bluuebunny/crossref_metadata_2025 huggingface dataset:
Knowledge mapping of metformin use on cancers: a bibliometric analysis (2013–2023)
Authors: Pan Chaomin , Wei Yiyi , Dai Jingping , Yang Li , Ding Zhuoyu , Xinke Wang
Published: August 2024

There is substantial evidence from clinical and preclinical studies suggesting an association between metformin use and a reduced risk of cancer. However, the effects of metformin use on cancers have not yet been subjected to bibliometric analysis. The goal of this study was to explore the potential effects of metformin use on cancers and to conduct a comprehensive assessment of research hotspots related to the use of metformin on cancers. The results of the literature analysis were visualized using various tools such as Adobe Illustrator CC 2018, VOSviewer, CiteSpace, and the R package “bibliometric.” The average annual publications from 2013 to 2023 was 372. In terms of journals and co-cited journals, a total of 1,064 journals published 1958 papers, and Oncotarget published the highest number of papers (n = 153, 7.81%), while Cancer Research (Co-citation = 5,125) was the most frequently cited journal. A total of 25,665 authors participated in the research on metformin use on cancers. Metformin has demonstrated improved outcomes in various types of cancer, including breast cancer (BC), lung cancer (LC), colorectal cancer (CRC), prostate cancer (PC), and pancreatic cancer. This bibliometric analysis reviews the current literature on the clinical data on metformin use on cancers and describes the preclinical evidence illustrating the potential mechanisms of metformin use on various cancers directly or indirectly.
Puerarin attenuates myocardial ischemic injury and endoplasmic reticulum stress by upregulating the Mzb1 signal pathway
Authors: Xue Jiaojiao , Ren Haolin , Zhang Qi , Gu Jing , Xu Qian , Sun Jiaxi , Zhang Lu , Zhou Ming-Sheng
Published: August 2024

Objective

This study investigated the role of Mzb1 in puerarin protection against heart injury and dysfunction in acute myocardial infarction (AMI) mice.

Methods

C57BL/6 mice were pretreated with and without puerarin at doses of 50 mg/kg and 100 mg/kg for 14 days before establishing the AMI model. An AMI model was induced by ligating the left descending anterior coronary artery, and AC16 cardiomyocytes were treated with H2O2in vitro. Echocardiography was performed to measure cardiac function. DHE staining, nicotinamide adenine dinucleotide phosphate (NADPH) oxidase assay, and DCFH-DA oxidative fluorescence staining were used to determine reactive oxygen species (ROS) production in vivo and in vitro. Bioinformatics analysis was used to predict potential upstream transcription factors of Mzb1.

Results

Puerarin dose-dependently reduced myocardial infarction area and injury, accompanied by the improvement of cardiac function in AMI mice. AMI mice manifested an increase in myocardial oxidative stress, endoplasmic reticulum (ER) stress, apoptosis, and mitochondrial biogenesis dysfunction, which were inhibited by pretreatment with puerarin. Puerarin also prevented Mzb1 downregulation in the hearts of AMI mice or H2O2-treated AC16 cells. Consistent with the in vivo findings, puerarin inhibited H2O2-induced cardiomyocyte apoptosis, ER stress, and mitochondrial dysfunction, which were attenuated by siRNA Mzb1. Furthermore, the JASPAR website predicted that KLF4 may be a transcription factor for Mzb1. The expression of KLF4 was partially reversed by puerarin in the cardiomyocyte injury model, and KLF4 inhibitor (kenpaullone) inhibited Mzb1 expression and affected its function.

Conclusion

These results suggest that puerarin can protect against cardiac injury by attenuating oxidative stress and endoplasmic reticulum stress through upregulating the KLF4/Mzb1 pathway and that puerarin may expand our armamentarium for the prevention and treatment of ischemic heart diseases.
Metformin-mediated effects on mesenchymal stem cells and mechanisms: proliferation, differentiation and aging
Authors: Liu Xinjuan , Li Zekun , Liu Luyun , Zhang Ping , Wang Yue , Ding Gang
Published: August 2024

Mesenchymal stem cells (MSCs) are a type of pluripotent adult stem cell with strong self-renewal and multi-differentiation abilities. Their excellent biological traits, minimal immunogenicity, and abundant availability have made them the perfect seed cells for treating a wide range of diseases. After more than 60 years of clinical practice, metformin is currently one of the most commonly used hypoglycaemic drugs for type 2 diabetes in clinical practice. In addition, metformin has shown great potential in the treatment of various systemic diseases except for type 2 diabetes in recent years, and the mechanisms are involved with antioxidant stress, anti-inflammatory, and induced autophagy, etc. This article reviews the effects and the underlying mechanisms of metformin on the biological properties, including proliferation, multi-differentiation, and aging, of MSCs in vitro and in vivo with the aim of providing theoretical support for in-depth scientific research and clinical applications in MSCs-mediated disease treatment.
Fibre bundle models as a framework for the detachment dynamics of soft probabilistic fasteners
Authors: Filippov A. D. , Sharma P. , Helmendach F. , Dijksman J. A. , Hidalgo R. C.
Published: August 2024

