bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative analysis of cell shape and the cytoskeleton in developmental biology
Authors: Yevick Hannah G. , Martin Adam C.
Published: August 2018

Computational approaches that enable quantification of microscopy data have revolutionized the field of developmental biology. Due to its inherent complexity, elucidating mechanisms of development requires sophisticated analysis of the structure, shape, and kinetics of cellular processes. This need has prompted the creation of numerous techniques to visualize, quantify, and merge microscopy data. These approaches have defined the order and structure of developmental events, thus, providing insight into the mechanisms that drive them. This review describes current computational approaches that are being used to answer developmental questions related to morphogenesis and describe how these approaches have impacted the field. Our intent is not to comprehensively review techniques, but to highlight examples of how different approaches have impacted our understanding of development. Specifically, we focus on methods to quantify cell shape and cytoskeleton structure and dynamics in developing tissues. Finally, we speculate on where the future of computational analysis in developmental biology might be headed.

This article is categorized under:

Technologies > Analysis of Cell, Tissue, and Animal Phenotypes

Early Embryonic Development > Gastrulation and Neurulation

Early Embryonic Development > Development to the Basic Body Plan
The Market for Films in Postwar Italy: Evidence for Both National and Regional Patterns of Taste
Authors: SEDGWICK JOHN , MISKELL PETER , NICOLI MARINA
Published: August 2018

The postwar market for films in Italy resembles those found in other developed capitalist economies, in which supply adjusts to demand through a set of institutional arrangements designed to maximize revenue for the film distributor. The outcome is a statistical distribution of revenues that manifests extreme levels of inequality, indicating that the hits of the day were “giants” in relation to the median film and enjoyed throughout the territory. By drawing upon film industry–sourced box-office data for five cities, Milan and Turin in the north, Naples and Bari in the south, and Rome in the center, we can observe the market mechanism operating at the city level, allowing the exploration of differences in preferences between the cities. A relative popularity index (RelPOP) is introduced to measure variation in film popularity across the five cities, and clear evidence is found to support the coexistence of national and local taste. This phenomenon is examined with respect to those films that were exceptionally popular throughout, and those with particular geographically specific audiences. The example of the many films that starred Totò, appealing in particular to southern Italian audiences, is highlighted and contrasted with the Don Camillo series of films that were set in Emilia Romagna and appealed differentially to filmgoers in the north.
Preventing ventilator-associated pneumonia—a mixed-method study to find behavioral leverage for better protocol adherence
Authors: Wolfensberger Aline , Meier Marie-Theres , Clack Lauren , Schreiber Peter W. , Sax Hugo
Published: August 2018

Objective

Preventing ventilator-associated pneumonia (VAP) is an important goal for intensive care units (ICUs). We aimed to identify the optimal behavior leverage to improve VAP prevention protocol adherence.

Design

Mixed-method study using adherence measurements to assess 4 VAP prevention measures and qualitative analysis of semi-structured focus group interviews with frontline healthcare practitioners (HCPs).

Setting

The 6 ICUs in the 900-bed University Hospital Zurich in Zurich, Switzerland.

Patients and participants

Adherence to VAP prevention measures were assessed in patients with a device for invasive ventilation (ie, endotracheal tube, tracheostomy tube). Participants in focus group interviews included a convenience samples of ICU nurses and physicians.

Results

Between February 2015 and July 2017, we measured adherence to 4 protocols: bed elevation showed adherence at 27% (95% confidence intervals [CI], 23%–31%); oral care at 41% (95% CI, 36%–45%); sedation interruption at 81% (95% CI, 74%–85%); and subglottic suctioning at 88% (95% CI, 83%–92%). Interviews were analyzed first inductively according a grounded theory approach then deductively against the behavior change wheel (BCW) framework. Main behavioral facilitators belonged to the BCW component ‘reflective motivation’ (ie, perceived seriousness of VAP and self-efficacy to prevent VAP). The main barriers belonged to ‘physical capability’ (ie, lack of equipment and staffing and side-effects of prevention measures). Furthermore, 2 primarily technical approaches (ie, ‘restructuring environment’ and ‘enabling HCP’) emerged as means to overcome these barriers.

Conclusions

Our findings suggest that technical, rather than education-based, solutions should be promoted to improve VAP prevention. This theory-informed mixed-method approach is an effective means of guiding infection prevention efforts.
Opportunities and Challenges of Engaged Indigenous Scholarship
Authors: Van de Ven Andrew H. , Meyer Alan D. , Jing Runtian
Published: August 2018

Management and Organization Review(MOR) is announcing a renewed initiative that seeks to encourage and publish research reporting engaged indigenous scholarship in China. MOR invites empirical as well as conceptual studies of indigenous phenomena related to management and organizations. MOR welcomes exploratory studies of new, emerging, and/or poorly understood indigenous research questions that employ abductive reasoning and creative hunches, as opposed to testing hypotheses deduced from non-indigenous Western theories. Data on indigenous phenomena can come from any source, including qualitative and quantitative data from case studies, field surveys, experiments, and ethnographies.
Spatial and temporal variations in river terrace formation, preservation, and morphology in the Lower Meuse Valley, The Netherlands
Authors: Woolderink Hessel Antonius Gerardus , Kasse Cornelis , Cohen Kim Mikkel , Hoek Wim Zacharias , Van Balen Ronald Theodorus
Published: August 2018

