bluuebunny/crossref_metadata_2025 huggingface dataset:
When Evidence Isn't Enough: Suspension, Evidentialism, and Knowledge-first Virtue Epistemology
Authors: Miracchi Lisa
Published: November 2019

I motivate and develop a novel account of the epistemic assessability of suspension as a development of my knowledge-first, virtue-epistemological research program. First, I extend an argument of Ernest Sosa's for the claim that evidentialism cannot adequately account for the epistemic assessability of suspension. This includes a kind of knowledge-first evidentialism of the sort advocated by Timothy Williamson. I agree with Sosa that the reasons why evidentialism fails motivate a virtue-epistemological approach, but argue that my knowledge-first account is preferable to his view. According to my account, rational belief is belief that manifests proper practical respect for what it takes to know. Beliefs are the only primary bearers of epistemic evaluation since they are the only candidates for knowledge. However, suspension can manifest a derivative kind of practical respect for what it takes to know. Thus, we can explain why the same sort of assessment is applicable to both belief and suspension (epistemic rationality), and why belief has a privileged claim to these properties. Lastly, I'll look at Sosa's and Williamson's treatments of Pyrrhonian skepticism, which treats a certain kind of suspension as the epistemically superior practice, and argue that my account provides a better anti-skeptical response than either of their approaches.
HOMOGENEOUS SASAKI AND VAISMAN MANIFOLDS OF UNIMODULAR LIE GROUPS
Authors: ALEKSEEVSKY D. , HASEGAWA K. , KAMISHIMA Y.
Published: November 2019

A Vaisman manifold is a special kind of locally conformally Kähler manifold, which is closely related to a Sasaki manifold. In this paper, we show a basic structure theorem of simply connected homogeneous Sasaki and Vaisman manifolds of unimodular Lie groups, up to holomorphic isometry. For the case of unimodular Lie groups, we obtain a complete classification of simply connected Sasaki and Vaisman unimodular Lie groups, up to modification.
Electoral Cycles in Government Policy Making: Strategic Timing of Austerity Reform Measures in Western Europe
Authors: Strobl Daniel , Bäck Hanna , Müller Wolfgang C. , Angelova Mariyana
Published: November 2019

This article investigates whether governing parties strategically time austerity policies to help them win re-election. It contributes to existing research by focusing directly on government policy output, analyzing over 1,200 welfare and taxation austerity measures in thirteen Western European countries over twenty years. In line with previous research, the authors find that governments become less likely to introduce austerity measures as elections approach. The study introduces original hypotheses about which governments have theabilityandopportunityto strategically time policy decisions. The authors suggest that minimal winning cabinets with leadership change (new prime ministers) face less complex bargaining environments and can credibly shift responsibility for austerity measures to the preceding government. The empirical analyses show that these governments are most likely to strategically time austerity policies.
Heterogeneity in the Ediacaran–Cambrian coastal oceans: a sulphur isotope perspective
Authors: Lin Ying , Wu Nanping , Li Da , Ling Hong-Fei
Published: November 2019

Multiple sulphur isotope compositions of sedimentary pyrites across the Ediacaran–Cambrian (Ed–C) transition and into the early Cambrian from the Xiaotan section, Yunnan, South China, are presented to explore the evolution of the sulphur cycle. The values of δ34Spyrange from 13.5 ‰ to 35.8 ‰, and the values of Δ33Spyrange from −0.044 ‰ to 0.063 ‰. The first-order observation of highly positive δ34Spyis consistent with sulphur isotope records from other sedimentary successions (with various degrees of enrichment in34S), reflecting a common feature in cycling of sulphur among ocean basins. The positive values suggest that pyrite was formed in a depositional setting with limiting availability of sulphate that suppressed the expression of microbial fractionations. The first-order observation of a 10-million-year period of negative Δ33Spybeginning around the Ed–C boundary likely reflects changes in isotopic compositions of sulphur influx to the oceans. Such changes are suggested to be linked to a pulse of preferred weathering of sulphides (with negative Δ33S) relative to sulphate, which may reflect enhanced exposure of pyrites in continental margins due to reorganization of continents at this time. Both δ34Spyand Δ33Spydata imply low seawater sulphate levels, and possibly heterogeneity in sulphate concentrations in the world’s coastal oceans. The predictions about sulphur isotope signatures of evolved seawater (with highly positive δ34S and negative Δ33S) at the Xiaotan section are testable with future measurements of carbonate-associated sulphate (CAS), a proxy of ancient oceanic sulphate that carries information about the operation of sulphur cycling on a global scale.
The effect of second-language vocabulary on word retrieval in the native language
Authors: Higby Eve , Donnelly Seamus , Yoon Jungmee , Obler Loraine K.
Published: November 2019

When bilinguals produce words in one language, their translation equivalents in the other language are thought to be activated as well. A common assumption is that this parallel co-activation produces interference, which slows down word retrieval. The current study aimed to evaluate the assumption of lexical interference during word retrieval by testing whether late Portuguese–English bilinguals were slower to name pictures in their native language when they knew the word in their second language compared to when they only knew the native language label. Instead of interfering with production, knowing the second-language label facilitated speed of word retrieval in the native language for both cognate and non-cognate translation-equivalent pairs. We suggest that using the second language may provide an indirect frequency boost for translation-equivalent words in the native language. This frequency boost has both long-term and short-term effects, strengthening connections to native-language labels when the translation equivalent is retrieved.
Fatwas and Democracy: Majelis Ulama Indonesia (MUI, Indonesian Ulema Council) and Rising Conservatism in Indonesian Islam
Authors: Hasyim Syafiq
Published: November 2019

