Molecular graphics

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.

Inauthentic text

An inauthentic text is a computer-generated expository document meant to appear as genuine, but which is actually meaningless. Frequently they are created in order to be intermixed with genuine documents and thus manipulate the results of search engines, as with Spam blogs. They are also carried along in email in order to fool spam filters by giving the spam the superficial characteristics of legitimate text. Sometimes nonsensical documents are created with computer assistance for humorous effect, as with Dissociated press or Flarf poetry. They have also been used to challenge the veracity of a publication—MIT students submitted papers generated by a computer program called SCIgen to a conference, where they were initially accepted. This led the students to claim that the bar for submissions was too low. With the amount of computer generated text outpacing the ability of people to humans to curate it, there needs some means of distinguishing between the two. Yet automated approaches to determining absolutely whether a text is authentic or not face intrinsic challenges of semantics. Noam Chomsky coined the phrase "Colorless green ideas sleep furiously" giving an example of grammatically correct, but semantically incoherent sentence; some will point out that in certain contexts one could give this sentence (or any phrase) meaning. The first group to use the expression in this regard can be found below from Indiana University. Their work explains in detail an attempt to detect inauthentic texts and identify pernicious problems of inauthentic texts in cyberspace. The site has a means of submitting text that assesses, based on supervised learning, whether a corpus is inauthentic or not. Many users have submitted incorrect types of data and have correspondingly commented on the scores. This application is meant for a specific kind of data; therefore, submitting, say, an email, will not return a meaningful score.

Conceptions of Library and Information Science

Conceptions of Library and Information Science (CoLIS) is a series of conferences about historical, empirical and theoretical perspectives in Library and Information Science. == CoLIS conferences == CoLIS 1 1991 in Tampere, Finland CoLIS 2 1996 in Copenhagen, Denmark CoLIS 3 1999 in Dubrovnik, Croatia CoLIS 4 2002 in Seattle, US CoLIS 5 2005 in Glasgow, Scotland CoLIS 6 2007 in Borås, Sweden CoLIS 7 June 2010 in London, at City University London. CoLIS 8 August 19–22, 2013, in Copenhagen, Denmark, at The Royal School of Library and Information Science. CoLIS 9 June 27–29, 2016, in Uppsala, Sweden, at Uppsala University. CoLIS 10 June 16–19, 2019, in Ljubljana, Slovenia, Faculty of Arts CoLIS 11 May 29–June 1, 2022, in Oslo, Norway, Oslo Metropolitan University.

Novell File Reporter

Novell File Reporter (NFR) is software that allows network administrators to identify files stored on the network and generates reports regarding the size of individual files, file type, when files were last accessed, and where duplicates exist. Additionally, the File Reporter tracks storage volume capacity and usage. It is a component of the Novell File Management Suite. == How it works == Novell File Reporter examines and reports on terabytes of data via a central reporting engine (NFR Engine) and distributed agents (NFR Agents). The NFR Engine schedules the scans of file instances conducted by NFR Agents, processes and compiles the scans for reporting purposes, and provides report information to the user interface. In addition to the standard reports it can generate, the NFR Engine can also produce "trigger reports" in response to specific events (a server volume crossing a capacity threshold, for example). Accordingly, the NFR Engine monitors the data gathered by the NFR Agents in order to identify these "triggers." The NFR Engine when working in either eDirectory or Active Directory connects to the directory via a Directory Services Interface (DSI) and thus can monitor and check file permissions.

Higuchi dimension

In fractal geometry, the Higuchi dimension (or Higuchi fractal dimension (HFD)) is an approximate value for the box-counting dimension of the graph of a real-valued function or time series. This value is obtained via an algorithmic approximation so one also talks about the Higuchi method. It has many applications in science and engineering and has been applied to subjects like characterizing primary waves in seismograms, clinical neurophysiology and analyzing changes in the electroencephalogram in Alzheimer's disease. == Formulation of the method == The original formulation of the method is due to T. Higuchi. Given a time series X : { 1 , … , N } → R {\displaystyle X:\{1,\dots ,N\}\to \mathbb {R} } consisting of N {\displaystyle N} data points and a parameter k m a x ≥ 2 {\displaystyle k_{\mathrm {max} }\geq 2} the Higuchi Fractal dimension (HFD) of X {\displaystyle X} is calculated in the following way: For each k ∈ { 1 , … , k m a x } {\displaystyle k\in \{1,\dots ,k_{\mathrm {max} }}\} and m ∈ { 1 , … , k } {\displaystyle m\in \{1,\dots ,k}\} define the length L m ( k ) {\displaystyle L_{m}(k)} by L m ( k ) = N − 1 ⌊ N − m k ⌋ k 2 ∑ i = 1 ⌊ N − m k ⌋ | X N ( m + i k ) − X N ( m + ( i − 1 ) k ) | . {\displaystyle L_{m}(k)={\frac {N-1}{\lfloor {\frac {N-m}{k}}\rfloor k^{2}}}\sum _{i=1}^{\lfloor {\frac {N-m}{k}}\rfloor }|X_{N}(m+ik)-X_{N}(m+(i-1)k)|.} The length L ( k ) {\displaystyle L(k)} is defined by the average value of the k {\displaystyle k} lengths L 1 ( k ) , … , L k ( k ) {\displaystyle L_{1}(k),\dots ,L_{k}(k)} , L ( k ) = 1 k ∑ m = 1 k L m ( k ) . {\displaystyle L(k)={\frac {1}{k}}\sum _{m=1}^{k}L_{m}(k).} The slope of the best-fitting linear function through the data points { ( log ⁡ 1 k , log ⁡ L ( k ) ) } {\displaystyle \left\{\left(\log {\frac {1}{k}},\log L(k)\right)\right\}} is defined to be the Higuchi fractal dimension of the time-series X {\displaystyle X} . == Application to functions == For a real-valued function f : [ 0 , 1 ] → R {\displaystyle f:[0,1]\to \mathbb {R} } one can partition the unit interval [ 0 , 1 ] {\displaystyle [0,1]} into N {\displaystyle N} equidistantly intervals [ t j , t j + 1 ) {\displaystyle [t_{j},t_{j+1})} and apply the Higuchi algorithm to the times series X ( j ) = f ( t j ) {\displaystyle X(j)=f(t_{j})} . This results into the Higuchi fractal dimension of the function f {\displaystyle f} . It was shown that in this case the Higuchi method yields an approximation for the box-counting dimension of the graph of f {\displaystyle f} as it follows a geometrical approach (see Liehr & Massopust 2020). == Robustness and stability == Applications to fractional Brownian functions and the Weierstrass function reveal that the Higuchi fractal dimension can be close to the box-dimension. On the other hand, the method can be unstable in the case where the data X ( 1 ) , … , X ( N ) {\displaystyle X(1),\dots ,X(N)} are periodic or if subsets of it lie on a horizontal line (see Liehr & Massopust 2020).

