bluuebunny/crossref_metadata_2025_split huggingface dataset:
CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images
Authors: Tao Yicheng , Feng Fan , Luo Xin , Reihsmann Conrad , Hopkirk Alexander , Saunders Diane , Brissova Marcela , Parker Stephen , Liu Jie 
Published: November 2022

Abstract
Recent studies show that cellular neighborhoods play an important role in evolving biological events such as cancer and diabetes. Therefore, it is critical to accurately and efficiently identify cellular neighborhoods from spatially-resolved single-cell transcriptomic data or single-cell resolution tissue imaging data. In this work, we develop CNTools, a computational toolbox for end-to-end cellular neighborhood analysis on annotated cell images, comprising both the identification and analysis steps. It includes state-of-the-art cellular neighborhood identification methods and post-identification smoothing techniques, with our newly proposed Cellular Neighbor Embedding (CNE) method and Naive Smoothing technique, as well as several established downstream analysis approaches. We applied CNTools on three real-world CODEX datasets and evaluated identification methods with smoothing techniques quantitatively and qualitatively. It shows that CNE with Naive Smoothing overall outperformed other methods and revealed more convincing biological insights. Suggestions on how to choose identification methods and smoothing techniques according to input data are provided at last.
Growth rate and projected age at sexual maturity for immature hawksbill turtles and green turtles foraging in the remote marine protected area of Aldabra Atoll
Authors: Sanchez Cheryl , Bunbury Nancy , Mortimer Jeanne A , A'Bear Luke , Betts Michael , von Brandis Rainer , Burt April J , Cooke Lorraine , de Crommenacker Janske van , Currie Jock C , Doak Naomi , Fleischer-Dogley Frauke , Mederic Emma , Mels Bruno , Pistorius Pierre , Richards Heather , Casale Paolo 
Published: November 2022

Abstract
Changes in marine ecosystems from human stressors, and concerns over how species will respond to these changes have emphasized the importance of understanding and monitoring crucial demographic parameters for population models. Long-lived, migratory, marine vertebrates such as sea turtles are particularly vulnerable to changes. Life-history parameters like growth in body size can be largely influenced by environmental processes which can impact population growth. We analyzed a 40-year (1981–2021) capture-mark-recapture dataset from the protected UNESCO World Heritage Site, Aldabra Atoll, Seychelles, to estimate key population parameters, including body growth, for immature green turtles (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata). Curved carapace length (CCL) ranged from 34.3–110.9 cm (mean ± SD: 51.0 ± 11.4 cm, n = 1191) for green turtles and 28.7–89.4 cm (47.7 ± 14.4 cm, n = 538) for hawksbill turtles. Recapture events, with an 11-month minimum period, revealed a mean annual growth rate of 3.2 ± 1.5 cm year-1 for green turtles (n = 75) and 2.8 ± 1.4 cm year-1 for hawksbill turtles (n = 110). Hawksbill turtles exhibited a non-monotonic growth rate while no significant growth-size relationship was detected for green turtles. Green turtle mean annual growth per 10-cm size class was highest in the larger size classes. Hawksbill turtle growth rate was highest in the larger size classes (50‒69.9 cm) then declined in the largest size class (80‒79.9 cm). Per the growth functions, green turtles and hawksbill turtles may spend > 8 and 18 years, respectively, using Aldabra as a foraging ground.
An efficient method for high-density multimodal salt-and-pepper noise removal of MRI images
Authors: Ebrahimnejad Javad , Naghsh Alireza 
Published: November 2022

Abstract
Medical image noise reduction is a significant and challenging area in image processing. A new adaptive window-based solution for the removal of high-density multimodal salt-and-pepper noise of the brain MRI images is proposed in this paper. In this efficient method, for each pixel of the noisy input image, an adaptive n x n window is considered in the neighborhood of that pixel, where n depends on the noise value. The higher the noise density, the larger the window size in which healthy pixels are found. If they are not noisy, the pixels of this window are weighted according to their distance from the desired pixel. The greater the distance, the less weight they gain. Then, the weighted sum of the neighboring pixels is averaged, and the noisy pixel replaces with the resulting value. To evaluate the proposed method against multimodal salt-and-pepper noise, which simultaneously appears in an image from 1–98%, 208 images from seven MRI databases are applied. The results show the excellent performance of the proposed method. The mean Peak Signal to Noise Ratio (PSNR) of whole databases is 29.3465. As a preprocessing step, the efficient proposed method shows highly accurate results on the brain MRI images. After applying the noise removal method, the quality and the Structural Similarity (SSIM) increased. In this study, in addition to removing multimodal noise in an image, noise with a specific density (single mode) in each image is also removed with similar or better results.
Activation of NFAT by HGF and IGF-1 via ARF6 and its effector ASAP1 promotes uveal melanoma metastasis
Authors: Yoo Jae Hyuk , Richards Jackson , Shin Donghan , Pryor Rob , Sorensen Lise , Sun Zhonglou , So Wonmi , Park Garam , Wolff Roger , Truong Amanda , McMahon Martin , Grossmann Allie , Harbour William , Zhu Weiquan , Odelberg Shannon 
Published: November 2022