The role of Majelis Ulama Indonesia (Indonesian Ulema Council) in influencing the construction of democracy through its fatwas has fluctuated since its establishment in 1975. During the Suharto regime, which was characterised by authoritarian national leadership, MUI fatwas tended to serve the interests of the regime. Since the reform era, they have stimulated undemocratic circumstances in Indonesian Islam. This article examines MUI fatwas and their influence on democracy in the context of Indonesian Islam. The main argument of this article is that fatwas in themselves can improve or worsen the implementation of democracy. Fatwas may impede democracy if their contents are not aligned with democratic principles, while they may support the development of democracy if their contents promote democracy. Rising conservatism in Indonesia has been influenced by the issuance of fatwas that do not promote democratic values. In addition to examining the roles of fatwa givers and the methodology of fatwa issuance, this article analyses the social and political circumstances driving their issuance. This article presents examples of MUI fatwas that have democratic and undemocratic characteristics. It concludes that democratic circumstances can be achieved through opening spaces for fatwa issuance among additional fatwa institutions in Indonesia, as the monopolisation of fatwa issuance has created undemocratic tendencies in Indonesian Islam.
Solar Irradiance Variability: Comparisons of Models and Measurements
Authors: Coddington O. , Lean J. , Pilewskie P. , Snow M. , Richard E. , Kopp G. , Lindholm C. , DeLand M. , Marchenko S. , Haberreiter M. , Baranyi T.
Published: November 2019

The Earth system responds to solar variability on a wide range of timescales. Knowledge of total solar irradiance (TSI) and solar spectral irradiance (SSI) spanning minutes to centuries is needed by scientists studying a broad array of research applications. For these purposes, the NOAA National Centers for Environmental Information (NCEI) Climate Data Record Program established the Solar Irradiance Climate Data Record. Version 2 of the Naval Research Laboratory's solar variability models that are derived from and demonstrate consistency with irradiance observations specifies TSI and SSI for the Solar Irradiance Climate Data Record. We establish the veracity of the Naval Research Laboratory models on the timescales and over the wavelength range for which the Sun is known to vary and, thereby, specify the utility of these models. Through comparisons with irradiance observations and independent models, we validate NRLTSI2 estimates of TSI on solar rotational (~27‐day), solar cycle (~11‐year), and multidecadal (spacecraft era) variability timescales. Similarly, we validate NRLSSI2 estimates of SSI rotational variability in the ultraviolet through the mid‐visible spectrum. Validation of NRLSSI2 estimates at longer wavelengths, particularly in the near‐infrared, and for the full spectrum at solar cycle timescales and longer is not possible with the current observational record due to instrumental noise and instrument instability. We identify where key new data sets, such as observations from the Total and Spectral Solar Irradiance Sensor‐1, are expected to provide a fuller understanding of total and spectral solar irradiance variability on multiple timescales.
Nitrate Isotopic Composition in Precipitation at a Chinese Megacity: Seasonal Variations, Atmospheric Processes, and Implications for Sources
Authors: Li Zhengjie , Walters Wendell W. , Hastings Meredith G. , Zhang Yanlin , Song Linlin , Liu Dongwei , Zhang Wenqi , Pan Yuepeng , Fu Pingqing , Fang Yunting
Published: November 2019

Nitrogen stable isotope composition (δ15N) of nitrate (NO3−) deposition can aid in source apportionment of its precursor emissions, nitrogen oxides (NOx), with implications in mitigation policy to address serious air pollution. However, potential δ15N fractionation during atmospheric NO3− formation may hinder accurate quantification of NOx contributions. Previously, NOx photochemical reactions have been suggested to be the dominant δ15N fractionation process in NO3− formation. Here, we have quantified the potential fractionation effects associated with NOx photochemical reactions based upon δ15N‐NO3− measured in 1 year of daily‐based bulk deposition samples in Shenyang, a megacity with distinct seasonal fossil fuel combustion in northeastern China. The mean δ15N was 0.9 ± 4.0‰ and ranged from −4.9 to 8.3‰, with the lowest and highest values observed during summer and winter, respectively. Calculated NOx photochemical equilibrium fractionation may account for up to 42% of the observed seasonal δ15N change in NO3− deposition. However, the relative NOx source contribution trends, estimated based upon a δ15N Bayesian mixing model, were insensitive to NOx photochemical fractionation considerations. Overall, NOx source partitioning based upon averaged year‐long δ15N of bulk NO3− deposition estimated the following relative trend in NOx emission sources: coal combustion > biomass burning = vehicle emissions ≫ soil emissions. Seasonally, the increase of coal combustion emissions from summer to winter drives the seasonality of δ15N in NO3− deposition, indicating a necessity to control NOx emissions from coal combustion to improve wintertime air quality.
Validation of NeQuick 2 Model Topside Ionosphere and Plasmasphere Electron Content Using COSMIC POD TEC
Authors: Kashcheyev A. , Nava B.
Published: November 2019

