bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating Explainability Methods in Recurrent Neural Network Architectures for Financial Time Series Data
Authors: Freeborough Warren , van Zyl Terence
Published: January 2022

Statistical methods were traditionally primarily used for time series forecasting. However, new hybrid methods demonstrate competitive accuracy, leading to increased machine-learning-based methodologies in the financial sector. However, very little development has been seen in explainable AI (XAI) for financial time series prediction, with a growing mandate for explainable systems. This study aims to determine if the existing XAI methodology is transferable to the context of financial time series prediction. Four popular methods, namely, ablation, permutation, added noise, and integrated gradients, were applied to a recurrent neural network (RNN), long short-term memory (LSTM), and a gated recurrent unit (GRU) network trained on S&P 500 stocks data to determine the importance of features, individual data points, and specific cells in each architecture. The explainability analysis revealed that GRU displayed the most significant ability to retain long-term information, while the LSTM disregarded most of the given input and instead showed the most notable granularity to the considered inputs. Lastly, the RNN displayed features indicative of no long-term memory retention. The applied XAI methods produced complementary results, reinforcing paradigms on significant differences in how different architectures predict. The results show that these methods are transferable in the financial forecasting sector, but a more sophisticated hybrid prediction system requires further confirmation.
An In-House Cone-Beam Tomographic Reconstruction Package for Laboratory X-ray Phase-Contrast Imaging
Authors: Hofmann Jürgen , Zboray Robert
Published: January 2022

Phase-contrast, and in general, multi-modal, X-ray micro-tomography is proven to be very useful for low-density, low-attention samples enabling much better contrast than its attenuation-based pendant. Therefore, it is increasingly applied in bio- and life sciences primarily dealing with such samples. Although there is a plethora of literature regarding phase-retrieval algorithms, access to implementations of those algorithms is relatively limited and very few packages combining phase-retrieval methods with the full tomographic reconstruction pipeline are available. This is especially the case for laboratory-based phase-contrast imaging typically featuring cone-beam geometry. We present here an in-house cone-beam tomographic reconstruction package for laboratory X-ray phase-contrast imaging. It covers different phase-contrast techniques and phase retrieval methods. The paper explains their implementation and integration in the filtered back projection chain. Their functionality and efficiency will be demonstrated through applications on a few dedicated samples.
Position Sensing with a Compact 0.1 THz Amplitude Modulated Source
Authors: Krmac Tadej , Švigelj Andrej , Trontelj Janez
Published: January 2022

Position determination is an important manufacturing process in many modern industries. The objective of this paper is to present an affordable measurement system that can replace optical position measurement with a laser beam in an opaque environment that prevents the laser beam from penetrating through the fog of gases or other materials that are opaque to optical light. THz waves are a good example of replacing a laser beam, as shown in this article. It is known that THz rays can penetrate fabrics, wood, Styrofoam, etc. The triangulation method using an amplitude modulated THz source proved to be a cost-effective solution for position determination in opaque environments.
Tantalum Alloy Welding: Does the Thermal Cycle Influence the Microstructure?
Authors: Bernardo Sánchez Antonio , Presno Vélez Álvaro , Fernández-Columbié Tomás , Rodríguez-Gonzalez Isnel , Suárez Torres Ledennis , Álvarez de Prado Laura , Menéndez Fernández Marta
Published: January 2022

The aim of the present work is to verify the microstructural behavior of a B 521 tantalum alloy UNS Grade R05200 after welding, in relation to the welding thermal cycle. The joint design was a 1.5 mm thickness circumferential butt welding, on a 32 mm outside diameter pipe, welded in 1 G position (horizontal, flat, and rotating). The chosen welding process was gas tungsten arc welding (GTAW). The microstructural analysis showed the presence of coarse, dendritic-columnar structures, as well as a hexagonal cell, with no cracks noted. Hardness tests showed an increase in hardness, from 120 HV to 425 HV, in the heat-affected zone. Through finite element methods, the behavior of the temperature field was estimated and compared.
Valorisation of Spent Grain from Malt Whisky in the Spelt Pasta Formulation: Modelling and Optimization Study
Authors: Chetrariu Ancuța , Dabija Adriana
Published: January 2022

Although durum wheat flour is conventionally used to produce pasta, in this study, emphasis was placed on the use of spelt flour in the formulation of the pasta recipe, with the replacement with spent grain obtained from distilleries for its content of fiber and protein. D-optimal design was used to optimize the influence of spent grain addition for the quality attributes of spelt pasta. In order to optimize the spelt pasta matrix, the spent grain content was varied (5%, 10%, 15%, and 20%) so that all responses were optimized (maximize cohesiveness, fracturability, proteins, total dietary fiber, total phenolic content, and antioxidant activity, minimize cooking loss, in-range firmness, and color paste). The optimal addition of spent grain in the spelt pasta recipe was 11.70%, yielding values with differences of less than 5% from the values predicted by the model and producing finished products with good nutritional properties without negative consequences on quality. Spent grain is a valuable byproduct that deserves to be used for fortification in order to obtain pro-health food. This study presents a formulation of spelt pasta with the addition of spent grain using mathematical modeling and statistical optimization.
Intelligent Prediction of Prestressed Steel Structure Construction Safety Based on BP Neural Network
Authors: Zhu Haoliang , Wang Yousong
Published: January 2022