Abstract
Preventing or effectively treating metastatic uveal melanoma (UM) is critical because it occurs in about half of patients and confers a very poor prognosis. There is emerging evidence that hepatocyte growth factor (HGF) and insulin-like growth factor 1 (IGF-1) promote metastasis and contribute to the striking metastatic hepatotropism observed in UM metastasis. However, the molecular mechanisms by which HGF and IGF-1 promote UM liver metastasis have not been elucidated. ASAP1, which acts as an effector for the small GTPase ARF6, is highly expressed in the subset of uveal melanomas most likely to metastasize. Here, we found that HGF and IGF-1 hyperactivate ARF6, leading to its interaction with ASAP1, which then acts as an effector to induce nuclear localization and transcriptional activity of NFAT1. Inhibition of any component of this pathway impairs cellular invasiveness. Additionally, knocking down ASAP1 or inhibiting NFAT signaling reduces metastasis in a xenograft mouse model of UM. The discovery of this signaling pathway represents not only an advancement in our understanding of the biology of uveal melanoma metastasis but also identifies a novel pathway that could be targeted to treat or prevent metastatic uveal melanoma.
Study on Effect of O 2 /H 2 O on CH 4 and NO x Removal with NTP
Authors: Li Hongyu , Cai Yunkai , Lü Lin 
Published: November 2022

Abstract
In this paper, the influence mechanism of O2/H2O/CO2 on the removal of CH4 and NOx by non-thermal plasma (NTP) combined with selective catalytic reduction of NOx by CH4 (NTP-CH4-SCR) were investigated. The results show that the increase of NTP energy density (0 J/L-491 J/L) promoted the CH4 removal but inhibited the NOx removal in NTP-CH4-SCR. In CH4-SCR, H2O could significantly reduce catalyst activity, adding 0.5% H2O decreased the removal efficiency of CH4 and NOx from 30–2.9% and 58.4–1.8% respectively. In NTP-CH4-SCR, the increase of H2O content (0.5%-10.4%) contributed to formation of oxidizing free radicals such as OH and HO2, thus the CH4 removal efficiency increased from 24.1–37.4%. The increase of O2 content (0%-10%) promoted the adsorption of NO and the reaction of adsorption products with CH4 oxidation products, causing the CH4 removal efficiency increased from 1.3–32.3% and NOx removal efficiency increased from 1.5–61.6% in CH4-SCR. Increasing O2 (0–10%) produced more O and HO2 radicals in NTP-CH4-SCR, resulting in the increase of CH4 removal efficiency from 18.6–44.9%. However, these O and HO2 radicals would react with N radicals to form NO2, NO3 et al., thus decreasing NOx removal efficiency from 68–40.8%. The change of CO2 concentration has little effect on CH4 and NOx removal efficiency.
A Matlab code of topology optimization by imposing the implicit floating projection constraint
Authors: Huang Xiaodong 
Published: November 2022

Abstract
This paper presents a Matlab code to implement the three-field floating projection topology optimization (FPTO) method using the linear material interpolation scheme. The material penalization scheme in the traditional element-based topology optimization approaches makes an optimal solution being close to 0/1 to avoid handling a large number of 0/1 constraints of the design variables. Instead, the implicit floating projection constraint in the FPTO method numerically simulates 0/1 constraints of the design variables so that even a linear material interpolation scheme can be employed. By gradually tightening 0/1 constraints, more and more design variables are pushed to 0/1 until an optimized element-based design with a clear topology is accurately represented by a smooth design. The implicit floating projection constraint provides a numerical engine for topology optimization, which is fundamentally different from the physical engine by material penalization. The Matlab code in this paper will focus on the numerical implementation of such an implicit constraint integrated with the common-used optimizer, e.g., optimality criteria (OC) or the method of moving asymptotes (MMA), as well as the extraction and evaluation of the smooth design. The Matlab code of the three-field FPTO method is also extended to other topology optimization problems. The provided Matlab code enables the readers to understand the FPTO method better and test this newly-developed topology optimization method for their own topology optimization problems.
GREB1L overexpression associates with good clinical outcomes in breast cancer
Authors: Dong Ke , Geng Chenchen , Zhan Xiaohong , Sun Zhi , Pu Qian , Li Peng , Song Haiyun , Zhao Guanghui , Gao Haidong 
Published: November 2022

