bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of several laser systems on removal of smear layer with a variety of irrigation solutions
Authors: Ozbay Yagiz , Erdemir Ali 
Published: October 2018

AbstractTo evaluate which laser system is more effective on smear layer removal when distilled water or combination of sodium hypochlorite (NaOCl) and ethylenediaminetetraacetic acid (EDTA) are used as irrigants. Ninety‐six human mandibular premolar teeth were used. Standard access cavities were prepared and the root canals were enlarged using ProTaper system to size F4 and divided into two equal groups according to final irrigation solution. In Group 1, distilled water was used, whilst 2.5% NaOCI and 17% EDTA solutions were used in Group 2. Each group was divided into four equal subgroups according to the activation procedure. In Subgroups 1A (Control) and 2A, no activation protocol was applied. In other subgroups, Er:YAG laser using photon‐induced photoacoustic streaming (PIPS; 1B and 2B), Nd:YAG laser (1C and 2C) and Er,Cr:YSGG laser (1D and 2D) were applied for the activation. Teeth were split longitudinally and subjected to scanning electron microscopy evaluation. Smear layer was scored at 1000× magnification in all thirds. The data were analysed statistically using Kruskal‐Wallis and Mann–Whitney U test post hoc comparisons. The samples irrigated with distilled water had greater smear layer scores when compared with the combination of NaOCl and EDTA (p < .05). The efficacy of smear layer removal increased when using laser systems (p < .05). Smear layer was removed more effectively in the coronal and middle levels compared to the apical level (p < .05). The sequential use of NaOCl and EDTA is significantly more effective than distilled water in smear layer removal. Regardless of the type of irrigant, laser activated irrigation enhances smear layer removal.Research HighlightsThe use of laser systems for activation of NaOCl and EDTA is the most effective method in terms of smear layer removal. Photon‐induced photoacoustic streaming technique with Er:YAG laser was the most efficient smear layer removal method regardless of the solution used.
Bioinformatic data processing pipelines in support of next‐generation sequencing‐based HIV drug resistance testing: the Winnipeg Consensus
Authors: Ji Hezhao , Enns Eric , Brumme Chanson J. , Parkin Neil , Howison Mark , Lee Emma R. , Capina Rupert , Marinier Eric , Avila‐Rios Santiago , Sandstrom Paul , Van Domselaar Gary , Harrigan Richard , Paredes Roger , Kantor Rami , Noguera‐Julian Marc 
Published: October 2018

AbstractIntroductionNext‐generation sequencing (NGS) has several advantages over conventional Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and quantitation of low‐abundance variants bearing drug resistance mutations (DRMs). However, the high HIV genomic diversity, unprecedented large volume of data, complexity of analysis and potential for error pose significant challenges for data processing. Several NGS analysis pipelines have been developed and used in HIVDR research; however, the absence of uniformity in data processing strategies results in lack of consistency and comparability of outputs from different pipelines. To fill this gap, an international symposium on bioinformatic strategies for NGS‐based HIVDR testing was held in February 2018 in Winnipeg, Canada, convening laboratory scientists, bioinformaticians and clinicians involved in four recently developed, publicly available NGS HIVDR pipelines. The goal of this symposium was to establish a consensus on effective bioinformatic strategies for NGS data management and its use for HIVDR reporting.DiscussionEssential functionalities of an NGS HIVDR pipeline were divided into five analytic blocks: (1) NGS read quality control (QC)/quality assurance (QA); (2) NGS read alignment and reference mapping; (3) HIV variant calling and variant QC; (4) NGS HIVDR reporting; and (5) extended data applications and additional considerations for data management. The consensuses reached among the participants on all major aspects of these blocks are summarized here. They encompass not only recommended data management and analysis strategies, but also detailed bioinformatic approaches that help ensure accuracy of the derived HIVDR analysis outputs for both research and potential clinical use.ConclusionsWhile NGS is being adopted more broadly in HIVDR testing laboratories, data processing is often a bottleneck hindering its generalized application. The proposed standardization of NGS read QC/QA, read alignment and reference mapping, variant calling and QC, HIVDR reporting and relevant data management strategies in this “Winnipeg Consensus” may serve as a starting guideline for NGS HIVDR data processing that informs the refinement of existing pipelines and those yet to be developed. Moreover, the bioinformatic strategies presented here may apply more broadly to NGS data analysis of microbes harbouring significant genomic diversity.
Successes and challenges in optimizing the viral load cascade to improve antiretroviral therapy adherence and rationalize second‐line switches in Swaziland
Authors: Etoori David , Ciglenecki Iza , Ndlangamandla Mpumelelo , Edwards Celeste G , Jobanputra Kiran , Pasipamire Munyaradzi , Maphalala Gugu , Yang Chunfu , Zabsonre Inoussa , Kabore Serge M , Goiri Javier , Teck Roger , Kerschberger Bernhard 
Published: October 2018

