bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and flexural strength of the hot-pressed AlMgB14 ceramic
Authors: Tkachev Dmitrii , Nikitin Pavel , Zhukov Ilya , Vorozhtsov Alexander , Marchenko Ekaterina , Verkhoshanskiy Yanis , Belchikov Ivan
Published: December 2022

AlMgB14 materials were obtained by hot-pressing of the prereacted AlMgB14 powder. The phase composition, structure, hardness and flexural strength have been studied. The XRD studies shown that the phase composition of the obtained materials contains from 9 to 12 wt. % of the spinel MgAl2O4 phase except target AlMgB14-phase. The spinel content increases linearly with an increase in the hot-pressing temperature from 1400 °C to 1600 °C. It was found that the density of the studied materials non-linearly depends on the hot-pressing temperature. An increase in the hot-pressing temperature from 1400 °C to 1500 °C leads to an increase in the relative density of the samples from 84% to 93%, respectively. A further increase in the hot-pressing temperature to 1600 °C leads to a decrease in the relative density to 81% due to the complication of the densification processes with an increase in the spinel content. An increase in the relative density from 81% to 93% leads to an increase in the flexural strength from 121 to 314 MPa and an increase in the Vickers microhardness from 5.1 to 7.9 GPa, respectively.
Spectroscopy and carrier dynamics of one-dimensional nanostructures
Authors: Zhang Yutong , Zhu Zhuoya , Zhang Shuai , Wu Xianxin , Du Wenna , Liu Xinfeng
Published: December 2022

In recent years, one-dimensional (1D) nanomaterials have raised researcher's interest because of their unique structural characteristic to generate and confine the optical signal and their promising prospects in photonic applications. In this review, we summarized the recent research advances on the spectroscopy and carrier dynamics of 1D nanostructures. First, the condensation and propagation of exciton–polaritons in nanowires (NWs) are introduced. Second, we discussed the properties of 1D photonic crystal (PC) and applications in photonic–plasmonic structures. Third, the observation of topological edge states in 1D topological structures is introduced. Finally, the perspective on the potential opportunities and remaining challenges of 1D nanomaterials is proposed.
One-step hydrothermal synthesis of Sn-doped α-Fe2O3 nanoparticles for enhanced photocatalytic degradation of Congo red
Authors: Lam Van Nang , Vu Thi Bich , Do Quang Dat , Le Thi Thanh Xuan , Nguyen Tien Dai , Nguyen T.-Thanh-Bao , Do Hoang Tung , Nguyen Thi Tu Oanh
Published: December 2022

We report on the synthesis of Sn-doped hematite nanoparticles (Sn-α-Fe2O3 NPs) by the hydrothermal method. The prepared Sn-α-Fe2O3 NPs had a highly pure and well crystalline rhombohedral phase with an average particle size of 41.4 nm. The optical properties of as-synthesized α-Fe2O3 NPs show a higher bandgap energy (2.40–2.57 eV) than that of pure bulk α-Fe2O3 (2.1 eV). By doping Sn into α-Fe2O3 NPs, the Sn-doped hematite was observed a redshift toward a long wavelength with increasing Sn concentration from 0% to 4.0%. The photocatalytic activity of Sn-doped α-Fe2O3 NPs was evaluated by Congo red (CR) dye degradation. The degradation efficiency of CR dye using Sn-α-Fe2O3 NPs catalyst is higher than that of pure α-Fe2O3 NPs. The highest degradation efficiency of CR dye was 97.8% using 2.5% Sn-doped α-Fe2O3 NPs catalyst under visible-light irradiation. These results suggest that the synthesized Sn-doped α-Fe2O3 nanoparticles might be a suitable approach to develop a photocatalytic degradation of toxic inorganic dye in wastewater.
Emitter layer optimization in heterojunction bifacial silicon solar cells
Authors: Shariah Adnan , Mahasneh Feda
Published: December 2022

Silicon solar cells continue to dominate the market, due to the abundance of silicon and their acceptable efficiency. The heterojunction with intrinsic thin layer (HIT) structure is now the dominant technology. Increasing the efficiency of these cells could expand the development choices for HIT solar cells. We presented a detailed investigation of the emitter a-Si:H(n) layer of a p-type bifacial HIT solar cell in terms of characteristic parameters which include layer doping concentration, thickness, band gap width, electron affinity, hole mobility, and so on. Solar cell composition: (ZnO/nc-Si:H(n)/a-Si:H(i)/c-Si(p)/a-Si:H(i)/nc-Si:H(p)/ZnO). The results reveal optimal values for the investigated parameters, for which the highest computed efficiency is 26.45% when lighted from the top only and 21.21% when illuminated from the back only.
Humidity sensor based on BiOBr synthesized under ambient condition
Authors: Cao Chaofan , Xiao Guixian , Lu Yao
Published: December 2022

