bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-inflammatory mechanisms of the novel cytokine interleukin-38 in allergic asthma
Authors: Sun Xiaoyu , Hou Tianheng , Cheung Edwin , Iu Tiffany Nga-Teng , Tam Victor Wai-Hou , Chu Ida Miu-Ting , Tsang Miranda Sin-Man , Chan Paul Kay-Sheung , Lam Christopher Wai-Kei , Wong Chun-Kwok
Published: October 2019

We elucidated the anti-inflammatory mechanisms of IL-38 in allergic asthma. Human bronchial epithelial cells and eosinophils were cocultured upon stimulation with the viral RLR ligand poly (I:C)/LyoVec or infection-related cytokine TNF-α to induce expression of cytokines/chemokines/adhesion molecules. House dust mite (HDM)-induced allergic asthma and humanized allergic asthma NOD/SCID murine models were established to assess anti-inflammatory mechanisms in vivo. IL-38 significantly inhibited induced proinflammatory IL-6, IL-1β, CCL5, and CXCL10 production, and antiviral interferon-β and intercellular adhesion molecule-1 expression in the coculture system. Mass cytometry and RNA-sequencing analysis revealed that IL-38 could antagonize the activation of the intracellular STAT1, STAT3, p38 MAPK, ERK1/2, and NF-κB pathways, and upregulate the expression of the host defense-related genePOU2AF1and anti-allergic response geneRGS13. Intraperitoneal injection of IL-38 into HDM-induced allergic asthma mice could ameliorate airway hyperreactivity by decreasing the accumulation of eosinophils in the lungs and inhibiting the expression of the Th2-related cytokines IL-4, IL-5, and IL-13 in the bronchoalveolar lavage fluid (BALF) and lung homogenates. Histological examination indicated lung inflammation was alleviated by reductions in cell infiltration and goblet cell hyperplasia, together with reduced Th2, Th17, and innate lymphoid type 2 cell numbers but increased proportions of regulatory T cells in the lungs, spleen, and lymph nodes. IL-38 administration suppressed airway hyperreactivity and asthma-related IL-4 and IL-5 expression in humanized mice, together with significantly decreased CCR3+eosinophil numbers in the BALF and lungs, and a reduced percentage of human CD4+CRTH2+Th2 cells in the lungs and mediastinal lymph nodes. Together, our results demonstrated the anti-inflammatory mechanisms of IL-38 and provided a basis for the development of a regulatory cytokine-based treatment for allergic asthma.
Nickel sulfide nanocrystals on nitrogen-doped porous carbon nanotubes with high-efficiency electrocatalysis for room-temperature sodium-sulfur batteries
Authors: Yan Zichao , Xiao Jin , Lai Weihong , Wang Li , Gebert Florian , Wang Yunxiao , Gu Qinfen , Liu Hui , Chou Shu-Lei , Liu Huakun , Dou Shi-Xue
Published: October 2019

Polysulfide dissolution and slow electrochemical kinetics of conversion reactions lead to low utilization of sulfur cathodes that inhibits further development of room-temperature sodium-sulfur batteries. Here we report a multifunctional sulfur host, NiS2 nanocrystals implanted in nitrogen-doped porous carbon nanotubes, which is rationally designed to achieve high polysulfide immobilization and conversion. Attributable to the synergetic effect of physical confinement and chemical bonding, the high electronic conductivity of the matrix, closed porous structure, and polarized additives of the multifunctional sulfur host effectively immobilize polysulfides. Significantly, the electrocatalytic behaviors of the Lewis base matrix and the NiS2 component are clearly evidenced by operando synchrotron X-ray diffraction and density functional theory with strong adsorption of polysulfides and high conversion of soluble polysulfides into insoluble Na2S2/Na2S. Thus, the as-obtained sulfur cathodes exhibit excellent performance in room-temperature Na/S batteries.
Altered dendritic spine function and integration in a mouse model of fragile X syndrome
Authors: Booker Sam A. , Domanski Aleksander P. F. , Dando Owen R. , Jackson Adam D. , Isaac John T. R. , Hardingham Giles E. , Wyllie David J. A. , Kind Peter C.
Published: October 2019

Cellular and circuit hyperexcitability are core features of fragile X syndrome and related autism spectrum disorder models. However, the cellular and synaptic bases of this hyperexcitability have proved elusive. We report in a mouse model of fragile X syndrome, glutamate uncaging onto individual dendritic spines yields stronger single-spine excitation than wild-type, with more silent spines. Furthermore, fewer spines are required to trigger an action potential with near-simultaneous uncaging at multiple spines. This is, in part, from increased dendritic gain due to increased intrinsic excitability, resulting from reduced hyperpolarization-activated currents, and increased NMDA receptor signaling. Using super-resolution microscopy we detect no change in dendritic spine morphology, indicating no structure-function relationship at this age. However, ultrastructural analysis shows a 3-fold increase in multiply-innervated spines, accounting for the increased single-spine glutamate currents. Thus, loss of FMRP causes abnormal synaptogenesis, leading to large numbers of poly-synaptic spines despite normal spine morphology, thus explaining the synaptic perturbations underlying circuit hyperexcitability.
Single- and multi-component chiral supraparticles as modular enantioselective catalysts
Authors: Li Si , Liu Juan , Ramesar Naomi S. , Heinz Hendrik , Xu Liguang , Xu Chuanlai , Kotov Nicholas A.
Published: October 2019

