bluuebunny/crossref_metadata_2025 huggingface dataset:
Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements
Authors: Zheng Yanjiang , VanDusen Nathan J.
Published: March 2023

The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic cis-regulatory elements, generation of mice featuring transgenic reporters or cis-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identification and therefore results in biases introduced during the selection of candidates for validation. However, recent advances across a range of disciplines are converging to enable functional genomic assays that can be conducted in a high-throughput manner. Here, we review one such method, massively parallel reporter assays (MPRAs), in which the activities of thousands of candidate genomic regulatory elements are simultaneously assessed via the next-generation sequencing of a barcoded reporter transcript. We discuss best practices for MPRA design and use, with a focus on practical considerations, and review how this emerging technology has been successfully deployed in vivo. Finally, we discuss how MPRAs are likely to evolve and be used in future cardiovascular research.
Irritable Bowel Syndrome and the Gut Microbiome: A Comprehensive Review
Authors: Shaikh Sofia D. , Sun Natalie , Canakis Andrew , Park William Y. , Weber Horst Christian
Published: March 2023

Irritable Bowel Syndrome (IBS) is a functional disorder of the gastrointestinal tract characterized by abdominal pain and altered bowel habits. It has a prevalence of 10 to 25% in the United States and has a high disease burden, as evidenced by reduced quality of life, decreased work productivity and increased healthcare utilization and costs. IBS has been associated with several intra-intestinal and extra-intestinal conditions, including psychiatric comorbidities. Although the pathophysiology of IBS has not been fully elucidated, it involves dysregulation of communication between the brain and gut (brain–gut axis) which is associated with alterations in intestinal motility, gut permeability, visceral hypersensitivity and gut microbiota composition. The purpose of this article is to review the role the gut microbiota plays in the pathophysiology of IBS, understand factors that affect the gut microbiome and explore the microbiome as a target of treatment.
Microwave Ablation of Recurrent Hepatocellular Carcinoma after Curative Surgical Resection
Authors: Adwan Hamzah , Hammann Lars , Vogl Thomas J.
Published: March 2023

Purpose: To evaluate the efficacy and safety of microwave ablation (MWA) as a treatment for recurrent hepatocellular carcinoma (HCC) after initial successful surgical resection. Methods: This retrospective study included 40 patients (11 women and 29 men; mean age: 62.3 ± 11.7 years) with 48 recurrent lesions of HCC after initial surgical resection that were treated by percutaneous MWA. Several parameters including complications, technical success, local tumor progression (LTP), intrahepatic distant recurrence (IDR), overall survival (OS), and progression-free survival (PFS) were evaluated in order to investigate the safety and efficacy of MWA for these recurrent HCC lesions after surgical treatment. Results: All MWA treatments were performed without complications or procedure-related deaths. Technical success was achieved in all cases. Two cases developed LTP at a rate of 5%, and IDR occurred in 23 cases at a rate of 57.5% (23/40). The 1-, 2-, 3-, 4-, and 6-year OS rates were 97%, 89.2%, 80.3%, 70.2%, and 60.2%, respectively. The 1- and 3-year PFS rates were 50.2% and 34.6%, respectively. Conclusion: MWA is effective and safe as a local treatment for recurrent HCC after initial surgical resection.
Comparison of Pronase versus Manual Dechorionation of Zebrafish Embryos for Small Molecule Treatments
Authors: Hasegawa Eva H. , Farr Gist H. , Maves Lisa
Published: March 2023

Zebrafish are a powerful animal model for small molecule screening. Small molecule treatments of zebrafish embryos usually require that the chorion, an acellular envelope enclosing the embryo, is removed in order for chemical compounds to access the embryo from the bath medium. For large-scale studies requiring hundreds of embryos, manual dechorionation, using forceps, can be a time-consuming and limiting process. Pronase is a non-specific protease that is widely used as an enzymatic alternative for dechorionating zebrafish embryos. However, whether pronase treatments alter the effects of subsequent small molecule treatments has not been addressed. Here, we provide a detailed protocol for large-scale pronase dechorionation of zebrafish embryos. We tested whether pronase treatment can influence the efficacy of drug treatments in zebrafish embryos. We used a zebrafish model for Duchenne muscular dystrophy (DMD) to investigate whether the efficacies of trichostatin-A (TSA) or salermide + oxamflatin, small molecule inhibitors known to ameliorate the zebrafish dmd muscle degeneration phenotype, are significantly altered when embryos are treated with pronase versus manual dechorionation. We also tested the effects of pronase on the ability of the anthracycline cancer drug doxorubicin to induce cardiotoxicity in zebrafish embryos. When comparing pronase- versus forceps-dechorionated embryos used in these small molecule treatments, we found no appreciable effects of pronase on animal survival or on the effects of the small molecules. The significant difference that was detected was a small improvement in the ability of salermide + oxamflatin to ameliorate the dmd phenotype in pronase-treated embryos when compared with manual dechorionation. Our study supports the use of pronase treatment as a dechorionation method for zebrafish drug screening experiments.
A Genetic Algorithm Based One Class Support Vector Machine Model for Arabic Skilled Forgery Signature Verification
Authors: Abdulhussien Ansam A. , Nasrudin Mohammad F. , Darwish Saad M. , Alyasseri Zaid Abdi Alkareem
Published: March 2023

