bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxogenomic assessment and genomic characterisation of Weissella cibaria strain 92 able to metabolise oligosaccharides derived from dietary fibres
Authors: Månberger Anna , Verbrugghe Phebe , Guðmundsdóttir Elísabet Eik , Santesson Sara , Nilsson Anne , Hreggviðsson Guðmundur Óli , Linares-Pastén Javier A. , Nordberg Karlsson Eva 
Published: April 2020

AbstractThe importance of the gut microbiota in human health has led to an increased interest to study probiotic bacteria. Fermented food is a source of already established probiotics, but it also offers an opportunity to discover new taxa. Four strains of Weissella sp. isolated from Indian fermented food have been genome sequenced and classified into the species W. cibaria based on whole-genome phylogeny. The genome of W. cibaria strain 92, known to utilise xylooligosaccharides and produce lactate and acetate, was analysed to identify genes for oligosaccharide utilisation. Clusters including genes involved in transportation, hydrolysis and metabolism of xylooligosaccharides, arabinooligosaccharides and β-glucosides were identified. Growth on arabinobiose and laminaribiose was detected. A 6-phospho-β-glucosidase clustered with a phosphotransferase system was found upregulated during growth on laminaribiose, indicating a mechanism for laminaribiose utilisation. The genome of W. cibaria strain 92 harbours genes for utilising the phosphoketolase pathway for the production of both acetate and lactate from pentose and hexose sugars but lacks two genes necessary for utilising the pentose phosphate pathway. The ability of W. cibaria strain 92 to utilise several types of oligosaccharides derived from dietary fibres, and produce lactate and acetate makes it interesting as a probiotic candidate for further evaluation.
Interaction of atomic systems with quantum vacuum beyond electric dipole approximation
Authors: Kosik Miriam , Burlayenko Oleksandr , Rockstuhl Carsten , Fernandez-Corbaton Ivan , Słowik Karolina 
Published: April 2020

AbstractThe photonic environment can significantly influence emission properties and interactions among atomic systems. In such scenarios, frequently the electric dipole approximation is assumed that is justified as long as the spatial extent of the atomic system is negligible compared to the spatial variations of the field. While this holds true for many canonical systems, it ceases to be applicable for more contemporary nanophotonic structures. To go beyond the electric dipole approximation, we propose and develop in this article an analytical framework to describe the impact of the photonic environment on emission and interaction properties of atomic systems beyond the electric dipole approximation. Particularly, we retain explicitly magnetic dipolar and electric quadrupolar contributions to the light-matter interactions. We exploit a field quantization scheme based on electromagnetic Green’s tensors, suited for dispersive materials. We obtain expressions for spontaneous emission rate, Lamb shift, multipole-multipole shift and superradiance rate, all being modified with dispersive environment. The considered influence could be substantial for suitably tailored nanostructured photonic environments, as demonstrated exemplarily.
In vivo biodistribution analysis of transmission competent and defective RNA virus-based episomal vector
Authors: Komatsu Yumiko , Tanaka Chiaki , Komorizono Ryo , Tomonaga Keizo 
Published: April 2020

AbstractRNA virus-based episomal vector (REVec) is an emerging viral vector system that mediates long-term stable gene expression in variety of cell typesin vitro. However, little is known about its tissue tropism and persistence of gene expressionin vivo. Here, to evaluate the feasibility of REVec forin vivogene delivery, we conducted biodistribution analysis of transmission competent REVec and transmission defective ΔG-REVec in Lewis rats. Following intracranial administration of REVec, transgene expression was detected in various tissues. In contrast, transgene expression was only observed in the brain after ΔG-REVec administration. Low levels of vector shedding in the feces and blood and of neutralizing antibody in the serum were detected after REVec injection. In the brain, microglia, astrocytes and neurons were susceptible to REVec-mediated transduction. However, the animals administered with REVec, but not with ΔG-REVec showed a significant decrease in body weight compared to mock treated animals. Additionally, CD8 T cell infiltration was observed in the brain of these animals. In summary, we demonstrated that REVec promotes long-term transgene expressionin vivowithout causing high vector shedding or neutralizing antibody production; however, suggests the need to attenuate vector associated pathogenicity in the future.
Lactobacillus acidophilus and L. plantarum improve health status, modulate gut microbiota and innate immune response of marron (Cherax cainii)
Authors: Foysal Md Javed , Fotedar Ravi , Siddik Muhammad A. B. , Tay Alfred 
Published: April 2020

