bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses of fine-root biomass and production to drying depend on wetness and site nutrient regime in boreal forested peatland
Authors: Lampela Maija , Minkkinen Kari , Straková Petra , Bhuiyan Rabbil , He Wei , Mäkiranta Päivi , Ojanen Paavo , Penttilä Timo , Laiho Raija 
Published: June 2023

IntroductionPeatlands are terrestrial-carbon hotspots, where changes in carbon pools and fluxes potentially caused by drying or warming may have significant feedbacks to climate change. In forested peatlands, fine-root biomass (FRB), and production (FRP) are important carbon pools and fluxes, but they and their depth distribution and plant functional type (PFT) composition are poorly known.MethodsWe studied the effects of persistent water-table level (WTL) drawdown on these characteristics in four forested boreal peatland site types that varied in soil nutrient and WTL regimes, ground vegetation and tree stand characteristics. Each site type was represented by a pair of one undrained and one drained site. Two pairs were nutrient-poor, Scots pine dominated sites, one very wet and one relatively dry in their undrained condition. The other two pairs were nutrient-rich, Norway spruce dominated sites, again one wetter and one drier in the undrained condition. FRB was estimated by separating and visually identifying roots from soil cores extending down to 50 cm depth. FRP was estimated using ingrowth cores covering the same depth, and the separated roots were identified using infrared spectroscopy.Results and discussionBoth FRB and FRP varied widely both within and among the different types of boreal forested peatland. In FRB, the clearest differences were seen in the two originally wettest sites, nutrient-poor tall-sedge pine fen and nutrient-rich herb-rich spruce swamp: FRB was smaller in the drained site compared to the undrained site in the pine fen, but the opposite was true in the spruce swamp. FRP was generally higher in the nutrient-poor, pine-dominated sites than the nutrient-rich, spruce-dominates sites. The depth distribution of FRB was more superficial than that of FRP, except for the most nutrient-rich spruce swamp. Tree and shrub roots dominated both FRB and FRP, except for the undrained pine fen, where graminoids and forbs dominated. Even there, these PFTs were replaced by trees and shrubs at the drained site. Site wetness and nutrient regime both thus clearly regulated FRB and FRP of the forested peatland site types studied, and both need to be considered when making any generalizations.
An amino acid metabolism-based seventeen-gene signature correlates with the clinical outcome and immune features in pancreatic cancer
Authors: Hao Jie , Zhou Cancan , Wang Zheng , Ma Zhenhua , Wu Zheng , Lv Yi , Wu Rongqian 
Published: June 2023

Background: Pancreatic cancer is an aggressive tumor with a low 5-year survival rate and primary resistance to most therapy. Amino acid (AA) metabolism is highly correlated with tumor growth, crucial to the aggressive biological behavior of pancreatic cancer; nevertheless, the comprehensive predictive significance of genes that regulate AA metabolism in pancreatic cancer remains unknown.Methods: The mRNA expression data downloaded from The Cancer Genome Atlas (TCGA) were derived as the training cohort, and the GSE57495 cohort from Gene Expression Omnibus (GEO) database was applied as the validation cohort. Random survival forest (RSF) and the least absolute shrinkage and selection operator (LASSO) regression analysis were employed to screen genes and construct an AA metabolism-related risk signature (AMRS). Kaplan-Meier analysis and receiver operating characteristic (ROC) curve were performed to assess the prognostic value of AMRS. We performed genomic alteration analysis and explored the difference in tumor microenvironment (TME) landscape associated with KRAS and TP53 mutation in both high- and low-AMRS groups. Subsequently, the relationships between AMRS and immunotherapy and chemotherapy sensitivity were evaluated.Results: A 17-gene AA metabolism-related risk model in the TCGA cohort was constructed according to RSF and LASSO. After stratifying patients into high- and low-AMRS groups based on the optimal cut-off value, we found that high-AMRS patients had worse overall survival (OS) in the training cohort (a median OS: 13.1 months vs. 50.1 months, p &lt; 0.0001) and validation cohort (a median OS: 16.2 vs. 30.5 months, p = 1e-04). Genetic mutation analysis revealed that KRAS and TP53 were significantly more mutated in high-AMRS group, and patients with KRAS and TP53 alterations had significantly higher risk scores than those without. Based on the analysis of TME, low-AMRS group displayed significantly higher immune score and more enrichment of T Cell CD8+ cells. In addition, high-AMRS-group exhibited higher TMB and significantly lower tumor immune dysfunction and exclusion (TIDE) score and T Cells dysfunction score, which suggested a higher sensitive to immunotherapy. Moreover, high-AMRS group was also more sensitive to paclitaxel, cisplatin, and docetaxel.Conclusion: Overall, we constructed an AA-metabolism prognostic model, which provided a powerful prognostic predictor for the clinical treatment of pancreatic cancer.
The UK kidney donor risk index poorly predicts long-term transplant survival in paediatric kidney transplant recipients
Authors: Kim Jon Jin , Curtis Rebecca M. K. , Reynolds Ben , Marks Stephen D. , Drage Martin , Kosmoliaptsis Vasilis , Dudley Jan , Williams Alun 
Published: June 2023

