bluuebunny/crossref_metadata_2025_split huggingface dataset:
Texture Feature Extraction From Microscope Images Enables Robust Estimation of ER Body Phenotype in Arabidopsis
Authors: Basak Arpan Kumar , Mirzaei Mohamadreza , Strzałka Kazimierz , Yamada Kenji 
Published: June 2021

Abstract
Background:

Cellular components are controlled by genetic and physiological factors that define their shape and size. However, quantitively capturing the morphological characteristics and movement of cellular organelles from micrograph images is challenging, because the analysis deals with complexities of images that frequently lead to inaccuracy in the estimation of the features. Here we show a unique quantitative method to overcome biases and inaccuracy of biological samples from confocal micrographs.
Results:

We generated 2D images of cell walls and spindle-shaped cellular organelles, namely ER bodies, with a maximum contrast projection of 3D confocal fluorescent microscope images. The projected images were further processed and segmented by adaptive thresholding of the fluorescent levels in the cell walls. Micrographs are composed of pixels, which have information on position and intensity. From the pixel information we calculated three types of features (spatial, intensity and Haralick) in ER bodies corresponding to segmented cells. The spatial features include basic information on shape, e.g., surface area and perimeter. The intensity features include information on mean, standard deviation and quantile of fluorescence intensities within an ER body. Haralick features describe the texture features, which can be calculated mathematically from the interrelationship between the pixel information. Together these parameters were subjected to multivariate analysis to estimate the morphological diversity. Additionally, we calculated the displacement of the ER bodies using the positional information in a time-lapse image. We captured similar morphological diversity and movement within ER body phenotypes on several microscopy experiments performed in different settings and scanned under different objectives. We then described differences in morphology and movement of ER bodies between A. thaliana wild type and mutants deficient in ER body-related genes.
Conclusions:

The findings unexpectedly revealed multiple genetic factors that are involved in the shape and size of ER bodies in A. thaliana. This is the first report showing morphological characteristics in addition to the movement of cellular components and quantitatively summarises plant phenotypic differences even in plants that show similar cellular components. The estimation of morphological diversity was independent of the cell staining method and the objective lens used in the microscopy. Hence, our study enables a robust estimation of plant phenotypes by recognizing small differences of complex cell organelle shapes and their movement, which is beneficial in a comprehensive analysis of the molecular mechanism for cell organelle formation that is independent of technical variations.
How Phosphatidylserine Is Exposed on Tumor Cells Determines The Tumor’s Microenvironment and the Success or Failure of Checkpoint Therapy
Authors: Kennedy James Randall 
Published: June 2021

Abstract
One constant in all malignant somatic tumors is their continuous growth and it is hypothesized that there are only two types of cell mutations that can cause this and that their microenvironments are determined by how those mutated cells eventually die and by how phosphatidylserine (PS) is exposed on their surface. When a mutation in a cell causes its rate of mitotic cell division to continuously exceed the rate necessary for its replacement after its programed cell death (PCD) a continuously growing tumor will form and all of the tumor cells will expose PS by the Xkr8 transmembrane scramblase molecule when they die causing an inflammatory and immune suppressive microenvironment. When a mutation in a cell eliminates PCD a continuous tumor growth begins because all those cells will continue dividing until they die a senescent death where PS is exposed by the TMEM16F scramblase molecule and causes an inflammatory microenvironment. Inflammation stresses somatic cells to expose checkpoint molecules (CPMs) on them and on immune cells that could potentially eliminate them. Only in tumors where PCD has been eliminated will CPM be exposed and only in them will immune checkpoint inhibitors (ICIs) be effective.
CircPTK2 Suppresses the Progression of Gastric Cancer by Targeting miR-196a-3p/AATK Axis
Authors: Gao Ling , Xia Tingting , Qin Mingde , Xue Xiaofeng , Jiang Linhua , Zhu Xinguo 
Published: June 2021

