bluuebunny/crossref_metadata_2025 huggingface dataset:
Coumarin Derivatives: The Influence of Cycloalkyl Groups at the C-3 Position on Intermolecular Interactions—Synthesis, Structure and Spectroscopy
Authors: Szwaczko Katarzyna , Kamiński Daniel M. , Koziol Anna E.
Published: February 2024

In this study, we explore the synthesis and solid-state characterization of four coumarin-3-carboxylic acid esters, each modified at the C-3 position with different cycloalkyl groups: cyclohexyl, menthyl, and iso-pulegyl. We conducted a detailed analysis of these compounds utilizing a variety of techniques such as a single-crystal X-ray diffraction, nuclear magnetic resonance (NMR), and Fourier-transform infrared (FTIR) spectroscopy. Additionally, we calculated the dipole moments for these molecules. Our findings include a thorough structural assessment, highlighting the role of noncovalent interactions through Full Interaction Maps and Hirshfeld surface analysis. This study reveals the critical influence of the weak C-H…O hydrogen bonds in determining the solid-state architecture of these esters, whereas π-π stacking interactions appear to be negligible among the studied derivatives.
The Awakening of Sleep Medicine: A Global Quest for Quality Rest and Health
Authors: Ferri Raffaele
Published: February 2024

The burden of sleep disorders is a global health concern that affects millions of people worldwide [...]
Pine-Oil-Derived Sodium Resinate Inhibits Growth and Acid Production of Streptococcus mutans In Vitro
Authors: Rajala Otto , Mäntynen Matias , Loimaranta Vuokko
Published: February 2024

S. mutans is a key pathogen in dental caries initiation and progression. It promotes oral biofilm dysbiosis and biofilm acidification. Sodium resinate is a salt of pine-oil-derived resin which has antimicrobial properties. Pine-oil-derived resin consists of terpenes, diterpenes, and abietic acids. The aim of this study was to determine the effects of pine (Pinus sylvestris) oil resinate (RS) on growth and acid production of cariogenic S. mutans strains in planktonic form and biofilm. The S. mutans type strain NCTC10449 and clinical isolate CI2366 were grown on 96-well plates for testing of RS effects on growth and biofilm formation, and on plates with integrated pH-sensitive optical ensors for real-time measurements of the effects of RS on bacterial acid production. We found that even short-time exposure to RS inhibits the growth and acid production of S. mutans in the planktonic phase and biofilms. In addition, RS was able to penetrate the biofilm matrix and reduce acid production inside S. mutans biofilm. RS thus shows potential as a novel antibacterial agent against cariogenic bacteria in biofilm.
What If I Were the Exile? Linking Past and Present for Democratic History Teaching with Pre-Service Educators
Authors: San Pedro Veledo María Belén , Zagalaz-Sánchez María Luisa , González González de Mesa Carmen
Published: February 2024

The academic literature has fostered a debate in recent decades regarding the concept of historical empathy and the typology of activities that can help to treat and develop it, although there is no consensus as to the real effectiveness of narrative activities of a descriptive type that involve the projection of the person into the past. The aim of this research was to check whether the implementation of a programme that uses historical contextualisation, contact with primary testimonies, the use of sources and historical empathy, linking the situation of the exiles of the Spanish Civil War with the current refugees, can contribute to the development of tolerant attitudes towards the figure of the displaced in pre-service teachers and the degree to which these attitudes are modified after the application of the programme. The research design is quantitative and corresponds to a quasi-experimental design with a control and experimental group. A questionnaire was used to measure the attitudes of 101 pre-service teachers at a Spanish university towards refugees. The questionnaire was completed at two different times, before and after a historical empathy exercise on the exiles of the Spanish Civil War. The results indicate that programmes using historical contextualisation, testimonies close to refugees and historical empathy relating the situation of refugees to that of the exiles of the Spanish Civil War can contribute to increasing and/or reinforcing positive attitudes towards refugees in pre-service teachers.
Talking Like a Teacher—A Study of Pre-Service Teachers’ Voice and Speech Characteristics in Learning and Teaching Situations
Authors: Järvinen Kati , Kähkönen Anna-Leena , Nieminen Pasi , Mäntylä Terhi
Published: February 2024

Voice and speech are educational tools and a medium of pedagogy for teachers. Teachers tend to modify their voice and speech to support learning. This study aimed to investigate whether pre-service teachers modify their speech and voice in teaching compared to peer learning speech and whether the changes can promote learning and be beneficial for the speakers. Nine pre-service physics teachers’ voices were recorded in three learning situations and in one teaching session with similar external circumstances. Duration of speech turns, pausing, speech rate, fundamental frequency (F0) and its variation, sound pressure level (SPL) and its range, and voice quality were analyzed. Results showed that the participants had longer speech turns, decreased speech rate, and increased pausing when teaching compared to speech in peer learning situations. F0 and SPL were higher in teaching, indicating that the teaching situation was more stressful than the peer learning situation. For F0, this was confirmed by correlation analysis. From the learning point, increased pausing and slower speech rate may be beneficial, but increased F0 and SPL may, on the other hand, be harmful to future teachers as they can increase the risk of vocal overloading. Voice training for future teachers is strongly recommended.
Digital and Social-Civic Skills in Future Primary Education Teachers: A Study from the Didactics of Social Sciences for the Improvement of Teacher Training in Competences
Authors: Guerrero Elecalde Rafael , Contreras García Javier , Bonilla Martos Antonio Luis , Serrano Arnáez Begoña
Published: February 2024

