bluuebunny/crossref_metadata_2025 huggingface dataset:
Кадастровая оценка объектов недвижимости в условиях формирования конкурентного рынка недвижимости
Authors: Врублевская Сталина Сергеевна , Ильиных Анастасия Леонидовна
Published: November 2021

На современном этапе развития общества, в условиях, когда реформируется система оценочно-кадастровых работ, проблематика, касающаяся получения достоверной, актуальной и сопоставимой кадастровой стоимости объектов недвижимости, актуализируется достаточно отчетливо. Вместе с тем, количество публикаций, в которых авторы описывают методическое обеспечение кадастровой оценки в Российской Федерации, относительно невелико. Особенно это касается научных трудов последних лет. При рассмотрении вопросов кадастровой оценки объектов недвижимости в условиях формирования конкурентного рынка недвижимости в статье охарактеризованы ее структурные особенности. Рассмотрены элементы, составляющие сущность кадастровой оценки объектов недвижимости. Дана характеристика моделей кадастровой оценки, а также представлено сравнение подходов к массовой оценке недвижимости в разных странах. Обозначены ключевые проблемные вопросы кадастровой оценки объектов недвижимости в условиях формирования конкурентного рынка, а также направления их решения в России.
Parechovirus A Infection of the Intestinal Epithelium: Differences Between Genotypes A1 and A3
Authors: García-Rodríguez Inés , van Eijk Hetty , Koen Gerrit , Pajkrt Dasja , Sridhar Adithya , Wolthers Katja C.
Published: November 2021

Human parechovirus (PeV-A), one of the species within the Picornaviridae family, is known to cause disease in humans. The most commonly detected genotypes are PeV-A1, associated with mild gastrointestinal disease in young children, and PeV-A3, linked to severe disease with neurological symptoms in neonates. As PeV-A are detectable in stool and nasopharyngeal samples, entry is speculated to occur via the respiratory and gastro-intestinal routes. In this study, we characterized PeV-A1 and PeV-A3 replication and tropism in the intestinal epithelium using a primary 2D model based on human fetal enteroids. This model was permissive to infection with lab-adapted strains and clinical isolates of PeV-A1, but for PeV-A3, infection could only be established with clinical isolates. Replication was highest with infection established from the basolateral side with apical shedding for both genotypes. Compared to PeV-A1, replication kinetics of PeV-A3 were slower. Interestingly, there was a difference in cell tropism with PeV-A1 infecting both Paneth cells and enterocytes, while PeV-A3 infected mainly goblet cells. This difference in cell tropism may explain the difference in replication kinetics and associated disease in humans.
Prevalence of Fungal and Bacterial Co-Infection in Pulmonary Fungal Infections: A Metagenomic Next Generation Sequencing-Based Study
Authors: Zhao Zhan , Song Junxiu , Yang Changqing , Yang Lei , Chen Jie , Li Xinhui , Wang Yubao , Feng Jing
Published: November 2021

With the widespread use of antibacterial drugs and increasing number of immunocompromised patients, pulmonary fungal infections are becoming more common. However, the incidence of pulmonary fungal and bacterial co-infection is rarely reported. In this study, 119 patients definitively diagnosed with pulmonary fungal infections between July 2018 and March 2020 were assessed using metagenomic next-generation sequencing (mNGS) as well as traditional pathogen detection to gauge the incidence of fungal and bacterial co-infection and evaluate the associated risk factors. We found that of the 119 patients with fungal infections, 48 (40.3%) had pulmonary fungal and bacterial co-infection. We identified immunocompromised status and the presence of one or more pulmonary cavities as risk factors associated with fungal and bacterial co-infection. The most commonly isolated fungi species were Aspergillus, Pneumocystis, and Rhizopus. The most commonly isolated bacterial species were Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Seventy-nine (66.4%) patients had received empirical antibiotic treatment before their pathogenic test results became available, and 41.7% (fungal infection group) and 38.7% (fungal and bacterial co-infection group) of the patients had their antibacterial drug dosage changed accordingly. This mNGS-based study showed that the incidence of fungal and bacterial co-infection is significant. Our research outcomes can, thus, guide the use of antibacterial drugs in the treatment of clinical fungal infections.
Pneumococcal Extracellular Serine Proteases: Molecular Analysis and Impact on Colonization and Disease
Authors: Ali Murtadha Q. , Kohler Thomas P. , Schulig Lukas , Burchhardt Gerhard , Hammerschmidt Sven
Published: November 2021

The pathobiontStreptococcus pneumoniaecauses life-threatening diseases, including pneumonia, sepsis, meningitis, or non-invasive infections such as otitis media. Serine proteases are enzymes that have been emerged during evolution as one of the most abundant and functionally diverse group of proteins in eukaryotic and prokaryotic organisms.S. pneumoniaeexpresses up to four extracellular serine proteases belonging to the category of trypsin-like or subtilisin-like family proteins: HtrA, SFP, PrtA, and CbpG. These serine proteases have recently received increasing attention because of their immunogenicity and pivotal role in the interaction with host proteins. This review is summarizing and focusing on the molecular and functional analysis of pneumococcal serine proteases, thereby discussing their contribution to pathogenesis.
Slc39a2-Mediated Zinc Homeostasis Modulates Innate Immune Signaling in Phenylephrine-Induced Cardiomyocyte Hypertrophy
Authors: Fang Yu , Wang Shun , Lv Jian , Zhao Zhenyi , Guo Ningning , Wu Gang , Tong Jingjing , Wang Zhihua
Published: November 2021

