bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial effects and influencing factors of urban land intensive use in the Yangtze River Delta under high-quality development
Authors: Luo Xiang , Qin Jingjing , Cheng Chao , Pan Yue , Yang Tiantian
Published: August 2022

To integrate the concept of high-quality development into urban land use, this paper explores the spatial-temporal pattern characteristics of urban land intensive use (ULIU) in the Yangtze River Delta with a constructed evaluation index system, the comprehensive evaluation model and exploratory spatial data analysis based on the spatial panel data of 41 cities from 2010 to 2020. The paper also analyzes the spatial effects and influencing factors of ULIU with the spatial Durbin model and partial differential method. The results demonstrate that: 1) The ULIU in the Yangtze River Delta generally showed consistent growth from 2010 to 2020. However, there was significant spatial differentiation among different regions, as the land intensive use level was higher in cities along the Yangtze River and coastal cities around Hangzhou Bay, while relatively lower in the mountainous and hilly cities in Zhejiang and southwestern Anhui. 2) The ULIU level showed significant positive global spatial autocorrelations, while its local spatial characteristics mainly included four types dominated by high-high agglomeration and low-low agglomeration from 2010 to 2020. 3) Economic development, industrial structure and infrastructure could remarkably promote the ULIU of both local and neighboring cities. Scientific and technological innovation could significantly enhance the ULIU of local cities; population urbanization and government financial pressure showed significant negative effects on the ULIU of local cities; while all the above three factors had insignificant effects on the ULIU of neighboring cities. These findings are of great significance for revealing the internal mechanism underlying the spatial effect of land intensive use and provide some guidance for improving the level of ULIU in the Yangtze River Delta from the perspective of regional cooperation.
Sources and migration characteristics of fluorine in the river water of a small karst watershed influenced by coal mining
Authors: Du Shuangxue , An Li , Huang Jiangxun , Li Qingguang , Wu Pan , Guo Xingqiang
Published: August 2022

In high-fluorine geological background areas, the supergene geochemical process of fluorine has an impact on regional environmental health and safety, which has long been the focus of attention. However, in karst areas characterized by a high incidence of endemic fluorosis, the migration and transformation of fluorine in surface water have not received sufficient attention. This study investigated the joint influence of the weathering and erosion of carbonate rocks and coal-bearing strata on a typical small watershed. Accordingly, 239 samples representing 13 periods of hydrochemical samples were systematically collected to clarify the source, migration, and transformation characteristics of fluorine in surface water. The results revealed that the pH of the Huatan River was low in the rainy season and high in the dry season. The annual variation range of fluorine concentration was 0.11–0.40 mg/L. Although mining development produced acid mine drainage with high fluorine concentration, its impact at the watershed scale appeared to be limited. In terms of spatial scale, the concentration of fluorine in the Huatan River increased gradually from upstream to downstream. The dissolution of fluorite and other fluorine-bearing minerals had not reached the saturation state. The fluorine in the watershed primarily came from the dissolution of fluorine-bearing minerals, followed by the contribution of atmospheric precipitation. The release of fluorine adsorbed on the surface of clay minerals was not the main source of this element. The leaching of the watershed was shown to represent a critical transport process concerning fluorine in the Huatan River, and evaporation had a notable impact on the enrichment of fluorine in water.
Orchid diversity along an altitudinal gradient in the central Balkans
Authors: Djordjević Vladan , Tsiftsis Spyros , Kindlmann Pavel , Stevanović Vladimir
Published: August 2022

Understanding patterns of species diversity along an altitudinal gradient is the major topic of much biogeographical and ecological research. The aim of this study was to explore how richness and density of orchid species and subspecies in terms of different categories of underground organ systems and pollination systems vary along an altitudinal gradient in the central Balkans. The altitudinal gradient of the study area was divided into 21 100-m vertical intervals. Data were analyzed using both non-linear and linear regressions with three data sets (total orchids, orchids of forest habitats, orchids of non-forest habitats) in the case of species richness and three data sets (total orchids—total area, forest orchids—forest area, and orchids of non-forest habitats—non-forest area) in the case of species density. The results showed a hump-shaped pattern of orchid richness and density, peaking at 900–1,000 m. The richness and density of orchids of forest habitats are generally slightly greater than the richness and density of orchids of non-forest habitats in lowland areas, whereas the orchids of herbaceous vegetation types dominating at high altitudes. Tuberous orchids dominate in low and mid-altitude areas, orchids with palmately lobed and fusiform tubers (“intermediate orchids”) dominate at high altitudes, while rhizomatous orchids are predominate in mid-altitude forest stands. Both deceptive and self-pollinated orchids show a unimodal trend with a peak at mid-altitude areas. This study underlines the importance of low and mid-altitude areas for the survival of deceptive orchids and the importance of mid- and high-altitude areas for the survival of rewarding orchids. In addition, forest habitats at mid-altitudes have been shown to be crucial for the survival of self-pollinated orchids. The results suggest that the altitudinal patterns of orchid richness and density in the central Balkans are determined by mechanisms related to land area size and habitat cover, partially confirming the species-area relationship (SAR) hypothesis. This study contributes significantly to a better understanding of the potential impacts of habitat changes on orchid diversity, thereby facilitating more effective conservation planning.
Probiotics and live biotherapeutic products aiming at cancer mitigation and patient recover
Authors: Schemczssen-Graeff Zelinda , Pileggi Marcos
Published: August 2022

