bluuebunny/crossref_metadata_2025 huggingface dataset:
From universal profiles to universal scaling laws in X-ray galaxy clusters
Authors: Ettori S. , Lovisari L. , Sereno M.
Published: October 2020

As the end products of the hierarchical process of cosmic structure formation, galaxy clusters present some predictable properties, like those mostly driven by gravity, and some others more affected by astrophysical dissipative processes that can be recovered from observations and that show remarkable universal behaviour once rescaled by halo mass and redshift. However, a consistent picture that links these universal radial profiles and the integrated values of the thermodynamical quantities of the intracluster medium, also quantifying the deviations from the standard self-similar gravity-driven scenario, has to be demonstrated. In this work we use a semi-analytic model based on a universal pressure profile in hydrostatic equilibrium within a cold dark matter halo with a defined relation between mass and concentration to reconstruct the scaling laws between the X-ray properties of galaxy clusters. We also quantify any deviation from the self-similar predictions in terms of temperature dependence of a few physical quantities such as the gas mass fraction, the relation between spectroscopic temperature and its global value, and, if present, the hydrostatic mass bias. This model allows us to reconstruct both the observed profiles and the scaling laws between integrated quantities. We use the Planck Early Sunyaev-Zeldovich sample, a Planck-selected sample of objects homogeneously analysed in X-rays, to calibrate the predicted scaling laws between gas mass, temperature, luminosity, and total mass. Our universal model reproduces well the observed thermodynamic properties and provides a way to interpret the observed deviations from the standard self-similar behaviour, also allowing us to define a framework to modify accordingly the characteristic physical quantities that renormalise the observed profiles. By combining these results with the constraints on the observed YSZ − T relation we show how we can quantify the level of gas clumping affecting the studied sample, estimate the clumping-free gas mass fraction, and suggest the average level of hydrostatic bias present.
Comparaison de deux dispositifs d’ancrage pour la distalisation molaire
Authors: Scotti Anne-Charlotte , Boudehen Erwan , Thebault Benoît , Sorel Olivier , Brézulier Damien
Published: October 2020

La gestion de l’ancrage est un paramètre clé dans le succès des thérapeutiques orthodontiques. Parmi les nombreux systèmes classiquement décris, tels que les forces extra-orales, les pastilles de Nance, ou encore le ten-two system de Tweed, aucun n’est dénué d’effets indésirables. C’est pourquoi des dispositifs dits « d’ancrage absolu », sans appui dentaire et permettant de s’affranchir de la coopération du patient sont apparus. Ils sont représentés par l’ensemble des vis ou mini-implants à visée orthodontique.

Nous proposons d’étudier ici deux de ces dispositifs : les mini plaques d’ancrage d’une part et les minivis OBS décrites par Chris Chang d’autre part. Notre propos sera illustré au travers de deux cas cliniques traités par distalisation molaire. Nous verrons que ces deux systèmes sont des ancrages osseux temporaires dont la polyvalence rend possible les déplacements des dents dans les trois dimensions de l’espace. Nous montrerons cependant que la phase chirurgicale est plus simple avec les minivis OBS avec moins de comorbidités associées.
Orbita-Infektion mit Delftia acidovorans nach Katzenkratzer
Authors: Smits Walter Johannes , Feucht Heinz-Hubert , Oellig Frank , Zöllner Bernhard
Published: October 2020

Anamnese und klinischer Befund Die 60-jährige Patientin wurde vor 34 Monaten von ihrer Katze am linken Augenlid gekratzt. Danach kam es zu chronischen, langsam progredienten Hautveränderungen mit sich verstärkenden Kopfschmerzen. Therapieversuche mit Kortison, Pimecrolimus, Pregabalin und Metamizol waren erfolglos. Nach 24 Monaten klagte sie über starken Bulbus-Schmerz am linken Auge, zunehmende Schmerzen bei Augenbewegungen und große Lichtempfindlichkeit. Es zeigten sich granulomatöse Papeln im Bereich des Auges.

Untersuchungen und Diagnose Die interdisziplinären Untersuchungsbefunde und klinisch-chemischen Parameter waren unauffällig. Eine Biopsie aus dem Lidbereich erbrachte den Nachweis von Delftia acidovorans mittels bakterieller 16S-rRNA-PCR.

Therapie und Verlauf Unter der Therapie mit Piperacillin/Tazobactam 3-mal 4,5 g/d i. v. für 10 Tage kam es zu einer raschen klinischen Besserung, sodass die Patientin nach 11 Tagen entlassen werden konnte. Nach weiteren 10 Monaten war sie rezidiv- und beschwerdefrei.

