bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights from social media into public perspectives on investigative genetic genealogy
Authors: Huston Sara , Madden Diana , Villanes Andrea , Reed Nathan , Bash Brooks Whitney , Healey Christopher , Guerrini Christi
Published: January 2025

Social media sites like X (formerly Twitter) increasingly serve as spaces for the public to discuss controversial topics. Social media can spark extreme viewpoints and spread biased or inaccurate information while simultaneously allowing for debate around policy-relevant topics. The arrest of Joseph J. DeAngelo in April 2018 ignited a barrage of social media conversations on how DNA and genetic genealogy led to the suspect. These conversations continued over the following years as policies changed and as the use of the approach expanded. We examined social media coverage of investigative genetic genealogy (IGG) to characterize the volume and temporal patterns in the topics and sentiments of these public conversations. First, using a data analytics tool Brandwatch Consumer Research, we built flexible search strings to collect tweets from the social media platform Twitter/X for IGG-relevant content published from 2018 to 2022, resulting in 24,209 tweets. Second, we applied informatics tools to the dataset to generate topic clusters and analyze trends in cluster volume and distribution over time to define the top 25 peaks in tweet volume, representing the 25 events that generated the highest volume of conversation over the 5-year period. Third, drawing on the contextual framework of key IGG events, we selected three of the top ten events to code for sentiment along with a randomly sampled subset of tweets across the timeframe. Qualitative coding for position on IGG revealed a majority of tweets were supportive of the use of IGG, but key concerns were also voiced about the ethics of IGG. Over a third of conversations on Twitter/X were on either cases solved or suggestions for use of IGG. We archived the social media data for future research. These data highlight key areas of public support and concern within IGG processes and across application contexts.
Evaluation of controls, quality control assays, and protocol optimisations for PacBio HiFi sequencing on diverse and challenging samples
Authors: Bronner Iraad F. , Dawson Emma , Park Naomi , Piepenburg Olaf , Quail Michael A.
Published: January 2025

The Darwin Tree of Life (DToL) project aims to generate high-quality reference genomes for all eukaryotic organisms in Britain and Ireland. At the time of writing, PacBio HiFi reads are generated for all samples using the Sequel IIe systems by the Wellcome Sanger Institute’s Scientific Operations teams, however we expect lessons from this work to apply directly to the Revio system too, as core principles of SMRT sequencing remain the same. We observed that HiFi yield is highly variable for DToL samples. We have investigated what drives this variation, and potential mitigations. To support these investigations a number of controls were evaluated to ensure that the library and sequencing preparation procedures, reagents, consumables, and Sequel IIe instruments, were performing as expected. Our findings support that a primary factor driving variability in HiFi yield is the quality of the DNA prior to library construction, e.g., purity, size, and damage. We investigated whether quality assessment assays could link measurable DNA damage or purity to sequencing yield. Some correlation could be established, however no assay was predictive of sequencing yield for all samples, indicating that the variability is driven by multiple factors that may interact. We demonstrate that contaminants present in some samples are the cause of very low HiFi yield, and show that these contaminants can negatively affect the PacBio internal sequencing control and samples multiplexed on the same SMRT Cell. We found that consistently high yields could be obtained if an amplification workflow was utilised, namely PacBio’s ultra-low input library preparation protocol.
Differential regulation of apoptosis-related genes during long-term culture and differentiation of canine adipose-derived stem cells - a functional bioinformatical analysis
Authors: Jankowski Maurycy , Stefańska Katarzyna , Suchodolski Michał , Dompe Claudia , Wąsiatycz Grzegorz , Kempisty Bartosz , Nowicki Michał , Roszak Magdalena
Published: January 2025

Introduction

Stem cells derived from adipose tissue are gaining popularity in the field of regenerative medicine due to their adaptability and clinical potential. Their rapid growth, ability to differentiate, and easy extraction with minimal complications make adipose-derived stem cells (ADSCs) a promising option for many treatments, particularly those targeting bone-related diseases. This study analyzed gene expression in canine ADSCs subjected to long-term culture and osteogenic differentiation.

Methods

ADSCs were isolated from discarded surgical waste and cultured for 14 days with and without differentiation media to assess osteogenic changes. RNA sequencing (RNA-seq) and bioinformatical analysis were performed to obtain comprehensive transcriptomic data. A total of 17793 genes were detected and GO enrichment analysis was performed on the differentially expressed genes to identify significantly up- and downregulated Biological Process (BP) GO terms across each comparison.

Results

The upregulation of apoptosis-regulating genes and genes related to circulatory system development suggest an induction of these processes, while the downregulation of neurogenesis and gliogenesis genes points to reciprocal regulation during osteogenic differentiation of canine ADSCs.

