bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients
Authors: Rubio Teresa , Felipo Vicente , Tarazona Sonia , Pastorelli Roberta , Escudero-García Desamparados , Tosca Joan , Urios Amparo , Conesa Ana , Montoliu Carmina 
Published: January 2021

AbstractPatients with liver cirrhosis may develop minimal hepatic encephalopathy (MHE) which affects their quality of life and life span. It has been proposed that a shift in peripheral inflammation triggers the appearance of MHE. However, the mechanisms involved in this immune system shift remain unknown. In this work we studied the broad molecular changes involved in the induction of MHE with the goal of identifying (1) altered genes and pathways in peripheral blood cells associated to the appearance of MHE, (2) serum metabolites and cytokines with modified levels in MHE patients and (3) MHE-regulated immune response processes related to changes in specific serum molecules. We adopted a multi-omic approach to profile the transcriptome, metabolome and a panel of cytokines of blood samples taken from cirrhotic patients with or without MHE. Transcriptomic analysis supports the hypothesis of alternations in the Th1/Th2 and Th17 lymphocytes cell populations as major drivers of MHE. Cluster analysis of serum molecules resulted in six groups of chemically similar compounds, suggesting that functional modules operate during the induction of MHE. Finally, the multi-omic integrative analysis suggested a relationship between cytokines CCL20, CX3CL1, CXCL13, IL-15, IL-22 and IL-6 with alteration in chemotaxis, as well as a link between long-chain unsaturated phospholipids and the increased fatty acid transport and prostaglandin production. We found altered immune pathways that may collectively contribute to the mild cognitive impairment phenotype in MHE. Our approach is able to combine extracellular and intracellular information, opening new insights to the understanding of the disease.
Scalable synthesis of Cu–Sb–S phases from reactive melts of metal xanthates and effect of cationic manipulation on structural and optical properties
Authors: Alqahtani Tahani , Khan Malik Dilshad , Lewis David J. , Zhong Xiang Li , O’Brien Paul 
Published: January 2021

AbstractWe report a simple, economical and low temperature route for phase-pure synthesis of two distinct phases of Cu–Sb–S, chalcostibite (CuSbS2) and tetrahedrite (Cu12Sb4S13) nanostructures. Both compounds were prepared by the decomposition of a mixture of bis(O-ethylxanthato)copper(II) and tris(O-ethylxanthato)antimony(III), without the use of solvent or capping ligands. By tuning the molar ratio of copper and antimony xanthates, single-phases of either chalcostibite or tetrahedrite were obtained. The tetrahedrite phase exists in a cubic structure, where the Cu and Sb atoms are present in different coordination environments, and tuning of band gap energy was investigated by the incorporation of multivalent cationic dopants, i.e. by the formation of Zn-doped tetrahedrites Cu12−xZnxSb4S13 (x = 0.25, 0.5, 0.75, 1, 1.2 and 1.5) and the Bi-doped tetrahedrites Cu12Sb4−xBixS13 (x = 0.08, 0.15, 0.25, 0.32, 0.4 and 0.5). Powder X-ray diffraction (p-XRD) confirms single-phase of cubic tetrahedrite structures for both of the doped series. The only exception was for Cu12Sb4−xBixS13 with x = 0.5, which showed a secondary phase, implying that this value is above the solubility limit of Bi in Cu12Sb4S13 (12%). A linear increase in the lattice parameter a in both Zn- and Bi-doped tetrahedrite samples was observed with increasing dopant concentration. The estimated elemental compositions from EDX data are in line with the stoichiometric ratio expected for the compounds formed. The morphologies of samples were investigated using SEM and TEM, revealing the formation of smaller particle sizes upon incorporation of Zn. Incorporation of Zn or Bi into Cu12Sb4S13 led to an increase in band gap energy. The estimated band gap energies of Cu12−xZnxSb4S13 films ranges from 1.49 to 1.6 eV, while the band gaps of Cu12Sb4−xBixS13 films increases from 1.49 to 1.72 eV with increasing x.
An ab initio study of the magnetic properties of strontium hexaferrite
Authors: Tejera-Centeno C. , Gallego S. , Cerdá J. I. 
Published: January 2021

