bluuebunny/crossref_metadata_2025 huggingface dataset:
Taxonomic Identification of Rhabdochona Species Found in Oncorhynchus Clarki Using Scanning Electron Microscopy
Authors: Young D , Heckmann RA , Gardner J S
Published: July 2020

Adult Rhabdochona nematodes, commonly parasitizing fish, were present in the digestive tracts of cutthroat trout in Little Cottonwood Creek, Utah. Cutthroat trout, Oncorhyncus clarki, are known to serve as both intermediate and definitive hosts for parasitic nematodes. The larval stage parasitizes almost any tissue of its host, but the adult is always found in the digestive tract. Due to the lack of key morphological features, scanning electron microscopy (SEM) was used to identify specific structures leading to the nematode's taxonomic identification.

Cutthroat trout were obtained using a rod and reel and were dissected the same day. Nematodes were present in all 12 cutthroat trout residing in all parts of the digestive tract. The nematodes, Rhabdochona sp., were prepared for SEM using the following procedures. First, the parasites were fixed in 2% buffered glutaraldehyde, washed in sodium cacodylate buffer, and post fixed in a 1% solution of osmium tetroxide. The samples were then washed in the same buffer system and dehydrated through a graded alcohol series. Critical-point-drying removed the remaining fluids. Finally, the nematodes were placed on specimen stubs, sputter coated with gold, and each specimen examined with a JOEL-840 high resolution scanning electron microscope with micrographs taken at varying magnifications.
Aminoglycoside Damage to Young Rats Equilibrium
Authors: Hara Hirotaka , Meza Graciela , Bohne Barbara , Hara Jun , César D. Fermin
Published: July 2020

Chronic streptomycin (STP) administration to young rats for 49 consecutive days intramuscularly affected the rats equilibrium, and balance. Behavioral measures indicated motor-related impairment and rats inability to swim correctly or upright themselves when dunk in a water tank. Moreover, the affected rats failed to walk straight on a inclined platform. Upon termination of the STP administration, motor-related functions returned to pre-administration levels in some animals (recovered group), but not in others (un-recovered group) suggesting that organs involved in maintenance of equilibrium and balance of the body were affected, but later recuperated. The inner ear of both groups and sham controls were processed for histology and transmission electron microscopy and examined.

Twenty day old male Long Evans rats were injected daily in alternating hindlimbs with 400mg/Kg body weight STP. Control rats were injected physiological saline, up to 57 days when they began the recovery period of 8-12 weeks without further injections.
Effect of Calcium on Salt Tolerance of Leaf Epidermal Cells of Ruppia maritima at High Salinity
Authors: Barnabas AD , Jagels R , Przybylowicz WJ , Mesjasz-Przybylowicz J
Published: July 2020

Ruppia maritima L. is a submerged halophyte which occurs frequently in estuaries where sodium chloride is the dominant salt. Unlike terrestrial halophytes, R. maritima does not possess any specialised salt-secreting structures such as salt glands. Knowledge of salt tolerance mechanisms in this plant is important to our understanding of its biology. In a previous study it was shown that leaf epidermal cells of R. maritima, which possess transfer cell characteristics, are implicated in salt regulation. In the present investigation, the effect of calcium (Ca) on salt tolerance of leaf epidermal cells was studied since Ca has been found to be an important factor in resistance to salt stress in terrestrial plants.

Plants were grown in artificial seawater of high salinity (33%) and at two different Ca concentrations : 400 ppm (high Ca) and 100 ppm (low Ca).
Digital Image Correlation of Forescatter Detector Images for Simultaneous Strain and Orientation Mapping
Authors: Adams Derrik , Irfan Shamoon , Cramer Jeff , Miles Michael P. , Homer Eric R. , Brown Tyson , Mishra Raj K. , Fullwood David T.
Published: July 2020

Improved plasticity models require simultaneous experimental local strain and microstructural evolution data. Microscopy tools, such as electron backscatter diffraction (EBSD), that can monitor transformation at the relevant length-scale, are often incompatible with digital image correlation (DIC) techniques required to determine local deformation. In this paper, the viability of forescatter detector (FSD) images as the basis for the DIC study is investigated. Standard FSD and an integrated EBSD/FSD approach (Pattern Region of Interest Analysis System: PRIAS™) are analyzed. Simultaneous strain and microstructure maps are obtained for tensile deformation of Q&P 1180 steel up to ~14% strain. Tests on an undeformed sample that is simply shifted indicate a standard deviation of error in strain of around 0.4% without additional complications from a deformed surface. The method resolves strain bands at ~2 μm spacing but does not provide significant sub-grain strain resolution. Similar resolution was obtained for mechanically polished and electropolished samples, despite electropolished surfaces presenting a smoother, simpler topography. While the resolution of the PRIAS approach depends upon the EBSD step size, the 80 nm step size used provides seemingly similar resolution as 8,000× (22.7 nm) FSD images. Surface feature evolution prevents DIC analysis across large strain steps (>6% strain), but restarting DIC, using an FSD reference image from an interim strain step, allows reasonable DIC across the stress–strain curve. Furthermore, the data are obtained easily and provide complementary information for EBSD analysis.
Strange Bedfellows: Interrogating the Unintended Consequences of Integrating Countering Violent Extremism with the UN's Women, Peace, and Security Agenda in Kenya
Authors: Aroussi Sahla
Published: July 2020

