bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atmospheric Pollution Reduction in São Paulo City and the Social Isolation Effect
Authors: Rosse Vinicius Possato , Pereira Jaqueline Natiele , Boari Arthur , Costa Gabriel Vinicius , Ribeiro João Pedro Colombo , Vieira-Filho Marcelo 
Published: June 2020

Abstract
Since January 2020, some studies have been reporting a reduction in air pollution in several countries due to social isolation measures, which have been adopted in order to contain the coronavirus outbreak progress (Covid-19). This study aims to evaluate the change in the atmospheric pollution levels by NO and NO2 in São Paulo city in the social isolation period. The NO and NO2 hourly concentrations were obtained through air quality monitoring stations from CETESB, from January 14 to April 12, 2020. Mann-Kendall and the Pettitt tests were performed in the air pollutants time series. We observed an overall negative trend in all stations, indicating a decreasing temporal pattern in concentrations. Regarding NO, the highest decrease rates were observed in Congonhas (-6.39 µg.m-3month-1) and Marginal Tietê (-6.19 µg.m-3month-1) stations; regarding NO2, the highest rates were observed in Marginal Tietê (-4.45 µg.m-3month-1) and Cerqueira César (-4.34 µg.m-3month-1) stations. In addition, we identified a turning point in the NO and NO2 series trends that occurred close to the start date of the social isolation period (March 20, 2020). Moreover, from statistical analysis, it was found that NO2 is a suitable surrogate for monitoring economic activities during social isolation period. Thus, we concluded that social isolation measures implemented in March 20, 2020 caused significant changes in the air pollutants concentrations in São Paulo city (as high as -200% in NO2 levels).
Screening of Potential Molecular Targets for Proximal, Mid, and Distal Esophageal Cancers
Authors: Zhong Liping , Guo Zeying , Pan Yuefen , Zhu Xiaoyong , Chen Yurong 
Published: June 2020

Abstract
Objective: This study aimed to screen the potential molecular targets for proximal, mid, and distal esophageal cancers.Methods: The clinical data, RNA-seq data, and survival data for TCGA esophageal cancer were retrieved from UCSC Xena database. The samples with clinical information on the esophageal tumor central location were selected. Differential analyses on different groups (mid vs. proximal, distal vs. proximal, and distal vs. mid) were performed. Following the differentially expressed genes (DEGs) in three groups were analyzed, the common genes were subjected to survival analysis, miRNA prediction, and drug-gene analysis. The specific genes were annotated for functional and module analyses.Results: Six common genes, namely KCNA1, CCDC196, UNC5CL, CYP3A5, CA10, and REG3A, were analyzed among three comparison groups. The expression of CA10 and REG3A was significantly correlated in the prognosis of patients with esophageal cancer. The distal vs. mid groups screened 766 specific DEGs, and the mid vs. proximal group screened 99 specific DEGs. Functional analysis showed that the genes of distal vs. mid groups, including EDN3, CGA, CCR9, and GABRA2, as well as genes in the mid vs. proximal groups, including GCGR, OXTR, and MCHR2, were significantly enriched in neural functions. In the distal vs. proximal groups, there were 314 specific DEGs, including CYP2C8 and OXGR1.Conclusion: Six common genes may serve as the potential molecular targets for the treatment of all proximal, mid, and distal esophageal cancers.
An Open Source Chemical Structure Curation Pipeline using RDKit
Authors: Bento A Patrícia , Hersey Anne , Felix Eloy , Landrum Greg , Gaulton Anna , Atkinson Francis , Bellis Louisa J , De Veij Marleen , Leach Andrew R 
Published: June 2020

