bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thyroid Cancer Overdiagnosis and Overtreatment: a cross- sectional study at a thyroid cancer referral center in Ecuador
Authors: Solis-Pazmino Paola , Salazar-Vega Jorge , Lincango-Naranjo Eddy , Garcia Cristhian , Koupermann Gabriela Jaramillo , Ortiz-Prado Esteban , Ledesma Tannya , Rojas Tatiana , Alvarado-Mafla Benjamin , Carcamo Cesar , Ponce Oscar J. , Brito Juan P. 
Published: January 2021

Abstract
Background: In contrast to the rapid increase in thyroid cancer incidence, the mortality has remained low and stable over the last decades. In Ecuador, however, thyroid cancer mortality has increased. The objective of this study is to determine possible drivers of high rates of thyroid cancer mortality, through a cross-sectional analysis of all patients attending a thyroid cancer referral center in Ecuador.Methods: From June 2014 to December 2017, a cross-sectional study was conducted at the Hospital de Especialidades Eugenio Espejo, a regional reference public hospital for endocrine neoplasia in adults in Quito, Ecuador. We identified the mechanism of detection, histopathology and treatment modalities from a patient interview and review of clinical records. Results: Among 452 patients, 74.8% were young adults and 94.2% (426) were female. 13.7% had a family history of thyroid cancer, and patients’ median tumor size was 2 cm. The incidental finding was 54.2% whereas 45.8% was non-incidental. Thyroid cancer histology reported that 93.3% had papillary thyroid cancer (PTC), 2.7% follicular, 1.5% Hurtle cells, 1.6% medullary, 0.7% poor differentiated, and 0.2% anaplastic carcinoma. The mean MACIS (metastasis, age, completeness, invasion, and size) score was 4.95 (CI 4.15-5.95) with 76.2% of the thyroid cancer patients having MACIS score less than or equal to 6. The very low and low risk of recurrence was 18.1% (79) and 62% (271) respectively. An analysis of 319 patients with non-metastatic thyroid cancer showed that 10.7% (34) of patients had surgical complications. Moreover, around 62.5% (80 from 128 patients with thyroglobulin laboratory results) of TC patients had a stimulated-thyroglobulin value equal or higher than 2 ng/ml. Overall, a poor surgical outcome was present in 35.1% (112) patients. Out of 436 patients with differentiated thyroid carcinoma, 86% (375) received radioactive iodine. Conclusion: Thyroid cancer histological characteristics and method of diagnosis are like those described in other reports without any evidence of the high frequency of aggressive thyroid cancer histology. However, we observed evidence of overtreatment and poor surgical outcomes that demand additional studies to understand their association with thyroid cancer mortality in Ecuador.
Mmu-miR-27a-5p Promotes the Polarization of Macrophages to the M2 Phenotype at the Site of Spinal Cord Injury in Mice
Authors: Yang Mingkun , Dang Xiaoqian , Zhang Xu , Liu Chuan , He Min 
Published: January 2021

Abstract
BackgroundTo investigate the effect of mmu-miR-27a-5p on macrophage polarization in the injured spinal cord and the recovery of motor function after spinal cord injury (SCI) in mice.MethodsA total of 160 specific-pathogen-free male mice were randomly divided into sham, model, mmu-miR-27a-5p, mmu-miR-27a-5p-negative control (NC) groups, with 40 mice in each group. Hindlimb motor function was assessed using the Basso Mouse scale (BMS) before injury and at 1, 3, 7, and 14 days after surgery. Spinal cord tissue samples were obtained at 1, 3, 7, and 14 days after surgery, and macrophage polarization types were detected by using western blot analysis, immunofluorescence, flow cytometry and RT-qPCR.ResultsThe BMS score in the mmu-miR-27a-5p group was significantly higher than that in the model and mmu-miR-27a-5p-NC groups at 7 and 14 days after SCI (X2=26.45-57.62, P<0.05). No significant changes in the expression of M1 markers IL-1β, TNF-α and M2 markers IL-10, Arginase-1 at each time point in the sham group (P=0.96). The expression of IL-1β and TNF-α was significantly lower, while the expression of IL-10 and Arginase-1 were significantly higher in the mmu-miR-27a-5p group as compared to the model and mmu-miR-27a-5p-NC groups at 7 and 14 days after SCI (P<0.05).Conclusion﻿Administration of mmu-miR-27a-5p can promote the polarization of macrophages to the M2 phenotype in the injured spinal cord, and improve motor function recovery within 14 days after SCI in mice.
Health System Preparedness for Coincidence of Natural Disasters and COVID-19: A Systematic Literature Review
Authors: Sohrabizadeh Sanaz , Yousefian Shiva , Bahramzadeh Amir hosein , Vaziri Mohammad Hosein 
Published: January 2021