Nanoscale biological assemblies exemplified by exosomes, endosomes and capsids, play crucial roles in all living systems. Supraparticles (SP) from inorganic nanoparticles (NPs) replicate structural characteristics of these bioassemblies, but it is unknown whether they can mimic their biochemical functions. Here, we show that chiral ZnS NPs self-assemble into 70–100 nm SPs that display sub-nanoscale porosity associated with interstitial spaces between constituent NPs. Similarly to photosynthetic bacterial organelles, these SPs can serve as photocatalysts, enantioselectively converting L- or D-tyrosine (Tyr) into dityrosine (diTyr). Experimental data and molecular dynamic simulations indicate that the chiral bias of the photocatalytic reaction is associated with the chiral environment of interstitial spaces and preferential partitioning of enantiomers into SPs, which can be further enhanced by co-assembling ZnS with Au NPs. Besides replicating a specific function of biological nanoassemblies, these findings establish a path to enantioselective oxidative coupling of phenols for biomedical and other needs.
Concerted dynamics of metallo-base pairs in an A/B-form helical transition
Authors: Schmidt Olivia P. , Jurt Simon , Johannsen Silke , Karimi Ashkan , Sigel Roland K. O. , Luedtke Nathan W.
Published: October 2019

Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-HgII-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-HgII-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-HgII-(N4)C base pairs and greater A-form characteristics. Ten-fold different1Jcoupling constants (15N,199Hg) are observed for (N3)C-HgII(114 Hz) versus (N4)C-HgII(1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-HgII-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding HgII, demonstrating that C-HgII-T has unique switching potential in DNA-based materials and devices.
Interfacial oxygen vacancies yielding long-lived holes in hematite mesocrystal-based photoanodes
Authors: Zhang Zhujun , Karimata Izuru , Nagashima Hiroki , Muto Shunsuke , Ohara Koji , Sugimoto Kunihisa , Tachikawa Takashi
Published: October 2019

Hematite (α-Fe2O3) is one of the most promising candidates as a photoanode materials for solar water splitting. Owing to the difficulty in suppressing the significant charge recombination, however, the photoelectrochemical (PEC) conversion efficiency of hematite is still far below the theoretical limit. Here we report thick hematite films (∼1500 nm) constructed by highly ordered and intimately attached hematite mesocrystals (MCs) for highly efficient PEC water oxidation. Due to the formation of abundant interfacial oxygen vacancies yielding a high carrier density of ∼1020 cm−3 and the resulting extremely large proportion of depletion regions with short depletion widths (<10 nm) in hierarchical structures, charge separation and collection efficiencies could be markedly improved. Moreover, it was found that long-lived charges are generated via excitation by shorter wavelength light (below ∼500 nm), thus enabling long-range hole transfer through the MC network to drive high efficiency of light-to-energy conversion under back illumination.
Sequence variants with large effects on cardiac electrophysiology and disease
Authors: Norland Kristjan , Sveinbjornsson Gardar , Thorolfsdottir Rosa B. , Davidsson Olafur B. , Tragante Vinicius , Rajamani Sridharan , Helgadottir Anna , Gretarsdottir Solveig , van Setten Jessica , Asselbergs Folkert W. , Sverrisson Jon Th. , Stephensen Sigurdur S. , Oskarsson Gylfi , Sigurdsson Emil L. , Andersen Karl , Danielsen Ragnar , Thorgeirsson Gudmundur , Thorsteinsdottir Unnur , Arnar David O. , Sulem Patrick , Holm Hilma , Gudbjartsson Daniel F. , Stefansson Kari
Published: October 2019

Features of the QRS complex of the electrocardiogram, reflecting ventricular depolarisation, associate with various physiologic functions and several pathologic conditions. We test 32.5 million variants for association with ten measures of the QRS complex in 12 leads, using 405,732 electrocardiograms from 81,192 Icelanders. We identify 190 associations at 130 loci, the majority of which have not been reported before, including associations with 21 rare or low-frequency coding variants. Assessment of genes expressed in the heart yields an additional 13 rare QRS coding variants at 12 loci. We find 51 unreported associations between the QRS variants and echocardiographic traits and cardiovascular diseases, including atrial fibrillation, complete AV block, heart failure and supraventricular tachycardia. We demonstrate the advantage of in-depth analysis of the QRS complex in conjunction with other cardiovascular phenotypes to enhance our understanding of the genetic basis of myocardial mass, cardiac conduction and disease.
Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action
Authors: Bule Pedro , Chuzel Léa , Blagova Elena , Wu Liang , Gray Melissa A. , Henrissat Bernard , Rapp Erdmann , Bertozzi Carolyn R. , Taron Christopher H. , Davies Gideon J.
Published: October 2019

