bluuebunny/crossref_metadata_2025_split huggingface dataset:
BIRDIE: A data pipeline to inform wetland and waterbird conservation at multiple scales
Authors: Cervantes Francisco , Altwegg Res , Strobbe Francis , Skowno Andrew , Visser Vernon , Brooks Michael , Stojanov Yvan , Harebottle Douglas M. , Job Nancy 
Published: March 2023

IntroductionEfforts to collect ecological data have intensified over the last decade. This is especially true for freshwater habitats, which are among the most impacted by human activity and yet lagging behind in terms of data availability. Now, to support conservation programmes and management decisions, these data need to be analyzed and interpreted; a process that can be complex and time consuming. The South African Biodiversity Data Pipeline for Wetlands and Waterbirds (BIRDIE) aims to help fast and efficient information uptake, bridging the gap between raw ecological datasets and the information final users need.MethodsBIRDIE is a full data pipeline that takes up raw data, and estimates indicators related to waterbird populations, while keeping track of their associated uncertainty. At present, we focus on the assessment of species abundance and distribution in South Africa using two citizen-science bird monitoring datasets, namely: the African Bird Atlas Project and the Coordinated Waterbird Counts. These data are analyzed with occupancy and state-space models, respectively. In addition, a suite of environmental layers help contextualize waterbird population indicators, and link these to the ecological condition of the supporting wetlands. Both data and estimated indicators are accessible to end users through an online portal and web services.Results and discussionWe have designed a modular system that includes tasks, such as: data cleaning, statistical analysis, diagnostics, and computation of indicators. Envisioned users of BIRDIE include government officials, conservation managers, researchers and the general public, all of whom have been engaged throughout the project. Acknowledging that conservation programmes run at multiple spatial and temporal scales, we have developed a granular framework in which indicators are estimated at small scales, and then these are aggregated to compute similar indicators at broader scales. Thus, the online portal is designed to provide spatial and temporal visualization of the indicators using maps, time series and pre-compiled reports for species, sites and conservation programmes. In the future, we aim to expand the geographical coverage of the pipeline to other African countries, and develop more indicators specific to the ecological structure and function of wetlands.
Deficiency of endothelial FGFR1 signaling via upregulation of ROCK2 activity aggravated ALI/ARDS
Authors: Deng Yue , Huang Xingming , Hu Yan , Zhong Weiting , Zhang Hua , Mo Chunheng , Wang Hongjun , Ding Bi-Sen , Wang Chen 
Published: March 2023

Vascular leakage and inflammation are pathological hallmarks of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). Endothelial cells (ECs) serve as a semipermeable barrier and play a key role in disease progression. It is well known that fibroblast growth factor receptor 1 (FGFR1) is required for maintaining vascular integrity. However, how endothelial FGFR1 functions in ALI/ARDS remains obscure. Here, we revealed that conditional deletion of endothelial FGFR1 aggravated LPS-induced lung injury, including inflammation and vascular leakage. Inhibition of its downstream Rho-associated coiled-coil–forming protein kinase 2 (ROCK2) by AAV Vec-tie-shROCK2 or its selective inhibitor TDI01 effectively attenuated inflammation and vascular leakage in a mouse model. In vitro, TNFα-stimulated human umbilical vein endothelial cells (HUVECs) showed decreased FGFR1 expression and increased ROCK2 activity. Furthermore, knockdown of FGFR1 activated ROCK2 and thus promoted higher adhesive properties to inflammatory cells and higher permeability in HUVECs. TDI01 effectively suppressed ROCK2 activity and rescued the endothelial dysfunction. These data demonstrated that the loss of endothelial FGFR1 signaling mediated an increase in ROCK2 activity, which led to an inflammatory response and vascular leakage in vivo and in vitro. Moreover, inhibition of ROCK2 activity by TDI01 provided great value and shed light on clinical translation.
Alterations of the fecal and vaginal microbiomes in patients with systemic lupus erythematosus and their associations with immunological profiles
Authors: Ling Zongxin , Cheng Yiwen , Gao Jie , Lei Wenhui , Yan Xiumei , Hu Xiaogang , Shao Li , Liu Xia , Kang Runfang 
Published: March 2023