Molecular biology techniques allowed access to non-culturable microorganisms, while studies using analytical chemistry, as Liquid Chromatography and Tandem Mass Spectrometry, showed the existence of a complex communication system among bacteria, signaled by quorum sensing molecules. These approaches also allowed the understanding of dysbiosis, in which imbalances in the microbiome diversity, caused by antibiotics, environmental toxins and processed foods, lead to the constitution of different diseases, as cancer. Colorectal cancer, for example, can originate by a dysbiosis configuration, which leads to biofilm formation, production of toxic metabolites, DNA damage in intestinal epithelial cells through the secretion of genotoxins, and epigenetic regulation of oncogenes. However, probiotic strains can also act in epigenetic processes, and so be use for recovering important intestinal functions and controlling dysbiosis and cancer mitigation through the metabolism of drugs used in chemotherapy, controlling the proliferation of cancer cells, improving the immune response of the host, regulation of cell differentiation and apoptosis, among others. There are still gaps in studies on the effectiveness of the use of probiotics, therefore omics and analytical chemistry are important approaches to understand the role of bacterial communication, formation of biofilms, and the effects of probiotics and microbiome on chemotherapy. The use of probiotics, prebiotics, synbiotics, and metabiotics should be considered as a complement to other more invasive and hazard therapies, such chemotherapy, surgery, and radiotherapy. The study of potential bacteria for cancer treatment, as the next-generation probiotics and Live Biotherapeutic Products, can have a controlling action in epigenetic processes, enabling the use of these bacteria for the mitigation of specific diseases through changes in the regulation of genes of microbiome and host. Thus, it is possible that a path of medicine in the times to come will be more patient-specific treatments, depending on the environmental, genetic, epigenetic and microbiome characteristics of the host.
A layer-wise fusion network incorporating self-supervised learning for multimodal MR image synthesis
Authors: Zhou Qian , Zou Hua
Published: August 2022

Magnetic resonance (MR) imaging plays an important role in medical diagnosis and treatment; different modalities of MR images can provide rich and complementary information to improve the accuracy of diagnosis. However, due to the limitations of scanning time and medical conditions, certain modalities of MR may be unavailable or of low quality in clinical practice. In this study, we propose a new multimodal MR image synthesis network to generate missing MR images. The proposed model comprises three stages: feature extraction, feature fusion, and image generation. During feature extraction, 2D and 3D self-supervised pretext tasks are introduced to pre-train the backbone for better representations of each modality. Then, a channel attention mechanism is used when fusing features so that the network can adaptively weigh different fusion operations to learn common representations of all modalities. Finally, a generative adversarial network is considered as the basic framework to generate images, in which a feature-level edge information loss is combined with the pixel-wise loss to ensure consistency between the synthesized and real images in terms of anatomical characteristics. 2D and 3D self-supervised pre-training can have better performance on feature extraction to retain more details in the synthetic images. Moreover, the proposed multimodal attention feature fusion block (MAFFB) in the well-designed layer-wise fusion strategy can model both common and unique information in all modalities, consistent with the clinical analysis. We also perform an interpretability analysis to confirm the rationality and effectiveness of our method. The experimental results demonstrate that our method can be applied in both single-modal and multimodal synthesis with high robustness and outperforms other state-of-the-art approaches objectively and subjectively.
Comprehensive analysis of the cancer driver genes constructs a seven-gene signature for prediction of survival and tumor immunity in hepatocellular carcinoma
Authors: Zou Jun , Qin Wan
Published: August 2022

Hepatocellular carcinoma (HCC) is a highly malignant and heterogeneous tumor with poor prognosis. Cancer driver genes (CDGs) play an important role in the carcinogenesis and progression of HCC. In this study, we comprehensively investigated the expression, mutation, and prognostic significance of 568 CDGs in HCC. A prognostic risk model was constructed based on seven CDGs (CDKN2C, HRAS, IRAK1, LOX, MYCN, NRAS, and PABPC1) and verified to be an independent prognostic factor in both TCGA and ICGC cohorts. The low-score group, which showed better prognosis, had a high proportion of CD8+ T cells and elevated expression of interferon-related signaling pathways. Additionally, we constructed a nomogram to extend the clinical applicability of the prognostic model, which exhibits excellent predictive accuracy for survival. Our study showed the important role of CDGs in HCC and provides a novel prognostic indicator for HCC.
The GNB3 c.825C>T (rs5443) polymorphism and protection against fatal outcome of corona virus disease 2019 (COVID-19)
Authors: Möhlendick Birte , Schönfelder Kristina , Zacher Christoph , Elsner Carina , Rohn Hana , Konik Margarethe J. , Thümmler Laura , Rebmann Vera , Lindemann Monika , Jöckel Karl-Heinz , Siffert Winfried
Published: August 2022

Background and aims: Albeit several factors which influence the outcome of corona virus disease (COVID-19) are already known, genetic markers which may predict the outcome of the disease in hospitalized patients are still very sparse. Thus, in this study, we aimed to analyze whether the single-nucleotide polymorphism (SNP) rs5443 in the gene GNB3, which was associated with higher T cell responses in previous studies, might be a suitable biomarker to predict T cell responses and the outcome of COVID-19 in a comprehensive German cohort.