AbstractThe magnetic properties of $${\text{SrFe}}_{12}{\text{O}}_{19}$$

SrFe
12

O
19

, a paradigmatic hexaferrite for permanent magnet applications, have been addressed in detail combining density functional theory including spin–orbit coupling and a Hubbard U term with Monte Carlo simulations. This multiscale approach allows to estimate the Néel temperature of the material from ab initio exchange constants, and to determine the influence of different computational conditions on the magnetic properties by direct comparison versus available experimental data. It is found that the dominant influence arises from the choice of the Hubbard U term, with a value in the 2–3 eV range as the most adequate to quantitatively reproduce the two most relevant magnetic properties of this material, namely: its large perpendicular magnetocrystalline anisotropy and its elevated Néel temperature.
Biting midge dynamics and bluetongue transmission: a multiscale model linking catch data with climate and disease outbreaks
Authors: Möhlmann Tim W. R. , Keeling Matt J. , Wennergren Uno , Favia Guido , Santman-Berends Inge , Takken Willem , Koenraadt Constantianus J. M. , Brand Samuel P. C. 
Published: January 2021

AbstractBluetongue virus (BTV) serotype 8 has been circulating in Europe since a major outbreak occurred in 2006, causing economic losses to livestock farms. The unpredictability of the biting activity of midges that transmit BTV implies difficulty in computing accurate transmission models. This study uniquely integrates field collections of midges at a range of European latitudes (in Sweden, The Netherlands, and Italy), with a multi-scale modelling approach. We inferred the environmental factors that influence the dynamics of midge catching, and then directly linked predicted midge catches to BTV transmission dynamics. Catch predictions were linked to the observed prevalence amongst sentinel cattle during the 2007 BTV outbreak in The Netherlands using a dynamic transmission model. We were able to directly infer a scaling parameter between daily midge catch predictions and the true biting rate per cow per day. Compared to biting rate per cow per day the scaling parameter was around 50% of 24 h midge catches with traps. Extending the estimated biting rate across Europe, for different seasons and years, indicated that whilst intensity of transmission is expected to vary widely from herd to herd, around 95% of naïve herds in western Europe have been at risk of sustained transmission over the last 15 years.
Thresholding of the Elliott-Yafet spin-flip scattering in multi-sublattice magnets by the respective exchange energies
Authors: Born Artur , Decker Régis , Büchner Robby , Haverkamp Robert , Ruotsalainen Kari , Bauer Karl , Pietzsch Annette , Föhlisch Alexander 
Published: January 2021

AbstractHow different microscopic mechanisms of ultrafast spin dynamics coexist and interplay is not only relevant for the development of spintronics but also for the thorough description of physical systems out-of-equilibrium. In pure crystalline ferromagnets, one of the main microscopic mechanism of spin relaxation is the electron-phonon (el-ph) driven spin-flip, or Elliott-Yafet, scattering. Unexpectedly, recent experiments with ferro- and ferrimagnetic alloys have shown different dynamics for the different sublattices. These distinct sublattice dynamics are contradictory to the Elliott-Yafet scenario. In order to rationalize this discrepancy, it has been proposed that the intra- and intersublattice exchange interaction energies must be considered in the microscopic demagnetization mechanism, too. Here, using a temperature-dependent x-ray emission spectroscopy (XES) method, we address experimentally the element specific el-ph angular momentum transfer rates, responsible for the spin-flips in the respective (sub)lattices of Fe$$_{20}$$

20

Ni$$_{80}$$

80

, Fe$$_{50}$$

50

Ni$$_{50}$$

50

and pure nickel single crystals. We establish how the deduced rate evolution with the temperature is linked to the exchange coupling constants reported for different alloy stoichiometries and how sublattice exchange energies threshold the related el-ph spin-flip channels. Thus, these results evidence that the Elliott-Yafet spin-flip scattering, thresholded by sublattice exchange energies, is the relevant microscopic process to describe sublattice dynamics in alloys and elemental magnetic systems.
Fabrication and temperature-dependent electrical characterization of a C-shape nanowire patterned by a DNA origami
Authors: Bayrak Türkan , Martinez-Reyes Amanda , Arce David Daniel Ruiz , Kelling Jeffrey , Samano Enrique C , Erbe Artur 
Published: January 2021