Abstract
BackgroundThe ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to consistent rules. In order to maintain the quality of the final database and to easily compare and integrate data on the same compound from different sources it is necessary for the chemical structures in the database to be appropriately standardised.ResultsA chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a Checker to test the validity of chemical structures and flag any serious errors; a Standardizer which formats compounds according to defined rules and conventions and a GetParent component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures. ConclusionAll the components of the structure pipeline have been made freely available for other researchers to use and adapt for their own use. The code is available in a GitHub repository and it can also be accessed via the ChEMBL Beaker webservices. It has been used successfully to standardise the nearly 2 million compounds in the ChEMBL database and the compound validity checker has been used to identify compounds with the most serious issues so that they can be prioritised for manual curation.
Identification of infrasonic and seismic components of tremors in single-station records: application to the 2013 and 2018 events at an isolated volcanic island, Ioto, Japan
Authors: Kurokawa Aika K. , Ichihara Mie 
Published: June 2020

Abstract
Infrasonic stations are sparse at many volcanoes, especially those on remote islands and those with less frequent eruptions. When only a single infrasound station is available, the seismic-infrasonic cross-correlation method has been used to extract infrasound from wind noise. However, it does not work with intense seismicity and sometimes mistakes ground-to-atmosphere signals as infrasound. This paper proposes a complementary method to identify the seismic component and the infrasonic component using a single microphone and a seismometer. We applied the method to estimate the surface activity on the isolated volcanic island, Ioto. We focused on volcanic tremors during the phreatic eruption on April 11, 2013, and during an unconfirmed event on September 12, 2018. We used the spectral amplitude ratios of the vertical ground motion to the pressure oscillation and compared those for the tremors with those for known signals generated by volcano-tectonic earthquakes and airplanes flying over the station. We were able to identify the infrasound component in the part of the seismic tremor with the 2013 eruption. On the other hand, the tremor with the unconfirmed 2018 event was accompanied by no apparent infrasound. We interpreted the results that the infrasound with the 2013 event was excited by the vent opening or the ejection of ballistic rocks, and the 2018 event was not an explosive eruption either on the ground or in the shallow water. If there was any gas (and ash) emission, it might have occurred gently undersea. As the method uses the relative values of on-site records instead of the absolute values, it is available even if the instrument sensitivity and the station site effects are poorly calibrated.
Neoadjuvant concurrent chemoradiotherapy followed by transanal total mesorectal excision assisted by single-port laparoscopic surgery for low-lying rectal adenocarcinoma: a single center study
Authors: Lu Yen-Jung , Chen Chien-Hsin , Lin En-Kwang , Wu Szu-Yuan 
Published: June 2020

Abstract
Purpose
To assess the feasibility and short-term outcomes of neoadjuvant chemoradiotherapy (CCRT) followed by transanal total mesorectal excision assisted by single-port laparoscopic surgery (TaTME-SPLS) for low-lying rectal adenocarcinoma.
Methods and materials:
A total of 23 patients with clinical stage II-III low-lying (from anal verge 0–8 cm) rectal adenocarcinoma who underwent neoadjuvant CCRT followed by TaTME-SPLS consecutively from December 2015 to December 2018, were enrolled into our study. Chi-squared testing and Student’s t testing were used to make parametric comparisons, and Fisher’s exact test or the Mann–Whitney U-test were used to make nonparametric comparisons.
Results
Conversion rate in patients who underwent neoadjuvant CCRT followed by TaTME-SPLS was only 4%. The mean operation time was 366 minutes and the inter-sphincter resection (ISR) was done for 14 patients (60%). The mean number of lymph nodes harvested were 15. There was no surgical mortality, but the 30-day morbidity rate was 21% (5 patients were Clavien-Dindo I-II). Pathological complete response was 21.74% with 100% organ preservation and 100% clear distal margin after neoadjuvant CCRT followed by TaTME-SPLS.
Conclusion
Neoadjuvant CCRT followed by TaTME-SPLS can be a safe and an effective sphincter-preserving procedure with acceptable morbidity rate for Asian patients with low-lying rectal adenocarcinoma.
Febrile infants without respiratory symptoms or sick contacts: Are chest radiographs or RSV/influenza testing indicated?
Authors: Ozcan Ali , Laskowski Evelyn , Sahai Shashi , Levasseur Kelly 
Published: June 2020

