bluuebunny/crossref_metadata_2025_split huggingface dataset:
Production-Strategy Insights Using Machine Learning: Application for Bakken Shale
Authors: Luo Guofan , Tian Yao , Bychina Mariia , Ehlig-Economides Christine 
Published: May 2019

Summary
Researchers from both industry and academia have intensively studied tight oil resources in the past decade since the successful development of Bakken Shale and Eagle Ford Shale, and have made tremendous progress. It has been recognized that locating the sweet spots in the regionally pervasive plays is of great significance. However, we are still struggling to determine whether the dominant control on shale-well productivity is geologic or technical. Given certain geological properties, what is the best completion strategy?
Most of the previous studies either analyze the completion data alone or divide the entire play into different data clusters by map coordinates and depth, which might neglect the heterogeneity in thickness and reservoir-quality parameters. In our study, we first conducted stratigraphic and petrophysical analyses, using the regional variation in depth, thickness, porosity, and water saturation to capture the regional heterogeneity in the Bakken Shale petroleum system. We selected approximately 2,000 horizontal wells, targeting the Middle Bakken Formation with detailed completion records and initial production dates during 2013 and 2014. Completion data inputs include normalized stage length (NSL), stage counts, normalized volume of fluid (NVF), and normalized volume of proppant (NVP).
We investigated the relationship between the geological and completion features, and its effect on the first year of production. Then, we built a neural-network model to identify the relationship between the first-year oil production and the selected features. We separated the data into three sets for training, validation, and testing. After we trained the model using the training and validation set, we tested the model to estimate its robustness. Through sensitivity analysis, we demonstrated how the completion parameters combined with geological input would affect the production.
The developed technique provides a method to identify the best well location, understand the effectiveness of the completion strategy, and predict the well production. Although the data used came from wells in the Bakken Shale, the methodology applies in a similar way to other tight oil plays.
Assessment of anterior chamber configuration changes after phacoemulsification with swept-source optical coherence tomography
Authors: Hu Man , Zheng Qian , Li Zhangliang , Chang Pingjun , Zhao Yun-e 
Published: May 2019

Abstract
Background

To assess the changes of anterior chamber angle in patients with shallow anterior chamber and normal anterior chamber after phacoemulsification and intraocular lens implantation (IOL) using anterior segment swept-source optical coherence tomography (AS-SS-OCT).

Methods

This was a prospective case control study; 60 eyes of 60 patients who underwent cataract surgery. Based on anterior chamber depth (ACD) and gonioscopy findings, the eyes were classified into two groups, shallow anterior chamber group (30 eyes) and normal anterior chamber group (30 eyes). AS-SS-OCT was used to measure ACD and angle parameters angle opening distance (AOD), angle recess area (ARA), trabecular iris space area(TISA), and trabecular iris angle (TIA). Serial changes in each group were measured before and 3 months after phacoemulsification and IOL, and the differences between the two groups were compared.

Results

All angle parameters including ACD, AOD, ARA, TISA, and TIA in both groups at 3 months after cataract surgery were significantly different from the preoperative values (p<0.01). In addition, we found significant differences of all angle parameters between groups of shallow anterior chamber (SAC) and normal anterior chamber (NAC) (All P< 0.05). Besides, the TISA750 in superior quadrant and anterior chamber volume (ACV) were significantly smaller in the group of SAC than those in the group of NAC (P = 0.041 and 0.002, respectively).

