bluuebunny/crossref_metadata_2025 huggingface dataset:
Changed cerebral function and morphology serve as neuroimaging evidence for subclinical type 2 diabetic polyneuropathy
Authors: Zhao Lin-Mei , Chen Xin , Zhang You-Ming , Qu Min-Li , Selvarajah Dinesh , Tesfaye Solomon , Yang Fang-Xue , Ou Chu-Ying , Liao Wei-Hua , Wu Jing
Published: November 2022

Introduction

Central and peripheral nervous systems are all involved in type 2 diabetic polyneuropathy mechanisms, but such subclinical changes and associations remain unknown. This study aims to explore subclinical changes of the central and peripheral and unveil their association.

Methods

A total of 55 type-2 diabetes patients consisting of symptomatic (n = 23), subclinical (n = 12), and no polyneuropathy (n = 20) were enrolled in this study. Cerebral morphology, function, peripheral electrophysiology, and clinical information were collected and assessed using ANOVA and post-hoc analysis. Gaussian random field correction was used for multiple comparison corrections. Pearson/Spearman correlation analysis was used to evaluate the association of the cerebral with the peripheral.

Results

When comparing the subclinical group with no polyneuropathy groups, no statistical differences were shown in peripheral evaluations except amplitudes of tibial nerves. At the same time, functional connectivity from the orbitofrontal to bilateral postcentral and middle temporal cortex increased significantly. Gray matter volume of orbitofrontal and its functional connectivity show a transient elevation in the subclinical group compared with the symptomatic group. Besides, gray matter volume in the orbitofrontal cortex negatively correlated with the Neuropathy Symptom Score (r = -0.5871, p < 0.001), Neuropathy Disability Score (r = -0.3682, p = 0.009), and Douleur Neuropathique en 4 questions (r = -0.4403, p = 0.003), and also found correlated positively with bilateral peroneal amplitude (r > 0.4, p < 0.05) and conduction velocities of the right sensory sural nerve(r = 0.3181, p = 0.03). Similarly, functional connectivity from the orbitofrontal to the postcentral cortex was positively associated with cold detection threshold (r = 0.3842, p = 0.03) and negatively associated with Neuropathy Symptom Score (r = -0.3460, p = 0.01).

Discussion

Function and morphology of brain changes in subclinical type 2 diabetic polyneuropathy might serve as an earlier biomarker. Novel insights from subclinical stage to investigate the mechanism of type 2 diabetic polyneuropathy are warranted.
The ADRENAL score: A comprehensive scoring system for standardized evaluation of adrenal tumor
Authors: Zhou Xiaochen , Li Xuwen , Fu Bin , Liu Weipeng , Zhang Cheng , Xia Yu , Gong Honghan , Zhu Lingyan , Lei Enjun , Kaplan Joshua , Deng Yaoliang , Eun Daniel , Wang Gongxian
Published: November 2022

Objectives

To propose an original and standardized scoring system to quantify the functional and anatomical characteristics of adrenal tumor.

Materials and methods

Four groups of consecutive adrenalectomies (n = 458) with heterogeneity in tumor characteristics and surgical approaches, including 212 laparoscopic cases (Group 1) and 105 robotic cases (Group 2) from The First Affiliated Hospital of Nanchang University, 28 robotic cases from Temple University Hospital (Group 3) and 113 laparoscopic cases from The First Affiliated Hospital of Guangxi Medical University (Group 4). All patients were followed up for 4.5 to 5.5 years. Six parameters including functional status or suspicion of malignancy, tumor size, relationship to adjacent organs, intratumoral enhancement on CT, nearness of the tumor to major vessels and body mass index were assessed and scored on a 0, 1 and 2 points scale. Correlation between the sum of the 6 scores and tumor laterality (ADRENAL score) verse operative time (OT), estimated blood loss (EBL), perioperative complications, transfusion, conversion and length of hospital stay was analyzed.

Results

ADRENAL score was a strong predictor of both OT and EBL in all four groups (p < 0.05 for all tests). In Group 2 and 4, higher ADRENAL score seemed to correlate with longer hospital stay. No statistically significant correlation between ADRENAL score and complication, transfusion or conversion was noted yet.

Conclusions

ADRENAL score appears to be a valid predictor of surgical outcomes. It may provide a common reference for adrenal surgery training program, preoperative risk assessment and stratified comparative analysis of adrenal surgeries via different techniques and approaches.
Sensorless control of marine permanent magnet synchronous propulsion motor based on adaptive extended Kalman filter
Authors: Chen Zaifa , Liu Yancheng
Published: November 2022

Gross error interference or noise statistical deviation is the main factor that leads to the accuracy deterioration of extended Kalman filter (EKF) in estimating the speed and rotor position of ship propulsion permanent magnet synchronous motor (PMSM). In this paper, an adaptive extended Kalman filter (AEKF) algorithm based on innovation sequence is proposed. In the proposed method, gross error interference is first added to EKF to analyze its influence on the observation accuracy. Then, the weighting coefficient is set in the calculation of innovation covariance. By adjusting the weight of the innovation covariance matrix at the adjacent time, the innovation covariance difference is calculated and then used in the calculation of Kalman gain. The observation performance comparison between AEKF and EKF strategies is conducted with subject to gross error interference and noise statistics deviate. Simulation and experimental results demonstrate that the proposed AEKF has stronger robustness and higher prediction accuracy of speed and rotor position.
Toward diverse seed sourcing to upscale ecological restoration in the Brazilian Cerrado
Authors: Silva Mateus C. , Moonlight Peter , Oliveira Rafael S. , Pennington R. Toby , Rowland Lucy
Published: November 2022