Recently, signature verification systems have been widely adopted for verifying individuals based on their handwritten signatures, especially in forensic and commercial transactions. Generally, feature extraction and classification tremendously impact the accuracy of system authentication. Feature extraction is challenging for signature verification systems due to the diverse forms of signatures and sample circumstances. Current signature verification techniques demonstrate promising results in identifying genuine and forged signatures. However, the overall performance of skilled forgery detection remains rigid to deliver high contentment. Furthermore, most of the current signature verification techniques demand a large number of learning samples to increase verification accuracy. This is the primary disadvantage of using deep learning, as the figure of signature samples is mainly restricted to the functional application of the signature verification system. In addition, the system inputs are scanned signatures that comprise noisy pixels, a complicated background, blurriness, and contrast decay. The main challenge has been attaining a balance between noise and data loss, since some essential information is lost during preprocessing, probably influencing the subsequent stages of the system. This paper tackles the aforementioned issues by presenting four main steps: preprocessing, multifeature fusion, discriminant feature selection using a genetic algorithm based on one class support vector machine (OCSVM-GA), and a one-class learning strategy to address imbalanced signature data in the practical application of a signature verification system. The suggested method employs three databases of signatures: SID-Arabic handwritten signatures, CEDAR, and UTSIG. Experimental results depict that the proposed approach outperforms current systems in terms of false acceptance rate (FAR), false rejection rate (FRR), and equal error rate (EER).
Language: Its Origin and Ongoing Evolution
Authors: Markov Ilia , Kharitonova Kseniia , Grigorenko Elena L.
Published: March 2023

With the present paper, we sought to use research findings to illustrate the following thesis: the evolution of language follows the principles of human evolution. We argued that language does not exist for its own sake, it is one of a multitude of skills that developed to achieve a shared communicative goal, and all its features are reflective of this. Ongoing emerging language adaptations strive to better fit the present state of the human species. Theories of language have evolved from a single-modality to multimodal, from human-specific to usage-based and goal-driven. We proposed that language should be viewed as a multitude of communication techniques that have developed and are developing in response to selective pressure. The precise nature of language is shaped by the needs of the species (arguably, uniquely H. sapiens) utilizing it, and the emergence of new situational adaptations, as well as new forms and types of human language, demonstrates that language includes an act driven by a communicative goal. This article serves as an overview of the current state of psycholinguistic research on the topic of language evolution.
Numerical Investigation into the Performance of an OWC Device under Regular and Irregular Waves
Authors: Cannata Giovanni , Simone Marco , Gallerano Francesco
Published: March 2023

A numerical investigation into the hydrodynamic efficiency of an oscillating water column (OWC) device for the production of energy from sea waves under the conditions of regular and irregular waves is proposed. The numerical simulations were carried out using a two-dimensional version of a recently published three-dimensional free-surface nonhydrostatic numerical model, which is based on a conservative form of the contravariant Navier–Stokes equations written for a moving co-ordinate system. The governing equations are spatially discretized by a finite volume shock-capturing scheme based on high-order wave-targeted essentially nonoscillatory reconstructions and an exact Riemann solver. Time discretization was performed by a predictor-corrector method that took into account the nonhydrostatic pressure component. The proposed numerical model allowed us to highlight the significant differences between the hydrodynamic efficiency obtained under irregular waves and those obtained under regular monochromatic waves and provides more realistic evaluations of the OWC device performances. The results of the above comparison showed a reduction in the hydrodynamic efficiency of the OWC from 0.78 to about 0.54 when passing from regular waves to the corresponding irregular ones. The model was applied to assess the potential energy production obtainable by a set of OWCs at the Cetraro harbor (southern Italy). The numerical results show that, by adopting the optimal dimensions of the OWC, the estimated mean annual energy production obtainable at the Cetraro harbor is equal to 1540.52 MWh, which corresponds to the energy production of about 10 wind turbines with a nominal power of 60 KW.
A CFD-FEA Method for Hydroelastic Analysis of Floating Structures
Authors: Gu Nan , Liang Deli , Zhou Xueqian , Ren Huilong
Published: March 2023

The so-called large multi-body floating offshore structure is a new type of offshore structure with a huge and extremely flat deck area, which has a promising prospect as a floating port and also in applications in the area of marine space exploitation. Due to its unique structural form, the hydrodynamic and structural response characteristics are very complex. Specifically, due to the instantaneous position variation in the body surface, the nonlinearity of the free surface, the interactions between floating bodies, and the elastic deformation of floating bodies, the nonlinear factors are significant and cannot be neglected. For these kinds of problems, methods based on CFD-FEA (computation fluid dynamics–finite element analysis) coupling simulation have significant advantages over traditional methods. In the present paper, the hydrodynamic and structural response characteristics of a large multi-body floating offshore structure are studied using a CFD-FEA method, and the results are compared with those obtained by the potential-flow-based commercial code SESAM/WADAM, and a three-dimensional nonlinear hydroelastic analysis commercial code COMPASS-WALCS-NE. The comparison and the analysis of the results show that the CFD-FEA method presented in this study can well simulate the behavior of the hydroelastic responses of flexible floating structures and has the potential to capture complex nonlinear behaviors.
Respiration, Production, and Growth Efficiency of Marine Pelagic Fungal Isolates
Authors: Heitger Marilena , Baltar Federico
Published: March 2023