AbstractIntroductionAs antiretroviral therapy (ART) is scaled up, more patients become eligible for routine viral load (VL) monitoring, the most important tool for monitoring ART efficacy. For HIV programmes to become effective, leakages along the VL cascade need to be minimized and treatment switching needs to be optimized. However, many HIV programmes in resource‐constrained settings report significant shortfalls.MethodsFrom a public sector HIV programme in rural Swaziland, we evaluated the VL cascade of adults (≥18 years) on ART from the time of the first elevated VL (>1000 copies/mL) between January 2013 and June 2014 to treatment switching by December 2015. We additionally described HIV drug resistance for patients with virological failure. We used descriptive statistics and Kaplan–Meier estimates to describe the different steps along the cascade and regression models to determine factors associated with outcomes.Results and DiscussionOf 828 patients with a first elevated VL, 252 (30.4%) did not receive any enhanced adherence counselling (EAC). Six hundred and ninety‐six (84.1%) patients had a follow‐up VL measurement, and the predictors of receiving a follow‐up VL were being a second‐line patient (adjusted hazard ratio (aHR): 0.72; p = 0.051), Hlathikhulu health zone (aHR: 0.79; p = 0.013) and having received two EAC sessions (aHR: 1.31; p = 0.023). Four hundred and ten patients (58.9%) achieved VL re‐suppression. Predictors of re‐suppression were age 50 to 64 (adjusted odds ratio (aOR): 2.02; p = 0.015) compared with age 18 to 34 years, being on second‐line treatment (aOR: 3.29; p = 0.003) and two (aOR: 1.66; p = 0.045) or three (aOR: 1.86; p = 0.003) EAC sessions. Of 278 patients eligible to switch to second‐line therapy, 120 (43.2%) had switched by the end of the study. Finally, of 155 successfully sequenced dried blood spots, 144 (92.9%) were from first‐line patients. Of these, 133 (positive predictive value: 92.4%) had resistance patterns that necessitated treatment switching.ConclusionsPatients on ART with high VLs were more likely to re‐suppress if they received EAC. Failure to re‐suppress after counselling was predictive of genotypically confirmed resistance patterns requiring treatment switching. Delays in switching were significant despite the ability of the WHO algorithm to predict treatment failure. Despite significant progress in recent years, enhanced focus on quality care along the VL cascade in resource‐limited settings is crucial.
Methods for the determination of levoglucosan and other sugar anhydrides as biomass burning tracers in environmental samples – A review
Authors: Janoszka Katarzyna , Czaplicka Marianna 
Published: October 2018

AbstractNowadays, there is a great pressure on finding an alternative source of energy. One such source is biomass combustion. Biomass is any organic matter such as wood, crops, seaweed, and animal wastes that during combustion emits energy but also smoke and solid residue. Biomass burning tracers, such as levoglucosan, mannosan and galactosan, are sugar anhydrides produced during burning of biomass that contain cellulose and hemicellulose. Analysis of environmental samples for tracers is the source of information about the type of biofuel burned. In this article, a literature review of the preparation and determination of biomass burning tracers for environmental samples was presented. The review discusses the preparation of different samples (particulate matter, soils, sediments, biological samples), extraction, derivatization, and determination. Amongst determination methods the most popular was gas chromatography with mass spectrometry but other techniques were also used, such as high‐performance liquid chromatography with aerosol charge detection, capillary electrophoresis with pulsed amperometric detection, and ion chromatography with pulsed amperometric detection.
Optimization of solid‐phase extraction of parabens and benzophenones in water samples using a combination of Plakett‐Burman and Box‐Behnken designs
Authors: Chávez‐Moreno Carmin A. , Hinojosa‐Reyes Laura , Ruiz‐Ruiz Edgar J. , Hernández‐Ramírez Aracely , Guzmán‐Mar Jorge L. 
Published: October 2018

