bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplified Expansion Stimulated Emission Depletion Microscopy
Authors: Kim Doyeon , Kim Taeyeon , Lee Jooyong , Shim Sang‐Hee 
Published: January 2019

AbstractExpansion microscopy (ExM) enhances spatial resolution by using a swellable polymer that expands the sample volume by a factor of ≈4 in one dimension and a factor of ≈64 in volume. Combining ExM with stimulated emission depletion (STED) microscopy, referred to as ExSTED, increases the resolution to up to 10 nm. However, photobleaching is a critical issue in ExSTED because the sample expansion lowers the fluorophore density whereas high‐resolution STED requires high depletion intensity. To overcome these issues, we developed extremely bright expansion nanoscopy by using biotin–avidin signal amplification to increase the labeling density. Our method provides up to sevenfold increases in fluorescence signal intensity in expanded samples, thus enabling the use of STED imaging with maximum depletion intensities of a commercial microscope in the order of GW cm−2. We demonstrated the method by using biotinylated antibodies and genetic incorporation approaches that allow localization of biotin in a specific molecule or organelle.
The role of indirect genetic effects in the evolution of interacting reproductive behaviors in the burying beetle,Nicrophorus vespilloides
Authors: Carter Mauricio J. , Wilson Alastair J. , Moore Allen J. , Royle Nick J. 
Published: January 2019

AbstractSocial interactions can give rise to indirect genetic effects (IGEs), which occur when genes expressed in one individual affect the phenotype of another individual. The evolutionary dynamics of traits can be altered when there are IGEs. Sex often involves indirect effects arising from first‐order (current) or second‐order (prior) social interactions, yet IGEs are infrequently quantified for reproductive behaviors. Here, we use experimental populations of burying beetles that have experienced bidirectional selection on mating rate to test for social plasticity and IGEs associated with focal males mating with a female either without (first‐order effect) or with (second‐order effect) prior exposure to a competitor, and resource defense behavior (first‐order effect). Additive IGEs were detected for mating rate arising from (first‐order) interactions with females. For resource defense behavior, a standard variance partitioning analysis provided no evidence of additive genetic variance—either direct or indirect. However, behavior was predicted by focal size relative to that of the competitor, and size is also heritable. Assuming that behavior is causally dependent on relative size, this implies that both DGEs and IGEs do occur (and may potentially interact). The relative contribution of IGEs may differ among social behaviors related to mating which has consequences for the evolutionary trajectories of multivariate traits.
Soluble CD93 is an apoptotic cell opsonin recognized by αxβ2
Authors: Blackburn Jack W. D. , Lau Darius H. C. , Liu Elaine Y. , Ellins Jessica , Vrieze Angela M. , Pawlak Emily N. , Dikeakos Jimmy D. , Heit Bryan 
Published: January 2019

AbstractEfferocytosis is essential for homeostasis and prevention of the inflammatory and autoimmune diseases resulting from apoptotic cell lysis. CD93 is a transmembrane glycoprotein previously implicated in efferocytosis, with mutations in CD93 predisposing patients to efferocytosis‐associated diseases. CD93 is a cell surface protein, which is proteolytically shed under inflammatory conditions, but it is unknown how CD93 mediates efferocytosis or whether its efferocytic activity is mediated by the soluble or membrane‐bound form. Herein, using cell lines and human monocytes and macrophages, we demonstrate that soluble CD93 (sCD93) potently opsonizes apoptotic cells but not a broad range of microorganisms, whereas membrane‐bound CD93 has no phagocytic, efferocytic, or tethering activity. Using mass spectrometry, we identified αxβ2 as the receptor that recognizes sCD93, and via deletion mutagenesis determined that sCD93 binds to apoptotic cells via its C‐type lectin‐like domain and to αxβ2 by its EGF‐like repeats. The bridging of apoptotic cells to αxβ2 markedly enhanced efferocytosis by macrophages and was abrogated by αxβ2 knockdown. Combined, these data elucidate the mechanism by which CD93 regulates efferocytosis and identifies a previously unreported opsonin‐receptor system utilized by phagocytes for the efferocytic clearance of apoptotic cells.
Economic assessment of advanced biofuel production via gasification using cost data from the GoBiGas plant
Authors: Thunman Henrik , Gustavsson Christer , Larsson Anton , Gunnarsson Ingemar , Tengberg Freddy 
Published: January 2019

