bluuebunny/crossref_metadata_2025 huggingface dataset:
Early-season and refined mapping of winter wheat based on phenology algorithms - a case of Shandong, China
Authors: Liu Xiuyu , Li Xuehua , Gao Lixin , Zhang Jinshui , Qin Dapeng , Wang Kun , Li Zhenhai
Published: July 2023

Winter wheat is one of the major food crops in China, and timely and effective early-season identification of winter wheat is crucial for crop yield estimation and food security. However, traditional winter wheat mapping is based on post-season identification, which has a lag and relies heavily on sample data. Early-season identification of winter wheat faces the main difficulties of weak remote sensing response of the vegetation signal at the early growth stage, difficulty of acquiring sample data on winter wheat in the current season in real time, interference of crops in the same period, and limited image resolution. In this study, an early-season refined mapping method with winter wheat phenology information as priori knowledge is developed based on the Google Earth Engine cloud platform by using Sentinel-2 time series data as the main data source; these data are automated and highly interpretable. The normalized differential phenology index (NDPI) is adopted to enhance the weak vegetation signal at the early growth stage of winter wheat, and two winter wheat phenology feature enhancement indices based on NDPI, namely, wheat phenology differential index (WPDI) and normalized differential wheat phenology index (NDWPI) are developed. To address the issue of “ different objects with the same spectra characteristics” between winter wheat and garlic, a plastic mulched index (PMI) is established through quantitative spectral analysis based on the differences in early planting patterns between winter wheat and garlic. The identification accuracy of the method is 82.64% and 88.76% in the early overwintering and regreening periods, respectively, These results were consistent with official statistics (R2 = 0.96 and 0.98, respectively). Generalization analysis demonstrated the spatiotemporal transferability of the method across different years and regions. In conclusion, the proposed methodology can obtain highly precise spatial distribution and planting area information of winter wheat 4_6 months before harvest. It provides theoretical and methodological guidance for early crop identification and has good scientific research and application value.
Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis
Authors: Yuan Shuai , Nie Cong , Jia Shangang , Liu Tianqi , Zhao Junming , Peng Jinghan , Kong Weixia , Liu Wei , Gou Wenlong , Lei Xiong , Xiong Yi , Xiong Yanli , Yu Qingqing , Ling Yao , Ma Xiao
Published: July 2023

Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.
A Sec-dependent effector, CLIBASIA_04425, contributes to virulence in ‘Candidatus Liberibater asiaticus’
Authors: Zhang Shushe , Wang Xuefeng , He Jun , Zhang Song , Zhao Tingchang , Fu Shimin , Zhou Changyong
Published: July 2023

Citrus Huanglongbing (HLB) is the most destructive citrus disease worldwide, mainly caused by ‘Candidatus Liberibacter asiaticus’ (CLas). It encodes a large number of Sec-dependent effectors that contribute to HLB progression. In this study, an elicitor triggering ROS burst and cell death in Nicotiana benthamiana, CLIBASIA_04425 (CLas4425), was identified. Of particular interest, its cell death-inducing activity is associated with its subcellular localization and the cytoplasmic receptor Botrytis-induced kinase 1 (BIK1). Compared with CLas infected psyllids, CLas4425 showed higher expression level in planta. The transient expression of CLas4425 in N. benthamiana and its overexpression in Citrus sinensis enhanced plant susceptibility to Pseudomonas syringae pv. tomato DC3000 ΔhopQ1-1 and CLas, respectively. Furthermore, the salicylic acid (SA) level along with the expression of genes NPR1/EDS1/NDR1/PRs in SA signal transduction was repressed in CLas4425 transgenic citrus plants. Taken together, CLas4425 is a virulence factor that promotes CLas proliferation, likely by interfering with SA-mediated plant immunity. The results obtained facilitate our understanding of CLas pathogenesis.
Online ‘chats’: fostering communitas and psychosocial support for people working across arts and play for health and wellbeing
Authors: Warran Katey , Wright Laura H. V.
Published: July 2023

Loss of work, furlough, and increased social isolation were prevalent for many working in the broad context of cultural and community engagement for health and wellbeing. This study set out to explore if and how regular online group interactions may foster social cohesion and provide support for these individuals during the critical time of the COVID-19 global pandemic. It was conducted in the context of the ‘social cohesion chat’ series led by a network called the Arts Play Health Community which was initiated in response to the pandemic as a way to bring those working in or connected to arts, play and health together during times of social isolation. Two qualitative focus groups with creative, participatory components were conducted with artists, researchers, evaluators, and arts/play managers (n= 11), and then analyzed using thematic analysis. Researcher ethnographic reflections and fieldnotes were also collected and analyzed. The authors engaged in reflexive online discussions to integrate and synthesize findings across different data. Four themes were constructed through the analysis procedure: (1) ‘Building an online community as processes of communitas’, spotlighting the importance of the non-hierarchical structure of the ‘chats’ particularly in relation to there being ‘no end goal’ to the online dialogues; (2) ‘Individual and shared emotional experiences’ that underpinned feelings of connection to others and the online space; (3) ‘Psychosocial benefits’ such as improving confidence and providing an opportunity to ‘have a voice’ in the community; and (4) ‘The importance of facilitation’, highlighting the opportunities the chats provided for participants to feel validated and valued as an active member of the community. The article concludes that constructing an inclusive and welcoming online community, where active participation is at the heart of regular social interactions can provide support for those working across arts and play for health and wellbeing. This was particularly important during the societal turbulence of the COVID-19 pandemic. It further concludes by noting the unique structure of these online dialogues as not being connected to institutions, with this playing a key role in allowing those in the community to ‘be themselves’ within it.
Assessing the causal association of trauma with subsequent psychiatric disorders by a Mendelian randomization study trauma and common psychiatric disorders
Authors: Gu Dongqing , Ou Shan , Liu Guodong
Published: July 2023

