bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal Linear Networks for Magnetic Resonance Image Reconstruction
Authors: Liberman Gilad , Poser Benedikt A. 
Published: December 2019

AbstractModern sequences for Magnetic Resonance Imaging (MRI) trade off scan time with computational challenges, resulting in ill-posed inverse problems and the requirement to account for more elaborated signal models. Various deep learning techniques have shown potential for image reconstruction from reduced data, outperforming compressed sensing, dictionary learning and other advanced techniques based on regularization, by characterization of the image manifold. In this work we suggest a framework for reducing a “neural” network to the bare minimum required by the MR physics, reducing the network depth and removing all non-linearities. The networks performed well both on benchmark simulated data and on arterial spin labeling perfusion imaging, showing clear images while preserving sensitivity to the minute signal changes. The results indicate that the deep learning framework plays a major role in MR image reconstruction, and suggest a concrete approach for probing into the contribution of additional elements.
Not all birds have a single dominantly expressed MHC-I gene: Transcription suggests that siskins have many highly expressed MHC-I genes
Authors: Drews Anna , Westerdahl Helena 
Published: December 2019

AbstractPasserine birds belong to the most species rich bird order and are found in a wide range of habitats. The extremely polymorphic adaptive immune system of passerines, identified through their major histocompatibility complex class I genes (MHC-I), may explain some of this extreme radiation. Recent work has shown that passerines have higher numbers of MHC-I gene copies than other birds, but little is currently known about expression and function of these gene copies. Non-passerine birds have a single highly expressed MHC-I gene copy, a pattern that seems unlikely in passerines. We used high-throughput sequencing to study MHC-I alleles in siskins (Spinus spinus) and determined gene expression, phylogenetic relationships and sequence divergence. We verified between six and 16 MHC-I alleles per individual and 97% of these were expressed. Strikingly, up to five alleles per individual had high expression. Out of 88 alleles 18 were putatively non-classical with low sequence divergence and expression, and found in a single phylogenetic cluster. The remaining 70 alleles were classical, with high sequence divergence and variable degrees of expression. Our results contradict the suggestion that birds only have a single dominantly expressed MHC-I gene by demonstrating several highly expressed MHC-I gene copies in a passerine.
Precision cancer monitoring using a novel, fully integrated, microfluidic array partitioning digital PCR platform
Authors: Dueck Megan E. , Lin Robert , Zayac Andrew , Gallagher Steve , Chao Alexander K. , Jiang Lingxia , Datwani Sammy S. , Hung Paul , Stieglitz Elliot 
Published: December 2019

AbstractA novel digital PCR (dPCR) platform combining off-the-shelf reagents, a micro-molded plastic microfluidic consumable with a fully integrated single dPCR instrument was developed to address the needs for routine clinical diagnostics. This new platform offers a simplified workflow that enables: rapid time-to-answer; low potential for cross contamination; minimal sample waste; all within a single integrated instrument. Here we showcase the capability of this fully integrated platform to detect and quantify non-small cell lung carcinoma (NSCLC) rare genetic mutants (EGFR T790M) with precision cell-free DNA (cfDNA) standards. Next, we validated the platform with an established chronic myeloid leukemia (CML) fusion gene (BCR-ABL1) assay down to 0.01% mutant allele frequency to highlight the platform’s utility for precision cancer monitoring. Thirdly, using a juvenile myelomonocytic leukemia (JMML) patient-specific assay we demonstrate the ability to precisely track an individual cancer patient’s response to therapy and show the patient’s achievement of complete molecular remission. These three applications highlight the flexibility and utility of this novel fully integrated dPCR platform that has the potential to transform personalized medicine for cancer recurrence monitoring.
Optimization of double diffusive mixed convection in a BFS channel filled with Alumina nanoparticle using Taguchi method and utility concept
Authors: Nath Ratnadeep , Krishnan Murugesan 
Published: December 2019