Despite recent studies suggesting that marine fungi are ubiquitous in oceanic systems and involved in organic matter degradation, their role in the carbon cycle of the oceans is still not characterized and fungal respiration and production are understudied. This study focused on determining fungal growth efficiencies and its susceptibility to temperature differences and nutrient concentration. Hence, respiration and biomass production of three fungal isolates (Rhodotorula mucilaginosa, Rhodotorula sphaerocarpa, Sakaguchia dacryoidea) were measured in laboratory experiments at two temperatures and two nutrient concentrations. We found that fungal respiration and production rates differed among species, temperature, and nutrient concentration. Fungal respiration and production were higher at higher temperatures, but higher fungal growth efficiencies were observed at lower temperatures. Nutrient concentration affected fungal respiration, production, and growth efficiency, but its influence differed among species. Altogether, this study provides the first growth efficiency estimates of pelagic fungi, providing novel insights into the role of fungi as source/sink of carbon during organic matter remineralization. Further research is now needed to unravel the role of pelagic fungi in the marine carbon cycle, a topic that gains even more importance in times of increasing CO2 concentrations and global warming.
LIFEHOUSE’s Functional Nutrition Examination (Physical Exam, Anthropometrics, and Selected Biomarkers) Informs Personalized Wellness Interventions
Authors: Stone Michael , Lukaczer Dan , D’Adamo Christopher R. , Dotson Nicole , Volkov Andrey , Minich Deanna , Metti Dina , Leary Michelle , Class Monique , Carullo Malisa , Lundquist Erik , Eck Brent , Ordovas Jose , Lamb Joseph , Bland Jeffrey
Published: March 2023

Each individual has a unique and interacting set of genetic, lifestyle, and environmental factors that are reflected in their physical exam and laboratory biomarkers and significantly impact their experience of health. Patterns of nutrient deficiency signs and biomarker levels below health-promoting thresholds have been identified in national nutrition surveys. However, identifying these patterns remains a challenge in clinical medicine for many reasons, including clinician training and education, clinical time restraints, and the belief that these signs are both rare and recognizable only in cases of severe nutritional deficiencies. With an increased interest in prevention and limited resources for comprehensive diagnostic evaluations, a functional nutrition evaluation may augment patient-centered screening evaluations and personalized wellness programs. During LIFEHOUSE, we have documented physical exam, anthropometric, and biomarker findings that may increase the recognition of these wellness-challenging patterns in a population of 369 adult employees working in two occupational areas: administrative/sales and manufacturing/warehouse. Distinct and significant physical exam differences and constellations of biomarker abnormalities were identified. We present these patterns of physical exam findings, anthropometrics, and advanced biomarkers to assist clinicians in diagnostic and therapeutic interventions that may stem the loss of function that precedes the development of the non-communicable chronic diseases of aging.
Analysis of Spatiotemporal Interaction Characteristics and Decoupling Effects of Urban Expansion in the Central Plains Urban Agglomeration
Authors: Wang Zhaolan , Wang Li , Zhao Biao , Pei Qian
Published: March 2023

In recent years, the rapid improvement in the urbanization level of the Central Plains urban agglomeration is bound to bring about significant changes in urban land expansion and economic development. However, at present, there is little attention paid to the research on the spatiotemporal interaction characteristics of urban expansion and the interaction between urban expansion and economic development in this region, and existing research lacks a geographical analysis perspective. This study uses spatial autocorrelation, hot spot analysis, LISA time path, and standard deviation ellipse models to analyze the spatiotemporal interaction characteristics of urban expansion in the Central Plains urban agglomeration from 1990 to 2020, and it uses bilateral spatial autocorrelation and decoupling models to analyze the spatial correlation and decoupling effects of urban expansion and economic development. The results show that (1) the urban built-up area of the Central Plains urban agglomeration as a whole is growing in a “J” shape, and the expansion rate has increased rapidly in the past 10 years. (2) The spatial expansion of the city is mainly in the direction of “northwest–southeast”; the directionality has been gradually strengthened in the past 10 years, mainly in the direction of several prefecture-level cities under the jurisdiction of Anhui Province, and the spatial center of gravity of the city has shifted significantly to the south. (3) The spatial agglomeration characteristics of urban expansion in the Central Plains urban agglomeration are not obvious; local hot spots are concentrated in Jiaozuo and its surrounding areas, and urban expansion has local spatial structural instability. (4) During the 2005–2020 period, the risk of uncoordinated urban expansion and economic growth in the Central Plains urban agglomeration increased. This study is of great significance for the rational control of regional development, providing empirical reference for the formulation of the development planning of the Central Plains urban agglomeration, as well as providing a reference for research ideas and methods related to urbanization.
Quantitative Acoustic versus Deep Learning Metrics of Lenition
Authors: Wayland Ratree , Tang Kevin , Wang Fenqi , Vellozzi Sophia , Sengupta Rahul
Published: March 2023

