bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stratification of diabetic kidney diseases via data-independent acquisition proteomics–based analysis of human kidney tissue specimens
Authors: Huang Qinghua , Fei Xianming , Zhong Zhaoxian , Zhou Jieru , Gong Jianguang , Chen Yuan , Li Yiwen , Wu Xiaohong 
Published: November 2022

AimThe aims of this study were to analyze the proteomic differences in renal tissues from patients with diabetes mellitus (DM) and diabetic kidney disease (DKD) and to select sensitive biomarkers for early identification of DKD progression.MethodsPressure cycling technology–pulse data-independent acquisition mass spectrometry was employed to investigate protein alterations in 36 formalin-fixed paraffin-embedded specimens. Then, bioinformatics analysis was performed to identify important signaling pathways and key molecules. Finally, the target proteins were validated in 60 blood and 30 urine samples.ResultsA total of 52 up- and 311 down-regulated differential proteins were identified as differing among the advanced DKD samples, early DKD samples, and DM controls (adjusted p&lt;0.05). These differentially expressed proteins were mainly involved in ion transport, apoptosis regulation, and the inflammatory response. UniProt database analysis showed that these proteins were mostly enriched in signaling pathways related to metabolism, apoptosis, and inflammation. NBR1 was significantly up-regulated in both early and advanced DKD, with fold changes (FCs) of 175 and 184, respectively (both p&lt;0.01). In addition, VPS37A and ATG4B were significantly down-regulated with DKD progression, with FCs of 0.140 and 0.088, respectively, in advanced DKD and 0.533 and 0.192, respectively, in early DKD compared with the DM control group (both p&lt;0.01). Bioinformatics analysis showed that NBR1, VPS37A, and ATG4B are closely related to autophagy. We also found that serum levels of the three proteins and urine levels of NBR1 decreased with disease progression. Moreover, there was a significant difference in serum VPS37A and ATG4B levels between patients with early and advanced DKD (both p&lt;0.05). The immunohistochemistry assaay exhibited that the three proteins were expressed in renal tubular cells, and NBR1 was also expressed in the cystic wall of renal glomeruli.ConclusionThe increase in NBR1 expression and the decrease in ATG4B and VPS37 expression in renal tissue are closely related to inhibition of the autophagy pathway, which may contribute to DKD development or progression. These three proteins may serve as sensitive serum biomarkers for early identification of DKD progression.
Effects of landscape restoration on migration of lead and cadmium at an abandoned mine site
Authors: Zhang Feiying , Li Hepeng 
Published: November 2022

Abandoned lead and zinc (Pb/Zn) mining wastes represent a serious environmental hazard because heavy metals (e.g., Pb and Cd) are continuously released into the environment, threatening ecological and human health. This study was devoted to investigate the stability of Pb and Cd in the soil at an abandoned Pb/Zn mine site after landscape restoration by five-year monitoring. Chemical extraction was applied to measure the distribution of metals. The results showed that the bioavailability of Pb and Cd in soil increased, during the accumulation of soil organic matter of about seven g/kg, and that the soil pH value decreased from 4.82 to 4.44. Soil organic matter and soil pH significantly affected the distribution of metals. Long-term afforestation can lead to continuous soil acidification. There was a significant negative correlation between the carbonate-bound state distribution and soil pH. With the decrease in pH, the decomposition of carbonates was promoted, and relative abundances of Pb and Cd in the distribution associated with the fulvic and humic complex of organic matter increased by 0.54% and 3.17%, respectively. Pb and Cd showed different migration behavior in pine. Compared with Cd, Pb was more concentrated in roots. These results have important implications for the long-term sustainable management of forests formed by the phytostabilization of contaminated soil.
Accelerated gross nitrogen cycling following garlic mustard invasion is linked with abiotic and biotic changes to soils
Authors: Edwards Joseph D. , Cook Allison M. , Yannarell Anthony C. , Yang Wendy H. 
Published: November 2022

