bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification
Authors: Kalinin Alexandr A. , Allyn-Feuer Ari , Ade Alex , Fon Gordon-Victor , Meixner Walter , Dilworth David , Husain Syed S. , de Wet Jeffrey R. , Higgins Gerald A. , Zheng Gen , Creekmore Amy , Wiley John W. , Verdone James E. , Veltri Robert W. , Pienta Kenneth J. , Coffey Donald S. , Athey Brian D. , Dinov Ivo D. 
Published: September 2018

AbstractQuantitative analysis of morphological changes in a cell nucleus is important for the understanding of nuclear architecture and its relationship with pathological conditions such as cancer. However, dimensionality of imaging data, together with a great variability of nuclear shapes, presents challenges for 3D morphological analysis. Thus, there is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analysis. We propose a new approach that combines modeling, analysis, and interpretation of morphometric characteristics of cell nuclei and nucleoli in 3D. We used robust surface reconstruction that allows accurate approximation of 3D object boundary. Then, we computed geometric morphological measures characterizing the form of cell nuclei and nucleoli. Using these features, we compared over 450 nuclei with about 1,000 nucleoli of epithelial and mesenchymal prostate cancer cells, as well as 1,000 nuclei with over 2,000 nucleoli from serum-starved and proliferating fibroblast cells. Classification of sets of 9 and 15 cells achieved accuracy of 95.4% and 98%, respectively, for prostate cancer cells, and 95% and 98% for fibroblast cells. To our knowledge, this is the first attempt to combine these methods for 3D nuclear shape modeling and morphometry into a highly parallel pipeline workflow for morphometric analysis of thousands of nuclei and nucleoli in 3D.
Interleukin-17D and Nrf2 mediate initial innate immune cell recruitment and restrict MCMV infection
Authors: Seelige Ruth , Saddawi-Konefka Robert , Adams Nicholas M. , Picarda Gaëlle , Sun Joseph C. , Benedict Chris A. , Bui Jack D. 
Published: September 2018

AbstractInnate immune cells quickly infiltrate the site of pathogen entry and not only stave off infection but also initiate antigen presentation and promote adaptive immunity. The recruitment of innate leukocytes has been well studied in the context of extracellular bacterial and fungal infection but less during viral infections. We have recently shown that the understudied cytokine Interleukin (IL)-17D can mediate neutrophil, natural killer (NK) cell and monocyte infiltration in sterile inflammation and cancer. Herein, we show that early immune cell accumulation at the peritoneal site of infection by mouse cytomegalovirus (MCMV) is mediated by IL-17D. Mice deficient in IL-17D or the transcription factor Nuclear factor (erythroid-derived 2)-like 2 (Nrf2), an inducer of IL-17D, featured an early decreased number of innate immune cells at the point of viral entry and were more susceptible to MCMV infection. Interestingly, we were able to artificially induce innate leukocyte infiltration by applying the Nrf2 activatortert-butylhydroquinone (tBHQ), which rendered mice less susceptible to MCMV infection. Our results implicate the Nrf2/IL-17D axis as a sensor of viral infection and suggest therapeutic benefit in boosting this pathway to promote innate antiviral responses.
Gene expression analysis of Atlantic salmon gills reveals mucin 5 and interleukin 4/13 as key molecules during amoebic gill disease
Authors: Marcos-López Mar , Calduch-Giner Josep A. , Mirimin Luca , MacCarthy Eugene , Rodger Hamish D. , O’Connor Ian , Sitjà-Bobadilla Ariadna , Pérez-Sánchez Jaume , Piazzon M. Carla 
Published: September 2018

