bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lonidamine, a Novel Modulator for the BvgAS System of Bordetella Species
Authors: Ota Natsuko , Nishida Takashi , Standley Daron M. , Sherif Aalaa Alrahman , Iwano Satoshi , Nugraha Dendi Krisna , Ueno Toshiya , Horiguchi Yasuhiko 
Published: December 2024

ABSTRACTThe Gram‐negative bacteria Bordetella pertussis, B. parapertussis, and B. bronchiseptica cause respiratory diseases in various mammals. They share the BvgAS two‐component system, which regulates the phenotypic conversion between the virulent Bvg+ and avirulent Bvg– phases. In the BvgAS system, the sensor kinase BvgS senses environmental cues and transduces a phosphorelay signal to the response regulator BvgA, which leads to the expression of Bvg+ phase‐specific genes, including virulence factor genes. Bacteria grown at 37°C exhibit the Bvg+ phenotype. In contrast, at lower than 26°C or in the presence of modulators, such as MgSO4 and nicotinic acid, the BvgAS system is inactivated, leading bacteria to the avirulent Bvg– phase. Therefore, effective modulators are expected to provide a therapeutic measure for Bordetella infection; however, no such modulators are currently available, and the mechanism by which modulators inactivate the BvgAS system is poorly understood. In the present study, we identified lonidamine as a novel modulator after screening an FDA‐approved drug library using bacterial reporter systems with the Bvg+‐specific and Bvg–‐specific promoters. Lonidamine directly bound to the VFT2 domain of BvgS and inactivated the BvgAS system at concentrations as low as 50 nM, which was at least 2000‐ to 20,000‐fold lower than the effective concentrations of known modulators. Lonidamine significantly reduced the adherence of B. pertussis to cultured cells but unexpectedly exacerbated bacterial colonization of the mouse nasal septum. These results provide insights into the structural requirements for BvgAS modulators and the role of Bvg phenotypes in the establishment of infection.
Recent innovations for improving the techno‐functional properties of plant‐based egg analogs and egg‐mimicking products to promote their industrialization and commercialization
Authors: Khalifa Ibrahim , Li Zhihua , Nawaz Asad , Walayat Noman , Sobhy Remah , Jia Yangyang , Korin Ali , Zou Xiaobo , Maqsood Sajid 
Published: December 2024

AbstractRecent advancements in plant‐based egg analogs (PBEAs) and plant‐based egg‐mimicking products (PEMP) are driven by growing consumer demand and the need for alternatives to animal‐derived products. This movement is being encouraged by several factors, including a drive toward specifically sustainability, increased allergenicity, and consumer preferences for flexitarian diets. We comprehensively overviewed the current research on the formulation and characterization of PBEAs and PEMP that are vital for diverse food applications. We also highlighted the techno‐functional features of these ingredients and their impact in PBEA and PEMP‐based formulas and evaluated up‐to‐date outcomes that display the availability of economically viable substitutes. However, to efficiently mimic the sensorial and textural features of eggs, further innovation and intensive work are still needed. For instance, challenges persist in achieving desired quality attributes, controlling costs, and scaling‐up the production, which limit broader market adoption of PBEAs and PEMP. Addressing these obstacles through persistent research and development can improve the functionality and acceptance of PBEAs in the food industry, aligning with evolving consumer preferences for plant‐based protein alternative options.
Ricemilks made from pigmented and aromatic rice varieties: Sensory analysis and physiochemical properties
Authors: Ardoin Ryan , Chaffee Olivia , Lea Jeanne , Sookraj Alysza , Boue Stephen , Smith Brennan , Dupre Rebecca , Olson Douglas W. , Broussard William , Priddy Daniel 
Published: December 2024

