bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Ply Misalignment in Material Characterization of Composite Laminates
Authors: Franz Michael , Radjef Racim , Eisenbart Boris , Wartzack Sandro
Published: November 2024

Carbon fiber reinforced plastic (CFRP) parts find a rising number of applications as structural components. Therefore, new manufacturing technologies are developed, enabling high volume production of such parts. With those higher volumes, variation management during product design becomes more critical. While manufacturing variations in CFRP materials occur on different scales, detecting and considering those on the meso (ply) scale becomes more important. Thus, the question arises whether such variations can be detected with standardized testing methods. In this study, artificial fiber misalignment has been introduced into the outer plies of standardized tensile specimens to explore the influence of such variations on the mechanical properties. A simulation model was developed to identify these variations and the test results were used to calibrate and optimize the material parameters of the simulation model. The effects of the artificially induced variation were distinguishable in the test data as well as in the simulation models. Furthermore, the simulation models showed good agreement with the experimental data, which leads to the conclusion that the utilized measuring techniques are well suited to characterize the fiber misalignment. The developed simulation models can be used to investigate the effects of fiber misalignment within the product development process without the need for physical testing.
Research on Wildfire and Soil Water: A Bibliometric Analysis from 1990 to 2023
Authors: Zuo Fenglin , Yao Qichao , Shi Lamei , Wang Zhou , Bai Maowei , Fang Keyan , Guo Futao , Yuan Lihua , Zhang Weikang
Published: November 2024

In the context of climate change, wildfires occur more frequently and significantly impact the vegetation–soil–water continuum. Soil water is a critical factor for understanding wildfire occurrence and predicting wildfire hazards. However, there is a lack of specific bibliometric analysis of the research on the mechanisms by which soil water influences wildfire occurrence. Therefore, this study conducted a bibliometric analysis of wildfire and soil water, aiming to understand their relationship, research characteristics, and future development trends. We used the Bibliometrix software package in R 4.4.0, which provides different methods for analyzing bibliometric data. A total of 1585 publications were analyzed from 1990 to 2023. The results of the study showed that the number of publications showed an overall growth trend during the period, with an average annual increase rate of 4.4%. The average annual citations per paper exhibited a pattern of rapid increase, followed by slow growth, and then rapid decrease. Ten highly productive authors in the field contributed 12.2% of the total publications during this period. Over the past 30 years, the University of Aveiro has consistently ranked first in terms of paper quantity. Most of the top ten productive institutions are in the United States, Australia, and several European countries. Fifty-eight countries engage in research related to wildfires and soil water, with close collaboration observed between the United States, Canada, and Spain. The four most frequently used keywords are “wildfire”, “fire”, “water repellency”, and “runoff” (with a total frequency of 1385). Water properties relevant to soil characteristics in the word cloud primarily include hydrophobicity, runoff, erosion, and infiltration. Erosion, wildfires, and runoff are crucial in the field but have yet to receive substantial development. The correlation of post-wildfire soil water properties with infiltration, runoff, and erosion processes is most likely to be addressed in future research. The findings will help researchers assess the post-wildfire disaster chain and its impact on the ecological environment, with clear trends, gaps, and research directions in the areas.
The Effects of Predominantly Chemoautotrophic Versus Heterotrophic Biofloc Systems on Nitrifying Bacteria, Planktonic Microorganisms, and Growth of Penaeus vannamei, and Oreochromis niloticus in an Integrated Multitrophic Culture
Authors: Sena Raysa Pâmela Oliveira , Krummenauer Dariano , Wasielesky Wilson , Pimentel Otávio Augusto Lacerda Ferreira , Bezerra Aline , dos Santos Junior Jorge Renato Tagliaferro , Carvalho Andrezza , Ravagnan Elisa , Bagi Andrea , Poersch Luis H. S.
Published: November 2024

The aim of this study was to evaluate the effect of predominantly chemoautotrophic and heterotrophic biofloc systems on ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and planktonic microorganisms in an integrated Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. Shrimp and tilapia were stocked at a density of 400 shrimp m−2 and 45 fish m−3, respectively. The trial consisted of two biofloc treatments, with three replicates each: chemoautotrophic and heterotrophic. The identification and quantification of the planktonic microorganisms (ciliates, flagellates, microalgae, and total bacteria) and nitrifying bacteria were carried out through direct counting and fluorescence in situ hybridization, respectively. At the end of the trial, heterotrophic treatment had resulted in higher total abundance of bacteria. The relative abundance of AOB and NOB in relation to the total abundance was less than 0.1% for both treatments. The system was dominated by flagellates in both treatment groups. The abundance of microalgae and ciliates was higher with chemoautotrophic treatment. After 43 days, the shrimp weights were higher in the chemoautotrophic group, while the final weights of the tilapia were not significantly different between the two treatments. The type of biofloc system (Chemoautotrophic vs. Heterotrophic) did not significantly alter the establishment of AOB and NOB in a Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. The two treatments proved to be equally efficient for maintaining good water quality, but the chemoautotrophic treatment resulted in better shrimp growth. Thus, our study demonstrated that chemoautotrophic biofloc is a promising approach in integrated multitrophic aquaculture.
Texture Evaluation and In Vivo Oral Tactile Perceptions of Cooked Wheat Pasta Sheets Partially Substituted with Pea Protein
Authors: Yang Chengyi , Leong Sze Ying , King Jessie , Kim Esther H.-J. , Morgenstern Marco P. , Peng Mei , Agyei Dominic , Sutton Kevin , Oey Indrawati
Published: November 2024