AbstractThis study aimed to investigate the combined effects of two most potent probiotic bacteria Lactobacillus acidophilus and Lactobacillus plantarum on overall health and immune status of freshwater crayfish, marron under laboratory conditions. A total of 36 marron were distributed into six different tanks and two different feeding groups, control and probiotic-fed group. After acclimation, control group was fed with basal diet while probiotic group was fed 109 CFU/mL per kg of bacterial supplemented feed for 60 days. The results showed no significant differences in weight gain, however, probiotic feed significantly enhanced some hemolymph parameters and biochemical composition of tail muscle. Histology data revealed better hepatopancreas health and higher microvilli counts in the marron gut fed probiotic diet. The probiotic bacteria triggered significant shift of microbial communities at different taxa level, mostly those reported as beneficial for crayfish. The probiotic diet also enriched the metabolic functions and genes associated with innate immune response of crayfish. Further correlation analysis revealed significant association of some taxa with increased activity for hemolymph and immune genes. Therefore, dietary Lactobacillus supplementation can modulate the overall health and immunity as well as gut microbial composition and interaction network between gut microbiota and immune system in crayfish.
Plant resistance does not compromise parasitoid-based biocontrol of a strawberry pest
Authors: Weber Daniela , Egan Paul A. , Muola Anne , Ericson Lars E. , Stenberg Johan A. 
Published: April 2020

AbstractPlant nutritional quality can influence interactions between herbivores and their parasitoids. While most previous work has focused on a limited set of secondary plant metabolites, the tri-trophic effects of overall phenotypic resistance have been understudied. Furthermore, the joint effects of secondary and primary metabolites on parasitoids are almost unexplored. In this study, we compared the performance and survival of the parasitoid species Asecodes parviclava Thompson on wild woodland strawberry (Fragaria vesca L.) genotypes showing variation in resistance against the parasitoid’s host, the strawberry leaf beetle (Galerucella tenella L.). Additionally, we related the metabolic profiles of these plant genotypes to the tritrophic outcomes in order to identify primary and secondary metabolites involved in regulating plant potential to facilitate parasitism. We found that parasitoid performance was strongly affected by plant genotype, but those differences in plant resistance to the herbivore were not reflected in parasitoid survival. These findings could be explained in particular by a significant link between parasitoid survival and foliar carbohydrate levels, which appeared to be the most important compounds for parasitism success. The fact that plant quality strongly affects parasitism should be further explored and utilized in plant breeding programs for a synergistic application in sustainable pest management.
Metal concentrations and biological effects from one of the largest mining disasters in the world (Brumadinho, Minas Gerais, Brazil)
Authors: Vergilio Cristiane dos Santos , Lacerda Diego , Oliveira Braulio Cherene Vaz de , Sartori Echily , Campos Gabriela Munis , Pereira Anna Luiza de Souza , Aguiar Diego Borges de , Souza Tatiana da Silva , Almeida Marcelo Gomes de , Thompson Fabiano , Rezende Carlos Eduardo de 
Published: April 2020

