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Single particle analysis

Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, making interpretation difficult. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a three-dimensional reconstruction of the particle. Using cryo-electron microscopy it has become possible to generate reconstructions with sub-nanometer, near-atomic resolution resolution first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well. == Techniques == Single particle analysis can be done on both negatively stained and vitreous ice-embedded transmission electron cryomicroscopy (CryoTEM) samples. Single particle analysis methods are, in general, reliant on the sample being homogeneous, although techniques for dealing with conformational heterogeneity are being developed. Images (micrographs) are taken with an electron microscope using charged-coupled device (CCD) detectors coupled to a phosphorescent layer (in the past, they were instead collected on film and digitized using high-quality scanners). The image processing is carried out using specialized software programs, often run on multi-processor computer clusters. Depending on the sample or the desired results, various steps of two- or three-dimensional processing can be done. === Alignment and classification === Biological samples, and especially samples embedded in thin vitreous ice, are highly radiation sensitive, thus only low electron doses can be used to image the sample. This low dose, as well as variations in the metal stain used (if used) means images have high noise relative to the signal given by the particle being observed. By aligning several similar images to each other so they are in register and then averaging them, an image with higher signal-to-noise ratio can be obtained. As the noise is mostly randomly distributed and the underlying image features constant, by averaging the intensity of each pixel over several images only the constant features are reinforced. Typically, the optimal alignment (a translation and an in-plane rotation) to map one image onto another is calculated by cross-correlation. However, a micrograph often contains particles in multiple different orientations and/or conformations, and so to get more representative image averages, a method is required to group similar particle images together into multiple sets. This is normally carried out using one of several data analysis and image classification algorithms, such as multi-variate statistical analysis and hierarchical ascendant classification, or k-means clustering. Often data sets of tens of thousands of particle images are used, and to reach an optimal solution an iterative procedure of alignment and classification is used, whereby strong image averages produced by classification are used as reference images for a subsequent alignment of the whole data set. === Image filtering === Image filtering (band-pass filtering) is often used to reduce the influence of high and/or low spatial frequency information in the images, which can affect the results of the alignment and classification procedures. This is particularly useful in negative stain images. The algorithms make use of fast Fourier transforms (FFT), often employing Gaussian shaped soft-edged masks in reciprocal space to suppress certain frequency ranges. High-pass filters remove low spatial frequencies (such as ramp or gradient effects), leaving the higher frequencies intact. Low-pass filters remove high spatial frequency features and have a blurring effect on fine details. === Contrast transfer function === Due to the nature of image formation in the electron microscope, bright-field TEM images are obtained using significant underfocus. This, along with features inherent in the microscope's lens system, creates blurring of the collected images visible as a point spread function. The combined effects of the imaging conditions are known as the contrast transfer function (CTF), and can be approximated mathematically as a function in reciprocal space. Specialized image processing techniques such as phase flipping and amplitude correction / Wiener filtering can (at least partially) correct for the CTF, and allow high resolution reconstructions. === Three-dimensional reconstruction === Transmission electron microscopy images are projections of the object showing the distribution of density through the object, similar to medical X-rays. By making use of the projection-slice theorem a three-dimensional reconstruction of the object can be generated by combining many images (2D projections) of the object taken from a range of viewing angles. Proteins in vitreous ice ideally adopt a random distribution of orientations (or viewing angles), allowing a fairly isotropic reconstruction if a large number of particle images are used. This contrasts with electron tomography, where the viewing angles are limited due to the geometry of the sample/imaging set up, giving an anisotropic reconstruction. Filtered back projection is a commonly used method of generating 3D reconstructions in single particle analysis, although many alternative algorithms exist. Before a reconstruction can be made, the orientation of the object in each image needs to be estimated. Several methods have been developed to work out the relative Euler angles of each image. Some are based on common lines (common 1D projections and sinograms), others use iterative projection matching algorithms. The latter works by beginning with a simple, low resolution 3D starting model and compares the experimental images to projections of the model and creates a new 3D to bootstrap towards a solution. Methods are also available for making 3D reconstructions of helical samples (such as tobacco mosaic virus), taking advantage of the inherent helical symmetry. Both real space methods (treating sections of the helix as single particles) and reciprocal space methods (using diffraction patterns) can be used for these samples. === Tilt methods === The specimen stage of the microscope can be tilted (typically along a single axis), allowing the single particle technique known as random conical tilt. An area of the specimen is imaged at both zero and at high angle (~60-70 degrees) tilts, or in the case of the related method of orthogonal tilt reconstruction, +45 and −45 degrees. Pairs of particles corresponding to the same object at two different tilts (tilt pairs) are selected, and by following the parameters used in subsequent alignment and classification steps a three-dimensional reconstruction can be generated relatively easily. This is because the viewing angle (defined as three Euler angles) of each particle is known from the tilt geometry. 3D reconstructions from random conical tilt suffer from missing information resulting from a restricted range of orientations. Known as the missing cone (due to the shape in reciprocal space), this causes distortions in the 3D maps. However, the missing cone problem can often be overcome by combining several tilt reconstructions. Tilt methods are best suited to negatively stained samples, and can be used for particles that adsorb to the carbon support film in preferred orientations. The phenomenon known as charging or beam-induced movement makes collecting high-tilt images of samples in vitreous ice challenging. === Map visualization and fitting === Various software programs are available that allow viewing the 3D maps. These often enable the user to manually dock in protein coordinates (structures from X-ray crystallography, NMR, or a computational model such as one found in the AlphaFold Protein Structure Database) of subunits into the electron density. Several programs can also fit subunits computationally; as of the 2020s using these programs tend to produce better accuracy than manual docking because they can perform labor-intensive tasks such as: The scale of SPA-derived maps depends on knowing the pixel size (angstorms per pixel), which is not always accurate. Programs can automatically correct for this difference by using coordinate data or by using knowledge of chemical bonds. Many proteins are made up of several roughly rigid protein domains linked by flexible parts. Pre-existing coordinate data, whether experimental or computational, may not exactly match the inter-domain positioning of the cyro-EM map. Modern programs can automatically "chop" pre-existing coordinate data into individual domains and fit them in individually. For higher-resolution structures, it is pos
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Foreign key

