bluuebunny/crossref_metadata_2025 huggingface dataset:
A Temperature Correction Method Based On Deep Learning
Authors: Hao Chenfei , Du Xinyu , Wang Jiarun
Published: March 2023

This paper presents a numerical model based on product temperature prediction deep learning error correction method, using two-dimensional convolution both short-term and long-term memory network model, using the European Centre for Medium-Range Weather Forecasts in 2018 numerical weather prediction model 2m temperature forecast products and part of China’s meteorological site data, using meteorological site temperature, wind speed, pressure, relative humidity, four elements. The spatio-temporal characteristics of the observed data were mined and combined with the model 2m temperature forecast results to train the deep learning model, and the prediction results of the short-and medium-term grid forecast products of the model 2m temperature in 2018 were interpolated to the station to correct the deviation. The results show that the Bi-Conv-LSTM model can reduce the overall root mean square error of temperature forecast from 4.35 °C to 2.75 °C, which is 44.6% lower. The Bi-Conv-LSTM model has an obvious effect on the correction of the temperature forecast error of the station, which verifies the application ability of deep learning in the field of meteorological correction.
Physical design of fusion target with edge computing
Authors: GaoyangLiu  , Peng Dongfang , Xiong Wenbin , Gao Qiang , Qu Fanyu , Tang Zhangchun , Liu Pan
Published: March 2023

The physical design of the fusion target is an important part of controlled thermonuclear fusion, and the geometric model and material selection of the target is also critical to achieving fusion ignition. We have modularised the target and introduced digital modeling, edge computing, and deep learning technologies to build a data-driven hybrid computing framework. We construct physical models and integrate them into a unified digital model of a multi-domain system; simulate and iteratively modify the physical model, and use edge computing technologies for information modeling. Edge computing is well applied to the calculation of each module of the target. Each module is both correlated and independent, and the values of the fusion ignition temperature and density achieved in the target are obtained, and the neutron products in the ignition and main fuel regions are 1016- 1017and 1019respectively. This will be an important reference value for the design of actual fusion targets.
Research on Attitude Calculation Based on MEMS Sensor
Authors: Zhang Cheng , Lin Guomin , Chen Zhen
Published: March 2023

According to the requirement of attitude measurement of moving carriers, the MPU9250 sensor is used to collect real-time data on moving carriers. However, the accuracy of the sensor is low, and there is a large error between the calculated attitude value and the real value. Therefore, in this paper, the adaptive complementary filtering algorithm and ellipse fitting method are adopted, which effectively reduces the error and makes the attitude angle more accurate. Based on the Euler angle and quaternion differential equation, the attitude angles
ϕ
and
θ
are obtained by correcting the gyroscope value according to the adaptive complementary filtering algorithm. Then the magnetometer in the MPU9250 sensor is processed by ellipse fitting based on the least square method, and the heading angle
ψ
of the moving carrier is calculated. Through static and dynamic experiments, it can be seen that the attitude angle obtained by adaptive complementary filtering and ellipse fitting is more accurate and stable.
An adjustable active noise control algorithm based on Bark scale
Authors: Su Haitao , Hu Chunjing , Chen Jiaxuan , Hu Hongzhi , Xu Cuifeng
Published: March 2023

An adjustable active noise control algorithm is proposed based on human auditory perception. Because of the FELMS algorithm, the Bark scale decomposition is used for simulating the decomposition of the human ears to the acoustic signal, and the real time response of the human ears to the noise is calculated. Residual filter is designed based on this real-time response so that the noise reduction effect is more in line with the human beings auditory perception. In the meantime, the adjustment parameter is set to adjust the amplitude-frequency response of the designed residual filter so that the noise reduction effect can be adjusted artificially under the condition of preserving the noise characteristics. Computer simulation results show that, match with the convention FXLMS algorithm, the algorithm put forward in this paper makes the residual noise, and the original noise has a similar energy change trend in Barks. This algorithm makes the noise reduction effect more aligned with the human auditory perception. It can retain the noise characteristics and artificially adjust the noise reduction effect.
Inkjet OLED printing planning based on deep reinforcement learning and reward-based TLO
Authors: Lian Zekai , Lv Cixing , Lu Wei
Published: March 2023

With the increasing use of OLED screens in electronic products, there is a focus on how to print OLED screens more efficiently. Deep reinforcement learning is being used to solve the OLED printing planning problem because it effectively uses historical data and is also real-time. This paper uses a modified TLO method to combine deep reinforcement learning for multi-objective optimization of OLED printing. Through experiments, the method is compared with the linear weighting method commonly used in multi-objective reinforcement learning, which is more effective in optimization.
Application of new power flow calculation in ship power system
Authors: Wang Wenxuan , WeifengShi
Published: March 2023