Sialic acids are a family of related sugars that play essential roles in many biological events intimately linked to cellular recognition in both health and disease. Sialidases are therefore orchestrators of cellular biology and important therapeutic targets for viral infection. Here, we sought to define if uncharacterized sialidases would provide distinct paradigms in sialic acid biochemistry. We show that a recently discovered sialidase family, whose first member EnvSia156 was isolated from hot spring metagenomes, defines an unusual structural fold and active centre constellation, not previously described in sialidases. Consistent with an inverting mechanism, EnvSia156 reveals a His/Asp active center in which the His acts as a Brønsted acid and Asp as a Brønsted base in a single-displacement mechanism. A predominantly hydrophobic aglycone site facilitates accommodation of a variety of 2-linked sialosides; a versatility that offers the potential for glycan hydrolysis across a range of biological and technological platforms.
Compositional boundary layers trigger liquid unmixing in a basaltic crystal mush
Authors: Honour Victoria C. , Holness Marian B. , Charlier Bernard , Piazolo Sandra C. , Namur Olivier , Prosa Ty J. , Martin Isabelle , Helz Rosalind T. , Maclennan John , Jean Marlon M.
Published: October 2019

The separation of immiscible liquids has significant implications for magma evolution and the formation of magmatic ore deposits. We combine high-resolution imaging and electron probe microanalysis with the first use of atom probe tomography on tholeiitic basaltic glass from Hawaii, the Snake River Plain, and Iceland, to investigate the onset of unmixing of basaltic liquids into Fe-rich and Si-rich conjugates. We examine the relationships between unmixing and crystal growth, and the evolution of a nanoemulsion in a crystal mush. We identify the previously unrecognised role played by compositional boundary layers in promoting unmixing around growing crystals at melt-crystal interfaces. Our findings have important implications for the formation of immiscible liquid in a crystal mush, the interpretations of compositional zoning in crystals, and the role of liquid immiscibility in controlling magma physical properties.
Hyperdirect insula-basal-ganglia pathway and adult-like maturity of global brain responses predict inhibitory control in children
Authors: Cai Weidong , Duberg Katherine , Padmanabhan Aarthi , Rehert Rachel , Bradley Travis , Carrion Victor , Menon Vinod
Published: October 2019

Inhibitory control is fundamental to children’s self-regulation and cognitive development. Here we investigate cortical-basal ganglia pathways underlying inhibitory control in children and their adult-like maturity. We first conduct a comprehensive meta-analysis of extant neurodevelopmental studies of inhibitory control and highlight important gaps in the literature. Second, we examine cortical-basal ganglia activation during inhibitory control in children ages 9–12 and demonstrate the formation of an adult-like inhibitory control network by late childhood. Third, we develop a neural maturation index (NMI), which assesses the similarity of brain activation patterns between children and adults, and demonstrate that higher NMI in children predicts better inhibitory control. Fourth, we show that activity in the subthalamic nucleus and its effective connectivity with the right anterior insula predicts children’s inhibitory control. Fifth, we replicate our findings across multiple cohorts. Our findings provide insights into cortical-basal ganglia circuits and global brain organization underlying the development of inhibitory control.
Protein folding while chaperone bound is dependent on weak interactions
Authors: Wu Kevin , Stull Frederick , Lee Changhan , Bardwell James C. A.
Published: October 2019

It is generally assumed that protein clients fold following their release from chaperones instead of folding while remaining chaperone-bound, in part because binding is assumed to constrain the mobility of bound clients. Previously, we made the surprising observation that the ATP-independent chaperone Spy allows its client protein Im7 to fold into the native state while continuously bound to the chaperone. Spy apparently permits sufficient client mobility to allow folding to occur while chaperone bound. Here, we show that strengthening the interaction between Spy and a recently discovered client SH3 strongly inhibits the ability of the client to fold while chaperone bound. The more tightly Spy binds to its client, the more it slows the folding rate of the bound client. Efficient chaperone-mediated folding while bound appears to represent an evolutionary balance between interactions of sufficient strength to mediate folding and interactions that are too tight, which tend to inhibit folding.
Ballistic transport and boundary resistances in inhomogeneous quantum spin chains
Authors: Biella Alberto , Collura Mario , Rossini Davide , De Luca Andrea , Mazza Leonardo
Published: October 2019

Transport phenomena are central to physics, and transport in the many-body and fully-quantum regime is attracting an increasing amount of attention. It has been recently revealed that some quantum spin chains support ballistic transport of excitations at all energies. However, when joining two semi-infinite ballistic parts, such as the XX and XXZ spin-1/2 models, our understanding suddenly becomes less established. Employing a matrix-product-state ansatz of the wavefunction, we study the relaxation dynamics in this latter case. Here we show that it takes place inside a light cone, within which two qualitatively different regions coexist: an inner one with a strong tendency towards thermalization, and an outer one supporting ballistic transport. We comment on the possibility that even at infinite time the system supports stationary currents and displays a non-zero Kapitza boundary resistance. Our study paves the way to the analysis of the interplay between transport, integrability, and local defects.
Mechanical adaptability of artificial muscles from nanoscale molecular action
Authors: Lancia Federico , Ryabchun Alexander , Nguindjel Anne-Déborah , Kwangmettatam Supaporn , Katsonis Nathalie
Published: October 2019