A foreign key is a set of attributes in a table that refers to the primary key of another table, linking these two tables. In the context of relational databases, a foreign key is subject to an inclusion dependency constraint that the tuples consisting of the foreign key attributes in one relation, R, must also exist in some other (not necessarily distinct) relation, S; furthermore that those attributes must also be a candidate key in S. In other words, a foreign key is a set of attributes that references a candidate key. For example, a table called TEAM may have an attribute, MEMBER_NAME, which is a foreign key referencing a candidate key, PERSON_NAME, in the PERSON table. Since MEMBER_NAME is a foreign key, any value existing as the name of a member in TEAM must also exist as a person's name in the PERSON table; in other words, every member of a TEAM is also a PERSON. == Summary == The table containing the foreign key is called the child table, and the table containing the candidate key is called the referenced or parent table. In database relational modeling and implementation, a candidate key is a set of zero or more attributes, the values of which are guaranteed to be unique for each tuple (row) in a relation. The value or combination of values of candidate key attributes for any tuple cannot be duplicated for any other tuple in that relation. Since the purpose of the foreign key is to identify a particular row of referenced table, it is generally required that the foreign key is equal to the candidate key in some row of the primary table, or else have no value (the NULL value.). This rule is called a referential integrity constraint between the two tables. Because violations of these constraints can be the source of many database problems, most database management systems provide mechanisms to ensure that every non-null foreign key corresponds to a row of the referenced table. For example, consider a database with two tables: a CUSTOMER table that includes all customer data and an ORDER table that includes all customer orders. Suppose the business requires that each order must refer to a single customer. To reflect this in the database, a foreign key column is added to the ORDER table (e.g., CUSTOMERID), which references the primary key of CUSTOMER (e.g. ID). Because the primary key of a table must be unique, and because CUSTOMERID only contains values from that primary key field, we may assume that, when it has a value, CUSTOMERID will identify the particular customer which placed the order. However, this can no longer be assumed if the ORDER table is not kept up to date when rows of the CUSTOMER table are deleted or the ID column altered, and working with these tables may become more difficult. Many real world databases work around this problem by 'inactivating' rather than physically deleting master table foreign keys, or by complex update programs that modify all references to a foreign key when a change is needed. Foreign keys play an essential role in database design. One important part of database design is making sure that relationships between real-world entities are reflected in the database by references, using foreign keys to refer from one table to another. Another important part of database design is database normalization, in which tables are broken apart and foreign keys make it possible for them to be reconstructed. Multiple rows in the referencing (or child) table may refer to the same row in the referenced (or parent) table. In this case, the relationship between the two tables is called a one to many relationship between the referencing table and the referenced table. In addition, the child and parent table may, in fact, be the same table, i.e. the foreign key refers back to the same table. Such a foreign key is known in SQL:2003 as a self-referencing or recursive foreign key. In database management systems, this is often accomplished by linking a first and second reference to the same table. A table may have multiple foreign keys, and each foreign key can have a different parent table. Each foreign key is enforced independently by the database system. Therefore, cascading relationships between tables can be established using foreign keys. A foreign key is defined as an attribute or set of attributes in a relation whose values match a primary key in another relation. The syntax to add such a constraint to an existing table is defined in SQL:2003 as shown below. Omitting the column list in the REFERENCES clause implies that the foreign key shall reference the primary key of the referenced table. Likewise, foreign keys can be defined as part of the CREATE TABLE SQL statement. If the foreign key is a single column only, the column can be marked as such using the following syntax: Foreign keys can be defined with a stored procedure statement. child_table: the name of the table or view that contains the foreign key to be defined. parent_table: the name of the table or view that has the primary key to which the foreign key applies. The primary key must already be defined. col3 and col4: the name of the columns that make up the foreign key. The foreign key must have at least one column and at most eight columns. == Referential actions == Because the database management system enforces referential constraints, it must ensure data integrity if rows in a referenced table are to be deleted (or updated). If dependent rows in referencing tables still exist, those references have to be considered. SQL:2003 specifies 5 different referential actions that shall take place in such occurrences: CASCADE RESTRICT NO ACTION SET NULL SET DEFAULT === CASCADE === Whenever rows in the parent (referenced) table are deleted (or updated), the respective rows of the child (referencing) table with a matching foreign key column will be deleted (or updated) as well. This is called a cascade delete (or update). === RESTRICT === A value cannot be updated or deleted when a row exists in a referencing or child table that references the value in the referenced table. Similarly, a row cannot be deleted as long as there is a reference to it from a referencing or child table. To understand RESTRICT (and CASCADE) better, it may be helpful to notice the following difference, which might not be immediately clear. The referential action CASCADE modifies the "behavior" of the (child) table itself where the word CASCADE is used. For example, ON DELETE CASCADE effectively says "When the referenced row is deleted from the other table (master table), then delete also from me". However, the referential action RESTRICT modifies the "behavior" of the master table, not the child table, although the word RESTRICT appears in the child table and not in the master table! So, ON DELETE RESTRICT effectively says: "When someone tries to delete the row from the other table (master table), prevent deletion from that other table (and of course, also don't delete from me, but that's not the main point here)." RESTRICT is not supported by Microsoft SQL 2012 and earlier. === NO ACTION === NO ACTION and RESTRICT are very much alike. The main difference between NO ACTION and RESTRICT is that with NO ACTION the referential integrity check is done after trying to alter the table. RESTRICT does the check before trying to execute the UPDATE or DELETE statement. Both referential actions act the same if the referential integrity check fails: the UPDATE or DELETE statement will result in an error. In other words, when an UPDATE or DELETE statement is executed on the referenced table using the referential action NO ACTION, the DBMS verifies at the end of the statement execution that none of the referential relationships are violated. This is different from RESTRICT, which assumes at the outset that the operation will violate the constraint. Using NO ACTION, the triggers or the semantics of the statement itself may yield an end state in which no foreign key relationships are violated by the time the constraint is finally checked, thus allowing the statement to complete successfully. === SET NULL, SET DEFAULT === In general, the action taken by the DBMS for SET NULL or SET DEFAULT is the same for both ON DELETE or ON UPDATE: the value of the affected referencing attributes is changed to NULL for SET NULL, and to the specified default value for SET DEFAULT. === Triggers === Referential actions are generally implemented as implied triggers (i.e. triggers with system-generated names, often hidden.) As such, they are subject to the same limitations as user-defined triggers, and their order of execution relative to other triggers may need to be considered; in some cases it may become necessary to replace the referential action with its equivalent user-defined trigger to ensure proper execution order, or to work around mutating-table limitations. Another important limitation appears with transaction isolation: your changes to a row may not be able to fully cascade because the row is ref
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Czekanowski distance