The use of technology, especially among young people, is providing new possibilities, including in the academic field, and requires teacher training through the development of skills and competences. At this point, Social Science Didactics plays a fundamental role, as it prepares future teachers to teach social knowledge in order to achieve useful and meaningful learning for students and society. Using an online questionnaire, structured with the Likert scale, which had previously been validated and published by Professors Peart, Gutiérrez-Esteban, and Cubo-Delgado, 156 students of the Degree in Primary Education of the subject Didactics of Social Sciences at the University of Granada (Spain) participated (academic year 2023–2024), with the aim of investigating the digital and socio-civic competences of trainee teachers in order to seek ways to improve their training. The results were processed in the IBM SPSS Statistics 25 programme, carrying out a descriptive statistical analysis, considering the mode and the variance ratio. The participating students mainly use digital environments to communicate with acquaintances and, although they know and value a democratic society, they do not exercise their citizenship on the Internet. This makes it even more necessary to train future teachers in digital competences, based on digital and socio-civic skills, as only in this way will they be able to train citizens capable of facing the challenges of the knowledge society.
Effects of Reduced Seawater pH and Oil Contamination on Bacterial Communities and Biochemical Markers of Estuarine Animal Hosts
Authors: Louvado António , Galhano Victor , Lima Fernanda , Cleary Daniel F. R. , Lopes Isabel , Gomes Newton C. M. , Coelho Francisco J. R. C.
Published: February 2024

Ecosystem functioning depends on complex interactions between microorganisms, hosts, and the environment. Changes in environmental conditions (e.g., ocean acidification) in combination with anthropogenic pollution have been shown to affect the composition and function of free-living microbial communities, but little is known about the effects these stressors on host-associated communities. This study aims to characterize the response of host-associated bacterial communities of the bottom-dwelling polychaete Hediste diversicolor and the epibenthic gastropod Peringia ulvae to oil contamination and reduced seawater pH. The independent and interactive effects of both stressors were simulated under controlled conditions. The response of host-associated bacterial communities was assessed using the high-throughput sequencing of the 16S rRNA gene and several biochemical markers related to host metabolic pathways, e.g., neurotransmission, anaerobic metabolism, biotransformation, oxidative stress, and energy consumption. In H. diversicolor, reduced seawater pH was associated with a high relative abundance of Cyanobacteria, while in P. ulvae oil contamination was associated with a reduction in the relative abundance of Chitinophagales. In P. ulvae, enrichment with oil hydrocarbon-degrading bacteria suggests a possible role of these organisms in the dispersion of oil hydrocarbon degraders. Furthermore, oil supplementation shifted some specific biochemical markers of gastropods related to oxidative stress and energy consumption, which suggests host stress. In general, the bacterial communities and biochemical markers of the gastropod were more affected by stressors than those of the polychaete. Overall, this study contributes to a better understanding of the response of host-associated bacterial communities of benthic macrofauna to anthropogenic contamination and environmental change.
Charting the Research Terrain for Large Old Trees: Findings from a Quantitative Bibliometric Examination in the Twenty-First Century
Authors: Xie Chunping , Liu Chang , Liu Dawei , Jim C. Y.
Published: February 2024

Despite their relatively small numbers, large old trees play disproportionately important roles in global biodiversity and ecosystem functions. There is a lack of systematic reviews and quantitative analyses of the accumulated literature. Understanding the research context and evolution could pump prime research and conservation endeavors. Using the comprehensive Web of Science, we applied VOSviewer (1.6.19) and CiteSpace (6.1R2) bibliometric software to examine the large old tree research field in 2000–2022. The queries of the bibliographic database generated quantitative–visual depictions in the form of knowledge maps. The nodes denote research intensity, and inter-node linkages denote the pathways and frequencies of collaborative activities. The research outputs differed significantly in terms of regions, countries, institutions, high-citation articles, productive researchers, hot topics, and research frontiers. Conspicuous spatial disparities were displayed, with the U.S.A., China, and Australia leading in publication counts and a cluster of European countries making considerable collective contributions. The research collaboration demonstrated a dichotomy: European countries networked more by geographical propinquity, and the top three countries connected by long-distance leap-frog jumps. The entrenched discrepancies between the endowed developed domains vis-à-vis the deprived developing domains were clearly expressed. The research productivity progressed through three stages: initial, growth, and flourishing. The leading institutions, researchers, and highly cited papers were recognized. The keyword analysis pinpointed diverse research hotspots: growth dynamics, conservation and management, ecological functions, and environmental response. This study informs recommendations for future research directions and cooperation on longevity mechanisms, evolutionary adaptation, dynamic monitoring, and temporal–spatial patterns. The integrated application of GIS, machine learning, and big data technologies could strengthen research capability.
Predicting Individual Tree Mortality of Larix gmelinii var. Principis-rupprechtii in Temperate Forests Using Machine Learning Methods
Authors: Yang Zhaohui , Duan Guangshuang , Sharma Ram P. , Peng Wei , Zhou Lai , Fan Yaru , Zhang Mengtao
Published: February 2024

