Algoa Bay, South Africa) to study their foraging behaviour and vocal activity at sea. Group formation was derived from the camera footage. During ~42 h, calls were recorded on 72 occasions from 16 birds. Vocalization exclusively took place in the presence of conspecifics and mostly in feeding aggregations (81% of the vocalizations). From the observation of the behaviours of birds associated with the emission of calls, we suggest that the calls were emitted to avoid collisions between birds. Our observations show that at least some seabirds use acoustic communication when foraging at sea. These findings open up new perspectives for research on seabirds foraging ecology and their interactions at sea.
Influence of low-temperature nitriding on the strain-induced martensite and laser-quenched austenite in a magnetic encoder made from 304L stainless steel
Authors: Leskovšek Vojteh , Godec Matjaž , Kogej Peter 
Published: August 2016

AbstractWe have investigated the possibility of producing a magnetic encoder by an innovative process. Instead of turning grooves in the encoder bar for precise positioning, we incorporated the information in 304L stainless steel by transforming the austenite to martensite after bar extrusion in liquid nitrogen and marking it with a laser, which caused a local transformation of martensite back into austenite. 304L has an excellent corrosion resistance, but a low hardness and poor wear resistance, which limits its range of applications. However, nitriding is a very promising way to enhance the mechanical and magnetic properties. After low-temperature nitriding at 400 °C it is clear that both ε- and α′-martensite are present in the deformed microstructure, indicating the simultaneous stress-induced and strain-induced transformations of the austenite. The effects of a laser surface treatment and the consequent appearance of a non-magnetic phase due to the α′ → γ transformation were investigated. The EDS maps show a high concentration of nitrogen in the alternating hard surface layers of γNand α′N(expanded austenite and martensite), but no significantly higher concentration of chromium or iron was detected. The high surface hardness of this nitride layer will lead to steels and encoders with better wear and corrosion resistance.
Metabolic activities of five botryticides against Botrytis cinerea examined using the Biolog FF MicroPlate
Authors: Wang Hancheng , Wang Jin , Li Licui , Hsiang Tom , Wang Maosheng , Shang Shenghua , Yu Zhihe 
Published: August 2016

AbstractTobacco grey mold caused by Botrytis cinerea is an important fungal disease worldwide. Boscalid, carbendazim, iprodione, pyrimethanil and propiconazole are representative botryticides for grey mold management. This research investigated the sensitivities of B. cinerea from tobacco to these chemicals using the Biolog FF Microplate. All five chemicals showed inhibitory activity, with average EC50 values of 0.94, 0.05, 0.50, 0.61 and 0.31 μg ml−1, respectively. B. cinerea metabolized 96.8% of tested carbon sources, including 29 effectively and 33 moderately, but the metabolic fingerprints differed under pressures imposed by these botryticides. For boscalid, B. cinerea was unable to metabolize many substrates related to tricarboxylic acid cycle. For carbendazim, carbon sources related to glycolysis were not metabolized. For iprodione, use of most carbon substrates was weakly inhibited, and the metabolic profile was similar to that of the control. For propiconazole, no carbon substrates were metabolized and the physiological and biochemical functions of the pathogen were totally inhibited. These findings provide useful information on metabolic activities of these botryticides, and may lead to future applications of the Biolog FF Microplate for examining metabolic effects of other fungicides on other fungi, as well as providing a metabolic fingerprint of B. cinerea that could be useful for identification.
The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa
Authors: Gouran Hossein , Gillespie Hyrum , Nascimento Rafael , Chakraborty Sandeep , Zaini Paulo A. , Jacobson Aaron , Phinney Brett S. , Dolan David , Durbin-Johnson Blythe P. , Antonova Elena S. , Lindow Steven E. , Mellema Matthew S. , Goulart Luiz R. , Dandekar Abhaya M. 
Published: August 2016

