bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of low-cost media for Bacillus thuringiensis subspecies israelensis
Authors: Mo-on Phuwana , Panprivech Siriwan , Kunathigan Viyada
Published: August 2022

Bacillus thuringiensis subspecies israelensis (Bti) has been used as a mosquito control agent in agricultural field and residences. The production of Bti by conventional medium was expensive. The objective of this study was to investigate low-cost media for Bti’s production with a cost analysis of the medium formulated. Soybean Casein Digest Medium (TSB) was used as a conventional medium to compare with Saberi medium at room temperature (approximately 21.5˚C) on static and agitation (by obituary shaker at 100 rpm). Saberi medium was also modified to vary the percentage of nitrogen and carbon source to observe the growth rate and sporulation, compared to the Saberi medium. The growth of Bti in TSB with agitation for 24 hours yielded the highest growth rate. Sporulation of Bti in TSB with agitation at room temperature was 6 days which was faster than Bti in the Saberi medium. Modified Saberi nitrogen source and carbon source medium could not support the growth of Bti due to an imbalance in the percentage of nitrogen source and carbon source. Determination of sugar utilization showed sugar in the medium was utilized mostly in the exponential phase of Bti, from 3 hours to 6 hours. The price of TSB was 76.80 Thai baht per liter while Saberi medium’s cost was 20.43 Thai baht per liter. In this study, the Saberi medium may not be able to replace TSB in terms of growth rate and period of sporulation. Further study will be needed to optimize the media that use agro-industrial wastes as ingredients following the concept of circular economy and sustainability.
In situ alloying of Ti10Mo fused tracks and layers via laser powder bed fusion
Authors: Dzogbewu Thywill Cephas , du Preez Willie Bouwer
Published: August 2022

Optimum process parameters for manufacturing a Ti10Mo alloy for biomedical applications via the laser powder bed fusion (LPBF) process were determined. Fused tracks were produced over a wide range of laser powers and scanning speeds, and layers were fused at varied hatch distances. The samples were analysed for continuity of the fused tracks, melting and distribution of the Mo powder particles in the Ti10Mo alloy layers, surface roughness, homogeneity of Mo in the alloy matrix and microhardness. The analysis revealed that the Mo powder particles melted completely in the alloy matrix with only pockets of Mo concentrations, mostly at the peripheries of the fused tracks due to the pushing effect. Complete melting of Mo in the Ti10Mo alloy matrix was due to the small size (1 μm) of the Mo powder particles used in the current experiment. The addition of Mo enhanced the wetting of the powder bed and prevented a pronounced balling effect. From this study, the parameter sets 150 W, 0.5 m/s and 200 W, 1.0 m/s both at a hatch distance of 80 μm, were obtained as the optimum process parameters. However, the Mo concentrations at the peripheries of the molten pool indicated that further research was required before a ‘completely’ homogenous sample could be manufactured via the LPBF process using elemental powder blends.
Fine-Grained Access Control Mechanism of Energy Internet
Authors: MIAO Siwei , ZHANG Xiaojuan , LIU Zhe
Published: August 2022

The Energy Internet has generated huge amounts of information on the production devices, transmission devices, and energy consumption devices. The leakage of data in the collection, transmission, and storage process will cause serious security problems. The existing Energy Internet security methods rely on traditional access control mechanisms and specific network boundary defense mechanisms, which has the limitations of static strategies and coarse design. We combine the advantages of role-based access control (RBAC) and attribute-based access control (ABAC), and propose a trusted Energy Internet fine-grained access control model based on devices' attribute and users' roles. We have not only achieved fine-grained Energy Internet resource allocation, but also ensured that the access control process is related to the security status of the environment in real time. Experimental results show that the access control model can safely and accurately execute access decisions in the Energy Internet scenario, and the processing performance is more stable.
Range-Angle Dependent Beampattern Synthesis Method for OFDM-Based Passive Radar
Authors: RAO Yunhua , HE Hao , WAN Xianrong , YI Jianxin
Published: August 2022

Frequency diverse array (FDA) radar applies a tiny frequency offset across its adjacent transmitting array elements to generate a range-angle-dependent beampattern. The increased degrees-of-freedom (DOFs) in range domain can help improve the performance of radar in target detection, localization, and clutter suppression. Passive radar utilizes uncontrollable external signal as illuminator, which makes it difficult to apply traditional frequency diverse process method. However, the third-party illuminator such as Orthogonal Frequency Division Multiplexing (OFDM) signal usually consists of several closely spaced modulated carriers, and it has been widely selected as the illuminator for passive radar in recent years. Considering the orthogonality between even separated subcarriers, we propose a new frequency diverse process method by extracting and processing each subcarrier of received data independently and attempt to provide a range-angle dependent beampattern for OFDM passive radar. Numerical results and real data analyses verify the superiority of frequency diversity process on the received data of OFDM passive radar.
Der subjektive Stellenwert von Bewegungs- und Sporttherapie bei
Menschen mit schwerer psychischer Erkrankung in Deutschland
Authors: Richter Daniel , Riedel-Heller Steffi , Breilmann Johanna , Hasan Alkomiet , Falkai Peter , Kilian Reinhold , Allgoewer Andreas , Ajayi Klemens , Baumgaertner Jessica , Brieger Peter , Frasch Karel , Heres Stephan , Jäger Markus , Küthmann Andreas , Putzhammer Albert , Schneeweiß Bertram , Schwarz Michael , Becker Thomas , Kösters Markus , Gühne Uta
Published: August 2022

Ziel der Studie Untersucht werden der subjektive Stellenwert und
Erfahrungen mit der Bewegungs- und Sporttherapie (BST) bei Patienten mit
schweren psychischen Erkrankungen.

