bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-resolution, spatially explicit estimate of fossil-fuel CO2 emissions from the Tokyo Metropolis, Japan
Authors: Cong Richao , Saito Makoto , Fukui Tetsuo , Hirata Ryuichi , Ito Akihiko 
Published: June 2020

Abstract
Background: The quantification of urban greenhouse gas (GHG) emissions is an important task in combating climate change. Emission inventories that include spatially explicit emission estimates facilitate the accurate tracking of emission changes, identification of emission sources, and formulation of policies for climate-change mitigation. Many currently available gridded emission estimates are based on the disaggregation of country- or state-wide emission estimates, which may be useful in describing city-wide emissions but are of limited value in tracking changes at subnational levels. Urban GHG emissions should therefore be quantified with a true bottom-up approach. Results: Multi-resolution, spatially explicit estimates of fossil-fuel carbon dioxide (FFCO2 ) emissions from the Tokyo Metropolis, Japan, were derived. Spatially explicit emission data were collected for point (e.g., power plants and waste incinerators), line (mostly traffic), and area (e.g., residential and commercial areas) sources. Emissions were mapped on the basis of emission rates calculated for source locations. Activity, emissions, and spatial data were integrated, and the results were visualized using a geographic information system approach. Conclusions: The annual total FFCO2 emissions from the Tokyo Metropolis in 2014 were 44,855 Gg CO2 , with the road-transportation sector (16,323 Gg CO2 ) accounting for 36.4% of the total. Spatial emission patterns were verified via a comparison with the East Asian Air Pollutant Emission Grid Database for Japan (EAGrid-Japan), which demonstrated the applicability of this methodology to other prefectures and therefore the entire country.
Barriers and associated factors for adequate antenatal care among Afghan women in Iran; findings from a community-based survey
Authors: Dadras Omid , Dadras Fateme , Taghizade Ziba , Seyedalinaghi Seyedahmad , Ono-Kihara Masako , Kihara Masahiro , Nakayama Takeo 
Published: June 2020

Abstract
Background: Almost a third of Afghan women living in Iran are at childbearing age. Antenatal care (ANC) is an inextricable part of healthy pregnancy and could prevent the adverse birth outcomes. Almost 97% of Iranian expectant women are receiving adequate ANC (4 or more visits). However, the situation for pregnant Afghan women is unclear. Some studies indicated low access to ANC among Afghan women. In the present study, we aimed to explore the sociodemographic factors and potential barriers associated with adequate ANC among Afghan women in Iran. Methods: A cross sectional study was conducted between June 2019 and August 2019. Using time location sampling (TLS), we recruited 424 Afghan women aged 18-45 years old at three health centers in south region of Tehran. The data were collected on sociodemographic characteristics and the reported reasons for inadequate ANC using a questionnaire and analyzed applying bivariate, and multivariate analyses. Factor analysis was performed to reduce the number of potential reasons for inadequate ANC in order to improve the precision of regression analysis. Results: Almost a third of Afghan women in this study had adequate ANC (≥ 8 visits). The women in older age group, those with higher education and family income, women with longer length of stay, those of legal status were more likely to have adequate ANC. In multivariate analysis, the poor knowledge and attitude toward ANC (AOR = 0.06; 95% CI [0.03-0.15]), the poor quality of services (AOR = 0.17 95% CI [0.07-0.41]); and to some extent, the difficulties in access (AOR = 0.33; 95% CI [0.11-1.00]) were the main obstacles toward adequate ANC among the study population. Conclusion: Our study emphasized the important role of the personal knowledge and attitude toward ANC with adequate antenatal care among Afghan women in Iran. This could be addressed by well-oriented interventions and health education for Afghan women. The collaboration between central government with international agencies should be directed toward enhancing the social support, promoting the awareness and knowledge, and expanding the safety net services to improve the access and quality care among Afghan women in Iran.
Systematic review and meta-analysis of diagnostic delay in axial spondyloarthritis
Authors: Zhao Sizheng , Pittam Bradley , Harrison Nicholas L , Ahmed Ashar E , Nursiah Karishma , Goodson Nicola J , Hughes David M 
Published: June 2020