The Czekanowski distance (sometimes shortened as CZD) is a per-pixel quality metric that estimates quality or similarity by measuring differences between pixels. Because it compares vectors with strictly non-negative elements, it is often used to compare colored images, as color values cannot be negative. This different approach has a better correlation with subjective quality assessment than PSNR. == Definition == Androutsos et al. give the Czekanowski coefficient as follows: d z ( i , j ) = 1 − 2 ∑ k = 1 p min ( x i k , x j k ) ∑ k = 1 p ( x i k + x j k ) {\displaystyle d_{z}(i,j)=1-{\frac {2\sum _{k=1}^{p}{\text{min}}(x_{ik},\ x_{jk})}{\sum _{k=1}^{p}(x_{ik}+x_{jk})}}} Where a pixel x i {\displaystyle x_{i}} is being compared to a pixel x j {\displaystyle x_{j}} on the k-th band of color – usually one for each of red, green and blue. For a pixel matrix of size M × N {\displaystyle M\times N} , the Czekanowski coefficient can be used in an arithmetic mean spanning all pixels to calculate the Czekanowski distance as follows: 1 M N ∑ i = 0 M − 1 ∑ j = 0 N − 1 ( 1 − 2 ∑ k = 1 3 min ( A k ( i , j ) , B k ( i , j ) ) ∑ k = 1 3 ( A k ( i , j ) + B k ( i , j ) ) ) {\displaystyle {\frac {1}{MN}}\sum _{i=0}^{M-1}\sum _{j=0}^{N-1}{\begin{pmatrix}1-{\frac {2\sum _{k=1}^{3}{\text{min}}(A_{k}(i,j),\ B_{k}(i,j))}{\sum _{k=1}^{3}(A_{k}(i,j)+B_{k}(i,j))}}\end{pmatrix}}} Where A k ( i , j ) {\displaystyle A_{k}(i,j)} is the (i, j)-th pixel of the k-th band of a color image and, similarly, B k ( i , j ) {\displaystyle B_{k}(i,j)} is the pixel that it is being compared to. == Uses == In the context of image forensics – for example, detecting if an image has been manipulated –, Rocha et al. report the Czekanowski distance is a popular choice for Color Filter Array (CFA) identification.
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New York Institute of Technology Computer Graphics Lab

The New York Institute of Technology Computer Graphics Lab is a computer lab located at the New York Institute of Technology (NYIT), founded by Alexander Schure. It was originally located at the "pink building" on the NYIT campus. It has played an important role in the history of computer graphics and animation, as founders of Pixar and Lucasfilm Limited, including Turing Award winners Edwin Catmull and Patrick Hanrahan, began their research there. It is the birthplace of entirely 3D CGI films. The lab was initially founded to produce a short high-quality feature film with the project name of The Works. The feature, which was never completed, was a 90-minute feature that was to be the first entirely computer-generated CGI movie. Production mainly focused around DEC PDP and VAX machines. Many of the original CGL team now form the elite of the CG and computer world with members going on to Silicon Graphics, Microsoft, Cisco, NVIDIA and others, including Pixar president, co-founder and Turing laureate Ed Catmull, Pixar co-founder and Microsoft graphics fellow Alvy Ray Smith, Pixar co-founder Ralph Guggenheim, Walt Disney Animation Studios chief scientist Lance Williams, Netscape and Silicon Graphics founder Jim Clark, Tableau co-founder and Turing laureate Pat Hanrahan, Microsoft graphics fellow Jim Blinn, Thad Beier, Oscar and Bafta nominee Jacques Stroweis, Andrew Glassner, and Tom Brigham. Systems programmer Bruce Perens went on to co-found the Open Source Initiative. Researchers at the New York Institute of Technology Computer Graphics Lab created the tools that made entirely 3D CGI films possible. Among NYIT CG Lab's many innovations was an eight-bit paint system to ease computer animation. NYIT CG Lab was regarded as the top computer animation research and development group in the world during the late 70s and early 80s. == The 21st century == The lab is presently located at NYIT's Long Island campus, and NYIT currently offers a Ph.D. program in Computer Science.
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SemEval

