bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vaccine Adverse Event Enrichment Tests
Authors: Zhao Lili , Li Shuoran 
Published: August 2020

Abstract
Background: Vaccination safety is critical for individual and public health. Many existing methods have been used to conduct safety studies with the VAERS (Vaccine Adverse Event Reporting System) database. However, these methods frequently identify many adverse event (AE) signals and they are often hard to interpret in a biological context. The AE ontology introduces biologically meaningful structures to the VAERS database by connecting similar AEs, which provides meaningful interpretation for the underlying safety issues. In this paper, we develop rigorous statistical methods to identify interesting AE groups by performing AE enrichment analysis. Results: We extend existing gene enrichment tests to perform AE enrichment analysis. Unlike the continuous gene expression data, AE data are counts. Therefore, AE data has many zeros and ties. We propose two enrichment tests, AEFisher and AEKS. AEFisher is a modified Fisher's exact test based on pre-selected significant AEs, while AEKS is based on a modified Kolmogorov-Smirnov statistic. Both tests incorporate the special features of the AE data. The proposed methods were evaluated using simulation studies and were further illustrated on two studies using VAERS data. Conclusion: By appropriately addressing the issues of ties and excessive zeros in AE count data, our enrichment tests performed well as demonstrated by simulation studies and analyses of VAERS data. The proposed methods were implemented in R package AEenrich and can be installed from the Comprehensive R Archive Network, CRAN, and source code are available at https://github.com/umich-biostatistics/AEenrich.
Decomposition and stabilization of the organic matter in an old-growth tropical riparian forest: effects of soil properties and vegetation structure
Authors: Fernandes Pedro , Souza Andrea Teixeira , Tanaka Marcel , Sebastiani Renata 
Published: August 2020

Abstract
Background: Nutrient cycling in tropical forests has large importance for primary productivity, and decomposition of litterfall is a major process influencing nutrient balance in forest soils. Although large-scale factors strongly influence decomposition patterns, small-scale factors can have major influences, especially in old-growth forests that have high structural complexity and strong plant-soil correlations. Methods: We evaluated decomposition rates and stabilization of soil organic matter using the Tea Bag Index in an old-growth riparian forest in southeastern Brazil. We buried 50 pairs of green and red tea at two distances from the watercourse to evaluate the effects of forest structure and soil properties on decomposition processes. Forest structure and soil properties were described using Principal Components Analysis (PCA). The main axes for each analysis were considered predictors of decomposition processes using a structural equations model.Results: Decomposition rates presented a large variation among tea bags and were positively correlated with forest structure, as characterized by higher basal area, larger trees, and tree density. Higher decomposition rates were probably correlated with higher litter production and microbial activity. On the other hand, stabilization factor was related mainly to soil chemical properties, with higher values with increased soil fertility as indicated by the PCA axes. Further analyses evaluated the effects of clay content, soil moisture, soil organic matter, soil base saturation, and soil fertility as predictors of the stabilization factor. These predictors were highly correlated, but clay content was the best predictor, explaining 79% of the variation among plots. Conclusions: These results showed that this old-growth forest presented high heterogeneity in both forest structure and soil properties at small spatial scales, that influenced decomposition processes and contributed to small-scale variation in nutrient cycling. Heterogeneity in ecological processes can contribute to the resilience of old-growth forests, strengthening ecosystem functions such as nutrient cycling and carbon fixation, and highlighting the importance of restoration strategies focused in the recovery of ecosystem processes
Clinical Outcomes and Adverse Events of the Stomach Endoscopic Submucosal Dissection of the Mid to Upper Stomach Under General Anesthesia and Monitored Anesthetic Care
Authors: Chang Jong-In , Kim Tae Jun , Hwang Na Young , Sohn Insuk , Min Yang Won , Lee Hyuk , Min Byung-Hoon , Lee Jun Haeng , Rhee Poong-Lyul , KIM JAE 
Published: August 2020