Folgerung D. acidovorans ist bislang nicht als zoonotischer Erreger in Erscheinung getreten, sollte aber bei Verletzungen durch Tiere in die differenzialdiagnostischen Erwägungen einbezogen werden.
Wie antikoaguliert man ältere und fragile Patienten?
Authors: Herold Joerg , Bauersachs Rupert
Published: October 2020

Mit zunehmendem Alter steigt das Risiko für Thrombosen, Blutungen und Nierenfunktionsstörungen. Die Wirksamkeit und Sicherheit der direkten oralen Antikoagulanzien (DOAKs) bei fragilen Patienten (Alter 75 Jahre und/oder Kreatinin-Clearance < 50 ml/min und/oder Körpergewicht unter 50 kg) mit Indikation zur Antikoagulation ist eines der schwierigsten Themen in der aktuellen kardiovaskulären Medizin. Neue Registerdaten aus Subgruppenanalysen großer Studien und Register weisen auf die Überlegenheit von DOAKs im Vergleich mit VKA hin. In diesem Artikel werden sowohl Daten aus neuen Studien als auch Subgruppenanalysen von wegweisenden Studien ausgewertet, um neue Erkenntnisse zu gewinnen und Wege für die Antikoagulation bei fragilen Patienten zu beschreiben.
Behandlungskonzepte der Frühmobilisation
Authors: Siegemund Kerstin
Published: October 2020

Eine frühfunktionelle Behandlung nach Beugesehnennaht kann Adhäsionen der Sehne mit dem umliegenden Gewebe reduzieren und so die Beweglichkeit der betroffenen Finger verbessern. Die funktionellen Ergebnisse sind bedeutend besser als nach einer Immobilisation. Je nachdem ob die Flexion der Finger postoperativ durch eigene Muskelkraft oder durch den Therapeuten erfolgt, sprechen wir von aktiver oder passiver Frühmobilisation.
Late-Stage Alkylation of N-Containing Heteroarenes Enabled by Homolysis of Alkyl-1,4-dihydropyridines under Blue LED Irradiation
Authors: Wang Ping , Chen Xiaoping , Luo Xiaosheng , Wang Kaiqian , Liang Feng
Published: October 2020

Alkylated heteroarenes are widely found in bioactive molecules and pharmaceuticals. Therefore, there is great interest in developing a chemoselective alkylation of heteroarenes under mild conditions, particularly during a late-stage functionalization step for the purpose of rapid derivatization. Herein, we introduce an efficient visible-light-promoted C–H alkylation of nitrogen-containing heteroarenes by using C4-alkyl 1,4-dihydropyridines (DHPs) as radical precursors at ambient temperatures. A broad scope of heteroarenes, such as 4-hydroxyquinazoline and its derivatives, including those bearing electron-donating or electron-withdrawing groups, can be successfully alkylated in good yields by using various C4-alkyl DHPs.
Information: a missing component in understanding and mitigating social epidemics
Authors: Magarey Roger D. , Trexler Christina M.
Published: October 2020

Social epidemics or behaviorally based non-communicable diseases are becoming an increasingly important problem in developed countries including the United States. It is the aim of our paper to propose a previously understudied aspect of the spread of social epidemics, the role of information in both causing and mitigating social epidemics. In this paper, we ask, can information be harmful, contagious, and a causal factor in social epidemics? In the spread of biological epidemics, the causal agents are biological pathogens such as bacteria or viruses. We propose that in the spread of social epidemics, one of the causal agents is harmful information, which is increasing exponentially in the age of the internet. We ground our idea in the concept of the meme and define the concept of an infopathogen as harmful information that can spread or intensify a social epidemic. Second, we ask, what are the best tools to understand the role of information in the spread of social epidemics? The epidemiological triad that includes a host, agents (and vectors), and the environment is extended into a quad by including information agents. The quad includes the role of information technologies as vectors and the impact of the social environment. The “life cycles” of pathogens in biological epidemics and infopathogens in social epidemics are compared, along with mitigations suggested by the epidemiological quad. Challenges to the theory of infopathogens, including the complexities associated with the spread of memes and the role of behavior in the spread of epidemics are discussed. Implications of the theory including the classification of harmfulness, the freedom of speech, and the treatment of infected individuals are also considered. We believe the application of the epidemiological quad provides insights into social epidemics and potential mitigations. Finally, we stress that infopathogens are only part of social epidemic development; susceptible hosts, a favorable environment, and availability of physical agents are all also required.
Interpretation of frequency modulation TN-LCD embedded with metal nanoparticles using equivalent circuit analysis
Authors: Kobayashi Shunsuke , Shiraishi Yukihide , Miyama Tomohiro , Toshima Naoki
Published: October 2020

A twisted nematic (TN) liquid crystal display (LCD) with embedded Ag nanoparticles (NPs) covered with a diffusion cloud exhibits peculiar frequency dependent behavior. In particular, no TN response is observed below the dielectric relaxation frequency, fR, whereas above this frequency, revival of the TN response occurs. Such a device is called a frequency modulation (FM) TN-LCD, and its behavior is attributed to the reduction of the dielectric anisotropy Δɛ far below the relaxation frequency, fR. However, above this frequency, the revival of the torque driving the TN-LCD occurs, and the TN-LCD operation is revived with a fast response speed. The reduction of Δɛ may be due to the prevalence of the amplified dielectric constant caused by the inclusions covering the entire region. However, above fR, this amplification gradually vanishes, and the normal TN-operation is revived due to the revival of dielectric torque force. In this paper, an interpretation of the FM-LCD operation through dielectric spectroscopy and equivalent circuit analysis is presented. Interpretation of the dielectric constant amplification [whose factor, AC, is equal to 52 through a postulation of negative ɛ2 for the inclusions (NPs and diffusion cloud)] is also presented.
The UBC27–AIRP3 ubiquitination complex modulates ABA signaling by promoting the degradation of ABI1 in Arabidopsis
Authors: Pan Wenbo , Lin Baoying , Yang Xiaoyuan , Liu Lijing , Xia Ran , Li Jigang , Wu Yaorong , Xie Qi
Published: October 2020

