bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of optimization algorithms based fuzzy controller in achieving induction motor performance enhancement
Authors: Hannan M. A. , Ali Jamal Abd. , Hossain Lipu M. S. , Mohamed A. , Ker Pin Jern , Indra Mahlia T. M. , Mansor M. , Hussain Aini , Muttaqi Kashem M. , Dong Z. Y.
Published: July 2020

Three-phase induction motors (TIMs) are widely used for machines in industrial operations. As an accurate and robust controller, fuzzy logic controller (FLC) is crucial in designing TIMs control systems. The performance of FLC highly depends on the membership function (MF) variables, which are evaluated by heuristic approaches, leading to a high processing time. To address these issues, optimisation algorithms for TIMs have received increasing interest among researchers and industrialists. Here, we present an advanced and efficient quantum-inspired lightning search algorithm (QLSA) to avoid exhaustive conventional heuristic procedures when obtaining MFs. The accuracy of the QLSA based FLC (QLSAF) speed control is superior to other controllers in terms of transient response, damping capability and minimisation of statistical errors under diverse speeds and loads. The performance of the proposed QLSAF speed controller is validated through experiments. Test results under different conditions show consistent speed responses and stator currents with the simulation results.
Structural order in plasmonic superlattices
Authors: Schulz Florian , Pavelka Ondřej , Lehmkühler Felix , Westermeier Fabian , Okamura Yu , Mueller Niclas S. , Reich Stephanie , Lange Holger
Published: July 2020

The assembly of plasmonic nanoparticles into ordered 2D- and 3D-superlattices could pave the way towards new tailored materials for plasmonic sensing, photocatalysis and manipulation of light on the nanoscale. The properties of such materials strongly depend on their geometry, and accordingly straightforward protocols to obtain precise plasmonic superlattices are highly desirable. Here, we synthesize large areas of crystalline mono-, bi- and multilayers of gold nanoparticles >20 nm with a small number of defects. The superlattices can be described as hexagonal crystals with standard deviations of the lattice parameter below 1%. The periodic arrangement within the superlattices leads to new well-defined collective plasmon-polariton modes. The general level of achieved superlattice quality will be of benefit for a broad range of applications, ranging from fundamental studies of light–matter interaction to optical metamaterials and substrates for surface-enhanced spectroscopies.
Associations of cardiovascular biomarkers and plasma albumin with exceptional survival to the highest ages
Authors: Hirata Takumi , Arai Yasumichi , Yuasa Shinsuke , Abe Yukiko , Takayama Michiyo , Sasaki Takashi , Kunitomi Akira , Inagaki Hiroki , Endo Motoyoshi , Morinaga Jun , Yoshimura Kimio , Adachi Tetsuo , Oike Yuichi , Takebayashi Toru , Okano Hideyuki , Hirose Nobuyoshi
Published: July 2020

Supercentenarians (those aged ≥110 years) are approaching the current human longevity limit by preventing or surviving major illness. Identifying specific biomarkers conducive to exceptional survival might provide insights into counter-regulatory mechanisms against aging-related disease. Here, we report associations between cardiovascular disease-related biomarkers and survival to the highest ages using a unique dataset of 1,427 oldest individuals from three longitudinal cohort studies, including 36 supercentenarians, 572 semi-supercentenarians (105–109 years), 288 centenarians (100–104 years), and 531 very old people (85–99 years). During follow-up, 1,000 participants (70.1%) died. Overall, N-terminal pro-B-type natriuretic peptide (NT-proBNP), interleukin-6, cystatin C and cholinesterase are associated with all-cause mortality independent of traditional cardiovascular risk factors and plasma albumin. Of these, low NT-proBNP levels are statistically associated with a survival advantage to supercentenarian age. Only low albumin is associated with high mortality across age groups. These findings expand our knowledge on the biology of human longevity.
Polypeptide formation in clusters of β-alanine amino acids by single ion impact
Authors: Rousseau Patrick , Piekarski Dariusz G. , Capron Michael , Domaracka Alicja , Adoui Lamri , Martín Fernando , Alcamí Manuel , Díaz-Tendero Sergio , Huber Bernd A.
Published: July 2020

The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of β-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.
Identification of relevant genetic alterations in cancer using topological data analysis
Authors: Rabadán Raúl , Mohamedi Yamina , Rubin Udi , Chu Tim , Alghalith Adam N. , Elliott Oliver , Arnés Luis , Cal Santiago , Obaya Álvaro J. , Levine Arnold J. , Cámara Pablo G.
Published: July 2020

Large-scale cancer genomic studies enable the systematic identification of mutations that lead to the genesis and progression of tumors, uncovering the underlying molecular mechanisms and potential therapies. While some such mutations are recurrently found in many tumors, many others exist solely within a few samples, precluding detection by conventional recurrence-based statistical approaches. Integrated analysis of somatic mutations and RNA expression data across 12 tumor types reveals that mutations of cancer genes are usually accompanied by substantial changes in expression. We use topological data analysis to leverage this observation and uncover 38 elusive candidate cancer-associated genes, including inactivating mutations of the metalloproteinase ADAMTS12 in lung adenocarcinoma. We show thatADAMTS12−/−mice have a five-fold increase in the susceptibility to develop lung tumors, confirming the role ofADAMTS12as a tumor suppressor gene. Our results demonstrate that data integration through topological techniques can increase our ability to identify previously unreported cancer-related alterations.
STAT3 serine phosphorylation is required for TLR4 metabolic reprogramming and IL-1β expression
Authors: Balic Jesse J. , Albargy Hassan , Luu Kevin , Kirby Francis J. , Jayasekara W. Samantha N. , Mansell Finbar , Garama Daniel J. , De Nardo Dominic , Baschuk Nikola , Louis Cynthia , Humphries Fiachra , Fitzgerald Katherine , Latz Eicke , Gough Daniel J. , Mansell Ashley
Published: July 2020