IntroductionAlliaria petiolata (garlic mustard), an invasive forest herb in North America, often alters nutrient availability in its non-native ecosystems, but the mechanisms driving these changes have yet to be determined. We hypothesized three potential mechanisms through which garlic mustard could directly influence soil nitrogen (N) cycling: by increasing soil pH, by modifying soil microbial community composition, and by altering nutrient availability through litter inputs.Materials and methodsTo test these hypotheses, we evaluated garlic mustard effects on soil pH and other soil properties; fungal and prokaryotic (bacterial and archaeal) community composition; and soil N cycling rates (gross N mineralization and nitrification rates, microbial N assimilation rates, and nitrification- versus denitrification-derived nitrous oxide fluxes); and we assessed correlations among these variables. We collected soil samples from garlic mustard present, absent, and removed treatments in eight forests in central Illinois, United States, during the rosette, flowering, and senescence phenological stages of garlic mustard life cycle.ResultsWe found that garlic mustard increased soil pH, altered fungal and prokaryotic communities, and increased rates of N mineralization, nitrification, nitrification-derived net N2O emission. Significant correlations between soil pH and microbial community composition suggest that garlic mustard effects on soil pH could both directly and indirectly influence soil N cycling rates.DiscussionCorrespondence of gross rates of N mineralization and nitrification with microbial community composition suggest that garlic mustard modification of soil microbial communities could directly lead to changes in soil N cycling. We had expected that early season, nutrient-rich litter inputs from mortality of young garlic mustard could accelerate gross N mineralization and microbial N assimilation whereas late season, nutrient poorer litter inputs from senesced garlic mustard could suppress N mineralization, but we did not observe these patterns in support of the litter input mechanism. Together, our results elucidate how garlic mustard effects on soil pH and microbial community composition can accelerate soil N cycling to potentially contribute to the invasion success of garlic mustard.
Why vaccines fail against Piscirickettsiosis in farmed salmon and trout and how to avoid it: A review
Authors: Valenzuela-Aviles Paula , Torrealba Débora , Figueroa Carolina , Mercado Luis , Dixon Brian , Conejeros Pablo , Gallardo-Matus José 
Published: November 2022

Piscirickettsiosis is the most severe, persistent, and damaging disease that has affected the Chilean salmon industry since its origins in the 1980s. As a preventive strategy for this disease, different vaccines have been developed and used over the last 30 years. However, vaccinated salmon and trout frequently die in the sea cages and the use of antibiotics is still high demonstrating the low efficiency of the available vaccines. The reasons why the vaccines fail so often are still debated, but it could involve different extrinsic and intrinsic factors. Among the extrinsic factors, mainly associated with chronic stress, we can distinguish: 1) biotic including coinfection with sea lice, sealions attacks or harmful algal blooms; 2) abiotic including low oxygen or high temperature; and 3) farm-management factors including overcrowding or chemical delousing treatments. Among the intrinsic factors, we can distinguish: 1) fish-related factors including host’s genetic variability (species, population and individual), sex or age; 2) pathogen-related factors including their variability and ability to evade host immune responses; and 3) vaccine-related factors including low immunogenicity and poor matches with the circulating pathogen strain. Based on the available evidence, in order to improve the development and the efficacy of vaccines against P. salmonis we recommend: a) Do not perform efficacy evaluations by intraperitoneal injection of pathogens because they generate an artificial protective immune response, instead cohabitation or immersion challenges must be used; b) Evaluate the diversity of pathogen strains in the field and ensure a good antigenic match with the vaccines; c) Investigate whether host genetic diversity could be improved, e.g. through selection, in favor of better and longer responses to vaccination; d) To reduce the stressful effects at the cage level, controlling the co-infection of pathogens and avoiding fish overcrowding. To date, we do not know the immunological mechanisms by which the vaccines against P. salmonis may or may not generate protection. More studies are required to identify what type of response, cellular or molecular, is required to develop effective vaccines.
M2 macrophage-related gene signature in chronic rhinosinusitis with nasal polyps
Authors: Zhu Ying , Sun Xiwen , Tan Shaolin , Luo Chunyu , Zhou Jiayao , Zhang Shiyao , Li Zhipeng , Lin Hai , Zhang Weitian 
Published: November 2022