Significance

The coreceptors of phytohormone ABA, such as ABI1, are the central regulator of plant tolerance to drought and other abiotic stresses. Tight regulation of ABI1 through ubiquitination is vital for ABA signaling and drought tolerance. In this study, we identified a mechanism to reduce ABI1 protein levels by an E2-E3 pair UBC27–AIRP3. UBC27 directly binds ABI1 and cooperates with AIRP3 in the degradation of ABI1 and ABA signaling. ABA further activates the expression of
UBC27
and
AIRP3
, inhibits the degradation of UBC27, and enhances the interaction between UBC27 and ABI1, establishing a positive feedback regulatory loop to control UBC27 activity under stress conditions. Our results identify a layer of ABA-pathway regulation that terminates ABI1 by the ubiquitination complex UBC27–AIRP3.
Sanctuary policies reduce deportations without increasing crime
Authors: Hausman David K.
Published: October 2020

Significance

Opponents of sanctuary policies, including the federal government, assert that they harm public safety. This report shows that that claim is not supported by the evidence. This report estimates the effect of sanctuary on deportations, finding that sanctuary policies reduce deportations by one-third, but that those policies do not reduce deportations of people with violent criminal convictions. It also finds that sanctuary has no measurable effect on crime.
From local to national metabolism: a review and a scale-up framework
Authors: Yan Ningyu , Liu Gengyuan , Ripa Maddalena , Wang Ning , Zheng Hongmei , Gonella Francesco
Published: October 2020

Research background
: Countries are likely the most important subjects involved in the environmental control and response to global environmental issues, while the majority of the related metabolic analyses are focused on the metabolism at the city scale.

Objective
: Analyzing why and how to scale up the metabolic study from city to country.

Methods
: Combining quantitative analysis with a literature review socio-metabolic research, since it is an effective method to study resource and environmental issues and has been applied at different scales.

Results
: 1) A single city or a smaller area is hardly self-sufficient, and its sustainability and resilience needs the support of the surrounding environment; 2) At the country scale, systems exhibit a higher level of self-organization and a corresponding higher level of complexity, addressing the need for applying the metabolic theory at the national scale; 3) The emergy analysis methods show its advantages in study metabolic processes for national metabolism; 4) Input-output analysis plays an important role in and region coordination.

Conclusions
: The interactions among and within the scales are nested, as well as the goals and methods. Therefore, socio-metabolic research on scales differ in their priority goals, and the methods adopted must be targeted.
Deep learning-based real-time volumetric imaging for lung stereotactic body radiation therapy: a proof of concept study
Authors: Lei Yang , Tian Zhen , Wang Tonghe , Higgins Kristin , Bradley Jeffrey D , Curran Walter J , Liu Tian , Yang Xiaofeng
Published: October 2020

Due to the inter- and intra- variation of respiratory motion, it is highly desired to provide real-time volumetric images during the treatment delivery of lung stereotactic body radiation therapy (SBRT) for accurate and active motion management. In this proof-of-concept study, we propose a novel generative adversarial network integrated with perceptual supervision to derive instantaneous volumetric images from a single 2D projection. Our proposed network, named TransNet, consists of three modules, i.e. encoding, transformation and decoding modules. Rather than only using image distance loss between the generated 3D images and the ground truth 3D CT images to supervise the network, perceptual loss in feature space is integrated into loss function to force the TransNet to yield accurate lung boundary. Adversarial supervision is also used to improve the realism of generated 3D images. We conducted a simulation study on 20 patient cases, who had received lung SBRT treatments in our institution and undergone 4D-CT simulation, and evaluated the efficacy and robustness of our method for four different projection angles, i.e. 0°, 30°, 60° and 90°. For each 3D CT image set of a breathing phase, we simulated its 2D projections at these angles. For each projection angle, a patient’s 3D CT images of 9 phases and the corresponding 2D projection data were used to train our network for that specific patient, with the remaining phase used for testing. The mean absolute error of the 3D images obtained by our method are 99.3 ± 14.1 HU. The peak signal-to-noise ratio and structural similarity index metric within the tumor region of interest are 15.4 ± 2.5 dB and 0.839 ± 0.090, respectively. The center of mass distance between the manual tumor contours on the 3D images obtained by our method and the manual tumor contours on the corresponding 3D phase CT images are within 2.6 mm, with a mean value of 1.26 mm averaged over all the cases. Our method has also been validated in a simulated challenging scenario with increased respiratory motion amplitude and tumor shrinkage, and achieved acceptable results. Our experimental results demonstrate the feasibility and efficacy of our 2D-to-3D method for lung cancer patients, which provides a potential solution for in-treatment real-time on-board volumetric imaging for tumor tracking and dose delivery verification to ensure the effectiveness of lung SBRT treatment.
Stretchable electromagnetic interference shielding and antenna for wireless strain sensing by anisotropic micron-steel-wire based conductive elastomers*
Authors: Hu Xiaoyu , Mou Linlin , Liu Zunfeng
Published: October 2020

