Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function

2013 ◽  
Vol 53 (4) ◽  
pp. 1007-1015 ◽  
Author(s):  
Christopher Pfleger ◽  
Prakash Chandra Rathi ◽  
Doris L. Klein ◽  
Sebastian Radestock ◽  
Holger Gohlke
Keyword(s):  
Network Analysis ◽  
Software Package ◽  
Constraint Network ◽  
Structure Flexibility ◽  
Thermo Stability ◽  
And Function

scholarly journals NetFACS: Using network science to understand facial communication systems

2021 ◽  
Author(s):  
Alexander Mielke ◽  
Bridget M. Waller ◽  
Claire Pérez ◽  
Alan V. Rincon ◽  
Julie Duboscq ◽  
...  
Keyword(s):  
Network Analysis ◽  
Communication Systems ◽  
Network Science ◽  
Coding System ◽  
Communication Tool ◽  
Resampling Methods ◽  
Facial Movements ◽  
The Face ◽  
Analyse Data ◽  
And Function

AbstractUnderstanding facial signals in humans and other species is crucial for understanding the evolution, complexity, and function of the face as a communication tool. The Facial Action Coding System (FACS) enables researchers to measure facial movements accurately, but we currently lack tools to reliably analyse data and efficiently communicate results. Network analysis can provide a way to use the information encoded in FACS datasets: by treating individual AUs (the smallest units of facial movements) as nodes in a network and their co-occurrence as connections, we can analyse and visualise differences in the use of combinations of AUs in different conditions. Here, we present ‘NetFACS’, a statistical package that uses occurrence probabilities and resampling methods to answer questions about the use of AUs, AU combinations, and the facial communication system as a whole in humans and non-human animals. Using highly stereotyped facial signals as an example, we illustrate some of the current functionalities of NetFACS. We show that very few AUs are specific to certain stereotypical contexts; that AUs are not used independently from each other; that graph-level properties of stereotypical signals differ; and that clusters of AUs allow us to reconstruct facial signals, even when blind to the underlying conditions. The flexibility and widespread use of network analysis allows us to move away from studying facial signals as stereotyped expressions, and towards a dynamic and differentiated approach to facial communication.

scholarly journals Articulação em rede: o cuidado a usuários de drogas na perspectiva da análise de redes sociais/ Networking articulation: care for drug users from the perspective of social network analysis

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Débora Schlotefeldt Siniak ◽  
Leandro Barbosa de Pinho ◽  
Otávio Neves da Silva Bittencourt ◽  
Pedro Henrique Antunes da Costa ◽  
Maria Gabriela Curubeto Godoy
Keyword(s):  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Software Package ◽  
Drug Users ◽  
Rio Grande ◽  
Rio Grande Do Sul ◽  
The Social

Objetivo: Estudo quantitativo, descritivo que se propõe a analisar a articulação entre um centro de atenção psicossocial e a rede de saúde intersetorial. Metodologia: A coleta de dados ocorreu de agosto à dezembro de 2017, em um município da fronteira oeste do Estado do Rio Grande do Sul, Brasil. A análise dos dados foi organizada a partir da utilização do Software Package for the Social Network Analysis - UCINET. O estudo norteia-se pelo referencial metodológico de análise de redes sociais. Resultados: Os resultados apontaram a existência de 37 atores envolvidos no cuidado às pessoas que usam drogas. Foi possível observar diversos setores de justiça e segurança pública que prestavam cuidados diretos ou indiretos aos usuários. Contudo, os resultados indicaram certo distanciamento desses atores no tocante ao desenvolvimento de programas conjuntos e coordenação de casos com outros serviços da rede. Verificou-se, através das métricas investigadas, um baixo grau de interação entre os dispositivos, demonstrando a dificuldade por parte da rede em atuar de forma integrada e construir possibilidades de cuidado conjuntas. Considerações finais: Discute-se a necessidade de maior articulação intersetorial nos níveis de interação analisados neste estudo. Para isso, é preciso pensar em políticas municipais que favoreçam essa “costura” entre os atores.

Graphical Spreadsheets as Convenient Tools for Turbomachinery Education

2001 ◽  
Author(s):  
Timothy F. Miller
Keyword(s):  
Software Package ◽  
Design Tool ◽  
Design Tools ◽  
Primary Reason ◽  
Educational Design ◽  
Analysis And Design ◽  
Radial Pump ◽  
And Function ◽  
Design Aspect ◽  
Spreadsheet Software

An unfortunate aspect of engineering education in general, and turbomachinery education in specific, has been the difficulty of incorporating the design aspect of instruction with the time-consuming components that make up theoretical instruction. The primary reason for this difficulty is the extremely limited time (typically three months) allocated to teach turbomachinery as a senior-level quarter or semester technical elective. It is desirable to develop an educational design tool that can be simultaneously exercised by a student to perform various design tasks and function as a means of theoretical instruction. Such a tool can permit the students both greater depth and breadth of exposure and may be subsequently used by the students in their future capacity as professional engineers. In this paper, this tool is illustrated by several applications of a commercial “graphical spreadsheet” software package (MathCAD, though others such as Mathmatica and Macsyma are appropriate as well). Some graphical spreadsheet design tools are presented, and these tools are applied to the analysis and design of a radial pump, centrifugal compressor, and radial-inflow turbine.