Abstract
Objectives: Serious bacterial infection rates in febrile infants <60 days are about 8-11%. Less than 1% of febrile infants with no respiratory symptoms will have pneumonia however, chest radiography (CXR) rates remain between 30-60%. Rapid Respiratory Syncytial Virus (RSV) and influenza (flu) testing is common, however, there is not enough data to determine if febrile infants without any respiratory symptoms should be tested. The goal of this study is to determine the rate of positive CXR and RSV/flu results in febrile infants with no respiratory symptoms and no sick contacts. Methods: Well-appearing febrile infants between 7-60 days of age who presented to the pediatric emergency department (PED) from September 1 st , 2015 through October 30 th , 2017 were enrolled. Demographic data, respiratory symptoms, CXR findings and RSV/flu results were collected. SAS statistical software was used for analysis. Results: 129 infants met enrollment criteria. Of the 129 infants, 58 (45.0%) had no respiratory symptoms and no sick contacts. Of these 58, 36 (62%) received a CXR and none of them had any abnormal findings, 48 (83%) had RSV/flu testing, no patients tested positive for RSV and only one patient tested positive for flu. Costs of CXR and RSV/flu testing for this cohort was $19,788. Conclusion: The absence of positive CXRs in this patient population reinforces the current recommendations that CXR is not indicated. The low incidence of RSV/flu indicate that routine testing may not be necessary in this population especially outside of the flu season. Reduced testing could decrease overall costs to the healthcare system as well as radiation exposure to this population.
Construction of an RNA Binding Protein-based Model for Prognosis Prediction of Colorectal Cancer
Authors: li Ting , Hui Wenjia , Halike Halina , Gao Feng 
Published: June 2020

Abstract
Background: Colorectalcancer (CRC) is a prevalent gastrointestinal tumor with high incidence and mortality. Dysregulation of RNA binding proteins (RBPs) has been found in a variety of cancers and is related to oncogenesis and progression. This study aimed to develop and validate new biomarkers related to CRC prognosis by a series of bioinformatics analysis.Methods: We mined the gene expression data of 510 CRC samples from The Cancer Genome Atlas (TCGA) database, differentially expressed genes were screened and prognosis-related genes were identified. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out. A prognosis-related gene signature was constructed by univariate and multivariate Cox analysis. Kaplan–Meier curves and time-dependent receiver operating characteristic (ROC) curves were utilized to evaluate the signature,The test set was used to validate the RBPs risk score model.Survival analysis was carried out to determine the independent prognostic significance of the signature. A nomogram combined with the gene signature was constructed.Results: A total of 224 aberrantly expressed RBPs were obtained, comprising 78 downregulated and 146 upregulatedRBPs. 13 RBPs with p < 0.005 were revealed in univariateCox regression analysis of train group, then stepwise multivariate Cox regression was applied for constituting an eight- RBP (BRCA1, TERT, TDRD7, PPARGC1A, LUZP4, CELF4, ZC3H12C, PNLDC1) signature prognostic biomarkers. Further analysis demonstrated that high risk score for patients was significantly related to poor overall survival according to the model. The area under the time-dependent receiver operator characteristic curve of the prognostic model was 0.730 at 5 years. The signature-based risk score was an independent prognostic factor in CRC patients. We also established a nomogram based on eight RBPs and internal validation in the train set, which displayed a favorable discriminating ability for Colorectal cancer.Conclusions: The established eight-RBP signature may serve as a novel independent prognostic factor that could be an important tool to predict the prognostic outcome of CRC patients. However, the specific biological mechanism needs further verification.
Analysis of the expression and potential molecular mechanism of interleukin-1 receptor antagonist (IL1RN) in papillary thyroid cancer via bioinformatics methods
Authors: Xie Zhenyu , Li Xin , He YuZhen , Wu Song , Wang Shiyue , Sun Jianjian , He Yuchen , Lun Yu , Xin Shijie , Zhang Jian 
Published: June 2020

