bluuebunny/crossref_metadata_2025 huggingface dataset:
Archaean Plate Tectonics in the North Atlantic Craton of West Greenland Revealed by Well-Exposed Horizontal Crustal Tectonics, Island Arcs and Tonalite-Trondhjemite-Granodiorite Complexes
Authors: Garde Adam Andreas , Windley Brian Frederick , Kokfelt Thomas Find , Keulen Nynke
Published: December 2020

The 700 km-long North Atlantic Craton (NAC) in West Greenland is arguably the best exposed and most continuous section of Eo-to Neoarchaean crust on Earth. This allows a close and essential correlation between geochemical and isotopic data and primary, well-defined and well-studied geological relationships. The NAC is therefore an excellent and unsurpassed stage for the ongoing controversial discussion about uniformitarian versus non-uniformitarian crustal evolution in the Archaean. The latest research on the geochemistry, structural style, and Hf isotope geochemistry of tonalite-trondhjemite-granodiorite (TTG) complexes and their intercalated mafic to intermediate volcanic belts strongly supports previous conclusions that the NAC formed by modern-style plate tectonic processes with slab melting of wet basaltic oceanic crust in island arcs and active continental margins. New studies of the lateral tectonic convergence and collision between juvenile belts in the NAC corroborate this interpretation. Nevertheless, it has repeatedly been hypothesised that the Earth’s crust did not develop by modern-style, subhorizontal plate tectonics before 3.0 Ga, but by vertical processes such as crustal sinking and sagduction, and granitic diapirism with associated dome-and-keel structures. Many of these models are based on supposed inverted crustal density relations, with upper Archaean crust dominated by heavy mafic ridge-lavas and island arcs, and lower Archaean crust mostly consisting of felsic, supposedly buoyant TTGs. Some of them stem from older investigations of upper-crustal Archaean greenstone belts particularly in the Dharwar craton, the Slave and Superior provinces and the Barberton belt. These interpreted interactions between these upper and lower crustal rocks are based on the apparent down-dragged greenstone belts that wrap around diapiric granites. However, in the lower crustal section of the NAC, there is no evidence of any low-density granitic diapirs or heavy, downsagged or sagducted greenstone belts. Instead, the NAC contains well-exposed belts of upper crustal, arc-dominant greenstone belts imbricated and intercalated by well-defined thrusts with the protoliths of the now high-grade TTG gneisses, followed by crustal shortening mainly by folding. This shows us that the upper and lower Archaean crustal components did not interact by vertical diapirism, but by subhorizontal inter-thrusting and folding in an ambient, mainly convergent plate tectonic regime.
L2 Vocabulary Teaching by Social Robots: The Role of Gestures and On-Screen Cues as Scaffolds
Authors: Demir-Lira Ö. Ece , Kanero Junko , Oranç Cansu , Koşkulu Sümeyye , Franko Idil , Göksun Tilbe , Küntay Aylin C.
Published: December 2020

Social robots are receiving an ever-increasing interest in popular media and scientific literature. Yet, empirical evaluation of the educational use of social robots remains limited. In the current paper, we focus on how different scaffolds (co-speech hand gestures vs. visual cues presented on the screen) influence the effectiveness of a robot second language (L2) tutor. In two studies, Turkish-speaking 5-year-olds (n = 72) learned English measurement terms (e.g., big, wide) either from a robot or a human tutor. We asked whether (1) the robot tutor can be as effective as the human tutor when they follow the same protocol, (2) the scaffolds differ in how they support L2 vocabulary learning, and (3) the types of hand gestures affect the effectiveness of teaching. In all conditions, children learned new L2 words equally successfully from the robot tutor and the human tutor. However, the tutors were more effective when teaching was supported by the on-screen cues that directed children's attention to the referents of target words, compared to when the tutor performed co-speech hand gestures representing the target words (i.e., iconic gestures) or pointing at the referents (i.e., deictic gestures). The types of gestures did not significantly influence learning. These findings support the potential of social robots as a supplementary tool to help young children learn language but suggest that the specifics of implementation need to be carefully considered to maximize learning gains. Broader theoretical and practical issues regarding the use of educational robots are also discussed.
PAS Kinase: A Nutrient and Energy Sensor “Master Key” in the Response to Fasting/Feeding Conditions
Authors: Hurtado-Carneiro Verónica , Pérez-García Ana , Alvarez Elvira , Sanz Carmen
Published: December 2020

The protein kinase with PAS domains (PASK) is a nutrient and energy sensor located in the cells of multiple organs. Many of the recent findings for understanding PASK functions in mammals have been reported in studies involving PASK-deficient mice. This minireview summarizes the PASK role in the control of fasting and feeding responses, focusing especially on the hypothalamus and liver. In 2013, PASK was identified in the hypothalamic areas involved in feeding behavior, and its expression was regulated under fasting/refeeding conditions. Furthermore, it plays a role in coordinating the activation/inactivation of the hypothalamic energy sensors AMPK and mTOR/S6K1 pathways in response to fasting. On the other hand, PASK deficiency prevents the development of obesity and non-alcoholic fatty liver in mice fed with a high-fat diet. This protection is explained by the re-establishment of several high-fat diet metabolic alterations produced in the expression of hepatic transcription factors and key enzymes that control the main metabolic pathways involved in maintaining metabolic homeostasis in fasting/feeding responses. This minireview covers the effects of PASK inactivation in the expression of certain transcription factors and target enzymes in several metabolic pathways under situations such as fasting and feeding with either a standard or a high-fat diet.
Participatory Modeling With QUICKScan to Shape Sustainable Urban Development
Authors: Verweij Peter , Cormont Anouk , Eupen Michiel van , Winograd Manuel , Hardoy Jorgelina
Published: December 2020