AbstractThe rupture of the Brumadinho mining tailings dam in Brazil is considered one of the largest mining disasters in the world, resulting in 244 deaths and 26 missing people, in addition to the environmental consequences. The present study aims to evaluate the concentrations of multiple elements and the biological effects on water and sediments of the Paraopeba River after the Brumadinho Dam rupture. The tailings are formed by fine particulate material with large amounts of Fe, Al, Mn, Ti, rare earth metals and toxic metals. In the water, the levels of Fe, Al, Mn, Zn, Cu, Pb, Cd and U were higher than those allowed by Brazilian legislation. In the sediments, Cr, Ni, Cu and Cd levels were higher than the established sediment quality guidelines (TEL-NOAA). The differences in metal concentrations in the water and sediments between the upstream and downstream sides of the dam illustrate the effect of the tailings in the Paraopeba River. Toxicological tests demonstrated that the water and sediments were toxic to different trophic levels, from algae to microcrustaceans and fish. The fish exposed to water and sediments containing mine ore also accumulated metals in muscle tissue. This evaluation emphasizes the necessity of long-term monitoring in the affected area.
On the widespread enhancement in fine particulate matter across the Indo-Gangetic Plain towards winter
Authors: Ojha Narendra , Sharma Amit , Kumar Manish , Girach Imran , Ansari Tabish U. , Sharma Som K. , Singh Narendra , Pozzer Andrea , Gunthe Sachin S. 
Published: April 2020

AbstractFine particulate matter (PM2.5, aerodynamic diameter ≤2.5 µm) impacts the climate, reduces visibility and severely influences human health. The Indo-Gangetic Plain (IGP), home to about one-seventh of the world’s total population and a hotspot of aerosol loading, observes strong enhancements in the PM2.5 concentrations towards winter. We performed high-resolution (12 km × 12 km) atmospheric chemical transport modeling (WRF-Chem) for the post-monsoon to winter transition to unravel the underlying dynamics and influences of regional emissions over the region. Model, capturing the observed variations to an extent, reveals that the spatial distribution of PM2.5 having patches of enhanced concentrations (≥100 µgm−3) during post-monsoon, evolves dramatically into a widespread enhancement across the IGP region during winter. A sensitivity simulation, supported by satellite observations of fires, shows that biomass-burning emissions over the northwest IGP play a crucial role during post-monsoon. Whereas, in contrast, towards winter, a large-scale decline in the air temperature, significantly shallower atmospheric boundary layer, and weaker winds lead to stagnant conditions (ventilation coefficient lower by a factor of ~4) thereby confining the anthropogenic influences closer to the surface. Such changes in the controlling processes from post-monsoon to winter transition profoundly affect the composition of the fine aerosols over the IGP region. The study highlights the need to critically consider the distinct meteorological processes of west-to-east IGP and changes in dominant sources from post-monsoon to winter in the formulation of future pollution mitigation policies.
Multi-objective optimization for EEG channel selection and accurate intruder detection in an EEG-based subject identification system
Authors: Moctezuma Luis Alfredo , Molinas Marta 
Published: April 2020

AbstractWe present a four-objective optimization method for optimal electroencephalographic (EEG) channel selection to provide access to subjects with permission in a system by detecting intruders and identifying the subject. Each instance was represented by four features computed from two sub-bands, extracted using empirical mode decomposition (EMD) for each channel, and the feature vectors were used as input for one-class/multi-class support vector machines (SVMs). We tested the method on data from the event-related potentials (ERPs) of 26 subjects and 56 channels. The optimization process was performed by the non-dominated sorting genetic algorithm (NSGA), which found a three-channel combination that achieved an accuracy of 0.83, with both a true acceptance rate (TAR) and a true rejection rate (TRR) of 1.00. In the best case, we obtained an accuracy of up to 0.98 for subject identification with a TAR of 0.95 and a TRR 0.93, all using seven EEG channels found by NSGA-III in a subset of subjects manually created. The findings were also validated using 10 different subdivisions of subjects randomly created, obtaining up to 0.97 ± 0.02 of accuracy, a TAR of 0.81 ± 0.12 and TRR of 0.85 ± 0.10 using eight channels found by NSGA-III. These results support further studies on larger datasets for potential applications of EEG in identification and authentication systems.
Similar history biases for distinct prospective decisions of self-performance
Authors: Mei Ning , Rankine Sean , Olafsson Einar , Soto David 
Published: April 2020