BackgroundChronic rhinosinusitis with nasal polyps (CRSwNP) is a common sinonasal inflammatory disorder with high heterogeneity. Increasing evidence have indicated that the infiltration of macrophages especially M2 macrophages play pivotal roles in the pathogenesis of CRSwNP, but the underlying mechanisms remain undetermined. This study sought to identify potential biomarkers related to M2 macrophages in CRSwNP.MethodsThe expression datasets of GSE136825 and GSE179265 were download from Gene Expression Omnibus (GEO) database and merged. Then, CIBERSORT and weighted gene co-expression network analysis (WGCNA) algorithms were applied to identify M2 macrophage-related gene modules. Thereafter, differentially expressed genes (DEGs) related to M2 macrophages were selected to perform functional enrichment analyses. A protein-protein interaction (PPI) network was built to identify hub genes and quantitative real-time reverse transcriptions PCR was used to verify the bioinformatics results.ResultsA total of 92 DEGs associated with M2 macrophages were identified for further analysis. The results of Gene ontology (GO) and Kyoto Encyclopedia of genes and genomes (KEGG) analyses illustrated that M2 macrophage-associated DEGs primarily enriched in immune responses and extracellular matrix structure. PPI network analysis identified 18 hub genes related to M2 macrophages that might be pivotal in the pathogenesis of CRSwNP. After verification, AIF1, C1QA, C1QB, C3AR1, CCR1, CD163, CD4, CD53, CD86, CSF1R, CYBB, FCER1G, FCGR3A, IL10RA, ITGB2, LAPTM5, PLEK, TYROBP were identified as potential M2 macrophage-related biomarkers for CRSwNP.ConclusionThese findings yield new insights into the hub genes and mechanisms related to M2 macrophages in the pathogenesis of CRSwNP. Further studies of these hub genes would help better understand the disease progression and identify potential treatment targets.
T cell-intrinsic protein kinase D3 is dispensable for the cells’ activation
Authors: Koutník Jiří , Leitges Michael , Siegmund Kerstin 
Published: November 2022

Protein kinases D (PKDs) are implicated in T cell receptor (TCR) signaling. Of the two T cell-expressed isoforms PKD2 and PKD3, however, only the former one is rather well understood in this immune cell type. Recently, we have observed a putative hyper-phenotype of T cells from conventional PKD3-knockout mice, which we explained as a secondary effect due to a skewed T cell compartment from naïve towards effector/memory T cells already under steady state conditions. Nonetheless, to this end it is not clear whether these aberrations are mediated by a T cell-intrinsic or -extrinsic function of PKD3. To address this question, we have investigated mice lacking PKD3 specifically in the T cell compartment. We could show that T cells from CD4-Cre-driven conditional knockout mice did not phenocopy the ones from conventional PKD3-knockout mice. In brief, no skewing in the T cell compartment of peripheral lymphoid organs, no hyper-activation upon stimulation in vitro or in vivo as well as no aberrations in follicular helper T cells (TFH) upon immunization were observed. Hence, although PKD3 is strongly regulated upon TCR stimulation, in T cells this kinase seems to be dispensable for their activation. The described skewing in the T cell compartment of conventional PKD3-deficient mice seems to be mediated by T cell-extrinsic mechanisms, thus once more emphasizing the importance of cell type-specific mouse models.
Differentially induced immunity in buccal and nasal mucosae after vaccination for SARS–CoV–2: Prospects for mass scale immunity-screening in large populations
Authors: Tsamadou Chrysanthi , Ludwig Carolin , Scholz Judith , Proffen Matthias , Hägele Janina , Rode Immanuel , Körper Sixten , Fabricius Dorit , Jahrsdörfer Bernd , Neuchel Christine , Amann Elisa , Schrezenmeier Hubert , Fürst Daniel 
Published: November 2022