Abstract
Background. Delay to diagnosis in axial spondyloarthritis (axSpA) is longer than many other rheumatic diseases. Prolonged delay has been shown to associate with poorer outcomes including functional impairment and quality of life. Our aims were to describe 1) global variation in delay to diagnosis, 2) factors associated with delay, and 3) differences in diagnostic delay between axSpA and psoriatic arthritis (PsA).Methods. We searched Medline, PubMed, EMBASE and Web of Science using a predefined protocol in accordance with PRISMA guidelines. Delay to diagnosis was defined as years between age at symptom onset and age at diagnosis. We pooled mean diagnostic delay using random-effects inverse variance meta-analysis. We examined variations in pooled estimates using pre-specified subgroup analyses and sources of heterogeneity using meta-regression.Results. A total of 64 studies reported mean diagnostic delay in axSpA patients. The pooled mean delay was 6.7 years (95% confidence interval 6.2 to 7.2) with high levels of heterogeneity. Delay to diagnosis did not improve over time when stratifying results by year of publication. Studies from high-income countries (defined by the World Bank) reported longer delay than those from middle-income countries. Factors consistently reported to be associated with longer delay were: lower education levels, younger age at symptom onset and absence of extra-articular manifestations. Pooled estimate for diagnostic delay from 8 PsA studies was significantly shorter, at 2.6 years (95%CI 1.6 to 3.6). Conclusion. For axSpA patients, delay to diagnosis remains unacceptably prolonged in many parts of the world, although some countries have reported remarkable improvements. Patient factors (education) and disease presentation (age at onset and extra-articular manifestations) should inform awareness campaigns to improve delay. Targets for improvement should aim to resemble delays in other spondyloarthritis patients.
Biodegradation of Atrazine and Ligninolytic Enzyme Production by Basidiomycete Strains
Authors: Henn Caroline , Monteiro Diego Alves , Boscolo Mauricio , Silva Roberto da , Gomes Eleni 
Published: June 2020

Abstract
Atrazine is one of the most widespread chlorinated herbicides, leaving large bulks in soils and groundwater. The metabolic pathways of biodegradation of atrazine by bacteria are well described, but many aspects of the fungal biodegradation of this compound remain unclear. Thus, we investigated the toxicity and degradation of atrazine by 13 rainforest basidiomycete strains. In liquid medium, Pluteus cubensis SXS320, Gloelophyllum striatum MCA7, and Agaricales MCA17 removed 30, 37, and 38%, respectively, of initial 25 mg L -1 of herbicide within 20 days. Deficiency of nitrogen drove atrazine degradation by Pluteus cubensis SXS320; this strain removed 30% of atrazine within 20 days in a culture medium with 2.5mM of N, raising three metabolites; in a medium with 25mM of N, only 21% of initial atrazine were removed after 40 days, and two metabolites appeared in culture extracts. This is the first report of such different outcomes linked to nitrogen availability during the biodegradation of atrazine by basidiomycetes. The herbicide also induced synthesis and secretion of extracellular laccases by Datronia caperata MCA5, Pycnoporus sanguineus MCA16, and Polyporus tenuiculus MCA11. Laccase levels in contaminated medium of P. tenuiculus MCA11 were 13.3-fold superior than in control; the possible role on this enzyme on atrazine biodegradation was evaluated, considering the strong induction and the removal of 13.9% of the herbicide in vivo . Although 88% of initial laccase activity remained after 6h, no evidence of in vitro degradation was observed, even though ABTS was present as mediator. Further studies, including a full characterization of the metabolites obtained, are desirable to assess the security of the use of these strains as in situ bioremediation tools. The search for other ligninolytic extracellular enzymes and cell-bound mechanisms implicated on the degradation would enlightens key aspects of the role of nitrogen in atrazine metabolism by basidiomycetes.
The regeneration of Acer rubrum L. "October Glory" through embryonic callus
Authors: Dai Chongwen , YAN Yang-yang , Liu Yumin , LIU Ya-min , DENG Yuan-wei , YAO Hong-yu 
Published: June 2020

Abstract
Background: Tissue culture and rapid propagation technology is an important way to solve the difficulties of plant propagation. This experiment aims to explore the appropriate conditions at each stage of the red maple’s tissue culture process and to obtain plantlets, thus providing a theoretical basis for the establishment of the red maple’s tissue culture system. Results: The results showed that the stem segment is the most suitable explant for inducing embryogenic callus. The MS (Murashige&Skoog) +0.8 mg/L TDZ (Thidiazuron) +1.0 mg/L 6-BA (6-Benzylaminopurine) +0.5 mg/L IAA(Indole-3-acetic acid) +35 g/L sucrose+7.5 g/L semi-fixed medium was the best for callus formation. When selecting type Ⅵ callus as embryonic callus induction material, MS+0.6 mg/L TDZ+0.5 mg/L 6-BA +2.0 mg/L IAA +35 g/L sucrose+7.5 g/L semi-fixed medium can get embryonic callus. The optimal medium for adventitious bud induction is MS+1.0 mg/L TDZ+3.0 mg/L 6-BA+0.2 mg/L NAA (1-Naphthaleneacetic acid)+1.2 mg/L IAA+35 g/L sucrose+7.5 g/L semi-fixed medium. The induction rate of adventitious roots in MS+0.6 mg/L TDZ+1.0 mg/L 6-BA+3 mg/L NAA+35 g/L sucrose+7.5 g/L semi-fixed medium was the highest, reaching 76%. Conclusions: In the course of our research, we found that PGRs play an important role in the callus induction stage, and the effect of TDZ is particularly obvious; The callus cells grow and proliferate according to the "S" growth curve, and can be sub-cultured when the highest growth point is reached to maintain the rapid proliferation of the callus cells and to avoid inactivation of callus caused by tight niche.
Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani
Authors: Motyka-Pomagruk Agata , Zoledowska Sabina , Misztak Agnieszka Emilia , Sledz Wojciech , Mengoni Alessio , Lojkowska Ewa 
Published: June 2020