The Lower Meuse Valley crosses the Roer Valley Rift System and provides an outstanding example of well-preserved late glacial and Holocene river terraces. The formation, preservation, and morphology of these terraces vary due to reach-specific conditions, a phenomenon that has been underappreciated in past studies. A detailed palaeogeographic reconstruction of the terrace series over the full length of the Lower Meuse Valley has been performed. This reconstruction provides improved insight into successive morphological responses to combined climatic and tectonic external forcing, as expressed and preserved in different ways along the river. New field data and data obtained from past studies were integrated using a digital mapping method in GIS. Results show that late glacial river terraces with diverse fluvial styles are best preserved in the Lower Meuse Valley downstream sub-reaches (traversing the Venlo Block and Peel Block), while Holocene terrace remnants are well-developed and preserved in the upstream sub-reaches (traversing the Campine Block and Roer Valley Graben). This reach-to-reach spatial variance in river terrace preservation and morphology can be ascribed to tectonically driven variations in river gradient and subsurface lithology, and to river-driven throughput of sediment supply.
A clinical guideline onDientamoeba fragilisinfections
Authors: van Gestel Rosanne SFE , Kusters Johannes G , Monkelbaan Jan F
Published: August 2018

Dientamoeba fragilis(D. fragilis) is an intestinal parasite frequently detected in humans with abdominal pain and diarrhoea, but it is also commonly found in asymptomatic subjects. Hence its clinical relevance is often disputed. The introduction of polymerase chain reaction (PCR) is a versatile and sensitive diagnostic technique for the detection of intestinal parasites, and in some Western world countries PCR has almost completely replaced microscopic diagnostics. PCR has however resulted in an increase in the number ofD. fragilis-positive patients. The disputed pathogenic nature of this intestinal parasite and an apparent increase in the incidence of patients with positive PCR results have renewed the discussions between clinicians and microbiologists on how to deal with an infected patient. Moreover, treatment guidelines differ throughout the world which makes it difficult for clinicians to choose an optimal therapeutic regimen.

Aim

To summarize and discuss the current knowledge on the pathogenicity, best diagnostic approach, treatment and follow-up of children and adults infected withD. fragilis.
Mass Resettlement and Political Violence
Authors: McNamee Lachlan
Published: August 2018

This article examines the relationship between mass resettlement and political conflict. The author theorizes that states can use mass resettlement to extend control over contested frontiers. Settlers whose land rights are politically contested will disproportionately participate in violence to defend the incumbent regime. The theory is tested using data on resettlement and violence in postcolonial Rwanda. The author shows that the Hutu revolutionary regime resettled some 450,000 Hutus after independence to frontier and Tutsi-dominated areas to defend itself against external Tutsi militias. The author contends that the invasion of the Tutsi-led Rwandan Patriotic Front (RPF) in the 1990s threatened the Hutu settler population because the RPF sought the repatriation of Tutsis onto redistributed land and that consequent land insecurity incentivized violence against Tutsis in 1994. The article identifies the positive effect of resettlement on locality violence during the genocide via a geographic regression discontinuity design. A process tracing of one notoriously violent resettled commune supports the theorized causal sequence. In light of these findings, the author suggests that research should refocus on the way that conflict shapes ethnic demography and that, to understand participation in state-sponsored violence, scholars should attend to the threat posed by regime change to individual livelihoods.
Preliminary survival and movement data for a declining population of Flesh-footed Shearwater Ardenna carneipes in Western Australia provides insights into marine threats
Authors: LAVERS JENNIFER L. , LISOVSKI SIMEON , BOND ALEXANDER L.
Published: August 2018

Seabirds face diverse threats on their breeding islands and while at sea. Human activities have been linked to the decline of seabird populations, yet over-wintering areas typically receive little or no protection. Adult survival rates, a crucial parameter for population persistence in long-lived species, tend to be spatially or temporally restricted for many seabird species, limiting our understanding of factors driving population trends at some sites. We used bio-loggers to study the migration of Western Australian Flesh-footed Shearwaters Ardenna carneipes carneipes and estimated adult survival over five years. Western Australia is home to around 35% of the world’s breeding Flesh-footed Shearwaters, a population which was up-listed to Vulnerable in 2015. During the austral winter, shearwaters migrated across the central Indian Ocean to their non-breeding grounds off western Sri Lanka. Low site fidelity on breeding islands, mortality of adult birds at sea (e.g. fisheries bycatch), and low annual breeding frequency likely contributed to the low estimated annual adult survival (2011–2015: ϕ = 0.634-0.835).
Human Activities Create Corridors of Change in Aquatic Zones
Authors: Bianchi Thomas , Morrison Elise
Published: August 2018

Canals, dammed reservoirs, irrigation ditches, and pollution are changing species diversity, microbial communities, and nutrient levels in aquatic zones across the planet.
Investigating the Onset of Strain Localization Within Anisotropic Shale Using Digital Volume Correlation of Time‐Resolved X‐Ray Microtomography Images
Authors: McBeck Jessica , Kobchenko Maya , Hall Stephen A. , Tudisco Erika , Cordonnier Benoit , Meakin Paul , Renard François
Published: August 2018

