bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges with gas hydrate formation
Authors: Kelland M A 
Published: November 2019

Abstract
Many multiphase flow lines are prone to hydrate formation unless prevention methods are put in place. Chemical management of hydrate formation is traditionally done with thermodynamic hydrate inhibitors but in the last 25 years low dosage hydrate inhibitors (LDHIs) have been developed which can offer economic, environmental and other benefits. LDHIs are divided into two main categories, kinetic inhibitors (KHIs) and anti-agglomerants (AAs), both of which are successfully being used in field applications. This paper briefly reviews the hydrate management tools available to the operator. Then the review focuses on LDHIs, their structure-performance relationships and the various classes that have been designed and tested. The environmental challenges of both AAs and KHIs are also discussed.
Study on application of colloidal particles of metal oxides to increase the oil recovery factor
Authors: Lesin V I , Eremin N A 
Published: November 2019

Abstract
The extraction of heavy oil, including bitumen, is complicated by the extremely high viscosity of the fluid in the reservoir. The adsorption of heavy oil fractions on the surface of minerals leads to the hydrophobization of the pore space. The magnetic colloidal particles of iron oxides present in the composition of the water remove adsorbed oil from the surface of pores, which manifests itself as an increase in the oil recovery factor and the injectivity of injection wells. Iron particles of submicron size, located on the surface of an electrically charged gas bubble, are concentrated at the water-oil interface. Due to the high adsorption energy on the surface of the iron particle, oil is deposited on the iron oxide particles. The drop-in bottom pressure of injection and production wells contributes to the movement of the gas bubble with oil and iron oxides to the bottom of production wells. The study of the mechanism of exposure to electromagnetic radiation showed that the electromagnetic field selectively heats the particles of iron oxide, causing catalytic cracking of oil, and contributes to an increase in the oil recovery factor and well productivity index.
Applying of the associative polymer solutions to enhance oil recovery
Authors: Abirov R Zh , Eremin N A 
Published: November 2019

Abstract
Purpose of this report to inform the petroleum readership of recent advances in areas of the associative polymer flooding. Polymer flooding is the industrial enhanced oil recovery method, which successfully has applied in various types of reservoirs. The polymer flooding for high-temperature and high-salinity reservoir faces enormous challenges. Hydrolyzed polymer has been used as the main polymer type for the polymer flooding. Now researchers have turned their attention to associative polymer solutions. This report presents an overview of the associative polymer flooding. Some recent projects have shown an expanding technology. This report reviews published results of the use of associative polymers to enhance oil recovery in recent years. The associative polymer flooding is one enhanced oil recovery (EOR) method being developed recently to increase the oil supply. Polymer flooding application in high-temperature and high-salinity reservoirs is currently limited by polymers chemically and thermally degradation at high temperature and salinity. The associative polymer solutions improve the over-all reservoir conformance by providing mobility control. Water is injected after the polymer solution. Based on the number of new laboratory and pilot tests, field activity is continuing at a moderate level.
Conjecture of new inequalities for some selected thermophysical properties values
Authors: Hohm Uwe 
Published: November 2019

AbstractIn 2005 it was rigorously shown with string theory methods that there is a lower bound for the ratio of the shear viscosityηand the volume density of entropys = S/Vgiven byη/s≥ℏ/(4πkB). Here we extend this result in a heuristic manner to other ratios of thermophysical properties. We conjectured that there are rigorous non-zero lower bounds for the Lorenz numberLas well as other combinations of equilibrium and transport properties. We suggest that the lower bounds and the corresponding inequalities can be written in terms of the Planck units. We show that some of the proposed new inequalities set severe constraints on the behavior and properties of ordinary matter.
A software to prevent delirium in hospitalised older adults: development and feasibility assessment
Authors: Alvarez Evelyn A , Garrido Maricel , Ponce Daniela P , Pizarro Gaspar , Córdova Andres A , Vera Felipe , Ruiz Rocio , Fernández Raul , Velásquez Juan D , Tobar Eduardo , Salech Felipe 
Published: November 2019