The motion of artificial molecular machines has been amplified into the shape transformation of polymer materials that have been compared to muscles, where mechanically active molecules work together to produce a contraction. In spite of this progress, harnessing cooperative molecular motion remains a challenge in this field. Here, we show how the light-induced action of artificial molecular switches modifies not only the shape but also, simultaneously, the stiffness of soft materials. The heterogeneous design of these materials features inclusions of free liquid crystal in a liquid crystal polymer network. When the magnitude of the intrinsic interfacial tension is modified by the action of the switches, photo-stiffening is observed, in analogy with the mechanical response of activated muscle fibers, and in contrast to melting mechanisms reported so far. Mechanoadaptive materials that are capable of active tuning of rigidity will likely contribute to a bottom-up approach towards human-friendly and soft robotics.
Dopant-tuned stabilization of intermediates promotes electrosynthesis of valuable C3 products
Authors: Zhuang Tao-Tao , Nam Dae-Hyun , Wang Ziyun , Li Hui-Hui , Gabardo Christine M. , Li Yi , Liang Zhi-Qin , Li Jun , Liu Xiao-Jing , Chen Bin , Leow Wan Ru , Wu Rui , Wang Xue , Li Fengwang , Lum Yanwei , Wicks Joshua , O’Brien Colin P. , Peng Tao , Ip Alexander H. , Sham Tsun-Kong , Yu Shu-Hong , Sinton David , Sargent Edward H.
Published: October 2019

The upgrading of CO2/CO feedstocks to higher-value chemicals via energy-efficient electrochemical processes enables carbon utilization and renewable energy storage. Substantial progress has been made to improve performance at the cathodic side; whereas less progress has been made on improving anodic electro-oxidation reactions to generate value. Here we report the efficient electroproduction of value-added multi-carbon dimethyl carbonate (DMC) from CO and methanol via oxidative carbonylation. We find that, compared to pure palladium controls, boron-doped palladium (Pd-B) tunes the binding strength of intermediates along this reaction pathway and favors DMC formation. We implement this doping strategy and report the selective electrosynthesis of DMC experimentally. We achieve a DMC Faradaic efficiency of 83 ± 5%, fully a 3x increase in performance compared to the corresponding pure Pd electrocatalyst.
One thousand plant transcriptomes and the phylogenomics of green plants
Authors:   One Thousand Plant Transcriptomes Initiative
Published: October 2019

Green plants (Viridiplantae) include around 450,000–500,000 species1,2of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
A cone-beam X-ray computed tomography data collection designed for machine learning
Authors: Der Sarkissian Henri , Lucka Felix , van Eijnatten Maureen , Colacicco Giulia , Coban Sophia Bethany , Batenburg Kees Joost
Published: October 2019

Unlike previous works, this open data collection consists of X-ray cone-beam (CB) computed tomography (CT) datasets specifically designed for machine learning applications and high cone-angle artefact reduction. Forty-two walnuts were scanned with a laboratory X-ray set-up to provide not only data from a single object but from a class of objects with natural variability. For each walnut, CB projections on three different source orbits were acquired to provide CB data with different cone angles as well as being able to compute artefact-free, high-quality ground truth images from the combined data that can be used for supervised learning. We provide the complete image reconstruction pipeline: raw projection data, a description of the scanning geometry, pre-processing and reconstruction scripts using open software, and the reconstructed volumes. Due to this, the dataset can not only be used for high cone-angle artefact reduction but also for algorithm development and evaluation for other tasks, such as image reconstruction from limited or sparse-angle (low-dose) scanning, super resolution, or segmentation.
Classification of GABAergic interneurons by leading neuroscientists
Authors: Mihaljević Bojan , Benavides-Piccione Ruth , Bielza Concha , Larrañaga Pedro , DeFelipe Javier
Published: October 2019

There is currently no unique catalog of cortical GABAergic interneuron types. In 2013, we asked 48 leading neuroscientists to classify 320 interneurons by inspecting images of their morphology. That study was the first to quantify the degree of agreement among neuroscientists in morphology-based interneuron classification, showing high agreement for the chandelier and Martinotti types, yet low agreement for most of the remaining types considered. Here we present the dataset containing the classification choices by the neuroscientists according to interneuron type as well as to five prominent morphological features. These data can be used as crisp or soft training labels for learning supervised machine learning interneuron classifiers, while further analyses can try to pinpoint anatomical characteristics that make an interneuron especially difficult or especially easy to classify.
Validation of Reference Genes for Normalization of Relative qRT-PCR Studies in Papillary Thyroid Carcinoma
Authors: Razavi S. Adeleh , Afsharpad Mandana , Modarressi Mohammad Hossein , Zarkesh Maryam , Yaghmaei Parichehreh , Nasiri Shirzad , Tavangar S. Mohammad , Gholami Hanieh , Daneshafrooz Afsoon , Hedayati Mehdi
Published: October 2019