Detection of microbial components such as lipopolysaccharide (LPS) by Toll-like receptor 4 (TLR4) on macrophages induces a robust pro-inflammatory response that is dependent on metabolic reprogramming. These innate metabolic changes have been compared to aerobic glycolysis in tumour cells. However, the mechanisms by which TLR4 activation leads to mitochondrial and glycolytic reprogramming are unknown. Here we show that TLR4 activation induces a signalling cascade recruiting TRAF6 and TBK-1, while TBK-1 phosphorylates STAT3 on S727. Using a genetically engineered mouse model incapable of undergoing STAT3 Ser727 phosphorylation, we show ex vivo and in vivo that STAT3 Ser727 phosphorylation is critical for LPS-induced glycolytic reprogramming, production of the central immune response metabolite succinate and inflammatory cytokine production in a model of LPS-induced inflammation. Our study identifies non-canonical STAT3 activation as the crucial signalling intermediary for TLR4-induced glycolysis, macrophage metabolic reprogramming and inflammation.
Author Correction: Dynamic reconfiguration of functional brain networks during working memory training
Authors: Finc Karolina , Bonna Kamil , He Xiaosong , Lydon-Staley David M. , Kühn Simone , Duch Włodzisław , Bassett Danielle S.
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Interactome of miRNAs and transcriptome of human umbilical cord endothelial cells exposed to short-term simulated microgravity
Authors: Kasiviswanathan Dharanibalan , Chinnasamy Perumal Rajadurai , Bhuvaneswari Srinivasan , Kumar Pavitra , Sundaresan Lakshmikirupa , Philip Manuel , Puthenpurackal Krishnankutty Sajesh , Chatterjee Suvro
Published: July 2020

Adaptation of humans in low gravity conditions is a matter of utmost importance when efforts are on to a gigantic leap in human space expeditions for tourism and formation of space colonies. In this connection, cardiovascular adaptation in low gravity is a critical component of human space exploration. Deep high-throughput sequencing approach allowed us to analyze the miRNA and mRNA expression profiles in human umbilical cord vein endothelial cells (HUVEC), cultured under gravity (G), and stimulated microgravity (MG) achieved with a clinostat. The present study identified totally 1870 miRNAs differentially expressed in HUVEC under MG condition when compared to the cells subjected to unitary G conditions. The functional association of identified miRNAs targeting specific mRNAs revealed that miRNAs, hsa-mir-496, hsa-mir-151a, hsa-miR-296-3p, hsa-mir-148a, hsa-miR-365b-5p, hsa-miR-3687, hsa-mir-454, hsa-miR-155-5p, and hsa-miR-145-5p differentially regulated the genes involved in cell adhesion, angiogenesis, cell cycle, JAK-STAT signaling, MAPK signaling, nitric oxide signaling, VEGF signaling, and wound healing pathways. Further, the q-PCR based experimental studies of upregulated and downregulated miRNA and mRNAs demonstrate that the above reported miRNAs influence the cell proliferation and vascular functions of the HUVEC in MG conditions effectively. Consensus on the interactome results indicates restricted fluctuations in the transcriptome of the HUVEC exposed to short-term MG that could lead to higher levels of endothelial functions like angiogenesis and vascular patterning.
Author Correction: Global karst springs hydrograph dataset for research and management of the world’s fastest-flowing groundwater
Authors: Olarinoye Tunde , Gleeson Tom , Marx Vera , Seeger Stefan , Adinehvand Rouhollah , Allocca Vincenzo , Andreo Bartolome , Apaéstegui James , Apolit Christophe , Arfib Bruno , Auler Augusto , Bailly-Comte Vincent , Barberá Juan Antonio , Batiot-Guilhe Christelle , Bechtel Timothy , Binet Stephane , Bittner Daniel , Blatnik Matej , Bolger Terry , Brunet Pascal , Charlier Jean-Baptiste , Chen Zhao , Chiogna Gabriele , Coxon Gemma , De Vita Pantaleone , Doummar Joanna , Epting Jannis , Fleury Perrine , Fournier Matthieu , Goldscheider Nico , Gunn John , Guo Fang , Guyot Jean Loup , Howden Nicholas , Huggenberger Peter , Hunt Brian , Jeannin Pierre-Yves , Jiang Guanghui , Jones Greg , Jourde Herve , Karmann Ivo , Koit Oliver , Kordilla Jannes , Labat David , Ladouche Bernard , Liso Isabella Serena , Liu Zaihua , Maréchal Jean-Christophe , Massei Nicolas , Mazzilli Naomi , Mudarra Matías , Parise Mario , Pu Junbing , Ravbar Nataša , Sanchez Liz Hidalgo , Santo Antonio , Sauter Martin , Seidel Jean-Luc , Sivelle Vianney , Skoglund Rannveig Øvrevik , Stevanovic Zoran , Wood Cameron , Worthington Stephen , Hartmann Andreas
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Projections of global-scale extreme sea levels and resulting episodic coastal flooding over the 21st Century
Authors: Kirezci Ebru , Young Ian R. , Ranasinghe Roshanka , Muis Sanne , Nicholls Robert J. , Lincke Daniel , Hinkel Jochen
Published: July 2020