Zinc dyshomeostasis has been involved in the pathogenesis of cardiac hypertrophy; however, the dynamic regulation of intracellular zinc and its downstream signaling in cardiac hypertrophy remain largely unknown. Using Zincpyr1 staining, we found a significant decrease of intracellular Zinc concentration in phenylephrine (PE)-induced hypertrophy of neonatal rat ventricular myocytes (NRVMs). We then screened SLC39 family members responsible for zinc uptake and identified Slc39a2 as the only one altered by PE treatment. Slc39a2 knockdown in NRVMs reduced the intracellular Zinc level, and exacerbated the hypertrophic responses to PE treatment. In contrast, adenovirus-mediated Slc39a2 overexpression enhanced zinc uptake and suppressed PE-induced Nppb expression. RNA sequencing analysis showed a pro-hypertrophic transcriptome reprogramming after Slc39a2 knockdown. Interestingly, the innate immune signaling pathways, including NOD signaling, TOLL-like receptor, NFκB, and IRFs, were remarkably enriched in the Slc39a2-regulated genes. Slc39a2 deficiency enhanced the phosphorylation of P65 NFκB and STAT3, and reduced the expression of IκBα. Finally, the expression of IRF7 was significantly increased by Slc39a2 knockdown, which was in turn suppressed by IRF7 knockdown. Our data demonstrate that zinc homeostasis mediated by a Slc39a2/IRF7 regulatory circuit contributes to the alteration of innate immune signaling in cardiomyocyte hypertrophy.
A Call to Expand Avian Vocal Development Research
Authors: Loo Yen Yi , Cain Kristal E.
Published: November 2021

Birds are our best models to understand vocal learning – a vocal production ability guided by auditory feedback, which includes human language. Among all vocal learners, songbirds have the most diverse life histories, and some aspects of their vocal learning ability are well-known, such as the neural substrates and vocal control centers, through vocal development studies. Currently, species are classified as either vocal learners or non-learners, and a key difference between the two is the development period, extended in learners, but short in non-learners. But this clear dichotomy has been challenged by the vocal learning continuum hypothesis. One way to address this challenge is to examine both learners and canonical non-learners and determine whether their vocal development is dichotomous or falls along a continuum. However, when we examined the existing empirical data we found that surprisingly few species have their vocal development periods documented. Furthermore, we identified multiple biases within previous vocal development studies in birds, including an extremely narrow focus on (1) a few model species, (2) oscines, (3) males, and (4) songs. Consequently, these biases may have led to an incomplete and possibly erroneous conclusions regarding the nature of the relationships between vocal development patterns and vocal learning ability. Diversifying vocal development studies to include a broader range of taxa is urgently needed to advance the field of vocal learning and examine how vocal development patterns might inform our understanding of vocal learning.
Exploring Biological Impacts of Prenatal Nutrition and Selection for Residual Feed Intake on Beef Cattle Using Omics Technologies: A Review
Authors: Foroutan Aidin , Wishart David S. , Fitzsimmons Carolyn
Published: November 2021

Approximately 70% of the cost of beef production is impacted by dietary intake. Maximizing production efficiency of beef cattle requires not only genetic selection to maximize feed efficiency (i.e., residual feed intake (RFI)), but also adequate nutrition throughout all stages of growth and development to maximize efficiency of growth and reproductive capacity, even during gestation. RFI as a measure of feed efficiency in cattle has been recently accepted and used in the beef industry, but the effect of selection for RFI upon the dynamics of gestation has not been extensively studied, especially in the context of fluctuating energy supply to the dam and fetus. Nutrient restriction during gestation has been shown to negatively affect postnatal growth and development as well as fertility of beef cattle offspring. This, when combined with the genetic potential for RFI, may significantly affect energy partitioning in the offspring and subsequently important performance traits. In this review, we discuss: 1) the importance of RFI as a measure of feed efficiency and how it can affect other economic traits in beef cattle; 2) the influence of prenatal nutrition on physiological phenotypes in calves; 3) the benefits of investigating the interaction of genetic selection for RFI and prenatal nutrition; 4) how metabolomics, transcriptomics, and epigenomics have been employed to investigate the underlying biology associated with prenatal nutrition, RFI, or their interactions in beef cattle; and 5) how the integration of omics information is adding a level of deeper understanding of the genetic architecture of phenotypic traits in cattle.
A Cholesterol Homeostasis-Related Gene Signature Predicts Prognosis of Endometrial Cancer and Correlates With Immune Infiltration
Authors: Chen Yili , Lee Kaping , Liang Yanchun , Qin Shuhang , Zhu Yuan , Liu Junxiu , Yao Shuzhong
Published: November 2021

Background: Endometrial cancer (EC) is one of the most common gynecological malignancies in women. Cholesterol metabolism has been confirmed to be closely related to tumor proliferation, invasion and metastasis. However, the correlation between cholesterol homeostasis-related genes and prognosis of EC remains unclear.

Methods: EC patients from the Cancer Genome Atlas (TCGA) database were randomly divided into training cohort and test cohort. Transcriptome analysis, univariate survival analysis and LASSO Cox regression analysis were adopted to construct a cholesterol homeostasis-related gene signature from the training cohort. Subsequently, Kaplan-Meier (KM) plot, receiver operating characteristic (ROC) curve and principal component analysis (PCA) were utilized to verify the predictive performance of the gene signature in two cohorts. Additionally, enrichment analysis and immune infiltration analysis were performed on differentially expressed genes (DEGs) between two risk groups.

