bluuebunny/crossref_metadata_2025 huggingface dataset:
Disentangling species-specific krill responses to local oceanography and predator’s biomass: The case of the Humboldt krill and the Peruvian anchovy
Authors: Díaz-Astudillo Macarena , Riquelme-Bugueño Ramiro , Bernard Kim S. , Saldías Gonzalo S. , Rivera Reinaldo , Letelier Jaime
Published: October 2022

Euphausiids (hereafter “krill”) are one of the main components of the pelagic communities of the Humboldt Current System (HCS). Their community dynamics have been well studied in central-southern Chile where upwelling is strongly seasonal, but little is known about the permanent-upwelling area of the HCS, which yields the largest fishery in the world, the Peruvian anchovy. We applied hierarchical generalized additive models with environmental and biological predictors to determine the main drivers of krill abundance, adjusting species-specific functions. We used a time series of 16 bi-annual surveys to study annual, seasonal, and spatial scales of variability of the four numerically dominant taxa: Euphausia mucronata (Humboldt krill), E. eximia, Stylocheiron affine, and Nematoscelis spp. The spatial pattern of the Humboldt krill (the dominant species) proved it is an upwelling-associated species, with higher abundances within 10 km from the coast. The other 3 taxa showed opposite spatial patterns with higher abundances offshore. The main covariates explaining krill abundances were the depth of the upper limit of the oxygen minimum zone (dOMZ) and the mean temperature of the water column. Humboldt krill was negatively correlated to both drivers, and the opposite effect was observed for the other taxa. Although many krill species are metabolically adapted to cope with the severe hypoxic conditions of this system, the Humboldt krill was the only species with higher modeled abundances when dOMZ was shallower. Chlorophyll-a remained high during all sampling periods, and it was an insignificant predictor for all taxa, suggesting food is not a limitation for krill in this highly productive system. The acoustic biomass of the Peruvian anchovy had a negative non-linear effect on the abundances of the Humboldt krill, and higher Humboldt krill abundances were found in areas with no anchovy hotspots. Our results indicate that krill in this system are susceptible to changes in temperature, oxygen, and upwelling conditions. Extreme events (e.g. heatwaves and ENSO events) are expected to increase in frequency and intensity, while climate change scenarios show a potential intensification of upwelling. These conditions could lead to distribution displacements and alter trophic interactions by modifying the distribution and biomass of the predator.
Dynamic analysis of an axially moving underwater pipe conveying pulsating fluid
Authors: Luo Yangyang , Zhang Dapeng
Published: October 2022

In this paper, both linear and non-linear dynamics of a slender and uniform pipe conveying pulsating fluid, which is axially moving in an incompressible fluid, are comprehensively studied. The vibration equations of the system are established by considering various factors, including a coordinate conversion system, an “axial added mass coefficient” describing the additional inertia forces caused by the external fluid, the Kelvin–Voigt viscoelastic damping, a kind of non-linear additional axial tension, and the pulsating internal fluid. The vibration equations are discretized by the Galerkin procedure and solved by the Runge–Kutta approach, and the validity of the solution procedure is carefully checked. After that, the linear and non-linear responses of the system are studied when the internal flow velocity and the axially moving speed of the pipe are small. For linear responses, the Kelvin–Voigt viscoelastic damping has great influences on the second and third modes of the system. For the non-linear dynamic, the results are rich and changeful, including the first and second principal parametric resonances, the secondary resonance, the combination resonance, period-1 motion, quasi-periodic motion, and chaotic motion. Finally, the influence of several key system parameters on the non-linear responses is analyzed.
Self-healing mechanism of deposited carbonates in cement cracks under CO2 storage well conditions
Authors: Xing Xuesong , Zhong Guangrong , Wu Zhiqiang , Cai Jingxuan , Cheng Xiaowei
Published: October 2022

In CO2 geological storage wells, the leakage of CO2 along the micro-cracks of the cement sheath of abandoned wells is one of the main risks of CO2 leakage. The chemical reaction between CO2 and oil well cement can realize self-healing of micro-cracks in the cement sheath. In this study, self-healing experiments of artificial cracks in cement-based materials were carried out by simulating the working conditions of high temperature, high pressure and CO2-rich CCS. The formation process and self-healing effect of calcium carbonate (CaCO3) in oil well cement-based materials induced by CO2 under different exposure environments were explored, and the self-healing products were analyzed by X-ray diffraction (XRD) and environmental scanning electron microscopy (ESEM and EDX). X-ray computed tomography (μ-CT) was used to reconstruct the changes of cracks in 3D, and compressive strength, porosity, and permeability were used to evaluate the self-healing properties of cement-based material cracks. The results indicated that for the CS-28 (the samples reacted with humid CO2 for 28 days) and AS-28 (the samples reacted with humid air for 28 days) samples, the compressive strength increased by 56.67% and 10.38%, the porosity decreased by 59.37% and 18.19%, and the permeability decreased by 59.91% and 28.07%, respectively. The crack-volume reduction rate of the CS-28 specimen was 57.08%, and the pore-volume reduction rate was 69.20%. Many massive, needle shaped CaCO3 crystals were formed in the pores and cracks of the sample. The reconstruction of the 3D structure of self-healing cement shows that the micro-cracks of the cement are sealed but the pores are increased. The damage prediction based on von Mises stress shows that under the axial force, the healing layer is not prone to damage. This study provides a theoretical and experimental basis for applying self-healing technology in CCS downhole environment, improving the service life of cement sheath and preventing the leakage of stored CO2.
Artificial intelligence to improve polyp detection and screening time in colon capsule endoscopy
Authors: Gilabert Pere , Vitrià Jordi , Laiz Pablo , Malagelada Carolina , Watson Angus , Wenzek Hagen , Segui Santi
Published: October 2022