BackgroundExploring the human microbiome in multiple body niches is beneficial for clinicians to determine which microbial dysbiosis should be targeted first. We aimed to study whether both the fecal and vaginal microbiomes are disrupted in SLE patients and whether they are correlated, as well as their associations with immunological features.MethodsA group of 30 SLE patients and 30 BMI-age-matched healthy controls were recruited. Fecal and vaginal samples were collected, the 16S rRNA gene was sequenced to profile microbiomes, and immunological features were examined.ResultsDistinct fecal and vaginal bacterial communities and decreased microbial diversity in feces compared with the vagina were found in SLE patients and controls. Altered bacterial communities were found in the feces and vaginas of patients. Compared with the controls, the SLE group had slightly lower gut bacterial diversity, which was accompanied by significantly higher bacterial diversity in their vaginas. The most predominant bacteria differed between feces and the vagina in all groups. Eleven genera differed in patients’ feces; for example, Gardnerella and Lactobacillus increased, whereas Faecalibacterium decreased. Almost all the 13 genera differed in SLE patients’ vaginas, showing higher abundances except for Lactobacillus. Three genera in feces and 11 genera in the vagina were biomarkers for SLE patients. The distinct immunological features were only associated with patients’ vaginal microbiomes; for example, Escherichia−Shigella was negatively associated with serum C4.ConclusionsAlthough SLE patients had fecal and vaginal dysbiosis, dysbiosis in the vagina was more obvious than that in feces. Additionally, only the vaginal microbiome interacted with patients’ immunological features.
Association of rheumatoid arthritis with bronchial asthma and asthma-related comorbidities: A population-based national surveillance study
Authors: Kim Jung Gon , Kang Jiyeon , Lee Joo-Hyun , Koo Hyeon-Kyoung 
Published: March 2023

BackgroundThe aim of this study was to investigate the impact of rheumatoid arthritis (RA) on the prevalence of bronchial asthma and asthma-related comorbidities. We also aimed to identify the influence of RA on interrelationship between asthma and asthma-related comorbidities.MethodsFrom the Korean National Health and Nutrition Examination Survey, participants &gt;40 years of age who completed questionnaires and spirometry tests were enrolled. Patient data on RA, asthma, allergic rhinitis, atopic dermatitis, chronic obstructive pulmonary disease (COPD), sinusitis, otitis media, and body mass index (BMI) were collected. Logistic regression and network analyses were performed.ResultsA total of 14,272 subjects were enrolled, among which, 334 (2.4%) had RA. RA was significantly associated with asthma (OR 2.32; 95% CI 1.51–3.57), allergic rhinitis (OR 1.51; 95% CI 1.08–2.10), and sinusitis (OR 1.64; 95% CI 1.08–2.50). The network analysis of total patients revealed a positive interrelationship between asthma and allergic rhinitis, sinusitis, otitis media, atopic dermatitis, BMI, and RA. The interrelationship between asthma and sinusitis was stronger in the RA group. Of note, the relationship between asthma and BMI was distinctively found only in the RA group (r = 0.214, P &lt; 0.05). In patients with asthma, the prevalence of obesity was 64% in the presence of RA, and 40% in the absence of RA (P = 0.034).ConclusionThis study supports the positive association of RA with asthma, allergic rhinitis, and sinusitis. Our analysis suggests a notable interrelationship between the presence of asthma and higher BMI values in patients with RA, indicating that asthma is more obesity-related in patients with RA.
White matter and gray matter changes related to cognition in community populations
Authors: Li Wen-Xin , Yuan Jing , Han Fei , Zhou Li-Xin , Ni Jun , Yao Ming , Zhang Shu-Yang , Jin Zheng-Yu , Cui Li-Ying , Zhai Fei-Fei , Zhu Yi-Cheng 
Published: March 2023