Results: Seven cholesterol homeostasis-related genes were selected to establish a gene signature. KM plot, ROC curve and PCA in two cohorts demonstrated that the gene signature was an efficient independent prognostic indicator. The enrichment analysis and immune infiltration analysis indicated that the high-risk group generally had lower immune infiltrating cells and immune function.

Conclusion: We constructed and validated a cholesterol homeostasis-related gene signature to predict the prognosis of EC, which correlated to immune infiltration and expected to help the diagnosis and precision treatment of EC.
Human Organoids for Predictive Toxicology Research and Drug Development
Authors: Matsui Toshikatsu , Shinozawa Tadahiro
Published: November 2021

Organoids are three-dimensional structures fabricated in vitro from pluripotent stem cells or adult tissue stem cells via a process of self-organization that results in the formation of organ-specific cell types. Human organoids are expected to mimic complex microenvironments and many of the in vivo physiological functions of relevant tissues, thus filling the translational gap between animals and humans and increasing our understanding of the mechanisms underlying disease and developmental processes. In the last decade, organoid research has attracted increasing attention in areas such as disease modeling, drug development, regenerative medicine, toxicology research, and personalized medicine. In particular, in the field of toxicology, where there are various traditional models, human organoids are expected to blaze a new path in future research by overcoming the current limitations, such as those related to differences in drug responses among species. Here, we discuss the potential usefulness, limitations, and future prospects of human liver, heart, kidney, gut, and brain organoids from the viewpoints of predictive toxicology research and drug development, providing cutting edge information on their fabrication methods and functional characteristics.
TNF-α Regulated Endometrial Stroma Secretome Promotes Trophoblast Invasion
Authors: You Yuan , Stelzl Patrick , Joseph Dana N. , Aldo Paulomi B. , Maxwell Anthony J. , Dekel Nava , Liao Aihua , Whirledge Shannon , Mor Gil
Published: November 2021

Successful implantation requires the coordinated migration and invasion of trophoblast cells from out of the blastocyst and into the endometrium. This process relies on signals produced by cells in the maternal endometrium. However, the relative contribution of stroma cells remains unclear. The study of human implantation has major technical limitations, therefore the need of in vitro models to elucidate the molecular mechanisms. Using a recently described 3D in vitro models we evaluated the interaction between trophoblasts and human endometrial stroma cells (hESC), we assessed the process of trophoblast migration and invasion in the presence of stroma derived factors. We demonstrate that hESC promotes trophoblast invasion through the generation of an inflammatory environment modulated by TNF-α. We also show the role of stromal derived IL-17 as a promoter of trophoblast migration through the induction of essential genes that confer invasive capacity to cells of the trophectoderm. In conclusion, we describe the characterization of a cellular inflammatory network that may be important for blastocyst implantation. Our findings provide a new insight into the complexity of the implantation process and reveal the importance of inflammation for embryo implantation.
Role of microRNA Shuttled in Small Extracellular Vesicles Derived From Mesenchymal Stem/Stromal Cells for Osteoarticular Disease Treatment
Authors: Lara-Barba Eliana , Araya María Jesús , Hill Charlotte Nicole , Bustamante-Barrientos Felipe A. , Ortloff Alexander , García Cynthia , Galvez-Jiron Felipe , Pradenas Carolina , Luque-Campos Noymar , Maita Gabriela , Elizondo-Vega Roberto , Djouad Farida , Vega-Letter Ana María , Luz-Crawford Patricia
Published: November 2021

Osteoarticular diseases (OD), such as rheumatoid arthritis (RA) and osteoarthritis (OA) are chronic autoimmune/inflammatory and age-related diseases that affect the joints and other organs for which the current therapies are not effective. Cell therapy using mesenchymal stem/stromal cells (MSCs) is an alternative treatment due to their immunomodulatory and tissue differentiation capacity. Several experimental studies in numerous diseases have demonstrated the MSCs’ therapeutic effects. However, MSCs have shown heterogeneity, instability of stemness and differentiation capacities, limited homing ability, and various adverse responses such as abnormal differentiation and tumor formation. Recently, acellular therapy based on MSC secreted factors has raised the attention of several studies. It has been shown that molecules embedded in extracellular vesicles (EVs) derived from MSCs, particularly those from the small fraction enriched in exosomes (sEVs), effectively mimic their impact in target cells. The biological effects of sEVs critically depend on their cargo, where sEVs-embedded microRNAs (miRNAs) are particularly relevant due to their crucial role in gene expression regulation. Therefore, in this review, we will focus on the effect of sEVs derived from MSCs and their miRNA cargo on target cells associated with the pathology of RA and OA and their potential therapeutic impact.
Running With Scissors: Evolutionary Conflicts Between Viral Proteases and the Host Immune System
Authors: Tsu Brian V. , Fay Elizabeth J. , Nguyen Katelyn T. , Corley Miles R. , Hosuru Bindhu , Dominguez Viviana A. , Daugherty Matthew D.
Published: November 2021

