bluuebunny/crossref_metadata_2025 huggingface dataset:
Lower-hybrid drift waves and their interaction with plasmas in a 3D symmetric reconnection simulation with zero guide field
Authors: Wang Shan , Chen Li-Jen , Ng Jonathan , Bessho Naoki , Hesse Michael
Published: July 2021

We investigate lower-hybrid drift waves (LHDW) in symmetric magnetic reconnection with zero guide field using three-dimensional particle-in-cell simulations. The long-wavelength mode with kρiρe∼1 develops in the bifurcated electron current layer around the X-line within the width of the electron meandering motion from the mid-plane, where ρi(e) is the ion (electron) gyroradius. The short-wavelength mode with kρe∼1 develops in the separatrix region downstream of the electron outflow jet, producing electron vortices in the background flow frame. Electrons follow the E × B drift with corrections from the diamagnetic drift and are heated inside the vortices with diverging electric fields. In the vortices, ions have comparable E × B and inertia drifts, which together mostly cancel the diamagnetic drift. Toward the center of diverging field vortices, ions are decelerated, leading to a decrease in the perpendicular temperature, while the loss of low-energy ions results in an increase in the parallel temperature. Parallel electric fields exist as a combination of the LHDW wave field projected to the magnetic field direction and the penetration of whistler waves that are mainly outside of the LHDW layer. The magnetic flux tube is twisted in the vortices. The twist may potentially lead to slippage reconnection, as indicated by the non-uniform parallel potential variation across field lines, while the periodic variations of the twisting directions are a limiting factor.
Effect of a probiotic (
Authors: Azizi Tayebe , Daneshyar Mohsen , Allymehr Manoochehr , Tukmechi Amir , Behroozyar Hamed Khalilvandi , Jalali Ali Shalizar
Published: July 2021

Context Deoxynivalenol (DON) contamination of feedstuffs causes detrimental effects on animals and poultry. Dietary inclusion of microbial feed additives, such as probiotics and/or yeast, seems to be a useful approach for DON detoxification and reducing the toxin absorption from the gut. Aims This study was conducted to evaluate the synergetic effects of a probiotic (Lactobacillus spp.), yeast (Saccharomyces cerevisiae) and mycotoxin detoxifier on performance, serum chemical parameters and immune status of broiler chickens fed a DON-contaminated diet. Methods A total of 200 1-day-old female broilers (Hubbard®) were allocated to five dietary treatments with four replicates each in a completely randomised design. Experimental diets consisted of: (1) control diet (basal diet), (2) DON diet (basal diet contaminated with 10 mg/kg DON), (3) DON diet supplemented with 0.25% mycotoxin detoxifier (Mycofix® Plus), (4) DON diet supplemented with a combination of 0.4 g/kg probiotic and 1.5 g/kg yeast, and (5) DON diet supplemented with a combination of a probiotic, yeast and mycotoxin detoxifier. Key results The results showed that the DON diet significantly increased the feed conversion ratio compared with mycotoxin detoxifier and control diets. Administration of 0.4 g/kg probiotic along with 1.5 g/kg yeast to a DON-contaminated diet caused a significant enhancement of dressing percentage, leg relative weight and aspartate aminotransferase enzyme activity. The DON-contaminated diet reduced total protein, albumin, triglyceride and cholesterol concentrations, but consumption of a probiotic, yeast and mycotoxin detoxifier improved the levels of these parameters. The DON-treated birds showed a reduction in haematocrit, haemoglobin, red blood cells and blood lymphocyte percentage in comparison with control levels. The inclusion of a combination of a probiotic and yeast along with mycotoxin detoxifier diminished the increased heterophil: lymphocyte ratio by DON administration. The antibody titre against Newcastle disease virus vaccine increased by inclusion of a probiotic, yeast and Mycofix. Conclusions In summary, a combination of a probiotic and yeast along with mycotoxin detoxifier can improve the enzyme activity, immunity and haematological attributes, which are useful for DON-contaminated diet detoxification. Implications Dietary supplementation with a probiotic, yeast and mycotoxin detoxifier could be used as an alternative to detoxification DON in broiler chickens.
Utilising dual-purpose crops effectively to increase profit and manage risk in meat production systems
Authors: McGrath S. R. , Behrendt R. , Friend M. A. , Moore A. D.
Published: July 2021