BackgroundThe UK kidney offering scheme introduced a kidney donor risk index (UK-KDRI) to improve the utility of deceased-donor kidney allocations. The UK-KDRI was derived using adult donor and recipient data. We assessed this in a paediatric cohort from the UK transplant registry.MethodsWe performed Cox survival analysis on first kidney-only deceased brain-dead transplants in paediatric (&lt;18 years) recipients from 2000-2014. The primary outcome was death-censored allograft survival &gt;30 days post-transplant. The main study variable was UK-KDRI derived from seven donor risk-factors, categorised into four groups (D1-low risk, D2, D3 and D4-highest risk). Follow-up ended on 31-December-2021.Results319/908 patients experienced transplant loss with rejection as the main cause (55%). The majority of paediatric patients received donors from D1 donors (64%). There was an increase in D2-4 donors during the study period, whilst the level of HLA mismatching improved. The KDRI was not associated with allograft failure. In multi-variate analysis, increasing recipient age [adjusted HR and 95%CI: 1.05(1.03-1.08) per-year, p&lt;0.001], recipient minority ethnic group [1.28(1.01-1.63), p&lt;0.05), dialysis before transplant [1.38(1.04-1.81), p&lt;0.005], donor height [0.99 (0.98-1.00) per centimetre, p&lt;0.05] and level of HLA mismatch [Level 3: 1.92(1.19-3.11); Level 4: 2.40(1.26-4.58) versus Level 1, p&lt;0.01] were associated with worse outcomes. Patients with Level 1 and 2 HLA mismatches (0 DR +0/1 B mismatch) had median graft survival &gt;17 years regardless of UK-KDRI groups. Increasing donor age was marginally associated with worse allograft survival [1.01 (1.00-1.01) per year, p=0.05].SummaryAdult donor risk scores were not associated with long-term allograft survival in paediatric patients. The level of HLA mismatch had the most profound effect on survival. Risk models based on adult data alone may not have the same validity for paediatric patients and therefore all age-groups should be included in future risk prediction models.
Early diagenesis and benthic fluxes of redox-sensitive metals in eastern China shelf sediments
Authors: Wang Xiaojing , Li Li , Ren Yijun , Cao Peng , Zhu Aimei , Liu Jihua , Shi Xuefa 
Published: June 2023

Thirteen Short sediment cores (30-50 cm) were collected from Bohai Sea, Yellow Sea and Changjiang Estuary in China, and the early diagenesis of several redox sensitive metals (Fe, Mn, Mo, U and V, referring to as RSMs) in sediment were studied. The recycling process of Mo and Mn was closely correlated with each other, generating benthic fluxes diffusing upward from sediment to overlying water column, and the flux rates are related to the organic carbon oxidation rates. The recycling of U and V were more tightly coupled with Fe oxides, generating benthic fluxes going downward into the sediment in most cores. Significant authigenic accumulation of U, in contrary to little to no accumulation of Mo and V, were found in the study region, even in Changjiang Estuary where hypoxic condition was often found during summer. Benthic diffusive fluxes were compared with authigenic mass accumulate rates (MAR), which indicated that, besides the benthic diffusion process, there are other processes controlling the authigenic accumulation of the RSMs. The close relationships between authigenic accumulation of RSMs with OCburial and OCburial with Sburial, indicating the authigenic accumulation of RSMs is a consequence of redox environment in shelf sediment, which directly influencing the organic carbon degradation process. Compared with other continental margin, moderate enrichment of U was found in China continental sediment. The authigenic U accumulation in BS and NYS sediments accounted for 20 - 68% of the Yellow River input, whilst in SYS sediments accounted for ~ 64% of the Yellow River and Changjiang River input, which acting as important U sinks that cannot be ignored.
Efficacy of acupuncture for pain relief in patients receiving extracorporeal shock wave lithotripsy: a meta-analysis of randomized controlled studies
Authors: Chen Hsiao-Tien , Hung Kuo-Chuan , Hsu Yao-Chin , Kuo Jinn-Rung , Chang Ying-Jen , Chen I-Wen , Sun Cheuk-Kwan 
Published: June 2023

