bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bronchoalveolar lavage fluid and lung biopsy tissue metagenomic next-generation sequencing in the diagnosis of pulmonary cryptococcosis
Authors: Huang Jinbao , Weng Heng , Ye Ling , Jiang Meiqin , Chen Lulu , Li Yangyu , Li Hongyan 
Published: October 2024

ObjectiveTo evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens.MethodsIn this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared.ResultsAmong the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%–91.7%), 98.7% (95% CI, 96.4%–99.6%), and 97.2% (95% CI, 94.7%–98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P &gt; 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046).ConclusionThe sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC.
Achieving land degradation neutrality: land-use planning and ecosystem approach
Authors: Saik Pavlo , Koshkalda Iryna , Bezuhla Liudmyla , Stoiko Nataliia , Riasnianska Alona 
Published: October 2024

IntroductionThe research purpose is to scientifically substantiate an integrated approach to solving the problem of land degradation, based on the idea of land degradation neutrality (LDN), taking into account ecosystem services when planning land use to maximize the conservation of natural capital. The methodological basis of the research is the provisions and principles of the concepts of sustainable development, achieving LDN, and ecosystem services, as well as the research results revealing various aspects of land use, particularly their degradation.MethodsThe following research methods are used in the paper: dialectical – to determine the cause-and-effect conditions of land degradation; analysis – to highlight the current state of land use in Ukraine and the factors that have led to land degradation; synthesis – for global trends towards achieving LDN; deduction – to explore the possibility of introducing global experience in achieving LDN in Ukraine; structural-functional analysis – to substantiate the feasibility of introducing an ecosystem approach to land-use planning to achieve LDN.ResultsAs a result of the research, the current land degradation state in Ukraine has been analyzed, and ways of achieving LDN in land-use planning through the prism of an ecosystem approach have been substantiated. Based on statistical data, the current and potential levels of arability of the territory of Ukraine have been calculated by natural-climatic zones, and the areas of eroded arable lands in Ukraine have been determined by the erodibility factor (low-eroded, mediumeroded,and highly-eroded).DiscussionFor the first time, a structural-logical scheme has been developed for organizational-economic support for the effective use of degraded and low-productive agricultural lands in the context of implementing the idea of LDN, which is a tool for rational allocation and use of degraded lands. This scheme can serve as a basis for the development of land-use planning strategies for territorial communities, for institutions, and organizations competent in the field of land management.
Agricultural carbon emissions in China: measurement, spatiotemporal evolution, and influencing factors analysis
Authors: Huang Xiujing , Wu Xinyu , Guo Xiaoyang , Shen Yang 
Published: October 2024

IntroductionThe agricultural sector is the second largest emitter of greenhouse gases, accounting for 23% of global anthropogenic carbon emissions. Analysis of the basic state of carbon emissions from China's agriculture is helpful to achieve carbon reduction targets.MethodsAgricultural carbon emissions were calculated using the emission factor method, based on data from the China Rural Statistical Yearbook and various provincial statistical yearbooks. To analyze spatial patterns, the standard deviation ellipse method and the center of gravity migration model were employed, uncovering the migration path of agricultural carbon emissions. Regional disparities and the driving factors of agricultural carbon emissions were further examined using the Theil index and the Logarithmic Mean Divisia Index (LMDI) model.ResultsThe analysis indicated that the emissions center has gradually shifted towards the central and western regions, reflecting changes in agricultural production activity areas. Intraregional differences are the primary contributors to the imbalance in agricultural carbon emissions, with pronounced disparities in grain production and consumption balance regions. Key influencing factors include agricultural production efficiency, adjustments in agricultural industrial structure, economic structure and output, and urbanization levels. The economic output effect and urbanization effect are identified as the main drivers of increased carbon emissions, while declining production efficiency has hindered emission reduction efforts.ConclusionThe findings provide valuable insights for regional management and policymaking in China's agricultural sector, highlighting the need to enhance production efficiency and optimize agricultural structure to reduce emissions.
Drivers of greenhouse gas emissions in agricultural soils: the effect of residue management and soil type
Authors: Singh Dharmendra , Lenka Sangeeta , Kanwar Rameshwar S. , Yadav Shashi S. , Saha Madhumonti , Sarkar Abhijit , Yadav Dinesh Kumar , Vassanda Coumar M. , Lenka Narendra Kumar , Adhikari Tapan , Jadon Priyanka , Gami Vijay 
Published: October 2024

