bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental citizen science practices in the ILTER community: Remarks from a case study at global scale
Authors: Bergami Caterina , Campanaro Alessandro , Davis Cathlyn , L’Astorina Alba , Pugnetti Alessandra , Oggioni Alessandro
Published: March 2023

In the last decades, citizen science (CS) has experienced an increasing interest as a practice in which scientists and citizens collaborate to produce new knowledge for science, society and policy. Environmental and ecological sciences are among the most active in proposing CS activities and new models for citizen participation in research. In addition to environmental dimensions, these fields necessarily include social and cultural dimensions to confront the complex local and global environmental challenges. This is particularly evident in the International Long-Term Ecological Research (ILTER) network, where the integration of social sciences has become a recognized priority. ILTER offers a valuable landscape to explore common CS features across a wide range of different cultural and socio-ecological contexts, as well as worldviews of science-society interactions. In 2020, we surveyed scientists working at ILTER sites across the globe to identify key features of CS initiatives in which they are/were involved and the levels of participation of the volunteers. We consider these features in the context of the internationally-developed “Ten Principles of Citizen Science” by examining scientific outcomes and societal/policy impact, type of volunteers’ involvement, and sharing of data/findings and feedbacks and acknowledging volunteers. Our results indicate that the ILTER community demonstrated a good predisposition toward environmentally-focused CS initiatives with diverse scientific questions including biodiversity, water quality, ecosystem services and climate change. Most of the respondents reported that the volunteers were involved mainly in collecting samples or recording data; some other activities, such as dissemination of the project conclusions and discussion and translation of the results into action, were also mentioned. Volunteers were usually trained for these initiatives and acknowledged in peer-reviewed publication, however data from the initiatives were only partially shared openly. We conclude with remarks and suggestions for expanding design and implementation of CS in the ILTER community.
Smart digital platforms for carbon neutral management and services: Business models based on ITU standards for green digital transformation
Authors: Liao Han-Teng , Pan Chung-Lien , Zhang Yuan
Published: March 2023

This brief research report focuses on the effects of artificial intelligence (AI) on the environment, by analyzing the latest documents issued by major standard organizations such as the International Telecommunication Union (ITU) and the Internet Society of China (ISC). By outlining the latest developments into a platform canvas for carbon neutrality management and services, this report identifies the potential of “AI of the environment” (i.e., the material composition and environmental impact of AI itself) and “AI for the environment” (i.e., the purposeful use of smart applications to benefit the environment). The role of AI is contextualized in the digital platform design for the provision of services on carbon emission data, which serves as the material foundation for smart services facing both the producers and the consumers of such information. Contributing to the design of business models that enable open innovations, this report discusses the emission impact reduction mechanisms that can optimize, substitute, induce, manage, and facilitate processes and services, indicating the potential of AI-enabled smart services such as forecasting, planning, and recommendation systems. Despite the limited disciplinary considerations and detailed discussions on specific AI technologies, this report provides a simple, practical, and flexible technology roadmap that can be used as a guide for researchers and practitioners to refine their operations and designs and to follow best practices. This report succinctly visualizes key elements of digital platforms of/for GHG emission reduction and their enabling mechanisms, serving as an AI technology roadmap for future research and innovation in the field.
Emissions of volatile organic compounds from Norway spruce and potential atmospheric impacts
Authors: Hakola Hannele , Taipale Ditte , Praplan Arnaud , Schallhart Simon , Thomas Steven , Tykkä Toni , Helin Aku , Bäck Jaana , Hellén Heidi
Published: March 2023

Published biogenic volatile organic compound (BVOC) emission rates of Norway spruces vary a lot. In this study we combined published Norway spruce emission rates measured in boreal forests and added our new, unpublished emission data from Southern (SF) and Northern Finland (NF). Standardized summer monthly mean emission potentials of isoprene vary from below the detection limit to 7 μg g–1(dw) h–1, and monoterpene (MT) and sesquiterpene (SQT) emission potentials 0.01–3 μg g–1(dw) h–1 and 0.03–2.7 μg g–1(dw) h–1, respectively. In this study, we found much higher SQT emissions from Norway spruces than previously measured, and on average SQTs had higher emission potentials than isoprene or MTs. The highest monthly mean SQT emission potential of 13.6 μg g–1(dw) h–1 was observed in September in Southern Finland. We found that none of the younger (33–40 years) trees in Hyytiälä, Southern Finland, emitted isoprene, while one 50-year-old tree was a strong isoprene emitter. The difference due to age could not be confirmed, since all measured small trees were growing in Hyytiälä, so this could also be due to the same genetic origin. On average, older trees (>80 years) emitted about ten times more isoprene and MTs than younger ones (<80 years), but no clear difference was seen in SQT emissions. SQT emissions can be more related to stress effects. As shown here for Norway spruce, it is possible that the emission factor of SQTs is significantly higher than what is currently used in models, which may have significant effects on the prediction of formation and growth of new particles, since the secondary organic aerosol (SOA) formation potential of SQTs is high, and this may have significant effects on the formation and growth of new particles. Due to the high secondary organic aerosol (SOA) formation potentials of SQTs, the impact on SOA formation and mass could be even higher.
Prenatal diagnosis by trio exome sequencing in fetuses with ultrasound anomalies: A powerful diagnostic tool
Authors: Tran Mau-Them Frédéric , Delanne Julian , Denommé-Pichon Anne-Sophie , Safraou Hana , Bruel Ange-Line , Vitobello Antonio , Garde Aurore , Nambot Sophie , Bourgon Nicolas , Racine Caroline , Sorlin Arthur , Moutton Sébastien , Marle Nathalie , Rousseau Thierry , Sagot Paul , Simon Emmanuel , Vincent-Delorme Catherine , Boute Odile , Colson Cindy , Petit Florence , Legendre Marine , Naudion Sophie , Rooryck Caroline , Prouteau Clément , Colin Estelle , Guichet Agnès , Ziegler Alban , Bonneau Dominique , Morel Godelieve , Fradin Mélanie , Lavillaureix Alinoé , Quelin Chloé , Pasquier Laurent , Odent Sylvie , Vera Gabriella , Goldenberg Alice , Guerrot Anne-Marie , Brehin Anne-Claire , Putoux Audrey , Attia Jocelyne , Abel Carine , Blanchet Patricia , Wells Constance F. , Deiller Caroline , Nizon Mathilde , Mercier Sandra , Vincent Marie , Isidor Bertrand , Amiel Jeanne , Dard Rodolphe , Godin Manon , Gruchy Nicolas , Jeanne Médéric , Schaeffer Elise , Maillard Pierre-Yves , Payet Frédérique , Jacquemont Marie-Line , Francannet Christine , Sigaudy Sabine , Bergot Marine , Tisserant Emilie , Ascencio Marie-Laure , Binquet Christine , Duffourd Yannis , Philippe Christophe , Faivre Laurence , Thauvin-Robinet Christel
Published: March 2023

