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26 results on '"Kazemi, Sina"'

2. Transition between Boundary-Limited Scaling and Mixing-Length Scaling of Turbulent Transport in Internally Heated Convection

Author

Kazemi, Sina, Ostilla-Mónico, Rodolfo, and Goluskin, David

Subjects
Physics - Fluid Dynamics
Abstract

Heat transport in turbulent thermal convection increases with the thermal forcing, but in almost all studies the rate of this increase is slower than it would be if transport became independent of the molecular diffusivities -- the heat transport scaling is slower than the mixing-length (or `ultimate') scaling. In configurations driven by either thermal boundary conditions or internal heating, thermal boundary layers instead lead to a boundary-limited (or `classical') scaling. With net-zero internal heating and cooling in different regions, mixing-length scaling can occur because heat need not cross a boundary. We report numerical simulations in which heating and cooling are unequal, as in various natural systems, at a Prandtl number of unity. As heating and cooling rates are made closer, the scaling exponent of heat transport varies from its boundary-limited value to its mixing-length value.

Published
2021
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4. Investigating The Effect of Promoting Changes and Transformations in Nursing Shift Work on the Satisfaction of Emergency Department Nurses.

Author

Kazemi, Sina, Mahmoudi, Hosein, Hashemi, Saeed, and Rahmani, Ali

Subjects
WORK environment, NURSING interventions, HOSPITALS, NURSING, HOSPITAL emergency services, JOB satisfaction, MEDICAL communication, NURSES' attitudes, QUALITY assurance, EMERGENCY nurses, SHIFT systems
Abstract

Background and Aim: Nursing care is complex and critical, making it vital to communicate health information using standardized methods. By using the SBAR (Situation - Background - Assessment - Recommendation) method, nurses can provide a complete and clear clinical picture of the patient's condition to the nurse receiving the patient. Conducting a shift handover audit allows for a comparison of the current shift handover process with the standard procedure, enabling the identification and resolution of any issues. Improving the shift handover process is crucial for the effective transfer of health information and addressing challenges that may arise during shift work delivery. The present study was conducted to investigate the effect of promoting changes in nursing shift work on the satisfaction of nurses in the emergency department of at Baqiyatallah Hospital in Tehran, Iran. The standard SBAR tool was utilized for this purpose. Methods: The present study is a semi-experimental study conducted before and after an intervention on 35 nurses who were randomized based on entry criteria in the emergency department of Baqiyatollah Hospital in Tehran from 2023 to 2024. Initially, the delivery of shift work in the emergency department and nurses' satisfaction levels were assessed through a questionnaire. Subsequently, the current situation was compared with the SBAR checklist, and an SBAR training program for nurses was developed based on identified deficiencies. Following the training sessions, a review of the materials and clarification of any issues were conducted. Subsequently, the practical application of shift delivery on patients' beds was assessed using the SBAR checklist. All participants were then asked to complete the nurses' satisfaction survey once again. Results: This study revealed that the SBAR score after the intervention (49.49) was significantly higher than the average SBAR score before the intervention (21.31) (P<0.05). Additionally, the satisfaction scores of nurses after the intervention were significantly higher than those of nurses before the intervention (P<0.05). Conclusion: Implementing the SBAR standard method for shift work delivery addresses the challenges faced in nursing shift work and enhances the nursing care process, ultimately boosting nurse satisfaction. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR

Author

Möbius, Kristin, Kazemi, Sina, Güntert, Peter, Jakob, Andreas, Heckel, Alexander, Becker-Baldus, Johanna, and Glaubitz, Clemens

Subjects
Diacylglycerol Kinase, Magnetic Resonance Spectroscopy, lcsh:R, Lipid Bilayers, lcsh:Medicine, Article, Diglycerides, Kinetics, Catalytic Domain, ddc:540, Escherichia coli, lcsh:Q, Amino Acid Sequence, Phosphorylation, lcsh:Science, Signal Transduction
Abstract

Escherichia coli diacylglycerol kinase (DGK) is an integral membrane protein, which catalyses the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatic acid (PA). It is a unique trimeric enzyme, which does not share sequence homology with typical kinases. It exhibits a notable complexity in structure and function despite of its small size. Here, chemical shift assignment of wild-type DGK within lipid bilayers was carried out based on 3D MAS NMR, utilizing manual and automatic analysis protocols. Upon nucleotide binding, extensive chemical shift perturbations could be observed. These data provide evidence for a symmetric DGK trimer with all of its three active sites concurrently occupied. Additionally, we could detect that the nucleotide substrate induces a substantial conformational change, most likely directing DGK into its catalytic active form. Furthermore, functionally relevant interprotomer interactions are identified by DNP-enhanced MAS NMR in combination with site-directed mutagenesis and functional assays., Scientific Reports, 9 (1), ISSN:2045-2322

