Evaluation of ontology structural metrics based on public repository data

2019 ◽  
Vol 21 (2) ◽  
pp. 473-485
Author(s):  
Manuel Franco ◽  
Juana María Vivo ◽  
Manuel Quesada-Martínez ◽  
Astrid Duque-Ramos ◽  
Jesualdo Tomás Fernández-Breis
Keyword(s):  
Evaluation Method ◽  
Measurement Instrument ◽  
Public Repository ◽  
Standard Methods ◽  
The Past ◽  
Biological Ontologies ◽  
Quality Aspects ◽  
Ontology Metrics ◽  
The Stability ◽  
Structural Metrics

Abstract The development and application of biological ontologies have increased significantly in recent years. These ontologies can be retrieved from different repositories, which do not provide much information about quality aspects of the ontologies. In the past years, some ontology structural metrics have been proposed, but their validity as measurement instrument has not been sufficiently studied to date. In this work, we evaluate a set of reproducible and objective ontology structural metrics. Given the lack of standard methods for this purpose, we have applied an evaluation method based on the stability and goodness of the classifications of ontologies produced by each metric on an ontology corpus. The evaluation has been done using ontology repositories as corpora. More concretely, we have used 119 ontologies from the OBO Foundry repository and 78 ontologies from AgroPortal. First, we study the correlations between the metrics. Second, we study whether the clusters for a given metric are stable and have a good structure. The results show that the existing correlations are not biasing the evaluation, there are no metrics generating unstable clusterings and all the metrics evaluated provide at least reasonable clustering structure. Furthermore, our work permits to review and suggest the most reliable ontology structural metrics in terms of stability and goodness of their classifications. Availability: http://sele.inf.um.es/ontology-metrics

Stability and Folding of the Unusually Stable Hemoglobin from Synechocystis is Subtly Optimized and Dependent on the Key Heme Pocket Residues.

2020 ◽  
Vol 27 ◽  
Author(s):  
Sheetal Uppal ◽  
Mohd. Asim Khan ◽  
Suman Kundu
Keyword(s):  
Molten Globule ◽  
Life Forms ◽  
Model System ◽  
Heme Pocket ◽  
The Past ◽  
Specific Manner ◽  
Delivery Vehicles ◽  
The Stability ◽  
Key Residues ◽  
Synechocystis Sp

Aims: The aim of our study is to understand the biophysical traits that govern the stability and folding of Synechocystis hemoglobin, a unique cyanobacterial globin that displays unusual traits not observed in any of the other globins discovered so far. Background: For the past few decades, classical hemoglobins such as vertebrate hemoglobin and myoglobin have been extensively studied to unravel the stability and folding mechanisms of hemoglobins. However, the expanding wealth of hemoglobins identified in all life forms with novel properties, like heme coordination chemistry and globin fold, have added complexity and challenges to the understanding of hemoglobin stability, which has not been adequately addressed. Here, we explored the unique truncated and hexacoordinate hemoglobin from the freshwater cyanobacterium Synechocystis sp. PCC 6803 known as “Synechocystis hemoglobin (SynHb)”. The “three histidines” linkages to heme are novel to this cyanobacterial hemoglobin. Objective: Mutational studies were employed to decipher the residues within the heme pocket that dictate the stability and folding of SynHb. Methods: Site-directed mutants of SynHb were generated and analyzed using a repertoire of spectroscopic and calorimetric tools. Result: The results revealed that the heme was stably associated to the protein under all denaturing conditions with His117 playing the anchoring role. The studies also highlighted the possibility of existence of a “molten globule” like intermediate at acidic pH in this exceptionally thermostable globin. His117 and other key residues in the heme pocket play an indispensable role in imparting significant polypeptide stability. Conclusion: Synechocystis hemoglobin presents an important model system for investigations of protein folding and stability in general. The heme pocket residues influenced the folding and stability of SynHb in a very subtle and specific manner and may have been optimized to make this Hb the most stable known as of date. Other: The knowledge gained hereby about the influence of heme pocket amino acid side chains on stability and expression is currently being utilized to improve the stability of recombinant human Hbs for efficient use as oxygen delivery vehicles.