Adhesives can be made by patterning surfaces with discrete adhesive elements. Nature uses this approach to provide animals with highly adaptive and robust approaches towards gaining an effective grip on surfaces. The mechanism of patterned surface adhesion involve many different attachment principles, adhesive site interactions, and probabilistic effects, the interplay of which is not understood. This limits our ability to design patterned surface adhesives for engineering applications. In this work, we quantify how a mechanically patterned adhesive based on passive mushroom-shaped elements performs. We explore a range of surface design features and model the mechanical adhesion dynamics with an approach based on the fiber bundle model (FBM). We find that the fiber bundle model can be used to rationalize the observations after modifying it to capture the initial non-linear force response of the adhesives. Additionally, we investigate the behavior of the system’s elastic energy and damage energy, as it is stretched under strain-controlled conditions. Our experimental data indicates that the elastic energy has a maximum that appears after the macroscopic strength (σc), corresponding to strains where a full rupture of the system can no longer be prevented. Moreover, we observed that below the maximum of the constitutive curve σc, the elastic energy consistently exceeds the damage energy. Finally, we found that the derivative of the elastic energy has a maximum, which always appears before σc. Therefore, the derivative of the elastic energy would serve as a reliable signal of upcoming catastrophic failure in experiments under stress-controlled conditions.
Metabolite profiling of chickpea (Cicer arietinum) in response to necrotrophic fungus Ascochyta rabiei
Authors: Raman Rosy , Morris Stephen , Sharma Niharika , Hobson Kristy , Moore Kevin
Published: August 2024

Introduction

Ascochyta blight (AB) caused by the necrotrophic fungus Ascochyta rabiei is one of the most significant diseases that limit the production of chickpea. Understanding the metabolic mechanisms underlying chickpea-A.rabiei interactions will provide important clues to develop novel approaches to manage this disease.

Methods

We performed metabolite profiling of the aerial tissue (leaf and stem) of two chickpea accessions comprising a moderately resistant breeding line (CICA1841) and a highly susceptible cultivar (Kyabra) in response to one of the highly aggressive Australian A. rabiei isolates TR9571 via non-targeted metabolomics analysis using liquid chromatography-mass spectrometry.

Results

The results revealed resistance and susceptibility-associated constitutive metabolites for example the moderately resistant breeding line had a higher mass abundance of ferulic acid while the levels of catechins, phthalic acid, and nicotinic acid were high in the susceptible cultivar. Further, the host-pathogen interaction resulted in the altered levels of various metabolites (induced and suppressed), especially in the susceptible cultivar revealing a possible reason for susceptibility against A.r abiei. Noticeably, the mass abundance of salicylic acid was induced in the aerial tissue of the susceptible cultivar after fungus colonization, while methyl jasmonate (MeJA) was suppressed, elucidating the key role of phytohormones in chickpea-A. rabiei interaction. Many differential metabolites in flavonoid biosynthesis, phenylalanine, Aminoacyl-tRNA biosynthesis, pentose and glucuronate interconversions, arginine biosynthesis, valine, leucine, and isoleucine biosynthesis, and alanine, aspartate, and glutamate metabolism pathways were up- and down-regulated showing the involvement of these metabolic pathways in chickpea-A. rabiei interaction.

Discussion

Taken together, this study highlights the chickpea − A. rabiei interaction at a metabolite level and shows how A. rabiei differentially alters the metabolite profile of moderately resistant and susceptible chickpea accessions and is probably exploiting the chickpea defense pathways in its favour.
Unlocking the puzzle: non-defining mutations in SARS-CoV-2 proteome may affect vaccine effectiveness
Authors: Ulzurrun Eugenia , Grande-Pérez Ana , del Hoyo Daniel , Guevara Cesar , Gil Carmen , Sorzano Carlos Oscar , Campillo Nuria E.
Published: August 2024

Introduction

SARS-CoV-2 variants are defined by specific genome-wide mutations compared to the Wuhan genome. However, non-clade-defining mutations may also impact protein structure and function, potentially leading to reduced vaccine effectiveness. Our objective is to identify mutations across the entire viral genome rather than focus on individual mutations that may be associated with vaccine failure and to examine the physicochemical properties of the resulting amino acid changes.

Materials and methods

Whole-genome consensus sequences of SARS-CoV-2 from COVID-19 patients were retrieved from the GISAID database. Analysis focused on Dataset_1 (7,154 genomes from Italy) and Dataset_2 (8,819 sequences from Spain). Bioinformatic tools identified amino acid changes resulting from codon mutations with frequencies of 10% or higher, and sequences were organized into sets based on identical amino acid combinations.

Results

Non-defining mutations in SARS-CoV-2 genomes belonging to clades 21 L (Omicron), 22B/22E (Omicron), 22F/23A (Omicron) and 21J (Delta) were associated with vaccine failure. Four sets of sequences from Dataset_1 were significantly linked to low vaccine coverage: one from clade 21L with mutations L3201F (ORF1a), A27- (S) and G30- (N); two sets shared by clades 22B and 22E with changes A27- (S), I68- (S), R346T (S) and G30- (N); and one set shared by clades 22F and 23A containing changes A27- (S), F486P (S) and G30- (N). Booster doses showed a slight improvement in protection against Omicron clades. Regarding 21J (Delta) two sets of sequences from Dataset_2 exhibited the combination of non-clade mutations P2046L (ORF1a), P2287S (ORF1a), L829I (ORF1b), T95I (S), Y145H (S), R158- (S) and Q9L (N), that was associated with vaccine failure.