Spanish voiced stops /b, d, ɡ/ surfaced as fricatives [β, ð, ɣ] in intervocalic position due to a phonological process known as spirantization or, more broadly, lenition. However, conditioned by various factors such as stress, place of articulation, flanking vowel quality, and speaking rate, phonetic studies reveal a great deal of variation and gradience of these surface forms, ranging from fricative-like to approximant-like [β⊤, ð⊤, ɣ⊤]. Several acoustic measurements have been used to quantify the degree of lenition, but none is standard. In this study, the posterior probabilities of sonorant and continuant phonological features in a corpus of Argentinian Spanish estimated by a deep learning Phonet model as measures of lenition were compared to traditional acoustic measurements of intensity, duration, and periodicity. When evaluated against known lenition factors: stress, place of articulation, surrounding vowel quality, word status, and speaking rate, the results show that sonorant and continuant posterior probabilities predict lenition patterns that are similar to those predicted by relative acoustic intensity measures and are in the direction expected by the effort-based view of lenition and previous findings. These results suggest that Phonet is a reliable alternative or additional approach to investigate the degree of lenition.
Unbiased Quantitative Single-Cell Morphometric Analysis to Identify Microglia Reactivity in Developmental Brain Injury
Authors: St. Pierre Mark , Duck Sarah Ann , Nazareth Michelle , Fung Camille , Jantzie Lauren L. , Chavez-Valdez Raul
Published: March 2023

Microglia morphological studies have been limited to the process of reviewing the most common characteristics of a group of cells to conclude the likelihood of a “pathological” milieu. We have developed an Imaris-software-based analytical pipeline to address selection and operator biases, enabling use of highly reproducible machine-learning algorithms to quantify at single-cell resolution differences between groups. We hypothesized that this analytical pipeline improved our ability to detect subtle yet important differences between groups. Thus, we studied the temporal changes in Iba1+ microglia-like cell (MCL) populations in the CA1 between P10–P11 and P18–P19 in response to intrauterine growth restriction (IUGR) at E12.5 in mice, chorioamnionitis (chorio) at E18 in rats and neonatal hypoxia–ischemia (HI) at P10 in mice. Sholl and convex hull analyses differentiate stages of maturation of Iba1+ MLCs. At P10–P11, IUGR or HI MLCs were more prominently ‘ameboid’, while chorio MLCs were hyper-ramified compared to sham. At P18–P19, HI MLCs remained persistently ‘ameboid’ to ‘transitional’. Thus, we conclude that this unbiased analytical pipeline, which can be adjusted to other brain cells (i.e., astrocytes), improves sensitivity to detect previously elusive morphological changes known to promote specific inflammatory milieu and lead to worse outcomes and therapeutic responses.
Non-Viral Carriers for Nucleic Acids Delivery: Fundamentals and Current Applications
Authors: Shtykalova Sofia , Deviatkin Dmitriy , Freund Svetlana , Egorova Anna , Kiselev Anton
Published: March 2023

Over the past decades, non-viral DNA and RNA delivery systems have been intensively studied as an alternative to viral vectors. Despite the most significant advantage over viruses, such as the lack of immunogenicity and cytotoxicity, the widespread use of non-viral carriers in clinical practice is still limited due to the insufficient efficacy associated with the difficulties of overcoming extracellular and intracellular barriers. Overcoming barriers by non-viral carriers is facilitated by their chemical structure, surface charge, as well as developed modifications. Currently, there are many different forms of non-viral carriers for various applications. This review aimed to summarize recent developments based on the essential requirements for non-viral carriers for gene therapy.
Pyrolysis and Torrefaction—Thermal Treatment of Creosote-Impregnated Railroad Ties as a Method of Utilization
Authors: Kazimierski Paweł , Kosmela Paulina , Piersa Piotr , Szufa Szymon
Published: March 2023

A fundamental issue of waste management and the rail transport industry is the problem of utilizing used railroad ties. Wooden railroad ties are treated with a preservative, usually creosote. Due to their high toxicity, railroad ties are considered hazardous waste and must be utilized under various directives. It is proposed to utilize the troublesome waste by using the pyrolysis and torrefaction process. The research proves that the thermal method is effective for disposing of this type of waste. Torrefaction up to 250 °C gives high efficiency of impregnation removal, while pyrolysis up to 400 °C completely neutralizes waste. A series of experiments were conducted for various final pyrolysis temperatures to determine a minimum temperature for which the obtained solid products are free from creosote. Extraction with the use of the Soxhlet technique was performed for the raw materials and the obtained solid products—chars. The oil content for liquid fraction was also examined for each sample. As a result of the thermal treatment of the waste, fuel with combustion parameters better than wood was obtained. For a high final temperature of the process, the calorific value of char is close to that of hard coal.
Design Strategy of Corrosion-Resistant Electrodes for Seawater Electrolysis
Authors: Zhao Li , Li Xiao , Yu Jiayuan , Zhou Weijia
Published: March 2023