Abstract
Background
Breast cancer is a malignant tumor with the highest incidence among women in the world. GREB1L is a protein coding gene. Previous studies have shown that GREB1L played an important role in lung adenocarcinoma and gastric adenocarcinoma. Currently, there is no relevant report about its role in breast cancer.
Methods
The Cancer Genome Atlas database was used to compare the expression level of GREB1L; TISIDB website was used for prognosis analysis; LinkedOmics database was used to predict the potential biological mechanism of GREB1L in breast cancer; Immunohistochemistry was used to detect the GREB1L expression level in breast tissue; Western blot was used to detect the GREB1L expression level in cell lines; Transwell assays, CCK8 cell proliferation assays and clone formation assays were used to detect the migration, invasion and proliferation and clone formation abilities of cells.
Results
GREB1L was highly expressed in breast cancer tissues and breast cancer cells; KEGG enrichment analysis suggested that GREB1L might participate in the regulation of Hedgehog signaling pathway; GREB1L affected the migration and invasion abilities of MCF7 and MDA-MB-231 cells, but not affected their proliferation and clone formation abilities. The overexpression of GREB1L in breast cancer predicted a favorable prognosis.
Conclusion
These results showed that GREB1L was involved in the development of breast cancer, and it may be a potential molecular marker to predict the prognosis of breast cancer.
Application of 4D Two-Colour LIF to Explore the Temperature Field of Laterally Confined Turbulent Rayleigh-Bénard Convection
Authors: Kashanj Sina , Nobes David S. 
Published: November 2022

Abstract
Recent studies show the significant effect of the third dimension and flow unsteadiness of laterally confined Rayleigh-Bénard convection (RBC). However, there are limited studies investigating 4D flow properties. The application of 4D two-colour laser-induced fluorescence to explore a laterally confined RBC at high Rayleigh number of Ra = 9.9 × 107 and Prandtl number of Pr = 6.1 is investigated using a scanning laser system. A two-colour, two dyes approach was employed to resolve the laser sheet intensity variations due to refractive index variations caused mainly by the generation of thermal plumes. Two temperature-sensitive fluorescent dyes with opposite sensitivities were used to enhance the overall temperature sensitivity to 7.3 % /℃. Details of the experimental procedure and optical system employed to reach such a high sensitivity is demonstrated. From the whole field temperature distribution, the dimensionless heat transfer coefficient, the Nusselt number, and its evolution was calculated for both hot and cold boundaries. Temperature field and Nusselt number obtained from 3D and 2D fields are reported to compare the results for these two scenarios. Thermal plumes were found to have a conical shape in the laterally confined RBC compared to the conventional mushroom shape. From visualization of the time-resolved 3D temperature field and 2D distribution of the Nusselt number, it was also found that only by volumetric measurement, temporal and spatial variations of the temperature and heat transfer can be evaluated. This shows that to evaluate the classic and ultimate theories, volumetric measurement is required for a coherent understanding of the physics.
Point-of-care Diagnosis and Monitoring of Hypofibrinolysis in the Critically Ill: Results from a Feasibility Study.
Authors: Coupland Lucy A. , Rabbolini David J. , Schoenecker Jonathan G. , Crispin Philip J. , Miller Jennene J. , Ghent Tony , Medcalf Robert L. , Aneman E. Anders 
Published: November 2022

