bluuebunny/crossref_metadata_2025_split huggingface dataset:
Separation of Cohorts on the Basis of Bacterial Type IV Conjugation Systems Identified From Metagenomic Assemblies
Authors: Joris Benjamin R , Browne Tyler S , Hamilton Thomas A , Edgell David R , Gloor Gregory B 
Published: June 2021

Abstract
BackgroundConjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identification of these systems in metagenomic samples clinically important. ResultsHere, we outline two distinct methods to identify conjugative elements in the human gut microbiome. We first show that conjugative elements exhibit strong population and age-level stratification. Furthermore, the taxonomic compositions of the conjugative elements differ from the composition of the metagenome assembled genomes, both in terms of the number of assembled elements and the relative abundances of the assembled systems. Finally, we demonstrate that the majority of assembled conjugative elements are not included within metagenomic bins, and that only a small proportion of the binned conjugative systems are included in "high-quality" metagenomic bins. Our findings highlight that conjugative systems differ between a North American inflammatory bowel disease cohort and a cohort of North American pre-term infants, but in a manner different than metagenome assembled genomes, revealing a potential use as an age-related biomarker. Additionally, conjugative systems can distinguish between other geographical-based cohorts. ConclusionsAnalysis of the human gut microbiome by shotgun metagenomic sequencing has revealed numerous connections to human health outcomes. Our findings emphasize the need to identify and analyze conjugative systems outside of standard metagenomic binning pipelines. We suggest that analysis of type IV conjugative systems should be added to the current metagenomic analysis approaches as they contain much information that could explain differences between cohorts beyond those we investigated.
Graph Theoretical Network Analysis and Pharmacoinformatics-Based Investigation of Bioactive Compounds of Rasam (South Indian Recipe) Against Human Cancer
Authors: Kalimuthu Arjun Kumar , Panneerselvam Theivendran , Parasuraman Pavadai , Pandian Sureshbabu Ram Kumar , Murugesan Sankaranarayanan , Ammunje Damodar Nayak , Kumar Sattanathan , Arunachalam Sankarganesh , Kunjiappan Selvaraj 
Published: June 2021

Abstract
Spice-rich recipes are referred to as "functional foods" because they include a variety of bioactive chemicals that have health-promoting properties in addition to their nutritional value. Using pharmacoinformatics-based analysis, we explored the relevance of bioactive chemicals found in rasam (a south Indian cuisine) against oxidative stress-induced human malignancies. The rasam is composed of twelve main ingredients, each of which contains a variety of bioactive chemicals. Sixty-six bioactive compounds were found from these ingredients, and their structures were downloaded from Pubchem. To find the right target via graph theoretical analysis (mitogen-activated protein kinase (MAPK)) and display their signaling route, a network was built. Among the identified compounds sixty-six bioactive compounds were used for in silico molecular docking study against MAPK, the top four compounds were chosen for further study based on their docking score and binding affinities. In silico predicted ADMET characteristics of the titled compounds were used to assess their drug-likeness. Molecular dynamics (MD) simulation modelling methodology were also used to analyze the effectiveness and safety profile of top four selected bioactive chemicals based on the docking score, as well as to assess the stability of the MAPK-ligand complex structure. Surprisingly, the discovered docking scores against MAPK revealed that the titled bioactive chemicals distribution varied between -3.5 and -10.6 kcal/mol. MD simulation validated the stability of four chemicals at the MAPK binding pockets, including Assafoetidinol A (ASA), Naringin (NAR), Rutin (RUT), and Tomatine (TOM). According to the results obtained, fifty of the sixty-six compounds showed higher binding affinity (-6.1 to -10.6 kcal/mol), and four of these compounds may be used as lead compounds to protect cells against oxidative stress-induced human malignancies.
Association of Increased Remnant Cholesterol and The Risk of Coronary Artery Disease: A Retrospective Study
Authors: Wang Kexin , Ding Yaodong , Gao Wen , Wang Rui , Yang Jiaxin , Liu Xiali , Shen Hua , Ge Hailong 
Published: June 2021

