bluuebunny/crossref_metadata_2025 huggingface dataset:
Usefulness of cutting planes in the hierarchical segmentation of cardiac anatomical structures
Authors: Vera M , Valbuena O , Huérfano Y , Vera M I , Gelvez-Almeida E , Salazar-Torres J
Published: November 2019

A spatial geometric plane is defined by the three-dimensional coordinates of a pair of spatial points and the direction that the normal vector establishes, which is formed by joining those points by means of an oriented line segment. This type of planes, in three-dimensional images, is extremely useful as an alternative solution to the problem of low contrast that exhibit the anatomical structures present in cardiac computed tomography images. To do this, after using a predetermined filter bank and in order to define a region of interest, a smart operator based on least squares support vector machines is trained and validated in order to detect the aforementioned coordinates which enables the location of the plane, in the three-dimensional space that contains the considered images. Once the structure that is required to segment is identified, a discriminant function is used that cancels all information not linked to this structure. In this work, the segmentation of the left ventricle, based on region growing technique, is firstly considered and then the left atrium is segmented considering region growing technique and an inverse discriminant function. The results show an excellent correspondence relationship when the spatial union of both structures is made.
Testing GeoGebra as an effective tool to improve the understanding of the concept of limit on engineering students
Authors: Aréchiga Maravillas J C , Díaz S Arceo , Salazar-Torres J , Andrade D A Sierra
Published: November 2019

The impact GeoGebra on the teaching of the concept of limit was analyzed. Two groups of engineering students, studying differential calculus, served as control and test groups. The traditional teaching, based on examples solved by hand, was given to the control group while a series of activities involving the usage of the mathematical software GeoGebra were applied in an attempt of improving the degree of assimilation on the concept of limits.
Conceptions and pedagogical practices on the mathematical processes of teachers
Authors: Hernández C A , Prada R , Gamboa A
Published: November 2019

The objective of this research work is to establish the disciplinary, didactic and pedagogical conceptions of teachers in the area of mathematics in basic education against the formative process by competences and mathematical processes. The relationship between the standards developed in the institution against those stipulated by the “Ministerio de Educación Nacional” of Colombia was analyzed. This research was developed considering a hermeneutical historical paradigm, guided by the integrated qualitative approach, from an ethnographic design and therefore microetnography as a method. The research contributes from the epistemological, pedagogical and didactic categories, towards the achievement of evidence related to the classroom practices of teachers where contextualized problematic situations do not prevail so that the classes of the students are routine, not very impactful and the environment or Space becomes unmanageable, they do not have an adequate use of educational texts, and the use of educational material such as technological tools is not evident.
Errors and difficulties in solving algebraic procedures in secondary school students
Authors: Diaz A , Hernández C A , Paz L S
Published: November 2019

The research presented was aimed at determining the errors and difficulties presented by secondary school students in a Colombian public educational institution when faced with the solution of algebraic procedures. A contribution is sought to contribute to studies that monitor the performance of the teaching and learning processes of students. The methodology was based on the quantitative paradigm with a descriptive design, for which two instruments were applied to detect errors and difficulties in students. The results allowed to detect that, of the 12 errors that were taken as dimensions, six are significantly replicated, the most significant being the simple calculation error, unfinished procedure and the errors when performing arithmetic-algebraic operations. Participants allege associated difficulties, mostly to teaching problems, which generated guidelines aimed at teachers in order to raise didactic situations related to error as a source of learning.
Rules for teaching to deaf students: A creative action that overpass the inclusive education
Authors: Pilonieta-Cortés L , Martínez-Lozano J J , Vergel Ortega M
Published: November 2019

The research aims to create guidelines to guide pedagogical processes for hearing-impaired children. The methodology used was supported for a qualitative paradigm, oriented under the ethnomethodology, type field; used was observation techniques and non-structured interviews. For this effect was selected teachers that works with deaf students as key informers in different schools from Bogotá-Colombia. Results show that learning times of deaf students and hearing students are different, who are associated with a specific pedagogical and didactic strategy. It is concluded that guidelines in teaching deaf children incorporate adaptations that implement tangible visual material, experiential and experimental projects.
Mobile devices for the development of critical thinking in the learning of differential equations
Authors: Rincón Leal L , Vergel Ortega M , Paz Montes L S
Published: November 2019