In the construction process of a prestressed steel structure, it is a point of research interest to obtain the safety state of the structure according to the design parameters and working conditions of the structure. The intelligent prediction of structural construction safety provides the basis for safety control. This study proposes an intelligent prediction method of structural construction safety based on a back propagation (BP) neural network. Firstly, the correlation mechanism of structural construction safety performance parameters is established, which involves structural design parameters and mechanical parameters. According to the basic principle of a BP neural network, the relationship between design parameters and mechanical parameters is captured. The virtual model of a structure construction process is established based on digital twins (DTs). The DTs and BP neural network are combined to form a structural safety intelligent prediction framework and theoretical method, setting working conditions in a twin model to obtain mechanical parameters. Mechanical parameters are intelligently predicted by design parameters in neural networks. The safety performance of structure construction is evaluated according to mechanical parameters. Finally, the intelligent prediction method is applied to the construction process of string beam. Based on DTs and BP neural network, the intelligent analysis of structural construction safety is carried out. This provides a reliable basis for safety control. The feasibility of this research method is verified by comparing the predicted results of the theoretical method with the measured data on site.
Ontology-Based Methodology for Knowledge Acquisition from Groupware
Authors: Uwasomba Chukwudi Festus , Lee Yunli , Yusoff Zaharin , Chin Teck Min
Published: January 2022

Groupware exist, and they contain expertise knowledge (explicit and tacit) that is primarily for solving problems, and it is collected on-the-job through virtual teams; such knowledge should be harvested. A system to acquire on-the-job knowledge of experts from groupware in view of the enrichment of intelligent agents has become one of the important technologies that is very much in demand in the field of knowledge technology, especially in this era of textual data explosion including due to the ever-increasing remote work culture. Before acquiring new knowledge from sentences in groupware into an existing ontology, it is vital to process the groupware discussions to recognise concepts (especially new ones), as well as to find the appropriate mappings between the said concepts and the destination ontology. There are several mapping procedures in the literature, but these have been formulated on the basis of mapping two or more independent ontologies using concept-similarities and it requires a significant amount of computation. With the goal of lowering computational complexities, identification difficulties, and complications of insertion (hooking) of a concept into an existing ontology, this paper proposes: (1) an ontology-based framework with changeable modules to harvest knowledge from groupware discussions; and (2) a facts enrichment approach (FEA) for the identification of new concepts and the insertion/hooking of new concepts from sentences into an existing ontology. This takes into consideration the notions of equality, similarity, and equivalence of concepts. This unique approach can be implemented on any platform of choice using current or newly constructed modules that can be constantly revised with enhanced sophistication or extensions. In general, textual data is taken and analysed in view of the creation of an ontology that can be utilised to power intelligent agents. The complete architecture of the framework is provided and the evaluation of the results reveal that the proposed methodology performs significantly better compared to the universally recommended thresholds as well as the existing works. Our technique shows a notable high improvement on the F1 score that measures precision and recall. In terms of future work, the study recommends the development of algorithms to fully automate the framework as well as for harvesting tacit knowledge from groupware.
Black Carbon in Bulgaria—Observed and Modelled Concentrations in Two Cities for Two Months
Authors: Hristova Elena , Georgieva Emilia , Veleva Blagorodka , Neykova Nadya , Naydenova Stela , Gonsalvesh-Musakova Lenia , Neykova Rozeta , Petrov Anton
Published: January 2022

Black carbon (BC) is one of the particulate matter (PM) components that both affects human health and contributes to climate change. In this study, we present the preliminary results of the investigation of BC concentrations in PM2.5 for two Bulgarian cites—Sofia and Burgas. The parallel PM2.5 samplings were organized in October 2020 and January 2021. The Multi-Wavelength Absorption Black carbon Instrument (MABI) was used for the evaluation of light-absorbing carbon. In addition, we compared the observed BC and PM2.5 values to modelled ones and analyzed the spatial distribution over the country, using data from advanced operational chemical transport models (CTM)—the European (regional) air quality system established at the Copernicus Atmosphere Monitoring Service (CAMS). Generally, the observed BC and PM2.5 values were higher in January than in October for both cities. In October, the model underestimated the observed BC concentrations (Sofia—2.44 μg.m−3, Burgas—1.63 μg.m−3) by 17% and 51%. In January 2021, the observed monthly BC concentrations were higher (Sofia—3.62 μg.m−3, Burgas—1.75 μg.m−3), and the bias of the model was less than that in October, with an overestimation of 22% for Sofia. The relative bias for PM2.5 in October (17% for Sofia and −6% for Burgas) was less than the relative bias in January when the model underestimated PM2.5 monthly mean concentrations by 20% (Sofia) and 42% (Burgas). In addition, we also elaborate on two episodes with high observed BC concentrations in view of the meteorological conditions.
Estimating Urban Wind Speeds and Wind Power Potentials Based on Machine Learning with City Fast Fluid Dynamics Training Data
Authors: Mortezazadeh Mohammad , Zou Jiwei , Hosseini Mirata , Yang Senwen , Wang Liangzhu
Published: January 2022