Many pathogens encode proteases that serve to antagonize the host immune system. In particular, viruses with a positive-sense single-stranded RNA genome [(+)ssRNA], including picornaviruses, flaviviruses, and coronaviruses, encode proteases that are not only required for processing viral polyproteins into functional units but also manipulate crucial host cellular processes through their proteolytic activity. Because these proteases must cleave numerous polyprotein sites as well as diverse host targets, evolution of these viral proteases is expected to be highly constrained. However, despite this strong evolutionary constraint, mounting evidence suggests that viral proteases such as picornavirus 3C, flavivirus NS3, and coronavirus 3CL, are engaged in molecular ‘arms races’ with their targeted host factors, resulting in host- and virus-specific determinants of protease cleavage. In cases where protease-mediated cleavage results in host immune inactivation, recurrent host gene evolution can result in avoidance of cleavage by viral proteases. In other cases, such as recently described examples in NLRP1 and CARD8, hosts have evolved ‘tripwire’ sequences that mimic protease cleavage sites and activate an immune response upon cleavage. In both cases, host evolution may be responsible for driving viral protease evolution, helping explain why viral proteases and polyprotein sites are divergent among related viruses despite such strong evolutionary constraint. Importantly, these evolutionary conflicts result in diverse protease-host interactions even within closely related host and viral species, thereby contributing to host range, zoonotic potential, and pathogenicity of viral infection. Such examples highlight the importance of examining viral protease-host interactions through an evolutionary lens.
Effect of Magnesium-Based Coatings on Titanium or Zirconia Substrates on Bone Regeneration and Implant Osseointegration- A Systematic Review
Authors: Almehmadi Ahmad H
Published: November 2021

Magnesium (Mg) is an essential trace element that has a significant role in the human body through its effects on bone metabolism. It has various applications in orthodpaedics and dentistry and the interest of this systematic review lies in its potential role as a dental implant surface coating. The dental implants can fail at different stages starting with its osseointegration phase to the restorative stage in the oral cavity. The biological loss of bone integration to the implant surface has been classified as one of the primary reasons for dental implant failure. There have been numerous strategies that have been shown to compensate this reason for implant failure, among which are the dental implant surface coatings. These coatings have been shown to improve the enhance the adhesion as well as the process of osseointegration. There are numerous studies in the existing literature that have analyzed the effects of Mg-based coatings on cellular as well as biological processes in bone-implant integration. A systematic search of various databases yielded 175 articles, of which 14 in vitro and experimental animal studies that analyzed the effect of Mg-based coatings and compared it to other coatings or no surface coatings were included in this systematic review. The main outcomes of this systematic review have been cellular behavior, osseointegration, and osteogenic markers and the effects of Mg-based coatings in these parameters have been highlighted in this review.
Identification of Cross-Pathway Connections via Protein-Protein Interactions Linked to Altered States of Metabolic Enzymes in Cervical Cancer
Authors: Kumar Krishna , Bose Sarpita , Chakrabarti Saikat
Published: November 2021

Metabolic reprogramming is one of the emerging hallmarks of cancer cells. Various factors, such as signaling proteins (S), miRNA, and transcription factors (TFs), may play important roles in altering the metabolic status in cancer cells by interacting with metabolic enzymes either directly or via protein-protein interactions (PPIs). Therefore, it is important to understand the coordination among these cellular pathways, which may provide better insight into the molecular mechanism behind metabolic adaptations in cancer cells. In this study, we have designed a cervical cancer-specific supra-interaction network where signaling pathway proteins, TFs, and microRNAs (miRs) are connected to metabolic enzymes via PPIs to investigate novel molecular targets and connections/links/paths regulating the metabolic enzymes. Using publicly available omics data and PPIs, we have developed a Hidden Markov Model (HMM)-based mathematical model yielding 94, 236, and 27 probable links/paths connecting signaling pathway proteins, TFs, and miRNAs to metabolic enzymes, respectively, out of which 83 paths connect to six common metabolic enzymes (RRM2, NDUFA11, ENO2, EZH2, AKR1C2, and TYMS). Signaling proteins (e.g., PPARD, BAD, GNB5, CHECK1, PAK2, PLK1, BRCA1, MAML3, and SPP1), TFs (e.g., KAT2B, ING1, MED1, ZEB1, AR, NCOA2, EGR1, TWIST1, E2F1, ID4, RBL1, ESR1, and HSF2), and miR (e.g., mir-147a, mir-593-5p, mir-138-5p, mir-16-5p, and mir-15b-5p) were found to regulate two key metabolic enzymes, EZH2 and AKR1C2, with altered metabolites (L-lysine and tetrahydrodeoxycorticosterone, THDOC) status in cervical cancer. We believe, the biology-based approach of our system will pave the way for future studies, which could be aimed toward identifying novel signaling, transcriptional, and post-transcriptional regulators of metabolic alterations in cervical cancer.
Leveraging of SARS-CoV-2 PCR Cycle Thresholds Values to Forecast COVID-19 Trends
Authors: Yin Nicolas , Dellicour Simon , Daubie Valery , Franco Nicolas , Wautier Magali , Faes Christel , Van Cauteren Dieter , Nymark Liv , Hens Niel , Gilbert Marius , Hallin Marie , Vandenberg Olivier
Published: November 2021

Introduction: We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic's dynamics at local and national levels and for improving forecasting models.

Methods: SARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.

Results: Over 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were strongly correlated with the 14-day mean confirmed cases in the Brussels-Capital and in Belgium with coinciding start, peak, and end of the different waves of the epidemic. Ct values decreased concurrently with the forecasted phase-shifts of the diagram. Similarly, the evolution of 14-day median Ct values was negatively correlated with daily estimated prevalence for all age-classes.