Seed markets are vital to scaling up ecosystem restoration in the Brazilian Cerrado, home of the world’s most species-rich grasslands and savannas. We compiled lists of species traded by four major Cerrado seed supply systems to investigate the representativeness of the species currently available for seed-based restoration. We also identified whether dominant ground-layer species are being sourced for seed production. Seeds from 263 Cerrado species can be purchased for restoration, of which 68% are trees, particularly legumes (24%). 63% of the traded species were found in only one seed supply system. The five most dominant graminoids of the Cerrado ground layer were available for sale, but two additional species uncommon in old-growth areas represented 44% of the sales of a key seed trader in Central Brazil. The expansion of Cerrado seed supply systems should be supported to further increase the number of species on the market. Sourcing seeds from a diversity of herbaceous species is central to facilitating the restoration of species-rich grasslands and savannas in the Cerrado. Recovering the diversity and functioning of old-growth open ecosystems through seeds will depend on increasing the supply and demand for species typical of Cerrado’s ground layer.
Analyzing the Korean reference genome with meta-imputation increased the imputation accuracy and spectrum of rare variants in the Korean population
Authors: Hwang Mi Yeong , Choi Nak-Hyeon , Won Hong Hee , Kim Bong-Jo , Kim Young Jin
Published: November 2022

Genotype imputation is essential for enhancing the power of association-mapping and discovering rare and indels that are missed by most genotyping arrays. Imputation analysis can be more accurate with a population-specific reference panel or a multi-ethnic reference panel with numerous samples. The National Institute of Health, Republic of Korea, initiated the Korean Reference Genome (KRG) project to identify variants in whole-genome sequences of ∼20,000 Korean participants. In the pilot phase, we analyzed the data from 1,490 participants. The genetic characteristics and imputation performance of the KRG were compared with those of the 1,000 Genomes Project Phase 3, GenomeAsia 100K Project, ChinaMAP, NARD, and TOPMed reference panels. For comparison analysis, genotype panels were artificially generated using whole-genome sequencing data from combinations of four different ancestries (Korean, Japanese, Chinese, and European) and two population-specific optimized microarrays (Korea Biobank Array and UK Biobank Array). The KRG reference panel performed best for the Korean population (R2 = 0.78–0.84, percentage of well-imputed is 91.9% for allele frequency >5%), although the other reference panels comprised a larger number of samples with genetically different background. By comparing multiple reference panels and multi-ethnic genotype panels, optimal imputation was obtained using reference panels from genetically related populations and a population-optimized microarray. Indeed, the reference panels of KRG and TOPMed showed the best performance when applied to the genotype panels of KBA (R2 = 0.84) and UKB (R2 = 0.87), respectively. Using a meta-imputation approach to merge imputation results from different reference panels increased the imputation accuracy for rare variants (∼7%) and provided additional well-imputed variants (∼20%) with comparable imputation accuracy to that of the KRG. Our results demonstrate the importance of using a population-specific reference panel and meta-imputation to assess a substantial number of accurately imputed rare variants.
Do the diverse phenotypes of Prader-Willi syndrome reflect extremes of covariation in typical populations?
Authors: Salminen Iiro , Read Silven , Crespi Bernard
Published: November 2022

The phenotypes of human imprinted neurogenetic disorders can be hypothesized as extreme alterations of typical human phenotypes. The imprinted neurogenetic disorder Prader-Willi syndrome (PWS) features covarying phenotypes that centrally involve altered social behaviors, attachment, mood, circadian rhythms, and eating habits, that can be traced to altered functioning of the hypothalamus. Here, we conducted analyses to investigate the extent to which the behavioral variation shown in typical human populations for a set of PWAS-associated traits including autism spectrum cognition, schizotypal cognition, mood, eating, and sleeping phenotypes shows covariability that recapitulates the covariation observed in individuals with PWS. To this end, we collected data from 296 typical individuals for this set of phenotypes, and showed, using principal components analysis, evidence of a major axis reflecting key covarying PWS traits. We also reviewed the literature regarding neurogenetic syndromes that overlap in their affected traits with PWS, to determine their prevalence and properties. These findings demonstrate that a notable suite of syndromes shows phenotypic overlap with PWS, implicating a large set of imprinted and non-imprinted genes, some of which interact, in the phenotypes of this disorder. Considered together, these findings link variation in and among neurogenetic disorders with variation in typical populations, especially with regard to pleiotropic effects mediated by the hypothalamus. This work also implicates effects of imprinted gene variation on cognition and behavior in typical human populations.
DNA computing for gastric cancer analysis and functional classification
Authors: Chen Congzhou , Chen Xin , Li Xin , Shi Xiaolong
Published: November 2022

