bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrant Expression of Fgl-1 and Lag-3 in Adenomyosis
Authors: Sun Wenjing , Qin Xiaoyan , Yuan Guangxi , Li Na , Liang Junhui , Li Chunyan , Li Changzhong , Li Mingjiang , Zhao Xingbo , Zhang Hui 
Published: March 2021

Abstract
Background: The presence of ectopic functional endometrial glands and stroma in the myometrium of the uterine cavity is considered as adenomyosis. Various inflammatory, vascular and mechanical factors are involved in the symptoms and evolution of this pathology. Lymphocyte-activation gene 3 (Lag-3) is an immune inhibitory receptor and fibrinogen-like protein 1 (Fgl-1) is a major functional ligand of Lag-3. The binding of Lag-3 and Fgl-1 leads to inhibition of T-cell immunity, which is an important target of immunotherapy. The objective of this study was to evaluate the expression of Lag-3 and Fgl-1 in normal endometrium and adenomyosis.Methods: The expression of the Lag-3 and Fgl-1 in normal endometrium (proliferative phase: n=15; secretory phase: n=15) and adenomyotic endometrium (proliferative phase: n=15; secretory phase: n=15) were determined using immunohistochemistry and immunofluorescence analysis.Results: In normal and adnomyotic endometrium, no significant difference of Fgl-1 expression was noted between proliferative and secretory phases. Compared with normal endometrium, eutopic and ectopic endometrium of adenomyosis showed increased expression of Fgl-1. Lag-3 was almost negative in endometrial glands of normal and adenomyosis. Compared with normal endometrium, Lag-3 positive T-lymphocytes were more common in the stroma of adenomyosis.Conclusions: Our data suggest that aberrant expression of Lag-3 and Fgl-1 is present in the eutopic and ectopic endometrium of adenomyosis. We conclude that Lag-3/Fgl-1 signaling may be involved in the pathogenesis and development of adenomyosis.
A Spread Model of COVID-19 With Some Strict Anti-epidemic Measures
Authors: Yang Bo , Yu Zhenhua , Cai Yuanli 
Published: March 2021

Abstract
In the absence of specific drugs and vaccines, the best way to control the spread of COVID-19 is to adopt and diligently implement effective and strict anti-epidemic measures. In this paper, a mathematical spread model is proposed based on strict epidemic prevention measures and the known spreading characteristics of COVID-19. The equilibriums and the basic regenerative number of the model are widely analyzed. As a validation, the model is used to simulate the spread of COVID-19 in Hubei Province of China for a period of time. The model parameters are estimated and the model is validated by the actual data related to COVID-19 in Hubei. Simulation results show that themodel can accurately describe the spread dynamics of COVID-19. Sensitivity analysis of the parameters is also done to provide the basis for formulating prevention and control measures.
Experimental Study on the Thermal Characteristics of Urban Mockups With Different Paved Streets
Authors: Qin Yinghong , Wei Peiyuan , Wang Junsong , TAN Kanghao 
Published: March 2021

Abstract
Pavements in urban area absorb more sunlight due to the canyon-like geomorphology of the urban geometry, and store more heat due to the great thermal bulk properties of concrete. Heat released from pavements warms up the urban air, contributing to the urban heat island. Recently, the uses of cool pavements to reduce the pavement temperature as an urban heat island mitigation have gained momentum. Understanding the temperature and solar insolation of a pavement in an urban area is important to adopt the right cool pavement option for the right place. This study measured the temperature of paved streets in an urban mockup for four days in summer. It is found that east-west (EW) streets are the hottest place in an urban area, followed by the intersection, and finally the south-north (SN) street; and that increasing the pavements albedo reduces the pavement temperature effectively. The dark grey pavement in open space is hotter than those in an urban canyon. The heat storage in the building blocks keeps the pavement warmer more than 2oC at nightime. The EW street is exposed to solar insolation for long hours, so it is suitable for preferentially developing of reflective cool pavements.
Modeling Moisture Redistribution of Pulse Drip Irrigation Systems by Soil and System Parameters: New Regression-based Approaches
Authors: Karimi Bakhtiar , Karimi Nazir , Shiri Jalal , Sanikhani Hadi 
Published: March 2021