Flexible humidity sensors are effective portable devices for human respiratory monitoring. However, the current preparation of sensitive materials need harsh terms and the small production output limits their practicability. Here, we report a synthesis method of single-crystal BiOBr nanosheets under room temperature and atmospheric pressure based on a sonochemical strategy. A flexible humidity sensor enabled by BiOBr nanosheets deliver efficient sensing performance, a high humidity sensitivity (I
g/I
0 = 550%) with relative humidity from 40% to 100%, an excellent selectivity, and a detection response/recovery time of 11 and 6 s, respectively. The flexible humidity sensor shows a potential application value as a wearable monitoring device for respiratory disease prevention and health monitoring.
Towards 2D dosimetry using monolithic active pixel sensors and a copper grating
Authors: Beck L. , Velthuis J.J. , De Sio C. , Pritchard J.L. , Li Y. , Hugtenburg R.P.
Published: December 2022

Higher energy and intensity X-ray radiotherapy treatments are coming into wider use, having the benefit of requiring fewer treatment fractions and fewer hospital visits per patient. However, small percentage errors in multileaf collimator positioning and dose become bigger problems with higher doses per fraction. Hence, real-time treatment verification becomes essential. Where devices downstream from the patient suffer from scattering in the patient, upstream devices can disturb the therapeutic beam. Here, a method is proposed for performing dosimetry upstream using monolithic active pixel sensors, which can be made thin enough to disturb the beam by <1%. In order to calculate the dose to the tumour, a verification device needs to make a measurement of the photon field. Some photons will Compton scatter an electron in the silicon and generate a signal. However, this signal is obscured by energy deposits from contamination electrons, originating from Compton scattering in the accelerator head and air. Often extensive build-up material is added to verification devices to reduce the electron contamination and enhance the photon signal. However, this leads to degradation of the beam intensity to the patient. Instead we propose using thin strips of 50 µm thick copper in a grating pattern and measuring the difference in the signal with and without it. The contamination electrons are relatively undisturbed by the presence of the thin copper strips and the photon signal generated via Compton scattering is enhanced under the strips. Hence the difference in the two signals mostly consists of energy deposits originating from the therapeutic photons. From this the dose to the patient can be derived. The 50 μm of copper is thin enough to keep the beam attenuation below 1%, but in itself would give a total signal response which consists of 38% contamination electrons. Using the grating technique, we show that the electron contamination can be reduced to 2.6% of the total signal. This allows the photon signal only to be extracted from the data and thus the dose to patient with a very thin upstream detector can be calculated using a Monte Carlo model to extrapolate the photon flux into the tumour.
Particle size amplification of black carbon by scattering measurement due to morphology diversity
Authors: Wu Yu , Cheng Tianhai , Zheng Lijuan , Zhang Yonggen , Zhang Lili
Published: December 2022

Black carbon (BC) is an important aerosol species due to its strong heating of the atmosphere accompanied by cooling of the Earth’s surface, but its radiative forcing is poorly constrained by different regional size distributions due to uncertain reproductions of a morphologically simplified model. Here, we quantify the BC morphological effect on measuring the particle size using an aggregate model. We show that the size distributions of loose BC particles could account for up to 45% underestimation by morphological simplification, leading to up to 25% differences, by relying on a simplified model to estimate radiative forcing. We find that the BC particle size is remarkably amplified for looser and larger BC aggregates by angular scattering observations. We suggest that the BC morphological diversity can be neglected in forward scattering angles (<30°), which is a useful supplement to reduce the uncertainty of radiative forcing assessment.
Enhancement of Arctic surface ozone during the 2020–2021 winter associated with the sudden stratospheric warming
Authors: Xia Yan , Xie Fei , Lu Xiao
Published: December 2022

Surface ozone is an important pollutant causing damage to human health and ecosystems. Here, we find that the Arctic surface ozone during the 2020–2021 winter was evidently enhanced after the sudden stratospheric warming (SSW) onset based on reanalysis data and simulations of a state-of-the-art chemistry-climate model. Further analysis suggests that this enhancement of Arctic surface ozone is primarily a result of the strengthening of the stratosphere-to-troposphere transport associated with the SSW. It is found that the SSW leads to more ozone in the Arctic stratosphere and enhanced downward transport with SSW-related downdraft. The 2021 SSW may also lead to positive anomalies in surface ozone in the northern midlatitudes, which are associated with cold air outbreaks. Our results indicate that the SSW not only affects the weather and climate in the troposphere but may also affect the surface air quality.
Design and Performance Improvement of 10T SRAM Using Sleepy Keeper and Drain Gating Techniques
Authors: Chaurasia Ranu , Kumar Brijesh , Verma Sudhanshu , Kumar Akhilesh
Published: December 2022

This paper presents the sleepy keeper and drain gating technique to improve the performance of 10T SRAM cell. The behavior of 10T SRAM cell is evaluated using benchmarked industry standard GPDK 45nm Technology Node of the Cadence Virtuoso EDA tool. The performance is analyzed in terms of dynamic and static parameters of 10T SRAM cell and compared with 6T SRAM, where find the reduction in dynamic power and static power dissipation. Besides this, observed the reduction in leakage current using sleepy keeper and drain gating technique. The proposed modified topology applicable in single-ended write and differential read operation. The read delay product and the write delay product is decreased by 36.7 % and 67.5 %, respectively. The major goal of the suggested architecture is to provide the improved stability, reduction in delay, as well as reduction in leakage current.
Design of Two Stage OTA based Sixth Order Butter-worth Low Pass Filter using CMOS 180nm Technology
Authors: Agrawal Anikesh , Ajnar D S , Khatri Rajesh
Published: December 2022