Discussion

These findings underscore the potential of ADSCs in bone regeneration and offer valuable insights for advancing tissue engineering, however further studies, including proteomic analyses, are needed to confirm these patterns and their biological significance.
A breeding method for Ogura CMS restorer line independent of restorer source in Brassica napus
Authors: Wang Xuesong , Liang Xingyu , Wang Rui , Gao Yuan , Li Yun , Shi Haoran , Gong Wanzhuo , Saleem Saira , Zou Qiong , Tao Lanrong , Kang Zeming , Yang Jin , Yu Qin , Wu Qiaobo , Liu Hailan , Fu Shaohong
Published: January 2025

The Ogura cytoplasmic male sterility (CMS) line of Brassica napus has gained significant attention for its use in harnessing heterosis. It remains unaffected by temperature and environment and is thorough and stable. The Ogura cytoplasmic restorer line of Brassica napus is derived from the distant hybridization of Raphanus sativus L. and B. napus, but it carried a large number of radish fragments into Brassica napus, because there is no homologous allele of the restorer gene in B. napus, transferring it becomes challenging. In this study, the double haploid induction line in B. napus was used as the male parent for hybridization with the Ogura CMS of B. napus. Surprisingly, fertile plants appeared in the offspring. Further analysis revealed that the cytoplasmic type, ploidy, and chromosome number of the fertile offspring were consistent with the sterile female parent. Moreover, the mitochondrial genome similarity between the fertile offspring and the sterile female parent was 97.7% indicates that the cytoplasm of the two is the same, while the nuclear gene difference between fertile offspring and sterile female parent was only 10.33%, indicates that new genes appeared in the offspring. To further investigate and locate the restorer gene, the BSA method was employed to construct extreme mixed pools. As a result, the restorer gene was mapped to three positions: A09 chromosome 10.99–17.20 Mb, C03 chromosome 5.07–5.34 Mb, and C09 chromosome 18.78–36.60 Mb. The experimental results have proved that induction does produce restorer genes. The induction of the Ogura CMS restorer gene through DH induction line provides a promising new approach for harnessing heterosis in B. napus.
Chemokine family significance and prognostic value in colorectal cancer
Authors: Ding Yi , Chen Yinnan , Xie Siyun , Qiu Quanpeng , Guo Xiaolong , Feng Yun , Li Hongxia , Zhu Fang , Liu Yaping
Published: January 2025

Background

Colorectal cancer (CRC) poses a substantial global health concern, exhibits inconspicuous early symptoms, and is typically diagnosed at advanced stages leading to unfavorable outcomes. The intricate tumor microenvironment plays a crucial role in CRC development and progression, where chemokines contribute significantly. These chemokines exhibit widespread expression within tumor cells, facilitating immune cell infiltration, angiogenesis, and the establishment of distant metastases. The dysregulation of various chemokines in the context of CRC has emerged as a pivotal factor in the disease's pathogenesis.

Methods

To explore the relationship between chemokine gene expression and CRC patient survival, as well as to clarify their biological roles,We conducted RNA-sequencing (RNA-seq) analysis on a cohort of 88 CRC patients with tumor samples, thereby enabling a detailed exploration of chemokine involvement in CRC. This study was rigorously augmented using comprehensive datasets from The Cancer Genome Atlas (TCGA), ensuring a robust analysis of gene expression patterns associated with clinical outcomes.

Results

Through data analysis, we identified key genes from the chemokine family thought pertinent to CRC outcomes. Consequently, we constructed a novel prognostic model based on the risk score derived from these chemokine expressions. Validation against clinical metadata, executed through immunohistochemistry analysis, affirmed the relevance and accuracy of our model in predicting patient survival.

Conclusion

Our findings illuminate the critical role of chemokines in shaping the immune microenvironment of CRC, thereby highlighting potential therapeutic targets for future treatment strategies. Our new prognostic model could provide important information for the development of targeted therapies for CRC, enhancing personalized treatment approaches andultimately improving survival for CRC patients.
Single-cell transcriptome atlas of peripheral immune features to Omicron breakthrough infection under booster vaccination strategies
Authors: Zhang Yuwei , Han Shanshan , Sun Qingshuai , Liu Tao , Wen Zixuan , Yao Mingxiao , Zhang Shu , Duan Qing , Zhang Xiaomei , Pang Bo , Kou Zengqiang , Jiang Xiaolin
Published: January 2025

Introduction

The high percentage of Omicron breakthrough infection in vaccinees is an emerging problem, of which we have a limited understanding of the phenomenon.

Methods

We performed single-cell transcriptome coupled with T-cell/B-cell receptor (TCR/BCR) sequencing in 15 peripheral blood mononuclear cell (PBMC) samples from Omicron infection and naïve with booster vaccination.

Results

We found that after breakthrough infection, multiple cell clusters showed activation of the type I IFN pathway and widespread expression of Interferon-stimulated genes (ISGs); T and B lymphocytes exhibited antiviral and proinflammatory-related differentiation features with pseudo-time trajectories; and large TCR clonal expansions were concentrated in effector CD8 T cells, and clonal expansions of BCRs showed a preference for IGHV3. In addition, myeloid cells in the BA.5.2 breakthrough infection with the fourth dose of aerosolized Ad5-nCoV were characterized by enhanced proliferation, chemotactic migration, and antigen presentation.

Discussion

Collectively, our study informs the comprehensive understandings of immune characterization for Omicron breakthrough infection, revealing the positive antiviral potential induced by booster doses of vaccine and the possible "trained immunity" phenomenon in the fourth dose of aerosolized Ad5-nCoV, providing a basis for the selection of vaccination strategies.
Therapeutic effects of platelet-derived extracellular vesicles on viral myocarditis correlate with biomolecular content
Authors: Beetler Danielle J. , Giresi Presley , Di Florio Damian N. , Fliess Jessica J. , McCabe Elizabeth J. , Watkins Molly M. , Xu Vivian , Auda Matthew E. , Bruno Katelyn A. , Whelan Emily R. , Kocsis Stephen P. C. , Edenfield Brandy H. , Walker Sierra A. , Macomb Logan P. , Keegan Kevin C. , Jain Angita , Morales-Lara Andrea C. , Chekuri Isha , Hill Anneliese R. , Farres Houssam , Wolfram Joy , Behfar Atta , Stalboerger Paul G. , Terzic Andre , Cooper Leslie T. , Fairweather DeLisa
Published: January 2025

Introduction

Extracellular vesicles (EVs) can potently inhibit inflammation yet there is a lack of understanding about the impact of donor characteristics on the efficacy of EVs. The goal of this study was to determine whether the sex and age of donor platelet-derived EVs (PEV) affected their ability to inhibit viral myocarditis.