scholarly journals Copper Phyllosilicates-Derived Catalysts in the Production of Alcohols from Hydrogenation of Carboxylates, Carboxylic Acids, Carbonates, Formyls, and CO2: A Review

Catalysts ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 255
Author(s):  
Dien-Thien To ◽  
Yu-Chuan Lin
Keyword(s):  
Carboxylic Acids ◽  
Catalytic Performance ◽  
Spatial Effect ◽  
Synthesis Methods ◽  
The Past ◽  
Surface Areas ◽  
Preparation Conditions ◽  
Remedial Actions ◽  
The Stability ◽  
Size Interaction

Copper phyllosilicates-derived catalysts (CuPS-cats) have been intensively explored in the past two decades due to their promising activity in carbonyls hydrogenation. However, CuPS-cats have not been completely reviewed. This paper focuses on the aspects concerning CuPS-cats from synthesis methods, effects of preparation conditions, and dopant to catalytic applications of CuPS-cats. The applications of CuPS-cats include the hydrogenation of carboxylates, carboxylic acids, carbonates, formyls, and CO2 to their respective alcohols. Besides, important factors such as the Cu dispersion, Cu+ and Cu0 surface areas, particles size, interaction between Cu and supports and dopants, morphologies, and spatial effect on catalytic performance of CuPS-cats are discussed. The deactivation and remedial actions to improve the stability of CuPS-cats are summarized. It ends up with the challenges and prospective by using this type of catalyst.

scholarly journals Identifying Stabilising Effects on Survey Based Life Satisfaction Using Quasi-maximum Likelihood Estimation

2021 ◽  
Author(s):  
Johannes Klement
Keyword(s):  
Life Satisfaction ◽  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Negative Binomial ◽  
Measurement Instrument ◽  
Likelihood Estimation ◽  
Satisfaction Scale ◽  
Quasi Maximum Likelihood ◽  
The Stability

AbstractTo which extent do happiness correlates contribute to the stability of life satisfaction? Which method is appropriate to provide a conclusive answer to this question? Based on life satisfaction data of the German SOEP, we show that by Negative Binomial quasi-maximum likelihood estimation statements can be made as to how far correlates of happiness contribute to the stabilisation of life satisfaction. The results show that happiness correlates which are generally associated with a positive change in life satisfaction, also stabilise life satisfaction and destabilise dissatisfaction with life. In such as they lower the probability of leaving positive states of life satisfaction and increase the probability of leaving dissatisfied states. This in particular applies to regular exercise, volunteering and living in a marriage. We further conclude that both patterns in response behaviour and the quality of the measurement instrument, the life satisfaction scale, have a significant effect on the variation and stability of reported life satisfaction.

scholarly journals Reliability Estimation of Reinforced Slopes to Prioritize Maintenance Actions

2021 ◽  
Vol 18 (2) ◽  
pp. 373
Author(s):  
Farshad BahooToroody ◽  
Saeed Khalaj ◽  
Leonardo Leoni ◽  
Filippo De Carlo ◽  
Gianpaolo Di Bona ◽  
...  
Keyword(s):  
Urban Areas ◽  
Evaluation Method ◽  
Likelihood Function ◽  
Reliability Estimation ◽  
Analytical Models ◽  
Geotechnical Structures ◽  
Reinforced Slopes ◽  
The Stability ◽  
Methods Analytical ◽  
Asset Managers