Methodik Querschnittserhebung bei Patienten mit schweren psychischen
Erkrankungen (18 bis 65 Jahre, N=385). Untersuchung möglicher
Zusammenhänge zwischen dem subjektiven Stellenwert der BST und
soziodemografischen und krankheitsassoziierten Variablen durch eine
binäre logistische Regression.

Ergebnisse 84,4% der Befragten (n=325) schätzen
den Stellenwert einer BST als hoch ein. Ein noch größerer Anteil
der Befragten (90,6%, n=349) konnte bereits Erfahrungen mit
einer entsprechenden Therapie sammeln. Studienteilnehmende mit einem
höheren Funktionsniveau (höherer GAF-Wert, p=0,041) und
wohnhaft in einem großstädtischem Wohnumfeld (p=0,011)
maßen der BST einen höheren subjektiven Stellenwert bei.
44,1% (n=143) der Befragten, die den BST einen hohen subjektiven
Stellenwert beimessen, treiben regelmäßig Sport.

Schlussfolgerung Die meisten der hier befragten schwer psychisch kranken
Menschen messen den BST einen überraschend hohen Stellenwert bei. Dies
erweist sich vor dem Hintergrund der zunehmenden Evidenz zu den positiven
Effekten dieser Therapien als exzellenter Ansatzpunkt, diese im
Gesamtbehandlungsplan fester zu verankern. Gleichzeitig gilt es, Strategien
für einen Alltagstransfer stärker zu implementieren.
Carrier lifetimes in high-lifetime silicon wafers and solar cells measured by photoexcited muon spin spectroscopy
Authors: Murphy J. D. , Grant N. E. , Pain S. L. , Niewelt T. , Wratten A. , Khorani E. , Markevich V. P. , Peaker A. R. , Altermatt P. P. , Lord J. S. , Yokoyama K.
Published: August 2022

Photoexcited muon spin spectroscopy (photo-μSR) is used to study excess charge carrier lifetimes in silicon. Experiments are performed on silicon wafers with very high bulk lifetimes with the surface passivation conditions intentionally modified to control the effective lifetime. When the effective lifetime is low (<500 μs), implanting the muons to different depths enables the reliable measurement of carrier lifetime as a function of distance from a surface. It is also demonstrated that the photo-μSR technique can measure effective carrier lifetimes in completed commercial gallium doped silicon passivated emitter and rear cell devices, with results validated with harmonically modulated photoluminescence imaging. It is discovered, however, that prolonged muon irradiation of samples with very long effective lifetimes (>10 ms) results in detectable degradation of the measured lifetime. Re-passivation of degraded samples with a temporary room temperature superacid-based passivation scheme demonstrates that degradation occurs in the silicon bulk. Deep-level transient spectroscopy measurements reveal the existence of several defect-related traps near the muon-exposed surface in concentrations of order 1010 cm−3 that are not present near the surface not exposed to muons. In contrast to the common perception of the μSR technique, our results demonstrate that muons are not inert probes and that beam-induced recombination activity modifies the bulk lifetime significantly in samples with high effective carrier lifetimes.
Evaluation of the Nusselt number for a fluid sphere in Stokes flow
Authors: Shaw B. D. , Vang C. L.
Published: August 2022

The Nusselt number Nu is evaluated for an isothermal fluid sphere immersed in a Stokes flow. The dimensionless convective-diffusive conservation equation is solved asymptotically for the case where the Peclet number based on the sphere radius, ε, is small relative to unity. The Nusselt number is evaluated by integrating the derivative of the asymptotic solution over the surface of the sphere. The conservation equation is also solved numerically. A comparison of the numerical and asymptotic solutions shows that the asymptotic expression for Nu is valid only for the Peclet number being small relative to unity. An alternative asymptotic expression for Nu is developed, and it is shown that this expression is valid for Peclet numbers of order unity.
Effects of dietary flaxseed oil with or without products with antioxidant properties on pig performance, carcass characteristics, meat quality and oxidative stability
Authors: Bernardi Daniela Miotto , Bertol Teresinha Marisa , Coldebella Arlei , Cunha Junior Anildo , Silveira-Almeida Bárbara Cristina , Rodrigues Juliana Bürger , Barrera-Arellano Daniel , Godoy Helena Teixeira , Meinhart Adriana Dillenburg , de Paris Leandro Daniel , Sgarbieri Valdemiro Carlos
Published: August 2022