The purpose of this research was to establish a relationship between mobile devices and the development of critical thinking in students of the differential equations subject. The research had a quantitative and qualitative methodological approach with quasi-experimental design, the sample was 110 students. Results: The integration of mobile applications favored and motivated the learning of the applications of differential equations, where the student develops critical thinking at the moment that creates, discovers, imagines and assumes. At the same time, when interacting with colleagues, it implements autonomous and collaborative learning, with the ease of access to information. Conclusion: Regarding the perception of students about this tool, 40% highlight its usefulness in understanding the topics and 51.2% step by step methodology. The average age of the students was 20 years with a standard deviation of 2.01 years.
Fostering mathematical logical intelligence in primary school students
Authors: Márquez Patiño R A , Gallardo Pérez H J , Vergel Ortega M
Published: November 2019

Education must form thinking people, who develop all their potentialities, among them, those referring to mathematical logical intelligence. The objective is to elaborate a didactic proposal that fosters mathematical logical intelligence in students. For this, the research was framed in a quantitative approach with fieldwork design and at a descriptive level. The survey was applied as a technique and as instruments a questionnaire for teachers and a test for students. The population was made up of all teachers and students in basic primary education. An intentional non-probability sample was applied, made up of 22 teachers who attend primary school programs and 30 students of the same educational level. The results identify the lack of strategies related to the processes of classification, serialization, and number of primary school teachers during their pedagogical work. Next, we describe the shortcomings that students have in applying mathematical logic processes in a series of activities proposed in the evaluative test. Finally, didactic strategies are defined according to the conditions of the learning environment analyzed so that from the work of the classroom it is possible to promote logical mathematical intelligence in the students.
Mathematical entrepreneurship in educational institutions
Authors: Palácios R A Fonseca , Paz Montes L S , Alvarez Paz D M
Published: November 2019

In the present investigation, a reflection was made on the teaching practices in the area of mathematics that entails educational institutions conducive academic spaces to generate entrepreneurial attitudes in students. These are personalized from the voices of the participants, involving the student in the development of the entrepreneurial culture and in the basic competences generated from the mathematics. The complexity present in the teaching practice becomes significant in the student when it is possible to establish an interrelation with their social, cultural, economic environment and, above all, in the proactive action that the student develops in the face of any situation in life. A new feeling that allows manifestations in students of: autonomy, responsibility, innovation, creativity and to generate in them citizen awareness.
Development of math skills in first semester students of public accounting
Authors: Alvarado gallardo O A , Gallardo Pérez H J , Vergel Ortega M
Published: November 2019

This research project describes the results of applying two pedagogical methodologies: problem-based learning and the use of new information technologies through GeoGebra in the development of the theme of functions for students of public accounting. The research was developed from a positivist paradigm, quantitative approach of quasi-experimental type of pretest and posttest with control and experimental group. In order to determine the development of competencies, a diagnostic test was initially applied to evaluate the mathematical knowledge with which the students enter; then pretest and posttest tests were applied to the control and experimental groups, in which by means of an intervention plan to the experimental group in the posttest stage, favorable results were evidenced by improving the proportion of correct answers and the development of competencies in geometric algebraic reasoning compared to the pretest stage. One of the conclusions reached in the research is that applying other methodologies in class such as problem-based learning with the support of GeoGebra software encourages the process of teaching learning and students find applicability to the topics treated by associating them with situations of practical life.
Mathematical argumentation in the classroom
Authors: Salazar-Torres J , Vera M , Contreras Y , Gelvez-Almeida E , Valbuena O , Barrera D , Rincon O
Published: November 2019

The article shares some elements of comprehensive type about “mathematical argumentation in the classroom”; whose analysis, was made from two fundamental categories in the development of an oral mathematical argumentation process for the conviction, contradiction and validation of a written mathematical argumentation process. The research addressed two central categories of argumentation as a discursive form, the first one is the epistemic position, and the second one is the discursive position that students unveil at the time of mathematically arguing the solution to a problem situation. The research was developed under the interpretative paradigm through the design of a case study directed by the theory and technique of a focal group, for the collection of information. In the findings, difficulties in the passage were evidenced from the semantic to the theoretical from the epistemic position; regarding the discursive position, the presence of three discursive forms was revealed: description, explanation and argumentation, the latter being the least used by the students.
Experimental study of turbulent syngas/methane/air flames at a sub-atmospheric condition
Authors: Cardona A , García A , Cano F , Arrieta C E , Yepes H A , Amell A
Published: November 2019