Electrocatalytic water splitting for hydrogen (H2) production has attracted more and more attention in the context of energy shortages. The use of scarce pure water resources, such as electrolyte, not only increases the cost but also makes application difficult on a large scale. Compared to pure water electrolysis, seawater electrolysis is more competitive in terms of both resource acquisition and economic benefits; however, the complex ionic environment in seawater also brings great challenges to seawater electrolysis technology. Specifically, chloride oxidation-related corrosion and the deposition of insoluble solids on the surface of electrodes during seawater electrolysis make a significant difference to electrocatalytic performance. In response to this issue, design strategies have been proposed to improve the stability of electrodes. Herein, basic principles of seawater electrolysis are first discussed. Then, the design strategy for corrosion-resistant electrodes for seawater electrolysis is recommended. Finally, a development direction for seawater electrolysis in the industrialization process is proposed.
Optimization of Tensile Strength in the Paper Material Cutting Process Based on CO2 Laser Process Parameters
Authors: Pincjer Ivan , Miketic Nada , Gvoic Vesna , Maricic Katarina , Vukelic Djordje , Prica Miljana
Published: March 2023

This paper examines the impact of the CO2 laser parameters on the tensile strength, which is one of the most important properties of paper packaging in the process of cutting paper material. The study was performed on a paper material sample Fbb Board/Ningbo Spark C1S Ivory Board by examination of the influence of four independent variables: paper material grammage, cutting speed, laser power, and resolution on the tensile strength by using definitive screening design. Optimum process conditions of four variables that maximize the tensile strength were predicted and validated accordingly. Results confirm that laser power, paper material grammage, and cutting speed are the main process parameters that mostly affect the tensile strength. Besides individual parameters, two statistically significant interactions were obtained: laser power and cutting speed, and cutting speed and laser resolution. Maximum tensile strength values (20.37 N/mm) were achieved using the laser power of 60.6%, cutting speed of 3.24%, resolution of 2500 Hz, and a paper material grammage of 326.85 g/m2. With laser power at middle values and at a lower speed, a maximum tensile strength value can be obtained. Increasing the laser power and cutting speed will produce a slight lowering of tensile strength.
On the Role of Microstructure and Defects in the Room and High-Temperature Tensile Behavior of the PBF-LB A357 (AlSi7Mg) Alloy in As-Built and Peak-Aged Conditions
Authors: Tonelli Lavinia , Liverani Erica , Di Egidio Gianluca , Fortunato Alessandro , Morri Alessandro , Ceschini Lorella
Published: March 2023

Additive processes like Laser Beam Powder Bed Fusion (PBF-LB) result in a distinctive microstructure characterized by metastability, supersaturation, and finesse. Post-process heat treatments modify microstructural features and tune mechanical behavior. However, the exposition at high temperatures can induce changes in the microstructure. Therefore, the present work focuses on the analyses of the tensile response at room and high (200 °C) temperature of the A357 (AlSi7Mg0.6) alloy processed by PBF-LB and subjected to tailored T5 (direct aging) and T6R (rapid solution treatment, quenching, and aging) treatments. Along with the effect of microstructural features in the as-built T5 and T6R alloy, the role of typical process-related defects is also considered. In this view, the structural integrity of the alloy is evaluated by a deep analysis of the work-hardening behavior, and quality indexes have been compared. Results show that T5 increases tensile strength at room temperature without compromising ductility. T6R homogenizes the microstructure and enhances the structural integrity by reducing the detrimental effect of defects, resulting in the best trade-off between strength and ductility. At 200 °C, tensile properties are comparable, but if resilience and toughness moduli are considered, as-built and T5 alloys show the best overall mechanical performance.
Comorbidity Patterns in Patients at Cardiovascular Hospital Admission
Authors: Soysaler Cezara-Andreea , Andrei Cătălina Liliana , Ceban Octavian , Sinescu Crina-Julieta
Published: March 2023

Hypertension frequently coexists with obesity, diabetes, hyperlipidemia, or metabolic syndrome, anditsassociation with cardiovascular disease is well established. The identification and management of these risk factors is an important part of overall patient management. In this paper, we find the most relevant patterns of hospitalized patients with cardiovascular diseases, consideringaspects of their comorbidities, such as triglycerides, cholesterol, diabetes, hypertension, and obesity. To find the most relevant patterns, several clusterizations were made, playing with the dimensions of comorbidity and the number of clusters. There are three main patient types who require hospitalization: 20% whose comorbidities are not so severe, 44% with quite severe comorbidities, and 36% with fairly good triglycerides, cholesterol, and diabetes but quite severe hypertension and obesity. The comorbidities, such as triglycerides, cholesterol, diabetes, hypertension, and obesity, were observed in different combinations in patients upon hospital admission.
Alteration of Community Metabolism by Prebiotics and Medicinal Herbs
Authors: Peterson Christine Tara , Pérez-Santiago Josué , Iablokov Stanislav N. , Rodionov Dmitry A. , Peterson Scott N.
Published: March 2023

Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here, we used the in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic medicine, followed by 16S rRNA sequencing. We applied a genome-wide metabolic reconstruction of enumerated communities to compare and contrast the structural and functional impact of prebiotics and medicinal herbs. In doings so, we examined the relationships between discrete variations in sugar composition and sugar linkages associated with each prebiotic to drive changes in microbiota composition. The restructuring of microbial communities with glycan substrates alters community metabolism and its potential impact on host physiology. We analyzed sugar fermentation pathways and products predicted to be formed and prebiotic-induced changes in vitamin and amino acid biosynthesis and degradation. These results highlight the utility of combining a genome-wide metabolic reconstruction methodology with 16S rRNA sequence-based community profiles to provide insights pertaining to community metabolism. This process also provides a rational means for prioritizing in vivo analysis of prebiotics and medicinal herbs in vivo to test hypotheses related to therapeutic potential in specific diseases of interest.
Detection of Pathogens and Ticks on Sedentary and Migratory Birds in Two Corsican Wetlands (France, Mediterranean Area)
Authors: Defaye Baptiste , Moutailler Sara , Vollot Benjamin , Galon Clémence , Gonzalez Gaëlle , Moraes Rayane Amaral , Leoncini Antoine-Simon , Rataud Amalia , Le Guillou Gilles , Pasqualini Vanina , Quilichini Yann
Published: March 2023

Birds are one of the most species-diverse vertebrate groups and are susceptible to numerous hematophagous ectoparasites. Migratory birds likely contribute to the circulation of these ectoparasites and their associated pathogens. One of the many migration paths crosses the Mediterranean islands including Corsica and its wetlands, which are migration stopovers. In our study, we collected blood samples and hematophagous ectoparasites in migratory and sedentary bird populations in two coastal lagoons: Biguglia and Gradugine. A total of 1377 birds were captured from which 762 blood samples, 37 louse flies, and 44 ticks were collected. All the louse flies were identified as Ornithomya biloba and all the ticks were from the Ixodes genus: Ixodes sp. (8.5%), I. accuminatus/ventalloi (2.9%), I. arboricola/lividus (14.3%), I. frontalis (5.7%) and I. ricinus (68.6%). Five pathogens were detected: Anaplasma phagocytophilum, Erhlichia chaffeensis, and Rickettsia helvetica in ticks, and Trypanosoma sp. in louse flies. Ehrlichia chaffeensis and the West Nile virus were both detected in bird blood samples in Corsica. This is the first report of these tick, louse fly and pathogen species isolated on the bird population in Corsica. Our finding highlights the importance of bird populations in the presence of arthropod-borne pathogens in Corsican wetlands.
Genome-Wide Pathway Exploration of the Epidermidibacterium keratini EPI-7T
Authors: Oh Yunseok , Mun Seyoung , Choi Young-Bong , Jo HyungWoo , Lee Dong-Geol , Han Kyudong
Published: March 2023

Functional cosmetics industries using skin microbiome screening and beneficial materials isolated from key microorganisms are receiving increasing attention. Since Epidermidibacterium keratini EPI-7T was first discovered in human skin, previous studies have confirmed that it can produce a new pyrimidine compound, 1,1′-biuracil, having anti-aging effects on human skin. Therefore, we conducted genomic analyses to judge the use value of E. keratini EPI-7T and provide up-to-date information. Whole-genome sequencing analysis of E. keratini EPI-7T was performed to generate new complete genome and annotation information. E. keratini EPI-7T genome was subjected to comparative genomic analysis with a group of closely-related strains and skin flora strains through bioinformatic analysis. Furthermore, based on annotation information, we explored metabolic pathways for valuable substances that can be used in functional cosmetics. In this study, the whole-genome sequencing (WGS) and annotation results of E. keratini EPI-7T were improved, and through comparative analysis, it was confirmed that the E. keratini EPI-7T has more metabolite-related genes than comparison strains. In addition, we annotated the vital genes for biosynthesis of 20 amino acids, orotic acid, riboflavin (B2) and chorismate. In particular, we were able to prospect that orotic acid could accumulate inside E. keratini EPI-7T under uracil-enriched conditions. Therefore, through a genomics approach, this study aims to provide genetic information for the hidden potential of E. keratini EPI-7T and the strain development and biotechnology utilization to be conducted in further studies.
Special Issue: Beneficial Properties and Safety of Lactic Acid Bacteria
Authors: Holzapfel Wilhelm Heinrich , Todorov Svetoslav Dimitrov
Published: March 2023

The application of LAB in various sectors, including in the biotechnical and food industry, in human and veterinary practice, and in health-promoting practices and cosmetics, has been the subject of intensive research across the globe, with a range of traditional and innovative methods currently being explored [...]
Co-Occurrence of Taste and Odor Compounds and Cyanotoxins in Cyanobacterial Blooms: Emerging Risks to Human Health?
Authors: Manganelli Maura , Testai Emanuela , Tazart Zakaria , Scardala Simona , Codd Geoffrey A.
Published: March 2023