ObjectiveFurther studies are needed to improve the understanding of the pathological process underlying cognitive impairments. The purpose of this study is to investigate the global and topographic changes of white matter integrity and cortical structure related to cognitive impairments in a community-based population.MethodsA cross-sectional analysis was performed based on 995 subjects (aged 56.8 ± 9.1 years, 34.8% males) from the Shunyi study, a community-dwelling cohort. Cognitive status was accessed by a series of neurocognitive tests including Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), category Verbal Fluency Test (VFT), Digit Span Test (DST), and Trail Making Tests A and B (TMT-A and TMT-B). Structural and diffusional MRI data were acquired. White matter integrity was assessed using fractional anisotropy (FA), mean diffusivity (MD), and peak width of skeletonized mean diffusivity (PSMD). Cortical surface area, thickness, and volume were measured using Freesurfer. Probabilistic tractography was further conducted to track the white matter fibers connecting to the cortical regions related to cognition. General linear models were used to investigate the association between brain structure and cognition.ResultsGlobal mean FA and MD were significantly associated with performances in VFT (FA, β 0.119, p &lt; 0.001; MD, β −0.128, p &lt; 0.001). Global cortical surface area, thickness, and volume were not related to cognitive scores. In tract-based spatial statistics analysis, disruptive white matter integrity was related to cognition impairment, mainly in visuomotor processing speed, semantic memory, and executive function (TMT-A and VFT), rather than verbal short-term memory and working memory (DST). In the whole brain vertex-wise analysis, surface area in the left orbitofrontal cortex, right posterior-dorsal part of the cingulate gyrus, and left central sulcus were positively associated with MMSE and MoCA scores, and the association were independent of the connecting white matter tract.ConclusionDisrupted white matter integrity and regional cortical surface area were related to cognition in community-dwelling populations. The associations of cortical surface area and cognition were independent of the connecting white matter tract.
Factors impacting quality of life in multiple system atrophy
Authors: Ali Nabila , Nesspor Vanessa , Bang Jee , Scholz Sonja W. , Pantelyat Alexander 
Published: March 2023

BackgroundMultiple system atrophy (MSA) is an atypical parkinsonian disorder marked by autonomic dysfunction, parkinsonism, cerebellar dysfunction, and poor response to dopaminergic medications such as levodopa. Patient-reported quality of life is an important benchmark for clinicians and clinical trials. The Unified Multiple System Atrophy Rating Scale (UMSARS) allows healthcare providers to rate and assess MSA progression. The MSA-QoL questionnaire is a health-related quality of life scale intended to provide patient-reported outcome measures. In this article, we investigated inter-scale correlations between the MSA-QoL and UMSARS to determine factors impacting the quality of life of patients with MSA.MethodsTwenty patients at the Johns Hopkins Atypical Parkinsonism Center's Multidisciplinary Clinic with a diagnosis of clinically probable MSA and who filled out the MSA-QoL and UMSARS questionnaires within 2 weeks of each other were included. Inter-scale correlations between MSA-QoL and UMSARS responses were examined. Linear regressions were also performed to examine relationships between both scales.ResultsSignificant inter-scale correlations were found between the MSA-QoL and UMSARS, both between MSA-QoL total score and UMSARS Part I subtotal scores and for individual scale items. There were no significant correlations between MSA-QoL life satisfaction rating and UMSARS subtotal scores or any specific UMSARS items. Linear regression analysis found significant associations between MSA-QoL total score and UMSARS Part I and total scores, and between MSA-QoL life satisfaction rating and UMSARS Part I, Part II, and total scores (after adjustment for age).ConclusionsOur study demonstrates significant inter-scale correlations between MSA-QoL and UMSARS, particularly relating to activities of daily living and hygiene. MSA-QoL total score and UMSARS Part I subtotal scores, which assess patients' functional status, were significantly correlated. The lack of significant associations between MSA-QoL life satisfaction rating and any UMSARS item suggests there may be aspects to quality of life that are not fully captured by this assessment. Larger cross-sectional and longitudinal analyses utilizing UMSARS and MSA-QoL are warranted and modification of the UMSARS should be considered.
The effects of COVID-19 on the vestibular system
Authors: Zaubitzer Lena , Ludwig Sonja , Berkemann Michelle , Walter Beatrice , Jungbauer Frederic , Held Valentin , Hegemann Stefan C. A. , Rotter Nicole , Schell Angela 
Published: March 2023