In October 2015, the United Nations Security Council adopted Resolution 2242 calling on member states to work toward the greater integration of the women, peace, and security (WPS) agenda with efforts to counter terrorism and violent extremism. While the rapprochement between counterterrorism and WPS may appear to be a step forward, particularly for those seeking to increase women's participation in areas traditionally dominated by men, it is also potentially dangerous. This article makes a significant contribution to the larger debate on the WPS agenda by studying the impact and unintended consequences of linking WPS with countering violent extremism on the ground in Kenya. Based on original research in the field, including key informant interviews, I argue that in the Kenyan context, connecting WPS with violent extremism has had several damaging consequences for women and their communities. Far from advancing the WPS agenda, this new policy shift has caused tension between local and international priorities, precipitated the redirection of donor funding away from important gender initiatives and toward countering violent extremism, and resulted in women's additional stigmatization, insecurity, and exclusion.
Home and Motor insurance joined at a household level using multivariate credibility
Authors: Pechon Florian , Denuit Michel , Trufin Julien
Published: July 2020

Actuarial ratemaking is usually performed at product and guarantee level, meaning that each product and guarantee is considered in isolation. Moreover, independence between policyholders is generally assumed. In this paper, we propose a multivariate Poisson mixture, with random effects correlated using a hierarchical structure, to accommodate for the dependence that may exist between unobserved risk factors across Home and Motor insurance and between policyholders from the same household. The hierarchical structure accounts for the fact that Home insurance covers the whole household, whereas Motor insurance policies are subscribed by specific policyholders within the household. The model allows to periodically correct the a priori expected claim frequencies using the reported number of claims in any of the considered products. Applications show that the impact of the number of claims reported in Motor insurance on the number of claims expected in Home insurance is larger than the other way around. Moreover, an out-of-sample analysis validates an improved predictive power. Also, the model allows to identify more rapidly the riskiest households.
Survey of Cryogenic Nitrogen Thermomechanical Property Data Relevant to Outer Solar System Bodies
Authors: Sagmiller Dylan , Hartwig Jason
Published: July 2020

The outer Solar System has many bodies of interest that have continued to captivate the planetary science community, recently Triton, a captured Kuiper belt object (KBO) of Neptune, and Pluto. Limited fly‐by observational data shows evidence that nitrogen is the dominant constituent on these two bodies, potentially also existing on other KBOs as well. Current simulations related to answering fundamental science questions and also to develop future mission science packages and vehicles require accurate, reliable thermodynamic, and mechanical property data of solid and gaseous nitrogen at relevant surface and atmospheric conditions. This paper thus presents an exhaustive review of all available experimental N2property data dating back to 1887. Each historical study is systematically analyzed and summarized and then the consolidated database is assembled. Comments are made on the validity of data sets, with an emphasis on specific heat capacity at constant pressure and constant volume (CP,Cv), thermal conductivity (κ), volume thermal expansion (αV), density (ρ), equilibrium vapor pressure (Pvap), heat of sublimation (ΔHS), heat of transition (ΔHT), Gruneisen parameter (γG), adiabatic and isothermal compressibility (xS,xT) and moduli of elasticity (C11,C12,C13,C33,C44). Results here can be used directly and immediately to perform new simulations on N2‐based bodies as well as to determine gaps in the consolidated database for future experiments.
Magnitude of the 1920 Haiyuan Earthquake Reestimated Using Seismological and Geomorphological Methods
Authors: Ou Q. , Kulikova G. , Yu J. , Elliott A. , Parsons B. , Walker R.
Published: July 2020

Reported magnitudes ranging between 7.8 and 8.7 highlight a confusion about the true size of the 1920 Haiyuan earthquake, the largest earthquake recorded in the northeast Tibetan Plateau. We compiled a global data set of previously unlooked‐at historical seismograms and performed modern computational analyses on the digitized seismic records. We found the epicenter to be near Haiyuan town and obtained a moment magnitude of MW=7.9±0.2. Following traditional approaches, we obtained mB=7.9±0.3 with data from 21 stations and MS(20)=8.1±0.2 with data from three stations. Geomorphologically, we mapped the surface rupture and horizontal offsets on high‐resolution Pleiades satellite and drone imagery that covered the entire western and middle sections of the 1920 Haiyuan earthquake rupture and compiled offsets reported on the eastern section from field measurements in the 1980s. Careful discrimination between single‐event and cumulative offsets suggests average horizontal slips of 3.0±1.0 m on the western section, 4.5±1.5 m on the middle section, and 3.5±0.5 m on the eastern section, indicating a total moment magnitude of MW=7.8±0.1. Thus, the seismological and geomorphological results agree within the uncertainties, a weighted average giving a moment magnitude of MW=7.9±0.2 for the 1920 Haiyuan earthquake. It is likely that earthquake magnitudes based on the historical M were systematically overestimated.
Fifty Years of Research on the Madden‐Julian Oscillation: Recent Progress, Challenges, and Perspectives
Authors: Jiang Xianan , Adames Ángel F. , Kim Daehyun , Maloney Eric D. , Lin Hai , Kim Hyemi , Zhang Chidong , DeMott Charlotte A. , Klingaman Nicholas P.
Published: July 2020