AbstractAmoebic gill disease (AGD) is one of the main diseases affecting Atlantic salmon (Salmo salarL.) mariculture. Hallmarks of AGD are hyperplasia of the lamellar epithelium and increased production of gill mucus. This study investigated the expression of genes involved in mucus secretion, cell cycle regulation, immunity and oxidative stress in gills using a targeted 21-gene PCR array. Gill samples were obtained from experimental and naturalNeoparamoeba peruransinfections, and sampling points included progressive infection stages and post-freshwater treatment. Up-regulation of genes related to mucin secretion and cell proliferation, and down-regulation of pro-inflammatory and pro-apoptotic genes were associated with AGD severity, while partial restoration of the gill homeostasis was detected post-treatment. Mucins and Th2 cytokines accoun ted for most of the variability observed between groups highlighting their key role in AGD. Two mucins (muc5,muc18) showed differential regulation upon disease. Substantial up-regulation of the secretedmuc5was detected in clinical AGD, and the membrane boundmuc18showed an opposite pattern. Th2 cytokines,il4/13aandil4/13b2, were significantly up-regulated from 2 days post-infection onwards, and changes were lesion-specific. Despite the differences between experimental and natural infections, both yielded comparable results that underline the importance of the studied genes in the respiratory organs of fish, and during AGD progression.
The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2)
Authors: Pisciotta Annalisa , Manteca Angel , Alduina Rosa 
Published: September 2018

AbstractStreptomyces coelicolor is a Gram-positive microorganism often used as a model of physiological and morphological differentiation in streptomycetes, prolific producers of secondary metabolites with important biological activities. In the present study, we analysed Streptomyces coelicolor growth and differentiation in the presence of the hypo-methylating agent 5′-aza-2′-deoxycytidine (5-aza-dC) in order to investigate whether cytosine methylation has a role in differentiation. We found that cytosine demethylation caused a delay in spore germination, aerial mycelium development, sporulation, as well as a massive impairment of actinorhodin production. Thus, we searched for putative DNA methyltransferase genes in the genome and constructed a mutant of the SCO1731 gene. The analysis of the SCO1731::Tn5062 mutant strain demonstrated that inactivation of SCO1731 leads to a strong decrease of cytosine methylation and almost to the same phenotype obtained after 5-aza-dC treatment. Altogether, our data demonstrate that cytosine methylation influences morphological differentiation and actinorhodin production in S. coelicolor and expand our knowledge on this model bacterial system.
Alterations of blood pulsations parameters in carotid basin due to body position change
Authors: Kamshilin Alexei A. , Krasnikova Tatiana V. , Volynsky Maxim A. , Miridonov Serguei V. , Mamontov Oleg V. 
Published: September 2018

AbstractThe velocity of the pulse wave (PWV) propagating through the vascular tree is an essential parameter for diagnostic the state of the cardiovascular system especially when it is measured in the pool of carotid arteries. In this research, we showed for the first time that the time of the blood-pressure-wave propagation from the heart to the face is a function of the body position. Significant asymmetry and asynchronicity of blood pulsations in the facial area were found in a recumbent position. Parameters of blood pulsations were measured by an advanced camera-based photoplethysmography system in 73 apparently healthy subjects. Most likely, observed changes of the blood-pulsation parameters are caused by variations of the arterial blood pressure due to hydrostatic pressure changes, and secondary reaction of blood vessels in response to these variations. Demonstrated feasibility of PWV measurements in the pool of carotid arteries provides considerable advantages over other technologies. Moreover, possibilities of the method to estimate physiological regulation of the peripheral blood flow (particularly, as a response to the gravitational changes) have been demonstrated. The proposed concept allows development of non-invasive medical equipment capable of solving a wide range of scientific and practical problems related to vascular physiology.
Long-reach 60-GHz MMWoF link with free-running laser diodes beating
Authors: Tsai Cheng-Ting , Li Chien-Cheng , Lin Chi-Hsiang , Lin Chun-Ting , Chi Sien , Lin Gong-Ru 
Published: September 2018