BackgroundThis meta-analysis aimed at investigating the efficacy of acupuncture for pain relief in patients receiving extracorporeal shock wave lithotripsy (ESWL).MethodsRandomized controlled trials comparing the efficacy of acupuncture with conventional treatments were retrieved from major electronic databases (e.g., MEDLINE, EMBASE, and Cochrane Library) until August 28, 2022. The primary outcome was the response rate (i.e., rate of pain relief), while secondary outcomes included stone-free rate, satisfaction rate, duration of ESWL, peri-/post-procedural pain score, and risk of adverse events.ResultsThirteen eligible studies involving 1,220 participants published between 1993 and 2022 were analyzed. Pooled results indicated that acupuncture had a better response rate compared to conventional treatments (RR = 1.17, 95% CI: 1.06–1.3, p = 0.003, seven trials, n = 832). Despite no difference in ESWL duration (MD = 0.02 min, 95% CI: −1.53 to 1.57, p = 0.98, three trials, n = 141), stone-free rate (RR = 1.11, 95% CI: 1–1.25, p = 0.06, six trials, n = 498), and satisfaction rate (RR = 1.51, 95% CI: 0.92–2.47, p = 0.1, three trials, n = 334) between the two groups, the acupuncture group had a lower risk of adverse events (RR = 0.51, 95% CI: 0.33–0.79, p = 0.003, five trials, n = 327), peri- (MD = −1.91 points, 94% CI: −3.53 to −0.28, p = 0.02, four trials, n = 258 patient) and post-procedural (MD = −1.07, 95% CI: −1.77 to −0.36, p = 0.003, four trials, n = 335) pain score.ConclusionThe results of this meta-analysis showed that the use of acupuncture in patients receiving ESWL was associated with a higher pain relief rate and a lower risk of adverse events, suggesting feasibility of its use in this clinical setting.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier: CRD42022356327.
Historical eye on IPF: a cohort study redefining the mortality scenario
Authors: Tomassetti Sara , Ravaglia Claudia , Piciucchi Sara , Ryu Jay , Wells Athol , Donati Luca , Dubini Alessandra , Klersy Catherine , Luzzi Valentina , Gori Leonardo , Rosi Elisabetta , Lavorini Federico , Poletti Venerino 
Published: June 2023

RationaleTherapies that slow idiopathic pulmonary fibrosis (IPF) progression are now available and recent studies suggest that the use of antifibrotic therapy may reduce IPF mortality.ObjectivesThe aim of the study was to evaluate whether, to what extent, and for which factors the survival of IPF in a real-life setting has changed in the last 15 years.MethodsHistorical eye is an observational study of a large cohort of consecutive IPF patients diagnosed and treated in a referral center for ILDs with prospective intention. We recruited all consecutive IPF patients seen at GB Morgagni Hospital, Forlì, Italy between January 2002 and December 2016 (15 years). We used survival analysis methods to describe and model the time to death or lung transplant and Cox regression to model prevalent and incident patient characteristics (time-dependent Cox models were fitted).Measurements and main resultsThe study comprised 634 patients. The year 2012 identifies the time point of mortality shift (HR 0.58, CI 0.46–0.63, p &lt; 0.001). In the more recent cohort, more patients had better preserved lung function, underwent cryobiopsy instead of surgery, and were treated with antifibrotics. Highly significant negative prognostic factors were lung cancer (HR 4.46, 95% CI 3.3–6, p &lt; 0.001), hospitalizations (HR 8.37, 95% CI 6.5–10.7, p &lt; 0.001), and acute exacerbations (HR 8.37, 95% CI 6.52–10.7, p &lt; 0.001). The average antifibrotic treatment effect estimated using propensity score matching showed a significant effect in the reduction of all-cause mortality (ATE coeff −0.23, SE 0.04, p &lt; 0.001), acute exacerbations (ATE coeff −0.15, SE 0.04, p &lt; 0.001), and hospitalizations (ATE coeff −0.15, SE 0.04, p &lt; 0.001) but no effect on lung cancer risk (ATE coeff −0.03, SE 0.03, p = 0.4).ConclusionAntifibrotic drugs significantly impact hospitalizations, acute exacerbations, and IPF survival. After the introduction of cryobiopsy and antifibrotic drugs, the prognosis of IPF patients has significantly improved together with our ability to detect IPF at an earlier stage.
Nebulized mesenchymal stem cell derived conditioned medium ameliorates Escherichia coli induced pneumonia in a rat model
Authors: González Héctor E. , McCarthy Sean D. , Masterson Claire , Laffey John G. , MacLoughlin Ronan , O’Toole Daniel 
Published: June 2023