AbstractThis research work focuses on the implementation of Taguchi method and utility concept for optimization of flow, geometrical and thermo-physical parameters for mixed convective heat and mass transfer in a backward facing step (BFS) channel filled with Alumina nanoparticle doped in water-ethylene glycol mixture. Mass, momentum, energy and solutal conservation equations for the flow field are cast in velocity-vorticity form of Navier-Stokes equations, which are solved using Galerkin’s weighted residual finite element method through isoparametric formulation. The following six parameters, expansion ratio of the BFS channel (H/h), Reynolds number (Re), buoyancy ratio (N), nanoparticle volume fraction (χ), shape of nanoparticles and thermal Grashof number (GrT) at three levels are considered as controlling parameters for optimization using Taguchi method. An L27 orthogonal array has been chosen to get the levels of the six parameters for the 27 trial runs. Simulation results were obtained for 27 trial runs from which three different sets of optimum levels of the control parameters were obtained for maximum Nu and Sh and minimum wall shear stress during double diffusive mixed convection in the channel. Then, in order to obtain a single set of optimum levels of the control parameters to achieve maximum heat and mass transfer and minimum wall shear stress concurrently, utility concept has been implemented. Taguchi results indicate that expansion ratio and volume fraction of nanoparticles are the significant contributing parameters to achieve maximum heat and mass transfer and minimum wall shear stress. Utility concept predicts the average Nusselt number less by 2% and Sherwood number less by 3% compared to the Taguchi method with equal weightage of 40% assumed for Nusselt and Sherwood numbers and 20% for wall shear stress.
Reaction rate of pyruvate and hydrogen peroxide: assessing antioxidant capacity of pyruvate under biological conditions
Authors: Guarino Victoria A. , Oldham William M. , Loscalzo Joseph , Zhang Ying-Yi 
Published: December 2019

AbstractPyruvate, a pivotal glucose metabolite, is an α-ketoacid that reacts with hydrogen peroxide (H2O2). Its pharmacological precursor, ethyl pyruvate, has shown anti-inflammatory/anti-tissue injury effects in various animal models of disease, but failed in a multicenter clinical trial. Since rodents, but not humans, can convert ethyl pyruvate to pyruvate in blood plasma, this additional source of extracellular pyruvate may have contributed to the discrepancy between the species. To examine this possibility, we investigated the kinetics of the reaction under biological conditions and determined the second order rate constant k as 2.360 ± 0.198 M−1 s−1. We then calculated the time required for H2O2 elimination by pyruvate. The results show that, with an average intracellular concentration of pyruvate (150 µM), elimination of 95% H2O2 at normal to pathological concentrations (0.01–50 µM) requires 141–185 min (2.4–3 hour). With 1,000 µM pyruvate, a concentration that can only exist extracellularly or in cell culture media, 95% elimination of H2O2 at 5–200 µM requires 21–25 min. We conclude that intracellular pyruvate, or other α-ketoacids, whose endogenous concentration is controlled by metabolism, have little role in H2O2 clearance. An increased extracellular concentration of pyruvate, however, does have remarkable peroxide scavenging effects, considering minimal peroxidase activity in this space.
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype
Authors: Mihelčić Matej , Šmuc Tomislav , Supek Fran 
Published: December 2019

AbstractGenes with similar roles in the cell cluster on chromosomes, thus benefiting from coordinated regulation. This allows gene function to be inferred by transferring annotations from genomic neighbors, following the guilt-by-association principle. We performed a systematic search for co-occurrence of >1000 gene functions in genomic neighborhoods across 1669 prokaryotic, 49 fungal and 80 metazoan genomes, revealing prevalent patterns that cannot be explained by clustering of functionally similar genes. It is a very common occurrence that pairs of dissimilar gene functions – corresponding to semantically distant Gene Ontology terms – are significantly co-located on chromosomes. These neighborhood associations are often as conserved across genomes as the known associations between similar functions, suggesting selective benefits from clustering of certain diverse functions, which may conceivably play complementary roles in the cell. We propose a simple encoding of chromosomal gene order, the neighborhood function profiles (NFP), which draws on diverse gene clustering patterns to predict gene function and phenotype. NFPs yield a 26–46% increase in predictive power over state-of-the-art approaches that propagate function across neighborhoods, thus providing hundreds of novel, high-confidence gene function inferences per genome. Furthermore, we demonstrate that copy number-neutral structural variation that shapes gene function distribution across chromosomes can predict phenotype of individuals from their genome sequence.
Analysis of free radical production capacity in mouse faeces and its possible application in evaluating the intestinal environment: a pilot study
Authors: Wakita Yoshihisa , Saiki Asako , Kaneda Hirotaka , Segawa Shuichi , Tsuchiya Youichi , Kameya Hiromi , Okamoto Susumu 
Published: December 2019