Abstract
Background and AimsLow-density lipoprotein cholesterol (LDL-C) is the primary target in lipid-lowering therapy in coronary artery disease (CAD). But some patients with normal levels of LDL-C still suffer from CAD progression and malignant outcomes (e.g., MACEs), and the mechanism is unclear. Previous prospective studies demonstrated that remnant cholesterol (RC) and non-HDL-C were capable to predict the risk of CAD. This study evaluated the association between RC and non-HDL-C with the risk of CAD.Methods12,563 patients were enrolled in our study. We categorized patients into four concordance/discordance groups according to the median of RC, LDL-C and non-HDL-C. Then we performed a propensity score matching (PSM) strategy. Unadjusted and adjusted multivariate logistic regression models were used to evaluate the relationship between lipid concentrations.Results8,658 (68.9%) patients were male with a median age of 61 (54,67) years. The multivariate logistic regression showed the OR of RC was 1.952 (CI=1.276-2.988, p＝0.002). The OR of low RC/high LDL-C group was 0.574 (CI=0.462-0.714, p＜0.001) and the OR of low RC/high non-HDL-C group was 0.574 (CI=0.462-0.714, p＜0.001). The p for interaction between RC and hypertension, diabetes were both <0.001.ConclusionsOur study showed a significant association between RC and CAD. The level of RC was more capable to reflect the risk of CAD than LDL-C and non-HDL-C. There was an interaction relationship between remnant cholesterol and age, gender, hypertension, diabetes in CAD. But we didn’t find whether there was a relationship between non-HDL-C and CAD.
The Acute Single and Mixture Toxicity of Paraquat Dichloride and Deltamethrin to Guppy (Poecillia reticulata)
Authors: Nugroho Rully Adi , Gestel Cornelis van 
Published: June 2021

Abstract
Although herbicide and insecticide contamination of surface waters normally occurs in the form of mixtures, the toxicity interactions displayed by such mixtures have only rarely been characterized. This study evaluated the acute effects of single pesticides (paraquat dichloride and deltamethrin, tested in their commercial formulations Gramoxone 276 SL and Decis 25EC) and their equitoxic mixtures on the survival of adult male guppy fish (Poecilia reticulata). Mixture toxicity was evaluated against the reference models of Concentration Addition (CA) and Independent Action (IA). In the single treatments, the 72h LC10 and LC50 values were 1.5 and 6.0 mg a.s. L-1 and 0.53 and 3.6 µg a.s. L-1 for paraquat dichloride and deltamethrin, respectively. The equitoxic mixtures showed significant paraquat dichloride-deltamethrin antagonism, both based on the CA and the IA model, without significant dose-level dependent deviations.
A feasibility study characterising tumour microenvironment of longitudinally collected biopsies of pancreatic tumours upon endoscopic ultrasound guided radiofrequency ablation
Authors: Lawrence Patrick V. , Desai Krisha , Wadsworth Christopher , Mangal Nagina , Habib Nagy , Sadanandam Anguraj , Sodergren Mikael 
Published: June 2021