Developing successful mitigation strategies for greenhouse gases (GHGs) from crop residue returned to the soil can be difficult due to an incomplete understanding of factors controlling their magnitude and direction. Therefore, this study investigates the effects of varying levels of wheat residue (WR) and nutrient management on GHGs emissions (CO2, N2O, and CH4) across three soil types: Alfisol, Vertisol, and Inceptisol. A combination of laboratory-based measurements and a variety of data analysis techniques was used to assess the GHG responses under four levels of WR inputs (0, 5, 10, and 15 Mg/ha; WR0, WR5, WR10, and WR15) and three levels of nutrient (NP0: no nutrient, NP1: nutrients (N and P) were added to balance the residue C/nutrient stoichiometry of C/N/P= 100: 8.3: 2.0 to achieve 30% stabilization of added residue C input at 5 Mg/ha (R5), and NP2: 3 × NP1). The results of this study clearly showed that averaged across residue and nutrient input, Inceptisol showed negative N2O flux, suggesting consumption which was supported by its high legacy phosphorus (19.7 mg kg⁻1), elevated pH (8.49), and lower clay content (13%), which reduced microbial activity, as indicated by lower microbial biomass carbon (MBC) and alkaline phosphatase (Alk-P) levels. N2O emissions were more responsive to nutrient inputs, particularly in Vertisol under high WR (15 Mg/ha) input, while CH4 fluxes were significantly reduced under high residue inputs, especially in Vertisol and Inceptisol. Alfisol exhibited the highest total carbon mineralization and GWP, with cumulative GWP being 1.2 times higher than Vertisol and 1.4 times higher than Inceptisol across residue and nutrient input. The partial least square (PLS) regression revealed that anthropogenic factors significantly influenced CO2 and N2O fluxes more than CH4. The anthropogenic drivers contributed 62% and 44% of the variance explained for N2O and CH4 responses. Our study proves that different biogeochemical mechanisms operate simultaneously depending on the stoichiometry of residue C and nutrients influencing soil GHG responses. Our findings provide insight into the relative contribution of anthropogenic and natural drivers to agricultural GHG emissions, which are relevant for developing process-based models and addressing the broader challenge of climate change mitigation through crop residue management.
Number of human protein interactions correlates with structural, but not regulatory conservation of the respective genes
Authors: Mekic Rijalda , Zolotovskaia Marianna A. , Sorokin Maksim , Mohammad Tharaa , Shaban Nina , Musatov Ivan , Tkachev Victor , Modestov Alexander , Simonov Alexander , Kuzmin Denis , Buzdin Anton 
Published: October 2024

IntroductionThe differential ratio of nonsynonymous to synonymous nucleotide substitutions (dN/dS) is a common measure of the rate of structural evolution in proteincoding genes. In addition, we recently suggested that the proportion of transposable elements in gene promoters that host functional genomic sites serves as a marker of the rate of regulatory evolution of genes. Such functional genomic regions may include transcription factor binding sites and modified histone binding loci.MethodsHere, we constructed a model of the human interactome based on 600,136 documented molecular interactions and investigated the overall relationship between the number of interactions of each protein and the rate of structural and regulatory evolution of the corresponding genes.ResultsBy evaluating a total of 4,505 human genes and 1,936 molecular pathways we found a general correlation between structural and regulatory evolution rate metrics (Spearman 0.08–0.16 and 0.25–0.37 for gene and pathway levels, respectively, p &lt; 0.01). Further exploration revealed in the established human interactome model lack of correlation between the rate of gene regulatory evolution and the number of protein interactions on gene level, and weak negative correlation (∼0.15) on pathway level. We also found a statistically significant negative correlation between the rate of gene structural evolution and the number of protein interactions (Spearman −0.11 and −0.3 for gene and pathway levels, respectively, p &lt; 0.01).DiscussionOur result suggests stronger structural rather than regulatory conservation of genes whose protein products have multiple interaction partners.
Alpha-Pinene-encapsulated lipid nanoparticles diminished inflammatory responses in THP-1 cells and imiquimod-induced psoriasis-like skin injury and splenomegaly in mice
Authors: Li Tao-Yu , Liang Wan-Li , Zhao Yi-Ming , Chen Wan-Dong , Zhu Hong-Xia , Duan Yuan-Yuan , Zou Han-Bo , Huang Sha-Sha , Li Xiao-Jun , Zhang Wei Kevin 
Published: October 2024