Colon Capsule Endoscopy (CCE) is a minimally invasive procedure which is increasingly being used as an alternative to conventional colonoscopy. Videos recorded by the capsule cameras are long and require one or more experts' time to review and identify polyps or other potential intestinal problems that can lead to major health issues. We developed and tested a multi-platform web application, AI-Tool, which embeds a Convolution Neural Network (CNN) to help CCE reviewers. With the help of artificial intelligence, AI-Tool is able to detect images with high probability of containing a polyp and prioritize them during the reviewing process. With the collaboration of 3 experts that reviewed 18 videos, we compared the classical linear review method using RAPID Reader Software v9.0 and the new software we present. Applying the new strategy, reviewing time was reduced by a factor of 6 and polyp detection sensitivity was increased from 81.08 to 87.80%.
Machine learning algorithm-based identification and verification of characteristic genes in acute kidney injury
Authors: Li Yinghao , Du Yiwei , Zhang Yanlong , Chen Chao , Zhang Jian , Zhang Xin , Zhang Min , Yan Yong
Published: October 2022

Background

Acute kidney injury is a common renal disease with high incidence and mortality. Early identification of high-risk acute renal injury patients following renal transplant could improve their prognosis, however, no biomarker exists for early detection.

Methods

The GSE139061 dataset was used to identify hub genes in 86 DEGs between acute kidney injury and control samples using three machine learning algorithms (LASSO, random forest, and support vector machine-recursive feature elimination). We used GSEA to identify the related signal pathways of six hub genes. Finally, we validated these potential biomarkers in an in vitro hypoxia/reoxygenation injury cell model using RT-qPCR.

Results

Six hub genes (MDFI, EHBP1L1, FBXW4, MDM4, RALYL, and ESM1) were identified as potentially predictive of an acute kidney injury. The expression of ESM1 and RALYL were markedly increased in control samples, while EHBP1L1, FBXW4, MDFI, and MDM4 were markedly increased in acute kidney injury samples.

Conclusion

We screened six hub genes related to acute kidney injury using three machine learning algorithms and identified genes with potential diagnostic utility. The hub genes identified in this study might play a significant role in the pathophysiology and progression of AKI. As such, they might be useful for the early diagnosis of AKI and provide the possibility of improving the prognosis of AKI patients.
Efficacy of preventive use of oxygen therapy after planned extubation in high-risk patients with extubation failure: A network meta-analysis of randomized controlled trials
Authors: Zheng Xiaozhuo , Wang Rui , Giri Mohan , Duan Jun , Ma Mengyi , Guo Shuliang
Published: October 2022

Background

Extubation failure is common in critically ill patients, especially those with high-risk factors, and is associated with poor prognosis. Prophylactic use of oxygen therapy after extubation has been gradually introduced. However, the best respiratory support method is still unclear.

Purpose

This study aimed to evaluate the efficacy of four post-extubation respiratory support approaches in reducing reintubation and respiratory failure in patients at high-risk of extubation failure.

Methods

A comprehensive search was performed in Cochrane Central Register of Controlled Trials, PubMed, EMBASE, and Web of Science from inception to June 2022. Randomized controlled trials (RCTs) comparing post-extubation preventive use of respiratory management strategies, including conventional oxygen therapy (COT), non-invasive ventilation (NIV), and high-flow nasal catheter (HFNC) in high-risk patients with extubation failure were reviewed. Primary outcomes were reintubation rate and respiratory failure. Secondary outcomes included intensive care unit (ICU) mortality, ICU stay and length of hospital stay (LOS).

Results

Seventeen RCTs comprising 2813 participants were enrolled. Compared with COT, the three respiratory support methods (NIV, HFNC, NIV + HFNC) were all effective in preventing reintubation [odds ratio (OR) 0.46, 95% confidence interval (CI) 0.32–0.67; OR 0.26, 95% CI 0.14–0.48; OR 0.62, 95% CI 0.39–0.97, respectively] and respiratory failure (OR 0.23, 95% CI 0.10–0.52; OR 0.15, 95% CI 0.04–0.60; OR 0.26, 95% CI 0.10–0.72, respectively). NIV and NIV + HFNC also reduced ICU mortality (OR 0.40, 95% CI 0.22–0.74; OR 0.32, 95% CI 0.12–0.85). NIV + HFNC ranked best in terms of reintubation rate, respiratory failure and ICU mortality based on the surface under the cumulative ranking curve (SUCRA) (99.3, 87.1, 88.2, respectively). Although there was no significant difference in shortening ICU stay and LOS among the four methods, HFNC ranked first based on the SUCRA.