AbstractThis paper describes an economic analysis of the GoBiGas plant, which is a first‐of‐its‐kind industrial installation for advanced biofuel production (ABP) via gasification, in which woody biomass is converted to biomethane. A previous technical evaluation of the demonstration unit confirmed that it is technically feasible to construct advanced biofuel production plants, using commercially available and widely used components. Thus, significant cost reductions for equipment cannot be expected as a consequence of learning effects. However, the equipment itself accounted for <20% of the total investment cost at GoBiGas and there exists the potential to reduce the production cost through learning how to assemble the process and reduce project‐specific costs. The analysis shows that a plant with capacity of 200 MW of biomethane is an attractive scale for future stand‐alone ABP plants with respect to limiting the production cost. For a 200‐MW ABP plant operated using forest residues as fuel, the production cost for biomethane is estimated at approximately 600 SEK/MWh, (60€/MWh, 75US$/MWh), which is equivalent to 5.4 SEK/liter gasoline [0.54 €/liter, or 2.5USD per gallon (9.9 SEK/€, 8 SEK/USD)], where the feedstock accounts for about 36% of the production cost. The most significant uncertainty factors pertaining to the estimated production costs are expected to relate to: trade conditions; the location of the installation; and the local price of feedstock. Thus, there is some potential for implementing cost‐competitive ABP systems of smaller capacity if low‐grade feedstocks (eg, waste‐derived woody biomass) can be utilized, and/or if the unit can be integrated with the already existing infrastructure.
Experimental investigations into the influence of biofilms and environmental factors on short‐term microtopographic fluctuations of supratidal sandstone
Authors: Yuan Runjie , Kennedy David M. , Stephenson Wayne J. , Gómez‐Pujol Lluís 
Published: January 2019

AbstractIn this study laboratory experiments were used to explore the role of biofilms, formed by lithobiontic microorganism communities, in causing hourly surface changes of supratidal sandstone and the potential linkage to long‐term rock decay. To isolate the influence of individual environmental factors (temperature and humidity) on rock surface changes (expansion and contraction), a colonized (biofilm‐covered) and a non‐colonized sandstone block (biofilm‐free) underwent the same univariate microclimatic simulations closely controlled by an environmental chamber. Simulations were run under three different light conditions, with a natural light lamp on, on and off at 20‐min intervals and off, to investigate the impact of light on rock surface dynamics. Measured with a traversing micro‐erosion meter (TMEM), two‐hourly microtopographic fluctuations of these two sandstone blocks were compared in the same environment. Induced by microclimatic variations, surface movements of significantly higher magnitude (12–120% under varying tempeature and 121–154% under varying humidity) and different change patterns were observed on the colonized block, indicating the primary role of biofilm in driving microtopographic fluctuations of supratidal sandstone. However, thermally driven changes of similar magnitude and pattern were observed on both surfaces, suggesting other mechanisms also operating on the non‐colonized rock surface in this process. Due to the sensitivity of biofilm microorganism communities to light, the magnitude and pattern of surface changes was impacted by light condition. Because biofilms increased the magnitude and number of cycles of expansion and contraction of the experimental rock surface, we propose that lithobiontic biofilms facilitate the detachment of grains and granular disintegration on the rock surface, consequently contributing to rock decay and accelerating the rate of breakdown of supratidal rock. This short‐term episode therefore needs to be superimposed on longer term studies to fully understand the role of biofilms in rock surface change. © 2019 John Wiley & Sons, Ltd.
A rapid method of preparing complex organohalogen extracts from avian eggs: Applications to in vitro toxicogenomics screening
Authors: Crump Doug , Williams Kim L. , Chiu Suzanne , Periard Luke , Letcher Robert J. 
Published: January 2019