Abstract
BackgroundGastric cancer is a type of malignant tumor with high morbidity and mortality. It has been shown that circular RNAs (circRNAs) exert critical functions in gastric cancer progression via working as microRNA (miRNA) sponges to regulate gene expression. However, the role and potential molecular mechanism of circRNAs in gastric cancer remain largely unknown.MethodsCircPTK2 (hsa_circ_0005273) was identified by bioinformatics analysis and validated by RT-qPCR assay. Bioinformatics prediction, dual-luciferase reporter and RNA pull down assays were used to determine the interaction between circPTK2, miR-196a-3p, AATK.ResultsThe level of circPTK2 was markedly downregulated in gastric cancer tissues. Upregulation of circPTK2 suppressed the proliferation, migration and invasion of gastric cancer cells, while downregulation of circPTK2 exhibited opposite effects. Mechanically, circPTK2 could competitively bind to miR-196a-3p and prevent miR-196a-3p to reduce the expression of AATK. In addition, circPTK2 overexpression inhibited tumorigenesis in a xenograft mouse model of gastric cancer.ConclusionCollectively, circPTK2 functions as a tumor suppressor to suppress gastric cancer cell proliferation through regulating miR-196a-3p/AATK axis, suggesting that circPTK2 may serve as novel therapeutic target for gastric cancer.
Allometric Models for Aboveground Biomass of Six Common Subtropical Shrubs and Small Trees
Authors: Huang Cheng , Feng Chun , Ma Yuhua , Liu Hua , Wang Zhaocheng , Yang Shaobo , Wang Wenjing , Fu Songling , Chen Han Y. H. 
Published: June 2021

Abstract
Background: The aboveground biomass (AGB) of shrubs and small trees is the main component for the productivity and carbon storage of understory vegetation in subtropical natural secondary forests. However, few allometric models exist for shrubs and small trees, even though they can accurately evaluate understory vegetative biomass. Methods: To estimate the ABG of six common shrub and small tree species, we utilized harvesting to sample 206 individuals, and developed species-specific and multi-species allometric models based on four predictors including height (H), stem diameter (D), crown area (Ca), and wood density (ρ). Results: As expected, these six shrub and small tree species possessed greater biomass in their stems in contrast to branches, with the lowest biomass in the leaves. Species-specific allometric models that employed D and the combined variables of D2H and ρDH as predictors, could accurately estimate the components and total AGB, with R2 values ranging from between 0.602 and 0.971. A multi-species shrub allometric model revealed that ρDH was the best predictor, with R2 values ranging from between 0.809 and 0.890. Conclusions: These results indicated that H and D were effective predictors for the models to estimate the AGB of the six shrub and small tree species, and the introduction of ρ improved their accuracy. The optimal model selected in this study could be applied to estimate the biomass of shrubs and small trees in the subtropical regions.
Preparation and Characterization of Sodium Alginate Polymeric Scaffold by Electrospinning Method for Skin Tissue Engineering Application
Authors: Jadbabaei Sorour , Naiemi Farid , Ebadi-Dehaghani Hassan , Kolahdoozan Majid 
Published: June 2021

Abstract
Sodium alginate (SA) approved its high potential in tissue engineering and regenerative medicine. One of the main weaknesses of this polysaccharide is its low spinnability which nanofiber based scaffolds are the interest of scientists in biomedical engineering. The main aim of this study was to improve the spinnability of SA in combination with polyvinyl alcohol (PVA). It was also tried to optimize the main parameters in electrospinning of the optimized SA;PVA ratio including voltage, flow rate, and working space. To aim this, Response surface methodology under central composite design was employed to design the experiments scientifically. The final nanofiber scaffolds were studied using scanning electron microscopy, Fourier transform infrared spectroscopy, degradability, swelling, tensile strength, porosity, nanofiber diameter, contact angle, and cytotoxicity. Based on the results, the best ratio for SA:PVA was 1:6.5. The solution with this concentration was spinnable in various values for the process parameters. The fabricated scaffolds under these conditions revealed good physical, chemical, mechanical, and biological features. L929 cell lines revealed high viability during 48 h of culture. The results revealed the uniform and homogeneous nanofibers with the regular size distribution (166 nm) were obtained at 30 kV, 0.55 µl/h, and 12.5 cm. To sum up, the optimized ratio under the reported conditions can be a good biologically compatible candidate for skin tissue engineering.
Study Of The Effect Of Different Ratios of Forage To Concentrate On Performance And Carcass Traits Of Zel Fattening Lambs
Authors: Kashani Seyed Mohsen Mousavi , Gharahveysi Shahabodin , Khorshidi Kaveh Jafari 
Published: June 2021