Early identification of key biomarkers of malignant cancer is vital for patients’ prognosis and therapies. There is research demonstrating that microRNAs are important biomarkers for cancer analysis. In this article, we used the DNA strand displacement mechanism (DSD) to construct the DNA computing system for cancer analysis. First, gene chips were obtained through bioinformatical training. These microRNA data and clinical traits were obtained from the Cancer Genome Atlas (TCGA) dataset. Second, we analyzed the expression data by using a weighted gene co-expression network (WGCNA) and found four biomarkers for two clinic features, respectively. Last, we constructed a DSD-based DNA computing system for cancer analysis. The inputs of the system are these identified biomarkers; the outputs are the fluorescent signals that represent their corresponding traits. The experiment and simulation results demonstrated the reliability of the DNA computing system. This DSD simulation system is lab-free but clinically meaningful. We expect this innovative method to be useful for rapid and accurate cancer diagnosis.
Non-coding RNAs in ossification of the posterior longitudinal ligament
Authors: Zhang Haoran , Zhang Qingyu , Yuan Zenong , Dong Jun
Published: November 2022

Ossification of the posterior longitudinal ligament (OPLL) is a kind of disease that involves a variety of factors leading to ectopic bone deposition of the spinal ligament. Although the detailed mechanism is not clear, genetic factors play important roles in the development of this disease. Noncoding RNA (ncRNA) refers to an RNA molecule that is not translated into a protein but participates in the regulation of gene expression. Functionally important types of ncRNA associated with OPLL include long noncoding RNA, microRNA, and circular RNA. We listed the differentially expressed ncRNAs in OPLL patients and normal controls to find the ncRNAs most relevant to the pathogenesis of the disease. The potential regulatory networks of ncRNA in OPLL cells were analyzed based on their most abundant signal transduction pathway data. The analysis of the highly connected ncRNAs in the regulatory network suggests that they play an important role in OPLL. These findings provide new directions for the study of OPLL pathogenesis and therapeutic targets. In this paper, we reviewed and analyzed the literature on ncRNAs in OPLL published in recent years, aiming to help doctors better understand and treat this disease.
Cell atlas of the immune microenvironment in gastrointestinal cancers: Dendritic cells and beyond
Authors: Wang Yinuo , Yang Ting , Liang Huan , Deng Mi
Published: November 2022

Gastrointestinal (GI) cancers occur in the alimentary tract and accessory organs. They exert a global burden with high morbidity and mortality. Inside the tumor microenvironment, dendritic cells (DCs) are the most efficient antigen-presenting cells and are necessary for adaptive immune responses such as T and B-cell maturation. However, the subsets of DCs revealed before were mostly based on flow cytometry and bulk sequencing. With the development of single-cell RNA sequencing (scRNA-seq), the tumor and microenvironment heterogeneity of GI cancer has been illustrated. In this review, we summarize the classification and development trajectory of dendritic cells at the single-cell level in GI cancer. Additionally, we focused on the interaction of DCs with T cells and their effect on the response to immunotherapy. Specifically, we focused on the newly identified tumor-infiltrating dendritic cells and discuss their potential function in antitumor immunity.
A flow cytometry-based neutralization assay for simultaneous evaluation of blocking antibodies against SARS-CoV-2 variants
Authors: Egia-Mendikute Leire , Bosch Alexandre , Prieto-Fernández Endika , Vila-Vecilla Laura , Zanetti Samanta Romina , Lee So Young , Jiménez-Lasheras Borja , García del Río Ana , Antoñana-Vildosola Asier , de Blas Ander , Velasco-Beltrán Paloma , Serrano-Maciá Marina , Iruzubieta Paula , Mehrpouyan Majid , Goldberg Edward M. , Bornheimer Scott J. , Embade Nieves , Martínez-Chantar María L. , López-Hoyos Marcos , Mato José M. , Millet Óscar , Palazón Asís
Published: November 2022

Vaccines against SARS-CoV-2 have alleviated infection rates, hospitalization and deaths associated with COVID-19. In order to monitor humoral immunity, several serology tests have been developed, but the recent emergence of variants of concern has revealed the need for assays that predict the neutralizing capacity of antibodies in a fast and adaptable manner. Sensitive and fast neutralization assays would allow a timely evaluation of immunity against emerging variants and support drug and vaccine discovery efforts. Here we describe a simple, fast, and cell-free multiplexed flow cytometry assay to interrogate the ability of antibodies to prevent the interaction of Angiotensin-converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of the original Wuhan-1 SARS-CoV-2 strain and emerging variants simultaneously, as a surrogate neutralization assay. Using this method, we demonstrate that serum antibodies collected from representative individuals at different time-points during the pandemic present variable neutralizing activity against emerging variants, such as Omicron BA.1 and South African B.1.351. Importantly, antibodies present in samples collected during 2021, before the third dose of the vaccine was administered, do not confer complete neutralization against Omicron BA.1, as opposed to samples collected in 2022 which show significant neutralizing activity. The proposed approach has a comparable performance to other established surrogate methods such as cell-based assays using pseudotyped lentiviral particles expressing the spike of SARS-CoV-2, as demonstrated by the assessment of the blocking activity of therapeutic antibodies (i.e. Imdevimab) and serum samples. This method offers a scalable, cost effective and adaptable platform for the dynamic evaluation of antibody protection in affected populations against variants of SARS-CoV-2.
B cell fate mapping reveals their contribution to the memory immune response against helminths
Authors: Haase Paul , Schäfer Simon , Gerlach Roman G. , Winkler Thomas H. , Voehringer David
Published: November 2022