Abstract

Double-crested cormorants are piscivorous birds that breed in variably contaminated colonies across the Laurentian Great Lakes of North America. Collection and preparation of environmentally relevant extracts from eggs that contain variable concentrations of organohalogen contaminants represents a minimally invasive approach to characterize potential effects of exposure using in vitro bioassays. In the present study, a rapid, efficient lipid freeze-filtration extraction method was used to prepare extracts from double-crested cormorant eggs collected from 5 breeding colonies that had variable organohalogen contaminant burdens. Extracts, solubilized in dimethyl sulfoxide, were administered to chicken embryonic hepatocytes (CEHs) to determine effects on cell viability, 7-ethoxyresorufin-O-deethylase (EROD) activity, and messenger RNA expression using a chicken ToxChip polymerase chain reaction (PCR) array. The EROD median effect concentration (EC50) values were lower for extracts with greater organohalogen contaminant burdens and thus permitted an initial ranking of colonies based on the efficacy of eliciting an aryl hydrocarbon receptor–mediated response. The ToxChip PCR array data provided a more exhaustive, pathway-based evaluation of extract effects; variability in the transcriptomic profiles was associated with organohalogen contaminant burdens. For example, extracts from Mud Island (Detroit River, MI, USA) had among the highest organohalogen contaminant burdens and elicited a greater biochemical (EROD EC50 = 0.005) and transcriptomic response (22/43 genes altered on the array) in CEHs compared with the least contaminated site, which was Mandarte Island (BC, Canada; EROD EC50 = 0.172; 8/43 genes altered). Avian eggs represent a useful biomonitoring tool for determining complex mixture effects, and the combination of a rapid extraction method, an in vitro bioassay, and targeted endpoint evaluation (biochemical and transcriptomic) shows great promise as an environmental effects monitoring approach. Environ Toxicol Chem 2019;38:811–819. © 2019 Crown in the right of Canada. Published by Wiley Periodicals Inc. on behalf of SETAC.
A grounded theory study of the narrative behind Indian physiotherapists global migration
Authors: Grafton Kate , Gordon Frances 
Published: January 2019

SummaryIt is estimated that an additional 6.4 million allied health professionals are required to address India's health challenges. Physiotherapy is amongst the largest of these professions. Over the last decade, thousands of Indian physiotherapists have sought to study and work overseas. In this study, 19 physiotherapists from across India were interviewed. Data were collected and analysed using construct+ivist grounded theory methods. The findings indicate that the Indian physiotherapy profession faces many political and clinical hierarchical challenges within the Indian healthcare infrastructure. The profession's education provision has developed, and the private clinical sector has grown, but there are significant disparities in quality and standards across the sector. The profession in India has variable autonomy, is not nationally regulated, is poorly paid, and the leadership has been divided. The political, educational, and clinical context in Indian physiotherapy impacts upon physiotherapists' ability to practise effectively to their professional satisfaction. Individual physiotherapists are frustrated by their workplace and travel overseas where they hear that the physiotherapy profession and practice is different. Whilst the disjunctures influencing these factors continue, and overseas physiotherapy practice is perceived as different and superior, Indian physiotherapists will continue to seek to migrate overseas, and facilitating their return will be challenging.
Dual‐Cure Coatings: Spiroorthoesters as Volume‐Controlling Additives in Thiol–Ene Reactions
Authors: Marx Philipp , Romano Angelo , Fischer Roland , Roppolo Ignazio , Sangermano Marco , Wiesbrock Frank 
Published: January 2019

AbstractMost thiol–ene systems exhibit shrinkage during cross‐linking, potentially resulting in micro‐cracks and delamination. Oligocyclic monomers like spiroorthoesters (SOEs), on the contrary, show expansion during the ring‐opening polymerization. In this communication, a photocurable thiol–ene system composed of a trifunctional thiol, a bisfunctional allyl‐bisphenol A compound, and an SOE compound bearing one olefin function shows expansion in the range from −3.07 to +1.70 vol% if the SOE content is increased from 0–30 wt%. Network formation can be accomplished under visible light if a radical as well as a cationic photoinitiator (dual‐cure mechanism) and a sensitizer are used. The elasticity of the cured resin increases upon the addition of the SOE; correspondingly, the glass‐transition temperature shows a (minor) decrease from 16 to 3 °C. A tailor‐made combination of the allyl‐bisphenol A compound (90 wt%) and the SOE (10 wt%) yields networks that are volume‐neutral during curing.
Single mutations in BraRS confer high resistance against nisin A in Staphylococcus aureus
Authors: Arii Kaoru , Kawada‐Matsuo Miki , Oogai Yuichi , Noguchi Kazuyuki , Komatsuzawa Hitoshi 
Published: January 2019