Dual-purpose cropping (sowing crops with the intention of both grazing them during vegetative growth and harvesting grain thereafter) has become a widespread farming practice in southern Australia. This synopsis paper integrates research from a multi-institutional research project conducted at three nodes located near Hamilton (south-western Victoria), Wagga Wagga (southern NSW) and Canberra (ACT), and sets out 11 principles for the effective utilisation of dual-purpose crops in meat production systems to increase profit and manage risk. Dual-purpose crops can be used to overcome feed quality gaps in late summer–autumn or feed quantity gaps in late autumn/winter. They provide large quantities of high-quality forages for grazing in summer, autumn and winter and can provide a substantial contribution to the annual number of grazing days on a farm. Utilisation of the high-quality dry matter provided by dual-purpose crops is most effective when directed at young growing stock for sale or future reproduction rather than reproducing adult ewes. For example, sale weight of yearlings per ewe was increased by 16% in systems at the Canberra node when dual-purpose crops were prioritised for grazing by weaners. Wool production was also increased in systems that included grazing of dual-purpose crops. Grazing crops in winter does not necessarily reduce supplementary feeding costs for winter or spring lambing. Modelling suggests that inclusion of dual-purpose crops does not substantially change the optimum time of lambing for sheep meat systems. Financial analysis of the experimental data from the Canberra node showed that although cash expenses per hectare were increased in the crop-grazing systems, the overall profitability of those systems over the life of the experiment was greater by AU$207/ha.year than that of the pasture-only system. Factors driving improved profitability included income from grain, higher income from meat and wool, and lower supplementary feeding costs. However, increasing the area sown to crop from 10% to 30% of the farm area in this Southern Tablelands system appeared to increase risk. In south-western Victoria, spring-sown canola carried risk similar to or less than other options assessed to achieve ewe-lamb mating weight. It is likely that at least part of the reduction in risk occurs through the diversification in income from the canola produced as part of the system. It was concluded that the grazing of cereal and canola crops for livestock production can be profitable and assist in managing risk.
Microbiome analysis of the skin of sheep that are resistant or susceptible to breech flystrike
Authors: Greeff J. C. , Paz E. A. , Munyard K. , Schlink A. C. , Smith J. , Karlsson L. J. E. , Martin G. B. , Groth D.
Published: July 2021

Context Breech strike is a serious disease for wool sheep. Skin wrinkle and dags are known predisposing factors for breech strike; however, a large part of the variation among sheep is unknown. Aims We studied the natural diversity and difference in microbial populations in the skin around the breech area in Merino sheep genetically resistant and susceptible to breech strike, by using 16S rRNA gene sequence analysis. Methods The sheep were from the breech strike flocks at the Mount Barker research station in Western Australia and from the CSIRO research station near Armidale in New South Wales. Skin samples were collected from the breech of all 2013-born progeny in both flocks before they were struck. Yearling ewes and rams were then naturally exposed to challenge by Lucilia cuprina blowflies. Breeding values for breech strike were estimated and used with phenotypic data to identify breech strike-resistant and -susceptible sheep. Skin samples of 78 unstruck and 73 struck sheep were selected, their microbiomes were analysed using 16S rRNA meta-barcoding, and operational taxonomic unit counts were analysed. Results The diversity analyses showed that the two flocks in the different environments had different microbiome profiles, but no difference was found between sexes or between breech strike-resistant and -susceptible sheep in either flock. Conclusions The results indicated that microbial differences on the skin of sheep are not associated with differences in susceptibility to breech strike. Implications Microbial differences do not offer opportunities to manage breech strike in Merino sheep.
“We have no Chinese classmates”
Authors: Liu Meng , Le Ha Phan
Published: July 2021

This paper draws on a small-scale qualitative study with international students enrolled in various English- and
Chinese-medium instruction programs in Chinese universities. It seeks to explore these students’ educational experiences and their
perceptions of China and China’s higher education. Our study provides ample evidence about the irrelevance of Chinese language in
the current policies and practices of Chinese universities regarding internationalization and international students. It also
counters earlier studies that show how deeply rooted the discourses of native speaker and native-speaking varieties of English are
in English-medium-instruction programs around the world. All in all, the paper makes theoretical and empirical contributions to
the emerging literature on international students’ education and academic experiences in China. Through accounts obtained from
international students of varied backgrounds, the paper also sheds light on nuances of internationalization, medium of
instruction, and academic mobilities.
The E’s of TNHE and EMI
Authors: Reynolds Dudley
Published: July 2021

Questions asked as part of phenomenographic research are used to critically synthesize findings from the case
studies in this issue of English-medium instruction (EMI) in transnational higher education (TNHE). With respect to whether EMI in
TNHE can be considered a phenomenon, it is suggested that the phenomenon is more discursive than empirical. Student and instructor
perceptions of the phenomenon reveal a critical awareness of the policies that structure the learning environment and agency that
takes advantage of the policies’ discursive nature to create alternative, multilingual language practices and improve learning. A
gap between policy and practice that allows for negotiation of the E’s in EMI and TNHE, English and education, is hence called
for.
Analog dual to a 2 + 1-dimensional holographic superconductor
Authors: Bilic Neven , Fabris Júlio C
Published: July 2021

We study an analog hydrodynamic model that mimics a 3 + 1 AdS planar BH spacetime dual to a 2 + 1-dimensional superconductor. We demonstrate that the AdS4 bulk and its holographic dual could be realized in nature in an analog gravity model based on fluid dynamics. In particular we mimic the metric of an O
2 holographic superconductor and calculate the entanglement entropy of a conveniently designed subsystem at the boundary of the analog AdS4 bulk.
A comparison of Ashtekar’s and Friedrich’s formalisms of spatial infinity
Authors: Ali Mohamed Mariem Magdy , Valiente Kroon Juan A
Published: July 2021

Penrose’s idea of asymptotic flatness provides a framework for understanding the asymptotic structure of gravitational fields of isolated systems at null infinity. However, the studies of the asymptotic behaviour of fields near spatial infinity are more challenging due to the singular nature of spatial infinity in a regular point compactification for spacetimes with non-vanishing ADM mass. Two different frameworks that address this challenge are Friedrich’s cylinder at spatial infinity and Ashtekar’s definition of asymptotically Minkowskian spacetimes at spatial infinity that give rise to the three-dimensional asymptote at spatial infinity