Wind power is known as a major renewable and eco-friendly power generation source. As a clean and cost-effective energy source, wind power utilization has grown rapidly worldwide. A roof-mounted wind turbine is a wind power system that lowers energy transmission costs and benefits from wind power potential in urban areas. However, predicting wind power potential is a complex problem because of unpredictable wind patterns, particularly in urban areas. In this study, by using computational fluid dynamics (CFD) and the concept of nondimensionality, with the help of machine learning techniques, we demonstrate a new method for predicting the wind power potential of a cluster of roof-mounted wind turbines over an actual urban area in Montreal, Canada. CFD simulations are achieved using city fast fluid dynamics (CityFFD), developed for urban microclimate simulations. The random forest model trains data generated by CityFFD for wind prediction. The accuracy of CityFFD is investigated by modeling an actual urban area and comparing the numerical data with measured data from a local weather station. The proposed technique is demonstrated by estimating the wind power potential in the downtown area with more than 250 buildings for a long-term period (2020–2049).
The Intraseasonal Variations of the Leading Mode of Summer Precipitation Anomalies in Meiyu Area of East Asia
Authors: Jia Zikang , Zheng Zhihai , Feng Guolin , Tong Mingjun
Published: January 2022

The intraseasonal variations of summer precipitation anomalies in the Meiyu area of East Asia are analyzed by applying a combined empirical orthogonal function (CEOF) of the latest meteorological reanalysis data ERA5 of European Center for Medium-Range Weather Forecasts for the period from 1991 to 2020, and the circulation structures and sources of variability of CEOF are also investigated. The first mode of the intraseasonal variations shows an in-phase pattern over the Meiyu area in June, July, and August, accounting for 22.2% of the total variance in the intraseasonal variations of summer precipitation anomalies. The positive (negative) CEOF1 is accompanied by the negative (positive) East Asia/Pacific pattern, including strong westerly wind anomalies in the upper troposphere and southwest monsoon in the lower troposphere, and the Western Pacific Subtropical High extending westward and its ridge line slightly south. The positive CEOF1 is preceded by decay of El Niño episodes, including the abnormal warm sea surface temperature anomalies (SSTAs) in the equatorial Central-Eastern Pacific in spring and warm SSTAs in the equatorial Indian Ocean in summer. The second mode shows an opposite precipitation anomaly in June and July, and the distribution in August is not significant. The corresponding geopotential height circulation of positive CEOF2 shows the large negative anomaly in the region north of 40° N and a positive anomaly over Japan in June, whereas the pattern reverses in July. At the same time, there is a radical reversion from abnormal eastly to westly wind in the upper troposphere. The structure of CEOF2 is somewhat induced by local SSTAs over the Northern Indian Ocean and South China Sea.
High-Resolution Measurements of SO2, HNO3 and HCl at the Urban Environment of Athens, Greece: Levels, Variability and Gas to Particle Partitioning
Authors: Liakakou Eleni , Fourtziou Luciana , Paraskevopoulou Despina , Speyer Orestis , Lianou Maria , Grivas Georgios , Myriokefalitakis Stelios , Mihalopoulos Nikolaos
Published: January 2022

High-resolution measurements of sulfur dioxide (SO2), nitric acid (HNO3), and hydrochloric acid (HCl) were conducted in Athens, Greece, from 2014 to 2016 via a wet rotating annular denuder system paired with an ion chromatograph. Decreased mean annual levels of SO2 and HNO3 (equal to 3.3 ± 4.8 μg m−3 and 0.7 ± 0.6 μg m−3, respectively) were observed relative to the past, whereas for HCl (mean of 0.4 μg m−3 ) no such comparison was possible as the past measurements are very scarce. Regional and local emission sources regulated the SO2 levels and contributed to both the December and the July maxima of 6.6 μg m−3 and 5.5 μg m−3, respectively. Similarly, the significant enhancement at noon and during the winter nighttime was due to transported SO2 and residential heating, respectively. The oxidation of NO2 by OH radicals and the heterogeneous reactions of HNO3 on sea salt seemed to drive the HNO3 and HCl formation, respectively, whereas nighttime biomass burning affected only the former by almost 50%. During summer, the sulfate anions dominated over the SO2, in contrast to the chloride and nitrate ions that prevailed during the winter and were linked to the aerosol acidity that influences their lifetime as well as their impact on ecosystems.
A Numerical Simulation of the “1907” Kaiyuan Tornado Weather Process in Liaoning, Northeast China
Authors: Wang Yiping , Wang Tong , Yang Pu , Xue Wei
Published: January 2022