Introduction: Prenatal ultrasound (US) anomalies are detected in around 5%–10% of pregnancies. In prenatal diagnosis, exome sequencing (ES) diagnostic yield ranges from 6% to 80% depending on the inclusion criteria. We describe the first French national multicenter pilot study aiming to implement ES in prenatal diagnosis following the detection of anomalies on US.

Patients and methods: We prospectively performed prenatal trio-ES in 150 fetuses with at least two US anomalies or one US anomaly known to be frequently linked to a genetic disorder. Trio-ES was only performed if the results could influence pregnancy management. Chromosomal microarray (CMA) was performed before or in parallel.

Results: A causal diagnosis was identified in 52/150 fetuses (34%) with a median time to diagnosis of 28 days, which rose to 56/150 fetuses (37%) after additional investigation. Sporadic occurrences were identified in 34/56 (60%) fetuses and unfavorable vital and/or neurodevelopmental prognosis was made in 13/56 (24%) fetuses. The overall diagnostic yield was 41% (37/89) with first-line trio-ES versus 31% (19/61) after normal CMA. Trio-ES and CMA were systematically concordant for identification of pathogenic CNV.

Conclusion: Trio-ES provided a substantial prenatal diagnostic yield, similar to postnatal diagnosis with a median turnaround of approximately 1 month, supporting its routine implementation during the detection of prenatal US anomalies.
Methodological quality assessment of genetic studies on brain arteriovenous malformation related hemorrhage: A cross-sectional study
Authors: Jiang Junhao , Qin Zhuo , Yan Junxia , Liu Junyu
Published: March 2023

Objectives: Rupture of a brain arteriovenous malformation (bAVM) can cause intracranial hemorrhage and severe clinical outcomes. At present, the mechanisms of bAVM-related hemorrhage are poorly understood. This study aimed to summarize the potential genetic risk factors for bAVM-related hemorrhage and appraise the methodological quality of existing genetic studies on bAVM-related hemorrhage using a cross-sectional design.

Methods: A systematic literature search was conducted on genetic studies associated with bAVM-related hemorrhage published in PubMed, Embase, Web of Science, China National Knowledge Internet, and Wangfang databases, up to November 2022. Subsequently, a cross-sectional study was performed to describe the potential candidate genetic variants of bAVM associated with risk of hemorrhage and to evaluate the methodological quality of the identified studies using the Newcastle–Ottawa quality assessment scale and Q-genie tool.

Results: Of the 1811 records identified in the initial search, nine studies met the filtering criteria and were included. Twelve single nucleotide polymorphisms (SNPs), including IL6 rs1800795, IL17A rs2275913, MMP9 rs9509, VEGFA rs1547651, and EPHB4 rs314353, rs314308, and rs314313, were associated with bAVM-related hemorrhage. However, only 12.5% of the evaluated SNPs showed statistical power> 0.80 (α = 0.05). Methodological quality assessment revealed significant flaws in the designs of the included studies, such as less reliable representativeness of recruited individuals, short follow-up periods in cohort studies, and less comparability between groups of hemorrhagic and non-hemorrhagic patients.