Digital volume correlation analysis of time‐resolved X‐ray microtomography scans acquired during in situ triaxial compression of Green River shale cores provided time series of 3‐D incremental strain fields that elucidated evolving deformation processes by quantifying microscopic strain localization. With these data, we investigated the impact of mechanical anisotropy on microscopic strain localization culminating in macroscopic shear failure. We conducted triaxial compression experiments with the maximum compressive stress, σ1, aligned perpendicular and parallel to lamination planes in order to investigate end‐member stress states that arise within sedimentary basins. When the preexisting laminations were perpendicular to σ1, a lamination‐parallel region with high axial compaction developed within the macroscopically linear deformation phase of the experiment and then thickened with increasing applied differential stress. Scanning electron microscopy images indicate that this axial compaction occurred within a lower density lamination and that more axial compaction occurred within the center of the core than near its sides. Boundary element method simulations suggest that this compacting volume promoted shear fracture development within the upper portion of the shale. When the laminations were parallel to σ1, lamination‐parallel dilation bands formed, thickened, and intensified in dilation. Population densities of the distributions of incremental shear strain, radial dilation, and axial contraction calculated by digital volume correlation analysis enabled quantification of the evolving overall impact of, and interplay between, these various deformation modes.
Interdecadal Change of the Impact of Eurasian Snow on Spring Precipitation Over Southern China
Authors: Jia Xiaojing , Cao Ding Rui , Ge Jing Wen , Wang Min
Published: August 2018

This study investigates the interdecadal changes in the relationship between the Eurasian snow cover extent (SCE) and spring precipitation over southern China. The results show that the spring precipitation over southern China has experienced an obvious change from an active to a quiet period since the late 1980s. The entire data set is divided into two subperiods, that is, 1972–1987 (P1) and 1988–2009 (P2). The interannual variation of the spring precipitation of southern China is found to be significantly related to Eurasian SCE anomalies around northwest of Lake Baikal. Less‐than‐normal SCE northwest of Lake Baikal corresponds to more‐than‐normal spring precipitation over southern China. The result of a numerical experiment performed using a baroclinic atmospheric model indicates that the Eurasian snow anomalies around northwest of Lake Baikal can impact the variation of spring precipitation over southern China by modulating the atmospheric circulations over eastern Asia and the western North Pacific region. Further examination shows that the SCE anomalies around Lake Baikal contribute differently to the variation of spring precipitation over southern China before and after the late 1980s. During P1, the SCE anomalies around Lake Baikal contribute to the variation of spring precipitation over China in the form of a mono‐sign pattern, which is similar to the first empirical orthogonal function mode of spring precipitation, while in P2, the SCE anomalies around Lake Baikal favor a north‐south dipole mode of the spring precipitation variation, which bears considerable similarity to the second empirical orthogonal function mode of spring precipitation over China.
Falling Snow Radiative Effects Enhance the Global Warming Response of the Tropical Pacific Atmosphere
Authors: Chen Chao‐An , Li J.‐L. F. , Richardson Mark , Lee Wei‐Liang , Fetzer Eric , Stephens G. , Hsu Huang‐Hsiung , Wang Yi‐Hui , Yu Jia‐Yuh
Published: August 2018

Most models from the Coupled Model Intercomparison Project phase 5 (CMIP5) do not include the radiative effects of falling snow. This has been shown to bias simulations of radiation and circulation in the Pacific present‐day mean state. Here we explore how precipitating ice radiative effects contribute to simulated Pacific climate change via a pair of sensitivity experiments with and without snow radiative effects (SnowOn/SnowOff) using 1pctCO2 simulations of the Community Earth System Model version 1 (CESM1) climate model, in which atmospheric CO2 increases at 1% per year for 140 years. In addition, we compare our results with the CMIP5 ensemble mean. The initial climate state of each 1pctCO2 run shows similar patterns to present‐day simulations. Under global warming, the regions of convective activity tend to intensify and shift eastward. These changes are stronger in the SnowOn simulation, which also displays a stronger zonal gradient of sea surface temperature warming relative to SnowOff. The changes in convective activity and the associated precipitation are particularly notable: with reduced precipitation around the maritime continent, and an approximate doubling of the precipitation increase over parts of the western Pacific in SnowOn. CESM1 SnowOff patterns of change are similar to those in CMIP5 models that exclude snow radiative effects, hinting that future warming‐driven changes in precipitation and circulation over the Pacific might be stronger than those simulated by most CMIP5 models.
Precipitation Partitioning in Multiscale Atmospheric Simulations: Impacts of Stability Restoration Methods
Authors: He Jian , Alapaty Kiran
Published: August 2018

Proper simulation of high‐resolution surface precipitation distribution and variability is important to local aspects of environmental pollution and climate. Global and regional climate and weather models routinely evaluate total precipitation using available measurements, but quantitative evaluation of contributions by the individual components (convective and nonconvective) to the total precipitation is not routinely performed. Wet bias in one component can alleviate dry bias in the other component, making the total precipitation look comparable to measurements, leading to an invisible bias. To study this aspect, Tropical Rainfall Measuring Mission (TRMM) measurements for precipitation components were used to quantitatively evaluate convective fractions simulated by a cumulus parameterization scheme in a regional climate simulation using 12‐km grid spacing. Results indicated a wet bias in convective precipitation as compared to TRMM measurements. This wet bias helped to counter a dry bias in grid‐scale precipitation and led to a total precipitation comparable to Parameter‐elevation Regressions on Independent Slopes Model and TRMM measurements. A new formulation has been developed for convective cloud adjustment time scale alleviating wet bias in convective precipitation when compared to the old formulation and TRMM measurements. Results for different grid spacing also indicate that the new method produces lower subgrid‐scale precipitation with overall better precipitation estimates. Our results also suggest that evaluating both components of the surface precipitation rather than just the total itself can inform a need to improve cloud formulations, as demonstrated in this study. This study calls for the development of methods to routinely produce measurements for precipitation components that help evaluating global and regional climate and weather models.
Distinguishing Anthropogenic CO2 Emissions From Different Energy Intensive Industrial Sources Using OCO‐2 Observations: A Case Study in Northern China
Authors: Wang Songhan , Zhang Yongguang , Hakkarainen Janne , Ju Weimin , Liu Yongxue , Jiang Fei , He Wei
Published: August 2018