Accurate prediction of individual tree mortality is essential for informed decision making in forestry. In this study, we proposed machine learning models to forecast individual tree mortality within the temperate Larix gmelinii var. principis-rupprechtii forests in Northern China. Eight distinct machine learning techniques including random forest, logistic regression, artificial neural network, generalized additive model, support vector machine, gradient boosting machine, k-nearest neighbors, and naive Bayes models were employed, to construct an ensemble learning model based on comprehensive dataset from this specific ecosystem. The random forest model emerged as the most accurate, demonstrating 92.9% accuracy and 92.8% sensitivity, making it the best model among those tested. We identified key variables impacting tree mortality, and the results showed that a basal area larger than the target trees (BAL), a diameter at 130 cm (DBH), a basal area (BA), an elevation, a slope, NH4-N, soil moisture, crown density, and the soil’s available phosphorus are important variables in the Larix Principis-rupprechtii individual mortality model. The variable importance calculation results showed that BAL is the most important variable with an importance value of 1.0 in a random forest individual tree mortality model. By analyzing the complex relationships of individual tree factors, stand factors, environmental, and soil factors, our model aids in decision making for temperate Larix gmelinii var. principis-rupprechtii forest conservation.
Potential Distribution Projections for Senegalia senegal (L.) Britton under Climate Change Scenarios
Authors: Fang Jiaqi , Shi Jianfei , Zhang Ping , Shao Minghao , Zhou Na , Wang Yongdong , Xu Xinwen
Published: February 2024

The gum acacia Senegalia senegal (L.) Britton (Fabales: Fabaceae) is a drought-tolerant plant belonging to the genus Acacia of the Leguminosae family, possessing significant economic and ecological value. Despite its importance, there is a knowledge gap regarding the potential impact of climate change on the distribution of S. senegal, crucial for the conservation of plant resources and optimizing its use in introductory silviculture. In this study, we selected 23 environmental variables and utilized the optimized maximum entropy (MaxEnt) model to analyze the key environmental factors affecting the distribution of S. senegal worldwide and simulate the current and future distribution range of S. senegal in Pakistan under the SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5 climate change scenarios. The results highlight key environmental factors influencing the distribution of S. senegal, including BIO3 (isothermally), BIO4 (coefficient of seasonal variation of temperature), BIO11 (mean temperature of the coldest season), and BIO12 (annual precipitation). Regions with higher and less fluctuating temperatures exhibit a higher potential for S. senegal distribution. Currently, suitable habitats of S. senegal are concentrated in the southern region of Pakistan, covering provinces such as Punjab, Sindh, and Balochistan, with highly suitable habitats accounting for 6.06% of the total area. Under the current climatic conditions, this study identifies the spatial patterns of suitable habitats and their concentration in specific regions. With climate change, a notable expansion of suitable habitats towards higher latitudes is observed, with the most significant expansion under the extremely severe climate change scenario (SSP5-8.5), reaching 223.45% of the current level. The results of this study enhance our understanding of the dynamics of S. senegal distribution under climate change and offer valuable insights into the long-term introduction of S. senegal for afforestation and soil conservation in Pakistan. This study provides theoretical support for the sustainable development of the local ecosystem and socio-economy, emphasizing the importance of proactive measures to adapt to changing climatic conditions.
CsAFS2 Gene from the Tea Plant Intercropped with Chinese Chestnut Plays an Important Role in Insect Resistance and Cold Resistance
Authors: Wang Jianzhao , Dao Mei , Yang Ziyun , Bai Yan , Qin Ying , Wu Tian
Published: February 2024

α-Farnesene, a crucial secondary metabolite in sesquiterpenes, is crucial for plant biotic and abiotic stress resistance. In this study, we screened an AFS gene from transcriptome data of tea plants (Camellia sinensis) intercropped with Chinese chestnut (Castanea mollissima), resulting in the cloning of CsAFS2. CsAFS2 expression increased following treatment with MJ (Methyl jasmonate), SA (Salicylic acid), GA3 (Gibberellin A3), and various plant growth regulators, as well as under high-salt, drought, and low-temperature conditions. The heterologous genetic transformation of tobacco with CsAFS2 led to an enhanced resistance to low-temperature stress and aphid feeding, evident from elevated levels of osmotic regulatory substances, increased protective enzyme activity, and the upregulation of cold and insect resistance-related genes. Trichomes, crucial in cold and insect resistance, exhibited significantly greater length and density in transgenic tobacco as compared to control plants. These results confirm the vital role of CsAFS2 in enhancing cold and insect resistance, providing comprehensive insights into stress regulation mechanisms in tea plants and advancing stress-resistant tea plant breeding.
Urban Vegetation Classification for Unmanned Aerial Vehicle Remote Sensing Combining Feature Engineering and Improved DeepLabV3+
Authors: Cao Qianyang , Li Man , Yang Guangbin , Tao Qian , Luo Yaopei , Wang Renru , Chen Panfang
Published: February 2024