This paper shows the design of 6th order Butter-worth low pass filter based on operational trans-conductance amplifier (OTA). The designing and simulation results are obtained using Cadence Virtuoso tool with 180nm (0.18μm) technology. The simulation results of OTA have a gain of about 97.3dB. The simulation results of butter-worth low pass filter for 1.25V supply voltage and 20μA biasing current gives -96.4mdB gain and 2.9GHz bandwidth for a frequency range of 100Hz to 10GHz. The results are presented in this paper.
Advanced Safety Programmable Logic Controller and Operational Programmable Logic Controller for Data Acquisition Control System of SADHANA Sodium Loop
Authors: Shanmugasundaram M. , Thirugnanamurthy D. , Srinivasan V.S. , SriDevi T. , Nashine B.K.
Published: December 2022

The SAfety Decay Heat Analysis in NAtrium (SADHANA) sodium loop is designed with two PLC controllers. All safety control interlocks are monitored by a Safety programmable logic controller (SPLC), and temperature control, including averaging ON/OFF heaters, is managed by an Operational PLC (OPLC).The decay heat exchange system of the SADHANA sodium loop is evaluated using these combined safety and operational PLCs. In the case of reactor loss of offsite and onsite power, decay heat generated in the reactor core after shutdown is removed by four Safety Grade Decay Heat Removal (SGDHR) systems [1,2,3,4,5]. Each exchanger (AHX) is located outside the reactor containment building, and a sodium loop circulation is created by natural convection [6,7,8,9,10]. The purpose of construction of SADHANA loop, with simulated models of DHX and AHX to study the performance of the SGDHR system, has been planned [11,12,13,14,15]. The SADHANA sodium loop has been commissioned, operating at isothermal temperatures of 300°C and hot temperatures of 500°C/& 550°C. The smart instrumentation and control system comprising Loop Operational Data Acquisition and Control System (LODACS) and Experimental Data Acquisition System (EDAS) are used in the SADHANA sodium loop. During the tests, LODACS personal computer and Instrumentation panel monitor loop parameters such as sodium level, leak, and pressure. In SADHANA loop DHX and AHX temperature decay heat changes monitoring by EDAS. The temperature of the pool in Test vessel 4 (TV-4) is controlled by immersion type sodium heaters via PID controllers. Currently, the loop consists of 64 surface heaters, 30 immersion type sodium heaters, and 205 thermocouples (84 Nos. of operational thermocouples and 121 Nos. of experimental thermocouples). According to the experimental thermocouples are being monitored by a separate fast data acquisition (scan rate of 10 seconds) by in-house developed software. This technical paper also describes the implementation of PLCs in different data acquisition control systems.
Performance Comparison of Channel Coding Techniques for OFDM System
Authors: Lakshmi M. Vijaya , Reddy G. Gagana , Sucharitha Alamur , Akshara N. , Vaishnavi N.
Published: December 2022

Wireless communication is one of the speedily evolving and dynamic technology areas in the realm of communication. OFDM is an acronym for Orthogonal Frequency Division Multiplexing. It is a version of FDM in which orthogonal subcarriers are closely spaced to maximize bandwidth consumption. By decreasing Inter Symbol Interference (ISI) and increasing the Signal-to-Noise ratio (SNR), it has enhanced the quality of long-distance communication. It’s commonly employed in digital communication systems to safeguard digital data from noise and interference while also reducing bit mistakes. Convolutional codes, Block codes, are the two fundamental forms of channel codes. Block codes are based on abstract algebra and finite field arithmetic. They are capable of detecting and correcting faults. This category includes LDPC and Reed Solomon codes. Convolution codes, alternatively are created using a distinct strong mathematical framework and are generally utilised for real-time error correction. They combine all of the data into a single codeword. Reed-Solomon codes are block-based error correcting codes used in digital communications, storage, and ADSL, among other uses. The BER performance of an OFDM system is investigated in this paper using various channel coding algorithms.
Edge Blending to Enhance the Flow Over Double delta wing configuration during re-entry
Authors: Jaiswal Krishna , Ganorkar Pratik , Shinde Sunil
Published: December 2022

During re-entry of space vehicle, the vehicle undergoes flow variation from hypersonic flow to subsonic flow, which causes huge heat transfer over the wing configuration. The double delta wing of configuration 76 degree - 40 degree is considered and effect of blending the wing at edges showed variation and enhancement of flow over the double delta wing configuration. Heat flux calculations were carried out at regions of shock-shock interactions and the effect of blend radius at edges were analyzed using simulations done in ANSYS Fluent. It was observed that aerodynamic efficiency increases with the edge blending which ultimately enhanced the flow field over the double delta wing.
Tensile and thermal behaviour of linear low-density polyethylene nanocomposite films
Authors: Chandra R B Jagadeesh , Shivamurthy B , Vishwanatha HM , kumar M Sathish
Published: December 2022