Since its discovery in the early 1970s, the crucial role of the Madden‐Julian Oscillation (MJO) in the global hydrological cycle and its tremendous influence on high‐impact climate and weather extremes have been well recognized. The MJO also serves as a primary source of predictability for global Earth system variability on subseasonal time scales. The MJO remains poorly represented in our state‐of‐the‐art climate and weather forecasting models, however. Moreover, despite the advances made in recent decades, theories for the MJO still disagree at a fundamental level. The problems of understanding and modeling the MJO have attracted significant interest from the research community. As a part of the AGU's Centennial collection, this article provides a review of recent progress, particularly over the last decade, in observational, modeling, and theoretical study of the MJO. A brief outlook for near‐future MJO research directions is also provided.
A Brief Analysis of Conceptual Model Structure Uncertainty Using 36 Models and 559 Catchments
Authors: Knoben W. J. M. , Freer J. E. , Peel M. C. , Fowler K. J. A. , Woods R. A.
Published: July 2020

The choice of hydrological model structure, that is, a model's selection of states and fluxes and the equations used to describe them, strongly controls model performance and realism. This work investigates differences in performance of 36 lumped conceptual model structures calibrated to and evaluated on daily streamflow data in 559 catchments across the United States. Model performance is compared against a benchmark that accounts for the seasonality of flows in each catchment. We find that our model ensemble struggles to beat the benchmark in snow‐dominated catchments. In most other catchments model structure equifinality (i.e., cases where different models achieve similar high efficiency scores) can be very high. We find no relation between the number of model parameters and performance during either calibration or evaluation periods nor evidence of increased risk of overfitting for models with more parameters. Instead, the choice of model parametrization (i.e., which equations are used and how parameters are used within them) dictates the model's strengths and weaknesses. Results suggest that certain model structures are inherently better suited for certain objective functions and thus for certain study purposes. We find no clear relationships between the catchments where any model performs well and descriptors of those catchments' geology, topography, soil, and vegetation characteristics. Instead, model suitability seems to relate strongest to the streamflow regime each catchment generates, and we have formulated several tentative hypotheses that relate commonalities in model structure to similarities in model performance. Modeling results are made publicly available for further investigation.
Galectin-9 promotes a suppressive microenvironment in human cancer by enhancing STING degradation
Authors: Zhang Chuan-xia , Huang Dai-jia , Baloche Valentin , Zhang Lin , Xu Jing-xiao , Li Bo-wen , Zhao Xin-rui , He Jia , Mai Hai-qiang , Chen Qiu-yan , Zhang Xiao-shi , Busson Pierre , Cui Jun , Li Jiang
Published: July 2020

Galectin-9 (Gal-9) is known to enhance the expansion of myeloid-derived suppressor cells (MDSCs) in murine models. Its contribution to the expansion of MDSCs in human malignancies remain to be investigated. We here report that Gal-9 expression in nasopharyngeal carcinoma (NPC) cells enhances the generation of MDSCs (CD33+CD11b+HLA-DR−) from CD33+ bystander cells. The underlying mechanisms involve both the intracellular and secreted Gal-9. Inside carcinoma cells, Gal-9 up-regulates the expression of a variety of pro-inflammatory cytokines which are critical for MDSC differentiation, including IL-1β and IL-6. This effect is mediated by accelerated STING protein degradation resulting from direct interaction of the Gal-9 carbohydrate recognition domain 1 with the STING C-terminus and subsequent enhancement of the E3 ubiquitin ligase TRIM29-mediated K48-linked ubiquitination of STING. Moreover, we showed that extracellular Gal-9 secreted by carcinoma cells can enter the myeloid cells and trigger the same signaling cascade. Consistently, high concentrations of tumor and plasma Gal-9 are associated with shortened survival of NPC patients. Our findings unearth that Gal-9 induces myeloid lineage-mediated immunosuppression in tumor microenvironments by suppressing STING signaling.
Correction: Association between sedentary behavior and the risk of dementia: a systematic review and meta-analysis
Authors: Yan Shijiao , Fu Wenning , Wang Chao , Mao Jing , Liu Bing , Zou Li , Lv Chuanzhu
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Evolutionary conserved role of neural cell adhesion molecule-1 in memory
Authors: Vukojevic Vanja , Mastrandreas Pavlina , Arnold Andreas , Peter Fabian , Kolassa Iris-T. , Wilker Sarah , Elbert Thomas , de Quervain Dominique J.-F. , Papassotiropoulos Andreas , Stetak Attila
Published: July 2020