Addressing the problems of misclassification and omissions in urban vegetation fine classification from current remote sensing classification methods, this research proposes an intelligent urban vegetation classification method that combines feature engineering and improved DeepLabV3+ based on unmanned aerial vehicle visible spectrum images. The method constructs feature engineering under the ReliefF algorithm to increase the number of features in the samples, enabling the deep learning model to learn more detailed information about the vegetation. Moreover, the method improves the classical DeepLabV3+ network structure based on (1) replacing the backbone network using MoblieNetV2; (2) adjusting the atrous spatial pyramid pooling null rate; and (3) adding the attention mechanism and the convolutional block attention module. Experiments were conducted with self-constructed sample datasets, where the method was compared and analyzed with a fully convolutional network (FCN) and U-Net and ShuffleNetV2 networks; the migration of the method was tested as well. The results show that the method in this paper is better than FCN, U-Net, and ShuffleNetV2, and reaches 92.27%, 91.48%, and 85.63% on the accuracy evaluation indices of overall accuracy, MarcoF1, and mean intersection over union, respectively. Furthermore, the segmentation results are accurate and complete, which effectively alleviates misclassifications and omissions of urban vegetation; moreover, it has a certain migration ability that can quickly and accurately classify the vegetation.
Analysis of Basidiomycete Fungal Communities in Soil and Wood from Contrasting Zones of the AWPA Biodeterioration Hazard Map across the United States
Authors: Kirker Grant T. , Bishell Amy B. , Cappellazzi Jed , Glass Samuel V. , Palmer Jonathan A. , Bechle Nathan J. , Hickey William J.
Published: February 2024

Wood deterioration due to basidiomycetous decay fungi shortens the useful life span of wood and wood-based materials. Prescriptive preservative treatment is the most effective way to reduce the detrimental effects of these microorganisms, particularly in soil contact and areas of critical use (difficult to replace or vital to structure). Current American Wood Protection Association (AWPA) guidelines in the standardized use category system specify 3 zones of severity regarding wood decay fungal hazards but contain very little information on the diversity and abundance of these fungi colonizing soil and wood. In this study, amplicon based sequencing was utilized to compare fungal communities in wood and adjacent soil to provide baseline data on the fungi involved in the process. A thorough understanding of decay hazards is critical for the proper selection and use of wood in soil contact. The goal of this work is to provide baseline data on basidiomycete fungal diversity and species composition in different zones of the existing 3-zone AWPA hazard map as compared to the previous 5-zone hazard map and Scheffer decay indices and discuss the ecological implications for wood decay.
Contrasting Effects of Nitrogen Deposition and Phosphorus Addition on Soil Organic Carbon in a Subtropical Forest: Physical Protection versus Chemical Stability
Authors: Wang Xiaodong , Wu Anqi , Chen Fu-Sheng , Fang Xiangmin , Wang Huimin , Wang Fangchao
Published: February 2024

Soil organic carbon (SOC) not only contributes to maintain soil health, but is also important in regulating global climate change. How atmospheric nitrogen (N) deposition and phosphorus (P) addition affects SOC dynamics remains unclear, especially in subtropical forests. The response of SOC in three layers to N deposition and P addition in this study is estimated by analyzing the soil aggregates and C chemical stability composition fertilized with N (100 kg N hm−2 a−1) and/or P (50 kg P hm−2 a−1) over 9 years in a Chinese fir (Cunninghamia lanceolata) plantation. Treatments involving N deposition increased the SOC concentration, while P addition alone decreased the SOC concentration in soil layers above 10 cm. The addition of N significantly increased the mean diameter of topsoil aggregates, macroaggregates SOC concentration, and the contribution of N to total SOC. P addition decreased the relative abundances of aromatic and aliphatic functional groups while decreasing the chemical stability of SOC in the topsoil. A structural equation model indicated that N deposition promoted SOC concentration by mainly improving the physical protection of soil aggregates, while P addition reduced SOC sequestration by decreasing the chemical stability of SOC. Our research suggested that elevated N deposition might promote the soil C sink, while P fertilization would not be recommended under increased N deposition to protect soil C storage in subtropical forests.
Empirical Study on the Impact of Different Types of Forest Environments in Wuyishan National Park on Public Physiological and Psychological Health
Authors: Weng Yuxi , Zhu Yujie , Huang Yabing , Chen Qimei , Dong Jianwen
Published: February 2024