Methods

PEV, isolated from men and women of all ages, was compared to PEV obtained from women under 50 years of age, which we termed premenopausal PEV (pmPEV). Because of the protective effect of estrogen against myocardial inflammation, we hypothesized that pmPEV would be more effective than PEV at inhibiting myocarditis. We injected PEV, pmPEV, or vehicle control in a mouse model of viral myocarditis and examined histology, gene expression, protein profiles, and performed proteome and microRNA (miR) sequencing of EVs.

Results

We found that both PEV and pmPEV significantly inhibited myocarditis; however, PEV was more effective, which was confirmed by a greater reduction of inflammatory cells and proinflammatory and profibrotic markers determined using gene expression and immunohistochemistry. Proteome and miR sequencing of EVs revealed that PEV miRs specifically targeted antiviral, Toll-like receptor (TLR)4, and inflammasome pathways known to contribute to myocarditis while pmPEV contained general immunoregulatory miRs.

Discussion

These differences in EV content corresponded to the differing anti-inflammatory effects of the two types of EVs on viral myocarditis.
The emergence of DNAM-1 as the facilitator of NK cell-mediated killing in ovarian cancer
Authors: Pounds Rachel , Croft Wayne , Pearce Hayden , Hossain Tasnia , Singh Kavita , Balega Janos , Jeevan David N. , Sundar Sudha , Kehoe Sean , Yap Jason , Moss Paul , Zuo Jianmin
Published: January 2025

Introduction

Ovarian cancer (OC) is the sixth most common malignancy in women and the poor 5-year survival emphasises the need for novel therapies. NK cells play an important role in the control of malignant disease but the nature of tumour-infiltrating and peripheral NK cells in OC remains unclear.

Methods

Using flow cytometric analysis, we studied the phenotype and function of NK cells in blood, primary tumour and metastatic tissue in 80 women with OC. The cell type contexture of metastatic OC tissue was explored utilising scRNAseq analysis, with a focus on portraying an immunogenic tumour microenvironment and determining the characteristics of a dysfunctional NK cell population.

Results

The proportion of peripheral NK cells was markedly elevated with a highly activated profile and increased cytotoxicity. In contrast, NK cell numbers in primary tumour and metastasis were substantially reduced, with downregulation of activatory receptors together with elevated PD-1 expression. scRNA-Seq identified 5 NK cell subpopulations along with increased exhausted and immature NK cells within tumour tissue compared to normal tissue. These features were attenuated following chemotherapy where higher levels of activated and cytotoxic NK cells associated with improved disease-free survival. Correlation of NK cell phenotype with clinical outcomes revealed high levels of DNAM-1 expression on tissue-localised and peripheral NK cells to be associated with reduced survival. Expression of PVR, the DNAM-1 ligand, was significantly increased on tumours and DNAM-1 mediated NK cell lysis of primary tumour tissue was observed in vitro.

Discussion

These findings reveal profound modulation of the tumour tissue and systemic profile of NK cells which likely contributes to the high rates of local progression and metastasis seen with OC. Immunotherapeutic approaches that overcome local immune suppression and enhance DNAM-1-targeted lysis of OC offer the potential to improve disease control.
SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells
Authors: Bernhardt Melissa , Rech Anne , Berthold Marion , Lappe Melina , Herbel Jan-Niklas , Erhard Florian , Paschen Annette , Schilling Bastian , Schlosser Andreas
Published: January 2025

Background

The immunopeptidome is constantly monitored by T cells to detect foreign or aberrant HLA peptides. It is highly dynamic and reflects the current cellular state, enabling the immune system to recognize abnormal cellular conditions, such as those present in cancer cells. To precisely determine how changes in cellular processes, such as those induced by drug treatment, affect the immunopeptidome, quantitative immunopeptidomics approaches are essential.

Methods

To meet this need, we developed a pulsed SILAC-based method for quantitative immunopeptidomics. Metabolic labeling with lysine, arginine, and leucine enabled isotopic labeling of nearly all HLA peptides across all allotypes (> 90% on average). We established a data analysis workflow that integrates the de novo sequencing-based tool Peptide-PRISM for comprehensive HLA peptide identification with MaxQuant for accurate quantification.

Results

We employed this strategy to explore the modulation of the immunopeptidome upon MAPK pathway inhibition (MAPKi) and to investigate alterations associated with early cellular responses to inhibitor treatment and acquired resistance to MAPKi. Our analyses demonstrated significant changes in the immunopeptidome early during MAPKi treatment and in the resistant state. Moreover, we identified putative tumor-specific cryptic HLA peptides linked to these processes that might represent exploitable targets for cancer immunotherapy.