Discussion

Vaccine coverage associations appear to be influenced by the mutations harbored by marketed vaccines. An analysis of the physicochemical properties of amino acid revealed that primarily hydrophobic and polar amino acid substitutions occurred. Our results suggest that non-defining mutations across the proteome of SARS-CoV-2 variants could affect the extent of protection of the COVID-19 vaccine. In addition, alteration of the physicochemical characteristics of viral amino acids could potentially disrupt protein structure or function or both.
Association analyses between urinary concentrations of multiple trace elements and gastric precancerous lesions and gastric cancer in Anhui province, eastern China
Authors: Qian Shiqing , Xu Fang , Wang Min , Zhang Meng , Ding Shaopeng , Jin Guoqing , Zhang Xiaohui , Cheng Wenli , Wang Li , Zhu Yuting , Wang Wuqi , Ofosuhemaa Princess , Wang Tingting , Lin Xiao , Zhu Yu , Lv Yaning , Hu Anla , Yang Wanshui , He Gengsheng , Zhao Qihong
Published: August 2024

Background

Limited epidemiological evidence suggests that exposure to trace elements adversely impacts the development of gastric precancerous lesions (GPL) and gastric cancer (GC). This study aimed to estimate the association of individual urinary exposure to multiple elements with GPL and GC.

Methods

A case-control investigation was conducted in Anhui Province from March 2021 to December 2022. A total of 528 subjects (randomly sampled from 1,020 patients with GPL, 200 patients with GC, and 762 normal controls) were included in our study. Urinary levels of iron (Fe), copper (Cu), zinc (Zn), nickel (Ni), strontium (Sr), and Cesium (Cs) were measured using inductively coupled plasma mass spectrometry (ICP-MS). Four different statistical approaches were employed to explore the risk of GPL and GC with mixed exposure, including multivariate logistic regression, weighted quantile regression (WQS), quantile g-computation (Qgcomp), and the Bayesian kernel machine regression (BKMR) model.

Results

The WQS model indicated that urinary exposure to a mixture of elements is positively correlated with both GPL and GC, with ORs for the mixture exposure of 1.34 (95% CI: 1.34-1.61) for GPL and 1.38 (95% CI: 1.27-1.50) for GC. The Qgcomp and BKMR models also demonstrated a statistically significant positive correlation between the mixture and both GPL and GC.

Conclusion

Considering the limitations of case-control studies, future prospective studies are warranted to elucidate the combined effects and mechanisms of trace elements exposure on human health.
Linking drivers of food insecurity and ecosystem services in Africa
Authors: Aryee Gregory Ayitey , Sardinha Idalina Dias , Branquinho Cristina
Published: August 2024

Food insecurity is a multidimensional and intricate problem, known to have significant implications for individuals, communities, and countries worldwide. Africa has become the continent that is experiencing this uncertainty the most. Food Security (FS) encompasses several aspects such as availability, accessibility, nutrient use, and supply system stability with time and, more recently, other obliges to governance/agency and sustainability. Knowing the interconnection between these aspects and the Ecosystems Services (ES) and understanding the relationship and interactions between FS and ES is important. Moreover, this knowledge may contribute to supporting policies that promote long-term sustainable and secure food systems. Hereby, a conceptual framework is presented, that examines interactions between food insecurity drivers and ecosystem change drivers and the combined influence on ES. Our review further introduces existing trade-offs between ES on account of agricultural intensification vs. key existing strategies to promote sustainable agricultural production. These strategies include climate-smart agriculture, sustainably managed land, and effective handling of water resources. In the end, the potential of Payment for Ecosystem Services (PES), as a suitable approach to ensuring these strategies are adopted, especially in African countries where sustainable financial incentives are currently under-explored is discussed. In resume, this review aims to make a conceptual contribution to understanding how drivers of food insecurity influence drivers of ecosystem changes, the impact of these influences on the services of ecosystems, and how sustainable agro approaches and PES introduction can help to reduce such negative impacts.
Innovation: ice cream in the recovery room rules out chylothorax after thoracic lymphadenectomy and affords same-day chest tube removal
Authors: Cerfolio Robert J. , McCormack Ashley J.
Published: August 2024

Objectives

Early removal of chest tubes reduces pain and morbidity. This study aimed to remove chest tubes immediately after robotic pulmonary resection with complete thoracic lymphadenectomy by administering ice cream to rule out chylothorax.

Methods

This quality improvement study utilized prospectively gathered data from one thoracic surgeon. Patients were given 3.6 fl oz of ice cream in the recovery room within 1 h after their operation. Chest tubes were removed within 4 h if there was no chylous drainage and air leak on the digital drainage system.

Results

From January 2022 to August 2023, 343 patients underwent robotic pulmonary resection with complete thoracic lymphadenectomy. The median time to ingest the ice cream was 1.5 h after skin closure. The incidence of chylothorax was 0.87% (3/343). Two patients were diagnosed with chylothorax after consuming ice cream within 4 h of surgery. One patient, whose chest tube remained in place due to an air leak, had a chylothorax diagnosed on postoperative day 1 (POD1). All three patients were discharged home on POD1 with their chest tubes in place, adhering to a no-fat, medium-chain triglyceride diet. All chylothoraces resolved within 6 days. None of the remaining patients developed chylothorax postoperatively with a minimum follow-up period of 90 days.