AbstractBackgroundnon-pharmacological interventions to prevent delirium are useful in hospitalised older adults. However, they are poorly implemented in clinical practice. We aimed to develop a software for bedside use by hospitalised older adults and to improve their access to these interventions.Methodsa transdisciplinary team composed of healthcare professionals, designers, engineers and older adults participated in the development of the software. Scrum methodology was used to coordinate the work of the team, and the software was evaluated in a feasibility study.Resultsa software for touchscreen mobile devices that supports Android 5.0 or later was produced, including modules for time-spatial re-orientation, cognitive stimulation, early mobilisation, sensorial support use promotion, sleep hygiene and pain management optimisation. Horizontal disposition, use of colour contrast and large interaction areas were used to improve accessibility. The software’s usability and accessibility were evaluated in 34 older adults (average age 73.2 ± 9.1 years) showing that 91.1% of them got access to all the software functions without previous instructions. The clinical feasibility assessment showed that 83.3% of the 30 enrolled hospitalised patients (76 ± 8 years) completed the 5-day protocol of software usage during hospitalisation. Software use was associated with a decreased trend in delirium incidence of 5 of 32 (15.6%) at baseline to 2 of 30 (6.6%) after its implementation.Conclusiona highly accessible and implementable software, designed to improve access to non-pharmacological interventions to prevent delirium in hospitalised older adults, was developed. The effectiveness of the software will be evaluated in a randomised clinical trial.
Alcohol Tolerance in Human Laboratory Studies for Development of Medications to treat Alcohol Use Disorder
Authors: Haass-Koffler Carolina L , Perciballi Roberta 
Published: November 2019

Abstract

Aims
Human laboratory studies have contributed extensively in the research and development of novel medications to treat alcohol use disorder (AUD). Alcohol tolerance may represent one additional variable that can be utilized to expand the understanding of the AUD wide phenotypic profile and provide support to the medication development process. Tolerance is characterized as an individual’s subjective response to alcohol and has been recognized as a predictor of AUD progression. Tolerance can be evaluated both by self-reported response (e.g. assessments) and objective measurements (e.g. motor impairment); as such, it represents an exploitable variable in the field of alcohol research.

Methods
This Narrative Review focuses on the use of alcohol tolerance, specifically within alcohol laboratory studies, for medication development. It seeks to identify a research gap and a research opportunity in clinical studies to evaluate biobehavioral responses captured in order to develop medications to treat AUD.

Results
Alcohol tolerance may provide additional information on the safety and tolerability of medications to treat AUD, in particular, when novel medications are co-administered with alcohol within the AUD population.

Conclusions
As such, alcohol tolerance represents an additional outcome that may be included in randomized clinical trial (RCT) protocols designed for developing AUD pharmacotherapies.
Advances in therapeutic application of CRISPR-Cas9
Authors: Sun Jinyu , Wang Jianchu , Zheng Donghui , Hu Xiaorong 
Published: November 2019

AbstractClustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has been widely applied in countless areas, including genome editing, gene function investigation and gene therapy both in vitro and in vivo. In this paper, we briefly introduce the mechanisms of CRISPR-Cas9 tool in genome editing. More importantly, we review the recent therapeutic application of CRISPR-Cas9 in various diseases, including hematologic diseases, infectious diseases and malignant tumor. Finally, we discuss the current challenges and consider thoughtfully what advances are required in order to further develop the therapeutic application of CRISPR-Cas9 in the future.
Designing a general method for predicting the regulatory relationships between long noncoding RNAs and protein-coding genes based on multi-omics characteristics
Authors: Zhang Yuwei , Yi Tianfei , Ji Huihui , Zhao Guofang , Xi Yang , Dong Changzheng , Zhang Lina , Zhang Xiaohong , Zhao Jinshun , Liao Qi 
Published: November 2019

Abstract

Motivation
Long noncoding RNA (lncRNA) has been verified to interact with other biomolecules especially protein-coding genes (PCGs), thus playing essential regulatory roles in life activities and disease development. However, the inner mechanisms of most lncRNA–PCG relationships are still unclear. Our study investigated the characteristics of true lncRNA–PCG relationships and constructed a novel predictor with machine learning algorithms.

Results
We obtained the 307 true lncRNA-PCG pairs from database and found that there are significant differences in multiple characteristics between true and random lncRNA–PCG sets. Besides, 3-fold cross-validation and prediction results on independent test sets show the great AUC values of LR, SVM and RF, among which RF has the best performance with average AUC 0.818 for cross-validation, 0.823 and 0.853 for two independent test sets, respectively. In case study, some candidate lncRNA–PCG relationships in colorectal cancer were found and HOTAIR–COMP interaction was specially exemplified. The proportion of the reported pairs in the predicted positive results was significantly higher than that in negative results (P &lt; 0.05).

Supplementary information
Supplementary data are available at Bioinformatics online.
NextPolish: a fast and efficient genome polishing tool for long-read assembly
Authors: Hu Jiang , Fan Junpeng , Sun Zongyi , Liu Shanlin 
Published: November 2019

Abstract

Motivation
Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors.