We prepare stretchable elastic electromagnetic interference (EMI) shielding and stretchable antenna for wireless strain sensing using an elastic composite comprising commercial steel wool as a conducting element. The prepared elastic conductor shows anisotropic electrical properties in response to the external force. In the stretchable range, the electrical resistance abnormally decreases with the increase of tensile deformation. The EMI shielding effectiveness of the elastic conductor can reach above –30 dB under 80% tensile strain. The resonance frequency of the dipole antenna prepared by the elastic conductor is linearly correlated with the tensile strain, which can be used as a wireless strain sensor. The transmission efficiency is stable at about –15 dB when stretched to 50% strain, with attenuation less than 5%. The current research provides an effective solution for stretchable EMI shielding and wireless strain sensing integrated with signal transmission by an antenna.
Stable water droplets on composite structures formed by embedded water into fully hydroxylated β-cristobalite silica*
Authors: Gong Hanqi , Qi Chonghai , Yang Junwei , Chen Jige , Lei Xiaoling , Zhao Liang , Wang Chunlei
Published: October 2020

Using molecular dynamics simulations, we have revealed a novel wetting phenomenon with a droplet on composite structures formed by embedded water into (111) surface of β-cristobalite hydroxylated silica. This can be attributed to the formation of a composite structure composed of embedded water molecules and the surface hydroxyl (–OH) groups, which reduces the number of hydrogen bonds between the composite structure and the water droplet above the composite structure. Interestingly, a small uniform strain (±3%) applied to the crystal lattice of the hydroxylated silica surface can result in a notable change of the contact angles (>40°) on the surface. The finding provides new insights into the correlation between the molecular-scale interfacial water structures and the macroscopic wettability of the hydroxylated silica surface.
Phoretic self-assembly of active colloidal molecules*
Authors: Lei Lijie , Wang Shuo , Zhang Xinyuan , Lai Wenjie , Wu Jinyu , Gao Yongxiang
Published: October 2020

We simulate the self-assembly of active colloidal molecules from binary mixtures of spherical particles using a Brownian dynamics algorithm. These particles interact via phoretic interactions, which are determined by two independently tunable parameters, surface activity and surface mobility. In systems composed of equal-size particles, we observe the formation of colloidal molecules with well-defined coordination numbers and spatial arrangement, which also display distinct dynamic functions, such as resting, translating, and rotating. By changing the size ratio to 2 : 1 between the two species, we further observe the formation of colloidal molecules with new structures arising from breaking the size symmetry. By tuning the mutual interactions between the smaller species via their surface mobility, we are able to control their spacing as well as the coordination number of the colloidal molecules. This study highlights the importance of tuning surface parameters and size asymmetry in controlling the structure and the active dynamics of colloidal molecules.
Constructing refined null models for statistical analysis of signed networks*
Authors: Li Ai-Wen , Xiao Jing , Xu Xiao-Ke
Published: October 2020

The establishment of effective null models can provide reference networks to accurately describe statistical properties of real-life signed networks. At present, two classical null models of signed networks (i.e., sign and full-edge randomized models) shuffle both positive and negative topologies at the same time, so it is difficult to distinguish the effect on network topology of positive edges, negative edges, and the correlation between them. In this study, we construct three refined edge-randomized null models by only randomizing link relationships without changing positive and negative degree distributions. The results of nontrivial statistical indicators of signed networks, such as average degree connectivity and clustering coefficient, show that the position of positive edges has a stronger effect on positive-edge topology, while the signs of negative edges have a greater influence on negative-edge topology. For some specific statistics (e.g., embeddedness), the results indicate that the proposed null models can more accurately describe real-life networks compared with the two existing ones, which can be selected to facilitate a better understanding of complex structures, functions, and dynamical behaviors on signed networks.
Characterization of Surface Topographies Generated using Circular- and Cylindrical-Face EDT
Authors: Jithin S , Bhandarkar Upendra V , Joshi Suhas S
Published: October 2020