Abstract
Fattening refers to the proper management and feeding of livestock to achieve maximum weight gain at a minimum cost over a specified period of time. This study aimed to determine the most effective ratio of forage to concentrate on feed intake, performance, and carcasses of male Zel fattening lambs. The present study was performed using 20 lambs of 16-week-old for 90 days in a completely randomized design with four treatments and five replications at the Islamic Azad University of Qaemshahr. Experimental treatments included different ratios of forage to concentrate (80:20, 70:30, 60:40, and 50:50). Traits were measured during the fattening period. The collected data were analyzed by LSmeans procedure and regression in SAS software. Effect of different ratios of forage to concentrate was significant on all performance traits (p < 0.01), slaughter weight (p < 0.05), weight gain during rearing (p < 0.05), daily weight gain (p < 0.05), feed intake (p < 0.01), feed conversion ratio (p < 0.01), the weight of digestive system contents (p < 0.05), hot and cold carcass weight (p < 0.05), carcass percentage (p < 0.05) and thickness Backfat (p < 0.05). The linear change in the mentioned traits is due to the increase of the concentrate to forage ratio (p < 0.01). As the percentage of concentrate in the ration increases, feed intake increases. The concentrate is palatable and contains more energy and nutrients than forage. Therefore, lambs that consumed more concentrate had higher body weight and slaughter weight. Based on the results for optimal performance in fattening lambs, a ration with the ratio of forage to concentrate equal (50:50) is recommended.
Cantharidin-Loaded Biomimetic MOF Nanoparticles Cascade To Enhance Fenton Reaction Based On Amplified Photothermal Therapy
Authors: Cheng Xiao , Liu Ye , Zhou Hao , Leng Junke , Dai Xiaofeng , Wang Dong , Ma Kun , Cui Changhao , Fu Jijun , Guo Zhaoming 
Published: June 2021

Abstract
The treatment efficiency of Fenton reaction is expected to be greatly restricted due to problems such as inefficient delivery of Fenton catalysis, limited H 2 O 2 concentration and uneven tumour tissue. Accurate photothermal therapy (PTT) can to some extent improve the efficiency of Fenton catalysis by raising temperature. However, the heat shock response (HSR) of tumour cells caused by PTT and Fenton reaction can attenuate the treatment effect. In this study, we developed a combined treatment platform based on the Fenton reaction mediated by iron ions consisting of a metal organic framework, i.e., PPy-CTD@MIL-100@MPCM nanoparticles (PCMM NPs), and we explored the inhibitory effect of PCMM NPs on the heat shock response (HSR). PCMM NPs can be recruited into tumour tissues through the response of biomacromolecules on the surface of macrophage cell membranes (MPCMs) to tumour cell signaling molecules, thereby increasing retention and accumulation. The photothermal effect of polypyrrole (PPy) can stimulate the HSR of tumour, and loaded HSP inhibitor-cantharidin (CTD) can inhibit this response to a large extent. In addition, the heat generated during the PTT process can accelerate the release of iron ions from the PCMM NPs and simultaneously improve the efficiency of the Fenton reaction to achieve a combined treatment of tumour PTT, Fenton therapy and chemotherapy.
Influence of the Key Process Parameters in Hydrodynamic Deep Drawing Utilizing a Combined Floating and Static Die Cavity
Authors: Wang Huiting , Kong Jianfei , Pan Hongbo , Fang Jinxiu , Shen Xiaohui 
Published: June 2021

Abstract
This study focus on the effects of the key process parameters during a modified hydrodynamic deep drawing utilizing a combined floating and static die cavity (HDDC). A two-stage hydraulic loading path is recommended in the novel process, and each stage of the hydraulic loading path is a linear loading path with an inflection point. The method to evaluate the wrinkle and forming dimension precision of the formed parts is introduced at first. Then the influence of the key parameters of the two-stage hydraulic loading path as well as the blank holder force on the dimension accuracy and surface quality of the formed parts was studied in detail. The results showed that the influence of the liquid pressure during the second stage is more significant than that in the first stage in hydrodynamic deep drawing utilizing a combined floating and static die cavity. The initial pressure of the second stage and the maximum pressure arriving moment during this stage have a significant impact on the dimensional accuracy of the formed parts, and the smaller initial pressure or the later the maximum pressure of the second stage arrives, the higher the accuracy of the formed part is. Similarly, the influence of the blank holder force in the second stage on the forming accuracy is more significant than that in the first stage.
Old Age, Number and Specific Comorbidities are Closely Related to Progression and Poor Prognosis in Patients with COVID-19
Authors: Liu Dafeng , Zheng Yongli , Kang Jun , Wang Dongmei , Bai Lang , Mao Yi , Zha Guifang , Tang Hong , Zhang Rengqing 
Published: June 2021