Objective

Trauma has been proposed as a risk factor for the development of psychiatric disorders. This study aimed to determine the causal role of trauma in six common psychiatric disorders.

Methods

We obtained summary-level data for genetic variants associated with trauma and the corresponding association with psychiatric disorders from previous genome-wide association studies. Two-sample Mendelian randomization analyzes were performed to estimate the causal association between trauma and psychiatric disorders, with inverse variance weighted used as the main method.

Results

Genetically predisposed trauma was associated with an increased risk of psychiatric disorders [odds ratio (OR) =1.24, 95%, confidence interval (CI), 1.09–1.40], anxiety disorder (OR = 1.30, 95% CI, 1.10–1.52) and schizophrenia (OR = 1.48, 95% CI, 1.18–1.84). However, the associations between trauma and sleep disorder (OR = 1.17, 95% CI, 1.01–1.35), as well as depression (OR = 1.09, 95% CI, 1.02–1.16) did not reach a Bonferroni corrected significance level. Besides, no association was observed between trauma and risk of bipolar disorder (OR = 1.21, 95% CI, 0.98–1.48) and eating disorder (OR = 1.28, 95% CI, 0.88–1.86).

Conclusion

Trauma might be causally associated with an increased risk of some common psychiatric disorders such as anxiety disorder and schizophrenia. However, little evidence supported an association between trauma and risk of depression, bipolar disorder, sleep disorder, and eating disorder. Our findings offered novel insights into the trauma-mediated development mechanism of psychiatric disorders, and psychological intervention to patients with trauma may be an effective prevention strategy for psychological diseases.
Suicide risk detection using artificial intelligence: the promise of creating a benchmark dataset for research on the detection of suicide risk
Authors: Parsapoor (Mah Parsa) Mahboobeh , Koudys Jacob W. , Ruocco Anthony C.
Published: July 2023

Suicide is a leading cause of death that demands cross-disciplinary research efforts to develop and deploy suicide risk screening tools. Such tools, partly informed by influential suicide theories, can help identify individuals at the greatest risk of suicide and should be able to predict the transition from suicidal thoughts to suicide attempts. Advances in artificial intelligence have revolutionized the development of suicide screening tools and suicide risk detection systems. Thus, various types of AI systems, including text-based systems, have been proposed to identify individuals at risk of suicide. Although these systems have shown acceptable performance, most of them have not incorporated suicide theories in their design. Furthermore, directly applying suicide theories may be difficult because of the diversity and complexity of these theories. To address these challenges, we propose an approach to develop speech- and language-based suicide risk detection systems. We highlight the promise of establishing a benchmark textual and vocal dataset using a standardized speech and language assessment procedure, and research designs that distinguish between the risk factors for suicide attempt above and beyond those for suicidal ideation alone. The benchmark dataset could be used to develop trustworthy machine learning or deep learning-based suicide risk detection systems, ultimately constructing a foundation for vocal and textual-based suicide risk detection systems.
Finding a way forward with the community: qualitative inquiry in the generalized HIV epidemic in Mizoram, India
Authors: Rao Amrita , Mamulwar Megha , Panda Samiran , Pachuau Henry Zodinliana , Vanlalvenzuali H. , Lalruatsanga  , Roy Tarun , Lalnuntlangi Nunui
Published: July 2023

Introduction

Mizoram, the northeastern State of India bordering Myanmar, is presently witnessing a burgeoning generalized HIV epidemic along with the highest State-level HIV prevalence among female sex workers (FSWs, 24.7%) and people who inject drugs (PWID,19.8%) in the country. The present study was conducted against such background to understand the current situation of HIV prevention and care services in Mizoram, and capture community voices as well as concerns so that the way forward could be informed appropriately.

Methods

The study period was October through December 2020 (in the midst of COVID-restrictions) in the districts of Aizawl, Mamit, Kolasib, Lunglei, and Champhai where HIV prevalence crossed 1% among ante-natal clinic (ANC) attending women. Contrastingly, the national average HIV prevalence among ANC attendees is 0.24%, which formed the basis for selecting the aforementioned five high burden districts for this current inquiry. In-depth-interviews were conducted with community members and youth leaders, vulnerable and general population groups as well as HIV-program officials. Interviews were recorded, transcribed, translated and later coded for analysis following thematic approach.