Abstract
One of the strategies for increasing water use efficiency and reducing deep percolation drip irrigation systems is considering the patterns of moisture redistribution after cut-offing the irrigation process. An experimental study was conducted in the present research to evaluate the moisture redistribution process under surface and subsurface pulse drip irrigation systems and developing new regression-based methodologies for estimating moisture redistribution dimensions using both the soil and system parameters together. A physical model was made and the experiments were performed on three different types of soil texture (light, medium, and heavy) with three emitter flow rates (2, 4, and 6 lit/hr) in three emitter installation depths (0, 15, and 30 cm). The experiments were conducted for both continuous (CI) and pulse (PI) irrigation modes. The results showed that significant amounts of wetting dimensions and wetted area of the moisture bulb are related to post-cut-offing stage. Then, using the nonlinear regression analysis, several models were proposed to estimate the horizontal and vertical redistribution pattern as well as the wetted area (upper and lower parts of the emitter). The comparison of the measured and the stimulated values indicated that the non-linear regression models simulated the parameters associated with redistribution, accurately.
Spatial frameworks for prioritization of agricultural research and development
Authors: Edreira Juan Rattalino , Andrade Jose , Cassman Kenneth , Ittersum Martin van , Loon Marloes van , Grassini Patricio 
Published: March 2021

Abstract
Food security interventions and policies need reliable estimates of actual crop production and the scope to enhance production on existing cropland. We assess the performance of two widely used “top-down” gridded frameworks (GAEZ and AgMIP) versus an alternative “bottom-up” approach that estimates extra production potential locally, for a number of representative sites, and then upscales the results to larger spatial scales (GYGA). Our results show that estimates from top-down frameworks are alarmingly unlikely, with estimated potential production being lower than current production at some locations. The consequences of using these coarse estimates to predict food security are illustrated by an example from sub-Saharan Africa. Our study shows that current foresights on food security, land use, and climate change and associate priority setting on AR&D based on yield potential and yield gaps derived from top-down approaches are subject to a high degree of uncertainty and would benefit from incorporating estimates from bottom-up approaches.
TN14003 attenuates cartilage degeneration by targeted blocking of the SDF-1/CXCR4 signaling pathway in knee osteoarthritis
Authors: Li Yanlin , Wang Kun , He Chuan , Wang Guoliang , Cai Guofeng , Yang Xianguang , Song En , Han Rui 
Published: March 2021

Abstract
In order to investigate the effect of TN14003 and its mechanism on cartilage degeneration in vitro and in vivo. P1 chondrocytes isolated from cartilage tissues of OA patients who underwent total knee arthroplasty were randomly assigned to blank control group, TN14003 group, T140 group, and AMD3100 group in vitro. Each group cells were cultured for 1, 2, 4, 6, 8, 10 days. Cell morphology were observed under inverted phase-contrast microscope and examined using MTT assay, flow cytometry, ELISA (MMPs in the chondrocyte medium) and quantitative real-time PCR (mRNA expressions of Col II and ACAN). Moreover, 96 male Hartley guinea pigs with spontaneous OA were randomly assigned to examine the effect of TN14003, T140, and AMD3100 in vivo. After 12 weeks, guinea pigs were sacrificed, the knee articular cartilage histopathology was analyzed. No difference in morphology, proliferation rate and apoptosis among four groups (P > 0.05). The content of MMP-3 and MMP-13, mRNA expression levels of ACAN and Col II were significantly lower in TN14003 group compared with other groups (P < 0.05). TN14003 had stronger effect in decreasing cartilage degeneration compared with T140 and AMD3100 in vivo. TN14003 could effective targeted to prevention and treatment of OA.
Hyperspectral Characterization and Chlorophyll Content Inversion Study of Reclaimed Vegetation in Rare Earth Mines
Authors: Li Hengkai , Xu Feng , Zhou Beibei , Wei Zhian 
Published: March 2021