scholarly journals Gender Differences in Social Support Received by Informal Caregivers: A Personal Network Analysis Approach

2018 ◽  
Vol 16 (1) ◽  
pp. 91 ◽  
Author(s):  
María Rodríguez-Madrid ◽  
María del Río-Lozano ◽  
Rosario Fernandez-Peña ◽  
Jaime Jiménez-Pernett ◽  
Leticia García-Mochón ◽  
...  
Keyword(s):  
Social Support ◽  
Gender Differences ◽  
Network Analysis ◽  
Descriptive Analysis ◽  
Perceived Health ◽  
Personal Network ◽  
Convenience Sample ◽  
Caregiver Support ◽  
Traditional Gender Roles ◽  
And Function

Social support is an important predictor of the health of a population. Few studies have analyzed the influence of caregivers’ personal networks from a gender perspective. The aim of this study was to analyze the composition, structure, and function of informal caregiver support networks and to examine gender differences. It also aimed to explore the association between different network characteristics and self-perceived health among caregivers. We performed a social network analysis study using a convenience sample of 25 female and 25 male caregivers. A descriptive analysis of the caregivers and bivariate analyses for associations with self-perceived health were performed. The structural metrics analyzed were density; degree centrality mean; betweenness centrality mean; and number of cliques, components, and isolates. The variability observed in the structure of the networks was not explained by gender. Some significant differences between men and women were observed for network composition and function. Women received help mainly from women with a similar profile to them. Men’s networks were broader and more diverse and they had more help from outside family circles, although these outcomes were not statistically significant. Our results indicate the need to develop strategies that do not reinforce traditional gender roles, but rather encourage a greater sharing of responsibility among all parties.

scholarly journals Trading off stability against activity in extremophilic aldolases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Markus Dick ◽  
Oliver H. Weiergräber ◽  
Thomas Classen ◽  
Carolin Bisterfeld ◽  
Julia Bramski ◽  
...  
Keyword(s):  
Network Analysis ◽  
Rational Design ◽  
Enzyme Stability ◽  
Disulfide Bridge ◽  
High Turnover ◽  
Dimer Interface ◽  
Constraint Network ◽  
Hyperthermophilic Enzymes ◽  
Monomeric Proteins ◽  
Hyperthermophilic Organisms

Abstract Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding α-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.

scholarly journals Genome-wide analysis of lncRNAs and mRNAs expression during the differentiation of abdominal preadipocytes in chicken

2016 ◽  
Author(s):  
Tao Zhang ◽  
Xiangqian Zhang ◽  
Kunpeng Han ◽  
Genxi Zhang ◽  
Jinyu Wang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Rna Sequencing ◽  
Early Stage ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Valuable Resource ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
And Function ◽  
Jinghai Yellow Chicken

AbstractlncRNAs regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in preadipocytes differentiation of chicken. Here, we identified lncRNAs in preadipocytes of different differentiation stages by RNA-sequencing using Jinghai Yellow chicken. A total of 1,300,074,528 clean reads and 27,023 lncRNAs were obtained from twenty samples. 3095 genes (1,336 lncRNAs and 1,759 mRNAs) were differentially expressed among different stages, of which the number of DEGs decreased with the differentiation, demonstrating that the early stage might be most important for chicken preadipocytes differentiation. Furthermore, 3,095 DEGs were clustered into 8 clusters with their expression patterns by K-means clustering. We identified six stage-specific modules related to A0, A2 and A6 stages using weighted co-expression network analysis. Many well-known/novel pathways associated with preadipocytes differentiation were found. We also identified highly connected genes in each module and visualized them by cytoscape. Many well-known genes related to preadipocytes differentiation were found such as IGFBP2 and JUN. Yet, the majority of high connected genes were unknown in chicken preadipocytes. This study provides a valuable resource for chicken lncRNA study and contributes to batter understanding the biology of preadipocytes differentiation in chicken.

Data-Driven Platform Design: Patent Data and Function Network Analysis

2018 ◽  
Vol 141 (2) ◽  
Author(s):  
Binyang Song ◽  
Jianxi Luo ◽  
Kristin Wood
Keyword(s):  
Network Analysis ◽  
Product Variety ◽  
Data Driven ◽  
Patent Data ◽  
Product System ◽  
Platform Design ◽  
Economy Of Scale ◽  
Product Systems ◽  
And Function ◽  
Platform System

A properly designed product-system platform seeks to reduce the cost and lead time for design and development of the product-system family. A key goal is to achieve a tradeoff between economy of scope from product variety and economy of scale from platform sharing. Traditionally, product platform planning uses heuristic and manual approaches and relies almost solely on expertise and intuition. In this paper, we propose a data-driven method to draw the boundary of a platform-system, complementing the other platform design approaches and assisting designers in the architecting process. The method generates a network of functions through relationships of their co-occurrences in prior designs of a product or systems domain and uses a network analysis algorithm to identify an optimal core–periphery structure. Functions identified in the network core co-occur cohesively and frequently with one another in prior designs, and thus, are suggested for inclusion in the potential platform to be shared across a variety of product-systems with peripheral functions. We apply the method to identify the platform functions for the application domain of spherical rolling robots (SRRs), based on patent data.

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