Conclusions

Providing ice cream to patients after pulmonary resection and complete thoracic lymphadenectomy is an effective and reliable technique to rule out chylothorax early in the postoperative period and facilitates early chest tube removal. Further studies are needed to ensure that this simple, inexpensive test is reproducible.
Genomic revelations: investigating rotavirus a presence in wild ruminants and its zoonotic potential
Authors: Šenica Petra , Žele Vengušt Diana , Vengušt Gorazd , Kuhar Urška
Published: August 2024

Introduction

Rotaviruses A (RVA) are a major cause of acute viral gastroenteritis in humans worldwide and are responsible for about two million hospitalizations per year. They can also infect other mammals such as pigs, calves, goats, lambs, and horses, in which they are also considered a major cause of viral diarrhea. While RVA is well studied in humans and domestic animals, its occurrence in wild ruminants is not well known. The RVA genome is a double-stranded RNA consisting of 11 segments, and genotyping is based on the VP7 (G) and VP4 (P) segments. Currently, there are 42G genotypes and 58P genotypes. RVA has a high mutation rate, and some combinations of G and P genotypes can infect different animal species, leading to speculation about the potential for zoonotic transmission.

Materials and methods

A total of 432 fecal samples were collected from roe deer, red deer, chamois, mouflon and Alpine ibex in Slovenia between 2017 and 2021. To investigate the presence of RVA in wild ruminants, real-time RT-PCR was used. Positive samples were subjected to next generation sequencing (NGS) using RIP-seq method.

Results and discussion

In total, 7 samples were RVA positive. Complete genomes were determined and phylogenetically analyzed for all 7 RVAs. Four different genotype constellations were present in 7 positive RVA animals: G8-P[14]-I2- R2-C2-M2-A3-N2-T6-E2-H3, G6-P [14]-I2-R2-C2-M2-A11-N2-T6-E2-H3, G10-P [15]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P [15]-I2-R2-C2-M2-A11- N2-T6-E2-H3. Genotypes G6P[14] and G10P[15] were found in both roe deer and red deer, representing the first confirmed occurrence of RVA in red deer. In addition, genotype G8P[14] was found in chamois, representing the first known case of positive RVA in this species. Some of these genotypes have also been found in humans, indicating the potential for zoonotic transmission.
A Virtual Machine Platform Providing Machine Learning as a Programmable and Distributed Service for IoT and Edge On-Device Computing: Architecture, Transformation, and Evaluation of Integer Discretization
Authors: Bosse Stefan
Published: August 2024

Data-driven models used for predictive classification and regression tasks are commonly computed using floating-point arithmetic and powerful computers. We address constraints in distributed sensor networks like the IoT, edge, and material-integrated computing, providing only low-resource embedded computers with sensor data that are acquired and processed locally. Sensor networks are characterized by strong heterogeneous systems. This work introduces and evaluates a virtual machine architecture that provides ML as a service layer (MLaaS) on the node level and addresses very low-resource distributed embedded computers (with less than 20 kB of RAM). The VM provides a unified ML instruction set architecture that can be programmed to implement decision trees, ANN, and CNN model architectures using scaled integer arithmetic only. Models are trained primarily offline using floating-point arithmetic, finally converted by an iterative scaling and transformation process, demonstrated in this work by two tests based on simulated and synthetic data. This paper is an extended version of the FedCSIS 2023 conference paper providing new algorithms and ML applications, including ANN/CNN-based regression and classification tasks studying the effects of discretization on classification and regression accuracy.
A System Design Perspective for Business Growth in a Crowdsourced Data Labeling Practice
Authors: Hajipour Vahid , Jalali Sajjad , Santos-Arteaga Francisco Javier , Vazifeh Noshafagh Samira , Di Caprio Debora
Published: August 2024

Data labeling systems are designed to facilitate the training and validation of machine learning algorithms under the umbrella of crowdsourcing practices. The current paper presents a novel approach for designing a customized data labeling system, emphasizing two key aspects: an innovative payment mechanism for users and an efficient configuration of output results. The main problem addressed is the labeling of datasets where golden items are utilized to verify user performance and assure the quality of the annotated outputs. Our proposed payment mechanism is enhanced through a modified skip-based golden-oriented function that balances user penalties and prevents spam activities. Additionally, we introduce a comprehensive reporting framework to measure aggregated results and accuracy levels, ensuring the reliability of the labeling output. Our findings indicate that the proposed solutions are pivotal in incentivizing user participation, thereby reinforcing the applicability and profitability of newly launched labeling systems.
Uptake and Economic Value of Macro- and Micronutrient Minerals in Wheat Residue
Authors: Adams Curtis B. , Rogers Christopher W. , Marshall Juliet M. , Hatzenbuehler Patrick , Walsh Olga S. , Thurgood Garrett , Dari Biswanath , Loomis Grant , Tarkalson David D.
Published: August 2024