Abstract
Background: Interleukin-1 receptor antagonist (IL1RN) has been reported as a biomarker of many cancers. However, the biological function of IL1RN in papillary thyroid carcinoma (PTC) remains undetermined.Methods: We obtained IL1RN expression data from The Cancer Genome Atlas (TCGA) database. Enrichment analysis of coexpressed genes and IL1RN methylation analysis were performed via LinkedOmics. The correlations between IL1RN and immune infiltrates were investigated via ESTIMATE, TIMER and TISIDB. We analyzed the association of IL1RN expression with pancancer overall survival (OS) via Gene Expression Profiling Interactive Analysis (GEPIA).Results: IL1RN showed higher expression levels and lower methylation levels in PTC tissues than in normal tissues. Higher IL1RN expression was significantly associated with shorter progression-free survival (PFS), advanced tumor stage, tumor metastasis, increased incidence of BRAF mutations, and decreased incidence of N-RAS and H-RAS mutations. Genes coexpressed with IL1RN participate primarily in immune-related pathways. IL1RN expression was positively correlated with immune infiltration, tumor progression and poor overall survival for all cancers.Conclusions: IL1RN is a good prognostic and diagnostic biomarker for PTC. IL1RN may promote thyroid cancer progression through immune-related pathways. Methylation may act as an upstream regulator of IL1RN expression and biological function. Additionally, IL1RN was shown to have broad prognostic value in a pancancer cohort.
Are Fiscal Deficits Inflationary in Nigeria? Evidence From Cointegration With Structural Breaks
Authors: Fasanya Ismail , Fajobi Ayinke , Adetokunbo Abiodun 
Published: June 2020

Abstract
In this paper, we model the relationship between fiscal deficit and inflation for Nigeria using annual data from 1980 to 2019. We employ the Linear ARDL approach and also account for structural breaks using the Bai and Perron (2003) test that allows for multiple structural changes in regression models.The paper finds that fiscal deficit is a major determinant of inflation along with other macroeconomic factors considered in the study. However, we observe that it may be necessary to pre-test for structural breaks when modelling the relationship between fiscal deficit and price level as it performs better than when structural events are not considered.The results imply that a fiscal management process that does not encourage increased revenue and reduce fiscal deficits in Nigeria will further worsen the level of inflation in the country.
Incidence and predictors of surgical site infection after distal femur fractures treated by open reduction and internal fixation: a prospective single-center study
Authors: Zhang Junzhe , Li Junyong , Zhao Kuo , Meng Hongyu , Zhu Yanbin , Zhang Yingze 
Published: June 2020

Abstract
Background: There remain limited data on the epidemiological characteristics and related predictors of surgical site infection (SSI) after open reduction and internal fixation (ORIF) for distal femur fractures. We designed this single-centre prospective study to explore and resolve these clinical problems.Methods：From October 2014 to December 2018, 364 patients with distal femur fractures were treated with ORIF and followed for complete data within one year. Receiver operating characteristic (ROC) analyses, univariate Chi-square analyses, and multiple logistic regression analyses were used to screen the adjusted predictors of SSI.Results: The incidence of SSI was 6% (22/364): 2.4% for superficial SSIs and 3.6% for deep SSIs. Staphylococcus aureus (methicillin-resistant S. aureus in 2 cases) was the most common pathogenic bacteria (7, 36.8%). In multivariate analysis, parameters independently associated with SSI were: Open fracture (OR: 7.27, p = 0.003), drain use (OR: 4.11, p = 0.037), and incision cleanliness (OR: 3.53, p = 0.002). An albumin/globulin (A/G) level ≥ 1.35 (OR: 0.23, p = 0.042) was an adjusted protective factor for SSI. Conclusions: The SSI after ORIF affected approximately one in 15 patients with distal femur fractures. We recommend that maintaining A/G levels higher than 1.35 is introduced during hospitalization and elaborative evaluation of drain use is conducted for reducing the risk of post-operative SSI. Trial registration: NO 2014-015-1, October 15, 2014. We registered our trial prospectively in October 15, 2014 before the first participant was enrolled. This study protocol was conducted according to the Declaration of Helsinki and approved by the Institutional Review Board. The ethics committee approved the Surgical Site Infection in Orthopaedic Surgery (NO 2014-015-1). Data used in this study were obtained from the patients who underwent orthopaedic surgeries between October 2014 to December 2018. Keywords : predictor, surgical site infection, distal femoral fracture, internal fixation surgery
I felt so much conflict instead of joy: An analysis of narratives from pregnant people in British Columbia who declined care recommendations
Authors: Stoll Kathrin , Wang Jessie J. , Niles Paulomi , Wells Lindsay , Vedam Saraswathi 
Published: June 2020

