scholarly journals Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting

2021 ◽  
Author(s):  
Daipayan Sarkar ◽  
Hyungro Lee ◽  
John W Vant ◽  
Matteo Turilli ◽  
Shantenu Jha ◽  
...  
Keyword(s):  
Decision Making ◽  
High Performance ◽  
Protein Structures ◽  
System Size ◽  
Physical Models ◽  
Stationary Structure ◽  
Density Maps ◽  
Essential Components ◽  
Adaptive Decision Making

Recent advances in cryo-electron microscopy (cryo-EM) has enabled modeling macromolecular complexes that are essential components of life. The density maps obtained from cryo-EM experiments is often integrated with ab-initio, knowledge-driven or first principles-based computational methods to build, fit and refine protein structures inside the electron density maps. Going beyond a single stationary-structure determination scheme, it is becoming more common to interpret the experimental data with a set of multiple physical models all of which contributes to the average observation seen by the experiment. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. In this work, we demonstrate such adaptive decision making capabilities during flexible fitting of biomolecules. Our solution uses RADICAL tools (RCT) and we test this new implementation in exascale high performance computing environment for two proteins, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). Our results indicate that using multiple replicas in flexible fitting with adaptive decision making improves the overall quality of fit and model by 40 % improvement when compared against the traditional flexible fitting approach. These advances are agnostic to system-size and computing environments.

High Performance Work Systems and Organizational Outcomes: The Mediating Role of Information Quality

ILR Review ◽  
2003 ◽  
Vol 56 (4) ◽  
pp. 590-605 ◽  
Author(s):  
Gil A. Preuss
Keyword(s):  
Decision Making ◽  
High Performance ◽  
Information Quality ◽  
Knowledge Work ◽  
Care Hospital ◽  
Quality Of Information ◽  
Work Systems ◽  
High Performance Work Systems ◽  
Performance Quality

Using data on registered nurses and nursing assistants in 50 acute-care hospital units, the author explores the relationships among high performance work systems, information quality, and performance quality within a context shaped by equivocal information—information that can be interpreted in multiple and sometimes conflicting ways. He finds that the quality of information available for decision-making, which largely depends on the interpretative skills of the workers who are exposed to important equivocal information, partially mediates how employee knowledge, work design, and total quality management systems affect organizational performance (which is measured as the inverse of medication error incidence). Providing employees with extensive relevant knowledge and enabling them to use their skills during even seemingly routine tasks improves the effective quality of information they bring to decision-making, and thereby promotes high performance quality.

Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques

2014 ◽  
Vol 70 (7) ◽  
pp. 1994-2006 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Giuliana Comunale ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Model Building ◽  
Protein Structures ◽  
Experimental Information ◽  
Atomic Resolution ◽  
Data Sets ◽  
Density Maps ◽  
Combined Use ◽  
Final Electron ◽  
Automatic Model Building

Phasing proteins at non-atomic resolution is still a challenge for anyab initiomethod. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (Cmap), theVLD(vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and thefree lunchextrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use ofARP/wARPto check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures:e.g.the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version ofSIR2014.

Study on the Compatibility between Naphthalene-Based Superplasticizer and Low Alkali Cement

2013 ◽  
Vol 639-640 ◽  
pp. 309-312
Author(s):  
La Na Tang
Keyword(s):  
High Performance ◽  
High Performance Concrete ◽  
Essential Components ◽  
Test Materials ◽  
Durability Of Concrete

Concrete admixture has become one of essential components of the high performance concrete in recent years; however, the quality of high performance concrete fluctuates according to the compatibility between cement and admixture it used. Considering lower alkali cement is often provided by cement producers in order to get better durability of concrete, so low alkali cement and naphthalene-based superplasticizer were used as the main test materials in this paper. The causes of the compatibility between low alkali cement and superplasticizer were studied, and then several measures were proposed to improve the compatibility.

Evaluation of the Academic Setting in Spain 1This study was financed by the University of Oviedo.

1995 ◽  
Vol 11 (2) ◽  
pp. 133-137 ◽  
Author(s):  
Juan Fernández ◽  
Miguel A. Mateo ◽  
José Muñiz
Keyword(s):  
Higher Education ◽  
Decision Making ◽  
Social Climate ◽  
Three Dimensions ◽  
Academic Setting ◽  
Teaching And Research ◽  
Evaluation Questionnaire ◽  
University Teachers ◽  
The University

The conditions are investigated in which Spanish university teachers carry out their teaching and research functions. 655 teachers from the University of Oviedo took part in this study by completing the Academic Setting Evaluation Questionnaire (ASEQ). Of the three dimensions assessed in the ASEQ, Satisfaction received the lowest ratings, Social Climate was rated higher, and Relations with students was rated the highest. These results are similar to those found in two studies carried out in the academic years 1986/87 and 1989/90. Their relevance for higher education is twofold because these data can be used as a complement of those obtained by means of students' opinions, and the crossing of both types of data can facilitate decision making in order to improve the quality of the work (teaching and research) of the university institutions.