Results

The emerging issues were grouped in three thematic layers; (1) HIV vulnerability, (2) challenges pertaining to prevention and care services, and (3) program elements and future roadmap. Discrimination at the community level, unfriendly behavior of some of the HIV-service staff, occasional interruption in supplies of anti-retroviral treatment and sterile syringes and needles were voiced as deterrents to accessing HIV prevention and care services by the participants. Community engagement, based on restorative approach rather than retribution and ensuring enhanced performance of the district AIDS program control units emerged as necessary programmatic elements.

Conclusion

This inquiry highlighted macro-social and structural forces contributing to stigma and discrimination toward people at risk of HIV. It is urgent that HIV-services are re-aligned through de-centralized district level innovations and creation of safer spaces at the physical, societal and familial level. These, even during the time of stress such as a pandemic, would help health services to remain resilient. HIV outreach, sensitization of the community leaders and health-care professionals through strategic communication and ownership of the communities in these endeavors appeared paramount.
A zöld átállás hatása az ásványi nyersanyagokkal való ellátásra
Authors: András József , Yannick Harrell , Tashchi Eugène
Published: July 2023

Az ásványi anyagok a mai gyorsan növekvő tisztaenergia-technológiák számos részének alapvető alkotóelemei – a szélturbináktól és villamosenergia-hálózatoktól kezdve az elektromos járművekig. Az ezen ásványok iránti kereslet gyorsan növekedni fog, ahogy a tiszta energiára való átállás felgyorsul. A jelen előadás az ásványok és energiaágazat zöld átállása közötti összetett kapcsolatok átalakulásának egyes kilátásait vizsgálja, főleg az elektromos járművek elterjedésére fókuszálva, és ehhez kötődő ásványinyersanyag-igény növekedésére.
An Online Generation Method of Terminal-Area Trajectories for Wave-Rider Using Deep Neural Networks
Authors: Liu Zhe , Yan Jie , Ai Bangcheng , Fan Yonghua , Luo Kai , Cai Guodong , Qin Jiankai
Published: July 2023

This paper presents a deep neural network-based online trajectory generation method for the aerodynamic characteristic description and terminal-area energy management of wave-rider aircrafts. First, the flight dynamics equations in the energy domain are linearized and discretized to generate numerous aircraft trajectory samples with sequential convex optimization (SCO) methods. Then, an optimization objective function is designed to promote the smoothness of the control variables and improve the trajectory similarity. Compared to the nonlinear programming (NLP), the proposed trajectory sample generation method is more suitable for the training of deep neural networks (DNNs). Finally, deep neural networks are formulated and trained for the control variables and state variables, using the generated obtained trajectory samples, so that the reference trajectories can be obtained online during the energy management process of the wave-rider’s terminal phase. Numerical simulations validate the high accuracy of the trajectories generated with the deep neural network. Meanwhile, this proposed method enables smaller storage usage, which is highly suitable for integration into on-board flight control systems.
The Dynamics and Driving Mechanisms of Rural Revitalization in Western China
Authors: Yang Xiaojuan , Li Weiwei , Zhang Ping , Chen Hua , Lai Min , Zhao Sidong
Published: July 2023

By constructing a rural revitalization index evaluation system and using measurement models and software such as AHP, the entropy method, the BCG matrix, and GeoDetector, this paper quantitatively analyzed the evolution mode and driving mechanism of rural revitalization performance based on the research of 131 cities and autonomous prefectures in western China to further put forward relevant policy suggestions and establish a new framework that integrates “performance evaluation, evolution model, driving mechanism, and management strategy”. Findings: firstly, rural revitalization in western China showed slow development and significant regional heterogeneity, with a coefficient of variation of 0.46 or even higher; secondly, the different dimensions of rural revitalization and development varied greatly, with the order being: thriving businesses (about 0.04) < effective governance (about 0.06) < pleasant living environment (about 0.09) < social etiquette and civility (about 1.0) < prosperity (about 0.23); thirdly, the growth and decline of rural revitalization performance coexisted in the context of rapid development in western China, and the evolution was in diversified patterns; fourthly, there were many factors affecting the change of rural revitalization performance, and different factors exhibited significant synergistic effects with each other, with super-interacting factor pairs having a force of over 0. 7 (maximum 1), including permanent population, urbanization rate, added value of primary industry, and per capita GDP as key factors; fifthly, based on the superposition analysis of the evolution pattern and driving forces of rural revitalization, western cities are classified into 8 types (including external assistance zone, general development zone, general retention zone, general demonstration zone, internal governance zone, important development zone, important retention zone, important demonstration zone) for establishment of a zoning planning and management system and design of differentiated development policies, providing a basis for “evidence-based decision-making” for the government.
Comparison of PCR Techniques in Adulteration Identification of Dairy Products
Authors: Li Baiyi , Yu Mingxue , Xu Weiping , Chen Lu , Han Juan
Published: July 2023

