bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway
Authors: Agić Heda , Högström Anette E. S. , Moczydłowska Małgorzata , Jensen Sören , Palacios Teodoro , Meinhold Guido , Ebbestad Jan Ove R. , Taylor Wendy L. , Høyberget Magne 
Published: October 2019

AbstractEukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic.Cyathinema digermulensegen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration.C.digermulenseshares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity,C.digermulensewas a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstätten.
In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria
Authors: Blaskovich Mark A. T. , Elliott Alysha G. , Kavanagh Angela M. , Ramu Soumya , Cooper Matthew A. 
Published: October 2019

AbstractAcne is a common skin affliction that involves excess sebum production and modified lipid composition, duct blockage, colonization by bacteria, and inflammation. Acne drugs target one or more of these steps, with antibiotics commonly used to treat the microbial infection for moderate to severe cases. Whilst a number of other acne therapies are purported to possess antimicrobial activity, this has been poorly documented in many cases. We conducted a comparative analysis of the activity of common topical acne drugs against the principal etiological agent associated with acne: the aerotolerant anaerobic Gram-positive organism Propionibacterium acnes (recently renamed as Cutibacterium acnes). We also assessed their impact on other bacteria that could also be affected by topical treatments, including both antibiotic-sensitive and antibiotic-resistant strains, using broth microdilution assay conditions. Drugs designated specifically as antibiotics had the greatest potency, but lost activity against resistant strains. The non-antibiotic acne agents did possess widespread antimicrobial activity, including against resistant strains, but at substantially higher concentrations. Hence, the antimicrobial activity of non-antibiotic acne agents may provide protection against a background of increased drug-resistant bacteria.
Topological Indices of Proteins
Authors: Melnikov Dmitry , Niemi Antti J. , Sedrakyan Ara 
Published: October 2019

AbstractProtein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons to introduce a topological classification of folded states of proteins, for example, using the self-linking number of the corresponding framed curves. In this paper we extend this classification to the discrete version, taking advantage of the “randomness” of such curves. Known definitions of the self-linking number apply to non-singular framings: for example, the Frenet framing cannot be used if the curve has inflection points. However, in the discrete proteins the special points are naturally resolved. Consequently, a separate integer topological characteristics can be introduced, which takes into account the intrinsic features of the special points. This works well for the proteins in our analysis, for which we compute integer topological indices associated with the singularities of the Frenet framing. We show how a version of the Calugareanu’s theorem is satisfied for the associated self-linking number of a discrete curve. Since the singularities of the Frenet framing correspond to the structural motifs of proteins, we propose topological indices as a technical tool for the description of the folding dynamics of proteins.
Epidemiological and time series analysis of haemorrhagic fever with renal syndrome from 2004 to 2017 in Shandong Province, China
Authors: Zhang Chao , Fu Xiao , Zhang Yuanying , Nie Cuifang , Li Liu , Cao Haijun , Wang Junmei , Wang Baojia , Yi Shuying , Ye Zhen 
Published: October 2019

AbstractShandong Province is an area of China with a high incidence of haemorrhagic fever with renal syndrome (HFRS); however, the general epidemic trend of HFRS in Shandong remains unclear. Therefore, we established a mathematical model to predict the incidence trend of HFRS and used Joinpoint regression analysis, a generalised additive model (GAM), and other methods to evaluate the data. Incidence data from the first half of 2018 were included in a range predicted by a modified sum autoregressive integrated moving average-support vector machine (ARIMA-SVM) combination model. The highest incidence of HFRS occurred in October and November, and the annual mortality rate decreased by 7.3% (p < 0.05) from 2004 to 2017. In cold months, the incidence of HFRS increased by 4%, −1%, and 0.8% for every unit increase in temperature, relative humidity, and rainfall, respectively; in warm months, this incidence changed by 2%, −3%, and 0% respectively. Overall, HFRS incidence and mortality in Shandong showed a downward trend over the past 10 years. In both cold and warm months, the effects of temperature, relative humidity, and rainfall on HFRS incidence varied. A modified ARIMA-SVM combination model could effectively predict the occurrence of HFRS.
Improvements on activated sludge settling and flocculation using biomass-based fly ash as activator
Authors: Chen Xiaoqian , Kong Fangong , Fu Yingjuan , Si Chuanling , Fatehi Pedram 
Published: October 2019

