bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational fluid dynamics model to predict the dynamical behavior of the cerebrospinal fluid through implementation of physiological boundary conditions
Authors: Vandenbulcke Sarah , De Pauw Tim , Dewaele Frank , Degroote Joris , Segers Patrick 
Published: November 2022

Cerebrospinal fluid (CSF) dynamics play an important role in maintaining a stable central nervous system environment and are influenced by different physiological processes. Multiple studies have investigated these processes but the impact of each of them on CSF flow is not well understood. A deeper insight into the CSF dynamics and the processes impacting them is crucial to better understand neurological disorders such as hydrocephalus, Chiari malformation, and intracranial hypertension. This study presents a 3D computational fluid dynamics (CFD) model which incorporates physiological processes as boundary conditions. CSF production and pulsatile arterial and venous volume changes are implemented as inlet boundary conditions. At the outlets, 2-element windkessel models are imposed to simulate CSF compliance and absorption. The total compliance is first tuned using a 0D model to obtain physiological pressure pulsations. Then, simulation results are compared with in vivo flow measurements in the spinal subarachnoid space (SAS) and cerebral aqueduct, and intracranial pressure values reported in the literature. Finally, the impact of the distribution of and total compliance on CSF pressures and velocities is evaluated. Without respiration effects, compliance of 0.17 ml/mmHg yielded pressure pulsations with an amplitude of 5 mmHg and an average value within the physiological range of 7–15 mmHg. Also, model flow rates were found to be in good agreement with reported values. However, when adding respiration effects, similar pressure amplitudes required an increase of compliance value to 0.51 ml/mmHg, which is within the range of 0.4–1.2 ml/mmHg measured in vivo. Moreover, altering the distribution of compliance over the four different outlets impacted the local flow, including the flow through the foramen magnum. The contribution of compliance to each outlet was directly proportional to the outflow at that outlet. Meanwhile, the value of total compliance impacted intracranial pressure. In conclusion, a computational model of the CSF has been developed that can simulate CSF pressures and velocities by incorporating boundary conditions based on physiological processes. By tuning these boundary conditions, we were able to obtain CSF pressures and flows within the physiological range.
Nanocellulose coated paper diagnostic to measure glucose concentration in human blood
Authors: Hossain Laila , De Francesco Marisa , Tedja Patricia , Tanner Joanne , Garnier Gil 
Published: November 2022

A new generation of rapid, easy to use and robust colorimetric point of care (POC) nanocellulose coated-paper sensors to measure glucose concentration in blood is presented in this study. The cellulose gel containing the enzyme with co-additive is coated and dried onto a paper substrate. Nanocellulose gel is used to store, immobilize and stabilize enzymes within its structure to prolong enzyme function and enhance its availability. Here, we immobilize glucose oxidase within the gel structure to produce a simple colorimetric blood glucose sensor. Increase in blood glucose concentration increases the concentration of reaction product which decreases the system pH detected by the pH indicative dye entrapped in the nanocellulose gel. The sensor produces a color change from red to orange as pH decreases due to the enzymatic reaction of glucose into gluconic acid and hydrogen peroxide. This sensor can measure glucose concentrations of 7–13 mM (medical range for diabetes control) at temperatures of 4°C–40°C. Stability tests confirm that no denaturation of enzyme occurs by measuring enzyme activity after 4 weeks. A prototype device is designed to instantly measure the glucose concentration from blood in a two steps process: 1) red blood cell separation and 2) quantification of glucose by color change. This study demonstrates nanocellulose sensor as an economical, robust, and sensitive diagnostic technology platform for a broad spectrum of diseases.
Comparative glycoproteomics study on the surface of SKOV3 versus IOSE80 cell lines
Authors: Zhou Ying , Cai Xiaoyu , Wu Linwen , Lin Nengming 
Published: November 2022