The neural cell adhesion molecule 1 (NCAM-1) has been implicated in several brain-related biological processes, including neuronal migration, axonal branching, fasciculation, and synaptogenesis, with a pivotal role in synaptic plasticity. Here, we investigated the evolutionary conserved role of NCAM-1 in learning and memory. First, we investigated sustained changes in ncam-1 expression following aversive olfactory conditioning in C. elegans using molecular genetic methods. Furthermore, we examined the link between epigenetic signatures of the NCAM1 gene and memory in two human samples of healthy individuals (N = 568 and N = 319) and in two samples of traumatized individuals (N = 350 and N = 463). We found that olfactory conditioning in C. elegans induced ncam-1 expression and that loss of ncam-1 function selectively impaired associative long-term memory, without causing acquisition, sensory, or short-term memory deficits. Reintroduction of the C. elegans or human NCAM1 fully rescued memory impairment, suggesting a conserved role of NCAM1 for memory. In parallel, DNA methylation of the NCAM1 promoter in two independent healthy Swiss cohorts was associated with memory performance. In two independent Sub-Saharan populations of conflict zone survivors who had faced severe trauma, DNA methylation at an alternative promoter of the NCAM1 gene was associated with traumatic memories. Our results support a role of NCAM1 in associative memory in nematodes and humans, and might, ultimately, be helpful in elucidating diagnostic markers or suggest novel therapy targets for memory-related disorders, like PTSD.
First results from five multidisciplinary diagnostic centre (MDC) projects for non-specific but concerning symptoms, possibly indicative of cancer
Authors: Chapman D. , Poirier V. , Vulkan D. , Fitzgerald K. , Rubin G. , Hamilton W. , Duffy S. W. ,   on behalf of the ACE MDC projects,   Airedale MDC pilot, Thomas Alan Hart , Gulliford Dawn , Rolfe Helena ,   Airedale MDC clinical team,   Greater Manchester MDC pilots, Hohmann Matthias , Repperday Chris , Sykes Susan , Taylor Sarah ,   Greater Manchester MDC clinical teams,   Leeds MDC pilot, Craig Angie , Dawson James , Forbes Sarah , Ryan Helen , Turner Rob ,   Leeds ACE MDC Clinical Team and Steering Group,   London MDC pilots, Ahmad Mush , Chung Donna , Graham David , Millar Andrew , Taiyari Sara ,   London MDC clinical teams,   Oxford MDC pilot, Smith Claire Friedemann , Gleeson Fergus , Hayles Shelley , Kaveney Zoe , Nicholson Brian ,   Oxford MDC clinical team
Published: July 2020

Background

Patients with non-specific symptoms often experience longer times to diagnosis and poorer clinical outcomes than those with site-specific symptoms. This paper reports initial results from five multidisciplinary diagnostic centre (MDC) projects in England, piloting rapid referral for patients with non-specific symptoms.

Methods

The evaluation covered MDC activity from 1st December 2016 to 31st July 2018, with projects using a common dataset. Logistical regression analyses were conducted, with a diagnosis of any cancer as the dependent variable. Exploratory analysis was conducted on presenting symptoms and diagnoses of cancer, and on comparisons within these groupings.

Results

In total, 2961 patients were referred into the MDCs and 241 cancers were diagnosed. The pathway detected cancers across a broad range of tumour sites, including several rare and less common cancers. An association between patient age and cancer was identified (p < 0.001). GP ‘clinical suspicion’ was identified as a strong predictor of cancer (p = 0.006), with a reduced association with cancer observed in patients with higher numbers of GP consultation before referral (p = 0.008).

Conclusions

The MDC model diagnoses cancer in patients with non-specific symptoms, with a conversion rate of 8%, demonstrating the diagnostic potential of a non-site-specific symptomatic referral pathway.
PD-L1 promotes tumor growth and progression by activating WIP and β-catenin signaling pathways and predicts poor prognosis in lung cancer
Authors: Yu Wendan , Hua Yijun , Qiu Huijuan , Hao Jiaojiao , Zou Kun , Li Zongjuan , Hu Sheng , Guo Ping , Chen Manyu , Sui Silei , Xiong Yuqing , Li Fengzhou , Lu Jianjun , Guo Wei , Luo Guangyu , Deng Wuguo
Published: July 2020

PD-L1 is overexpressed in tumor cells and contributes to cancer immunoevasion. However, the role of the tumor cell-intrinsic PD-L1 in cancers remains unknown. Here we show that PD-L1 regulates lung cancer growth and progression by targeting the WIP and β-catenin signaling. Overexpression of PD-L1 promotes tumor cell growth, migration and invasion in lung cancer cells, whereas PD-L1 knockdown has the opposite effects. We have also identified WIP as a new downstream target of PD-L1 in lung cancer. PD-L1 positively modulates the expression of WIP. Knockdown of WIP also inhibits cell viability and colony formation, whereas PD-L1 overexpression can reverse this inhibition effects. In addition, PD-L1 can upregulate β-catenin by inhibiting its degradation through PI3K/Akt signaling pathway. Moreover, we show that in lung cancer cells β-catenin can bind to the WIP promoter and activate its transcription, which can be promoted by PD-L1 overexpression. The in vivo experiments in a human lung cancer mouse model have also confirmed the PD-L1-mediated promotion of tumor growth and progression through activating the WIP and β-catenin pathways. Furthermore, we demonstrate that PD-L1 expression is positively correlated with WIP in tumor tissues of human adenocarcinoma patients and the high expression of PD-L1 and WIP predicts poor prognosis. Collectively, our results provide new insights into understanding the pro-tumorigenic role of PD-L1 and its regulatory mechanism on WIP in lung cancer, and suggest that the PD-L1/Akt/β-catenin/WIP signaling axis may be a potential therapeutic target for lung cancers.
Review of data and knowledge gaps regarding yellow fever vaccine-induced immunity and duration of protection
Authors: Staples J. Erin , Barrett Alan D. T. , Wilder-Smith Annelies , Hombach Joachim
Published: July 2020