AbstractBiomass-based fly ash and wastewater are undesired products of the pulping industry. Recently, the use of biomass-based fly ash as an adsorbent (i.e., a valued material) for constituents of wastewater effluents was reported. In this work, the settling performance and properties of activated sludge were studied in the presence of fly ash. Upon mixing, fly ash increased the zeta potential of the sludge from −31 mV to −28 mV, which was due to the release of cationic ions from fly ash in the sludge suspension. The sludge settling and its flocculation affinity were improved through the complexation of flocs and released cation ions from fly ash. The relationships between the protein/polysaccharide (PN/PS) ratio and the content of extracellular polymeric substances (EPS) as well as the ratio and the properties of the sludge flocs were determined. A correlation between the total loosely bound-EPS (LB-EPS) content and the effluent suspended solids (ESS) (Pearson’s coefficient, rp = 0.83) was observed. The performance of sludge flocculation and settling were much more closely correlated with LB-EPS than with tightly bound EPS (TB-EPS). Scanning electron microscopy (SEM) analysis of sludge flocs before and after EPS extraction showed that the sludge flocs contained a large number of microorganisms, mainly Bacillus and Cocci. The amount of LB-EPS had an adverse influence on bioflocculation, effluent clarification and sludge settling affinity. The sludge properties had a moderate relationship with the PN/PS ratio of LB-EPS. Also, no correlation could be established between the ratio and the TB-EPS content.
TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes
Authors: Jensen Kamilla Kjærgaard , Rantos Vasileios , Jappe Emma Christine , Olsen Tobias Hegelund , Jespersen Martin Closter , Jurtz Vanessa , Jessen Leon Eyrich , Lanzarotti Esteban , Mahajan Swapnil , Peters Bjoern , Nielsen Morten , Marcatili Paolo 
Published: October 2019

AbstractThe interaction between the class I major histocompatibility complex (MHC), the peptide presented by the MHC and the T-cell receptor (TCR) is a key determinant of the cellular immune response. Here, we present TCRpMHCmodels, a method for accurate structural modelling of the TCR-peptide-MHC (TCR-pMHC) complex. This TCR-pMHC modelling pipeline takes as input the amino acid sequence and generates models of the TCR-pMHC complex, with a median Cα RMSD of 2.31 Å. TCRpMHCmodels significantly outperforms TCRFlexDock, a specialised method for docking pMHC and TCR structures. TCRpMHCmodels is simple to use and the modelling pipeline takes, on average, only two minutes. Thanks to its ease of use and high modelling accuracy, we expect TCRpMHCmodels to provide insights into the underlying mechanisms of TCR and pMHC interactions and aid in the development of advanced T-cell-based immunotherapies and rational design of vaccines. The TCRpMHCmodels tool is available at http://www.cbs.dtu.dk/services/TCRpMHCmodels/.
Dynamical transitions during the collapse of inertial holes
Authors: Lu Jiakai , Corvalan Carlos M 
Published: October 2019

AbstractAt the center of a collapsing hole lies a singularity, a point of infinite curvature where the governing equations break down. It is a topic of fundamental physical interest to clarify the dynamics of fluids approaching such singularities. Here, we use scaling arguments supported by high-fidelity simulations to analyze the dynamics of an axisymmetric hole undergoing capillary collapse in a fluid sheet of small viscosity. We characterize the transitions between the different dynamical regimes —from the initial inviscid dynamics that dominate the collapse at early times to the final Stokes dynamics that dominate near the singularity— and demonstrate that the crossover hole radii for these transitions are related to the fluid viscosity by power-law relationships. The findings have practical implications for the integrity of perforated fluid films, such as bubble films and biological membranes, as well as fundamental implications for the physics of fluids converging to a singularity.
Minimization of energy transduction confers resistance to phosphine in the rice weevil, Sitophilus oryzae
Authors: Kim Kyeongnam , Yang Jeong Oh , Sung Jae-Yoon , Lee Ji-Young , Park Jeong Sun , Lee Heung-Sik , Lee Byung-Ho , Ren Yonglin , Lee Dong-Woo , Lee Sung-Eun 
Published: October 2019

AbstractInfestation of phosphine (PH3) resistant insects threatens global grain reserves. PH3 fumigation controls rice weevil (Sitophilus oryzae) but not highly resistant insect pests. Here, we investigated naturally occurring strains of S. oryzae that were moderately resistant (MR), strongly resistant (SR), or susceptible (wild-type; WT) to PH3 using global proteome analysis and mitochondrial DNA sequencing. Both PH3 resistant (PH3–R) strains exhibited higher susceptibility to ethyl formate-mediated inhibition of cytochrome c oxidase than the WT strain, whereas the disinfectant PH3 concentration time of the SR strain was much longer than that of the MR strain. Unlike the MR strain, which showed altered expression levels of genes encoding metabolic enzymes involved in catabolic pathways that minimize metabolic burden, the SR strain showed changes in the mitochondrial respiratory chain. Our results suggest that the acquisition of strong PH3 resistance necessitates the avoidance of oxidative phosphorylation through the accumulation of a few non-synonymous mutations in mitochondrial genes encoding complex I subunits as well as nuclear genes encoding dihydrolipoamide dehydrogenase, concomitant with metabolic reprogramming, a recognized hallmark of cancer metabolism. Taken together, our data suggest that reprogrammed metabolism represents a survival strategy of SR insect pests for the compensation of minimized energy transduction under anoxic conditions. Therefore, understanding the resistance mechanism of PH3–R strains will support the development of new strategies to control insect pests.
Nestling carcasses from colonially breeding wading birds: patterns of access and energetic relevance for a vertebrate scavenger community
Authors: Gabel Wray , Frederick Peter , Zabala Jabi 
Published: October 2019