Global models of tide, storm surge, and wave setup are used to obtain projections of episodic coastal flooding over the coming century. The models are extensively validated against tide gauge data and the impact of uncertainties and assumptions on projections estimated in detail. Global “hotspots” where there is projected to be a significant change in episodic flooding by the end of the century are identified and found to be mostly concentrated in north western Europe and Asia. Results show that for the case of, no coastal protection or adaptation, and a mean RCP8.5 scenario, there will be an increase of 48% of the world’s land area, 52% of the global population and 46% of global assets at risk of flooding by 2100. A total of 68% of the global coastal area flooded will be caused by tide and storm events with 32% due to projected regional sea level rise.
Loss of Caveolin-1 and caveolae leads to increased cardiac cell stiffness and functional decline of the adult zebrafish heart
Authors: Grivas Dimitrios , González-Rajal Álvaro , Guerrero Rodríguez Carlos , Garcia Ricardo , de la Pompa José Luis
Published: July 2020

Caveolin-1 is the main structural protein of caveolae, small membrane invaginations involved in signal transduction and mechanoprotection. Here, we generatedcav1-KOzebrafish lacking Cav1 and caveolae, and investigated the impact of this loss on adult heart function and response to cryoinjury. We found that cardiac function was impaired in adultcav1-KOfish, which showed a significantly decreased ejection fraction and heart rate. Using atomic force microscopy, we detected an increase in the stiffness of epicardial cells and cells of the cortical zone lacking Cav1/caveolae. This loss of cardiac elasticity might explain the decreased cardiac contraction and function. Surprisingly,cav1-KOmutants were able to regenerate their heart after a cryoinjury but showed a transient decrease in cardiomyocyte proliferation.
Reversible visible/near-infrared light responsive thin films based on indium tin oxide nanocrystals and polymer
Authors: Wu Jian , Mu Chenzhong , Yang Jinglei
Published: July 2020

In this study, we design a novel thermo- and photo-responsive nanocomposite film prepared by depositing indium tin oxide nanocrystals via the coating of amphiphilic copolymer on polycaprolactone substrates (INCP). The INCP film shows reversible surface morphology change properties by changing temperature as well as turning ON/OFF NIR laser. Especially, as the temperature changes from 25 to 75 °C, the film could regulate light transmittance from 75 to 90% across the visible and near-infrared region (500–1,750 nm). In addition, the film also exhibits excellent recycle and thermal stability at different temperature. Our results reveal that reversible surface morphology change properties are caused by curvature adjustment of film, which is owing to the coupling effect between copolymer and PCL with different thermal expansion strains. Our results suggest a possible strategy for the preparation of smart responsive materials in the future, which provides a reference for the development of new energy-saving materials.
Vulnerability of a top marine predator to coastal storms: a relationship between hydrodynamic drivers and stranding rates of newborn pinnipeds
Authors: Sepúlveda M. , Quiñones R. A. , Esparza C. , Carrasco P. , Winckler P.
Published: July 2020

Coastal storms have increased in recent decades, affecting many species, including the South American sea lion (Otaria byronia). Reports of stranded sea lion pups are becoming common in Chile, presumably due to the increase in the frequency and intensity of coastal storms. To validate this assumption, a 10-year database was built by coupling wave generation and coastal propagation models to correlate pure wave parameters (significant wave height Hs, peak period Tp, normalized wave power Hs2Tp) and wave parameters including the tidal level (maximum surface elevation η, modified wave power η2Tp) with records of stranded pups in Cobquecura, the largest breeding colony in central Chile. The correlation between the number of pups stranded per day and wave parameters in the first half of January and the last half of February is poor, while they are stronger for the second half of January and the first half of February. The higher number of stranded pups coincide with coastal storms with normalized wave power values exceeding a threshold of 100 m2/s. Conversely, below this threshold there is wide dispersion between the number of strandings and wave parameters. Identifying wave parameter thresholds could be used to predict when newborn pups will be most affected by coastal storms, and thus help institutions to develop remediation techniques for animals at risk.
The Gly82Ser mutation in AGER contributes to pathogenesis of pulmonary fibrosis in combined pulmonary fibrosis and emphysema (CPFE) in Japanese patients
Authors: Kinjo Takumi , Kitaguchi Yoshiaki , Droma Yunden , Yasuo Masanori , Wada Yosuke , Ueno Fumika , Ota Masao , Hanaoka Masayuki
Published: July 2020