Abstract
Background
In critical conditions such as sepsis, severe trauma, COVID-19 and non-COVID acute respiratory failure, hypofibrinolysis is associated with multi-organ dysfunction syndrome and death. The mechanisms underpinning hypofibrinolysis may include reduced tissue plasminogen activator (t-PA) and/or plasmin effect due to elevated inhibitor levels, reduced expression and/or exhaustion. This study in critically ill patients with hypofibrinolysis aimed to evaluate the ability of t-PA and plasminogen supplementation to restore fibrinolysis assessed by bedside viscoelastic testing (VET).
Methods
Prospective observational and interventional studies were undertaken in 28 critically ill patients identified as hypercoagulant and hypofibrinolytic using standard ClotPro VET. Hypercoagulation was defined as above normal values for clot amplitude on the EX-test (tissue factor (TF) activated coagulation) or FIB-test (TF activated coagulation with platelet inhibition). Hypofibrinolysis was defined as a clot lysis time > 300 seconds on the TPA-test (TF activated coagulation with t-PA accelerated fibrinolysis). In experimental VET, repeat TPA-tests were spiked with additional t-PA and/or plasminogen and the effect on lysis time determined. In a hypofibrinolytic patient, alteplase was administered intravenously over a 24-hr period with standard ClotPro VET repeated frequently throughout to monitor the effect on coagulation and fibrinolysis.
Results
In the ex-vivo studies, distinct response groups emerged with increased fibrinolysis observed following (i) additional t-PA supplementation only, or (ii) combined plasminogen and t-PA supplementation. A baseline TPA-test lysis time of > 1000 sec associated with the latter group. In the interventional study, alteplase administered as a 2-hr bolus (25 mg) followed by a 22-hr infusion (1 mg/hr) resulted in a gradual reduction in serial TPA-test lysis times.
Conclusions
ClotPro viscoelastic testing, the associated TPA-test and the novel spiked ex-vivo assays may be utilised to (i) investigate the potential mechanisms of hypofibrinolysis, (ii) guide corrective treatment, and (iii) monitor in real-time the treatment effect. Such a precision-medicine and personalised treatment approach to the management of hypofibrinolysis has the potential to increase treatment benefit, whilst minimising adverse events in hypofibrinolytic critically ill patients.
Trial Registration:
VETtiPAT ARF, a clinical trial evaluating the use of ClotPro-guided tissue plasminogen activator (alteplase) administration in hypofibrinolytic patients with acute respiratory failure is ongoing (ClinicalTrials.gov NCT05540834, registered 15 September 2022, retrospectively registered).
Effect of trabeculectomy on corneal clarity in primary open-angle glaucoma patients
Authors: IRGAT Saadet GÜLTEKİN , ÖZCURA Fatih , ALTUNEL Orhan 
Published: November 2022

Abstract
Purpose
To examine possible changes in Scheimpflug corneal densitometry 12 months after trabeculectomy and compare these measurements with healthy controls.
Methods
In the patient group, corneal densitometry with Scheimpflug Pentacam HR corneal topography was evaluated in three different corneal regions (0–2, 2–6, 6–10 mm) and four quadrants (upper, lower, temporal, nasal) before trabeculectomy and 12 months after surgery. It was compared with the control group. The number and duration of use of IOP-lowering agents, daily applications, and benzalkonium chloride (BAC) content were recorded before surgery.
Results
Mean IOP from 25.8 ± 4.7 to 14.5 ± 3.0 mm Hg (p < 0.001) and amount of pressure reducing agents from 3.5 ± 0.5 to 0.4 ± 0.5 ( P < 0.001) there was a statistically significant decrease. 85% of the topical agents contained benzalkonium chloride.Total corneal densitometry values at the 12th month before and after surgery in the POAG patient group were significantly decreased in all zones and quadrants except the nasal quadrant in the 2–6 mm zone and the temporal quadrant in the 6–10 mm zone. There was no statistically significant difference in all zones and quadrants when compared with the control group after surgery (p > 0.05).
Conclusion
Glaucoma surgeries not only reduce eye pressure but also protect corneal health.
Comparative genomic analysis of Halomonas campaniensis wild-type and ultraviolet radiation-mutated strains reveal genomic differences associated with increased ectoine production
Authors: Wang Zhibo , Li Yongzhen , Gao Xiang , Xing Jiangwa , Wang Rong , Zhu Derui , Shen Guoping 
Published: November 2022

