bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Differential Weathering on The Magnetic Properties of Paleosols: A Case Study of Magnetic Enhancement vs. Magnetic Depletion in the Pleistocene Blackwater Draw Formation, Texas
Authors: Stine J. , Geissman J.W. , Sweet D.E. , Baird H. 
Published: June 2021

The type-section of the Blackwater Draw Formation (BDF) consists of a series of five paleosol horizons developed on eolian deposits and an overlying surficial soil. Previous work has shown that magnetic properties (e.g., χ, ARM, and IRM) as a function of depth in this type-section, display both magnetically enhanced and magnetically depleted signals for different paleosols. To better understand the magnetic mineralogy responsible for these varying responses, various rock-magnetic experiments, scanning electron microscopy, and Mössbauer spectroscopy were conducted on representative samples from the six soil units which constitute the BDF type-section. Our results show that sub-micron hematite [with a minor contribution from single-domain sized hematite (Hc = ∼500 mT) dominates all the soils in terms of weight percent concentration. Whereas, low coercivity (Hc = ∼35 mT or less) magnetite/maghemitized-magnetite grains, largely in the PSD state (Mr/Ms=∼0.14 +/– 0.03588, Hcr/Hc=∼2.68 +/– 0.298789), dominate the magnetic signal. Magnetically depleted soils show a relatively higher proportion of goethite, while magnetically enhanced soils show an increased contribution from SP/SSD magnetite/maghemite phases.By combining our data-set with geochemically-derived climofunctions, we have correlated the magnetically preserved, depleted, and enhanced sections of the type-section to three distinct environmental phases (I-III). The basal sediments of Phase I displays relatively homogenous (neither enhanced nor depleted) magnetic properties due to relatively arid conditions and minimal alteration of southerly derive eolian sands. Conversely, Phase II-III represents a change in weathering intensities and provenance, resulting in a mix of southerly derived sands and northerly derived silts. Phase II, experienced greater precipitation levels, resulting in the dissolution of Fe-oxide phases and thus magnetic depletion. The uppermost Phase III experienced intermediate precipitation intensities resulting in magnetic enhancement.Using previously published age models we tentatively interpret these changing environmental conditions to be influenced by the Middle-Pleistocene Transition (1.2-0.7 Ma), where the Earth’s climatic cycles shifted from a ∼41 kyr to ∼100 kyr cycles. However, ambiguities persist due to uncertainties in the currently published age model. Due to the complexity of the magnetic signal, we recommend future studies utilize a holistic approach, incorporating rock-magnetic, geochemical, and microscopy observations for more accurate reconstruction of regional paleoenvironments.
Combining Argo and Satellite Data Using Model-Derived Covariances: Blue Maps
Authors: Oke Peter R. , Chamberlain Matthew A. , Fiedler Russell A. S. , Bastos de Oliveira Hugo , Beggs Helen M. , Brassington Gary B. 
Published: June 2021

Blue Maps aims to exploit the versatility of an ensemble data assimilation system to deliver gridded estimates of ocean temperature, salinity, and sea-level with the accuracy of an observation-based product. Weekly maps of ocean properties are produced on a 1/10°, near-global grid by combining Argo profiles and satellite observations using ensemble optimal interpolation (EnOI). EnOI is traditionally applied to ocean models for ocean forecasting or reanalysis, and usually uses an ensemble comprised of anomalies for only one spatiotemporal scale (e.g., mesoscale). Here, we implement EnOI using an ensemble that includes anomalies for multiple space- and time-scales: mesoscale, intraseasonal, seasonal, and interannual. The system produces high-quality analyses that produce mis-fits to observations that compare well to other observation-based products and ocean reanalyses. The accuracy of Blue Maps analyses is assessed by comparing background fields and analyses to observations, before and after each analysis is calculated. Blue Maps produces analyses of sea-level with accuracy of about 4 cm; and analyses of upper-ocean (deep) temperature and salinity with accuracy of about 0.45 (0.15) degrees and 0.1 (0.015) practical salinity units, respectively. We show that the system benefits from a diversity of ensemble members with multiple scales, with different types of ensemble members weighted accordingly in different dynamical regions.
The Value of Different Single or Combined Indexes of the Captopril Challenge Test in the Diagnosis of Primary Aldosteronism
Authors: Xiang Qiao , Chen Tao , Yu Kai , Li Yuanmei , Li Qianrui , Tian Haoming , Ren Yan 
Published: June 2021