Yellow fever (YF) virus is a mosquito-borne flavivirus found in Sub-Saharan Africa and tropical South America. The virus causes YF, a viral hemorrhagic fever, which can be prevented by a live-attenuated vaccine, strain 17D. Despite the vaccine being very successful at decreasing disease risk, YF is considered a re-emerging disease due to the increased numbers of cases in the last 30 years. Until 2014, the vaccine was recommended to be administered with boosters every 10 years, but in 2014 the World Health Organization recommended removal of booster doses for all except special populations. This recommendation has been questioned and there have been reports of waning antibody titers in adults over time and more recently in pediatric populations. Clearly, the potential of waning antibody titers is a very important issue that needs to be carefully evaluated. In this Perspective, we review what is known about the correlate of protection for full-dose YF vaccine, current information on waning antibody titers, and gaps in knowledge. Overall, fundamental questions exist on the durability of protective immunity induced by YF vaccine, but interpretation of studies is complicated by the use of different assays and different cut-offs to measure seroprotective immunity, and differing results among certain endemic versus non-endemic populations. Notwithstanding the above, there are few well-characterized reports of vaccine failures, which one would expect to observe potentially more with the re-emergence of a severe disease. Overall, there is a need to improve YF disease surveillance, increase primary vaccination coverage rates in at-risk populations, and expand our understanding of the mechanism of protection of YF vaccine.
Interconnection of bacterial and phytoplanktonic communities with hydrochemical parameters from ice and under-ice water in coastal zone of Lake Baikal
Authors: Bukin Yu. S. , Bondarenko N. A. , Rusanov I. I. , Pimenov N. V. , Bukin S. V. , Pogodaeva T. V. , Chernitsyna S. M. , Shubenkova O. V. , Ivanov V. G. , Zakharenko A. S. , Zemskaya T. I.
Published: July 2020

We analysed the relationship between the chemical complex (concentration of dissolved ions, nutrients, pH) and biological parameters (primary production, biomass of phytoplankton, abundance and activity of bacterial communities) at estuaries of rivers and coastal waters of Southern Baikal during the under-ice period. Correlation network analysis revealed CO2 to be the main limiting factor for the development of algae and microbial communities in the coastal zone of Lake Baikal. This study indicates that primarily reverse synthesis of bicarbonate and carbonate ions associated with the development of phytoplankton and accumulation of dissolved CO2 during photosynthesis regulates pH in the Baikal water. We did not detect the anthropogenic factors that influence the change in pH and acidification. Near the Listvyanka settlement (Lake Baikal, Listvennichnaya Bay), there was a great number of organotrophs and thermotolerant bacteria with low bacterioplankton activity and high concentration of organic carbon. This evidences eutrophication due to the influx of organic matter having an anthropogenic source. Nutrients produced during the bacterial destruction of this matter may explain the changes in bottom phytocenoses of Listvennichnaya Bay.
Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov.
Authors: Khodadadi Fatemeh , González Jonathan B. , Martin Phillip L. , Giroux Emily , Bilodeau Guillaume J. , Peter Kari A. , Doyle Vinson P. , Aćimović Srđan G.
Published: July 2020

Apple bitter rot caused by Colletotrichum species is a growing problem worldwide. Colletotrichum spp. are economically important but taxonomically un-resolved. Identification of Colletotrichum spp. is critical due to potential species-level differences in pathogenicity-related characteristics. A 400-isolate collection from New York apple orchards were morphologically assorted to two groups, C. acutatum species complex (CASC) and C. gloeosporioides species complex (CGSC). A sub-sample of 44 representative isolates, spanning the geographical distribution and apple varieties, were assigned to species based on multi-locus phylogenetic analyses of nrITS, GAPDH and TUB2 for CASC, and ITS, GAPDH, CAL, ACT, TUB2, APN2, ApMat and GS genes for CGSC. The dominant species was C. fioriniae, followed by C. chrysophilum and a novel species, C. noveboracense, described in this study. This study represents the first report of C. chrysophilum and C. noveboracense as pathogens of apple. We assessed the enzyme activity and fungicide sensitivity for isolates identified in New York. All isolates showed amylolytic, cellulolytic and lipolytic, but not proteolytic activity. C. chrysophilum showed the highest cellulase and the lowest lipase activity, while C. noveboracense had the highest amylase activity. Fungicide assays showed that C. fioriniae was sensitive to benzovindiflupyr and thiabendazole, while C. chrysophilum and C. noveboracense were sensitive to fludioxonil, pyraclostrobin and difenoconazole. All species were pathogenic on apple fruit with varying lesion sizes. Our findings of differing pathogenicity-related characteristics among the three species demonstrate the importance of accurate species identification for any downstream investigations of Colletotrichum spp. in major apple growing regions.
Unspoken Assumptions in Multi-layer Modularity maximization
Authors: Hanteer Obaida , Magnani Matteo
Published: July 2020