AbstractComplex interplay between the intestinal environment and the host has attracted considerable attention and has been well studied with respect to the gut microbiome and metabolome. Oxygen free radicals such as superoxide and the hydroxyl radical (•OH) are generated during normal cellular metabolism. They are toxic to both eukaryotic and prokaryotic cells and might thus affect intestinal homeostasis. However, the effect of oxygen free radicals on the intestinal environment has not been widely studied. Herein, we applied electron spin resonance spectroscopy with spin trapping reagents to evaluate oxygen free radical production capacity in the intestinal lumen and the faeces of mice. •OH was generated in faeces and lumens of the small and large intestines. There were no remarkable differences in •OH levels between faeces and the large intestine, suggesting that faeces can be used as alternative samples to estimate the •OH production capacity in the colonic contents. We then compared free radical levels in faecal samples among five different mouse strains (ddY, ICR, C57BL/6, C3H/HeJ, and BALB/c) and found that strain ddY had considerably higher levels than the other four strains. In addition, strain ddY was more susceptible to dextran sulphate sodium-induced colitis. These differences were possibly related to the relative abundance of the gut bacterial group Candidatus Arthromitus, which is known to modulate the host immune response. From these results, we suggest that the production capacity of oxygen free radicals in mouse faeces is associated with intestinal homeostasis.
Empathy and compassion toward other species decrease with evolutionary divergence time
Authors: Miralles Aurélien , Raymond Michel , Lecointre Guillaume 
Published: December 2019

AbstractCurrently the planet is inhabited by several millions of extremely diversified species. Not all of them arouse emotions of the same nature or intensity in humans. Little is known about the extent of our affective responses toward them and the factors that may explain these differences. Our online survey involved 3500 raters who had to make choices depending on specific questions designed to either assess their empathic perceptions or their compassionate reactions toward an extended photographic sampling of organisms. Results show a strong negative correlation between empathy scores and the divergence time separating them from us. However, beyond a certain time of divergence, our empathic perceptions stabilize at a minimum level. Compassion scores, although based on less spontaneous choices, remain strongly correlated to empathy scores and time of divergence. The mosaic of features characterizing humans has been acquired gradually over the course of the evolution, and the phylogenetically closer a species is to us, the more it shares common traits with us. Our results could be explained by the fact that many of these traits may arouse sensory biases. These anthropomorphic signals could be able to mobilize cognitive circuitry and to trigger prosocial behaviors usually at work in human relationships.
Ab initio Molecular Dynamics Simulation Study of Dissociation Electron Attachment to Lactic Acid and Isomer
Authors: Zhang Ying , Xu Zhongfeng , Zhao Yongtao , Zhang Xiaoan 
Published: December 2019

AbstractDissociation processes of lactic acid and its isomer formed by low-energy dissociation electron attachment (DEA) in the gas phase are investigated by using ab initio molecular dynamics (MD) simulations. The ab initio MD simulations using an atom-centered density matrix propagation (ADMP) method are carried out to investigate the DEA dissociation process of lactic acid and its isomer. The analysis of the simulated dissociation trajectories of lactic acid and its isomer indicates that the C-C, C-H, and C-O bonds are cleaved within femtoseconds of the simulation time scale in the DEA dissociation process, and the difference in dissociation trajectory depends on the size of the three basis sets. The simulation results enable us to gain insights into the DEA dissociation process of lactic acid and its isomer. In this work, we present a comparative study of the 6-31 + G(d,p), 6-311++G(2d,2p), and Aug-cc-pVDZ basis sets of the DEA dissociation simulation of lactic acid and its isomer. The comparative study results indicate that the 6-311++G(2d,2p) is an excellent basis set for the ADMP trajectory simulation of lactic acid and its isomer in the DEA dissociation process. The natural bond orbital (NBO) analysis is carried out to characterize variation in the charge population and charge transfer accompanied by the C-C, C-H, and C-O bond dissociation processes for lactic acid and its isomer in the ADMP trajectory simulation. ADMP simulation and NBO analysis of the dissociation trajectory is considered an important initial and decisive step in DEA dissociation dynamics for lactic acid and its isomer.
Controlling properties of human neural progenitor cells using 2D and 3D conductive polymer scaffolds
Authors: Song Shang , Amores Danielle , Chen Cheng , McConnell Kelly , Oh Byeongtaek , Poon Ada , George Paul M. 
Published: December 2019