AbstractEnergy transfer is fundamental to ecosystem processes, affecting productivity and community structure. Large aggregations of colonially breeding birds are known as nutrient sources through deposition of feces, but also may deposit large quantities of energy in the form of dead nestlings. The magnitude and ecological relevance of this process to the scavenger community is poorly understood. We used trail cameras to monitor the fates of size-appropriate chicken carcasses in heron colonies in order to quantify the proportion of available fallen nestlings that were consumed by scavengers in the Everglades of Florida, USA. Overall, 85% of 160 carcasses were consumed, with Turkey Vultures (Cathartes aura, 47%) and American Alligators (Alligator mississippiensis, 29%) being the primary consumers. Probability of consumption by alligators or vultures was related to distance from nest to water, local nesting density, and colony type. Consumption probabilities of both scavengers in relation to habitat covariates suggested clear resource partitioning promoting coexistence. We estimate fallen nestlings throughout this ecosystem could support 16% of the alligator population and 147 adult Turkey Vultures during a nesting season. This work indicates that fallen nestlings can serve as an important source of energy for scavengers at colonial breeding aggregations, particularly in oligotrophic systems.
Timing of follow-up blood cultures for community-onset bacteremia
Authors: Lee Ching-Chi , Yang Chao-Yung , Hsieh Chih-Chia , Hong Ming-Yuan , Lee Chung-Hsun , Tang Hung-Jen , Ko Wen-Chien 
Published: October 2019

AbstractBacteremia is associated with high morbidity and mortality, but the utility and optimal timing of follow-up blood cultures (FUBCs) remain undefined. To assess the optimal timing of FUBCs related to appropriate antibiotic therapy (AAT), adults with community-onset bacteremia and FUBCs after bacteremia onset were retrospectively studied during the 6-year period in two hospitals. Based on the time gap between the initiation of AAT and FUBC sampling, 1,247 eligible patients were categorized as FUBCs prior to AAT (65 patients, 5.2%), 0–3 days (202, 16.2%), 3.1–6 days (470, 37.7%), 6.1–9 days (299, 24.0%), and ≥9 days (211, 16.9%) after AAT. The prognostic impact of the growth of the same bacteria in FUBCs on 30-day mortality was evidenced only in patients with FUBCs at 3.1–6 days after AAT (adjusted odds ratio [AOR], 3.75; P < 0.001), not in those with FUBCs prior to AAT (AOR, 2.86; P = 0.25), 0–3 days (AOR, 0.39; P = 0.08), 6.1–9 days (AOR, 2.19; P = 0.32), and ≥9 days (AOR, 0.41; P = 0.41) of AAT, after adjusting independent factors of 30-day mortality recognized by the multivariable regression in each category. Conclusively, persistent bacteremia in FUBCs added prognostic significance in the management of adults with community-onset bacteremia after 3.1–6 days of AAT.
DNA sequence-dependent chromatin architecture and nuclear hubs formation
Authors: Jabbari Kamel , Chakraborty Maharshi , Wiehe Thomas 
Published: October 2019

AbstractIn this study, by exploring chromatin conformation capture data, we show that the nuclear segregation of Topologically Associated Domains (TADs) is contributed by DNA sequence composition. GC-peaks and valleys of TADs strongly influence interchromosomal interactions and chromatin 3D structure. To gain insight on the compositional and functional constraints associated with chromatin interactions and TADs formation, we analysed intra-TAD and intra-loop GC variations. This led to the identification of clear GC-gradients, along which, the density of genes, super-enhancers, transcriptional activity, and CTCF binding sites occupancy co-vary non-randomly. Further, the analysis of DNA base composition of nucleolar aggregates and nuclear speckles showed strong sequence-dependant effects. We conjecture that dynamic DNA binding affinity and flexibility underlay the emergence of chromatin condensates, their growth is likely promoted in mechanically soft regions (GC-rich) of the lowest chromatin and nucleosome densities. As a practical perspective, the strong linear association between sequence composition and interchromosomal contacts can help define consensus chromatin interactions, which in turn may be used to study alternative states of chromatin architecture.
Stateful Three-Input Logic with Memristive Switches
Authors: Siemon A. , Drabinski R. , Schultis M. J. , Hu X. , Linn E. , Heittmann A. , Waser R. , Querlioz D. , Menzel S. , Friedman J. S. 
Published: October 2019