H

. Both frameworks address the singularity at spatial infinity although the link between the two approaches had not been investigated in the literature. This article aims to show the relation between Friedrich’s cylinder and the asymptote as spatial infinity. To do so, we initially consider this relation for Minkowski spacetime. It can be shown that the solution to the conformal geodesic equations provides a conformal factor that links the cylinder and the asymptote. For general spacetimes satisfying Ashtekar’s definition, the conformal factor cannot be determined explicitly. However, proof of the existence of this conformal factor is provided in this article. Additionally, the conditions satisfied by physical fields on the asymptote

H

are derived systematically using the conformal constraint equations. Finally, it is shown that a solution to the conformal geodesic equations on the asymptote can be extended to a small neighbourhood of spatial infinity by making use of the stability theorem for ordinary differential equations. This solution can be used to construct a conformal Gaussian system in a neighbourhood of

H

.
Undamped plasmon modes and enhanced superconductivity in metal diborides
Authors: Gao Han , Ding Chao , Geng Wenhui , Ma Xikui , Li Yangyang , Zhao Mingwen
Published: July 2021

The anisotropic geometric and electronic structures of metal diborides (MB2) leads to many unusual optical and electronic properties. Here, we present a first-principles study on the low-energy collective electronic excitations and the superconducting performance of the MB2 (M = Be, Mg, Al, and Ca). We demonstrate the undamped cosine-like plasmon modes and the sine-like acoustic plasmons in these metal diborides. Interestingly, the energy of the acoustic plasmons shows a positive correlation with the E
2g
phonon modes which are negatively correlated with the superconducting transition temperature (T
c) of the MB2 materials. Moreover, hole doping can lower the energy of the acoustic plasmons and enhance the T
c of CaB2 up to 48.2 K. Our work offers a theoretical guidance to regulate the plasmonic properties, as well as a new predictive factor for superconductivity.
First neutral beam experiments on Wendelstein 7-X
Authors: Lazerson Samuel A. , Ford Oliver , Äkaslompolö Simppa , Bozhenkov Sergey , Slaby Christoph , Vanó Lilla , Spanier Annabelle , McNeely Paul , Rust Norbert , Hartmann Dirk , Poloskei Peter , Buttenschoゆ Birger , Burhenn Rainer , Tamura Naoki , Bussiahn Rene , Wegner Thomas , Drevlak Michael , Turkin Yuriy , Ogawa Kunihiro , Knauer Jens , Brunner Kai Jakob , Pasch Ekkehard , Beurskens Marc , Damm Hannes , Fuchert Golo , Nelde Philipp , Scott Evan , Pablant Novimir , Langenberg Andreas , Traverso Peter , Valson Pranay , Hergenhahn Uwe , Pavone Andrea , Rahbarnia Kian , Andreeva Tamara , Schilling Jonathan , Brandt Christian , Neuner Ulrich , Thomsen Henning , Chaudhary Neha , Höefel Udo , Stange Torsten , Weir Gavin , Marushchenko Nikolai , Jakubowski Marcin , Ali Adnan , Gao Yu , Niemann Holger , Puig Sitjes Aleix , Koenig Ralf , Schroeder Ralf , den Harder Niek , Heinemann Bernd , Hopf Christian , Riedl Rudolf , Wolf Robert C. , W7-X Team the
Published: July 2021

In the previous divertor campaign, the Wendelstein 7-X (W7-X) device injected 3.6 MW of neutral beam heating power allowing for the achievement of densities approaching 2 × 1020 m−3, and providing the first initial assessment of fast ion confinement in a drift optimized stellarator. The neutral beam injection (NBI) system on W7-X is comprised of two beam boxes with space for four radio frequency sources each. The 3.6 MW of heating reported in this work was achieved with two sources in the NI21 beam box. The effect of combined electron-cyclotron resonance heating (ECRH) and NBI was explored through a series of discharges varying both NBI and ECRH power. Discharges without ECRH saw a linear increase in the line-integrated plasma density, and strong peaking of the core density, over the discharge duration. The presence of 1 MW of ECRH power was found to be sufficient to control a continuous density rise during NBI operation. Simulations of fast ion wall loads were found to be consistent with experimental infrared camera images during operation. In general, NBI discharges were free from the presence of fast ion induced Alfvénic activity, consistent with low beam betas. These experiments provide data for future scenario development and initial assessment of fast-ion confinement in W7-X, a key topic of the project.
First record of Thelohanellus wuhanensis Xiao & Chen, 1993 (Myxozoa: Myxosporea) in Iraq on the gills of Carassius auratus (Linnaeus, 1758)
Authors: Abdul-Ameer Kefah Naser , Obaid Aisha Sulaiman
Published: July 2021

In the current study, the myxobolid, Thelohanellus wuhanensis Xiao & Chen, 1993 was recorded for the first time in Iraq from the gills of Carassius auratus (Linnaeus, 1758) that was caught from Tigris river near Al-Shawwaka location in Baghdad city during the period from May to October 2020. With this registration, T. wuhanensis become the fourth species of the genus Thelohanellus so far recorded from the Iraqi fish. The description and measurements of this external parasite as well as its illustrations are given.
The effective of the inner radius of the iron free coil on the paraxial ray for magnetic lenses
Authors: Al-kadumi AhmedK. , Al-Baghdadi M.
Published: July 2021