Plant proteins are increasingly incorporated into food products to enhance their nutritional value. However, little is known about how this alters the textural perceptions of such products. This study investigated the substitution of up to 35% wheat flour with pea protein isolate (PPI) into pasta sheets to determine how this influenced texture. Furthermore, an in vivo human mastication test (n = 116 participants) was conducted to evaluate oral tactile perceptions (perceived firmness, stickiness, and brittleness) and chewing time associated with PPI-containing pasta. Cooked pasta hardness decreased from 145 to 96 N at 5% PPI substitution due to the disruption of gluten network but increased to 144 N at 15–25% PPI substitution, indicating a stronger protein network at higher PPI substitution levels. In vivo, pasta substituted with 25% PPI required a shorter chewing time and was perceived as less firm, less sticky, and more brittle than wheat flour-only pasta. Regardless of pasta samples, fast chewers (average chewing time ≤13 s) were better at recognizing differences in pasta firmness, while slow chewers (>13 s) were more sensitive to changes in stickiness and brittleness. The results obtained in this study could contribute to the design of protein-rich pasta tailored to populations with specific texture requirements (e.g., softer texture for the elderly).
Exploration of Bioactive Umami Peptides from Wheat Gluten: Umami Mechanism, Antioxidant Activity, and Potential Disease Target Sites
Authors: Chen Haowen , Zhao Huiyan , Li Cuiling , Zhou Chunxia , Chen Jianxu , Xu Wenjie , Jiang Guili , Guan Jingjing , Du Zhuorong , Luo Donghui
Published: November 2024

Umami peptides have the ability to enhance food flavours and have potential health benefits. The objective of this study was to conduct a comprehensive investigation into the umami intensity, taste mechanism, and antioxidant activity of six umami peptides derived from wheat gluten hydrolysates (WGHs) and fermented WGHs. The e-tongue analysis demonstrated that the peptides exhibited a direct proportionality in terms of umami value and concentration, and were capable of enhancing the umami of commercially available condiments. The molecular dynamics simulations demonstrated that the peptides interacted with T1R1/T1R3 receptors via hydrogen bonds, hydrophobic interactions, ionic interactions, and water bridges, thereby producing umami. Furthermore, the DPPH, ABTS, hydroxyl radical-scavenging, and FRAP assays demonstrated that the six peptides exhibited antioxidant activity in vitro. Ultimately, the network pharmacology and molecular docking results indicated that AKT1, JUN, and CASP3 may serve as the core targets for the peptides in the treatment of oxidative diseases. In conclusion, this work offers novel insights into the use of bioactive umami peptides, emphasising their prospective applications in the food and health supplement industries.
Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species
Authors: Jahuey-Martínez Francisco J. , Martínez-Quintana José A. , Rodríguez-Almeida Felipe A. , Parra-Bracamonte Gaspar M.
Published: November 2024

Background: Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species’ genomes is crucial for animal genetics research. Objectives: This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL distribution and evaluating the correlation between QTL, gene density, and chromosome size with the aim to identify QTL-enriched genomic regions. Methods: Data from 211,715 QTL (1994–2021) were retrieved from the AnimalQTLdb and analyzed using R software v4.2.1. Unique QTL annotations were identified, and redundant or inconsistent data were removed. Statistical analyses included Pearson correlations and binomial, hypergeometric, and bootstrap-based enrichment tests. Results: QTL densities per Mbp were 10 for bovine, 4 for pig, 1 for sheep, and 3 for chicken genomes. Analysis of QTL distribution across chromosomes revealed uneven patterns, with certain regions enriched for QTL. Correlation analysis revealed a strong positive relationship between QTL and gene density/chromosome size across all species (p < 0.05). Enrichment analysis identified pleiotropic regions, where QTL affect multiple traits, often aligning with known candidate and major genes. Significant QTL-enriched windows (p < 0.05) were detected, with 699 (187), 355 (68), 50 (15), and 38 (17) genomic windows for cattle, pigs, sheep, and chickens, respectively, associated with overall traits (and specific phenotypic categories). Conclusions: This study provides critical insights into QTL distribution and its correlation with gene density, offering valuable data for advancing genetic research in livestock species. The identification of QTL-enriched regions also highlights key areas for future exploration in trait improvement programs.
Disentangling the Genetic Landscape of Peripartum Depression: A Multi-Polygenic Machine Learning Approach on an Italian Sample
Authors: Harrington Yasmin A. , Fortaner-Uyà Lidia , Paolini Marco , Poletti Sara , Lorenzi Cristina , Spadini Sara , Melloni Elisa M. T. , Agnoletto Elena , Zanardi Raffaella , Colombo Cristina , Benedetti Francesco
Published: November 2024