ObjectiveThe result interpretation of the captopril challenge test (CCT) for the diagnosis of primary aldosteronism (PA) is not standardized. Superiorities of different indexes in the CCT have not been fully investigated. We aimed to comprehensively evaluate the value and influence factors of different CCT-associated indexes in the diagnosis of PA.MethodsWe enrolled 312, 85, 179 and 97 patients in the groups of PA, essential hypertension (EH), unilateral PA (UPA) and bilateral PA (BPA), respectively. For each single index investigated, we computed diagnostic estimates including the area under the receiver operating characteristic curve (AUC). We performed pre-specified subgroup analyses to explore influence factors. We assessed the diagnostic value of combined indexes in binary logistic regression models.ResultsPost-CCT aldosterone to renin ratio (ARR) (AUC = 0.8771) and plasma aldosterone concentration (PAC) (AUC = 0.8769) showed high value in distinguishing PA from EH, and their combination (AUC = 0.937) was even superior to either alone. The diagnostic efficacy was moderately high for post-CCT aldosterone to angiotensin II ratio (AA2R) (AUC = 0.834) or plasma renin activity (PRA) (AUC = 0.795) but low for the suppression percentage of PAC (AUC = 0.679). Post-CCT PAC had a significantly higher AUC in the UPA than BPA subgroup (AUC = 0.914 vs 0.827, P&lt;0.05).ConclusionWe can take post-CCT ARR and PAC altogether into account to distinguish PA from EH, while caution should be taken to interpret CCT results with the suppression percentage of PAC. Post-CCT PAC may perform better to identify the unilateral than bilateral form of PA.
Detection and Sourcing of CDOM in Urban Coastal Waters With UV-Visible Imaging Spectroscopy
Authors: Harringmeyer Joshua P. , Kaiser Karl , Thompson David R. , Gierach Michelle M. , Cash Curtis L. , Fichot Cédric G. 
Published: June 2021

Ultraviolet (UV)-visible imaging spectroscopy is an emerging and highly anticipated technology, expected to improve the remote sensing of coastal waters and expand its range of applications. Upcoming NASA satellite missions including PACE and GLIMR will feature imaging spectrometers capable of measuring hyperspectral remote-sensing reflectance (Rrs) across the visible range and well into the near-infrared and ultraviolet domains. The availability of UV reflectance is expected to facilitate the remote sensing of chromophoric dissolved organic matter (CDOM) in optically complex waters, thereby improving coastal water-quality monitoring. Although this argument is well supported by the dominance of CDOM absorption in the UV domain, few studies have directly evaluated the potential advantages conferred by UV reflectance for monitoring CDOM-related coastal water quality. Here, we took advantage of a 6-week wastewater diversion event in Santa Monica Bay, California in 2015 and the availability of Portable Remote Imaging SpectroMeter (PRISM) imagery acquired during the diversion to assess if UV-visible imaging spectroscopy could facilitate the detection of CDOM and help differentiate wastewater effluent-derived CDOM from other sources. A comparison of local empirical algorithms with varying amounts of spectral information implemented on PRISM data showed that incorporating UV Rrs as a predictor significantly improved retrieval of CDOM absorption coefficients (ag). Optimal performance was reached when combining Rrs(365), Rrs(400), and Rrs(700) as predictors of ag in a multiple linear regression. The use of the entire UV-visible spectrum (365–700 nm) in a partial-least-squares regression (PLSR) did not improve retrievals, indicating that a few carefully chosen predictors in the UV-visible domain were sufficient to empirically differentiate CDOM from phytoplankton in coastal waters minimally influenced by sediments or bottom reflectance. Finally, the development of a new fluorescence-based indicator of effluent-derived CDOM (effluent fluorescence ratio, EFR) helped demonstrate the feasibility of remotely detecting CDOM from wastewater. A PLSR-based algorithm using Rrs(365–700) provided reasonable EFR retrievals and successfully identified effluent-derived CDOM at the wastewater outfall when implemented on PRISM imagery. Although further work should investigate the influence of effluent-CDOM fluorescence on Rrs more mechanistically, these results confirmed that UV-visible imaging spectrometers can facilitate coastal CDOM-related water quality monitoring and expand its range of applications.
Genetic Determinants for Bacterial Osteomyelitis: A Focused Systematic Review of Published Literature
Authors: Xie Xiaoping , Li Jiangbi , Gu Feng , Zhang Ke , Su Zilong , Wen Qiangqiang , Sui Zhenjiang , Zhou Pengcheng , Yu Tiecheng 
Published: June 2021