Economic profit-driven food adulteration has become widespread in the dairy industry. One of the most common forms of dairy adulteration is the substitution of low-priced milk for high-priced milk. This has prompted regulatory authorities to focus on various means of authenticity testing. So far, many methods have been developed. Since milk adulteration has been upgraded, which has forced the testing methods to meet the needs of detection, which include DNA-based PCR methods. PCR and PCR-derived methods exhibit multiple advantages for authenticity testing, such as high stability, fast speed, and high efficiency, which meet the needs of modern testing. Therefore, it is important to develop rapid, reliable, and inexpensive PCR-based assays for dairy adulteration identification. In order to provide perspectives for improving adulteration identification methods, this review first summarizes the DNA extraction methods, then compares the advantages and disadvantages of various PCR authenticity testing methods, and finally proposes the directions for improving dairy product adulteration identification methods.
Developing Fermentation Liquid of Bacillus amyloliquefaciens PMB04 to Control Bacterial Leaf Spot of Sweet Pepper
Authors: Wang Fei , Chao Szu-Han , Tsai Chen-Hsuan , Blanco Sabrina Diana , Yang Yung-Yu , Lin Yi-Hsien
Published: July 2023

Sweet pepper is an important vegetable in the world. Bacterial leaf spot, caused by the pathogen Xanthomonas perforans, is a limiting factor that significantly reduces the quality and yield of sweet peppers. The use of chemical fungicides is currently the main disease-control method for bacterial leaf spot disease. It is important to develop an eco-friendly biocontrol method by using antagonistic microorganisms. Bacillus amyloliquefaciens PMB04 has strong antagonistic effects against pathogens and can inhibit the occurrence of diseases. B. amyloliquefaciens PMB04 has the potential for the development of a disease-control product. Primarily, PMB04 contained a strong inhibitory effect against all isolated X. perforans strains. In the inoculation assay, the severity of bacterial leaf spot disease on sweet peppers was reduced by PMB04 bacterial suspensions. To increase the convenience of field applications in future prospects, the development of the PMB04 fermentation liquid was carried out using different ratios of brown sugar and yeast extract in a 30 L fermentation tank. The results exhibited that the fermentation liquid of the 3-1 and 2-1 formulas obtained the highest bacterial population in a 30 L fermentation tank. The fermentation liquid of the 0.5-0.5 formula was the most stable formula for two different conditions in terms of a consistent bacterial population and sporulation. In addition, the 200-fold dilution of the 3-1 and 0.5-0.5 fermentation liquids revealed the best control efficacy on bacterial leaf spot disease of sweet peppers. Additionally, the results of the 0.5-0.5 fermentation liquid (PMB4FL) with different dilution concentrations also demonstrated that the 200- and 500-fold dilutions had the best control efficacy. To understand the effect of commonly used copper-containing fungicides on sweet peppers on the application of microbial agent PMB4FL, the effects of copper hydroxide and tribasic copper sulfate on the growth of X. perforans strains and B. amyloliquefaciens PMB04 were assayed. The results exhibited that the above two fungicides did not have any inhibitory effect on the growth of PMB04 but had a strong inhibitory effect on the X. perforans strain. In the follow-up control experiment, the treatment of copper hydroxide had no synergistic effect with PMB4FL to control bacterial leaf spot disease. We concluded that the use of the PMB4FL fermentation liquid alone on the leaves could effectively control the occurrence of bacterial leaf spots in sweet pepper crops.
Runoff Mitigation in Croplands: Evaluating the Benefits of Straw Mulching and Polyacrylamide Techniques
Authors: Argaman Eli , Stavi Ilan
Published: July 2023

Water loss through surface runoff is a significant constraint for rainfed agricultural lands across the Mediterranean region. Using straw-mulch cover (SMC) as a runoff mitigator has been successfully utilized to negate the impact of raindrop splashing. However, this practice is uncommon due to the high demand for crop residue as feed or fodder for livestock. Therefore, the application of synthetic polyacrylamide (PAM) has become a common practice. Although many studies have shown the positive impact of PAM on runoff control, most were conducted under laboratory conditions, where interactions with crop phenology and runoff dynamics were disregarded. In this study, on-site rainfall simulation was used to determine the efficiency of PAM and SMC to control runoff from foxtail millet (Setaria italica) fields under three seasonal conditions: (1) high-intensity rainfall, characteristic of autumn, on bare soil surfaces; (2) moderate-intensity rainfall, characteristic of winter, following crop tillering; and (3) high-intensity rainfall, characteristic of spring, following the flowering phase. The effect of SMC during the autumn and spring simulations was significantly better than that of the PAM and control treatments. For the winter simulation, runoff rates and runoff ratios were similar for all treatments. The most prominent finding was obtained for the spring simulation, where SMC yielded no runoff, whereas the PAM and control treatments yielded similar runoff rates and runoff ratios.
Genome-Wide Scan for Genetic Signatures Based on the Whole-Genome Resequencing of Salt- and Drought-Tolerant Rice Varieties
Authors: Jiang Conghui , Wang Yulong , Zhou Jinjun , Rashid Muhammad Abdul Rehman , Li Yaping , Peng Yongbin , Xie Lixia , Zhou Guanhua , He Yanan , Sun Wei , Zheng Chongke , Xie Xianzhi
Published: July 2023