Conclusions

We have developed a new mass spectrometric approach that allowed us to investigate the effects of common MAPK inhibitors on the immunopeptidome of melanoma cells. This finally led to the discovery of new potential targets for cancer immunotherapy.
Extracellular acyl-CoA-binding protein as an independent biomarker of COVID-19 disease severity
Authors: Isnard Stephane , Mabanga Tsoarello , Royston Léna , Berini Carolina A. , Bu Simeng , Aiyana Orthy , Feng Hansen , Lebouché Bertrand , Costiniuk Cecilia T. , Cox Joseph , Kroemer Guido , Durand Madeleine , Routy Jean-Pierre ,   the Biobanque Québécoise de la COVID-19 (BQC-19)
Published: January 2025

Background

Factors leading to severe COVID-19 remain partially known. New biomarkers predicting COVID-19 severity that are also causally involved in disease pathogenesis could improve patient management and contribute to the development of innovative therapies. Autophagy, a cytosolic structure degradation pathway is involved in the maintenance of cellular homeostasis, degradation of intracellular pathogens and generation of energy for immune responses. Acyl-CoA binding protein (ACBP) is a key regulator of autophagy in the context of diabetes, obesity and anorexia. The objective of our work was to assess whether circulating ACBP levels are associated with COVID-19 severity, using proteomics data from the plasma of 903 COVID-19 patients.

Methods

Somalogic proteomic analysis was used to detect 5000 proteins in plasma samples collected between March 2020 and August 2021 from hospitalized participants in the province of Quebec, Canada. Plasma samples from 903 COVID-19 patients collected during their admission during acute phase of COVID-19 and 295 hospitalized controls were assessed leading to 1198 interpretable proteomic profiles. Levels of anti-SARS-CoV-2 IgG were measured by ELISA and a cell-binding assay.

Results

The median age of the participants was 59 years, 46% were female, 65% had comorbidities. Plasma ACBP levels correlated with COVID-19 severity, in association with inflammation and anti-SARS-CoV-2 antibody levels, independently of sex or the presence of comorbidities. Samples collected during the second COVID-19 wave in Quebec had higher levels of plasma ACBP than during the first wave. Plasma ACBP levels were negatively correlated with biomarkers of T and NK cell responses interferon-γ, tumor necrosis factor-α and interleukin-21, independently of age, sex, and severity.

Conclusions

Circulating ACBP levels can be considered a biomarker of COVID-19 severity linked to inflammation. The contribution of extracellular ACBP to immunometabolic responses during viral infection should be further studied.
The rapid infilling of a tide-dominated channel on the southern Yangtze Delta plain during the Medieval Climate Anomaly
Authors: Wu Zhuoxuan , Wang Jianwen , Nian Xiaomei , Qiu Fengyue , Wang Zhanghua
Published: January 2025

The response of ports and navigation channels in tide-dominated or tide-influenced estuaries to climate warming is of significant practical relevance. However, studies utilizing sedimentary records to understand these dynamics remain limited. This study investigates the rapid siltation of the palaeo-Qinglong channel during the Song dynasty and its relationship to climate change. Three cores were drilled in the lower reaches of the palaeo-Wusong River, and surface sediment samples were collected from the Huangpu River in the southern plain of the Yangtze Delta. Using AMS 14C and optically stimulated luminescence (OSL) dating, sedimentological and alkaline earth metal analyses, this study explores the formation and silting history of the palaeo-Qinglong channel. The results indicate that the palaeo-channel was formed about 2,000 years ago as a fluvial-dominated channel but transitioned into a tide-dominated environment, as evidenced by the prevalence of muddy sediments. Rapid siltation occurred during the 11th and 12th centuries, characterized by increased Sr content and Sr/Ba ratio, which indicate intensified salinity intrusion. This rapid infilling is attributed to the increased storm frequency during the Song dynasty, which enhanced the mud import into the channel. A brief period of strengthened fluvial processes, characterized by the occurrence of sandy bedload in the sediments near Qinglong Town, likely reflects channel regulation projects undertaken along the lower reaches of the palaeo-Wusong River during the Northern Song dynasty. The findings suggest that the climate warming and relative sea-level rise during the Medieval Climate Anomaly (MCA) amplified tidal processes in the lower palaeo-Wusong River. This study provides valuable insights into fluvial-marine interactions and their implications for managing ports and navigation channels in tidally influenced estuaries.
Gut microbiota and inflammasome-mediated pyroptosis: a bibliometric analysis from 2014 to 2023
Authors: Zhang Hang , Zhao Tian , Gu Juan , Tang Fushan , Zhu Lei
Published: January 2025

Background

The role of gut microbiota in inflammatory disease development and progression has been recognized more recently. Inflammasome-mediated pyroptosis in involved in these diseases. This complex relationship between gut microbiota and inflammasome-mediated pyroptosis provides an important field of research. Bibliometric analysis provides a comprehensive understanding of this relationship, offering valuable insights into emerging research trends.

Materials and methods

Leveraging data spanning from 2014 to 2023 sourced from the Web of Science Core Collection, our analysis was conducted using advanced tools such as SCImago Graphica, VOSviewer, and CiteSpace software. Visualizations were created using GraphPad Prism software. We explored the nuanced aspects of research hotspots, collaborative networks, and developing trends in this field.

Results

A global bibliometric analysis identified 520 relevant studies spanning 41 countries and 887 institutions. Over the past decade, publication trends have shown consistent growth, with China and the United States leading the research output. Southern Medical University and Nanjing Medical University in China emerged as leading institutions in this filed. Prominent contributors include Jia Sun, Yuan Zhang, Wei Chen, Jing Wang, and Hongtao Liu from China, alongside Eicke Latz from Germany. High-impact journals such as Frontiers in Immunology and Nature Communications have been pivotal in disseminating research in this domain. Keyword analysis highlighted a primary focus on gut microbiota, NLRP3 inflammasome, pyroptosis pathways, and inflammatory diseases, themes that persist in recent studies. Furthermore, burst keyword analysis identified “butyrate” as the sole term currently experiencing a marked increase in research interest.