Conclusion: We provide preliminary evidence that trends of Ct values can help to both follow and predict the epidemic's trajectory at local and national levels, underlining that consolidated microbiology laboratories can act as epidemic sensors as they gather data that are representative of the geographical area they serve.
Development and Validation of a Novel Risk Prediction Model Using Recursive Feature Elimination Algorithm for Acute-on-Chronic Liver Failure in Chronic Hepatitis B Patients With Severe Acute Exacerbation
Authors: Yu Mingxue , Li Xiangyong , Lu Yaxin , Jie Yusheng , Li Xinhua , Shi Xietong , Zhong Shaolong , Wu Yuankai , Xu Wenli , Liu Zifeng , Chong Yutian
Published: November 2021

Background: Patients with chronic hepatitis B (CHB) with severe acute exacerbation (SAE) are at a progression stage of acute-on-chronic liver failure (ACLF) but uniform models for predicting ACLF occurrence are lacking. We aimed to present a risk prediction model to early identify the patients at a high risk of ACLF and predict the survival of the patient.

Methods: We selected the best variable combination using a novel recursive feature elimination algorithm to develop and validate a classification regression model and also an online application on a cloud server from the training cohort with a total of 342 patients with CHB with SAE and two external cohorts with a sample size of 96 and 65 patients, respectively.

Findings: An excellent prediction model called the PATA model including four predictors, prothrombin time (PT), age, total bilirubin (Tbil), and alanine aminotransferase (ALT) could achieve an area under the receiver operating characteristic curve (AUC) of 0.959 (95% CI 0.941–0.977) in the development set, and AUC of 0.932 (95% CI 0.876–0.987) and 0.905 (95% CI 0.826–0.984) in the two external validation cohorts, respectively. The calibration curve for risk prediction probability of ACLF showed optimal agreement between prediction by PATA model and actual observation. After predictive stratification into different risk groups, the C-index of predictive 90-days mortality was 0.720 (0.675–0.765) for the PATA model, 0.549 (0.506–0.592) for the end-stage liver disease score model, and 0.648 (0.581–0.715) for Child–Turcotte–Pugh scoring system.

Interpretation: The highlypredictive risk model and easy-to-use online application can accurately predict the risk of ACLF with a poor prognosis. They may facilitate risk communication and guidetherapeutic options.
Diversification of Escherichia albertii H-Antigens and Development of H-Genotyping PCR
Authors: Nakae Koji , Ooka Tadasuke , Murakami Koichi , Hara-Kudo Yukiko , Imuta Naoko , Gotoh Yasuhiro , Ogura Yoshitoshi , Hayashi Tetsuya , Okamoto Yasuhiro , Nishi Junichiro
Published: November 2021

Escherichia albertii is a recently recognized human enteropathogen that is closely related to Escherichia coli. As E. albertii sometimes causes outbreaks of gastroenteritis, rapid strain typing systems, such as the O- and H-serotyping systems widely used for E. coli, will be useful for outbreak investigation and surveillance. Although an O-genotyping system has recently been developed, the diversity of E. albertii H-antigens (flagellins) encoded by fliC genes remains to be systematically investigated, and no H-serotyping or genotyping system is currently available. Here, we analyzed the fliC genes of 243 genome-sequenced E. albertii strains and identified 73 sequence types, which were grouped into four clearly distinguishable types designated E. albertii H-genotypes 1–4 (EAHg1–EAHg4). Although there was a clear sign of intraspecies transfer of fliC genes in E. albertii, none of the four E. albertii H-genotypes (EAHgs) were closely related to any of the 53 known E. coli H-antigens, indicating the absence or rare occurrence of interspecies transfer of fliC genes between the two species. Although the analysis of more E. albertii strains will be required to confirm the low level of variation in their fliC genes, this finding suggests that E. albertii may exist in limited natural hosts or environments and/or that the flagella of E. albertii may function in a limited stage(s) in their life cycle. Based on the fliC sequences of the four EAHgs, we developed a multiplex PCR-based H-genotyping system for E. albertii (EAH-genotyping PCR), which will be useful for epidemiological studies of E. albertii infections.
Metagenomic Analysis of Biocide-Treated Neotropical Oil Reservoir Water Unveils Microdiversity of Thermophile Tepidiphilus
Authors: Bedoya Katherine , Niño Jhorman , Acero Julia , Jaimes-Prada Ronald , Cabarcas Felipe , Alzate Juan F.
Published: November 2021

Microorganisms are capable of colonizing extreme environments like deep biosphere and oil reservoirs. The prokaryotes diversity in exploited oil reservoirs is composed of indigenous microbial communities and artificially introduced microbes. In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located in the Orinoquia region of Colombia, South America. Tepidiphilus is the dominant bacteria found in both injection and produced waters. The produced water has a higher microbial richness and exhibits a Tepidiphilus microdiversity. The reservoir injected water is recycled and treated with the biocides glutaraldehyde and tetrakis-hydroxymethyl-phosphonium sulfate (THPS) to reduce microbial load. This process reduces microbial richness and selects a single Tepidiphilus genome (T. sp. UDEAICP_D1) as the dominant isolate. Thermus and Hydrogenobacter were subdominants in both water systems. Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage. Comparative analysis of the Tepidiphilus genomes revealed several genes that might be related to the biocide-resistant phenotype and the tolerance to the stress conditions imposed inside the oil well, like RND efflux pumps and type II toxin-antitoxin systems. Comparing the abundance of Tepidiphilus protein-coding genes in both water systems shows that the biocide selected Tepidiphilus sp. UDEAICP_D1 genome has enriched genes annotated as ABC-2 type transporter, ABC transporter, Methionine biosynthesis protein MetW, Glycosyltransferases, and two-component system NarL.
Protective Effect of an Exopolysaccharide Produced by Lactiplantibacillus plantarum BGAN8 Against Cadmium-Induced Toxicity in Caco-2 Cells
Authors: Brdarić Emilija , Soković Bajić Svetlana , Đokić Jelena , Đurđić Slađana , Ruas-Madiedo Patricia , Stevanović Magdalena , Tolinački Maja , Dinić Miroslav , Mutić Jelena , Golić Nataša , Živković Milica
Published: November 2021