AbstractAn automated method for the analysis of methylparaben, propylparaben, benzophenone‐3, and benzophenone‐4 in water effluents via on‐line solid‐phase extraction coupled with high‐performance liquid chromatography/ultraviolet detection was proposed. The preconcentration parameters were studied using Plackett‐Burman and Box‐Behnken experimental designs using a C18 sorbent material. The results demonstrated that the eluent volume, composition, and sorbent amount were statistically significant. Optimal conditions for these variables were an eluent volume of 1.55 mL, eluent composition of acetonitrile 100% v/v, and sorbent amount of 100 mg. The eluted sample was analyzed on‐line using high‐performance liquid chromatography equipped with a reversed‐phase C18 column and ultraviolet detection. Separation of the analytes was achieved in 15 min using gradient elution with acetonitrile/water. A simple, sensitive, and rapid analytical method was proposed for personal care compounds without sophisticated or expensive equipment. The limits of detection were 1.20, 1.73, 2.51, and 4.67 μg/L for propylparaben, methylparaben, benzophenone‐3, and benzophenone‐4, respectively. The analysis time was 48 min, consuming only 1.59 mL of eluent acetonitrile for the solid phase extraction step, with minimal sample handling. The method was applied to the analysis of spiked swimming pool and wastewater, with recoveries between 65–107%. These results indicate the reliability of the flow‐based procedure.
Effects of scale and land cover on loggerhead shrike occupancy
Authors: Froehly Jennifer L. , Tegeler Amy K. , Jachowski Catherine M. Bodinof , Jachowski David S. 
Published: October 2018

ABSTRACTThe loggerhead shrike (Lanius ludovicianus) is a species of concern throughout its range because of severe population declines over the past 7 decades. Grassland habitat loss and fragmentation is widely viewed as contributing to the decline. Habitat associations have primarily been studied up to the territory scale, with few studies assessing shrike habitat selection at landscape scales. We conducted roadside passive‐active point counts for loggerhead shrikes in the coastal plain of South Carolina to evaluate detection probability and how land use and habitat fragmentation at multiple spatial scales influenced the occupancy of loggerhead shrikes. Detection probability increased with fair weather to 63% with clear skies, with temperature to 83% at 28°C, and with declining noise to 63% at no noise. High probability of detection at mean covariate conditions (P = 0.49 ± 0.08 [SE]) indicated support for the application of passive point counts in future loggerhead shrike monitoring. Occupancy was best predicted by percentage of pasture within 1 km, where predicted occupancy increased from 2 ± 0.02% when there was 0% pasture in a 1‐km radius, to 98 ± 0.03% occupancy when there was 43% pasture in a 1‐km radius, though our model‐averaged occupancy estimate was low (ψ = 0.17 ± 0.05). Extrapolation of our averaged model suggested that only 8% of the South Carolina coastal plain was occupied by loggerhead shrikes in the 2016 and 2017 breeding seasons. Our results highlight the importance of habitat beyond breeding territories and highlight the need for the establishment of higher concentrations of pasture and grassland at a 1‐km scale to increase the proportion of area in South Carolina occupied by shrikes. © 2018 The Wildlife Society.
Photomodulated Morphologies in Halogen Bond–Driven Assembly during Gel–Sol Transition
Authors: Hu Haisi , Qiu Yuan , Wang Jing , Zhao Dongxu , Wang Hong , Wang Qin , Liao Yonggui , Peng Haiyan , Xie Xiaolin 
Published: October 2018