Conclusion

Research has been deeply focused on the gut microbiota and inflammasome triggered pyroptosis in years. Over the past decade, the exploration of how gut microbiota and NLRP3 or NLRP6 inflammasome-mediated pyroptosis has been an area of interest. Future investigations in this filed may primarily revolve around understanding the correlation between butyrate and NLRP3 inflammasome induced pyroptosis in relation to conditions. However, an in-depth analysis, through studies is crucial to uncover and elucidate the complex mechanisms linking these elements.
The response of soil microbial community to application of organic amendment to saline land
Authors: Cong Peifei , Huang Pengfei , Huang Zhisheng
Published: January 2025

Introduction

The salinization of coastal soils is a primary cause of global land degradation. The aim of this study was to evaluate the effect of organic amendment on the soil microbial community within a saline gradient.

Methods

The study was designed with five levels of electrical conductivity (EC): 0.33, 0.62, 1.13, 1.45 and 2.04 ds m−1. By conducting indoor potted plant experiments, determine the effects of applying microbial organic fertilizer on the physicochemical properties of soil and the structure of soil microbial communities under different salinity concentrations.

Results

Compared with the control, higher OM content, total N, and higher crop biomass were observed in samples with organic amendment at the same salinity level. At the same salinity levels, the mean bacterial activity (AUC) and the mean number of substrates were higher than in the soil without organic amendment according to analyses by means of Biolog ECO MicroPlate. The results of canonical correspondence analysis indicate that after the application of organic amendments, the composition of loam and clay replaces soil pH, and aboveground biomass replaces root biomass as key indicators closely monitoring Community level physiological profiling (CLPP). In soil with the same salinity level, the application of microbial organic fertilizer led to an increase in the proportion of Actinobacteriota and a decrease in the proportion of Chloroflexi. In 0.3dS m-1 soil, the abundance of actinomycetes increased from 23% to 27% after application of microbial organic fertilizer, while the abundance of basidiomycetes decreased from 20% to 6%. In addition, after the application of microbial organic fertilizer, RB41, blastococcus and solirubrobacter significantly increased, while Melothermus and Herpetosiphon significantly decreased.

Discussion

This study provides a strong theoretical basis for using microbial organic fertilizers to improve saline-alkali soil.
MicroRNA-3145 as a potential therapeutic target for hepatitis B virus: inhibition of viral replication via downregulation of HBS and HBX
Authors: Muchtar Amrizal , Onomura Daichi , Ding Dan , Nishitsuji Hironori , Shimotohno Kunitada , Okada Shunpei , Ueda Keiji , Watashi Koichi , Wakita Takaji , Iida Kei , Yoshiyama Hironori , Iizasa Hisashi
Published: January 2025

Current treatments for hepatitis B virus (HBV), such as interferons and nucleic acid analogs, have limitations due to side effects like depression and the development of drug-resistant mutants, highlighting the need for new therapeutic approaches. In this study, we identified microRNA-3145 (miR-3145) as a host-derived miRNA with antiviral activity that is upregulated in primary hepatocytes during HBV infection. The expression of its precursor, pri-miR-3145, increased in response to the the virus infection, and miR-3145 downregulated the hepatitis B virus S (HBS) antigen and hepatitis B virus X (HBX), thereby inhibiting viral replication. The binding site for miR-3145 was located in the HBV polymerase (pol) region, as experimentally confirmed. Moreover, overexpression of HBS and HBX induced pri-miR-3145 expression through endoplasmic reticulum stress. The expression of pri-miR-3145 showed a strong correlation with the Nance–Horan syndrome-like 1 (NHSL1) gene, as it is encoded within an intron of NHSL1, and higher NHSL1 expression in hepatocellular carcinoma patients with HBV infection was associated with better prognosis. These findings suggest that miR-3145-3p, along with small molecules targeting its binding sites, holds promise as a potential therapeutic candidate for HBV treatment.
Structures and determinants of soil microbiomes along a steep elevation gradient in Southwest China
Authors: Li Ting , Gao Ziyan , Zhou Ping , Huang Mingmin , Wang Gangzheng , Xu Jianping , Deng Wangqiu , Wang Mu
Published: January 2025

Soil microbial communities play a vital role in accelerating nutrient cycling and stabilizing ecosystem functions in forests. However, the diversity of soil microbiome and the mechanisms driving their distribution patterns along elevational gradients in montane areas remain largely unknown. In this study, we investigated the soil microbial diversity along an elevational gradient from 650 m to 3,800 m above sea level in southeast Tibet, China, through DNA metabarcode sequencing of both the bacterial and fungal communities. Our results showed that the dominant bacterial phyla across elevations were Proteobacteria, Acidobacteriota and Actinobacteriota, and the dominant fungal phyla were Ascomycota and Basidiomycota. The Simpson indices of both soil bacteria and fungi demonstrated a hollow trend along the elevational gradient, with an abrupt decrease in bacterial and fungal diversity at 2,600 m a.s.l. in coniferous and broad-leaved mixed forests (CBM). Soil bacterial chemoheterotrophy was the dominant lifestyle and was predicted to decrease with increasing elevation. In terms of fungal lifestyles, saprophytic and symbiotic fungi were the dominant functional communities but their relative abundance was negatively correlated with increasing elevation. Environmental factors including vegetation type (VEG), altitude (ALT), soil pH, total phosphorus (TP), nitrate nitrogen (NO3−-N), and polyphenol oxidase (ppo) all exhibited significant influence on the bacterial community structure, whereas VEG, ALT, and the carbon to nitrogen ratio (C/N) were significantly associated with the fungal community structure. The VPA results indicated that edaphic factors explained 37% of the bacterial community variations, while C/N, ALT, and VEG explained 49% of the total fungal community variations. Our study contributes significantly to our understanding of forest ecosystems in mountainous regions with large elevation changes, highlighting the crucial role of soil environmental factors in shaping soil microbial communities and their variations in specific forest ecosystems.
Iron-oxidizing microorganisms affect the iron-bound organic carbon in the subsoil of alpine grassland during the thawing of seasonal frozen soil
Authors: Tian Yuxin , Abulaizi Maidinuer , Yang Zailei , Kou Tianle , Jia Yuanbin , Hu Yunpeng , Chen Mo , Jia Hongtao
Published: January 2025