BackgroundMesenchymal stem cells (MSC) have shown immense therapeutic promise in a range of inflammatory diseases, including acute respiratory distress syndrome (ARDS), and are rapidly advancing through clinical trials. Among their multimodal mechanisms of action, MSCs exert strong immunomodulatory effects via their secretome, which contains cytokines, small molecules, extracellular vesicles, and a range of other factors. Recent studies have shown that the MSC secretome can recapitulate many of the beneficial effects of the MSC itself. We aimed to determine the therapeutic capacity of the MSC secretome in a rat bacterial pneumonia model, especially when delivered directly to the lung by nebulization which is a technique more appropriate for the ventilated patient.MethodsConditioned medium (CM) was generated from human bone marrow derived MSCs in the absence of antibiotics and serum supplements. Post-nebulization lung penetration was estimated through nebulization of CM to a cascade impactor and simulated lung and quantification of collected total protein and IL-8 cytokine. Control and nebulized CM was added to a variety of lung cell culture models and injury resolution assessed. In a rat E. coli pneumonia model, CM was instilled or administered by nebulization and lung injury and inflammation assessed at 48 h.ResultsMSC-CM was predicted to have good distal lung penetration and delivery when administered by nebulizer. Both control and nebulized CM reduced NF-κB activation and inflammatory cytokine production in lung cell culture, while promoting cell viability and would closure in oxidative stress and scratch wound models. In a rat bacterial pneumonia model, both instilled and nebulizer delivered CM improved lung function, increasing blood oxygenation and reducing carbon dioxide levels compared to unconditioned medium controls. A reduction in bacterial load was also observed in both treatment groups. Inflammatory cytokines were reduced significantly by both liquid and aerosol CM administration, with less IL-1β, IL-6, and CINC1 in these groups compared to controls.ConclusionMSC-CM is a potential therapeutic for pneumonia ARDS, and administration is compatible with vibrating mesh nebulization.
Serum metabolic signatures for acute pulmonary embolism identified by untargeted metabolomics
Authors: Xie Ming , Liu Yu , Zheng Hui , Gao Xiaoli , Liu Ran 
Published: June 2023

Background and aimsThe important metabolic features of acute pulmonary embolism (APE) risk stratification and their underlying biological basis remain elusive. Our study aims to develop early diagnostic models and classification models by analyzing the plasma metabolic profile of patients with APE.Materials and methodsSerum samples were collected from 68 subjects, including 19 patients with confirmed APE, 35 patients with confirmed NSTEMI, and 14 healthy individuals. A comprehensive metabolic assessment was performed using ultra-performance liquid chromatography-mass spectrometry based on an untargeted metabolomics approach. In addition, an integrated machine learning strategy based on LASSO and logistic regression was used for feature selection and model building.ResultsThe metabolic profiles of patients with acute pulmonary embolism and NSTEMI is significantly altered relative to that of healthy individuals. KEGG pathway enrichment analysis revealed differential metabolites between acute pulmonary embolism and healthy individuals mainly involving glycerophosphate shuttle, riboflavin metabolism, and glycerolipid metabolism. A panel of biomarkers was defined to distinguish acute pulmonary embolism, NSTEMI, and healthy individuals with an area under the receiver operating characteristic curve exceeding 0.9 and higher than that of D-dimers.ConclusionThis study contributes to a better understanding of the pathogenesis of APE and facilitates the discovery of new therapeutic targets. The metabolite panel can be used as a potential non-invasive diagnostic and risk stratification tool for APE.
Collagen co-localized with macrovesicular steatosis better differentiates fibrosis progression in non-alcoholic fatty liver disease mouse models
Authors: Wang Xiao-Xiao , Jin Rui , Li Xiao-He , Yang Qiang , Teng Xiao , Liu Fang-Fang , Wu Nan , Rao Hui-Ying , Liu Feng 
Published: June 2023