From 17:00 to 18:00 local standard time (LST) on 3 July 2019, a rare strong tornado occurred in Kaiyuan, Liaoning Province, northeast China. NCEP/NCAR 0.25° × 0.25° reanalysis data and WRF4.0 numerical prediction models were used to carry out the numerical simulation. Double nesting was adopted, and the horizontal grid distance was 9 km by 3 km. Based on the observation data of China meteorological observation stations, surface and upper charts, Doppler radar data, Himawari(HMW)-8 satellite images and numerical simulation results, the mesoscale structure and mechanism of the tornado were studied. The results show that: (1) At the northwest edge of the subtropical high, and the northeast cold vortex located in Northeast China, when the transverse trough moves southward, cold air is supplied continuously. Under the joint influence of the surface northeast cyclone, these are the main synoptic features of the tornado; (2) The northeast cold vortex cloud system was located at the junction of Heilongjiang and Jilin Provinces, and a squall line cloud system is formed. The tornado occurred at the tail of the squall line, and the strongest echo reached 65 dBZ. A mesocyclone, a 20 km northwest–southeast convergence belt, V-shaped gap, echo overhang structure and tornado vortex feature (TVS) were detected by the Doppler radar; (3) Before the tornado occurred, dry and cold air intruded from the northwest of the cold vortex, and a water vapor convergence zone appeared south of the squall line. The water vapor saturation zone with 80% relative humidity in northeast China was concentrated at 700 hPa, and the 20% dry column dropped down to 500 hPa between 115 and 124° E from the west. On the 850 hPa physical fields, there was a −20 × 10−5 s−1 convergence zone, and a 16 × 10−5 s−1 divergence belt appeared south and north of the squall line. A negative vorticity belt and a positive vorticity belt appeared south and north of the squall line, respectively. Kaiyuan is located at the smallest vertical shear, which is the junction place of three large vertical shear belts; (4) After 10:00 LST, the westerly wind 20 (10) m·s−1 dropped to 400 (800) hPa between 126 and 127° E. The northerly gale at 300 hPa north of 45° N moved southward. The rising center of the low level at 17:00 LST at approximately 45° N moved southward, and a sinking center appeared above it; (5) Several pairs of positive and negative vorticity columns formed between the lower troposphere and the place where the tornado occurred. There was convective instability at the lower level. CAPE increased, 0–3 km vertical wind shear increased, and LCL decreased remarkably during the afternoon.
Exploring the Impact of Planetary Boundary Layer Schemes on Rainfall Forecasts for Typhoon Mujigae, 2015
Authors: Shen Wenqi , Lu Zebin , Ye Guilin , Zhang Yu , Chen Siqi , Xu Jianjun
Published: January 2022

Sensitivity experiments were conducted on Typhoon Mujigae, which occurred in 2015, wherein the Weather Research and Forecasting Advanced Research (WRF-ARW) model was used to select two local and two nonlocal planetary boundary layer (PBL) parameterization schemes: the quasi-normal scale elimination (QNSE) and Mellor–Yamada–Janjic (MYJ) schemes, and the Yonsei University (YSU) and medium-range forecast (MRF) schemes, respectively. The differences in rainfall response in the typhoon’s inner core and outer region were evaluated by comparing the anomaly rainfall distribution, heat transmission, and mixing processes in the boundary layer among the PBL schemes. The results show that the simulated rainfall in typhoon Mujigae has large uncertainty among the PBL schemes and a significant difference between the inner and outer regions. Compared with the observation, the simulated rainfall was significantly higher in the inner core and slightly lower in the outer region. All PBL schemes accurately identified the rainfall location, although the amounts differed between the schemes. The rainfall levels in the MRF scheme were closest to the observation, followed by those in the YSU and MYJ schemes; the QNSE scheme showed the largest deviation. In general, rainfall simulation using a nonlocal boundary layer scheme such as MRF had the best results for both the inner core and the outer region.
The Different Impacts of Emissions and Meteorology on PM2.5 Changes in Various Regions in China: A Case Study
Authors: Zhang Wenjie , Wang Hong , Zhang Xiaoye , Peng Yue , Liu Zhaodong , Zhong Junting , Wang Yaqiang , Che Huizheng , Zhao Yifan
Published: January 2022

Emissions and meteorology are significant factors affecting aerosol pollution, but it is not sufficient to understand their relative contributions to aerosol pollution changes. In this study, the observational data and the chemical model (GRAPES_CUACE) are combined to estimate the drivers of PM2.5 changes in various regions (the Beijing–Tianjin–Hebei (BTH), the Central China (CC), the Yangtze River Delta (YRD), and the Pearl River Delta (PRD)) between the first month after COVID-19 (FMC_2020) (i.e., from 23 January to 23 February 2020) and the corresponding period in 2019 (FMC_2019). The results show that PM2.5 mass concentration increased by 26% (from 61 to 77 µg m−3) in the BTH, while it decreased by 26% (from 94 to 70 µg m−3) in the CC, 29% (from 52 to 37 µg m−3) in the YRD, and 32% (from 34 to 23 µg m−3) in the PRD in FMC_2020 comparing with FMC_2019, respectively. In the BTH, although emissions reductions partly improved PM2.5 pollution (−5%, i.e., PM2.5 mass concentration decreased by 5% due to emissions) in FMC_2020 compared with that of FMC_2019, the total increase in PM2.5 mass concentration was dominated by more unfavorable meteorological conditions (+31%, i.e., PM2.5 mass concentration increased by 31% due to meteorology). In the CC and the YRD, emissions reductions (−33 and −36%) played a dominating role in the total decrease in PM2.5 in FMC_2020, while the changed meteorological conditions partly worsened PM2.5 pollution (+7 and +7%). In the PRD, emissions reductions (−23%) and more favorable meteorological conditions (−9%) led to a total decrease in PM2.5 mass concentration. This study reminds us that the uncertainties of relative contributions of meteorological conditions and emissions on PM2.5 changes in various regions are large, which is conducive to policymaking scientifically in China.
A Dataset for Emotion Recognition Using Virtual Reality and EEG (DER-VREEG): Emotional State Classification Using Low-Cost Wearable VR-EEG Headsets
Authors: Suhaimi Nazmi Sofian , Mountstephens James , Teo Jason
Published: January 2022