Large area texturing using EDT is challenging due to surface damage resulted from inefficient discharges, such as arcs and short-circuits. Also, three-dimensional analyses of surface topography generated during electrical discharge texturing (EDT) are scarcely performed in the available literature. Therefore, in this work, two modes of EDT were developed for large area texturing based on the mode of electrode movement resulting in texture generation on work surfaces: circular-face EDT (CirEDT) and cylindrical-face EDT (CylEDT), and the generated surface topographies are characterized in terms of topography images, areal texture parameters, and scanning electron microscopy images. Parametric analyses are also performed to study the influences of the operating parameters, such as discharge current, pulse on-time, and peripheral velocity, on different areal texture parameters. Topography analyses reveal that these surfaces have a characteristic stochastic distribution of microstructures in shape, size, and location. Height parameter analyses reveal that CylEDT surfaces are twice positively skewed and have a higher kurtosis as compared to the CirEDT surfaces. Spatial parameter analyses reveal that both surfaces display dominance of isotropic nature and non-directional structures. CirEDT surfaces have higher lubricant retention capacity, but lesser wear volume available for running-in period as compared to CylEDT surfaces, as per volume parameter analyses. Discharge current and pulse on-time are identified as the significant parameters influencing the majority of the areal texture parameters analyzed. SEM analysis revealed that CylEDT results in a textured surface with sea-wave-like structures, whereas CirEDT results in a textured surface with lunar-craters-like structures.
Deep subwavelength manipulation of THz waves by plasmonic surface
Authors: Guo Baoshan
Published: October 2020

Deep subwavelength manipulation of terahertz (THz) wave is a key method to realize compact on chip THz devices. It is demonstrated that the refractive index change in a deep subwavelength region of a dielectric layer can effectively manipulate the surface THz wave propagation by the simulation study. The feature size of this area is only 10 μm (∼1/8 λ). A slight change of refractive index, position or size of this region is enough to manipulate the surface THz waves with high efficiency, such as the transmissivity or reflectivity of different THz frequencies. Moreover, the change of the deep subwavelength region can be controlled by an ultrafast laser to achieve ultrafast dynamic manipulation of THz waves. This is a concise and efficient method of manipulating electromagnetic waves on the deep subwavelength scale and to fabricate more compact integrated optical devices.
Hg adatoms on graphene: A first-principles study
Authors: Fenta A S , Amorim C O , Gonçalves J N , Fortunato N , Barbosa M B , Araujo J P , Houssa M , Cottenier S , Van Bael M J , Correia J G , Amaral V S , Pereira L M C
Published: October 2020

The interest in understanding the interaction between graphene and atoms that are adsorbed on its surface (adatoms) spans a wide range of research fields and applications, for example, to controllably change the properties of graphene in electronic devices or to detect those changes in graphene-based sensors. We present a density functional theory study of the interaction between graphene and Hg adatoms. Binding energy, electronic structure and electric field gradient (EFG) were calculated for various high-symmetry atomic configurations, from isolated adatoms to a continuous Hg monolayer. Hg as isolated adatom was found to be the most stable configuration, with a binding energy of 188 meV. Whereas isolated adatoms have a minor effect on the electronic structure of graphene (small acceptor effect), Hg monolayer configurations induce a metallic state, with the Fermi level moving well above the Dirac point (donor behavior). Based on the EFG calculated for the various configurations, we discuss how hyperfine techniques (perturbed angular correlation spectroscopy, in particular) can be used to experimentally study Hg adsorption on graphene.
Impact of hot electrons on optical excitation of terahertz radiation by beating of supergaussian lasers in electron-positron collisional plasma
Authors: Divya S
Published: October 2020

The mechanism of generation of terahertz (THz) radiation with beating of two supergausssian lasers in corrugated density plasma containing hot electron-positron (e-p) is revisited. Resonance condition for optical excitation of THz emission is reported to be modified due to finite temperature of plasma species (electrons-positrons to the few order keV range) in the presence of weak collisions. The collision frequency is optimized to the range ν ≤ 0.5ω

p
in the e-p plasma depending on the temperature and collisional rates. The effect of electron temperature, collision frequency and suitability of supergaussian laser is investigated on phase modulation to achieve highest emitted THz field with 6% efficiency of the mechanism.
Transverse strain measurements in polymer-embedded, polarization-maintaining Fiber Bragg Gratings
Authors: Gouws Andre , Ford Kurtis R , Jones Brad H
Published: October 2020

Fiber Bragg gratings (FBGs) have numerous advantages over traditional foil strain gages, most notably in that they can be embedded in host materials and used to evaluate local deformation. Among the wide variety of grating architectures that have been studied, FBGs inscribed in polarization-maintaining (PM) or other birefringent fibers provide a unique, quantifiable response to strain transverse to the fiber axis. In this work, we show that a PM FBG can accurately predict the asymmetry in transverse strain of a host material in embedded configurations. We do this by diametrically loading an epoxy cylinder that has a uniform PM FBG embedded in the center. We use elasticity and finite element modeling (FEM) to correlate the mechanical response of an embedded fiber with that of the host. An analytical solution of the nominal relationship between Bragg wavelength and strain is included for this loading condition.
Automated multi-layer optical design via deep reinforcement learning
Authors: Wang Haozhu , Zheng Zeyu , Ji Chengang , Jay Guo L
Published: October 2020