Cadmium (Cd) ranks seventh on the list of most significant potential threats to human health based on its suspected toxicity and the possibility of exposure to it. It has been reported that some bacterial exopolysaccharides (EPSs) have the ability to bind heavy metal ions. We therefore investigated the capacity of eight EPS-producing lactobacilli to adsorb Cd in the present study, and Lactiplantibacillus plantarum BGAN8 was chosen as the best candidate. In addition, we demonstrate that an EPS derived from BGAN8 (EPS-AN8) exhibits a high Cd-binding capacity and prevents Cd-mediated toxicity in intestinal epithelial Caco-2 cells. Simultaneous use of EPS-AN8 with Cd treatment prevents inflammation, disruption of tight-junction proteins, and oxidative stress. Our results indicate that the EPS in question has a strong potential to be used as a postbiotic in combatting the adverse effects of Cd. Moreover, we show that higher concentrations of EPS-AN8 can alleviate Cd-induced cell damage.
Vitamin A Deficiency Exacerbates Gut Microbiota Dysbiosis and Cognitive Deficits in Amyloid Precursor Protein/Presenilin 1 Transgenic Mice
Authors: Chen Bo-Wen , Zhang Kai-Wen , Chen Si-Jia , Yang Chun , Li Peng-Gao
Published: November 2021

Vitamin A deficiency (VAD) plays an essential role in the pathogenesis of Alzheimer’s disease (AD). However, the specific mechanism by which VAD aggravates cognitive impairment is still unknown. At the intersection of microbiology and neuroscience, the gut-brain axis is undoubtedly contributing to the formation and function of neurological systems, but most of the previous studies have ignored the influence of gut microbiota on the cognitive function in VAD. Therefore, we assessed the effect of VAD on AD pathology and the decline of cognitive function in AD model mice and determined the role played by the intestinal microbiota in the process. Twenty 8-week-old male C57BL/6J amyloid precursor protein/presenilin 1 (APP/PS1) transgenic mice were randomly assigned to either a vitamin A normal (VAN) or VAD diet for 45 weeks. Our results show that VAD aggravated the behavioral learning and memory deficits, reduced the retinol concentration in the liver and the serum, decreased the transcription of vitamin A (VA)-related receptors and VA-related enzymes in the cortex, increased amyloid-β peptides (Aβ40 and Aβ42) in the brain and gut, upregulate the translation of beta-site APP-cleaving enzyme 1 (BACE1) and phosphorylated Tau in the cortex, and downregulate the expression of brain-derived neurotrophic factor (BDNF) and γ-aminobutyric acid (GABA) receptors in the cortex. In addition, VAD altered the composition and functionality of the fecal microbiota as exemplified by a decreased abundance of Lactobacillus and significantly different α- and β-diversity. Of note, the functional metagenomic prediction (PICRUSt analysis) indicated that GABAergic synapse and retinol metabolism decreased remarkably after VAD intervention, which was in line with the decreased expression of GABA receptors and the decreased liver and serum retinol. In summary, the present study provided valuable facts that VAD exacerbated the morphological, histopathological, molecular biological, microbiological, and behavioral impairment in the APP/PS1 transgenic mice, and the intestinal microbiota may play a key mediator role in this mechanism.
Neural Mechanisms of Visual Motion Anomalies in Autism: A Two-Decade Update and Novel Aetiology
Authors: Spiteri Samuel , Crewther David
Published: November 2021

The 21st century has seen dramatic changes in our understanding of the visual physio-perceptual anomalies of autism and also in the structure and development of the primate visual system. This review covers the past 20 years of research into motion perceptual/dorsal stream anomalies in autism, as well as new understanding of the development of primate vision. The convergence of this literature allows a novel developmental hypothesis to explain the physiological and perceptual differences of the broad autistic spectrum. Central to these observations is the development of motion areas MT+, the seat of the dorsal cortical stream, central area of pre-attentional processing as well as being an anchor of binocular vision for 3D action. Such development normally occurs via a transfer of thalamic drive from the inferior pulvinar → MT to the anatomically stronger but later-developing LGN → V1 → MT connection. We propose that autistic variation arises from a slowing in the normal developmental attenuation of the pulvinar → MT pathway. We suggest that this is caused by a hyperactive amygdala → thalamic reticular nucleus circuit increasing activity in the PIm → MT via response gain modulation of the pulvinar and hence altering synaptic competition in area MT. We explore the probable timing of transfer in dominance of human MT from pulvinar to LGN/V1 driving circuitry and discuss the implications of the main hypothesis.
Evaluation of the Partial Replacement of Dietary Fish Meal With Fermented or Untreated Soybean Meal in Juvenile Silver Barb, Barbonymus gonionotus
Authors: Jahan Halima , Tumpa Israt Jahan , Qasem Wafaa A. , Moniruzzaman Mohammad , Pervin Mst. Arzu , Akter Rabeya , Omri Abdelwahab , Min Taesun , Hossain Zakir
Published: November 2021

