scholarly journals Seven quick tips for beginners in protein crystallography

2021 ◽  
Author(s):  
Katarzyna Kurpiewska ◽  
Tomasz Borowski
Keyword(s):  
Structural Biology ◽  
Structure Determination ◽  
Biological Function ◽  
Protein Crystallography ◽  
Structural Features ◽  
Trial And Error ◽  
Short Overview ◽  
Whole Process ◽  
Selection Of ◽  
Crystallization Structure

The aim of this brief review is to provide a roadmap for beginning crystallographers who have little or no experience in structural biology and yet are keen to produce protein crystals and analyze their 3D structures to understand their biological roles. To achieve this goal it is crucial to perform crystallization, structure determination, visualization and analysis of the protein’s structural features related to its biological function. Keeping that objective in mind, tips presented herein cover the most important steps in a crystallographic endeavor and present a selection of databases and software which can aid and accelerate the whole process. We hope that this short overview will help novices coming from different disciplines to navigate a protein crystallography project and, hopefully, allow avoiding some costly mistakes, even though being a crystallographer means learning by trial and error.

From classrooms to Centres: Mary and David Medd’s contribution to postwar school design in Britain

2020 ◽  
Vol 24 (3) ◽  
pp. 251-264
Author(s):  
Paula Lacomba Montes ◽  
Alejandro Campos Uribe
Keyword(s):  
Great Britain ◽  
Design Process ◽  
School Design ◽  
Ministry Of Education ◽  
Learning Spaces ◽  
Close Collaboration ◽  
Innovative Strategies ◽  
Whole Process ◽  
Conventional School ◽  
Selection Of

This paper reports on the primary school design processes carried out around the 1940s in the County of Hertfordshire in Great Britain, which later evolved into innovative strategies developed by Mary and David Medd in the Ministry of Education from the late 1950s. The whole process, undertaken during more than three decades, reveals a way of breaking with the traditional spatial conception of a school. The survey of the period covered has allowed an in-depth understanding of how learning spaces could be transformed by challenging the conventional school model of closed rooms, suggesting a new way of understanding learning spaces as a group of Centres rather than classrooms. Historians have thoroughly shown the ample scope of this process, which involved many professionals, fostering a true cross-disciplinary endeavour where the curriculum and the learning spaces were developed in close collaboration. A selection of schools built in the county has been used to typologically analyse how architectural changes began to arise and later flourished at the Ministry of Education. The Medds had indeed a significant role through the development of a design process known as the Built-in variety and the Planning Ingredients. A couple of examples will clarify some of these strategies, revealing how the design of educational space could successfully respond to an active way of learning.

scholarly journals The quantum mitochondrion and optimal health

2016 ◽  
Vol 44 (4) ◽  
pp. 1101-1110 ◽  
Author(s):  
Alistair V.W. Nunn ◽  
Geoffrey W. Guy ◽  
Jimmy D. Bell
Keyword(s):  
Natural Selection ◽  
Energy Production ◽  
Healthy Aging ◽  
Evolutionary Process ◽  
Emergent Behaviour ◽  
Whole Process ◽  
Optimal Health ◽  
Response To Stress ◽  
Will Self ◽  
Selection Of

A sufficiently complex set of molecules, if subject to perturbation, will self-organize and show emergent behaviour. If such a system can take on information it will become subject to natural selection. This could explain how self-replicating molecules evolved into life and how intelligence arose. A pivotal step in this evolutionary process was of course the emergence of the eukaryote and the advent of the mitochondrion, which both enhanced energy production per cell and increased the ability to process, store and utilize information. Recent research suggest that from its inception life embraced quantum effects such as ‘tunnelling’ and ‘coherence’ while competition and stressful conditions provided a constant driver for natural selection. We believe that the biphasic adaptive response to stress described by hormesis–a process that captures information to enable adaptability, is central to this whole process. Critically, hormesis could improve mitochondrial quantum efficiency, improving the ATP/ROS ratio, whereas inflammation, which is tightly associated with the aging process, might do the opposite. This all suggests that to achieve optimal health and healthy aging, one has to sufficiently stress the system to ensure peak mitochondrial function, which itself could reflect selection of optimum efficiency at the quantum level.