A relevant mathematical model regarding the calculation of tidal currents in ship power systems is constructed for the actual situation of ship power systems. The nodal is used to verify the applicability of its method in the ship power system. The algorithm program for the ship power system using radiation networks is prepared using MATLAB, and the accuracy of the algorithm is verified by an example. Verification of ship power flow calculation and its stability by Newton method,which will greatly help to improve the operation of the ship’s electric power system.
Multi-parameter infrared sensing method for operation state of power equipment
Authors: Song Qingwu , Fengjiang  , Li Chunpeng , Wang Yifan , Bao Zhengjun , Shao Shanrui
Published: March 2023

Aiming at the problems of difficult extraction and reconstruction of multi-parameter signals and poor perception effect of power equipment operation status, a multi-parameter infrared perception method of power equipment operation status is proposed. The multi-parameter (sound, light, electricity, vibration, heat, and environment) sensors of power equipment operation status are selected, the multi-parameter sensor integration framework is built based on the Internet of things technology, the multi-parameter sensors are effectively integrated, the power equipment operation status parameter signals are collected and reconstructed, the power equipment operation status perception model is built, the unsupervised classification and AR algorithm are introduced, and the reconstructed signals are fitted, to realize the infrared perception of power equipment operation status. The experimental data show that the integrity of power equipment operation state parameters and the accuracy of power equipment operation state perception obtained by the proposed method are higher, which proves that the proposed method has a good effect on power equipment operation state perception.
Study of a planar cascaded GEM TEPC with sealed chamber for the radiation detection in microdosimetry
Authors: Wang H.Y. , Hu C.C. , Ruan S.Z. , Qi H.R. , Jiao L.
Published: March 2023

In the field of radiation detection in microdosimetry, the
Tissue Equivalent Proportional Counters (TEPCs) are the key detector
options in determining the radiation quality. In this paper, two
different structures of TEPCs were introduced, and their electric
field uniformity and angular dependence were disscussed. A planar
cascaded GEM TEPC with sealed chamber was developed in the
laboratory and the general materials used in the detector were
tested for outgassing characteristics. The experimental results
showed that the polyether ether ketone (PEEK) had the lowest
outgassing rate among all tested materials and were selected as the
main assembly materials of the TEPC detector. The 241Am was
used as the built-in radioactive source for detector calibration,
and the detector gain characteristics were studied. The long-term
operating stability was tested at working pressure of 54.72 kPa,
with a gain consistency of better than 97.8% over 7 days
(168 hours) and relative gain variation less than 1% over 4 days
(96 hours).
Water Stress Index application to assess water scarcity of Lower Vu Gia - Thu Bon River Basin in Vietnam
Authors: Mai D T T , Vo D N , Tran N T V
Published: March 2023

The role of water security is the importance of sustainable development in a country. This study used the water stress index (WSI) to evaluate the status of water resources and water exploitation in the Vu Gia - Thu Bon river basin. In the study, the Vu Gia - Thu Bon river basin was divided into 15 areas to calculate the water stress index (WSI) through the following calculation: The water availability is calculated by the simulation software MIKE SHE; Demand water (domestic, industry, agriculture); Environmental water requirement (EWR) to maintain environmental stability of the river. The findings have shown that 1) There is WSI differences beetwen upper and lower Vu Gia Thu Bon; 2) In the downstream areas, WSI value is up to 4 in the dry season. WSI exceeds 1 times is during the period from April to June. Water scarcity becomes more serious than in the middle and upstream areas, especially, the exploitation area to supply water for domestic and industry in Da Nang city.
Validation of Hershfield probable maximum precipitation estimation using homogeneous region in Malaysia
Authors: Paramasivam R , Alias N E , Lokoman R M
Published: March 2023

Probable maximum precipitation (PMP) is used to design major hydraulic structures, such as dams and spillways, flood protection works, and nuclear power plants. Long observation data are required for PMP estimates using the Hershfield statistical approach. In Malaysia, the PMP calculated using state boundary is commonly used, but the estimated PMP values are close to historical maximums. Homogeneous regions are regions containing stations with similar rainfall characteristics. Therefore, homogeneous region boundaries could be used for PMP estimations. In this paper, 1-day rainfall data of more than 25 years for 161 stations in Peninsular Malaysia; were analysed to estimate the PMP for 1-day duration based on an appropriate frequency factor by considering homogeneous regions. Using PMP estimates, a generalised graph was prepared to show the spatial distribution of 1-day PMP. The 1-day PMP estimates in Peninsular Malaysia by considering state boundary, varied from 146 to 1364.7 mm and by considering the homogeneous regions, the 1-day PMP estimates varied from 208.5 to 2094 mm. Hence, the PMP considering homogeneous regions is considered more accurate and safe to be used in designs.
Rapid production of organic fertilizer using subcritical water treatment on waste biomass
Authors: Huzir N M , Hussin M H , Rosly M B , Amin A N R , Asmadi A A , Md Ali A H , Balasundram V , Yen L P , Goto M , Tamunaidu P
Published: March 2023