Wheat (Triticum aestivum, L.) producers have the choice to retain or remove residue from the cropping system following grain harvest. In the U.S. Pacific Northwest and other regions, wheat residue is often sold to increase operational profitability, especially from higher-yielding systems. But there are several benefits to retaining residue, including recycling of mineral nutrients contained therein, though this is understudied. Therefore, the primary objectives of this research were to collect and analyze a large and diverse dataset on wheat residue nutrient uptake (N, P, K, Ca, Mg, S, Fe, Zn, Mn, Cu), develop tools to estimate nutrient amounts in residue, and make economic estimates of the fertilizer replacement value of those nutrients. This was accomplished by conducting replicated variety trials on five classes of wheat across many Pacific Northwest sites over two years, then collecting and analyzing data on wheat residue biomass, residue nutrient concentrations, and grain yield. The results showed that wheat residue contained a significant amount of nutrients, but was particularly concentrated in K. Production environment had the most substantial effect on residue mineral uptake amounts, due to site differences in yield and soil nutrient availability. To enable simple estimation of residue nutrient uptake across a broad range of wheat production levels, two estimation tools are presented herein. Economic analysis showed the substantial monetary value of residual nutrients. For example, in a high-yielding wheat crop (9 Mg ha−1), the average fertilizer replacement value of just residue N, P, K, and S was similar to the entire fertilizer budget to grow the crop (~$211 vs. $205 ha−1), not considering micronutrients in the residue or any nutrients removed through grain harvest. In making residue management decisions, wheat producers should consider the tradeoff between the immediate economic gains of residue sale and the multifaceted benefits of residue retention, including savings on future nutrient costs.
Spatial and Temporal Variability of Soil pH, Organic Matter and Available Nutrients (N, P and K) in Southwestern China
Authors: Guo Bao-Xiu , Zhou Jia , Zhan Lin-Qing , Wang Zi-Yu , Wu Wei , Liu Hong-Bin
Published: August 2024

Knowledge of the spatial and temporal variations in soil nutrients is crucial for designing efficient site-specific nutrient management plans, which can improve crop yields and maximize nutrient use efficiency. The present study was conducted to evaluate and compare the status and spatio-temporal distribution pattern of available nitrogen (AHN), phosphorus (AP) and potassium (AK) and some selected soil properties [soil pH and soil organic matter (SOM)] in cultivated soils of Southwestern China over a 15-year period (2007–2022). We visualized the correlations among soil properties, AHN, AP and AK and analyzed the spatial structures of these parameters. A total of 3845 topsoil (0–20 cm) samples (3331 in 2007 and 514 in 2022) were collected from the cultivated areas of Jiangjin District, Chongqing, Southwestern China. Soil pH, SOM, AHN and AK showed moderate variability with coefficient of variation (CV) values varying between 10 and 100%, except AP (CV > 100%, high variability). The mean soil pH, SOM, AP and AK in 2022 were significantly higher than those in 2007. AHN was significantly positively correlated with SOM (r = 0.531, p < 0.01 in 2007, r = 0.768, p < 0.01 in 2022) and significantly negatively correlated with soil pH (r = −0.186, p < 0.01 in 2007, r = −0.102, p < 0.05 in 2022). AP was significantly negatively correlated with soil pH (r = −0.075, p < 0.01 in 2007, r = −0.126, p < 0.01 in 2022). AK was significantly positively correlated with SOM (r = 0.164, p < 0.01 in 2007, r = 0.229, p < 0.01 in 2022), ANH (r = 0.131, p < 0.01 in 2007, r = 0.251, p < 0.01 in 2022) and AP (r = 0.145, p < 0.01 in 2007, r = 0.52, p < 0.01 in 2022). The exponential function performed best for the soil properties and all three nutrients, with higher R2 values (0.203 to 0.93 in 2007 and 0.316 to 0.796 in 2022) in both years. The nugget/sill ratios (which varied from 31.58% to 72% in 2007 and from 29.31% to 47.02% in 2022) indicated the moderate spatial dependence of all soil parameters, except AK in 2022 (nugget/sill ratio = 23.81%, strong spatial dependence). During the study period, soil pH, AP and AK increased in the central and northern areas; SOM increased in the northern and southwestern parts; AHN decreased in the central areas. The current study highlighted the change in spatial variability of soil pH, AHN, AP and AK in the study area over 15 years.
A Tool for the Design of the Minimal Fingerprinting SNP Set: Use Case for Barley
Authors: Ermolaev Aleksey , Samarina Mariya , Strembovskiy Ilya , Kroupin Pavel , Karlov Gennady , Kharchenko Pyotr , Voronov Sergey , Eroshenko Lyubov , Kryuchenko Elizaveta , Laptina Yulia , Avdeev Sergey , Shirnin Sergey , Igonin Vladimir , Divashuk Mikhail
Published: August 2024