Context The inclusion of natural products with antioxidant properties in animal diets as well as the use of different lipid sources has been tested to improve the nutritional quality of meat. Aim The aim of this work was to compare natural products with antioxidant properties and vitamin E in swine diets containing flaxseed oil. Methods Ninety-six animals were allocated to six treatments: control diet (C), diet with 3% flaxseed oil (F), diet with 3% flaxseed oil + 10% grape pomace (FGP), diet with 3% flaxseed oil + 0.0022% grape seed extract (FGE), diet with 3% flaxseed oil + 5% Nile tilapia carcass hydrolysate (FH), and diet with 3% flaxseed oil + 200 ppm vitamin E supplement (FVitE). Key results The treatments had no effect on growth performance or serum total antioxidant status, while low-magnitude effects on carcass traits were observed. The addition of flaxseed oil to the diet increased the omega-3 and total polyunsaturated fatty acid concentrations and decreased saturated fatty acid and monounsaturated fatty acid concentrations in meat; high concentrations of total tocopherol were observed in the treatments FVitE, FGE, and FH, while a higher oxidative stability (Rancimat®) of backfat was observed for the treatment FVitE. The thiobarbituric acid-reactive substances assay and the sensory evaluation of mini-burgers revealed that vitamin E was the most efficient antioxidant throughout the storage, although the treatments FH and FGE have presented a mild effect. Conclusions Problems of oxidative stability of pork resulting from including flaxseed oil in the diet of pigs due to increases in omega-3 fatty acids were better overcome by dietary vitamin E than by the use of the other natural antioxidants assessed here. However, this study also demonstrated that both the tilapia hydrolysate and grape seed extract have potential to be used as natural antioxidants, although further studies are required. Implications The results impact the meat industry in regard to the nutritional quality and oxidative stability of meat. Pork with higher omega-3 content and natural antioxidants can meet consumer demand for a healthier diet, besides providing higher stability throughout storage, providing an additional market niche for the pork industry.
Revisiting the role of age in second language speech acquisition
Authors: Lee Andrew H.
Published: August 2022

The present study investigated whether age of acquisition (AOA) is a significant predictor of the extent to which Korean learners of English perceive and produce two nonnative vowels and the extent to which their speech perception and production accuracy are linked. A total of 100 Korean learners of English with a varying range of AOA participated in the study by completing perception and production measurement tasks. Overall, there were significant AOA effects found in the case of Korean participants who moved to Canada before the age breakpoint range of 17.0 to 25.5, after which AOA failed to be a significant predictor of their perception and production accuracy. In addition, compared to late second language (L2) learners, early L2 learners more consistently demonstrated instances of significant perception-production correlation. This study concludes by highlighting the role of AOA in L2 speech acquisition, supporting the existence of a critical period for intelligible L2 pronunciation.
Future projections on the anomalous WWγγ couplings in hadron–hadron interactions at the FCC-hh
Authors: Gutiérrez-Rodríguez A , Ari V , Gurkanli E , Köksal M , Hernández-Ruíz M A
Published: August 2022

We carry out a study in the approach of a dimension-eight effective field theory on the anomalous quartic WWγγ couplings that arise from the process pp → Wγγ at the Future Circular Collider-hadron hadron (FCC-hh). The process is sensitive to the WWγγ vertex, and future projections on the anomalous f

M,i
/Λ4 and f

T,j
/Λ4 couplings can be put by measurements of Wγγ production. We illustrate the physics opportunities and reach of the FCC-hh operating for a high integrated luminosity scenario of

L
=
1
,
5
,
10
,
30

a
b

−
1

of proton–proton collisions at a center-of-mass energy of

s

=
100

TeV and systematic uncertainties of δ
sys = 0%, 3%, 5%, 10%. Production cross-sections of the signal and the sensitivity constraints on the anomalous f

M,i
/Λ4 and f

T,j
/Λ4 couplings at 95% C.L. are identified through the leptonic and hadronic decay modes of the W-boson. The FCC-hh sensitivity on these anomalous couplings is expected might reach up to the order of magnitude

O

(

1

0

−
4

−
1

0

1

)

. These sensitivity perspectives indicate that the pp → Wγγ channel at the FCC-hh has a greater potential to search for the anomalous quartic WWγγ couplings and to search for new physics than present colliders.
Cavity optomechanics in a fiber cavity: the role of stimulated Brillouin scattering
Authors: Beregi A , Pontin A , Barker P F
Published: August 2022

We study the role of stimulated Brillouin scattering in a fiber cavity by numerical simulations and a simple theoretical model and find good agreement between experiment, simulation and theory. We also investigate an optomechanical system based on a fiber cavity in the presence of the nonlinear Brillouin scattering. Using simulation and theory, we show that this hybrid optomechanical system increases optomechanical damping for low mechanical resonance frequencies in the unresolved sideband regime. Furthermore, optimal damping occurs for blue detuning in stark contrast to standard optomechanics. We investigate whether this hybrid optomechanical system is capable of cooling a mechanical oscillator to the quantum ground state.
Fast population transfer with a superconducting qutrit via non-Hermitian shortcut to adiabaticity
Authors: Dong Xin-Ping , Feng Zhi-Bo , Lu Xiao-Jing , Li Ming , Zhao Zheng-Yin
Published: August 2022