Waste biomass are highly valuable and have potential to be converted to organic fertilizers or compost. This is a great alternative to replace the uses of commercial chemical fertilizers towards sustainable agriculture. However, due to its complex molecular structure and high lignin content, it hinders full decomposition of these wastes into mature compost. Therefore, subcritical water (SCW) pre-treatment was studied to enhance the hydrolytic degradation of biomass waste such as rice straw, banana peel, and chicken feathers to be converted into mature compost within a shorter time. Validation on the maturity of the treated substrates and measurements of the level of phytotoxicity in the compost were studied based on the germination index (GI) of Japanese mustard seeds. Results showed that all treated substrates provided high GI of more than 60% at its optimum concentration which indicates the significant contribution of SCW pre-treatment to produce effective mature compost.
Route selection for road vehicle real-driving emissions test using GIS
Authors: Yusof N , Abas M A , Rohana N A , Mohd Perang M R
Published: March 2023

The European Commission has developed a Real-Driving Emissions (RDE) test for road vehicles that complies with the urban, rural and motorway criteria to ensure the exhaust emission produced could be accurately evaluated. Therefore, careful measures are taken in selecting the best routes to ensure the testing fulfils the targeted criteria. As there is no common method exist to select the testing route, analysis on the testing route selection was implemented using Geographic Information System (GIS) platform that is capable to deal with large vector data. Thus, the proposed framework facilitates the testing route selection process which is difficult to determine without a proper spatial analysis of network data. Specific route information comprises of road categories, route speed range and route classes were collected from the Open StreetMap (OSM) database. The generated route density and the topological route network structure were used to further analyse the suitability route as the requirement of Real-Driving Emissions test. As a result, five candidates of Real-Driving Emissions test route have been selected in Malaysia as a case study using GIS platform.
Low resistance electrical contacts to few-layered MoS2 by local pressurization
Authors: Manzanares-Negro Yolanda , Quan Jiamin , Rassekh Maedeh , Moaied Mohammed , Li Xiaoqin , Ares Pablo , Palacios Juan José , Gomez-Herrero Julio , Gomez-Navarro Cristina
Published: March 2023

The performance of electronic and optoelectronic devices is dominated by charge carrier injection through the metal–semiconductor contacts. Therefore, creating low-resistance electrical contacts is one of the most critical challenges in the development of devices based on new materials, particularly in the case of two-dimensional semiconductors. Herein, we report a strategy to reduce the contact resistance of MoS2 via local pressurization. We fabricated electrical contacts using an atomic force microscopy tip and applied variable pressure ranging from 0 to 25 GPa. By measuring the transverse electronic transport properties, we show that MoS2 undergoes a reversible semiconducting-metallic transition under pressure. Planar devices in field effect configuration with electrical contacts performed at pressures above ∼15 GPa show up to 30-fold reduced contact resistance and up to 25-fold improved field-effect mobility when compared to those measured at low pressure. Theoretical simulations show that this enhanced performance is due to improved charge injection to the MoS2 semiconductor channel through the metallic MoS2 phase obtained by pressurization. Our results suggest a novel strategy for realizing improved contacts to MoS2 devices by local pressurization and for exploring emergent phenomena under mechano-electric modulation.
Interlayer exciton polaritons in homobilayers of transition metal dichalcogenides
Authors: König Jonas K , Fitzgerald Jamie M , Hagel Joakim , Erkensten Daniel , Malic Ermin
Published: March 2023

Transition metal dichalcogenides integrated within a high-quality microcavity support well-defined exciton polaritons. While the role of intralayer excitons in 2D polaritonics is well studied, interlayer excitons have been largely ignored due to their weak oscillator strength. Using a microscopic and material-realistic Wannier–Hopfield model, we demonstrate that MoS2 homobilayers in a Fabry–Perot cavity support polaritons that exhibit a large interlayer exciton contribution, while remaining visible in linear optical spectra. Interestingly, with suitable tuning of the cavity length, the hybridization between intra- and interlayer excitons can be ‘unmixed’ due to the interaction with photons. We predict formation of polaritons where

>
90

% of the total excitonic contribution is stemming from the interlayer exciton. Furthermore, we explore the conditions on the tunneling strength and exciton energy landscape to push this to 100%. Despite the extremely weak oscillator strength of the underlying interlayer exciton, optical energy can be effectively fed into the polaritons once the critical coupling condition of balanced radiative and scattering decay channels is met. These findings have a wide relevance for fields ranging from nonlinear optoelectronic devices to Bose–Einstein condensation.
Study on the formation of arc plasma on the resistive wall liquid metal current limiter
Authors: LI Jinjin , DUAN Xiongying , HUANG Zhihui , XIE Weiying , LIAO Minfu , MA Chang , TAO Jia
Published: March 2023

Due to its significant attributes, the liquid metal current limiter (LMCL) is considered a new strategy for limiting short-circuit current in the power grid. A resistive wall liquid metal current limiter (RWLMCL) is designed to advance the starting current-limiting time. Experiments are performed to investigate the dynamic behaviors of liquid metal, and the influence of different currents on the liquid metal self-shrinkage effect is compared and analyzed. Furthermore, the liquid metal self-shrinkage effect is mathematically modeled, and the reason for the formation of arc plasma is obtained by simulation. The laws of arc plasma formation and the current transfer in the cavity are revealed, and the motion mechanisms are explained by physical principles. The simulations are in accordance with the test data. It is demonstrated that the sudden change of the current density at both ends of the wall causes the liquid metal to shrink and depress under the electromagnetic force, and the current starts to transfer from the liquid metal path to the wall resistance path. The RWLMCL can effectively advance the starting current-limiting time.
China’s grassland ecological compensation policy achieves win-win goals in Inner Mongolia
Authors: Zhou Ting , Yang Hongbo , Qiu Xiao , Sun Hailian , Song Peilin , Yang Wu
Published: March 2023