An accurate representation of the topside ionosphere and plasmasphere electron content is still one of the important issues for ionospheric models, particularly for those used in GNSS applications. In this work, a validation of NeQuick 2 empirical ionospheric model has been performed in terms of ionosphere topside and plasmasphere electron content in the altitude range ~800–20,200 km. For this purpose, total electron content (TEC) data derived from precise orbit determination (POD) antennas onboard COSMIC low earth orbit (LEO) satellites tracking GPS signals have been used. The data span the period from 2006 to 2018 and correspond to different heliogeophysical conditions. In order to remove unrealistic TEC values from the validation process, a specific filtering procedure has been applied to POD‐derived TEC data. Subsequently, the statistical analysis of the difference between the modeled and the corresponding experimentally derived TEC values has been performed on data obtained during geomagnetically quiet periods. The results are presented as a function of solar activity level, season, local time, and geomagnetic latitude plots. They show that NeQuick 2 model underestimates the ionosphere topside and plasmasphere electron content, particularly during the early morning hours. The conditions under which the discrepancy between the model and experimental data is the highest have been also identified and considered as indications for future model improvements.
Toward Improved Probabilistic Predictions for Flood Forecasts Generated Using Deterministic Models
Authors: Jiang Xiaolei , Gupta Hoshin V. , Liang Zhongmin , Li Binquan
Published: November 2019

Uncertainties in flood forecasts are inevitable, and the key issue is to develop probabilistic predictions so that the predictive uncertainty (PU) bounds can be estimated. We develop and test a general method for probabilistic forecasting and PU estimation that is based on a theoretical and practical analysis of the actual nature of the model residuals, which reveals that the residual mean, standard deviation, and distributional form can all vary with time. Our approach is to condition the nature of the residual distribution on the magnitude of the corresponding streamflow value, but other kinds of conditioning are also possible. Using real data, we illustrate seven progressively more realistic sets of assumptions regarding the model residuals, ranging from homogenous Gaussian to fully heterogeneous non‐Gaussian. Our results show that the estimated probabilistic predictions become progressively better as the assumptions better conform to the actual properties of the residuals. As benchmarks, we compare against results from the state‐of‐the‐art power transformation approach. Our method is generally applicable to any situation where a deterministic model is used to generate predictions, and where empirical probabilistic predictions are required without developing a stochastic version of that model.
The transcription factor FoxM1 activates Nurr1 to promote intestinal regeneration after ischemia/reperfusion injury
Authors: Zu Guo , Guo Jing , Zhou Tingting , Che Ningwei , Liu Baiying , Wang Dong , Zhang Xiangwen
Published: November 2019

FoxM1 is involved in the regeneration of several organs after injury and expressed in the intestinal mucosa. The intrinsic mechanism of FoxM1 activity in the mucosa after intestinal ischemia/reperfusion (I/R) injury has not been reported. Therefore, we investigated the role of FoxM1 in mediating intestinal mucosa regeneration after I/R injury. Expression of FoxM1 and the proliferation of intestinal mucosa epithelial cells were examined in rats with intestinal I/R injury and an IEC-6 cell hypoxia/reperfusion (H/R) model. The effects of FoxM1 inhibition or activation on intestinal epithelial cell proliferation were measured. FoxM1 expression was consistent with the proliferation of intestinal epithelial cells in the intestinal mucosa after I/R injury. Inhibition of FoxM1 expression led to the downregulation of Ki-67 expression mediated by the inhibited expression of Nurr1, and FoxM1 overexpression promoted IEC-6 cell proliferation after H/R injury through activating Nurr1 expression. Furthermore, FoxM1 directly promoted the transcription of Nurr1 by directly binding the promoter of Nurr1. Further investigation showed low expression levels of FoxM1, Nurr1, and Ki-67 in the intestinal epithelium of patients with intestinal ischemic injury. FoxM1 acts as a critical regulator of intestinal regeneration after I/R injury by directly promoting the transcription of Nurr1. The FoxM1/Nurr1 signaling pathway represents a promising therapeutic target for intestinal I/R injury and related clinical diseases.
Improved polygenic prediction by Bayesian multiple regression on summary statistics
Authors: Lloyd-Jones Luke R. , Zeng Jian , Sidorenko Julia , Yengo Loïc , Moser Gerhard , Kemper Kathryn E. , Wang Huanwei , Zheng Zhili , Magi Reedik , Esko Tõnu , Metspalu Andres , Wray Naomi R. , Goddard Michael E. , Yang Jian , Visscher Peter M.
Published: November 2019