Current spatial planning methods are often technocratic, slow, fail to use the right kind of evidence or do not involve (all) the actors needed to create support and consensus. We present a method that facilitates the use of evidence (data) in participatory spatial planning processes, resulting in a joint understanding of the most important causalities, as a means to build capacity across actors. QUICKScan is a participatory modeling method that links stakeholder- and decision maker knowledge and preferences to available spatial and spatio-statistical data, and is designed for group use in a multi-stakeholder workshop setting. We describe four urban QUICKScan applications, that vary in objective, scale and institutional setting. The most critical in organizing a QUICKScan session is to: (i) include crucial participants in a single plenary workshop (decision maker, local data expert, and local thematic experts), (ii) create an open atmosphere in which each and everyone's opinion is treated equally, (iii) dialogue is more important than an abundance of detailed spatial data, and (iv) start with simple modeling rules and iterate often while expanding the set of rules and trying out alternatives.
Soil Physical Quality and Relationship to Changes in Termite Community in Northwestern Colombian Amazon
Authors: Duran-Bautista Ervin Humprey , Muñoz Chilatra Yolima , Galindo Juan Diego , Ortiz Tania Alexandra , Bermúdez María Fernanda
Published: December 2020

Conversion from Amazon forest to low-management pasture or agriculture causes not only degradation of aboveground vegetation but also negative changes in soil properties and ecosystem services. This study aimed to evaluate the impact of physical soil degradation on termite community changes in three contrasting land uses (natural regeneration, rubber plantations, and silvopastoral systems). Soil physical quality was assessed through a set of physical variables, such as bulk density, porosity, soil macro-aggregation state, Visual Evaluation of Soil Structure (VESS) and penetration resistance, which were summarized in an overall synthetic indicator of physical quality. Besides, transects of 20 × 2 m were established in each land use; each transect was divided into four sections of 5 m to search and collect termites during 1 hour in each section; likewise, termites were collected from blocks of soil 25 × 25 × 10 cm (length, width, and depth, respectively) adapted from the Tropical Soil Biology and Fertility (TSBF) method. In total, 60 transects were evaluated, 20 in each land use. A total of 41 species were collected across the three land uses evaluated: natural regeneration presented 60% of the collected species (25 species), silvopastoral systems 53% (22 species), and rubber plantations 39% (16 species). Additionally, composition species from the silvopastoral, agroforestry systems, and natural regeneration were different, and a close association between these last land uses was observed. Soil physical characteristics showed significant variations between land uses. The rubber plantations presented lowest values of soil physical quality, while the natural regeneration showed high soil physical quality. These changes affected termite community and lead to changes in its composition with disproportionate loss of some species; however, there are some that can acclimate well to the decline in the soil physical quality.
Machine Learning Prediction of Crossbred Pig Feed Efficiency and Growth Rate From Single Nucleotide Polymorphisms
Authors: Tusell Llibertat , Bergsma Rob , Gilbert Hélène , Gianola Daniel , Piles Miriam
Published: December 2020

This research assessed the ability of a Support Vector Machine (SVM) regression model to predict pig crossbred (CB) performance from various sources of phenotypic and genotypic information for improving crossbreeding performance at reduced genotyping cost. Data consisted of average daily gain (ADG) and residual feed intake (RFI) records and genotypes of 5,708 purebred (PB) boars and 5,007 CB pigs. Prediction models were fitted using individual PB genotypes and phenotypes (trn.1); genotypes of PB sires and average of CB records per PB sire (trn.2); and individual CB genotypes and phenotypes (trn.3). The average of CB offspring records was the trait to be predicted from PB sire’s genotype using cross-validation. Single nucleotide polymorphisms (SNPs) were ranked based on the Spearman Rank correlation with the trait. Subsets with an increasing number (from 50 to 2,000) of the most informative SNPs were used as predictor variables in SVM. Prediction performance was the median of the Spearman correlation (SC, interquartile range in brackets) between observed and predicted phenotypes in the testing set. The best predictive performances were obtained when sire phenotypic information was included in trn.1 (0.22 [0.03] for RFI with SVM and 250 SNPs, and 0.12 [0.05] for ADG with SVM and 500–1,000 SNPs) or when trn.3 was used (0.29 [0.16] with Genomic best linear unbiased prediction (GBLUP) for RFI, and 0.15 [0.09] for ADG with just 50 SNPs). Animals from the last two generations were assigned to the testing set and remaining animals to the training set. Individual’s PB own phenotype and genotype improved the prediction ability of CB offspring of young animals for ADG but not for RFI. The highest SC was 0.34 [0.21] and 0.36 [0.22] for RFI and ADG, respectively, with SVM and 50 SNPs. Predictive performance using CB data for training leads to a SC of 0.34 [0.19] with GBLUP and 0.28 [0.18] with SVM and 250 SNPs for RFI and 0.34 [0.15] with SVM and 500 SNPs for ADG. Results suggest that PB candidates could be evaluated for CB performance with SVM and low-density SNP chip panels after collecting their own RFI or ADG performances or even earlier, after being genotyped using a reference population of CB animals.
Signatures of Selection in Composite Vrindavani Cattle of India
Authors: Singh Akansha , Mehrotra Arnav , Gondro Cedric , Romero Andrea Renata da Silva , Pandey Ashwni Kumar , Karthikeyan A. , Bashir Aamir , Mishra B. P. , Dutt Triveni , Kumar Amit
Published: December 2020