Emotions are viewed as an important aspect of human interactions and conversations, and allow effective and logical decision making. Emotion recognition uses low-cost wearable electroencephalography (EEG) headsets to collect brainwave signals and interpret these signals to provide information on the mental state of a person, with the implementation of a virtual reality environment in different applications; the gap between human and computer interaction, as well as the understanding process, would shorten, providing an immediate response to an individual’s mental health. This study aims to use a virtual reality (VR) headset to induce four classes of emotions (happy, scared, calm, and bored), to collect brainwave samples using a low-cost wearable EEG headset, and to run popular classifiers to compare the most feasible ones that can be used for this particular setup. Firstly, we attempt to build an immersive VR database that is accessible to the public and that can potentially assist with emotion recognition studies using virtual reality stimuli. Secondly, we use a low-cost wearable EEG headset that is both compact and small, and can be attached to the scalp without any hindrance, allowing freedom of movement for participants to view their surroundings inside the immersive VR stimulus. Finally, we evaluate the emotion recognition system by using popular machine learning algorithms and compare them for both intra-subject and inter-subject classification. The results obtained here show that the prediction model for the four-class emotion classification performed well, including the more challenging inter-subject classification, with the support vector machine (SVM Class Weight kernel) obtaining 85.01% classification accuracy. This shows that using less electrode channels but with proper parameter tuning and selection features affects the performance of the classifications.
Ecocultural or Biocultural? Towards Appropriate Terminologies in Biocultural Diversity
Authors: Franco F. Merlin
Published: January 2022

Biocultural diversity has made notable contributions that have furthered our understanding of the human culture-nature interrelationship. However, the usage of the term ‘biocultural’ is not unique to biocultural diversity. It was first used in biocultural studies within anthropology decades ahead of biocultural diversity. The existing literature on biocultural diversity does not acknowledge the prior existence of biocultural studies, or provide a clear demarcation between usages of the two terms. In this article, I discuss the varying contexts in usage of the term ‘biocultural’ between biocultural diversity and biocultural anthropology. While biocultural diversity deals with the linkages between biological, cultural, and linguistic diversity, biocultural studies in anthropology deal with the deterministic influence of physical and social environment on human biology and wellbeing. In biocultural studies, ‘biocultural’ refers to the integration of methodically collated cultural data with biological and environmental data. ‘Bio’ in biocultural anthropology therefore denotes biology, unlike biocultural diversity where it refers to biodiversity. Both biocultural studies and biocultural diversity apply ‘biocultural’ as descriptor to generate overlapping terminologies such as ‘biocultural approach’. Such a confusing scenario is not in the interest of biocultural diversity, as it would impede theoretical advancements. I propose that advocates of biocultural diversity explore its harmonies with ecoculturalism and the possibilities of suitably adapting the term ‘ecoculture’ in lieu of ‘bioculture’. Using ‘ecocultural’ instead of ‘biocultural’ as a descriptor to coin terminologies could solve confusions arising from the expanding usage of the term ‘bioculture’.
High-Throughput Chemical Screening and Structure-Based Models to Predict hERG Inhibition
Authors: Krishna Shagun , Borrel Alexandre , Huang Ruili , Zhao Jinghua , Xia Menghang , Kleinstreuer Nicole
Published: January 2022

Chemical inhibition of the human ether-a -go-go-related gene (hERG) potassium channel leads to a prolonged QT interval that can contribute to severe cardiotoxicity. The adverse effects of hERG inhibition are one of the principal causes of drug attrition in clinical and pre-clinical development. Preliminary studies have demonstrated that a wide range of environmental chemicals and toxicants may also inhibit the hERG channel and contribute to the pathophysiology of cardiovascular (CV) diseases. As part of the US federal Tox21 program, the National Center for Advancing Translational Science (NCATS) applied a quantitative high throughput screening (qHTS) approach to screen the Tox21 library of 10,000 compounds (~7871 unique chemicals) at 14 concentrations in triplicate to identify chemicals perturbing hERG activity in the U2OS cell line thallium flux assay platform. The qHTS cell-based thallium influx assay provided a robust and reliable dataset to evaluate the ability of thousands of drugs and environmental chemicals to inhibit hERG channel protein, and the use of chemical structure-based clustering and chemotype enrichment analysis facilitated the identification of molecular features that are likely responsible for the observed hERG activity. We employed several machine-learning approaches to develop QSAR prediction models for the assessment of hERG liabilities for drug-like and environmental chemicals. The training set was compiled by integrating hERG bioactivity data from the ChEMBL database with the Tox21 qHTS thallium flux assay data. The best results were obtained with the random forest method (~92.6% balanced accuracy). The data and scripts used to generate hERG prediction models are provided in an open-access format as key in vitro and in silico tools that can be applied in a translational toxicology pipeline for drug development and environmental chemical screening.
Should All Fractions of the Boar Ejaculate Be Prepared for Insemination Rather Than Using the Sperm Rich Only?
Authors: Luongo Chiara , Llamas-López Pedro José , Hernández-Caravaca Iván , Matás Carmen , García-Vázquez Francisco Alberto
Published: January 2022