Abstract
Background— Some patients with comorbidities and rapid disease progression have a poor prognosis.Aim—In this study, we aimed to investigate the distribution characteristics of comorbidities and their relationship with disease progression and outcomes of COVID-19 patients.Methods— A total of 718 COVID-19 patients were divided into five clinical type groups and eight age-interval groups. The distribution characteristics of comorbidities were compared between the different clinical type groups and between the different age-interval groups, and their relationships with disease progression and outcomes of COVID-19 patients were assessed.Results—Approximately 88.62% (637/718) of the COVID-19 patients were twenty to fifty-nine years old. Approximately 65.73% (554/718) had one or more comorbidities, and common comorbidities included non-alcoholic fatty liver disease (NAFLD), hyperlipidaemia, hypertension, diabetes mellitus (DM), chronic hepatitis B (CHB), hyperuricaemia and gout. COVID-19 patients with comorbidities were older, especially those with chronic obstructive pulmonary disease (COPD) and cardiovascular disease (CVD). Hypertension, DM, COPD, chronic kidney disease (CKD) and CVD were mainly found in severe COVID-19 patients, and hypertension, CKD and CVD were primarily associated with those who died. Risk factors included the number of comorbidities and hyperlipidaemia for disease severity, age, the number of comorbidities, hyperlipidaemia, NAFLD and COPD for the virus negative conversion time, and the number of comorbidities and CKD for prognosis. Number of comorbidities played a predictive role in disease progression and outcomes.Conclusions—These findings provide a reference for clinicians to focus on the number and specific comorbidities in COVID-19 patients to predict disease progression and prognosis.Clinical Trial Registry: Chinese Clinical Trial Register ChiCTR2000034563
Short-term Effects of a Three-week Inpatient Post-COVID-19 Pulmonary Rehabilitation Program - a Prospective Observational Study
Authors: Hayden Markus C. , Limbach Matthias , Schuler Michael , Merkl Steffen , Schwarzl Gabriele , Jakab Katalin , Nowak Dennis , Schultz Konrad 
Published: June 2021

Abstract
Background:The clinical course of coronavirus disease 2019 (COVID-19) varies distinctly. Particularly after severe or critical courses, i.e., after hospitalization, clinical manifestations frequently persist after the acute phase. However, symptoms may also persist after initially milder courses that can be treated in an outpatient setting. For patients who remain symptomatic after COVID-19, pulmonary rehabilitation (PR) is recommended. However, only few studies investigated the effectiveness of PR, especially considering different disease courses. The main objective was to evaluate the feasibility, safety, and efficacy of post-COVID-19 PR.Methods:A total of 120 post-COVID-19 patients who were referred to the Bad Reichenhall Clinic between April 2020 and January 2021 were asked to participate in this prospective observational study. PR was tailored to each patient’s individual needs and was based on the current recommendations. The primary outcome dyspnea was assessed with numerical rating scales and the modified Medical Research Council (mMRC) dyspnea scale. Secondary outcomes included other symptoms such as cough and sputum; physical capacity; lung function; fatigue; quality of life (QoL); depression; and anxiety. Furthermore, patients rated the overall effectiveness of PR and their subjective change in health status.Results:A total of 108 patients (mean age 55.6±10.1 years, 45.4% female) were included and were assigned to 3 groups depending on the referral mode (A: severe acute; B: severe after interval, C: mild after interval). At the end of PR, we detected improvements in the intensity of exertional dyspnea, physical capacity, QoL, fatigue, and depression in the overall group, with large effect sizes (Cohen’s d>0.8). Moderate effect sizes (0.5≤d<0.8) were found for resting dyspnea and the mMRC-dyspnea scale. Cohen’s d>0.4 was found for vital capacity, forced expiratory volume in one second, partial oxygen pressure, and anxiety. Significant but rather small effect sizes (0.2<d<0.4) were found for cough, sputum, pain, and other lung function parameters.Conclusions:PR is feasible, safe, and effective after acute COVID-19, which was true for all 3 groups analyzed, with a trend toward greater efficacy after severe courses of COVID-19 and an earlier start of PR after acute COVID-19. Therefore, all post-COVID-19 patients who remain symptomatic should be offered PR.Trial registration: German Clinical Trials Register, DRKS00023180. Registered 01 September 2020 – Retrospectively registered, https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00023180
Real-World Data from Selective Laser Trabeculoplasty in Brazil
Authors: Abe Ricardo Y. , Maestrini Heloísa A. , Guedes Guilherme B. , Nascimento Marcelo M. , Iguma Camila I. , Santos Hérika Danielle Miranda , Nasr Muna Georges , Lucena-Junior Ricarte P , Prata Tiago S. 
Published: June 2021