Conclusion

Preventive use of NIV + HFNC after scheduled extubation is probably the most effective respiratory support method for preventing reintubation, respiratory failure and ICU death in high-risk patients with extubation failure. HFNC alone seems to be the best method to shorten ICU stay and LOS.

Systematic review registration

[https://www.crd.york.ac.uk/prospero/], identifier [CRD42022340623].
Probiotics and probiotic-based vaccines: A novel approach for improving vaccine efficacy
Authors: Kazemifard Nesa , Dehkohneh Abolfazl , Baradaran Ghavami Shaghayegh
Published: October 2022

Vaccination is defined as the stimulation and development of the adaptive immune system by administering specific antigens. Vaccines' efficacy, in inducing immunity, varies in different societies due to economic, social, and biological conditions. One of the influential biological factors is gut microbiota. Cross-talks between gut bacteria and the host immune system are initiated at birth during microbial colonization and directly control the immune responses and protection against pathogen colonization. Imbalances in the gut microbiota composition, termed dysbiosis, can trigger several immune disorders through the activity of the adaptive immune system and impair the adequate response to the vaccination. The bacteria used in probiotics are often members of the gut microbiota, which have health benefits for the host. Probiotics are generally consumed as a component of fermented foods, affect both innate and acquired immune systems, and decrease infections. This review aimed to discuss the gut microbiota's role in regulating immune responses to vaccination and how probiotics can help induce immune responses against pathogens. Finally, probiotic-based oral vaccines and their efficacy have been discussed.
The CRTh2 polymorphism rs533116 G > A associates with asthma severity in older females
Authors: Shrestha Palikhe Nami , Mackenzie Constance A. , Licskai Christopher , Kim Richard B. , Vliagoftis Harissios , Cameron Lisa
Published: October 2022

Background

CRTh2 is G protein coupled receptor for prostaglandin D2 (PGD)2expressed by immune cells that drive type 2 inflammation such as CD4+T cells (Th2), eosinophils and group 2 innate lymphoid cells (ILC2) as well as structural cells including smooth muscle and epithelium. CRTh2-expressing cells are increased in the blood and airways of asthmatics and severe asthma is characterized by increased activity of the PGD2-CRTh2 pathway. TheCRTh2single nucleotide polymorphism (SNP) rs533116 G > A is associated with development of asthma and increased Th2 cell differentiation.

Objective

To examine whether CRTh2 rs533116G > A associates with asthma severity. Since severe asthma is more common in females than males, we performed a sex-stratified analysis.

Methods

Clinical data from asthmatics (n= 170) were obtained from clinic visits and chart review. Asthma severity was assessed according to ERS/ATS guidelines. Peripheral blood cells were characterized by flow cytometry and qRT-PCR. Genotyping was performed by TaqMan assay.

Results

Older females (≥45 years) homozygous for minor A allele of rs533116 were more likely to have severe asthma, lower FEV1, a higher prescribed dose of inhaled corticosteroid and more type 2 inflammation than females carrying GA or GG genotypes. Comparing females and males with the AA genotype also revealed that women had more type 2 inflammation.

Conclusions and significance

The polymorphism CRTh2 rs533116 G > A associates with severe asthma and type 2 inflammation in older females. This study reveals a gene-sex-aging interaction influencing the effect of CRTh2 on asthma severity.
How does self-compassion help people adjust to chronic skin conditions? A template analysis study
Authors: Clarke Elaine N. , Norman Paul , Thompson Andrew R.
Published: October 2022

Objectives

Skin conditions can greatly impact people's lives, but greater understanding of the processes involved in positive adjustment is required. Self-compassion has strong links to wellbeing and adaptive functioning and therefore may play an important role in adjustment to skin conditions.

Design

Template analysis was used to explore how self-compassion operates in people living with skin conditions, with reference to existing theories of self-compassion.

Methods

Semi-structured interviews were conducted with highly self-compassionate people with chronic skin conditions (N = 10). Theoretical models of self-compassion were used in the development of the initial template and interview schedule. Participants were purposively selected on the basis of having high scores on a measure of self-compassion.

Results

Participants reported a variety of ongoing skin-related difficulties and their ways of managing these. Sensitivity to distress and care for wellbeing were identified as foundation themes: necessary components of a compassionate response to distress. Eleven types of difficulty-management strategies built upon these foundation themes: empathy, non-judgement, distress tolerance, self-kindness, mindful attention, perspective-taking, self-talk, self-care, using social support, concealment, and idiosyncratic coping strategies.