SemEval (Semantic Evaluation) is an ongoing series of evaluations of computational semantic analysis systems; it evolved from the Senseval word sense evaluation series. The evaluations are intended to explore the nature of meaning in language. While meaning is intuitive to humans, transferring those intuitions to computational analysis has proved elusive. This series of evaluations provides a mechanism to characterize in more precise terms exactly what is necessary to compute in meaning. As such, the evaluations provide an emergent mechanism to identify the problems and solutions for computations with meaning. These exercises have evolved to articulate more of the dimensions that are involved in our use of language. They began with apparently simple attempts to identify word senses computationally. They have evolved to investigate the interrelationships among the elements in a sentence (e.g., semantic role labeling), relations between sentences (e.g., coreference), and the nature of what we are saying (semantic relations and sentiment analysis). The purpose of the SemEval and Senseval exercises is to evaluate semantic analysis systems. "Semantic Analysis" refers to a formal analysis of meaning, and "computational" refer to approaches that in principle support effective implementation. The first three evaluations, Senseval-1 through Senseval-3, were focused on word sense disambiguation (WSD), each time growing in the number of languages offered in the tasks and in the number of participating teams. Beginning with the fourth workshop, SemEval-2007 (SemEval-1), the nature of the tasks evolved to include semantic analysis tasks outside of word sense disambiguation. Triggered by the conception of the SEM conference, the SemEval community had decided to hold the evaluation workshops yearly in association with the SEM conference. It was also the decision that not every evaluation task will be run every year, e.g. none of the WSD tasks were included in the SemEval-2012 workshop. == History == === Early evaluation of algorithms for word sense disambiguation === From the earliest days, assessing the quality of word sense disambiguation algorithms had been primarily a matter of intrinsic evaluation, and “almost no attempts had been made to evaluate embedded WSD components”. Only very recently (2006) had extrinsic evaluations begun to provide some evidence for the value of WSD in end-user applications. Until 1990 or so, discussions of the sense disambiguation task focused mainly on illustrative examples rather than comprehensive evaluation. The early 1990s saw the beginnings of more systematic and rigorous intrinsic evaluations, including more formal experimentation on small sets of ambiguous words. === Senseval to SemEval === In April 1997, Martha Palmer and Marc Light organized a workshop entitled Tagging with Lexical Semantics: Why, What, and How? in conjunction with the Conference on Applied Natural Language Processing. At the time, there was a clear recognition that manually annotated corpora had revolutionized other areas of NLP, such as part-of-speech tagging and parsing, and that corpus-driven approaches had the potential to revolutionize automatic semantic analysis as well. Kilgarriff recalled that there was "a high degree of consensus that the field needed evaluation", and several practical proposals by Resnik and Yarowsky kicked off a discussion that led to the creation of the Senseval evaluation exercises. === SemEval's 3, 2 or 1 year(s) cycle === After SemEval-2010, many participants feel that the 3-year cycle is a long wait. Many other shared tasks such as Conference on Natural Language Learning (CoNLL) and Recognizing Textual Entailments (RTE) run annually. For this reason, the SemEval coordinators gave the opportunity for task organizers to choose between a 2-year or a 3-year cycle. The SemEval community favored the 3-year cycle. Although the votes within the SemEval community favored a 3-year cycle, organizers and coordinators had settled to split the SemEval task into 2 evaluation workshops. This was triggered by the introduction of the new SEM conference. The SemEval organizers thought it would be appropriate to associate our event with the SEM conference and collocate the SemEval workshop with the SEM conference. The organizers got very positive responses (from the task coordinators/organizers and participants) about the association with the yearly SEM, and 8 tasks were willing to switch to 2012. Thus was born SemEval-2012 and SemEval-2013. The current plan is to switch to a yearly SemEval schedule to associate it with the SEM conference but not every task needs to run every year. ==== List of Senseval and SemEval Workshops ==== Senseval-1 took place in the summer of 1998 for English, French, and Italian, culminating in a workshop held at Herstmonceux Castle, Sussex, England on September 2–4. Senseval-2 took place in the summer of 2001, and was followed by a workshop held in July 2001 in Toulouse, in conjunction with ACL 2001. Senseval-2 included tasks for Basque, Chinese, Czech, Danish, Dutch, English, Estonian, Italian, Japanese, Korean, Spanish and Swedish. Senseval-3 took place in March–April 2004, followed by a workshop held in July 2004 in Barcelona, in conjunction with ACL 2004. Senseval-3 included 14 different tasks for core word sense disambiguation, as well as identification of semantic roles, multilingual annotations, logic forms, subcategorization acquisition. SemEval-2007 (Senseval-4) took place in 2007, followed by a workshop held in conjunction with ACL in Prague. SemEval-2007 included 18 different tasks targeting the evaluation of systems for the semantic analysis of text. A special issue of Language Resources and Evaluation is devoted to the result. SemEval-2010 took place in 2010, followed by a workshop held in conjunction with ACL in Uppsala. SemEval-2010 included 18 different tasks targeting the evaluation of semantic analysis systems. SemEval-2012 took place in 2012; it was associated with the new SEM, First Joint Conference on Lexical and Computational Semantics, and co-located with NAACL, Montreal, Canada. SemEval-2012 included 8 different tasks targeting at evaluating computational semantic systems. However, there was no WSD task involved in SemEval-2012, the WSD related tasks were scheduled in the upcoming SemEval-2013. SemEval-2013 was associated with NAACL 2013, North American Association of Computational Linguistics, Georgia, USA and took place in 2013. It included 13 different tasks targeting at evaluating computational semantic systems. SemEval-2014 took place in 2014. It was co-located with COLING 2014, 25th International Conference on Computational Linguistics and SEM 2014, Second Joint Conference on Lexical and Computational Semantics, Dublin, Ireland. There were 10 different tasks in SemEval-2014 evaluating various computational semantic systems. SemEval-2015 took place in 2015. It was co-located with NAACL-HLT 2015, 2015 Conference of the North American Chapter of the Association for Computational Linguistics – Human Language Technologies and SEM 2015, Third Joint Conference on Lexical and Computational Semantics, Denver, USA. There were 17 different tasks in SemEval-2015 evaluating various computational semantic systems. == SemEval Workshop framework == The framework of the SemEval/Senseval evaluation workshops emulates the Message Understanding Conferences (MUCs) and other evaluation workshops ran by ARPA (Advanced Research Projects Agency, renamed the Defense Advanced Research Projects Agency (DARPA)). Stages of SemEval/Senseval evaluation workshops Firstly, all likely participants were invited to express their interest and participate in the exercise design. A timetable towards a final workshop was worked out. A plan for selecting evaluation materials was agreed. 'Gold standards' for the individual tasks were acquired, often human annotators were considered as a gold standard to measure precision and recall scores of computer systems. These 'gold standards' are what the computational systems strive towards. In WSD tasks, human annotators were set on the task of generating a set of correct WSD answers (i.e. the correct sense for a given word in a given context) The gold standard materials, without answers, were released to participants, who then had a short time to run their programs over them and return their sets of answers to the organizers. The organizers then scored the answers and the scores were announced and discussed at a workshop. == Semantic evaluation tasks == Senseval-1 & Senseval-2 focused on evaluation WSD systems on major languages that were available corpus and computerized dictionary. Senseval-3 looked beyond the lexemes and started to evaluate systems that looked into wider areas of semantics, such as Semantic Roles (technically known as Theta roles in formal semantics), Logic Form Transformation (commonly semantics of phrases, clauses or sentences were represented
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Security information management