Abstract
Taking the Lingbei rare earth mining area in Dingnan county of Jiangxi Province as the research object of the reclaimed vegetation, the original spectrum, derivative spectrum and the continuum removed spectrum of the reclaimed vegetation were detected. The spectral characteristics and variation regularity of the typical reclaimed vegetation were analyzed, the correlation between chlorophyll content and spectral characteristic index of reclaimed vegetation was analyzed, and the sensitive spectral parameters were extracted. Partial Least Squares Algorithm, Back Propagation Neural Network Algorithm and Sparse Autoencoder Network Algorithm were selected to construct the estimation model of chlorophyll content, and compare the accuracy. The results show that; The vegetation spectrum of rare earth mine reclamation has the spectral characteristics of higher reflectance in visible region, red shift of green peak and red valley, blue shift of “red edge”, with less spectral variation in bamboo willow; Variability in the sensitive spectral parameters extracted from different vegetation; Sparse Autoencoder network algorithm is the optimal estimation model (R2 value of three vegetation is 0.9117,0.7418 and 0.9815 respectively). In the case of the small sample, it has higher estimation precision and universality for different reclaimed vegetation.
Explainable artificial intelligence for predicting remission in patients with rheumatoid arthritis treated with biologics
Authors: Koo Bon San , Eun Seongho , Shin Kichul , Yoon Hyemin , Hong Chaelin , Kim Do-Hoon , Hong Seokchan , Kim Yong-Gil , Lee Chang-Keun , Yoo Bin , Oh Ji Seon 
Published: March 2021

Abstract
Background: We developed a model to predict remissions in patients treated with biologic disease-modifying anti-rheumatic drugs (bDMARDs) and to identify important clinical features associated with remission using explainable artificial intelligence (XAI).Methods: We gathered the follow-up data of 1204 patients treated with bDMARDs (etanercept, adalimumab, golimumab, infliximab, abatacept, and tocilizumab) from the Korean College of Rheumatology Biologics and Targeted Therapy Registry. Remission was predicted at one-year follow-up using baseline clinical data obtained at the time of enrollment. Machine learning methods (e.g., lasso, ridge, support vector machine, random forest, and XGBoost) were used for the predictions. The Shapley additive explanation (SHAP) value was used for interpretability of the predictions.Results: The ranges for accuracy and area under the receiver operating characteristic of the newly developed machine learning model for predicting remission were 52.8%–72.9% and 0.511–0.694, respectively. The Shapley plot in XAI showed that the impacts of the variables on predicting remission differed for each bDMARD. The most important features were age for adalimumab, rheumatoid factor for etanercept, erythrocyte sedimentation rate for infliximab and golimumab, disease duration for abatacept, and C-reactive protein for tocilizumab, with mean SHAP values of -0.250, -0.234, -0.514, -0.227, -0.804, and 0.135, respectively.Conclusions: Our proposed machine learning model successfully identified clinical features that were predictive of remission in each of the bDMARDs. This approach may be useful for improving treatment outcomes by identifying clinical information related to remissions in patients with rheumatoid arthritis.
Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS
Authors: Prieto-Alhambra Daniel , Kostka Kristin , Duarte-Salles Talita , Prats-Uribe Albert , Sena Anthony , Pistillo Andrea , Khalid Sara , Lai Lana , Golozar Asieh , Alshammari Thamir M , Dawoud Dalia , Nyberg Fredrik , Wilcox Adam , Andryc Alan , Williams Andrew , Ostropolets Anna , Areia Carlos , Jung Chi Young , Harle Christopher , Reich Christian , Blacketer Clair , Morales Daniel , Dorr David A. , Burn Edward , Roel Elena , Tan Eng Hooi , Minty Evan , DeFalco Frank , de Maeztu Gabriel , Lipori Gigi , Alghoul Heba , Zhu Hong , Thomas Jason , Bian Jiang , Park Jimyung , Roldán Jordi Martínez , Posada Jose , Banda Juan M , Horcajada Juan P , Kohler Julianna , Shah Karishma , Natarajan Karthik , Lynch Kristine , Liu Li , Schilling Lisa , Recalde Martina , Spotnitz Matthew , Gong Mengchun , Matheny Michael , Valveny Neus , Weiskopf Nicole , Shah Nigam , Alser Osaid , Casajust Paula , Park Rae Woong , Schuff Robert , Seager Sarah , DuVall Scott , You Seng Chan , Song Seokyoung , Fernández-Bertolín Sergio , Fortin Stephen , Magoc Tanja , Falconer Thomas , Subbian Vignesh , Huser Vojtech , Ahmed Waheed-Ul-Rahman , Carter William , Guan Yin , Galvan Yankuic , He Xing , Rijnbeek Peter , Hripcsak George , Ryan Patrick , Suchard Marc 
Published: March 2021