A principled approach to recover communities in social networks is to find a clustering of the network nodes into modules (i.e groups of nodes) for which the modularity over the network is maximal. This guarantees partitioning the network nodes into sparsely connected groups of densely connected nodes. A popular extension of modularity has been proposed in the literature so it applies to multi-layer networks, that is, networks that model different types/aspects of interactions among a set of actors. In this extension, a new parameter, the coupling strength ω, has been introduced to couple different copies (i.e nodes) of the same actor with specific weights across different layers. This allows two nodes that refer to the same actor to reward the modularity score with an amount proportional to ω when they appear in the same community. While this extension seems to provide an effective tool to detect communities in multi-layer networks, it is not always clear what kind of communities maximising the generalised modularity can identify in multi-layer networks and whether these communities are inclusive to all possible community structures possible to exist in multi-layer networks. In addition, it has not been thoroughly investigated yet how to interpret ω in real-world scenarios, and whether a proper tuning of ω, if exists, is enough to guarantee an accurate recoverability for different types of multi-layer community structures. In this article, we report the different ways used in the literature to tune ω. We analyse different community structures that can be recovered by maximising the generalised modularity in relation to ω. We propose different models for multi-layer communities in multiplex and time-dependent networks and test if they are recoverable by modularity-maximization community detection methods under any assignment of ω. Our main finding is that only few simple models of multi-layer communities in multiplex and time-dependent networks are recoverable by modularity maximisation methods while more complex models are not accurately recoverable under any assignment of ω.
Evolutionary-driven C-MYC gene expression in mammalian fibroblasts
Authors: Moura Marcelo T. , Silva Roberta L. O. , Cantanhêde Ludymila F. , Ferreira-Silva José C. , Nascimento Pábola S. , Benko-Iseppon Ana M. , Oliveira Marcos A. L.
Published: July 2020

The extent to which mammalian cells share similar transcriptomes remains unclear. Notwithstanding, such cross-species gene expression inquiries have been scarce for defined cell types and most lack the dissection of gene regulatory landscapes. Therefore, the work was aimed to determineC-MYCrelative expression across mammalian fibroblasts (Ovis ariesandBos taurus) via cross-species RT-qPCR and comprehensively explore its regulatory landscape by in silico tools. The prediction of transcription factor binding sites inC-MYCand its 2.5 kb upstream sequence revealed substantial variation, thus indicating evolutionary-driven re-wiring of cis-regulatory elements.C-MYCand its downstream targetTBX3were up-regulated inBos taurusfibroblasts. The relative expression ofC-MYCregulators [RONIN(also known asTHAP11),RXRβ, andTCF3] and theC-MYC-associated transcript elongation factorCDK9did not differ between species. Additional in silico analyses suggestedBos taurus-specificC-MYCexonization, alternative splicing, and binding sites for non-coding RNAs.C-MYCprotein orthologs were highly conserved, while variation was in the transactivation domain and the leucine zipper motif. Altogether, mammalian fibroblasts display evolutionary-drivenC-MYCrelative expression that should be instructive for understanding cellular physiology, cellular reprogramming, andC-MYC-related diseases.
Effects of biochar-based controlled release nitrogen fertilizer on nitrogen-use efficiency of oilseed rape (Brassica napus L.)
Authors: Liao Jiayuan , Liu Xiangrong , Hu Ang , Song Haixing , Chen Xiuzhi , Zhang Zhenhua
Published: July 2020

Biochar-based controlled release nitrogen fertilizers (BCRNFs) have received increasing attention due to their ability to improve nitrogen-use efficiency (NUE) and increase crop yields. We previously developed a novel BCRNF, but its effects on soil microbes, NUE, and crop yields have not been reported. Therefore, we designed a pot experiment with five randomised treatments: CK (without urea and biochar), B (addition biochar without urea), B + U (biochar mixed urea), Urea (addition urea without biochar), and BCRNF (addition BCRNF), to investigate the effects of BCRNF on nitrifiers and denitrifiers, and how these impact nitrogen supply and NUE. Results of high-throughput sequencing revealed bacterial community groups with higher nutrient metabolic cycling ability under BCRNF treatment during harvest stage. Compared to Urea treatment, BCRNF treatment stimulated nitrification by increasing the copy number of the bacterial amoA gene and reducing nitrous oxide emission by limiting the abundance of nirS and nirK. Eventually, BCRNF successfully enhanced the yield (~ 16.6%) and NUE (~ 58.79%) of rape by slowly releasing N and modulating the abundance of functional microbes through increased soil nitrification and reduced denitrification, as compared with Urea treatment. BCRNF significantly improved soil NO3−, leading to an increase in N uptake by rape and NUE, thereby promoting rape growth and increasing grain yield.
Y2O3–Al2O3 microsphere crystallization analyzed by electron backscatter diffraction (EBSD)
Authors: Wisniewski Wolfgang , Švančárek Peter , Prnová Anna , Parchovianský Milan , Galusek Dušan
Published: July 2020

The crystallization of glass microspheres in the Y2O3–Al2O3-system produced from precursor powders of four different nominal compositions via flame synthesis is analyzed in detail by electron microscopy with a focus on electron backscatter diffraction (EBSD). Growth models are formulated for individual microspheres crystallized during flame synthesis as well as after an additional heat treatment step. 16 different types of crystallized bodies are cataloged for future reference. They are presented without regard for their relative occurrence; some are extremely rare but illustrate the possibilities of flame synthesis in the analyzed system. All three phases in the binary Y2O3–Al2O3-phase diagram (Y3Al5O12, YAlO3 and Y4Al2O9) and α-alumina are located by EBSD. Energy dispersive X-ray spectrometry results obtained from these microspheres show that their chemical composition can deviate from the nominal composition of the precursor powder. The multitude of differing microsphere types showing polygon and dendritic crystal growth as well as phase separation indicate that flame synthesis can lead to a wide variety of parameters during microsphere production, e.g. via irregular flight paths through the flame, contaminants or irregular cooling rates.
The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica
Authors: Britt Adrian , Bernini Megan , McSweeney Benjamin , Dalapati Sony , Duchin Sophia , Cavanna Kathryn , Santos Nicolette , Donovan Grace , O’Byrne Katherine , Noyes Sarah , Romero Manuela , Poonacha Kavery Nivana Theethira , Scully Tara
Published: July 2020