AbstractPhotoresponsive supramolecular gels with various applications are being constantly pursued; however, achieving well‐defined morphology changes of gels via light irradiation remains a formidable challenge. In this study, a gel is prepared through halogen bond between azopyridine‐containing Azopy‐C10 and 1,4‐tetrafluorodiiodobenzene. The gel exhibits gel–sol transition due to trans–cis isomerization of the azopyridine moiety upon UV irradiation. During this transition, the morphologies vary from flake to fluffy bobble‐like and finally to peony‐like with increasing exposure time, which is difficult to achieve in traditional assembly systems. The microstructure change is attributed to the variations of cis‐isomer content and halogen‐bonding strength. The supramolecular gel provides a novel method to achieve photomodulated morphologies and broadens the applications of such kind of materials, ranging from information storage to high‐tech anticounterfeit.
Color My World
Authors: Giordano Geoff 
Published: October 2018

With material regulations getting stricter and performance requirements getting tougher, suppliers of custom colors for plastics are meeting the demand with highly specific formulations, production of small lots, and faster turnaround timesWhether to meet legal requirements that limit toxic materials or market needs for impact resistance, fire prevention, shelf presence, and more, several color companies are investing heavily and expanding capacity rapidly to rise to the challenge
Redefining Tissue Crosstalk via Shotgun Proteomic Analyses of Plasma Extracellular Vesicles
Authors: Whitham Martin , Febbraio Mark A. 
Published: October 2018

AbstractProtein signaling between tissues, or tissue cross‐talk is becoming recognized as a fundamental biological process that is incompletely understood. Shotgun proteomic analyses of tissues and plasma to explore this concept are regularly challenged by high dynamic range of protein abundance, which limits the identification of lower abundance proteins. In this viewpoint article, it is highlighted how a focus on proteins contained within extracellular vesicles (EVs) not only partially addresses this issue, but can also reveal an underappreciated complexity of the circulating proteome in various physiological and pathological contexts. Furthermore, how quantitative proteomics can inform EV mediated crosstalk is highlighted and the importance of high coverage, sensitive proteomic analyses of EVs to identify both the optimal methods to isolate EV subtypes of interest and proteins that characterize them is stressed.
Extracellular Vesicles: A Prevalent Tool for Microbial Gene Delivery?
Authors: Ben‐Hur Sharon , Biton Mirit , Regev‐Rudzki Neta 
Published: October 2018

AbstractGenetic plasticity of prokaryotic microbial communities is largely dependent on the ongoing exchange of genetic determinants by Horizontal Gene Transfer (HGT). HGT events allow beneficial genetic transitions to occur throughout microbial life, thus promoting adaptation to changing environmental conditions. Here, the significance of secreted vesicles in mediating HGT between microorganisms is discussed, while focusing on the benefits gained by vesicle‐mediated gene delivery and its occurrence under different environmental cues. The potential use of secreted DNA‐harboring vesicles as a mechanism of currently unresolved HGT events in eukaryotic microbes is further discussed.
Synthesis and testing of novel alternative oxidase (AOX) inhibitors with antifungal activity against Moniliophthora perniciosa (Stahel), the causal agent of witches' broom disease of cocoa, and other phytopathogens
Authors: Barsottini Mario RO , Pires Bárbara A , Vieira Maria L , Pereira José GC , Costa Paulo CS , Sanitá Jaqueline , Coradini Alessandro , Mello Fellipe , Marschalk Cidnei , Silva Eder M , Paschoal Daniele , Figueira Antonio , Rodrigues Fábio HS , Cordeiro Artur T , Miranda Paulo CML , Oliveira Paulo SL , Sforça Maurício L , Carazzolle Marcelo F , Rocco Silvana A , Pereira Gonçalo AG 
Published: October 2018