Abstract
BackgroundMost patients with pancreatic ductal adenocarcinoma (PDAC) are metastatic at presentation with dismal prognosis warranting improved systemic therapy options. Longitudinal sampling for assessment of treatment response poses a challenge for validating novel therapies. In this feasibility study, we evaluate the role of endoscopic ultrasound (EUS)-guided serial fine-needle aspiration biopsies (FNABs) to study the molecular changes associated with radiofrequency ablation (RFA).MethodsTwo stage III inoperable gemcitabine-treated PDAC patients were recruited in the treatment arm of ARDEO (ethically approved Phase-II prospective randomized clinical study). Post examination, targeted RFA was delivered thrice, and sequential FNABs of tumour were taken before and after treatment and analysed using a custom NanoString panel (144 genes) consisting of cancer and cancer-associated fibroblast (CAFs) subtypes and immune changes. CAF culture was established from one FNAB and characterised by immunofluorescence and immunoblotting.ResultsSerial EUS-RFA treatments were well tolerated with no complications. Both patients had stable disease immediately after EUS-RFA, however, with different survival outcomes. Two-course RFA led to upregulation of CD1E gene (involved in antigen presentation) in both, patient 1 and 2 (4.5 and 3.9-fold) compared to baseline. Patient 1 showed increased T cell genes (CD4 – 8.7-fold, CD8 – 35.7-fold), cytolytic function (6.4-fold) and inflammatory response (8-fold). Greater than 2-fold upregulation of immune checkpoint genes was observed post 2nd RFA in patient 1, patient 2 or both. Further, two-course RFA led to increased PDGFRa (4.5-fold) and CAF subtypes B and C genes in patient 1 and subtypes A, B and D genes in patient 2. Patient2-derived CAFs post 1st RFA showed expression of PDGFRα, POSTN and MYH11 proteins. Finally, RFA led to downregulation of classical PDA subtype in both patients. ConclusionsFor the first time, this feasibility study validates longitudinal sampling by EUS-FNABs as an appropriate research tool to study tumour microenvironmental changes associated with local PDAC immunomodulatory treatments like RFA.
Retrospective Assessment of Donkeys’ Health and Welfare problems in Dale Sadi District Haro Sabbu Veterinary Clinic, Oromia, Ethiopia
Authors: Bekele Firaol , Goshu Desita , Lulu Darge , Wankila Ebisa 
Published: June 2021

Abstract
Background: Although donkey contributed vital role in human livelihoods through direct and indirect contributions to financial, human and social capital, emphasis has not been given to study the welfare issue which include health problems and management requirement. A retrospective study and questionnaire survey was conducted to assess the health and the welfare problem of donkeys coming to the Haro Sabbu Veterinary clinic for treatment at the Dale Sadi district, Haro SabbuVeterinary clinic, Oromia, Ethiopia. Data on 448 donkeys from 2018 to 2020 were analyzed from the data record sheet kept by the clinic. Results: The most common case for wound occurrence were back sore 135(30.1%), chest wound 37(8.3%), bite 27(6.0%) and combined wound of both back and bite 14(3.1%). The finding indicated that the occurrence of wound in donkeys having poor 170 (64.4%), medium 41(33.6%) and good 7(11.6%) body condition and this was found to be statistically significantly associated (p=0.000). Among the common health problems and abnormalities encountered in donkeys back sore wound 135(30.1%), lameness 92(20.5%), parasitic infestation 60(13.6%), chest wound 37(8.3) and signs of colic 34 (7.6%) were the major problems encountered in donkeys coming to clinic for treatment with there was no a statistically significant difference among different years. In addition to body condition, the occurrence of wounds was found to be statistically significantly associated with age category and work type. In addition, pack donkeys experienced higher lameness occurrences as compared to cart donkeys and it was statistically significant (P>0.05). In addition to health related problems, the questionnaire survey conducted also revealed welfare problems such as management condition, overloading, working hour, housing problems, and wounds due to harnessing were the major welfare problems of donkeys in the study area.Conclusion: This retrospective study and questionnaire survey revealed the significant health and welfare problems of donkeys that need to be addressed in order to improve welfare status, their health and working efficiency. Therefore, there should be immediate awareness creation for community, government, community, local service providers and policy makers on welfare issue of donkey and health management in the study area in particular and in the country in general.
Stroke volume variation is a good predictor of fluid responsiveness in cardiac surgery patients with implanted intra-arortic balloon pump
Authors: Enev Rostislav , Abedinov Filip , Bakalova Neda 
Published: June 2021

Abstract
There is a vast body of evidence in favor of individualising fluid therapy using dynamic hemodynamic indices like stroke volume variation (SVV). Patients with implanted intra-aortic balloon pump (IABP) are excluded from this approach because of pulse contour artifacts caused by the pump. The aim of this work is to test whether SVV can be used for fluid responsiveness prediction in these patients. Materials and methods: Patients after cardiac surgery with implanted IABP were included in this study. SVV was measured after placing the IABP on standy mode for one minute. Cardiac output (CO) measurement was obtained via Swan-Ganz catheter before and after a 6 ml/kg fluid challenge. Fluid responsiveness was defined as increase of CO by at least 10%. Results: SVV above 8.5% showed a good correlation with fuid responsiveness. Sensitivity was 95 (95% CI 85 to 100) and specificity 82 (95% CI 72 to 92). SVV had an area under the ROC curve 0.91 (95% CI 0.81 to 1.0) Conclusion: SVV is a good predictor of fluid responsiveness in patients with IABP. SVV should not be excluded as a fluid therapy guide for these patients. Placing the pump on standby for one minute allows obtaining an accurate measurement of this important variable.
Development of a Mathematical Model to Forecast Solar Radiation and Validating Results Using Machine Learning Technique
Authors: Herath H.M.K.K.M.B. , Ariyathunge S.V.A.S.H. , Karunasena G.M.K.B. 
Published: June 2021