Background: The genetic determinants of peripartum depression (PPD) are not fully understood. Using a multi-polygenic score approach, we characterized the relationship between genome-wide information and the history of PPD in patients with mood disorders, with the hypothesis that multiple polygenic risk scores (PRSs) could potentially influence the development of PPD. Methods: We calculated 341 PRSs for 178 parous mood disorder inpatients affected by major depressive disorder (MDD) or bipolar disorder (BD) with (n = 62) and without (n = 116) a history of PPD. We used partial least squares regression in a novel machine learning pipeline to rank PRSs based on their contribution to the prediction of PPD, in the whole sample and separately in the two diagnostic groups. Results: The PLS linear regression in the whole sample defined a model explaining 27.12% of the variance in the presence of PPD history, 56.73% of variance among MDD, and 42.96% of variance in BD. Our findings highlight that multiple genetic factors related to circadian rhythms, inflammation, and psychiatric diagnoses are top contributors to the prediction of PPD. Specifically, in MDD, the top contributing PRS was monocyte count, while in BD, it was chronotype, with PRSs for inflammation and psychiatric diagnoses significantly contributing to both groups. Conclusions: These results confirm previous literature about the immune system dysregulation in postpartum mood disorders, and shed light on which genetic factors are involved in the pathophysiology of PPD.
Survive and Thrive: Outcomes of Children Enrolled in a Follow-Up Clinic for Small and Sick Newborns in Rural Rwanda
Authors: Nshimyiryo Alphonse , Barnhart Dale A. , Nemerimana Mathieu , Beck Kathryn , Wilson Kim , Mutaganzwa Christine , Bigirumwami Olivier , Shema Evelyne , Uwamahoro Alphonsine , Itangishaka Cécile , Havugarurema Silas , Sayinzoga Felix , Baganizi Erick , Magge Hema , Kirk Catherine M.
Published: November 2024

Introduction: Children born small or sick are at risk of death and poor development, but many lack access to preventative follow-up services. We assessed the impact of Pediatric Development Clinics (PDC), which provide structured follow-up after discharge from hospital neonatal care units, on children’s survival, nutrition and development in rural Rwanda. Methods: This quasi-experimental study compared a historic control group to children receiving PDC in Kayonza and Kirehe districts. Study populations in both districts included children born preterm or with birthweight < 2000 g and discharged alive. Kirehe additionally included children with hypoxic ischemic encephalopathy (HIE). Home-based cross-sectional surveys were conducted in Kayonza among children with expected chronological age 11–36 months in 2014 (controls) and 2018 (PDC group) and in Kirehe among children with expected chronological age 17–39 months in 2018 (controls) and 2019 (PDC group). Outcomes were measured using anthropometrics and the Ages and Stages Questionnaires. We used weighted logistic regression to control for confounding and differential non-participation. Results: PDC children (n = 464/812, 57.1%) were significantly more likely to participate in surveys (83.0% vs. 65.5%), have very low birthweight (27.6% vs. 19.0%), and be younger at the survey (26.2 vs. 31.1 months). 6.9% (n = 56) died before the survey. PDC was associated with reduced odds of death (aOR = 0.49, 95% CI: 0.26–0.92) and reduced odds of developmental delay (aOR = 0.48, 95% CI: 0.30–0.77). In Kayonza, PDC was associated with reduced stunting (aOR = 0.52, 95% CI: 0.28–0.98). PDC was not associated with reduced underweight or wasting. Conclusions: PDC was associated with improved survival and development among children born preterm, with low birthweight, or with HIE. Increased access to PDC, scale-up across Rwanda, and implementation of similar services and early intervention in other low-resource settings could support children born small or sick.
Multi-Analytical Characterization of Illuminated Choirbooks from the Royal Audience of Quito
Authors: Romero-Bastidas Martha , Guacho-Pachacama Katherine , Vásquez-Mora Carlos , Espinoza-Guerra Fernando , Díaz-Benalcázar Rita , Ramírez-Bustamante Johanna , Ramos-Guerrero Luis
Published: November 2024

Choirbooks are historical heritage manuscripts used for the performance of vocal music in religious ceremonies in colonial times. This study aimed to understand the characteristics of choirbook manuscripts produced in the Real Audiencia de Quito during the 17th century. The methodology combined non-invasive techniques, such as infrared false-color imaging (IRFC) and X-ray fluorescence (XRF), together with spot analysis by scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX) and Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR). The analytical results revealed the use of pumice, chalk and lime carbonate as support materials in the manufacturing process and surface treatment of the parchment. In the illuminations, three pictorial techniques based on protein, polysaccharide and lipid binders were recognized, establishing that the pigments used with greater regularity in the illuminations were vermilion, minium, verdigris, orpiment, azurite, and indigo, preferably in a pure state. Materials used less regularly were also identified, such as yellow ochre, saffron, smalt, red ochre, and bone black, among others. Regarding the vulnerability of the pictorial materials, it was determined that, although most of the pigments exhibit chemical stability, they present some vulnerabilities associated with their intrinsic composition and the medium that contains them.
History and Acoustics of Preaching in Notre-Dame de Paris
Authors: Canfield-Dafilou Elliot K. , Katz Brian F. G. , Caseau Chevallier Beatrice
Published: November 2024

This article investigates the audibility and intelligibility of preaching in a loud voice inside the Cathedral Notre-Dame de Paris during the Middle Ages, after the construction of the Gothic cathedral, until the late 19th century. Through this time period, the locations where oration took place changed along with religious practices inside the cathedral. Here, we combine a historical approach with room acoustic modelling to evaluate the locations inside the cathedral where one would hear sermons well. In a reverberant cathedral such as Notre-Dame, speech would be most intelligible in areas near the orator. Until the introduction of electronically amplified public address systems, speech would not be intelligible throughout the entire cathedral.
Multi-Approach Unveils Potential Gene Introgression of Oil Camellias
Authors: Fan Menglong , Song Zhixin , Zhang Ying , Li Xinlei , Sun Zhenyuan
Published: November 2024