AbstractBackgroundMoniliophthora perniciosa (Stahel) Aime & Phillips‐Mora is the causal agent of witches' broom disease (WBD) of cocoa (Theobroma cacao L.) and a threat to the chocolate industry. The membrane‐bound enzyme alternative oxidase (AOX) is critical for M. perniciosa virulence and resistance to fungicides, which has also been observed in other phytopathogens. Notably AOX is an escape mechanism from strobilurins and other respiration inhibitors, making AOX a promising target for controlling WBD and other fungal diseases.ResultsWe present the first study aimed at developing novel fungal AOX inhibitors. N‐Phenylbenzamide (NPD) derivatives were screened in the model yeast Pichia pastoris through oxygen consumption and growth measurements. The most promising AOX inhibitor (NPD 7j‐41) was further characterized and displayed better activity than the classical AOX inhibitor SHAM in vitro against filamentous fugal phytopathogens, such as M. perniciosa, Sclerotinia sclerotiorum and Venturia pirina. We demonstrate that 7j‐41 inhibits M. perniciosa spore germination and prevents WBD symptom appearance in infected plants. Finally, a structural model of P. pastoris AOX was created and used in ligand structure‐activity relationships analyses.ConclusionWe present novel fungal AOX inhibitors with antifungal activity against relevant phytopathogens. We envisage the development of novel antifungal agents to secure food production. © 2018 Society of Chemical Industry
Immunomodulatory effect of Cynara scolymus (artichoke) in rats
Authors: Hueza Isis Machado , Gotardo André Tadeu , da Silva Mattos Maria Izabel , Górniak Silvana Lima 
Published: October 2018

Cynara scolymus is a plant used both as food as well as medicinal plant worldwide. Cynarin is one of the main active principles of the plant, and it is also present in species such as Echinacea purpurae, which is known to have immunomodulatory activity. Thus, the objective of this study is to evaluate the immune effects of C. scolymus in rats. Rats were treated with 1.0‐, 2.0‐, or 4.0‐g/kg body weight of C. scolymus extract for 28 days. Haemogram, serum biochemistry, lymphoid organs weight, and their cell phenotypes were evaluated. Macrophages and neutrophils oxidative burst, specific humoral immune response, and the delayed‐type hypersensitivity (DTH) were studied. No changes in the haemogram, biochemical profile, antibody titers, lymphoid organs, and in their cellularities were observed. An increase in the basal activity of reactive oxygen species from male's macrophage was observed. There was a suppression of the DTH response in both gender when treated with the highest dose of C. scolymus. This study is the first in the literature that revealed an immunosuppressive effect of C. scolymus. We also verified that the doses of artichoke extract here employed did not cause general toxicity.
Extracting at the borders: Negotiating political and ecological geographies of movement in mineral frontiers
Authors: Ali Saleem H. 
Published: October 2018

AbstractThis paper questions the drive towards more ecologically determined porosity across national borders in the context of incongruent economic regulation and incentives. The push towards regionalization and less austere border conditions have socio‐ecological salience and deserve consideration. However, mining creates human and financial capital flows across “mineral frontiers” which deserve greater attention by policy‐makers who are advocating for more relaxed border conditions. While minerals frontiers can be areas of cooperation under certain circumstances, they are highly vulnerable to acting as threat multipliers if not effectively monitored. A typology from border studies is used to develop a framework of how mineral resource projects can lead to human movement across borders. While mining projects in resource frontiers can be a means of fostering regional cooperation, they can also create vulnerabilities involving the migrants. The ways in which development donors and companies can facilitate more constructive harmonization of regulatory mechanisms to prevent such vulnerabilities are examined.
Performance persistence in the presence of higher‐order resources
Authors: Wibbens Phebo D. 
Published: October 2018

Research SummaryThis paper presents a formal model of how higher‐order resources affect profit persistence. Higher‐order resources provide an abstract representation of dynamic capabilities, and are defined as resources that do not affect profit directly, but can affect other resources that in turn affect profit over time. The model shows that higher‐order resources lead to persistence not only in the level of profit, but also in its growth. Estimation of the model using empirical profit data of more than 4,000 U.S. firms over 30 years implies an average duration of competitive advantage of about 18 years, which is almost four times as long as implied by traditionally used autoregressive models that exclude the effect of higher‐order resources.Managerial SummaryIf firms want to make more profit than their competitors for prolonged periods of time, they must have access to resources that competitors cannot effectively obtain, such as brands, patents, captive customers, or specialized plants. This paper shows that not only these “operating resources” drive long‐term profit differences across firms, but also “higher‐order resources,” such as strategic planning, M&A capabilities, and superior forecasts. Such higher‐order resources do not affect profits directly, but allow firms to obtain superior operating resources over time. A mathematical model incorporating higher‐order resources suggests an average duration of competitive advantage of about 18 years, almost four times as long as implied by traditionally used models.