Accurate prediction of an individual’s phenotype from their DNA sequence is one of the great promises of genomics and precision medicine. We extend a powerful individual-level data Bayesian multiple regression model (BayesR) to one that utilises summary statistics from genome-wide association studies (GWAS), SBayesR. In simulation and cross-validation using 12 real traits and 1.1 million variants on 350,000 individuals from the UK Biobank, SBayesR improves prediction accuracy relative to commonly used state-of-the-art summary statistics methods at a fraction of the computational resources. Furthermore, using summary statistics for variants from the largest GWAS meta-analysis (n ≈ 700, 000) on height and BMI, we show that on average across traits and two independent data sets that SBayesR improves prediction R2 by 5.2% relative to LDpred and by 26.5% relative to clumping and p value thresholding.
Cav2.3 channels contribute to dopaminergic neuron loss in a model of Parkinson’s disease
Authors: Benkert Julia , Hess Simon , Roy Shoumik , Beccano-Kelly Dayne , Wiederspohn Nicole , Duda Johanna , Simons Carsten , Patil Komal , Gaifullina Aisylu , Mannal Nadja , Dragicevic Elena , Spaich Desirée , Müller Sonja , Nemeth Julia , Hollmann Helene , Deuter Nora , Mousba Yassine , Kubisch Christian , Poetschke Christina , Striessnig Joerg , Pongs Olaf , Schneider Toni , Wade-Martins Richard , Patel Sandip , Parlato Rosanna , Frank Tobias , Kloppenburg Peter , Liss Birgit
Published: November 2019

Degeneration of dopaminergic neurons in the substantia nigra causes the motor symptoms of Parkinson’s disease. The mechanisms underlying this age-dependent and region-selective neurodegeneration remain unclear. Here we identify Cav2.3 channels as regulators of nigral neuronal viability. Cav2.3 transcripts were more abundant than other voltage-gated Ca2+channels in mouse nigral neurons and upregulated during aging. Plasmalemmal Cav2.3 protein was higher than in dopaminergic neurons of the ventral tegmental area, which do not degenerate in Parkinson’s disease. Cav2.3 knockout reduced activity-associated nigral somatic Ca2+signals and Ca2+-dependent after-hyperpolarizations, and afforded full protection from degeneration in vivo in a neurotoxin Parkinson’s mouse model. Cav2.3 deficiency upregulated transcripts for NCS-1, a Ca2+-binding protein implicated in neuroprotection. Conversely, NCS-1 knockout exacerbated nigral neurodegeneration and downregulated Cav2.3. Moreover, NCS-1 levels were reduced in a human iPSC-model of familial Parkinson’s. Thus, Cav2.3 and NCS-1 may constitute potential therapeutic targets for combatting Ca2+-dependent neurodegeneration in Parkinson’s disease.
Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data
Authors: Zhou Yitao , Xiao Shijun , Lin Gang , Chen Duo , Cen Wan , Xue Ting , Liu Zhiyu , Zhong Jianxing , Chen Yanting , Xiao Yijun , Chen Jianhua , Guo Yunhai , Chen Youqiang , Zhang Yanding , Hu Xuefeng , Huang Zhen
Published: November 2019

Pufferfish are ideal models for vertebrate chromosome evolution studies. The yellowbelly pufferfish, Takifugu flavidus, is an important marine fish species in the aquaculture industry and ecology of East Asia. The chromosome assembly of the species could facilitate the study of chromosome evolution and functional gene mapping. To this end, 44, 27 and 50 Gb reads were generated for genome assembly using Illumina, PacBio and Hi-C sequencing technologies, respectively. More than 13 Gb full-length transcripts were sequenced on the PacBio platform. A 366 Mb genome was obtained with the contig of 4.4 Mb and scaffold N50 length of 15.7 Mb. 266 contigs were reliably assembled into 22 chromosomes, representing 95.9% of the total genome. A total of 29,416 protein-coding genes were predicted and 28,071 genes were functionally annotated. More than 97.7% of the BUSCO genes were successfully detected in the genome. The genome resource in this work will be used for the conservation and population genetics of the yellowbelly pufferfish, as well as in vertebrate chromosome evolution studies.
Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments
Authors: Sinkko Hanna , Hepolehto Iina , Lyra Christina , Rinta-Kanto Johanna M. , Villnäs Anna , Norkko Joanna , Norkko Alf , Timonen Sari
Published: November 2019

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology
Authors: Taylor Tonya L. , Volkening Jeremy D. , DeJesus Eric , Simmons Mustafa , Dimitrov Kiril M. , Tillman Glenn E. , Suarez David L. , Afonso Claudio L.
Published: November 2019

U.S. public health agencies have employed next-generation sequencing (NGS) as a tool to quickly identify foodborne pathogens during outbreaks. Although established short-read NGS technologies are known to provide highly accurate data, long-read sequencing is still needed to resolve highly-repetitive genomic regions and genomic arrangement, and to close the sequences of bacterial chromosomes and plasmids. Here, we report the use of long-read nanopore sequencing to simultaneously sequence the entire chromosome and plasmid of Salmonella enterica subsp. enterica serovar Bareilly and Escherichia coli O157:H7. We developed a rapid and random sequencing approach coupled with de novo genome assembly within a customized data analysis workflow that uses publicly-available tools. In sequencing runs as short as four hours, using the MinION instrument, we obtained full-length genomes with an average identity of 99.87% for Salmonella Bareilly and 99.89% for E. coli in comparison to the respective MiSeq references. These nanopore-only assemblies provided readily available information on serotype, virulence factors, and antimicrobial resistance genes. We also demonstrate the potential of nanopore sequencing assemblies for rapid preliminary phylogenetic inference. Nanopore sequencing provides additional advantages as very low capital investment and footprint, and shorter (10 hours library preparation and sequencing) turnaround time compared to other NGS technologies.
Feasibility Study of Thorium-Plutonium Mixed Oxide Assembly In Light Water Reactors
Authors: Mustafa S. S. , Amin E. A.
Published: November 2019