The complex phylogenetic relationship of polyploid species provides an opportunity for a comprehensive study of gene introgression. Oil camellias refer to a class of important woody oil plant in the camellia genus, including octoploid, hexaploid, tetraploid, and diploid plants, but the phylogeny relationship of these species remains poorly investigated. Here, based on multiple types of evidence, including phylogenetic conflict, gene flow analysis, and representative metabolite, we reconstructed the phylogenetic relationship of oil camellias. Camellia shensiensis and C. grijsii formed a distinct branch. Phylogenetic conflict suggested that hexaploid C. oleifera probably originated from hybridization and clustered with diploid C. kissi and tetraploid C. meiocarpa. Tetraploid C. confusa probably originated from crossing the ancestor of C. kissi and C. brevistyla, and C. brevistyla probably was the maternal progenitor of hexaploid C. sasanqua. Furthermore, the composition of anthocyanin in tender leaves showed a strong correlation with phylogenetic distinctions. This study proves the feasibility of using iconic metabolic components to solve phylogenetic relationships and lays a foundation for analyzing genetic breeding and utilizing oil camellia resources.
Understanding Mental Health Impact of COVID-19 on Puerto Rican Youth: Influence of Parental Stress
Authors: Martínez-Seda Gabriela M. , Vélez-Pastrana María C. , Nicasio-Infante Andel
Published: November 2024

The COVID-19 pandemic disrupted all areas of society. The socioemotional effects of isolation, financial instability, and educational and employment uncertainty are anticipated to have a ripple effect on the mental health of parents and children, which has not yet been studied in the Puerto Rican context. To examine the impact of COVID-19 on Puerto Rican families, we used a cross-sectional, correlational research design that studied the following: (a) Adverse experiences (AE) related to the COVID-19 pandemic reported by parents; (b) Parental stress; (c) Parental psychopathology: (d) The mental health of their children. We hypothesized that AEs have direct and indirect effects on child mental health, which are mediated by parental mental health and stress. One hundred and thirty-five parents with children aged 4 to 18 years completed an anonymous online survey from March to May 2022. Results show that COVID-19 AEs have significant direct and indirect effects on child mental health, which are mediated by parental stress and parental psychopathology. We observed medium-to-large effect sizes in the associations between child mental health and COVID-19 AEs, which are mediated by parental stress and psychopathology. Children’s mental health symptoms worsen as parental stress and parental psychopathology increase in the context of COVID-19 AEs.
The Use of Wearable Systems for Assessing Work-Related Risks Related to the Musculoskeletal System—A Systematic Review
Authors: Motta Filippo , Varrecchia Tiwana , Chini Giorgia , Ranavolo Alberto , Galli Manuela
Published: November 2024

Work-related musculoskeletal disorders (WRMSDs) are a leading cause of chronic conditions among working-age adults. Preventing these disorders is crucial to reducing their impact, and quantitative analysis through sensors can help identify their causes and guide ergonomic solutions. This systematic review aims to compile research from 2000 to 2023 published in English and sourced from Web of Science, Scopus, or PubMed that examines workers’ movements during tasks using wearable sensor systems that are applicable in workplace settings. The goal is to identify the job sectors that have been studied and highlight tasks lacking ergonomic risk research. A total of 111 papers were selected through a screening process across three databases, assessed using the McMaster risk of bias tool. The studies span various job sectors and report on the use of different technologies for data collection and study population sizes. The review identifies existing research on WRMSD risks utilizing wearable systems in different job sectors, drawing attention to under-researched areas that warrant further study. It serves as a foundation for future research aimed at understanding the causes of WRMSDs and developing solutions supported by wearable technologies to mitigate these risks.
Persistent Elevation in Urinary Neutrophil Gelatinase-Associated Lipocalin Levels Can Be a Predictor of Urinary Tract Infection Recurrence or Persistence in Women
Authors: Liu Min-Ching , Jiang Yuan-Hong , Jhang Jia-Fong , Chang Tien-Lin , Yang Chia-Cheng , Kuo Hann-Chorng
Published: November 2024