Optical multi-layer thin films are widely used in optical and energy applications requiring photonic designs. Engineers often design such structures based on their physical intuition. However, solely relying on human experts can be time-consuming and may lead to sub-optimal designs, especially when the design space is large. In this work, we frame the multi-layer optical design task as a sequence generation problem. A deep sequence generation network is proposed for efficiently generating optical layer sequences. We train the deep sequence generation network with proximal policy optimization to generate multi-layer structures with desired properties. The proposed method is applied to two energy applications. Our algorithm successfully discovered high-performance designs, outperforming structures designed by human experts in task 1, and a state-of-the-art memetic algorithm in task 2.
Assessment of antibacterial and anticancer capability of silver nanoparticles extracellularly biosynthesized using Aspergillus terreus
Authors: Kumari R Mankamna , Kumar Vikram , Kumar Manish , Pareek Nidhi , Nimesh Surendra
Published: October 2020

The present study explores biosynthesis of silver nanoparticles (AgNPs) employing extracellular extract of Aspergillus terreus ITCC 9932.15. Modulation of various variables that dictate the biosynthesis of AgNPs, suggested of optimal AgNPs synthesis using AgNO3, 1 mM at pH 8 and temperature, 35 °C. The biosynthesis of AgNPs was observed to be time dependent with incremental particle synthesis till 24 h. Various studies were undertaken to authenticate formation and characterization of AgNPs for size, crystallinity and biomolecules involved. A sharp SPR peak observed at 420 nm in the UV–vis absorption spectra validated synthesis of nanoparticles. These particles exhibited spherical morphology with size ∼25 nm and −16 mV of zeta potential. Further, the existence of proteins and other biomolecules onto the surface of AgNPs was confirmed with FTIR studies. The SAED pattern investigated by employing TEM authenticated the crystallinity of AgNPs. The AgNPs also exhibited potential antibacterial activity against Gram-negative and Gram-positive bacteria (E. coli and P. aeruginosa). In addition, remarkable anticancer activity was obtained in breast cancer cell line (MCF-7).
Cancer Incidence and Mortality in the Oldest Old: A Nationwide Study in Finland
Authors: Tanskanen Tomas , Seppä Karri J M , Virtanen Anni , Malila Nea K , Pitkäniemi Janne M
Published: October 2020

The world’s population is aging rapidly. This study reports the burden of cancer in the “oldest old” (aged ≥85 years) in Finland, 1953–2017, and estimates age-specific cancer rates in the older population (65–99 years) for 1988–2017. The Finnish Cancer Registry provided data on all cancer diagnoses, cancer deaths, and other deaths in cancer patients in Finland for 1953–2017. Between 1953–1957 and 2013–2017, the proportion of incident cancers in those aged ≥85 years increased from 1.5% to 9.6% (597 to 15,360 new cases), and in 2013–2017, more new cancers were diagnosed at ages ≥85 years than ages <50 years. Cancer incidence and excess mortality attributable to cancer peaked at ages 85–94 years and declined subsequently, whereas cancer-specific mortality continued to increase or plateaued. Due to demographic changes, the number of new cancers in the oldest old has increased substantially in Finland, and currently nearly 1 in 10 cancers are diagnosed in this age group. The increasing cancer burden in the oldest old poses a major challenge for health care and needs to be addressed in designing clinical research and reporting of cancer registries. In older populations with competing risks of death, we propose excess cancer mortality as a measure of cancer-related mortality.
Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq
Authors: Vivek A T , Kumar Shailesh
Published: October 2020

Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
DriverGroup: a novel method for identifying driver gene groups
Authors: Pham Vu V H , Liu Lin , Bracken Cameron P , Goodall Gregory J , Li Jiuyong , Le Thuc D
Published: October 2020

Motivation

Identifying cancer driver genes is a key task in cancer informatics. Most existing methods are focused on individual cancer drivers which regulate biological processes leading to cancer. However, the effect of a single gene may not be sufficient to drive cancer progression. Here, we hypothesize that there are driver gene groups that work in concert to regulate cancer, and we develop a novel computational method to detect those driver gene groups.

Results

We develop a novel method named DriverGroup to detect driver gene groups by using gene expression and gene interaction data. The proposed method has three stages: (i) constructing the gene network, (ii) discovering critical nodes of the constructed network and (iii) identifying driver gene groups based on the discovered critical nodes. Before evaluating the performance of DriverGroup in detecting cancer driver groups, we firstly assess its performance in detecting the influence of gene groups, a key step of DriverGroup. The application of DriverGroup to DREAM4 data demonstrates that it is more effective than other methods in detecting the regulation of gene groups. We then apply DriverGroup to the BRCA dataset to identify driver groups for breast cancer. The identified driver groups are promising as several group members are confirmed to be related to cancer in literature. We further use the predicted driver groups in survival analysis and the results show that the survival curves of patient subpopulations classified using the predicted driver groups are significantly differentiated, indicating the usefulness of DriverGroup.

Availability and implementation

DriverGroup is available at https://github.com/pvvhoang/DriverGroup

Supplementary information

Supplementary data are available at Bioinformatics online.
Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files
Authors: Saremi Babak , Kohls Moritz , Liebig Pamela , Siebert Ursula , Jung Klaus
Published: October 2020

Motivation

High-throughput sequencing data can be affected by different technical errors, e.g. from probe preparation or false base calling. As a consequence, reproducibility of experiments can be weakened. In virus metagenomics, technical errors can result in falsely identified viruses in samples from infected hosts. We present a new resampling approach based on bootstrap sampling of sequencing reads from FASTQ-files in order to generate artificial replicates of sequencing runs which can help to judge the robustness of an analysis. In addition, we evaluate a mixture model on the distribution of read counts per virus to identify potentially false positive findings.