An estimated quarter of the human world population is infected with gastrointestinal helminths causing major socioeconomic problems in endemic countries. A better understanding of humoral immune responses against helminths is urgently needed to develop effective vaccination strategies. Here, we used a fate mapping (FM) approach to mark germinal center (GC) B cells and their developmental fates by induced expression of a fluorescent protein during infection of mice with the helminth Nippostrongylus brasiliensis. We could show that FM+ cells persist weeks after clearance of the primary infection mainly as CD80+CD73+PD-L2+ memory B cells. A secondary infection elicited expansion of helminth-specific memory B cells and plasma cells (PCs). Adoptive transfers and analysis of somatic mutations in immunoglobulin genes further revealed that FM+ B cells rapidly convert to PCs rather than participating again in a GC reaction. These results provide new insights in the population dynamics of the humoral immune response against helminths.
In patients with primary Sjögren’s syndrome innate-like MAIT cells display upregulated IL-7R, IFN-γ, and IL-21 expression and have increased proportions of CCR9 and CXCR5-expressing cells
Authors: Hinrichs Anneline C. , Kruize Aike A. , Leavis Helen L. , van Roon Joel A. G.
Published: November 2022

Introduction

Mucosal-associated invariant T (MAIT) cells might play a role in B cell hyperactivity and local inflammation in primary Sjögren’s syndrome (pSS), just like previously studied mucosa-associated CCR9+ and CXCR5+ T helper cells. Here, we investigated expression of CCR9, CXCR5, IL-18R and IL-7R on MAIT cells in pSS, and assessed the capacity of DMARDs to inhibit the activity of MAIT cells.

Methods

Circulating CD161+ and IL-18Rα+ TCRVα7.2+ MAIT cells from pSS patients and healthy controls (HC) were assessed using flow cytometry, and expression of CCR9, CXCR5, and IL-7R on MAIT cells was studied. Production of IFN-γ and IL-21 by MAIT cells was measured upon IL-7 stimulation in the presence of leflunomide (LEF) and hydroxychloroquine (HCQ).

Results

The numbers of CD161+ and IL-18Rα+ MAIT cells were decreased in pSS patients compared to HC. Relative increased percentages of CD4 MAIT cells in pSS patients caused significantly higher CD4/CD8 ratios in MAIT cells. The numbers of CCR9 and CXCR5-expressing MAIT cells were significantly higher in pSS patients. IL-7R expression was higher in CD8 MAIT cells as compared to all CD8 T cells, and changes in IL-7R expression correlated to several clinical parameters. The elevated production of IL-21 by MAIT cells was significantly inhibited by LEF/HCQ treatment.

Conclusion

Circulating CD161+ and IL-18Rα+ MAIT cell numbers are decreased in pSS patients. Given their enriched CCR9/CXCR5 expression this may facilitate migration to inflamed salivary glands known to overexpress CCL25/CXCL13. Given the pivotal role of IL-7 and IL-21 in inflammation in pSS this indicates a potential role for MAIT cells in driving pSS immunopathology.
Dynamics and immunomodulation of cognitive deficits and behavioral changes in non-severe experimental malaria
Authors: Rosa-Gonçalves Pamela , de Sousa Luciana Pereira , Maia Aline Barbosa , Ribeiro-Gomes Flávia Lima , Gress Caroline Cristhiani Tavares de Lima , Werneck Guilherme Loureiro , Souza Diogo Onofre , Almeida Roberto Farina , Daniel-Ribeiro Cláudio Tadeu
Published: November 2022

Data recently reported by our group indicate that stimulation with a pool of immunogens capable of eliciting type 2 immune responses can restore the cognitive and behavioral dysfunctions recorded after a single episode of non-severe rodent malaria caused byPlasmodium bergheiANKA. Here we explored the hypothesis that isolated immunization with one of the type 2 immune response-inducing immunogens, the human diphtheria-tetanus (dT) vaccine, may revert damages associated with malaria. To investigate this possibility, we studied the dynamics of cognitive deficits and anxiety-like phenotype following non-severe experimental malaria and evaluated the effects of immunization with both dT and of a pool of type 2 immune stimuli in reversing these impairments. Locomotor activity and long-term memory deficits were assessed through the open field test (OFT) and novel object recognition task (NORT), while the anxiety-like phenotype was assessed by OFT and light/dark task (LDT). Our results indicate that poor performance in cognitive-behavioral tests can be detected as early as the 12thday after the end of antimalarial treatment with chloroquine and may persist for up to 155 days post infection. The single immunization strategy with the human dT vaccine showed promise in reversal of long-term memory deficits in NORT, and anxiety-like behavior in OFT and LDT.
Inducing ferroptosis has the potential to overcome therapy resistance in breast cancer
Authors: Qi Xiaowen , Wan Zhixing , Jiang Baohong , Ouyang Yuhan , Feng Wenjie , Zhu Hongbo , Tan Yeru , He Rongfang , Xie Liming , Li Yuehua
Published: November 2022