BackgroundNon-alcoholic fatty liver disease (NAFLD) is a global commonly occurring liver disease. However, its exact pathogenesis is not fully understood. The purpose of this study was to quantitatively evaluate the progression of steatosis and fibrosis by examining their distribution, morphology, and co-localization in NAFLD animal models.MethodsSix mouse NAFLD groups were established: (1) western diet (WD) group; (2) WD with fructose in drinking water (WDF) group; (3) WDF + carbon tetrachloride (CCl4) group, WDF plus intraperitoneal injection of CCl4; (4) high-fat diet (HFD) group, (5) HFD with fructose (HFDF) group; and (6) HFDF + CCl4 group, HFDF plus intraperitoneal injection of CCl4. Liver tissue specimens from NAFLD model mice were collected at different time points. All the tissues were serially sectioned for histological staining and second-harmonic generation (SHG)/two-photon excitation fluorescence imaging (TPEF) imaging. The progression of steatosis and fibrosis was analyzed using SHG/TPEF quantitative parameters with respect to the non-alcoholic steatohepatitis Clinical Research Network scoring system.ResultsqSteatosis showed a good correlation with steatosis grade (R: 0.823–0.953, p &lt; 0.05) and demonstrated high performance (area under the curve [AUC]: 0.617-1) in six mouse models. Based on their high correlation with histological scoring, qFibrosis containing four shared parameters (#LongStrPS, #ThinStrPS, #ThinStrPSAgg, and #LongStrPSDis) were selected to create a linear model that could accurately identify differences among fibrosis stages (AUC: 0.725-1). qFibrosis co-localized with macrosteatosis generally correlated better with histological scoring and had a higher AUC in six animal models (AUC: 0.846-1).ConclusionQuantitative assessment using SHG/TPEF technology can be used to monitor different types of steatosis and fibrosis progression in NAFLD models. The collagen co-localized with macrosteatosis could better differentiate fibrosis progression and might aid in developing a more reliable and translatable fibrosis evaluation tool for animal models of NAFLD.
Establishment of a novel cytokine-related 8-gene signature for distinguishing and predicting the prognosis of triple-negative breast cancer
Authors: Liu Xiaojun , Zhang Liang , Chen Liang 
Published: June 2023

BackgroundTriple-negative breast cancer (TNBC) is a common carcinoma in women, and the prognosis of TNBC is the worst. Using data from The Cancer Genome Atlas (TCGA) database, we analyzed the functional roles of cytokine-related genes in TNBC.MethodsThe clinical and transcriptome data of TNBC patients were downloaded from TCGA database. A systematical analyses of the data from TCGA database were conducted to screen the prognostic genes and identify the main cytokine-related pathways related to TNBC.ResultsWe identified 499 prognostic genes in TNBC patients from TCGA database and the cytokine-related pathways closely related to TNBC. TCGA-TNBC patients were divided into the high-risk cluster (C1) group and the low-risk cluster (C2) group based on the cytokine-related genes. The C1 group patients exhibited tumor metastasis and an advanced tumor stage. The functional analysis revealed that the upregulated differentially expressed genes (DEGs) in the C1 group were mainly associated with the extracellular matrix (ECM)-receptor interaction, stem cell proliferation, focal adhesion, and cyclic adenosine monophosphate (cAMP) signaling pathway, while the downregulated DEGs in the C1 group were mainly associated with cytokine and cytokine receptors, T-helper 17 (Th17) cell differentiation, and primary immunodeficiency. The immune activity of C1 group was lower than that of C2 group, and the identified half-maximal inhibitory concentration scores of 3 chemotherapy drugs (i.e., doxorubicin, methotrexate, and paclitaxel) were lower in C2 group than C1 group. More importantly, we constructed a novel prognostic signature and identified the following 8 genes: CCL25, CXCL13, IL12RB2, IL21, TNFRSF13C, TNFRSF8, CCL7 and GDF5.ConclusionThe status of the cytokine-related pathway was closely related to tumor classification and immune activity in the TNBC patients. The gene signature of the cytokine-related genes showed an good performance in predicting the prognosis of TNBC patients, and could predict the prognosis of TNBC patients.