Energy intensive industries, such as iron and steel industry and coal‐processing industry, are one of the major anthropogenic fossil fuel carbon dioxide (CO2) emission sources, especially in China. Monitoring the localized CO2 emissions from these industrial point sources is valuable to improve emission estimates and inform on policy discussion. However, spatiotemporally explicit information on CO2 emissions from different energy intensive industrial sources is still limited. In this study, we use remote sensing data sets with high spatial resolution to detect the patterns of CO2 enhancements of carbon emission intensive industries, taking northern China as the case study area. CO2 anomalies are derived from spaceborne column‐averaged CO2 mixing ratio (XCO2) data measured by the Orbiting Carbon Observatory 2 (OCO‐2). The Gaussian plume model is used to select the XCO2 data when the CO2 emissions from plants are localized, which allows us to distinguish CO2 emissions from different industrial point sources. We demonstrate that high‐emission areas with industrial plants are detectable by CO2 anomalies compared to natural background area and the average enhancement is about 1.8 ppm. The XCO2 data also show a higher CO2 emission from a cluster of iron and steel plants than that of coal‐processing plants, which is consistent with emission inventories. Furthermore, anthropogenic CO2 emission hotspots are possible to be identified from surrounding natural background. Our results suggest the potential of satellite data for characterizing strong localized carbon emission from different industrial sources both in space and time.
Study of the Quasi‐5‐Day Wave in the MLT Region by a Meteor Radar Chain
Authors: Gong Yun , Li Chun , Ma Zheng , Zhang Shaodong , Zhou Qihou , Huang Chunming , Huang Kaiming , Li Guozhu , Ning Baiqi
Published: August 2018

An extensive analysis of quasi 5‐day waves (5DWs) in the mesosphere and lower thermosphere and their responses to a major sudden stratospheric warming (SSW) event (January 2013) are presented. The analysis is based on data conducted from a meteor radar chain in the period from December 2008 to November 2017 and Aura Microwave Limb Sounder satellite. The radar chain includes three stations located at Mohe (MH, 53.5°N, 122.3°E), Beijing (BJ, 40.3°N, 116.2°E), and Wuhan (WH, 30.5°N, 114.6°E). The 5DWs present clear interannual and seasonal variations, which are observed by both the radar wind data and Aura‐temperature data. Interestingly, the ter‐annual oscillation is found to be as important as the commonly recognized annual oscillation and semiannual oscillation at the three stations in both neutral wind components. The 5DWs are strong mainly during the August/September in the meridional component, while they are primarily enhanced in the period of January, April/May, and late summer in the zonal component. An enhancement of 5DWs is observed during the 2013 SSW event in the mesosphere and lower thermosphere region at the three stations. The amplitudes during the SSW are more than 2 times larger than the January average. The strength of the amplification is most prominent at MH and reduces as latitude decreases. According to the results obtained from the radar wind and Aura temperature, the enhanced 5DW modes are W1 at MH, and W2 at BJ and WH. Our results indicate that the amplification of the 5DWs is very likely associated with the 2013 SSW.
Modal energy transfer by thermally induced refractive index gratings in Yb-doped fibers
Authors: Stihler Christoph , Jauregui Cesar , Tünnermann Andreas , Limpert Jens
Published: August 2018

Thermally induced refractive index gratings in Yb-doped fibers lead to transverse mode instability (TMI) above an average power threshold, which represents a severe problem for many applications. To obtain a deeper understanding of TMI, the evolution of the strength of the thermally induced refractive index grating with the average output power in a fiber amplifier is experimentally investigated for the first time. This investigation is performed by introducing a phase shift between the refractive index grating and modal interference pattern, which is obtained by applying a pump power variation to the fiber amplifier. It is demonstrated that the refractive index grating is sufficiently strong to enable modal energy coupling at powers that are significantly below the TMI threshold if the induced phase shift is sufficiently large. The experiments indicate that at higher powers, the refractive index grating becomes more sensitive to such phase shifts, which will ultimately trigger TMI. Furthermore, the experimental results demonstrate beam cleaning above the TMI threshold via the introduction of a positive phase shift. This finding paves the way for the development of a new class of mitigation strategies for TMI that are based on controlling the phase shift between the thermally induced refractive index grating and modal interference pattern.
Localized recombination drives diversification of killing spectra for phage-derived syringacins
Authors: Baltrus David A , Clark Meara , Smith Caitlin , Hockett Kevin L
Published: August 2018

