scholarly journals PROSS 2: a new server for the design of stable and highly expressed protein variants

2020 ◽  
Author(s):  
Jonathan Jacob Weinstein ◽  
Adi Goldenzweig ◽  
ShlomoYakir Hoch ◽  
Sarel Jacob Fleishman
Keyword(s):  
Sequence Analysis ◽  
Heterologous Expression ◽  
Sequence Alignment ◽  
Design Method ◽  
Automated Analysis ◽  
Designed Proteins ◽  
Analysis Error ◽  
Design Calculations ◽  
Protein Variants

ABSTRACT   Summary: Many natural and designed proteins are only marginally stable limiting their usefulness in research and applications. Recently, we described an automated structure and sequence-based design method, called PROSS, for optimizing protein stability and heterologous expression levels that has since been validated on dozens of proteins. Here, we introduce improvements to the method, workflow and presentation, including more accurate sequence analysis, error handling and automated analysis of the quality of the sequence alignment that is used in design calculations. Availability and implementation PROSS2 is freely available for academic use at https://pross.weizmann.ac.il.

Ego Psychoanalytic Rorschach Interpretation

2017 ◽  
Vol 38 (1) ◽  
pp. 22-32 ◽  
Author(s):  
Irving B. Weiner
Keyword(s):  
Differential Diagnosis ◽  
Sequence Analysis ◽  
Treatment Planning ◽  
Well Being ◽  
Adjustment Difficulties ◽  
Behavioral Features ◽  
Defensive Style ◽  
Cognitive Slippage ◽  
Interpretive Process

Abstract. This article concerns the utility of ego psychoanalytic perspectives in Rorschach interpretation. Psychoanalytic ego psychology focuses on how people cope with events in their lives and how effectively they can meet challenges to their sense of well-being. The way people deal with experienced distress constitutes their defensive style and determines to a large extent what kind of person they are. Adequate defenses against anxiety promote comfortable and productive adjustment, whereas ineffective defenses typically cause adjustment difficulties and susceptibility to psychological disorders. In Rorschach assessment, the nature and effectiveness of a person’s defensive style can often be identified with a sequence analysis that integrates the structural, thematic, and behavioral features in the protocol. In particular, the sequential quality of responses, especially preceding and following instances of cognitive slippage, can help identify causes of upsetting concerns, defensive efforts to alleviating these concerns, and the adequacy of these defensive efforts in restoring equanimity. This interpretive process is illustrated with attention to implications for differential diagnosis and treatment planning in the Rorschach protocol of a 20-year-old suicidal woman.

COMPARATIVE PERFORMANCE EVALUATION OF PMB and CRMB WITH PARTIAL REPLACEMENT OF BITUMEN (VG-30) USING MARSHALL MIX DESIGN METHOD-A REVIEW

2018 ◽  
Vol 5 (02) ◽  
Author(s):  
N. SATHEESHKANNA
Keyword(s):  
Performance Evaluation ◽  
Design Method ◽  
Mix Design ◽  
Partial Replacement ◽  
Comparative Performance

Waste generated from industries and from various places around us not only contains rubber or plastics but contains lot many harmful pollutants whichare hazardous if disposed continuously in open and leftto degrade in our environment.Our project aims to study properties of different materials which may help in utilising the waste as well as improve the quality of roads and make them efficient, stable, durable and long lasting. Some of the materials that we have studied and considered to be tested in the partial replacement of bitumen are PMB and CRMB.

Research on the Optimal Design Method of the Main Components for the Wheelchair Pickup

2013 ◽  
Vol 791-793 ◽  
pp. 799-802
Author(s):  
Ya Ping Wang ◽  
H.R. Shi ◽  
L. Gao ◽  
Z. Wang ◽  
X.Y. Jia ◽  
...  
Keyword(s):  
Parametric Design ◽  
Design Method ◽  
Basic Function ◽  
Design Parameters ◽  
Algorithm Optimization ◽  
Optimization Analysis ◽  
Research Designs ◽  
Optimal Design Method ◽  
Main Components

With the increasing of the aging of population all over the world, and With the inconvenience coming from diseases and damage, there will be more and more people using the wheelchair as a tool for transport. When it cant be short of the wheelchair in the daily life, the addition of the function will bring the elevation of the quality of life for the unfortunate. Staring with this purpose, the research designs a pickup with planetary bevel gear for the wheelchair. After determining the basic function of the wheelchair aids, the study determines the design parameters by using the knowledge of parametric design and completes the model for the system with Pro/E, on the other hand, it completes key components optimization analysis which is based on genetic algorithm optimization.