Approximately 10% of China’s grasslands are severely degraded and 90% of them are overgrazed. To protect ecosystems and boost human well-being, payments for ecosystem services programs have been implemented to generate win-win outcomes for pastoralists and the grasslands. Taking a payment for ecosystem services program in Damao County, Inner Mongolia as an example, our study evaluated the ecological effects of the Grassland Ecological Compensation Policy (GECP) based on historical trends at the pixel, parcel, and county levels. We also evaluated the socioeconomic effects of GECP using both objective and subjective well-being at the household level. Our results show that: (1) at the pixel level, the percentages of additionally increased Normalized Difference Vegetation Index (NDVI) and Net Primary Production (NPP) were 93.4% and 93.3% after GECP implementation, corresponding to the average additional effects of 0.08 and 58.99 g C/m2, respectively. At the parcel level, the GECP additionally increased NDVI between 0.02–0.17 (average of 0.08) and increased NPP between 28.36–115.15 (average of 60.30) g C/m2, respectively. At the county level, the GECP additionally increased grassland NDVI and NPP by 0.07 (∼3.4% annually) and 53.63 g C/m2 (∼4.5% annually) from 2008 to 2020, respectively; and (2) the GECP implementation significantly improved pastoralists’ objective well-being (P < 0.01) while the effects on subjective well-being indices were mixed. Our results also show that GECP effects on objective and subjective well-being significantly differ from households with large rangeland to those with small rangeland. We further discussed the experience, challenges, and opportunities of GECP. The long-term sustainability of GECP, particularly socioeconomic sustainability, still remains challenging and relies on guiding pastoralists to find alternative livelihoods. For future research and policy improvement, we call for the establishment of a better policy compensation mechanism that jointly considers the ecological effectiveness, economic efficiency, and social equity.
Optimal placement and sizing of custom power devices using APSO and JAYA optimization in radial distribution network
Authors: Munnu Mandeep Kumar , Choudhary Jayanti
Published: March 2023

With the recent advancement in the field of power electronics devices and an increasing number of nonlinear loads in the power system, the maintenance of good power quality at the consumers’ end is one of the major concerns of today’s power distribution systems. The introduction of a large number of power electronics devices in the system introduces power quality issues like voltage flicker, voltage distortions, harmonic distortions, voltage sag-swell, etc. Due to this, the maintenance of good power quality at the consumer end becomes a major challenge for distribution companies. The Custom power devices (CPD) have been used in the power system to address these issues and improve power quality. However, optimal placement and sizing of CPD is a challenge itself. In this paper, the optimal location and rating of CPD (STATCOM and APLC) have been determined using the APSO and JAYA optimization techniques,both of these techniques are known for their robustness. The main objective of the paper is to minimize the total harmonic distortion, total CPD size, harmonic transmission line loss, telephone influence factor, and motor load loss. Further, the performances of allocated CPD in controlling the voltage quality and reactive power are evaluated. The performanced from the APSO and JAYA algorithm on an IEEE-16 bus and 69 bus distribution system has been compared to each other.
Bioinspired smooth neuromorphic control for robotic arms
Authors: Polykretis Ioannis , Supic Lazar , Danielescu Andreea
Published: March 2023

Beyond providing accurate movements, achieving smooth motion trajectories is a long-standing goal of robotics control theory for arms aiming to replicate natural human movements. Drawing inspiration from biological agents, whose reaching control networks effortlessly give rise to smooth and precise movements, can simplify these control objectives for robot arms. Neuromorphic processors, which mimic the brain’s computational principles, are an ideal platform to approximate the accuracy and smoothness of biological controllers while maximizing their energy efficiency and robustness. However, the incompatibility of conventional control methods with neuromorphic hardware limits the computational efficiency and explainability of their existing adaptations. In contrast, the neuronal subnetworks underlying smooth and accurate reaching movements are effective, minimal, and inherently compatible with neuromorphic hardware. In this work, we emulate these networks with a biologically realistic spiking neural network for motor control on neuromorphic hardware. The proposed controller incorporates experimentally-identified short-term synaptic plasticity and specialized neurons that regulate sensory feedback gain to provide smooth and accurate joint control across a wide motion range. Concurrently, it preserves the minimal complexity of its biological counterpart and is directly deployable on Intel’s neuromorphic processor. Using the joint controller as a building block and inspired by joint coordination in human arms, we scaled up this approach to control real-world robot arms. The trajectories and smooth, bell-shaped velocity profiles of the resulting motions resembled those of humans, verifying the biological relevance of the controller. Notably, the method achieved state-of-the-art control performance while decreasing the motion jerk by 19% to improve motion smoothness. Overall, this work suggests that control solutions inspired by experimentally identified neuronal architectures can provide effective, neuromorphic-controlled robots.
The Evaluation of Worker Exposure to Airborne Silica Dust During Five OSHA Table I Construction Tasks
Authors: Cothern Emily J , Brazile William J , Autenrieth Daniel A
Published: March 2023