Conclusion:IL1B, IL6, IL17A, APOE, MMP9, VEGFA and EPHB4 were potentially associated with bAVM-related hemorrhage. The methodological designs of the analyzed studies required improvement in order to obtain more reliable results. Regional alliances and rare disease banks need to be established to recruit large numbers of bAVM patients (especially familial and extreme-trait cases) in a multicenter, prospective cohort study with an adequate follow-up period. Furthermore, it is important to use advanced sequencing techniques and efficient measures to filter candidate genetic variants.
Modeling the effects of cigarette smoke extract on influenza B virus infections in mice
Authors: Chavez Jerald R. , Yao Wangyuan , Dulin Harrison , Castellanos Jasmine , Xu Duo , Hai Rong
Published: March 2023

Influenza B virus (IBV) is a major respiratory viral pathogen. Due to a lack of pandemic potential for IBV, there is a lag in research on IBV pathology and immunological responses compared to IAV. Therefore, the impact of various lifestyle and environmental factors on IBV infections, such as cigarette smoking (CS), remains elusive. Despite the increased risk and severity of IAV infections with CS, limited information exists on the impact of CS on IBV infections due to the absence of suitable animal models. To this end, we developed an animal model system by pre-treating mice for two weeks with cigarette smoke extract (CSE), then infected them with IBV and monitored the resulting pathological, immunological, and virological effects. Our results reveal that the CSE treatment decreased IBV specific IgG levels yet did not change viral replication in the upper airway/the lung, and weight recovery post infection. However, higher concentrations of CSE did result in higher mortality post infection. Together, this suggests that CS induced inflammation coupled with IBV infection resulted in exacerbated disease outcome.
C1q and central nervous system disorders
Authors: Zhang Wenjie , Chen Yuan , Pei Hui
Published: March 2023

C1q is a crucial component of the complement system, which is activated through the classical pathway to perform non-specific immune functions, serving as the first line of defense against pathogens. C1q can also bind to specific receptors to carry out immune and other functions, playing a vital role in maintaining immune homeostasis and normal physiological functions. In the developing central nervous system (CNS), C1q functions in synapse formation and pruning, serving as a key player in the development and homeostasis of neuronal networks in the CNS. C1q has a close relationship with microglia and astrocytes, and under their influence, C1q may contribute to the development of CNS disorders. Furthermore, C1q can also have independent effects on neurological disorders, producing either beneficial or detrimental outcomes. Most of the evidence for these functions comes from animal models, with some also from human specimen studies. C1q is now emerging as a promising target for the treatment of a variety of diseases, and clinical trials are already underway for CNS disorders. This article highlights the role of C1q in CNS diseases, offering new directions for the diagnosis and treatment of these conditions.
Deciphering the roles of myeloid derived suppressor cells in viral oncogenesis
Authors: Glover Alexander , Zhang Zhaoqin , Shannon-Lowe Claire
Published: March 2023

Myeloid derived suppressor cells (MDSCs) are a heterogenous population of myeloid cells derived from monocyte and granulocyte precursors. They are pathologically expanded in conditions of ongoing inflammation where they function to suppress both innate and adaptive immunity. They are subdivided into three distinct subsets: monocytic (M-) MDSC, polymorphonuclear (or neutrophilic) (PMN-) MDSC and early-stage (e-) MDSC that may exhibit differential function in different pathological scenarios. However, in cancer they are associated with inhibition of the anti-tumour immune response and are universally associated with a poor prognosis. Seven human viruses classified as Group I carcinogenic agents are jointly responsible for nearly one fifth of all human cancers. These viruses represent a large diversity of species, including DNA, RNA and retroviridae. They include the human gammaherpesviruses (Epstein Barr virus (EBV) and Kaposi’s Sarcoma-Associated Herpesvirus (KSHV), members of the high-risk human papillomaviruses (HPVs), hepatitis B and C (HBV, HCV), Human T cell leukaemia virus (HTLV-1) and Merkel cell polyomavirus (MCPyV). Each of these viruses encode an array of different oncogenes that perturb numerous cellular pathways that ultimately, over time, lead to cancer. A prerequisite for oncogenesis is therefore establishment of chronic infection whereby the virus persists in the host cells without being eradicated by the antiviral immune response. Although some of the viruses can directly modulate the immune response to enable persistence, a growing body of evidence suggests the immune microenvironment is modulated by expansions of MDSCs, driven by viral persistence and oncogenesis. It is likely these MDSCs play a role in loss of immune recognition and function and it is therefore essential to understand their phenotype and function, particularly given the increasing importance of immunotherapy in the modern arsenal of anti-cancer therapies. This review will discuss the role of MDSCs in viral oncogenesis. In particular we will focus upon the mechanisms thought to drive the MDSC expansions, the subsets expanded and their impact upon the immune microenvironment. Importantly we will explore how MDSCs may modulate current immunotherapies and their impact upon the success of future immune-based therapies.
Microbe-mineral interactions in the Plastisphere: Coastal biogeochemistry and consequences for degradation of plastics
Authors: Dodhia Maya S. , Rogers Kelsey L. , Fernández-Juárez Victor , Carreres-Calabuig Joan A. , Löscher Carolin R. , Tisserand Amandine A. , Keulen Nynke , Riemann Lasse , Shashoua Yvonne , Posth Nicole R.
Published: March 2023