Objective:Site-and structure-specific quantitative N-glycoproteomics study of differential cell-surface N-glycosylation of ovarian cancer SKOV3 cells with the non-cancerous ovarian epithelial IOSE80 cells as the control.Methods:C18-RPLC-MS/MS (HCD with stepped normalized collision energies) was used to analyze the 1: 1 mixture of labeled intact N-glycopeptides from SKOV3 and IOSE80 cells, and the site- and structure-specific intact N-glycopeptide search engine GPSeeker was used to conduct qualitative and quantitative search on the obtained raw datasets.Results:With the control of the spectrum-level false discovery rate ≤1%, 13,822 glycopeptide spectral matches coming from 2,918 N-glycoproteins with comprehensive N-glycosite and N-glycan structure information were identified; 3,733 N-glycosites and 3,754 N-glycan sequence structures were confirmed by site-determining and structure-diagnostic fragment ions, respectively. With the control of no less than two observations among the three technical replicates, fold change ≥1.5, andp-value ≤ 0.05, 746 DEPGs in SKOV3 cells relative to IOSE80 cells were quantified, where 421 were upregulated and 325 downregulated.Conclusion:Differential cell-surface N-glycosylation of ovarian cancer SKOV3 cells were quantitatively analyzed by isotopic labeling and site- and structure-specific N-glycoproteomics. This discovery study provides putative N-glycoprotein biomarker candidates for future validation study using multiple reaction monitoring and biochemical methods.
Machine learning opportunities to conduct high-fidelity earthquake simulations in multi-scale heterogeneous geology
Authors: Lehmann Fanny , Gatti Filippo , Bertin Michaël , Clouteau Didier 
Published: November 2022

The 2019 Le Teil earthquake is an illustrative example of a moderate (MW4.9) yet damaging event, occurring at shallow depth (≈1 km) in a region with little to no geophysical data available. Therefore, using a high-fidelity wave propagation code, we performed numerical simulations of the Le Teil earthquake in a highly uncertain framework, investigating several seismic sources and geological set-ups. With respect to the former aspect, a point-source model and an extended kinematic fault model were compared. The latter aspect was investigated by comparing a 1D-layered to a 3D geological model. Those models were enhanced with random fluctuations, in order to obtain three alternative non-stationary random geological fields. The synthetic waveforms obtained from regional geophysical models were globally coherent with the recorded ones. The extended fault source model seemed more realistic than the point-source model. In addition, some geological random fields improved the synthetics’ agreement with the recordings. However, the three random field samplings led to a high variability in induced ground motion responses. Given the computational burden of high-fidelity simulations, we used two dimensionality reduction methods, namely the Principal Component Analysis (PCA) and a deep neural network (3D UNet), to investigate this variability. The methods were applied to a database of 40,000 3D geological random fields. Both the PCA and the 3D UNet condensed the variability of the 3D geological fields into a few components. These were sufficient to reconstruct the original fields with great accuracy. More importantly, the seismic response arising from the propagation throughout the reconstructed fields was in excellent agreement with the response of the original geological fields in more than 75% of the dataset. By building a structured ensemble of complex geological fields from their reduced representation, it may become possible to find a relationship between the reduced representation and the generated ground motion. Thus, our study proves the interest of dimensionality reduction to perform uncertainty analyses in complex geological media.
Progress and prospect of ecological risks of land use change
Authors: Cao Congjie , Song Wei 
Published: November 2022

Ecological risks reflect the extent to which ecosystems are threatened by human activities and environmental changes. Changes in land use/land cover can have profound impacts on the regional ecological environment, such as land desertification, soil erosion, a sharp reduction in forest resources, and biodiversity loss. To objectively reveal the current research status, we conducted an econometric analysis of relevant research papers from 1991 to 2021, published in Web of Science. The results are as follows: 1) In the past 30 years, the number of publications in the field of ecological risks of land use change increased, and the period from 1991 to 2021 can be divided into three stages: the budding period from 1991 to 2008, the rising period from 2009 to 2015, and the high-yield period from 2016 to 2021. 2) Research in this field covered 104 countries or regions, mainly in Asia, the Americas, and Europe. The top three cited countries were the US, China, and the UK. 3) The high-frequency keywords of land use change in the field of ecological risks mainly included “land use”, “management”, “climate change”, and “risk and ecology”. Keywords frequently appeared in Tree Map, such as “dynamics”, “framework”, and “model”, indicating the main research methods in this field. Based on the results, we suggest that for the future development of this research field, the evaluation method system should be improved and multidisciplinary research should be strengthened, ultimately exploring new ways to solve the current ecological problems.
Causal effects of homocysteine levels on the components of sarcopenia: A two-sample mendelian randomization study
Authors: Yu Hongwei , Luo Gan , Sun Tianwei , Tang Qiong 
Published: November 2022