Women commonly experience urinary tract infection (UTI) recurrence. However, there is no effective tool for predicting recurrent UTI after the first UTI episode. Hence, this study aimed to investigate potential urinary inflammatory biomarkers and specific biomarkers for predicting UTI recurrence or persistence after antibiotic treatment in women. Forty women who had a history of recurrent UTI within 1 year after the initial episode and acute bacterial cystitis were treated with broad-spectrum antibiotics for 1 week. To measure inflammatory biomarker levels, urine samples were collected at the baseline and after 1 week, 1 month, and 3 months. The levels of urinary pro-inflammatory proteins such as neutrophil gelatinase-associated lipocalin (NGAL), nerve growth factor, CXC-motif chemokine ligand (CXCL)-1, interleukin-8, CXCL-10, monocyte chemoattractant protein-1, and tumor necrosis factor-alpha were measured using commercial kits. Seven healthy age-matched women were included as controls. The changes in urinary biomarker levels at the baseline and various time points were compared between women with and without UTI recurrence within 1 month or within 3 months after the initial antibiotic therapy. At the baseline, patients with a higher urinary white blood cell count had a significantly higher NGAL level than the controls and those with a low white blood cell count. Of the 40 patients with a history of recurrent UTI, 12 presented with UTI persistence or recurrence within 1 month and 19 within 3 months after the initial antibiotic treatment. Among the 28 patients without UTI recurrence at 1 month after treatment, 7 had UTI recurrence within 3 months. Compared with patients without UTI recurrence, those with UTI recurrence had significantly higher urinary NGAL levels at 1 week, 1 month, and 3 months after the initial treatment. This study concludes that persistent elevation in urinary NGAL levels after the initial antibiotic treatment indicated persistent bladder inflammation. Further, it could be a predictor of UTI persistence or recurrence within 1 or 3 months after the initial antibiotic treatment. Patients with a history of recurrent UTI and high urinary NGAL levels after antibiotic treatment might require a longer treatment duration to completely eradicate or prevent UTI recurrence.
gnas Knockdown Induces Obesity and AHO Features in Early Zebrafish Larvae
Authors: Abbas Alaa , Hammad Ayat S , Zakaria Zain Z. , Al-Asmakh Maha , Hussain Khalid , Al-Shafai Mashael
Published: November 2024

GNAS (Guanine Nucleotide-Binding Protein, Alpha Stimulating) is a complex gene that encodes the alpha subunit of the stimulatory G protein (Gsα), critical for signaling through various G protein-coupled receptors. Inactivating genetic and epigenetic changes in GNAS, resulting in Gsα deficiency, cause different variants of pseudohypoparathyroidism, which may manifest features of Albright hereditary osteodystrophy (AHO, a syndrome characterized by early-onset obesity and other developmental defects). Recent findings have linked Gsα deficiency with isolated, severe, early-onset obesity, suggesting it as a potential, underrecognized cause of monogenic, non-syndromic obesity. This study was prompted by identifying several GNAS variants of uncertain significance (VUSs) in pediatric patients presenting with unexplained, severe, early-onset obesity at Sidra Medicine in Qatar. To functionally characterize these variants, we developed the first zebrafish model of Gsα deficiency, offering numerous advantages over other model systems. This was achieved by knockdown of the ortholog through microinjection of translation-blocking Morpholino antisense oligonucleotides into the yolks of 1-8-cell-stage zebrafish embryos. The morphant larvae displayed an obese phenotype, marked by significantly enlarged yolk sacs, increased neutral lipid accumulation, and reduced metabolic rates, among other developmental abnormalities resembling those in AHO. This zebrafish model lays the foundation for efficient functional characterization of GNAS VUSs and paves the way for enhancing our understanding of Gsα deficiency-associated early-onset obesity.
Incorporating Water Molecules into Highly Accurate Binding Affinity Prediction for Proteins and Ligands
Authors: Zhang Diya , Meng Qiaozhen , Guo Fei
Published: November 2024

In the binding process between proteins and ligand molecules, water molecules play a pivotal role by forming hydrogen bonds that enable proteins and ligand molecules to bind more strongly. However, current methodologies for predicting binding affinity overlook the importance of water molecules. Therefore, we developed a model called GraphWater-Net, specifically designed for predicting protein–ligand binding affinity, by incorporating water molecules. GraphWater-Net employs topological structures to represent protein atoms, ligand atoms and water molecules, and their interactions. Leveraging the Graphormer network, the model extracts interaction features between nodes within the topology, alongside the interaction features of edges and nodes. Subsequently, it generates embeddings with attention weights, inputs them into a Softmax function for regression prediction, and ultimately outputs the predicted binding affinity value. Experimental results on the Comparative Assessment of Scoring Functions (CASF) 2016 test set show that the introduction of water molecules into the complex significantly improves the prediction performance of the proposed model for protein and ligand binding affinity. Specifically, the Pearson correlation coefficient (Rp) exceeds that of current state-of-the-art methods by a margin of 0.022 to 0.129. By integrating water molecules, GraphWater-Net has the potential to facilitate the rational design of protein–ligand interactions and aid in drug discovery.
Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
Authors: Burge Kathryn Y. , Zhong Hua , Wilson Adam P. , Chaaban Hala
Published: November 2024

Human milk (HM) is rich in bioactive factors promoting postnatal small intestinal development and maturation of the microbiome. HM is also protective against necrotizing enterocolitis (NEC), a devastating inflammatory condition predominantly affecting preterm infants. The HM glycosaminoglycan, hyaluronan (HA), is present at high levels in colostrum and early milk. Our group has demonstrated that HA with a molecular weight of 35 kDa (HA35) promotes maturation of the murine neonatal intestine and protects against two distinct models of NEC. However, the molecular mechanisms underpinning HA35-induced changes in the developing ileum are unclear. CD-1 mouse pups were treated with HA35 or vehicle control daily, from P7 to P14, and we used network and functional analyses of bulk RNA-seq ileal transcriptomes to further characterize molecular mechanisms through which HA35 likely influences intestinal maturation. HA35-treated pups separated well by principal component analysis, and cell deconvolution revealed increases in stromal, Paneth, and mature enterocyte and progenitor cells in HA35-treated pups. Gene set enrichment and pathway analyses demonstrated upregulation in key processes related to antioxidant and growth pathways, such as nuclear factor erythroid 2-related factor-mediated oxidative stress response, hypoxia inducible factor-1 alpha, mechanistic target of rapamycin, and downregulation of apoptotic signaling. Collectively, pro-growth and differentiation signals induced by HA35 may present novel mechanisms by which this HM bioactive factor may protect against NEC.
The Untapped Potential of Hairy Root Cultures and Their Multiple Applications
Authors: Mirmazloum Iman , Slavov Aleksandar K. , Marchev Andrey S.
Published: November 2024