In this paper, the magnetic flux density was studied using a mathematical model and different inner radius has been used for the iron free coil. The maximum value of magnetic field and the magnetic scalar potential was calculated. The paraxial ray can be studied using rung Kutta to solve the differential equation in the infinite and zero magnification condition, all results are determined using MATLAB program.
Web Mining Techniques and Technologies: A Landscape View
Authors: Ibrahim Kareem K. , Obaid Ahmed J.
Published: July 2021

Web mining is the process of discovering important information and patterns in a weblog file. And contains loads of information. It consists of pages of various formats (HTML documents, images, etc.). And the data for this record is still increasing at a very high rate. So the process of retrieving information from it is a very difficult task. In order to obtain the required information from the network. This requires mining the weblog file. In this paper, the researcher conducted a review of previous studies and what researchers have dealt with in web prospecting. Explain web mining concepts. And how to obtain information and the visitors’ patterns through the techniques and algorithms used in Web usage mining.
Effectiveness of Heterogenous Catalyst In Biodiesel Production Process: The Use of Zeolite, ZnO and Al2O3
Authors: Pasae Y , Melawaty L. , Ruswanto  , Bulo L , Allo E L
Published: July 2021

One of the most important needs in the biodiesel industry is the availability of catalysts. The catalyst most commonly used in making biodiesel is a homogeneous catalyst. However, the use of this catalyst has a weakness, namely that it is difficult to separate from the reaction mixture so that it will be wasted as waste which can cause environmental pollution. To overcome this, it is necessary to substitute a homogeneous base catalyst with a heterogeneous base catalyst. In this study, biodiesel production was carried out through the transesterification reaction of palm oil and methanol using three types of heterogeneous catalysts, namely zeolite, ZnO, and Al2O3. The results showed that the three types of catalysts can be used to become catalysts in the biodiesel production process. Of the three catalysts, the most effective use for biodiesel production from palm oil is the Al2O3. The characteristics of the biodiesel produced also meet the quality standards set out in the Indonesian National Standard.
Removal of Hg2+ and CH3Hg+ by a polyphosphonate ligand from water
Authors: Abate C , Foti C , Giuffrè O
Published: July 2021

The potential of employing a polyphosphonate ligand, diethylenetriamine-N,N,N′,N″,N″-pentakis(methylenephosphonic) acid (DTPMP), in the removal from water of Hg2+ and (CH3)Hg+ was studied. Metal-ligand systems were investigated by potentiometry in aqueous solution at t = 25°C, 0.1 < I / mol L1 < 1 for Hg2+, I = 0.1 mol L1 for (CH3)Hg+. The formation of several complex species was evidenced. The analysis of the results showed that species stability of Hg2+ complex species was significantly higher than that of (CH3)Hg+. The sequestering capacity, determined under typical conditions of natural waters, showed highest potential towards Hg
2+
, also respect to those of other polyphosphonate ligand, such as etidronic acid ((1-Hydroxy-1,1-ethanediyl)bis(phosphonic) acid, HEDPA). This quantitative study is useful to evaluate the possible employment of this polyphosphonate in the decontamination of natural waters from toxic metals.
Analysis of the effect of doped metal ions in the tricalcium phosphate bioceramic
Authors: Macedo D F , Silva A P
Published: July 2021

Calcium phosphate bioceramics such as hydroxyapatite (HA) and tricalcium phosphate (TCP) were successfully used in medical fields such as dentistry, orthopedics, and facial surgery due to their resorption and bioactivity characteristics. This work aims to obtain an osteoinductive ceramic matrix doped with metal ions. First, TCP doped with 10 mol.% of MgO was selected for the initial matrix due to the increased of HA content, microstructure densification (90%), and mechanical strength (27 MPa). Second, the addition of others metal ions (Zn, Mn, and Fe), at most 5 mol.%, to this initial matrix was evaluated by means of statistical analysis applying design of experiments (DOE). The presence of metal ions was studied by XRD and SEM-EDX analysis. The trace plots and equations were obtained for apparent and relative densities, apparent porosity, and diametral compression resistance, all for a 95% confidence interval and maximum error of p < 0,05. The results show a strong dependency between the addition of these metal ions and all studied properties.
Accuracy controlled data assimilation for parabolic problems
Authors: Dahmen Wolfgang , Stevenson Rob , Westerdiep Jan
Published: July 2021

This paper is concerned with the recovery of (approximate) solutions to parabolic problems from incomplete and possibly inconsistent observational data, given on a time-space cylinder that is a strict subset of the computational domain under consideration. Unlike previous approaches to this and related problems our starting point is a regularized least squares formulation in a continuous infinite-dimensional setting that is based on stable variational time-space formulations of the parabolic partial differential equation. This allows us to derive a priori as well as a posteriori error bounds for the recovered states with respect to a certain reference solution. In these bounds the regularization parameter is disentangled from the underlying discretization. An important ingredient for the derivation of a posteriori bounds is the construction of suitable Fortin operators which allow us to control oscillation errors stemming from the discretization of dual norms. Moreover, the variational framework allows us to contrive preconditioners for the discrete problems whose application can be performed in linear time, and for which the condition numbers of the preconditioned systems are uniformly proportional to that of the regularized continuous problem. In particular, we provide suitable stopping criteria for the iterative solvers based on the a posteriori error bounds. The presented numerical experiments quantify the theoretical findings and demonstrate the performance of the numerical scheme in relation with the underlying discretization and regularization.
New congruence properties for Ramanujan’s 𝜙 function
Authors: Xia Ernest
Published: July 2021