Methods: We analyzed the influence of demographics, pre-existing disorders, laboratory parameters at the time of hospitalization, and GNB3 rs5443 genotype in a comprehensive cohort (N = 1570) on the outcome of COVID-19. In a sub cohort, we analyzed SARS-CoV-2-specific T cell responses and associated GNB3 rs5443 genotypes. We investigated the influence of all factors on COVID-19 fatality in multivariable analysis.

Results: We found a younger patient age, normotension or absence of diabetes mellitus or cardiovascular diseases, normal blood cell counts, and low inflammatory markers at hospital admission were protective factors against fatal course of disease. In addition, the rs5443 TT genotype was significantly associated with protection against COVID-19 fatality (OR: 0.60, 95% CI: 0.40–0.92, p = 0.02). We also observed significantly increased SARS-CoV-2-specific T cell responses in rs5443 TT genotype carriers (p = 0.01). Although we observed a significant association of the factors described previously in univariate analysis, only a younger age of the patients, normal blood cell counts, and the GNB3 rs5443 TT genotype remained independent predictors against COVID-19 fatality in multivariable analysis.

Conclusion: Immutable predictors for COVID-19 fatality are relatively rare. In this study we could show that the TT genotype of the SNP rs5443 in the gene GNB3 is associated with protection against COVID-19 fatality. It was as well correlated to higher SARS-CoV-2-specific T cell responses, which could result in a milder course of disease in those patients. Based on those observations we hereby provide a further prognostic biomarker, which might be used in routine diagnostics as a predictive factor for COVID-19 mortality already upon hospitalization.
Black raspberry extract inhibits regulatory T-cell activity in a murine model of head and neck squamous cell carcinoma chemoprevention
Authors: Ryan Nathan M. , Lamenza Felipe F. , Upadhaya Puja , Pracha Hasan , Springer Anna , Swingler Michael , Siddiqui Arham , Oghumu Steve
Published: August 2022

Head and neck squamous cell carcinomas (HNSCC) are one of the most diagnosed malignancies globally, with a 5-year survival rate of approximately 40% to 50%. Current therapies are limited to highly invasive surgery, aggressive radiation, and chemotherapies. Recent reports have demonstrated the potential phytochemical properties of black raspberries in inhibiting the progression of various cancers including HNSCCs. However, the effects of black raspberry extracts on immune cells of the tumor microenvironment, specifically regulatory T cells during HNSCC, have not been investigated. We used a mouse model of 4-nitroquinoline-1-oxide (4NQO) chemically induced HNSCC carcinogenesis to determine these effects. C57BL/6 mice were exposed to 4NQO for 16 weeks and regular water for 8 weeks. 4NQO-exposed mice were fed the AIN-76A control mouse diet or the AIN76 diet supplemented with black raspberry extract. At terminal sacrifice, tumor burdens and immune cell recruitment and activity were analyzed in the tumor microenvironment, draining lymph nodes, and spleens. Mice fed the BRB extract-supplemented diet displayed decreased tumor burden compared to mice provided the AIN-76A control diet. Black raspberry extract administration did not affect overall T-cell populations as well as Th1, Th2, or Th17 differentiation in spleens and tumor draining lymph nodes. However, dietary black raspberry extract administration inhibited regulatory T-cell recruitment to HNSCC tumor sites. This was associated with an increased cytotoxic immune response in the tumor microenvironment characterized by increased CD8+ T cells and enhanced Granzyme B production during BRB extract-mediated HNSCC chemoprevention. Interestingly, this enhanced CD8+ T-cell antitumoral response was localized at the tumor sites but not at spleens and draining lymph nodes. Furthermore, we found decreased levels of PD-L1 expression by myeloid populations in draining lymph nodes of black raspberry-administered carcinogen-induced mice. Taken together, our findings demonstrate that black raspberry extract inhibits regulatory T-cell recruitment and promotes cytotoxic CD8 T-cell activity at tumor sites during HNSCC chemoprevention. These results demonstrate the immunomodulatory potential of black raspberry extracts and support the use of black raspberry-derived phytochemicals as a complementary approach to HNSCC chemoprevention and treatment.
Migration and homeostasis of regulatory T cells in rheumatoid arthritis
Authors: Kotschenreuther Konstantin , Yan Shuaifeng , Kofler David M.
Published: August 2022

Regulatory T (Treg) cells are garnering increased attention in research related to autoimmune diseases, including rheumatoid arthritis (RA). They play an essential role in the maintenance of immune homeostasis by restricting effector T cell activity. Reduced functions and frequencies of Tregcells contribute to the pathogenesis of RA, a common autoimmune disease which leads to systemic inflammation and erosive joint destruction. Tregcells from patients with RA are characterized by impaired functions and by an altered phenotype. They show increased plasticity towards Th17 cells and a reduced suppressive capacity. Besides the suppressive function of Tregcells, their effectiveness is determined by their ability to migrate into inflamed tissues. In the past years, new mechanisms involved in Tregcell migration have been identified. One example of such a mechanism is the phosphorylation of vasodilator-stimulated phosphoprotein (VASP). Efficient migration of Tregcells requires the presence of VASP. IL-6, a cytokine which is abundantly present in the peripheral blood and in the synovial tissue of RA patients, induces posttranslational modifications of VASP. Recently, it has been shown in mice with collagen-induced arthritis (CIA) that this IL-6 mediated posttranslational modification leads to reduced Tregcell trafficking. Another protein which facilitates Tregcell migration is G-protein-signaling modulator 2 (GPSM2). It modulates G-protein coupled receptor functioning, thereby altering the cellular activity initiated by cell surface receptors in response to extracellular signals. The almost complete lack of GPSM2 in Tregcells from RA patients contributes to their reduced ability to migrate towards inflammatory sites. In this review article, we highlight the newly identified mechanisms of Tregcell migration and review the current knowledge about impaired Tregcell homeostasis in RA.
When liquid-liquid phase separation meets viral infections
Authors: Wei Wenqiang , Bai Lu , Yan Bing , Meng Weiquan , Wang Hongju , Zhai Jingbo , Si Fusheng , Zheng Chunfu
Published: August 2022