Plants are rich sources of specialized metabolites, such as alkaloids, terpenes, phenolic acids, flavonoids, coumarins, and volatile oils, which provide various health benefits including anticancer, anti-inflammatory, antiaging, skin-altering, and anti-diabetic properties. However, challenges such as low and inconsistent yields, environment and geographic factors, and species-specific production of some specialized metabolites limit the supply of raw plant material for the food, cosmetic, or pharmaceutical industries. Therefore, biotechnological approaches using plant in vitro systems offer an appealing alternative for the production of biologically active metabolites. Among these, hairy root cultures induced by Rhizobium rhizogenes have firmed up their position as “green cell factories” due to their genotypic and biosynthetic stability. Hairy roots are valuable platforms for producing high-value phytomolecules at a low cost, are amenable to pathway engineering, and can be scaled up in bioreactors, making them attractive for commercialization. This review explores the potential of hairy roots for specialized metabolites biosynthesis focusing on biotechnology tools to enhance their production. Aspects of morphological peculiarities of hairy roots, the diversity of bioreactors design, and process intensification technologies for maximizing biosynthetic capacity, as well as examples of patented plant-derived (green-labeled) products produced through hairy root cultivation at lab and industrial scales, are addressed and discussed.
Biosynthesis of Phenolic Compounds of Medicago truncatula After Inoculation with Selected PGPR Strains
Authors: Kisiel Anna , Miller Tymoteusz , Łobodzińska Adrianna , Rybak Kinga
Published: November 2024

The phenylpropanoid biosynthesis pathway is involved in the response of plants to stress factors, including microorganisms. This paper presents how free-living strains of rhizobacteria Pseudomonas brassicacearum KK5, P. corrugata KK7, Paenibacillus borealis KK4, and the symbiotic strain Sinorhizobium meliloti KK13 affect the expression of genes encoding phenylalanine ammonia-lyase (PAL), the activity of this enzyme, and the production of phenolic compounds in Medicago truncatula. Seedlings were inoculated with rhizobacteria, then at T0, T24, T72, and T168 after inoculation, the leaves and roots were analyzed for gene expression, enzyme activity, and the content of phenolic compounds. All bacteria affected PAL gene expression, in particular, MtPAL2, MtPAL3, and MtPAL4. Pseudomonas strains had the greatest impact on gene expression. The inoculation affected PAL activity causing it to increase or decrease. The most stimulating effect on enzyme activity was observed 168 h after inoculation. A varied effect was also observed in the case of the content of phenolic compounds. The greatest changes were observed 24 h after inoculation, especially with the KK7 strain. The influence of the studied rhizobacteria on the biosynthesis of phenolic compounds at the molecular level (expression of MtPAL genes) and biochemical level (PAL activity and content of phenolic compounds) was confirmed. The MtPAL3 gene underwent the most significant changes after inoculation and can be used as a marker to assess the interaction between M. truncatula and rhizobacteria. The Pseudomonas strains had the greatest influence on the biosynthesis pathway of phenolic compounds.
A Repetitive Acipenser gueldenstaedtii Genomic Region Aligning with the Acipenser baerii IGLV Gene Cluster Suggests a Role as a Transcription Termination Element Across Several Sturgeon Species
Authors: Chouljenko Alexander V. , Stanfield Brent A. , Melnyk Tetiana O. , Dutta Ojasvi , Chouljenko Vladimir N.
Published: November 2024

This study focuses on the common presence of repetitive sequences within the sturgeon genome that may contribute to enhanced immune responses against infectious diseases. A repetitive 675 bp VAC-2M sequence in Russian sturgeon DNA that aligns with the Siberian sturgeon IGLV gene cluster was identified. A specific 218 bp long portion of the sequence was found to be identical between Acipenser gueldenstaedtii, A. baerii and A. stellatus species, and NCBI blast analysis confirmed the presence of this DNA segment in the A. ruthenus genome. Multiple mutated copies of the same genomic region were detected by PCR analysis, indicating that different versions of this highly repetitive sequence exist simultaneously within the same organism. The selection toward specific genetic differences appears to be highly conserved based on the sequence variations within DNA originating from fish grown at distant geographical regions and individual caviar grains from the same fish. The corresponding A. baerii genomic region encompassing the 357 bp DNA sequence was cloned either ahead or after the human cytomegalovirus immediate early promoter (HCMV-IE) into a pBV-Luc reporter vector expressing the luciferase gene. The DNA segment significantly reduced luciferase expression in transient transfection/expression experiments. The results indicate that this genomic region functions as a transcription termination element that may affect antibody production in sturgeons.
Research Progress and Application of Miniature CRISPR-Cas12 System in Gene Editing
Authors: Xuan Qiangbing , Wang Junjie , Nie Yuanqing , Fang Chaowei , Liang Weihong
Published: November 2024