The aim of this work was determined turbulent burning velocities of air-syngas-methane flames at sub-atmospheric conditions using the angle method and Schlieren imaging. We analyzed a high hydrogen content syngas that can be obtained with a Conoco-Phillips coal gasification process. Equivalence ratios evaluated here correspond to lean combustion conditions: 0.8-1.0. Experiments were carried out at room temperature of 297 K and 849 mbar. The chemical-turbulence interaction was evaluated considering geometric parameters, laminar flame properties, and turbulence length scales. It was found that the turbulent burning velocity and the ratio between turbulent and laminar burning velocities increases with the turbulence intensity. Additionally, the addition of syngas to methane increases the laminar and turbulent burning velocity.
Drinking water treatment sludge as a partial substitute for clays in non-structural brick production
Authors: Fonseca Herreño L C , Valdés Solano D M , Rodríguez Sarabia K D , Cabello Pérez J O , Muñoz Quintero A A
Published: November 2019

The sludge as by-products of the water treatment is composed of particles of sand, silt and clay, colloidal organic matter and chemical substances that have been added to the water source during the treatment processes, this has aroused interest in its study as an economic and sustainable alternative in the making of non-structural and ornamental materials, among others. This research was carried out in a water treatment plant in the municipality of Ocaña, Colombia, which does not have a system for the adequate treatment and final disposal of the sludge generated, resulting in the discharge of this waste directly into the body of water, Algodonal river. Sampling of the sludge was taken from the plant for the analysis of its physical properties; subsequently, bricks with different mixing ratios are made and subjected to resistance tests according to national and international standards. It was found that the sludge generated in the sedimentation tank of the water treatment plant has a potential for the manufacture of non-structural brick, taking into account that the results of the tests showed similar or superior properties in comparison with a commercial brick produced in the region.
Methodology to determine the wear on the cutting tool during milling-planning in a computer numerical control machining center
Authors: Espinel-Blanco E , Arévalo-Ruedas J H , Florez-Solano E
Published: November 2019

The increased service life of cutting tools used in material removal processes results in significant savings in terms of production time and costs. Machining downtimes, especially those related to tool changes, represent a significant percentage of machine downtimes, which reduces efficiency. A proposed methodology is presented for the analysis of the behavior of the cutting tool through the application of the ISO standard, for which roughness and wear were determined and micrographs were used as indicators for the verification of the condition of the tool. The effectiveness of the proposed methodology that can be used in manufacturing processes to avoid failures in the workpiece due to improper use of the cutting tool was tested.
Carbon dioxide mixtures for organic power cycles using waste heat sources
Authors: Noriega Sanchez C J , Afanador García N , Guerrero Gómez G
Published: November 2019

The theoretical study proposed here is based on the energy recovery of sensible heat sources of medium and low temperature levels from Rankine power cycles in which binary mixtures of carbon dioxide and organic fluids are the working fluids. In this sense, the impact of these blends on performance parameters in the basic Rankine cycle configuration is addressed, as well as, optimization analyses of global conductance to ensure the highest production of net power cycle. The results allowed identifying what mixtures stand out in each performance indicator, particularly at net power and first law efficiency.
Impact of information and communication technologies on organizational learning
Authors: Manzano O , Peñaranda M , Páez H
Published: November 2019

The use of information and communication technologies a strategic tool has become one of the greatest benefits that has given a total shift to the different tactics that could be implemented to improve processes within organizations. The purpose of the research was to determine the relationship between information and communication technologies and organizational learning in the “micro, pequeñas y medianas empresas” of the city of Ocaña, Colombia. The focus of the research was quantitative correlation type; with non-experimental transactional field design given that the impact of the information and communication technologies variable on organizational learning was analyzed at a moment of time and without manipulating the variables. In order to collect the information, a Likert instrument with a Cronbach’s Alpha coefficient of 89.70% was validated. The results through the analysis of variance could show that information and communication technologies have a positive and significant impact on the organizational learning variable. The calculated correlation coefficient was 72.30%, showing that there is a high and positive correlation between the two variables. The information and communication technologies tools that managed to improve the competitiveness of companies are intranet, email, video conferences, social networks, search engines, document management, electronic commerce, databases and support applications for each type of organization.
Numerical analysis of the influence of friction conditions on the pile-up effect in Vickers hardness measurements
Authors: Trzepiecinski T , Lemu H G
Published: November 2019