AbstractMetacognition can be deployed retrospectively -to reflect on the correctness of our behavior- or prospectively -to make predictions of success in one’s future behavior or make decisions about strategies to solve future problems. We investigated the factors that determine prospective decision making. Human participants performed a visual discrimination task followed by ratings of visibility and response confidence. Prior to each trial, participants made prospective judgments. In Experiment 1, they rated their belief of future success. In Experiment 2, they rated their decision to adopt a focused attention state. Prospective beliefs of success were associated with no performance changes while prospective decisions to engage attention were followed by better self-evaluation of the correctness of behavioral responses. Using standard machine learning classifiers we found that the current prospective decision could be predicted from information concerning task-correctness, stimulus visibility and response confidence from previous trials. In both Experiments, awareness and confidence were more diagnostic of the prospective decision than task correctness. Notably, classifiers trained with prospective beliefs of success in Experiment 1 predicted decisions to engage in Experiment 2 and vice-versa. These results indicate that the formation of these seemingly different prospective decisions share a common, dynamic representational structure.
Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus
Authors: Wildeman Peter , Tevell Staffan , Eriksson Carl , Lagos Amaya Campillay , Söderquist Bo , Stenmark Bianca 
Published: April 2020

AbstractStaphylococcus aureus is a commensal colonizing the skin and mucous membranes. It can also act as a pathogen, and is the most common microorganism isolated from prosthetic joint infections (PJIs). The aim of this study was to explore the genomic relatedness between commensal and PJI S. aureus strains as well as microbial traits and host-related risk factors for treatment failure. Whole-genome sequencing (WGS) was performed on S. aureus isolates obtained from PJIs (n = 100) and control isolates from nares (n = 101). Corresponding clinical data for the PJI patients were extracted from medical records. No PJI-specific clusters were found in the WGS phylogeny, and the distribution of the various clonal complexes and prevalence of virulence genes among isolates from PJIs and nares was almost equal. Isolates from patients with treatment success and failure were genetically very similar, while the presence of an antibiotic-resistant phenotype and the use of non-biofilm-active antimicrobial treatment were both associated with failure.In conclusion, commensal and PJI isolates of S. aureus in arthroplasty patients were genetically indistinguishable, suggesting that commensal S. aureus clones are capable of causing PJIs. Furthermore, no association between genetic traits and outcome could be demonstrated, stressing the importance of patient-related factors in the treatment of S. aureus PJIs.
Dynamics at the crystal-melt interface in a supercooled chalcogenide liquid near the glass transition
Authors: Li Jianheng , Jangid Rahul , Zhu Weidi , Kohne Chris , Fluerasu Andrei , Zhang Yugang , Sen Sabyasachi , Kukreja Roopali 
Published: April 2020

AbstractDirect quantitative measurements of nanoscale dynamical processes associated with structural relaxation and crystallization near the glass transition are a major experimental challenge. These type of processes have been primarily treated as macroscopic phenomena within the framework of phenomenological models and bulk experiments. Here, we report x-ray photon correlation spectroscopy measurements of dynamics at the crystal-melt interface during the radiation induced formation of Se nano-crystallites in pure Se and in binary AsSe4 glass-forming liquids near their glass transition temperature. We observe a heterogeneous dynamical behaviour where the intensity correlation functions g2(q, t) exhibits either a compressed or a stretched exponential decay, depending on the size of the Se nano-crystallites. The corresponding relaxation timescale for the AsSe4 liquid increases as the temperature is raised, which can be attributed to changes in the chemical composition of the melt at the crystal-melt interface with the growth of the Se nano-crystallites.
Nitrogen Pollution Impact and Remediation through Low Cost Starch Based Biodegradable polymers
Authors: Ibrahim K. A. , Naz M. Y. , Shukrullah S. , Sulaiman S. A. , Ghaffar A. , AbdEl-Salam N. M. 
Published: April 2020