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.
Clinical Utility of Exome Sequencing and Reinterpreting Genetic Test Results in Children and Adults With Epilepsy
Authors: Jiang Yong-li , Song Changgeng , Wang Yuanyuan , Zhao Jingjing , Yang Fang , Gao Qiong , Leng Xiuxiu , Man Yulin , Jiang Wen
Published: December 2020

The clinical utility of genetic testing for epilepsy has been enhanced with the advancement of next-generation sequencing (NGS) technology along with the rapid updating of publicly available databases. The aim of this study was to evaluate the diagnostic yield of NGS and assess the value of reinterpreting genetic test results in children and adults with epilepsy. We performed genetic testing on 200 patients, including 82 children and 118 adults. The results were classified into three categories: positive, inconclusive, or negative. The reinterpretation of inconclusive results was conducted in April 2020. Overall, we identified disease-causing variants in 12% of the patients in the original analysis, and 14.5% at reinterpretation. The diagnostic yield for adults with epilepsy was similar to that for children (11 vs. 19.5%, p = 0.145). After reinterpretation, 9 of the 86 patients who initially had inconclusive results obtained a clinically significant change in diagnosis. Among these nine revised cases, five obtained positive diagnoses, representing a diagnosis rate of 5.8% (5/86). Manual searches for additional evidence of pathogenicity for candidate variants and updated patient clinical information were the main reasons for diagnostic reclassification. This study emphasizes the diagnostic potential of combining NGS and reinterpretation of inconclusive genetic test reports in children and adults with epilepsy.
Predicting Rice Heading Date Using an Integrated Approach Combining a Machine Learning Method and a Crop Growth Model
Authors: Chen Tai-Shen , Aoike Toru , Yamasaki Masanori , Kajiya-Kanegae Hiromi , Iwata Hiroyoshi
Published: December 2020

Accurate prediction of heading date under various environmental conditions is expected to facilitate the decision-making process in cultivation management and the breeding process of new cultivars adaptable to the environment. Days to heading (DTH) is a complex trait known to be controlled by multiple genes and genotype-by-environment interactions. Crop growth models (CGMs) have been widely used to predict the phenological development of a plant in an environment; however, they usually require substantial experimental data to calibrate the parameters of the model. The parameters are mostly genotype-specific and are thus usually estimated separately for each cultivar. We propose an integrated approach that links genotype marker data with the developmental genotype-specific parameters of CGMs with a machine learning model, and allows heading date prediction of a new genotype in a new environment. To estimate the parameters, we implemented a Bayesian approach with the advanced Markov chain Monte-Carlo algorithm called the differential evolution adaptive metropolis and conducted the estimation using a large amount of data on heading date and environmental variables. The data comprised sowing and heading dates of 112 cultivars/lines tested at 7 locations for 14 years and the corresponding environmental variables (day length and daily temperature). We compared the predictive accuracy of DTH between the proposed approach, a CGM, and a single machine learning model. The results showed that the extreme learning machine (one of the implemented machine learning models) was superior to the CGM for the prediction of a tested genotype in a tested location. The proposed approach outperformed the machine learning method in the prediction of an untested genotype in an untested location. We also evaluated the potential of the proposed approach in the prediction of the distribution of DTH in 103 F2segregation populations derived from crosses between a common parent, Koshihikari, and 103 cultivars/lines. The results showed a high correlation coefficient (ca. 0.8) of the 10, 50, and 90th percentiles of the observed and predicted distribution of DTH. In this study, the integration of a machine learning model and a CGM was better able to predict the heading date of a new rice cultivar in an untested potential environment.
Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
Authors: Yu Zhe , Zheng Chunfang , Albert Victor A. , Sankoff David
Published: December 2020

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.
Mycobacterium bovis Bacille-Calmette-Guérin Infection Aggravates Atherosclerosis
Authors: Huaman Moises A. , Qualls Joseph E. , Jose Shinsmon , Schmidt Stephanie M. , Moussa Anissa , Kuhel David G. , Konaniah Eddy , Komaravolu Ravi K. , Fichtenbaum Carl J. , Deepe George S. , Hui David Y.
Published: December 2020