Abstract
Solar radiation or also referred to as solar power is the general expression for electromagnetic radiation emitted by the Sun. Direct solar radiation is an important factor in global solar radiation and is very influential in the efficiency evaluation of various applications for solar energy. For countries like Sri Lanka, installing a solar radiation instrument in rural areas is a challenge. Thus, both scientific and economically, measuring solar radiation without installing measuring instruments is an advantage. The aim of this study is to development of a mathematical model to predict solar radiation where solar radiation measurement instruments are not installed. The Artificial Neural Network (ANN) was used to verify the predictions of the mathematical model. Multiple Linear Regression (MLR) analysis was used for the development of a mathematical model to predict solar radiation. The model with the highest R2 value (0.5973) was chosen from the 127 equations as the best model that describes the solar radiation that reaches the surface of the earth. The dataset used for this study was meteorological data from the four month HI-SEAS weather station and are composed of ten attributes including date, time, radiation (H), temperature (Tair), pressure (P), humidity (φ), sunrise time, sunset time, wind direction (D), and speed (S). The angle of declination (δ) and sunshine hours (N) were calculated using the dataset. For the training of the neural network, 80 % of the data from the HI-SEAS dataset was used. The remaining data were used for testing both mathematical and ANN models. Results obtained from the multiple linear regression method and the ANN method was compared with the measured values. The experimental results suggested that the mathematical model was predicted the solar radiation with ±100 Wm-2 tolerance for both measured and ANN values.
Influence of COVID-19 Lockdown on Aerosol Optical Depth over Pokhara and Kyanjin Gompa in Nepal
Authors: Silwal Ashok , Gautam Sujan Prasad , Karki Monika , Poudel Prakash , Thapa Arati , Chapagain Narayan Prasad , Adhikari Binod 
Published: June 2021

Abstract
The outbreak of the COVID-19 pandemic and the subsequent global economic shutdown provided an opportunity to conduct a real-time experiment assessing the influence of global emission reductions in the Aerosol Optical Depth (AOD) level, an indicator of air pollution over Nepal. Nepal's government imposed a lockdown on the country for approximately three months (from 24 March onwards) in 2020. The purpose of this study is to examine the temporal fluctuation in Aerosol Optical Depth (AOD) caused by the COVID-19 shutdown by comparing its value during the same time period of the past year over two sites: Pokhara and Kyanjin Gompa. We comparatively analyzed the variation of diurnal mean and monthly average AOD of two selected sites, from the month of January to May 2020 and January to May 2018. By examining the time-series graph of daily average AOD prior to and during the lockdown period, our study showed an apparent fluctuation in AOD throughout the studied areas. The major findings of the research revealed that after the lockdown, a significant variation in monthly averaged AOD was observed, ranging from 20–60% deviation over Pokhara and 25–50% deviation in Kyanjin Gompa at different wavelengths. This confirms previous studies on aerosols and other particulate matter during COVID-19 lockdown, as well as theoretical assumptions. In addition, we performed the heatmap correlation analysis among AOD, Total precipitable water (Tpw), Angstrom exponent (α), Turbidity coefficient (β), and Visibility (V) during the studied period with possible explanations. We believe this research work serves as a crucial reference for our government to implement appropriate policies for pollution control over the studied areas in the future.
ANALYSIS OF CANCER-TESTIS ANTIGENS AS POTENTIAL MARKERS FOR DISSEMINATION OF PRIMARY HUMAN SKIN MELANOMA
Authors: Mikhaylova I. N. , Treshalina H. M. , Utyashev I. A. , Kiselevsky M. V. , Lushnikova A. A. , Shubina I. Zh. 
Published: June 2021