Results

The evaluation of our approach on an artificially generated dataset with known viral sequence content shows in general a high reproducibility of uncovering viruses in sequencing data, i.e. the correlation between original and mean bootstrap read count was highly correlated. However, the bootstrap read counts can also indicate reduced or increased evidence for the presence of a virus in the biological sample. We also found that the mixture-model fits well to the read counts, and furthermore, it provides a higher accuracy on the original or on the bootstrap read counts than on the difference between both. The usefulness of our methods is further demonstrated on two freely available real-world datasets from harbor seals.

Availability and implementation

We provide a Phyton tool, called RESEQ, available from https://github.com/babaksaremi/RESEQ that allows efficient generation of bootstrap reads from an original FASTQ-file.

Supplementary information

Supplementary data are available at Bioinformatics online.
Simultaneous Determination of Paracetamol, Propyphenazone and Caffeine in Presence of Paracetamol Impurities Using Dual-Mode Gradient HPLC and TLC Densitometry Methods
Authors: Ibrahim Hany , Hamdy Abdallah M , Merey Hanan A , Saad Ahmed S
Published: October 2020

Two chromatographic methods were validated for the determination of the widely prescribed analgesic and antipyretic drug combination of paracetamol (PC) (recently integrated into the supportive treatment of COVID-19), propyphenazone (PZ) and caffeine (CF) in the presence of two PC impurities, namely 4-aminophenol and 4-nitrophenol. A “dual-mode” gradient high-performance liquid chromatography method was developed, where the separation was achieved via “dual-mode” gradient by changing both the ternary mobile phase composition (acetonitrile: methanol: water) and the flow rate. This enables a good resolution within a relatively shorter analysis time. The analysis was realized using Zorbax Eclipse XDB column C18, 5 μm (250 × 4.6 mm) and the UV detector was set at 220 nm. The other method is a thin-layer chromatography densitometry method, where the separation was achieved using a mobile phase composed of chloroform: toluene: ethyl acetate: methanol: acetic acid (6: 6: 1: 2: 0.1, by volume). Densitometric detection was performed at 220 nm on silica gel 60 F254 plates. The developed methods were fully validated as per the ICH guidelines and proved to be accurate, robust, specific and suitable for application as purity indicating methods for routine analysis of PC in pure form or in pharmaceuticals with PZ and CF in quality control laboratories.
Quantitative Determination of Fosfomycin in 10 μL of Plasma and Dialysate by Hydrophilic Interaction Liquid Chromatography Electrospray Ionization Mass Spectrometry
Authors: Shopova Teodora , Hüppe Tobias , Wolf Beate , Sessler Daniel I , Volk Thomas , Groesdonk Heinrich V , Kreuer Sascha , Maurer Felix
Published: October 2020

Fosfomycin is an antibiotic with a broad spectrum of activity against many multidrug-resistant bacterial strains. It is mainly excreted unchanged by the kidneys, and its half-life therefore depends on kidney function which varies considerably among individuals, and within individuals over time. Proper fosfomycin dosing thus depends on assaying blood concentration of the drug. We developed and validated a simple, sensitive and specific chromatography assay, which was coupled to electrospray ionization mass spectrometry for determination of fosfomycin. Separation of fosfomycin was based on the method of the hydrophilic interaction liquid chromatography; specifically, plasma and dialysate samples were acidified and the protein precipitated with acetonitrile. The calibration curves showed excellent coefficients of determination (R2 > 0.999) over the relevant concentration range of 25–700 μg/mL. Intraday precision was 1.1–1.2% and accuracy was −5.9% to 0.9% for quality control samples. Interday precision was 2.9–3.4% and accuracy was −3.7% to 5.5%. Extraction recovery was ≥87% and matrix effects ranged from 2.2% to 4.3%. After laboratory validation, the method was successfully applied to clinical samples.
Scope and heterogeneity of outcomes reported in randomized trials in patients receiving peritoneal dialysis
Authors: Manera Karine E , Johnson David W , Cho Yeoungjee , Sautenet Benedicte , Shen Jenny , Kelly Ayano , Yee-Moon Wang Angela , Brown Edwina A , Brunier Gillian , Perl Jeffrey , Dong Jie , Wilkie Martin , Mehrotra Rajnish , Pecoits-Filho Roberto , Naicker Saraladevi , Dunning Tony , Craig Jonathan C , Tong Allison
Published: October 2020

Background

Randomized trials can provide evidence to inform decision-making but this may be limited if the outcomes of importance to patients and clinicians are omitted or reported inconsistently. We aimed to assess the scope and heterogeneity of outcomes reported in trials in peritoneal dialysis (PD).

Methods

We searched the Cochrane Kidney and Transplant Specialized Register for randomized trials in PD. We extracted all reported outcome domains and measurements and analyzed their frequency and characteristics.