Boar ejaculate is released in several well-characterized fractions, differing in terms of sperm concentration, seminal plasma volume, and composition. However, the inclusion of the last part of the ejaculate for artificial insemination (AI) purposes is still under debate due to its controversial effects. Thus, there is a need to study the potential synergistic impact of the different ejaculate fractions. We aimed to evaluate the effect of accumulative ejaculate fractions on sperm conservation, AI performance, and offspring health. Ejaculates (n = 51) were collected and distributed as follows: F1: sperm-rich fraction; F2: sperm-rich + intermediate fractions; F3: sperm-rich + intermediate + poor fractions. Each group was diluted in a commercial extender, packaged in seminal doses (2000 × 106 sperm/60 mL), and stored at ~16 °C. On day 3 of conservation, sperm were analyzed and used for AI (n = 174). High sperm quality was observed after storage without a significant difference between the groups (p > 0.05). Moreover, no differences were obtained for AI performance (pregnancy and farrowing rates, and litter size; p > 0.05) and offspring health (growth and blood analysis; p > 0.05). Conclusively, the presence of all ejaculate fractions within the seminal doses does not impair the reproductive performance, reporting important economic savings according to the economic model included here.
Transcriptomic Analysis Reveals Functional Interaction of mRNA–lncRNA–miRNA in Steroidogenesis and Spermatogenesis of Gynogenetic Japanese Flounder (Paralichthys olivaceus)
Authors: Cheng Jie , Yang Fan , Liu Saisai , Zhao Haitao , Lu Wei , Zhang Quanqi
Published: January 2022

Teleost fishes exhibit extraordinary diversity, plasticity and adaptability with their sex determination and sexual development, and there is growing evidence that non-coding RNAs (ncRNAs) are emerging as critical regulators of reproduction. Japanese flounder (Paralichthys olivaceus) is an important marine cultured fish that presents significant sexual dimorphism with bigger females, in which gynogenesis has been applied for aquaculture industry. In order to reveal the regulatory mechanisms of sexual development in gynogenetic female and sex-reversed neo-male P. olivaceus, the lncRNA–miRNA–mRNA interactions were investigated using high-throughput sequencing. A total of 6772 differentially expressed mRNAs (DEmRNAs), 2284 DElncRNAs, and 244 DEmiRNAs were obtained between gynogenetic female ovaries and sex-reversed neo-male testes. Genes in the steroid hormone biosynthesis and secretion pathway were enriched and mostly significantly upregulated in neo-male testes. Subsequently, network analysis uncovered high functional specificity for gynogenetic P. olivaceus sperm motility, as co-expressed DEmRNAs were significantly enriched in microtubule and cytoskeleton-related biological processes. Clustered miRNAs were characterized in the P. olivaceus genome with examples of the largest conserved let-7 clusters. The 20 let-7 members are distributed in 11 clusters and may not transcribe together with their neighboring miR-125b, with let-7 repressing cyp11a and miR-125b repressing esr2b, both as key steroidogenesis pathway genes. In summary, this study provides comprehensive insights into the mRNA–miRNA–lncRNA functional crosstalk in teleost sexual development and gametogenesis and will expand our understanding of ncRNA biology in teleost gynogenesis.
Elements and COVID-19: A Comprehensive Overview of Studies on Their Blood/Urinary Levels and Supplementation with an Update on Clinical Trials
Authors: Ścibior Agnieszka , Wnuk Ewa
Published: January 2022

The current report provides a brief overview of the clinical features, hematological/biochemical abnormalities, biomarkers, and AI-related strategies in COVID-19; presents in a nutshell the pharmacological and non-pharmacological therapeutic options; and concisely summarizes the most important aspects related to sociodemographic and behavioral factors as well as comorbidities having an impact on this disease. It also gives a brief outline of the effect of selected elements on immune response and collects data on the levels of micro-/macro-elements and toxic metals in the blood/urine of SARS-CoV-2 infected patients and on supplementation with minerals in COVID-19 subjects. Moreover, this review provides an overview of clinical trials based on the use of minerals alone or in combination with other agents that can provide effective responses toward SARS-CoV-2 infection. The knowledge compiled in this report lays the groundwork for new therapeutic treatments and further research on biomarkers that should be as informative as possible about the patient’s condition and can provide more reliable information on COVID-19 course and prognosis. The collected results point to the need for clarification of the importance of mineral supplementation in COVID-19 and the relationships of the levels of some minerals with clinical improvement.
Evaluation of Different Techniques, including Modified Atmosphere, under Vacuum Packaging, Washing, and Latilactobacillus sakei as a Bioprotective Agent, to Increase the Shelf-Life of Fresh Gutted Sea Bass (Dicentrarchus labrax) and Sea Bream (Sparus aurata) Stored at 6 ± 2 °C
Authors: Iacumin Lucilla , Jayasinghe Am Stefania , Pellegrini Michela , Comi Giuseppe
Published: January 2022