In 2012, Chan proved a number of congruences for the coefficients of Ramanujan’s

ϕ
\phi

function. In this paper, we prove some new congruences modulo powers of 2 and 3 for Ramanujan’s

ϕ
\phi

function by employing Newman’s identities and theta function identities.
The arithmetic local Nori fundamental group
Authors: Romagny Matthieu , Tonini Fabio , Zhang Lei
Published: July 2021

In this paper we introduce the local Nori fundamental group scheme of a reduced scheme or algebraic stack over a perfect field

k
k

. We give particular attention to the case of fields: to any field extension

K

/

k

K/k

we attach a pro-local group scheme over 

k
k

. We show how this group has many analogies, but also some crucial differences, with the absolute Galois group. We propose two conjectures, analogous to the classical Neukirch-Uchida Theorem and Abhyankar Conjecture, providing some evidence in their favor. Finally we show that the local fundamental group of a normal variety is a quotient of the local fundamental group of an open, of its generic point (as it happens for the étale fundamental group) and even of any smooth neighborhood.
Existence of curves with constant geodesic curvature in a Riemannian 2-sphere
Authors: Cheng Da Rong , Zhou Xin
Published: July 2021

We prove the existence of immersed closed curves of constant geodesic curvature in an arbitrary Riemannian 2-sphere for almost every prescribed curvature. To achieve this, we develop a min-max scheme for a weighted length functional.
Effect of the single mutation N9Y on the catalytical properties of xylanase Xyn11A from Cellulomonas uda: a biochemical and molecular dynamic simulation analysis
Authors: Cayetano-Cruz Maribel , Caro-Gómez Luis A , Plascencia-Espinosa Miguel , Santiago-Hernández Alejandro , Benítez-Cardoza Claudia G , Campos Jorge E , Hidalgo-Lara María Eugenia , Zamorano-Carrillo Absalom
Published: July 2021

Cellulomonas uda produces Xyn11A, moderately thermostable xylanase, with optimal activity at 50 °C and pH 6.5. An improvement in the biochemical properties of Xyn11A was achieved by site-directed mutagenesis approach. Wild-type xylanase, Xyn11A-WT, and its mutant Xyn11A-N9Y were expressed in Escherichia coli, and then both enzymes were purified and characterized. Xyn11A-N9Y displayed optimal activity at 60 °C and pH 7.5, an upward shift of 10 °C in the optimum temperature and an upward shift of 1 unit in optimum pH; also, it manifested an 11-fold increase in thermal stability at 60 °C, compared to that displayed by Xyn11A-WT. Molecular dynamics simulations of Xyn11A-WT and Xyn11A-N9Y suggest that the substitution N9Y leads to an array of secondary structure changes at the N-terminal end and an increase in the number of hydrogen bonds in Xyn11A-N9Y. Based on the significant improvements, Xyn11A-N9Y may be considered as a candidate for several biotechnological applications.
Forsythiae Fructus aqueous extract attenuates cisplatin-induced kaolin consumption (pica) by inhibiting NLRP3 inflammasome activation in rats
Authors: Meng Qi , Bi Pingping , Zhang Guanglong , Li Yaqi , Chen Siqi , Nie Ke
Published: July 2021

The present study was conducted to evaluate the effect of Forsythiae Fructus aqueous extract (FAE) against cisplatin-induced emesis and to explore the antiemetic mechanism of FAE by focusing on NLRP3 inflammasome activation in a rat pica model. Our results showed that FAE significantly ameliorated cisplatin-induced acute and delayed pica in rats. Moreover, FAE improved the gastrointestinal histopathological injury and reduced the levels of serum ROS, IL-1β, and IL-18 in cisplatin-treated rats. In addition, the expressions of NLRP3, ASC, caspase-1, and IL-1β and the colocalization of the NLRP3 with ASC or caspase-1 in rat gastric antrum and ileum were also suppressed by FAE. Taken together, our findings indicate that FAE has a therapeutic effect against CINV, which may be related to its inhibition of the activation of NLRP3 inflammasome.
Deep fusion learning facilitates anatomical therapeutic chemical recognition in drug repurposing and discovery
Authors: Wang Xiting , Liu Meng , Zhang Yiling , He Shuangshuang , Qin Caimeng , Li Yu , Lu Tao
Published: July 2021

The advent of large-scale biomedical data and computational algorithms provides new opportunities for drug repurposing and discovery. It is of great interest to find an appropriate data representation and modeling method to facilitate these studies. The anatomical therapeutic chemical (ATC) classification system, proposed by the World Health Organization (WHO), is an essential source of information for drug repurposing and discovery. Besides, computational methods are applied to predict drug ATC classification. We conducted a systematic review of ATC computational prediction studies and revealed the differences in data sets, data representation, algorithm approaches, and evaluation metrics. We then proposed a deep fusion learning (DFL) framework to optimize the ATC prediction model, namely DeepATC. The methods based on graph convolutional network, inferring biological network and multimodel attentive fusion network were applied in DeepATC to extract the molecular topological information and low-dimensional representation from the molecular graph and heterogeneous biological networks. The results indicated that DeepATC achieved superior model performance with area under the curve (AUC) value at 0.968. Furthermore, the DFL framework was performed for the transcriptome data–based ATC prediction, as well as another independent task that is significantly relevant to drug discovery, namely drug–target interaction. The DFL-based model achieved excellent performance in the above-extended validation task, suggesting that the idea of aggregating the heterogeneous biological network and node’s (molecule or protein) self-topological features will bring inspiration for broader drug repurposing and discovery research.
Chemsearch: collaborative compound libraries with structure-aware browsing
Authors: Gaffney Stephen G , Smaga Sarah , Schepartz Alanna , Townsend Jeffrey P
Published: July 2021