Iron (Fe) minerals possess a huge specific surface area and high adsorption affinity, usually considered as “rust tanks” of organic carbon (OC), playing an important role in global carbon storage. Microorganisms can change the chemical form of Fe by producing Fe-chelating agents such as side chains and form a stable complex with Fe(III), which makes it easier for microorganisms to use. However, in seasonal frozen soil thawing, the succession of soil Fe-cycling microbial communities and their coupling relationship with Fe oxides and Fe-bound organic carbon (Fe-OC) remains unclear. We characterized changes in the Fe phase, Fe-OC, Fe-oxidizing bacteria (FeOB), and Fe-reducing bacteria (FeRB) in the subsoil and analyzed the microbial mechanism underlying Fe-OC changes in alpine grassland by constructing a composite structural equation model (SEM). We found that the Fe(III) content consistently exceeded that of Fe(II). Among the three types of Fe oxides, organically complex Fe (Fep) decreased from 2.54 to 2.30 g·kg−1, whereas the opposite trend was observed for poorly crystalline Fe (Feo). The Fe-OC content also decreased (from 10.31 to 9.47 g·kg−1; p < 0.05). Fe-cycling microorganisms were markedly affected by the thawing of frozen soil (except FeRB). Fep and Feo directly affected changes in Fe-OC. Soil moisture (SM) and FeOB were significant indirect factors affecting Fe-OC changes. Freeze–thaw changes in the subsoil of alpine grassland in Central Asia significantly affected FeOB and Fe oxides, thus affecting the Fe-OC content. To the best of our knowledge, this was the first study to examine the influence of Fe-cycling microorganisms on the Fe phase and Fe-OC in the soil of alpine grassland in Central Asia. Overall, our findings provide scientific clues for exploring the biogeochemical cycle process in future climate change.
MSGU-Net: a lightweight multi-scale ghost U-Net for image segmentation
Authors: Cheng Hua , Zhang Yang , Xu Huangxin , Li Dingliang , Zhong Zejian , Zhao Yinchuan , Yan Zhuo
Published: January 2025

U-Net and its variants have been widely used in the field of image segmentation. In this paper, a lightweight multi-scale Ghost U-Net (MSGU-Net) network architecture is proposed. This can efficiently and quickly process image segmentation tasks while generating high-quality object masks for each object. The pyramid structure (SPP-Inception) module and ghost module are seamlessly integrated in a lightweight manner. Equipped with an efficient local attention (ELA) mechanism and an attention gate mechanism, they are designed to accurately identify the region of interest (ROI). The SPP-Inception module and ghost module work in tandem to effectively merge multi-scale information derived from low-level features, high-level features, and decoder masks at each stage. Comparative experiments were conducted between the proposed MSGU-Net and state-of-the-art networks on the ISIC2017 and ISIC2018 datasets. In short, compared to the baseline U-Net, our model achieves superior segmentation performance while reducing parameter and computation costs by 96.08 and 92.59%, respectively. Moreover, MSGU-Net can serve as a lightweight deep neural network suitable for deployment across a range of intelligent devices and mobile platforms, offering considerable potential for widespread adoption.
Iconography of abnormal non-neuronal cells in pediatric focal cortical dysplasia type IIb and tuberous sclerosis complex
Authors: Zhang Joyce , Argueta Deneen , Tong Xiaoping , Vinters Harry V. , Mathern Gary W. , Cepeda Carlos
Published: January 2025

Once believed to be the culprits of epileptogenic activity, the functional properties of balloon/giant cells (BC/GC), commonly found in some malformations of cortical development including focal cortical dysplasia type IIb (FCDIIb) and tuberous sclerosis complex (TSC), are beginning to be unraveled. These abnormal cells emerge during early brain development as a result of a hyperactive mTOR pathway and may express both neuronal and glial markers. A paradigm shift occurred when our group demonstrated that BC/GC in pediatric cases of FCDIIb and TSC are unable to generate action potentials and lack synaptic inputs. Hence, their role in epileptogenesis remained obscure. In this review, we provide a detailed characterization of abnormal non-neuronal cells including BC/GC, intermediate cells, and dysmorphic/reactive astrocytes found in FCDIIb and TSC cases, with special emphasis on electrophysiological and morphological assessments. Regardless of pathology, the electrophysiological properties of abnormal cells appear more glial-like, while others appear more neuronal-like. Their morphology also differs in terms of somatic size, shape, and dendritic elaboration. A common feature of these types of non-neuronal cells is their inability to generate action potentials. Thus, despite their distinct properties and etiologies, they share a common functional feature. We hypothesize that, although the exact role of abnormal non-neuronal cells in FCDIIb and TSC remains mysterious, it can be suggested that cells displaying more glial-like properties function in a similar way as astrocytes do, i.e., to buffer K+ ions and neurotransmitters, while those with more neuronal properties, may represent a metabolic burden due to high energy demands but inability to receive or transmit electric signals. In addition, due to the heterogeneity of these cells, a new classification scheme based on morphological, electrophysiological, and gene/protein expression in FCDIIb and TSC cases seems warranted.
Hypercoagulable states in young adults with ischemic stroke in a Stroke Belt state: a retrospective study
Authors: Gordon David Lee , Durica Sarah R.
Published: January 2025