Identifying elite stress-tolerant varieties and elucidating the genetic mechanisms mediating stress resistance can help breeders develop and exploit new rice germplasm resources. In this study, we identified five salt-tolerant varieties and five drought-tolerant upland rice varieties by survival rate and drought tolerance grade and constructed variation maps of the resistance using a deep-sequencing approach. Using 116 rice accessions from the 3000 Rice Genomes Project, we characterized the population structure of sequenced varieties. Through comparative genomics and transcriptome analysis, we screened 39 salt-response candidate genes. Natural variation analysis on root length-related drought candidate gene showed that Hap1 and Hap4 were the predominant haplotypes in indica, while Hap5 was the predominant haplotype in japonica. Gene Ontology (GO) analysis showed that carbohydrate metabolic process, defense response, and response to stimulus were the common GO terms associated with salt and drought tolerance. Selective signatures in elite stress-tolerant varieties indicated that multiple important stress tolerance genes, namely OsRac1, Pikp-2, Xa26, OsSIRP4, and wsl1, were selected and utilized in these sequenced rice varieties. These findings may be useful for clarifying the genetic variations among elite stress-tolerant varieties, while also laying the foundation for a more comprehensive investigation of the genetic basis of salt and drought tolerance.
Estimation Model of Rice Aboveground Dry Biomass Based on the Machine Learning and Hyperspectral Characteristic Parameters of the Canopy
Authors: Wang Xiaoke , Xu Guiling , Feng Yuehua , Peng Jinfeng , Gao Yuqi , Li Jie , Han Zhili , Luo Qiangxin , Ren Hongjun , You Xiaoxuan , Lu Wei
Published: July 2023

Accurately estimating aboveground dry biomass (ADB) is crucial. The ADB of rice has primarily been estimated using vegetation indices with several discrete bands; nevertheless, these indices cannot take advantage of continuous bands available with hyperspectral remote sensing. This study analyzed the quantitative relationship between canopy hyperspectral characteristic parameters (HCPs) and the ADB of rice. Twenty HCPs were used, including red edge area (SDr), blue edge area (SDb), and others. The variable-screening methods involved stepwise regression (SR), a regression coefficient (RC), variable importance in projection (vip), and random forest (RF). Stepwise and partial least squares regression methods were employed with traditional linear regression as well as machine learning methods including random forest (RF), a support vector machine (SVM), a BP artificial neural network (BPNN), and an extreme learning machine. Whole- and screening-variable models were constructed to estimate rice ADB at jointing, booting, heading, and maturing stages and across growth stages. Screening-variable models include SVM models based on SR (SVM-sr), RF models based on vip (RF-vip), and others. The results show that the HCPs had a significant correlation with ADB containing elements in the red edge region, namely SDr, SDr/SDb, and (SDr − SDb)/(SDr + SDb) at each growth stage. In addition, the screening performance of vip and SR was better than that of RC and RF, and fewer variables were screened. Moreover, the HCPs of the red edge region were screened using different screening methods at each growth stage. Among them, SDr/SDb and (SDr − SDb)/(SDr + SDb) appeared frequently, indicating they are important. Furthermore, at each growth stage, ADB could be well-estimated using diverse models with the RF modeling method based on vip screening variables found to be the best modeling method for ADB estimation; the independent variables of the RF-vip model involved the (SDr − SDb)/(SDr + SDb) at each growth stage.
Self-Similarity and Spatial Periodicity in Cerebral Cortical Patterning: Structural Design Notes for Neural Tissue Architects
Authors: Rouleau Nicolas , Murugan Nirosha J.
Published: July 2023

Tissue engineering is a powerful tool with which to systematically identify the determinants of biological functions. Applied to the design and fabrication of biomimetic brains, tissue engineering serves to disentangle the complex anatomy of neural circuits and pathways by recapitulating structure-function relationships in simplified model systems. The complex neuroanatomy of the cerebral cortex, with its enigmatic columnar and stratified cytoarchitectonic organization, represents a major challenge toward isolating the minimal set of elements that are required to assemble neural tissues with cognitive functions. Whereas considerable efforts have highlighted important genetic and physical correlates of early cortical tissue patterning, no substantive attempt to identify the determinants of how the cortices acquire their relatively conserved, narrow range of numbered layers is evident in the literature. Similarly, it is not yet clear whether cortical columns and laminae are functionally relevant or epiphenomena of embryonic neurodevelopment. Here, we demonstrate that spatial frequencies (m−1) derived from the width-to-height ratios of cerebral cortical columns predict sinusoids with a narrow range of spatial cycles over the average cortical thickness. The resulting periodicities, denoted by theoretical wavenumbers, reflect the number of observed cortical layers among humans and across several other species as revealed by a comparative anatomy approach. We present a hypothesis that cortical columns and their periodic layers are emergent of the intrinsic spatial dimensions of neurons and their nested, self-similar aggregate structures including minicolumns. Finally, we discuss the implications of periodic tissue patterns in the context of neural tissue engineering.
Discovery of Bactericidal Proteins from Staphylococcus Phage Stab21 Using a High-Throughput Screening Method
Authors: Nyhamar Ellisiv , Webber Paige , Liong Olivia , Yilmaz Özgenur , Pajunen Maria , Skurnik Mikael , Wan Xing
Published: July 2023