Chemsearch is a cross-platform server application for developing and managing a chemical compound library and associated data files, with an interface for browsing and search that allows for easy navigation to a compound of interest, similar compounds or compounds that have desired structural properties. With provisions for access control and centralized document and data storage, Chemsearch supports collaboration by distributed teams.

Availability and implementation

Chemsearch is a free and open-source Flask web application that can be linked to a Google Workspace account. Source code is available at https://github.com/gem-net/chemsearch (GPLv3 license). A Docker image allowing rapid deployment is available at https://hub.docker.com/r/cgemcci/chemsearch.
BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis
Authors: Liu Hualin , Zheng Jinshui , Bo Dexin , Yu Yun , Ye Weixing , Peng Donghai , Sun Ming
Published: July 2021

Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of genetically modified crops against pests. We previously developed a web-based insecticidal gene mining tool BtToxin_scanner. It has been frequently used by many researchers worldwide. However, it can only handle the genome one by one online. To facilitate efficiently mining toxin genes from large-scale sequence data, we re-designed this tool with a new workflow and the novel bacterial pesticidal protein database. Here, we present BtToxin_Digger, a comprehensive and high-throughput Bt toxin mining tool. It can be used to predict Bt toxin genes from thousands of raw genome and metagenome data, and provides accurate results for downstream analysis and experiment testing. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the replacement of the database.

Availability and implementation

The BtToxin_Digger codes and web services are freely available at https://github.com/BMBGenomics/BtToxin_Digger and https://bcam.hzau.edu.cn/BtToxin_Digger, respectively.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Sensitive HPLC–MS/MS Method for Determination of Obeticholic Acid in Human Plasma: Application to a Pharmacokinetic Study in Healthy Volunteers
Authors: Hu Can , Li Ya , Liu Yujie , Lai Yong , Ding Li
Published: July 2021

A rapid and sensitive LC-MS/MS method was developed and fully validated for the determination of obeticholic acid in human plasma. Glimepiride was used as internal standard. For this method, liquid–liquid extraction was performed to extract analyte from the plasma samples. Chromatographic separation was performed on a C18 (2.1 × 50 mm, 2.7 μm, Agilent) column with isocratic elution using water containing 0.1% formic acid and acetonitrile containing 0.1% formic acid at a flow rate of 0.4 mL/min. The mass detection was performed in negative mode. The precursor-product ion pairs for MRM were m/z 465.3 → 419.3 for obeticholic acid and m/z 489.3 → 224.8 for the IS. The method exhibited great linearity over the concentration range of 0.150–100 ng/mL for obeticholic acid. The sensitivity, linearity, accuracy, precision, recovery, matrix effect and stability of this method were all within the acceptable limits. The method was successfully validated and applied to the pharmacokinetic studies in healthy Chinese volunteers after a single oral dose administration of obeticholic acid tablets of 10 mg, and the pharmacokinetic characteristics of obeticholic acid in human were reported for the first time.
Interpretative Labor and the Bane of Nonstandardized Metadata in Public Health Surveillance and Food Safety
Authors: Pettengill James B , Beal Jennifer , Balkey Maria , Allard Marc , Rand Hugh , Timme Ruth
Published: July 2021

Open-source DNA sequence databases have long been touted as beneficial to public health, including the facilitation of earlier detection and response to infectious disease outbreaks. Of critical importance to harnessing these benefits is the metadata that describe general and other domain-specific attributes (eg, collection location, isolate type) of a sample. Unlike the sequence data, metadata are often incomplete and lack adherence to an international standard. Here, we describe the problem posed by such variable and incomplete metadata in terms of interpretative labor costs (the time and energy necessary to make sense of the signal in the genetic data) and the impact such metadata have on foodborne outbreak detection and response. Improving the quality of sequence-associated metadata would allow for earlier detection of emerging food safety hazards and allow faster response to foodborne outbreaks.
The spatial distribution of the photosynthetic picoeukaryotes community structure in Lake Hongze
Authors: Wu Fan , Zhang Min , Liu Changqing , Yang Jinsheng , Ren Mindong , Wu Qing Long , Shi Xiaoli
Published: July 2021