Non-Hermitian dissipation dynamics, capable of turning the conventionally detrimental decoherence effects to useful resources for state engineering, is highly attractive to quantum information processing. In this work, an effective scheme is developed for implementing fast population transfer with a superconducting qutrit via the non-Hermitian shortcut to adiabaticity (STA). We first deal with a Λ-configuration interaction between the qutrit and microwave drivings, in which the dephasing-assisted qubit state inversion requiring an overlarge dephasing rate is constructed non-adiabatically. After introducing a feasible ancillary driving that directly acts upon the qubit states, the target state transfer can be well realized but with an accessible qubit dephasing rate. Moreover, a high fidelity could be numerically obtained in the considered system. The strategy could provide a new route towards the non-Hermitian shortcut operations on superconducting quantum circuits.
Unusual thermodynamics of low-energy phonons in the Dirac semimetal Cd3As2
Authors: Wang Zhen , Zhao Hengcan , Lyu Meng , Xiang Junsen , Dong Qingxin , Chen Genfu , Zhang Shuai , Sun Peijie
Published: August 2022

By studying the thermal conductivity, specific heat, elastic modulus, and thermal expansion as a function of temperature for Cd3As2, we have unveiled a couple of important thermodynamic features of the low-energy phonons strongly interacting with Dirac electrons. The existence of soft optical phonons, as inferred from the extremely low thermal conductivity, is unambiguously confirmed by low-temperature specific heat revealing significant deviation from Debye’s description. The estimated Debye temperature is small in the range of 100–200 K and varies significantly depending upon the measurement used in its experimental determination. The thermodynamic Grüneisen ratio γ reveals a remarkable reduction below about 100 K, an energy scale that is highly relevant to the Dirac states, towards negative values below about 10 K that are indicative of lattice instability.
Dynamic stabilization of atomic ionization in a high-frequency laser field with different initial angular momenta
Authors: Zhang Di-Yu , Qiao Yue , Lan Wen-Di , Wang Jun , Guo Fu-Ming , Yang Yu-Jun , Ding Da-Jun
Published: August 2022

We investigated the ionization of an atom with different orbital angular momenta in a high-frequency laser field by solving the time-dependent Schrödinger equation. The results showed that the ionization stabilization features changed with the relative direction between the angular momentum of the initial state and the vector field of the laser pulse. The ionization mechanism of the atom irradiated by a high frequency was explained by calculating the transition matrix and evolution of the time-dependent wave packet. This study can provide comprehensive understanding to improve atomic nonadiabatic ionization.
Chronically underestimated: a reassessment of US heat waves using the extended heat index
Authors: Romps David M , Lu Yi-Chuan
Published: August 2022

The heat index, or apparent temperature, was never defined for extreme heat and humidity, leading to the widespread adoption of a polynomial extrapolation designed by the United States National Weather Service. Recently, however, the heat index has been extended to all combinations of temperature and humidity, presenting an opportunity to reassess past heat waves. Here, three-hourly temperature and humidity are used to evaluate the extended heat index over the contiguous United States during the years 1984–2020. It is found that the 99.9th percentile of the daily maximum heat index is highest over the Midwest. Identifying and ranking heat waves by the spatially integrated exceedance of that percentile, the Midwest once again stands out as home to the most extreme heat waves, including the top-ranked July 2011 and July 1995 heat waves. The extended heat index can also be used to evaluate the physiological stress induced by heat and humidity. It is found that the most extreme Midwest heat waves tax the cardiovascular system with a skin blood flow that is elevated severalfold, approaching the physiological limit. These effects are not captured by the National Weather Service’s polynomial extrapolation, which also underestimates the heat index by as much as 10 ∘C (20 ∘F) during severe heat waves.
Overview on plasma electrolytic oxidation of magnesium alloys for medical and engineering applications
Authors: Patrascu I , Ducu M C , Negrea A D , Moga S G , Plaiasu A G
Published: August 2022

The scope of this review article is to offer a general view of the recent advances in the plasma electrolytic oxidation of Mg and Mg alloys with emphasis of the Plasma Electrolytic Oxidation (PEO) processing parameters used to obtain key surface properties for medical and engineering applications. The paper presents the different dependencies of the PEO process, first of all depending on the composition of the substrate, the electrolyte used, the applied electrical regime, as well as the way of their interaction, with direct implications on the properties designed to satisfy concrete applications for magnesium alloys. Magnesium-deformable alloys are of particular interest for the manufacture of parts for the for medical and engineering applications and industry due to the possibility of obtaining a more homogeneous structure and better mechanical properties, compared to cast parts. Also, magnesium alloys find its place to a broad range of aerospace, electronics, commercial and sport-related applications. In general, the interactions of the substrate / electrolyte combination with the electrical regime are complex and still the subject of ample research. Because, unlike other electrolytic surface treatment methods, PEO results in the formation of high-strength ohmic layers, they affect, especially in the case of current-controlled regimes, the extent to which the predefined electrical pulse is projected correctly in the setting experimental data.
Millisecond pulsed laser welding of AISI 316 stainless steel
Authors: Stanciu E M , Pascu A , Roată I C , Iatan C , Moldovan E R , Tierean M H
Published: August 2022