AbstractWe introduce a method based on directed molecular self-assembly to manufacture and electrically characterise C-shape gold nanowires which clearly deviate from typical linear shape due to the design of the template guiding the assembly. To this end, gold nanoparticles are arranged in the desired shape on a DNA-origami template and enhanced to form a continuous wire through electroless deposition. C-shape nanowires with a size below 150nm on a $${\hbox {SiO}_2}/\hbox {Si}$$

SiO
2

/
Si

substrate are contacted with gold electrodes by means of electron beam lithography. Charge transport measurements of the nanowires show hopping, thermionic and tunneling transports at different temperatures in the 4.2K to 293K range. The different transport mechanisms indicate that the C-shape nanowires consist of metallic segments which are weakly coupled along the wires.
Three-dimensional modeling of in-ground cathodic protection systems with deforming anodes
Authors: Mansouri Abraham , Binali Alreem Essa , Khan Najeeb , Zamanzadeh Mehrooz , Taheri Peyman 
Published: January 2021

AbstractThe design of sacrificial cathodic protection (CP) systems conventionally involves steady-state assumptions, which means design parameters are considered constant during the in-service life of CP systems. In contrast, it is evident by experimental observations (including field measurements) that cathodic protection is a transient process due to variations in electrolyte properties such as seasonal changes in electrical conductivity of soil, depletion of anodes, and formation of corrosion deposits on anode material surface, to name a few. The lack of practical time-dependent models on this critical issue is apparent in the literature; accordingly, in this study, a pseudo transient electrochemical model is adopted to highlight the transient behavior of cathodic protection systems and investigate key differences with steady-state behavior. For the sake of demonstration, the developed model is used to simulate the time-dependent performance of a sacrificial anode bed for cathodic protection of screw-pile foundations. The methodology proposed in this study can be used by corrosion engineers to improve and optimize the design of CP systems and numerically estimate the performance of sacrificial anodes and the level of protection over time.
LIM Homeobox 4 (lhx4) regulates retinal neural differentiation and visual function in zebrafish
Authors: Guo Rui , Ge Kangkang , Wang Yuying , Lu Minxia , Li Fei , Tian Lili , Gan Lin , Sheng Donglai 
Published: January 2021

AbstractLIM homeobox 4 (LHX4) is expressed in the photoreceptors (PRs) of the outer nuclear layer (ONL) and bipolar cells (BCs) of the inner nuclear layer (INL) in mouse and chicken retina. It regulates the subtype-specific development of rod BCs and cone BCs in the mouse retina. However, no report has been published on its expression and function in the zebrafish retina. In this study, we assessed the expression of Lhx4 using in situ hybridization (ISH) technique and explored its role in zebrafish (Danio rerio) retinal development via morpholino (MO) technology. We found that the expression oflhx4in the zebrafish retina begins 48 h post-fertilization (hpf) and is continuously expressed in the ONL and INL. A zebrafish model constructed withlhx4knockdown in the eyes through vivo-MO revealed that:lhx4knockdown inhibits the differentiation of Parvalbumin+amacrine cells (ACs) and Rhodopsin+rod photoreceptors (RPs), enhances the expression of visual system homeobox 2 (vsx2); and damages the responses of zebrafish to light stimulus, without affecting the differentiation of OFF-BCs and rod BCs, and apoptosis in the retina. These findings reveal thatlhx4regulates neural differentiation in the retina and visual function during zebrafish embryonic development.
A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity
Authors: Bernhardt Laura , Dittrich Marcus , El-Merahbi Rabih , Saliba Antoine-Emmanuel , Müller Tobias , Sumara Grzegorz , Vogel Jörg , Nichols-Burns Stefanie , Mitchell Megan , Haaf Thomas , El Hajj Nady 
Published: January 2021

AbstractPaternal obesity is known to have a negative impact on the male’s reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of theSamd4bandGata6gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of bothGata6andSamd4bduring differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.
A set of composite, non-redundant EEG measures of NREM sleep based on the power law scaling of the Fourier spectrum
Authors: Bódizs Róbert , Szalárdy Orsolya , Horváth Csenge , Ujma Péter P. , Gombos Ferenc , Simor Péter , Pótári Adrián , Zeising Marcel , Steiger Axel , Dresler Martin 
Published: January 2021