Tuberculosis has been associated with increased risk of atherosclerotic cardiovascular disease. To examine whether mycobacterial infection exacerbates atherosclerosis development in experimental conditions, we infected low-density lipoprotein receptor knockout (Ldlr-/-) mice with Mycobacterium bovis Bacille-Calmette-Guérin (BCG), an attenuated strain of the Mycobacterium tuberculosis complex. Twelve-week old male Ldlr-/- mice were infected with BCG (0.3–3.0x106 colony-forming units) via the intranasal route. Mice were subsequently fed a western-type diet containing 21% fat and 0.2% cholesterol for up to 16 weeks. Age-matched uninfected Ldlr-/- mice fed with an identical diet served as controls. Atherosclerotic lesions in aorta were examined using Oil Red O staining. Changes induced by BCG infection on the immunophenotyping profile of circulating T lymphocytes and monocytes were assessed using flow cytometry. BCG infection increased atherosclerotic lesions in en face aorta after 8 weeks (plaque ratio; 0.021±0.01 vs. 0.013±0.01; p = 0.011) and 16 weeks (plaque ratio, 0.15±0.13 vs. 0.06±0.02; p = 0.003). No significant differences in plasma cholesterol or triglyceride levels were observed between infected and uninfected mice. Compared to uninfected mice, BCG infection increased systemic CD4/CD8 T cell ratio and the proportion of Ly6Clow non-classical monocytes at weeks 8 and 16. Aortic plaque ratios correlated with CD4/CD8 T cell ratios (Spearman’s rho = 0.498; p = 0.001) and the proportion of Ly6Clow non-classical monocytes (Spearman’s rho = 0.629; p < 0.001) at week 16. In conclusion, BCG infection expanded the proportion of CD4+ T cell and Ly6Clow monocytes, and aggravated atherosclerosis formation in the aortas of hyperlipidemic Ldlr-/- mice. Our results indicate that mycobacterial infection is capable of enhancing atherosclerosis development.
Humoral Responses and Serological Assays in SARS-CoV-2 Infections
Authors: Galipeau Yannick , Greig Matthew , Liu George , Driedger Matt , Langlois Marc-André
Published: December 2020

In December 2019, the novel betacoronavirus Severe Acute Respiratory Disease Coronavirus 2 (SARS-CoV-2) was first detected in Wuhan, China. SARS-CoV-2 has since become a pandemic virus resulting in hundreds of thousands of deaths and deep socioeconomic implications worldwide. In recent months, efforts have been directed towards detecting, tracking, and better understanding human humoral responses to SARS-CoV-2 infection. It has become critical to develop robust and reliable serological assays to characterize the abundance, neutralization efficiency, and duration of antibodies in virus-exposed individuals. Here we review the latest knowledge on humoral immune responses to SARS-CoV-2 infection, along with the benefits and limitations of currently available commercial and laboratory-based serological assays. We also highlight important serological considerations, such as antibody expression levels, stability and neutralization dynamics, as well as cross-reactivity and possible immunological back-boosting by seasonal coronaviruses. The ability to accurately detect, measure and characterize the various antibodies specific to SARS-CoV-2 is necessary for vaccine development, manage risk and exposure for healthcare and at-risk workers, and for monitoring reinfections with genetic variants and new strains of the virus. Having a thorough understanding of the benefits and cautions of standardized serological testing at a community level remains critically important in the design and implementation of future vaccination campaigns, epidemiological models of immunity, and public health measures that rely heavily on up-to-date knowledge of transmission dynamics.
Alternative Pathways of IL-1 Activation, and Its Role in Health and Disease
Authors: Pyrillou Katerina , Burzynski Laura C. , Clarke Murray C. H.
Published: December 2020

Cytokines activate or inhibit immune cell behavior and are thus integral to all immune responses. IL-1α and IL-1β are powerful apical cytokines that instigate multiple downstream processes to affect both innate and adaptive immunity. Multiple studies show that IL-1β is typically activated in macrophages after inflammasome sensing of infection or danger, leading to caspase-1 processing of IL-1β and its release. However, many alternative mechanisms activate IL-1α and IL-1β in atypical cell types, and IL-1 function is also important for homeostatic processes that maintain a physiological state. This review focuses on the less studied, yet arguably more interesting biology of IL-1. We detail the production by, and effects of IL-1 on specific innate and adaptive immune cells, report how IL-1 is required for barrier function at multiple sites, and discuss how perturbation of IL-1 pathways can drive disease. Thus, although IL-1 is primarily studied for driving inflammation after release from macrophages, it is clear that it has a multifaceted role that extends far beyond this, with various unconventional effects of IL-1 vital for health. However, much is still unknown, and a detailed understanding of cell-type and context-dependent actions of IL-1 is required to truly understand this enigmatic cytokine, and safely deploy therapeutics for the betterment of human health.
A Potent SARS-CoV-2 Neutralizing Human Monoclonal Antibody That Reduces Viral Burden and Disease Severity in Syrian Hamsters
Authors: Fagre Anna C. , Manhard John , Adams Rachel , Eckley Miles , Zhan Shijun , Lewis Juliette , Rocha Savannah M. , Woods Catherine , Kuo Karina , Liao Wuxiang , Li Lin , Corper Adam , Challa Dilip , Mount Emily , Tumanut Christine , Tjalkens Ronald B. , Aboellail Tawfik , Fan Xiaomin , Schountz Tony
Published: December 2020