Automated phase attribute-based picking applied to reflection seismics

Geophysics ◽  
2016 ◽  
Vol 81 (2) ◽  
pp. V141-V150 ◽  
Author(s):  
Emanuele Forte ◽  
Matteo Dossi ◽  
Michele Pipan ◽  
Anna Del Ben
Keyword(s):  
Signal To Noise Ratio ◽  
Phase Method ◽  
Data Sets ◽  
Reflection Seismic ◽  
Instantaneous Phase ◽  
Whole Process ◽  
Specific Analysis ◽  
Reflection Seismics ◽  
Selection Of ◽  
Energy Package

We have applied an attribute-based autopicking algorithm to reflection seismics with the aim of reducing the influence of the user’s subjectivity on the picking results and making the interpretation faster with respect to manual and semiautomated techniques. Our picking procedure uses the cosine of the instantaneous phase to automatically detect and mark as a horizon any recorded event characterized by lateral phase continuity. A patching procedure, which exploits horizon parallelism, can be used to connect consecutive horizons marking the same event but separated by noise-related gaps. The picking process marks all coherent events regardless of their reflection strength; therefore, a large number of independent horizons can be constructed. To facilitate interpretation, horizons marking different phases of the same reflection can be automatically grouped together and specific horizons from each reflection can be selected using different possible methods. In the phase method, the algorithm reconstructs the reflected wavelets by averaging the cosine of the instantaneous phase along each horizon. The resulting wavelets are then locally analyzed and confronted through crosscorrelation, allowing the recognition and selection of specific reflection phases. In case the reflected wavelets cannot be recovered due to shape-altering processing or a low signal-to-noise ratio, the energy method uses the reflection strength to group together subparallel horizons within the same energy package and to select those satisfying either energy or arrival time criteria. These methods can be applied automatically to all the picked horizons or to horizons individually selected by the interpreter for specific analysis. We show examples of application to 2D reflection seismic data sets in complex geologic and stratigraphic conditions, critically reviewing the performance of the whole process.

The Sizer-Dissector for Aneurysm Clip Selection: Technical Note

Neurosurgery ◽  
2002 ◽  
Vol 50 (3) ◽  
pp. 669-671 ◽  
Author(s):  
Steven L. Giannotta
Keyword(s):  
Technical Note ◽  
Trial And Error ◽  
Aneurysm Clip ◽  
Blade Length ◽  
Permanent Occlusion ◽  
The Wire ◽  
Selection Of

Abstract OBJECTIVE: Appropriate clip selection frequently becomes a matter of trial and error because of inadequate dissection of the pathway for each clip blade. To facilitate selection of the proper clip size, a series of dissectors have been designed that mimic the exact caliber of each category of Sugita clips. METHODS: Three lines of sizer-dissectors reflecting the wire size of the most commonly used Sugita clips were developed by attaching a single aneurysm clip blade to a rounded microdissector handle. Each sizer-dissector is scaled in millimeters and is available in straight and angled configurations. Once dissection is presumed to be complete, the device is passed through the pathway of the intended aneurysm clip blades, and the clip with the appropriate caliber and length for permanent occlusion is selected. RESULTS: During dissection and clip ligation of 83 aneurysms, the sizer-dissector was used to select the blade length in 16 lesions and the blade caliber in 5 lesions. There were no complications associated with deployment of the device. CONCLUSION: By use of the sizer-dissector before attempting clip placement, clip selection is facilitated, safety is enhanced, and clip wastage is reduced.

scholarly journals Optimization of Magnetic Properties of Magnetic Microwires by Post-Processing

Processes ◽  
2020 ◽  
Vol 8 (8) ◽  
pp. 1006
Author(s):  
Valentina Zhukova ◽  
Paula Corte-Leon ◽  
Lorena González-Legarreta ◽  
Ahmed Talaat ◽  
Juan Maria Blanco ◽  
...  
Keyword(s):  
Magnetic Properties ◽  
Chemical Composition ◽  
Hysteresis Loops ◽  
Structural Features ◽  
Post Processing ◽  
Soft Magnetic ◽  
Magnetic Microwires ◽  
Prepared State ◽  
Induced Magnetic Anisotropy ◽  
Selection Of

The influence of post-processing conditions on the magnetic properties of amorphous and nanocrystalline microwires has been thoroughly analyzed, paying attention to the influence of magnetoelastic, induced and magnetocrystalline anisotropies on the hysteresis loops of Fe-, Ni-, and Co-rich microwires. We showed that magnetic properties of glass-coated microwires can be tuned by the selection of appropriate chemical composition and geometry in as-prepared state or further considerably modified by appropriate post-processing, which consists of either annealing or glass-coated removal. Furthermore, stress-annealing or Joule heating can further effectively modify the magnetic properties of amorphous magnetic microwires owing to induced magnetic anisotropy. Devitrification of microwires can be useful for either magnetic softening or magnetic hardening of the microwires. Depending on the chemical composition of the metallic nucleus and on structural features (grain size, precipitating phases), nanocrystalline microwires can exhibit either soft magnetic properties or semi-hard magnetic properties. We demonstrated that the microwires with coercivities from 1 A/m to 40 kA/m can be prepared.