AbstractWith the remote beating of two mutually incoherent laser carriers, the local-oscillator-free long-reach millimeter-wave over fiber (MMWoF) link at 60-GHz band is demonstrated. The unique schemes of the proposed MMWoF are the wavelength-locked colorless laser diode (CLD) modulator, the mutually incoherent optical carrier for heterodyne MMW generation, and the square-law power envelope detection at receiving end. By directly encoding the single-mode with the CLD modulator, the single-carrier modulated QAM-OFDM data is achieved to release the RF power fading after fiber transmission. The mutually incoherent laser beating enables the optical heterodyne MMW generation with two independent optical carriers, which provides the advantages of local-oscillator-free operation and rules out the requirement of dual-mode optical carrier delivery from central office. At the wireless receiving end, the received QAM-OFDM data is self-down-converted to the baseband by employing the square-law power envelope detection. This eliminates the requirement of local oscillator and rules out the influence of the MMW carrier frequency fluctuation between two mutually incoherent lasers (used at central office and remote node), which effectively provides the MMW carrier immunity against the down-conversion instability caused by clock jitter or carrier incoherence. This architecture ensures the transmission of 16.5-Gbit/s 32-QAM OFDM data over 50 km in SMF and 3 m in free-space with the FEC certificated error vector magnitude of 12%, signal-to-noise ratio (SNR) of 18.4 dB, and bit error rate of 3.8 × 10−3. For multi-channel DWDM-PON applications, the proposed local-oscillator-free MMWoF link can successfully perform 11 DWDM channels of 32-QAM OFDM data access at 16.5 Gbit/s per channel via the wavelength controlling of the CLD modulation stage and the detuning of the beating carrier at remote node.
Affective computing in virtual reality: emotion recognition from brain and heartbeat dynamics using wearable sensors
Authors: Marín-Morales Javier , Higuera-Trujillo Juan Luis , Greco Alberto , Guixeres Jaime , Llinares Carmen , Scilingo Enzo Pasquale , Alcañiz Mariano , Valenza Gaetano 
Published: September 2018

AbstractAffective Computing has emerged as an important field of study that aims to develop systems that can automatically recognize emotions. Up to the present, elicitation has been carried out with non-immersive stimuli. This study, on the other hand, aims to develop an emotion recognition system for affective states evoked through Immersive Virtual Environments. Four alternative virtual rooms were designed to elicit four possible arousal-valence combinations, as described in each quadrant of the Circumplex Model of Affects. An experiment involving the recording of the electroencephalography (EEG) and electrocardiography (ECG) of sixty participants was carried out. A set of features was extracted from these signals using various state-of-the-art metrics that quantify brain and cardiovascular linear and nonlinear dynamics, which were input into a Support Vector Machine classifier to predict the subject’s arousal and valence perception. The model’s accuracy was 75.00% along the arousal dimension and 71.21% along the valence dimension. Our findings validate the use of Immersive Virtual Environments to elicit and automatically recognize different emotional states from neural and cardiac dynamics; this development could have novel applications in fields as diverse as Architecture, Health, Education and Videogames.
The induced by an electromagnetic field coexistence of types I and II spectra in Weyl semimetals
Authors: Alisultanov Zaur Z. 
Published: September 2018

AbstractDue to their unique properties, Weyl semimetals (WSMs) are promising materials for the future electronics. Currently, the two types (I and II) of WSMs are discovered experimentally. These types of WSMs differ from each other in their topological properties. In this paper we showed that a coexistence of types I and II Weyls spectra is possible in some WSMs under crossed magnetic and electric fields. This is possible in systems with non-equivalent Weyl points (WPs). In particular, it is possible in strained WSMs. Such phase, controlled by electromagnetic field, is principally new for topological matter physics. It is obvious, that in this regime new features of electron transport will appear. We showed that this effect can also be considered as a mechanism of strain induced type-I-type-II transition.
Antimicrobial promotion of pig growth is associated with tissue-specific remodeling of bile acid signature and signaling
Authors: Ipharraguerre Ignacio R. , Pastor Jose J. , Gavaldà-Navarro Aleix , Villarroya Francesc , Mereu Alessandro 
Published: September 2018

AbstractThe spread of bacterial resistance to antimicrobials (AMA) have intensified efforts to discontinue the non-therapeutic use of AMA in animal production. Finding alternatives to AMA, however, is currently encumbered by the obscure mechanism that underlies their growth-promoting action. In this report, we demonstrate that combinations of antibiotics and zinc oxide at doses commonly used for stimulating growth or preventing post-weaning enteritis in pigs converge in promoting microbial production of bile acids (BA) in the intestine. This leads to tissue-specific modifications in the proportion of BA, thereby amplifying BA signaling in intestine, liver, and white adipose tissue (WAT). Activation of BA-regulated pathways ultimately reinforces the intestinal protection against bacterial infection and pathological secretion of fluids and electrolytes, attenuates inflammation in colon and WAT, alters protein and lipid metabolism in liver, and increases the circulating levels of the hormone FGF19. Conceivably, these alterations could spare nutrients for growth and improve the metabolic efficiency of AMA-treated animals. This work provides evidence that BA act as signaling molecules that mediate host physiological, metabolic, and immune responses to the AMA-induced alterations in gut microbial metabolism, eventually permitting the growth-promoting action of AMA. Consequently, BA emerge as a promising target for developing efficacious alternatives to AMA.
The serine/threonine kinase Stk and the phosphatase Stp regulate cell wall synthesis in Staphylococcus aureus
Authors: Jarick Marcel , Bertsche Ute , Stahl Mark , Schultz Daniel , Methling Karen , Lalk Michael , Stigloher Christian , Steger Mirco , Schlosser Andreas , Ohlsen Knut 
Published: September 2018