Amidst the challenges of global environmental change and urbanization, the salutary effects of natural environments on public health are increasingly being recognized. This study investigates the specific effects of varied forest environments in China’s Wuyishan National Park on physiological and psychological health. Eight distinct forest environments were carefully selected, and a repeated-measures ANOVA approach was used to evaluate 41 participants over three days. Physiological assessments included Heart Rate Variability, Skin Conductance Level, and surface Electromyography, complemented by psychological evaluations using the Profile of Mood States. The key findings include the following: (1) Notable variations in physiological indicators were observed among different forest types. In valley tea gardens and broadleaf forest streamside, significant changes in heart rate indicators highlighted the influence of these settings on autonomic nervous activities. Skin Conductance Level and surface Electromyography also indicated varying emotional arousal and pleasure across the forests. The mixed broadleaf and coniferous forest valley, along with the rock-bedded streamscape, elicited emotions of low arousal but high pleasure, inducing feelings of calmness and pleasure. The valley’s tea gardens were associated with low arousal and pleasure, suggesting tranquility without positive emotional induction, while the broadleaf ridge forest induced high arousal and pleasure, reflecting an exciting and joyful environment. (2) The study found that different forest environments had a notable impact on participants’ mood states, indicating reductions in tension, anger, fatigue, and depression, along with an increase in vigor levels. In summary, forest environments offer unique psychological and physiological health benefits compared to urban settings. These findings underscore the importance of integrating forest environments into urban development and public health frameworks, and the need to further explore their impact on the health of diverse populations.
The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis
Authors: Zhang Shulin , Chen Zhuo , Feng Luying , Zhi Zhaokun , Liu Yiteng , Zhang Mengmeng , Yue Huafeng , Zhu Gao-Pu , Gao Fuling
Published: February 2024

Jujube (Ziziphus jujuba Mill.) stands as a pivotal fruit tree with significant economic, ecological, and social value. Recent years have witnessed remarkable strides in multi-omics-based biological research on jujube. This review began by summarizing advancements in jujube genomics. Subsequently, we provided a comprehensive overview of the integrated application of genomics, transcriptomics, and metabolomics to explore pivotal genes governing jujube domestication traits, quality attributes (including sugar synthesis, terpenoids, and flavonoids), and responses to abiotic stress and discussed the transcriptional regulatory mechanisms underlying these traits. Furthermore, challenges in multi-omics research on jujube biological traits were outlined, and we proposed the integration of resources such as pan-genomics and sRNAome to unearth key molecules and regulatory networks influencing diverse biological traits. Incorporating these molecules into practical breeding strategies, including gene editing, transgenic approaches, and progressive breeding, holds the potential for achieving molecular-design breeding and efficient genetic enhancement of jujube.
System Identification and Fractional-Order Proportional–Integral–Derivative Control of a Distributed Piping System
Authors: Zhang Xiaomeng , Zhang Shuo , Xiong Furui , Liu Lu , Zhang Lichuan , Han Xuan , Wang Heng , Zhang Yanzhu , Ren Ranzhen
Published: February 2024

The vibration of piping systems is one of the most important causes of accelerated equipment wear and reduced work efficiency and safety. In this study, an active vibration control method based on a fractional-order proportional–integral–derivative (PID) controller was proposed to suppress pipeline vibration and reduce pipeline damage. First, a mathematical model of the distributed piping system was established using the finite element analysis method, and the characteristics of the distributed piping system were studied effectively. Further, the time-frequency domain parameter identification method was used to realise the system identification of the cross-point vibration transfer function between the brake and sensor, and the particle swarm optimisation algorithm was utilised to further optimise the transfer function parameters to improve the system identification accuracy. Therefore, a fractional-order PID controller was designed using the D-decomposition method, and the optimal controller parameters were obtained. The experimental and numerical simulation results show that the improved system identification algorithm can significantly improve modelling accuracy. In addition, the designed fractional-order PID controller can effectively reduce the system’s overshoot, oscillation time, and adjustment time, thereby reducing the vibration response of piping systems.
Hydrogel of Thyme-Oil-PLGA Nanoparticles Designed for Skin Inflammation Treatment
Authors: Folle Camila , Díaz-Garrido Natalia , Mallandrich Mireia , Suñer-Carbó Joaquim , Sánchez-López Elena , Halbaut Lyda , Marqués Ana M. , Espina Marta , Badia Josefa , Baldoma Laura , Calpena Ana Cristina , García Maria Luisa
Published: February 2024