We theorize that the southeastern United States has a higher stroke mortality rate and higher recurrent ischemic stroke rate than the rest of the United States due to (1) an increased prevalence of hypercoagulable states among young adults in the region, (2) failure to diagnose hypercoagulable states as the cause of ischemic stroke in young adults, and (3) underutilization of anticoagulation for ischemic stroke secondary prevention in young adults with hypercoagulable states. In an attempt to investigate this hypothesis, we conducted a retrospective chart review of 311 inpatients with first-ever ischemic stroke from age 18 to 55 years at an Oklahoma academic medical center from 1 July 2011 to 30 April 2017. Using Chi-squared test, we compared the stroke etiologic diagnosis of the attending neurologist at discharge—when hypercoagulable profile results were rarely available—to the diagnosis of a vascular neurologist postdischarge who had access to all available etiologic test results. The inpatient neurologists identified the stroke etiology as hypercoagulable state in 79 patients (25.57%) and undetermined etiology in 105 (33.98%). With the benefit of final hypercoagulable profile results, the postdischarge vascular neurologist identified the stroke etiology as hypercoagulable state in 167 (54.22%, 95% CI 48.64–59.70%, p-value <2.2e-16) and undetermined etiology in 28 (9.09%, 95% CI 6.36–12.83%, p-value 1.03e-14). There was no significant change in the proportion of ischemic strokes classified under all other stroke etiologies. We conclude that hypercoagulable states are a common and underrecognized cause of ischemic stroke in young adults in the U.S. Stroke Belt.
Applicability of a serodiagnostic line blot for idiopathic inflammatory myopathy: the muscle biopsy is not all
Authors: Fontana Pedro Nogueira , da Silva Vinícius Gomes , Corazzini Roseli , Athayde Natália Merten , Ferreira da Silva Ana Marina Dutra , Brockhausen Igor , Correia Carolina da Cunha , Sobreira Cláudia Ferreira da Rosa , Tomaselli Pedro José , Petean Flávio , de Oliveira Rodrigo , Feitoza Pablo Vinícius , Moraes Soane Michel , Saraiva Natália , Hidalgo Rafaela , Fideles Cláudia , Feder David , Carvalho Alzira Alves de Siqueira
Published: January 2025

Introduction

Differential diagnosis of rare idiopathic inflammatory myopathies (IIM) is mainly based on clinical aspects, muscle biopsy analysis, and auxiliary assays that determine myositis-specific and associated autoantibodies (MSA and MAA). While MSAs are considered specific for their respective IIM subclass, MAAs can be present in more than one subclass and in other conditions. This study compares results of a multispecific line blot assay with the final diagnosis of IIM patients based on clinical features and muscle biopsy to draw conclusions for the test's applicability in the diagnostic workflow.

Methods

Samples from patients (n = 50) diagnosed with various forms of IIM, including patients (n = 5) with other myopathies, were analyzed using the EUROLINE Autoimmune Inflammatory Myopathies 16 Ag (IgG), an anti-HMGCR (IgG) line blot, and the Anti-cN-1A ELISA (IgG, all EUROIMMUN).

Results

MSA and MAA were detected in 74.0% (37/50) of sera and were concordant with the final diagnosis in 64.8% (24/37), discordant in 16.2% (6/37) and not evaluable in 18.9% (7/37) of cases. In 100% (5/5) of patients with other myopathies, no MSA was found. MSA/MAA-co-positivity was observed in 18.0% (9/50) of patients. In 30.0% (15/50) of cases, the muscle biopsy analysis was essential to establish the final diagnosis.

Conclusion

The agreement between serodiagnostic results and final diagnosis highlights the applicability of the EUROIMMUN myositis-related diagnostic test as first line diagnostic tool in the IIM diagnosis workflow and suggests morphological analysis in cases of inconclusive or negative serology. However, results of diagnostic assays shall always be interpreted in combination with clinical features.
NORDIC denoising on VASO data
Authors: Knudsen Lasse , Vizioli Luca , De Martino Federico , Faes Lonike K. , Handwerker Daniel A. , Moeller Steen , Bandettini Peter A. , Huber Laurentius
Published: January 2025