The dominant pathogenesis underlying the combined pulmonary fibrosis and emphysema (CPFE) remains unresolved. The receptor for advanced glycation end-products (RAGE) is highly expressed in lung tissues and interacts with distinct multiple ligands, implicating it in certain lung diseases. To elucidate the pathogenesis of CPFE, we genotyped three single nucleotide polymorphisms (SNPs: rs2070600, rs1800625, and rs2853807) of the gene encoding RAGE (AGER) in 111 CPFE patients and 337 chronic obstructive pulmonary disease (COPD) patients of Japanese by using StepOne Real-Time PCR System for SNP genotyping assay. Serum levels of soluble RAGE (sRAGE) were measured by ELISA. We found that the allele frequency of rs2070600 was significantly different between the two groups [corrected P (Pc) = 0.015]. In addition, the minor allele was associated with CPFE patients relative to COPD patients in a dominant effect model (Odds Ratio = 1.93; Pc = 0.018). Moreover, the serum sRAGE level was significantly lower in the CPFE group than the COPD group (P = 0.014). The rs2070600 minor allele was significantly associated with reduced sRAGE level in CPFE patients and independently affected sRAGE level reduction in this group (P = 0.020). We concluded that the AGER rs2070600 minor allele (Gly82Ser mutation) is associated with the pathogenesis of pulmonary fibrosis in CPFE in Japanese patients.
Gene knockdown via electroporation of short hairpin RNAs in embryos of the marine hydroid Hydractinia symbiolongicarpus
Authors: Quiroga-Artigas Gonzalo , Duscher Alexandrea , Lundquist Katelyn , Waletich Justin , Schnitzler Christine E.
Published: July 2020

Analyzing gene function in a broad range of research organisms is crucial for understanding the biological functions of genes and their evolution. Recent studies have shown that short hairpin RNAs (shRNAs) can induce gene-specific knockdowns in two cnidarian species. We have developed a detailed, straightforward, and scalable method to deliver shRNAs into fertilized eggs of the hydrozoan cnidarian Hydractinia symbiolongicarpus via electroporation, yielding effective gene-targeted knockdowns that can last throughout embryogenesis. Our electroporation protocol allows for the transfection of shRNAs into hundreds of fertilized H. symbiolongicarpus eggs simultaneously with minimal embryo death and no long-term harmful consequences on the developing animals. We show RT-qPCR and detailed phenotypic evidence of our method successfully inducing effective knockdowns of an exogenous gene (eGFP) and an endogenous gene (Nanos2), as well as knockdown confirmation by RT-qPCR of two other endogenous genes. We also provide visual confirmation of successful shRNA transfection inside embryos through electroporation. Our detailed protocol for electroporation of shRNAs in H. symbiolongicarpus embryos constitutes an important experimental resource for the hydrozoan community while also serving as a successful model for the development of similar methods for interrogating gene function in other marine invertebrates.
Intracellular G-actin targeting of peripheral sensory neurons by the multifunctional engineered protein C2C confers relief from inflammatory pain
Authors: Allen Derek , Zhou You , Wilhelm Audrey , Blum Paul
Published: July 2020

The engineered multifunctional protein C2C was tested for control of sensory neuron activity by targeted G-actin modification. C2C consists of the heptameric oligomer, C2II-CI, and the monomeric ribosylase, C2I. C2C treatment of sensory neurons and SH-SY5Y cells in vitro remodeled actin and reduced calcium influx in a reversible manner. C2C prepared using fluorescently labeled C2I showed selective in vitro C2I delivery to primary sensory neurons but not motor neurons. Delivery was dependent on presence of both C2C subunits and blocked by receptor competition. Immunohistochemistry of mice treated subcutaneously with C2C showed colocalization of subunit C2I with CGRP-positive sensory neurons and fibers but not with ChAT-positive motor neurons and fibers. The significance of sensory neuron targeting was pursued subsequently by testing C2C activity in the formalin inflammatory mouse pain model. Subcutaneous C2C administration reduced pain-like behaviors by 90% relative to untreated controls 6 h post treatment and similarly to the opioid buprenorphene. C2C effects were dose dependent, equally potent in female and male animals and did not change gross motor function. One dose was effective in 2 h and lasted 1 week. Administration of C2I without C2II-CI did not reduce pain-like behavior indicating its intracellular delivery was required for behavioral effect.
Elafin inhibits obesity, hyperglycemia, and liver steatosis in high-fat diet-treated male mice
Authors: Wang Jiani , Ortiz Christina , Fontenot Lindsey , Mukhopadhyay Riya , Xie Ying , Law Ivy Ka Man , Shih David Q. , Mattai S. Anjani , Li Zhaoping , Koon Hon Wai
Published: July 2020

Elafin is an antimicrobial and anti-inflammatory protein. We hypothesize that elafin expression correlates with diabetes. Among non-diabetic and prediabetic groups, men have significantly higher serum elafin levels than women. Men with type 2 diabetes mellitus (T2DM) have significantly lower serum elafin levels than men without T2DM. Serum elafin levels are inversely correlated with fasting blood glucose and hemoglobin A1c levels in men with T2DM, but not women with T2DM. Lentiviral elafin overexpression inhibited obesity, hyperglycemia, and liver steatosis in high-fat diet (HFD)-treated male mice. Elafin-overexpressing HFD-treated male mice had increased serum leptin levels, and serum exosomal miR181b-5p and miR219-5p expression. Transplantation of splenocytes and serum exosomes from elafin-overexpressing HFD-treated donor mice reduced food consumption and fat mass, and increased adipose tissue leptin mRNA expression in HFD-treated recipient mice. Elafin improved leptin sensitivity via reduced interferon-gamma expression and induced adipose leptin expression via increased miR181b-5p and miR219-5p expression. Subcutaneous and oral administration of modified elafin inhibited obesity, hyperglycemia, and liver steatosis in the HFD-treated mice. Circulating elafin levels are associated with hyperglycemia in men with T2DM. Elafin, via immune-derived miRNAs and cytokine, activates leptin sensitivity and expression that subsequently inhibit food consumption, obesity, hyperglycemia, and liver steatosis in HFD-treated male mice.
Rapid fragmentation of microplastics by the freshwater amphipod Gammarus duebeni (Lillj.)
Authors: Mateos-Cárdenas Alicia , O’Halloran John , van Pelt Frank N. A. M. , Jansen Marcel A. K.
Published: July 2020