AbstractAlong with dairy allergic/intolerant and vegetarian/vegan individuals, flexitarian consumers contribute to the market for plant‐based milk alternatives. Niche pigmented (purple and red) and/or aromatic (aromatic brown and white) rice varieties were used to formulate ricemilks, which were compared to a product made from commercial nonaromatic white rice. Descriptive sensory analysis (9 trained panelists) and affective sensory testing (161 consumers) were used to explore perceptions of ricemilks. Additional sample differences were characterized by instrumental color, viscosity, 2‐acetyl‐1‐pyrroline (2‐AP), starch quality, total phenolic content (TPC), oxygen radical absorbance capacity (ORAC), and proximate analyses. Compared to nonaromatic white ricemilk, increased bioactive and antioxidant potential was exhibited for pigmented varieties (TPC ranging 56.6–64.5 µg/mL; ORAC ranging 628–753 µM Trolox equivalents). However, the pigments also resulted in decreased acceptability of product color. For red ricemilk, this was overcome after tasting, resulting in the highest grouping of overall liking scores along with aromatic brown and aromatic white ricemilks (5.6–5.7 on a 9‐point hedonic scale)—all associated with a desirable “popcorn” aromatic from 2‐AP. Highest purchase intent was found for aromatic brown ricemilk (47% overall and 69% among regular dairy and nondairy milk consumers) which was associated with the “dairy” aromatic. Consumers also favored colors and mouthfeel more reminiscent of dairy milk. Ricemilks made from niche pigmented and/or aromatic rices provided unique flavors and outperformed nonaromatic white ricemilk in overall acceptability. Ricemilks made from aromatic whole grain varieties can offer a new health‐promoting functional beverage option to consumers, and a new use of niche rice varieties.
Cold atmospheric plasma inactivation of polyphenol oxidase: Focus on the protective and boosting effect of mono‐ and disaccharides
Authors: Laika Jessica , Sabatucci Annalaura , Sacchetti Giampiero , Di Michele Alessandro , Molina Hernandez Junior Bernardo , Ricci Antonella , Dalla Rosa Marco , Chaves Lopez Clemencia , Neri Lilia 
Published: December 2024

AbstractPolyphenol oxidase (PPO) is among the most detrimental enzymes in processed plant foods, being responsible for enzymatic browning. To propose a “mild” alternative to traditional enzymatic inactivation methods, this study investigated the effect of cold atmospheric plasma (CAP) on PPO inactivation and highlighted the role of different sugars on both inactivation and structural modification of this enzyme. Different model systems were prepared in phosphate buffer using a purified PPO either alone or added with glucose, fructose, sucrose, and trehalose at different concentrations. CAP treatments (6 KV; 23 KHz; duty cycle 10%) were applied at times ranging from 5 to 30 min. Different spectroscopic analyses were conducted before and after treatments to evaluate the PPO activity and changes in tertiary and secondary structures. CAP induced a significant reduction (p < 0.05) in PPO activity across all systems, ranging from 70% to 94% after 30 min of treatment. Among sugars, fructose enhanced (p < 0.05) the PPO inactivation (+23% on average with respect to the phosphate buffer system), possibly by promoting the loss of secondary structures containing the copper‐binding site of the catalytic pocket. The effect of other sugars on PPO inactivation was strictly dependent on their type and concentration; specifically, disaccharides at the highest concentrations and treatment times showed a protective effect on the structure and functionality of the protein. Thus, the results of this study highlight that sugars can modulate the effectiveness of CAP, offering promising perspectives for optimizing this food processing technology.Practical ApplicationCold atmospheric plasma (CAP) is a promising nonthermal technology for food preservation. In particular, surface dielectric barrier discharge (SDBD) CAP could be applied as an alternative to chemical and thermal treatments to inactivate polyphenol oxidase (PPO), an enzyme responsible for browning reactions and quality loss in most processed fruit and vegetable products. However, as shown by this study, PPO inactivation induced by CAP is affected by sugars. Specifically, fructose can positively influence the inactivation of this enzyme. Therefore, CAP potentially could find main applications for the PPO stabilization of high fructose‐content plants (e.g., pears, apples, bananas, grapes, peppers, and squashes).
Supercritical fluid extrusion of pea flour and pea protein concentrate: Effects on functional and structural attributes
Authors: Hosseini Abdul Fateh , Iqbal Aamir , Rizvi Syed S. H. 
Published: December 2024