Abstract
Background: In December 2019, the Chinese city of Wuhan has reported a novel pneumonia caused by COVID-19. While the COVID-19 pandemic has been increasingly affecting the world, the occurrence of natural disasters resulted in complex emergencies. The present review is aimed to identify the research focused on coincidence of natural disasters and COVID-19 and describe the preparedness and response actions applied by affected countries. Methods: This study was conducted and reported based on PRISMA checklist. The databases of Web of Sciences, PubMed, Scopus, Google Scholar and World Health Organization Library were searched. The inclusion criteria were all forms of published articles which investigated the dual risk or coincidence of natural disasters and COVID-19 pandemic. Once the studies selection was completed and the relevant papers was finalized, the analysis was done.Findings: Out of 1245 studies generated by initial search, a number of 13 articles was selected for final analysis. Earthquake was the most frequent disaster which its coincidence with COVID-19 was studied by researchers (31%). The implications of researchers for healthcare system were explained in three sections of climatic events, earthquakes and all hazard approach in relation to COVID-19.Conclusion: Extracting the lessons learned from the regions affected by disasters at the time of COVID-19 pandemic can be helpful for healthcare professionals and policy-makers to modify their preparedness and response plans for cascading risk of natural disasters and a serious pandemic such as COVID-19. Further research is needed to identify the factors strengthen the preparedness of health system for the dual risk of natural hazards and pandemics.
MCAs in Arabidopsis are Ca2+-permeable mechanosensitive channels innately sensitive to membrane tension
Authors: Yoshimura Kenjiro , Iida Kazuko , Iida Hidetoshi 
Published: January 2021

Abstract
Mechanosensitive (MS) ion channels respond to mechanical stress and convert it to electric and ionic signals that activate appropriate cellular mechanisms. Although the force-sensing mechanisms of MS channels remain obscure, the following have been proposed: activation by force from membrane lipids and activation by force delivered from associated proteins. Five MS channel families have been identified to date in plants, including the Arabidopsis thaliana Mid1-Complementing Activity (MCA) channel; however, their activation mechanisms have not yet been elucidated in detail. We herein demonstrated that the MCA2 channel is a Ca2+-permeable mechanosensitive channel that is directly activated by membrane tension. The N-terminal 173 residues of MCA1 and MCA2 were synthesized in vitro, purified, and reconstituted into artificial liposome membranes. Ca2+ fluorometry demonstrated that liposomes reconstituted with MCA1(1-173) or MCA2(1-173) mediated Ca2+ influx. The patch-clamp technique revealed that the application of pressure to the membrane reconstituted with MCA2(1-173) elicited channel currents. This channel was also activated by voltage. Blockers for mechanosensitive channels inhibited stretch, but not voltage, activation. Since MCA proteins are found exclusively in plants, these results suggest that MCA represents a plant-type MS channel that opens directly with membrane stretch.
Exploratory Analysis of Machine Learning Methods in Predicting Subsurface Temperature and Geothermal Gradient of Northeastern United States
Authors: Shahdi Arya , Lee Seho , Karpatne Anuj , Nojabaei Bahareh 
Published: January 2021

Abstract
Geothermal scientists have used bottom hole temperature data from extensive oil and gas well datasets to generate heat flow and temperature-at-depth maps to locate potential geothermally active regions. Considering that there are some uncertainties and simplifying assumptions associated with the current state of physics-based models, in this study, the applicability of several machine learning models is evaluated for predicting temperature-at-depth and geothermal gradient parameters. Through our exploratory analysis, it is found that XGBoost results in the highest accuracy for subsurface temperature prediction with average mean-absolute-error and root-mean-square-error of 3.19[°C] and 4.94[°C], respectively. Furthermore, we apply our model to regions around the sites to provide 2D continuous temperature maps at three different depths using XGBoost model, which can be used to locate prospective geothermally active regions. We also validate the proposed XGBoost and DNN models using an extra dataset containing measured temperature data along the depth for fifty-eight wells in the state of West Virginia. Accuracy measures show that machine learning models are highly comparable to the physics-based model and can even outperform the thermal conductivity model. Also, a geothermal gradient map is derived for the whole region by fitting linear regression to the XGBoost predicted temperatures along the depth. Finally, thorough our analysis, the most favorable geological locations are suggested for potential future geothermal developments.
Long-read metagenomics retrieve complete single-contig bacterial genomes from canine feces
Authors: Cusco Anna , Pérez Daniel , Viñes Joaquim , Fàbregas Norma , Francino Olga 
Published: January 2021