AbstractPierce’s disease (PD) is a deadly disease of grapevines caused by the Gram-negative bacterium Xylella fastidiosa. Though disease symptoms were formerly attributed to bacteria blocking the plant xylem, this hypothesis is at best overly simplistic. Recently, we used a proteomic approach to characterize the secretome of X. fastidiosa, both in vitro and in planta and identified LesA as one of the pathogenicity factors of X. fastidiosa in grapevines that leads to leaf scorching and chlorosis. Herein, we characterize another such factor encoded by PD0956, designated as an antivirulence secreted protease “PrtA” that displays a central role in controlling in vitro cell proliferation, length, motility, biofilm formation and in planta virulence. The mutant in X. fastidiosa exhibited reduced cell length, hypermotility (and subsequent lack of biofilm formation) and hypervirulence in grapevines. These findings are supported by transcriptomic and proteomic analyses with corresponding plant infection data. Of particular interest, is the hypervirulent response in grapevines observed when X. fastidiosa is disrupted for production of PrtA and that PD-model tobacco plants transformed to express PrtA exhibited decreased symptoms after infection by X. fastidiosa.
Constructal approach to bio-engineering: the ocular anterior chamber temperature
Authors: Lucia Umberto , Grisolia Giulia , Dolcino Daniela , Astori Maria Rosa , Massa Eugenio , Ponzetto Antonio 
Published: August 2016

AbstractThe aim of this work was to analyse the pressure inside the eyes anterior chamber, namedintraocular pressure (IOP), in relation to the biomechanical properties of corneas. The approach used was based on the constructal law, recently introduced in vision analysis. Results were expressed as the relation between the temperature of the ocular anterior chamber and the biomechanical properties of the cornea. The IOP, the elastic properties of the cornea and the related refractive properties of the eye were demonstrated to be dependent on the temperature of the ocular anterior chamber. These results could lead to new perspectives for experimental analysis of the IOP in relation to the properties of the cornea.
HIV-1 Tat exacerbates lipopolysaccharide-induced cytokine release via TLR4 signaling in the enteric nervous system
Authors: Guedia Joy , Brun Paola , Bhave Sukhada , Fitting Sylvia , Kang Minho , Dewey William L. , Hauser Kurt F. , Akbarali Hamid I. 
Published: August 2016

AbstractThe loss of gut epithelium integrity leads to translocation of microbes and microbial products resulting in immune activation and drives systemic inflammation in acquired immunodeficiency syndrome (AIDS) patients. Although viral loads in HIV patients are significantly reduced in the post-cART era, inflammation and immune activation persist and can lead to morbidity. Here, we determined the interactive effects of the viral protein HIV-1 Tat and lipopolysaccharide (LPS) on enteric neurons and glia. Bacterial translocation was significantly enhanced in Tat-expressing (Tat+) mice. Exposure to HIV-1 Tat in combination with LPS enhanced the expression and release of the pro-inflammatory cytokines IL-6, IL-1β and TNF-α in the ilea of Tat+ mice and by enteric glia. This coincided with enhanced NF-κB activation in enteric glia that was abrogated in glia from TLR4 knockout mice and by knockdown (siRNA) of MyD88 siRNA in wild type glia. The synergistic effects of Tat and LPS resulted in a reduced rate of colonic propulsion in Tat+ mice treated with LPS. These results show that HIV-1 Tat interacts with the TLR4 receptor to enhance the pro-inflammatory effects of LPS leading to gastrointestinal dysmotility and enhanced immune activation.
Self‐capacitor voltage balancing method for optimally hybrid modulated cascaded H‐bridge D‐STATCOM
Authors: Vural Ahmet Mete 
Published: August 2016

A hybrid modulation (HM) for cascaded H‐bridge converters is suggested which is a fusion of selective harmonic elimination (SHE) and carrier based bipolar pulse width modulation. It differs from its counterparts in the sense that only one triangular carrier for all H‐bridges is used as opposed to multi‐triangle waveform set and only one level of capacitor voltage and single type of semiconductor are considered. HM eliminates calculating and storing offline delay angles for each modulation index as in case of SHE. A novel self‐voltage balancing mechanism is also proposed for HM which is based on strategically swapping redundant switching states. This mechanism is free from voltage sorting, current measurement, extra circuitry, or additional controllers. The comparison with phase and level shift pulse width modulation schemes reveal that the HM has 15% more DC voltage utilisation, and lower harmonic content for wide interval of modulation index. Moreover, HM has low semiconductor losses, as low as 0.55%. The tests on 1500 kVAR distribution static synchronous compensator shows that HM generates only 4% voltage ripple at the cost of few increase in average switching frequency. Voltage and reactive power balancing in each phase are also established with high power efficiency.
Expanding Surgical Opportunities: Endoscopic Harvesting of the Vena Saphena Parva in Supine Position
Authors: Rustenbach Christian , Franke Ulrich , Baumbach Hardy , Wachter Kristina 
Published: August 2016