The emergence of COVID-19 has led to a pandemic that has caused millions of cases of disease, variable morbidity and hundreds of thousands of deaths. Currently, only remdesivir and dexamethasone have demonstrated limited efficacy, only slightly reducing disease burden, thus novel approaches for clinical management of COVID-19 are needed. We identified a panel of human monoclonal antibody clones from a yeast display library with specificity to the SARS-CoV-2 spike protein receptor binding domain that neutralized the virus in vitro. Administration of the lead antibody clone to Syrian hamsters challenged with SARS-CoV-2 significantly reduced viral load and histopathology score in the lungs. Moreover, the antibody interrupted monocyte infiltration into the lungs, which may have contributed to the reduction of disease severity by limiting immunopathological exacerbation. The use of this antibody could provide an important therapy for treatment of COVID-19 patients.
Marine Pollution Mitigation by Waste Oils Recycling Onboard Ships: Technical Feasibility and Need for New Policy and Regulations
Authors: Mazzoccoli Michela , Altosole Marco , Vigna Veronica , Bosio Barbara , Arato Elisabetta
Published: December 2020

About 80% of the total pollution from ships is caused by operational oil discharges into the sea, often made deliberately and in violation of international rules; the main reasons can be due to cost savings or lack of adequate facilities in ports to receive waste oils. Therefore, reducing waste oil discharges is crucial for a proper protection of the marine environment. In this regard, the paper presents the preliminary feasibility of a particular waste recycling technology, aimed at obtaining marine fuel oil from sludge, through a pyrolysis process to be carried out in a small reactor onboard. The originality of the research consists in the adaptation of pyrolysis to oily waste produced by ships, since this technology is traditionally applied to solid waste and biomass. Furthermore, the plant has to be designed for operation on board the ship, therefore under very different constraints compared to traditional land plants. Although the preliminary lab tests and simulation results in the chemical process are promising enough, there are still some technical criticalities due to the energy optimization of the reactor for an efficient use onboard of the whole system. In addition, the possibility of recycling waste, directly onboard ships, is not yet covered by mandatory regulations, which is why shipowners generally still feel unmotivated to invest in such technologies.
Fabrication and Characterisation of Magnetorheological Shear Thickening Fluids
Authors: Sokolovski Vladimir , Tian Tongfei , Ding Jie , Li Weihua
Published: December 2020

In this article, a magnetorheological shear thickening fluid (MRSTF) was fabricated based on magnetorheological (MR) material and shear thickening fluid (STF). The STF was firstly fabricated as the liquid phase, and carbonyl iron particles were then mixed with the prefabricated STF to synthesise a series of MRSTFs with various iron concentrations. Then, a rheometer was used to measure their viscosities by varying the shear rate under various magnetic fields. Both static and dynamic tests were conducted to study the rheology of MRSTFs under different magnetic fields. The tested results revealed that the MRSTF showed shear thickening under zero magnetic field and MR effect with increasing applied magnetic field. It was also noted that the viscosity of the MRSTFs can be controlled by both shear rate and the applied magnetic field. The concentration of iron particles played an important role in the MRSTFs’ rheological properties. The MRSTFs with higher iron particle concentrations revealed lower shear thickening effects but higher MR effects, which means the MRSTF with higher iron concentration can be treated as an effective MR fluid. Meanwhile, the MRSTF with low iron concentration displays good shear thickening effect under weak magnetic field. To summarise the behavior of MRSTFs with various iron concentrations and under different magnetic fields, three regions were proposed to provide guidelines to design MRSTFs and assist in their applications.
Iron and Chronic Kidney Disease: Still a Challenge
Authors: Wojtaszek Ewa , Glogowski Tomasz , Malyszko Jolanta
Published: December 2020

Anemia is a clinical feature of chronic kidney disease (CKD). Most common causes are iron and erythropoietin deficiency. The last two decades have yielded significant advances in understanding iron balance's physiology, including iron trafficking and the crosstalk between iron, oxygen, and erythropoiesis. This knowledge sheds new light on the regulation and disturbance of iron homeostasis in CKD and holds the promise for developing new diagnostic and therapeutic tools to improve the management of iron disorders. Hepcidin–ferroportin axis has a central role in regulating body iron balance and coordinating communication between tissues and cells that acquire, store, and utilize iron. Recent research has revealed a bidirectional relationship between fibroblast growth factor 23 (FGF23) and iron status, anemia, and inflammation, as well as the role of erythroferrone (ERFE) in iron homeostasis. However, ERFE concentrations and actions are not well-characterized in CKD patients. Studies on ERFE in CKD are limited with slightly conflicting results. Despite general interest in iron metabolism in kidney diseases, studies on the less prevalent renal replacement therapy mode, such as peritoneal dialysis or hemodiafiltration, are scarce. Slightly more was published on hemodialysis. There are several novel options on the horizon; however, clinical data are limited. One should be aware of the potential risks and benefits of the novel, sophisticated therapies. An inhibition of hepcidin on the different pathways might be also a viable adjunctive therapeutic option in other clinical situations.
Evaluating SARS-CoV-2 Seroconversion Following Relieve of Confinement Measures
Authors: Gonçalves Juliana , Sousa Rita L. , Jacinto Maria J. , Silva Daniela A. , Paula Filipe , Sousa Rute , Zahedi Sara , Carvalho Joana , Cabral M. Guadalupe , Costa Manuela , Branco Jaime C. , Canhão Helena , Alves José D. , Rodrigues Ana M. , Soares Helena
Published: December 2020