Breast cancer is the most common type of malignancy among women. Due to the iron-dependent character of breast cancer cells, they are more sensitive to ferroptosis compared to normal cells. It is possible to reverse tumor resistance by inducing ferroptosis in breast cancer cells, thereby improving tumor treatment outcomes. Ferroptosis is highly dependent on the balance of oxidative and antioxidant status. When ferroptosis occurs, intracellular iron levels are significantly increased, leading to increased membrane lipid peroxidation and ultimately triggering ferroptosis. Ferroptotic death is a form of autophagy-associated cell death. Synergistic use of nanoparticle-loaded ferroptosis-inducer with radiotherapy and chemotherapy achieves more significant tumor suppression and inhibits the growth of breast cancer by targeting cancer tissues, enhancing the sensitivity of cells to drugs, reducing the drug resistance of cancer cells and the toxicity of drugs. In this review, we present the current status of breast cancer and the mechanisms of ferroptosis. It is hopeful for us to realize effective treatment of breast cancer through targeted ferroptosis.
Single-cell transcriptomics in bone marrow delineates CD56dimGranzymeK+ subset as intermediate stage in NK cell differentiation
Authors: Melsen Janine E. , van Ostaijen-ten Dam Monique M. , Schoorl Dorenda J. A. , Schol Pieter J. , van den Homberg Daphne A. L. , Lankester Arjan C. , Lugthart Gertjan , Schilham Marco W.
Published: November 2022

Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56brightCD16+, CD56dimCD16+ and CD69+CXCR6+ lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells.
High-resolution variability of dissolved and suspended organic matter in the Cape Verde Frontal Zone
Authors: Campanero Rubén , Burgoa Nadia , Fernández-Castro Bieito , Valiente Sara , Nieto-Cid Mar , Martínez-Pérez Alba M. , Gelado-Caballero María Dolores , Hernández-Hernández Nauzet , Marrero-Díaz Ángeles , Machín Francisco , Rodríguez-Santana Ángel , Hernández-García Inés , Delgado-Huertas Antonio , Martínez-Marrero Antonio , Arístegui Javier , Álvarez-Salgado Xosé Antón
Published: November 2022

Distributions of dissolved (DOM) and suspended (POM) organic matter, and their chromophoric (CDOM) and fluorescent (FDOM) fractions, are investigated at high resolution (< 10 km) in the Cape Verde Frontal Zone (CVFZ) during fall 2017. In the epipelagic layer (< 200 m), meso- and submesoscale structures (meanders, eddies) captured by the high resolution sampling dictate the tight coupling between physical and biogeochemical parameters at the front. Remarkably, fluorescent humic-like substances show relatively high fluorescence intensities between 50 and 150 m, apparently not related to local mineralization processes. We hypothesize that it is due to the input of Sahara dust, which transports highly re-worked DOM with distinctive optical properties. In the mesopelagic layer (200-1500 m), our results suggest that DOM and POM mineralization occurs mainly during the transit of the water masses from the formation sites to the CVFZ. Therefore, most of the local mineralization seems to be due to fast-sinking POM produced in situ or imported from the Mauritanian upwelling. These local mineralization processes lead to the production of refractory CDOM, an empirical evidence of the microbial carbon pump mechanism. DOM released from these fast-sinking POM is the likely reason behind the observed columns of relatively high DOC surrounded by areas of lower concentration. DOM and POM dynamics in the CVFZ has turned out to be very complex, in parallel to the complexity of meso- and submesoscale structures present in the area. On top of this high resolution variability, the input of Sahara dust or the release of DOM from sinking particles have been hypothesized to explain the observed distributions.
Productivity and nutrient removal by the microalga Chlamydopodium fusiforme grown outdoors in BG-11 and piggery wastewater
Authors: Zittelli Graziella Chini , Silva Benavides Ana Margarita , Silovic Tina , Ranglová Karolína , Masojídek Jiří , Cicchi Bernardo , Faraloni Cecilia , Touloupakis Eleftherios , Torzillo Giuseppe
Published: November 2022

The objective of this work was to test the growth of the freshwater microalgaChlamydopodium fusiformeMACC-430 in diluted piggery wastewater (PWW) for biomass production which is a potential producer of biostimulating and antimicrobial compounds. The productivity and effectiveness in removing nitrogen and phosphorus by the cultures were tested outdoors in open ponds by comparing the mineral medium BG-11 medium (control) and piggery wastewater (PWW). Daily biomass yields were found 14.7 ± 4.6g m-2d-1in BG-11 and 17.6 ± 6.7g m-2d-1in 10-fold diluted wastewater (PWW10) with deionized water. Further increase in the biomass productivity yield (33.1 ± 5.6g m-2d-1) was achieved with more concentrated PWW (5-fold dilution – PWW5). Nitrogen removal rate (N-NH4+) reached 21.4 ± 2.9mg L-1d-1in cultures grown in PWW10 and increased to 38.4±16.3mg L-1d-1using the PWW5. The use of undiluted PWW strongly increased the bacterial load, which caused the loss of the culture. The photosynthetic performance measured as the maximum fluorescence yield Fv/Fmratio in both the PWW10 and BG-11 cultures showed a cyclic behavior, as it decreased during the day and recovered at night. However, in the cultures grown in diluted PWW the Fv/Fmratio slightly increased throughout the cultivation. Between PWW10 and BG-11, no significant differences were observed in photosynthetic oxygen evolution; on the contrary, PWW5 showed a 30% reduction compared to PWW10 and BG-11. Significantly lower chlorophyll and carotenoid contents were found in the cultures grown in PWW compared to BG-11. Biochemical composition showed a slightly higher protein content in biomass grown in PWW10 (53.4%) compared to BG-11 (52.7%). The protein content further increased (61.3%) when the more concentrated PWW5 was used. The biomass, particularly that produced on PWW, revealed antimicrobial activity against plant pathogens, including fungi, and oomycete, while rather weak biostimulant activity was determined for theC. fusiformebiomass independently of the cultivation medium. Results demonstrated thatC. fusiformeis a robust strain suitable to be grown in diluted PWW outdoors with a high nutrient removal rate.
Marine monitoring in transition: On the verge of technological revolution?
Authors: Korpinen Samuli , Kahlert Maria , Kuosa Harri , Mack Leoni , Meissner Kristian , Pitkänen Heikki , Pyhälahti Timo , Uusitalo Laura
Published: November 2022