In the escalating battle against antimicrobial resistance, there is an urgent need to discover and investigate new antibiotic strategies. Bacteriophages are untapped reservoirs of such potential antimicrobials. This study focused on Hypothetical Proteins of Unknown Function (HPUFs) from a Staphylococcus phage Stab21. We examined its HPUFs for bactericidal activity against E. coli using a Next Generation Sequencing (NGS)-based approach. Among the 96 HPUFs examined, 5 demonstrated cross-species toxicity towards E. coli, suggesting the presence of shared molecular targets between E. coli and S. aureus. One toxic antibacterial HPUF (toxHPUF) was found to share homology with a homing endonuclease. The implications of these findings are profound, particularly given the potential broad applicability of these bactericidal agents. This study confirms the efficacy of NGS in streamlining the screening process of toxHPUFs, contributes significantly to the ongoing exploration of phage biology, and offers promises in the search for potent antimicrobial agents.
The Prevalence of the Virulence Genes of Staphylococcus aureus in Sickle Cell Disease Patients at KSUMC, Riyadh, Saudi Arabia
Authors: Abdulmanea Adel A. , Alharbi Naiyf S. , Somily Ali M. , Khaled Jamal M. , Algahtani Farjah H.
Published: July 2023

Staphylococcus aureus in the blood of sickle cell disease (SCD) patients may result in a significant increase in morbidity and mortality. S. aureus strains contain various virulence characteristics, including the ability to create a variety of toxins and develop drug resistance. The current study sought to assess the prevalence of S. aureus in SCD patients and to identify the pathogen’s virulence characteristics. Between 2017 and 2021, blood samples and data were collected at King Saud University Medical City (KSUMC) in Riyadh, Saudi Arabia. The Vitek system PCR and gene sequencing methods were used for identification, antibiotic resistance patterns, and genetic analysis. During the study period, 47 S. aureus blood isolates (methicillin-resistant S. aureus (MRSA) 41.6% and non-MRSA 58.4%) were isolated from 2406 SCD patients. The prevalence percentages of virulence genes (finbB, sdrC, sdrD, icaA, coa, nuc, hlg, hla, finbA, clfA, efb, pvl, agr, spa, seb, sea, sec, tst, and sed) among all the isolates from the SCD patients compared with non-SCD patients (control group) were as follows: (100% vs. 100%), (100% vs. 100%), (100% vs. 100%), (100% vs. 87.5%), (100% vs. 81.3%), (100% vs. 100%), (100% vs. 100%), (100% vs. 100%), (97.9% vs. 81.3%), (97.9% vs. 100%), (97.9% vs. 87.5%), (54.3% vs. 56.3%), (46.8% vs. 75%), (42.6% vs. 43.8%), (27.7% vs. 0%), (25.5% vs. 12.5%), (12.8% vs. 6.3%), (4.3% vs. 12.5%), and (4.3% vs. 0%). Regarding the resistance genes (plaZ, mecA, ermA, ermC, tetK, tetM, and ermB) of the S. aureus strains isolated from the SCD patients compared with non-SCD patients (control group), the prevalence percentages were as follows: (100% vs. 100%), (100% vs. 56.3%), (0% vs. 31.3%), (31.9% vs. 18.8%), (40.4% vs. 25%), (0% vs. 0%), and (0% vs. 0%). As for the antibiotic (ampicillin, penicillin, amoxicillin, cefazolin, imipenem, oxacillin, erythromycin, tetracycline, azithromycin, ciprofloxacin, moxifloxacin, and levofloxacin) resistance of the S. aureus strains isolated from the SCD patients compared with non-SCD patients (control group), the prevalence percentages were as follows: (100% vs. 100%), (97.9% vs. 100%), (72.3% vs. 25%), (68.1% vs. 37.5%), (68.1% vs. 25%), (66% vs. 25%), (36.2% vs. 18.8%), (23.4% vs. 12.5%), (19.1% vs. 12.5%), (17% vs. 12.5%), (14.9% vs. 25%), and (10.6% vs. 18.7%). This study concluded that several virulence genes were present in the S. aureus strains recovered from the SCD patients at KSUMC, with all the isolates containing the finbB, sdrC, sdrD, icaA, coa, nuc, hlg, and hla genes.
Streptococcus mitis as a New Emerging Pathogen in Pediatric Age: Case Report and Systematic Review
Authors: Colomba Claudia , Garbo Valeria , Boncori Giovanni , Albano Chiara , Bagarello Sara , Condemi Anna , Giordano Salvatore , Canduscio Laura A. , Gallo Cristina , Parrinello Gaspare , Cascio Antonio
Published: July 2023

Streptococcus mitis, a normal inhabitant of the oral cavity, is a member of Viridans Group Streptococci (VGS). Generally recognized as a causative agent of invasive diseases in immunocompromised patients, S. mitis is considered to have low pathogenic potential in immunocompetent individuals. We present a rare case of sinusitis complicated by meningitis and cerebral sino-venous thrombosis (CSVT) caused by S. mitis in a previously healthy 12-year-old boy with poor oral health status. With the aim of understanding the real pathogenic role of this microorganism, an extensive review of the literature about invasive diseases due to S. mitis in pediatric patients was performed. Our data define the critical role of this microorganism in invasive infections, especially in immunocompetent children and in the presence of apparently harmful conditions such as sinusitis and caries. Attention should be paid to the choice of therapy because of VGS’s emerging antimicrobial resistance patterns.
Biosynthesis, Deficiency, and Supplementation of Coenzyme Q
Authors: Staiano Carmine , García-Corzo Laura , Mantle David , Turton Nadia , Millichap Lauren E. , Brea-Calvo Gloria , Hargreaves Iain
Published: July 2023