IntroductionThe symptoms and severity of SARS-CoV-2 infection vary greatly across the spectrum, from asymptomatic infection to severe pneumonia with acute respiratory distress syndrome and even death. Dizziness is a frequently reported symptom of SARS-CoV-2 viral infection. However, the extent to which this symptom results from the effect of SARS-CoV-2 on the vestibular system remains unclear.Materials and methodsIn the present single-center, prospective cohort study, patients with a previous SARS-CoV-2 infection underwent a vestibular assessment consisting of the Dizziness Handicap Inventory to assess dizziness during and after infection, a clinical examination, the video head impulse test, and the subjective visual vertical test. When the subjective visual vertical test result was abnormal, vestibular-evoked myogenic potentials were performed. Vestibular testing results were compared to pre-existing normative data of healthy controls. In addition, we performed a retrospective data analysis of patients admitted to hospital presenting with acute symptoms of dizziness who were also diagnosed with acute SARS-CoV-2 infection.ResultsA total of 50 participants have been enrolled. During and after the SARS-CoV-2 infection, women were significantly more likely than men to suffer from dizziness. A significantly reduced semicircular canal or otolith function was not observed in either women or men. Acute SARS-CoV-2 infection was diagnosed in nine patients who presented to the emergency room with acute vestibular syndrome. Six of the patients exhibited acute unilateral peripheral vestibulopathy upon diagnosis. A different patient was diagnosed with vestibular migraine, and two individuals had a posterior inferior cerebellar artery infarct revealed by magnetic resonance imaging.Discussion/conclusionOverall, a persisting structural affection of the vestibular system by SARS-CoV-2 seems to be unlikely and could not be confirmed by vHIT, SVV, and VEMPS in our study. It seems possible but unlikely that SARS-CoV-2 induces acute vestibulopathy. Nevertheless, dizziness is a common symptom in patients with COVID-19, which should be taken and worked through seriously.
In vivo evaluation of integrin αvβ6-targeting peptide in NSCLC and brain metastasis
Authors: Fan Di , Zhang Chengkai , Luo Qi , Li Baowang , Ai Lin , Li Deling , Jia Wang 
Published: March 2023

IntroductionIntegrin αvβ6, which is upregulated in malignancies and remains absent or weak in normal tissue, is a promising target in molecular imaging therapeutics. In vivo imaging of integrin αvβ6 could therefore be valuable for early tumor detection and intraoperative guidance.MethodsIn this study, integrin αvβ6-targeting probe G2-SFLAP3 was labeled with near-infrared (NIR) dye Cy5.5 or radioisotope 68Ga. The resulting probes were evaluated in integrin αvβ6-positive A549 and αvβ6-negative H1703 xenograft mice models.ResultsThe cellar uptake of G2-SFLAP3-Cy5.5 was consistent with the expression of integrin αvβ6. Both subcutaneous and brain metastatic A549 tumors could be clearly visualized by NIR fluorescent imaging of G2-SFLAP3-Cy5.5. A549 tumors demonstrated the highest G2-SFLAP3-Cy5.5 accumulation at 4h post-injection (p.i.) and remain detectable at 84h p.i. The fluorescent signal of G2-SFLAP3-Cy5.5 was significantly reduced in H1703 and A549-blocking groups. Consistently, small-animal PET imaging showed tumor-specific accumulation of 68Ga-DOTA-G2-SFLAP3.DiscussionG2-SFLAP3 represents a promising agent for noninvasive imaging of non-small cell lung cancer (NSCLC) and brain metastases.
CT-based radiomics with various classifiers for histological differentiation of parotid gland tumors
Authors: Lu Yang , Liu Haifeng , Liu Qi , Wang Siqi , Zhu Zuhui , Qiu Jianguo , Xing Wei 
Published: March 2023

ObjectiveThis study assessed whether radiomics features could stratify parotid gland tumours accurately based on only noncontrast CT images and validated the best classifier of different radiomics models.MethodsIn this single-centre study, we retrospectively recruited 249 patients with a diagnosis of pleomorphic adenoma (PA), Warthin tumour (WT), basal cell adenoma (BCA) or malignant parotid gland tumours (MPGTs) from June 2020 to August 2022. Each patient was randomly classified into training and testing cohorts at a ratio of 7:3, and then, pairwise comparisons in different parotid tumour groups were performed. CT images were transferred to 3D-Slicer software and the region of interest was manually drawn for feature extraction. Feature selection methods were performed using the intraclass correlation coefficient, t test and least absolute shrinkage and selection operator. Five common classifiers, namely, random forest (RF), support vector machine (SVM), logistic regression (LR), K-nearest neighbours (KNN) and general Bayesian network (Gnb), were selected to build different radiomics models. The receiver operating characteristic curve, area under the curve (AUC), accuracy, sensitivity, specificity and F-1 score were used to assess the prediction performances of these models. The calibration of the model was calculated by the Hosmer–Lemeshow test. DeLong’s test was utilized for comparing the AUCs.ResultsThe radiomics model based on the RF, SVM, Gnb, LR, LR and RF classifiers obtained the highest AUC in differentiating PA from MPGTs, WT from MPGTs, BCA from MPGTs, PA from WT, PA from BCA, and WT from BCA, respectively. Accordingly, the AUC and the accuracy of the model for each classifier were 0.834 and 0.71, 0.893 and 0.79, 0.844 and 0.79, 0.902 and 0.88, 0.602 and 0.68, and 0.861 and 0.94, respectively.ConclusionOur study demonstrated that noncontrast CT-based radiomics could stratify refined pathological types of parotid tumours well but could not sufficiently differentiate PA from BCA. Different classifiers had the best diagnostic performance for different parotid tumours. Our study findings add to the current knowledge on the differential diagnosis of parotid tumours.
Development and validation of a CECT-based radiomics model for predicting IL1B expression and prognosis of head and neck squamous cell carcinoma
Authors: Xie Yang , Wang Min , Xia Haibin , Sun Huifang , Yuan Yi , Jia Jun , Chen Liangwen 
Published: March 2023