Security information management (SIM) is an information security industry term for the collection of data such as log files into a central repository for trend analysis. == Overview == SIM products generally are software agents running on the computer systems that are monitored. The recorded log information is then sent to a centralized server that acts as a "security console". The console typically displays reports, charts, and graphs of that information, often in real time. Some software agents can incorporate local filters to reduce and manipulate the data that they send to the server, although typically from a forensic point of view you would collect all audit and accounting logs to ensure you can recreate a security incident. The security console is monitored by an administrator who reviews the consolidated information and takes action in response to any alerts issued. The data that is sent to the server to be correlated and analyzed are normalized by the software agents into a common form, usually XML. Those data are then aggregated in order to reduce their overall size. == Terminology == The terminology can easily be mistaken as a reference to the whole aspect of protecting one's infrastructure from any computer security breach. Due to historic reasons of terminology evolution; SIM refers to just the part of information security which consists of discovery of 'bad behavior' or policy violations by using data collection techniques. The term commonly used to represent an entire security infrastructure that protects an environment is commonly called information security management (InfoSec). Security information management is also referred to as log management and is different from SEM (security event management), but makes up a portion of a SIEM (security information and event management) solution. == Regulatory compliance == Security information management systems support compliance with regulatory frameworks that require centralized collection and analysis of security data. The Health Insurance Portability and Accountability Act (HIPAA) Security Rule requires covered entities to implement audit controls that record and examine activity in information systems containing electronic protected health information (45 CFR 164.312(b))."45 CFR § 164.312 - Technical safeguards". Legal Information Institute. Retrieved April 1, 2026. SIM platforms aggregate these audit records to support the required regular review of information system activity records (45 CFR 164.308(a)(1)(ii)(D)). The December 2024 HIPAA Security Rule NPRM proposed requiring regulated entities to deploy automated systems capable of monitoring and recording access to ePHI, including the ability to detect unauthorized access attempts in near real-time."HIPAA Security Rule To Strengthen the Cybersecurity of Electronic Protected Health Information". Federal Register. January 6, 2025. Retrieved April 1, 2026. The Payment Card Industry Data Security Standard (PCI DSS) similarly requires centralized log management and daily review of security events (Requirements 10.4 and 10.6)."PCI DSS v4.0" (PDF). PCI Security Standards Council. March 2022. Retrieved April 1, 2026. NIST Special Publication 800-53 addresses security information management through the AU (Audit and Accountability) control family, which specifies requirements for audit event generation, content, storage, and analysis."NIST SP 800-53 Rev. 5: Security and Privacy Controls". National Institute of Standards and Technology. September 2020. Retrieved April 1, 2026.
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Adrozek

Adrozek is malware that injects fake ads into online search results. Microsoft announced the malware threat on 10 December 2020, and noted that many different browsers are affected, including Google Chrome, Microsoft Edge, Mozilla Firefox and Yandex Browser. The malware was first detected in May 2020 and, at its peak in August 2020, controlled over 30,000 devices a day. But during the December 2020 announcement, Microsoft claimed "hundreds of thousands" of infected devices worldwide between May and September 2020. According to Microsoft, if not detected and blocked, Adrozek adds browser extensions, modifies a specific DLL per target browser, and changes browser settings to insert additional, unauthorized ads into web pages, often on top of legitimate ads from search engines. For each user tricked into clicking on the fake ads, the scammers earn affiliate advertising dollars. The malware has been observed to extract device data and, in some cases, steal credentials, sending them to remote servers. Users may unintentionally install the malware because of a drive-by download, by visiting a tampered website, opening an e-mail attachment, or clicking on a deceptive link or a deceptive pop-up window. The main malware program is downloaded to the “Programs Files” folder using file names such as Audiolava.exe, QuickAudio.exe, and converter.exe. According to PC Magazine, a good way to avoid, or mitigate, infection by Adrozek is to keep browser and related software programs up to date.
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Data item

A data item describes an atomic state of a particular object concerning a specific property at a certain time point. A collection of data items for the same object at the same time forms an object instance (or table row). Any type of complex information can be broken down to elementary data items (atomic state). Data items are identified by object (o), property (p) and time (t), while the value (v) is a function of o, p and t: v = F(o,p,t). Values typically are represented by symbols like numbers, texts, images, sounds or videos. Values are not necessarily atomic. A value's complexity depends on the complexity of the property and time component. When looking at databases or XML files, the object is usually identified by an object name or other type of object identifier, which is part of the "data". Properties are defined as columns (table row), properties (object instance) or tags (XML). Often, time is not explicitly expressed and is an attribute applying to the complete data set. Other data collections provide time on the instance level (time series), column level, or even attribute/property level.
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Companion robot