Eukaryotic cells have both membranous and membraneless organelles. While the formation mechanism of membranous organelles is well understood, the formation mechanism of membraneless organelles remains unknown. Many biomolecules in the cytoplasm transition from the liquid phase to the agglutinated phase are known as liquid-liquid phase separation (LLPS). The biomolecular agglomerates’ physical properties enable them to function as dynamic compartments that respond to external pressures and stimuli. Scientists have gradually recognized the importance of phase separation during viral infections. LLPS provides a powerful new framework for understanding the viral life cycle from viral replication to evasion of host immune surveillance. As a result, this review focuses on the progress of LLPS research in viral infection and immune regulation to provide clues for antiviral therapeutic strategies.
Engineered nanoceria alleviates thermally induced oxidative stress in free-living Breviolum minutum (Symbiodiniaceae, formerly Clade B)
Authors: Roger Liza M. , Russo Joseph A. , Jinkerson Robert E. , Giraldo Juan Pablo , Lewinski Nastassja A.
Published: August 2022

The breakdown of symbiotic mutualism between cnidarian hosts and dinoflagellate algae partners (i.e., bleaching) has been linked to an immune-like response pathway brought on by a nitro-oxidative burst, a symptom of thermal stress. Stress induced by reactive oxygen species (ROS)/reactive nitrogen species is a problem common to aerobic systems. In this study, we tested the antioxidant effects of engineered poly(acrylic acid)-coated cerium dioxide nanoparticles (CeO2, nanoceria) on free-living Symbiodiniaceae (Breviolum minutum), a dinoflagellate alga that forms symbiotic relationships with reef-building corals and anemones. Results show that poly(acrylic acid)-coated CeO2 with hydrodynamic diameters of ~4 nm are internalized by B. minutum in under 30 min and subsequently localized in the cytosol. Nanoceria exposure does not inhibit cell growth over time, with the treated cultures showing a similar growth trend over the 25-day exposure. Aerobic activity and thermal stress when held at 34°C for 1 h (+6°C above control) led to increased intracellular ROS concentration with time. A clear ROS scavenging effect of the nanoceria was observed, with a 5-fold decrease in intracellular ROS levels during thermal stress. The nitric oxide (NO) concentration decreased by ~17% with thermal stress, suggesting the rapid involvement of NO scavenging enzymes or proteins within 1 h of stress onset. The presence of nanoceria did not appear to influence NO concentration. Furthermore, aposymbiotic anemones (Exaiptasia diaphana, ex Aiptasia pallida) were successfully infected with nanoceria-loaded B. minutum, demonstrating that inoculation could serve as a delivery method. The ability of nanoceria to be taken up by Symbiodiniaceae and reduce ROS production could be leveraged as a potential mitigation strategy to reduce coral bleaching.
A model for predicting fall risks of hospitalized elderly in Taiwan-A machine learning approach based on both electronic health records and comprehensive geriatric assessment
Authors: Chu Wei-Min , Kristiani Endah , Wang Yu-Chieh , Lin Yen-Ru , Lin Shih-Yi , Chan Wei-Cheng , Yang Chao-Tung , Tsan Yu-Tse
Published: August 2022

Backgrounds

Falls are currently one of the important safety issues of elderly inpatients. Falls can lead to their injury, reduced mobility and comorbidity. In hospitals, it may cause medical disputes and staff guilty feelings and anxiety. We aimed to predict fall risks among hospitalized elderly patients using an approach of artificial intelligence.

Materials and methods

Our working hypothesis was that if hospitalized elderly patients have multiple risk factors, their incidence of falls is higher. Artificial intelligence was then used to predict the incidence of falls of these patients. We enrolled those elderly patients aged >65 years old and were admitted to the geriatric ward during 2018 and 2019, at a single medical center in central Taiwan. We collected 21 physiological and clinical data of these patients from their electronic health records (EHR) with their comprehensive geriatric assessment (CGA). Data included demographic information, vital signs, visual ability, hearing ability, previous medication, and activity of daily living. We separated data from a total of 1,101 patients into 3 datasets: (a) training dataset, (b) testing dataset and (c) validation dataset. To predict incidence of falls, we applied 6 models: (a) Deep neural network (DNN), (b) machine learning algorithm extreme Gradient Boosting (XGBoost), (c) Light Gradient Boosting Machine (LightGBM), (d) Random Forest, (e) Stochastic Gradient Descent (SGD) and (f) logistic regression.

Results

From modeling data of 1,101 elderly patients, we found that machine learning algorithm XGBoost, LightGBM, Random forest, SGD and logistic regression were successfully trained. Finally, machine learning algorithm XGBoost achieved 73.2% accuracy.