IntroductionIt is necessary to explore a noninvasive method to stratify head and neck squamous cell carcinoma (HNSCC)’s prognosis and to seek new indicators for individualized precision treatment. As a vital inflammatory cytokine, IL1B might drive a new tumor subtype that could be reflected in overall survival (OS) and predicted using the radiomics method.MethodsA total of 139 patients with RNA-Seq data from The Cancer Genome Atlas (TCGA) and matched CECT data from The Cancer Image Archive (TCIA) were included in the analysis. The prognostic value of IL1B expression in patients with HNSCC was analyzed using Kaplan-Meier analysis, Cox regression analysis and subgroup analysis. Furthermore, the molecular function of IL1B on HNSCC was explored using function enrichment and immunocytes infiltration analyses. Radiomic features were extracted with PyRadiomics and processed using max-relevance minredundancy, recursive feature elimination, and gradient boosting machine algorithm to construct aradiomics model for predicting IL1B expression. The area under the receiver operating characteristic curve (AUC), calibration curve, precision recall (PR) curve, and decision curve analysis (DCA) curve were used to examine the performance of the model.ResultsIncreased IL1B expression in patients with HNSCC indicated a poor prognosis (hazard ratio [HR] = 1.56, P = 0.003) and was harmful in patients who underwent radiotherapy (HR = 1.87, P = 0.007) or chemotherapy (HR = 2.514, P &lt; 0.001). Shape_Sphericity, glszm_SmallAreaEmphasis, and firstorder_Kurtosis were included in the radiomics model (AUC: training cohort, 0.861; validation cohort, 0.703). The calibration curves, PR curves and DCA showed good diagnostic effect of the model. The rad-score was close related to IL1B (P = 4.490*10-9), and shared the same corelated trend to EMT-related genes with IL1B. A higher rad-score was associated with worse overall survival (P = 0.041).DiscussionThe CECT-based radiomics model provides preoperative IL1B expression predictionand offers non-invasive instructions for the prognosis and individualized treatment of patients withHNSCC.
Pharmacokinetics and tissue distribution of bleomycin-induced idiopathic pulmonary fibrosis rats treated with cryptotanshinone
Authors: He Xiangjun , Zhong Zhi , Wang Quan , Jia Zhenmao , Lu Jing , Chen Jianwen , Liu Peiqing 
Published: March 2023

Introduction: Cryptotanshinone(CTS), a compound derived from the root of Salvia miltiorrhiza, has been linked to various of diseases, particularly pulmonary fibrosis. In the current study, we investigated the benefit of CTS on Sprague-Dawley (SD) rats induced by bleomycin (BLM) and established high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) methods to compare pharmacokinetics and tissue distribution in subsequent normal and modulated SD rats.Methods: The therapeutic effect of CTS on BLM-induced SD rats was evaluated using histopathology, lung function and hydroxyproline content measurement, revealing that CTS significantly improved SD rats induced by BLM. Additionally, a simple, rapid, sensitive and specific HPLC-MS/MS method was developed to determine the pharmacokinetics of various components in rat plasma.Results: Pharmacokinetic studies indicated that CTS was slowly absorbed by oral administration and had low bioavailability and a slow clearance rate. The elimination of pulmonary fibrosis in 28-day rats was slowed down, and the area under the curve was increased compared to the control group. Long-term oral administration of CTS did not accumulate in vivo, but the clearance was slowed down, and the steady-state blood concentration was increased. The tissue distribution study revealed that CTS exposure in the lungs and liver.Discussion: The lung CTS exposure was significantly higher in the model group than in the control group, suggesting that the pathological changes of pulmonary fibrosis were conducive to the lung exposure of CTS and served as the target organ of CTS.