A companion robot is a robot created to create real or apparent companionship for human beings. Target markets for companion robots include the elderly and single children. Companions robots are expected to communicate with non-experts in a natural and intuitive way. They offer a variety of functions, such as monitoring the home remotely, communicating with people, or waking people up in the morning. Their aim is to perform a wide array of tasks including educational functions, home security, diary duties, entertainment and message delivery services, etc. The idea of companionship with robots has already existed on science fictions of 1970s, like R2-D2. Starting from the late 20th century, companion robots became a reality, mostly as robotic pets. Besides entertainment purposes, interactive robots were also introduced as a personal service robot for elderly care around 2000. == Characteristics == Companion robots try to interact with users. They gather information about users based on their interactions and yield feedback. This procedure varies slightly based on their specific roles. For example, social-companion robots make simple conversations, while pet-companion robots mimic being real pets. == Types == Companion robots can perform a variety of tasks and they are produced in a specialized manner according to their purpose or target audience in order to increase convenience and end user satisfaction. === Social companion robots === Social companion robots are designed to provide companionship and be a solution for unwanted solitude. They often mimic adult human, child or pet behaviours appealing to the user base. Robots which are specifically devised for simple conversations, conveying emotions and respond to user feelings fall under this category. === Assistive companion robots === Assistive companion robots are aimed at people who require constant care because of age, disability or rehabilitation purposes. Such robots can help disadvantaged users with their daily tasks, act as reminders (e.g., for regular medication) and facilitate mobility in everyday actions. Assistive companion robots reduce the intensity of labour that should be performed by caretakers, nurses and legal guardians. === Educational companion robots === Educational companion robots perform tutorship for students, regardless of their ages, and can teach desired subjects with activities tailored for the user such as interactive assignments and games. Rather than replacing teachers and instructors, educational companion robots are aides to them. === Therapeutic companion robots === Designed for individuals coping with stress (PTSD in severe cases), anxiety and loneliness; therapeutic companion robots support users' emotional and mental wellbeing. Such robots can be utilized in hospitals and care facilities as well as dwellings where the distressed user may need the most help. Therapeutic companion robots bear a vast resemblance to assistive companion robots to the extent of being a branch of them; the nuance between these two types of companion robots is that the former is for long-term/lifetime usage while the latter is mostly for the duration of the therapy received by the user. === Pet companion robots === Pet companion robots are for individuals who seek an alternative to live pets as live animals demand a considerable amount of care and may not be eligible for people with allergies. These robots aim to be perfect imitations of a pet while diminishing the chore aspect of having one. === Entertainment companion robots === Entertainment companion robots are designed solely for entertainment and can provide numerous ways of entertainment, ranging from dancing to playing games with the user. People who would appreciate an individual to have fun with are the main audience of such products. === Personal assistant robots === Personal assistant robots help people with daily tasks, management, scheduling, reminding etc. Their area of activity can be offices as well as homes and public spaces. === Sex robots === Sex robots are anthropomorphic robotic sex dolls that have human-like movement or behavior, and some degree of artificial intelligence. As of 2026, although elaborately instrumented sex dolls have been created by a number of inventors, no fully animated sex robots yet exist. Simple devices have been created which can speak, make facial expressions, or respond to touch. There is controversy as to whether developing them would be morally justifiable. In 2015, robot ethicist Kathleen Richardson called for a ban on the creation of anthropomorphic sex robots with concerns about normalizing relationships with machines and reinforcing female dehumanization. Questions about their ethics, effects, and possible legal regulations have been discussed since then. == Examples == There are several companion robot prototypes, and these include Paro, CompanionAble, and EmotiRob, among others. === Paro === Paro is a pet-type robot system developed by Japan's National Institute of Advanced Industrial Science and Technology (AIST). The robot, which looked like a small harp seal, was designed as a therapeutic tool for use in hospitals and nursing homes. The robot is programmed to cry for attention and respond to its name. Experiments showed that Paro facilitated elderly residents to communicate with each other, which led to psychological improvements. === CompanionAble === This robot is classified as an FP 7 EU project. It is built to "cooperate with Ambient Assistive Living environment". The autonomous device, which is also built to support the elderly, helps its owner interact with smart home environment as well as caregivers. The robot functions as a mobile friend, by which natural interaction is possible via speech and the touchscreen to detect and track people at home. === EmotiRob === EmotiRob is developed in a robotics project which is the continuity of the MAPH (Active Media For the Handicap) project in emotion synthesis. The aim of the project was to maintain emotional interaction with children. EmotiRob designed in a way that a child can hold it in a his/her arms and with which he/she could interact by talking to it, and then the robot would express itself through body postures or facial expressions. It has cognitive capabilities, which are further extended so that the robot can have a natural linguistic interaction with its owner through the DRAGON speech-recognition software developed by a company called NUANCE. Such interaction is expected to facilitate a child's cognitive development and develop new learning patterns. === LOVOT === Lovot is a Japanese company robot whose only purpose is "to make you happy". It features over 50 sensors that mimic the behavior of a human baby or small pet, a 360° camera with a microphone, the ability to distinguish humans from objects, neoteny eyes, and an internal warmth of 30° celsius. An interactive Lovot Café was opened in Japan October 3, 2020. === NICOBO === Nicobo was developed by Panasonic and was influenced by the loneliness of lockdowns created as a measure of the COVID-19 pandemic. It was designed to appear vulnerable, which creates empathy in its owners. Nicobo's name derives from the Japanese word for "smile". It wags its tail, engages in baby talk, and stays as a housemate. === Hyodol === Hyodol is an advanced care robot designed to support the elderly by reminding them to take their medications and monitoring their movements to keep their guardians informed. Additionally, this innovative robot can detect and respond to the emotional states of its elderly users, adding a layer of personalized care. Hyodol is designed with the appearance and speech style of a 7-year-old Korean grandchild, featuring a soft fabric exterior and user interaction methods such as striking the head or patting the back. It is equipped with various sensors and wireless communication technologies to collect and process data, supporting mobile apps and PC web monitoring systems for remote monitoring from anywhere. In South Korea, approximately 10,000 Hyodol robots are deployed to the homes of elderly individuals living alone, providing essential support and companionship. Local governments, including provincial and county offices, have embraced Hyodol as a solution to address social challenges stemming from the country's rapidly aging society.Furthermore, the robot is widely utilized in the treatment of dementia patients at a university hospital in Gangwon province. Hyodol was honored with the Mobile World Congress (MWC) Global Mobile Awards (GLOMO) in the "Best Mobile Innovation for Connected Health and Wellbeing" category on February 29, 2024. === Moxie === Moxie was a companion robot for autistic children developed by a company called Embodied. Although it had limited motion, it presented itself as a lifelike avatar. It was designed to help the children learn emotional cognition, using remotely hosted large language models to direct its respons
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Alerts.in.ua