Thyme oil (THO) possesses excellent antibacterial and antioxidant properties which are suitable for skin inflammatory disorders such as acne vulgaris. However, THO is insoluble in water and its components are highly volatile. Therefore, these drawbacks may be overcome by its encapsulation in biodegradable PLGA nanoparticles (THO-NPs) that had been functionalized using several strategies. Moreover, cell viability was studied in HaCat cells, confirming their safety. In order to assess therapeutic efficacy against acne, bacterial reduction capacity and antioxidant properties were assessed. Moreover, the anti-inflammatory and wound-healing abilities of THO-NPs were also confirmed. Additionally, ex vivo antioxidant assessment was carried out using pig skin, demonstrating the suitable antioxidant properties of THO-NPs. Moreover, THO and THO-NPs were dispersed in a gelling system, and stability, rheological properties, and extensibility were assessed. Finally, the biomechanical properties of THO-hydrogel and THO-NP-hydrogel were studied in human volunteers, confirming the suitable activity for the treatment of acne. As a conclusion, THO has been encapsulated into PLGA NPs, and in vitro, ex vivo, and in vivo assessments had been carried out, demonstrating excellent properties for the treatment of inflammatory skin disorders.
Micro and Macro Flooding Mechanism and Law of a Gel Particle System in Strong Heterogeneous Reservoirs
Authors: Ye Rongjun , Wang Lei , Xu Wenjun , Zhang Jianpeng , Chen Zhengbang
Published: February 2024

To address the issue of ineffective injection resulting from the consistent channeling of injected water through highly permeable channels in ultra-deep, high-temperature, high-salinity, and strongly heterogeneous reservoirs during the production process, a gel particle profile control agent suitable for high-temperature and high-salinity conditions was chosen. With the help of the glass etching visual microscopic model and the heterogeneous long core model, the formation mechanism of a water flooding channeling path and the distribution law of the remaining oil were explored, the microscopic profile control mechanism of the different parameters was clarified, and the profile control effect of macroscopic core displacement was analyzed. The research shows that the formation mechanism of a water flooding channeling path is dominated by the distribution law of the permeability section and the connection mode between different penetration zones. The remaining oil types after water flooding are mainly contiguous block, parallel throats, and multi-branch clusters. The profile control effect of gel particles on reservoir vertical heterogeneity is better than that of reservoir lateral heterogeneity. It was found that 10 wt% submicron particles with a median diameter of 600 nm play a good role in profiling and plugging pores of 5–20 μm. In addition, 10 wt% micron-sized particles with a median diameter of 2.63 μm mainly play a strong plugging role in the pores of 20–30 μm, and 5 wt% micron-sized particles with a median diameter of 2.63 μm mainly form a weak plugging effect on the pores of 10–20 μm. The overall profile control effect of 10 wt% submicro particles is the best, and changes in concentration parameters have a more significant effect on the profile control effect. In the macroscopic core profile control, enhanced oil recovery (EOR) can reach 16%, and the gel particles show plugging, deformation migration, and re-plugging. The research results provide theoretical guidance for tapping the potential of the remaining oil in strong heterogeneous reservoirs. To date, the gel particles have been applied in the Tahe oilfield and have produced an obvious profile control effect; the oil production has risen to the highest value of 26.4 t/d, and the comprehensive water content has fallen to the lowest percentage of 32.1%.
The Identification of Goat KCNJ15 Gene Copy Number Variation and Its Association with Growth Traits
Authors: Zhao Jiahao , Liu Zhe , Wang Xianwei , Xin Xiaoling , Du Lei , Zhao Huangqing , An Qingming , Ding Xiaoting , Zhang Zijing , Wang Eryao , Xu Zejun , Huang Yongzhen
Published: February 2024

(1) Background: Copy number variation (CNV) is a critical component of genome structural variation and has garnered significant attention. High-throughput screening of the KCNJ15 gene has revealed a correlation between the CNV region and the growth traits of goats. We aimed to identify the CNV of the KCNJ15 gene in five goat breeds and analyze its association with growth characteristics. (2) Methods: We utilized 706 goats from five breeds: Guizhou black goat (GZB), Guizhou white goat (GZW), Bohuai goat (BH), Huai goat (HH), and Taihang goat (TH). To evaluate the number of copies of the KCNJ15 gene using qPCR, we analyzed the correlation between the CNV and growth characteristics and then used a universal linear model. The findings revealed variations in the distribution of different copy number types among the different goat breeds. (3) Results: Association analysis revealed a positive influence of the CNV in the KCNJ15 gene on goat growth. In GZB, individuals with duplication types exhibited superior performance in terms of cannon bone circumference (p < 0.05). In HH, individuals with duplication types exhibited superior performance in terms of body slanting length (p < 0.05). Conversely, normal TH demonstrated better body height and body weight (p < 0.05), while in GZW, when CN = 3, it performed better than other types in terms of body weight and chest circumference (p < 0.05). However, in BH, it had no significant effect on growth traits. (4) Conclusions: We confirmed that the CNV in the KCNJ15 gene significantly influences the growth characteristics of four distinct goat breeds. The correlation between KCNJ15 gene CNVs and goat growth traits offers valuable insights to breeders, enabling them to employ precise and efficient breeding methods that enhance livestock welfare, productivity, and overall economic benefits in the industry.
Economy of Effort or Sophisticated Programming? The Prevalence of Bidirectional Promoter Complexes in the Human Genome
Authors: Anderson Erik M. , Anderson Stephen K.
Published: February 2024