In this work Graphene nanoplatelets (GNPs) filled with Linear low-density polyethylene (LLDPE), nanocomposite films designated as LLDPE+1%GNP and LLDPE+5% GNP were manufactured using LLDPE pristine granules, 1 wt. % GNPs-LLDPE, and 5wt. % GNPs-LLDPE masterbatch granules by the extrusion-blow molding process. It was found that the ductile behaviour of neat LLDPE film and nanocomposite films are anisotropic in the machine direction (MD) and transverse direction (TD). The tensile strength of neat LLDPE films in the MD and TD is 25.93 & 20MPa. LLDPE+1GNPs nanocomposite films showed higher tensile strength in the MD and TD 28.38 & 23MPa, and LLDPE+5GNPs nanocomposite films showed 24.36 & 23MPa respectively. The high concentration of GNPs in LLDPE acts as plasticizers increased the elongation, reduced the strength, and increased the rate of thermal degradation. The XRD results reveal additional peeks observed in LLDPE+5GNPs nanocomposite films infer the slight change in crystallinity as compared to neat LLDPE film. This is evident in the change of tensile behaviour of nanocomposite as compared to LLDPE.
Investigation of Dielectric Spectroscopy of Tellurium (Te) doped Bismuth Antimony (BiSb) pellet
Authors: Panchal Reena , Jani Maunik , Vyas S M , Pavagadhi Himanshu
Published: December 2022

Tellurium (Te) doped Bismuth Antimony (BiSb) sample has been prepared in the form of the pellet (Bulk) with the help of a compression method using a Pelletizer. Using Tellurium (Te) doped Bismuth antimony (BiSb) pellet was used for the study of dielectric properties through VNA (Vector Network Analysis) in the high range of frequency 200 MHz to 20 GHz. From initial data obtained for the study, DC conductivity, Dielectric loss, Dielectric constant, AC conductivity, and Real & Imaginary Electric modulus have been figured. All these properties have been used for exploring different mechanisms involved in the examination of dielectric spectroscopy.
Structural, Dielectric and Ferroelectric Characterizations of Sol-gel Prepared Ba1-xSrxTiO3 Nanoceramics
Authors: Singh Devendra , Dixit Anju , Dobal Pramod S
Published: December 2022

Ba1-xSrxTiO3 (0.0 ≤ x ≤ 0.5) nanoceramics were synthesized via sol-gel route and the structural and electric properties of the resulting compositions were investigated. revealed A tetragonal crystal structures for x = 0.0 - 0.3 and a cubic structure for x = 0.5 compositions was revealed by X-ray diffraction. The smaller ionic radii of Sr ions resulted in the lowering of c/a ratio with increasing x and a tetragonal to cubic structural transformation was observed at around x = 0.4. The average crystallite size gradually decreased with increasing x from 0 to 0.5. This trend was visible in electron micrographs. The room temperature dielectric constant in these nanoceramics increases with increasing Sr and a maximum value of 1553 was observed for x=0.3. Curie temperature (Tc
) of 125 °C was obtained for x=0.0, which shifted toward lower temperature with increasing x value. The value of Tc
was observed as 100 and 75 °C for x = 0.1 and 0.3, respectively. The remnant polarization (Pr
), saturation polarization (Ps
), and coercive field (Ec
) decreased with increasing Sr concentration in BT due to the structural modifications. Value of Pr
decreases from 0.637 to 0.229 μC/cm2, Ps
decreases from 8.910 to 3.238 μC/cm2 and Ec
decreases from 0.631 to 0.255 kV/cm with increasing x from 0 to 0.5.
Surface analyses of corrosion products formed on API X-70 steel in sour brine after testing in a pipe loop
Authors: Cervantes-Tobón A , Díaz-Cruz M , Domínguez-Aguilar M A , Cabrera-Sierra R , García-Murillo A , de J Carrillo-Romo F , Ortega-Cárdenas J Angélica
Published: December 2022

Flow assisted corrosion (FAC) is a problem of pipeline systems that handle high flow rates and strong direction changes. In the present investigation, FAC was tested on carbon steel exposed to the NACE 1D-196 environment by means an experimental pipe loop. As the exposure time increased, corrosion products formed a mixture of oxides, sulfides, and an apparent sulfate (rhombohedral mikasaite Fe2 (SO4)3), which was found in greater proportion and appeared to have a significant effect on decreasing corrosion rate. Transmission electron microscopy and x ray diffraction patterns seemed to confirm the presence of a sulfate and some oxides as the major chemical species contained in the corrosion products.
Euclidean volumes of hyperbolic knots
Authors: Abrosimov Nikolay , Kolpakov Alexander , Mednykh Alexander
Published: December 2022