Nowadays, there is an increasing demand for AISI 316 stainless steel for automotive, medical, aerospace, for tool manufacturing and for nuclear industry. Compared with continuous beam laser welding, pulse temporal shape, pulse duration and the repetition rate are fundamental parameters that have a direct influence on the quality on the welded joint [2]. The laser welding of AISI 316 stainless steel thin sheets by millisecond pulsed laser will be analysed within this research by addressing to pulsed laser parameters influence on the geometry and appearing of the welding joint. The influence of laser power, pulse duration and repetition rate were determined by tracking fusion lines on specimen’s plates and butt weld stainless steel welding were obtained by using the determined optimal welding parameters. All the parameters have a major influence on the geometrical appearance of the weld bead.
Optically controllable coupling between edge and topological interface modes of graphene metasurfaces
Authors: Wang Yupei , Panoiu Nicolae C
Published: August 2022

Nonlinear topological photonics has been attracting increasing research interest, as it provides an exciting photonic platform that combines the advantages of active all-optical control offered by nonlinear optics with the unique features of topological photonic systems, such as topologically-protected defect-immune light propagation. In this paper, we demonstrate that topological interface modes and trivial edge modes of a specially designed graphene metasurface can be coupled in a tunable and optically controllable manner, thus providing an efficient approach to transfer optical power to topologically protected states. This is achieved in a pump-signal configuration, in which an optical pump propagating in a bulk mode of the metasurface is employed to tune the band structure of the photonic system and, consequently, the coupling coefficient and wave-vector mismatch between edge and topological interface modes. This tunable coupling mechanism is particularly efficient due to the large Kerr coefficient of graphene. Importantly, we demonstrate that the required pump power can be significantly reduced if the optical device is operated in the slow-light regime. We perform our analysis using both ab initio full-wave simulations and a coupled-mode theory that captures the main physics of this active coupler and observe a good agreement between the two approaches. This work may lead to the design of active topological photonic devices with new or improved functionality.
Dependence of size distribution of nanoparticles on hole size uniformity in membrane emulsification
Authors: Yanagishita Takashi , Maejima Yukari , Masuda Hideki
Published: August 2022

Metal oxide nanoparticles were fabricated by membrane emulsification using alumina through-hole membranes with different hole size uniformity. Hole size of alumina through-hole membrane used for membrane emulsification and the size of obtained nanoparticles were evaluated by SEM observation, and the relationship between the uniformity of hole size and the size distribution of the obtained nanoparticles was investigated. As a result, nanoparticles with higher size uniformity were obtained when the RSD (relative standard deviation) of hole size was 3.8%. This indicates that the hole size uniformity of the emulsification membrane is important for the fabrication of droplets and nanoparticles of uniform size by membrane emulsification.
Appendix: Kantian Internalism
Authors: Cummiskey David
Published: August 2022

Kant maintained that morality is a system of categorical imperatives. Categorical imperatives are supposed to have some for of rational necessity. Through a critical discussion of Williams's account of internal and external reasons and Korsgaard's account of Kantian practical reason, we see that Kant defended a plausible combination of strong reason internalism and weak motive internalism. An internalist approach to morality must begin with the perspective of the deliberating moral agent. In this very important sense, moral principles are necessarily agent‐centered. Consequentialism, however, can be fully agent‐centered in the requisite sense. The requirement to promote the good of all can be an agent‐centered requirement and even an agent‐centered constraint of the maximization of one's own good. Kantian internalism is fully compatible with a consequentialist categorical imperative.
Occupational Exposure to β-d-Glucans, Mould Allergens, Endotoxins and Cultivable Fungi in Pig Farms
Authors: Kraemer Julia G , Hilty Markus , Oppliger Anne
Published: August 2022

Airborne concentrations of organic dust on animal farms are known to be very high. This dust is partly composed of microorganisms such as bacteria, fungi and their components [endotoxins, (1→3)-β-d-glucans, mould allergens, mycotoxins], recognised as being responsible for numerous health effects. Several cross-sectional studies have measured levels of airborne bacteria, fungi and endotoxins on pig farms. However, the temporal dynamics of organic dust’s components throughout the year have rarely been assessed, and airborne concentrations of (1→3)-β-d-glucans and mould allergens remain poorly understood in these work environments. This longitudinal, four-season study measured cultivable fungi, endotoxins, (1→3)-β-d-glucans, Aspergillus versicolor (AveX), Aspergillus fumigatus (Asp f1) and Alternaria sp (Alt a1) allergens on 31 pig farms in Switzerland. Results showed that exposure to AveX occurred in all four seasons. Total mean airborne concentration of endotoxins were between 3 and 4 times higher than the Swiss recommended limit value of 1000 EU m-3 and mean airborne concentrations of fungi were between 30 and 50 times higher than the Swiss recommended limit value of 1000 cfu m-3. Finally, accumulations of faecal matter on floors, humidity and dusty pathways were associated with increased concentrations of (1→3)-β-d-glucans. In conclusion, pig farmers require better information about biological occupational risks, and measures to improve air quality should be implemented, especially in winter.
GREAP: a comprehensive enrichment analysis software for human genomic regions
Authors: Yang Yongsan , Qian Fengcui , Li Xuecang , Li Yanyu , Zhou Liwei , Wang Qiuyu , Zhou Xinyuan , Zhang Jian , Song Chao , Yu Zhengmin , Cui Ting , Feng Chenchen , Zhu Jiang , Shang Desi , Liu Jiaqi , Sun Mengfei , Zhang Yuexin , Tang Huifang , Li Chunquan
Published: August 2022