Conclusions

The parameters of anterior chamber increased significantly in both two groups but not increase to the same extent 3 months after phacoemulsification. Iris thickening may also be one of the narrow angle factors,not just age-related lens thickening.
Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites
Authors: Ye Chenxu , Rasheed Humaira , Ran Yuehua , Yang Xiaojuan , Xing Lianxi , Su Xiaohong 
Published: May 2019

Abstract
Background: The reproductive plasticity of termite workers provides colonies with tremendous flexibility to respond to environmental changes, which is the basis for evolutionary and ecological success. Although it is known that all colony members share the same genetic background and that differences in castes are caused by differences in gene expression, the pattern of the specific expression of genes involved in the differentiation of workers into reproductives remains unclear. In this study, the transition of the female workers into neotenic reproductives (NRs) was induced by a groups of isolated workers (IWs) of Reticulitermes labralis, and then comparative transcriptomes were used for the first time to reveal the molecular mechanisms underlying the reproductive plasticity of workers.
Results: We identified 38,070 differentially expressed genes and found profile 5 to be the pattern of gene expression involved in the differentiation of the workers into reproductives. 12,543 genes were specifically upregulated in the IWs. Twenty-five signal transduction pathways classified into environmental information processing were related to the differentiation of workers into NRs. Ras functions as a signalling switch regulated the reproductive plasticity of workers.The catalase gene which is related to longevity was up-regulated in NRs.
Conclusion: We demonstrate that workers leaving the natal colony can induce the expression of stage-specific genes in the workers, which leads to the differentiation of workers into queens and suggests that the signal transduction along the Ras-MAPK pathway crucially controls the reproductive plasticity of the workers. This study also provides an important model for revealing the molecular mechanism of longevity changes.
Transcriptome Analysis of Muscle Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Duroc Pigs
Authors: Zhao Xueyan , Hu Hongmei , Wang Cheng , Wang Yanping , Lin Haichao , Wang Jiying 
Published: May 2019

Abstract
Background
Intramuscular fat (IMF) content plays a key role in meat quality of pork. Duroc is a common commercial pig breed, which is extensively used as the terminal male parent of DLY (Duroc × Landrace × Yorkshire) commercial pigs. For identification potential candidate genes and pathways, IMF content of 28 purebred Duroc pigs were measured, and transcriptome differences of muscles from individuals with divergent IMF content were analyzed based on RNA sequencing.
Results
As a result, a total of 309 DEGs were detected using edgeR and DESeq2 (p < 0.05, |log2(fold change)| ≥ 1) between the the IMF-High and -Low groups. Functional analysis of the DEGs revealed 27 Gene Ontology (GO) terms, two pathways (q < 0.05) and 23 key DEGs, which closely related to lipid metabolism and fat cell differentiation. Among these key DEGs, LEP, SFRP1, CIDEC, PNPLA3 and MT3, are potential candidate genes affecting IMF content due to their biological functions, the significant correlation between these genes’ expression with IMF content values in the 28 Duroc samples and proofs from previous studies. Meanwhile, a weighted gene co-expression network analysis (WGCNA) also revealed seven out of these key DEGs, including ADIPOQ, FABP4, PLIN1, CIDEA, ACAA1, CYP2A19 and ADIRF, were hub genes in turquoise module which may exhibit important functions in influencing IMF content. Furthermore, two pathways, regulation of lipolysis in adipocytes and PPAR signaling pathway, were potential pathways affecting IMF content because of their significant enrichment for the DEGs and co-expression genes of turquoise modules.
Conclusions
Our study demonstrates that some DEGs and pathways detected have essential role in regulating IMF content, and are supposed to be potential candidate genes and pathways affecting the trait in Duroc pigs. The study provides information for understanding molecular mechanism of IMF content, and would be of help for improving pork quality of Duroc pigs.
RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this Toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection
Authors: Yang Shuxin , Hu Wanbin , Shimada Yasuhito , Münch Magnus , Marín-Juez Rubén , Meijer Annemarie H. , Spaink Herman P. 
Published: May 2019