Fifty-one (51) personal silica air samples were collected over 13 days on 19 construction employees while they performed five different construction tasks found in the Occupational Safety and Health Administration’s (OSHA) respirable crystalline silica standard for construction, Table 1, which specifies engineering, work practice, and respiratory protection controls that employers can use in lieu of exposure monitoring to adhere to the standard. The average construction task time was 127 min (range: 18–240 min) with a mean respirable silica concentration of 85 μg m−3 (standard deviation [SD] = 176.2) for all 51 measured exposures. At least one OSHA-specified silica dust control measure was used during all 51 samples collected. The mean silica concentrations for the five tasks were: core drilling 11.2 μg m−3 (SD = 5.31 μg m−3), cutting with a walk-behind saw 126 μg m−3 (SD = 115 μg m−3), dowel drilling 99.9 μg m−3 (SD = 58.7 μg m−3), grinding 172 μg m−3 (SD = 145 μg m−3), and jackhammering 23.2 μg m−3 (SD = 5.19 μg m−3). Twenty four of 51 (47.1%) workers were exposed above the OSHA Action Level (AL) of 25 μg m−3 and 15 of 51 (29.4%) were exposed above the OSHA Permissible Exposure Limit (PEL) of 50 μg m−3 when exposures were extrapolated to an 8-h shift. When silica exposures were extrapolated to 4 h, 15 of 51 (29.4%) of workers sampled were exposed over the OSHA AL and 8 of 51 (15.7%) were exposed over the OSHA PEL. A total of 15 area airborne respirable crystalline silica samples were collected on days where the personal task-based silica samples were taken, with an average sampling time of 187 min. Of the 15 area respirable crystalline silica samples, only four were greater than the laboratory reporting limit of 5 μg m−3. The four area silica samples with reportable concentrations revealed background silica concentrations of 23 μg m−3, 5 μg m−3, 40 μg m−3, and 100 μg m−3. Odds ratios were used to analyze the apparent association between dichotomous background construction site exposures to respirable crystalline silica (detectable or not detectable), and personal exposure category (over or not over the OSHA AL and PEL) when exposure times were extrapolated to 8 h. The associations were strongly positive and significant between detectable background exposures and personal overexposures for workers conducting the five Table 1 tasks with engineering controls in place. The results of this study suggest that exposure to hazardous levels of respirable crystalline silica may be present even when OSHA-specified engineering controls are implemented. The current study findings also suggest that background construction site silica concentrations may potentially cause task-based overexposures, even when the OSHA Table 1 control methods have been put in place.
A comprehensive review of bioinformatics tools for chromatin loop calling
Authors: Liu Li , Han Kaiyuan , Sun Huimin , Han Lu , Gao Dong , Xi Qilemuge , Zhang Lirong , Lin Hao
Published: March 2023

Precisely calling chromatin loops has profound implications for further analysis of gene regulation and disease mechanisms. Technological advances in chromatin conformation capture (3C) assays make it possible to identify chromatin loops in the genome. However, a variety of experimental protocols have resulted in different levels of biases, which require distinct methods to call true loops from the background. Although many bioinformatics tools have been developed to address this problem, there is still a lack of special introduction to loop-calling algorithms. This review provides an overview of the loop-calling tools for various 3C-based techniques. We first discuss the background biases produced by different experimental techniques and the denoising algorithms. Then, the completeness and priority of each tool are categorized and summarized according to the data source of application. The summary of these works can help researchers select the most appropriate method to call loops and further perform downstream analysis. In addition, this survey is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.
ProFeatMap: a highly customizable tool for 2D feature representation of protein sets
Authors: Bich Goran , Monsellier Elodie , Travé Gilles , Nominé Yves
Published: March 2023

Motivation

Studies of sets of proteins are a central point in biology. In particular, the application of omics in the last decades has generated lists of several hundreds or thousands of proteins or genes. However, these lists are often not inspected globally, possibly due to the lack of tools capable of simultaneously visualizing the feature architectures of a large number of proteins.

Results

Here, we present ProFeatMap, an intuitive Python-based website. For a given set of proteins, it allows to display features such as domains, repeats, disorder or post-translational modifications and their organization along the sequences, into a highly customizable 2D map. Starting from a user-defined protein list of UniProt accession codes, ProFeatMap extracts the most important annotated features available for each protein from one of the well-established databases such as Uniprot or InterPro, allocates shapes and colors, potentially depending on quantitative or qualitative data and sorts the protein list based on homologous feature content. The resulting publication-quality map allows even large protein families to be explored, and to classify them based on shared features. It can help to gain insights, for example, feature redundancy or feature pattern, that were previously overlooked. ProFeatMap is freely available on the web at: https://profeatmap.pythonanywhere.com/.