High-throughput genomic technologies are enabling the identification of thousands or even millions of single-nucleotide polymorphisms (SNPs). SNP markers are frequently used to analyze crop varieties, with the marker data summarized in a common VCF file. At present, it is difficult to identify the minimal SNP set, the smallest sets that can distinguish between all crop varieties listed in a VCF file, due to the absence of available ready-to-use tools capable of such characterization. Here, we describe the development of the ready-to-use open-source tool MDSearch (Minimal Discriminatory SNP Set Search) based on the identification of the MDS (minimal discriminatory set) of SNPs using random walking staring from the maximal discriminatory set. MDSearch can be used for disploid as well as poliploid species and both phased and unphased VCF files. MDSearch has been validated using a publicly available dataset of barley SNPs obtained by genotyping-by-sequencing. As a result, we have successfully identified a discriminating set of 19 SNP markers capable of distinguishing all 254 barley varieties included in our study. We expect that this program will prove useful to genomics researchers to support a variety of certifications.
A Roadmap to Toxocariasis Infection Control: A Comprehensive Study on Its Impact, Seroprevalence, and Allergic Implications in Latin America
Authors: Silva Raphael Chagas , Silva Jaqueline Wang da , Fernandes Antônio Márcio Santana , Figueiredo Camila Alexandrina Viana de , Coneglian Natália Gomes de Morais , Alcântara Neves Neuza Maria , Pinheiro Carina da Silva
Published: August 2024

This study was conducted using data from the SCAALA (Social Change Asthma and Allergy in Latin America) cohort in Brazil from 2005 to 2013. We examined the seroprevalence and risk factors of toxocariasis, a parasitic infection leading to conditions such as visceral larva migrans, utilizing an indirect ELISA with T. canis antigens, alongside with data from questionnaires, eosinophil counts, sIgE to aeroallergens, IL-10 levels, and Skin Prick Test results; the research provided insights into the disease’s dynamics. The prevalence of anti-Toxocara spp. IgG increased from 48% to 53% over the studied period, with a 25% increase in new cases in 2013. The significant risk factors included age and pet exposure, while higher maternal education and living on paved streets were found to offer protection. The study uncovered a complex interaction between Toxocara spp. infection and the immune system, indicating that the infection could both trigger inflammation and modulate skin reactions. Based on these findings, the study proposed a roadmap for controlling toxocariasis, which includes strategies such as enhancing public education about the disease and preventive measures, improving environmental sanitation, strengthening veterinary control measures like pet deworming, increasing access to healthcare and screening, and implementing community-based interventions to address the identified risk factors. These measures aim to reduce the prevalence of toxocariasis and its impact on public health by addressing environmental and socioeconomic risk factors, providing a pathway to significantly reduce the burden of this parasitic infection.
Optimizing Supply Chain Efficiency Using Innovative Goal Programming and Advanced Metaheuristic Techniques
Authors: Douaioui Kaoutar , Benmoussa Othmane , Ahlaqqach Mustapha
Published: August 2024

This paper presents an optimization approach for supply chain management that incorporates goal programming (GP), dependent chance constraints (DCC), and the hunger games search algorithm (HGSA). The model acknowledges uncertainty by embedding uncertain parameters that promote resilience and efficiency. It focuses on minimizing costs while maximizing on-time deliveries and optimizing key decision variables such as production setups, quantities, inventory levels, and backorders. Extensive simulations and numerical results confirm the model’s effectiveness in providing robust solutions to dynamically changing supply chain problems when compared to conventional models. However, the integrated model introduces substantial computational complexity, which may pose challenges in large-scale real-world applications. Additionally, the model’s reliance on precise probabilistic and fuzzy parameters may limit its applicability in environments with insufficient or imprecise data. Despite these limitations, the proposed approach has the potential to significantly enhance supply chain resilience and efficiency, offering valuable insights for both academia and industry.
An Alternative Series Solution for Free Vibration Analysis of Asymmetric L-Shaped Membranes
Authors: Chang Kao-Hao , Kuo Wen-Ten
Published: August 2024

This study revisits the freely vibrating problem of asymmetric L-shaped membranes using a three-segmented domain decomposition (3-SDD) strategy. Motivated by the need for more accurate and flexible methods, the 3-SDD strategy is compared with the previously proposed two-segmented domain decomposition (2-SDD) strategy. The region-matching technique is used to derive an alternative series solution, and the eigenvalues obtained are compared with those in existing research. The convergence behavior and sensitivity analyses reveal that the 3-SDD strategy offers improved accuracy and stability, particularly for higher truncation terms. Detailed comparisons of the first four eigenvalue squares show strong agreement between the 3-SDD and 2-SDD strategies, confirming the reliability of both methods. This research establishes a foundation for the vibration analysis of complex membrane structures, emphasizing the benefits of the 3-SDD approach for upcoming engineering applications and showcasing its potential for broader applicability in practical scenarios. The findings underscore the importance of utilizing multi-segmented decomposition strategies to enhance the accuracy and flexibility of free vibration analysis.
Tribological Analysis of Fused Filament Fabrication PETG Parts Coated with IGUS
Authors: Batista Moises , Tenorio Delia , Del Sol Irene , Vazquez-Martinez Juan Manuel
Published: August 2024

This paper studied the tribological behaviour of parts manufactured using fused filament fabrication (FFF) technology with PETG (polyethylene terephthalate glycol) coated with IGUS tribological filaments. The research focuses on analysing how these multi-material parts behave under different loads. The objective of this study is to evaluate the wear resistance and friction coefficient of parts coated with different thicknesses of IGUS material. The methodology employs pin-on-disc (PoD) tribological tests to measure behaviour under various load conditions and coating thicknesses. The results indicate that increasing the coating thickness improves surface stability and reduces roughness, although it does not significantly affect the average friction coefficient. This research concludes that coating thickness has a moderate impact on surface quality and that the applied load significantly influences the depth and width of the wear groove. This contribution is valuable for the field of additive manufacturing as it provides a better understanding of how to optimise the tribological properties of parts manufactured using FFF, which is crucial for industrial applications where wear and friction are critical factors. The practical application includes the potential improvement of components in the automotive and aerospace industries.
Cable Tension of Long-Span Steel Box Tied Arch Bridges Based on Radial Basis Function-Support Vector Machine Optimized by Quantum-Behaved Particle Swarm Optimization
Authors: Shi Hongcai , Shi Menglin , Xu Weisheng
Published: August 2024