To better understand the potential for antagonistic interactions between members of the same bacterial species, we have surveyed bacteriocin killing activity across a diverse suite of strains of the phytopathogen Pseudomonas syringae. Our data demonstrate that killing activity from phage-derived bacteriocins of P. syringae (R-type syringacins) is widespread. Despite a high overall diversity of bacteriocin activity, strains can broadly be classified into five main killing types and two main sensitivity types. Furthermore, we show that killing activity switches frequently between strains and that switches correlate with localized recombination of two genes that together encode the proteins that specify bacteriocin targeting. Lastly, we demonstrate that phage-derived bacteriocin killing activity can be swapped between strains simply through expression of these two genes in trans. Overall, our study characterizes extensive diversity of killing activity for phage-derived bacteriocins of P. syringae across strains and highlights the power of localized recombination to alter phenotypes that mediate strain interactions during evolution of natural populations and communities.
Unexpected stability of aqueous dispersions of raspberry-like colloids
Authors: Lan Yang , Caciagli Alessio , Guidetti Giulia , Yu Ziyi , Liu Ji , Johansen Villads E. , Kamp Marlous , Abell Chris , Vignolini Silvia , Scherman Oren A. , Eiser Erika
Published: August 2018

Aqueous colloidal suspensions, both man-made and natural, are part of our everyday life. The applicability of colloidal suspensions, however, is limited by the range of conditions over which they are stable. Here we report a novel type of highly monodisperse raspberry-like colloids, which are prepared in a single-step synthesis that relies on simultaneous dispersion and emulsion polymerisation. The resulting raspberry colloids behave almost like hard spheres. In aqueous solutions, such prepared raspberries show unexpected stability against aggregation over large variations of added salt concentrations without addition of stabilisers. We present simple Derjaguin–Landau–Verwey–Overbeek (DLVO) calculations performed on raspberry-like and smooth colloids showing that this stability results from our raspberries’ unique morphology, which extends our understanding of colloidal stability against salting. Further, the raspberries’ stability facilitates the formation of superspheres and thin films in which the raspberry colloids self-assemble into hexagonally close-packed photonic crystals with exquisite reproducibility.
LY6E mediates an evolutionarily conserved enhancement of virus infection by targeting a late entry step
Authors: Mar Katrina B. , Rinkenberger Nicholas R. , Boys Ian N. , Eitson Jennifer L. , McDougal Matthew B. , Richardson R. Blake , Schoggins John W.
Published: August 2018

Interferons (IFNs) contribute to cell-intrinsic antiviral immunity by inducing hundreds of interferon-stimulated genes (ISGs). In a screen to identify antiviral ISGs, we unexpectedly found that LY6E, a member of the LY6/uPAR family, enhanced viral infection. Here, we show that viral enhancement by ectopically expressed LY6E extends to several cellular backgrounds and affects multiple RNA viruses. LY6E does not impair IFN antiviral activity or signaling, but rather promotes viral entry. Using influenza A virus as a model, we narrow the enhancing effect of LY6E to uncoating after endosomal escape. Diverse mammalian orthologs of LY6E also enhance viral infectivity, indicating evolutionary conservation of function. By structure-function analyses, we identify a single amino acid in a predicted loop region that is essential for viral enhancement. Our study suggests that LY6E belongs to a class of IFN-inducible host factors that enhance viral infectivity without suppressing IFN antiviral activity.
Imaging of Murine Whole Lung Fibrosis by Large Scale 3D Microscopy aided by Tissue Optical Clearing
Authors: Ochoa Lorenzo F. , Kholodnykh Alexander , Villarreal Paula , Tian Bing , Pal Rahul , Freiberg Alexander N. , Brasier Allan R. , Motamedi Massoud , Vargas Gracie
Published: August 2018

Pulmonary fibrosis, characterized by excessive collagen deposition in the lungs, comprises a key and debilitating component of chronic lung diseases. Methods are lacking for the direct visualization of fibrillar collagen throughout the whole murine lung, a capability that would aid the understanding of lung fibrosis. We combined an optimized organ-level optical clearing (OC) approach with large-scale, label-free multiphoton microscopy (MPM) and second harmonic generation microscopy (SHGM) to reveal the complete network of fibrillar collagen in whole murine lungs. An innate inflammation-driven model based on repetitive poly(I:C) challenge was evaluated. Following OC, mosaic MPM/SHGM imaging with 3D reconstruction and whole organ quantitative analysis revealed significant differences in collagen deposition between PBS and poly(I:C) treated lungs. Airway specific analysis in whole lung acquisitions revealed significant sub-epithelial fibrosis evident throughout the proximal conductive and distal airways with higher collagen deposition in the poly(I:C) group vs PBS group. This study establishes a new, powerful approach based on OC and MPM/SHGM imaging for 3D analysis of lung fibrosis with macroscopic views of lung pathology based on microscopy and providing a new way to analyze the whole lung while avoiding regional sampling bias.
The aerobic diagenesis of Mesoproterozoic organic matter
Authors: Wang Xiaomei , Zhao Wenzhi , Zhang Shuichang , Wang Huajian , Su Jin , Canfield Donald E. , Hammarlund Emma U.
Published: August 2018