Background: Currently, it is unclear whether there is a causal association between genetically predicted plasma homocysteine (Hcy) levels and the risk of sarcopenia. We performed a Mendelian randomization (MR) study to assess the association between circulating Hcy levels and the components [grip strength, walking pace, and appendicular lean mass (ALM)] of sarcopenia.Methods: Independent single nucleotide polymorphisms (SNPs) significantly associated with plasma Hcy levels served as instrumental variables. Summary-level data regarding the components of sarcopenia. Were obtained from the UK Biobank. Inverse variance weighted (IVW) as the primary method was used for Mendelian randomization (MR) analysis. We also use four models, weighted median, MR-Egger regression, Maximum likelihood, and Penalised weighted median, as supplementary methods to IVW. The MR-Egger intercept test, Cochran’s Q test, and “leave-one-out” sensitivity analysis were performed to evaluate the horizontal pleiotropy, heterogeneities, and stability of the causal association between Hcy levels and the components of sarcopenia.Results: The IVW-MR analysis suggested significant negative associations of increased plasma Hcy levels with grip strength (right: effect = −0.036, SE = 0.032, p = 5.53E-4; left: effect = −0.045, SE = 0.010, p = 1.45E-5), walking pace (effect = −0.038, SE = 0.011, p = 3.18E-4), and ALM (effect = −0.058, 0.013, p = 1.03E-5). However, there were no significant associations of decreased plasma Hcy levels with grip strength (right: effect = 0.005, SE = 0.021, p = 0.82; left: effect = −0.006, SE = 0.014, p = 0.64), walking pace (effect = 0.01, 0.020, p = 0.61), or ALM (effect = -0.034, SE = 0.018, p = 0.06).The accuracy and robustness of these findings were confirmed by sensitivity tests.Conclusion: Increased circulating Hcy levels were associated with lower grip strength, slower walking pace, and decreased ALM.
Identification of immune-related features involved in Duchenne muscular dystrophy: A bidirectional transcriptome and proteome-driven analysis
Authors: Wu Xuan , Dong Nan , Yu Liqiang , Liu Meirong , Jiang Jianhua , Tang Tieyu , Zhao Hongru , Fang Qi 
Published: November 2022

BackgroundWe aimed to investigate the biological mechanism and feature genes of Duchenne muscular dystrophy (DMD) by multi-omics and experimental verification strategy.MethodsWe integrated the transcriptomic and proteomic methods to find the differentially expressed mRNAs (DEMs) and proteins (DEPs) between DMD and Control groups. Weighted gene co-expression network analysis (WGCNA) was then used to identify modules of highly correlated genes and hub genes. In the following steps, the immune and stromal cells infiltrations were accomplished by xCELL algorithm. Furthermore, TF and miRNA prediction were performed with Networkanalyst. ELISA, western blot and external datasets were performed to verify the key proteins/mRNAs in DMD patient and mouse. Finally, a nomogram model was established based on the potential biomarkers.Results4515 DEMs and 56 DEPs were obtained from the transcriptomic and proteomic study respectively. 14 common genes were identified, which is enriched in muscle contraction and inflammation-related pathways. Meanwhile, we observed 33 significant differences in the infiltration of cells in DMD. Afterwards, a total of 22 miRNAs and 23 TF genes interacted with the common genes, including TFAP2C, MAX, MYC, NFKB1, RELA, hsa-miR-1255a, hsa-miR-130a, hsa-miR-130b, hsa-miR-152, and hsa-miR-17. In addition, three genes (ATP6AP2, CTSS, and VIM) showed excellent diagnostic performance on discriminating DMD in GSE1004, GSE3307, GSE6011 and GSE38417 datasets (all AUC &gt; 0.8), which is validated in patients (10 DMD vs. 10 controls), DMD with exon 55 mutations, mdx mouse, and nomogram model.ConclusionTaken together, ATP6AP2, CTSS, and VIM play important roles in the inflammatory response in DMD, which may serve as diagnostic biomarkers and therapeutic targets.
Crosstalk between cytotoxic CD8+ T cells and stressed cardiomyocytes triggers development of interstitial cardiac fibrosis in hypertensive mouse hearts
Authors: Brassington Kurt , Kanellakis Peter , Cao Anh , Toh Ban-Hock , Peter Karlheinz , Bobik Alex , Kyaw Tin 
Published: November 2022