Abstract
Background: Endoscopic submucosal dissection (ESD) of gastric tumors in the mid to upper stomach is a technically challenging procedure. This study compared the therapeutic outcomes and adverse events following ESD of tumors in this area, performed in conjunction with either general anesthesia (GA) or monitored anesthetic care (MAC).Methods: Between 2012 and 2018, 674 patients underwent ESD of gastric tumors in the midbody, high body, fundus, or cardia (100 patients received GA; 574 received MAC). The results were analyzed using propensity score (PS)-matched (1:1) patients receiving either GA or MAC.Results: PS matching identified 95 patients who received GA and 95 matched patients who received MAC. Both groups showed high rates of en-bloc resection (GA, 98.5%; MAC, 98.9%; p = 0.18) and complete resection, defined as tumors excised with histologically confirmed negative margins (GA, 82.1%; MAC, 90.5%; p = 0.14). There were no significant differences in the frequencies of adverse events (GA, 16.8%; MAC, 9.5%; p = 0.13) between the anesthetic groups. A logistic regression analysis indicated that the anesthetic method was not a factor impacting the frequencies of complete resection or adverse events. Conclusion: At our high-volume center, good therapeutic outcomes were achieved following ESD of tumors in the mid to upper stomach, regardless of the anesthetic method used. Our results demonstrate the efficacy and safety non-inferiority of the ESD procedure performed in conjunction with MAC, compared with GA.
Statistical methods for the analysis of adverse event data in randomised controlled trials: a comprehensive review and taxonomy
Authors: Phillips Rachel , Sauzet Odile , Cornelius Victoria 
Published: August 2020

Abstract
Background Statistical methods for the analysis of harm outcomes in randomised controlled trials (RCTs) are rarely used, and there is a reliance on simple approaches to display information such as in frequency tables. We aimed to identify whether any statistical methods had been specifically developed to analyse prespecified secondary harm outcomes and non-specific emerging adverse events (AEs). Methods A scoping review was undertaken to identify articles that proposed original methods or the original application of existing methods for the analysis of AEs that aimed to detect potential adverse drug reactions (ADRs) in phase II-IV parallel controlled group trials. Methods where harm outcomes were the (co)-primary outcome were excluded. Information was extracted on methodological characteristics such as: whether the method required the event to be prespecified or could be used to screen emerging events; and whether it was applied to individual events or aggregate events. Each statistical method was appraised and a taxonomy was developed for classification.Results Forty-four eligible articles proposing 73 individual methods were included. A taxonomy was developed and articles were categorised as: visual summary methods (8 articles proposing 20 methods); hypothesis testing methods (11 articles proposing 16 methods); estimation methods (15 articles proposing 24 methods); or methods that provide decision-making probabilities (10 articles proposing 13 methods). Methods were further classified according to whether they required a prespecified event (9 articles proposing 12 methods), or could be applied to emerging events (35 articles proposing 61 methods); and if they were (group) sequential methods (10 articles proposing 12 methods) or methods to perform final/one analyses (34 articles proposing 61 methods). Conclusions This review highlighted that a broad range of methods exist for AE analysis. Immediate implementation of some of these could lead to improved inference for AE data in RCTs. For example, a well-designed graphic can be an effective means to communicate complex AE data and methods appropriate for counts, time-to-event data and that avoid dichotomising continuous outcomes can improve efficiencies in analysis. Previous research has shown that adoption of such methods in the scientific press is limited and that strategies to support change are needed.
Daily, Oral FMT for Long-Term Maintenance Therapy in Ulcerative Colitis: Results of a Single-Center, Prospective, Randomized Pilot Study.
Authors: Crothers Jessica Wood , Chu Nathaniel D. , Nguyen Le Thanh Tu , Phillips Magen , Collins Cheryl , Fortner Karen , Rio-Geurra Roxana del , Lavoie Brigitte , Callas Peter , Velez Mario , Cohn Aaron , Elliott Ryan J. , Wong Wing Fei , Vo Elaine , Wilcox Rebecca , Smith Mark , Kassam Zain , Budd Ralph , Alm Eric J. , Mawe Gary M. , Moses Peter L 
Published: August 2020