Conclusion

This is the first machine-learning based study using both EHR and CGA to predict fall risks of elderly. Multiple risk factors of falls in hospitalized elderly patients can be put into a machine learning model to predict future falls for early planned actions. Future studies should be focused on the model fitting and accuracy of data analysis.
A prognosis model for clear cell renal cell carcinoma based on four necroptosis-related genes
Authors: Qiu Qiangmin , Li Yanze , Zhang Ye , Hou Yanguang , Hu Juncheng , Wang Lei , Chen Zhiyuan , Lei Yourong , Du Yang , Liu Xiuheng
Published: August 2022

Necroptosis is a type of caspase-independent cell death, and it plays a critical role in regulating the development of cancer. To date, little is known about the role of necroptosis-related genes (NRGs) in clear cell renal cell carcinoma (ccRCC). In this study, we downloaded data regarding the expression of NRGs and overall survival (OS) from The Cancer Genome Atlas (TCGA) database and constructed a risk model to determine the prognostic features of necroptosis using COX regression analysis. Patients with ccRCC were divided into low-risk and high-risk groups based on their risk scores. Thereafter, Kaplan–Meier curves were used to evaluate OS, and receiver operating characteristic (ROC) curves were used to determine the accuracy of prediction. Stratified analyses were performed according to different clinical variables. Furthermore, we assessed the correlation between clinical variables and risk scores; the NRGs with differential expression were mainly enriched in positive regulation of intracellular transport and platinum resistance pathways. We constructed prognostic signatures for OS based on four NRGs and showed that the survival time was significantly longer in the low-risk groups than in the high-risk groups (p < 0.001). The area of the ROC curve for OS was 0.717, indicating excellent predictive accuracy of the established model. Therefore, a predictive model based on NRGs was constructed, which can predict the prognosis of patients and provides insights into the biological mechanisms underlying necroptosis in patients with ccRCC.
Predicting treat-and-extend outcomes and treatment intervals in neovascular age-related macular degeneration from retinal optical coherence tomography using artificial intelligence
Authors: Bogunović Hrvoje , Mares Virginia , Reiter Gregor S. , Schmidt-Erfurth Ursula
Published: August 2022

Purpose

To predict visual outcomes and treatment needs in a treat & extend (T&E) regimen in neovascular age-related macular degeneration (nAMD) using a machine learning model based on quantitative optical coherence tomography (OCT) imaging biomarkers.

Materials and methods

Study eyes of 270 treatment-naïve subjects, randomized to receiving ranibizumab therapy in the T&E arm of a randomized clinical trial were considered. OCT volume scans were processed at baseline and at the first follow-up visit 4 weeks later. Automated image segmentation was performed, where intraretinal (IRF), subretinal (SRF) fluid, pigment epithelial detachment (PED), hyperreflective foci, and the photoreceptor layer were delineated using a convolutional neural network (CNN). A set of respective quantitative imaging biomarkers were computed across an Early Treatment Diabetic Retinopathy Study (ETDRS) grid to describe the retinal pathomorphology spatially and its change after the first injection. Lastly, using the computed set of OCT features and available clinical and demographic information, predictive models of outcomes and retreatment intervals were built using machine learning and their performance evaluated with a 10-fold cross-validation.

Results

Data of 228 evaluable patients were included, as some had missing scans or were lost to follow-up. Of those patients, 55% reached and maintained long (8, 10, 12 weeks) and another 45% stayed at short (4, 6 weeks) treatment intervals. This provides further evidence for a high disease activity in a major proportion of patients. The model predicted the extendable treatment interval group with an AUROC of 0.71, and the visual outcome with an AUROC of up to 0.87 when utilizing both, clinical and imaging features. The volume of SRF and the volume of IRF, remaining at the first follow-up visit, were found to be the most important predictive markers for treatment intervals and visual outcomes, respectively, supporting the important role of quantitative fluid parameters on OCT.

Conclusion

The proposed Artificial intelligence (AI) methodology was able to predict visual outcomes and retreatment intervals of a T&E regimen from a single injection. The result of this study is an urgently needed step toward AI-supported management of patients with active and progressive nAMD.
Pyoluteorin and 2,4-diacetylphloroglucinol are major contributors to Pseudomonas protegens Pf-5 biocontrol against Botrytis cinerea in cannabis
Authors: Balthazar Carole , St-Onge Renée , Léger Geneviève , Lamarre Simon G. , Joly David L. , Filion Martin
Published: August 2022