The use of submillimeter resolution functional magnetic resonance imaging (fMRI) is increasing in popularity due to the prospect of studying human brain activation non-invasively at the scale of cortical layers and columns. This method, known as laminar fMRI, is inherently signal-to-noise ratio (SNR)-limited, especially at lower field strengths, with the dominant noise source being of thermal origin. Furthermore, laminar fMRI is challenged with signal displacements due to draining vein effects in conventional gradient-echo blood oxygen level-dependent (BOLD) imaging contrasts. fMRI contrasts such as cerebral blood volume (CBV)-sensitive vascular space occupancy (VASO) sequences have the potential to mitigate draining vein effects. However, VASO comes along with another reduction in detection sensitivity. NOise Reduction with DIstribution Corrected (NORDIC) PCA (principal component analysis) is a denoising technique specifically aimed at suppressing thermal noise, which has proven useful for increasing the SNR of high-resolution functional data. While NORDIC has been examined for BOLD acquisitions, its application to VASO data has been limited, which was the focus of the present study. We present a preliminary analysis to evaluate NORDIC’s capability to suppress thermal noise while preserving the VASO signal across a wide parameter space at 3T. For the data presented here, with a proper set of parameters, NORDIC reduced thermal noise with minimal bias on the underlying signal and preserved spatial resolution. Denoising performance was found to vary with different implementation strategies and parameter choices, for which we provide recommendations. We conclude that when applied properly, NORDIC has the potential to overcome the sensitivity limitations of laminar-specific VASO fMRI. Since very few groups currently have 3T VASO data, by sharing our analysis and code, we can compile and compare the effects of NORDIC across a broader range of acquisition parameters and study designs. Such a communal effort will help develop robust recommendations that will increase the utility of laminar fMRI at lower field strengths.
Alternations of interhemispheric functional connectivity in patients with acute acquired concomitant esotropia: a resting state fMRI study using voxel-mirrored homotopic connectivity
Authors: Chen Jiayu , Hao Jie , Liu Jiawen , Li Huijian , Meng Zhaojun , Fu Jing
Published: January 2025

Purpose

To investigate the changes in cerebral hemispheric functional connections in patients with acute acquired concomitant esotropia (AACE) and their relationship with clinical manifestations, utilizing voxel-mirrored homotopic connectivity (VMHC).

Methods

A prospective, observational study was conducted involving 32 AACE patients and 31 age-, sex-, and education-matched healthy controls (HC). The resting-state functional magnetic resonance imaging (rs-fMRI) signals, binocular vision function, and psychometric scale scores were collected rs-fMRI data and structural image data were analyzed for VMHC, and a two-sample t-test was used to analyze the differences in VMHC between groups. Spearman correlation analysis evaluated the relationship between fMRI indicators and clinical features.

Results

There was no statistical difference between the two groups concerning sex, age, height and weight. VMHC levels in the superior frontal gyrus and anterior cingulate were significantly lower in the AACE group (p < 0.05). In the AACE group, the VMHC values of the left caudate positively correlated with near vision work duration (r = 0.381, p = 0.034), the deviation angles at near (r = 0.428, p = 0.015) and at distance (r = 0.416, p = 0.018). The VMHC values in the bilateral olfactory cortex also positively correlated with the near vision work duration (Right: r = 0.389, p = 0.031; Left: r = 0.372, p = 0.039) while Beck Depression Inventory (BDI) scores negatively correlated with the VMHC values of the left olfactory cortex (r = −0.359, p = 0.048).

Conclusion

The dysfunction of the medial frontal gyrus and anterior cingulate gyrus is the underlying neuropathological mechanism of AACE, and these dysfunctions may be related to poor eye habits and the severity of deviation.
Comparative efficacy of neuroprotective agents for improving neurological function and prognosis in acute ischemic stroke: a network meta-analysis
Authors: Wang Yuchen , Li Mengqi , Jiang Yuye , Ji Qiuhong
Published: January 2025

Background

Ischemic stroke is the second leading cause of death and the third leading cause of combined disability and mortality globally. While reperfusion therapies play a critical role in the management of acute ischemic stroke (AIS), their applicability is limited, leaving many patients with significant neurological deficits and poor prognoses. Neuroprotective agents have garnered attention for their potential as adjunct therapies; however, their relative efficacy remains unclear. This study utilized a network meta-analysis (NMA) to systematically compare the efficacy of neuroprotective agents in improving neurological function and prognosis in stroke patients.

Methods

This study adhered to PRISMA guidelines and the Cochrane Handbook for systematic reviews. Randomized controlled trials (RCTs) were identified through comprehensive searches of the PubMed, Embase, and Cochrane Library databases. Two independent reviewers conducted the selection process, data extraction, and quality assessment. Outcomes included 90-day modified Rankin Scale (90d-mRS), change of National Institutes of Health Stroke Scale score from baseline to 90-day/14-day/7-day (90d/14d/7d-NIHSS) and 90-day/14-day Barthel Index (90d/14d-BI). Data analyses were performed using RevMan 5.4 and Stata 14.0.

Results

A total of 42 RCTs involving 12,210 participants were included in this analysis. The interventions assessed included Cerebrolysin, Citicoline, Edaravone, Edaravone Dextranol, Human urinary kallidinogenase, Minocycline, Nerinetide, Butylphthalide, Vinpocetine, and Control. The NMA results demonstrated that NBP ranked highest for the 90d-mRS, 90d-NIHSS, 14d-NIHSS, and 14d-BI outcomes. Edaravone was found to be the most effective intervention for the 7d-NIHSS and 90d-BI outcomes.

Conclusion

The findings of this study indicate that different neuroprotective agents exhibit distinct advantages at specific stages of recovery. NBP showed outstanding performance in improving 90d-mRS and 90d-NIHSS, underscoring its potential in long-term rehabilitation. Edaravone demonstrated significant superiority in 7d-NIHSS scores, highlighting its role in early neuroprotection. These results provide valuable insights for individualized clinical treatment. To further validate the efficacy and safety of neuroprotective agents, future studies should involve larger sample sizes and conduct multicenter, large-scale randomized controlled trials.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=601346, identifier CRD42024601346.