Background: Osteomyelitis is an inflammatory process characterized by progressive bone destruction. Moreover, chronic bacterial osteomyelitis is regarded as a difficult-to-treat clinical entity due to its long-standing course and frequent infection recurrence. However, the role of genetic factors in the occurrence and development of bacterial osteomyelitis is poorly understood.Methods: We performed a systematic review to assess the frequency of individual alleles and genotypes of single-nucleotide polymorphisms (SNPs) among patients with bacterial osteomyelitis and healthy people to identify whether the SNPs are associated with the risk of developing bacterial osteomyelitis. Then, gene ontology and Kyoto Encyclopedia of Gene and Genomes analyses were performed to identify the potential biological effects of these genes on the pathogenesis of bacterial osteomyelitis.Result: Fourteen eligible studies containing 25 genes were analyzed. In this review, we discovered that the SNPs in IL1B, IL6, IL4, IL10, IL12B, IL1A, IFNG, TNF, PTGS2, CTSG, vitamin D receptor (VDR), MMP1, PLAT, and BAX increased the risk of bacterial osteomyelitis, whereas those in IL1RN and TLR2 could protect against osteomyelitis. The bioinformatic analysis indicated that these osteomyelitis-related genes were mainly enriched in inflammatory reaction pathways, suggesting that inflammation plays a vital role in the development of bacterial osteomyelitis. Furthermore, functional notation for 25 SNPs in 17 significant genes was performed using the RegulomeDB and NCBI databases. Four SNPs (rs1143627, rs16944, rs2430561, and rs2070874) had smaller scores from regulome analysis, implying significant biological function.Conclusion: We systematically summarized several SNPs linked to bacterial osteomyelitis and discovered that these gene polymorphisms could be a genetic factor for bacterial osteomyelitis. Moreover, further large-scale cohort studies are needed to enhance our comprehensive understanding of the development of osteomyelitis to provide earlier individualized preventions and interventions for patients with osteomyelitis in clinical practice.
PER1 Is a Prognostic Biomarker and Correlated With Immune Infiltrates in Ovarian Cancer
Authors: Chen Mali , Zhang Lili , Liu Xiaolong , Ma Zhen , Lv Ling 
Published: June 2021

Background: Period circadian protein homolog 1 (PER1) is an important component of the biorhythm molecular oscillation system and plays an important part in the development and progression of mammalian cancer. However, the correlations of PER1 with prognosis and tumor-infiltrating lymphocytes in ovarian cancer (OV) remain unclear.Methods: The Oncomine and TIMER databases were used to examine the expression of PER1 in OV. Kaplan–Meier Plotter and PrognoScan were used to evaluate the relationship between PER1 and prognosis. Kaplan–Meier Plotter was used to analyze the relationships between PER1 and clinicopathological features of OV patients. The relationship between PER1 expression and immune infiltration in OV was investigated using the TIMER database and CIBERSORT algorithm. The STRING database was used to analyze PER1-related protein functional groups, the GeneMANIA online tool was used to analyze gene groups with similar functions to those of PER1, and Network Analyst was used to identify transcription factors that regulate PER1. The correlation between PER1 and immunoinvasion of OV was analyzed using TIMER. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect PER1 expression.Results: PER1 was differentially expressed in different cancer tissues, and its expression in various OV subtypes was lower than that in normal ovarian tissue. OV patients with low PER1 expression had a reduced overall survival rate. Decreased PER1 expression in stage 1 and stage 1+2 OV patients was related to poor prognosis, while increased PER1 expression in stage 3+4 patients and TP53 mutation were related to poor overall survival and progression-free survival. We identified eight genes whose expression was strongly correlated with that of PER1, as well as four transcription factors that regulate PER1. In OV, PER1 expression levels were positively correlated with infiltration levels of cells including neutrophils, regulatory T cells, and M2 macrophages, and closely related to a variety of immune markers. Reduced expression of PER1 was significantly associated with poor overall survival.Conclusion: These findings suggest that PER1 could be used as a prognostic biomarker to determine prognosis and immune infiltration in OV patients.
9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma
Authors: Yan Kexin , Lu Yuxiu , Yan Zhangyong , Wang Yutao 
Published: June 2021