Availability and implementation

Source code is freely accessible at https://github.com/profeatmap/ProFeatMap under the GPL license.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
TopEnzyme: a framework and database for structural coverage of the functional enzyme space
Authors: van der Weg Karel J , Gohlke Holger
Published: March 2023

Motivation

TopEnzyme is a database of structural enzyme models created with TopModel and is linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database to provide an overview of structural coverage of the functional enzyme space for over 200 000 enzyme models. It allows the user to quickly obtain representative structural models for 60% of all known enzyme functions.

Results

We assessed the models with TopScore and contributed 9039 good-quality and 1297 high-quality structures. Furthermore, we compared these models to AlphaFold2 models with TopScore and found that the TopScore differs only by 0.04 on average in favor of AlphaFold2. We tested TopModel and AlphaFold2 for targets not seen in the respective training databases and found that both methods create qualitatively similar structures. When no experimental structures are available, this database will facilitate quick access to structural models across the currently most extensive structural coverage of the functional enzyme space within Swiss-Prot.

Availability and implementation

We provide a full web interface to the database at https://cpclab.uni-duesseldorf.de/topenzyme/.
A Bayesian approach to estimating COVID-19 incidence and infection fatality rates
Authors: Slater Justin J , Bansal Aiyush , Campbell Harlan , Rosenthal Jeffrey S , Gustafson Paul , Brown Patrick E
Published: March 2023

Naive estimates of incidence and infection fatality rates (IFR) of coronavirus disease 2019 suffer from a variety of biases, many of which relate to preferential testing. This has motivated epidemiologists from around the globe to conduct serosurveys that measure the immunity of individuals by testing for the presence of SARS-CoV-2 antibodies in the blood. These quantitative measures (titer values) are then used as a proxy for previous or current infection. However, statistical methods that use this data to its full potential have yet to be developed. Previous researchers have discretized these continuous values, discarding potentially useful information. In this article, we demonstrate how multivariate mixture models can be used in combination with post-stratification to estimate cumulative incidence and IFR in an approximate Bayesian framework without discretization. In doing so, we account for uncertainty from both the estimated number of infections and incomplete deaths data to provide estimates of IFR. This method is demonstrated using data from the Action to Beat Coronavirus erosurvey in Canada.
NanoString analysis of mycosis fungoides reveals individual molecular identity
Authors: Alonso-Alonso Ruth , Rodríguez Marta , García-Díaz Nuria , Tomás-Roca Laura , Borregón Jennifer  , Cabezuelo-Rodríguez Marta , Rebollo-González Marcos , Gallego-Manzano Luis , Cereceda Laura , Rodriguez-Pinilla Socorro María , Córdoba Raúl , Fernando García Juan , Torre-Castro Juan , García-Álvarez Carmen M , del Mar Onteniente Gomis María , Rivera-Díaz Raquel , Rodriguez-Peralto José Luis , Vaqué José Pedro , Ortiz-Romero Pablo Luis , Piris Miguel Á
Published: March 2023

Gene profiling using a customized NanoString platform can be applied to routine mycosis fungoides (MF) samples, revealing their specific molecular features. This study shows that MF samples carry a signature derived from individual molecular features found in consecutive biopsies.
Localization of depressive symptoms based on focal brain lesions: adding ‘resilience’ to ‘risk’
Authors: Klingbeil Julian , Saur Dorothee
Published: March 2023

This scientific commentary refers to ‘Large-scale lesion symptom mapping of depression identifies brain regions for risk and resilience’ by Trapp et al. (https://doi.org/10.1093/brain/awac361).
A new approach to digitized cognitive monitoring: validity of the SelfCog in Huntington’s disease
Authors: Lunven Marine , Hernandez Dominguez Karen , Youssov Katia , Hamet Bagnou Jennifer , Fliss Rafika , Vandendriessche Henri , Bapst Blanche , Morgado Graça , Remy Philippe , Schubert Robin , Reilmann Ralf , Busse Monica , Craufurd David , Massart Renaud , Rosser Anne , Bachoud-Lévi Anne-Catherine
Published: March 2023

Cognitive deficits represent a hallmark of neurodegenerative diseases, but evaluating their progression is complex. Most current evaluations involve lengthy paper-and-pencil tasks which are subject to learning effects dependent on the mode of response (motor or verbal), the countries’ language or the examiners. To address these limitations, we hypothesized that applying neuroscience principles may offer a fruitful alternative. We thus developed the SelfCog, a digitized battery that tests motor, executive, visuospatial, language and memory functions in 15 min. All cognitive functions are tested according to the same paradigm, and a randomization algorithm provides a new test at each assessment with a constant level of difficulty.