AbstractThe world does not have too much time to ensure that the fast-growing population has enough land, food, water and energy. The rising food demand has brought a positive surge in fertilizers’ demand and agriculture-based economy. The world is using 170 million tons of fertilizer every year for food, fuel, fiber, and feed. The nitrogenous fertilizers are being used to meet 48% of the total food demand of the world. High fertilizer inputs augment the reactive nitrogen levels in soil, air, and water. The unassimilated reactive nitrogen changes into a pollutant and harms the natural resources. The use of controlled-release fertilizers for slowing down the nutrients’ leaching has recently been practiced by farmers. However, to date, monitoring of the complete discharge time and discharge rate of controlled released fertilizers is not completely understood by the researchers. In this work, corn starch was thermally processed into a week gel-like coating material by reacting with urea and borate. The granular urea was coated with native and processed starch in a fluidized bed reactor having bottom-up fluid delivery system. The processed starch exhibited better thermal and mechanical stability as compared to the native starch. Unlike the pure starch, the storage modulus of the processed starch dominated the loss modulus. The release time of urea, coated with processed starch, remained remarkably larger than the uncoated urea.
Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau
Authors: Roy Chayan , Rameez Moidu Jameela , Haldar Prabir Kumar , Peketi Aditya , Mondal Nibendu , Bakshi Utpal , Mapder Tarunendu , Pyne Prosenjit , Fernandes Svetlana , Bhattacharya Sabyasachi , Roy Rimi , Mandal Subhrangshu , O’Neill William Kenneth , Mazumdar Aninda , Mukhopadhyay Subhra Kanti , Mukherjee Ambarish , Chakraborty Ranadhir , Hallsworth John Edward , Ghosh Wriddhiman 
Published: April 2020

AbstractLittle is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite calledShivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent,Shivlinga’s geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% ofShivlinga’s microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated byAquificae/Deinococcus-Thermus, thenChlorobi/Chloroflexi/Cyanobacteria, and finallyBacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C.Shivlinga’s geomicrobiology highlights the possibility that the system’s kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.
Axial stretch regulates rat tail collecting lymphatic vessel contractions
Authors: Razavi Mohammad S. , Leonard-Duke Julie , Hardie Becky , Dixon J. Brandon , Gleason Rudolph L. 
Published: April 2020

AbstractLymphatic contractions play a fundamental role in maintaining tissue and organ homeostasis. The lymphatic system relies on orchestrated contraction of collecting lymphatic vessels, via lymphatic muscle cells and one-way valves, to transport lymph from the interstitial space back to the great veins, against an adverse pressure gradient. Circumferential stretch is known to regulate contractile function in collecting lymphatic vessels; however, less is known about the role of axial stretch in regulating contraction. It is likely that collecting lymphatic vessels are under axial strain in vivo and that the opening and closing of lymphatic valves leads to significant changes in axial strain throughout the pumping cycle. The purpose of this paper is to quantify the responsiveness of lympatic pumping to altered axial stretch. In situ measurements suggest that rat tail collecting lymphatic vessels are under an axial stretch of ~1.24 under normal physiological loads. Ex vivo experiments on isolated rat tail collecting lymphatics showed that the contractile metrics such as contractile amplitude, frequency, ejection fraction, and fractional pump flow are sensitive to axial stretch. Multiphoton microscopy showed that the predominant orientation of collagen fibers is in the axial direction, while lymphatic muscle cell nuclei and actin fibers are oriented in both circumferential and longitudinal directions, suggesting an axial component to contraction. Taken together, these results demonstrate the significance of axial stretch in lymphatic contractile function, suggest that axial stretch may play an important role in regulating lymph transport, and demonstrate that changes in axial strains could be an important factor in disease progression.