IntroductionPsoriasis, a persistent skin condition caused by the disorder of the immune system, impacts approximately 1.25 million individuals globally. Nevertheless, the presence of adverse effects in conventional clinical drugs necessitates further exploration of novel medications or combination therapies to mitigate these reactions and enhance their effectiveness.MethodsHence, our intention here in this paper is to utilize the lipid nanoparticle delivery system for overcoming the volatility and hydrophobic properties of α-pinene, a naturally occurring compound renowned for its anti-inflammatory and antiviral effects, and further explore its potential pharmacological applications both in vitro and in vivo.ResultsThe production of α-pinene lipid nanoparticles (APLNs) was achieved through the utilization of high pressure homogenization methods. APLNs was successfully fabricated with enhanced stability and water solubility. Meanwhile, the application of APLNs could drastically reduce the expression of lipopolysaccharide (LPS)-induced inflammation-related factors in THP-1 cells. Administration of APLNs to a mouse model of auricular swelling could effectively reduce redness and swelling in the auricles of mice as well. Furthermore, APLNs were also found to alleviate skin damage in mice with Imiquimod (IMQ)-induced psoriasis model, as well as decrease the levels of psoriasis-related protein nuclear factor kappa-B (NF-κB) and interleukin-17 (IL-17), interleukin-23 (IL-23), and other inflammation-related cytokines. More importantly, utilization of APLNs successfully mitigated the systemic inflammatory reactions in mice, resulting in the reduction of spleen-to-body ratio (wt%) and of inflammatory cytokines’ expression in the serum.DiscussionOverall, our results suggest that with the help of lipid nanoparticle encapsulation, APLNs possess a better pharmacological effect in anti-inflammation and could potentially serve as an anti-psoriasis drug.
Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis
Authors: Pappa Theodora , Rivas Ariel L. , Iandiorio Michelle J. , Hoogesteijn Almira L. , Fair Jeanne M. , Rojas Gil Andrea Paola , Burriel Angeliki R. , Bagos Pantelis G. , Chatzipanagiotou Stylianos , Ioannidis Anastasios 
Published: October 2024

IntroductionData overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis.MethodsBlood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions.ResultsThe reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named ‘early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other’). Mortality data validated these labels: both ‘suppression’ subsets revealed 100% mortality, the ‘immunocompetence’ group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the ‘intermediary’ suppression expressed an impaired monocyte-related function, the ‘late’ suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine.DiscussionThe data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the ‘other’ group, additional studies are recommended.
YTHDC1 Regulates the Migration, Invasion, Proliferation, and Apoptosis of Rheumatoid Fibroblast-Like Synoviocytes
Authors: Feng Zhi-wei , Yang Chen-fei , Xiao He-fang , Yuan Fa , Chen Feng , Zhang Bo , Zhang Jun , Tan Min , Guo Ming-gang 
Published: October 2024

BackgroundRheumatoid arthritis (RA), a chronic autoimmune condition, is characterized by persistent synovial inflammation, bone degradation, and progressive joint deterioration. Despite considerable research efforts, the precise molecular mechanism underlying RA remains elusive. This investigation aims to elucidate the potential role and molecular mechanism of N6-methyladenosine (m6A) methylation regulators in the pathogenesis of RA.MethodsIn this study, we employed bioinformatics tools to elucidate the association between RA and m6A modifications, aiming to identify potential biological markers. We extracted datasets GSE12021, GSE55235, and GSE55457 from the Gene Expression Omnibus (GEO) database for comprehensive analysis. Utilizing differential expression analysis, protein-protein interaction (PPI) analysis, and single-cell sequencing techniques, we identified pivotal hub genes implicated in the pathogenesis of RA. Subsequently, we assessed the correlation between these hub genes and the pathogenesis of RA using Gene Set Enrichment Analysis (GSEA). Both in vivo and in vitro experiments were performed to confirm the expression and functional roles of the identified key hub gene in RA.ResultsDifferential expression analysis, PPI analysis, and single-cell analysis identified three key hub genes (YTHDC1, YTHDC2, and YTHDF2) associated with RA. GSEA results further revealed that these genes are enriched in pathways associated with inflammatory responses. Subsequent correlation analysis demonstrated a significant negative correlation between YTHDC1 expression and CD8+ T cell levels. Notably, the gene and protein expression levels of YTHDC1 and YTHDF2 were significantly reduced in the synovial tissue of RA patients. Furthermore, silencing YTHDC1 in fibroblast-like synoviocytes (FLSs) significantly inhibited their migration, invasion, proliferation, and induced apoptosis.ConclusionYTHDC1 may potentially be involved in the pathogenesis of RA through its regulation of migration, invasion, proliferation, and apoptosis in FLSs.
An early HMGB1 rise 12 hours before creatinine predicts acute kidney injury and multiple organ failure in a smoke inhalation and burn swine model
Authors: Yang Zhangsheng , Cancio Tomas S. , Willis Robert P. , Young Matthew D. , Kneifel Dustin M. , Salinas Jose , Meyer Andrew D. 
Published: October 2024