Efforts to renew marine ecosystem monitoring to include advanced technology and cost-effective methods have been repeatedly called for. The current environmental legislation in European Union (EU) requires also ecosystem monitoring beyond the scope of conventional methods and sampling strategies. Despite several studies showing the benefits of new methods, the progress to adopt the methods in national monitoring programmes under legal requirements has been slow. In this study, we have reviewed the current use of a set of methods in marine monitoring programmes under the EU marine strategy framework directive (MSFD), which calls for a holistic view of the marine environment and thus requires tens of monitoring parameters by different methods. Here we assess how widely the new methods are being adopted in the EU member states implementing the MSFD. Our results show a relatively high adoption rate for certain methods, while others are widely ignored. We compare the results also with the monitoring strategies of the four regional sea conventions. We argue that the adoption of methods in European and regional programmes may positively influence the national use of new methods.
Understanding the impact of environmental variability and fisheries on the red sea urchin population in Baja California
Authors: Medellín–Ortiz Alfonso , Montaño–Moctezuma Gabriela , Álvarez–Flores Carlos , Santamaría-del-Ángel Eduardo , García–Nava Hector , Beas–Luna Rodrigo , Cavanaugh Kyle
Published: November 2022

Introduction

The red sea urchin fishery is one of the most important fisheries in Baja California and the only urchin fishery in México; yet little is known on understanding how local, regional, and oceanic environmental variability may affect red sea urchin populations.

Methods

We analyzed how food availability, predator abundance and environmental variability could affect red sea urchin populations developing generalized linear models under different temperature conditions: Pre-heat wave, heat wave, and post–heatwave, including sites where sea surface temperature was above, below, and on average. Models included: a) biological variables: Macrocystis pyrifera (kelp) biomass, red sea urchin (Mesocentrotus franciscanus) density, sheephead (Semicossyphus pulcher), kelp bass (Paralabrax clathratus) and spiny lobster (Panulirus interruptus) catches, and b) oceanographic variables: sea surface temperature, wave power, upwelling index, multivariate El Niño index and North Pacific Gyre Oscillation index.

Results

Between 65 and 82% of the variability observed in red sea urchin populations was explained by different combinations of variables, depending on the thermal condition analyzed. We observed that local environmental variability, such as food availability and predator harvest are highly important factors in determining red sea urchin population changes, compared to regional and oceanic scale variables such as upwelling, El Niño, or the North Pacific Gyre Oscillation. Results show that the relative importance of these variables changed depending on the spatial and temporal scale being analyzed, meaning that under “normal or average” conditions one set of variables is important, compared to extreme environmental conditions such as El Niño or “the Blob” when a different set of variables explained the observed variability. Urchin predators’ catches were correlated with urchin density during the pre-heatwave scenario, suggesting that under “average temperature” conditions the effect of fishing on predators, and consequently on urchin density is higher than local temperature, the most important variable during warm conditions.

Discussion

This study suggests that in Baja California, red sea urchin harvest has become the most important red sea urchin population control, so efforts should be encouraged and supported by state and federal agencies to promote more resilient ecosystems in the face of environmental uncertainty. Improving management of the commercial species that inhabit kelp forest, could yield benefits for the entire ecosystem, fishers, and the red sea urchin population in Mexico.
Using nanomaterials to address SARS-CoV-2 variants through development of vaccines and therapeutics
Authors: Hangad Maria Victoria , Keshvani Sarah , Kelpin Niya , Walters-Shumka Jonathan , Hood McKayla , Volk Cameo , Pal Danika , Willerth Stephanie M.
Published: November 2022