Pseudomonas protegensPf-5 is an effective biocontrol agent that protects many crops against pathogens, including the fungal pathogenBotrytis cinereacausing gray mold disease inCannabis sativacrops. Previous studies have demonstrated the important role of antibiotics pyoluteorin (PLT) and 2,4-diacetylphloroglucinol (DAPG) in Pf-5-mediated biocontrol. To assess the potential involvement of PLT and DAPG in the biocontrol exerted by Pf-5 againstB. cinereain the phyllosphere ofC. sativa, two knockout Pf-5 mutants were generated by in-frame deletion of genespltDorphlA, required for the synthesis of PLT or DAPG respectively, using a two-step allelic exchange method. Additionally, two complemented mutants were constructed by introducing a multicopy plasmid carrying the deleted gene into each deletion mutant.In vitroconfrontation assays revealed that deletion mutant ∆pltDinhibitedB. cinereagrowth significantly less than wild-type Pf-5, supporting antifungal activity of PLT. However, deletion mutant ∆phlAinhibited mycelial growth significantly more than the wild-type, hypothetically due to a co-regulation of PLT and DAPG biosynthesis pathways. Both complemented mutants recoveredin vitroinhibition levels similar to that of the wild-type. In subsequent growth chamber inoculation trials, characterization of gray mold disease symptoms on infected cannabis plants revealed that both ∆pltDand ∆phlAsignificantly lost a part of their biocontrol capabilities, achieving only 10 and 19% disease reduction respectively, compared to 40% achieved by inoculation with the wild-type. Finally, both complemented mutants recovered biocontrol capabilitiesin plantasimilar to that of the wild-type. These results indicate that intact biosynthesis pathways for production of PLT and DAPG are required for the optimal antagonistic activity ofP. protegensPf-5 againstB. cinereain the cannabis phyllosphere.
Precision targeting of food biofilm-forming genes by microbial scissors: CRISPR-Cas as an effective modulator
Authors: Ghosh Sreejita , Lahiri Dibyajit , Nag Moupriya , Sarkar Tanmay , Pati Siddhartha , Edinur Hisham Atan , Kumar Manoj , Mohd Zain Muhammad R. A. , Ray Rina Rani
Published: August 2022

The abrupt emergence of antimicrobial resistant (AMR) bacterial strains has been recognized as one of the biggest public health threats affecting the human race and food processing industries. One of the causes for the emergence of AMR is the ability of the microorganisms to form biofilm as a defense strategy that restricts the penetration of antimicrobial agents into bacterial cells. About 80% of human diseases are caused by biofilm-associated sessile microbes. Bacterial biofilm formation involves a cascade of genes that are regulated via the mechanism of quorum sensing (QS) and signaling pathways that control the production of the extracellular polymeric matrix (EPS), responsible for the three-dimensional architecture of the biofilm. Another defense strategy utilized commonly by various bacteria includes clustered regularly interspaced short palindromic repeats interference (CRISPRi) system that prevents the bacterial cell from viral invasion. Since multigenic signaling pathways and controlling systems are involved in each and every step of biofilm formation, the CRISPRi system can be adopted as an effective strategy to target the genomic system involved in biofilm formation. Overall, this technology enables site-specific integration of genes into the host enabling the development of paratransgenic control strategies to interfere with pathogenic bacterial strains. CRISPR-RNA-guided Cas9 endonuclease, being a promising genome editing tool, can be effectively programmed to re-sensitize the bacteria by targeting AMR-encoding plasmid genes involved in biofilm formation and virulence to revert bacterial resistance to antibiotics. CRISPRi-facilitated silencing of genes encoding regulatory proteins associated with biofilm production is considered by researchers as a dependable approach for editing gene networks in various biofilm-forming bacteria either by inactivating biofilm-forming genes or by integrating genes corresponding to antibiotic resistance or fluorescent markers into the host genome for better analysis of its functions both in vitro and in vivo or by editing genes to stop the secretion of toxins as harmful metabolites in food industries, thereby upgrading the human health status.
Chitosan encompassed Aniba rosaeodora essential oil as innovative green candidate for antifungal and antiaflatoxigenic activity in millets with emphasis on cellular and its mode of action
Authors: Singh Bijendra Kumar , Chaudhari Anand Kumar , Das Somenath , Tiwari Shikha , Maurya Akash , Singh Vipin Kumar , Dubey Nawal Kishore
Published: August 2022

The present study demonstrates first time investigation on encapsulation of Aniba rosaeodora essential oil into chitosan nanoemulsion (AREO-CsNe) with the aim of improvement of its antifungal, and aflatoxin B1 (AFB1) inhibitory performance in real food system. The GC–MS analysis of AREO revealed the presence of linalool (81.46%) as a major component. The successful encapsulation of EO into CsNe was confirmed through SEM, FTIR, and XRD analysis. The in-vitro release study showed the controlled release of AREO. AREO-CsNe caused complete inhibition of Aspergillus flavus (AFLHPSi-1) growth and AFB1 production at 0.8 and 0.6 μl/ml, respectively, which was far better than AREO (1.4 and 1.2 μl/ml, respectively). Impairment of ergosterol biosynthesis coupled with enhancement of cellular materials leakage confirmed plasma membrane as the possible antifungal target of both AREO and AREO-CsNe. Significant inhibition of methylglyoxal (AFB1 inducer) synthesis in AFLHPSi-1 cells by AREO and AREO-CsNe confirmed their novel antiaflatoxigenic mode of action. In-silico molecular docking studies revealed effective interaction of linalool with Ver-1 and Omt-A proteins, leading to inhibition of AFB1 biosynthesis. Further, AREO-CsNe showed enhanced antioxidant activity with IC50 values 3.792 and 1.706 μl/ml against DPPH• and ABTS•+ radicals, respectively. In addition, AREO-CsNe caused 100% protection of stored millets (Setaria italica seeds) from AFB1 contamination and lipid peroxidation over a period of 1 year without compromising its sensory properties and exhibited high safety profile with LD50 value 9538.742 μl/kg body weight. Based on enhanced performance of AREO-CsNe over AREO, it can be recommended as a novel substitute of synthetic preservative for preservation of stored millets.
Biological and transcriptional studies reveal VmeL is involved in motility, biofilm formation and virulence in Vibrio parahaemolyticus
Authors: Liu Peng-xuan , Zhang Xiao-yun , Wang Quan , Li Yang-yang , Sun Wei-dong , Qi Yu , Zhou Kai , Han Xian-gan , Chen Zhao-guo , Fang Wei-huan , Jiang Wei
Published: August 2022