To investigate hanger force during the construction phase of large-span steel box tie arch bridges, the challenge of low accuracy in force identification due to multifactor coupling was addressed. An energy method was employed to derive formulas for calculating forces under different boundary conditions. Utilizing the QPSO-RBF-SVM machine learning algorithm model, predictions of bridge formation stage forces were conducted, integrating findings from actual engineering case studies. Error analysis on hanger force was performed, revealing that the quantum particle swarm optimization (QPSO) algorithm optimizes parameters in the radial basis function support vector machine (RBF-SVM). The model was trained on datasets, achieving an average relative error of 0.65% in predicted cable force values compared with measured values in the test set, with a coefficient of determination of 0.97. These results demonstrate superior accuracy compared with calculations derived from the energy method and other machine learning algorithms. This algorithmic model presents a promising approach for accurately assessing cable forces in large-span steel box tie arch bridges.
Flexural Performance of Carbon Fiber-Reinforced Polymer Prestressed Spun High-Strength Concrete Pile
Authors: Tan Cheng , Jiang Xu , Qiang Xuhong , Fan Mingxin
Published: August 2024

Prestressed spun high-strength concrete (PHC) piles are commonly used in various types of structures, including bridges, buildings and marine infrastructures. However, piles installed in aggressive environments are vulnerable to corrosion of the steel, which can lead to rapid degradation of the piles. As a corrosion-resistant material, carbon fiber-reinforced polymer (CFRP) is considered an alternative to steel tendons for durability enhancement. In this study, a new pile system with CFRP was proposed. Experimental tests of three full-scale piles and a numerical analysis of eight piles with various parameters were performed to investigate the flexural performance of CFRP prestressed spun high-strength concrete pile. The proposed piles were loaded under four-point bending after prestressing. The experimental and numerical results verified the feasibility of the proposed system, and the CFRP pile exhibited twice of flexural capacity of that of steel-reinforced piles. The flexural performance of the CFRP PHC pile was significantly affected by the reinforcement ratio, prestressing level and modulus of the CFRP. An analytical approach predicting the flexural capacity of the CFRP PHC pile was proposed based on the parametric study. Ninety percent accuracy was achieved for the proposed analytical approach. The presented study can significantly promote the application of CFRP in pile foundations and improve the durability of PHC piles.
Influence of Time–Activity Patterns on Indoor Air Quality in Italian Restaurant Kitchens
Authors: Keller Marta , Campagnolo Davide , Borghi Francesca , Carminati Alessio , Fanti Giacomo , Rovelli Sabrina , Zellino Carolina , Del Vecchio Rocco Loris , De Vito Giovanni , Spinazzé Andrea , Mihucz Viktor Gábor , Dossi Carlo , Carrieri Mariella , Cattaneo Andrea , Cavallo Domenico Maria
Published: August 2024

This study aims to delve deeper into the relationship between the professional activities carried out in restaurant kitchens and some key air pollutants. The ultrafine particles (UFPs), nitrogen dioxide (NO2), ozone (O3), Total Volatile Organic Compounds (TVOCs) and formaldehyde (HCHO) indoor air concentrations were determined using real-time monitors. Simultaneously, the kitchen environment was characterized using video recordings with the aim to retrieve information pertaining to cooking, cookware washing and surface cleaning activities. Statistical analysis was carried out separately for the winter and summer campaigns. The obtained results confirmed that the professional activities carried out in restaurant kitchens had a significant impact on the concentrations of all the selected pollutants. Specifically, this study revealed the following key results: (i) indoor UFPs and NO2 concentrations were significantly higher during cooking than during washing activities (e.g., about +60% frying vs. handwashing and dishwasher running), mainly in the winter; (ii) washing activity had a statistically significant impact on the TVOC (+39% on average) and HCHO (+67% on average) concentrations compared to other activities; (iii) some specific sources of short-term pollutant emissions have been identified, such as the different types of cooking and opening the dishwasher; and (iv) in some restaurants, a clear time-dependent relationship between O3 and UFP, TVOC and HCHO has been observed, underlining the occurrence of ozonolysis reactions.
Exploring Fixed-Point Theorems in k-Fuzzy Metric Spaces: A Comprehensive Study
Authors: Nazam Muhammad , Attique Seemab , Hussain Aftab , Alsulami Hamed H.
Published: August 2024