Microplastics have become ubiquitous in all environments. Yet, their environmental fate is still largely unknown. Plastic fragmentation is a key component of plastic degradation, which is mostly caused by abiotic processes over prolonged time scales. Here, it is shown that the freshwater amphipod Gammarus duebeni can rapidly fragment polyethylene microplastics, resulting in the formation of differently shaped and sized plastic fragments, including nanoplastics. Fragments comprised 65.7% of all observed microplastic particles accumulated in digestive tracts. Higher numbers of fragments were found in response to longer exposure times and/or higher microplastic concentrations. Furthermore, the proportion of smaller plastic fragments was highest when food was present during the depuration process. It is concluded that G. duebeni can rapidly fragment polyethylene microplastics and that this is closely associated with the feeding process. These results highlight the crucial role, currently understudied, that biota may play in determining the fate of microplastics in aquatic ecosystems.
Simultaneous time-varying viscosity, elasticity, and mass measurements of single adherent cancer cells across cell cycle
Authors: Adeniba Olaoluwa O. , Corbin Elise A. , Ganguli Anurup , Kim Yongdeok , Bashir Rashid
Published: July 2020

Biophysical studies on single cells have linked cell mechanics to physiology, functionality and disease. Evaluation of mass and viscoelasticity versus cell cycle can provide further insights into cell cycle progression and the uncontrolled proliferation of cancer. Using our pedestal microelectromechanical systems resonant sensors, we have developed a non-contact interferometric measurement technique that simultaneously tracks the dynamic changes in the viscoelastic moduli and mass of adherent colon (HT-29) and breast cancer (MCF-7) cells from the interphase through mitosis and then to the cytokinesis stages of their growth cycle. We show that by combining three optomechanical parameters in an optical path length equation and a two-degree-of-freedom model, we can simultaneously extract the viscoelasticity and mass as a function of the nano-scaled membrane fluctuation of each adherent cell. Our measurements are able to discern between soft and stiff cells across the cell cycle and demonstrated sharp viscoelastic changes due to cortical stiffening around mitosis. Cell rounding before division can be detected by measurement of mechanical coupling between the cells and the sensors. Our measurement device and method can provide for new insights into the mechanics of single adherent cells versus time.
Cutibacterium acnes regulates the epidermal barrier properties of HPV-KER human immortalized keratinocyte cultures
Authors: Bolla Beáta Szilvia , Erdei Lilla , Urbán Edit , Burián Katalin , Kemény Lajos , Szabó Kornélia
Published: July 2020

Our skin provides a physical barrier to separate the internal part of our body from the environment. Maintenance of complex barrier functions is achieved through anatomical structures in the skin, the stratified squamous epithelium specialized junctional organelles, called tight junctions (TJs). Several members of our microbial communities are known to affect the differentiation state and function of the colonized organ. Whether and how interactions between skin cells and cutaneous microbes, including Cutibacterium acnes (C. acnes), modify the structure and/or function of our skin is currently only partly understood. Thus, in our studies, we investigated whether C. acnes may affect the epidermal barrier using in vitro model systems. Real-time cellular analysis showed that depending on the keratinocyte differentiation state, the applied C. acnes strains and their dose, the measured impedance values change, together with the expression of selected TJ proteins. These may reflect barrier alterations, which can be partially restored upon antibiotic–antimycotic treatment. Our findings suggest that C. acnes can actively modify the barrier properties of cultured keratinocytes, possibly through alteration of tight cell-to-cell contacts. Similar events may play important roles in our skin, in the maintenance of cutaneous homeostasis.
Controlling osteoblast morphology and proliferation via surface micro-topographies of implant biomaterials
Authors: Rabel Kerstin , Kohal Ralf-Joachim , Steinberg Thorsten , Tomakidi Pascal , Rolauffs Bernd , Adolfsson Erik , Palmero Paola , Fürderer Tobias , Altmann Brigitte
Published: July 2020

Current research on surface modifications has yielded advanced implant biomaterials. Various implant surface modifications have been shown to be promising in improving bone target cell response, but more comprehensive studies whether certain implant surface modifications can directly target cell behavioural features such as morphogenesis and proliferation are needed. Here, we studied the response of primary alveolar bone cells on various implant surface modifications in terms of osteoblast morphology and proliferation in vitro. Analyses of surface modifications led to surface-related test parameters including the topographical parameters micro-roughness, texture aspect and surface enlargement as well as the physicochemical parameter surface wettability. We compared osteoblast morphology and proliferation towards the above-mentioned parameters and found that texture aspect and surface enlargement but not surface roughness or wettability exhibited significant impact on osteoblast morphology and proliferation. Detailed analysis revealed osteoblast proliferation as a function of cell morphology, substantiated by an osteoblast size- and morphology-dependent increase in mitotic activity. These findings show that implant surface topography controls cell behavioural morphology and subsequently cell proliferation, thereby opening the road for cell instructive biomaterials.
Two Dyakonov–Voigt surface waves guided by a biaxial–isotropic dielectric interface
Authors: Zhou Chenzhang , Mackay Tom G. , Lakhtakia Akhlesh
Published: July 2020