Thorium-plutonium mixed oxide, (Th,Pu)OX, is currently used as an alternative fuel in the light water reactors in the world. The main objective of this paper is not only to show the benefits of using the thorium, but mainly to study how the way thorium is introduced in the fuel affects the neutron parameters. Among these benefits is the possibility of extending the operating cycle length and the reduction of the increasing stockpiles of plutonium. The first investigated method is introducing thorium as (Th,Pu)OX. The second one is a homogeneous model of thorium plutonium oxide. It is carried out by adding an amount of plutonium separated from the uranium oxide cycle at 50 GWd/ton of heavy metal to the same amount of thorium. Thus, we studied three assemblies; the reference assembly is uranium oxide of 4.2% enrichment containing borated water as a moderator of concentration 500 ppm (part per million) of B-10. The second is a (Th,Pu)OX and the third one is an assembly with homogenized thorium plutonium. All three assemblies are modeled using MCNPX. A comparison is held between the results of the three lattices. The factors compared are the effective multiplication factor, the inventory of plutonium and uranium isotopes, and the depletion of B-10, the pin by pin power distribution at 0 and 60 GWd/ton and the relative pin radial power for the three lattices. The comparison is aimed to show the effect on the cycle length, the reduction in the Pu content and the power flattening across the assembly. It is found that the evolution of the multiplication factors shows a similar behaviour using (Th-Pu)OX fuel in the assembly as UOX cycle inspite of lowering the K-eff of fresh (Th-Pu)OX fuel (1.19847). The power flattening which is favorable in reactor operation is clearer in (Th,Pu)OX fuel. It is noticed that the mass of Pu-239 decreases by 1.07% from its initial value at the end of life. For homogeneous (Th,Pu)OX, the mass decreases by 0.0832%. The high power peaking factor for (Th,Pu)OX is not expected to cause significant effects during reactor operation but it can be reduced by adding burnable poisons.
Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters
Authors: Chénard Caroline , Wijaya Winona , Vaulot Daniel , Lopes dos Santos Adriana , Martin Patrick , Kaur Avneet , Lauro Federico M.
Published: November 2019

Singapore, an equatorial island in South East Asia, is influenced by a bi-annual reversal of wind directions which defines two monsoon seasons. We characterized the dynamics of the microbial communities of Singapore coastal waters by collecting monthly samples between February 2017 and July 2018 at four sites located across two straits with different trophic status, and sequencing the V6-V8 region of the small sub-unit ribosomal RNA gene (rRNA gene) of Bacteria, Archaea, and Eukaryota. Johor Strait, which is subjected to wider environmental fluctuations from anthropogenic activities, presented a higher abundance of copiotrophic microbes, including Cellvibrionales and Rhodobacterales. The mesotrophic Singapore Strait, where the seasonal variability is caused by changes in the oceanographic conditions, harboured a higher proportion of typically marine microbe groups such as Synechococcales, Nitrosupumilales, SAR11, SAR86, Marine Group II Archaea and Radiolaria. In addition, we observed seasonal variability of the microbial communities in the Singapore Strait, which was possibly influenced by the alternating monsoon regime, while no seasonal pattern was detected in the Johor Strait.
Humoral Immunogenicity and Efficacy of a Single Dose of ChAdOx1 MERS Vaccine Candidate in Dromedary Camels
Authors: Alharbi Naif Khalaf , Qasim Ibrahim , Almasoud Abdulrahman , Aljami Haya A. , Alenazi Mohamed W. , Alhafufi Ali , Aldibasi Omar S. , Hashem Anwar M. , Kasem Samy , Albrahim Raed , Aldubaib Musaad , Almansour Ali , Temperton Nigel J. , Kupke Alexandra , Becker Stephan , Abu-obaidah Ali , Alkarar Ali , Yoon In-Kyu , Azhar Esam , Lambe Teresa , Bayoumi Faisal , Aldowerij Ali , Ibrahim Osman H. , Gilbert Sarah C. , Balkhy Hanan H.
Published: November 2019

MERS-CoV seronegative and seropositive camels received a single intramuscular dose of ChAdOx1 MERS, a replication-deficient adenoviral vectored vaccine expressing MERS-CoV spike protein, with further groups receiving control vaccinations. Infectious camels with active naturally acquired MERS-CoV infection, were co-housed with the vaccinated camels at a ratio of 1:2 (infected:vaccinated); nasal discharge and virus titres were monitored for 14 days. Overall, the vaccination reduced virus shedding and nasal discharge (p = 0.0059 and p = 0.0274, respectively). Antibody responses in seropositive camels were enhancedby the vaccine; these camels had a higher average age than seronegative. Older seronegative camels responded more strongly to vaccination than younger animals; and neutralising antibodies were detected in nasal swabs. Further work is required to optimise vaccine regimens for younger seronegative camels.
Learning leads to bounded rationality and the evolution of cognitive bias in public goods games
Authors: Leimar Olof , McNamara John M.
Published: November 2019