The rapid development of genomic high-throughput sequencing has identified a large number of DNA regulatory elements with abundant epigenetics markers, which promotes the rapid accumulation of functional genomic region data. The comprehensively understanding and research of human functional genomic regions is still a relatively urgent work at present. However, the existing analysis tools lack extensive annotation and enrichment analytical abilities for these regions. Here, we designed a novel software, Genomic Region sets Enrichment Analysis Platform (GREAP), which provides comprehensive region annotation and enrichment analysis capabilities. Currently, GREAP supports 85 370 genomic region reference sets, which cover 634 681 107 regions across 11 different data types, including super enhancers, transcription factors, accessible chromatins, etc. GREAP provides widespread annotation and enrichment analysis of genomic regions. To reflect the significance of enrichment analysis, we used the hypergeometric test and also provided a Locus Overlap Analysis. In summary, GREAP is a powerful platform that provides many types of genomic region sets for users and supports genomic region annotations and enrichment analyses. In addition, we developed a customizable genome browser containing >400 000 000 customizable tracks for visualization. The platform is freely available at http://www.liclab.net/Greap/view/index.
MultiGran-SMILES: multi-granularity SMILES learning for molecular property prediction
Authors: Jiang Jing , Zhang Ruisheng , Zhao Zhili , Ma Jun , Liu Yunwu , Yuan Yongna , Niu Bojuan
Published: August 2022

Motivation

Extracting useful molecular features is essential for molecular property prediction. Atom-level representation is a common representation of molecules, ignoring the sub-structure or branch information of molecules to some extent; however, it is vice versa for the substring-level representation. Both atom-level and substring-level representations may lose the neighborhood or spatial information of molecules. While molecular graph representation aggregating the neighborhood information of a molecule has a weak ability in expressing the chiral molecules or symmetrical structure. In this article, we aim to make use of the advantages of representations in different granularities simultaneously for molecular property prediction. To this end, we propose a fusion model named MultiGran-SMILES, which integrates the molecular features of atoms, sub-structures and graphs from the input. Compared with the single granularity representation of molecules, our method leverages the advantages of various granularity representations simultaneously and adjusts the contribution of each type of representation adaptively for molecular property prediction.

Results

The experimental results show that our MultiGran-SMILES method achieves state-of-the-art performance on BBBP, LogP, HIV and ClinTox datasets. For the BACE, FDA and Tox21 datasets, the results are comparable with the state-of-the-art models. Moreover, the experimental results show that the gains of our proposed method are bigger for the molecules with obvious functional groups or branches.

Availability and implementation

The code and data underlying this work are available on GitHub at https://github. com/Jiangjing0122/MultiGran.

Supplementary information

Supplementary data are available at Bioinformatics online.
medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata
Authors: Kimble M , Allers S , Campbell K , Chen C , Jackson L M , King B L , Silverbrand S , York G , Beard K
Published: August 2022

Motivation

Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software.

Results

We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019).

Availability and implementation

The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data
Authors: Chen Guangyi , Liu Zhi-Ping
Published: August 2022

Motivation

Single-cell RNA sequencing (scRNA-seq) data provides unprecedented opportunities to reconstruct gene regulatory networks (GRNs) at fine-grained resolution. Numerous unsupervised or self-supervised models have been proposed to infer GRN from bulk RNA-seq data, but few of them are appropriate for scRNA-seq data under the circumstance of low signal-to-noise ratio and dropout. Fortunately, the surging of TF-DNA binding data (e.g. ChIP-seq) makes supervised GRN inference possible. We regard supervised GRN inference as a graph-based link prediction problem that expects to learn gene low-dimensional vectorized representations to predict potential regulatory interactions.

Results

In this paper, we present GENELink to infer latent interactions between transcription factors (TFs) and target genes in GRN using graph attention network. GENELink projects the single-cell gene expression with observed TF-gene pairs to a low-dimensional space. Then, the specific gene representations are learned to serve for downstream similarity measurement or causal inference of pairwise genes by optimizing the embedding space. Compared to eight existing GRN reconstruction methods, GENELink achieves comparable or better performance on seven scRNA-seq datasets with four types of ground-truth networks. We further apply GENELink on scRNA-seq of human breast cancer metastasis and reveal regulatory heterogeneity of Notch and Wnt signalling pathways between primary tumour and lung metastasis. Moreover, the ontology enrichment results of unique lung metastasis GRN indicate that mitochondrial oxidative phosphorylation (OXPHOS) is functionally important during the seeding step of the cancer metastatic cascade, which is validated by pharmacological assays.