Abstract
Background
The function of Toll-like receptor 2 (TLR2) in host defense against pathogens, especially Mycobacterium tuberculosis (Mtb) is poorly understood. To investigate the role of TLR2 during mycobacterial infection, we analyzed the response of tlr2 zebrafish mutant larvae to infection with Mycobacterium marinum (Mm), a close relative to Mtb, as a model for tuberculosis. We measured infection burdens and transcriptome responses using RNA deep sequencing in mutant and control larvae.
Results
tlr2 mutant embryos at 2 dpf do not show morphological alterations or differences in the number of macrophages and neutrophils when compared to control embryos. However, we found substantial changes in gene expression in these mutants, particularly in developmental and metabolic pathways, when compared with the heterozygote tlr2+/- control. After Mm infection, bacterial burden was six to ten fold higher in tlr2-/- larvae than in tlr2+/-, or tlr2+/+ larvae, indicating that Tlr2 acts as a protective factor in zebrafish host defense. RNAseq analysis of infected tlr2-/- versus tlr2+/- shows that the number of up-regulated and down-regulated genes in response to infection was greatly diminished in tlr2 mutants by at least 2 fold and 10 fold, respectively. Analysis of the transcriptome data and qPCR validation shows that Mm infection of tlr2 mutants leads to decreased mRNA levels of genes involved in inflammation and immune responses, including il1b, tnfb, cxcl11aa/ac, fosl1a, and cebpb. Furthermore, RNAseq analyses revealed that the expression of genes for Maf family transcription factors, vitamin D receptors, and Dicps proteins is significantly altered in tlr2 mutants with or without infection. In addition, the data indicate a function of Tlr2 in the control of induction of cytokines and chemokines, such as the CXCR3-CXCL11 signaling axis.
Conclusion
The transcriptome and infection burden analyses give support for a function of TLR2 in host defense against mycobacteria. Transcriptome analysis revealed tlr2-specific pathways involved in Mm infection, which are related to responses to Mtb infection in human macrophages. Considering its dominant function in control of transcriptional processes that govern defense responses and metabolism, the TLR2 protein can be expected to be also of importance for other infectious diseases and interactions with the microbiome.
Complete Mitogenome of Threespot Flounder Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae) and Study on the Mechanism of Gene Rearrangement in 13 Bothids
Authors: Luo Hairong , Kong Xiaoyu , Chen Shixi , Shi Wei 
Published: May 2019

Abstract
Background: The mitochondrial genomes (mitogenomes) of 12 bothids (Pleuronectiformes) from eight genera have been obtained. From the data, the genomic-scale and various gene rearrangements revealed the high diversity of variation in these mitogenomes.

Results: A total of 18170 bp of Grammatobothus polyophthalmus mitogenome was determined including 37 genes and two control regions (CRs). Genes encoded by L-strand were grouped to an eight-genes cluster (Q-A-C-Y-S1-ND6-E-P) except for the tRNA-N, other genes encoded by H-strand were grouped together (F-12S … CytB-T) except for the tRNA-D that was translocated to inside of the eight-genes cluster. The mitogenome of G. polyophthalmus and that of 12 known bothids possessed the similar genomic-scale rearrangements with the only differences in the various combinations of CR, tRNA-D and eight-genes cluster, and the shuffling of tRNA-V. Based on the structure character of all 13 bothid mitogenomes, the Dimer-Mitogenome and Non-Random Loss (DMNR) model was fitted to account for all these rearrangements. And the translocation of tRNA-D occurring after the DMNR process in 10 of 13 bothid mitogenomes was confirmed. The striking finding was that each of degenerated genes existing in the gene rearrangement process in 13 bothids had their counterparts of intergenic spaces.

Conclusions: The result of corresponding relationship between degenerated genes and intergenic spaces provided the significant evidence to support the possibility of the DMNR model, as well as, the existing of dimeric mitogenome in mitochondrion. The findings of this study were rare phenomenona in teleost fish, which not only promoted the understanding of mitogenome structural diversity, but also shed light on studying of mitochondrial rearrangement and replication.
Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples
Authors: Bhagwate Aditya Vijay , Liu Yuanhang , Winham Stacey J. , McDonough Samantha J. , Stallings-Mann Melody L. , Heinzen Ethan P. , Davila Jaime I. , Vierkant Robert A. , Hoskin Tanya L. , Frost Marlene , Carter Jodi M. , Radisky Derek C. , Cunningham Julie M. , Degnim Amy , Wang Chen 
Published: May 2019

Abstract
Background

Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples.