Results
When evaluated for the speed and efficiency using human and a plant (Arabidopsis thaliana) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy.

Availability and implementation
NextPolish is implemented in C and Python. The source code is available from https://github.com/Nextomics/NextPolish.

Supplementary information
Supplementary data are available at Bioinformatics online.
pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences
Authors: Zerihun Mehari B , Pucci Fabrizio , Peter Emanuel K , Schug Alexander 
Published: November 2019

Abstract

Motivation
The ongoing advances in sequencing technologies have provided a massive increase in the availability of sequence data. This made it possible to study the patterns of correlated substitution between residues in families of homologous proteins or RNAs and to retrieve structural and stability information. Direct coupling analysis (DCA) infers coevolutionary couplings between pairs of residues indicating their spatial proximity, making such information a valuable input for subsequent structure prediction.

Results
Here, we present pydca, a standalone Python-based software package for the DCA of protein- and RNA-homologous families. It is based on two popular inverse statistical approaches, namely, the mean-field and the pseudo-likelihood maximization and is equipped with a series of functionalities that range from multiple sequence alignment trimming to contact map visualization. Thanks to its efficient implementation, features and user-friendly command line interface, pydca is a modular and easy-to-use tool that can be used by researchers with a wide range of backgrounds.

Availability and implementation
pydca can be obtained from https://github.com/KIT-MBS/pydca or from the Python Package Index under the MIT License.

Supplementary information
Supplementary data are available at Bioinformatics online.
PyIOmica: longitudinal omics analysis and trend identification
Authors: Domanskyi Sergii , Piermarocchi Carlo , Mias George I 
Published: November 2019

Abstract

Summary
PyIOmica is an open-source Python package focusing on integrating longitudinal multiple omics datasets, characterizing and categorizing temporal trends. The package includes multiple bioinformatics tools including data normalization, annotation, categorization, visualization and enrichment analysis for gene ontology terms and pathways. Additionally, the package includes an implementation of visibility graphs to visualize time series as networks.

Availability and implementation
PyIOmica is implemented as a Python package (pyiomica), available for download and installation through the Python Package Index (https://pypi.python.org/pypi/pyiomica), and can be deployed using the Python import function following installation. PyIOmica has been tested on Mac OS X, Unix/Linux and Microsoft Windows. The application is distributed under an MIT license. Source code for each release is also available for download on Zenodo (https://doi.org/10.5281/zenodo.3548040).

Supplementary information
Supplementary data are available at Bioinformatics
APTANI2: update of aptamer selection through sequence-structure analysis
Authors: Caroli Jimmy , Forcato Mattia , Bicciato Silvio 
Published: November 2019

Abstract

Summary
Here we present APTANI2, an expanded and optimized version of APTANI, a computational tool for selecting target-specific aptamers from high-throughput-Systematic Evolution of Ligands by Exponential Enrichment data through sequence-structure analysis. As compared to its original implementation, APTANI2 ranks aptamers and identifies relevant structural motifs through the calculation of a score that combines frequency and structural stability of each secondary structure predicted in any aptamer sequence. In addition, APTANI2 comprises modules for a deeper investigation of sequence motifs and secondary structures, a graphical user interface that enhances its usability, and coding solutions that improve performances.

Availability and implementation
Source code, documentation and example command lines can be downloaded from http://aptani.unimore.it. APTANI2 is implemented in Python 3.4, released under the GNU GPL3.0 License, and compatible with Linux, Mac OS and the MS Windows subsystem for Linux.

Supplementary information
Supplementary information is available at Bioinformatics online
Struo: a pipeline for building custom databases for common metagenome profilers
Authors: de la Cuesta-Zuluaga Jacobo , Ley Ruth E , Youngblut Nicholas D 
Published: November 2019

Abstract

Summary
Taxonomic and functional information from microbial communities can be efficiently obtained by metagenome profiling, which requires databases of genes and genomes to which sequence reads are mapped. However, the databases that accompany metagenome profilers are not updated at a pace that matches the increase in available microbial genomes, and unifying database content across metagenome profiling tools can be cumbersome. To address this, we developed Struo, a modular pipeline that automatizes the acquisition of genomes from public repositories and the construction of custom databases for multiple metagenome profilers. The use of custom databases that broadly represent the known microbial diversity by incorporating novel genomes results in a substantial increase in mappability of reads in synthetic and real metagenome datasets.