Availability and implementation

The code and data are available at https://github.com/zpliulab/GENELink.

Supplementary information

Supplementary data are available at Bioinformatics online.
Self-modulation of motor cortex activity after stroke: a randomized controlled trial
Authors: Sanders Zeena-Britt , Fleming Melanie K , Smejka Tom , Marzolla Marilien C , Zich Catharina , Rieger Sebastian W , Lührs Michael , Goebel Rainer , Sampaio-Baptista Cassandra , Johansen-Berg Heidi
Published: August 2022

Real-time functional MRI neurofeedback allows individuals to self-modulate their ongoing brain activity. This may be a useful tool in clinical disorders that are associated with altered brain activity patterns. Motor impairment after stroke has previously been associated with decreased laterality of motor cortex activity. Here we examined whether chronic stroke survivors were able to use real-time fMRI neurofeedback to increase laterality of motor cortex activity and assessed effects on motor performance and on brain structure and function.

We carried out a randomized, double-blind, sham-controlled trial (ClinicalTrials.gov: NCT03775915) in which 24 chronic stroke survivors with mild to moderate upper limb impairment experienced three training days of either Real (n = 12) or Sham (n = 12) neurofeedback. Assessments of brain structure, brain function and measures of upper-limb function were carried out before and 1 week after neurofeedback training. Additionally, measures of upper-limb function were repeated 1 month after neurofeedback training. Primary outcome measures were (i) changes in lateralization of motor cortex activity during movements of the stroke-affected hand throughout neurofeedback training days; and (ii) changes in motor performance of the affected limb on the Jebsen Taylor Test (JTT).

Stroke survivors were able to use Real neurofeedback to increase laterality of motor cortex activity within (P = 0.019), but not across, training days. There was no group effect on the primary behavioural outcome measure, which was average JTT performance across all subtasks (P = 0.116). Secondary analysis found improvements in the performance of the gross motor subtasks of the JTT in the Real neurofeedback group compared to Sham (P = 0.010). However, there were no improvements on the Action Research Arm Test or the Upper Extremity Fugl–Meyer score (both P > 0.5). Additionally, decreased white-matter asymmetry of the corticospinal tracts was detected 1 week after neurofeedback training (P = 0.008), indicating that the tracts become more similar with Real neurofeedback. Changes in the affected corticospinal tract were positively correlated with participants neurofeedback performance (P = 0.002).

Therefore, here we demonstrate that chronic stroke survivors are able to use functional MRI neurofeedback to self-modulate motor cortex activity in comparison to a Sham control, and that training is associated with improvements in gross hand motor performance and with white matter structural changes.
Faecal microbiota transplant ameliorates gut dysbiosis and cognitive deficits in Huntington’s disease mice
Authors: Gubert Carolina , Choo Jocelyn M , Love Chloe J , Kodikara Saritha , Masson Bethany A , Liew Jamie J M , Wang Yiwen , Kong Geraldine , Narayana Vinod K , Renoir Thibault , Lê Cao Kim Anh , Rogers Geraint B , Hannan Anthony J
Published: August 2022

Huntington’s disease is a neurodegenerative disorder involving psychiatric, cognitive and motor symptoms. Huntington’s disease is caused by a tandem-repeat expansion in the huntingtin gene, which is widely expressed throughout the brain and body, including the gastrointestinal system. There are currently no effective disease-modifying treatments available for this fatal disorder. Despite recent evidence of gut microbiome disruption in preclinical and clinical Huntington’s disease, its potential as a target for therapeutic interventions has not been explored. The microbiota–gut–brain axis provides a potential pathway through which changes in the gut could modulate brain function, including cognition. We now show that faecal microbiota transplant (FMT) from wild-type into Huntington’s disease mice positively modulates cognitive outcomes, particularly in females. In Huntington’s disease male mice, we revealed an inefficiency of FMT engraftment, which is potentially due to the more pronounced changes in the structure, composition and instability of the gut microbial community, and the imbalance in acetate and gut immune profiles found in these mice. This study demonstrates a role for gut microbiome modulation in ameliorating cognitive deficits modelling dementia in Huntington’s disease. Our findings pave the way for the development of future therapeutic approaches, including FMT and other forms of gut microbiome modulation, as potential clinical interventions for Huntington’s disease.
Detection of Influenza in Managed Quarantine in Australia and the Estimated Risk of Importation
Authors: Peck Heidi , Anbumurali Nithila , McMahon Kimberley , Freeman Kevin , Aziz Ammar , Gillespie Leah , Yang Bingyi , Moselen Jean , Deng Yi-Mo , Cowling Benjamin J , Barr Ian G , Subbarao Kanta , Sullivan Sheena G
Published: August 2022

Background

Influenza circulated at historically low levels during 2020/2021 due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic travel restrictions. In Australia, international arrivals were required to undergo a 14-day hotel quarantine to limit new introduction of SARS-CoV-2.

Methods

We usedtesting data for travelers arriving on repatriation flights to Darwin, Australia, from 3 January 2021 to 11 October 2021 to identify importations of influenza virus into Australia. We used this information to estimate the risk of a case exiting quarantine while still infectious. Influenza-positive samples were sequenced, and cases were followed up to identify transmission clusters. Data on the number of cases and total passengers were used to infer the risk of influenza cases exiting quarantine while infectious.