alerts.in.ua is an online service that visualizes information about air alerts and other threats on the map of Ukraine. == History == The idea of the site appeared in the first weeks of the 2022 Russian invasion of Ukraine, during the development of other projects related to alerting the population about alarms. So, on March 2, 2022, the "Lviv Siren" bot was created, which reported on air alarms in Lviv on Twitter. Later, the idea arose to monitor alarms all over Ukraine and display them on a map. However, the lack of a single official source reporting alarms made this task much more difficult. On March 15, 2022, the Ajax Systems company announced the creation of the official Telegram channel "Air Alarm". This channel receives signals from the "Air Alarm" application and instantly publishes messages about the start and end of alarms in different regions of Ukraine. This immediately solved the problem with the source of information and gave impetus to the further implementation of the project. On March 22, 2022, the first version of the "Air Alarm Map" website was published, located on the war.ukrzen.in.ua domain. The map quickly gained popularity in social networks. It, like several other similar projects, began to be widely distributed by the mass media: Suspilne, Novyi Kanal, UNIAN, DW, Fakty ICTV, Vikna TV, Ukrainian Radio, STB, Espresso, dev.ua, itc.ua and state bodies: Center for Countering Disinformation at the National Security and Defense Council of Ukraine, Verkhovna Rada of Ukraine, Khmelnytska OVA, etc. On April 8, 2022, the site moved to the alerts.in.ua domain, where it is still available today. On August 25, 2022, the service began monitoring local official channels in addition to the main "Air Alarm". On September 11, 2022, the English version of the site was published. On March 22, 2023, its own Android application was published. The project is actively developing and has its own community. == Description == The main part of the site is a map of Ukraine, on which the regions where an air alert or other threats have been declared are highlighted in real time. As of October 16, 2022, 5 types of threats are supported: Air alarm. The threat of artillery fire. The threat of street fighting. Chemical threat. Nuclear threat. Additionally, based on media reports, information is published about other dangerous events, such as explosions, demining, etc. On the site, you can view the history of announced alarms with links to sources. Alarm statistics for different time periods are also available. For developers, there is an API that allows you to develop your own services based on information about declared alarms. The site is available in Ukrainian, English, Polish and Japanese. == Use == The map is used by: To monitor the situation in the country and the region. To illustrate the alarms announced in the mass media: TSN, Ukrainian truth, Channel 24, Suspilne, RBC Ukraine, Gromadske, Glavkom. As a map of alarms in mobile applications, there is Alarm and AirAlert. As an API for its services, including alternative alarm maps, Telegram, Viber channels, Discord bots, IoT projects, etc. == Statistics == 89.5% of users use the map from a mobile phone, 10% from a PC and 1% from a tablet. Top 6 countries by visit: Ukraine, United States, Poland, Germany, Great Britain and Japan . == Alternative projects == eMap was created by the developer Vadym Klymenko. AlarmMap is an online from the Ukrainian office of Agroprep. The official map of air alarms was developed by Ajax Systems together with the developer Artem Lemeshev, Stfalcon with the support of the Ministry of Statistics.
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Connection string

In computing, a connection string is a string that specifies information about a data source and the means of connecting to it. It is passed in code to an underlying driver or provider in order to initiate the connection. Whilst commonly used for a database connection, the data source could also be a spreadsheet or text file. The connection string may include attributes such as the name of the driver, server and database, as well as security information such as user name and password. == Examples == This example shows a PostgreSQL connection string for connecting to wikipedia.com with SSL and a connection timeout of 180 seconds: DRIVER={PostgreSQL Unicode};SERVER=www.wikipedia.com;SSL=true;SSLMode=require;DATABASE=wiki;UID=wikiuser;Connect Timeout=180;PWD=ashiknoor Users of Oracle databases can specify connection strings: on the command line (as in: sqlplus scott/tiger@connection_string ) via environment variables ($TWO_TASK in Unix-like environments; %TWO_TASK% in Microsoft Windows environments) in local configuration files (such as the default $ORACLE_HOME/network/admin.tnsnames.ora) in LDAP-capable directory services
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Multimedia database

A Multimedia database (MMDB) is a collection of related for multimedia data. The multimedia data include one or more primary media data types such as text, images, graphic objects (including drawings, sketches and illustrations) animation sequences, audio and video. A Multimedia Database Management System (MMDBMS) is a framework that manages different types of data potentially represented in a wide diversity of formats on a wide array of media sources. It provides support for multimedia data types, and facilitate for creation, storage, access, query and control of a multimedia database. == Contents of MMDB == A Multimedia Database (MMDB) hosts one or more multimedia data types (i.e. text, images, graphic objects, audio, video, animation sequences). These data types are broadly categorized into three classes: Static media (time-independent: image and graphic object). Dynamic media (time-dependent: audio, video and animation). Dimensional media(3D game and computer aided drafting programs). === Comparison of multimedia data types === Additionally, a Multimedia Database (MMDB) needs to manage additional information pertaining to the actual multimedia data. The information is about the following: Media data: the actual data representing an object. Media format data: information about the format of the media data after it goes through the acquisition, processing, and encoding phases. Media keyword data: the keyword descriptions, usually relating to the generation of the media data. Media feature data: content dependent data such as contain information about the distribution of colours, the kinds of textures and the different shapes present in an image. The last three types are called metadata as they describe several different aspects of the media data. The media keyword data and media feature data are used as indices for searching purpose. The media format data is used to present the retrieved information. == Requirements of Multimedia databases == Like the traditional databases, Multimedia databases should address the following requirements: Integration Data items do not need to be duplicated for different programs invocations Data independence Separate the database and the management from the application programs Concurrency control Allows concurrent transactions Persistence Data objects can be saved and re-used by different transactions and program invocations Privacy Access and authorization control Integrity control Ensures database consistency between transactions Recovery Failures of transactions should not affect the persistent data storage Query support Allows easy querying of multimedia data Multimedia databases should have the ability to uniformly query data (media data, textual data) represented in different formats and have the ability to simultaneously query different media sources and conduct classical database operations across them. (Query support) They should have the ability to retrieve media objects from a local storage device in a good manner. (Storage support) They should have the ability to take the response generated by a query and develop a presentation of that response in terms of audio-visual media and have the ability to deliver this presentation. (Presentation and delivery support) == Issues and challenges == Multimedia data consists of a variety of media formats or file representations including TIFF, BMP, PPT, IVUE, FPX, JPEG, MPEG, AVI, MID, WAV, DOC, GIF, EPS, PNG, etc. Because of restrictions on the conversion from one format to the other, the use of the data in a specific format has been limited as well. Usually, the data size of multimedia is large such as video; therefore, multimedia data often require a large storage. Multimedia database consume a lot of processing time, as well as bandwidth. Some multimedia data types such as video, audio, and animation sequences have temporal requirements that have implications on their storage, manipulation and presentation, but images, video and graphics data have special constraints in terms of their content. == Application areas == Examples of multimedia database application areas: Digital Libraries News-on-Demand Video-on-Demand Music database Geographic Information Systems (GIS) Telemedicine
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Adobe ImageReady