Conclusions

Components of self-compassion helped people adjust to chronic skin conditions in a wide variety of ways, indicating that psychological adjustment is not a simple, linear process. Sometimes compassionate responses occurred automatically and sometimes with deliberate effort. Further research on compassion-based interventions for people with skin conditions is warranted.
Development of an innovative in vivo model of PJI treated with DAIR
Authors: Poilvache Hervé , Van Bambeke Françoise , Cornu Olivier
Published: October 2022

Introduction

Prosthetic Joint Infection (PJI) are catastrophic complications of joint replacement. Debridement, implant retention, and antibiotic therapy (DAIR) is the usual strategy in acute infections but fails in 45% of MRSA infections. We describe the development of a model of infected arthroplasty in rabbits, treated with debridement and a course of vancomycin with clinically relevant dosage.

Materials and methods

A total of 15 rabbits were assigned to three groups: vancomycin pharmacokinetics (A), infection (B), and DAIR (C). All groups received a tibial arthroplasty using a Ti-6Al-4V implant. Groups B and C were infected per-operatively with a 5.5 log10 MRSA inoculum. After 1 week, groups C infected knees were surgically debrided. Groups A and C received 1 week of vancomycin. Pharmacokinetic profiles were obtained in group A following 1st and 5th injections. Animals were euthanized 2 weeks after the arthroplasty. Implants and tissue samples were processed for bacterial counts and histology.

Results

Average vancomycin AUC0–12 h were 213.0 mg*h/L (1st injection) and 207.8 mg*h/L (5th injection), reaching clinical targets. All inoculated animals were infected. CFUs were reproducible in groups B. A sharp decrease in CFU was observed in groups C. Serum markers and leukocytes counts increased significantly in infected groups.

Conclusion

We developed a reproducible rabbit model of PJI treated with DAIR, using vancomycin at clinically relevant concentrations.
Integration of artificial intelligence and precision oncology in Latin America
Authors: Sussman Liliana , Garcia-Robledo Juan Esteban , Ordóñez-Reyes Camila , Forero Yency , Mosquera Andrés F. , Ruíz-Patiño Alejandro , Chamorro Diego F. , Cardona Andrés F.
Published: October 2022

Next-generation medicine encompasses different concepts related to healthcare models and technological developments. In Latin America and the Caribbean, healthcare systems are quite different between countries, and cancer control is known to be insufficient and inefficient considering socioeconomically discrepancies. Despite advancements in knowledge about the biology of different oncological diseases, the disease remains a challenge in terms of diagnosis, treatment, and prognosis for clinicians and researchers. With the development of molecular biology, better diagnosis methods, and therapeutic tools in the last years, artificial intelligence (AI) has become important, because it could improve different clinical scenarios: predicting clinically relevant parameters, cancer diagnosis, cancer research, and accelerating the growth of personalized medicine. The incorporation of AI represents an important challenge in terms of diagnosis, treatment, and prognosis for clinicians and researchers in cancer care. Therefore, some studies about AI in Latin America and the Caribbean are being conducted with the aim to improve the performance of AI in those countries. This review introduces AI in cancer care in Latin America and the Caribbean, and the advantages and promising results that it has shown in this socio-demographic context.
Characterization and mechanism of aflatoxin degradation by a novel strain of Trichoderma reesei CGMCC3.5218
Authors: Yue Xiaofeng , Ren Xianfeng , Fu Jiayun , Wei Na , Altomare Claudio , Haidukowski Miriam , Logrieco Antonio F. , Zhang Qi , Li Peiwu
Published: October 2022

Aflatoxins, which are produced mainly by Aspergillus flavus and A. parasiticus, are recognized as the most toxic mycotoxins, which are strongly carcinogenic and pose a serious threat to human and animal health. Therefore, strategies to degrade or eliminate aflatoxins in agro-products are urgently needed. We investigated 65 Trichoderma isolates belonging to 23 species for their aflatoxin B1 (AFB1)-degrading capabilities. Trichoderma reesei CGMCC3.5218 had the best performance, and degraded 100% of 50 ng/kg AFB1 within 3 days and 87.6% of 10 μg/kg AFB1 within 5 days in a liquid-medium system. CGMCC3.5218 degraded more than 85.0% of total aflatoxins (aflatoxin B1, B2, G1, and G2) at 108.2–2323.5 ng/kg in artificially and naturally contaminated peanut, maize, and feed within 7 days. Box–Behnken design and response surface methodology showed that the optimal degradation conditions for CGMCC3.5218 were pH 6.7 and 31.3°C for 5.1 days in liquid medium. Possible functional detoxification components were analyzed, indicating that the culture supernatant of CGMCC3.5218 could efficiently degrade AFB1 (500 ng/kg) with a ratio of 91.8%, compared with 19.5 and 8.9% by intracellular components and mycelial adsorption, respectively. The aflatoxin-degrading activity of the fermentation supernatant was sensitive to proteinase K and proteinase K plus sodium dodecyl sulfonate, but was stable at high temperatures, suggesting that thermostable enzymes or proteins in the fermentation supernatant played a major role in AFB1 degradation. Furthermore, toxicological experiments by a micronucleus assay in mouse bone marrow erythrocytes and by intraperitoneal injection and skin irritation tests in mice proved that the degradation products by CGMCC3.5218 were nontoxic. To the best of our knowledge, this is the first comprehensive study on Trichoderma aflatoxin detoxification, and the candidate strain T. reesei CGMCC3.5218 has high efficient and environment-friendly characteristics, and qualifies as a potential biological detoxifier for application in aflatoxin removal from contaminated feeds.
Mirubactin C rescues the lethal effect of cell wall biosynthesis mutations in Bacillus subtilis
Authors: Kepplinger Bernhard , Wen Xin , Tyler Andrew Robert , Kim Byung-Yong , Brown James , Banks Peter , Dashti Yousef , Mackenzie Eilidh Sohini , Wills Corinne , Kawai Yoshikazu , Waldron Kevin John , Allenby Nicholas Edward Ellis , Wu Ling Juan , Hall Michael John , Errington Jeff
Published: October 2022