BackgroundAcute kidney injury (AKI) and multiple organ failure (MOF) are leading causes of mortality in trauma injuries. Early diagnosis of AKI and MOF is vital to improve outcomes, but current diagnostic criteria rely on laboratory markers that are delayed or unreliable. In this study, we investigated whether damage associated molecular patterns such as high-mobility group box 1 (HMGB1), syndecan-1 (SDC-1) and C3a correlate with the development of trauma-induced AKI and MOF. MethodsThirty-nine swine underwent smoke inhalation and severe burns, then received critical care for 72 hours or until death. AKI was defined by the KDIGO (Kidney Disease: Improving Global Outcomes) criteria, which labels AKI when a 1.5-fold increase in blood creatinine levels from baseline or a urine output &lt; 0.5 mL/kg/h for 6 hours or more occurs. MOF was defined by the presence of both AKI and acute respiratory distress syndrome (PaO2/FiO2&lt;300 for 4 hours). ResultsEight of 39 pigs developed AKI and seven of those developed MOF. Pathological analysis revealed that polytrauma induces significantly higher kidney injury scores compared to sham controls. The average time from injury to KDIGO AKI was 24 hours (interquartile range: 22.50-32.25). Twelve hours after injury, HMGB1 levels were significantly increased in animals that went on to develop AKI compared to those that did not (73.07 ± 18.66 ng/mL vs. 31.64 ± 4.15 ng/mL, p&lt;0.01), as well as in animals that developed MOF compared to those that did not (81.52±19.68 ng/mL vs. 31.19 ± 3.972 ng/mL, p&lt;0.05). SDC-1 and C3a levels were not significantly different at any time point between groups. ROC analysis revealed that HMGB1 levels at 12 hours post-injury were predictive of both AKI and MOF development (AKI: AUROC=0.81, cut-off value=36.41 ng/mL; MOF: AUROC=0.89, cut-off value=36.41 ng/mL). Spearman’s correlation revealed that HMGB1 levels at 12 hours correlated with multiple parameters of AKI, including blood urea nitrogen, blood creatinine, and blood myoglobin. ConclusionTwelve-hour post-injury HMGB1 levels predict AKI and MOF in a smoke inhalation and burn swine model. Further research is needed to validate this result in other polytrauma models and in critical combat causalities.
Arterial blood gases in SCUBA divers at depth
Authors: Paganini Matteo , Zucchi Lorenzo , Giacon Tommaso Antonio , Martani Luca , Mrakic-Sposta Simona , Garetto Giacomo , McKnight J. Chris , Camporesi Enrico M. , Moon Richard E. , Bosco Gerardo 
Published: October 2024

BackgroundCurrent diving physiology postulates that SCUBA divers’ arterial blood gas (ABG) levels vary proportionally to environmental pressure, but, to date, ABGs have only been obtained during simulated dives. Also, recent evidence supports the use of the arterial/alveolar (a:A) partial pressures of oxygen (PO2) ratio to predict the arterial PO2 (PaO2) under hyperbaric conditions from measurements obtained at 1 atmosphere absolute (ATA). This work summarizes ABGs obtained in SCUBA divers in real underwater conditions and aims to validate the a:A ratio in predicting PaO2 in this subset of individuals at depth.MethodsThe study was approved by the local ethics committee. After cannulating the radial artery of the non-dominant limb, ABGs were sampled at the surface before the dive (A), at depth (15 meters of freshwater (mfw) or 42 mfw) before (B) and after (C) pedaling on a submersed bicycle for 10 minutes, and back at surface (D). After calculating the surface alveolar PO2 for each subject, the a:A ratio was obtained and used to predict PaO2 at depth. A linear regression between measured and predicted PaO2 was reported, along with the goodness-of-fit F test.ResultsSix subjects performed the dive at 15 mfw, and four others at 42 mfw. The PaO2 proportionally increased at both depths, remaining stable before and after pedaling. The a:A calculated from the baseline ABG obtained at rest, out of the water, adequately predicted the PaO2 at depth (R2 = 0.97, p&lt;0.001), better at 15 mfw but losing accuracy at 42 mfw.ConclusionsThe ABGs confirmed the proportional rise of PaO2 in SCUBA divers underwater. The a:A ratio could be used to predict the magnitude of PaO2 rise at depth to limit exposure to hyperoxia, especially in repetitive recreational dives and professional divers.