Microbe-mineral interactions, such as mineral substrate utilization and aggregate formation, have played a key role in the cycling of elements through Earth evolution. In water, soils, and sediment biogeochemistry modulates microbial community composition and mineral formation over spatial and temporal scales. Plastic is a new material that is now widespread in the environment. Both microbial and mineral associations with plastic comprise the Plastisphere, which influences the fate of plastic. This study focuses on how the biogeochemical environment defines microbial and mineral association with polyethylene (PE) and polystyrene (PS) over a 12-month period in a temperate coastal harbor. The coastal harbor environment was separated into 3 conceptual compartments defined by physical and biogeochemical conditions, that allow transfer of electrons between species e.g., light penetration and redox setting. Microbe and mineral association were investigated in the water column, top sediment, and bottom sediment by applying a range of modern analytical techniques to identify changes in the chemical structures of plastics, microbial community development, metal, salt and mineral formation. The epiplastic microbial community was distinct to that of the surrounding environment across changing redox conditions. The type and oxidation state of metallic minerals formed on plastics or entrapped in the biofilm matrix related to the dominant abiotic and biotic processes across redox conditions. FTIR spectroscopy indicated the occurrence of PE and PS oxidation in the various biogeochemical environments. Combined, these findings demonstrate that redox conditions and surrounding biogeochemistry mediate the composition of mineralogical and biological loading of PE and PS in coastal marine environments. This suggests that the biogeochemical setting in which the plastics are stored constrains the development of plastic interfacial biogeochemistry and the potential for plastic degradation and transport over time.
Temporal trends of organophosphate esters in a sediment core from the tidal flat of Liao River estuary, Northeast China
Authors: Luo Qing , Wang Congcong , Gu Leiyan , Wu Zhongping , Li Yujie
Published: March 2023

The historical trends and inventory of organophosphate esters (OPEs) were investigated based on depth profiles of OPEs in sediment core collected from the tidal flat of the Liao River estuary in northeastern China. The concentration of ∑13OPEs in sediment core has increased continuously since records began, reaching a peak of 10.8 ng g-1 dry weight (dw) in the 1960s, then began to decline and fall to a low of 3.91 ng g-1 dw in the 1980s, before rising again and increasing to 20.4 ng g-1 dw in the 2000s. After a brief decline, It started to increase again and reached a peak of 27.0 ng g-1 dw in 2018. Tributyl-n-phosphate was found in each layer of the sediment core, accounting for 31.9 - 100% of ∑13OPEs. The fluxes of OPEs ranged from 46.5 to 105 ng cm-2 y-1 in the sediment layers deposited between 2007 and 2018. The inventory of OPEs in the sediment core was estimated to be 1541 ng cm-2. This work reports for the first time the historical contamination trends of OPEs in Chinese sediments, which is important for assessing the environmental risk of OPEs.
In-house vs. commercial boron-doped diamond electrodes for electrochemical degradation of water pollutants: A critical review
Authors: Brosler Priscilla , Girão Ana Violeta , Silva Rui F. , Tedim João , Oliveira Filipe J.
Published: March 2023

Boron-doped diamond (BDD) electrodes are eco-friendly and widely used in efficient water remediation through electrochemical advanced oxidation processes (EAOPs). These anodes can completely mineralize a wide range of pollutants, only requiring electrical energy. Over the last 2 decades, numerous commercially available BDD electrodes have emerged, but little is known about their electrooxidation performance, particularly if compared to laboratory-produced anodes by different research groups. In this critical review, a comparison between in-house-made and commercially available BDD electrodes based on a systematic literature review (SLR) is carried out. SLR was quite useful in locating and selecting the scientific publications relevant to the topic, enabling information gathering on dissemination, growth, and trends in the application of BDD electrodes in the degradation of water pollutants. More specifically, data concerning the origin of the employed BDD electrodes, and their physicochemical properties were extracted from a thorough selection of articles. Moreover, a detailed analysis of the main parameters affecting the BDD electrodes’ performance is provided and includes selection and pre-treatment of the substrate material, chemical vapor deposition (CVD) method, deposition parameters, characterization methods, and operational conditions. This discussion was carried out fully based on the numerous performance indicators found in the literature. Those clearly revealed that there are only a few analogous points across works, demonstrating the challenge of establishing an accurate comparison methodology. In this context, we propose a figure-of-merit equation which aims at normalizing BDD degradation results for a specific contaminant, even if working under different experimental conditions. Two case studies based on the degradation of solutions spiked with phenol and landfill leachate treatment with commercial or in-house-made BDD electrodes are also presented. Although it was not possible to conclude which electrode would be the best choice, we propose a set of guidelines detailing a consistent experimental procedure for comparison purposes in the future.
Sequence diversity of hepatitis D virus in Mongolia
Authors: Magvan Battur , Kloeble Anne Alina , Ptok Johannes , Hoffmann Daniel , Habermann Daniel , Gantumur Anuujin , Paluschinski Martha , Enebish Gerelmaa , Balz Vera , Fischer Johannes C. , Chimeddorj Battogtokh , Walker Andreas , Timm Jörg
Published: March 2023

Introduction

The Hepatitis Delta Virus (HDV) is a defective, single-stranded RNA virusoid encoding for a single protein, the Hepatitis Delta Antigen (HDAg), which requires the hepatitis B virus (HBV) envelope protein (HBsAg) for its transmission. Currently, hepatitis D is the most aggressive form of viral hepatitis and treatment options are limited. Worldwide 12 million people are chronically infected with HDV being at high risk for progression to cirrhosis and development of liver cancer.

Objectives

Although it is well established that Mongolia is the country with the highest prevalence of HDV infections, the information on the molecular epidemiology and factors contributing to HDV sequence diversity are largely unclear. The aim of the study was to characterize the sequence diversity of HDV in rural areas from Mongolia and to determine the extent of HLA class I-associated selection pressure.

Patients and methods

From the HepMongolia cohort from rural areas in Mongolia, 451 HBsAg-positive individuals were selected and anti-HDV, HDV-RNA and the sequence of the large HDAg was determined. For all individuals the HLA class I locus was genotyped. Residues under selection pressure in the presence of individual HLA class I types were identified with the recently published analysis tool HAMdetector.