Abstract
Background: Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response [1,2]. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) [3] Characterizing Health Associated Risks, and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD.Methods: We conducted a descriptive cohort study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11th June 2020 and are iteratively updated via GitHub [4]. Findings: We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19, and 113,627 hospitalized with COVID-19 requiring intensive services. All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts, and are available in an interactive website: https://data.ohdsi.org/Covid19CharacterizationCharybdis/. Interpretation: CHARYBDIS findings provide benchmarks that contribute to our understanding of COVID-19 progression, management and evolution over time. This can enable timely assessment of real-world outcomes of preventative and therapeutic options as they are introduced in clinical practice.
On the role of natural multidecadal oscillations on global warming and its hiatus
Authors: Pal Mayukha , Panigrahi Prasanta K 
Published: March 2021

Abstract
In this study, we investigate the role of the multidecadal oscillation patterns in the global temperature in the global warming hiatus. We analyze the global instrumental temperature records and multiple tree-ring temperature reconstruction records using wavelet transforms and register the presence of a multidecadal cycle of approximately 55-75 years. The hiatus and post-hiatus rise in temperature arises from the declining phase of the multidecadal oscillation which temporally compensates the rising phase. The unusual rise in the temperature after the hiatus is possibly explained by the positive uprising phase of this natural cycle. The origin of the global warming debate has been partly ascribed to faulty calculations or biased judgments. However, in these studies, little emphasis has been given to the possible presence of multidecadal oscillation patterns in the global temperature, which may lead to such an effect. Our result demonstrates that, phase of this cycle has accidentally played an important role in fueling the global warming debate. Therefore, while assessing any future climate changes, such possibilities should be accounted.
Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in populus trichocarpa
Authors: He Fang , Shi Yu-Jie , Zhao Qian , Zhao Kuang-Ji , Cui Xing-Lei , Chen Liang-Hua , Yang Han-Bo , Zhang Fan , Mi Jia-Xuan , Huang Jin-Liang , Wan Xue-Qin 
Published: March 2021

Abstract
Background: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic as well as biotic stress. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in plant resistance against biotic and abiotic stresses. Although the whole genome sequence of populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, insect feeding and hormone response at the whole genome level. Results: In the recent research, a genome-wide analysis of the Poplar PPOs family was finished and 18 PtrPPOs gene were identified. Then, bioinformatics and qRT-PCR were applied to analyze the gene structure, phylogeny, chromosomal localization, gene replication, Cis-elements, expression patterns of PtrPPOs. Sequence analysis revealed that 2/3 of the PtrPPO genes not contained introns. Phylogenetic analysis revealed that all PPOs gene were split into 11 subfamilies, and woody plants differentiated a large number of PPO genes. 18 PtrPPOs gene were disproportionally apportioned on 19 chromosomes, and the number of three pairs of segmented replication genes and four tandem repeat genomes were detected in poplars. Cis-acting element analysis identified a large number elements of growth and development, secondary metabolism process, and stress-related elements on the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferably in young plant tissues and fruits. In addition, some PtrPPOs could be significantly induced by PEG, ABA and JA, thus revealing their potential role in regulating stress response. Conclusions: Comprehensive analysis is helpful to select candidate PPO genes for the follow-up study of the biological function, and molecular genetic progress of stress resistance in forest trees provides genetic resources.
First report of Mesocriconema sphaerocephalum (Taylor, 1936) Loof, 1989 associated with wild grass in Botswana
Authors: Shokoohi Ebrahim 
Published: March 2021