Seroprevalence studies are crucial both for estimating the prevalence of SARS-CoV-2 exposure and to provide a measure for the efficiency of the confinement measures. Portuguese universities were closed on March 16th 2020, when Portugal only registered 62 SARS-CoV-2 infection cases per million. We have validated a SARS-CoV-2 ELISA assay to a stabilized full-length spike protein using 216 pre-pandemic and 19 molecularly diagnosed SARS-CoV-2 positive individual's samples. At NOVA University of Lisbon, presential work was partially resumed on May 25th with staggered schedules. From June 15th to 30th, 3–4 weeks after the easing of confinement measures, we screened 1,636 collaborators of NOVA university of Lisbon for the presence of SARS-CoV-2 spike specific IgA and IgG antibodies. We found that spike-specific IgG in 50 of 1,636 participants (3.0%), none of which had anti-spike IgA antibodies. As participants self-reported as asymptomatic or paucisymptomatic, our study also provides a measurement of the prevalence of asymptomatic/paucisymptomatic SARS-CoV-2 infections. Our study suggests that essential workers have a 2-fold increase in viral exposure, when compared to non-essential workers that observed confinement. Additional serological surveys in different population subgroups will paint a broader picture of the effect of the confinement measures in the broader community.
Comparative Genomic Analysis of Ochratoxin A Biosynthetic Cluster in Producing Fungi: New Evidence of a Cyclase Gene Involvement
Authors: Ferrara Massimo , Gallo Antonia , Perrone Giancarlo , Magistà Donato , Baker Scott E.
Published: December 2020

The widespread use of Next-Generation Sequencing has opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences and identifying gene clusters for known secondary metabolites as well as novel cryptic ones. However, most of these clusters still need to be examined in detail to completely understand the pathway steps and the regulation of the biosynthesis of metabolites. Genome sequencing approach led to the identification of the biosynthetic genes cluster of ochratoxin A (OTA) in a number of producing fungal species. Ochratoxin A is a potent pentaketide nephrotoxin produced byAspergillusandPenicilliumspecies and found as widely contaminant in food, beverages and feed. The increasing availability of several new genome sequences of OTA producer species in JGI Mycocosm and/or GenBank databanks led us to analyze and update the gene cluster structure in 19Aspergillusand 2PenicilliumOTA producing species, resulting in a well conserved organization of OTA core genes among the species. Furthermore, our comparative genome analyses evidenced the presence of an additional gene, previously undescribed, located between the polyketide and non-ribosomal synthase genes in the cluster of all the species analyzed. The presence of a SnoaL cyclase domain in the sequence of this gene supports its putative role in the polyketide cyclization reaction during the initial steps of the OTA biosynthesis pathway. The phylogenetic analysis showed a clustering of OTA SnoaL domains in accordance with the phylogeny of OTA producing species at species and section levels. The characterization of this new OTA gene, its putative role and its expression evidence in three important representative producing species, are reported here for the first time.
Serotype Is Associated With High Rate of Colistin Resistance Among Clinical Isolates of Salmonella
Authors: Luo Qixia , Wang Yuan , Fu Hao , Yu Xiao , Zheng Beiwen , Chen Yunbo , Berglund Björn , Xiao Yonghong
Published: December 2020

To investigate the prevalence, probable mechanisms and serotype correlation of colistin resistance in clinical isolates of Salmonella from patients in China, Salmonella isolates were collected from fecal and blood samples of patients. In this study, 42.8% (136/318) clinical isolated Salmonella were resistant to colistin. MIC distribution for colistin at serotype level among the two most prevalent serotypes originating from humans in China indicated that Salmonella Enteritidis (83.9% resistance, 125/149) were significantly less susceptible than Salmonella Typhimurium (15.3% resistance, 9/59, P < 0.01). mcr genes and mutations in PmrAB confer little for rate of colistin resistant Salmonella isolated from human patients. Phylogenetic tree based on core-genome single nucleotide polymorphisms (SNPs) was separately by the serotypes and implied a diffused distribution of MICs in the same serotype isolates. Relatvie expression levels of colistin resistant related pmr genes were significantly higher in non-mcr colistin resistant S. Typhimurium than in colistin sensitive S. Typhimurium, but no discernable differences between colistin resistant and sensitive S. Enteritidis, indicating a different mechanism between colistin resistant S. Typhimurium and S. Enteritidis. In conclusion, colistin susceptibility and colistin resistant mechanism of clinical isolated Salmonella were closely associated with specific serotypes, at least in the two most prevalent serotype Enteritidis and Typhimurium. We suggest clinical microbiology laboratory interpreting Salmonella colistin MIC results in the serotype level.
Comparative Analysis of the Gut Microbial Communities of the Eurasian Kestrel (Falco tinnunculus) at Different Developmental Stages
Authors: Zhou Lei , Huo Xiaona , Liu Boyu , Wu Hui , Feng Jiang
Published: December 2020