Fish meal (FM) has excellent protein and lipid profile. However, FM is losing its acceptability and substituted with plant protein due to FM has high price, high demand, and sustainability issues in global aquaculture production. In this study, experimental diets were prepared by substituting FM with fermented soybean meal (FSM) or normal and untreated soybean meal (SM) to assess the effects on growth, hematology, innate immunity, gut physiology, and digestive enzyme activities in juvenile silver barb, Barbonymus gonionotus. Five diets, that is, 40% FM (FM 40), 20% FM + 20% FSM (FM 20 + FSM 20), 20% FM + 20% SM (FM 20 + SM 20), 40% FSM (FSM 40), and 40% SM (SM 40) were fed to the fish two times daily for 90 days. After 90 days of feeding trial, FM 40, FM 20 + FSM 20, and FM 20 + SM 20 diet groups showed significantly higher weight gain (WG) and specific growth rate (SGR) compared to the FSM 40 and SM 40 diets. Hepatosomatic index (HSI) and viscerosomatic index (VSI) were significantly higher in fish fed with the FSM 40 and SM 40 diets than those of fish fed with the FM 40 diet. Hematocrit, hemoglobin, and erythrocyte count were significantly lower in fish fed with the SM 40 diet compared to fish fed with the FM 40 and FM 20 + FSM 20 diets. Superoxide dismutase and catalase activities in the liver were significantly higher in fish fed with the SM 40 diet compared to fish fed with the FM 40 diet. However, serum thiobarbituric acid reactive substances in fish fed with the experimental diets were unaltered. Fish showed significant reduction of villus height (Vh) in the anterior and posterior intestine of fish fed with the FSM 40 and SM 40 diets, whereas muscular thickness was opposite to the findings of Vh. Digestive enzyme activities in intestine were significantly higher in fish fed with the FM 40 diet compared to those in the SM 40 diet. The results of the present study revealed that the 50% of FM can be replaced by FSM or SM as a source of protein without affecting the growth of juvenile silver barb.
Results of the ECHO (Eating habits CHanges in Oncologic patients) Survey: An Italian Cross-Sectional Multicentric Study to Explore Dietary Changes and Dietary Supplement Use, in Breast Cancer Survivors
Authors: Caprara Greta , Tieri Maria , Fabi Alessandra , Guarneri Valentina , Falci Cristina , Dieci Maria Vittoria , Turazza Monica , Ballardini Bettina , Bin Alessandra , Cinieri Saverio , Vici Patrizia , Montagna Emilia , Zamagni Claudio , Mazzi Cristina , Modena Alessandra , Marchetti Fabiana , Verzè Matteo , Ghelfi Francesca , Titta Lucilla , Nicolis Fabrizio , Gori Stefania
Published: November 2021

The role of a healthy diet in cancer prevention is well recognized. Recent data indicate that following the same advices can also improve cancer survivors’ quality of life. Breast cancer (BC) patients are commonly concerned about diet and nutrition and frequently express the need to obtain health-related information and the will to change their diet and lifestyle. Hence, be aware of survivors’ dietary changes and information needs is crucial for healthcare professionals to guide them toward optimal lifestyle choices. In order to investigate eating habits changes in a BC survivors’ population, we conceived the cross-sectional multicentric study ECHO (Eating habits CHanges in Oncologic patients) Survey. Data were collected from 684 patients, diagnosed with invasive breast cancer, in order to investigate their changes in food consumption, use of supplements, or the beginning of a specific diet, after BC diagnosis. We also examined the sources of information used and if any modification in their diets was reported to the oncologist. We primarily observed that patients increased their consumption of vegetables, pulses, nuts, fruits, wholemeal bread/pasta, grains and fish; while decreasing red and processed meat, refined bread/pasta, baked good and animal fat consumption. Survivors also reported the use of dietary supplements, mainly vitamins, aimed at counteracting therapies’ side effects. Changes in nutritional habits were often adopted without asking or informing the oncologist. Despite BC survivors made some positive changes in their nutritional habits, those modifications were mostly pursued by less than half of them, while the majority of patients consumed nutritional supplements after diagnosis. These results, as well as the failure to communicate with the physicians, reinforce the need to both improve the patient-healthcare professional relationship and to develop tailored nutrition counselling and intervention programs for cancer survivors.
Survival Outcomes After Breast-Conserving Therapy Compared With Mastectomy for Patients With Early-Stage Invasive Micropapillary Carcinoma of the Breast: A SEER Population-Based Study
Authors: Wang Song , Zhang Yiyuan , Yin Fangxu , Wang Xiaohong , Yang Zhenlin
Published: November 2021

Background

Invasive micropapillary breast carcinoma (IMPC) is a relatively rare pathological type of invasive breast cancer. Little is currently known on the efficacy and safety of breast-conserving treatment (BCT, lumpectomy plus postsurgical radiation) compared with mastectomy in women diagnosed with early-stage IMPC. Accordingly, we sought to investigate the long-term prognostic differences between BCT and mastectomy in patients with T1-3N0-3M0 invasive micropapillary breast carcinoma using data from the Surveillance, Epidemiology, and End Results (SEER) database.

Materials and Methods

We retrospectively analyzed 1,203 female patients diagnosed with early-stage IMPC between 2004 and 2015 from the SEER database. The impact of different surgical approaches on patient prognosis was assessed by the Kaplan-Meier method and Cox proportional risk models.