AbstractHuman induced pluripotent stem cell-derived neural progenitor cells (hNPCs) are a promising cell source for stem cell transplantation to treat neurological diseases such as stroke and peripheral nerve injuries. However, there have been limited studies investigating how the dimensionality of the physical and electrical microenvironment affects hNPC function. In this study, we report the fabrication of two- and three-dimensional (2D and 3D respectively) constructs composed of a conductive polymer to compare the effect of electrical stimulation of hydrogel-immobilized hNPCs. The physical dimension (2D vs 3D) of stimulating platforms alone changed the hNPCs gene expression related to cell proliferation and metabolic pathways. The addition of electrical stimulation was critical in upregulating gene expression of neurotrophic factors that are important in regulating cell survival, synaptic remodeling, and nerve regeneration. This study demonstrates that the applied electrical field controls hNPC properties depending on the physical nature of stimulating platforms and cellular metabolic states. The ability to control hNPC functions can be beneficial in understanding mechanistic changes related to electrical modulation and devising novel treatment methods for neurological diseases.
Identification and ecology of alternative insect vectors of ‘Candidatus Phytoplasma solani’ to grapevine
Authors: Quaglino Fabio , Sanna Francesco , Moussa Abdelhameed , Faccincani Monica , Passera Alessandro , Casati Paola , Bianco Piero Attilio , Mori Nicola 
Published: December 2019

AbstractBois noir, a disease of the grapevine yellows complex, is associated with ‘CandidatusPhytoplasma solani’ and transmitted to grapevines in open fields by the cixiidsHyalesthes obsoletusandReptalus panzeri. In vine-growing areas where the population density of these vectors is low within the vineyard, the occurrence of bois noir implies the existence of alternative vectors. The aim of this study was to identify alternative vectors through screening of the Auchenorrhyncha community, phytoplasma typing bystampgene sequence analyses, and transmission trials. During field activities, conducted in Northern Italy in a vineyard where the bois noir incidence was extremely high, nine potential alternative insect vectors were identified according to high abundance in the vineyard agro-ecosystem, high infection rate, and harbouring phytoplasma strains characterized bystampgene sequence variants found also in symptomatic grapevines. Transmission trials coupled with molecular analyses showed that at least eight species (Aphrodes makarovi,Dicranotropis hamata,Dictyophara europaea,Euscelis incisus,Euscelidius variegatus,Laodelphax striatella,Philaenus spumarius, andPsammotettix alienus/confinis) are alternative vectors of ‘CandidatusPhytoplasma solani’ to grapevines. These novel findings highlight that bois noir epidemiology in vineyard agro-ecosystems is more complex than previously known, opening up new perspectives in the disease management.
Biochemical response of Rhodotorula mucilaginosa and Cladosporium herbarum isolated from aquatic environment on iron(III) ions
Authors: Cudowski A. , Pietryczuk A. 
Published: December 2019