Electromagnetic surface waves guided by the planar interface of an orthorhombic dielectric material and an isotropic dielectric material were analyzed theoretically and numerically. Both naturally occurring minerals (crocoite, tellurite, and cerussite) and engineered materials were considered as the orthorhombic partnering material. In addition to conventional Dyakonov surface waves, the analysis revealed that as many as two Dyakonov–Voigt surface waves can propagate in each quadrant of the interface plane, depending upon the birefringence of the orthorhombic partnering material. The coexistence of two Dyakonov–Voigt surface waves marks a fundamental departure from the corresponding case involving the planar interface of a uniaxial dielectric material and an isotropic dielectric material for which only one Dyakonov–Voigt surface wave is possible. The two Dyakonov–Voigt surface waves propagate in different directions in each quadrant of the interface plane, with different relative phase speeds and different penetration depths. Furthermore, the localization characteristics of the two Dyakonov–Voigt surface waves at the planar interface are quite different: the Dyakonov–Voigt surface wave with the higher relative phase speed is much less tightly localized at the interface in the isotropic dielectric partnering material.
Dopaminergic neurons regenerate following chemogenetic ablation in the olfactory bulb of adult Zebrafish (Danio rerio)
Authors: Godoy Rafael , Hua Khang , Kalyn Michael , Cusson Victoria-Marie , Anisman Hymie , Ekker Marc
Published: July 2020

Adult zebrafish have the ability to regenerate cells of the central nervous system. However, few neuronal regeneration studies in adult zebrafish addressed their ability to regenerate specific types of neurons following cell specific ablation. We show here that treatment of transgenic Tg(dat:CFP-NTR) adult zebrafish with the prodrug metronidazole (Mtz) according to our administration regimen predominantly ablates dopamine (DA) neurons within the olfactory bulb (OB) of adult fish. Loss of DA neurons was accompanied by an impaired olfaction phenotype, as early as 1-week post-treatment, in which fish were unable to sense the presence of the repulsive stimulus cadaverine. The olfactory impairment was reversed within 45 days and coincided with the recovery of DA neuron counts in the OB. A multi-label pulse-chase analysis with BrdU and EdU over the first seventeen days-post Mtz exposure showed that newly formed DA neurons were recruited within the first nine days following exposure and led to functional and morphological recovery of the OB.
A D-lactate dehydrogenase from rice is involved in conferring tolerance to multiple abiotic stresses by maintaining cellular homeostasis
Authors: Jain Muskan , Aggarwal Sakshi , Nagar Preeti , Tiwari Roopam , Mustafiz Ananda
Published: July 2020

D-lactate dehydrogenase (D-LDH) converts D-lactate (the end product of glyoxalase system) to pyruvate and thereby completes the detoxification process of methylglyoxal. D-LDH detoxifies and diverts the stress induced toxic metabolites, MG and D-lactate, towards energy production and thus, protects the cell from their deteriorating effects. In this study, a D-LDH enzyme from rice (OsD-LDH2, encoded by Os07g08950.1) was characterized for its role in abiotic stress tolerance. For this, a combination of in silico, molecular, genetic and biochemical approaches was used. The kinetic analysis revealed OsD-LDH2 to be the most efficient D-LDH enzyme in comparison to D-LDHs from other plant species. Heterologous overexpression of OsD-LDH2 provides tolerance against multiple abiotic stresses in E. coli, yeast and plant system. The analysis of D-LDH mutant and OsD-LDH2 overexpressing transgenic plants uncovered the crucial role of D-LDH in mitigation of abiotic stresses. OsD-LDH2 overexpressing plants maintained lower level of ROS and other toxic metabolites along with better functioning of antioxidant system. This is the first report on correlation of D-LDH with multiple abiotic stress tolerance. Overall, OsD-LDH2 emerged as a promising candidate which can open a new direction for engineering stress tolerant crop varieties by maintaining their growth and yield in unfavorable conditions.
Ultra-compact and high-performance polarization beam splitter assisted by slotted waveguide subwavelength gratings
Authors: Huang Chia-Chih , Huang Chia-Chien
Published: July 2020

We propose an ultra-short polarization beam splitter (PBS) consisting of two slot waveguides assisted by slotted waveguide subwavelength gratings (SWSWGs), located between the two slotted waveguides. By controlling the optical momentum of evanescent waves with the anisotropic characteristics of the SWSWGs, we considerably suppress and enhance the couplings of transverse-electric (TE) and transverse-magnetic (TM) modes, respectively, concurrently improving performances and reducing length of the proposed PBS, compared with conventional slotted waveguide couplers (CSWCs). Exceptionally, a transition point is found to show almost zero crosstalk between waveguides for the TE mode, i.e., infinite coupling length. Differing from conventional single-material SWGs, the SWSWGs not only simplify the fabrication process but improve polarization extinction ratio (PER). Numerical results demonstrate the improvement in PERTM (PERTE) from approximately 13 (23) dB for the CSWCs to 26 (24) dB for the present structure, with a > 70% reduction in device length, operating at the wavelength of λ = 1,550 nm. Our design achieves performance of PERTM > 25 dB and PERTE > 20 dB, and insertion loss (IL) < 0.05 dB for TE and < 0.3 dB for TM modes within a bandwidth width (BW) of ~ 50 nm from λ = 1,530 to 1,580 nm. Additionally, geometry deviation is also investigated to assess experimental tolerance. The present idea provides an approach for improving PER, device length, and operating BW of PBSs composed of various waveguide couplers.
SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach
Authors: Wang Mingyi , Luo Wen , Jones Kristine , Bian Xiaopeng , Williams Russell , Higson Herbert , Wu Dongjing , Hicks Belynda , Yeager Meredith , Zhu Bin
Published: July 2020