The hyperbolic structure on a

3
3

–dimensional cone–manifold with a knot as singularity can often be deformed into a limiting Euclidean structure. In the present paper we show that the respective normalised Euclidean volume is always an algebraic number, which is reminiscent of Sabitov’s theorem (the Bellows Conjecture). This fact also stands in contrast to hyperbolic volumes whose number–theoretic nature is usually quite complicated.
Estimates for truncated area functionals on the Bloch space
Authors: Efraimidis Iason , Mas Alejandro , Vukotić Dragan
Published: December 2022

Recently, Kayumov [Lobachevskii J. Math. 38 (2017), pp. 466–468] obtained a sharp estimate for the

n
n

-th truncated area functional for normalized functions in the Bloch space for

n
≤
5

n\le 5

and then, together with Wirths [Lobachevskii J. Math. 40 (2019), pp. 1319–1323], extended the result for

n
=
6

n=6

. We prove that for the functions with non-negative Taylor coefficients, the same sharp estimate is valid for all

n
n

. For arbitrary functions, we obtain an estimate that is asymptotically of the same order but slightly larger (roughly by a factor of

4

/

e

4/e

). We also consider related weighted estimates for functionals involving the powers

n
t

n^t

,

t
>
0

t>0

, and show that the exponent

t
=
1

t=1

represents the critical case for the expected sharp estimate.
A construction of Sbrana-Cartan hypersurfaces in the discrete class
Authors: Dajczer Marcos , Jimenez Miguel
Published: December 2022

The classical classifications of the locally isometrically deformable Euclidean hypersurfaces obtained by U. Sbrana in 1909 and E. Cartan in 1916 include four classes, among them the one formed by submanifolds that allow just a single deformation. The question of whether these Sbrana-Cartan hypersurfaces do, in fact, exist was not addressed by either of them. Positive answers to this question were given by Dajczer-Florit-Tojeiro in 1998 for the ones called of hyperbolic type and by Dajczer-Florit in 2004 when of elliptic type which is the other possibility. In both cases the examples constructed are rather special. The main result of this paper yields an abundance of examples of hypersurfaces of either type and seems to point in the direction of a classification although that goal remains elusive.
To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities
Authors: Zhou Jiayin , Song Wen , Tu Qichao
Published: December 2022

High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.
Large-scale prediction of adverse drug reactions-related proteins with network embedding
Authors: Park Jaesub , Lee Sangyeon , Kim Kwansoo , Jung Jaegyun , Lee Doheon
Published: December 2022

Motivation

Adverse drug reactions (ADRs) are a major issue in drug development and clinical pharmacology. As most ADRs are caused by unintended activity at off-targets of drugs, the identification of drug targets responsible for ADRs becomes a key process for resolving ADRs. Recently, with the increase in the number of ADR-related data sources, several computational methodologies have been proposed to analyze ADR–protein relations. However, the identification of ADR-related proteins on a large scale with high reliability remains an important challenge.

Results

In this article, we suggest a computational approach, Large-scale ADR-related Proteins Identification with Network Embedding (LAPINE). LAPINE combines a novel concept called single-target compound with a network embedding technique to enable large-scale prediction of ADR-related proteins for any proteins in the protein–protein interaction network. Analysis of benchmark datasets confirms the need to expand the scope of potential ADR-related proteins to be analyzed, as well as LAPINE’s capability for high recovery of known ADR-related proteins. Moreover, LAPINE provides more reliable predictions for ADR-related proteins (Value-added positive predictive value = 0.12), compared to a previously proposed method (P < 0.001). Furthermore, two case studies show that most predictive proteins related to ADRs in LAPINE are supported by literature evidence. Overall, LAPINE can provide reliable insights into the relationship between ADRs and proteomes to understand the mechanism of ADRs leading to their prevention.

Availability and implementation

The source code is available at GitHub (https://github.com/rupinas/LAPINE) and Figshare (https://figshare.com/articles/software/LAPINE/21750245) to facilitate its use.

Supplementary information

Supplementary data are available at Bioinformatics online.
Identification of a possible proteomic biomarker in Parkinson’s disease: discovery and replication in blood, brain and cerebrospinal fluid
Authors: Winchester Laura , Barber Imelda , Lawton Michael , Ash Jessica , Liu Benjamine , Evetts Samuel , Hopkins-Jones Lucinda , Lewis Suppalak , Bresner Catherine , Malpartida Ana Belen , Williams Nigel , Gentlemen Steve , Wade-Martins Richard , Ryan Brent , Holgado-Nevado Alejo , Hu Michele , Ben-Shlomo Yoav , Grosset Donald , Lovestone Simon
Published: December 2022