AbstractThe cell wall synthesis pathway producing peptidoglycan is a highly coordinated and tightly regulated process. Although the major components of bacterial cell walls have been known for decades, the complex regulatory network controlling peptidoglycan synthesis and many details of the cell division machinery are not well understood. The eukaryotic-like serine/threonine kinase Stk and the cognate phosphatase Stp play an important role in cell wall biosynthesis and drug resistance in S. aureus. We show that stp deletion has a pronounced impact on cell wall synthesis. Deletion of stp leads to a thicker cell wall and decreases susceptibility to lysostaphin. Stationary phase Δstp cells accumulate peptidoglycan precursors and incorporate higher amounts of incomplete muropeptides with non-glycine, monoglycine and monoalanine interpeptide bridges into the cell wall. In line with this cell wall phenotype, we demonstrate that the lipid II:glycine glycyltransferase FemX can be phosphorylated by the Ser/Thr kinase Stk in vitro. Mass spectrometric analyses identify Thr32, Thr36 and Ser415 as phosphoacceptors. The cognate phosphatase Stp dephosphorylates these phosphorylation sites. Moreover, Stk interacts with FemA and FemB, but is unable to phosphorylate them. Our data indicate that Stk and Stp modulate cell wall synthesis and cell division at several levels.
Achromatic linear polarization rotators by tandem twisted nematic liquid crystal cells
Authors: Chung Te-Yuan , Tsai Min-Cheng , Liu Cheng-Kai , Li Jia-Hao , Cheng Ko-Ting 
Published: September 2018

AbstractAn achromatic linear polarization rotator based on a tandem-2ϕ-twisted nematic liquid crystal cell (tandem-2ϕ-TNLC cell, where 2ϕ represents the total twisted angle) is theoretically analyzed and experimentally demonstrated. The tandem-2ϕ-TNLC cell comprises two conventional ϕ-TNLC cells with the required arrangement that the LC director close to the last layer of the first ϕ-TNLC cell should be perpendicular to that close to the first layer of the second ϕ-TNLC cell. With such a simple combination, the TNLC performances are considerably improved. According to the experimental results and theoretical analyses by Jones Calculus, the tandem-2ϕ-TNLC polarization rotator with suitable parameters is achromatic and insensitive to the polarization plane of incident light. Such properties provide these polarization rotators with potential for practical applications.
Agile research to complement agile development: a proposal for an mHealth research lifecycle
Authors: Wilson Kumanan , Bell Cameron , Wilson Lindsay , Witteman Holly 
Published: September 2018

AbstractMobile health (mHealth) technology is increasingly being used, but academic evaluations supporting its use are not keeping pace. This is partly due to the disconnect between the traditional pharmaceutical approach to product evaluation, with its incremental approach, and the flexible way in which mHealth products are developed. An important step to addressing these problems lies in establishing agile research methods that complement the agile development methodologies used to create modern digital health applications. We describe an mHealth research model that mirrors traditional clinical research methods in its attention to safety and efficacy, while also accommodating the rapid and iterative development and evaluation required to produce effective, evidence-based, and sustainable digital products. This approach consists of a project identification stage followed by four phases of clinical evaluation: Phase 1: User Experience Design, Development, & Alpha Testing; Phase 2: Beta testing; Phase 3: Clinical Trial Evaluation; and Phase 4: Post-Market Surveillance. These phases include sample gating questions and are adapted to accommodate the unique nature of digital product development.
Cellular-scale probes enable stable chronic subsecond monitoring of dopamine neurochemicals in a rodent model
Authors: Schwerdt Helen N. , Zhang Elizabeth , Kim Min Jung , Yoshida Tomoko , Stanwicks Lauren , Amemori Satoko , Dagdeviren Huseyin E. , Langer Robert , Cima Michael J. , Graybiel Ann M. 
Published: September 2018