Results

Of 431 HBsAg positive patients, 281 were anti-HDV positive (65%), and HDV-RNA could be detected in 207 of 281 (74%) of patients. The complete large HDAg was successfully sequenced from 131 samples. Phylogenetic analysis revealed that all Mongolian HDV isolates belong to genotype 1, however, they separate into several different clusters without clear regional association. In turn, from phylogeny there is strong evidence for recent local transmission events. Importantly, we found multiple residues with strong support for HLA class I-associated selection pressure consistent with a functional CD8+ T cell response directed against HDV.

Conclusion

HDV isolates from Mongolia are highly diverse. The molecular epidemiology suggests circulation of multiple subtypes and provides evidence for ongoing recent transmissions.
The effect of SMAD4 on the prognosis and immune response in hypopharyngeal carcinoma
Authors: Song Juanjuan , Wu Jialing , Ding Jiaxuan , Liang Yangxin , Chen Changlong , Liu Yimin
Published: March 2023

Objectives

In malignant tumors, elevated infiltration of intratumoral CD8+ cytotoxic T cells predicts a beneficial prognosis, whereas high levels of CD15+ neutrophils in peritumor tissues indicate poor prognosis. It is unclear how SMAD4, which promotes favorable clinical outcomes and antitumor immunoregulation, along with CD8+ cytotoxic T cells and CD15+ neutrophils exert an influence on hypopharyngeal carcinoma (HPC).

Materials and methods

Specimens were collected from 97 patients with HPC. Immunohistological analyses of SMAD4, CD8+ cytotoxic T cell and CD15+ neutrophil expression were performed. SMAD4 nuclear intensity was measured, meanwhile, CD8+ cytotoxic T cells and CD15+ neutrophils were counted under a microscope. The prognostic role of SMAD4 was determined using the log-rank test and univariate and multivariate analyses. The relationship among SMAD4, CD8+ cytotoxic T cells, and CD15+ neutrophils was estimated by Mann–Whitney U test.

Results

High levels of SMAD4 were associated with favorable overall survival (OS) and disease-free survival (DFS) in HPC. Multivariate analysis suggested that SMAD4 is an independent predictor of OS and DFS. A high density of intratumoral CD8+ cytotoxic T cells and low accumulation of CD15+ neutrophils in the peritumor area were associated with longer OS and DFS. Furthermore, SMAD4 was linked to the levels of intratumoral CD8+ cytotoxic T cells and peritumoral CD15+ neutrophils. Patients with high SMAD4/high intratumoral CD8+ cytotoxic T cells or high SMAD4/low peritumoral CD15+ neutrophils showed the best prognosis.

Conclusion

SMAD4, CD8+ cytotoxic T cell level, and CD15+ neutrophil level have prognostic value in HPC. SMAD4 is a promising prognostic marker reflecting immune response in HPC.
Evaluation of a gene signature related to thrombotic manifestations in antiphospholipid syndrome
Authors: Jacintho Bruna Cardoso , Mazetto Fonseca Bruna de Moraes , Hounkpe Bidossessi Wilfried , Oliveira Jose Diogo , dos Santos Ana Paula Rosa , Vaz Camila de Oliveira , de Paula Erich Vinicius , Orsi Fernanda Andrade
Published: March 2023

Thrombotic primary antiphospholipid syndrome (t-PAPS) is an acquired condition characterized by heterogeneous thrombotic manifestations, which is intriguing since venous and arterial thrombosis appear to have distinct pathogenesis. Gene expression analysis may constitute a new approach to evaluate potential similarities or differences between the clinical manifestations of t-PAPS. Recently, dysregulation of the ANXA3, TNFAIP6, TXK, BACH2, and SERPINB2 genes has been associated with both arterial and venous thrombosis in the general population. Therefore, the aim of this study was to examine whether ANXA3, TNFAIP6, TXK, BACH2, and SERPINB2 expression was associated with t-PAPS. Gene expression was quantified by qPCR of total leukocyte mRNA. In this case-control study, 102 t-PAPS patients, 17 asymptomatic antiphospholipid (aPL) carriers and 100 controls were evaluated. Increased expression of ANXA3 (P = 0.008) and TNFAIP6 (P = 0.001) and decreased expression of the TXK gene (P = 0.0001) were associated with an increased risk of t-PAPS compared to the control. ANXA3 upregulation was more evident in cases of arterial thrombosis and multiple thrombotic events. There was no difference in the expression of these genes between triple and non-triple aPL positivity. ANXA3, TNFAIP6, TXK, BACH2, and SERPINB2 expression levels were also similar between aPL carriers and controls (P = 0.77; P = 0.48; P = 0.08; P = 0.73, and P = 0.13, respectively). In conclusion, our results showed that genes related to hemostasis (ANXA3) and immunity (TNFAIP6, TXK) are dysregulated in t-PAPS compared to controls. Gene dysregulation was not detected in aPL carriers and was not related to the aPL profile, suggesting that this gene signature is related to thrombotic manifestations rather than to aPL burden. Our results suggest that innate immunity and hemostasis pathways are associated with t-PAPS at a molecular level and may play a role in disease severity.
Urinary-derived extracellular vesicles reveal a distinct microRNA signature associated with the development and progression of Fabry nephropathy
Authors: Levstek Tina , Vujkovac Bojan , Cokan Vujkovac Andreja , Trebušak Podkrajšek Katarina
Published: March 2023

Introduction

Early initiation is essential for successful treatment of Fabry disease, but sensitive and noninvasive biomarkers of Fabry nephropathy are lacking. Urinary extracellular vesicles (uEVs) represent a promising source of biomarkers of kidney involvement. Among them, microRNAs (miRNAs) are important post-transcriptional regulators of gene expression that contribute to the development and progression of various kidney diseases. We aimed to identify uEV-derived miRNAs involved in the development and/or progression of Fabry nephropathy.