Biomarkers to aid diagnosis and delineate the progression of Parkinson’s disease are vital for targeting treatment in the early phases of the disease. Here, we aim to discover a multi-protein panel representative of Parkinson’s and make mechanistic inferences from protein expression profiles within the broader objective of finding novel biomarkers. We used aptamer-based technology (SomaLogic®) to measure proteins in 1599 serum samples, 85 cerebrospinal fluid samples and 37 brain tissue samples collected from two observational longitudinal cohorts (the Oxford Parkinson’s Disease Centre and Tracking Parkinson’s) and the Parkinson’s Disease Brain Bank, respectively. Random forest machine learning was performed to discover new proteins related to disease status and generate multi-protein expression signatures with potential novel biomarkers. Differential regulation analysis and pathway analysis were performed to identify functional and mechanistic disease associations. The most consistent diagnostic classifier signature was tested across modalities [cerebrospinal fluid (area under curve) = 0.74, P = 0.0009; brain area under curve = 0.75, P = 0.006; serum area under curve = 0.66, P = 0.0002]. Focusing on serum samples and using only those with severe disease compared with controls increased the area under curve to 0.72 (P = 1.0 × 10−4). In the validation data set, we showed that the same classifiers were significantly related to disease status (P < 0.001). Differential expression analysis and weighted gene correlation network analysis highlighted key proteins and pathways with known relationships to Parkinson’s. Proteins from the complement and coagulation cascades suggest a disease relationship to immune response. The combined analytical approaches in a relatively large number of samples, across tissue types, with replication and validation, provide mechanistic insights into the disease as well as nominate a protein signature classifier that deserves further biomarker evaluation.
The upper thermal limit of epaulette sharks (Hemiscyllium ocellatum) is conserved across three life history stages, sex and body size
Authors: Wheeler Carolyn R , Lang Bethan J , Mandelman John W , Rummer Jodie L
Published: December 2022

Owing to climate change, most notably the increasing frequency of marine heatwaves and long-term ocean warming, better elucidating the upper thermal limits of marine fishes is important for predicting the future of species and populations. The critical thermal maximum (CTmax), or the highest temperature a species can tolerate, is a physiological metric that is used to establish upper thermal limits. Among marine organisms, this metric is commonly assessed in bony fishes but less so in other taxonomic groups, such as elasmobranchs (subclass of sharks, rays and skates), where only thermal acclimation effects on CTmax have been assessed. Herein, we tested whether three life history stages, sex and body size affected CTmax in a tropical elasmobranch, the epaulette shark (Hemiscyllium ocellatum), collected from the reef flats surrounding Heron Island, Australia. Overall, we found no difference in CTmax between life history stages, sexes or across a range of body sizes. Findings from this research suggest that the energetically costly processes (i.e. growth, maturation and reproduction) associated with the life history stages occupying these tropical reef flats do not change overall acute thermal tolerance. However, it is important to note that neither embryos developing in ovo, neonates, nor females actively encapsulating egg cases were observed in or collected from the reef flats. Overall, our findings provide the first evidence in an elasmobranch that upper thermal tolerance is not impacted by life history stage or size. This information will help to improve our understanding of how anthropogenic climate change may (or may not) disproportionally affect particular life stages and, as such, where additional conservation and management actions may be required.
Hexavalent chromium–induced epigenetic instability and transposon activation lead to phenotypic variations and tumors in Drosophila
Authors: Parikh Rasesh Y , Gangaraju Vamsi K
Published: December 2022

Developmental robustness represents the ability of an organism to resist phenotypic variations despite environmental insults and inherent genetic variations. Derailment of developmental robustness leads to phenotypic variations that can get fixed in a population for many generations. Environmental pollution is a significant worldwide problem with detrimental consequences of human development. Understanding the genetic basis for how pollutants affect human development is critical for developing interventional therapies. Here, we report that environmental stress induced by hexavalent chromium, Cr(VI), a potent industrial pollutant, compromises developmental robustness, leading to phenotypic variations in the progeny. These phenotypic variations arise due to epigenetic instability and transposon activation in the somatic tissues of the progeny rather than novel genetic mutations and can be reduced by increasing the dosage of Piwi - a Piwi-interacting RNA–binding protein, in the ovary of the exposed mother. Significantly, the derailment of developmental robustness by Cr(VI) exposure leads to tumors in the progeny, and the predisposition to develop tumors is fixed in the population for at least three generations. Thus, we show for the first time that environmental pollution can derail developmental robustness and predispose the progeny of the exposed population to develop phenotypic variations and tumors.
Processed food exports from developing countries: the effect of food safety compliance
Authors: Suanin Wanissa
Published: December 2022

The study investigates the impact of developing countries’ ability to comply with international food safety standards on processed food exports, based on the structural gravity modelling framework and a novel dataset from 2002 to 2018. The constructed variable on international food safety compliance is derived from import refusal records from the US Food and Drug Administration. The findings indicate that international food safety compliance is a significant factor in explaining inter-country differences in processed food export performance. The ability to meet international food safety standards matters for processed food exports from developing Asia to developing country markets and the USA, but it has a limited influence on Asian processed food exports to the European Union.
The Portuguese budgetary costs with First World War: a comparative perspective
Authors: Ferraz Ricardo
Published: December 2022