AbstractThis research investigated the effectiveness of supercritical fluid extrusion (SCFX) to modify the functional and structural characteristics of pea protein concentrate (PPC) and pea flour (PF). The results indicate that the SCFX process favorably modified the hydration properties of PPC and PF needed for developments in the structural and textural qualities of the meat analogs and other similar products. The water‐holding capacity of extruded PPC and PF improved significantly. The SCFX‐extruded samples showed greater emulsifying activity and stability index compared to the unextruded samples. The reduced solubility of the extruded samples indicates changes in the native protein structure and further denaturation due to the SCFX process. Denaturation is a prerequisite for protein texturization to produce meat analogs. Enhanced exposure of sulfhydryl (SH) groups indicates the favorable modification of the protein structure after extrusion. Free SH groups participate in covalent intramolecular disulfide linkages during the solidification process, enhancing the fibrous degree and formation of anisotropic structures. Additionally, the increase in surface hydrophobicity observed in the extruded samples demonstrates the ability of the SCFX process to enhance hydrophobic interactions among protein molecules, resulting in a stronger network formation. Overall, these findings showed the potential of SCFX processing as an innovative technique to effectively modify the structural and functional properties of PPC and PF, thereby enhancing their potential utility in creating novel food products from pea proteins.
Bacterial Communities From Two Freshwater Aquaculture Systems in Northern Germany
Authors: Clols‐Fuentes Júlia , Nguinkal Julien A. , Unger Patrick , Kreikemeyer Bernd , Palm Harry W. 
Published: December 2024

ABSTRACTThe microbial communities in aquaculture systems are primarily affected by changes in water quality, fish metabolism, feeding strategies and fish disease prevention treatments. Monitoring changes in aquatic microbiomes related to aquaculture activities is necessary to improve management strategies and reduce the environmental impact of aquaculture water discharge. This study assessed the effects of activities within two fish farms on water microbiome composition by analysing the water entering and leaving both systems. Additionally, pathogenic bacterial species associated with common fish diseases were identified. The abundance, diversity and identity of microorganisms were evaluated using 16S rRNA hypervariable gene region amplicon sequencing. Proteobacteria (38.2%) and Bacteroidetes (31.3%) were the most abundant phyla in all water samples. Changes in microbiome composition after passage through the fish tanks were observed in several taxa, such as Nitrospirae, Chloroflexi, Deferribacteres and Cyanobacteria. Flavobacterium sp. and Pseudomonas sp. were the predominant potential pathogens and heterotrophic bacteria detected in both farms. Several chemolithotrophic bacteria and archaea were found in the natural reservoir used for aquaculture activities, while water microbiomes in the aquaculture systems were generally dominated by heterotrophic organisms.
A bibliometric analysis of root canal irrigation: From laboratory to clinical practice
Authors: Deng Yudi , Zhang Jinglan , Wang Xinran , Yang Lei , He Qiang , Huang Dingming , Tan Xuelian 
Published: December 2024

AbstractThe study aims to conduct a bibliometric analysis on root canal irrigation to elucidate the development of this domain and pose the future research trends. Of 6722 articles retrieved from Clarivate Analytics' Web of Science Core Collection and PubMed, 6650 publications were included for bibliometric analysis. Irrigation field had received emerging attention for the last half century, peaking at 399 in 2022. The United States was revealed as the most influential contributor, with Journal of Endodontics representing the most voluminous resource. Franklin R Tay was regarded as the most productive author, while Siqueira, Jose. F. was the most prominent. Both keywords cluster analysis and burst analysis revealed the main research branch fields were irrigation protocols. Within this branch, the discussion of irrigants (with a frequency of 1135) ranked first. This bibliometric study revealed the research hotspot of irrigants, while suggesting the future directions of irrigants' creations and micro‐level mechanism elucidation.
Regulation of lipid storage and inflammation in the liver by CEACAM1
Authors: Najjar Sonia M. , Shively John E. 
Published: December 2024

AbstractThis review focuses on a special aspect of hepatic lipid storage and inflammation that occurs during nutritional excess in obesity. Mounting evidence supports that prolonged excess fatty acid (FA) uptake in the liver is strongly associated with hepatic lipid storage and inflammation and that the two processes are closely linked by a homeostatic mechanism. There is also strong evidence that bacterial lipids may enter the gut by a common mechanism with lipid absorption and that there is a set point to determine when their uptake triggers an inflammatory response in the liver. In fact, the progression from high uptake of FAs in the liver resulting in Metabolic dysfunction‐associated steatotic liver disease (MASLD) to the development of the more serious Metabolic dysfunction‐associated steatohepatitis (MASH) depends on the degree of inflammation and its progression from an acute to a chronic state. Thus, MASLD/MASH implicates both excess fatty acids and progressive inflammation in the aetiology of liver disease. We start the discussion by introduction of CD36, a major player in FA and lipopolysaccharide (LPS) uptake in the duodenum, liver and adipose tissue. We will then introduce CEACAM1, a major player in the regulation of hepatic de novo lipogenesis and the inflammatory response in the liver, and its dual association with CD36 in enterocytes and hepatocytes. We conclude that CEACAM1 and CD36 together regulate lipid droplet formation and inflammation in the liver.
The role of CEACAMs in neutrophil function
Authors: Skubitz Keith M. 
Published: December 2024