Growth of most rod-shaped bacteria is accompanied by the insertion of new peptidoglycan into the cylindrical cell wall. This insertion, which helps maintain and determine the shape of the cell, is guided by a protein machine called the rod complex or elongasome. Although most of the proteins in this complex are essential under normal growth conditions, cell viability can be rescued, for reasons that are not understood, by the presence of a high (mM) Mg2+ concentration. We screened for natural product compounds that could rescue the growth of mutants affected in rod-complex function. By screening > 2,000 extracts from a diverse collection of actinobacteria, we identified a compound, mirubactin C, related to the known iron siderophore mirubactin A, which rescued growth in the low micromolar range, and this activity was confirmed using synthetic mirubactin C. The compound also displayed toxicity at higher concentrations, and this effect appears related to iron homeostasis. However, several lines of evidence suggest that the mirubactin C rescuing activity is not due simply to iron sequestration. The results support an emerging view that the functions of bacterial siderophores extend well beyond simply iron binding and uptake.
Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China
Authors: Han Zhenzhi , Xiao Jinbo , Song Yang , Zhao Xiaonan , Sun Qiang , Lu Huanhuan , Zhang Keyi , Li Jichen , Li Junhan , Si Fenfen , Zhang Guoyan , Zhao Hehe , Jia Senquan , Zhou Jienan , Wang Dongyan , Zhu Shuangli , Yan Dongmei , Xu Wenbo , Fu Xiaoqing , Zhang Yong
Published: October 2022

Background

The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China.

Materials and methods

We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships.

Results

In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics.

Conclusion

Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.
The archaeal class Halobacteria and astrobiology: Knowledge gaps and research opportunities
Authors: Wu Jia-Hui , McGenity Terry J. , Rettberg Petra , Simões Marta F. , Li Wen-Jun , Antunes André
Published: October 2022

Water bodies on Mars and the icy moons of the outer solar system are now recognized as likely being associated with high levels of salt. Therefore, the study of high salinity environments and their inhabitants has become increasingly relevant for Astrobiology. Members of the archaeal class Halobacteria are the most successful microbial group living in hypersaline conditions and are recognized as key model organisms for exposure experiments. Despite this, data for the class is uneven across taxa and widely dispersed across the literature, which has made it difficult to properly assess the potential for species of Halobacteria to survive under the polyextreme conditions found beyond Earth. Here we provide an overview of published data on astrobiology-linked exposure experiments performed with members of the Halobacteria, identifying clear knowledge gaps and research opportunities.
Effects of captive and primate-focused tourism on the gut microbiome of Tibetan macaques
Authors: Xia Yingna , Xu Xiaojuan , Chen Huijuan , Yue Ran , Xia Dongpo , Wang Xi , Li Jinhua , Sun Binghua
Published: October 2022

Documenting the effects of anthropogenic activities on the gut microbiome of wild animals is important to their conservation practices. Captivity and ecotourism are generally considered two common anthropogenic disturbances on the health of nonhuman primates. Here, we examined the divergences of gut microbiome in different environments of Tibetan macaques. Our results showed that there were no significant differences in the alpha diversity, predominant families and genera of gut microbiomes between wild and tourist groups. However, these indexes decreased significantly in the captive individuals. In addition, the significant differences of beta diversity and community compositions between wild and tourism groups also were detected. In particular, higher potential pathogenic and predicted KEGG pathway of drug resistance (antimicrobial) were detected in the gut microbiome of individuals in captive environment. Our results indicated that living in the wild are beneficial to maintaining gut microbial diversity of Tibetan macaques, while captivity environment is harmful to the health of this macaque. Exploring ways to restore the native gut microbiome and its diversity of captive individual should pay more attention to in the future studies.
Metformin alleviates irradiation-induced intestinal injury by activation of FXR in intestinal epithelia
Authors: Yang Jing-Yu , Liu Meng-Jie , Lv Lin , Guo Jin-Rong , He Kai-Yue , Zhang Hong , Wang Ke-Ke , Cui Cui-Yun , Yan Bei-Zhan , Du Dan-Dan , Wang Jin-Hua , Ding Qiang , Liu Guo-Long , Xu Zhi-Xiang , Jian Yong-Ping
Published: October 2022