Long-standing evidence supports the importance of maintaining healthy populations of microbiota for the survival, homeostasis, and complete development of marine mollusks. However, the long-term ecological effects of agricultural runoff on these populations remains largely unknown. Atrazine (6-Chloro-n-ethyl-n′-(1-methylethyl)-triazine-2,4-diamine), a prevalent herbicide in the United States, is often used along tributaries of the Chesapeake Bay where oyster breeding programs are concentrated. To investigate any potential effects atrazine maybe having on mollusk-prokaryote interactions, we used 16S rRNA gene amplicons to evaluate how microbial compositions shift in response to exposure of environmentally relevant concentrations of atrazine previously found within the Chesapeake Bay. The dominant bacterial genera found within all groups included those belonging toPseudoalteromonas,Burkholderia,Bacteroides,Lactobacillis,Acetobacter,Allobaculum,Ruminococcus,andNocardia. Our results support previously published findings of a possible core microbial community inCrassostrea virginica. We also report a novel finding: oysters exposed to atrazine concentrations as low as 3 µg/L saw a significant loss of a key mutualistic microbial species and a subsequent colonization of a pathogenic bacteriaNocardia. We conclude that exposure to atrazine in the Chesapeake Bay may be contributing to a significant shift in the microbiomes of juvenile oysters that reduces fitness and impedes natural and artificial repopulation of the oyster species within the Bay.
Improving the accuracy of gastrointestinal neuroendocrine tumor grading with deep learning
Authors: Govind Darshana , Jen Kuang-Yu , Matsukuma Karen , Gao Guofeng , Olson Kristin A. , Gui Dorina , Wilding Gregory. E. , Border Samuel P. , Sarder Pinaki
Published: July 2020

The Ki-67 index is an established prognostic factor in gastrointestinal neuroendocrine tumors (GI-NETs) and defines tumor grade. It is currently estimated by microscopically examining tumor tissue single-immunostained (SS) for Ki-67 and counting the number of Ki-67-positive and Ki-67-negative tumor cells within a subjectively picked hot-spot. Intraobserver variability in this procedure as well as difficulty in distinguishing tumor from non-tumor cells can lead to inaccurate Ki-67 indices and possibly incorrect tumor grades. We introduce two computational tools that utilize Ki-67 and synaptophysin double-immunostained (DS) slides to improve the accuracy of Ki-67 index quantitation in GI-NETs: (1) Synaptophysin-KI-Estimator (SKIE), a pipeline automating Ki-67 index quantitation via whole-slide image (WSI) analysis and (2) deep-SKIE, a deep learner-based approach where a Ki-67 index heatmap is generated throughout the tumor. Ki-67 indices for 50 GI-NETs were quantitated using SKIE and compared with DS slide assessments by three pathologists using a microscope and a fourth pathologist via manually ticking off each cell, the latter of which was deemed the gold standard (GS). Compared to the GS, SKIE achieved a grading accuracy of 90% and substantial agreement (linear-weighted Cohen’s kappa 0.62). Using DS WSIs, deep-SKIE displayed a training, validation, and testing accuracy of 98.4%, 90.9%, and 91.0%, respectively, significantly higher than using SS WSIs. Since DS slides are not standard clinical practice, we also integrated a cycle generative adversarial network into our pipeline to transform SS into DS WSIs. The proposed methods can improve accuracy and potentially save a significant amount of time if implemented into clinical practice.
Four-dot masking in monoptic and dichoptic viewing
Authors: Nakamura Tomoya , Lavrenteva Sofia , Murakami Ikuya
Published: July 2020

In visual backward masking paradigms, the visibility of a target is reduced using various kinds of mask stimuli presented immediately after the target. Four-dot masking is one such kind of backward masking, caused by four surrounding dots neither spatially adjacent nor similar to the target. Four-dot masking is often considered to involve object-level interferences. However, low-level contributions such as lateral inhibition and motion detection are also possible. To elucidate the loci of the underlying mechanism within the visual hierarchy, we compared the masking effect between monoptic and dichoptic viewing conditions. A target and a four-dot mask, which also served as a spatial cue to the target location, were presented to the same eye in monoptic viewing, whereas they were presented to different eyes in dichoptic viewing. Observers were then asked to discriminate the target shape. We found a significant decline in the correct response rate compared to the baseline condition in which the four-dot mask was not presented, and the masking effect was equivalent between the monoptic and dichoptic viewings. These results demonstrate that four-dot masking stems exclusively from processing within the binocular pathway.
Societal attention toward extinction threats: a comparison between climate change and biological invasions
Authors: Jarić Ivan , Bellard Céline , Courchamp Franck , Kalinkat Gregor , Meinard Yves , Roberts David L. , Correia Ricardo A.
Published: July 2020