Adobe ImageReady was a bitmap graphics editor that was shipped with Adobe Photoshop for six years. It was available for Windows, Classic Mac OS and Mac OS X from 1998 to 2007. ImageReady was designed for web development and closely interacted with Photoshop. == Function == ImageReady was designed for web development rather than effects-intensive photo manipulation. To that end, ImageReady has specialized features such as animated GIF creation, image compression optimization, image slicing, adding rollover effects, and HTML generation. Photoshop versions with which ImageReady was released have an "Edit in ImageReady" button that enables editing of image directly in ImageReady. ImageReady, in turn, has an "Edit in Photoshop" button. ImageReady has strong resemblances to Photoshop; it can even use the same set of Photoshop filters. One set of tools that does not resemble the Photoshop tools, however, is the Image Map set of tools, indicated by a shape or arrow with a hand that varied depending upon the version. This toolbox has several features not found in Photoshop, including: Toggle Image Map Visibility and Toggle Slice Visibility tools: toggle between showing and hiding image maps and slices, respectively Export Animation Frames as Files option: saves all or specified frames for an alternate use, e.g., to e-mail slides for review Preview Document tool: provides a preview of rollover effects in ImageReady rather than previewing them in a browser Preview in Default Browser tool: previews the image in a browser, including any rollover or animation effects Edit in Photoshop button: opens the current image in Photoshop == History == Adobe ImageReady 1.0 was released in July 1998 as a standalone application. Version 2.0 was packaged with Photoshop 5.5, and the program was included with Photoshop through version 9.0 (CS2). Starting with Photoshop 7.0, Adobe changed the version numbers of ImageReady to match. With the release of the Creative Suite 3, ImageReady was discontinued. According to Adobe, ImageReady's most popular features were merged into Photoshop. (Even before discontinuation, some of ImageReady's web optimization functionality could be found in Photoshop's Save For Web & Devices tool.) Around the same time, Adobe purchased rival software developer Macromedia, whose application Fireworks had been a competitor to ImageReady.
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Kindara

Kindara is a femtech company headquartered in Colorado that develops apps that help women identify their fertile window. The products are used for women trying to get pregnant, or women who want to track their menstrual cycle for overall health. Their latest product, Priya Fertility and Ovulation Monitor, maximizes a woman's chance of getting pregnancy by identifying her most fertile days. == Overview == Kindara was founded in 2011 by husband-and-wife team Will Sacks and Kati Bicknell. The company launched its free mobile application in 2012. Kindara's mobile application allows women to track signs of fertility, such as basal body temperature, cervical fluid, and the position of the cervix to determine when ovulation is occurring. Kindara also sells a thermometer, Wink, which records basal body temperature and syncs automatically to the Kindara fertility application. In 2018, Kindara was acquired by the company Prima-Temp.
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Molecular graphics

Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically. == History == Prior to the use of computer graphics in representing molecular structure, Robert Corey and Linus Pauling developed a system for representing atoms or groups of atoms from hard wood on a scale of 1 inch = 1 angstrom connected by a clamping device to maintain the molecular configuration. These early models also established the CPK coloring scheme that is still used today to differentiate the different types of atoms in molecular models (e.g. carbon = black, oxygen = red, nitrogen = blue, etc). This early model was improved upon in 1966 by W.L. Koltun and are now known as Corey-Pauling-Koltun (CPK) models. The earliest efforts to produce models of molecular structure was done by Project MAC using wire-frame models displayed on a cathode ray tube in the mid 1960s. In 1965, Carroll Johnson distributed the Oak Ridge thermal ellipsoid plot (ORTEP) that visualized molecules as a ball-and-stick model with lines representing the bonds between atoms and ellipsoids to represent the probability of thermal motion. Thermal ellipsoid plots quickly became the de facto standard used in the display of X-ray crystallography data, and are still in wide use today. The first practical use of molecular graphics was a simple display of the protein myoglobin using a wireframe representation in 1966 by Cyrus Levinthal and Robert Langridge working at Project MAC. Among the milestones in high-performance molecular graphics was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres. Initially much of the technology concentrated on high-performance 3D graphics. During the 1970s, methods for displaying 3D graphics using cathode ray tubes were developed using continuous tone computer graphics in combination with electro-optic shutter viewing devices. The first devices used an active shutter 3D system, generating different perspective views for the left and right channel to provide the illusion of three-dimensional viewing. Stereoscopic viewing glasses were designed using lead lanthanum zirconate titanate (PLZT) ceramics as electronically controlled shutter elements. Active 3D glasses require batteries and work in concert with the display to actively change the presentation by the lenses to the wearer's eyes. Many modern 3D glasses use a passive, polarized 3D system that enables the wearer to visualize 3D effects based on their own perception. Passive 3D glasses are more common today since they are less expensive. The requirements of macromolecular crystallography also drove molecular graphics because the traditional techniques of physical model-building could not scale. The first two protein structures solved by molecular graphics without the aid of the Richards' Box were built with Stan Swanson's program FIT on the Vector General graphics display in the laboratory of Edgar Meyer at Texas A&M University: First Marge Legg in Al Cotton's lab at A&M solved a second, higher-resolution structure of staph. nuclease (1975) and then Jim Hogle solved the structure of monoclinic lysozyme in 1976. A full year passed before other graphics systems were used to replace the Richards' Box for modelling into density in 3-D. Alwyn Jones' FRODO program (and later "O") were developed to overlay the molecular electron density determined from X-ray crystallography and the hypothetical molecular structure. === Timeline === == Types == === Ball-and-stick models === In the ball-and-stick model, atoms are drawn as small sphered connected by rods representing the chemical bonds between them. === Space-filling models === In the space-filling model, atoms are drawn as solid spheres to suggest the space they occupy, in proportion to their van der Waals radii. Atoms that share a bond overlap with each other. === Surfaces === In some models, the surface of the molecule is approximated and shaded to represent a physical property of the molecule, such as electronic charge density. === Ribbon diagrams === Ribbon diagrams are schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the adjacent image. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and non-repetitive coils or loops as lines or thin tubes. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon.
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