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) in thyroid tumors require accurate data normalization, however, there are no sufficient studies addressing the suitable reference genes for gene expression analysis in malignant and normal thyroid tissue specimens. The purpose of this study was to identify valid internal control genes for normalization of relative qRT-PCR studies in human papillary thyroid carcinoma tissue samples. The expression characteristics of 12 candidate reference genes (GAPDH, ACTB, HPRT1, TBP, B2M, PPIA, 18SrRNA, HMBS, GUSB, PGK1, RPLP0, and PGM1) were assessed by qRT-PCR in 45 thyroid tissue samples (15 papillary thyroid carcinoma, 15 paired normal tissues and 15 multinodular goiters). These twelve candidate reference genes were selected by a systematic literature search. GeNorm, NormFinder, and BestKeeper statistical algorithms were applied to determine the most stable reference genes. The three algorithms were in agreement in identifying GUSB and HPRT1 as the most stably expressed genes in all thyroid tumors investigated. According to the NormFinder software, the pair of genes including ‘GUSB and HPRT1’ or ‘GUSB and HMBS’ or ‘GUSB and PGM1’ were the best combinations for selection of pair reference genes. The optimal number of genes required for reliable normalization of qPCR data in thyroid tissues would be three according to calculations made by GeNorm algorithm. These results suggest that GUSB and HPRT1 are promising reference genes for normalization of relative qRT-PCR studies in papillary thyroid carcinoma.
Tracing microplastics in aquatic environments based on sediment analogies
Authors: Enders Kristina , Käppler Andrea , Biniasch Oliver , Feldens Peter , Stollberg Nicole , Lange Xaver , Fischer Dieter , Eichhorn Klaus-Jochen , Pollehne Falk , Oberbeckmann Sonja , Labrenz Matthias
Published: October 2019

Microplastics (MP) data collection from the aquatic environment is a challenging endeavour that sets apparent limitations to regional and global MP quantification. Expensive data collection causes small sample sizes and oftentimes existing data sets are compared without accounting for natural variability due to hydrodynamic processes governing the distribution of particles. In Warnow estuarine sediments (Germany) we found significant correlations between high-density polymer size fractions (≥500 µm) and sediment grain size. Among potential predictor variables (source and environmental terms) sediment grain size was the critical proxy for MP abundance. The MP sediment relationship can be explained by the force necessary to start particle transport: at the same level of fluid motion, transported sediment grains and MP particles are offset in size by one to two orders of magnitude. Determining grain-size corrected MP abundances by fractionated granulometric normalisation is recommended as a basis for future MP projections and identification of sinks and sources.
Estimating numbers of intracellular molecules through analysing fluctuations in photobleaching
Authors: Bakker Elco , Swain Peter S.
Published: October 2019

The impact of fluorescence microscopy has been limited by the difficulties of expressing measurements of fluorescent proteins in numbers of molecules. Absolute numbers enable the integration of results from different laboratories, empower mathematical modelling, and are the bedrock for a quantitative, predictive biology. Here we propose an estimator to infer numbers of molecules from fluctuations in the photobleaching of proteins tagged with Green Fluorescent Protein. Performing experiments in budding yeast, we show that our estimates of numbers agree, within an order of magnitude, with published biochemical measurements, for all six proteins tested. The experiments we require are straightforward and use only a wide-field fluorescence microscope. As such, our approach has the potential to become standard for those practising quantitative fluorescence microscopy.
Extended stable equilibrium invaded by an unstable state
Authors: Castillo-Pinto Camila , Clerc Marcel G. , González-Cortés Gregorio
Published: October 2019

Coexistence of states is an indispensable feature in the observation of domain walls, interfaces, shock waves or fronts in macroscopic systems. The propagation of these nonlinear waves depends on the relative stability of the connected equilibria. In particular, one expects a stable equilibrium to invade an unstable one, such as occur in combustion, in the spread of permanent contagious diseases, or in the freezing of supercooled water. Here, we show that an unstable state generically can invade a locally stable one in the context of the pattern forming systems. The origin of this phenomenon is related to the lower energy unstable state invading the locally stable but higher energy state. Based on a one-dimensional model we reveal the necessary features to observe this phenomenon. This scenario is fulfilled in the case of a first order spatial instability. A photo-isomerization experiment of a dye-dopant nematic liquid crystal, allow us to observe the front propagation from an unstable state.
Author Correction: The effect of endothelial nitric oxide synthase on the hemodynamics and wall mechanics in murine arteriovenous fistulas
Authors: Pike Daniel , Shiu Yan-Ting , Cho Yun-Fang , Le Ha , Somarathna Maheshika , Isayeva Tatyana , Guo Lingling , Symons J. David , Kevil Christopher G. , Totenhagen John , Lee Timmy
Published: October 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Impact of geography and surgical approach on recurrence in global pilonidal sinus disease
Authors: Doll Dietrich , Orlik Andriu , Maier Katharina , Kauf Peter , Schmid Marco , Diekmann Maja , Vogt Andreas P. , Stauffer Verena K. , Luedi Markus M.
Published: October 2019