Methods

Patients with genetically confirmed Fabry disease and matched control subjects were included. EVs were isolated from the second morning urine by size exclusion chromatography, from which miRNAs were extracted. miRNA urine exosome PCR panels were used to characterize the miRNA signature in a discovery cohort. Individual qPCRs were performed on a validation cohort that included chronological samples. We identified the target genes of dysregulated miRNAs and searched for potential hub genes. Enrichment analyses were performed to identify their potential function.

Results

The expression of miR-21-5p and miR-222-3p was significantly higher in patients with stable renal function and those with progressive nephropathy compared with the corresponding controls. In addition, the expression of miR-30a-5p, miR-10b-5p, and miR-204-5p was significantly lower in patients with progressive nephropathy, however, in the chronological samples, this was only confirmed for miR-204-5p. Some of the identified hub genes controlled by the dysregulated miRNAs have been associated with kidney impairment in other kidney diseases.

Conclusion

The miRNA cargo in uEVs changes with the development and progression of Fabry nephropathy and, therefore, represents a potential biomarker that may provide a new option to prevent or attenuate the progression of nephropathy. Furthermore, dysregulated miRNAs were shown to be potentially associated with pathophysiological pathways in the kidney.
Biogeochemical behavior and pollution control of arsenic in mining areas: A review
Authors: Zhuang Fan , Huang Jingyi , Li Hongguang , Peng Xing , Xia Ling , Zhou Lei , Zhang Teng , Liu Zhenghua , He Qiang , Luo Feng , Yin Huaqun , Meng Delong
Published: March 2023

Arsenic (As) is one of the most toxic metalloids that possess many forms. As is constantly migrating from abandoned mining area to the surrounding environment in both oxidation and reducing conditions, threatening human health and ecological safety. The biogeochemical reaction of As included oxidation, reduction, methylation, and demethylation, which is closely associated with microbial metabolisms. The study of the geochemical behavior of arsenic in mining areas and the microbial remediation of arsenic pollution have great potential and are hot spots for the prevention and remediation of arsenic pollution. In this study, we review the distribution and migration of arsenic in the mining area, focus on the geochemical cycle of arsenic under the action of microorganisms, and summarize the factors influencing the biogeochemical cycle of arsenic, and strategies for arsenic pollution in mining areas are also discussed. Finally, the problems of the risk control strategies and the future development direction are prospected.
Upper respiratory tract mycobiome alterations in different kinds of pulmonary disease
Authors: Xu Xingye , Ding Fangping , Hu Xiangqi , Yang Fan , Zhang Ting , Dong Jie , Xue Ying , Liu Tao , Wang Jing , Jin Qi
Published: March 2023

Introduction

The human respiratory tract is considered to be a polymicrobial niche, and an imbalance in the microorganism composition is normally associated with several respiratory diseases. In addition to the well-studied bacteriome, the existence of fungal species in the respiratory tract has drawn increasing attention and has been suggested to have a significant clinical impact. However, the understanding of the respiratory fungal microbiota (mycobiome) in pulmonary diseases is still insufficient.

Methods

In this study, we investigated the fungal community composition of oropharynx swab (OS) samples from patients with five kinds of pulmonary disease, including interstitial lung disease (ILD), bacterial pneumonia (BP), fungal pneumonia (FP), asthma (AS) and lung cancer (LC), and compared them with healthy controls (HCs), based on high-throughput sequencing of the amplified fungal internal transcribed spacer (ITS) region.

Results

The results showed significant differences in fungal composition and abundance between disease groups and HCs. Malassezia was the most significant genus, which was much more abundant in pulmonary diseases than in the control. In addition, many common taxa were shared among different disease groups, but differences in taxa abundance and specific species in distinct disease groups were also observed. Based on linear discriminant analysis effect size (LefSe), each group had its characteristic species. Furthermore, some species showed a significant correlation with the patient clinical characteristics.

Discussion

Our study deepened our understanding of the respiratory tract mycobiome in some diseases that are less studied and identified the commonalities and differences among different kinds of pulmonary disease. These results would provide the solid basis for further investigation of the association between the mycobiome and pathogenicity of pulmonary diseases.
Development of a rapid reverse genetics system for feline coronavirus based on TAR cloning in yeast
Authors: Cao Hongmin , Gu Haorong , Kang Hongtao , Jia Honglin
Published: March 2023

Introduction

Reverse genetics has become an indispensable tool to gain insight into the pathogenesis of viruses and the development of vaccines. The yeast-based synthetic genomics platform has demonstrated the novel capabilities to genetically reconstruct different viruses.

Methods

In this study, a transformation-associated recombination (TAR) system in yeast was used to rapidly rescue different strains of feline infectious peritonitis virus, which causes a deadly disease of cats for which there is no effective vaccine.