Recently, k -fuzzy metric spaces were introduced by connecting the degree of nearness of two points with k parameters (t1,t2,t3,⋯,tk) and the authors presented an analogue of Grabiec’s fixed-point result in k-fuzzy metric spaces along with other necessary notions. The results presented only addressed continuous mappings. For discontinuous mappings, there is no result in k-fuzzy metric spaces. In this paper, we obtain some fixed-point results stating necessary conditions for the existence of fixed points of mappings eliminating the continuity requirement in k-fuzzy metric spaces. We illustrate the hypothesis of our findings with examples. We provide a common fixed-point theorem and fixed-point theorems for single-valued k-fuzzy Kannan type contractions. As an application, we use a fixed-point result to ensure the existence of solution of fractional differential equations.
Stable and Thin-Polymer-Based Modification of Neurovascular Stents with 2-Methacryloyloxyethyl Phosphorylcholine Polymer for Antithrombogenicity
Authors: Inuzuka Naoki , Shobayashi Yasuhiro , Tateshima Satoshi , Sato Yuya , Ohba Yoshio , Ishihara Kazuhiko , Teramura Yuji
Published: August 2024

The advent of intracranial stents has revolutionized the endovascular treatment of cerebral aneurysms. The utilization of stents has rendered numerous cerebral aneurysm amenable to endovascular treatment, thereby obviating the need for otherwise invasive open surgical options. Stent placement has become a mainstream approach because of its safety and efficacy. However, further improvements are required for clinically approved devices to avoid the frequent occurrence of thrombotic complications. Therefore, controlling the thrombotic complications associated with the use of devices is of significant importance. Our group has developed a unique stent coated with a 2-methacryloyloxyethyl phosphorylcholine (MPC)-based polymer. In this study, the surface characteristics of the polymer coating were verified using X-ray photoelectron spectroscopy and atomic force microscopy. Subsequently, the antithrombotic properties of the coating were evaluated by measuring platelet count and thrombin–antithrombin complex levels of whole human blood after 3 h of incubation in a Chandler loop model. Scanning electron microscopy was utilized to examine thrombus formation on the stent surface. We observed that MPC polymer-coated stents significantly reduced thrombus formation as compared to bare stents and several clinically approved devices. Finally, the coated stents were further analyzed by implanting them in the internal thoracic arteries of pigs. Angiographic imaging and histopathological examinations that were performed one week after implantation revealed that the vascular lumen was well maintained and coated stents were integrated within the vascular endothelium without inducing adverse effects. Thus, we demonstrated the efficacy of MPC polymer coating as a viable strategy for avoiding the thrombotic risks associated with neurovascular stents.
Solute Carrier Family 35 (SLC35)—An Overview and Recent Progress
Authors: Kamiyama Shin , Sone Hideyuki
Published: August 2024

The solute carrier family 35 (SLC35) comprises multiple members of transporters, including a group of proteins known as nucleotide sugar transporters (NSTs), an adenosine triphosphate (ATP) transporter, 3′-phosphoadenosine 5′-phosphosulfate (PAPS) transporters, and transporters of unknown function. To date, seven subfamilies (A to G) and 32 members have been classified into this large SLC35 family. Since the majority of glycosylation reactions occur within the lumen of the endoplasmic reticulum (ER) and Golgi apparatus, the functions of NSTs are indispensable for the delivery of substrates for glycosylation. Recent studies have revealed the diverse functions of this family of proteins in the regulation of numerous biological processes, including development, differentiation, proliferation, and disease progression. Furthermore, several congenital disorders of glycosylation (CDGs) resulting from variations in the SLC35 family member genes have been identified. To elucidate the pathology of these diseases, a variety of knockout mice harboring mutations in the family member genes have been generated and employed as animal models for CDGs. This review presents a historical overview of the SLC35 family, with a particular focus on recent advances in research on the functions of this family and their relationship to human diseases.
Generation of Two-Line Restorer Line with Low Chalkiness Using Knockout of Chalk5 through CRISPR/Cas9 Editing
Authors: Fan Gucheng , Jiang Jiefeng , Long Yu , Wang Run , Liang Famao , Liu Haiyang , Xu Junying , Qiu Xianjin , Li Zhixin
Published: August 2024

Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H+-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions.
Molecular Developmental Biology of Fibrodysplasia Ossificans Progressiva: Measuring the Giant by Its Toe
Authors: Towler O. Will , Shore Eileen M. , Kaplan Frederick S.
Published: August 2024

When a genetic disease is characterized by the abnormal activation of normal molecular pathways and cellular events, it is illuminating to critically examine the places and times of these activities both in health and disease. Therefore, because heterotopic ossification (HO) in fibrodysplasia ossificans progressiva (FOP) is by far the disease’s most prominent symptom, attention is also directed toward the pathways and processes of bone formation during skeletal development. FOP is recognizable by effects of the causative mutation on skeletal development even before HO manifests, specifically in the malformation of the great toes. This signature skeletal phenotype is the most highly penetrant, but is only one among several skeletal abnormalities associated with FOP. Patients may present clinically with joint malformation and ankylosis, particularly in the cervical spine and costovertebral joints, as well as characteristic facial features and a litany of less common, non-skeletal symptoms, all stemming from missense mutations in the ACVR1 gene. In the same way that studying the genetic cause of HO advanced our understanding of HO initiation and progression, insight into the roles of ACVR1 signaling during tissue development, particularly in the musculoskeletal system, can be gained from examining altered skeletal development in individuals with FOP. This review will detail what is known about the molecular mechanisms of developmental phenotypes in FOP and the early role of ACVR1 in skeletal patterning and growth, as well as highlight how better understanding these processes may serve to advance patient care, assessments of patient outcomes, and the fields of bone and joint biology.