Originally identified as a key component of the mitochondrial respiratory chain, Coenzyme Q (CoQ or CoQ10 for human tissues) has recently been revealed to be essential for many different redox processes, not only in the mitochondria, but elsewhere within other cellular membrane types. Cells rely on endogenous CoQ biosynthesis, and defects in this still-not-completely understood pathway result in primary CoQ deficiencies, a group of conditions biochemically characterised by decreased tissue CoQ levels, which in turn are linked to functional defects. Secondary CoQ deficiencies may result from a wide variety of cellular dysfunctions not directly linked to primary synthesis. In this article, we review the current knowledge on CoQ biosynthesis, the defects leading to diminished CoQ10 levels in human tissues and their associated clinical manifestations.
Ultrasound-Assisted Deep Eutectic Solvent Extraction of Phenolic Compounds from Thinned Young Kiwifruits and Their Beneficial Effects
Authors: Wu Ding-Tao , Deng Wen , Li Jie , Geng Jin-Lei , Hu Yi-Chen , Zou Liang , Liu Yi , Liu Hong-Yan , Gan Ren-You
Published: July 2023

Fruit thinning is a common practice employed to enhance the quality and yield of kiwifruits during the growing period, and about 30–50% of unripe kiwifruits will be thinned and discarded. In fact, these unripe kiwifruits are rich in nutrients and bioactive compounds. Nevertheless, the applications of thinned young kiwifruits and related bioactive compounds in the food and functional food industry are still limited. Therefore, to promote the potential applications of thinned young kiwifruits as value-added health products, the extraction, characterization, and evaluation of beneficial effects of phenolic compounds from thinned young fruits of red-fleshed Actinidia chinensis cv ‘HY’ were examined in the present study. A green and efficient ultrasound-assisted deep eutectic solvent extraction (UADE) method for extracting phenolic compounds from thinned young kiwifruits was established. A maximum yield (105.37 ± 1.2 mg GAE/g DW) of total phenolics extracted from thinned young kiwifruits by UADE was obtained, which was significantly higher than those of conventional organic solvent extraction (CSE, about 14.51 ± 0.26 mg GAE/g DW) and ultrasound-assisted ethanol extraction (UAEE, about 43.85 ± 1.17 mg GAE/g DW). In addition, 29 compounds, e.g., gallic acid, chlorogenic acid, neochlorogenic acid, catechin, epicatechin, procyanidin B1, procyanidin B2, quercetin-3-rhamnoside, and quercetin-3-O-glucoside, were identified in the kiwifruit extract by UPLC-MS/MS. Furthermore, the contents of major phenolic compounds in different kiwifruit extracts prepared by conventional organic solvent extraction (EE), ultrasound-assisted ethanol extraction (UEE), and ultrasound-assisted deep eutectic solvent extraction (UDE) were compared by HPLC analysis. Results revealed that the content of major phenolics in UDE (about 15.067 mg/g DW) was significantly higher than that in EE (about 2.218 mg/g DW) and UEE (about 6.122 mg/g DW), suggesting that the UADE method was more efficient for extracting polyphenolics from thinned young kiwifruits. In addition, compared with EE and UEE, UDE exhibited much higher antioxidant and anti-inflammatory effects as well as inhibitory effects against α-glucosidase and pancreatic lipase, which were closely associated with its higher content of phenolic compounds. Collectively, the findings suggest that the UADE method can be applied as an efficient technique for the preparation of bioactive polyphenolics from thinned young kiwifruits, and the thinned young fruits of red-fleshed A. chinensis cv ‘HY’ have good potential to be developed and utilized as functional foods and nutraceuticals.
DYNAMION—A Powerful Beam Dynamics Software Package for the Development of Ion Linear Accelerators and Decelerators
Authors: Yaramyshev Stepan , Barth Winfried , Lauber Simon , Miski-Oglu Maksym , Rubin Anna , Scheeler Uwe , Vormann Hartmut , Vossberg Markus
Published: July 2023

Numerous ambitious particle accelerator facilities, based on proton and ion linear accelerators, have recently been in development for fundamental research, as well as for industrial applications. The advanced design of such new machines, as well as the upgrade and optimization of existing linacs, requires adequate, precise and reliable tools to simulate beam dynamics. The software package DYNAMION, created about 30 years ago, is undergoing systematic improvement and further development in order to characterize modern ion linacs and to provide solutions for its intrinsic complex problems. The DYNAMION code features Front to End beam dynamics simulations under space charge conditions in a linac system, comprising an arbitrary sequence of accelerating-focusing structures and beam transport lines. The evolution of a macroparticle ensemble could be analyzed at a high level of specification. A 3D distribution of the external electrical field (RFQ, DTL) is modeled using integrated internal solvers. Optionally, a 3D electromagnetic field mapping, supplied by specialized external codes, could be used. The recent status of the DYNAMION software package is presented in this paper. Furthermore, the performance of the code is demonstrated on the basis of its application for various linear accelerator/decelerator projects.
Maximizing the Capacity of Edge Networks with Multicasting
Authors: Yuan Peiyan , Li Ming , Li Shuhong , Liu Chunhong , Zhao Xiaoyan
Published: July 2023