IntroductionHumoral immunity after SARS-CoV-2 vaccination has been extensively investigated in blood. Aim of this study was to develop an ELISA method in order to determine the prevalence of IgG and IgA SARS-CoV-2 domain 1 spike-protein (S) specific antibodies (Abs) in buccal and nasal mucosal surfaces of vaccinees.MethodsTo this end, we analyzed 69 individuals who received their first vaccine dose between February and July 2021. Vaccines administered were BNT162b2, mRNA-1273 or ChAdOx1-nCoV-19. Detection of IgG and IgA Abs was performed using commercial ELISA kits for both blood and swab samples after protocol modification for the latter.ResultsAnti-spike IgG and IgA Abs in the buccal and/or nasal swabs were detectable in &gt;81% of the study subjects after the second dose. The IgG measurements in buccal swabs appeared to correlate in a more consistent way with the respective measurements in blood with a correlation coefficient of r=0.74. It is of note that IgA Abs appeared to be significantly more prevalent in the nasal compared to the buccal mucosa. Optimal selection of the assay cut-off for the IgG antibody detection in buccal swabs conferred a sensitivity of 91.8% and a specificity of 100%. Last, individuals vaccinated with mRNA-based vaccines exhibited higher antibody levels in both blood and mucosal surfaces compared to those receiving ChAdOx1-nCoV-19 confirming previously reported results.ConclusionIn conclusion, our findings show a differential prevalence of anti-S Abs on mucosal surfaces after vaccination for SARS-CoV-2, while they also set the basis for potential future use of IgG antibody detection in buccal swabs for extended immunity screening in large populations.
Experimental investigation on the effects of magnetic field assistance on the quality of surface finish for sustainable manufacturing of ultra-precision single-point diamond turning of titanium alloys
Authors: Hatefi Shahrokh , Abou-El-Hossein Khaled 
Published: November 2022

Single-point diamond turning (SPDT) is the state-of-the-art technology for ultra-precision manufacturing of optical products with optical surface roughness down to 1 nm. The SPDT technology has an important role in advanced manufacturing of critical components in different fields of industry. In a SPDT process, different cutting mechanisms affect the optical surface generation and reduce the quality of the turned product. Different efforts have been undertaken to improve the machining conditions as well as optical surface generation mechanisms. Recently, the application of magnetic field assistance in non-conventional SPDT platforms has shown promising results in terms of improving the cutting stability as well as the quality of surface finish. The application of magnetic field assistance becomes more important in SPDT of hard-to-cut materials including titanium alloy. In this study, magnetic field assistance is used in SPDT of Ti-6Al-4V alloy. The machining results show that using this technique could significantly improve the machining conditions and the quality of optical surface generation. The magnetic field assisted SPDT with air coolant could successfully improve the quality of surface finish by 62.5% when compared to non-magnetic purely mechanical SPDT process in dry cutting conditions. Magnetic field assistance is a passive machining technique, environmentally friendly, and it can promote green manufacturing and clean production in ultra-precision SPDT applications.
Fluid overload and mortality in critically ill patients with severe heart failure and cardiogenic shock–An observational cohort study
Authors: Waskowski Jan , Michel Matthias C. , Steffen Richard , Messmer Anna S. , Pfortmueller Carmen A. 
Published: November 2022

ObjectivePatients with heart failure (HF) and cardiogenic shock are especially prone to the negative effects of fluid overload (FO); however, fluid resuscitation in respective patients is sometimes necessary resulting in FO. We aimed to study the association of FO at ICU discharge with 30-day mortality in patients admitted to the ICU due to severe heart failure and/or cardiogenic shock.MethodsRetrospective, single-center cohort study. Patients with admission diagnoses of severe HF and/or cardiogenic shock were eligible. The following exclusion criteria were applied: (I) patients younger than 16 years, (II) patients admitted to our intermediate care unit, and (III) patients with incomplete data to determine FO at ICU discharge. We used a cumulative weight-adjusted definition of fluid balance and defined more than 5% as FO. The data were analyzed by univariate and adjusted univariate logistic regression.ResultsWe included 2,158 patients in our analysis. 185 patients (8.6%) were fluid overloaded at ICU discharge. The mean FO in the FO group was 7.2% [interquartile range (IQR) 5.8–10%]. In patients with FO at ICU discharge, 30-day mortality was 22.7% compared to 11.7% in non-FO patients (p &lt; 0.001). In adjusted univariate logistic regression, we did not observe any association of FO at discharge with 30-day mortality [odds ratio (OR) 1.48; 95% confidence interval (CI) 0.81–2.71, p = 0.2]. No association between FO and 30-day mortality was found in the subgroups with HF only or cardiogenic shock (all p &gt; 0.05). Baseline lactate (adjusted OR 1.27; 95% CI 1.13–1.42; p &lt; 0.001) and cardiac surgery at admission (adjusted OR 1.94; 95% CI 1.0–3.76; p = 0.05) were the main associated factors with FO at ICU discharge.ConclusionIn patients admitted to the ICU due to severe HF and/or cardiogenic shock, FO at ICU discharge seems not to be associated with 30-day mortality.
Case report: Antiplatelet therapy on metastatic paraganglioma-associated cutaneous vascular disease and literature review
Authors: Gao Yinjie , Cui Yunying , Hu Zhonghui , Wang Yu , Li Tianyi , Liu Yuehua , Tong Anli 
Published: November 2022