AbstractMemristive switches are able to act as both storage and computing elements, which make them an excellent candidate for beyond-CMOS computing. In this paper, multi-input memristive switch logic is proposed, which enables the function X OR (Y NOR Z) to be performed in a single-step with three memristive switches. This ORNOR logic gate increases the capabilities of memristive switches, improving the overall system efficiency of a memristive switch-based computing architecture. Additionally, a computing system architecture and clocking scheme are proposed to further utilize memristive switching for computation. The system architecture is based on a design where multiple computational function blocks are interconnected and controlled by a master clock that synchronizes system data processing and transfer. The clocking steps to perform a full adder with the ORNOR gate are presented along with simulation results using a physics-based model. The full adder function block is integrated into the system architecture to realize a 64-bit full adder, which is also demonstrated through simulation.
Spatial Surface Charge Engineering for Electrochemical Electrodes
Authors: Xie Lingyun , Wang Peng , Qian Yinping , Rao Lujia , Yin Hongjie , Wang Xingyu , Chen Hedong , Zhou Guofu , Nötzel Richard 
Published: October 2019

AbstractWe introduce a novel concept for the design of functional surfaces of materials: Spatial surface charge engineering. We exploit the concept for an all-solid-state, epitaxial InN/InGaN-on-Si reference electrode to replace the inconvenient liquid-filled reference electrodes, such as Ag/AgCl. Reference electrodes are universal components of electrochemical sensors, ubiquitous in electrochemistry to set a constant potential. For subtle interrelation of structure design, surface morphology and the unique surface charge properties of InGaN, the reference electrode has less than 10 mV/decade sensitivity over a wide concentration range, evaluated for KCl aqueous solutions and less than 2 mV/hour long-time drift over 12 hours. Key is a nanoscale charge balanced surface for the right InGaN composition, InN amount and InGaN surface morphology, depending on growth conditions and layer thickness, which is underpinned by the surface potential measured by Kelvin probe force microscopy. When paired with the InN/InGaN quantum dot sensing electrode with super-Nernstian sensitivity, where only structure design and surface morphology are changed, this completes an all-InGaN-based electrochemical sensor with unprecedented performance.
Prion strain-dependent tropism is maintained between spleen and granuloma and relies on lymphofollicular structures
Authors: Al-Dybiat Iman , Moudjou Mohammed , Martin Davy , Reine Fabienne , Herzog Laetitia , Truchet Sandrine , Berthon Patricia , Laude Hubert , Rezaei Human , Andréoletti Olivier , Béringue Vincent , Sibille Pierre 
Published: October 2019

AbstractIn peripherally acquired prion diseases, prions move through several tissues of the infected host, notably in the lymphoid tissue, long before the occurrence of neuroinvasion. Accumulation can even be restricted to the lymphoid tissue without neuroinvasion and clinical disease. Several experimental observations indicated that the presence of differentiated follicular dendritic cells (FDCs) in the lymphoid structures and the strain type are critical determinants of prion extraneural replication. In this context, the report that granulomatous structures apparently devoid of FDCs could support prion replication raised the question of the requirements for prion lymphotropism. The report also raised the possibility that nonlymphoid tissue-tropic prions could actually target these inflammatory structures. To investigate these issues, we examined the capacity of closely related prions, albeit with opposite lymphotropism (or FDC dependency), for establishment in experimentally-induced granuloma in ovine PrP transgenic mice. We found a positive correlation between the prion capacity to accumulate in the lymphoid tissue and granuloma, regardless of the prion detection method used. Surprisingly, we also revealed that the accumulation of prions in granulomas involved lymphoid-like structures associated with the granulomas and containing cells that stain positive for PrP, Mfge-8 but not CD45 that strongly suggest FDCs. These results suggest that the FDC requirement for prion replication in lymphoid/inflammatory tissues may be strain-dependent.
Velocity-dependent friction enhances tribomechanical differences between monolayer and multilayer graphene
Authors: Ptak F. , Almeida C. M. , Prioli R. 
Published: October 2019

AbstractThe influence of sliding speed in the nanoscale friction forces between a silicon tip and monolayer and multilayer graphene were investigated with the use of an atomic force microscope. We found that the friction forces increase linearly with the logarithm of the sliding speed in a highly layer-dependent way. The increase in friction forces with velocity is amplified at the monolayer. The amplification of the friction forces with velocity results from the introduction of additional corrugation in the interaction potential driven by the tip movement. This effect can be interpreted as a manifestation of local thermally induced surface corrugations in nanoscale influencing the hopping dynamics of the atoms at the contact. These experimental observations were explained by modeling the friction forces with the thermally activated Prandtl-Tomlinson model. The model allowed determination of the interaction potential between tip and graphene, critical forces, and attempt frequencies of slip events. The latter was observed to be dominated by the effective contact stiffness and independent of the number of layers.