Abdominal irradiation (IR) destroys the intestinal mucosal barrier, leading to severe intestinal infection. There is an urgent need to find safe and effective treatments to reduce IR-induced intestinal injury. In this study, we reported that metformin protected mice from abdominal IR-induced intestinal injury by improving the composition and diversity of intestinal flora. The elimination of intestinal microbiota (Abx) abrogated the protective effects of metformin on irradiated mice. We further characterized that treatment of metformin increased the murine intestinal abundance of Lactobacillus, which mediated the radioprotective effect. The administration of Lactobacillus or fecal microbiota transplantation (FMT) into Abx mice considerably lessened IR-induced intestinal damage and restored the radioprotective function of metformin in Abx mice. In addition, applying the murine intestinal organoid model, we demonstrated that IR inhibited the formation of intestinal organoids, and metformin alone bore no protective effect on organoids after IR. However, a combination of metformin and Lactobacillus or Lactobacillus alone displayed a strong radioprotection on the organoid formation. We demonstrated that metformin/Lactobacillus activated the farnesoid X receptor (FXR) signaling in intestinal epithelial cells and hence upregulated tight junction proteins and mucins in intestinal epithelia, increased the number of goblet cells, and augmented the mucus layer thickness to maintain the integrity of intestinal epithelial barrier, which eventually contributed to reduced radiation intestinal injury. In addition, we found that Lactobacillus abundance was significantly increased in the intestine of patients receiving metformin while undergoing abdominal radiotherapy and the abundance was negatively correlated with the diarrhea duration of patients. In conclusion, our results demonstrate that metformin possesses a protective effect on IR-induced intestinal injury by upregulating the abundance of Lactobacillus in the intestine.
Biological and genomic characteristics of two bacteriophages isolated from sewage, using one multidrug-resistant and one non-multidrug-resistant strain of Klebsiella pneumoniae
Authors: Liang Bingchun , Zhao Wenpeng , Han Bo , Barkema Herman W. , Niu Yan D. , Liu Yongxia , Kastelic John P. , Gao Jian
Published: October 2022

Bovine mastitis caused by multi-drug resistant (MDR) Klebsiella pneumoniae is difficult to treat with antibiotics, whereas bacteriophages may be a viable alternative. Our objective was to use 2 K. pneumoniae strains, 1 MDR and the other non-MDR, to isolate phages from sewage samples and compare their biological and genomic characteristics. Additionally, phage infected mouse mammary gland was also analyzed by H&E staining and ELISA kits to compare morphology and inflammatory factors, respectively. Based on assessments with double agar plates and transmission electron microscopy, phage CM_Kpn_HB132952 had clear plaques surrounded by translucent halos on the bacterial lawn of K. pneumoniae KPHB132952 and belonged to Siphoviridae, whereas phage CM_Kpn_HB143742 formed a clear plaque on the bacterial lawn of K. pneumoniae KPHB143742 and belonged to Podoviridae. In 1-step growth curves, CM_Kpn_HB132952 and CM_Kpn_HB143742 had burst sizes of 0.34 and 0.73 log10 PFU/mL, respectively. The former had a latent period of 50 min and an optimal multiplicity of infection (MOI) of 0.01, whereas for the latter, the latent period was 30 min (MOI = 1). Phage CM_Kpn_HB132952 had better thermal and acid–base stability than phage CM_Kpn_HB143742. Additionally, both phages had the same host range rate but different host ranges. Based on Illumina NovaSeq, phages CM_Kpn_HB132952 and CM_Kpn_HB143742 had 140 and 145 predicted genes, respectively. Genomic sequencing and phylogenetic tree analysis indicated that both phages were novel phages belonging to the Klebsiella family. Additionally, the histopathological structure and inflammatory factors TNF-α and IL-1β were not significantly different among phage groups and the control group. In conclusion, using 1 MDR and 1 non-MDR strain of K. pneumoniae, we successfully isolated two phages from the same sewage sample, and demonstrated that they had distinct biological and genomic characteristics.
Genetic characterization of porcine reproductive and respiratory syndrome virus from Eastern China during 2017–2022
Authors: Zhou Lujia , Yang Yang , Xia Qiqi , Guan Zhixin , Zhang Junjie , Li Beibei , Qiu Yafeng , Liu Ke , Shao Donghua , Ma Zhiyong , Wang Xiaodu , Wei Jianchao
Published: October 2022