AimsCardiac fibrosis is central to heart failure (HF), especially HF with preserved ejection fraction (HFpEF), often caused by hypertension. Despite fibrosis causing diastolic dysfunction and impaired electrical conduction, responsible for arrhythmia-induced sudden cardiac death, the mechanisms are poorly defined and effective therapies are lacking. Here we show that crosstalk between cardiac cytotoxic memory CD8+ T cells and overly stressed cardiomyocytes is essential for development of non-ischemic hypertensive cardiac fibrosis.Methods and resultsCD8 T cell depletion in hypertensive mice, strongly attenuated CF, reduced cardiac apoptosis and improved ventricular relaxation. Interaction between cytotoxic memory CD8+ T cells and overly stressed cardiomyocytes is highly dependent on the CD8+ T cells expressing the innate stress-sensing receptor NKG2D and stressed cardiomyocytes expressing the NKG2D activating ligand RAE-1. The interaction between NKG2D and RAE-1 results in CD8+ T cell activation, release of perforin, cardiomyocyte apoptosis, increased numbers of TGF-β1 expressing macrophages and fibrosis. Deleting NKG2D or perforin from CD8+ T cells greatly attenuates these effects. Activation of the cytoplasmic DNA-STING-TBK1-IRF3 signaling pathway in overly stressed cardiomyocytes is responsible for elevating RAE-1 and MCP-1, a macrophage attracting chemokine. Inhibiting STING activation greatly attenuates cardiomyocyte RAE-1 expression, the cardiomyocyte apoptosis, TGF-β1 and fibrosis.ConclusionOur data highlight a novel pathway by which CD8 T cells contribute to an early triggering mechanism in CF development; preventing CD8+ T cell activation by inhibiting the cardiomyocyte RAE-1-CD8+ T cell-NKG2D axis holds promise for novel therapeutic strategies to limit hypertensive cardiac fibrosis.
Application of visual placement of a nasojejunal indwelling feeding tube in intensive care unit patients receiving mechanical ventilation
Authors: Chen Yuequn , Tian Xin , Liu Cheng , Zhang Liqin , Xv Yueyuan , Xv Shuang 
Published: November 2022

BackgroundCompared with nasogastric nutrition, nasojejunal nutrition may prevent some complications of critically ill patients by maintaining better nutritional status, and blind placement of nasojejunal dwelling feeding tubes is widely used. However, the visual placement seems to be safer and more effective than the blind placement, and is still seldom reported.ObjectiveWe tried to develop visual placement of a nasojejunal feeding tube in intensive care unit patients.MethodsA total of 122 patients receiving mechanical ventilation were admitted to the Department of Critical Care Medicine of the Fifth Affiliated Hospital of Wenzhou Medical University and received the placement of nasojejunal feeding tubes. These patients were randomly and evenly assigned into two groups, one group receiving visual placement of nasojejunal dwelling feeding tubes and another group receiving blind placement. Actual tube placement was confirmed by X-ray. The primary outcome included the success rates of first placement of feeding tubes. The secondary outcome included the time of tube placement, complications, the total cost, heart rates and respiratory rates.ResultsThe primary outcome showed that the success rates of first placement were 96.70% (59 cases/61 cases) in the visual placement group, and two cases failed due to pyloric stenosis and gastroparesis. The success rates were 83.6% (51 cases/61 cases) in the blind placement group and 10 cases failed due to either wrong placement or retrograde tube migration. The success rates in the visual placement group were higher than that in the blind placement group (P = 0.015). The secondary outcome showed that the time of tube placement in the visual placement group was shorter than that in the blind placement group (P &lt; 0.0001). The cost of tube placement in the visual placement group was higher than that in the blind placement group (P &lt; 0.0001). The statistical differences in complications, heart and respiratory rates were insignificant between the two groups (P &gt; 0.05).ConclusionCompared with the blind placement, the visual placement shortened the time of nasojejunal tube placement and increased success rates of first placement. The visual placement was more efficient, easy to operate, safe, and has potential clinical applications.
Preoperative plasma visfatin may have a dual effect on the occurrence of postoperative delirium
Authors: Kang Ning , Yang Ning , Zhao Kaixuan , Li Zhengqian , Zhang Wenchao , Han Yongzheng , Liu Kaixi , Song Yanan , Chen Lei , Li Yue , Hong Jingshu , Li Yitong , Guo Xiangyang , Wang Geng , Yuan Yi 
Published: November 2022