AbstractThe objective of the paper was to determine the influence of iron(III) ions on the growth and metabolism of fungi commonly occurring in waters: the yeast Rhodotorula mucilaginosa and filamentous fungus Cladosporium herbarum. Cells of R. mucilaginosa were shown to absorb the most iron(III) ions at a concentration of 1 mg/L iron(III) ions. Yeast cells showed a considerable increase in the content of proteins and monosaccharides, as well as biomass growth. At higher concentrations of iron(III) ions, the yeast limited the intake of iron(III) ions, and a decrease in the basic metabolites in cells was observed, as well as an increase in the secretion of such metabolites into the medium. Moreover, the activity of antioxidant enzymes increased in the fungal cells, suggesting that iron(III) ions have a toxic effect. Simultaneously, even at high concentrations of iron(III) ions in the medium, no decrease in the yeast biomass was recorded. It seems therefore that the potentially pathogenic R. mucilaginosa will likely be present in waters moderately contaminated with iron(III) ions. It can be useful as a water quality bioindicator. A considerably higher capacity for the biosorption of iron(III) ions was recorded for the filamentous fungus C. herbarum. Defensive mechanisms were observed for C. herbarum, which were manifested in a substantial increase in the content of proteins and monosaccharides, as well as an increase in the activity of antioxidant enzymes, particularly under the influence of high concentrations of iron(III) ions. Moreover, it was evidenced that in the filamentous fungus, iron(III) ions limited the extracellular secretion of metabolites. These results suggest that the fungus can actively accumulate iron(III) ions and therefore eliminate them from the aquatic environment. It can be useful in water treatment processes, which has a significant impact on water ecology.
Smoking and risk of incident end-stage kidney disease in general population: A Nationwide Population-based Cohort Study from Korea
Authors: Choi Hong Sang , Han Kyung-Do , Oh Tae Ryom , Kim Chang Seong , Bae Eun Hui , Ma Seong Kwon , Kim Soo Wan 
Published: December 2019

AbstractWe analyzed data from the Korean National Health Insurance Service (NHIS) to investigate whether smoking increases the risk of end-stage kidney disease (ESKD). This retrospective nationwide population-based cohort study included the data of 23,232,091 participants who underwent at least one health examination between 2009 and 2012. Smoking status was recorded at baseline. The incidence of ESKD was identified via ICD-10 codes and special medical aid codes from the Korean National Health Insurance Service database till December 2016. A Cox proportional-hazards model with multivariable adjustment was used to evaluate the association between smoking and ESKD incidence. Overall, 24.6% of participants were current smokers; 13.5% and 61.9%, were ex- and non-smokers, respectively. Overall, 45,143 cases of ESKD developed during the follow-up period. Current smokers (hazard ratio [HR], 1.39; 95% confidence interval [CI], 1.35–1.43) and ex-smokers (HR, 1.09; 95% CI, 1.06–1.12) demonstrated a significant increase in the adjusted risk of ESKD compared to non-smokers. The risk of ESKD was directly proportional to the smoking duration, number of cigarettes smoked daily, and pack-years. In conclusion, smoking is associated with a greater risk of ESKD in the general Korean population; the risk increases with an increase in the smoking duration, number of cigarettes smoked daily, and pack-years.
Spatial variations and controls of carbon use efficiency in China’s terrestrial ecosystems
Authors: Chen Zhi , Yu Guirui 
Published: December 2019

AbstractCarbon use efficiency (CUE), one of the most important eco-physiological parameters, represents the capacity of plants to transform carbon into new biomass. Understanding the variations and controls of CUE is crucial for regional carbon assessment. Here, we used 15-years of continuous remote sensing data to examine the variations of CUE across broad geographic and climatic gradients in China. The results showed that the vegetation CUE was averaged to 0.54 ± 0.11 with minor interannual variation. However, the CUE greatly varied with geographic gradients and ecosystem types. Forests have a lower CUE than grasslands and croplands. Evergreen needleleaf forests have a higher CUE than other forest types. Climate factors (mean annual temperature (MAT), precipitation (MAP) and the index of water availability (IWA)) dominantly regulated the spatial variations of CUE. The CUE exhibited a linear decrease with enhanced MAT and MAP and a parabolic response to the IWA. Furthermore, the responses of CUE to environmental change varied with individual ecosystem type. In contrast, precipitation exerted strong control on CUE in grassland, while in forest and cropland, the CUE was mainly controlled by the available water. This study identifies the variations and response of CUE to environmental drivers in China, which will be valuable for the regional assessment of carbon cycling dynamics under future climate change.