AbstractFeatures of sleep were shown to reflect aging, typical sex differences and cognitive abilities of humans. However, these measures are characterized by redundancy and arbitrariness. Our present approach relies on the assumptions that the spontaneous human brain activity as reflected by the scalp-derived electroencephalogram (EEG) during non-rapid eye movement (NREM) sleep is characterized by arrhythmic, scale-free properties and is based on the power law scaling of the Fourier spectra with the additional consideration of the rhythmic, oscillatory waves at specific frequencies, including sleep spindles. Measures derived are the spectral intercept and slope, as well as the maximal spectral peak amplitude and frequency in the sleep spindle range, effectively reducing 191 spectral measures to 4, which were efficient in characterizing known age-effects, sex-differences and cognitive correlates of sleep EEG. Future clinical and basic studies are supposed to be significantly empowered by the efficient data reduction provided by our approach.
On the stiffness of surfaces with non-Gaussian height distribution
Authors: Pérez-Ràfols Francesc , Almqvist Andreas 
Published: January 2021

AbstractIn this work, the stiffness, i.e., the derivative of the load-separation curve, is studied for self-affine fractal surfaces with non-Gaussian height distribution. In particular, the heights of the surfaces are assumed to follow a Weibull distribution. We find that a linear relation between stiffness and load, well established for Gaussian surfaces, is not obtained in this case. Instead, a power law, which can be motivated by dimensionality analysis, is a better descriptor. Also unlike Gaussian surfaces, we find that the stiffness curve is no longer independent of the Hurst exponent in this case. We carefully asses the possible convergence errors to ensure that our conclusions are not affected by them.
Ex vivo culture of intact human patient derived pancreatic tumour tissue
Authors: Kokkinos John , Sharbeen George , Haghighi Koroush S. , Ignacio Rosa Mistica C. , Kopecky Chantal , Gonzales-Aloy Estrella , Youkhana Janet , Timpson Paul , Pereira Brooke A. , Ritchie Shona , Pandzic Elvis , Boyer Cyrille , Davis Thomas P. , Butler Lisa M. , Goldstein David , McCarroll Joshua A. , Phillips Phoebe A. 
Published: January 2021

AbstractThe poor prognosis of pancreatic ductal adenocarcinoma (PDAC) is attributed to the highly fibrotic stroma and complex multi-cellular microenvironment that is difficult to fully recapitulate in pre-clinical models. To fast-track translation of therapies and to inform personalised medicine, we aimed to develop a whole-tissue ex vivo explant model that maintains viability, 3D multicellular architecture, and microenvironmental cues of human pancreatic tumours. Patient-derived surgically-resected PDAC tissue was cut into 1–2 mm explants and cultured on gelatin sponges for 12 days. Immunohistochemistry revealed that human PDAC explants were viable for 12 days and maintained their original tumour, stromal and extracellular matrix architecture. As proof-of-principle, human PDAC explants were treated with Abraxane and we observed different levels of response between patients. PDAC explants were also transfected with polymeric nanoparticles + Cy5-siRNA and we observed abundant cytoplasmic distribution of Cy5-siRNA throughout the PDAC explants. Overall, our novel model retains the 3D architecture of human PDAC and has advantages over standard organoids: presence of functional multi-cellular stroma and fibrosis, and no tissue manipulation, digestion, or artificial propagation of organoids. This provides unprecedented opportunity to study PDAC biology including tumour-stromal interactions and rapidly assess therapeutic response to drive personalised treatment.
Evaluation and comparison of recombinase polymerase amplification coupled with lateral-flow bioassay for Escherichia coli O157:H7 detection using different genes
Authors: Rani Alka , Ravindran Vivek B. , Surapaneni Aravind , Shahsavari Esmaeil , Haleyur Nagalakshmi , Mantri Nitin , Ball Andrew S. 
Published: January 2021