Nanomaterials have played a significant role in effectively combating the global SARS-CoV-2 pandemic that began in December 2019 through the development of vaccines as well as antiviral therapies. These versatile, tunable materials can interact and deliver a broad range of biologically relevant molecules for preventing COVID-19 infection, generating immunity against COVID-19, and treating infected patients. Application of these nanomaterials and nanotechnologies can further be investigated in conjunction with disease models of COVID-19 and this holds immense potential for accelerating vaccine or therapeutic process development further encouraging the elimination of animal model use during preclinical stages. This review examines the existing literature on COVID-19 related nanomaterial applications, including perspective on nanotechnology-based vaccines and therapeutics, and discusses how these tools can be adapted to address new SARS-CoV-2 variants of concern. We also analyze the limitations of current nanomaterial approaches to managing COVID-19 and its variants alongside the challenges posed when implementing this technology. We end by providing avenues for future developments specific to disease modelling in this ever-evolving field.
Serum IL-12p40: A novel biomarker for early prediction of minimal change disease relapse following glucocorticoids therapy
Authors: Bai Mengqiu , Zhang Jian , Su Xinwan , Yao Xi , Li Heng , Cheng Jun , Mao Jianhua , Li Xiayu , Chen Jianghua , Lin Weiqiang
Published: November 2022

Background

Minimal change disease (MCD) has a high recurrence rate, but currently, no biomarker can predict its recurrence. To this end, this study aimed at identifying potential serum cytokines as valuable biomarkers for predicting the risk of MCD recurrence.

Materials and methods

Raybiotech 440 cytokine antibody microarray was used to detect the serum samples of eight relapsed, eight non-relapsed MCD patients after glucocorticoid treatment, and eight healthy controls. The differentially expressed cytokines were confirmed by enzyme-linked immunosorbent assay (ELISA) with serum samples from 29 non-relapsed and 35 relapsed MCD patients. The study used the receiver operating characteristic (ROC) curve analysis to investigate the sensitivity and specificity of a serum biomarker for predicting the MCD relapse.

Results

Serum IL-12p40 levels increased significantly in the relapsed group. The Area Under the ROC Curve (AUC) of IL-12p40 was 0.727 (95%CI: 0.597–0.856; P < 0.01). The RNA-sequencing analysis and qPCR assay performed on the IL-12 treated mouse podocytes and the control group showed increased expression of podocyte damage genes, such as connective tissue growth factor (CTGF), matrix metallopeptidase 9 (MMP9), secreted phosphoprotein 1 (SPP1), and cyclooxygenase-2 (COX-2) in the former group.

Conclusion

IL-12p40 may serve as a new biomarker for predicting the risk of MCD recurrence after glucocorticoid treatment, and it may be involved in the pathogenesis and recurrence of MCD.
Identification of diagnostic gene biomarkers related to immune infiltration in patients with idiopathic pulmonary fibrosis based on bioinformatics strategies
Authors: Dai Xiangdong , Yang Zhihua , Zhang Wenjing , Liu Shuai , Zhao Qianru , Liu Tao , Chen Lu , Li Lin , Wang Yi , Shao Rui
Published: November 2022

Objective

The study aims to identify potential diagnostic markers of idiopathic pulmonary fibrosis (IPF) and analyze the significance of immune cell infiltration in this pathology.

Materials and methods

Download two publicly available gene expression profiles (GSE10667 and GSE24206 datasets) from the GEO database including 48 Idiopathic pulmonary fibrosis (IPF) samples and 21 human control samples and select for distinctly expressed genes (DEG) from them. Lasso regression model and support vector machine recursive feature elimination S,V,R,F analysis were used to check candidate biomarkers. The area under the subject’s work characteristic curve (AUC) value is used to evaluate its recognition ability. The GSE53845 dataset (40 IPF patients and 8 controls) continue to validate the expression level and diagnostic value of biomarkers in IPF. Comprehensive analysis of immune infiltrated cells of IPF was performed using R software and immune cell infiltration estimation analysis tool- deconvolution algorithm (CIBERSORT).

Results

43 DEGs were identified in total. The identified DEGs mostly involve pneumonia, lung disease, collagen disease, obstructive pulmonary disease and other diseases. The activation of IL-17 signaling pathways, amoebic disease, interaction of viral proteins with cytokines and cytokine receptors, protein digestion and absorption, and flaccid hormone signaling pathways in IPF were different from the control group. The expression degree of CRTAC1, COL10A1, COMP, RPS4Y1, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 in IPF tissue were prominently higher than the normal group. Immune cell infiltration analysis showed that CRTAC1, COL10A1, COMP, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 were associated with monocytes, plasma cells, neutrophils, and regulatory (treg) T cells.

Conclusion

CRTAC1, COL10A1, COMP, IGFL2, NECAB1, SCG5, SLC6A4, and SPP1 can be used as diagnostic markers for IPF, providing new ideas for the future study of IPF occurrence and molecular mechanisms.
Genomic analysis of methicillin-resistant Staphylococcus aureus clonal complex 239 isolated from Danish patients with and without an international travel history
Authors: Coppens Jasmine , Xavier Basil Britto , Vlaeminck Jelle , Larsen Jesper , Lammens Christine , Van Puyvelde Sandra , Goossens Herman , Larsen Anders Rhod , Malhotra-Kumar Surbhi
Published: November 2022

Introduction

International travel has been a major determinant for the introduction of pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) into naïve geographic areas. MRSA clonal complex 239 (CC239) is a highly virulent clone that is predominant in Asia. The objective of this study was to determine the geographic origin of MRSA CC239 isolates recovered from Danish cases with or without a history of international travel during 2004–2016.