Automatic verification method of progressive image model matching information based on machine learning

2021 ◽  
pp. 1-10
Author(s):  
Jie Yuan ◽  
Yuan Ji ◽  
Zhou Zhu ◽  
Liya Huang ◽  
Junfeng Qian ◽  
...  
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
Design Method ◽  
Large Error ◽  
Model Matching ◽  
Target Image ◽  
Image Model ◽  
Verification Method ◽  
Low Performance

In order to solve the problems of large error and low performance of traditional progressive image model matching information checking methods, an automatic progressive image model matching information checking method based on machine learning is proposed. The generation method of progressive image is analyzed, and the target image sample is obtained. On this basis, machine learning algorithm is used to segment progressive image samples. In each image segmentation part, crawler technology is used to automatically collect progressive image model matching information, and under the constraint of image model matching information checking standard, automatic checking of progressive image model matching information is realized from geometric structure, image content and other aspects. Experimental results show that the verification error of the design method is reduced by 0.687 Mb, and the quality of progressive image is improved.

scholarly journals IPG as a new method to improve the agility of the initial analysis of the inventive design

2021 ◽  
Vol 49 (3) ◽  
pp. 549-562
Author(s):  
Masih Hanifi ◽  
Hicham Chibane ◽  
Rémy Houssin ◽  
Denis Cavallucci
Keyword(s):  
Inverse Problem ◽  
Design Method ◽  
New Method ◽  
Significant Progress ◽  
Initial Analysis ◽  
The Subject ◽  
Time Required

TRIZ method has long proven its value without appearing to the industrial world as inevitable. Design researchers have therefore addressed the limitations of the TRIZ method and have overcome them with more systematic approaches. Among these, the Inventive Design Method (IDM) has been the subject of several articles and put into practice in the industry. It is considered an improvement over TRIZ but still suffers from some drawbacks in terms of the time-consuming nature of its implementation. We focused on the IDM process by trying to both identify its areas of inefficiencies while attempting to preserve the quality of its deliverables. Our approach consists of applying the precepts of Lean to IDM. The result is the Inverse Problem Graph (IPG) method, inspired by IDM, but offering significant progress in reducing the time required to mobilize experts while preserving its inventive outcomes. This article outlines our approach for the construction of this new method.

scholarly journals Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Ernesto Liñán-García ◽  
Lorena Marcela Gallegos-Araiza
Keyword(s):  
Simulated Annealing ◽  
Sequence Alignment ◽  
Simulated Annealing Algorithm ◽  
Multiple Sequence ◽  
Heating And Cooling ◽  
Dna Sequence Alignment ◽  
Alignment Problem ◽  
Simple Change ◽  
Annealing Algorithm

A new algorithm for solving sequence alignment problem is proposed, which is named SAPS (Simulated Annealing with Previous Solutions). This algorithm is based on the classical Simulated Annealing (SA). SAPS is implemented in order to obtain results of pair and multiple sequence alignment. SA is a simulation of heating and cooling of a metal to solve an optimization problem. In order to select randomly a current solution, SAPS algorithm chooses a solution from solutions that have been previously generated within the Metropolis Cycle. This simple change has led to increase the quality of the solution to the problem of aligning genomic sequences with respect to the classical Simulated Annealing algorithm. The parameters of SAPS, for certain instances, are tuned by an analytical method, and some parameters have experimentally been tuned. SAPS has generated high-quality results in comparison with the classical SA. The instances used are specific genes of the AIDS virus.