In this paper, I show that the Portuguese budgetary costs with the First World War represented, on average, practically 50% of state expenditure and 7% of GDP during 1914–1918. These costs caused different negative effects on public finances and were also negatively correlated with economic growth according to the estimated results of two dynamic models. Nevertheless, Portugal’s costs with this war appear to have been lower than those of the other belligerents for which data are available, as Austria-Hungary, Bulgaria, France, Greece, Great Britain, Italy, and the United States.
Ablation versus anti-arrhythmic therapy for reducing all hospital episodes from recurrent atrial fibrillation: a prospective, randomized, multi-centre, open label trial
Authors: Kanagaratnam Prapa , McCready James , Tayebjee Muzahir , Shepherd Ewen , Sasikaran Thiagarajah , Todd Derick , Johnson Nicholas , Kyriacou Andreas , Hayat Sajad , Hobson Neil A , Mann Ian , Balasubramaniam Richard , Whinnett Zachary , Earley Mark , Petkar Sanjiv , Veasey Rick , Kirubakaran Senthil , Coyle Clare , Kim Min-Young , Lim Phang Boon , O’Neill James , Davies D Wyn , Peters Nicholas S , Babalis Daphne , Linton Nicholas , Falaschetti Emanuela , Tanner Mark , Shah Jaymin , Poulter Neil
Published: December 2022

Aims

There is rising healthcare utilization related to the increasing incidence and prevalence of atrial fibrillation (AF) worldwide. Simplifying therapy and reducing hospital episodes would be a valuable development. The efficacy of a streamlined AF ablation approach was compared to drug therapy and a conventional catheter ablation technique for symptom control in paroxysmal AF.

Methods and results

We recruited 321 patients with symptomatic paroxysmal AF to a prospective randomized, multi-centre, open label trial at 13 UK hospitals. Patients were randomized 1:1:1 to cryo-balloon ablation without electrical mapping with patients discharged same day [Ablation Versus Anti-arrhythmic Therapy for Reducing All Hospital Episodes from Recurrent (AVATAR) protocol]; optimization of drug therapy; or cryo-balloon ablation with confirmation of pulmonary vein isolation and overnight hospitalization. The primary endpoint was time to any hospital episode related to treatment for atrial arrhythmia. Secondary endpoints included complications of treatment and quality-of-life measures. The hazard ratio (HR) for a primary endpoint event occurring when comparing AVATAR protocol arm to drug therapy was 0.156 (95% CI, 0.097–0.250; P < 0.0001 by Cox regression). Twenty-three patients (21%) recorded an endpoint event in the AVATAR arm compared to 76 patients (74%) within the drug therapy arm. Comparing AVATAR and conventional ablation arms resulted in a non-significant HR of 1.173 (95% CI, 0.639–2.154; P = 0.61 by Cox regression) with 23 patients (21%) and 19 patients (18%), respectively, recording primary endpoint events (P = 0.61 by log-rank test).

Conclusion

The AVATAR protocol was superior to drug therapy for avoiding hospital episodes related to AF treatment, but conventional cryoablation was not superior to the AVATAR protocol. This could have wide-ranging implications on how demand for AF symptom control is met.

Trial registration

Clinical Trials Registration: NCT02459574.
Scar border zone mass and presence of border zone channels assessed with cardiac magnetic resonance imaging are associated with ventricular arrhythmia in patients with ST-segment elevation myocardial infarction
Authors: Thomsen Anna F , Bertelsen Litten , Jøns Christian , Jabbari Reza , Lønborg Jacob , Kyhl Kasper , Göransson Christoffer , Nepper-Christensen Lars , Atharovski Kiril , Ekström Kathrine , Tilsted Hans-Henrik , Pedersen Frants , Køber Lars , Engstrøm Thomas , Vejlstrup Niels , Jacobsen Peter Karl
Published: December 2022

Aims

Late gadolinium enhancement cardiac magnetic resonance (CMR) permits characterization of left ventricular ischaemic scars. We aimed to evaluate if scar core mass, border zone (BZ) mass, and BZ channels are risk markers for subsequent ventricular arrhythmia (VA) in ST-segment elevation myocardial infarction (STEMI).

Methods and results

A sub-study of the DANish Acute Myocardial Infarction-3 multi-centre trial and Danegaptide phase II proof-of-concept clinical trial in which a total of 843 STEMI patients had a 3-month follow-up CMR. Of these, 21 patients subsequently experienced VA during 100 months of follow-up and were randomly matched 1:5 with 105 controls. A VA event was defined as: ventricular tachycardia, ventricular fibrillation, or sudden cardiac death. Ischaemic scar characteristics were automatically detected by specialized software. We included 126 patients with a median left ventricular ejection fraction of 51.0 ± 11.6% in cases with VA vs. 55.5 ± 8.5% in controls (P = 0.10). Cases had a larger mean BZ mass and more often BZ channels compared to controls [BZ mass: 17.2 ± 10.3 g vs. 10.3 ± 6.0 g; P = 0.0002; BZ channels: 17 (80%) vs. 44 (42%); P = 0.001]. A combination of ≥17.2 g BZ mass and the presence of BZ channels was five times more prevalent in cases vs. controls (P ≤ 0.00001) with an odds ratio of 9.40 (95% confidence interval 3.26–27.13; P ≤ 0.0001) for VA. This identified cases with 52% sensitivity and 90% specificity.