Abstract
Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.
Comparison of Ultrasound Cycloplasty and Transscleral Cyclophotocoagulation for Refractory Glaucoma in Chinese Population
Authors: Yu Qiuli , Liang Ya , Ji Fangfang , Yuan Zhilan 
Published: June 2020

Abstract
Background To compare the efficacy and safety of focused ultrasound cycloplasty (UCP) and transscleral cyclophotocoagulation (TSCP) in the treatment of refractory glaucoma in a Chinese population. Methods We retrospective compared twenty-eight eligible patients with refractory glaucoma, who were divided into the UCP group and TSCP group. Patients in these two groups underwent a corresponding procedure from June 2018 to February 2019. The intraocular pressure (IOP), visual acuity, the number of anti-glaucoma agents used and complications were reviewed and compared between groups. Proper statistical methods were selected according to comparison models under IBM SPSS 25 software. Results After the 12-months follow-up, postoperative IOP and number of anti-glaucoma agents used in the two groups were both reduced than the baseline level, and the differences were statistically significant (P<0.05). There were no significant differences in IOP, number of anti-glaucoma agents and the best-corrected visual acuity between the two groups at each follow-up time point (P＞0.05). In terms of complications, the pain at 1 day after surgery in the UCP group was significantly milder than that in the TSCP group (P<0.05). And there were no significant differences in other complications between the two groups (P>0.05). Conclusions Both UCP and TSCP are safe and effective methods for the treatment of refractory glaucoma. Nevertheless, pain is less severe after UCP.
A methylation‐based mRNA signature predicts survival in patients with gastric cancer
Authors: Li Yang , Sun Rongrong , Zhang Youwei , Yuan Yuan , Miao Yufeng 
Published: June 2020

Abstract
Background: Evidence suggests that altered DNA methylation plays a causative role in the occurrence, progression and prognosis of gastric cancer (GC). Thus, methylated-differentially expressed genes (MDEGs) could potentially serve as biomarkers and therapeutic targets in GC.Methods: Four genomics profiling datasets were used to identify MDEGs. Gene Ontology enrichment and Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis were used to explore the biological roles of MDEGs in GC. Univariate Cox and LASSO analysis were used to identify survival-related MDEGs and to construct a MDEGs-based signature. The prognostic performance was evaluated in two independent cohorts.Results: We identified a total of 255 MDEGs, including 192 hypermethylation-low expression and 63 Hypomethylation-high expression genes. The univariate Cox regression analysis showed that 83 MDEGs were associated with overall survival. Further we constructed an eight-MDEGs signature that was independent predictive of prognosis in the training cohort. By applying the eight-MDEGs signature, patients in the training cohort could be categorized into high-risk or low-risk subgroup with significantly different overall survival (HR = 2.62, 95%CI= 1.71-4.02, P < 0.0001). The prognostic value of the eight-MDEGs signature was confirmed in another independent GEO cohort (HR=1.35, 95% CI= 1.03-1.78, P= 0.0302) and TCGA-GC cohort (HR=1.85, 95% CI= 1.16-2.94, P= 0.0084). Multivariate cox regression analysis proved the eight-MDEGs signature was an independent prognostic factor for GC.Conclusion: We have thus established an innovative eight-MDEGs signature that is predictive of overall survival and could be a potentially useful guide for personalized treatment of GC patients.
Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2
Authors: Chen Hongzhi , Tang Lingli , Yu Xinling , Zhou Jie , Chang Yunfeng , Wu Xiang 
Published: June 2020