CRISPR-Cas system, a natural acquired immune system in prokaryotes that defends against exogenous DNA invasion because of its simple structure and easy operation, has been widely used in many research fields such as synthetic biology, crop genetics and breeding, precision medicine, and so on. The miniature CRISPR-Cas12 system has been an emerging genome editing tool in recent years. Compared to the commonly used CRISPR-Cas9 and CRISPR-Cas12a, the miniature CRISPR-Cas12 system has unique advantages, such as rich PAM sites, higher specificity, smaller volume, and cytotoxicity. However, the application of miniature Cas12 proteins and the methods to improve its editing efficiency have not been systematically summarized. In this review, we introduce the classification of CRISPR-Cas system and summarize the structural characteristics of type V CRISPR-Cas system and the cleavage mechanism of five miniature Cas12 proteins. The application of a miniature CRISPR-Cas12 system in the gene editing of animals, plants, and microorganisms is summarized, and the strategies to improve the editing efficiency of the miniature CRISPR-Cas12 system are discussed, aiming to provide reference for further understanding the functional mechanism and engineering modification of the miniature CRISPR-Cas12 system.
Accurate Multiplex qPCR Detection of Epstein–Barr Virus/Cytomegalovirus/BK Virus in Kidney Transplant Patients: Pilot Study
Authors: Damian Costin , Ursu Ramona Gabriela , Covic Adrian Constantin , Bădescu Aida Corina , Hogaș Simona Mihaela , Buzilă Elena Roxana , Duhaniuc Alexandru , Iancu Luminița Smaranda
Published: November 2024

Chronic kidney disease is a really important heath issue, and transplantation is an intervention that can greatly increase patient quality of life and survival. The aim of this study was to perform a comprehensive evaluation of the BK virus, CMV, and EBV in kidney transplant recipients (KTRs); to assess the prevalence of infections; and to test if our detection method would be feasible for use in follow-ups with KTRs. A total of 157 KTRs registered at the Clinical Hospital “Dr. C. I. Parhon”, Iași, Romania, were selected using specific inclusion/exclusion criteria. We tested the blood samples from each patient for BK, EBV, and CMV using a multiplex real-time PCR (qPCR) assay and the TaqMan PCR principle. The highest prevalence was detected for BKV (11/157, 7%), followed by CMV (9/157, 5.7%) and EBV (5/157, 3.2%). By simultaneously detecting three possible nephropathic viruses and oncogenes in KTRs using multiplex real-time PCR, we aimed to optimize their monitoring and follow-up. The prevalence of the tested nephropathogenic viruses—BKV, CMV, and EBV—was comparable to that analyzed in other studies. We demonstrate that the use of qPCR for viral detection in KTRs is a robust, cost-effective method for case monitoring.
Steroid Profiles and Precursor-to-Product Ratios Are Altered in Pregnant Women with Preeclampsia
Authors: Trummer Olivia , Stern Christina , Reintar Sharmaine , Mayer-Pickel Karoline , Cervar-Zivkovic Mila , Dischinger Ulrich , Kurlbaum Max , Huppertz Berthold , Fluhr Herbert , Obermayer-Pietsch Barbara
Published: November 2024

Steroid hormone imbalance is associated with the pathogenesis of preeclampsia. However, affected enzymes of steroid metabolism and gene and protein expression in serum and placenta have not been elucidated yet. We aimed to investigate steroid hormone profiles and precursor-to-product ratios in preeclamptic women compared to women with healthy pregnancy (controls) to identify potentially affected steroid hormones and their metabolizing enzymes. Also, we aimed to investigate whether the mRNA expression of these enzymes is different between the study groups and whether levels of serum mRNA expression reflect postnatal placental protein expression. Serum levels of 14 steroid hormones were measured at eight time points throughout pregnancy in nine preeclamptic women and 36 controls. Serum mRNA expression of selected steroid-metabolizing enzymes was assessed, and their protein expression was analyzed in additional nine preeclamptic women. Mean levels of sex steroid and corticosteroid hormones were significantly altered in preeclamptic women. Precursor-to-product ratios of 5α-reductase, aromatase and 11β-hydroxysteroid dehydrogenase 1 were significantly increased, those of steroid 17α-hydroxylase, 17β-hydroxysteroid-dehydrogenase, steroid 11β-hydroxylase and 11β-hydroxysteroid dehydrogenase 2 were significantly decreased. Serum mRNA expression and placenta protein expression were comparable between the groups. Results contribute to understanding the heterogeneity of preeclampsia and can thus promote future research in personalized medicine.
Evaluation of a New Tandem Mass Spectrometry Method for Sickle Cell Disease Newborn Screening
Authors: Renoux Céline , Roland Estelle , Ruet Séverine , Zouaghi Sarah , Michel Marie , Joly Philippe , Feray Cécile , Zhao Fanny , Gavanier Déborah , Gaucherand Pascal , Roumieu Fanny , Cannas Giovanna , Merazga Salima , Connes Philippe , Renom Gilles , Massardier Jérôme , Cheillan David
Published: November 2024