Vibrio parahaemolyticusis a marine pathogen thought to be the leading cause of seafood-borne gastroenteritis globally, urgently requiring efficient management methods.V. parahaemolyticusencodes 12 resistance/nodulation/division (RND) efflux systems. However, research on these systems is still in its infancy. In this study, we discovered that the inactivation of VmeL, a membrane fusion protein within the RND efflux systems, led to reduction of the ability of biofilm formation. Further results displayed that the decreased capacity of Congo red binding and the colony of ΔvmeLis more translucent compared with wild type strains, suggested reduced biofilm formation due to decreased production of biofilm exopolysaccharide uponvmeLdeletion. In addition, the deletion ofvmeLabolished surface swarming and swimming motility ofV. parahaemolyticus. Additionally, deletion ofvmeLweakened the cytotoxicity ofV. parahaemolyticustowards HeLa cells, and impaired its virulence in a murine intraperitoneal infection assay. Finally, through RNA-sequencing, we ascertained that there were 716 upregulated genes and 247 downregulated genes in ΔvmeLstrain. KEGG enrichment analysis revealed that quorum sensing, bacterial secretion systems, ATP-binding cassette transporters, and various amino acid metabolism pathways were altered due to the inactivation ofvmeL. qRT-PCR further confirmed that genes accountable to the type III secretion system (T3SS1) and lateral flagella were negatively affected byvmeLdeletion. Taken together, our results suggest that VmeL plays an important role in pathogenicity, making it a good target for managing infection withV. parahaemolyticus.
Day 1 neutrophil-to-lymphocyte ratio (NLR) predicts stroke outcome after intravenous thrombolysis and mechanical thrombectomy
Authors: Chen Siyan , Cheng Jianhua , Ye Qiang , Ye Zusen , Zhang Yanlei , Liu Yuntao , Huang Guiqian , Chen Feichi , Yang Ming , Wang Chuanliu , Duan Tingting , Liu Xiang , Zhang Zheng
Published: August 2022

Background

The neutrophil-to-lymphocyte ratio (NLR) is a biomarker reflecting the balance between inflammation (as indicated by the neutrophil count) and adaptive immunity (as indicated by the lymphocyte count). We aimed to estimate ability of NLR at admission and at day 1 for predicting stroke outcome after two reperfusion therapies: intravenous thrombolysis (IVT) and mechanical thrombectomy (MT).

Methods

A retrospective analysis was performed on patients who received recombinant human tissue plasminogen activator (IVT) and/or underwent MT for acute ischemic stroke (AIS) at the First Affiliated Hospital of Wenzhou Medical University (Wenzhou, China) from January 2018 to December 2020. Blood samples were taken on admission to hospital and on day 1 after stroke onset. Binary logistic regression models were applied to investigate potential associations between NLR at admission or day 1 and the following outcomes: symptomatic intracerebral hemorrhage (sICH), dependence, and mortality at 90 days. The ability of NLR to predict AIS outcome was analyzed using receiver operating characteristic (ROC) curves.

Results

Data for 927 patients (576 IVT and 351 MT) were reviewed. High admission NLR was associated with dependence in IVT treatment [adjusted odds ratio (OR) 1.21, 95% confidence interval (CI) 1.14–1.23] and 90-day mortality in MT patients (OR 1.09, 95% CI 1.04–1.13). In IVT patients, high NLR at day 1 predicted dependence (OR 1.09, 95% CI 1.02–1.11), sICH (OR = 1.07, 95% CI 1.01–1.12), and 90-day mortality (OR 1.06, 95% CI 1.01–1.15). In MT patients, high NLR at day 1 also predicted dependence (OR 1.08, 95% CI 1.02–1.11) and sICH (OR 1.03, 95% CI 1.01–1.09). ROC analysis confirmed that NLR at day 1 could predict dependence (cut-off 4.2; sensitivity 68.7%; specificity 79.6%), sICH (cut-off 5.1; sensitivity 57.9%, specificity 73.5%), and death (cut-off 5.4; sensitivity 78.8%; specificity 76.4%) in IVT patients. Z values of area under the curves were compared between admissioin and day 1 NLR in IVT patients and showed day 1 NLR can better predict dependence (Z = 2.8, p = 0.004) and 90-day death (Z = 2.8, p = 0.005).