Public attention and interest in the fate of endangered species is a crucial prerequisite for effective conservation programs. Societal awareness and values will largely determine whether conservation initiatives receive necessary support and lead to adequate policy change. Using text data mining, we assessed general public attention in France, Germany and the United Kingdom toward climate change and biological invasions in relation to endangered amphibian, reptile, bird and mammal species. Our analysis revealed that public attention patterns differed among species groups and countries but was globally higher for climate change than for biological invasions. Both threats received better recognition in threatened than in non-threatened species, as well as in native species than in species from other countries and regions. We conclude that more efficient communication regarding the threat from biological invasions should be developed, and that conservation practitioners should take advantage of the existing attention toward climate change.
FMR1 locus isoforms: potential biomarker candidates in fragile X-associated tremor/ataxia syndrome (FXTAS)
Authors: Zafarullah Marwa , Tang Hiu-Tung , Durbin-Johnson Blythe , Fourie Emily , Hessl David , Rivera Susan M. , Tassone Flora
Published: July 2020

Fragile X associated tremor/ataxia syndrome (FXTAS) is a late adult-onset neurodegenerative disorder that affects movement and cognition in male and female carriers of a premutation allele of 55–200 CGG repeats in the Fragile X mental retardation (FMR1) gene. It is currently unknown if and when an individual carrier of a premutation allele will develop FXTAS, as clinical assessment fails to identify carriers at risk before significant neurological symptoms are evident. The primary objective of this study was to investigate the alternative splicing landscape at the FMR1 locus in conjunction with brain measures in male individuals with a premutation allele enrolled in a very first longitudinal study, compared to age-matched healthy male controls, with the purpose of identifying biomarkers for early diagnosis, disease prediction and, a progression of FXTAS. Our findings indicate that increased expression of FMR1 mRNA isoforms, including Iso4/4b, Iso10/10b, as well as of the ASFMR1 mRNAs Iso131bp, are present in premutation carriers as compared to non-carrier healthy controls. More specifically, we observed a higher expression of Iso4/4b and Iso10/10b, which encode for truncated proteins, only in those premutation carriers who developed symptoms of FXTAS over time as compared to non-carrier healthy controls, suggesting a potential role in the development of the disorder. In addition, we found a significant association of these molecular changes with various measurements of brain morphology, including the middle cerebellar peduncle (MCP), superior cerebellar peduncle (SCP), pons, and midbrain, indicating their potential contribution to the pathogenesis of FXTAS. Interestingly, the high expression levels of Iso4/4b observed both at visit 1 and visit 2 and found to be associated with a decrease in mean MCP width only in those individuals who developed FXTAS over time, suggests their role as potential biomarkers for early diagnosis of FXTAS.
Automated spheroid generation, drug application and efficacy screening using a deep learning classification: a feasibility study
Authors: Benning Leo , Peintner Andreas , Finkenzeller Günter , Peintner Lukas
Published: July 2020

The last two decades saw the establishment of three-dimensional (3D) cell cultures as an acknowledged tool to investigate cell behaviour in a tissue-like environment. Cells growing in spheroids differentiate and develop different characteristics in comparison to their two-dimensionally grown counterparts and are hence seen to exhibit a more in vivo-like phenotype. However, generating, treating and analysing spheroids in high quantities remains labour intensive and therefore limits its applicability in drugs and compound research. Here we present a fully automated pipetting robot that is able to (a) seed hanging drops from single cell suspensions, (b) treat the spheroids formed in these hanging drops with drugs and (c) analyse the viability of the spheroids by an image-based deep learning based convolutional neuronal network (CNN). The model is trained to classify between ‘unaffected’, ‘mildly affected’ and ‘affected’ spheroids after drug exposure. All corresponding spheroids are initially analysed by viability flow cytometry analysis to build a labelled training set for the CNN to subsequently reduce the number of misclassifications. Hence, this approach allows to efficiently examine the efficacy of drug combinatorics or new compounds in 3D cell culture. Additionally, it may provide a valuable instrument to screen for new and individualized systemic therapeutic strategies in second and third line treatment of solid malignancies using patient derived primary cells.
Transmural difference in myocardial damage assessed by layer-specific strain analysis in patients with ST elevation myocardial infarction
Authors: Kim Sua , Cho Dong-Hyuk , Kim Mi-Na , Hong Soon-Jun , Yu Cheol Woong , Lim Do-Sun , Shim Wan Joo , Park Seong-Mi
Published: July 2020

We performed layer-specific strain analysis with speckle-tracking echocardiography to investigate the transmural difference of myocardial damage as the predicting factor for the viability of damaged myocardium in patients with ST segment elevation myocardial infarction (STEMI). We analysed patients with acute STEMI who had undergone primary percutaneous coronary intervention and echocardiography within 24 h from the intervention and 2 months after the event. Segmental strains of the left ventricular (LV) endocardium, myocardium, epicardium, and strain gradient (SG) between the endocardium and epicardium were evaluated. In 34 patients, 112 akinetic/dyskinetic and 94 hypokinetic segments were observed among 612 segments of the LV at baseline, and 65 akinetic/dyskinetic segments had viability. In our study, layer-specific strains were gradually deteriorated by their wall motion. SG was augmented in the hypokinetic segments where inhomogeneous wall motion impairment was progressed. SG in the akinetic/dyskinetic segments was different between the viable and non-viable myocardium and was maintained in viable segments. We therefore believe that significantly reduced SG is indicative of irreversible transmural damage in the acute stage of STEMI and can be suitably used as a parameter for predicting myocardial viability.