Results and discussion

Using this system, the viruses could be rescued rapidly and stably without multiple cloning steps. Considering its speed and ease of manipulation in virus genome assembly, the reverse genetics system developed in this study will facilitate the research of the feline coronaviruses pathogenetic mechanism and the vaccine development.
Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils
Authors: Ning Qi , Chen Lin , Li Fang , Zhou Guixiang , Zhang Congzhi , Ma Donghao , Zhang Jiabao
Published: March 2023

Stable soil organic carbon (SOC) formation in coastal saline soils is important to improve arable land quality and mitigate greenhouse gas emissions. However, how microbial life-history strategies and metabolic traits regulate SOC turnover in coastal saline soils remains unknown. Here, we investigated the effects of microbial life history strategy tradeoffs on microbial carbon use efficiency (CUE) and microbial-derived SOC formation using metagenomic sequencing technology in different salinity soils. The results showed that high-salinity is detrimental to microbial CUE and microbial-derived SOC formation. Moreover, the regulation of nutrients stoichiometry could not mitigate adverse effects of salt stress on microbial CUE, which indicated that microbial-derived SOC formation is independent of stoichiometry in high-salinity soil. Low-salinity soil is dominated by a high growth yield (Y) strategy, such as higher microbial biomass carbon and metabolic traits which are related to amino acid metabolism, carbohydrate metabolism, and cell processes. However, high-salinity soil is dominated by stress tolerance (S) (e.g., higher metabolic functions of homologous recombination, base excision repair, biofilm formation, extracellular polysaccharide biosynthesis, and osmolytes production) and resource acquisition (A) strategies (e.g., higher alkaline phosphatase activity, transporters, and flagellar assembly). These trade-offs of strategies implied that resource reallocation took place. The high-salinity soil microbes diverted investments away from growth yield to microbial survival and resource capture, thereby decreasing biomass turnover efficiency and impeding microbial-derived SOC formation. Moreover, altering the stoichiometry in low-salinity soil caused more investment in the A-strategy, such as the production of more β-glucosidase and β-N-acetyl-glucosaminidase, and increasing bacterial chemotaxis, which thereby reduced microbial-derived SOC formation. Our research reveals that shift the microbial community from S- and A- strategies to the Y-strategy is important to increase the microbial CUE, and thus enhance SOC turnover in coastal saline soils.
MADGAN:A microbe-disease association prediction model based on generative adversarial networks
Authors: Hu Weixin , Yang Xiaoyu , Wang Lei , Zhu Xianyou
Published: March 2023

Researches have demonstrated that microorganisms are indispensable for the nutrition transportation, growth and development of human bodies, and disorder and imbalance of microbiota may lead to the occurrence of diseases. Therefore, it is crucial to study relationships between microbes and diseases. In this manuscript, we proposed a novel prediction model named MADGAN to infer potential microbe-disease associations by combining biological information of microbes and diseases with the generative adversarial networks. To our knowledge, it is the first attempt to use the generative adversarial network to complete this important task. In MADGAN, we firstly constructed different features for microbes and diseases based on multiple similarity metrics. And then, we further adopted graph convolution neural network (GCN) to derive different features for microbes and diseases automatically. Finally, we trained MADGAN to identify latent microbe-disease associations by games between the generation network and the decision network. Especially, in order to prevent over-smoothing during the model training process, we introduced the cross-level weight distribution structure to enhance the depth of the network based on the idea of residual network. Moreover, in order to validate the performance of MADGAN, we conducted comprehensive experiments and case studies based on databases of HMDAD and Disbiome respectively, and experimental results demonstrated that MADGAN not only achieved satisfactory prediction performances, but also outperformed existing state-of-the-art prediction models.
A pan-cancer analysis reveals CHD1L as a prognostic and immunological biomarker in several human cancers
Authors: Soltan Mohamed A. , Eldeen Muhammad Alaa , Eid Refaat A. , Alyamani Najiah M. , Alqahtani Leena S. , Albogami Sarah , Jafri Ibrahim , Park Moon Nyeo , Alsharif Ghadi , Fayad Eman , Mohamed Gamal , Osman Rihab , Kim Bonglee , Zaki Mohamed Samir A.
Published: March 2023

Introduction: Several recent studies pointed out that chromodomain-helicase-DNA-binding protein 1-like (CHD1L) is a putative oncogene in many human tumors. However, up to date, there is no pan-cancer analysis performed to study the different aspects of this gene expression and behavior in tumor tissues.

Methods: Here, we applied several bioinformatics tools to make a comprehensive analysis for CHD1L. Firstly we assessed the expression of CHD1L in several types of human tumors and tried to correlate that with the stage and grade of the analyzed tumors. Following that, we performed a survival analysis to study the correlation between CHD1L upregulation in tumors and the clinical outcome. Additionally, we investigated the mutation forms, the correlation with several immune cell infiltration, and the potential molecular mechanisms of CHD1L in the tumor tissue.

Result and discussion: The results demonstrated that CHD1L is a highly expressed gene across several types of tumors and that was correlated with a poor prognosis for most cancer patients. Moreover, it was found that CHD1L affects the tumor immune microenvironment by influencing the infiltration level of several immune cells. Collectively, the current study provides a comprehensive overview of the oncogenic roles of CHD1L where our results nominate CHD1L as a potential prognostic biomarker and target for antitumor therapy development.
Cortical thinning in male obstructive sleep apnoea patients with excessive daytime sleepiness
Authors: Li Yezhou , Wang Jing , Ji Lirong , Cheng Chaohong , Su Tong , Wu Shuqing , Han Fei , Cox Daniel J. , Wang Erlei , Chen Rui
Published: March 2023

Background and purpose

Obstructive sleep apnoea is associated with excessive daytime sleepiness due to sleep fragmentation and hypoxemia, both of which can lead to abnormal brain morphology. However, the pattern of brain structural changes associated with excessive daytime sleepiness is still unclear. This study aims to investigate the effects of excessive daytime sleepiness on cortical thickness in patients with obstructive sleep apnoea.