Here, we assessed its validity, reliability and sensitivity to detect decline in early-stage Huntington’s disease in a prospective and international multilingual study (France, the UK and Germany). Fifty-one out of 85 participants with Huntington’s disease and 40 of 52 healthy controls included at baseline were followed up for 1 year. Assessments included a comprehensive clinical assessment battery including currently standard cognitive assessments alongside the SelfCog. We estimated associations between each of the clinical assessments and SelfCog using Spearman’s correlation and proneness to retest effects and sensitivity to decline through linear mixed models. Longitudinal effect sizes were estimated for each cognitive score. Voxel-based morphometry and tract-based spatial statistics analyses were conducted to assess the consistency between performance on the SelfCog and MRI 3D-T1 and diffusion-weighted imaging in a subgroup that underwent MRI at baseline and after 12 months.

The SelfCog detected the decline of patients with Huntington’s disease in a 1-year follow-up period with satisfactory psychometric properties. Huntington’s disease patients are correctly differentiated from controls. The SelfCog showed larger effect sizes than the classical cognitive assessments. Its scores were associated with grey and white matter damage at baseline and over 1 year. Given its good performance in longitudinal analyses of the Huntington’s disease cohort, it should likely become a very useful tool for measuring cognition in Huntington’s disease in the future. It highlights the value of moving the field along the neuroscience principles and eventually applying them to the evaluation of all neurodegenerative diseases.
Reduced likelihood of the Poggendorff illusion in cerebellar strokes: a clinical and neuroimaging study
Authors: Higashiyama Yuichi , Kuroki Miho , Kudo Yosuke , Hamada Tomoya , Morihara Keisuke , Saito Asami , Miyaji Yosuke , Kimura Katsuo , Joki Hideto , Kishida Hitaru , Doi Hiroshi , Ueda Naohisa , Takeuchi Hideyuki , Johkura Ken , Tanaka Fumiaki
Published: March 2023

This study aimed to test our hypothesis that the cerebellum plays an important role in the generation of the optical-geometric illusion known as the Poggendorff illusion, the mechanism of which has been explained by accumulated experience with natural scene geometry. A total of 79 participants, comprising 28 patients with isolated cerebellar stroke, 27 patients with isolated cerebral stroke and 24 healthy controls, performed Poggendorff illusion tasks and 2 different control tasks. We also investigated core brain regions underpinning changes in the experience of the illusion effect using multivariate lesion-symptom mapping. Our results indicate that patients with isolated cerebellar stroke were significantly less likely to experience the Poggendorff illusion effect than patients with isolated cerebral stroke or healthy controls (74.6, 90.5 and 89.8%, respectively; F(2,76) = 6.675, P = 0.002). However, there were no inter-group differences in the control tasks. Lesion-symptom mapping analysis revealed that the brain lesions associated with the reduced frequency of the Poggendorff illusion effect were mainly centred on the right posteromedial cerebellar region, including the right lobules VI, VII, VIII, IX and Crus II. Our findings demonstrated, for the first time, that patients with cerebellar damage were significantly less likely to experience the Poggendorff illusion effect and that right posteromedial cerebellar lesions played an important role in this effect. These results provide new insight into alterations of a geometric illusion effect in patients with cerebellar disorders and pave the way for future clinical use of the illusion task to detect cerebellar abnormalities.
A novel CLDN1 variant identified in a case of ILVASC with sparse curly hair
Authors: Cai Liangqi , Lin Zhimiao , Wang Huijun
Published: March 2023

ILVASC (ichthyosis, leukocyte vacuoles, alopecia and sclerosing cholangitis) is an extremely rare autosomal recessive syndromic ichthyosis. Herein we report on a Chinese ILVASC case with a novel phenotype of curly hair caused by a previously unrecorded homozygous mutation in CLDN1.
Clinical and experimental treatment of allergic asthma with an emphasis on allergen immunotherapy and its mechanisms
Authors: Fiala Scott , Fleit Howard B
Published: March 2023

Allergen immunotherapy (AIT) is currently the only form of treatment that modifies allergic asthma. Pharmacotherapy alone seeks to control the symptoms of allergic asthma, allergic rhinitis, and other atopic conditions. In contrast, AIT can induce long-term physiological modifications through the immune system. AIT enables individuals to live improved lives many years after treatment ends, where they are desensitized to the allergen(s) used or no longer have significant allergic reactions upon allergen provocation. The leading forms of treatment with AIT involve injections of allergen extracts with increasing doses via the subcutaneous route or drops/tablets via the sublingual route for several years. Since the initial attempts at this treatment as early as 1911 by Leonard Noon, the mechanisms by which AIT operates remain unclear. This literature-based review provides the primary care practitioner with a current understanding of the mechanisms of AIT, including its treatment safety, protocols, and long-term efficacy. The primary mechanisms underlying AIT include changes in immunoglobulin classes (IgA, IgE, and IgG), immunosuppressive regulatory T-cell induction, helper T cell type 2 to helper T cell type 1 cell/cytokine profile shifts, decreased early-phase reaction activity and mediators, and increased production of IL-10, IL-35, TGF-β, and IFN-γ. Using the databases PubMed and Embase, a selective literature search was conducted searching for English, full-text, reviews published between 2015 and 2022 using the keywords (with wildcards) “allerg*,” “immunotherap*,” “mechanis*,” and “asthma.” Among the cited references, additional references were identified using a manual search.
Autoimmune/inflammatory syndrome induced by adjuvants (ASIA): past, present, and future implications
Authors: Seida Isa , Alrais Mahmoud , Seida Ravend , Alwani Abdulkarim , Kiyak Zeynep , Elsalti Abdulrahman , Nil Esirgun Sevval , Abali Tunahan , Mahroum Naim
Published: March 2023