AbstractThe small saphenous vein (SSV) has proved to be a valid graft option for coronary artery bypass grafting (CABG), if other grafts are absent or unsuitable. Beside the described open technique we herein present our approach to endoscopic harvesting in supine position in seven patients. Harvesting was successful in six patients. Mean skin-to-skin time was 29.8 minutes. There were no infections or neurological deficits and the intraoperatively measured graft flow was excellent according to mean flow and low pulsatility index. Therefore, endoscopic harvesting of the SSV extends surgical opportunities not only in CABG, but also in surgery of peripheral artery disease.
Mike the Knight in the neo-liberal era
Authors: Lindstrand Fredrik , Insulander Eva , Selander Staffan 
Published: August 2016

Abstract
Goal-oriented learning seems to be a ubiquitous demand for almost all kind of play activities today. This demand, the article argues, is related to a specific neo-liberal discourse about the “superchild”. The article shows how this discourse is articulated multimodally in a number of media texts aimed at young children based around a trans-medial brand; Mike the Knight.
Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics
Authors: Wen Yalu , Chen Fushun , Zhang Qingzheng , Zhuang Yan , Li Zhiguang 
Published: August 2016

Motivation: DNA methylation is an important epigenetic modification that has essential role in gene regulation, cell differentiation and cancer development. Bisulfite sequencing is a widely used technique to obtain genome-wide DNA methylation profiles, and one of the key tasks of analyzing bisulfite sequencing data is to detect differentially methylated regions (DMRs) among samples under different treatment conditions. Although numerous tools have been proposed to detect differentially methylated single CpG site (DMC) between samples, methods for direct DMR detection, especially for complex study designs, are largely limited.
Results: We present a new software, GetisDMR, for direct DMR detection. We use beta-binomial regression to model the whole-genome bisulfite sequencing data, where variations in methylation levels and confounding effects have been accounted for. We employ a region-wise test statistic, which is derived from local Getis-Ord statistics and considers the spatial correlation between nearby CpG sites, to detect DMRs. Unlike existing methods, that attempt to infer DMRs from DMCs based on empirical criteria, we provide statistical inference for direct DMR detection. Through extensive simulations and an application to two mouse datasets, we demonstrate that GetisDMR achieves better sensitivities, positive predictive values, more exact locations and better agreement of DMRs with current biological knowledge.
Availability and Implementation: It is available at https://github.com/DMU-lilab/GetisDMR.
Contacts: y.wen@auckland.ac.nz or zhiguangli@dlmedu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of Erwinia rhapontici as the Causal Agent of Crown and Shoot Rot and Pink Seed of Pea in Nebraska
Authors: Adesemoye Anthony O. , Wei Hsin-Ho , Harveson Robert M. 
Published: August 2016

Dry yellow pea production has been increasing in the central High Plains. One of the emerging pathogens of pea in the region is Erwinia rhapontici. In a Nebraska disease survey, a pea field exhibited a high incidence of bacterial-like symptoms. Four of the isolates recovered from samples were identified as E. rhapontici by sequencing the 16s rDNA. Similar symptoms to those seen on the field were also reestablished by these strains in pathogenicity tests through rolled towel and greenhouse assays. Accepted for publication 2 June 2016. Published 6 July 2016.
Soybean Cyst Nematode HG Type Test Results Differ Among Multiple Samples from the Same Field but the Management Implications Are the Same
Authors: Beeman Augustine Q. , Harbach Chelsea J. , Marett Christopher C. , Tylka Gregory L. 
Published: August 2016

The objective of this study was to determine how HG type test results might vary among SCN populations in independent samples collected from the same field or area of a field. Accepted for publication 20 June 2016. Published 22 July 2016.
Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis
Authors: Malinverni Duccio , Lopez Alfredo Jost , Los Rios Paolo De , Hummer Gerhard , Barducci Alessandro 
Published: August 2016

AbstractThe interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.