Abstract
Purpose: Evaluate real-world data of outcomes from selective laser trabeculoplasty (SLT) performed in different regions of Brazil and also investigate potential predictors of success associated with treatment.Methods: Multicenter retrospective case series with patients who underwent a primary SLT procedure. Results: A total of 835 eyes from 835 patients were included. The mean follow-up was 916.8 ± 563.0 days. The mean age was 64.5 ± 14.9 years and 56.6% were women. We observed a intraocular pressure reduction comparing baseline to post-SLT measurements (18.4 ± 3.8mmHg versus 14.8 ± 3.5mmHg; P<0.001) and mean number of glaucoma medications (1.8 ± 1.3 versus 1.4 ± 1.4; P<0.001). We observed visual acuity loss over time (0.1 ± 0.3 versus 0.2 ± 0.3 logMAR, baseline and post-SLT, respectively, P=0.009) and decrease in visual field mean deviation values (-5.4 ± 5.9 versus -5.7 ± 6.0dB; P=0.054) The Kaplan-Meier survival analysis showed an estimated probability of treatment success of 88% at 12 months, declining to 70% at 24 months and 54% at 36 months post-SLT. In the multivariable model, we found that a denser angle pigmentation (HR 0.69; 95% CI: 0.57 – 0.85, P=0.001) and corticosteroid treatment following SLT (HR 0.59; 95% CI: 0.39 – 0.91, P=0.018) were significantly associated with a lower risk for failure. Conclusions: Primary SLT achieved relatively high success rates without sight-threating complications in this real-world study with a large sample of Brazilian patients. These findings corroborate previous studies regarding SLT outcomes and may help clinicians to identify the best candidates for laser treatment.
Realization of quantum nanomagnets in metal-free porphyrins
Authors: Wang Shiyong , Zhao Yan , Jiang Kaiyue , Li Can , Liu Yufeng , Zhu Gucheng , Guan Dandan , Li Yaoyi , Zheng Hao , Liu Canhua , Jia Jin-Feng , Zhuang Xiaodong 
Published: June 2021

Abstract
Quantum nanomagnets exhibit collective quantum behaviors beyond the usual long range ordered states due to the interplay of low dimension, competing interactions and strong quantum fluctuations. Despite numerous theoretical works treating quantum magnetism, the experimental study of individual quantum nanomagnets remains very challenge, greatly hindering the development of this cutting-edge field. Here, we demonstrate an effective strategy to realize individual quantum nanomagnets in metal-free porphyrins by using combined on-surface synthesis and atom manipulation approaches, with the ultimate ability to arrange coupled spins one by one as envisioned by Richard Feynman 60 years ago. A series of metal-free porphyrin nanomagnets have been constructed on Au(111) and their collective magnetic properties have been thoroughly characterized on the atomic scale by scanning probe microscopy together with theoretical calculations. Our results reveal that the constructed S=1/2 antiferromagnets host a gapped excitation in consistent with isotropic Heisenberg antiferromagnets S=1/2 model, while the S=1 antiferromagnets with odd-number units exhibit two zero-mode end states due to quantum fluctuations. Our achieved strategy not only provides a unique testing bed to study the strongly correlated effects of quantum magnetism in purely organic materials, but expands the functionalities of porphyrins with implications for quantum technological applications.