The Xiamaling Formation in the North China Block contains a well-preserved 1400 Ma sedimentary sequence with a low degree of thermal maturity. Previous studies have confirmed the dynamic and complex nature of this evolving marine setting, including the existence of an oxygen-minimum zone, using multi-proxy approaches, including iron speciation, trace metal dynamics, and organic geochemistry. Here, we investigate the prevailing redox conditions during diagenesis via the biomarkers of rearranged hopanes from the finely laminated sediments of the organic-rich black shales in Units 2 and 3 of the Xiamaling Formation. We find that rearranged hopanes are prominent in the biomarker composition of the oxygen-minimum zone sediment, which is completely different from that of the sediment in the overlying anoxic strata. Since the transition process from hopanes to rearranged hopanes requires oxygen via oxidation at the C-l6 alkyl position of 17α(H)-hopanes, we infer that dissolved oxygen led to the transformation of hopane precursors into rearranged hopanes during the early stages of diagenesis. The use of hopanoid hydrocarbons as biomarkers of marine redox conditions has rarely been previously reported, and the hydrocarbon signatures point towards oxic bottom waters during the deposition of Unit 3 of the Xiamaling Formation, which is consistent with the earlier oxygen-minimum zone environmental interpretation of this Unit.
Association of short-term exposure to ambient carbon monoxide with hospital admissions in China
Authors: Liu Hui , Tian Yaohua , Xiang Xiao , Li Man , Wu Yao , Cao Yaying , Juan Juan , Song Jing , Wu Tao , Hu Yonghua
Published: August 2018

Evidence on the acute effects of ambient carbon monoxide (CO) pollution on morbidity risk in developing countries is scarce and inconsistent. We conducted a multicity case-crossover study in 26 largest cities in China from January, 2014 to December, 2015 to examine the association between short-term exposure to CO and daily hospital admission. We fitted conditional logistic regression to obtain effect estimates of the associations. We also performed subset analyses to explore the health effects of CO at low levels. During the study period, a total of 14,569,622, 2,008,786 and 916,388 all-cause, cardiovascular and respiratory admissions were identified, respectively. A 1 mg/m3 increase in the CO concentrations corresponded to a 3.75% (95% CI, 3.63–3.87%), 4.39% (95% CI, 4.07–4.70%), and 4.44% (95% CI, 3.97–4.92%) increase in all-cause, cardiovascular, and respiratory admissions on the same day, respectively. The associations were robust to controlling for criteria co-pollutants. In subset analyses, negative effects of short-term CO exposure on hospital admission were observed at lower concentrations (<1 mg/m3), while positive effects were observed at higher concentrations (>2 mg/m3). In conclusion, current CO levels in China were significantly associated with increased daily hospital admissions.
A Relational Formulation of Quantum Mechanics
Authors: Yang Jianhao M.
Published: August 2018

Non-relativistic quantum mechanics is reformulated here based on the idea that relational properties among quantum systems, instead of the independent properties of a quantum system, are the most fundamental elements to construct quantum mechanics. This idea, combining with the emphasis that measurement of a quantum system is a bidirectional interaction process, leads to a new framework to calculate the probability of an outcome when measuring a quantum system. In this framework, the most basic variable is the relational probability amplitude. Probability is calculated as summation of weights from the alternative measurement configurations. The properties of quantum systems, such as superposition and entanglement, are manifested through the rules of counting the alternatives. Wave function and reduced density matrix are derived from the relational probability amplitude matrix. They are found to be secondary mathematical tools that equivalently describe a quantum system without explicitly calling out the reference system. Schrödinger Equation is obtained when there is no entanglement in the relational probability amplitude matrix. Feynman Path Integral is used to calculate the relational probability amplitude, and is further generalized to formulate the reduced density matrix. In essence, quantum mechanics is reformulated as a theory that describes physical systems in terms of relational properties.
Metallo supramolecular cylinders inhibit HIV-1 TAR-TAT complex formation and viral replication in cellulo
Authors: Cardo Lucia , Nawroth Isabel , Cail Peter J. , McKeating Jane A. , Hannon Michael J.
Published: August 2018

Shape-selective recognition of nucleic acid structures by supramolecular drugs offers the potential to treat disease. The Trans Activation Response (TAR) region is a region of high secondary structure within the human immunodeficiency virus-1 (HIV-1) RNA that complexes with the virus-encoded Transactivator protein (TAT) and regulates viral transcription. Herein, we explore different metallo-supramolecular triple stranded helicates (cylinders) that target the TAR bulge motif and inhibit the formation of TAR-TAT complexes and HIV infection. Cylinders that incorporate Ni(II) and Ru(II) showed the most potent anti-viral activity with limited evidence of cellular cytotoxicity. These metallo-supramolecular compounds provide an exciting avenue for developing a new class of anti-viral agents.
A potential link between gambling addiction severity and central dopamine levels: Evidence from spontaneous eye blink rates
Authors: Mathar David , Wiehler Antonius , Chakroun Karima , Goltz Dominique , Peters Jan
Published: August 2018