PurposeTo identify CD8+T cell-related factors and the co-expression network in melanoma and illustrate the interactions among CD8+T cell-related genes in the melanoma tumor microenvironment.MethodWe obtained melanoma and paracancerous tissue mRNA matrices from TCGA-SKCM and GSE65904. The CIBERSORT algorithm was used to assess CD8+T cell proportions, and the “estimate” package was used to assess melanoma tumor microenvironment purity. Weighted gene co-expression network analysis was used to identify the most related co-expression modules in TCGA-SKCM and GSE65904. Subsequently, a co-expression network was built based on the joint results in the two cohorts. Subsequently, we identified the core genes of the two most relevant modules of CD8+T lymphocytes according to the module correlation, and constructed the signature using ssGSEA. Later, we compared the signature with the existing classical pathways and gene sets, and confirmed the important prognostic significance of the signature in this paper.ResultsNine co-expressed genes were identified as CD8+T cell-related genes enriched in the cellular response to interferon−gamma process and antigen processing and presentation of peptide antigen. In the low expression level group, inflammation and immune responses were weaker. Single-cell sequencing and immunohistochemistry indicated that these nine genes were highly expressed in CD8+T cells group.ConclusionWe identified nine-gene signature, and the signature is considered as the biomarker for T lymphocyte response and clinical response to immune checkpoint inhibitors for melanoma
The Role of Ageing and Parenchymal Senescence on Macrophage Function and Fibrosis
Authors: Campbell Ross A. , Docherty Marie-Helena , Ferenbach David A. , Mylonas Katie J. 
Published: June 2021

In this review, we examine senescent cells and the overlap between the direct biological impact of senescence and the indirect impact senescence has via its effects on other cell types, particularly the macrophage. The canonical roles of macrophages in cell clearance and in other physiological functions are discussed with reference to their functions in diseases of the kidney and other organs. We also explore the translational potential of different approaches based around the macrophage in future interventions to target senescent cells, with the goal of preventing or reversing pathologies driven or contributed to in part by senescent cell load in vivo.
Targeted Transcriptomics of Frog Virus 3 in Infected Frog Tissues Reveal Non-Coding Regulatory Elements and microRNAs in the Ranaviral Genome and Their Potential Interaction with Host Immune Response
Authors: Tian Yun , Khwatenge Collins N. , Li Jiuyi , De Jesus Andino Francisco , Robert Jacques , Sang Yongming 
Published: June 2021

BackgroundFrog Virus 3 (FV3) is a large dsDNA virus belonging to Ranaviruses of family Iridoviridae. Ranaviruses infect cold-blood vertebrates including amphibians, fish and reptiles, and contribute to catastrophic amphibian declines. FV3 has a genome at ~105 kb that contains nearly 100 coding genes and 50 intergenic regions as annotated in its reference genome. Previous studies have mainly focused on coding genes and rarely addressed potential non-coding regulatory role of intergenic regions.ResultsUsing a whole transcriptomic analysis of total RNA samples containing both the viral and cellular transcripts from FV3-infected frog tissues, we detected virus-specific reads mapping in non-coding intergenic regions, in addition to reads from coding genes. Further analyses identified multiple cis-regulatory elements (CREs) in intergenic regions neighboring highly transcribed coding genes. These CREs include not only a virus TATA-Box present in FV3 core promoters as in eukaryotic genes, but also viral mimics of CREs interacting with several transcription factors including CEBPs, CREBs, IRFs, NF-κB, and STATs, which are critical for regulation of cellular immunity and cytokine responses. Our study suggests that intergenic regions immediately upstream of highly expressed FV3 genes have evolved to bind IRFs, NF-κB, and STATs more efficiently. Moreover, we found an enrichment of putative microRNA (miRNA) sequences in more than five intergenic regions of the FV3 genome. Our sequence analysis indicates that a fraction of these viral miRNAs is targeting the 3’-UTR regions of Xenopus genes involved in interferon (IFN)-dependent responses, including particularly those encoding IFN receptor subunits and IFN-regulatory factors (IRFs).ConclusionsUsing the FV3 model, this study provides a first genome-wide analysis of non-coding regulatory mechanisms adopted by ranaviruses to epigenetically regulate both viral and host gene expressions, which have co-evolved to interact especially with the host IFN response.
Immune Response, Viral Shedding Time, and Clinical Characterization in COVID-19 Patients With Gastrointestinal Symptoms
Authors: Yang Huan , Xi Xiangyu , Wang Weimin , Gu Bing 
Published: June 2021