Availability and implementation
Source code available for download at https://github.com/leylabmpi/Struo. Custom genome taxonomy database databases available at http://ftp.tue.mpg.de/ebio/projects/struo/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Rho Guanine Nucleotide Exchange Factors Regulate Horizontal Axon Branching of Cortical Upper Layer Neurons
Authors: Sasaki Kensuke , Arimoto Kei , Kankawa Kento , Terada Chikayo , Yamamori Tetsuo , Watakabe Akiya , Yamamoto Nobuhiko 
Published: November 2019

AbstractAxon branching is a crucial process for cortical circuit formation. However, how the cytoskeletal changes in axon branching are regulated is not fully understood. In the present study, we investigated the role of RhoA guanine nucleotide exchange factors (RhoA-GEFs) in branch formation of horizontally elongating axons (horizontal axons) in the mammalian cortex. In situ hybridization showed that more than half of all known RhoA-GEFs were expressed in the developing rat cortex. These RhoA-GEFs were mostly expressed in the macaque cortex as well. An overexpression study using organotypic cortical slice cultures demonstrated that several RhoA-GEFs strongly promoted horizontal axon branching. Moreover, branching patterns were different between overexpressed RhoA-GEFs. In particular, ARHGEF18 markedly increased terminal arbors, whereas active breakpoint cluster region-related protein (ABR) increased short branches in both distal and proximal regions of horizontal axons. Rho kinase inhibitor treatment completely suppressed the branch-promoting effect of ARHGEF18 overexpression, but only partially affected that of ABR, suggesting that these RhoA-GEFs employ distinct downstream pathways. Furthermore, knockdown of either ARHGEF18 or ABR considerably suppressed axon branching. Taken together, the present study revealed that subsets of RhoA-GEFs differentially promote axon branching of mammalian cortical neurons.
Predictive habitat suitability models for nesting woodpeckers following wildfire in the Sierra Nevada and Southern Cascades of California
Authors: Campos Brent R , Latif Quresh S , Burnett Ryan D , Saab Victoria A 
Published: November 2019

AbstractWoodpeckers are often focal species for informing management of recently burned forests. Snags generated by wildfire provide key nesting and foraging resources for woodpeckers, and nest cavities excavated by woodpeckers are subsequently used by many other species. Habitat suitability models applicable in newly burned forest are important management tools for identifying areas likely to be used by nesting woodpeckers. Here we present and test predictive models for mapping woodpecker nest-site habitat across wildfire locations that can be used to inform post-fire planning and salvage logging decisions. From 2009 to 2016, we monitored 313 nest sites of 4 species—Black-backed Woodpecker (Picoides arcticus), Hairy Woodpecker (Dryobates villosus), White-headed Woodpecker (D. albolarvatus), and Northern Flicker (Colaptes auratus)—from 3 wildfires in the Northern Sierra Nevada and Southern Cascades 1–5 yr after fire. Using these data, we developed habitat suitability index models that compared nest vs. non-nest sites for each species using (1) exclusively remotely sensed covariates, and (2) combinations of remotely sensed and field-collected covariates. We emphasized predictive performance across wildfire locations when selecting models to retain generalizable habitat relationships useful for informing management in newly burned locations. We identified models for all 4 species with strong predictive performance across wildfire locations despite notable variation in conditions among locations, suggesting broad applicability to guide post-fire management in the Sierra Nevada region. Top models for nest-site selection underscored the importance of high burn severity at the local scale, lower burn severity at the 1-km scale, mid-sized nest-tree diameters, and nest trees with broken tops. Models restricted to remotely sensed covariates exhibited similar predictive performance as combination models and are valuable for mapping habitat across entire wildfire locations to help delineate project areas or habitat reserves. Combination models are especially relevant for design of silvicultural prescriptions.
Peer Relationship Experiences Of Deaf And Hard-Of-Hearing Adolescents
Authors: Terlektsi E , Kreppner J , Mahon M , Worsfold S , Kennedy Colin R 
Published: November 2019

Abstract
Deaf and hard-of-hearing adolescents (DHH) experience more peer problems and lower levels of friendships than their hearing peers. This study used a qualitative approach to identify their experiences of peer problems and factors influencing them. A sample of 30, 13–19 year-old DHH adolescents with a moderate to profound hearing loss, drawn from a population-based cohort study in which their receptive language and social–emotional skills had been assessed, underwent semi-structured interviews. Interviews were analyzed using thematic analysis. Participants reported that, overall, they had developed positive and rewarding relationships with their peers, notwithstanding their earlier experience of being bullied. Conflicts and infrequency of interaction in their friendships were mainly reported by girls. Adolescents with moderate hearing loss were identified as facing the same or even more barriers than adolescents with severe to profound hearing loss in making new friends. Implications for educational practice are discussed.