Abstract
Background
No Canadian studies to date have examined the experiences of people who decline care during pregnancy and birth. The current analysis bridges this gap by describing narratives from 892 people in British Columbia (BC) who refused a test or procedure that their care provider recommended.
Methods
In the Changing Childbirth in BC study, childbearing people designed a mixed-methods study that captured experiences of receiving maternity care, including novel items describing provider-patient interactions. We conducted a descriptive quantitative content analysis of 1540 open ended comments about declining care recommendations.
Results
Close to half of people who participated in the survey (n = 892; 46%) declined a test or procedure. Participants most commonly declined genetic or gestational diabetes testing, ultrasounds, induction of labour, pharmaceutical pain management during labour, and eye prophylaxis for the newborn. Some people reported that care providers accepted or supported their decision, and others described pressure and coercion from providers. These negative interactions resulted in childbearing people feeling invisible, disempowered and in some cases traumatized. Loss of trust in healthcare providers were also described by childbearing people whose preferences were not respected whereas those who felt informed about their options and supported to make decisions about their care reported positive birth experiences.
Conclusions
Declining care is common during pregnancy and birth and care provider reactions and behaviours greatly influence how childbearing people experience these events. Our findings confirm that clinicians need further training in person-centred decision-making, including respectful communication even when choices fall outside of standard care.
Relationship of attitudes toward uncertainty and preventive health behaviors with breast cancer screening participation
Authors: Satoh Miho , Sato Naoko 
Published: June 2020

Abstract
Background: Early detection of breast cancer is effective for prolonging survival, but the participation rate in breast cancer screening among target Japanese women remains low. This study examined the relationships between tendencies in decision-making under uncertainty conditions, health behaviors, demographics, and breast cancer screening participation in Japanese women.Methods: Data for women aged 40 years or older obtained in the 2017 Keio Household Panel Survey were analyzed. Participants answered questions about breast cancer screening attendance in the last year, risk aversion, time preference, health behaviors (e.g., smoking habit, alcohol consumption, and medical treatment received in the last year), and demographic variables. Responses were analyzed using chi-squared tests, t-tests, and logistic regression analysis. Variables were entered into the regression model if they were significantly associated with breast cancer screening participation in univariate analysis.Results: A total of 2,729 of 2,945 households responded to the questionnaire. Data from 708 questionnaires were analyzed. Among the respondents, 28.8% had participated in breast cancer screening in the past year. Factors found to significantly contribute to breast cancer screening participation included higher risk aversity (odds ratio [OR], 2.34; 95% confidence interval [CI] = 1.03-5.32; p = 0.043), medical treatment received in the last year (OR, 1.56; 95%CI = 1.06-2.30; p = 0.026), higher self-rated health (OR, 1.47; 95% CI = 1.18-1.83; p = 0.001), living above the poverty line (OR, 2.31; 95% CI = 1.13-4.72; p = 0.022), and having children (OR, 1.57; 95% CI = 1.02-2.42; p = 0.042). Factors not significantly associated with screening participation were smoker (OR, 0.20; 95% CI = 0.10-0.42; p < 0.000), alcohol drinker (OR, 0.56; 95% CI = 0.37-0.86; p = 0.007), self-employed (OR, 0.22; 95% CI = 0.10-0.46; p < 0.000), and unemployed (OR, 0.48; 95% CI = 0.26-0.90; p = 0.022). No significant relationship was observed between time preference and screening participation.Conclusions: The results indicate that women who recognize the actual risk of developing breast cancer or have high awareness of breast cancer prevention tend to participate in breast cancer screening. Barriers to screening participation are not working for an enterprise that encourages screening and low income.