An abundance of antisense promoters in the vicinity of the transcriptional start site of coding genes suggests that they play an important role in gene regulation. The divergent transcription of housekeeping genes by a common central promoter region allows for coordinated regulation of genes in related pathways and is also linked to higher promoter activity. However, closely positioned transcription start sites can also result in competition between overlapping promoter elements and generate a binary switch element. Furthermore, the direct competition resulting from the presence of an antisense promoter immediately downstream of the transcription start site of the gene produces an element that can exist in only one of two stable transcriptional states: sense or antisense. In this review, we summarize analyses of the prevalence of antisense transcription in higher eukaryotes and viruses, with a focus on the antisense promoters competing with the promoters of coding genes. The structures of bidirectional promoters driving the simultaneous expression of housekeeping genes are compared with examples of human bidirectional elements that have been shown to act as switches. Since many bidirectional elements contain a noncoding RNA as the divergent transcript, we describe examples of functional noncoding antisense transcripts that affect the epigenetic landscape and alter the expression of their host gene. Finally, we discuss opportunities for additional research on competing sense/antisense promoters, uncovering their potential role in programming cell differentiation.
Improving Genomic Predictions in Multi-Breed Cattle Populations: A Comparative Analysis of BayesR and GBLUP Models
Authors: Ma Haoran , Li Hongwei , Ge Fei , Zhao Huqiong , Zhu Bo , Zhang Lupei , Gao Huijiang , Xu Lingyang , Li Junya , Wang Zezhao
Published: February 2024

Numerous studies have shown that combining populations from similar or closely related genetic breeds improves the accuracy of genomic predictions (GP). Extensive experimentation with diverse Bayesian and genomic best linear unbiased prediction (GBLUP) models have been developed to explore multi-breed genomic selection (GS) in livestock, ultimately establishing them as successful approaches for predicting genomic estimated breeding value (GEBV). This study aimed to assess the effectiveness of using BayesR and GBLUP models with linkage disequilibrium (LD)-weighted genomic relationship matrices (GRMs) for genomic prediction in three different beef cattle breeds to identify the best approach for enhancing the accuracy of multi-breed genomic selection in beef cattle. Additionally, a comparison was conducted to evaluate the predictive precision of different marker densities and genetic correlations among the three breeds of beef cattle. The GRM between Yunling cattle (YL) and other breeds demonstrated modest affinity and highlighted a notable genetic concordance of 0.87 between Chinese Wagyu (WG) and Huaxi (HX) cattle. In the within-breed GS, BayesR demonstrated an advantage over GBLUP. The prediction accuracies for HX cattle using the BayesR model were 0.52 with BovineHD BeadChip data (HD) and 0.46 with whole-genome sequencing data (WGS). In comparison to the GBLUP model, the accuracy increased by 26.8% for HD data and 9.5% for WGS data. For WG and YL, BayesR doubled the within-breed prediction accuracy to 14.3% from 7.1%, outperforming GBLUP across both HD and WGS datasets. Moreover, analyzing multiple breeds using genomic selection showed that BayesR consistently outperformed GBLUP in terms of predictive accuracy, especially when using WGS. For instance, in a mixed reference population of HX and WG, BayesR achieved a significant accuracy of 0.53 using WGS for HX, which was a substantial enhancement over the accuracies obtained with GBLUP models. The research further highlights the benefit of including various breeds in the reference group, leading to enhanced accuracy in predictions and emphasizing the importance of comprehensive genomic selection methods. Our research findings indicate that BayesR exhibits superior performance compared to GBLUP in multi-breed genomic prediction accuracy, achieving a maximum improvement of 33.3%, especially in genetically diverse breeds. The improvement can be attributed to the effective utilization of higher single nucleotide polymorphism (SNP) marker density by BayesR, resulting in enhanced prediction accuracy. This evidence conclusively demonstrates the significant impact of BayesR on enhancing genomic predictions in diverse cattle populations, underscoring the crucial role of genetic relatedness in selection methodologies. In parallel, subsequent studies should focus on refining GRM and exploring alternative models for GP.
GiOPARK Project: The Genetic Study of Parkinson’s Disease in the Croatian Population
Authors: Rački Valentino , Bergant Gaber , Papić Eliša , Kovanda Anja , Hero Mario , Rožmarić Gloria , Starčević Čizmarević Nada , Ristić Smiljana , Ostojić Saša , Kapović Miljenko , Maver Aleš , Peterlin Borut , Vuletić Vladimira
Published: February 2024