Pilonidal sinus disease (PSD) is increasing globally. A recent meta-analysis and merged-data analysis showed that recurrence rates in PSD depend essentially on follow-up time and specific surgical procedures. However, the global distribution of surgical approaches and respective recurrence rates have never been studied in PSD. We aimed at studying the impact of geographic distribution of surgical approaches to treat PSD and subsequent geography-specific recurrence rates. We searched relevant databases as described previously. Recurrence rates were then associated with reported follow-up times and geographic origin. We simulated individual patients to enable analogy across data. Globally, recurrence rates range from 0.3% for Limberg/Dufourmentel approaches (95% CI 0.2–0.4) and flaps (95% CI 0.1–0.5) and up to 6.3% for incision (95% CI 3.2–9.3) at 12 months. Recurrence rates range from 0.3% for Karydakis/Bascom approaches (95% CI 0.0–0.8) up to 67.2% for incision (95% CI 7.5–100) in the USA, and 0.0% for primary asymmetric closure in Germany (95% CI 0.0–0.0). Our analysis shows that recurrence rates in PSD not only depend on therapeutic approaches and follow-up time but also on geography. Primary asymmetric closure and various flap techniques remain superior regardless of the geographical region. Some approaches have extraordinarily good outcomes in specific countries.
Acetic acid: a cost-effective agent for mitigation of seawater-induced salt toxicity in mung bean
Authors: Rahman Md. Mezanur , Mostofa Mohammad Golam , Rahman Md. Abiar , Islam Md. Robyul , Keya Sanjida Sultana , Das Ashim Kumar , Miah Md. Giashuddin , Kawser A. Q. M. Robiul , Ahsan S. M. , Hashem Abeer , Tabassum Baby , Abd_Allah Elsayed Fathi , Tran Lam-Son Phan
Published: October 2019

The current study sought the effective mitigation measure of seawater-induced damage to mung bean plants by exploring the potential roles of acetic acid (AA). Principal component analysis (PCA) revealed that foliar application of AA under control conditions improved mung bean growth, which was interlinked to enhanced levels of photosynthetic rate and pigments, improved water status and increased uptake of K+, in comparison with water-sprayed control. Mung bean plants exposed to salinity exhibited reduced growth and biomass production, which was emphatically correlated with increased accumulations of Na+, reactive oxygen species and malondialdehyde, and impaired photosynthesis, as evidenced by PCA and heatmap clustering. AA supplementation ameliorated the toxic effects of seawater, and improved the growth performance of salinity-exposed mung bean. AA potentiated several physio-biochemical mechanisms that were connected to increased uptake of Ca2+ and Mg2+, reduced accumulation of toxic Na+, improved water use efficiency, enhanced accumulations of proline, total free amino acids and soluble sugars, increased catalase activity, and heightened levels of phenolics and flavonoids. Collectively, our results provided new insights into AA-mediated protective mechanisms against salinity in mung bean, thereby proposing AA as a potential and cost-effective chemical for the management of salt-induced toxicity in mung bean, and perhaps in other cash crops.
Propagation and Scattering of Lamb Waves at Conical Points in Plates
Authors: Stobbe David M. , Grünsteidl Clemens M. , Murray Todd W.
Published: October 2019

Lamb waves exhibit conical dispersion at zero wave number when an accidental degeneracy occurs between thickness mode longitudinal and shear resonances of the same symmetry. Here we investigate the propagation of Lamb waves generated at the conical point frequency and the interaction of these waves with defects and interfaces. The group velocity and mode shapes of Lamb waves at the conical point are found, and it is shown that as the wavenumber gets close to zero, considerable group velocity is seen only for material properties supporting a degeneracy or near-degeneracy. The unusual wave propagation and mode conversion of Lamb waves generated at the conical point are elucidated through numerical simulations. Experimental measurements of near conical point Lamb wave interaction with holes in a plate demonstrate that these waves flow around defects while maintaining a constant phase of oscillation across that plate surface.
Systematic comparison between methods for the detection of influential spreaders in complex networks
Authors: Erkol Şirag , Castellano Claudio , Radicchi Filippo
Published: October 2019

Influence maximization is the problem of finding the set of nodes of a network that maximizes the size of the outbreak of a spreading process occurring on the network. Solutions to this problem are important for strategic decisions in marketing and political campaigns. The typical setting consists in the identification of small sets of initial spreaders in very large networks. This setting makes the optimization problem computationally infeasible for standard greedy optimization algorithms that account simultaneously for information about network topology and spreading dynamics, leaving space only to heuristic methods based on the drastic approximation of relying on the geometry of the network alone. The literature on the subject is plenty of purely topological methods for the identification of influential spreaders in networks. However, it is unclear how far these methods are from being optimal. Here, we perform a systematic test of the performance of a multitude of heuristic methods for the identification of influential spreaders. We quantify the performance of the various methods on a corpus of 100 real-world networks; the corpus consists of networks small enough for the application of greedy optimization so that results from this algorithm are used as the baseline needed for the analysis of the performance of the other methods on the same corpus of networks. We find that relatively simple network metrics, such as adaptive degree or closeness centralities, are able to achieve performances very close to the baseline value, thus providing good support for the use of these metrics in large-scale problem settings. Also, we show that a further 2–5% improvement towards the baseline performance is achievable by hybrid algorithms that combine two or more topological metrics together. This final result is validated on a small collection of large graphs where greedy optimization is not applicable.
LiSep LSTM: A Machine Learning Algorithm for Early Detection of Septic Shock
Authors: Fagerström Josef , Bång Magnus , Wilhelms Daniel , Chew Michelle S.
Published: October 2019