Conclusion(s)

Scar characterization with CMR indicates that a combination of ≥17.2 g BZ mass and the presence of BZ channels had the strongest association with subsequent VA in STEMI patients.

ClinicalTrials.gov

Unique identifier: NCT01435408 (DANAMI 3-iPOST and DANAMI 3-DEFER), NCT01960933 (DANAMI 3-PRIMULTI), and NCT01977755 (Danegaptide).
Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens
Authors: Michaux Charlotte , Gerovac Milan , Hansen Elisabeth E , Barquist Lars , Vogel Jörg
Published: December 2022

Enterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA–protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA–protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA–protein complexes such as the 6S RNA–RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
Accurate and fast clade assignment via deep learning and frequency chaos game representation
Authors: Avila Cartes Jorge , Anand Santosh , Ciccolella Simone , Bonizzoni Paola , Della Vedova Gianluca
Published: December 2022

Background

Since the beginning of the coronavirus disease 2019 pandemic, there has been an explosion of sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus; most notably, the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade.

Results

In this article, we leverage the frequency chaos game representation (FCGR) and convolutional neural networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieved an $96.29\%$ overall accuracy, while a similar tool, Covidex, obtained a $77,12\%$ overall accuracy. As far as we know, our method is the first using deep learning and FCGR for intraspecies classification. Furthermore, by using some feature importance methods, CouGaR-g allows to identify k-mers that match SARS-CoV-2 marker variants.

Conclusions

By combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on random forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants.

Availability

The trained models can be tested online providing a FASTA file (with 1 or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.
Antigen Discovery for Next-Generation Pertussis Vaccines Using Immunoproteomics and Transposon-Directed Insertion Sequencing
Authors: Gregg Kelsey A , Wang Yihui , Warfel Jason , Schoenfeld Elizabeth , Jankowska Ewa , Cipollo John F , Mayho Matthew , Boinett Christine , Prasad Deepika , Brickman Timothy J , Armstrong Sandra K , Parkhill Julian , Da Silva Antunes Ricardo , Sette Alessandro , Papin James F , Wolf Roman , Merkel Tod J
Published: December 2022

Background

Despite high vaccination rates, the United States has experienced a resurgence in reported cases of pertussis after switching to the acellular pertussis vaccine, indicating a need for improved vaccines that enhance infection control.

Methods

Bordetella pertussis antigens recognized by convalescent-baboon serum and nasopharyngeal wash were identified by immunoproteomics and their subcellular localization predicted. Genes essential or important for persistence in the baboon airway were identified by transposon-directed insertion-site sequencing (TraDIS) analysis.

Results

In total, 314 B. pertussis antigens were identified by convalescent baboon serum and 748 by nasopharyngeal wash. Thirteen antigens were identified as immunogenic in baboons, essential for persistence in the airway by TraDIS, and membrane-localized: BP0840 (OmpP), Pal, OmpA2, BP1485, BamA, Pcp, MlaA, YfgL, BP2197, BP1569, MlaD, ComL, and BP0183.

Conclusions

The B. pertussis antigens identified as immunogenic, essential for persistence in the airway, and membrane-localized warrant further investigation for inclusion in vaccines designed to reduce or prevent carriage of bacteria in the airway of vaccinated individuals.
Antimicrobial activity of antibiotics on biofilm formed byStaphylococcus aureusandPseudomonas aeruginosain an open microfluidic model mimicking the diabetic foot environment
Authors: Pouget Cassandra , Pantel Alix , Dunyach-Remy Catherine , Magnan Chloé , Sotto Albert , Lavigne Jean-Philippe
Published: December 2022

Background

Diabetic foot infections (DFIs) represent a public health problem because of their frequency and the severity of their consequences, i.e. amputation and mortality. Polymicrobial biofilms on the skin surface of these ulcers complicate wound healing. Few in vitro models exist to study the antibiotics activity in this context.

Objectives

This study evaluated the in vitro activity of antibiotics against the two main bacteria isolated in DFI, Staphylococcus aureus and Pseudomonas aeruginosa, using a dynamic system (BioFlux™ 200) and a chronic wound-like medium (CWM) that mimic the foot ulcer environment.

Methods

Reference strains and two pairs of clinical S. aureus and P. aeruginosa isolated together from a DFI were cultivated in brain heart infusion and CWM media during 72 h at 37°C, alone and combined in the BioFlux™ 200 system. Antibiotic activity was evaluated after a mechanical debridement. The activities were measured by the reduction of biofilm percentage of bacteria in the microfluidic system using microscopy.

Results

Daptomycin for S. aureus and ceftazidime for P. aeruginosa showed excellent activity to reduce biofilm biomass, whereas linezolid action was more mitigated and dalbavancin was ineffective. Ceftazidime + daptomycin presented the most potent in vitro activity on a mixed biofilm.

Conclusions

The combination of CWM and the BioFlux™ microfluidic system represents a valuable tool to screen the potential antimicrobial activity of antibiotics under conditions mimicking those encountered in DFI. It could help clinicians in their management of chronic wounds.