The gut microflora play a very important role in the life of animals. Although an increasing number of studies have investigated the gut microbiota of birds in recent years, there is a lack of research work on the gut microbiota of wild birds, especially carnivorous raptors, which are thought to be pathogen vectors. There are also a lack of studies focused on the dynamics of the gut microbiota during development in raptors. In this study, 16S rRNA gene amplicon high-throughput sequencing was used to analyze the gut microbiota community composition of a medium-sized raptor, the Eurasian Kestrel (Falco tinnunculus), and to reveal stage-specific signatures in the gut microbiota of nestlings during the pre-fledging period. Moreover, differences in the gut microbiota between adults and nestlings in the same habitat were explored. The results indicated that the Eurasian Kestrel hosts a diverse assemblage of gut microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the primary phyla shared within the guts of adults and chicks. However, adults harbored higher abundances of Proteobacteria while nestlings exhibited higher abundances of Firmicutes and Actinobacteria, and consequently the majority of dominant genera observed in chicks differed from those in adults. Although no significant differences in diversity were observed across the age groups during nestling ontogeny, chicks from all growth stages harbored richer and more diverse bacterial communities than adults. In contrast, the differences in gut microbial communities between adults and younger nestlings were more pronounced. The gut microbes of the nestlings in the last growth stage were converged with those of the adults. This study provides basic reference data for investigations of the gut microbiota community structure of wild birds and deepens our understanding of the dynamics of the gut microflora during raptor development.
Nitrogen Fixation in a Changing Arctic Ocean: An Overlooked Source of Nitrogen?
Authors: von Friesen Lisa W. , Riemann Lasse
Published: December 2020

The Arctic Ocean is the smallest ocean on Earth, yet estimated to play a substantial role as a global carbon sink. As climate change is rapidly changing fundamental components of the Arctic, it is of local and global importance to understand and predict consequences for its carbon dynamics. Primary production in the Arctic Ocean is often nitrogen-limited, and this is predicted to increase in some regions. It is therefore of critical interest that biological nitrogen fixation, a process where some bacteria and archaea termed diazotrophs convert nitrogen gas to bioavailable ammonia, has now been detected in the Arctic Ocean. Several studies report diverse and active diazotrophs on various temporal and spatial scales across the Arctic Ocean. Their ecology and biogeochemical impact remain poorly known, and nitrogen fixation is so far absent from models of primary production in the Arctic Ocean. The composition of the diazotroph community appears distinct from other oceans – challenging paradigms of function and regulation of nitrogen fixation. There is evidence of both symbiotic cyanobacterial nitrogen fixation and heterotrophic diazotrophy, but large regions are not yet sampled, and the sparse quantitative data hamper conclusive insights. Hence, it remains to be determined to what extent nitrogen fixation represents a hitherto overlooked source of new nitrogen to consider when predicting future productivity of the Arctic Ocean. Here, we discuss current knowledge on diazotroph distribution, composition, and activity in pelagic and sea ice-associated environments of the Arctic Ocean. Based on this, we identify gaps and outline pertinent research questions in the context of a climate change-influenced Arctic Ocean – with the aim of guiding and encouraging future research on nitrogen fixation in this region.
Corynebacterium jeikeium Dormant Cell Formation and Photodynamic Inactivation
Authors: Shleeva Margarita , Savitsky Alexander , Kaprelyants Arseny
Published: December 2020

Pathogenic non-spore forming bacteria enter a dormant state under stressful conditions, which likely allows them to acquire resistance to various antibiotics. This work revealed the efficient formation of dormant “non-culturable” (NC) Corynebacterium jeikeium cells in stationary phase upon gradual acidification of the growth medium. Such cells were unable to form colonies and existed in a prolonged stationary phase. At an early stage of dormancy (approximately 14 days post-inoculation), dormant cells are able for resuscitation in liquid medium. However, those stored for long time in dormant state needed addition of supernatant taking from active C. jeikeium cultures for successful resuscitation. NC cells possessed low RNA synthesis and significant tolerance to antibiotics (rifampicin and vancomycin). They also accumulated free porphyrins, and 5-aminolevulinic acid addition enhanced free porphyrin accumulation which makes them potentially sensitive to photodynamic inactivation (PDI). PDI of dormant bacteria was accomplished by exposing cells to a 565 nm wavelength of light using a SOLIS-4C light-emitting diode for 60 min. This revealed that increased porphyrin concentrations were correlated with elevated PDI sensitivity. Results shown here demonstrate the potential utility of employing PDI to minimize levels of dormant, persistent corynebacteria and the C. jeikeium dormancy model developed here may be useful for finding new drugs and techniques for combatting persistent corynebacteria.
Creation of an Online Platform for Identification of Microorganisms: Peak Picking or Full-Spectrum Analysis
Authors: Starostin Konstantin V. , Demidov Evgeny A. , Ershov Nikita I. , Bryanskaya Alla V. , Efimov Vadim M. , Shlyakhtun Valeriya N. , Peltek Sergey E.
Published: December 2020