Results

Despite very low circulation of influenza globally, 42 cases were identified among 15 026 returned travelers, of which 30 were A(H3N2), 2 were A(H1N1)pdm09, and 10 were B/Victoria. Virus sequencing data identified potential in-flight transmission, as well as independent infections prior to travel. Under the quarantine strategy in place at the time, the probability that these cases could initiate influenza outbreaks in Australia neared 0. However, this probability rose as quarantine requirements relaxed.

Conclusions

Detection of influenza virus infections in repatriated travelers provided a source of influenza viruses otherwise unavailable and enabled development of the A(H3N2) vaccine seed viruses included in the 2022 Southern Hemisphere influenza vaccine. Failure to test quarantined returned travelers for influenza represents a missed opportunity for enhanced surveillance to better inform public health preparedness.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Testing and Detection During Peripartum Hospitalizations Among a Multicenter Cohort of Pregnant Persons: March 2020–February 2021
Authors: Delahoy Miranda J , Munoz Flor , Li De-Kun , Arriola Carmen Sofia , Bond Nanette Lee , Daugherty Michael , Ferber Jeannette , Ferguson Nickolas , Hadden Louise , Henderson Jillian T , Irving Stephanie A , Juergens Mary , Kancharla Venkatesh , Greenberg Mara , Odouli Roxana , Newes-Adeyi Gabriella , Nicholson Erin G , Reichle Lawrence , Sanyang Momodou , Snead Margaret , Dawood Fatimah S , Naleway Allison L
Published: August 2022

Background

Identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during peripartum hospitalizations is important to guide care, implement prevention measures, and understand infection burden.

Methods

This cross-sectional analysis used electronic health record data from hospitalizations during which pregnancies ended (peripartum hospitalizations) among a cohort of pregnant persons at 3 US integrated healthcare networks (sites 1–3). Maternal demographic, medical encounter, SARS-CoV-2 testing, and pregnancy and neonatal outcome information was extracted for persons with estimated delivery and pregnancy end dates during March 2020–February 2021 and ≥1 antenatal care record. Site-stratified multivariable logistic regression was used to identify factors associated with testing and compare pregnancy and neonatal outcomes among persons tested.

Results

Among 17 858 pregnant persons, 10 863 (60.8%) had peripartum SARS-CoV-2 testing; 222/10 683 (2.0%) had positive results. Testing prevalence varied by site and was lower during March–May 2020. Factors associated with higher peripartum SARS-CoV-2 testing odds were Asian race (adjusted odds ratio [aOR]: 1.36; 95% confidence interval [CI]: 1.03–1.79; referent: White) (site 1), Hispanic or Latino ethnicity (aOR: 1.33; 95% CI: 1.08–1.64) (site 2), peripartum Medicaid coverage (aOR: 1.33; 95% CI: 1.06–1.66) (site 1), and preterm hospitalization (aOR: 1.69; 95% CI: 1.19–2.39 [site 1]; aOR: 1.39; 95% CI: 1.03–1.88 [site 2]).

Conclusions

Findings highlight potential disparities in SARS-CoV-2 peripartum testing by demographic and pregnancy characteristics. Testing practice variations should be considered when interpreting studies relying on convenience samples of pregnant persons testing positive for SARS-CoV-2. Efforts to address testing differences between groups could improve equitable testing practices and care for pregnant persons with SARS-CoV-2 infections.
Successful treatment of recurrent cardiac sarcoidosis with the combination of corticosteroid and methotrexate monitored by 18F-fluoro-2-deoxyglucose positron emission tomography: case series
Authors: Ishizuka Masato , Uehara Masae , Katagiri Mikako , Ishida Junichi , Kojima Toshiya , Amiya Eisuke , Komuro Issei
Published: August 2022

Background

The standard treatment for cardiac sarcoidosis (CS) is corticosteroids, including prednisolone (PSL). Previous studies have shown that the addition of methotrexate (MTX) to PSL is effective for steroid-refractory and recurrent cases. 18F-fluoro-2-deoxyglucose positron emission tomography (FDG-PET) is an essential tool for the diagnosis of CS. However, it is unclear whether FDG-PET is useful for detecting recurrence of CS and monitoring the effectiveness of PSL and MTX combination therapy.

Case summary

We detected CS recurrence during PSL treatment using FDG-PET. Patient 1 was accompanied by increased FDG uptake in other organs, Patient 2 was complicated with a decrease in left ventricular ejection fraction, and Patient 3 showed enlargement of the late gadolinium enhancement area, which was compatible with the recurrence of CS. We successfully monitored the inflammation activity by FDG-PET and treated recurrent CS by increasing the PSL dose and adding MTX to suppress inflammation.

Discussion

FDG-PET is useful for detecting CS recurrence and monitoring the effectiveness of PSL and MTX combination therapy. Serial FDG-PET scans indicated that it might be more difficult to suppress inflammation in recurrent CS than in the initial treatment. The use of FDG-PET is necessary to monitor long-term disease activity.