AbstractNisin A is a lantibiotic produced by Lactococcus lactis that is widely used as a food preservative. In Staphylococcus aureus, the BraRS two‐component system (TCS) senses nisin A and regulates the expression of the ABC transporter VraDE, which is responsible for nisin A resistance. In this study, we exposed S. aureus to a sub‐minimum inhibition concentration of nisin A and obtained three spontaneous mutants that were highly resistant to this lantibiotic, designated as SAN (S. aureus nisin resistant) 1, SAN8, and SAN87. In the wild‐type S. aureus strain, VraDE expression was induced by nisin A. In contrast, SAN8 and SAN87 showed constitutively high VraDE expression, even in the absence of nisin A, while SAN1 showed higher BraRS expression, which resulted in high VraDE expression in the presence of nisin A. We identified a single mutation in the promoter region of braXRS in SAN1, whereas SAN8 and SAN87 had single mutations in braR and braS, respectively. Interestingly, even the unphosphorylated form of the mutant BraR protein induced VraDE expression. These results indicate that conformational changes in BraS or BraR resulting from the point mutations may result in the constitutive expression of VraDE, allowing S. aureus to adapt to high concentrations of nisin A.
Aquella oligotrophica gen. nov. sp. nov.: A new member of the family Neisseriaceae isolated from laboratory tap water
Authors: Chan Kok‐Gan , See‐Too Wah‐Seng , Chua Kah‐Ooi , Peix Álvaro , Goh Kian Mau , Hong Kar‐Wai , Yin Wai‐Fong , Lee Li‐Sin 
Published: January 2019

AbstractA bacterial strain designated as P08T was isolated from laboratory tap water during a water quality assessment in University of Malaya, Malaysia. The strain was a Gram‐negative, rod‐shaped, nonmotile, and aerobic bacterium. Complete genome of P08T comprised of a 2,820,660 bp chromosome with a G + C content of 36.43%. Both 16S rRNA phylogeny and phylogenetic tree inferred from the core gene matrix demonstrated that P08T formed a hitherto unknown subline within the family Neisseriaceae. Ortho average nucleotide identity (OrthoANI) values and the percentage of conserved proteins (POCP) calculated from complete genome sequence indicated low relatedness between P08T and its phylogenetic neighbors. Respiratory quinone analysis revealed Q‐8 as the only detectable quinone. The predominant cellular fatty acids were identified as C14:0, iso‐C15:0, and summed feature 3 (C16:1 ω7c/C16:1 ω6c). The polar lipids consisted of uncharacterized aminolipid, phosphatidylglycerol, and phosphatidylethanolamine. All aspects of phenotypic and phylogenetic data suggested that strain P08T represents a novel genus within family Neisseriaceae, for which the name Aquella gen. nov. is proposed. The type species of the genus is Aquella oligotrophica sp. nov., and the type strain is P08T (=LMG 29629T =DSM 100970T).
Investigating energy deposition in glandular tissues for mammography using multiscale Monte Carlo simulations
Authors: Oliver Patricia A. K. , Thomson Rowan M. 
Published: January 2019

PurposeTo investigate energy deposition in glandular tissues of the breast on macro‐ and microscopic length scales in the context of mammography.MethodsMultiscale mammography models of breasts are developed, which include segmented, voxelized macroscopic tissue structure as well as nine regions of interest (ROIs) embedded throughout the breast tissue containing explicitly‐modelled cells. Using a 30 kVp Mo/Mo spectrum, Monte Carlo (MC) techniques are used to calculate dose to ∼mm voxels containing glandular and/or adipose tissues, as well as energy deposition on cellular length scales. ROIs consist of at least 1000 mammary epithelial cells and ∼200 adipocytes; specific energy (energy imparted per unit mass; stochastic analogue of the absorbed dose) is calculated within mammary epithelial cell nuclei.ResultsMacroscopic dose distributions within segmented breast tissue demonstrate considerable variation in energy deposition depending on depth and tissue structure. Doses to voxels containing glandular tissue vary between ∼0.1 and ∼4 times the mean glandular dose (MGD, averaged over the entire breast). Considering microscopic length scales, mean specific energies for mammary epithelial cell nuclei are ∼30% higher than the corresponding glandular voxel dose. Additionally, due to the stochastic nature of radiation, there is considerable variation in energy deposition throughout a cell population within a ROI: for a typical glandular voxel dose of 4 mGy, the standard deviation of the specific energy for mammary epithelial cell nuclei is 85% relative to the mean. Thus, for a glandular voxel dose of 4 mGy at the centre of the breast, corresponding mammary epithelial cell nuclei will receive specific energies up to ∼9 mGy (considering the upper end of the 1σ standard deviation of the specific energy), while a ROI located 2 cm closer to the radiation source will receive specific energies up to ∼40 mGy. Energy deposition within mammary epithelial cell nuclei is sensitive to cell model details including cellular elemental compositions and nucleus size, underlining the importance of realistic cellular models.ConclusionsThere is considerable variation in energy deposition on both macro‐ and microscopic length scales for mammography, with glandular voxel doses and corresponding cell nuclei specific energies many times higher than the MGD in parts of the breast. These results should be considered for radiation‐induced cancer risk evaluation in mammography which has traditionally focused on a single metric such as the MGD.
hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data
Authors: Massignani Enrico , Cuomo Alessandro , Musiani Daniele , Jammula SriGanesh , Pavesi Giulio , Bonaldi Tiziana 
Published: January 2019