ContextTumor-associated cutaneous vascular disorder induced by PPGL was extremely rare, and the cutaneous manifestations could disappear after removal of the tumors. However, the definite pathological diagnosis and the potential mechanism remained unidentified. We presented a severe cutaneous vascular lesion manifested as diffuse erythema with ulceration and necrosis over the limbs in a female patient with metastatic paraganglioma. Skin biopsy was performed on her for defining the pathological diagnosis and potential mechanism. The patient was diagnosed as vascular disease according to the obvious angioectasia in dermis on cutaneous pathology, which might be caused by PPGL-induced hypercoagulability. We used the antiplatelet therapy with aspirin to treat the PPGL-associated cutaneous vascular disease for the first time, and the cutaneous lesions were relieved and healed gradually, further supporting the diagnosis of vascular disease.ConclusionFor metastatic PPGL patients like the case we reported, the definite diagnosis by skin biopsy and the early antiplatelet therapy might be effective to the cutaneous lesions caused by the hypercoagulable state of PPGL.
Gamma-glutamyl transferase to high-density lipoprotein cholesterol ratio has a non-linear association with non-alcoholic fatty liver disease: A secondary prospective cohort study in non-obese Chinese adults
Authors: Li Qiming , Han Yong , Hu Haofei , Zhuge Yuzheng 
Published: November 2022

ObjectiveThe evidence for a relationship between the ratio of gamma-glutamyl transferase (GGT) to high-density lipoprotein cholesterol (HDL-c) and non-alcoholic fatty liver disease (NAFLD) is currently inadequate. This study aimed to investigate the relationship between the GGT/HDL-c ratio and NAFLD.Materials and methodsThis study is a prospective cohort study that recruited a total of 11,891 non-obese volunteers in a Chinese hospital from January 2010 to December 2014 in a non-selective manner. The Cox proportional-hazards regression model was then used to investigate the relationship between baseline GGT/HDL-c ratio and the probability of developing NAFLD. The non-linear link between the GGT/HDL-c ratio and NAFLD was identified using a Cox proportional hazards regression with cubic spline functions and smooth curve fitting (cubic spline smoothing). Furthermore, we conducted several sensitivity and subgroup analyses. Data had been uploaded to the DATADRYAD website.ResultsThe mean age of study participants was 43.29 ± 14.95 years old, and 6,502 (54.68%) were male. The median (interquartile ranges) of GGT/HDL-c ratio was 15.56 (10.73–23.84). During a median follow-up of 29.35 months, 2028 (17.05%) participants were diagnosed with NAFLD. After adjusting for covariates, the results showed that GGT/HDL-c ratio was positively associated with incident NAFLD (HR = 1.014, 95% CI 1.011–1.017). There was also a non-linear relationship between GGT/HDL-c ratio and NAFLD, and the inflection point of the GGT/HDL-c ratio was 20.35. The effect sizes (HR) on the left and right sides of the inflection point were 1.113 (95% CI 1.096, 1.130) and 1.003 (95% CI 1.000–1.007), respectively. Moreover, the sensitivity analysis demonstrated the robustness of our results. Subgroup analysis showed that GGT/HDL-c ratio was more strongly associated with incident NAFLD in triglyceride (TG) &lt; 1.7 mmol/L participants. In contrast, the weaker association was probed in those with TG ≥ 1.7 mmol/L.ConclusionThe present study reveals a positive and non-linear relationship between the GGT/HDL-c ratio and NAFLD risk in a non-obese Chinese population. GGT/HDL-c ratio is strongly associated with NAFLD when GGT/HDL-c ratio is less than 20.35. Therefore, maintaining the GGT/HDL-c ratio lower than the inflection point is recommended from a treatment perspective.