Why Is Safe Science Good Science?

2018 ◽  
Author(s):  
Camilla Kao ◽  
Che-I Kao ◽  
Russell Furr
Keyword(s):  
Decision Making ◽  
Design Thinking ◽  
Good Science ◽  
Safety Issues ◽  
Safety Requirements ◽  
The Arts ◽  
Hands On ◽  
Obvious Benefit ◽  
New Ideas

In science, safety can seem unfashionable. Satisfying safety requirements can slow the pace of research, make it cumbersome, or cost significant amounts of money. The logic of rules can seem unclear. Compliance can feel like a negative incentive. So besides the obvious benefit that safety keeps one safe, why do some scientists preach "safe science is good science"? Understanding the principles that underlie this maxim might help to create a strong positive incentive to incorporate safety into the pursuit of groundbreaking science.<div><br></div><div>This essay explains how safety can enhance the quality of an experiment and promote innovation in one's research. Being safe induces a researcher to have <b>greater control</b> over an experiment, which reduces the <b>uncertainty</b> that characterizes the experiment. Less uncertainty increases both <b>safety</b> and the <b>quality</b> of the experiment, the latter including <b>statistical quality</b> (reproducibility, sensitivity, etc.) and <b>countless other properties</b> (yield, purity, cost, etc.). Like prototyping in design thinking and working under the constraint of creative limitation in the arts, <b>considering safety issues</b> is a hands-on activity that involves <b>decision-making</b>. Making decisions leads to new ideas, which spawns <b>innovation</b>.</div>

BIM-Based Quality Control for Safety Issues in the Design and Construction Phases

2015 ◽  
Vol 9 (3) ◽  
pp. 111 ◽  
Author(s):  
Seunghwa Park ◽  
Inhan Kim
Keyword(s):  
Decision Making ◽  
Traditional Method ◽  
Building Information Modeling ◽  
Safety Management ◽  
Information Modeling ◽  
Use Case ◽  
Safety Issues ◽  
Building Information ◽  
Building Safety

Today’s buildings are getting larger and more complex. As a result, the traditional method of manually checking the design of a building is no longer efficient since such a process is time-consuming and laborious. It is becoming increasingly important to establish and automate processes for checking the quality of buildings. By automatically checking whether buildings satisfy requirements, Building Information Modeling (BIM) allows for rapid decision-making and evaluation. In this context, the work presented here focuses on resolving building safety issues via a proposed BIM-based quality checking process. Through the use case studies, the efficiency and usability of the devised strategy is evaluated. This research can be beneficial in promoting the efficient use of BIM-based communication and collaboration among the project party concerned for improving safety management. In addition, the work presented here has the potential to expand research efforts in BIM-based quality checking processes.

QUALITY OF INDIVIDUAL AND GROUP LEVEL INTERVENTIONS FOR FIRST EPISODE PSYCHOSIS AT THE TERTIARY PSYCHIATRIC HOSPITAL IN UGANDA.

2020 ◽  
Author(s):  
Emmanuel Kiiza Mwesiga ◽  
Noeline Nakasujja ◽  
Lawrence Nankaba ◽  
Juliet Nakku ◽  
Seggane Musisi
Keyword(s):  
Psychiatric Hospital ◽  
Psychotic Disorders ◽  
First Episode Psychosis ◽  
First Episode ◽  
Group Level ◽  
Group Interventions ◽  
Episode Psychosis ◽  
Essential Components ◽  
The Individual

Introduction: Individual and group level interventions have the largest effect on outcomes in patients with the first episode of psychosis. The quality of these individual and group level interventions provided to first-episode psychosis patients in Uganda is unclear.Methods: The study was performed at Butabika National Psychiatric Teaching and referral hospital in Uganda. A retrospective chart review of recently discharged adult in-patients with the first episode of psychosis was first performed to determine the proportion of participants who received the different essential components for individual and group level interventions. From the different proportions, the quality of the services across the individual and group interventions was determined using the first-Episode Psychosis Services Fidelity Scale (FEPS-FS). The FEPS-FS assigns a grade of 1-5 on a Likert scale depending on the proportion of patients received the different components of the intervention. Results: The final sample included 156 first-episode psychosis patients. The median age was 27 years [IOR (24-36)] with 55% of participants of the female gender. 13 essential components across the individual and group interventions were assessed and their quality quantified. All 13 essential components had poor quality with the range of scores on the FEPS-FS of 1-3. Only one essential component assessed (use of single antipsychotics) had moderate quality.Discussion: Among current services at the National psychiatric hospital of Uganda, the essential for individual and group level interventions for psychotic disorders are of low quality. Further studies are required on how the quality of these interventions can be improved.

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