Edge networks employ local computing and caching resources to process data, thus alleviating the bandwidth pressure on backbone networks and improve users’ quality of experience. System capacity is one of the key metrics to evaluate the performance of edge networks. However, maximizing system capacity in edge scenarios faces challenges due to the dynamical user sessions and the changing content popularity. This study reports on the influence of multicast communication on the capacity of edge caching networks. When large amounts of content are requested simultaneously or over a short period, one-to-one unicast transmission will consume copious network resources due to repetitious transmission. To solve this problem, this study used the one-to-many multicast scheme to realize cooperative transmission between edge servers. First, multiple copies of the content are distributed to multiple small base stations (SBSs) based on the content’s popularity and the SBSs’ cache sizes. Second, a multicast tree is constructed by using, as the root node, the SBS that stores the content. Third, the content is transmitted along the path of the multicast tree to each end-user. Finally, a simulation platform is constructed to analyze the performance of the two transmission schemes. The results of simulating on edge caching networks show that multicast communication responds well to users’ requests even when the requested content requires sudden transmission, is highly popular or is requested often within short time. This system’s capacity has been significantly improved compared to the classical methods.
The Influence of Immersive and Collaborative Virtual Environments in Improving Spatial Skills
Authors: Conesa Julián , Mula Francisco José , Bartlett Kristin A. , Naya Ferran , Contero Manuel
Published: July 2023

The use of Virtual Reality (VR) is growing in popularity in educational contexts. In this work, we present a novel software application based on immersive VR in which users can interact simultaneously with a model in a shared virtual scene and maintain audiovisual communication. The 3D model-building activity within the application was designed to improve spatial skills. Twenty-nine industrial engineering students completed the modeling activity in groups of two or three. Post-test scores showed significant improvement over pre-test scores for both spatial tests used to measure the effectiveness of the instrument in improving spatial skills. Participants rated the application favorably in terms of usability and functionality. Results suggest that spatial training in a collaborative immersive virtual environment has the potential to be an effective approach to improving spatial skills.
A Stereo-Vision-Based Spatial-Positioning and Postural-Estimation Method for Miniature Circuit Breaker Components
Authors: Wu Ziran , Bao Zhizhou , Wang Jingqin , Yan Juntao , Xu Haibo
Published: July 2023

This paper proposes a stereo-vision-based method that detects and registers the positions and postures of muti-type, randomly placed miniature circuit breaker (MCB) components within scene point clouds acquired by a 3D stereo camera. The method is designed to be utilized in the flexible assembly of MCBs to improve the precision of gripping small-sized and complex-structured components. The proposed method contains the following stages: First, the 3D computer-aided design (CAD) models of the components are converted to surface point cloud models by voxel down-sampling to form matching templates. Second, the scene point cloud is filtered, clustered, and segmented to obtain candidate-matching regions. Third, point cloud features are extracted by Intrinsic Shape Signatures (ISSs) from the templates and the candidate-matching regions and described by Fast Point Feature Histogram (FPFH). We apply Sample Consensus Initial Alignment (SAC-IA) to the extracted features to obtain a rough matching. Fourth, fine registration is performed by employing Iterative Closest Points (ICPs) with a K-dimensional Tree (KD-tree) between the templates and the roughly matched targets. Meanwhile, Random Sample Consensus (RANSAC), which effectively solves the local optimal problem in the classic ICP algorithm, is employed to remove the incorrectly matching point pairs for further precision improvement. The experimental results show that the proposed method achieves spatial positioning errors smaller than 0.2 mm and postural estimation errors smaller than 0.5°. The precision and efficiency meet the requirements of the robotic flexible assembly for MCBs.
Using A Rotary Spring-Driven Gripper to Manipulate Objects of Diverse Sizes and Shapes
Authors: Lama Safal , Deemyad Taher
Published: July 2023

This paper introduces a new gripper mechanism that is capable of grasping objects of various sizes and shapes without the need for a closed-loop control system. Industries such as the food and beverage industry are seeking innovative soft grippers with a simplified control system. The proposed design utilizes a rotary mechanism with springs to achieve both force-closure and form-closure grasping. The design sets itself apart from most soft grippers with its ability to offer grasping forces in all lateral directions. The gripper is designed in a cylindrical shape and is actuated by a stepper motor with a gearbox to enhance the torque. Three stacked curvilinear and linear rails convert the motor’s rotational motion into linear motion. The grasping component consists of three curved parts, each incorporating numerous compression springs. Currently, the gripper can effectively grasp objects ranging from five to nine centimeters in diameter, with a maximum height of ten centimeters. However, the design is scalable based on specific application requirements. A comprehensive CAD model of the mechanism was developed, and multiple analyses were conducted, including motion, topology, and stress analyses. Finally, a functional prototype of the gripper was constructed and successfully tested for grasping fruits and vegetables of different sizes and shapes. This research can be further expanded to explore the application of the gripper in space exploration with its novel and completely electro-mechanical foundation.