Background and Aims: Gastrointestinal (GI) symptoms are frequently observed in coronavirus disease (COVID-19) symptoms. Previous studies have mainly focused on epidemiology and characteristics in patients with GI symptoms, little is known about the roles of the immune response in susceptibility to and severity of infection. Here, we analyzed COVID-19 cases to determine immune response and clinical characteristics in COVID-19 patients with GI symptoms.Methods: Based on the presence of GI symptoms, 79 patients in Xuzhou were divided into GI and non-GI groups. A retrospective study investigating the clinical characteristics, selected laboratory abnormalities, immune response, treatment, and clinical outcome was performed to compare patients with or without GI symptoms.Results: Approximately 25% of patients reported at least one GI symptom. Our results showed significantly higher rates of fatigue, increased LDH, increased CK, higher percentage increase neutrophil-to-lymphocyte ratio (NLR), lymphopenia, and bilateral pneumonia in patients with GI symptoms. No significant changes in serum amylase (SAA), immunoglobulin (Ig) G, IgM, C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6), viral shedding time, liver injury, and kidney injury between the two groups were observed. The clinical type on admission of patients with GI symptoms reported significantly higher rates of critical disease type (20 vs. 3.3%; p = 0.033). However, the survival rate did not differ between the two groups.Conclusions: Increase in total lymphocytes and NLR as well as the elevation of CRP, SAA, PCT, IL-6, CK, and LDH were closely associated with COVID-19 with GI symptoms, implying reliable indicators COVID-19 patients with GI symptoms were more likely to develop into a severe disease.
Comprehensive Analysis of Clinical Trials Registration for Lupus Nephritis Therapy on ClinicalTrials.gov
Authors: Gao Yanfang , Wang Yuhan , Li Rongshan , Zhou Xiaoshuang 
Published: June 2021

Objective: Clinical trials are the most effective method for evaluating therapeutic strategies. The purpose of this study was to comprehensively assess the characteristics of trials on lupus nephritis (LN) and provide a reference for LN treatment and research.Methods: Registered therapeutic trials on drug interventions for LN were obtained from ClinicalTrials.gov up to December 3, 2020. The general characteristics, methodological characteristics, detailed characteristics, investigated drugs, eligibility criteria, and outcome measures of these trials were analyzed.Results: A total of 126 eligible trials were evaluated, and these trials mainly investigated the initial treatment of adult proliferative LN. Half of the trials enrolled &lt;50 participants, and 70.7% of the trials lasted for 6–24 months. In total, 95.2% of trials adopted an interventional study design. Of intervention trials, 56.6% were in phase 2 or phase 3, 76.7% were randomized, 77.5% employed a parallel assignment, and 41.7% were masked. The eligibility criteria and outcome measures of the included trials varied and involved a variety of indicators. Chemical agents and biologics are the most widely studied immunotherapies, of which mycophenolate mofetil, tacrolimus, and rituximab are the most studied. In addition, some trials studied cell transplantation treatment.Conclusions: The majority of clinical trials for LN therapy registered on ClinicalTrials.gov investigated the initial treatment of adult proliferative LN, and most of these trials were randomized, parallel assigned, and insufficiently masked interventional trials with small scale, short duration, various eligibility criteria, and outcome measures. We hope that more large-scale, long-term multicenter, and high-quality RCT trials with standardized inclusion criteria/exclusion criteria and treatment effect evaluation systems will be conducted and that more energy and funding will be put into exploring biological products and stem cell therapies. In addition, trials for membranous LN, childhood-onset LN, and maintenance phase LN are needed to establish optimal treatment strategies.