Abstract
This randomized study was designed to assess the safety and feasibility of long-term fecal microbiota transplantation (FMT) in subjects with mild to moderate UC using frozen, encapsulated oral FMT (cFMT). FMT induction was implemented by colonoscopy, followed by 12 weeks of daily oral administration of frozen encapsulated cFMT. Ribosomal 16S bacterial sequencing was used to assess donor-induced changes in the gut microbiota. Changes in T regulatory (Treg) and mucosal associated invariant T (MAIT) cell populations were evaluated as an exploratory endpoint. Twelve subjects with active UC were randomized: 6 subjects completed the full 12-week course of FMT plus cFMT, and 6 subjects received sham treatment by colonic installation and longitudinal oral treatment. Chronic administration of cFMT was found to be safe and well-tolerated. Protocol adherence was high, and none of the study subjects experienced FMT-associated treatment emergent adverse events. While n-values were too small to draw firm conclusions, 3/6 subjects that received cFMT exhibited multiple signs of clinical improvement. These pilot data suggest that daily encapsulated cFMT may extend the durability of index FMT-induced changes in gut bacterial community structure and that an association between MAIT cell cytokine production and clinical response to FMT may exist in UC populations. Oral frozen encapsulated cFMT is a promising FMT delivery system and may be preferred for longterm treatment strategies in UC and other chronic diseases but further evaluations will have to address home storage concerns. Larger trials should be done to explore the benefits of cFMT and to determine its long-term impacts on the colonic microbiome. Trial registration: ClinicalTrials.gov (NCT02390726). Registered 17 March 2015, https://clinicaltrials.gov/ct2/show/NCT02390726?term=NCT02390726&draw=2&rank=1.
Quantitative determination of energy potential of refuse derived fuel from the waste recovered from Indian landfill
Authors: Cheela V R Sankar , John Michele , Dubey Brajesh 
Published: August 2020

Abstract
Landfills are urban stocks and resource reservoirs for potential energy recovery. The purpose of this study is to evaluate the amount of energy that could be recovered from aged waste (around 5 - 20 years old) recovered from landfills. Investigations were conducted on the physical and chemical properties of refuse-derived fuel (RDF) prepared from recovered landfill waste (RLW) in Andhra Pradesh, India. Waste characterization studies included determination of waste composition, proximity analysis, ultimate analysis, and energy content. The moisture content ranged between 25.70 to 31.30%, however, no trend was observed with age. In the ultimate analysis, the percentage of carbon increased from 42.94% to 71. 66% with the age of the samples, this is due to an increase in the plastic content over time. The calorific value of the recovered landfill waste ranged from 10.35 MJ/kg to 21.83 MJ/kg. From the findings, it can be summarized that the RDF can potentially be utilized as a feedstock for the recovery of energy from RLW. The results from this study will assist policy makers and local authorities in designing and developing strategies for resource and energy recovery from landfills in different urban cites across the globe.
Virulent Secondary Metabolites of Entomopathogenic Bacteria, Xenorhabdus and Photorhabdus, Inhibit PLA2 to Suppress Host Insect Immunity
Authors: Mollah Md. Mahi Imam , Kim Yonggyun 
Published: August 2020