Parkinson’s disease is a neurological disorder that affects motor function, autonomic functions, and cognitive abilities. It is likely that both genetic and environmental factors, along with age, contribute to the cause. However, there is no comprehensive guideline for genetic testing for Parkinson’s disease, and more research is needed to understand genetic variations in different populations. There has been no research on the genetic background of Parkinson’s disease in Croatia so far. Therefore, with the GiOPARK project, we aimed to investigate the genetic variants responsible for Parkinson’s disease in 153 Croatian patients with early onset, familial onset, and sporadic late-onset using whole-exome sequencing, along with multiplex ligation-dependent probe amplification and Sanger sequencing in select patients. We found causative variants in 7.84% of the patients, with GBA being the most common gene (4.58%), followed by PRKN (1.96%), ITM2B (0.65%), and MAPT (0.65%). Moreover, variants of uncertain significance were identified in 26.14% of the patients. The causative variants were found in all three subgroups, indicating that genetic factors play a role in all the analyzed Parkinson’s disease subtypes. This study emphasizes the need for more inclusive research and improved guidelines to better understand the genetic basis of Parkinson’s disease and facilitate more effective clinical management.
Further Delineation of Clinical Phenotype of ZMYND11 Variants in Patients with Neurodevelopmental Dysmorphic Syndrome
Authors: Bodetko Aleksandra , Chrzanowska Joanna , Rydzanicz Malgorzata , Borys-Iwanicka Agnieszka , Karpinski Pawel , Bladowska Joanna , Ploski Rafal , Smigiel Robert
Published: February 2024

Intellectual disability with speech delay and behavioural abnormalities, as well as hypotonia, seizures, feeding difficulties and craniofacial dysmorphism, are the main symptoms associated with pathogenic variants of the ZMYND11 gene. The range of clinical manifestations of the ZMYND phenotype is constantly being expanded by new cases described in the literature. Here, we present two previously unreported paediatric patients with neurodevelopmental challenges, who were diagnosed with missense variants in the ZMYND11 gene. It should be noted that one of the individuals manifested with hyperinsulinaemic hypoglycaemia (HH), a symptom that was not described before in published works. The reason for the occurrence of HH in our proband is not clear, so we try to explain the origin of this symptom in the context of the ZMYND11 syndrome. Thus, this paper contributes to knowledge on the range of possible manifestations of the ZMYND disease and provides further evidence supporting its association with neurodevelopmental challenges.
Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel
Authors: Gao Jionghao , Li Jianxin , Zhang Jihong , Sun Yan , Ju Xiaolong , Li Wenlong , Duan Haiyang , Xue Zhengjie , Sun Li , Hussain Sahito Javed , Fu Zhiyuan , Zhang Xuehai , Tang Jihua
Published: February 2024

Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.
Satellitome Analysis in the Southern Lapwing (Vanellus chilensis) Genome: Implications for SatDNA Evolution in Charadriiform Birds
Authors: Kretschmer Rafael , Toma Gustavo A. , Deon Geize Aparecida , dos Santos Natalia , dos Santos Rodrigo Zeni , Utsunomia Ricardo , Porto-Foresti Fabio , Gunski Ricardo José , Garnero Analía Del Valle , Liehr Thomas , de Oliveira Edivaldo Herculano Corra , de Freitas Thales Renato Ochotorena , Cioffi Marcelo de Bello
Published: February 2024

Vanellus (Charadriidae; Charadriiformes) comprises around 20 species commonly referred to as lapwings. In this study, by integrating cytogenetic and genomic approaches, we assessed the satellite DNA (satDNA) composition of one typical species, Vanellus chilensis, with a highly conserved karyotype. We additionally underlined its role in the evolution, structure, and differentiation process of the present ZW sex chromosome system. Seven distinct satellite DNA families were identified within its genome, accumulating on the centromeres, microchromosomes, and the W chromosome. However, these identified satellite DNA families were not found in two other Charadriiformes members, namely Jacana jacana and Calidris canutus. The hybridization of microsatellite sequences revealed the presence of a few repetitive sequences in V. chilensis, with only two out of sixteen displaying positive hybridization signals. Overall, our results contribute to understanding the genomic organization and satDNA evolution in Charadriiform birds.
Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform
Authors: Papa Mze Nasserdine , Fernand-Laurent Cécile , Daugabel Solen , Zanzouri Olfa , Marque Juillet Stéphanie
Published: February 2024

Genotypic testing is often recommended to improve the management of patients infected with human immunodeficiency virus (HIV). To help combat this major pandemic, next-generation sequencing (NGS) techniques are widely used to analyse resistance to antiretroviral drugs. In this study, we used a Vela Sentosa kit (Vela Diagnostics, Kendall, Singapore), which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to the Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and the Illumina Miseq platform, respectively. The average depth was 21,955 and 46,856 for Ion Torrent PGM and Illumina Miseq platforms, respectively. The cost of sequencing a run of eight samples was quite similar between the two platforms (about USD 1790 for Illumina Miseq and about USD 1833 for Ion Torrent PGM platform). We have shown for the first time that it is possible to adapt and use the Vela Sentosa kit for the Illumina Miseq platform to obtain high-quality results with a similar cost.