Results

As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit ("QA"), and QIAGEN GeneRead DNA FFPE Kit ("QGR"). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different library preparations.

In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92% of the uniquely called FFPE variants were of low allelic frequency range (<5%), and collectively shared a “C>T|G>A” mutational signature known to be representative of FFPE artifacts resulting fromcytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates.

Conclusions

Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency.
Intestinal DCs global gene expression dynamics affected by recombinant baker’s yeasts saccharomyces cerevisiae
Authors: Han Baoquan , Zhang Tingting , Li Xinyi , Zhao Rui , Ge Wei , Mu Lu , Xu Kun , Zhang Zhiying 
Published: May 2019

Abstract
Background

The baker’s yeast, saccharomyces cerevisiae, has been widely used throughout our daily life in diverse aspects for thousands of years. The saccharomyces cerevisiae was found to specifically target the dendritic cells (DCs) in mammalian with a manner of antigen-receptor interaction as described previously. It is necessary to investigate the effect of the baker’s yeasts on global gene expression dynamics of intestinal DCs and explore the possibilities of using baker’s yeast as gene delivery vehicle to modulate animal’s immune functions

Results

with a murine oral delivery model in vivo, we confirmed the feasibility of using budding yeast as gene delivery vehicle to the intestinal DCs using the Western blots. We then examined the transcriptome profile of the mouse intestinal DCs upon yeast stimulus. The enrichment analysis of unique transcripts indicated the beneficial role of yeast in modulating the DC-mediated adaptive immunity. Compared with previous study, we also found that a large fraction of the regulated genes is coincident with the response induced by other fungus, suggesting that the budding yeast induces a similar tailored unique genetic re-programming of DCs. Another analysis of transcriptome profile indicated that expression of β-catenin gene significantly changes DCs gene expression related to inflammatory response and cell adhesion.

Conclusions

Here, we defined the role of budding yeast on global gene expression of intestinal DCs, and confirmed the important role of β-catenin gene on the DCs-related inflammatory response, which provides a framework for the development of mucosa yeast-based DNA vaccine.
HERITAGE AND INNOVATION IN SERBIAN 21ST CENTURY ARCHITECTURE – GENUINE TRADITIONAL BUILDING TECHNIQUES
Authors: MILOŠEVIĆ Predrag , MILOŠEVIĆ Vladimir , MILOŠEVIĆ Grigor 
Published: May 2019

Abstract
The social integration of people, the common belief of a particular group of people, contributed to the creation of a very fine and sincere architecture, which celebrated the habits and lifestyles of a particular community. National, traditional architecture is not a style, but rather, a glimpse of the world and life, the nature and genius loci, attitude towards life processes and materials, towards climate and authenticity. Traditional construction and building techniques help us establish new innovative architecture, to improve our living conditions in as much as the environment.
RHEOLOGY OF MORTAR WITH PORTLAND-LIMESTONE CEMENT CEM II/A,B-LL IN RELATION TO PROPERTIES OF CEMENT
Authors: GOŁASZEWSKA Małgorzata 
Published: May 2019

Abstract
The paper presents the results of rheological research, conducted to examine how the properties and composition of cement affects the yield stress and plastic viscosity of Portland limestone cements. Portland limestone cements used in the research were obtained by mixing four Portland cements of various chemical and phase compositions with two limestones of different origin, in an amount of 6, 10, 20 and 30% of cement mass. The yield stress and plastic viscosity were determined using the Viskomat NT rheometer, after 5 and 60 minutes from combining the constituents. Obtained results indicate a significant effect of the C3A content in cement on the rheological properties of mortars, mainly yield stress. The specific surface area of the tested cements has a lesser effect on the rheological properties of mortars with Portland limestone cements.
APPLICATION OF POTASSIUM FERRATE(VI) FOR OXIDATION OF SELECTED POLLUTANTS IN AQUATIC ENVIRONMENT – SHORT REVIEW
Authors: KLIŚ Simona , BARBUSIŃSKI Krzysztof , THOMAS Maciej , MOCHNACKA Anna 
Published: May 2019