Conclusions

NLR is a readily available biomarker that can predict AIS outcome after reperfusion treatment and day 1 NLR is even better than admission NLR.
Body representation underlies response of proprioceptive acuity to repetitive peripheral magnetic stimulation
Authors: Xia Yunxiang , Tanaka Kento , Yang Man , Izumi Shinichi
Published: August 2022

Proprioceptive acuity is of great significance in basic research exploring a possible neural mechanism of fine motor control and in neurorehabilitation practice promoting motor function recovery of limb-disabled people. Moreover, body representation relies on the integration of multiple somatic sensations, including proprioception that is mainly generated in muscles and tendons of human joints. This study aimed to examine two hypotheses: First, different extension positions of wrist joint have different proprioceptive acuities, which might indicate different body representations of wrist joint in the brain. Second, repetitive peripheral magnetic stimulation (rPMS) applied peripherally to the forearm radial nerve and extensors could change proprioceptive acuity at the wrist joint. Thirty-five healthy participants were recruited then randomly divided into the real stimulation group (n = 15) and the sham stimulation group (n = 20). The participants’ non-dominant side wrist joint position sense was tested at six extension positions within the physiological joint motion range (i.e., 10°, 20°, 30°, 40°, 50°, 60°) both before stimulation and after stimulation. Results showed that proprioceptive bias (arithmetic difference of target position and replicated position) among six extension positions could be divided into lower-extension position (i.e., 10°, 20°, 30°) and higher-extension position (i.e., 40°, 50°, 60°). One session rPMS could influence proprioceptive bias in lower-extension position but not in higher-extension position. However, proprioceptive precision (standard deviation within lower-extension position and higher-extension position) was not influenced. To conclude, proprioceptive bias may vary between different wrist extension positions due to different hand postures being related to changes in body representation, and different functions relating to proprioceptive bias and proprioceptive precision may underlie two aspects of body representation.
Multiple spatial scale mapping of time-resolved brain network reconfiguration during evoked pain in patients with rheumatoid arthritis
Authors: Fanton Silvia , Altawil Reem , Ellerbrock Isabel , Lampa Jon , Kosek Eva , Fransson Peter , Thompson William H.
Published: August 2022

Functional brain networks and the perception of pain can fluctuate over time. However, how the time-dependent reconfiguration of functional brain networks contributes to chronic pain remains largely unexplained. Here, we explored time-varying changes in brain network integration and segregation during pain over a disease-affected area (joint) compared to a neutral site (thumbnail) in 28 patients with rheumatoid arthritis (RA) in comparison with 22 healthy controls (HC). During functional magnetic resonance imaging, all subjects received individually calibrated pain pressures corresponding to visual analog scale 50 mm at joint and thumbnail. We implemented a novel approach to track changes of task-based network connectivity over time. Within this framework, we quantified measures of integration (participation coefficient, PC) and segregation (within-module degree z-score). Using these network measures at multiple spatial scales, both at the level of single nodes (brain regions) and communities (clusters of nodes), we found that PC at the community level was generally higher in RA patients compared to HC during and after painful pressure over the inflamed joint and corresponding site in HC. This shows that all brain communities integrate more in RA patients than in HC for time points following painful stimulation to a disease-relevant body site. However, the elevated community-related integration seen in patients appeared to not pertain uniquely to painful stimulation at the inflamed joint, but also at the neutral thumbnail, as integration and segregation at the community level did not differ across body sites in patients. Moreover, there was no specific nodal contribution to brain network integration or segregation. Altogether, our findings indicate widespread and persistent changes in network interaction in RA patients compared to HC in response to painful stimulation.
Topography and distribution of adenosine A2A and dopamine D2 receptors in the human Subthalamic Nucleus
Authors: Emmi Aron , Antonini Angelo , Sandre Michele , Baldo Andrea , Contran Martina , Macchi Veronica , Guidolin Diego , Porzionato Andrea , De Caro Raffaele
Published: August 2022

The human Subthalamic Nucleus (STh) is a diencephalic lens-shaped structure located ventrally to the thalamus and functionally implicated in the basal ganglia circuits. Despite recent efforts to characterize the neurochemical and functional anatomy of the STh, little to no information is available concerning the expression and distribution of receptors belonging to the dopaminergic and purinergic system in the human STh. Both systems are consistently implicated in basal ganglia physiology and pathology, especially in Parkinson’s Disease, and represent important targets for the pharmacological treatment of movement disorders. Here, we investigate the topography and distribution of A2A adenosine and D2 dopamine receptors in the human basal ganglia and subthalamic nucleus. Our findings indicate a peculiar topographical distribution of the two receptors throughout the subthalamic nucleus, while colocalization between the receptors opens the possibility for the presence of A2AR- D2R heterodimers within the dorsal and medial aspects of the structure. However, further investigation is required to confirm these findings.
Biophysical characterization of light-gated ion channels using planar automated patch clamp
Authors: Govorunova Elena G. , Sineshchekov Oleg A. , Brown Leonid S. , Spudich John L.
Published: August 2022

Channelrhodopsins (ChRs) are proteins that guide phototaxis in protists and exhibit light-gated channel conductance when their genes are heterologously expressed in mammalian cells. ChRs are widely used as molecular tools to control neurons and cardiomyocytes with light (optogenetics). Cation- and anion-selective ChRs (CCRs and ACRs, respectively) enable stimulation and inhibition of neuronal activity by depolarization and hyperpolarization of the membrane, respectively. More than 400 natural ChR variants have been identified so far, and high-throughput polynucleotide sequencing projects add many more each year. However, electrophysiological characterization of new ChRs lags behind because it is mostly done by time-consuming manual patch clamp (MPC). Here we report using a high-throughput automated patch clamp (APC) platform, SyncroPatch 384i from Nanion Technologies, for ChR research. We find that this instrument can be used for determination of the light intensity dependence and current-voltage relationships in ChRs and discuss its advantages and limitations.