Identification of microorganisms by MALDI-TOF mass spectrometry is a very efficient method with high throughput, speed, and accuracy. However, it is significantly limited by the absence of a universal database of reference mass spectra. This problem can be solved by creating an Internet platform for open databases of protein spectra of microorganisms. Choosing the optimal mathematical apparatus is the pivotal issue for this task. In our previous study we proposed the geometric approach for processing mass spectrometry data, which represented a mass spectrum as a vector in a multidimensional Euclidean space. This algorithm was implemented in a Jacob4 stand-alone package. We demonstrated its efficiency in delimiting two closely related species of the Bacillus pumilus group. In this study, the geometric approach was realized as R scripts which allowed us to design a Web-based application. We also studied the possibility of using full spectra analysis (FSA) without calculating mass peaks (PPA), which is the logical development of the method. We used 74 microbial strains from the collections of ICiG SB RAS, UNIQEM, IEGM, KMM, and VGM as the models. We demonstrated that the algorithms based on peak-picking and analysis of complete data have accuracy no less than that of Biotyper 3.1 software. We proposed a method for calculating cut-off thresholds based on averaged intraspecific distances. The resulting database, raw data, and the set of R scripts are available online at https://icg-test.mydisk.nsc.ru/s/qj6cfZg57g6qwzN.
A Fast, Efficient and Easy to Implement Method to Purify Bacterial Pili From Lacticaseibacillus rhamnosus GG Based on Multimodal Chromatography
Authors: Dos Santos Morais Raphael , El-Kirat-Chatel Sofiane , Burgain Jennifer , Simard Blandine , Barrau Sarah , Paris Cédric , Borges Frédéric , Gaiani Claire
Published: December 2020

Pili are polymeric proteins located at the cell surface of bacteria. These filamentous proteins play a pivotal role in bacterial adhesion with the surrounding environment. They are found both in Gram-negative and Gram-positive bacteria but differ in their structural organization. Purifying these high molecular weight proteins is challenging and has certainly slowed down their characterization. Here, we propose a chromatography-based protocol, mainly relying on multimodal chromatography (core bead technology using Capto Core 700 resin), to purify sortase-dependent SpaCBA pili from the probiotic strain Lacticaseibacillus rhamnosus GG (LGG). Contrary to previously published methods, this purification protocol does not require specific antibodies nor complex laboratory equipment, including for the multimodal chromatography step, and provides high degree of protein purity. No other proteins were detectable by SDS-PAGE and the 260/280 nm ratio (∼0.6) of the UV spectrum confirmed the absence of any other co-purified macromolecules. One can obtain ∼50 μg of purified pili, starting from 1 L culture at OD600nm ≈ 1, in 2–3 working days. This simple protocol could be useful to numerous laboratories to purify pili from LGG easily. Therefore, the present work should boost specific studies dedicated to LGG SpaCBA pili and the characterization of the interactions occurring with their protein partners at the molecular level. Moreover, this straightforward purification process might be extended to the purification of sortase-dependant pili from other Gram-positive bacteria.
The fliK Gene Is Required for the Resistance of Bacillus thuringiensis to Antimicrobial Peptides and Virulence in Drosophila melanogaster
Authors: Attieh Zaynoun , Mouawad Carine , Rejasse Agnès , Jehanno Isabelle , Perchat Stéphane , Hegna Ida K. , Økstad Ole A. , Kallassy Awad Mireille , Sanchis-Borja Vincent , El Chamy Laure
Published: December 2020

Antimicrobial peptides (AMPs) are essential effectors of the host innate immune system and they represent promising molecules for the treatment of multidrug resistant microbes. A better understanding of microbial resistance to these defense peptides is thus prerequisite for the control of infectious diseases. Here, using a random mutagenesis approach, we identify the fliK gene, encoding an internal molecular ruler that controls flagella hook length, as an essential element for Bacillus thuringiensis resistance to AMPs in Drosophila. Unlike its parental strain, that is highly virulent to both wild-type and AMPs deficient mutant flies, the fliK deletion mutant is only lethal to the latter’s. In agreement with its conserved function, the fliK mutant is non-flagellated and exhibits highly compromised motility. However, comparative analysis of the fliK mutant phenotype to that of a fla mutant, in which the genes encoding flagella proteins are interrupted, indicate that B. thuringiensis FliK-dependent resistance to AMPs is independent of flagella assembly. As a whole, our results identify FliK as an essential determinant for B. thuringiensis virulence in Drosophila and provide new insights on the mechanisms underlying bacteria resistance to AMPs.