scholarly journals Grounded Theory for the Design of Mobile User Interfaces-Based on Space Retrieval Therapy

2021 ◽  
Vol 15 (12) ◽  
pp. 104
Author(s):  
Kholoud Abdulrahman Aljedaani ◽  
Reem Abdulaziz Alnanih
Keyword(s):  
Quality Of Life ◽  
Grounded Theory ◽  
Elderly People ◽  
User Interfaces ◽  
Design Method ◽  
User Model ◽  
User Centered Design ◽  
Cognitive Changes ◽  
Color Preferences

<span lang="EN-US">Technology plays a major role in our daily lives. In healthcare, technology assists in treating and detecting diseases and can improve patients’ quality of life. Alzheimer’s disease patients are generally elderly people who suffer from disabilities in vision, hearing, speech, and movement. The disease is one of the most common types of dementia. This paper proposes a design for a mobile application with an adaptive user interface for Alzheimer’s patients based on an elderly model developed using grounded theory. The application aims to improve the patients’ quality of life and allow them to remain engaged in society. The design of the application is based on spaced retrieval therapy (SRT), a method that helps Alzheimer’s patients to recall specific pieces of important information. User-centered design method was used to design and build this application. In the requirements phase, a user model for elderly people was elicited based on a classification developed through grounded theory. The prototype for the proposed model was designed and developed considering the default user interfaces and the adaptive user interfaces. A test was conducted with 15 elderly Arab users. The participants were 50–74 years old with varying levels of education and experience with technology. The authors proposed a user model for elderly people containing all the design implications in terms of physical and cognitive changes. The results of testing with elderly Arab users supported the proposed user model in terms of colors, fonts, pictures, and symbols. However, there were problems with the menu design and color preferences.</span>

scholarly journals Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

2021 ◽  
Author(s):  
Romain Feron ◽  
Robert Michael Waterhouse
Keyword(s):  
Large Scale ◽  
Automated Analysis ◽  
Single Copy ◽  
The United States ◽  
Community Resource ◽  
Assembly Quality ◽  
Sequencing Technologies ◽  
Analysis Workflow ◽  
Genome Assemblies

Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. In order to guide forthcoming genome generation efforts and promote efficient prioritisation of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data. Here we present an automated analysis workflow that surveys genome assemblies from the United States National Center for Biotechnology Information (NCBI), assesses their completeness using the relevant Benchmarking Universal Single-Copy Orthologue (BUSCO) datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, we examine how key assembly metrics relate to gene content completeness, and we compare results from using different BUSCO lineage datasets. These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritisations for ongoing and future sampling, sequencing, and genome generation initiatives.

scholarly journals PENERAPAN PENDEKATAN PSIKOLOGI ARSITEKTUR PADA SEKOLAH LUAR BIASA TUNARUNGU (SLB TIPE B) DI KOTA BEKASI

Arsitektura ◽  
2017 ◽  
Vol 15 (2) ◽  
pp. 525
Author(s):  
Ariani Nurfakhirah
Keyword(s):  
Hearing Impairment ◽  
Learning Process ◽  
Design Method ◽  
Special School ◽  
Deaf Students ◽  
Normal Children ◽  
Site Analysis ◽  
School For The Deaf ◽  
Deaf Persons

<p><em>The condition of special school for the deaf and the deaf itself are still apprehensive, especially in Bekasi, West Java. Meanwhile, deaf persons still need to get an education which equivalent to the education that normal children get. However, education for children with special needs, especially those with hearing impairment, requires special implementations based on deaf’s characteristics in some design aspects in order to improve physical and psychological comfort required by deaf students so they can be more comfortable adapting to school circumstances. Design method that seems appropriate to be applied to this special school for the deaf is psychological architecture approach that focuses on the characteristics of the deaf itself. Psychological architecture as design method that used in this special school is adjusted to the characteristics of hearing impaired in order to improve the quality of physical and psychological comfort of deaf students in the learning process and activities by applying the principles of psychological architecture on site analysis, school layout arrangement, and also the appearance of interior and exterior of special school for the deaf.</em></p>

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