AbstractChemical signaling underlies both temporally phasic and extended activity in the brain. Phasic activity can be monitored by implanted sensors, but chronic recording of such chemical signals has been difficult because the capacity to measure them degrades over time. This degradation has been attributed to tissue damage progressively produced by the sensors and failure of the sensors themselves. We report methods that surmount these problems through the development of sensors having diameters as small as individual neuronal cell bodies (<10 µm). These micro-invasive probes (µIPs) markedly reduced expression of detectable markers of inflammation and tissue damage in a rodent test model. The chronically implanted µIPs provided stable operation in monitoring sub-second fluctuations in stimulation-evoked dopamine in anesthetized rats for over a year. These findings demonstrate that monitoring of chemical activity patterns in the brain over at least year-long periods, long a goal of both basic and clinical neuroscience, is achievable.
A high-gain and high-fidelity coherent state comparison amplifier
Authors: Donaldson Ross J. , Mazzarella Luca , Collins Robert J. , Jeffers John , Buller Gerald S. 
Published: September 2018

AbstractOptical signals are subject to a distance-dependent loss as they propagate through transmission media. High-intensity, classical, optical signals can routinely be amplified to overcome the degradation caused by this loss. However, quantum optical states cannot be deterministically amplified and any attempt to do so will introduce intrinsic noise that spoils the desired quantum properties. Non-deterministic optical amplification, based on post-selection of the output depending on certain conditioning detection outcomes, is an emerging enabling technology in quantum measurement and quantum communications. Here we present an investigation into the properties of a simple, modular optical state comparison amplifier operating on weak coherent states. This amplifier requires no complex quantum resources and is based on linear optical components allowing for a high amplification rate at high gain and fidelity. We examine the amplifier’s performance in different configurations and develop an accurate analytical model that accounts for typical experimental scenarios.
Thiolation in arsenic metabolism: a chemical perspective
Authors: Fan Changjun , Liu Guangliang , Long Yanmin , Rosen Barry , Cai Yong 
Published: September 2018

Abstract
In recent years, methylated thioarsenicals have been widely detected in various biological and environmental matrices, suggesting their broad involvement and biological importance in arsenic metabolism. However, very little is known about the formation mechanism of methylated thioarsenicals and the relation between arsenic methylation and thiolation processes. It is timely and necessary to summarize and synthesize the reported information on thiolated arsenicals for an improved understanding of arsenic thiolation. To this end, we examined the proposed formation pathways of methylated oxoarsenicals and thioarsenicals from a chemical perspective and proposed a novel arsenic metabolic scheme, in which arsenic thiolation is integrated with methylation (instead of being separated from methylation as currently reported). We suggest in the new scheme that protein-bound pentavalent arsenicals are critical intermediates that connect methylation and thiolation, with protein binding of pentavalent methylated thioarsenical being a key step for arsenic thiolation. This informative review on arsenic thiolation from the chemical perspective will be helpful to better understand the arsenic metabolism at the molecular level and the toxicological effects of arsenic species.
Domination integrity of some graph classes
Authors: Besirik Ayse , Kilic Elgin 
Published: September 2018

The stability of a communication network has a great importance in network design. There are several vulnerability measures used to determine the resistance of network to the disruption in this sense. Domination theory provides a model to measure the vulnerability of a graph network. A new vulnerability measure of domination integrity was introduced by Sundareswaran in his Ph.D. thesis (Parameters of vulnerability in graphs (2010)) and defined as DI(G) = min{|S| + m(G − S):S ∈ V(G)} where m(G − S) denotes the order of a largest component of graph G − S and S is a dominating set of G. The domination integrity of an undirected connected graph is such a measure that works on the whole graph and also the remaining components of graph after any break down. Here we determine the domination integrity of wheel graph W1,n, Ladder graph Ln, Sm,n, Friendship graph Fn, Thorn graph of Pn and Cn which are commonly used graph models in network design.