Abstract
BackgroundLong-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample.ResultsWe used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to gain biological insights that are otherwise missed in short-read MAGs catalogs, as shown by the mobilome functions detected in the long-read HQ MAGs.ConclusionsWe recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly's contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertions and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes.
Anti-Inflammatory Diet Consumption Reduced Fatty Liver Indices: Finding From A Large Cohort Study in the Kurdish Population
Authors: Darbandi Mitra , Hamzeh Behrooz , Ayenepour Azad , Rezaeian Shahab , Najafi Farid , Shakiba Ebrahim , Pasdar Yahya 
Published: January 2021

Abstract
The aim of this study was the assess association between of dietary inflammatory index (DII) and non-invasive markers of liver status in adults. This cross-sectional study was performed on 8,520 adults, recruited in Ravansar Non-Communicable Diseases (RaNCD) cohort study, the west of Iran. DII score was calculated based on participants’ dietary intakes obtained from Food Frequency Questionnaire (FFQ). Fatty Liver Index (FLI) score was calculated by anthropometric measurements and some non-invasive markers of liver status. Linear regression models were used to estimate the associations and adjust for possible confounding factors. A greater DII score was significantly associated with higher energy intake, BMI (body mass index), BFM (body fat mass), blood pressure and FLI (P<0.001). Participants with the highest DII score had a significantly higher consumption saturated fat, trans fat and red meat than those in the lowest quartile (P<0.001). After adjustment for age and sex, participants in the highest quartile of DII score had a greater risk of FLI (β: 0.742, 95% CI: 0.254, 0.601). The more pro-inflammatory diet in participants was associated with higher FLI; DII score was positively associated with non-invasive liver markers. Thus having an anti-inflammatory diet can help balance liver enzymes, reduce obesity and fatty liver.
Assessment of the Role of NOGO Gene Block in Enhancing the Neuro-regenerative Effect of Mesenchymal Stem Cells.
Authors: Youssef Eman , Gabr Hala , Kishk Nirmeen A , Zickri Maha Baligh , Botros Shahira KA , Ashour Amal S. 
Published: January 2021

Abstract
Background: Amyotrophic Lateral Sclerosis (ALS) is a fatal disease. Mesenchymal stem cells (MSCs) have a therapeutic potential in neuronal diseases, factors as NOGO-A limit axonal regeneration. In this study, gene silencing was used to suppress Nogo-A expression in MSCs to enhance its neuro-regenerative role. Methods: mouse models of motor neuron degeneration were created, effect of non-modified and plasmid transfected MSCs were studied clinically and histologically. Group 1 received no treatment. Group 2 received IV injection of non modified MSCs and sacrificed after 8 days (subgroup 2a) and 15 days (subgroup 2b) following treatment, Group 3 received IV injection of transfected MSCs and were sacrificed after 8 days (subgroup 3a) and 15 days (subgroup 3b) following treatment. Results: A significant increase in weight and motor scores of subgroups 2a & 2b occurred in comparison to subgroups1a & 1b respectively (p values <0.001, <0.001, 0.001 & 0.026 respectively), GAP43 expression in group 2 mice was significantly higher compared to group 1 mice (p value <0.001). Deformed neurons and glial cells in group 2 were significantly lower compared to group 1 mice (p value <0.001). Deformed neurons and glial cells in subgroup 2b were significantly less in comparison to subgroup 2a (p values = 0.002 and 0.03) indicating an improvement with time. GAP43 in subgroup 2b was significantly higher compared to subgroup 2a (p value = 0.030).Weight and motor power in group 3 mice was significantly higher when compared to group 1 on days; 14 and 21 (p values <0.001, <0.001, <0.001 and 0.008) respectively. Deformed neurons and glial cells in group 3 mice were significantly lower when compared to group 1 mice (p values <0.001). GAP43 expression in group 3 mice was significantly higher when compared to group1 (p value <0.001). Deformed neurons in subgroup 3b was significantly less than subgroup 3a (p value <0.001). GAP43 expression in group 3 mice was significantly increased when compared to group 2 mice (p value <0.001).Conclusion: NOGO-A gene SiRNA is a potential enhancer of the neuro-regenerative action of MSCs.
A Recombinant Protein SARS-CoV-2 Candidate Vaccine Elicits High-titer Neutralizing Antibodies in Macaques.
Authors: Baisa Gary , Rancour David , Mansfield Keith , Burns Monika , Martin Lori , Cunha Daise , Fischer Jessica , Muecksch Frauke , Hatziioannou Theodora , Bieniasz Paul D. , Schomburg Fritz , Luke Kimberly 
Published: January 2021