Results

A total of 609 and 594 patients underwent mastectomy and BCT, respectively. Compared with patients who underwent a mastectomy, patients in the BCT group were older and had lower tumor diameters, lower rates of lymph nodes metastasis, and higher rates of ER receptor positivity and PR receptor positivity (p < 0.05). Kaplan-Meier plots showed that the overall survival (OS) and breast cancer-specific survival (BCSS) were higher in the BCT group than in the mastectomy group. In subgroup analysis, patients with T2 stage in the BCT group had better OS than the mastectomy group. Multivariate analysis showed no statistical difference in OS and BCSS for patients in the mastectomy group compared with the BCT group (hazard ratio (HR) = 0.727; 95% confidence interval (95% CI) 0.369–1.432, p = 0.357; HR = 0.762; 95% CI 0.302–1.923, p = 0.565; respectively). During the multivariate analysis and stratifying for the T stage, a better OS was found for patients with T2 stage in the BCT group than the mastectomy group (HR = 0.333, 95% CI: 0.149–0.741, p = 0.007). There was no significant difference in OS for patients with T1 and T3 stages between the BCT and mastectomy groups (p > 0.05).

Conclusion

In women with early-stage IMPC, BCT was at least equivalent to mastectomy in terms of survival outcomes. When both procedures are feasible, BCT should be recommended as the standard surgical treatment, especially for patients with T2 disease.
Trends in Intracranial Glioma Incidence and Mortality in the United States, 1975-2018
Authors: Lin Dongdong , Wang Ming , Chen Yan , Gong Jie , Chen Liang , Shi Xiaoyong , Lan Fujun , Chen Zhongliang , Xiong Tao , Sun Hu , Wan Shu
Published: November 2021

Purpose

Glioma incidence in the US seems to have stabilized over the past 20 years. It’s also not clear whether changes in glioblastoma incidence are associated with glioma mortality trends. Our study investigated trends in glioma incidence and mortality according to tumor characteristics.

Methods

This study obtained data from the Surveillance, Epidemiology, and End Results-9 (SEER-9) registries to calculate glioma incidence and mortality trends. Annual percent changes (APC) and 95% CIs were calculated using the Joinpoint program.

Results

62,159 patients (34,996 males and 55,424 whites) were diagnosed with glioma during 1975-2018, and 31,922 deaths occurred from 1995-2018. Glioblastoma (32,893 cases) and non-glioblastoma astrocytoma (17,406 cases) were the most common histologic types. During the study period, the incidence of glioma first experienced a significant increase (APC=1.8%, [95% CI, 1.3% to 2.3%]) from 1975 to 1987, and then experienced a slight decrease (APC=-0.4%, [95% CI, -0.5% to -0.3%]) from 1987 to 2018, while the APC was 0.8% for glioblastoma, -2.0% for non-glioblastoma astrocytoma, 1.1% for oligodendroglial tumors, 0.7% for ependymoma and -0.3% for glioma NOS during the study period. Glioblastoma incidence increased for all tumor size and tumor extension except for distant. From 1995 to 2018, glioma mortality declined 0.4% per year (95% CI: -0.6% to -0.2%) but only increased in patients older than 80 years [APC=1.0%, (95% CI, 0.4% to 1.6%)].

Conclusion

Significant decline in glioma incidence (1987-2018) and mortality (1995-2018) were observed. Epidemiological changes in non-glioblastoma astrocytoma contributed the most to overall trends in glioma incidence and mortality. These findings can improve understanding of risk factors and guide the focus of glioma therapy.
Clinical Significance of Screening Differential Metabolites in Ovarian Cancer Tissue and Ascites by LC/MS
Authors: Liu Miao , Liu Yu , Feng Hua , Jing Yixin , Zhao Shuang , Yang Shujia , Zhang Nan , Jin Shi , Li Yafei , Weng Mingjiao , Xue Xinzhu , Wang Fuya , Yang Yongheng , Jin Xiaoming , Kong Dan
Published: November 2021

Tumor cells not only show a vigorous metabolic state, but also reflect the disease progression and prognosis from their metabolites. To judge the progress and prognosis of ovarian cancer is generally based on the formation of ascites, or whether there is ascites recurrence during chemotherapy after ovarian cancer surgery. To explore the relationship between the production of ascites and ovarian cancer tissue, metabolomics was used to screen differential metabolites in this study. The significant markers leading to ascites formation and chemoresistance were screened by analyzing their correlation with the formation of ascites in ovarian cancer and the clinical indicators of patients, and then provided a theoretical basis. The results revealed that nine differential metabolites were screened out from 37 ovarian cancer tissues and their ascites, among which seven differential metabolites were screened from 22 self-paired samples. Sebacic acid and 20-COOH-leukotriene E4 were negatively correlated with the high expression of serum CA125. Carnosine was positively correlated with the high expression of serum uric acid. Hexadecanoic acid was negatively correlated with the high expression of serum γ-GGT and HBDH. 20a,22b-Dihydroxycholesterol was positively correlated with serum alkaline phosphatase and γ-GGT. In the chemotherapy-sensitive and chemotherapy-resistant ovarian cancer tissues, the differential metabolite dihydrothymine was significantly reduced in the chemotherapy-resistant group. In the ascites supernatant of the drug-resistant group, the differential metabolites, 1,25-dihydroxyvitamins D3-26, 23-lactonel and hexadecanoic acid were also significantly reduced. The results indicated that the nine differential metabolites could reflect the prognosis and the extent of liver and kidney damage in patients with ovarian cancer. Three differential metabolites with low expression in the drug-resistant group were proposed as new markers of chemotherapy efficacy in ovarian cancer patients with ascites.