Fish meat is very perishable because of indigenous and microbial enzymes, which determine spoilage and shelf life. The deterioration processes, which lead to an important, sequential, and progressive modification of the initial state of freshness, are fast and depend on rearing, harvesting, slaughtering, handling, and storage conditions. Usually, the shelf life of gutted fish stored at 4 ± 2 °C under vacuum packaging (VP—1.0 bar) and modified atmosphere packaging (MAP, 70% N2, <1% O2, 30% CO2) is approximately 9 days. The aim of this work was to improve the shelf life and preserve the microbiological and sensory quality of farmed gutted sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) using different methods, including VP, MAP, and bioprotective culture containing Latilactobacillus sakei, until 12–14 days. Microbiological, physicochemical, and sensory quality indices were monitored to confirm the effectiveness of biopreservation on product quality during proper refrigeration (4 ± 2 °C) or abuse (6 ± 2 °C, simulating supermarkets and consumer fridges) storage period. Considering the quality indexes represented by Enterobacteriaceae, total volatile nitrogen (TVB-N), and malonaldehyde concentrations (TBARS) and the sensorial analysis, the VP samples were more acceptable than the MAP fish, even though the shelf-life of the VP and MAP fish was similar at about 12 days. The second phase of the work was to evaluate the shelf-life of both VP fish stored at 6 ± 2 °C, which simulates the normal abuse temperature of supermarkets or consumer fridges. Data confirmed the previous results and demonstrated, despite the abuse temperature of storage, a shelf-life of about 12 days. Finally, the third phase consisted of prolonging the shelf life until 14 days of storage at 6 ± 2 °C by washing the gutted sea bass and sea bream in a suspension of bioprotective starter (7 log CFU/mL) with or without the addition of dextrose (0.1%) and by VP packaging. The bioprotective culture reduced the growth of spoilage microorganisms. Consequently, the total volatile nitrogen (TVB-N) concentration in both fish species was low (<35 mg N/100 g). Nonprofessional and untrained evaluators confirmed the acceptability of the inoculated samples by sensorial analysis.
New Insights into the Role of the Complement System in Human Viral Diseases
Authors: Ostrycharz Ewa , Hukowska-Szematowicz Beata
Published: January 2022

The complement system (CS) is part of the human immune system, consisting of more than 30 proteins that play a vital role in the protection against various pathogens and diseases, including viral diseases. Activated via three pathways, the classical pathway (CP), the lectin pathway (LP), and the alternative pathway (AP), the complement system leads to the formation of a membrane attack complex (MAC) that disrupts the membrane of target cells, leading to cell lysis and death. Due to the increasing number of reports on its role in viral diseases, which may have implications for research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this review aims to highlight significant progress in understanding and defining the role of the complement system in four groups of diseases of viral etiology: (1) respiratory diseases; (2) acute liver failure (ALF); (3) disseminated intravascular coagulation (DIC); and (4) vector-borne diseases (VBDs). Some of these diseases already present a serious global health problem, while others are a matter of concern and require the collaboration of relevant national services and scientists with the World Health Organization (WHO) to avoid their spread.
Insights into the Role of Gremlin-1, a Bone Morphogenic Protein Antagonist, in Cancer Initiation and Progression
Authors: Elemam Noha Mousaad , Malek Abdullah Imadeddin , Mahmoud Esraa Elaraby , El-Huneidi Waseem , Talaat Iman M.
Published: January 2022

The bone morphogenic protein (BMP) antagonist Gremlin-1 is a biologically significant regulator known for its crucial role in tissue differentiation and embryonic development. Nevertheless, it has been reported that Gremlin-1 can exhibit its function through BMP dependent and independent pathways. Gremlin-1 has also been reported to be involved in organ fibrosis, which has been correlated to the development of other diseases, such as renal inflammation and diabetic nephropathy. Based on growing evidence, Gremlin-1 has recently been implicated in the initiation and progression of different types of cancers. Further, it contributes to the stemness state of cancer cells. Herein, we explore the recent findings on the role of Gremlin-1 in various cancer types, including breast, cervical, colorectal, and gastric cancers, as well as glioblastomas. Additionally, we highlighted the impact of Gremlin-1 on cellular processes and signaling pathways involved in carcinogenesis. Therefore, it was suggested that Gremlin-1 might be a promising prognostic biomarker and therapeutic target in cancers.
Female Reproductive Factors and the Risk of Bronchiectasis: A Nationwide Population-Based Longitudinal Study
Authors: Yang Bumhee , Lee Dong-Hwa , Han Kyungdo , Choi Hayoung , Kang Hyung Koo , Shin Dong Wook , Lee Hyun
Published: January 2022