Abstract
Background: Xenorhabdus and Photorhabdus are entomopathogenic bacteria that cause septicemia and toxemia in insects. They produce secondary metabolites to induce host immunosuppression. Their metabolite compositions vary among bacterial species. Little is known about the relationship between metabolite compositions and the bacterial pathogenicity. The objective of this study was to compare pathogenicity and production of secondary metabolites of 14 bacterial isolates of Xenorhabdus and Photorhabdus. Results: All bacterial isolates exhibited insecticidal activities after hemocoelic injection to Spodoptera exigua (a lepidopteran insect) larvae, with median lethal doses ranging from 168.8 to 641.3 CFU per larva. Bacterial infection also led to immunosuppression by inhibiting eicosanoid biosynthesis. Bacterial culture broth was fractionated into four different organic extracts. All four organic extracts of each bacterial species exhibited insecticidal activities and resulted in immunosuppression. These organic extracts were subjected to GC-MS analysis which predicted 182 compounds, showing differential compositions for 14 bacteria isolates. There were positive correlations between total number of secondary metabolites produced by each bacterial culture broth and its bacterial pathogenicity based on immunosuppression and insecticidal activity. From these correlation results, 70 virulent compounds were selected from secondary metabolites of high virulent bacterial isolates by deducting those of low virulent bacterial isolates. These selected virulent compounds exhibited significant immunosuppressive activities by inhibiting eicosanoid biosynthesis. They also exhibited relatively high insecticidal activities. Conclusion: Virulence variation between Xenorhabdus and Photorhabdus is determined by their different compositions of secondary metabolites, of which PLA2 inhibitors play a crucial role.
Analysis of Sinmap in Landslide Susceptibility Mapping of Coonoor Watershed, Nilgiris, India
Authors: Saravanan Subbarayan , Jesudasan Jacinth Jennifer , Singh Leelambar , Devanantham Abijith 
Published: August 2020

Abstract
Landslide susceptibility mapping is crucial for risk management in mountainous Nilgiris district, Tamil Nadu, India. In this study, the spatially distributed Stability INdex MAPping (SINMAP) model was used to develop a landslide susceptibility model for Coonoor watershed, which is based on a steady-state hydrologic model coupled with an infinite-slope stability equation. Shuttle Radar Topography Mission (SRTM) digital elevation model was utilized to compute the slope and other topographic parameters. In-situ data collection and laboratory tests were executed to estimate the hydro-geotechnical parameters. A detailed field study was conducted, and 35 samples were taken from the landslide locations to perform laboratory tests to find the geotechnical parameters. Also, an inventory landslide map was generated to evaluate the model performance. Statistical results of SINMAP show that, under the fully saturated condition, 58.96% of the region was found to be stable, 16.79% moderately stable, 8.72% quasi-stable and 15.24% unstable. The Area under the Curve (AUC) value of the predicted result is 72.3% which infer that the underlying predictors perform good in classifying the outcome. Thus, the considered parameters in the model have played its part well in the classification of the region based on its stability.
Salivary Melatonin in Oral Squamous Cell Carcinoma Patients: A Cross-sectional Study
Authors: Salaric Ivan , Karmelic Ivana , Lovric Jasna , Bazdaric Ksenija , Rozman Marko , Cvrljevic Igor , Zajc Ivan , Brajdic Davor , Macan Darko 
Published: August 2020

Abstract
BACKGROUND: Around 55% of oral squamous cell carcinoma (OSCC) patients are diagnosed in the advanced stage. Poor sleep quality has been associated as a potential risk factor for several malignancies, including head and neck cancers. Melatonin’s role in circadian rhythm is well documented, as are its’ anti-oxidant, oncostatic and anti-inflammatory properties. The purpose of this study is to determine salivary melatonin (MLT) levels in OSCC patients, compare the salivary MLT levels with those in healthy individuals and compare the salivary and serum levels in OSCC patients. Furthermore, the aim is to evaluate sleep quality and to investigate the potential relationship between sleep quality and salivary MLT levels in OSCC patients. METHODS: Unstimulated and stimulated saliva were sampled from patients with T1N0M0 and T2N0M0 OSCC (N=34) and 33 sex and age matched healthy subjects. Serum samples were taken from 11 OSCC patients. Detailed medical history was taken before sampling and sleep quality measured using Pittsburgh Sleep Quality Index (PSQI) questionnaire. RESULTS: Melatonin levels in UWS and SWS were significantly higher in the OSCC group. Sleep quality was significantly lower in patients with OSCC (U=249.50; P = 0.0001). ROC analysis was found to be significant (P <0.001) in evaluating the MLT concentration limit in diagnosing OSCC. CONCLUSIONS: The expected relationship between sleep quality and salivary MLT levels in OSCC patients was not observed. Salivary melatonin could present a potential OSCC biomarker. However, larger prospective studies should validate the clinical utility of MLT as an OSCC biomarker.
Discontinuation and Switching of Postpartum Contraceptive Methods Over Twelve Months in Burkina Faso and the DRC: A Secondary Analysis of the Yam-Daabo trial
Authors: Coulibaly Abou , Millogo Tieba , Baguiya Adama , Tran Nguyen Toan , Yodi Rachel , Seuc Armando , Cuzin-Kihl Asa , Thieba Blandine , Landoulsi Sihem , Kiarie James , Mashinda Désiré , Kouanda Seni 
Published: August 2020