Purpose of the study: to analyze characteristics of cancer-testis antigens (Ctas) as potential biomarkers for dissemination of primary human skin melanoma (sm).Material and Methods. Recent publications from Pubmed, scopus and elibrary databases were analyzed for the available appropriate literature review. In total, 176 papers reported the description of Ctas and encoding genes and their potential for prognosis of primary sm dissemination. The authors included 52 of them in the given review.Results. Two sections of the paper comprise clinically significant characteristics of Ctas and their genes, including overexpression, which is selective for the heterogeneous tumor cell populations and mediated by humoral and/or cellular immune reactions; the association of tumor process and activation of Cta genes by demethylation of promotor sites, which is correlated with tumor progression; and the conditions required for effective immunotherapy involving Ctas and/or their genes.Conclusion. At present, there are no standards or clinical recommendations for the Cta-based prognosis of the early dissemination of primary skin melanoma. Therefore, it is important to study and analyze the Cta and encoding gene characteristics that reveal the connection between primary sm progression and tumor genesis including the role of circulating tumor cells (ctc), similar to stem cells, which have epithelial-mesenchymal transition (emt) phenotype, for clinical diagnostics of early sm dissemination. As a result of the study, the following Ctas could be considered as significant biomarkers of the early sm dissemination: mage-a1, mage-a4 and ny-eso-1, which expression correlates with the clinical pathological description of the disease progression, as well as with the relapse-free period and overall survival of the patients; magea3, which expression correlates with spag5 activation and Cd8+ t-cell abundance; ssx, a marker for stem cell migration including identification of the cells with emt and/or ctcs; and prame, signaling marker for dissemination of the uveal melanoma.
PRELIMINARY EVALUATION OF THE EFFECTIVENESS OF HIFU-THERAPY IN PATIENTS WITH PANCREATIC CANCER
Authors: Bolotina L. B. , Moskvicheva L. I. , Kornietskaya A. L. , Sidorov D. V. , Grishin N. A. , Lozhkin M. V. , Kaprin A. D. 
Published: June 2021

Purpose: to conduct a preliminary analysis of the safety and effectiveness of hifu-therapy with a lowenergy hifu-2001 device (shenzhen Huikang Medical apparatus Co., ltd) performed concurrently with chemotherapy in pancreatic cancer patients who are not suitable for surgery or chemoradiotherapy.Material and Method. The study included 24 pancreatic cancer patients who were treated at the Hertsen Moscow Oncology Research institute in the period from 2016 to 2019. There were 17 (71 %) women and 7 (29 %) men. The percentage of patients in the elderly group was 79 %. Stage iia pancreatic cancer was diagnosed in 3 (12.5 %) patients, stage ii in 5 (21 %) patients, stage iii in 9 (37.5 %) patients, and stage iv in 7 (29 %) patients. All patients received combination therapy, including systemic chemotherapy and hifu-therapy. Results. The most frequent adverse events of treatment were skin burns (n=6), with third-degree burns occurring in 2 (8.3 %) patients. Local sclerosis of subcutaneous adipose tissue was observed in 4 (17 %) patients; development of asymptomatic pancreatic pseudocysts in the area of hifu exposure was observed in 1 (4 %) patient. Pain control was achieved in 17 (85 %) patients, and local tumor control was achieved in 19 (79.2 %) patients. The follow-up time ranged from 5 to 30 months with a median time of 14.5 months. The median total life expectancy of patients was 16 months, and the median time to progression was 9 months. The overall 6-month survival rate was 100 %. The 1- and 1.5-year survival rates were 75.0 % and 41.7 %, respectively. The 2-year survival rate was 17.2 %. The 6-month and 1-year disease-free survival rates were 62.5 % and 12.5 %, respectively. Conclusion. The short- and long-term outcomes were consistent with those described in other studies, which indicated that a combination of systemic drug therapy and hifu-therapy is an appropriate approach for the treatment of patients with pancreatic cancer.