Cyanobacteria commonly form large blooms in waterbodies; they can produce cyanotoxins, with toxic effects on humans and animals, and volatile compounds, causing bad tastes and odors (T&O) at naturally occurring low concentrations. Notwithstanding the large amount of literature on either cyanotoxins or T&O, no review has focused on them at the same time. The present review critically evaluates the recent literature on cyanotoxins and T&O compounds (geosmin, 2-methylisoborneol, β-ionone and β-cyclocitral) to identify research gaps on harmful exposure of humans and animals to both metabolite classes. T&O and cyanotoxins production can be due to the same or common to different cyanobacterial species/strains, with the additional possibility of T&O production by non-cyanobacterial species. The few environmental studies on the co-occurrence of these two groups of metabolites are not sufficient to understand if and how they can co-vary, or influence each other, perhaps stimulating cyanotoxin production. Therefore, T&Os cannot reliably serve as early warning surrogates for cyanotoxins. The scarce data on T&O toxicity seem to indicate a low health risk (but the inhalation of β-cyclocitral deserves more study). However, no data are available on the effects of combined exposure to mixtures of cyanotoxins and T&O compounds and to combinations of T&O compounds; therefore, whether the co-occurrence of cyanotoxins and T&O compounds is a health issue remains an open question.
Antimicrobial Mechanism of Salt/Acid Solution on Microorganisms Isolated from Trimmed Young Coconut
Authors: Treesuwan Khemmapas , Jirapakkul Wannee , Tongchitpakdee Sasitorn , Chonhenchob Vanee , Mahakarnchanakul Warapa , Tongkhao Kullanart
Published: March 2023

This study investigated the inhibitory activity of organic solutions containing 5, 10, 15, 20 and 30% (w/v) sodium chloride and citric acid solution and 15:10, 15:15, 15:20 and 15:30% (w/v) sodium chloride (NaCl) combined with citric acid (CA) solution (salt/acid solution) for 10 min against microorganisms isolated from trimmed young coconut: Bacillus cereus, B. subtilis, Staphylococcus aureus, S. epidermidis, Enterobacter aerogenes, Serratia marcescens, Candida tropicalis, Lodderromyces elongisporus, Aspergillus aculeatus and Penicillium citrinum. Commercial antimicrobial agents such as potassium metabisulfite and sodium hypochlorite (NaOCl) were used as the controls. Results showed that 30% (w/v) NaCl solution displayed antimicrobial properties against all microorganisms, with s reduction range of 0.00–1.49 log CFU/mL. Treatment of 30% (w/v) CA solution inhibited all microorganisms in the reduction range of 1.50–8.43 log CFU/mL, while 15:20% (w/v) salt/acid solution was the minimum concentration that showed a similar antimicrobial effect with NaOCl and strong antimicrobial effect against Gram-negative bacteria. The mode of action of this solution against selected strains including B. cereus, E. aerogenes and C. tropicalis was also determined by scanning electron microscopy and transmission electron microscopy. B. cereus and E. aerogenes revealed degradation and detachment of the outer layer of the cell wall and cytoplasm membrane, while cytoplasmic inclusion in treated C. tropicalis cells changed to larger vacuoles and rough cell walls. The results suggested that a 15:20% (w/v) salt/acid solution could be used as an alternative antimicrobial agent to eliminate microorganisms on fresh produce.
Phenotypic and Molecular Characteristics of Carbapenem-Resistant Acinetobacter baumannii Isolates from Bulgarian Intensive Care Unit Patients
Authors: Strateva Tanya V. , Sirakov Ivo , Stoeva Temenuga J. , Stratev Alexander , Peykov Slavil
Published: March 2023

Carbapenem-resistant Acinetobacter baumannii (CRAB) is designated as an urgent public health threat, both due to its remarkable multidrug resistance and propensity for clonal spread. This study aimed to explore the phenotypic and molecular characteristics of antimicrobial resistance in CRAB isolates (n = 73) from intensive care unit (ICU) patients in two university hospitals in Bulgaria (2018–2019). The methodology included antimicrobial susceptibility testing, PCR, whole-genome sequencing (WGS), and phylogenomic analysis. The resistance rates were as follows: imipenem, 100%; meropenem, 100%; amikacin, 98.6%; gentamicin, 89%; tobramycin, 86.3%; levofloxacin, 100%; trimethoprim–sulfamethoxazole, 75.3%; tigecycline, 86.3%; colistin, 0%; and ampicillin–sulbactam, 13.7%. All isolates harbored blaOXA-51-like genes. The frequencies of distribution of other antimicrobial resistance genes (ARGs) were: blaOXA-23-like, 98.6%; blaOXA-24/40-like, 2.7%; armA, 86.3%; and sul1, 75.3%. The WGS of selected extensively drug-resistant A. baumannii (XDR-AB) isolates (n = 3) revealed the presence of OXA-23 and OXA-66 carbapenem-hydrolyzing class D β-lactamases in all isolates, and OXA-72 carbapenemase in one of them. Various insertion sequencies, such as ISAba24, ISAba31, ISAba125, ISVsa3, IS17, and IS6100, were also detected, providing increased ability for horizontal transfer of ARGs. The isolates belonged to the widespread high-risk sequence types ST2 (n = 2) and ST636 (n = 1) (Pasteur scheme). Our results show the presence of XDR-AB isolates, carrying a variety of ARGs, in Bulgarian ICU settings, which highlights the crucial need for nationwide surveillance, especially in the conditions of extensive antibiotic usage during COVID-19.
A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry
Authors: Qi Qin , Kamruzzaman Muhammad , Iredell Jonathan R.
Published: March 2023

Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin–antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.
Gut Dysbiosis: A Target for Protective Interventions against Parkinson’s Disease
Authors: Lima Illyane S. , Pêgo Ana C. , Martins Ana C. , Prada Ana R. , Barros João Tomás , Martins Gracelino , Gozzelino Raffaella
Published: March 2023

Sub-chronic inflammation, caused by age-related dysbiosis, primes the brain to neuroinflammation and neurodegenerative diseases. Evidence revealed that Parkinson’s disease (PD) might originate in the gut, demonstrating gastro-intestinal disturbances, as reported by PD patients long before developing motor symptoms. In this study, we conducted comparative analyses in relatively young and old mice maintained in conventional or gnotobiotic conditions. We aimed to confirm that the effects induced by age-related dysbiosis, rather than aging itself, sensitize to PD onset. This hypothesis was confirmed in germ-free (GF) mice, which proved resistant to the pharmacological induction of PD, regardless of their age. Contrary to conventional animals, old GF mice did not develop an inflammatory phenotype or an accumulation of iron in the brain, two catalysts sensitizing to disease onset. The resistance of GF mice to PD is reverted when colonized with stool collected from conventional old animals, but not if receiving bacterial content from young mice. Hence, changes in gut microbiota composition are a risk factor for PD development and can be targeted preventively by iron chelators, shown to protect the brain from pro-inflammatory intestinal priming that sensitizes to neuroinflammation and the development of severe PD.
Hot Water Extraction of Antioxidants from Tea Leaves—Optimization of Brewing Conditions for Preparing Antioxidant-Rich Tea Drinks
Authors: Cheng Yan , Xue Fumin , Yang Yu
Published: March 2023

There are billions of tea drinkers around the world. However, the optimized tea-brewing temperature and time conditions for achieving a higher concentration of antioxidants in tea drinks have not been thoroughly studied. Finding out the optimized brewing conditions can benefit tea drinkers significantly. In this work, we have studied ten antioxidants from seven different popular green, Oolong, black, and scented teas using hot water extraction followed by HPLC analysis. The antioxidant yield was evaluated at 25–100 °C with 5 to 720 min of brewing time. Our results show that the extraction efficiency was enhanced by increasing the water temperature and the highest yield of antioxidants was achieved at 100 °C. The antioxidant yield increased with prolonged brewing time. However, the degradation of antioxidants occurred when tea leaves were extracted for 120 to 720 min. Caffeine was found in all seven tea samples. At 100 °C, the caffein concentration in the tea extract ranged from 7.04 to 20.4 mg/g in Rizhao green tea. Longjing green tea contained the highest concentration of antioxidants (88 mg/g) in the 100 °C extract. Epigallocatechin and caffeine were the most abundant compounds found in all tea samples studied, ranging from 4.77 to 26.88 mg/g. The antioxidant yield was enhanced by increasing the extraction time to up to 60–120 min for all ten compounds studied.
Selenium Enrichment of the Edible Medicinal Mushroom Antrodia camphorata by Submerged Fermentation
Authors: Li Jin , Wen Sai , Zhang Baoyuan , Wang Fenghuan
Published: March 2023

Selenium (Se) is an essential nutrient element in human physiological metabolism and immune function. Supplementation of bioavailable Se will confer benefit on human life, especially when intake of this nutrient is inadequate. The edible and medicinal mushroom Antrodia camphorata is a unique fungus endemic to Taiwan, which has shown high therapeutic and nutritive value. This study is the first to demonstrate that A. camphorata can assimilate and transform sodium selenite into organic selenium. With an initial concentration of Se (IV) at 10 mg/L in 100 mL of the medium at 25 °C, the total selenium content in Se-enriched A. camphorata mycelia was 1281.3 ± 79.2 µg/g, in which the organic selenium content accounted for 88.1%. Further analysis demonstrated that selenium-enriched polysaccharide was the main form of Se present in A. camphorata (61.5% of the organic selenium). Four water-soluble Se-polysaccharide fractions were separated from A. camphorata, and ACP II was the major fraction of Se-polysaccharide. The scavenging efficiency of Se-polysaccharides on DPPH and ABTS radicals was determined, proving that selenium enrichment dramatically improved the in vitro antioxidant capacity of A. camphorata polysaccharide. Therefore, the selenium accumulation and transformation ability of A. camphorata provides an opportunity for developing this beneficent fungus into a novel selenium-enriched dietary or medicinal supplement.