The spatial dynamics of picophytoplankton were investigated by flow cytometry and high-throughput sequencing in Lake Hongze, a large river-connecting lake. Picophytoplankton were mainly composed of phycocyanin-rich picocyanobacteria (PCY) and photosynthetic picoeukaryotes (PPEs). Picocyanobacteria was the dominant picophytoplankton group since the contribution of PPEs to total picophytoplankton was only 11.78%. However, PPEs were highly diverse and were composed of Chlorophyta, Bacillariophyta and Chrysophyceae. Environmental factors showed spatial differences, particularly in total phosphorus (TP), suspended solids (SS) and chemical oxygen demand (CODMn), which showed relatively high concentrations around the river channel. The abundances of PPEs and PCY showed similar spatial patterns, which were relatively low in the river course since they were negatively related to SS and CODMn. The top 10 OTUs contributed 79.18% of the total PPEs reads and affiliated with main species in PPEs. CCA results showed that, PPEs community composition was significantly impacted by temperature and DO at sites away from river channel, while was only influenced by nitrite at sites around the river channel.
Human Molecular Genetics and the long road to treating cystic fibrosis
Authors: Harris Ann
Published: July 2021

The causative gene in cystic fibrosis (CF) was identified in 1989, 3 years before the publication of the first issue of Human Molecular Genetics. The cystic fibrosis transmembrane conductance regulator (CFTR) gene was among the first underlying a common inherited disorder to be cloned, and hence, its subsequent utilization toward a cure for CF provides a roadmap for other monogenic diseases. Over the past 30 years, the advances that built upon knowledge of the gene and the CFTR protein to develop effective therapeutics have been remarkable, and yet, the setbacks have also been challenging. Technological progress in other fields has often circumvented the barriers. This review focuses on key aspects of CF diagnostics and current approaches to develop new therapies for all CFTR mutations. It also highlights the major research advances that underpinned progress toward treatments and considers the remaining obstacles.
Endoscopic Prediction of Crohn’s Disease Postoperative Recurrence
Authors: De Cruz Peter , Hamilton Amy L , Burrell Kathryn J , Gorelik Alexandra , Liew Danny , Kamm Michael A
Published: July 2021

Background

The presence and severity of endoscopic recurrence after Crohn's disease intestinal resection predicts subsequent disease course. The Rutgeerts postoperative endoscopic recurrence score is unvalidated but has proven prognostically useful in many clinical studies. This study aimed to investigate the association between specific early endoscopic findings and subsequent disease course.

Methods

In the setting of a randomized controlled trial (the POCER study), 85 patients underwent colonoscopy at 6 and 18 months after intestinal resection. Patients received 3 months of metronidazole, and high-risk patients received a thiopurine (or adalimumab if they were thiopurine intolerant). For endoscopic recurrence (Rutgeerts score ≥i2) at 6 months, patients stepped up to a thiopurine, fortnightly adalimumab with thiopurine, or weekly adalimumab. Central readers confirmed Rutgeerts, Simple Endoscopic Score for Crohn’s Disease, Crohn’s Disease Endoscopic Index of Severity scores, and 5 newly tested endoscopic parameters: anastomotic ulcer depth (superficial vs deep), number of ulcers (0, ≤2, >2), ulcer size (1-5 mm, ≥6 mm), circumferential extent of ulceration (<25%, ≥25%), and the presence or absence of stenosis. The POCER index, based on the 6-month postoperative findings, was then developed in relation to predicting the endoscopic outcome at 18 months.

Results

Of the 5 parameters, the combination of ulcer depth and circumference at the anastomosis at 6 months was associated with endoscopic recurrence at 18 months (odds ratio [OR], 1.6; 95% confidence interval [CI], 1.03-2.50; P = 0.035) with an area under the receiver operating characteristic curve of 0.62 (95% CI, 0.5-0.75). The combination of these 2 parameters formed the basis of the POCER index (range, 0-4 with 0 denoting no ulcers and 4 denoting deep ulceration with >25% circumferential involvement). The new index had a strong correlation with the Rutgeerts score measured at the same time points: Spearmans’ r = .80 at 6 months and r = .77 at 18 months (P < 0.001 at both time points). A POCER index of ≥2 and a Rutgeerts score of ≥i2 both had a sensitivity of 0.41 for recurrence; however, the POCER index had a higher specificity (0.8 and 0.67, respectively). The POCER index at 6 months was associated with endoscopic recurrence at 18 months (OR, 1.5; 95% CI, 1.2-2.0; P = 0.002; area under the receiver operating characteristic curve of 0.70; 95% CI, 0.57-0.82), but the Rutgeerts score was not (OR, 1.2; 95% CI, 0.8-1.8; P = 0.402).

Conclusions

The POCER postoperative index comprises 2 key endoscopic factors related to the anastomosis that are associated with subsequent disease progression. A higher score, comprising the adverse prognostic factors of deep or circumferentially extensive anastomotic ulceration, may help identify patients who require more intensive therapy.
A new approach to the complex Helmholtz equation with applications to diffusion wave fields, impedance spectroscopy and unsteady Stokes flow
Authors: Hauge Jordan C , Crowdy Darren
Published: July 2021

A new transform pair representing solutions to the complex Helmholtz equation in a convex 2D polygon is derived using the theory of Bessel’s functions and Green’s second identity. The derivation is a direct extension of that given by Crowdy (2015, A transform method for Laplace’s equation in multiply connected circular domains. IMA J. Appl. Math., 80, 1902–1931) for ‘Fourier–Mellin transform’ pairs associated with Laplace’s equation in various domain geometries. It is shown how the new transform pair fits into the collection of ideas known as the Fokas transform where the key step in solving any given boundary value problem is the analysis of a global relation. Here we contextualize those global relations from the point of view of ‘reciprocal theorems’, which are familiar tools in the study of the effective properties of physical systems. A survey of the many uses of this new transform approach to the complex Helmholtz equation in applications is given. This includes calculation of effective impedance in electrochemical impedance spectroscopy and in other spectroscopy methods in diffusion wave field theory, application to the 3$\omega $ method for measuring thermal conductivity and to unsteady Stokes flow. A theoretical connection between this analysis of the global relations and Lorentz reciprocity in mathematical physics is also pointed out.
Emerging Themes in the Molecular Pathogenesis of Enterotoxigenic Escherichia coli
Authors: Fleckenstein James M , Sheikh Alaullah
Published: July 2021