Abstract
Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods : ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results : A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike 315-324 , Spike 333-338 , Spike 648-663 , Spike 1064-1079 ) exhibited high antigenicity score and good surface accessibility. 10 residues within spike protein (Gly 496 , Glu 498 , Pro 499 , Thr 500 , Leu 1141 , Gln 1142 , Pro 1143 , Glu 1144 , Leu 1145 , Asp 1146 ) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecule respectively. The peptides (Nucleocapsid 66-75 , Nucleocapsid 104-112 ) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions : B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.
Comparison of the effects of and usability of active and active-assistive rehabilitation robots for the upper extremity function among patients with stroke: a single-blinded randomized controlled pilot study
Authors: Park Jin Ho , Park Gyulee , Kim Ha Yeon , Lee Ji-Yeong , Ham Yeajin , Hwang Donghwan , Kwon Suncheol , Shin Joon-Ho 
Published: June 2020

Abstract
Background: Robotic rehabilitation of stroke survivors with upper extremity dysfunction yields different outcomes depending on the robot type. Considering that excessive dependence on assistive force provided by robots may interfere with the patient’s active learning and participation, we hypothesized that the use of an active-assistive robot does not lead to a more meaningful difference with respect to upper extremity rehabilitation than the use of an active robot. Accordingly, we aimed to evaluate the differences in the clinical and kinematic outcomes between active and active-assistive robotic rehabilitation among stroke survivors.Methods: In this single-blinded randomized controlled trial, we assigned 20 stroke survivors with upper extremity dysfunction (Medical Research Council scale score, 3 or 4) to the active (ACT) and active-assistive (ACAS) robotic rehabilitation groups in a 1:1 ratio and administered 20 sessions of 30-minute robotic intervention (5 days/week, 4 weeks). The primary (Wolf Motor Function Test [WMFT]-score and -time: measures activity), and secondary (Fugl-Meyer Assessment [FMA] and Stroke Impact Scale [SIS] scores: measure impairment and participation, respectively; kinematic outcomes) outcome measures were determined at baseline, after 2 and 4 weeks of the intervention, and 4 weeks after the end of the intervention. Furthermore, we evaluated the usability of the robotic devices by conducting interviews with the patients, therapists, and physiatrists. Results: In both the groups, the WMFT-score and -time improved over the course of the intervention. Time had a significant effect on the WMFT-score and -time, FMA-UE, FMA-prox, and SIS-strength; group × time interaction had a significant effect on SIS-function and SIS-social participation (all, p <0.05). The ACT group showed better improvement in participation and smoothness than the ACAS group. In contrast, the ACAS group exhibited better improvement in mean speed. Conclusions: There were no differences between the two groups regarding the impairment and activity domains. However, the ACT robots were more beneficial than ACAS robots regarding participation and smoothness. Considering the high cost and complexity of ACAS robots, ACT robots may be more suitable for robotic rehabilitation in stroke survivors who can perform voluntary movement.Trial registration: The trial was registered retrospectively on 14 March 2018 at ClinicalTrials.gov (NCT03465267).
Combining texture features of whole slide images improves prognostic prediction of recurrence-free survival for cutaneous melanoma patients
Authors: Peng Yanbin , Chu Yunfeng , Chen Zhong , Zhou Wen , Wan Shengxiang , Xiao Yingfeng , Zhang Youlong , Li Jialu 
Published: June 2020

Abstract
Background: Accurate prediction of recurrence-free survival (RFS) is important for the prognosis of cutaneous melanoma patients. The image-based pathological examination remains as the gold standard for diagnosis. It is of clinical interest to account for computer-aided processing of pathology image when performing prognostic analysis.Methods: We enrolled in this study a total of 152 patients from TCGA-SKCM (The Cancer Genome Atlas Skin Cutaneous Melanoma project) with complete information in recurrence-related survival time, baseline variables (clinicopathologic variables, mutation status of BRAF and NRAS genes), gene expression data and whole slide image (WSI) features. We preprocessed WSI to segment global or nucleus areas, and extracted 3 types of texture features from each region. We performed cross validation and used multiple evaluation metrics including C-index and time-dependent AUC to determine the best model of predicting recurrence events. We further performed differential gene expression analysis between the higher and lower-risk groups within AJCC pathologic tumor stage III patients to explore the underlying molecular mechanisms driving risk stratification. Results: The model combining baseline variables and WSI features had the best performance among models with any other types of data integration. The prognostic risk score generated by this model could provide a higher-resolution risk stratification within pathologically-defined subgroups. We found the selected image features captured important immune-related variations, such as the aberration of expression in T cell activation and proliferation gene sets, and therefore contributed to the improved prediction. Conclusions: Our study provided a prognostic model based on the combination of baseline variables and computer-processed WSI features. This model provided more accurate prediction than models based on other types of data combination in recurrence-free survival analysis. Trail registration: This study was based on public open data from TCGA and hence the study objects were retrospectively registered.