Published
2019

17. Hydrological controls on glacially exported microbial assemblages

Author

Dubnick, Ashley, Kazemi, Sina, Sharp, Martin, Wadham, Jemma, Hawkings, Jon, Beaton, Alexander, and Lanoil, Brian

Subjects
subglacial, Greenland, hydrology, bacteria, 16S rRNA gene sequencing
Abstract

The Greenland Ice Sheet (GrIS) exports approximately 400 km3 of freshwater annually to downstream freshwater and marine ecosystems. These meltwaters originate in a wide range of well-defined habitats that can be associated with very different physical environments within the ice sheet, ranging from oxygenated surface environments that are exposed to light and supplied with nutrients from atmospheric/aeolian sources to subglacial environments that are permanently dark, isolated from the atmosphere, and potentially anoxic. Hydrological conditions in the latter likely favor prolonged rock-water contact. The seasonally evolving hydrological system that drains meltwaters from the GrIS connects these distinct microbial habitats and exports the microbes contained within them to downstream ecosystems. The microbial assemblages exported in glacier meltwater may have an impact on downstream ecosystem function and development. We explored how the seasonal development of a glacial drainage system influences the character of microbial assemblages exported from the GrIS by monitoring the seasonal changes in hydrology, water chemistry, and microbial assemblage composition of meltwaters draining from a glacier in southwest Greenland. We found that the microbial assemblages exported in meltwaters varied in response to glacier hydrological flow path characteristics. Whether or not meltwaters passed through the subglacial environment was the first-order control on the composition of the microbial assemblages exported from the glacier, while water source (i.e., supraglacial or extraglacial) and subglacial residence times were second-order controls. Glacier hydrology therefore plays a fundamental role in determining the microbial exports from glaciated watersheds.

Published
2017
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25. Protein Flexibility and Mobility in Structure-Based Drug Design

Author

Ahmed, Aqeel, Kazemi, Sina, and Gohlke, Holger

Abstract

Initially, structure-based drug design (SBDD) approaches relied on the validity of the “lock and key” model, although this assumption leads to clear limitations. Thus, there are considerable efforts nowadays to incorporate the influence of (changes of) protein flexibility and mobility into recent drug design approaches. These efforts are grounded on the “induced-fit” and “conformational selection” models of ligand binding to proteins. Here we will summarize computational approaches in SBDD that address these issues, with a focus on methods that account for receptor plasticity. In particular, we consider how protein plasticity can be incorporated into docking strategies. Two requirements need to be met for this: first, one needs to detect what can move and how; second, this knowledge needs to be transformed into a docking algorithm. With regard to the former, knowledge about moving protein parts can be gained from experimental information as well as established techniques such as molecular dynamics simulations, graph theoretical and geometry-based approaches, or harmonic analysis-based methods. With regard to the latter, a plethora of approaches has been presented recently that range from considering protein plasticity only implicitly to modeling sidechain movements to also including backbone changes. A hallmark of all these approaches is that they need to balance accuracy and efficiency. Case studies of SBDD for which the inclusion of protein plasticity was crucial to success are noted along these lines. This provides a picture of scope and limitations of the current approaches as well as guidelines for further developments.

Published
2007

26. Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids.

Author

Krüger DM, Bergs J, Kazemi S, and Gohlke H

Abstract

The highly flexible nature of RNA provides a formidable challenge for structure-based drug design approaches that target RNA. We introduce an approach for modeling target conformational changes in RNA-ligand docking based on potential grids that are represented as elastic bodies using Navier's equation. This representation provides an accurate and efficient description of RNA-ligand interactions even in the case of a moving RNA structure. When applied to a data set of 17 RNA-ligand complexes, filtered out of the largest validation data set used for RNA-ligand docking so far, the approach is twice as successful as docking into an apo structure and still half as successful as redocking to the holo structure. The approach allows considering RNA movements of up to 6 Å rmsd and is based on a uniform and robust parametrization of the properties of the elastic potential grids, so that the approach is applicable to different RNA-ligand complex classes.

Published
2011
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