In France, sickle cell disease newborn screening (SCD NBS) has been targeted to at-risk regions since 1984, but generalization to the whole population will be implemented from November 2024. Although tandem mass spectrometry (MS/MS) is already used for the NBS of several inherited metabolic diseases, its application for SCD NBS has not been widely adopted worldwide. The aim of this study was to evaluate a dedicated MS/MS kit (Targeted MS/MS Hemo, ZenTech, LaCAR Company, Liege, Belgium) for SCD NBS and to compare the results obtained with those from an NBS reference center using matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and cation-exchange high-performance liquid chromatography (CE-HPLC, Variant NBS, Biorad Laboratories, Inc., Hercules, CA, USA) as confirmatory method. The MS/MS Hemo kit was used according to the manufacturer’s instructions and performed on a Waters Xevo TQ-D (Waters Corporation, USA). The software provided by the manufacturer was used for the calculation and analysis of peptide signal ratios. Among the 1333 samples, the results of 1324 samples were consistent with the HPLC and/or MALDI-TOF results (1263 FA, 50 FAS, 7 FAC, 1 FAO-Arab, and 3 FS). All the discordant results (one FAS on MS/MS vs. FA in CE-HPLC, one FA on MS/MS vs. FAS in CE-HPLC, seven FS on MS/MS vs. FAS in CE-HPLC) were corrected after modifying the peptide signal ratios thresholds, allowing the MS/MS Hemo kit to achieve near-100% sensitivity and specificity for SCD NBS. In conclusion, the MS/MS Hemo kit appears to be an effective method for SCD NBS, particularly for laboratories already equipped with MS/MS technology. However, these results should be confirmed in a larger cohort including a greater number of positive samples for SCD.
Interaction of Phenanthroline-Containing Copper Complexes with Model Phospholipid Membranes
Authors: Freddi Priscilla , Alvarez Natalia , Facchin Gianella , Costa-Filho Antonio J.
Published: November 2024

Medicinal Inorganic Chemistry has provided oncology with metallodrugs for cancer treatment, including several promising candidate drugs. In particular, copper(II) coordination compounds with phenanthroline stand out as potential anticancer agents. In this work, we used Differential Scanning Calorimetry and Electron Spin Resonance to investigate the interaction of the copper phenanthroline complexes [Cu(phen)]2+ and [Cu(L-dipeptide)(phenanthroline) (L-dipeptide: L-Ala-Gly and L-Ala-Phe)) with model lipid membranes (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC, and 1,2-dipalmitoyl-sn-glycero-3-phospho-(1′-rac-glycerol) sodium salt, DPPG). Our results showed that the complexes interact with the membrane models, fluidizing them. The [Cu(phen)]2+ presented a different localization than the free ligand phen. The dipeptide modulated the localization of the complex in the membrane and the modifications induced in the physicochemical properties of the lipid vesicles. A stronger interaction with DPPG anionic membranes was observed, which mimic membranes with negatively charged surfaces, as found on several tumor cells.
Naturally Occurring Microbiota-Accessible Borates: A Focused Minireview
Authors: Biţă Andrei , Scorei Ion Romulus , Mogoşanu George Dan , Bejenaru Ludovic Everard , Biţă Cristina Elena , Dinescu Venera Cristina , Rău Gabriela , Ciocîlteu Maria Viorica , Bejenaru Cornelia , Croitoru Octavian
Published: November 2024

Recently, we discovered and proved the essentiality of organic boron species (OBS), such as borate–pectic polysaccharides and borate–phenolic esters, for healthy symbiosis (HS) between microbiota and human/animal (H/A) host. The essentiality of OBS will provide new options for B supplementation in H/A nutrition for a healthy and long life. New knowledge on the essentiality of naturally occurring microbiota-accessible borate species for HS between microbiota and H/A host will allow the use of natural B-based dietary supplements to target the H/A microbiome (the gut, skin, oral, scalp, and vaginal microbiome). In the literature, there is evidence that certain bacteria need B (autoinducer-2 borate) for communication and our preliminary data show that HS takes place when the colonic mucus gel layer contains B. Subsequently, OBS become novel prebiotic candidates and target the colon as novel colonic foods.
Use of Chemical and Colorimetric Changes to Age Cryptotermes brevis Frass for Termite Management
Authors: Haigh William , Hassan Babar , Yi Tengfei , Hayes R. Andrew
Published: November 2024

Drywood termites are problematic timber pests worldwide. Cryptotermes brevis, the West Indian drywood termite, is among the most important of these pests, in part due to its cryptic nature, making it hard to detect in structures and thereby easy to transport. Primary detections are commonly made by the observation of frass deposits evacuated through kick-holes, often leading to fumigation of the building to effectively eradicate the pest. However, after treatment, new frass piles are often discovered. It is, then, challenging to determine whether this frass represents reinfestation or is simply old frass dislodged from inactive nests. This may lead to unchecked termite proliferation or expensive fumigation when it is not needed. The ability to assess the age of the found frass would allow inspectors to determine whether a new infestation has occurred. Photocolorimetry has indicated that frass darkens over time, but large differences in the starting color of frass samples limit the usefulness of this as an aging method. Gas chromatographic-mass spectrometric analysis of the hexane extracts of C. brevis frass samples aged 0–22 months found differences between fresh frass (under 6 months) and those aged over 12 months but could not distinguish between 6- and 12-month-aged frass. Eight compounds accounted for over 70% of the differences between samples and are, thus, targets for chemical analysis of frass of unknown age. While this chemical frass analysis requires fairly sophisticated analytical tools, the cost associated with these processes would pale in comparison with those for unnecessarily fumigating a structure and thus merits further refinement to increase the accessibility of the method.