Vickers indentation load-depth curve may be used to determine basic mechanical properties of metallic materials such as hardness, yield stress, modulus of elasticity, and elastic and plastic work. The pile-up phenomenon observed during indentation causes underestimation of the projected contact area and the diagonal dimensions of the impression in different hardness measurement scales (nano-, micro-, and macro-). The aim of this paper is to conduct a numerical analysis of the effect of friction conditions on the pile-up phenomenon during testing of DC04 steel sheet. The mechanical properties of the sheet metal used for the modelling purpose were first characterized by tensile tests on samples cut along the rolling direction (0°), transverse to the rolling direction (90°) and at an angle of 45° to the rolling direction. The numerical computation was conducted using ABAQUS, which is one of the powerful finite element-based programs. A wide range of variation of friction coefficients, i.e. 0-0.3 has been used in the analysis. It has been observed that the results of indentation of anisotropic materials are significantly affected by friction. The difference in the pile-up height measured at rolling direction of sheet metal and transverse to the rolling direction decreases with the reduction of the maximum displacement of the indenter. For higher values of the coefficient of friction, the higher the value of the indenter displacement, the lower becomes the increase in the pile-up height value.
Contact stresses associated with the wedge-lock mechanism in a prototype subsea pipeline recovery tool
Authors: Xing Y , Eriksson N B , Ong M C , Knutsen C
Published: November 2019

This paper examines the contact stresses associated with the wedge-lock mechanism in a prototype subsea pipeline recovery tool (PRT) through numerical methods and experimental testing. The prototype PRT studied combines IK-Norway subsea plug technology in a subsea PRT. This allows the PRT to seal the subsea pipeline while it is being retrieved. The PRT can then flush the pipeline before retrieval and therefore providing for operational cost savings. This paper presents the first stage of the study which the sealing mechanism is not studied. The current wedge-lock mechanism uses a cone to press steel balls against the insides of the subsea pipeline thereby locking the PRT to the pipeline. Designing for sufficient contact stresses is critical to ensure that the PRT can grab the subsea pipeline tightly in order to ensure a successful recovery. The contact pressure distribution between the ball and cone in the wedge-lock mechanism is modelled using finite element method in Ansys. The resulting indentation depths occurring at the pipeline are compared against physical tests. It was found that the contact problem associated with the wedge-lock mechanism is complex and the actual contact stress/final gripping force is sensitive to the input parameters. Second, the results show that the Ansys numerical model is able to represent the contract stresses fairly accurately if the friction coefficient is well-controlled. Third, it was observed that a low friction coefficient ensures low indentation depths. Last, the results highlight that an increase in the cone-angle leads to a decrease in the indentation depth.
Implementation of linear, double-linear, and nonlinear fatigue damage accumulation rules for fatigue life prediction of offshore drilling top-drive tie-rods
Authors: Inoma J E , Pavlou D G , Zec J
Published: November 2019

The offshore oil and gas industry has been exposed to major challenges over the last decade, particularly demanding cost cuts and more effective technical solutions. Predictive systems and remaining life assessments for both machine and structural components are known to be one of the core areas that has gathered much attention lately. This paper focuses on multiaxial fatigue that is a problem in number of engineering structures and equipment. The ability to properly assess and quantify multiaxial fatigue of offshore equipment and structures has major benefits for owners of engineering assets both in terms of technical and safety integrity. Traditionally, Palmgren-Miner’s damage rule is used for life estimation involving multiaxial fatigue due to its ease of use. There are however some known shortcomings with Palmgren-Miner’s rule namely: it does not consider the loading sequences. This for instance can result in overestimation of fatigue life in scenarios where stress amplitudes are decreasing, and moreover underestimation of fatigue life in scenarios where stress amplitudes increase. This research work thus involves closely studying the application of Palmgren-Miner’s linear damage rule, Manson’s double linear damage rule, and Subramanyan’s non-linear damage rule for the purpose of enhancing the predictability of damage as well as accuracy of fatigue life assessments. Each of these techniques were applied for tie-rods of an offshore drilling top-drive having a known stress history. The loading histories were provided by a drilling company. The torque and axial force values are transformed to stress components for the corresponding critical spots. The “rainflow” counting technique is applied to the obtained stress histories and the mean stress effect is considered for the damage accumulation calculations. The fatigue life prediction of the three models are justified and discussed. This research work was aimed at contributing towards the utilization of more robust fatigue life estimation techniques such as Manson’s double linear damage rule and simplified non-linear damage rules which capture the true nature of the fatigue that equipment’s are subjected to, and thus to improve the reliability of the fatigue life predictions.
Predictive maintenance (PdM) analysis matrix: A tool to determine technical specifications for PdM ready-equipment
Authors: El-Thalji I
Published: November 2019