Geosynthetics are extensively utilized to improve the stability of geotechnical structures and slopes in urban areas. Among all existing geosynthetics, geotextiles are widely used to reinforce unstable slopes due to their capabilities in facilitating reinforcement and drainage. To reduce settlement and increase the bearing capacity and slope stability, the classical use of geotextiles in embankments has been suggested. However, several catastrophic events have been reported, including failures in slopes in the absence of geotextiles. Many researchers have studied the stability of geotextile-reinforced slopes (GRSs) by employing different methods (analytical models, numerical simulation, etc.). The presence of source-to-source uncertainty in the gathered data increases the complexity of evaluating the failure risk in GRSs since the uncertainty varies among them. Consequently, developing a sound methodology is necessary to alleviate the risk complexity. Our study sought to develop an advanced risk-based maintenance (RBM) methodology for prioritizing maintenance operations by addressing fluctuations that accompany event data. For this purpose, a hierarchical Bayesian approach (HBA) was applied to estimate the failure probabilities of GRSs. Using Markov chain Monte Carlo simulations of likelihood function and prior distribution, the HBA can incorporate the aforementioned uncertainties. The proposed method can be exploited by urban designers, asset managers, and policymakers to predict the mean time to failures, thus directly avoiding unnecessary maintenance and safety consequences. To demonstrate the application of the proposed methodology, the performance of nine reinforced slopes was considered. The results indicate that the average failure probability of the system in an hour is 2.8×10−5 during its lifespan, which shows that the proposed evaluation method is more realistic than the traditional methods.

scholarly journals Thermodynamic and Energy Efficiency Analysis of a Domestic Refrigerator Using Al2O3 Nano-Refrigerant

2021 ◽  
Vol 13 (10) ◽  
pp. 5659
Author(s):  
Farhood Sarrafzadeh Javadi ◽  
Rahman Saidur
Keyword(s):  
Temperature Gradient ◽  
Technological Changes ◽  
Nanoparticle Concentration ◽  
Evaporator Temperature ◽  
Domestic Refrigerator ◽  
The Past ◽  
Nano Lubricant ◽  
The Stability ◽  
Energy Efficiency Analysis ◽  
Al2o3 Nanofluid

Refrigeration systems have experienced massive technological changes in the past 50 years. Nanotechnology can lead to a promising technological leap in the refrigeration industry. Nano-refrigerant still remains unknown because of the complexity of the phase change process of the mixture including refrigerant, lubricant, and nanoparticle. In this study, the stability of Al2O3 nanofluid and the performance of a nano-refrigerant-based domestic refrigerator have been experimentally investigated, with the focus on the thermodynamic and energy approaches. It was found that by increasing the nanoparticle concentration, the stability of nano-lubricant was decreased and evaporator temperature gradient was increased. The average of the temperature gradient increment in the evaporator was 20.2% in case of using 0.1%-Al2O3. The results showed that the energy consumption of the refrigerator reduced around 2.69% when 0.1%-Al2O3 nanoparticle was added to the system.

scholarly journals Water confined in solutions of biological relevance

2020 ◽  
Vol 92 (10) ◽  
pp. 1563-1574
Author(s):  
Marie-Claire Bellissent-Funel
Keyword(s):  
Aqueous Solutions ◽  
Bulk Water ◽  
Biological Macromolecules ◽  
Organic Solutes ◽  
Confined Water ◽  
The Past ◽  
Structure And Dynamics ◽  
Biological Relevance ◽  
The Stability

AbstractIn many relevant situations, water is not in its bulk form but instead attached to some substrates or filling some cavities. We shall call water in the latter environment confined water as opposed to bulk water. It is known that the confined water is essential for the stability and the function of biological macromolecules. In this paper, we provide a review of the experimental and computational advances over the past decades concerning the understanding of the structure and dynamics of water confined in aqueous solutions of biological relevance. Examples involving water in solution of organic solutes (cryoprotectants such as dimethylsulfoxide (DMSO), sugars such as trehalose) are provided.

Future Directions in Surface Electromyography

Biofeedback ◽  
2010 ◽  
Vol 38 (2) ◽  
pp. 78-82 ◽  
Author(s):  
John G. Arena
Keyword(s):  
Surface Electromyography ◽  
Ambulatory Monitoring ◽  
Future Directions ◽  
The Past ◽  
Psychophysiological Assessment ◽  
The Future ◽  
The Stability

Abstract The use of surface electromyography (SEMG) has increased exponentially in the past four decades. SEMG is one of the most widespread measures employed today in psychophysiological assessment and one of three primary biofeedback modalities. This article briefly outlines three areas that the author believes are important for SEMG to address if it is to continue to flourish in the future: applications in telehealth, the use of telemetry and ambulatory monitoring, and studies on the stability or reliability of surface electromyography.