Accumulating evidence points at similarities between substance use disorders (SUD) and gambling disorder on the behavioral and neural level. In SUD, attenuation of striatal D2/3-receptor availability is a consistent finding, at least for stimulating substances. For gambling disorder, no clear association with striatal D2/3-receptor availability has been unveiled so far. With its presumably negligible dopaminergic toxicity, possible differences in receptor availability in gambling disorder might constitute a vulnerability marker. Spontaneous eye blink rate (sEBR) is discussed as a potential proxy measure for striatal dopamine D2/3-receptor availability. Here we examined sEBR in 21 male problem gamblers and 20 healthy control participants. In addition, participants completed a screening questionnaire for overall psychopathology and self-reported measures of alcohol and nicotine consumption. We found no significant difference in sEBR between gamblers and controls. However, in gamblers, sEBR was negatively associated with gambling severity and positively associated with psychopathology. A final exploratory analysis revealed that healthy controls with low sEBR displayed higher alcohol and nicotine consumption than healthy participants with high sEBR. Although the exact association between dopamine transmission and sEBR is still debated, our findings reveal that sEBR is sensitive to inter-individual differences in gambling disorder severity in problem gamblers.
European dog owner perceptions of obesity and factors associated with human and canine obesity
Authors: Muñoz-Prieto Alberto , Nielsen Liza Rosenbaum , Dąbrowski Roman , Bjørnvad Charlotte Reinhard , Söder Josefin , Lamy Elsa , Monkeviciene Ingrida , Ljubić Blanka Beer , Vasiu Iosif , Savic Sara , Busato Francesca , Yilmaz Zeki , Bravo-Cantero Antonio F. , Öhlund Malin , Lucena Sónia , Zelvyte Rasa , Aladrović Jasna , Lopez-Jornet Pia , Caldin Marco , Lavrador Catarina , Karveliene Birute , Mrljak Vladimir , Mazeikiene Jovita , Tvarijonaviciute Asta
Published: August 2018

Obesity is a common nutrition-related disorder leading to reduced life expectancy in both humans and dogs. With the aim of identifying new prevention and control options, the study objectives were (1) to investigate dog-owner perceptions about obesity in terms of themselves and their dogs, and (2) to identify factors associated with obesity and possible social, environmental and economic drivers for its development in dog owners and their pets. A cross-sectional questionnaire-based study was performed across multiple countries. The questionnaire focused on human and canine obesity, associated factors and potential drivers, and was distributed online and in the form of hard copies among dog owners in 11 European countries. In total, 3,185 responses from ten countries were included in multivariable analyses. Between 19.1% and 48.8% of the dog owners reported to be overweight/obese. Owner-reported overweight/obesity in dogs ranged from 6.0% to 31.3% based on body condition score charts, and 31.8% to 69.4% based on body fat index charts. Common factors associated with obesity in owners and their dogs were age, gender and owners’ attitudes to diet and physical activity. Dog owners who did not consider obesity to be a disease were more likely to have obese dogs.
Nebulisation of synthetic lamellar lipids mitigates radiation-induced lung injury in a large animal model
Authors: Collie David , Murchison John T. , Wright Steven H. , McLean Alec , Howard Lynsey , del-Pozo Jorge , Smith Sionagh , McLachlan Gerry , Lawrence Jessica , Kay Elaine , Schwarz Tobias , Parys Magdalena
Published: August 2018

Methods to protect against radiation-induced lung injury (RILI) will facilitate the development of more effective radio-therapeutic protocols for lung cancer and may provide the means to protect the wider population in the event of a deliberate or accidental nuclear or radiological event. We hypothesised that supplementing lipid membranes through nebulization of synthetic lamellar lipids would mitigate RILI. Following pre-treatment with either nebulised lamellar lipids or saline, anaesthetised sheep were prescribed fractionated radiotherapy (30 Gray (Gy) total dose in five 6 Gy fractions at 3–4 days intervals) to a defined unilateral lung volume. Gross pathology in radio-exposed lung 37 days after the first radiation treatment was consistent between treatment groups and consisted of deep red congestion evident on the pleural surface and firmness on palpation. Consistent histopathological features in radio-exposed lung were subpleural, periarteriolar and peribronchial intra-alveolar oedema, alveolar fibrosis, interstitial pneumonia and type II pneumocyte hyperplasia. The synthetic lamellar lipids abrogated radiation-induced alveolar fibrosis and reduced alpha-smooth muscle actin (ASMA) expression in radio-exposed lung compared to saline treated sheep. Administration of synthetic lamellar lipids was also associated with an increased number of cells expressing dendritic cell-lysosomal associated membrane protein throughout the lung.
Intrinsic refractive index matched 3D dSTORM with two objectives: Comparison of detection techniques
Authors: Schmidt Nora C. , Kahms Martin , Hüve Jana , Klingauf Jürgen
Published: August 2018

We have built a setup for 3D single molecule localisation microscopy (SMLM) where a very high resolution is achieved by, firstly, the use of two objectives instead of one and, secondly, minimizing optical aberrations by refractive index matching with a glycerol-water mixture as immersion medium in conjunction with glycerol-immersion objectives. Multiple optical paths of the microscope allow to switch between astigmatic and interferometric localisation along the optical axis, thus enabling a direct comparison of the performance of these localisation methods.
Time-advanced occurrence of moderate-size earthquakes in a stable intraplate region after a megathrust earthquake and their seismic properties
Authors: Hong Tae-Kyung , Lee Junhyung , Park Seongjun , Kim Woohan
Published: August 2018