Abstract
The paper provides comprehensive information on the recent progress of the use of potassium ferrate(VI) (K2FeO4) for the removal of selected pollutants from water and wastewater. K2FeO4 provides great potential for diverse environmental applications without harm to the natural environment. Therefore K2FeO4 was used in removal of cyanides from gold ore purification processes, degradation of dyes and organic compounds in wastewater and algae removal in the water treatment process. The quoted research results indicate that K2FeO4 due to its strong oxidizing and coagulating properties, could be an alternative to the use of Advanced Oxidation Processes (AOPs) or be an additional option to conventional methods of water and wastewater treatment. As a result of using K2FeO4, the emerge intermediates of the impurities decomposition are nontoxic or show less toxicity than the initial substrates. The use of K2FeO4 is also associated with certain limitations of technical and technological nature, which requires further research in order to use its high efficiency in the degradation of various types of contamination on a technical scale.
METHODOLOGY OF ECODIAGNOSTICS ON THE EXAMPLE OF RURAL AREAS
Authors: KOVAL Viktor V. , PETRASHEVSKA Angelina D. , POPOVA Olga L. , MIKHNO Inesa S. , GASKA Krzysztof 
Published: May 2019

Abstract
The present state of the environment in the rural area has been analyzed. The main factors which led to the existing situation have been revealed. The structure of Ukraine’s crops area and the amount of accumulated waste in Ukraine influencing the agricultural landscapes of rural areas have been analyzed. The dependence between the amount of accumulated waste and the incidence within the time interval was revealed. As a result of calculations, we have received the social losses due to an increase in the morbidity of the population living in the area of the impact of landfills, the coefficient of ecological stability of the studied territories was calculated and it was found that the presence of landfills reduces the coefficient of ecological stability. It has been revealed that with the help of satellite data monitoring of agricultural landscapes is possible, which can be used in calculating the price of land considering the quality factor of this land.
USE OF THE MACROMODEL DNS/SWAT TO CALCULATE THE NATURAL BACKGROUND OF TN AND TP IN SURFACE WATERS FOR THE RAC PARAMETER
Authors: WILK Paweł , ORLIŃSKA-WOŹNIAK Paulina 
Published: May 2019

Abstract
Total nitrogen (TN) and total phosphorus (TP) get into surface waters from both natural and anthropogenic sources. Anthropogenic sources have been relatively well recognised but the natural emmission of nutrients into the rivers, in the case of many catchments, remains a mystery. The paper describes the possibility of using a tool, the Macromodel DNS/SWAT (Discharge Nutrient Sea/Soil and Water Assessment Tool), to estimate the concentration and load of natural background (Natural Pollutant Concentration – NPC and Natural Pollution Load – NPL) for TN and TP and thus to specify the previously developed method of river absorption capacity – RAC. A variant scenario was developed allowing for a “virtual” change in the use of the area of an analysed catchment. This allowed the simulation of the amount of TN and TP in the waters of the main river, the Warta, in a situation where there was no anthropogenic phenomenon in the area. NPC and NPL results were obtained for six calculation profiles located on the central Warta main stream. On this basis, the total absorbency of the Total River Absorption Capacity – RACT River was calculated. The obtained results indicate an increasing pollution of the analyzed river on subsequent Surface Water Bodies (SWB). The values of RAC and RACt parameters for both TN and TP were reduced between the opening and closing profiles of the analyzed catchment by 2651 t/y (TN) and 86 t/y (TP), respectively.