Abstract
BackgroundVaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. MethodsWe assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain or an extended C-terminal domain containing the receptor-binding domain and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. ResultsA robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the N-terminal domain alone lacked this activity. Crucially, sera from animals immunized with the extended receptor binding domain but not the N-terminal domain had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. ConclusionsThese data support the utility of spike subunit-based antigens as a vaccine for use in humans.
Spatial Variability of Saturated Hydraulic Conductivity and its Links with other Soil Properties at the Commune Scale
Authors: Usowicz Boguslaw , Lipiec Jerzy 
Published: January 2021

Abstract
Saturated hydraulic conductivity (SHC) is a key property for evaluating soil water movement and quality. Most studies on spatial variability of SHC have been performed soil at a field or smaller scale. Therefore, the aim of this work was to assess (quantify) the spatial distribution of SHC at the commune scale and its relationship with other soil properties, including intrinsic sand, silt, and clay contents, relatively stable organic carbon, cation exchange capacity (CEC), dynamic water content (WC), total porosity (FI), and dry bulk density (BD) in the surface layer (0–20 cm). The spatial relationships were assessed using a semivariogram and a cross-semivariogram. The studied commune (140 km2) with predominantly permeable sandy soils with low fertility and productivity is located in the south-eastern part of Poland (Podlasie region). The mean sand and organic carbon contents are 74 andobablyctknąć, czy o to chodzid mniej znacznie mniejszed? ? 0.86 and their ranges (in %) are 45-95 and 0.002-3.75, respectively. The number of individual samples varied from 216–228 (for SHC, WC, BD, FI) to 691 for the other soil properties. The best fitting models were adjusted to the empirical semivariogram (exponential) and the cross-semivariogram (exponential, Gaussian, or linear) used to draw maps with kriging. The results showed that, among the soil properties studied, SHC was most variable (coefficient of variation 77.3%) and significantly (p <0.05) positively correlated with total porosity (r = 0.300) and negatively correlated with soil bulk density (r = –0.283). The mean SHC was 2.597 m day–1 and ranged from 0.01 up to 11.54 m day–1. The spatial autocorrelation (range) of SHC in the single (direct) semivariograms was 0.081° (8.1 km), while it favourably increased up to 0.149–0.81° (14.9–81 km) in the cross-semivariograms using the OC contents, textural fractions, and CEC as auxiliary variables. The generated spatial maps allowed outlining two sub-areas with predominantly high SHC above 3.0 m day–1 in the northern sandier (sand content >74%) and less silty (silt content <22%) part and, with lower SHC in the southern part of the commune. Generally, the spatial distribution of the SHC values in the commune area depended on the share of individual intrinsic textural fractions. On the other hand, the ranges of the spatial relationship between SHC and the intrinsic and relatively stable soil properties were much larger (from ~15 to 81 km) than between SHC and the dynamic soil properties (0.3-0.9 km). This knowledge is supportive for making decisions related to land management aimed at reduction of hydraulic conductivity and chemical leaching and improvement of soil water resources and crop productivity.
Corticosteroids Treatment for Patients With Coronavirus Disease-2019 (COVID-19) With Different Disease Severity: a Systematic Review and Meta-analysis Protocol
Authors: Lou Shaofei , Huang Kaizhuang , Jiang Jiao , Li Ningjun 
Published: January 2021

Abstract
Introduction: As the coronavirus disease 2019 (COVID-19) pandemic progresses, identifying effective antiviral agents to treat the COVID-19 is of most urgency. Efficacy and safety of corticosteroids in patients with COVID-19 still are debated. Because high-quality randomized clinical trials (RCTs) on the use of corticosteroids for patients with COVID-19 recently were published recently, we aim to conduct a systematic review and meta-analysis of RCTs on corticosteroids therapy in patients with different disease severity to ascertain the effect on survival. Methods: We will undertake a comprehensive literature search among PubMed, EMBASE, Cochrane Library, medRxiv, and bioRxiv from their inception onwards to identify relevant RCTs. Two reviewers will independently extract data and conduct risk of bias assessments. The primary outcome is all-cause mortality, mortality of mechanically ventilated patients and patients who did not receive oxygen therapy. Secondary outcomes include need for mechanical ventilation or oxygen therapy and incidence of adverse outcomes. Heterogeneity of the estimates across studies will be assessed. Outcomes will be analyzed to pooled risk ratio and pertinent 95% confidence interval. A subgroup analysis will be conducted by disease severity to explore the source of heterogeneity. The systematic review and meta-analysis will be presented according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses. Discussion: This systematic review will provide an overview of the current state of evidence concerning the effect of corticosteroids on survival of patients with COVID-19 depended on the disease severity. Also, this systematic review will show the limitations and strengths of the studies available in the literature, as well as recommendations for future avenues of research will be given. PROSPERO registration number: CRD42020227740.