AbstractBackgroundIn addition to the long‐known antibacterial actions of neutrophils, neutrophils are recognized to have a variety of other effects and are functionally diverse. Neutrophils can either stimulate or inhibit B cells and T cells, regulate NK development and activity, augment or direct the resolution of inflammation, act as myeloid‐derived suppressor cells, modulate tumour growth and metastasis and trigger autoimmune diseases. CEACAMs 1, 3, 6 and 8 are expressed on human neutrophils.MethodsA literature review was performed on the role of CEACAMs in neutrophil function.ResultsCEACAMs 1, 6 and 8 can be upregulated from intracellular stores, while CEACAM3, an opsonin‐independent phagocytic receptor, is constitutively expressed. CEACAM1 has an intracellular ITIM motif and an ITSM motif, and CEACAM3 has an ITAM‐like motif; CEACAMs 6 and 8 are glycosylphosphatidylinositol‐linked. CEACAM8 can also be released in a soluble form. These CEACAMs can interact with multiple other host CEACAMs as well as other molecules on bacteria, fungi and host cells, both transmitting and receiving signals. Known CEACAM‐binding pathogens bind the CFG face of the N domain which is also important in CEACAM‐CEACAM binding, although the ABDE face also appears to be involved in higher‐order oligomers.ConclusionsUnderstanding the exact role of each individual CEACAM in human neutrophils is complicated by the fact that the neutrophil CEACAMs can interact with multiple ligands. The data demonstrates some of the many roles of CEACAMs in neutrophil function and the extensive role of the neutrophil in human biology beyond its classical role as a short‐lived phagocyte.
Mechanism and function of CEACAM1 splice isoforms
Authors: Dery Kenneth J. , Najjar Sonia M. , Beauchemin Nicole , Shively John E. , Kupiec‐Weglinski Jerzy W. 
Published: December 2024

AbstractBackgroundAlternative splicing is a fundamental mechanism in the post‐transcriptional regulation of genes. The multifunctional transmembrane glycoprotein receptor carcinoembryonic antigen‐related cell adhesion molecule 1 (CEACAM1) undergoes extensive alternative splicing to allow for tunable functions in cell signalling, adhesion and modulation of immune and metabolic responses. Splice isoforms that differ in their ectodomain and short or long cytoplasmic tail (CEACAM1‐S/CEACAM1‐L) have distinct functional roles. The mechanisms that regulate CEACAM1 RNA splicing remain elusive.MethodsThis narrative review summarizes the current knowledge of the mechanism and function of CEACAM1 splice isoforms. Historical perspectives address the biological significance of the glycosylated Ig domains, the variable exon 7, and phosphorylation events that dictate its signal transduction pathways. The use of small antisense molecules to target mis‐spliced variable exon 7 is discussed.ResultsThe Ig variable‐like N domain mediates cell adhesion and immune checkpoint inhibitory functions. Gly and Tyr residues in the transmembrane (TM) domain are essential for dimerization. Calmodulin, Calcium/Calmodulin‐dependent protein kinase II delta (CamK2D), Actin and Annexin A2 are binding partners of CEACAM1‐S. Homology studies of the muCEACAM1‐S and huCEACAM1‐S TM predict differences in their signal transduction pathways. Hypoxia‐inducible factor 1‐α (HIF‐1‐α) induces alternative splicing to produce CEACAM1‐S under limited oxygen conditions. Antisense small molecules directed to exon 7 may correct faulty expression of the short and long cytoplasmic tail splicing isoforms.ConclusionMore pre‐clinical and clinical studies are needed to elucidate the precise mechanisms by which CEACAM1 RNA splicing may be exploited to develop targeted interventions towards novel therapeutic strategies.
Evolution of CEACAM pathogen decoy receptors in primates
Authors: Zimmermann Wolfgang , Kammerer Robert 
Published: December 2024