Porcine reproductive and respiratory syndrome (PRRS) is an immunosuppressive disease caused by PRSS virus (PRRSV). PRRSV mainly causes reproductive disorders in pregnant sows and respiratory diseases in piglets. Recently, it has emerged as one of the most important diseases of the pig industry across the globe. In this study, we have collected 231 samples from differently sized pig farms in Eastern China from 2017 to 2022 to investigate the epidemic characteristics of the disease. All samples were screened by RT-PCR and analyzed further using Nsp2 and ORF5 genes. The result showed that the positive rate of PRRSV was 24% (54/231). Phylogenetic analysis (13 positive samples) revealed that all isolates belonged to genotype 2, and they were mainly distributed in four lineages (i.e., lineage 1, 3, 5, and 8). Nsp2 is the most variable protein among all PRRSV NSPs, several isolates from this study had amino acid deletions within Nsp2 compared to that of strain VR-2332. The major structural protein glycoprotein (GP5) protein is encoded by ORF5. Epitope analysis of the 13 isolated strains and additional reference strains revealed that all 13 strains had some mutations on the decoy epitope, the primary neutralizing epitope, T cell epitopes, and B cell epitopes. This study showed that the prevalent PRRSV strain in Eastern China was still HP-PRRSV, while the proportion of NADC30-like and NADC34-like strains have increased. This study further enriches the epidemiological data of PRRS in Eastern China and provides a theoretical basis for vaccine development and prevention and control of the disease across the region.
The relation between avian coronaviruses and SARS-CoV-2 coronavirus
Authors: Al-Khalaifah Hanan , Alotaibi Mohammad , Al-Nasser Afaf
Published: October 2022

The coronaviruses (CoVs) are a family of ribonucleic acid viruses that are present in both mammals and birds. SARS-CoV and MERS-CoV originated in bats, and there is a possibility that this could be the case for SARS-CoV-2 as well. There is already evidence that a probable intermediary host is responsible for the emergence of viruses in humans as was the case for SARS-CoVs and MERS-CoV. As the SARS-CoV-2 originated from a live animal market, there is always the question if domestic animals are susceptible to these viruses and the possible risk of zoonotic transmission with mammals, including humans. This uncertainty of the transmission of the COVID-19 virus between humans and animals is of great significance worldwide. Hence, this paper focuses on the avian CoVs and their possible relation and interaction with SARS-CoV-2.
Incubation determines favorable microbial communities in Chinese alligator nests
Authors: Yu Qin-Zhang , Hu Meng-Yuan , Wang Li , Lin Jian-Qing , Fang Sheng-Guo
Published: October 2022

Nest materials are a major heat source due to rotting promoted by microbial activity. Additionally, they are a potential microbial source given their direct contact with eggshells. Microbial dynamics during incubation have been studied in wild birds; however, similar studies in reptiles remain elusive. Here, the study characterized microbial communities in the nest materials of Chinese alligator (Alligator sinensis) using high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) region sequences. The results showed that significant changes in the diversity and structure of microbial communities according to different incubation periods. The diversity and richness of bacterial species increased significantly over time, but the relative abundance of the most dominant bacteria in pre-incubation period, including some pathogenic bacteria, declined after incubation. In contrast, fungal species diversity and richness decreased significantly with time. Additionally, nest material composition significantly influenced microbial community structure rather than species diversity and richness. Notably, the fungal community structure showed a stronger response than bacteria to nest material composition, which varied due to differences in plant litter composition. Our results demonstrate the significant response of microbial community diversity and structure to differences in incubation periods and nest material composition in reptiles. It is further emphasized that the importance of incubation period in the conservation of the Chinese alligator and could inform similar studies in other reptiles and birds.
Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report
Authors: Oldoni Emanuela , Saunders Gary , Bietrix Florence , Garcia Bermejo Maria Laura , Niehues Anna , ’t Hoen Peter A. C. , Nordlund Jessica , Hajduch Marian , Scherer Andreas , Kivinen Katja , Pitkänen Esa , Mäkela Tomi Pekka , Gut Ivo , Scollen Serena , Kozera Łukasz , Esteller Manel , Shi Leming , Ussi Anton , Andreu Antonio L. , van Gool Alain J.
Published: October 2022

Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
Randomized, sham-controlled, clinical trial of repetitive transcranial magnetic stimulation for patients with Alzheimer’s dementia in Japan
Authors: Saitoh Youichi , Hosomi Koichi , Mano Tomoo , Takeya Yasushi , Tagami Shinji , Mori Nobuhiko , Matsugi Akiyoshi , Jono Yasutomo , Harada Hideaki , Yamada Tomomi , Miyake Akimitsu
Published: October 2022

Background

Several medications have been applied to Alzheimer’s dementia patients (AD) but their efficacies have been insufficient. The efficacy and safety of 4 weeks of repetitive transcranial magnetic stimulation (rTMS) in Japanese AD were evaluated in this exploratory clinical trial.

Methods

Forty-two patients, aged 60–93 years (average, 76.4 years), who were taking medication (> 6 months) and had Mini-Mental State Examination (MMSE) scores ≤ 25 and Clinical Dementia Rating Scale scores (CDR-J) of 1 or 2, were enrolled in this single-center, prospective, randomized, three-arm study [i.e., 120% resting motor threshold (120% RMT), 90% RMT for the bilateral dorsolateral prefrontal cortex, and Sham]. Alzheimer’s Disease Assessment Scale-Japanese Cognitive (ADAS-J cog), Montreal Cognitive Assessment (MoCA-J), Clinical Global Impression of Change (CGIC), Neuropsychiatric inventory (NPI), and EuroQOL 5 Dimensions 5-Level (EQ-5D-5L) were administered. The primary endpoint was the mean change from baseline in the MMSE score (week 4). An active rTMS session involved applying 15 trains bilaterally (40 pulses/train at 10 Hz; intertrain interval, 26 s). Participants received ≥ 8 interventions within the first 2 weeks and at least one intervention weekly in the 3rd and 4th weeks. Full Analysis set (FAS) included 40 patients [120% RMT (n = 15), 90% RMT (n = 13), and Sham (n = 12)].