In social interactions, including cooperation and conflict, individuals can adjust their behaviour over the shorter term through learning within a generation, and natural selection can change behaviour over the longer term of many generations. Here we investigate the evolution of cognitive bias by individuals investing into a project that delivers joint benefits. For members of a group that learn how much to invest using the costs and benefits they experience in repeated interactions, we show that overestimation of the cost of investing can evolve. The bias causes individuals to invest less into the project. Our explanation is that learning responds to immediate rather than longer-term rewards. There are thus cognitive limitations in learning, which can be seen as bounded rationality. Over a time horizon of several rounds of interaction, individuals respond to each other’s investments, for instance by partially compensating for another’s shortfall. However, learning individuals fail to strategically take into account that social partners respond in this way. Learning instead converges to a one-shot Nash equilibrium of a game with perceived rewards as payoffs. Evolution of bias can then compensate for the cognitive limitations of learning.
The use of canid tooth marks on bone for the identification of livestock predation
Authors: Yravedra José , Maté-González Miguel Ángel , Courtenay Lloyd A. , González-Aguilera Diego , Fernández Maximiliano Fernández
Published: November 2019

Historically wolves and humans have had a conflictive relationship which has driven the wolf to extinction in some areas across Northern America and Europe. The last decades have seen a rise of multiple government programs to protect wolf populations. Nevertheless, these programs have been controversial in rural areas, product of the predation of livestock by carnivores. As a response to such issues, governments have presented large scale economic plans to compensate the respected owners. The current issue lies in the lack of reliable techniques that can be used to detect the predator responsible for livestock predation. This has led to complications when obtaining subsidies, creating conflict between landowners and government officials. The objectives of this study therefore are to provide a new alternative approach to differentiating between tooth marks of different predators responsible for livestock predation. Here we present the use of geometric morphometrics and Machine Learning algorithms to discern between different carnivores through in depth analysis of the tooth marks they leave on bone. These results present high classification rates with up to 100% accuracy in some cases, successfully differentiating between wolves, dogs and fox tooth marks.
Human Health Risk Assessment associated with contaminants in the finest fraction of sidewalk dust collected in proximity to trafficked roads
Authors: Adamiec Ewa , Jarosz-Krzemińska Elżbieta
Published: November 2019

The objective of the study was to determine concentration of metals in sidewalk dust collected in close vicinity to heavily congested roads in Poland in order to assess non-carcinogenic and carcinogenic health risk for both children and adults associated with the ingestion, dermal contact and inhalation of sidewalk dust. Results revealed that sidewalk dust from Warsaw, Krakow, Wroclaw and Opole is heavily contaminated especially with Sb, Se, Cd, Cu, Zn, Pb, considered as indicators of traffic emission. Hazardous indices determined for different exposure pathways indicated that the greatest health risk for both children and adults is associated with the ingestion of sidewalk dust. Carcinogenic risk associated with the ingestion of sidewalk dust by children, calculated for As, Cd, Ni and Pb exceeded safe level of 1 × 10−4 in all cities except for Warsaw. Non-carcinogenic risk of ingestion for children was two orders of magnitude higher than dermal risk and four to five orders of magnitude higher than risk of inhalation. Non-carcinogenic risk associated with the ingestion of sidewalk dust by adults is comparable with dermal contact risk and five orders of magnitude higher when inhalation risk.
Species-wide Metabolic Interaction Network for Understanding Natural Lignocellulose Digestion in Termite Gut Microbiota
Authors: Kundu Pritam , Manna Bharat , Majumder Subham , Ghosh Amit
Published: November 2019

The structural complexity of lignocellulosic biomass hinders the extraction of cellulose, and it has remained a challenge for decades in the biofuel production process. However, wood-feeding organisms like termite have developed an efficient natural lignocellulolytic system with the help of specialized gut microbial symbionts. Despite having an enormous amount of high-throughput metagenomic data, specific contributions of each individual microbe to achieve this lignocellulolytic functionality remains unclear. The metabolic cross-communication and interdependence that drives the community structure inside the gut microbiota are yet to be explored. We have contrived a species-wide metabolic interaction network of the termite gut-microbiome to have a system-level understanding of metabolic communication. Metagenomic data of Nasutitermes corniger have been analyzed to identify microbial communities in different gut segments. A comprehensive metabolic cross-feeding network of 205 microbes and 265 metabolites was developed using published experimental data. Reconstruction of inter-species influence network elucidated the role of 37 influential microbes to maintain a stable and functional microbiota. Furthermore, in order to understand the natural lignocellulose digestion inside N. corniger gut, the metabolic functionality of each influencer was assessed, which further elucidated 15 crucial hemicellulolytic microbes and their corresponding enzyme machinery.
Changes in ventricular depolarisation vectors during exercise caused by regional myocardial ischaemia
Authors: Vellani Cameruddin W. , Hashmi Satwat , Mahmud Sadia , Yusuf Mohammad , Awan Safia , Kazmi Khawar
Published: November 2019