Materials and methods

61 male patients with newly diagnosed obstructive sleep apnoea were included in the present study. Polysomnography and structural MRI were performed for each participant. Subjective daytime sleepiness was assessed using the Epworth Sleepiness Scale score. Surface-based morphometric analysis was performed using Statistical Parametric Mapping 12 and Computational Anatomy 12 toolboxes to extract cortical thickness.

Results

Using the median Epworth Sleepiness Scale score, patients were divided into the non-sleepiness group and the sleepiness group. The cortical thickness was markedly thinner in the sleepiness group in the left temporal, frontal, and parietal lobe and bilateral pre- and postcentral gyri (pFWE < 0.05). There was a significant negative correlation between the cortical thickness and the Epworth Sleepiness Scale score. After adjusting for age, body mass index, and obstructive sleep apnoea severity, the Epworth Sleepiness Scale score remained an independent factor affecting the cortical thickness of the left middle temporal lobe, transverse temporal and temporal pole.

Conclusion

Subjective daytime sleepiness is associated with decreased cortical thickness, and the Epworth Sleepiness Scale score may be of utility as a clinical marker of brain injury in patients with obstructive sleep apnoea.
Clinical factors associated with functional outcomes in patients with single subcortical infarction with neurological deterioration
Authors: Yang Yi , He Yue , Han Wei , Xu JianHui , Cai ZhiRong , Zhao Tian , Shao YuanWei , Yu Ming
Published: March 2023

Objective

Factors that predict poor outcomes in patients with single subcortical infarction (SSI) may differ from those that predict poor outcomes in the SSI subgroup with neurological deterioration (ND). This study aimed to investigate the effect of ND on functional outcomes in patients with SSI and the clinical factors that predict poor outcomes in patients with SSI with ND (SSI-ND) and in all patients with SSI.

Methods

Patients with SSI were consecutively enrolled in this study. ND was defined as an increase of ≥2 points in the National Institutes of Health Stroke Scale (NIHSS) total score, an increase of ≥1 point in the NIHSS subscore of consciousness or motor function, or any new neurological deficit.

Results

A total of 255 patients were enrolled, and nine (3.53%) were lost to a follow-up. ND [adjusted relative risk (aRR) = 1.37, 95% confidence interval (CI) = 1.22–1.55, p < 0.001], female sex (aRR = 1.13, 95% CI = 1.03–1.24, p = 0.12), initial NIHSS (aRR = 1.08, 95% CI = 1.07–1.10, p < 0.001), and parental arterial disease (PAD) (aRR = 1.16, 95% CI = 1.07–1.26, p = 0.038) were associated with a poor 90-day outcome (the modified Rankin scale (mRS) > 2 points) in patients with SSI. In the SSI-ND subgroup, PAD (aRR = 2.15, 95% CI = 1.20–3.86, p = 0.01), glycosylated hemoglobin (aRR = 1.17, 95% CI = 1.01–1.35, p = 0.035), and severe NIHSS (aRR = 1.15, 95% CI = 1.06–1.25, p = 0.001) were predictive of a poor outcome, and PAD (aRR = 1.87, 95% CI = 1.19–2.95, p = 0.007) was correlated with higher/worsened NIHSS [> 2 points (median)]. For predicting poor outcomes in patients with SSI-ND with PAD, a more severe NIHSS (aRR = 1.09, 95% CI = 1.02–1.17, p = 0.01) was the only determinant, with a cutoff of 4.5 points, a sensitivity of 94.0%, and a specificity of 83.3%.

Conclusions

ND is an independent predictor of poor outcomes in patients with SSI, and poor outcome determinants in the SSI-ND subgroup and in all patients with SSI are not identical. For patients with SSI-ND, PAD could aggravate ND and was therefore an essential predictor of poor outcomes.
The initiator of neuroexcitotoxicity and ferroptosis in ischemic stroke: Glutamate accumulation
Authors: Fan Genhao , Liu Menglin , Liu Jia , Huang Yuhong
Published: March 2023

Glutamate plays an important role in excitotoxicity and ferroptosis. Excitotoxicity occurs through over-stimulation of glutamate receptors, specifically NMDAR, while in the non-receptor-mediated pathway, high glutamate concentrations reduce cystine uptake by inhibiting the System Xc-, leading to intracellular glutathione depletion and resulting in ROS accumulation, which contributes to increased lipid peroxidation, mitochondrial damage, and ultimately ferroptosis. Oxidative stress appears to crosstalk between excitotoxicity and ferroptosis, and it is essential to maintain glutamate homeostasis and inhibit oxidative stress responses in vivo. As researchers work to develop natural compounds to further investigate the complex mechanisms and regulatory functions of ferroptosis and excitotoxicity, new avenues will be available for the effective treatment of ischaemic stroke. Therefore, this paper provides a review of the molecular mechanisms and treatment of glutamate-mediated excitotoxicity and ferroptosis.