AbstractBackgroundCEACAM1 in leukocytes controls cell activation during inflammation. This and its expression in epithelial cells led to frequent independent appropriation of CEACAM1 as receptor by pathogens in humans and other species to gain host access and to downregulate its immune response. As a countermeasure, decoy receptors with CEACAM1‐like pathogen‐binding domains evolved. The granulocyte‐specific human CEACAM3 endocytic receptor diverts CEACAM1‐binding pathogens to neutrophils for internalization and destruction. The role of the glycosylphosphatidylinositol‐anchored CEACAM5 and CEACAM6 which can also bind CEACAM1‐targeting pathogens in humans is less clear.MethodsWe analyzed the selection of CEACAMs to avoid pathogen binding and to maintain similarity between pathogen receptors and decoy receptors in 148 primate species.ResultsNotably, functional CEACAM3 genes were not found in gibbons and New World monkeys. Interestingly, CEACAM6 in these primates exhibits similar high ratios of rates of nonsynonymous and synonymous substitution (dN/dS) in their pathogen‐binding N domain exons as found for CEACAM1. High dN/dS ratios are indicative of selection for diversification typically seen in pathogen receptors. Human CEACAM6 is expressed on granulocytes and epithelial cells. Therefore, CEACAM6 could substitute for the missing endocytic receptor CEACAM3. In nearly all investigated primate groups also N exons of the epithelially expressed CEACAM5 exhibit selection for diversification. In African populations, five high‐frequency polymorphisms are observed in the pathogen‐binding region of CEACAM5 (I80V, V83A, I100T, I112V, I113T) with 3‐4 polymorphisms combined in the same individual. These polymorphisms correspond to CEACAM1 pathogen‐binding domain sequences.ConclusionThe glycosylphosphatidylinositol‐anchored CEACAM5 and CEACAM6 are under selection to maintain similarity to the pathogen receptor CEACAM1 in most primate species, indicating a function as decoy receptors.
Integration of Morphology‐Based and Molecular Techniques to Study the Most Significant Diatom Order (Thalassiosirales) of Phytoplankton in the River Danube
Authors: Ács Éva , Korponai János László , Kiss Keve Tihamér , Bíró Tibor , Duleba Mónika , Grigorszky István , Szekeres József , Vadkerti Edit , Somlyai Imre 
Published: December 2024

ABSTRACT

Metabarcoding is a rapidly developing field for studying aquatic life and provides a promising alternative to microscopy. However, accurate assessments require that database errors and species boundaries be addressed, yet the use of only a short gene sequences in metabarcoding, may be insufficient for accurate species identification. This study examines the potential of metabarcoding in replacing traditional microscopic methods in planktic diatom identification.

Phytoplankton samples were collected monthly from May 2021 to April 2022 at 13 sites on the Hungarian section of the River Danube. Environmental variables were measured, and electron microscopy and metabarcoding analyses were conducted.

Both morphological and DNA analysis methods were used to study the Thalassiosirales order. Although there was some overlap in the taxa identified by both methods, there were also discrepancies, with certain taxa detected exclusively by one method. P‐distance analysis and BLAST search were used to correct misidentifications, revealing mismatches between database sequences and observed species.

Phytoplankton community exhibited varying temperature and nutrients optima and tolerance ranges, which influenced their distribution patterns. During spring, diatoms—particularly Thalassiosirales—dominated the phytoplankton, with proportions decreasing in summer. Algal biomass in the Danube was highest in March, decreasing sharply by the end of summer and remaining low until the end of the growing season, the decrease relating to changes in the TN:TP ratio, which was very low in the warm water period (mostly below 10), leading to nitrogen limitation.

Discrepancies between bioinformatic analysis and SEM observations revealed errors in the reference database. Our results clarify the functional group (FG) classification, which is important for both ecological status assessment and understanding of ecosystem functioning.

Temperature is one of the most fundamental drivers of microbial nitrogen dynamics in rivers. Global warming is driving up the average temperature of the Danube, creating more favourable conditions for denitrification since the speed of microbial processes is higher in warm water. The increasingly common nitrogen limitation could potentially limit algal growth.

Environmental factors, especially temperature and nutrient concentrations, significantly influenced the Danube's phytoplankton communities, with implications for ecosystem health and water quality assessment. Integrated approaches combining molecular techniques with traditional morphological analysis are needed for comprehensive ecological assessments, but accurate species identification and ecological status assessment require completeness in reference databases and the correction of database errors.