scholarly journals Sub-Frame Evaluation of Frame Synchronization for Camera Network Using Linearly Oscillating Light Spot

Sensors ◽  
2021 ◽  
Vol 21 (18) ◽  
pp. 6148
Author(s):  
Hyuno Kim ◽  
Masatoshi Ishikawa
Keyword(s):  
Visual Information ◽  
Evaluation Method ◽  
Measurement Instrument ◽  
Light Spot ◽  
Estimation Accuracy ◽  
Accurate Data ◽  
Frame Synchronization ◽  
Camera Network ◽  
Novel Method ◽  
Synchronization Accuracy

Precisely evaluating the frame synchronization of the camera network is often required for accurate data fusion from multiple visual information. This paper presents a novel method to estimate the synchronization accuracy by using inherent visual information of linearly oscillating light spot captured in the camera images instead of using luminescence information or depending on external measurement instrument. The suggested method is compared to the conventional evaluation method to prove the feasibility. Our experiment result implies that the estimation accuracy of the frame synchronization can be achieved in sub-millisecond order.

scholarly journals Stability Evaluation Method of Hole Wall for Bored Pile under Blasting Impact

Symmetry ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 79
Author(s):  
Qiuwei Yang ◽  
Zhikun Ba ◽  
Zhuo Zhao ◽  
Xi Peng ◽  
Yun Sun
Keyword(s):  
Pile Foundation ◽  
Evaluation Method ◽  
Impact Load ◽  
Stability Evaluation ◽  
Foundation Construction ◽  
Concentration Problem ◽  
Hole Wall ◽  
Failure Theory ◽  
Collapse Failure ◽  
The Stability

Blasting impact load may be encountered during the construction of some pile foundation projects. Due to the effect of blasting impact, hole collapse can easily occur in the hole-forming stage of pile foundation construction. In order to prevent hole collapse, it is very necessary to evaluate the stability of a pile hole wall before pile foundation construction. The calculation of hole collapse can usually be attributed to an axisymmetric circular hole stress concentration problem. However, the existing collapse failure theory of pile hole hardly considers the effect of blasting impact load. In view of this, this paper proposes the stability evaluation method of a pile hole wall under blasting impact. Compared with the existing collapse failure theory, the proposed method fully considers the effect of blasting impact stress. Using Mohr–Coulomb strength theory and symmetry analysis, the strength condition of collapse failure is established in this work for accurate evaluation of the stability of a hole wall. The proposed stability evaluation method is demonstrated by a pile foundation construction project of a bridge. Moreover, a shaking table test on the pile hole model was performed to verify the proposed method by experimental data. The results indicate the effectiveness and usability of the proposed method. The proposed method provides a feasible way for the stability analysis of a pile hole wall under blasting impact.

scholarly journals Spatial aspect of modern warfare: from traditional warfare to cyberwar

2021 ◽  
pp. 136-149
Author(s):  
Natalia Aleksandrovna Balakleets
Keyword(s):  
Military Leaders ◽  
The Past ◽  
The Earth ◽  
Total Destruction ◽  
Spatial Aspect ◽  
Pessimistic Scenario ◽  
The Stability ◽  
Military Activity ◽  
Modern Warfare ◽  
The Military

This author substantiates the thesis on the importance of spatial factors for conducting warfare. The article traces the evolution of warfare associated with the involvement of new territories and new types of spaces in the orbit of military activity. If the warfare of the past demonstrated a direct dependence on the geographical territory and the related “tensions” (C. von Clausewitz), the modern warfare are emancipated from the geographical shell of the Earth. The article explicates the factors that justify the need for arranging the new warfare spaces. Special attention is given to cyberspace, its structure, and conflicts unfolding therein. The scientific novelty of consists in the interpretation of cyberspace as an expected result of the spatial evolution of warfare. The conclusion is drawn that the emergence of cyberspace contributes to solution of the problem of information vagueness and creation of the stability zones for the military leaders, but at the same is a source of problems not less dangerous for the humanity. The cyberwar winner faces a tempting challenge of establishing global control over the territory of the plane using cyberweapon, or in most pessimistic scenario, its total destruction.

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