Abstract
Introduction: Women who use contraceptive methods sometimes stop early, use methods intermittently or switched contraceptive methods. All these events (discontinuations and switching) contribute to the occurrence of unwanted and close pregnancies. This study aimed to explore contraceptive discontinuation and switching during the Yam-Daabo project to measure the effect of interventions on the continuation of contraceptive methods use.Methods: We conducted a secondary analysis of the Yam-Daabo trial data. We choose the discontinuation and switching of a modern contraceptive method as outcome measures. We performed a survival analysis by using the Stata software package to estimate the effect of the interventions on contraceptive discontinuation. We also studied the main reasons for discontinuation and switching.Results: In total, 637 out of the 1,120 women used at least one contraceptive method (of any type), with 267 women in the control and 370 in the intervention group. Modern methods were used by 179 women of control group compared to 279 women of intervention group with 24 and 32 who discontinued, respectively. We observed no statistically significant association between interventions and modern methods discontinuation and switching. However, the discontinuation of modern methods was higher in pills and injectables users than implants and IUDs users. The pooled data comparison showed that, in reference to the women who had not switched while using a modern method, the likelihood of switching to a less or equal effectiveness method among the women of the control group was 3.8(95% CI: 1.8-8.0) times the likelihood of switching to a less or equal effectiveness method among the women of the intervention group. And this excess was statistically significant (p<0.001). The main reason for discontinuation and switching was method-related (141 over 199), followed by partner opposition with 20 women.Conclusion: The results of this study show no statistically significant association between interventions and modern methods discontinuation. Discontinuation is more related to the methods themselves than to any other factor. It is also important to set up specific actions targeting women's partners and influential people in the community to counter inhibiting beliefs.Trial registration: Pan African Clinical Trials Registry (PACTR201609001784334, https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=1784).
Development and Validation of a Gene-panel-based Nomogram for Prediction of Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma
Authors: Wu Xuejie , Chen Donglai , Wang Wenjia , Ye Fei , Sang Yonghua , Chen Yongbing , Yang Wentao 
Published: August 2020

Abstract
Background: Esophageal squamous cell carcinoma (ESCC) is one of the main histological subtypes of esophageal cancer. This study aimed to develop a gene-panel-based nomogram for identification of lymph node metastasis (LNM) in ESCC patients.Methods: RNA sequencing profiles of ESCC patients were obtained from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. A bioinformatic approach was employed to investigate differentially expressed genes (DEGs) between ESCC patients with LNM and those without. A 4-DEGs panel was eventually identified and integrated with clinical characteristics to construct a nomogram for predicting LNM. Predictive performance of the nomogram was further evaluated by calibration curves and concordance index (C-index). Results: A total of 179 ESCC patients with 32059 genes from the GEO dataset were included. Among these genes, 3524 DEGs were correlated with lymph node involvement. Meanwhile, TCGA dataset containing 93 ESCC patients was obtained, in which 82 DEGs were selected out of 18416 genes. Among the 11 communal DEGs, four genes were identified to be (ALG3, CPOX, LMLN, PSMD2) associated with LNM. A nomogram was established by integrating the four-gene panel and three clinical characteristics including T stage, G stage and tumor location. The nomogram exhibited good performance with C-indices of 0.710 and 0.693 in the GEO and TCGA datasets, respectively. Conclusion: Our novel 4-gene-based nomogram displayed its value in prediction of LNM in ESCC patients, which may be helpful in determining treatment approach for early-stage ESCC patients.