Sepsis is a major health concern with global estimates of 31.5 million cases per year. Case fatality rates are still unacceptably high, and early detection and treatment is vital since it significantly reduces mortality rates for this condition. Appropriately designed automated detection tools have the potential to reduce the morbidity and mortality of sepsis by providing early and accurate identification of patients who are at risk of developing sepsis. In this paper, we present “LiSep LSTM”; a Long Short-Term Memory neural network designed for early identification of septic shock. LSTM networks are typically well-suited for detecting long-term dependencies in time series data. LiSep LSTM was developed using the machine learning framework Keras with a Google TensorFlow back end. The model was trained with data from the Medical Information Mart for Intensive Care database which contains vital signs, laboratory data, and journal entries from approximately 59,000 ICU patients. We show that LiSep LSTM can outperform a less complex model, using the same features and targets, with an AUROC 0.8306 (95% confidence interval: 0.8236, 0.8376) and median offsets between prediction and septic shock onset up to 40 hours (interquartile range, 20 to 135 hours). Moreover, we discuss how our classifier performs at specific offsets before septic shock onset, and compare it with five state-of-the-art machine learning algorithms for early detection of sepsis.
Relationship between lifestyle pattern and blood pressure - Iranian national survey
Authors: Akbarpour Samaneh , Khalili Davood , Zeraati Hojjat , Mansournia Mohammad Ali , Ramezankhani Azra , Ahmadi Pishkuhi Mahin , Rostami Gooran Soroush , Fotouhi Akbar
Published: October 2019

We aimed to evaluate the relationship between different lifestyle patterns and blood pressure. This study is based on the national survey of the risk factors for non-communicable diseases in Iran in 2012. A total of 8244 people aged 25–70 years old have been enrolled in the survey. Clustering on the individual data of lifestyle factors (nutrition, physical activity, and smoking) were carried out using self-organizing neural network method. Multivariable regression models were used to determine the relationship between blood pressure and the clusters. This study revealed seven lifestyle clusters in the national survey. The first cluster had a healthier lifestyle (15%), and the rest of the clusters had at least one or more lifestyle-related risk factors. Among all the clusters, people in two clusters, i.e. one characterized by consumption of sugar-sweetened beverages, salt, and fast foods, and the other one characterized by physical inactivity, were more exposed to the risk of hypertension (odds ratios of 1.44 and 1.12, respectively). People in another cluster who were 100% smokers and had a very high level of work-related physical activity were about 30% less likely to experience elevated blood pressure. Although a lifestyle with cigarette smoking was associated with a reduction in blood pressure, this might be due to other related factors, such as work-related physical activity, which lower blood pressure. Of course, this hypothesis still needs to be further studied in the future.
Microstructure and superconducting properties of high-rate PLD-derived GdBa2Cu3O7−δ coated conductors with BaSnO3 and BaZrO3 pinning centers
Authors: Ovcharov Alexey V. , Degtyarenko Pavel N. , Chepikov Vsevolod N. , Vasiliev Alexander L. , Gavrilkin Sergey Yu. , Karateev Igor A. , Tsvetkov Alexey Yu. , Kaul Andrey R.
Published: October 2019

The microstructure of GdBa2Cu3O7−δ based on superconducting tapes with BaSnO3 and BaZrO3 artificial pinning centers formed by high-rate pulse laser deposition in SuperOx Japan was studied by scanning/transmission electron microscopy. The artificial pinning centers have adopted columnar morphology with average diameter of about 8 nm (BaSnO3-doped sample) and 6.5 nm (BaZrO3-doped sample) and density of 500 μm−2 for the both samples. The average length of the BaSnO3 nanocolumns is about two times higher than the BaZrO3 nanocolumns. The angular dependences of critical current in magnetic field up to 1 Tesla at 77 and 65 K have been obtained. The critical current and its anisotropy depend on artificial pinning centers presence and their type. The angular dependence of resistivity in the field up to 9 Tesla was also studied and discussed.
Phylogenetic comparative methods improve the selection of characters for generic delimitations in a hyperdiverse Neotropical orchid clade
Authors: Bogarín Diego , Pérez-Escobar Oscar A. , Karremans Adam P. , Fernández Melania , Kruizinga Jaco , Pupulin Franco , Smets Erik , Gravendeel Barbara
Published: October 2019