It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs.
Spectrochemical analysis of liquid biopsy harnessed to multivariate analysis towards breast cancer screening
Authors: Freitas Daniel L. D. , Câmara Ingrid M. , Silva Priscila P. , Wanderley Nathália R. S. , Alves Maria B. C. , Morais Camilo L. M. , Martin Francis L. , Lajus Tirzah B. P. , Lima Kassio M. G.
Published: July 2020

Mortality due to breast cancer could be reduced via screening programs where preliminary clinical tests employed in an asymptomatic well-population with the objective of identifying cancer biomarkers could allow earlier referral of women with altered results for deeper clinical analysis and treatment. The introduction of well-population screening using new and less-invasive technologies as a strategy for earlier detection of breast cancer is thus highly desirable. Herein, spectrochemical analyses harnessed to multivariate classification techniques are used as a bio-analytical tool for a Breast Cancer Screening Program using liquid biopsy in the form of blood plasma samples collected from 476 patients recruited over a 2-year period. This methodology is based on acquiring and analysing the spectrochemical fingerprint of plasma samples by attenuated total reflection Fourier-transform infrared spectroscopy; derived spectra reflect intrinsic biochemical composition, generating information on nucleic acids, carbohydrates, lipids and proteins. Excellent results in terms of sensitivity (94%) and specificity (91%) were obtained using this method in comparison with traditional mammography (88–93% and 85–94%, respectively). Additional advantages such as better disease prognosis thus allowing a more effective treatment, lower associated morbidity, fewer false-positive and false-negative results, lower-cost, and higher analytical frequency make this method attractive for translation to the clinical setting.
Drag reduction mechanism of Paramisgurnus dabryanus loach with self-lubricating and flexible micro-morphology
Authors: Wu Liyan , Wang Huan , Song Yuqiu , Zhang Benhua , Xu Yan , Liu Cuihong , Yan Yuying
Published: July 2020

Underwater machinery withstands great resistance in the water, which can result in consumption of a large amount of power. Inspired by the character that loach could move quickly in mud, the drag reduction mechanism ofParamisgurnus dabryanus loachis discussed in this paper. Subjected to the compression and scraping of water and sediments, a loach could not only secrete a lubricating mucus film, but also importantly, retain its mucus well from losing rapidly through its surface micro structure. In addition, it has been found that flexible deformations can maximize the drag reduction rate. This self-adaptation characteristic can keep the drag reduction rate always at high level in wider range of speeds. Therefore, even though the part of surface of underwater machinery cannot secrete mucus, it should be designed by imitating the bionic micro-morphology to absorb and store fluid, and eventually form a self-lubrication film to reduce the resistance. In the present study, theParamisgurnus dabryanus loachis taken as the bionic prototype to learn how to avoid or slow down the mucus loss through its body surface. This combination of the flexible and micro morphology method provides a potential reference for drag reduction of underwater machinery.
Developing intelligent medical image modality classification system using deep transfer learning and LDA
Authors: Hassan Mehdi , Ali Safdar , Alquhayz Hani , Safdar Khushbakht
Published: July 2020

Rapid advancement in imaging technology generates an enormous amount of heterogeneous medical data for disease diagnosis and rehabilitation process. Radiologists may require related clinical cases from medical archives for analysis and disease diagnosis. It is challenging to retrieve the associated clinical cases automatically, efficiently and accurately from the substantial medical image archive due to diversity in diseases and imaging modalities. We proposed an efficient and accurate approach for medical image modality classification that can used for retrieval of clinical cases from large medical repositories. The proposed approach is developed using transfer learning concept with pre-trained ResNet50 Deep learning model for optimized features extraction followed by linear discriminant analysis classification (TLRN-LDA). Extensive experiments are performed on challenging standard benchmark ImageCLEF-2012 dataset of 31 classes. The developed approach yields improved average classification accuracy of 87.91%, which is higher up-to 10% compared to the state-of-the-art approaches on the same dataset. Moreover, hand-crafted features are extracted for comparison. Performance of TLRN-LDA system demonstrates the effectiveness over state-of-the-art systems. The developed approach may be deployed to diagnostic centers to assist the practitioners for accurate and efficient clinical case retrieval and disease diagnosis.
Clinical outcomes and prognostic factors of robotic assisted rectal cancer resection alone versus robotic rectal cancer resection with natural orifice extraction: a matched analysis
Authors: Liu Dongning , Luo Rui , Wan Zhikai , Zhu Weiquan , He Penghui , Ye Shanping , Tang Cheng , Lei Xiong , Li Taiyuan
Published: July 2020