data a; * significance level; a=0.05; * variance of difference of two observations on the log scale; * sigmaW = within-subjects standard deviation; sigmaW=0.355; s=sqrt(2)*sigmaW; * total number of subjects (needs to be a multiple of 2); n=58; * error degrees of freedom for AB/BA cross-over with n subjects in total; n2=n-2; * ratio = mu_T/mu_R; ratio=1.00; run; data b; set a; * calculate power; t1=tinv(1-a,n-2); t2=-t1; nc1=(sqrt(n))*((log(ratio)-log(0.8))/s); nc2=(sqrt(n))*((log(ratio)-log(1.25))/s); df=(sqrt(n-2))*((nc1-nc2)/(2*t1)); prob1=probt(t1,df,nc1); prob2=probt(t2,df,nc2); answer=prob2-prob1; power=answer*100; run; proc print data=b; run; As an example of using this SAS code, suppose µ = 1, σ = 0.355, α = 0.05 and n = 58. The power (as a percentage) is calculated as 90.4. The required number of subjects to achieve a given power can easily be obtained by trial and error using a selection of values of n. An alternative approach is to use trial and error directly on the sample size n for a given power. For more on this see Phillips (1990) and Diletti et al. (1991), for example. 7.4 Individual bioequivalence As noted in Section 7.1, individual bioequivalence (IBE) is a criterion for deciding if a patient who is currently being treated with R can be

2003 ◽  
pp. 362-362
Keyword(s):  
Standard Deviation ◽  
Sample Size ◽  
Degrees Of Freedom ◽  
Trial And Error ◽  
Significance Level ◽  
Individual Bioequivalence ◽  
Alternative Approach ◽  
Within Subjects ◽  
Log Ratio ◽  
Selection Of

scholarly journals Protein microcrystallography using synchrotron radiation

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 529-539 ◽  
Author(s):  
Masaki Yamamoto ◽  
Kunio Hirata ◽  
Keitaro Yamashita ◽  
Kazuya Hasegawa ◽  
Go Ueno ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structural Features ◽  
X Ray ◽  
Data Collection Strategy ◽  
Technological Developments ◽  
Novel Method

The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as smallin mesocrystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

scholarly journals Effect of Different Local Vibration Frequencies on the Multiscale Regularity of Plantar Skin Blood Flow

Entropy ◽  
2020 ◽  
Vol 22 (11) ◽  
pp. 1288
Author(s):  
Fuyuan Liao ◽  
Keying Zhang ◽  
Lingling Zhou ◽  
Yanni Chen ◽  
Jeannette Elliott ◽  
...  
Keyword(s):  
Blood Flow ◽  
Skin Blood Flow ◽  
Metatarsal Head ◽  
Structural Features ◽  
Frequency Interval ◽  
Local Vibration ◽  
First Metatarsal ◽  
Before And After ◽  
The Right ◽  
Selection Of

Local vibration has shown promise in improving skin blood flow (SBF). However, there is no consensus on the selection of the best vibration frequency. An important reason may be that previous studies utilized time- and frequency-domain parameters to characterize vibration-induced SBF responses. These parameters are unable to characterize the structural features of the SBF response to local vibrations, thus contributing to the inconsistent findings seen in vibration research. The objective of this study was to provide evidence that nonlinear dynamics of SBF responses would be an important aspect for assessing the effect of local vibration on SBF. Local vibrations at 100 Hz, 35 Hz, and 0 Hz (sham vibration) with an amplitude of 1 mm were randomly applied to the right first metatarsal head of 12 healthy participants for 10 min. SBF at the same site was measured for 10 min before and after local vibration. The degree of regularity of SBF was quantified using a multiscale sample entropy algorithm. The results showed that 100 Hz vibration significantly increased multiscale regularity of SBF but 35 Hz and 0 Hz (sham vibration) did not. The significant increase of regularity of SBF after 100 Hz vibration was mainly attributed to increased regularity of SBF oscillations within the frequency interval at 0.0095–0.15 Hz. These findings support the use of multiscale regularity to assess effectiveness of local vibration on improving skin blood flow.

Mobile Speech Recognition

2009 ◽  
pp. 3468-3493
Author(s):  
Dirk Schnelle
Keyword(s):  
Speech Recognition ◽  
Business Case ◽  
Embedded Devices ◽  
Short Overview ◽  
Enterprise Applications ◽  
Selection Of ◽  
Current Business

This chapter gives an overview of the main architectures for enabling speech recognition on embedded devices. Starting with a short overview of speech recognition; an overview of the main challenges for the use on embedded devices is given. Each of the architectures has its own characteristic problems and features. This chapter gives a solid basis for the selection of an architecture that is most appropriate for the current business case in enterprise applications.

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