Adjuvants, as the name indicates, are adjoined material aimed to assist in functioning as when added to vaccines they are meant to boost the effect and strongly stimulate the immune system. The response of the immune system can be unpredictable, and the autoimmune/inflammatory syndrome induced by adjuvants (ASIA) was developed to address possible adverse reactions of an autoimmune and inflammatory type that may be caused by adjuvants. While ASIA, as a syndrome, was coined and defined in 2011; reports describing patients with vague and nonspecific clinical symptoms following vaccinations appeared much earlier. In other words, ASIA came to define, arrange, and unite the variety of symptoms, related to autoimmunity, caused not by the vaccine itself, rather by the adjuvant part of the vaccine such as aluminum, among others. Accordingly, the introduction of ASIA enabled better understanding, proper diagnosis, and early treatment of the disorder. Furthermore, ASIA was shown to be associated with almost all body systems and various rheumatic and autoimmune diseases such as systemic lupus erythematosus, antiphospholipid syndrome, and systemic sclerosis. In addition, the correlation between COVID-19 and ASIA was noticed during the pandemic. In this review, we summarized the reported effects of adjuvants and medical literature before and after ASIA was defined, the several ways ASIA can manifest and impact different systems of the body, and the incidences of ASIA during the COVID-19 pandemic. It is important to clarify, that vaccines are among, if not the, most effective means of fighting infectious diseases however, we believe that vaccines manufacturing is not above criticism, particularly when it comes to added substances possessing a risk of side effects.
Respiratory response to an odor throughout development in rats
Authors: Boulanger-Bertolus Julie , Courtiol Emmanuelle , Buonviso Nathalie , Mouly Anne-Marie
Published: March 2023

Odor-induced sniffing has proven to be a useful behavioral readout for assessing olfactory performance in adult rats. However, little is known about how the respiratory response changes throughout ontogeny. Thus, this study aimed at characterizing respiratory response to an odor in rats using paradigms suitable to infants, juveniles, and adults. We first analyzed the respiratory response to a neutral, novel odor. Then the value of the odor was changed either through its repeated presentation (odor habituation), or its association with a foot-shock (odor fear). In the habituation task, we found that the first presentation of the novel odor induced a clear sniffing response at all 3 ages, but the peak respiratory frequency was higher in adults than in juveniles and infants. When the odor was presented repeatedly, the sniffing response gradually faded and the younger the animal, the faster the fading of the response. In the fear conditioning task, the odor induced an increase in respiratory rate that persisted until the end of the session in adults and infants, but not in juveniles. In another group for which the odor was explicitly unpaired with the foot-shock, the respiratory response to the odor did not last as long over the session than in the paired condition at all 3 ages. Finally, we observed that shock delivery induced a similar respiratory response at the 3 investigated ages in the paired and unpaired conditions. Collectively, these data show that the respiratory response constitutes a faithful index to assess rat’s olfactory abilities throughout ontogeny.
Successful recovery from acute decompensated heart failure associated with left ventricular diastolic dysfunction and atrial fibrillation by urgent radiofrequency catheter ablation using mechanical haemodynamic support: a case report
Authors: Todoroki Wataru , Takemoto Masao , Sakai Togo , Tsuchihashi Takuya
Published: March 2023

Background

Atrial fibrillation (AF) and heart failure (HF) frequently coexist, and AF is associated with an exacerbation of HF. Catheter ablation (CA) of AF has proved to be an established treatment for patients with HF associated with AF. Ordinarily, CA of AF is an elective procedure.

Case summary

We present a 68-year-old male patient with chief complaints of palpitation and general malaise, and appetite loss, associated with acute decompensated HF (ADHF) resulting from drug-refractory AF and left ventricular (LV) diastolic dysfunction (DD). He underwent an urgent CA therapy for AF under mechanical support via intra-aortic balloon pumping (IABP), which dramatically improved his haemodynamic status and clinical outcomes.

Discussion

Despite their shared common risk factors, AF, HF, and LVDD subtypes exacerbate one another and create a vicious triad of AF, HF, and LVDD, developing into ADHF. Thus, it is important to break this vicious cycle using non-invasive and/or invasive strategies. Performing an urgent CA of AF for ADHF may be a challenging strategy, which has not been well established. However, urgent CA using mechanical haemodynamic support, including IABP, might be an effective and feasible strategy in patients with medically intractable, severe ADHF associated with LVDD and drug-refractory AF as in the present case. Haemodynamically unstable patients, as in the present case, require prompt and careful monitoring of their clinical condition. Thus, it may also be important to consider the appropriate timing for providing optimal treatment in these patients.