Enterotoxigenic Escherichia coli (ETEC) are ubiquitous diarrheal pathogens that thrive in areas lacking basic human needs of clean water and sanitation. These genetically plastic organisms cause tremendous morbidity among disadvantaged young children, in the form of both acute diarrheal illness and sequelae of malnutrition and growth impairment. The recent discovery of additional plasmid-encoded virulence factors and elucidation of their critical role in the molecular pathogenesis of ETEC may inform new approaches to the development of broadly protective vaccines. Although the pathogens have been closely linked epidemiologically with nondiarrheal sequelae, these conditions remain very poorly understood. Similarly, while canonical effects of ETEC toxins on cellular signaling promoting diarrhea are clear, emerging data suggest that these toxins may also drive changes in intestinal architecture and associated sequelae. Elucidation of molecular events underlying these changes could inform optimal approaches to vaccines that prevent acute diarrhea and ETEC-associated sequelae.
Vagus nerve-mediated intestinal immune regulation: therapeutic implications of inflammatory bowel diseases
Authors: Mikami Yohei , Tsunoda Junya , Kiyohara Hiroki , Taniki Nobuhito , Teratani Toshiaki , Kanai Takanori
Published: July 2021

The pathophysiology of inflammatory bowel diseases (IBDs) involves immunological, genetic and environmental factors. Through its ability to sense environmental stimuli, the autonomic nervous system plays a key role in the development and persistence of IBDs. The vagus nerve (VN), which contains sensory and motor neurons, travels throughout the body to innervate the gut and other visceral organs in the thoracic and abdominopelvic cavities. Recent studies show that the VN has anti-inflammatory effects via the release of acetylcholine, in what is known as the cholinergic anti-inflammatory pathway (CAIP). In the gut immune system, the CAIP is proposed to be activated directly by signals from the gut and indirectly by signals from the liver, which receives gut-derived bioactive substances via the portal vein and senses the status of the gut. The gut–brain axis and liver–brain–gut reflex arc regulate a wide variety of peripheral immune cells to maintain homeostasis in the gut. Therefore, targeting the neural reflex by methods such as VN stimulation is now under investigation for suppressing intestinal inflammation associated with IBDs. In this review, we describe the role of the VN in the regulation of intestinal immunity, and we discuss novel therapeutic approaches for IBDs that target neuroimmune interactions.
Ankle intention detection algorithm using electromyography signal
Authors: Kim Inwoo , Lee Taehoon , Lee Soo-Hong
Published: July 2021

In this study, an ankle intention detection algorithm was developed to calculate the torque the user wants to exert from the ankle starting from the user’s EMG signal. Since the subtalar joint axis of the ankle is very important for stability, the intent detection algorithm also calculates the torque of the eversion motion of the subtalar joint axis. A dry EMG sensor was used to measure the EMG signal, and an ankle biaxial torque measurement device was manufactured to measure the ankle torque to perform the experiment. The experiment was conducted on four healthy subjects (mean ± SD: height, 177.6 ± 7.3 cm; weight 70.2 ± 8.9 kg; and age, 27 ± 2 years), and the EMG signals and ankle torque were measured. Using the experimental results and a neural network, we developed an intention detection algorithm. When you input an EMG signal, the algorithm estimates the torque of eversion, dorsiflexion, and plantar flexion. The error of the algorithm is 0.37 Nm (subtalar) and 0.57 Nm (talocrural), which is 0.5% (subtalar) and 1.5% (talocrural) of the torque required for walking. Using the algorithm of this study, more accurate and stable exoskeleton robot control becomes possible.
Tissue-level transcriptomic responses to local and distal chilling reveal potential chilling survival mechanisms in maize
Authors: Xue Chunmei , Jiang Yuan , Wang Zhixue , Shan Xiaohui , Yuan Yaping , Hua Jian
Published: July 2021

Chilling is a major stress to plants of subtropical and tropical origins, including maize (Zea mays L.). To reveal the molecular mechanisms underlying chilling tolerance and survival in maize, we investigated transcriptomic responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity. The application of chilling stress to shoots or roots each contributed to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacities revealed that chilling survival is highly associated with the up-regulation of abscisic acid biosynthesis and responses as well as transcriptional regulators in leaves and crowns. It was also associated with the down-regulation of translation in leaves and the heat response in crowns. Chilling treatment of all or part of the plants revealed that the response to distal chilling is very distinct from, and sometimes opposite to, the response to local or whole-plant chilling in both leaves and roots, suggesting communication between shoots and roots in the environmental response. This study thus provides information on transcriptomic responses in leaves, roots, and crowns under different chilling stresses in maize, and reveals potential chilling tolerance and survival mechanisms, which lay the ground for improving chilling tolerance in crop plants.