Results

From 128 reports of 120 included trials, 80 different outcome domains were reported. Overall, 39 (49%) domains were surrogate, 23 (29%) patient-reported and 18 (22%) clinical. The five most commonly reported domains were PD-related infection [59 (49%) trials], dialysis solute clearance [51 (42%)], kidney function [45 (38%)], protein metabolism [44 (37%)] and inflammatory markers/oxidative stress [42 (35%)]. Quality of life was reported infrequently (4% of trials). Only 14 (12%) trials included a patient-reported outcome as a primary outcome. The median number of outcome measures (defined as a different measurement, aggregation and metric) was 22 (interquartile range 13–37) per trial. PD-related infection was the most frequently reported clinical outcome as well as the most frequently stated primary outcome. A total of 383 different measures for infection were used, with 66 used more than once.

Conclusions

Trials in PD include important clinical outcomes such as infection, but these are measured and reported inconsistently. Patient-reported outcomes are infrequently reported and nearly half of the domains were surrogate. Standardized outcomes for PD trials are required to improve efficiency and relevance.
Safety, Pharmacokinetics, and Efficacy of Olorinab, a Peripherally Acting, Highly Selective, Full Agonist of the Cannabinoid Receptor 2, in a Phase 2a Study of Patients With Chronic Abdominal Pain Associated With Crohn’s Disease
Authors: Yacyshyn Bruce R , Hanauer Stephen , Klassen Preston , English Brett A , Stauber Kathe , Barish Charles F , Gilder Kye , Turner Stewart , Higgins Peter D R
Published: October 2020

Background

This randomized, open-label phase 2a study investigated the safety/tolerability, pharmacokinetics, and efficacy of olorinab—a highly selective, peripherally acting, full agonist of the cannabinoid receptor 2—in patients with Crohn’s disease (CD) experiencing abdominal pain.

Methods

Eligible subjects 18–80 years of age with quiescent to mildly active CD were randomized to receive olorinab 25 or 100 mg three times daily for 8 weeks. The primary objective was to assess safety/tolerability.

Results

Fourteen subjects received olorinab 25 mg (N = 6) or 100 mg (N = 8). Ten subjects [4 (67%) in the 25-mg group and 6 (75%) in the 100-mg group] reported a total of 34 treatment-emergent adverse events (TEAEs; 32 grade 1/2, not serious events; 2 grade 3, serious, not treatment-related events). No dose reductions or discontinuations due to TEAEs or deaths were reported. Dose-proportional increases in olorinab exposure from 25 to 100 mg were observed, with minimal accumulation at both doses. At week 8, the mean (SD) change from baseline in average abdominal pain score at peak olorinab plasma concentrations was −4.61 (1.77) in the 25-mg group (P = 0.0043) and −4.57 (2.17) in the 100-mg group (P = 0.0036). The change from baseline at week 8 in the mean (SD) number of pain-free days per week was +1.60 (2.61) in the 25-mg group and +2.33 (3.62) in the 100-mg group. No subject required pain medication on study.

Conclusions

Patients with quiescent to mildly active CD receiving olorinab experienced mild-to-moderate adverse events and an improvement in abdominal pain scores in this study.
Long-term outcome of myocardial scarring and deformation with cardiovascular magnetic resonance in out of hospital cardiac arrest survivors
Authors: Baritussio Anna , Biglino Giovanni , Scatteia Alessandra , De Garate Estefania , Dastidar Amardeep Ghosh , Palazzuoli Alberto , Harries Iwan , Strange Julian W , Diab Ihab , Bucciarelli-Ducci Chiara
Published: October 2020

Aims

Cardiovascular magnetic resonance (CMR) is increasingly recognized as a diagnostic and prognostic tool in out of hospital cardiac arrest (OHCA) survivors. After assessing CMR findings early after ventricular fibrillation (VF) OHCA, we sought to explore the long-term outcome of myocardial scarring and deformation.

Methods and results

We included 121 consecutive VF OHCA survivors (82% male, median 62 years) undergoing CMR within 2 weeks from cardiac arrest. Late gadolinium-enhancement (LGE) was quantified using the full width at half maximum method and tissue tracking analysis software was used to assess myocardial deformation. LGE was found in 71% of patients (median LGE mass 6.2% of the left ventricle, LV), mainly with an ischaemic pattern. Myocardial deformation was overall impaired and showed a significant correlation with LGE presence and extent (P < 0.001). A composite end-point of all-cause mortality and appropriate ICD discharge/anti-tachycardia pacing was met in 24% of patients. Patients meeting the end-point had significantly greater LGE extent (8.6% of LV myocardium vs. 4.1%, P = 0.02), while there was no difference with regards to myocardial deformation. Survival rate was significantly lower in patients with LGE (P = 0.05) and LGE mass >4.4% of the LV identified a group of patients at higher risk of adverse events (P = 0.005).

Conclusions

We found a high prevalence of LGE, early after OHCA, and an overall impaired myocardial deformation. On long-term follow-up both LGE presence and extent showed a significant association with recurrent adverse events, while LV ejection fraction and myocardial deformation did not identify patients with an unfavourable outcome.