Robotic rectal cancer resection with natural orifice extraction is a recently developed minimally invasive surgery used in the treatment of patients with rectal cancer. However, its safety and feasibility remain undiscussed and controversial. This study reported the clinical outcomes and prognostic factors pertaining to traditional robotic assisted rectal cancer resection alone against that of robotic rectal cancer resection with natural orifice extraction to provide a discussion on this issue. 49 patients who underwent robotic rectal cancer resection with natural orifice extraction and 49 matched patients who underwent conventional robotic assisted rectal cancer resection were systematically analyzed in this study. Regarding the baseline characteristics, after matching, no significant differences were observed between the natural orifice specimen extraction (NOSE) group and the robotic assisted rectal cancer resection (RARC) group. Patients in the NOSE group had a reduced visual analog scale (p < 0.001), passed flatus more quickly (p = 0.002) and suffered less surgical stress than those in the RARC group. Moreover, 4 complications were observed in the NOSE group and 7 complications in the RARC group with no significant difference (p = 0.337) in terms of complications. The two groups had a similar survival outcomes, where the 3-year overall survival (p = 0.738) and 3-year progression-free survival (p = 0.986) were all comparable between the two groups. Histological differentiation and T stage could be regarded as independent prognostic factors for 3-year overall survival and 3-year progression-free survival. Robotic rectal cancer resection with natural orifice extraction is a safe and feasible minimally invasive surgery for patients suffering from rectal cancer as it encompasses considerable several advantages. Histological differentiation and T stage may serve as independent prognostic factors for 3-year overall survival and 3-year progression-free survival.
Erbium emission in Er:Y2O3 decorated fractal arrays of silicon nanowires
Authors: Lo Faro Maria Josè , Leonardi Antonio Alessio , Priolo Francesco , Fazio Barbara , Miritello Maria , Irrera Alessia
Published: July 2020

Disordered materials with new optical properties are capturing the interest of the scientific community due to the observation of innovative phenomena. We present the realization of novel optical materials obtained by fractal arrays of silicon nanowires (NWs) synthesized at low cost, without mask or lithography processes and decorated with Er:Y2O3, one of the most promising material for the integration of erbium in photonics. The investigated structural properties of the fractal Er:Y2O3/NWs demonstrate that the fractal morphology can be tuned as a function of the sputtering deposition angle (from 5° to 15°) of the Er:Y2O3 layer. We demonstrate that by this novel approach, it is possible to simply change the Er emission intensity by controlling the fractal morphology. Indeed, we achieved the increment of Er emission at 560 nm, opening new perspectives on the control and enhancement of the optical response of novel disordered materials.
Metal sensing-carbon dots loaded TiO2-nanocomposite for photocatalytic bacterial deactivation and application in aquaculture
Authors: Alexpandi Rajaiah , Gopi Chandu V. V. Muralee , Durgadevi Ravindran , Kim Hee-Je , Pandian Shunmugiah Karutha , Ravi Arumugam Veera
Published: July 2020

Nowadays, bioactive nanomaterials have been attracted the researcher’s enthusiasm in various fields. Herein, Diplocyclos palmatus leaf extract-derived green-fluorescence carbon dots (DP-CDs) were prepared using the hydrothermal method. Due to the strong fluorescence stability, the prepared DP-CDs were coated on filter-paper to make a fluorometric sensor-strip for Fe3+ detection. After, a bandgap-narrowed DP-CDs/TiO2 nanocomposite (DCTN) was prepared using the methanolic extract of D. palmatus. The prepared DCTN exhibited improved photocatalytic bacterial deactivation under sunlight irradiation. The DCTN-photocatalysis slaughtered V. harveyi cells by the production of reactive oxygen species, which prompting oxidative stress, damaging the cell membrane and cellular constituents. These results suggest the plausible mode of bactericidal action of DCTN-photocatalysis under sunlight. Further, the DCTN has shown potent anti-biofilm activity against V. harveyi, and thereby, DCTN extended the survival of V. harveyi-infected shrimps during the in vivo trial with Litopenaeus vannamei. Notably, this is the first report for the disinfection of V. harveyi-mediated acute-hepatopancreatic necrosis disease (AHPND) using nanocomposite. The reduced internal-colonization of V. harveyi on the hepatopancreas as well as the rescue action of the pathognomonic effect in the experimental animals demonstrated the anti-infection potential of DCTN against V. harveyi-mediated AHPND in aquaculture.
Deterministic control of photonic de Broglie waves using coherence optics
Authors: Ham Byoung S.
Published: July 2020

Photonic de Broglie waves offer a unique property of quantum mechanics satisfying the complementarity between the particle and wave natures of light, where the photonic de Broglie wavelength is inversely proportional to the number of entangled photons acting on a beam splitter. Very recently, the nonclassical feature of photon bunching has been newly interpreted using the pure wave nature of coherence optics [Sci. Rep. 10, 7,309 (2020)], paving the road to unconditionally secured classical key distribution [Sci. Rep. 10, 11,687 (2020)]. Here, deterministic photonic de Broglie waves are presented in a coherence regime to uncover new insights in both fundamental quantum physics and potential applications of coherence-quantum metrology.
Author Correction: Proteome-wide identification and functional analysis of ubiquitinated proteins in peach leaves
Authors: Song Yanbo , Shi Xiaojing , Zou Yanli , Guo Juanru , Huo Nan , Chen Shuangjian , Zhao Chengping , Li Hong , Wu Guoliang , Peng Yong
Published: July 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.