Abstract
Ectoine is a natural amino acid derivative and one of the most widely used compatible solutes produced by Halomonas species that affects both cellular growth and osmotic equilibrium. The positive effects of UV mutagenesis on both biomass and ectoine content production in ectoine-producing strains have yet to be reported. In this study, the wild-type H. campaniensis strain XH26 (CCTCCM2019776) was subjected to UV-mutagenesis to increase ectoine production. Eight rounds of mutagenesis were used to generate mutated XH26 strains with different UV-irradiation exposure times. Ectoine extract concentrations were then evaluated among all strains using high performance liquid chromatography (HPLC) analysis, alongside whole genome sequencing with the PacBio RS II platform and comparison of the wild type strain XH26 and the mutant strain G8-52 genomes. The mutant strain G8-52 (CCTCCM2019777) exhibited the highest cell growth rate and ectoine yields among mutated strains in comparison with strain XH26. Further, ectoine levels in the aforementioned strain significantly increased to 1.51 ± 0.01 g L− 1 (0.65 g g− 1 of cell dry weight), representing a two-fold increase compared to wild-type cells (0.51 ± 0.01 g L− 1) when grown in culture medium for ectoine accumulation (CMEA). Concomitantly, electron microscopy revealed that mutated strain G8-52 cells were obviously shorter than wild-type strain XH26 cells. Moreover, strain G8-52 produced a relatively stable ectoine yield (1.50 g L− 1) after 40 days of continuous subculture. Comparative genomics analysis suggested that strain XH26 harbored 24 mutations, including 10 nucleotide insertions, 10 nucleotide deletions, and unique single nucleotide polymorphisms. Notably, the genes orf00723 and orf02403 (lipA) of the wild type strain mutated to davT and gabD in strain G8-52 that encoded for 4-aminobutyrate-2-oxoglutarate transaminase and NAD-dependent succinate-semialdehyde dehydrogenase, respectively. Consequently, these genes may be involved in increased ectoine yields. These results suggest that continuous multiple rounds of UV-mutation represents a successful strategy for increasing ectoine production, and that the mutant strain G8-52 is suitable for large-scale fermentation applications.
Bayesian analysis of linear regression models with autoregressive symmetrical errors and incomplete data
Authors: Garay Aldo William Medina , Medina Francyelle Lima , de Freitas Suelem Torres , Davila Victor Hugo Lachos 
Published: November 2022

Abstract
Observations collected over time are often auto correlated rather than independent, and sometimes include incomplete information, e.g. censored values reported as less or more than a level of detection and/or missing values. Another complication arises when the data departs significantly from normality, such as asymmetry and fat tails. In this paper, we propose Bayesian analysis of linear regression models with autoregressive symmetrical errors. The model considers the symmetric class of scale mixture of normal distributions, which include the normal, slash, contaminated normal and Student-t distributions as special cases. A Markov-chain Monte Carlo (MCMC) algorithm is tailored to obtain Bayesian posterior distributions of the unknown quantities of interest. The likelihood function is utilized to compute some Bayesian model selection measures. We evaluate the proposed model under different settings of censored and/or missing levels using simulated data. Finally, we illustrate the usage of our proposal through the analysis of a real dataset.
Genetic diversity analysis and EST-SSR fingerprinting construction of natural Populus euphratica and Populus pruinosa populations
Authors: Chen Xiang X. , Gai Zhong S. , Zhai Jun T. , Guo Xue F. , Wu Zhi H. , Li Zhi J. 
Published: November 2022

Abstract
Populus euphratica and Populus pruinosa are important tree species in northwest China. In this study, the codominant EST-SSR markers related to drought resistance genes was used to reveal the genetic diversity of P. euphratica and P. pruinosa populations. The results showed that those populations exhibited rich genetic diversity levels. Compared with other P. euphratica and P. pruinosa populations respectively, the genetic diversity of populations in southern Xinjiang was all the highest. The average fixed index of different populations indicated that the genetic relationship among P. euphratica populations was relatively far, while the relationship among the P. pruinosa populations was closer. The molecular variance analysis showed that the variation within populations was bigger than that among populations in the P. euphratica and P. pruinosa populations respectively. The cluster analysis showed that P. euphratica and P. pruinosa populations could be mainly classified into two clades represented by southern and northern Xinjiang respectively. The population structure and principal co-ordinates analysis indicated that the 47 natural P. euphratica populations have been divided into 4 clades, represented by the two populations in southern or southern Xinjiang respectively. The 17 natural P. pruinosa populations had been divided into 4 clades, consisted by the three County in southern Xinjiang, and Nilka County in northern Xinjiang. At the same time, The EST-SSR fingerprintings of 47 natural Populus euphratica and 17 natural Populus pruinosa have been constructed successfully. This study laid the foundation for the later priority protection of the genetic diversity populations of excellent drought resistance.