The distance-dependent coseismic and postseismic displacements produced by the 2011MW9.0 Tohoku-Oki megathrust earthquake caused medium weakening and stress perturbation in the crust around the Korean Peninsula, increasing the seismicity with successiveML5-level earthquakes at the outskirts of high seismicity regions. The averageML5-level occurrence rate prior to the megathrust earthquake was 0.15 yr−1(0.05–0.35 yr−1at a 95% confidence level), and the rate has increased to 0.71 yr−1(0.23–1.67 yr−1at a 95% confidence level) since the megathrust earthquake. The 2016ML5-level midcrustal earthquakes additionally changed the stress field in adjacent regions, inducing the 15 November 2017ML5.4 earthquake. The successive 2016 and 2017 moderate-size earthquakes built complex stress fields in the southeastern Korean Peninsula, increasing the seismic hazard risks in the regions of long-term stress accumulation. The increased seismic risks may continue until the medium properties and stress field are recovered.
Analytical ultracentrifugation in saliva research: Impact of green tea astringency and its significance on the in-vivo aroma release
Authors: Dinu Vlad , Liu Chujiao , Ali Joseph , Ayed Charfedinne , Gershkovich Pavel , Adams Gary G. , Harding Stephen E. , Fisk Ian D.
Published: August 2018

Current saliva testing methods rely on cutting edge yet expensive techniques for the detection and analysis of genetic material, proteins and biomarkers for clinical use. However, these techniques are limited in scope and often cannot be used with complex food materials. We propose an efficient ex-vivo tool for evaluating biologically relevant interactions between food components and human saliva using sedimentation velocity analytical ultracentrifugation (SV-AUC). We evaluated macromolecular content from “unstimulated” (US) and “stimulated” (SS) samples pooled from 5 healthy volunteers. Over 90% of total saliva protein consisted of α-amylase and mucin, and up to 10% was secretory immunoglobulin A (SIgA). It was shown that α-amylase concentration increased upon parafilm stimulation, which lead to a decrease in the viscosity of saliva. Then, we used a simple food system (green tea) to evaluate changes in the salivary protein content caused by green tea polyphenols. It was found that aroma release from green tea is highly influenced by interactions between α-amylase and polyphenol epigallocatechin 3-gallate (EGCG). This interaction was found to increase the viscosity of the salivary bulk, suggested to contribute to astringency, and increased the concentrations of β-ionone, benzaldehyde and isovaleraldehyde (P < 0.01), suggested to play a significant role in the characteristic flavour of green tea.
Evaluation of alpha-II-spectrin breakdown products as potential biomarkers for early recognition and severity of aneurysmal subarachnoid hemorrhage
Authors: Papa Linda , Rosenthal Kimberly , Silvestri Francesca , Axley John C. , Kelly Jared M. , Lewis Stephen B.
Published: August 2018

This study assessed whether cytoskeletal protein alpha-II spectrin breakdown products (SBDP150, SBDP145, and SBDP120) would identify the presence of aSAH and be associated with severity (GCS score, WFNS grade and survival to hospital discharge). This prospective case-control study, conducted at a tertiary care Level I trauma center, enrolled adult patients with angiography confirmed aSAH who underwent ventriculostomy placement for cerebrospinal fluid (CSF) drainage. There were 40 patients enrolled in the study, 20 with aSAH and 20 control subjects. Patients with aSAH were a mean age of 54 (SD15) and 75% were female. There were significant differences in SBDP150, SBDP145, and SBDP120 CSF levels between patients with and without aSAH (p < 0.001), even in those presenting with a GCS Score of 15 and a WFNS Grade 1. The AUC for distinguishing aSAH from control subjects was 1.0 for SBDP150 and SBDP145, and 0.95 for SBDP120. SBDP150 and SBDP145 both yielded sensitivities and specificities of 100% and SBDP120 was 90% and 100% respectively. Moreover, there were significantly higher levels of SBDP150 and SBDP145 in the non-survivors than in the survivors (p < 0.001). This study demonstrates the potential that SBDP’s have as biomarkers for recognition and severity of aSAH. A larger prospective study is warranted.
The Impact of Blood Transfusion on Recurrence and Mortality Following Colorectal Cancer Resection: A Propensity Score Analysis of 4,030 Patients
Authors: Wu Hsiang-Ling , Tai Ying-Hsuan , Lin Shih-Pin , Chan Min-Ya , Chen Hsiu-Hsi , Chang Kuang-Yi
Published: August 2018

Whether blood transfusion exacerbates cancer outcomes after surgery in humans remains inconclusive. We utilized a large cohort to investigate the effect of perioperative blood transfusion on cancer prognosis following colorectal cancer (CRC) resection. Patients with stage I through III CRC undergoing tumour resection at a tertiary medical center between 2005 and 2014 were identified and evaluated through August 2016. Propensity score matching was used to cancel out imbalances in patient characteristics. Postoperative disease-free survival (DFS) and overall survival (OS) were analysed using Cox regression model. A total of 4,030 and 972 patients were analysed before and after propensity score matching. Cox regression analyses demonstrated blood transfusion associated with shorter DFS and OS before and after matching (hazard ratio: 1.41, 95% CI: 1.2–1.66 for DFS; 1.97, 95% CI: 1.6–2.43 for OS). Larger transfusion volume was linked to higher overall mortality (≤4 units vs. nil, HR = 1.58; >4 units vs. nil, HR = 2.32) but not more cancer recurrence. Preoperative anemia was not associated with decreased survival after adjusting covariates. Perioperative blood transfusion was associated with worse cancer prognosis after curative colorectal resection, independently of anemia status. Strategies aimed at minimizing transfusion requirements should be further developed.