Predictive maintenance (PdM) and operations optimisation are expected to generate the highest industrial and societal impact within the oil and gas industry. Such an optimistic expectation requires several changes in asset design and maintenance management. Nowadays, design for maintenance and maintenance support needs are mainly guided by the IEC 60706-2 standard. However, Designing for PdM ready-equipment is not yet part of that standard. To design PdM ready-equipment a specific analysis method shall be performed to evaluate the technical requirements and specifications of designed equipment to be PdM ready. Therefore, the purpose of this paper is to propose and demonstrate a PdM analysis method that helps to specify the technical specifications to monitor and predict the health of a specific physical asset. The proposed matrix is an evolution of further development of failure Mode, effect and criticality analysis (FMECA) and failure mode symptoms analysis (FMSA) rather than a revolutionary analysis. The case study method is used to extract stakeholders needs of what they expect from PdM analysis (PdMA) and how practical such type of analysis shall be. The developed PdMA matrix shows a simple relation between failure (their modes/levels) and measured abnormal symptoms and tracking and prediction indicators. The electric generator is used to demonstrate the use of the matrix. The PdMA matrix can be developed further to be more quantitative by including the probability of detection and probability of prediction.
A web based solution to track trawl vessel activities over pipelines in Norwegian Continental Shelf
Authors: Farmanbar M , Palanisamy A , Høydal A B , Keprate A , Haug G
Published: November 2019

Vessel activities such as trawling and anchoring potentially affect pipeline integrity. Therefore, the detailed information about the trawl activity in the area is essential for accurate assessment of pipeline, where to inspect and where to implement corrective intervention, based on up to date trawling intensity and equipment used. The main contribution of this paper is to present a detailed analysis of trawling vessels activities based on the automatic identification system (AIS) data combined with DNV GL ship register, data from HIS Maritime World Register of Ships and information gathered on the trawl equipment. In this aspect, an interactive web-based solution has been designed and developed to monitor and track trawl vessel activities in the Norwegian Continental Shelf which can be used for assessing integrity of pipelines. Data Analysis and visualization techniques have been utilized to transfer high-dimensional data by encoding it as visual objects contained in graphical presentations. The extracted knowledge result in the density mapping, vessel tracking, computing crossing points of trawl vessel paths, computing a buffered polygon around the pipeline for the chosen threshold and cross-over statistics of pipeline and vessels, etc. The use of such a framework is mostly advantageous for the port authorities, marine transportation, relevant fisheries management authority, etc.
Evaluation of ballast failures during operations of semi-submersible rigs
Authors: Unegbu N , Gudmestad O T
Published: November 2019

Risk analysis/assessment is one of the challenges encountered during operations of offshore units on the Norwegian Continental Shelf (NCS). In recent years, the Petroleum Safety Authority (PSA) has focused on hazards relating to floating installations and thus requested that more attention should be made by the industry on hazards relating to buoyancy loss and stability. Ballast systems play a very vital role to ensure vessel stability. Various failure modes of semi-submersible ballast systems are identified and possible barriers and consequences due to the ballast system failure during drilling operation are considered. The failure mode effect and criticality analysis (FMECA) of the main components of the semi-submersible’s ballast system is adopted to determine the failure causes and failure modes that could influence each components performance, and thus identifying the most critical component(s). The Structured What-If Technique (SWIFT) is used to compensate for hazard identification for the unidentified hazards (i.e., human errors), in the FMECA. By studying the most critical system components, a qualitative risk analysis is conducted to model accidental sequences by using the fault tree method to establish the chain of failure events. The result of the Structured What If Analysis (SWIFT) shows that maloperation of the ballast system is the main contributing failure cause. This involves, failure to properly describe ballast procedure, failure to follow ballast plan, wrong sequence of closing/opening valve, maloperation of valve, time pressure complacency, communication gap or general lack of knowledge of the system. The FMECA findings indicate that failure of valves to “close on demand” with a Risk Priority Number (RPN) of 60, is the most critical.
Challenges with gas hydrate formation
Authors: Kelland M A
Published: November 2019

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

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

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

In 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

Background

non-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.

Methods

a 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.

Results

a 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.

Conclusion

a 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

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

Clustered 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

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 < 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

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

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

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

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

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.
Resolution of pathogenic R-loops rescues motor neuron degeneration in spinal muscular atrophy
Authors: Hensel Niko , Detering Nora Tula , Walter Lisa Marie , Claus Peter
Published: November 2019

This scientific commentary refers to ‘ZPR1 prevents R-loop accumulation, upregulates SMN2 expression and rescues spinal muscular atrophy’, by Kannan et al. (doi: 10.1093/brain/awz373).
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

Axon 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.