BackgroundVisfatin is considered to be a “novel pro-inflammatory cytokine.” Neuroinflammatory response is one of the important mechanisms of postoperative delirium (POD). The relationship between preoperative plasma visfatin and POD is unclear.ObjectiveTo investigate the relationship between preoperative plasma visfatin concentrations and POD (primary outcome) in older hip fracture patients and to explore whether it affects POD through inflammatory factors.Materials and methodsThis prospective cohort study enrolled 176 elderly patients who were scheduled for hip fracture surgery. Preoperative plasma was collected on the morning of surgery, and visfatin levels were measured. Interleukin (IL)-1 and IL-6 were measured using patients’ plasma collected on the first day after surgery. We used the 3-min diagnostic interview for Confusion Assessment Method-defined delirium (3D-CAM) twice daily within the 2 days after surgery to assess whether POD had occurred. Restricted cubic splines and piecewise regression were used to explore the relationship between preoperative plasma visfatin concentrations and POD, and further mediation analysis was used to verify whether visfatin plays a role in POD through regulating inflammatory factors.ResultsThe incidence of POD was 18.2%. A J-shaped association was observed between preoperative plasma visfatin levels and POD. The risk of POD decreased within the lower visfatin concentration range up to 37.87 ng/ml, with a hazard ratio of 0.59 per 5 ng/ml [odds ratio (OR) = 0.59, 95% confidence interval (CI) = 0.37–0.95], but the risk increased above this concentration (P for non-linearity &lt; 0.001, with a hazard ratio of 1.116 per 10 ng/ml; OR = 1.10, 95% CI = 1.02–1.23). Mediation effect analysis showed that when the plasma visfatin concentration was higher than 37.87 ng/ml, the effect of visfatin on POD was mediated by IL-6 (p &lt; 0.01). A significant indirect association with postoperative plasma IL-6 was observed between preoperative plasma visfatin and POD (adjusted β = 0.1%; 95% CI = 4.8∼38.9%; p &lt; 0.01).ConclusionVisfatin is the protective factor in POD when the preoperative plasma visfatin concentration is below 37.87 ng/ml, but when it exceeds 37.87 ng/ml, the visfatin concentration is a risk factor for POD, which is mediated by postoperative plasma IL-6. The results suggest that preoperative visfatin may have a dual effect on the POD occurrence.Clinical trial registration[www.ClinicalTrials.gov], identifier [ChiCTR21 00052674].
Giant cell arteritis: A population-based retrospective cohort study exploring incidence and clinical presentation in Canterbury, Aotearoa New Zealand
Authors: Lyne Suellen A. , Ruediger Carlee , Lester Susan , Chapman Peter T. , Shanahan Ernst Michael , Hill Catherine L. , Stamp Lisa 
Published: November 2022

Background/aimTo determine the epidemiology and clinical features of giant cell arteritis (GCA) in Canterbury, Aotearoa New Zealand, with a particular focus on extra-cranial large vessel disease.MethodsPatients with GCA were identified from radiology and pathology reports, outpatient letters and inpatient hospital admissions in the Canterbury New Zealand from 1 June 2011 to 31 May 2016. Data was collected retrospectively based on review of electronic medical records.ResultsThere were 142 cases of GCA identified. 65.5% of cases were female with a mean age of 74.2 years. The estimated population incidence for biopsy-proven GCA was 10.5 per 100,000 people over the age of 50 and incidence peaked between 80 and 84 years of age. 10/142 (7%) people were diagnosed with large vessel GCA, often presenting with non-specific symptoms and evidence of vascular insufficiency including limb claudication, vascular bruits, blood pressure and pulse discrepancy, or cerebrovascular accident. Those with limited cranial GCA were more likely to present with the cardinal clinical features of headache and jaw claudication. Patients across the two groups were treated similarly, but those with large vessel disease had greater long-term steroid burden. Rates of aortic complication were low across both groups, although available follow-up data was limited.ConclusionThis study is the first of its kind to describe the clinical characteristics of large vessel GCA in a New Zealand cohort. Despite small case numbers, two distinct subsets of disease were recognized, differentiating patients with cranial and large vessel disease. Our results suggest that utilization of an alternative diagnostic and therapeutic approach may be needed to manage patients with large vessel disease.