Taxonomic delimitations are challenging because of the convergent and variable nature of phenotypic traits. This is evident in species-rich lineages, where the ancestral and derived states and their gains and losses are difficult to assess. Phylogenetic comparative methods help to evaluate the convergent evolution of a given morphological character, thus enabling the discovery of traits useful for classifications. In this study, we investigate the evolution of selected traits to test for their suitability for generic delimitations in the cladeLepanthes, one of the Neotropical species-richest groups. We evaluated every generic name proposed in theLepanthesclade producing densely sampled phylogenies with Maximum Parsimony, Maximum Likelihood, and Bayesian approaches. Using Ancestral State Reconstructions, we then assessed 18 phenotypic characters that have been traditionally employed to diagnose genera. We propose the recognition of 14 genera based on solid morphological delimitations. Among the characters assessed, we identified 16 plesiomorphies, 12 homoplastic characters, and seven synapomorphies, the latter of which are reproductive features mostly related to the pollination by pseudocopulation and possibly correlated with rapid diversifications inLepanthes. Furthermore, the ancestral states of some reproductive characters suggest that these traits are associated with pollination mechanisms alike promoting homoplasy. Our methodological approach enables the discovery of useful traits for generic delimitations in theLepanthesclade and offers various other testable hypotheses on trait evolution for future research on Pleurothallidinae orchids because the phenotypic variation of some characters evaluated here also occurs in other diverse genera.
Correlations and nonlinear partition of nonionic organic compounds by humus-like substances humificated from rice straw
Authors: Ren Liufen , Lin Daohui , Yang Kun
Published: October 2019

The debate on whether the nonlinear sorption of nonionic organic compounds (NOCs) by soil organic matter (SOM) is captured by nonlinear partition or adsorption has been going on for decades because the used SOM samples are complex mixtures from various precursors with varied humification degrees in natural environment. Therefore, in this study, hydrothermal method was employed to prepare humus-like substances from a sole precursor (i.e., rice straw) with various humification degrees for nonlinear sorption of 25 aromatic compounds, then to have an insight into the underlying mechanisms of the nonlinear sorption of NOCs by SOM. It was observed that the increasing humification degree of humus-like substances, i.e., decreasing in the polarity ((O + N)/C) and increasing in the aromaticity, result in the increase of isotherm nonlinearity and sorption capacity/affinity of NOCs. Sorption capacity of NOCs, obtained by isotherm fitting using Dubinin-Astakhov (DA) model and Dual-Mode (DM) model, are positively correlated with their solubility in water and octanol, indicating the nonlinear sorption could be captured by nonlinear partition mechanism. Specific interactions including hydrogen-bonding interaction and π-π interaction between aromatic structures of humus-like substances and organic molecules could be responsible for the nonlinear partition and the increase of sorption affinity with the enhancement of humification degree. These obtained correlations are valuable for understanding the underlying mechanisms of nonlinear sorption and elucidating the transport of NOCs in the environment.
Drug-induced PD-L1 expression and cell stress response in breast cancer cells can be balanced by drug combination
Authors: Gilad Yosi , Eliaz Yossi , Yu Yang , Han Sang Jun , O’Malley Bert W. , Lonard David M.
Published: October 2019

The impact of chemotherapy on tumor-immune system interaction can be either beneficial or harmful, which is represented by the immunogenic cell death (ICD) paradigm or overexpression of the immunosuppressive protein – programmed death ligand 1 (PD-L1). In this study we explore the impact of steroid receptor coactivator inhibitor, other targeted anti-cancer compounds and traditional chemotherapeutic agents on the expression of PD-L1 in four breast cancer (BC) cell lines. Our results show that these agents induce PD-L1 expression, yet the magnitude of this induction varies substantially across the different compounds. In addition, we utilized the E0771 ER + BC cells as a model to examine in greater detail the relationship between pharmacological pressure, cell stress and the induction of PD-L1. Our results imply that drug induced PD-L1 expression occurs in the broader context of cell-stress, without conferring acquired drug-resistance. Furthermore, a balance between BC cytotoxicity, induction of cell-stress and the overexpression of PD-L1 can be achieved through the selection of appropriate combinations of anti-cancer compounds. Therefore, we propose that drug combination can be employed not only for increasing the direct kill of cancer cells, but also as a strategy to minimize the activation of immunosuppressive and cancer cell pro-survival program responses during drug treatment.
Non-Polar and Complementary Resistive Switching Characteristics in Graphene Oxide devices with Gold Nanoparticles: Diverse Approach for Device Fabrication
Authors: Khurana Geetika , Kumar Nitu , Chhowalla Manish , Scott James F. , Katiyar Ram S.
Published: October 2019

Downscaling limitations and limited write/erase cycles in conventional charge-storage based non-volatile memories stimulate the development of emerging memory devices having enhanced performance. Resistive random-access memory (RRAM) devices are recognized as the next-generation memory devices for employment in artificial intelligence and neuromorphic computing, due to their smallest cell size, high write/erase speed and endurance. Unipolar and bipolar resistive switching characteristics in graphene oxide (GO) have been extensively studied in recent years, whereas the study of non-polar and complementary switching is scarce. Here we fabricated GO-based RRAM devices with gold nanoparticles (Au Nps). Diverse types of switching behavior are observed by changing the processing methods and device geometry. Tri-layer GO-based devices illustrated non-polar resistive switching, which is a combination of unipolar and bipolar switching. Five-layer GO-based devices depicted complementary resistive switching having the lowest current values ~12 µA; and this structure is capable of resolving the sneak path issue. Both devices show good retention and endurance performance. Au Nps in tri-layer devices assisted the conducting path, whereas in five-layer devices, Au Nps layer worked as common electrodes between co-joined cells. These GO-based devices with Au Nps comprising different configuration are vital for practical applications of emerging non-volatile resistive memories.