AbstractHeavy methyl Stable Isotope Labeling with Amino acids in Cell culture (hmSILAC) is a metabolic labeling strategy employed in proteomics to increase the confidence of global identification of methylated peptides by MS. However, to this day, the automatic and robust identification of heavy and light peak doublets from MS‐raw data of hmSILAC experiments is a challenging task, for which the choice of computational methods is very limited. Here, hmSEEKER, a software designed to work downstream of a MaxQuant analysis for in‐depth search of MS peak pairs that correspond to light and heavy methyl‐peptide within MaxQuant‐generated tables is described with good sensitivity and specificity. The software is written in Perl, and its code and user manual are freely available at Bitbucket (https://bit.ly/2scCT9u).
Insensitive High Explosives: III. Nitroguanidine – Synthesis – Structure – Spectroscopy – Sensitiveness
Authors: Koch Ernst‐Christian 
Published: January 2019

AbstractThis paper reviews the production, synthesis, crystallography, particle morphology and spectroscopy of the insensitive high explosive nitroguanidine, (NGu, CH4N4O2), CAS‐No: [556‐88‐7] and its isotopologues [2D4]‐NGu and [15N4]‐NGu]. When compared with standard insensitive high explosives such as 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB), 1,1‐diamino‐2,2‐dinitroethylene (FOX‐7) and N‐guanylurea dinitramide (FOX‐12), Nitroguanidine proves to be the least sensitive. The review gives 170 references to the public domain. For Part II see ref. [1].
Interrater reliability of the standardized Timed Up and Go Test when used in hospitalized and community‐dwelling older individuals
Authors: Kristensen Morten Tange , Bloch Mette Linding , Jønsson Line Rokkedal , Jakobsen Thomas Linding 
Published: January 2019

AbstractObjectiveThe purpose of this study was to determine the interrater reliability and measurement error of the standardized Timed Up and Go (TUG) Test manual using the fastest of the three timed TUG trials in hospitalized and community‐dwelling older individuals.MethodsThirty participants (19 from a hospital and 11 from an outpatient geriatric centre: 20 women, 10 men), 65 years or older, all of whom had been referred to physiotherapy due to a functional decline, were included. All participants performed the TUG Test across two sessions (three trials in each) on the same day, separated by a minimum of 30 min. The two raters were blinded to each other's ratings until the end of the study, and the rater order was randomized.ResultsParticipants from the outpatient centre had a higher prereferral functional level when evaluated with the New Mobility Score and performed the TUG Test significantly faster than the hospital group. Accordingly, reliability estimates are reported for each specific group. Interrater reliability was excellent for both groups (intraclass correlation coefficient2.1 ≥ 0.93), and no systematic between‐rater difference for obtained TUG times was found. The measurement error was acceptable both at the group (standard error of measurement [SEM] = 1.7 s and SEM% = 8 [hospital] vs. 0.7 s and 6 [outpatient]) and the individual (minimal detectable change [MDC95] = 4.6 s and MDC95% = 23 [hospital] vs. 1.8 s and 17 [outpatient]) level.ConclusionFindings suggest that using the fastest of the three TUG trials is highly reliable between raters and with acceptable measurement error. We, therefore, suggest that the standardized TUG manual with the fastest of the three timed trials be used for the assessment of functional mobility in hospitalized and community‐dwelling older individuals.