AbstractShiga toxin-producing Escherichia coli serotype O157:H7 is a food and waterborne zoonotic pathogen causing gastroenteritis in humans. Rapid and simple detection in water and food is imperative to control its spread. However, traditional microbial detection approaches are time-consuming, expensive and complex to operate at the point-of-care without professional training. We present a rapid, simple, sensitive, specific and portable method for detection of E. coli O157:H7 in drinking water, apple juice and milk. We evaluated the effect of gene selection in detecting E. coli O157:H7 using recombinase polymerase amplification coupled with a lateral flow assay using rfbE, fliC and stx gene targets. As low as 100 ag and 1 fg DNA, 4–5 CFU/mL and 101 CFU/mL of E. coli O157:H7 was detected using the stx and rfbE gene targets respectively with 100% specificity, whilst the detection limit was 10 fg DNA and 102 CFU/mL for the fliC gene target, with 72.8% specificity. The RPA-LFA can be completed within 8 min at temperatures between 37 and 42 °C with reduced handling and simple equipment requirements. The test threshold amplification of the target was achieved in 5–30 min of incubation. In conclusion, RPA-LFA represents a potential rapid and effective alternative to conventional methods for the monitoring of E. coli O157:H7 in food and water.
Chondroprotective effects of purple corn anthocyanins on advanced glycation end products induction through suppression of NF-κB and MAPK signaling
Authors: Chuntakaruk Hathaichanok , Kongtawelert Prachya , Pothacharoen Peraphan 
Published: January 2021

AbstractFormation of advanced glycation end products (AGEs), which are associated with diabetes mellitus, contributes to prominent features of osteoarthritis, i.e., inflammation-mediated destruction of articular cartilage. Among the phytochemicals which play a role in anti-inflammatory effects, anthocyanins have also been demonstrated to have anti-diabetic properties. Purple corn is a source of three major anthocyanins: cyanidin-3-O-glucoside, pelargonidin-3-O-glucoside and peonidin-3-O-glucoside. Purple corn anthocyanins have been demonstrated to be involved in the reduction of diabetes-associated inflammation, suggesting that they may have a beneficial effect on diabetes-mediated inflammation of cartilage. This investigation of the chondroprotective effects of purple corn extract on cartilage degradation found a reduction in glycosaminoglycans released from AGEs induced cartilage explants, corresponding with diminishing of uronic acid loss of the cartilage matrix. Investigation of the molecular mechanisms in human articular chondrocytes showed the anti-inflammatory effect of purple corn anthocyanins and the metabolite, protocatechuic acid (PCA) on AGEs induced human articular chondrocytes via inactivation of the NFκb and MAPK signaling pathways. This finding suggests that purple corn anthocyanins and PCA may help ameliorate AGEs mediated inflammation and diabetes-mediated cartilage degradation.
Enhanced polyhydroxybutyrate (PHB) production by newly isolated rare actinomycetes Rhodococcus sp. strain BSRT1-1 using response surface methodology
Authors: Trakunjae Chanaporn , Boondaeng Antika , Apiwatanapiwat Waraporn , Kosugi Akihiko , Arai Takamitsu , Sudesh Kumar , Vaithanomsat Pilanee 
Published: January 2021

AbstractPoly-β-hydroxybutyrate (PHB) is a biodegradable polymer, synthesized as carbon and energy reserve by bacteria and archaea. To the best of our knowledge, this is the first report on PHB production by a rare actinomycete species, Rhodococcus pyridinivorans BSRT1-1. Response surface methodology (RSM) employing central composite design, was applied to enhance PHB production in a flask scale. A maximum yield of 3.6 ± 0.5 g/L in biomass and 43.1 ± 0.5 wt% of dry cell weight (DCW) of PHB were obtained when using RSM optimized medium, which was improved the production of biomass and PHB content by 2.5 and 2.3-fold, respectively. The optimized medium was applied to upscale PHB production in a 10 L stirred-tank bioreactor, maximum biomass of 5.2 ± 0.5 g/L, and PHB content of 46.8 ± 2 wt% DCW were achieved. Furthermore, the FTIR and 1H NMR results confirmed the polymer as PHB. DSC and TGA analysis results revealed the melting, glass transition, and thermal decomposition temperature of 171.8, 4.03, and 288 °C, respectively. In conclusion, RSM can be a promising technique to improve PHB production by a newly isolated strain of R. pyridinivorans BSRT1-1 and the properties of produced PHB possessed similar properties compared to commercial PHB.