Although the oestrogen level is thought to be involved in the occurrence of bronchiectasis, limited data are available on the relationship between female reproductive factors and the risk of bronchiectasis. We performed a population-based retrospective cohort study of 959,523 premenopausal women and 1,362,401 postmenopausal women without a previous history of bronchiectasis who participated in a health screening exam in 2009 in South Korea. In premenopausal women, compared with a later age at menarche (≥16 years), an earlier menarche (<12 years) was associated with a reduced risk of bronchiectasis with an adjusted hazard ratio (aHR) (95% confidence interval (CI)) of 0.74 (0.67–0.81). However, there were no significant associations between other reproductive factors (breastfeeding, parity, or oral contraceptive use) and the risk of bronchiectasis. In postmenopausal women, the risk of bronchiectasis (aHR (95% CI)) was lower in those with an earlier menarche (0.79 (0.72–0.87) for <12 years vs. ≥16 years), a later menopause (0.90 (0.84–0.96) ≥55 years vs. <40 years), and a longer reproductive period (0.90 (0.86–0.94) for ≥40 years vs. <30 years). There was no significant relationship between parity and the risk of bronchiectasis. Although breastfeeding <1 year (aHR (95% CI) = 0.92 (0.87–0.97) for <0.5 years and 0.93 (0.88–0.97) for 0.5–1 years) and oral contraceptive use <1 year (0.97 (0.94–0.99)) reduced the risk of bronchiectasis, hormone replacement therapy ≥5 years increased the risk of bronchiectasis (1.24 (1.18–1.30)). Female reproductive factors are risk factors for developing bronchiectasis, showing a higher risk associated with shorter endogenous oestrogen exposure regardless of the menopausal status.
Acknowledgment to Reviewers of Biomedicines in 2021
Authors:   Biomedicines Editorial Office
Published: January 2022

Rigorous peer-reviews are the basis of high-quality academic publishing [...]
Rapid Detection of Virus Nucleic Acid via Isothermal Amplification on Plasmonic Enhanced Digitizing Biosensor
Authors: Wei Shih-Chung , Chang Chia-Chen , Chuang Tsung-Liang , Sung Kung-Bin , Lin Chii-Wann
Published: January 2022

Rapid detection for infectious diseases is highly demanded in diagnosis and infection prevention. In this work, we introduced a plasmonic enhanced digitizing biosensor for the rapid detection of nucleic acids. The sensor successfully achieved the detection of loop-mediated isothermal amplification for the hepatitis virus in this work. The sensor comprised a nanodisc array and Bst polymerases conjugated on the rough surface of a nanodisc. The rough surface of the nanodisc provided plasmonic hot spots to enhance the fluorescence signal. The virus DNA was detected by conducting a modified loop-mediated isothermal amplification with fluorescence resonance energy transfer reporter conjugated primers on the sensor. The modified isothermal amplification improved the signal contrast and detection time compared to the original assay. By integrating the modified amplification assay and plasmonic enhancement sensor, we achieved rapid detection of the hepatitis virus. Nucleic acid with a concentration of 10−3 to 10−4 mg/mL was detected within a few minutes by our design. Our digitizing plasmonic nanoarray biosensor also showed 20–30 min earlier detection compared to conventional loop-mediated isothermal amplification sensors.
Applications of Fluorescence Spectroscopy, RGB- and MultiSpectral Imaging for Quality Determinations of White Meat: A Review
Authors: Fan Ke-Jun , Su Wen-Hao
Published: January 2022

Fluorescence spectroscopy, color imaging and multispectral imaging (MSI) have emerged as effective analytical methods for the non-destructive detection of quality attributes of various white meat products such as fish, shrimp, chicken, duck and goose. Based on machine learning and convolutional neural network, these techniques can not only be used to determine the freshness and category of white meat through imaging and analysis, but can also be used to detect various harmful substances in meat products to prevent stale and spoiled meat from entering the market and causing harm to consumer health and even the ecosystem. The development of quality inspection systems based on such techniques to measure and classify white meat quality parameters will help improve the productivity and economic efficiency of the meat industry, as well as the health of consumers. Herein, a comprehensive review and discussion of the literature on fluorescence spectroscopy, color imaging and MSI is presented. The principles of these three techniques, the quality analysis models selected and the research results of non-destructive determinations of white meat quality over the last decade or so are analyzed and summarized. The review is conducted in this highly practical research field in order to provide information for future research directions. The conclusions detail how these efficient and convenient imaging and analytical techniques can be used for non-destructive quality evaluation of white meat in the laboratory and in industry.
A Sensitive Monoclonal-Antibody-Based ELISA for Forchlorfenuron Residue Analysis in Food Samples
Authors: Liu Xinmei , Xie Bo , Cheng Yongjian , Luo Lin , Liang Yifan , Xiao Zhili
Published: January 2022

In this study, forchlorfenuron (CPPU) was coupled with succinic anhydride to yield a CPPU hapten (CPPU-COOH), and a high-affinity monoclonal antibody (mAb) that can specifically recognize CPPU was produced. Using this mAb as a recognition reagent, a sensitive indirect competitive enzyme-linked immunosorbent assay (icELISA) for CPPU was optimized, which exhibits an IC50 of 1.04 ng/mL, a limit of detection of 0.16 ng/mL, and a linear range of 0.31–3.43 ng/mL for CPPU. Cross-reactivity percentages with six analogues were all below 6%. The average recovery rates for cucumber and orange samples were from 85.23% to 119.14%. The analysis results of this icELISA showed good consistency with those from liquid chromatography mass spectrometry. These results suggest that the proposed icELISA provides a sensitive, specific, and reliable strategy for CPPU detection in food samples.
Acknowledgment to Reviewers of Biosensors in 2021
Authors:   Biosensors Editorial Office
Published: January 2022

Rigorous peer-reviews are the basis of high-quality academic publishing [...]