Research at the Aga Khan University for several years has been directed to find a reliable, low-cost, portable, non-invasive method for identification of coronary artery disease, its location and extent. A new method has been devised to measure the magnitude and direction of cardiac electrical vectors in three perpendicular planes during physical exercise to identify reduction in myocardial excitability as the electrophysiological marker of hypoxia. This report shows that changes in electrical forces due to exercise-induced regional hypoxia serve as indicators of reversible myocardial ischaemia. Changes in the magnitude and direction of vectors at stages of the Bruce protocol were measured in healthy volunteers, and patients undergoing the same exercise protocol for distribution of a radioactive tracer injected intravenously at peak exercise and after recovery (myocardial perfusion scan). Alterations in the magnitude and direction of resultant vectors during exercise were scored to enable analysis. Analysis identified slow progression of myocardial depolarisation as the electrophysiological marker of regional hypoxia relative to physical work. Compared with myocardial perfusion scan the sensitivity and specificity of electrical vectors for identification of ischaemia were 88% and 71%, respectively. Accuracy of ischaemia shown by electrical vectors is being assessed in patients undergoing elective coronary angiography.
Freezing method for rock cross-cut coal uncovering I: Mechanical properties of a frozen coal seam for preventing outburst
Authors: Yue Jiwei , Yue Gaowei , Wang Zhaofeng , Li Minmin , Wang Binbin , An Fenghua
Published: November 2019

A comprehensive technology is proposed to realize fast and safe rock cross-cut coal uncovering (RCCCU) based on artificial freezing engineering method. This comprehensive technology includes four steps, namely, drilling a borehole, wetting the coal body by water injection, gas drainage and freezing the coal seam by liquid nitrogen injection. In this paper, the compressive strength, tensile strength and shear strength of frozen coal specimens are tested to obtain the mechanical parameters of the specimen. Then, for RCCCU under freezing temperatures, the outburst prevention effects are calculated and quantitatively analysed with regard to three aspects, namely, the enhancement of coal the mechanical properties, the reduction in the coefficient of outburst hazard (COH) in the distressed zone and the reduction in the interfacial elastic energy ratio (IEER) between the coal seam and the roof/floor. The results show that a considerable improvement in the mechanical properties of frozen coal and that the coal mechanical parameters, such as the compressive strength and the tensile strength, increase linearly with decreasing temperature. The coefficient of outburst hazard in the distressed zone decreases rapidly and drops from above 0.8 to below 0.3. The interfacial elastic energy ratio is greatly reduced from dozens of times of that of the roof/floor before freezing to several times of that of the roof/floor after freezing, which effectively weakens the sudden change of the elastic energy at the coal-rock interface.
Feline bocavirus-1 associated with outbreaks of hemorrhagic enteritis in household cats: potential first evidence of a pathological role, viral tropism and natural genetic recombination
Authors: Piewbang Chutchai , Kasantikul Tanit , Pringproa Kidsadagon , Techangamsuwan Somporn
Published: November 2019

Feline bocavirus-1 (FBoV-1) was identified in cats from different households with hemorrhagic enteritis during outbreaks of an unusual clinical presentation of feline panleukopenia virus (FPLV) in Thailand. Use of polymerase chain reaction revealed the presence of the FBoV-1 DNA in several tissues, suggesting hematogenous viremia, with the viral nucleic acid, detected by in situ hybridization (ISH), was localized in intestinal cells and vascular endothelium of intestinal mucosa and serosa, and in necrosis areas primarily in various lymph nodes while FPLV-immunohistochemical analysis revealed viral localization only in cryptal cells, neurons, and limited to leukocytes in the mesenteric lymph node. Full-length coding genome analysis of the Thai FBoV-1 strains isolated from moribund cats revealed three distinct strains with a high between-strain genetic diversity, while genetic recombination in one of the three FBoV-1 strains within the NS1 gene. This is the first report identifying natural genetic recombination of the FBoV-1 and describing the pathology and viral tropism of FBoV-1 infection in cats. Although the role of FBoV-1 associated with systemic infection of these cats remained undetermined, a contributory role of enteric infection of FBoV-1 is possible. Synergistic effects of dual infection with FPLV and FBoV-1 are hypothesized, suggesting more likely severe clinical presentations.
Impregnation of poly(L-lactide-ran-δ-valerolactone) with essential bark oil using supercritical carbon dioxide
Authors: Tsutsumi Chikara , Manabe Souta , Nakayama Susumu , Nakayama Yuushou , Shiono Takeshi
Published: November 2019