Materials and methods

Human MRSA isolates with spa types t030 and t037 (n = 60) were obtained from the National Reference Laboratory for Antimicrobial Resistance. For each case, the following data were collected from notification forms: sex, age, isolation year, specimen source (screening swab or clinical sample), infection type, and international travel history. All isolates were whole-genome sequenced, and a comparative genome and phylogenetic analysis was performed.

Results

The majority of isolates originated from skin and soft tissue (SST) infections and screening swabs. In 31 out of 60 cases reported international travel to different parts of the world. Fifty-four isolates belonged to CC239, including sequence type 239 (ST239) (n = 43), ST241 (n = 5), ST4377 (n = 2), ST4378 (n = 1), ST1465 (n = 1), ST343 (n = 1), and ST592 (n = 1). The majority of the CC239 MRSA isolates (40/54) belonged to well-known geographic clades, including the Asian (n = 12), Serbian (n = 11), South American (n = 2), and Turkish (n = 15). Most MRSA ST239 isolates belonging to the highly virulent Asian clade carried sasX and were recovered from individuals who had travelled to Asia, Africa and the Middle East.

Conclusion

Our data reveal multiple introductions of MRSA CC239 into Denmark through international travel, which highlights the importance of continued genomic surveillance of MRSA in persons returning from international travel to areas where MRSA is endemic.
UPLC-TOF/MS-based metabolomics reveals the chemical changes and in vitro biological effects in fermentation of white ginseng by four probiotics
Authors: Chen Yincui , Wang Yunsheng , Zhu Anqin , Zhang Liqin , Zhang Xiang , Zhang Jin , Zhang Chuanbo
Published: November 2022

Microbial fermentation is a useful method for improving the biological activity of Chinese herbal medicine. Herein, we revealed the effects of solid-state fermentation by Lactiplantibacillus plantarum, Bacillus licheniformis, Saccharomyces cerevisiae, Eurotium cristatum and multiple strains on total flavonoid content, total phenol content, as well as antioxidants, α-amylase inhibitory activities and α-glucosidase inhibitory activities in white ginseng (WG). Metabolite differences between non-fermented and fermented WG by different probiotics were comprehensively investigated using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS). Results showed that the total flavonoid content, ferric reducing antioxidant power, scavenging activities of DPPH radical and ABTS radical, α-amylase inhibitory activities and α-glucosidase inhibitory activities of WG were considerably enhanced after processing by solid-state fermentation in all strains. The total phenol content was increased by E. cristatum and B. licheniformis fermentation, but decreased by L. plantarum, S. cerevisiae and multi-strain fermentation. Additionally, E. cristatum exhibited stronger biotransformation activity on WG compared to other strains. Significant differential metabolites were mainly annotated as prenol lipids, carboxylic acids and derivatives, flavonoids, polyphenols, coumarins and derivatives. Correlation analysis further showed that changes of these metabolites were closely related to antioxidant and hypoglycemic effects. Our results confirmed that fermentation of WG by different probiotics has distinct effects on biological activities and metabolite composition, and indicating fermentation as an important novel strategy to promote components and bioactivities of WG.
Biocompatibility and biocidal effects of modified polylactide composites
Authors: Stachurová Tereza , Rybková Zuzana , Škrlová Kateřina , Malachová Kateřina , Havlíček Miroslav , Plachá Daniela
Published: November 2022

Polylactide (PLA) materials treated with antimicrobial fillers represent a suitable alternative to the production of medical devices. Their advantage is that they can prevent the growth of microorganisms and the formation of microbial biofilms on the surface and around composites. The work is focused on the evaluation of biocompatibility and biocide effect of PLA composite films filled with vermiculite and graphene oxide modified with silver (Ag+ and Ag nanoparticles), hexadecylpyridinium (HDP) and hexadecyltrimethylammonium (HDTMA) cations and their degradation leachates monitored at 1–3–6-month intervals. The antimicrobial effect of the leachates was detected by microdilution methods on gram-negative (Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis), gram-positive (Staphylococcus aureus, Streptococcus salivarius) bacteria and yeast (Candida albicans). The biocidal effect of composites on biofilm formation on the surface of composites was monitored by Christensen method and autoaggregation and motility tests. The biocompatibility of the composite and the leachates was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) cytotoxicity assay. The evaluation of the antimicrobial effect of the leachates demonstrated that leachates of PLA composite filled with graphene oxide and Ag+ showed a stronger antimicrobial effect than leachates of PLA composite filled with vermiculite and Ag+ and Ag nanoparticles. The leachates of PLA composites containing vermiculite with HDP and HDTMA cations had a higher antimicrobial effect on G+ bacteria and yeast than G– bacteria. Bacterial growth, biofilm formation, autoaggregation and motility of the tested bacteria were most inhibited by the composite with vermiculite and Ag+ and Ag nanoparticles. Even after a 6-month degradation of this composite, bacterial growth and biofilm formation continued to be strongly inhibited up to 42 and 91%, respectively. The cytotoxic effect was proved only in the leachate of the composite with vermiculite containing HDP after 6 months of its degradation. Tests evaluating the biocompatibility of materials have shown that the vermiculite is the most preferred carrier and can be used in the future to bind other compounds. The study confirmed that PLA composite filled with vermiculite and Ag+ and Ag nanoparticles was the most stable and effective composite with the best biocompatible and biocidal properties.