Abstract
During a survey on the biodiversity of plant-parasitic nematodes of natural areas in Botswana, Mesocriconema sphaerocephalum was discovered around the rhizosphere of the wild grass. The nematodes were extracted using the tray method and then fixed according to the available protocols. The morphological characters fit well with the M. sphaerocephalum. Besides, molecular aspects using 18S and 28S rDNA were studied. The phylogenetic analysis of 18S and 28S rDNA placed the examined population with other populations of M. sphaerocephalum in a group. According to the knowledge, this is the first report of M. spaherocephalum from Botswana.
Integrative taxonomy, distribution, and host associations of Geocenamus brevidens and Quinisulcius capitatus from southern Alberta, Canada
Authors: Munawar Maria , Yevtushenko Dmytro P. , Castillo Pablo 
Published: March 2021

Abstract
Two stunt nematode species, Geocenamus brevidens and Quinisulcius capitatus, were recovered from the potato growing regions of southern Alberta, described and characterized based on integrative taxonomy. Morphometrics, distribution, and host associations of both species are discussed. The Canadian populations of both species displayed minor variations in morphometrical characteristics (viz., slightly longer bodies and tails) from the original descriptions. The populations of G. brevidens and Q. capitatus species examined in this study are proposed as standard and reference populations for each respective species until topotype specimens become available and molecularly characterized. Phylogenetic analyses, based on partial 18S, 28S, and ITS sequences, placed both species with related stunt nematode species. The present study updates the taxonomic records of G. brevidens and Q. capitatus from a new location, southern Alberta, Canada, and will aid in the decision whether these stunt nematodes should be included in nematode management programs.
Expression, Rapid Purification and Functional Analysis of DnaK from Rhodococcus ruber
Authors: Fan Xin , Yuan Yuan , Zhang Fan , Ai Lei , Wu Zhonghao , Peng Ren 
Published: March 2021

Background:
Heat shock proteins (HSPs) represent a group of important proteins which
are produced by all kinds of organisms especially under stressful conditions. DnaK, an Hsp70 homolog
in prokaryotes, has indispensable roles when microbes was confronted with stress conditions.
However, few data on DnaK from Rhodococcus sp. were available in the literature. In a previous
study, we reported that toluene and phenol stress gave rise to a 29.87-fold and 3.93-fold increase
for the expression of DnaK from R. ruber SD3, respectively. Thus, we deduced DnaK was
in correlation with the organic solvent tolerance of R. ruber SD3.

Objective:
To elucidate the role of DnaK in the organic solvent tolerance of R. ruber SD3, expression,
purification and functional analysis of Dnak from R. ruber SD3 were performed in the present
paper.

Methods:
In this article, DnaK from R. ruber SD3 was heterologously expressed in E. coli
BL21(DE3) and purified by affinity chromatography. Functional analysis of DnaK was performed
using determination of kinetics, docking, assay of chaperone activity and microbial growth.

Results:
The recombinant DnaK was rapidly purified by affinity chromatography with the purification
fold of 1.9 and the recovery rate of 57.9%. Km, Vmax and Kcat for Dnak from R. ruber SD3
were 80.8 μM, 58.1 nmol/min and 374.3 S-1, respectively. The recombinant protein formed trimer
in vitro, with the calculated molecular weight of 214 kDa. According to in-silico analysis, DnaK interacted
with other molecular chaperones and some important proteins in the metabolism. The specific
activity of catalase in the presence of recombinant DnaK was 1.85 times or 2.00 times that in
the presence of BSA or Tris-HCl buffer after exposure to 54 °C for 1h. E. coli transformant with
pET28-dnak showed higher growth than E. coli transformant with pET28 at 43°C and in the presence
of phenol, respectively.

Conclusion:
The biochemical properties and the interaction analysis of DnaK from R. ruber SD3
deepened our understanding of DnaK function. DnaK played an important role in microbial growth
when R. ruber was subjected to various stress such as heating and organic solvent.