This work studied the incorporation of essential bark oil from Thujopsis dolabrata var. hondae, which is known to repel various insects, in poly(L-lactide-ran-δ-valerolactone) [poly(L-LA-ran-VL)] using supercritical carbon dioxide (scCO2). The poly(L-LA-ran-VL) was synthesized by first purifying the monomers by azeotropic distillation with benzene, followed by polymerization with Sn(oct)2 using the same equipment, representing an efficient one-pot process. The copolymerization of L-LA with VL using this technique at a feed ratio of 90/10 mol/mol gave poly(L-LA-ran-VL) (91/9) with a molecular weight of 6.48 × 104 g/mol and a high yield of 74.9%. Products with molecular weights over 5.0 × 104 g/mol were obtained at L-LA feed proportions of 70 to 90%. Impregnation trials were conducted between 40 and 120 °C at 14 MPa for 3 h. The oil content of a 73/27 specimen was found to increase significantly during processing at 100 or 120 °C. During enzymatic degradation with proteinase K, the 91/9 specimen showed the fastest degradation rate. Although the 71/29 sample was slowly hydrolyzed in a phosphate buffer at pH 7.0, the release of oil vapor from this material was slightly higher than that from the 91/9 specimen, and the vapor release rate continuously increased throughout the hydrolysis process.
Association of NCF1 polymorphism with systemic lupus erythematosus and systemic sclerosis but not with ANCA-associated vasculitis in a Japanese population
Authors: Yokoyama Nozomi , Kawasaki Aya , Matsushita Takashi , Furukawa Hiroshi , Kondo Yuya , Hirano Fumio , Sada Ken-ei , Matsumoto Isao , Kusaoi Makio , Amano Hirofumi , Nagaoka Shouhei , Setoguchi Keigo , Nagai Tatsuo , Shimada Kota , Sugii Shoji , Hashimoto Atsushi , Matsui Toshihiro , Okamoto Akira , Chiba Noriyuki , Suematsu Eiichi , Ohno Shigeru , Katayama Masao , Migita Kiyoshi , Kono Hajime , Hasegawa Minoru , Kobayashi Shigeto , Yamada Hidehiro , Nagasaka Kenji , Sugihara Takahiko , Yamagata Kunihiro , Ozaki Shoichi , Tamura Naoto , Takasaki Yoshinari , Hashimoto Hiroshi , Makino Hirofumi , Arimura Yoshihiro , Harigai Masayoshi , Sato Shinichi , Sumida Takayuki , Tohma Shigeto , Takehara Kazuhiko , Tsuchiya Naoyuki
Published: November 2019

Genome-wide association studies of systemic lupus erythematosus (SLE) in Chinese and Korean populations demonstrated strong association of single nucleotide polymorphisms (SNPs) located in theGTF2I-NCF1region, rs73366469 (GTF2I), rs117026326 (GTF2I), rs80346167(GTF2IRD1) and rs201802880 (NCF1). This region has also been associated with susceptibility to Sjögren syndrome and rheumatoid arthritis; however, association studies with systemic sclerosis (SSc) and ANCA-associated vasculitis (AAV) have not been reported. Here we made an attempt to confirm their associations with SLE in the Japanese population, to find the primarily associated SNP, and to investigate whether these SNPs are also associated with susceptibility to SSc and AAV. By genotyping these four SNPs on 842 SLE, 467 SSc, 477 AAV patients and 934 healthy controls, striking association was confirmed in Japanese SLE. In addition, these SNPs were significantly associated with susceptibility to SSc, but not with AAV. Conditional logistic regression analysis revealed that the association ofNCF1rs201802880, a missense SNP encoding p.Arg90His, can account for the association of other SNPs by linkage disequilibrium. These results suggested thatGTF2I-NCF1region is associated with susceptibility to multiple autoimmune rheumatic diseases but not with AAV, and the primarily associated variant may be the missense SNP inNCF1.
A robust, hand-powered, instrument-free sample preparation system for point-of-care pathogen detection
Authors: Zhao Fei , Lee Eun Yeong , Noh Geun Su , Shin Jaehyup , Liu Huifang , Qiao Zhen , Shin Yong
Published: November 2019

Here, we describe a simple, universal protocol for use in nucleic acid testing-based pathogen diagnostics, which requires only hand-powered sample preparation, including the processes of pathogen enrichment and nucleic acid isolation. The protocol uses low-cost amine-functionalized diatomaceous earth with a 1-μm Teflon filter as a reaction matrix in both stages of the process, using homobifunctional imidoesters. Using a simple syringe as a pump, the capture efficiency for a large sample volume (<50 mL) was enhanced by up to 98.3%, and the detection limit was 1 CFU/mL, 100-fold better than that of common commercial nucleic acid isolation kit. This protocol can also be combined with commercialized 96-well filter plates for robust sample preparation. Our proposed system is robust, simple, low-cost, universal, and rapid (taking <20 min), and it works regardless of the ambient environment and sample pretreatment, requiring no electricity or instruments. Its benefits include the simplicity of producing its components and its ease of operation, and it can be readily integrated with other assays for point-of-care diagnostics.
Author Correction: Label-free detection of nanoparticles using depth scanning correlation interferometric microscopy
Authors: Aygun Ugur , Urey Hakan , Yalcin Ozkumur Ayca
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Intermittent restraint stress induces circadian misalignment in the mouse bladder, leading to nocturia
Authors: Ihara Tatsuya , Nakamura Yuki , Mitsui Takahiko , Tsuchiya Sachiko , Kanda Mie , Kira Satoru , Nakagomi Hiroshi , Sawada Norifumi , Kamiyama Manabu , Shigetomi Eiji , Shinozaki Youichi , Yoshiyama Mitsuharu , Nakao Atsuhito , Koizumi Schuichi , Takeda Masayuki
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.