Results

In the FAS, MMSE, ADAS-J cog, MoCA-J, CDR-J, CGIC, NPI, and EQ-5D-5L scores between the three groups were not significantly different. Two patients were erroneously switched between the 120% RMT and 90% RMT groups, therefore, “as treated” patients were mainly analyzed. Post hoc analysis revealed significant treatment efficacy in participants with MMSE scores ≥ 15, favoring the 120% RMT group over the Sham group. Responder analysis revealed 41.7% of the 120% RMT group had a ≥ 3-point improvement in the ADAS-J cog versus 0% in the Sham group (Fisher’s exact test, p = 0.045). The MoCA-J showed the same tendency but was not significant. Efficacy disappeared in week 20, based on the ADAS-cog and MoCA-J. No intervention-related serious adverse events occurred.

Conclusion

This paper is the first report of using rTMS in Japanese AD patients. The treatment seems safe and moderate-mild stage AD should be target population of pivotal clinical trial with 120% RMT rTMS.
EEG functional brain connectivity strengthens with age during attentional processing to faces in children
Authors: Ramos-Loyo Julieta , Olguín-Rodríguez Paola V. , Espinosa-Denenea Sara E. , Llamas-Alonso Luis A. , Rivera-Tello Sergio , Müller Markus F.
Published: October 2022

Studying functional connectivity may generate clues to the maturational changes that occur in children, expressed by the dynamical organization of the functional network assessed by electroencephalographic recordings (EEG). In the present study, we compared the EEG functional connectivity pattern estimated by linear cross-correlations of the electrical brain activity of three groups of children (6, 8, and 10 years of age) while performingodd-balltasks containing facial stimuli that are chosen considering their importance in socioemotional contexts in everyday life. On the first task, the children were asked to identify the sex of faces, on the second, the instruction was to identify the happy expressions of the faces. We estimated the stable correlation pattern (SCP) by the average cross-correlation matrix obtained separately for the resting state and the task conditions and quantified the similarity of these average matrices comparing the different conditions. The accuracy improved with higher age. Although the topology of the SCPs showed high similarity across all ages, the two older groups showed a higher correlation between regions associated with the attentional and face processing networks compared to the youngest group. Only in the youngest group, the similarity metric decreased during the sex condition. In general, correlation values strengthened with age and during task performance compared to rest. Our findings indicate that there is a spatially extended stable brain network organization in children like that reported in adults. Lower similarity scores between several regions in the youngest children might indicate a lesser ability to cope with tasks. The brain regions associated with the attention and face networks presented higher synchronization across regions with increasing age, modulated by task demands.
Variation in stroke care at the hospital level: A cross-sectional multicenter study
Authors: Lens Charlotte , Coeckelberghs Ellen , Seys Deborah , Demeestere Jelle , Weltens Caroline , Vanhaecht Kris , Lemmens Robin
Published: October 2022

Introduction

Stroke is one of the leading causes of mortality and disability. Improving patient outcomes can be achieved by improving stroke care and adherence to guidelines. Since wide variation in adherence rates for stroke guidelines still exists, we aimed to describe and compare stroke care variability within Belgian hospitals.

Materials and methods

An observational, multicenter study was performed in 29 Belgian hospitals. We retrospectively collected patient characteristics, quality indicators, and time metrics from the last 30 consecutive patients per hospital, diagnosed with ischemic stroke in 2019 with structured questionnaires. Mean adherence ratios (%) ± SD (minimum – maximum) were calculated.

Results

We analyzed 870 patient records from 29 hospitals. Results showed large inter- and intrahospitals variations in adherence for various indicators. Almost all the patients received brain imaging (99.7%) followed by admission at a stroke unit in 82.9% of patients. Of patients not receiving thrombolysis, 92.5% of patients were started on antithrombotic drugs. Indicators with moderate median adherence but large interhospital variability were glycemia monitoring [82.3 ± 16.7% (26.7–100.0%)], performing clinical neurological examination and documentation of stroke severity [63.1 ± 36.8% (0–100%)], and screening for activities of daily living [51.1 ± 40.3% (0.0–100.0%)]. Other indicators lacked adequate adherence: swallowing function screening [37.0 ± 30.4% (0.0–93.3%)], depression screening [20.2 ± 35.8% (0.0–100%)], and timely body temperature measurement [15.1 ± 17.0% (0.0–60%)].

Conclusion

We identified high adherence to guidelines for some indicators, but lower rates with large interhospital variability for other recommendations also based on robust evidence. Improvement strategies should be implemented to improve the latter.