Security switch

A security switch is a hardware device designed to protect computers, laptops, smartphones and similar devices from unauthorized access or operation, distinct from a virtual security switch which offers software protection. Security switches should be operated by an authorized user only; for this reason, it should be isolated from other devices, in order to prevent unauthorized access, and it should not be possible to bypass it, in order to prevent malicious manipulation. The primary purpose of a security switch is to provide protection against surveillance, eavesdropping, malware, spyware, and theft of digital devices. Unlike other protections or techniques, a security switch can provide protection even if security has already been breached, since it does not have any access from other components and is not accessible by software. It can additionally disconnect or block peripheral devices, and perform "man in the middle" operations. A security switch can be used for human presence detection since it can only be initiated by a human operator. It can also be used as a firewall. == Types == === Hardware kill switch === A hardware kill switch (HKS) is a physical switch that cuts the signal or power line to the device or disable the chip running them. == Examples == A cellphone is compromised by malicious software, and the device initiates video and audio recording. When the user activates the “prevent capture of audio/video” mode of the security switch, that either physically disconnects or cut the power to the microphone and the camera, which stops the recording. A laptop that has an embedded security switch is stolen. The security switch detects a lack of communication from a specific external source for 12 hours, and responds by disconnecting the screen, keyboard and other key components, rendering the laptop useless, with no possibility of recovery, even with a full format. A user wishes to prevent tracking of their location. The user then activates geolocation protection and the security switch disables all GPS communication, eliminating the possibility of tracking the device's location. A user desires to eliminate the possibility of their PIN being copied from their smartphone. They can activate the secure input function, causing the security switch to disconnect the touch screen from the operating system, so input signals are not available to any devices except the switch. A security switch performs scheduled monitoring and finds that a program is attempting to download malicious content from the internet. It then activates internet security function and disables internet access, interrupting the download. If laptop software is compromised by air-gap malware, the user may activate the security switch and disconnect the speaker and microphone, so it can not establish communication with the device. == History == Google started to work on a hardware kill switch for AI in 2016. In 2019, Apple, and Google, along with a handful of smaller players, are designing “kill switches” that cut the power to the microphones or cameras in their devices. Googles first product that implemented this is Nest Hub Max. Hardware kill switches are already available and widely tested on the PinePhone, Librem, Shiftphone, to cut power to the input peripherals (microphone, camera) but also the network connectivity modules (wifi, cellular network).

Library history

Library history is a subdiscipline within library science and library and information science focusing on the history of libraries and their role in societies and cultures. Some see the field as a subset of information history. Library history is an academic discipline and should not be confused with its object of study (history of libraries): the discipline is much younger than the libraries it studies. Library history begins in ancient societies through contemporary issues facing libraries today. Topics include recording mediums, cataloguing systems, scholars, scribes, library supporters and librarians. == Earliest libraries == The earliest records of a library institution as it is presently understood can be dated back to around 5,000 years ago in the Southwest Asian regions of the world. One of the oldest libraries found is that of the ancient library at Ebla (circa 2500 BCE) in present-day Syria. In the 1970s, the excavation at Ebla's library unearthed over 20,000 clay tablets written in cuneiform script. === Library in Mesopotamia === The Assyrian King Assurbanipal created one of the greatest libraries in Nineveh in the seventh century BCE. The collection consisted of over 30,000 tablets written in a variety of languages. The collection was cataloged both by the shape of the tablet and by the subject of the content. The library had separate rooms for the different topics: government, history, law, astronomy, geography, and so on. The tablets also contained myths, hymns, and even jokes. Assurbanipal would send scribes to visit every corner of his kingdom to copy the content of other libraries. His library contained many of the most important literary works of the day, including the epic of Gilgamesh. Assurbanipal's Royal Library also had one of the first library catalogs. Unfortunately, Nineveh was eventually destroyed, and the library was lost in a fire. === Libraries in Ancient Greece === The Greek government was the first to sponsor public libraries. By 500 BCE both Athens and Samos had begun creating libraries for the public, though as most of the population was illiterate these spaces were serving a small, educated portion of the community. Athens developed a city archive at the Metroon in 405 BCE, where documents were stored in sealed jars. These would have saved the documents, but they would have been difficult to consult regularly. In Paros, around the same time, contracts were placed in the temple for safe keeping, and a book curse was placed for extra protection. === Library of Alexandria === The Library at Alexandria, Egypt, was renowned in the third century BCE while kings Ptolemy I Soter and Ptolemy II Philadelphus reigned. The library included a museum, garden, meeting areas and of course reading rooms. The Great Library, as it is known, was one of many in Alexandria. From its inception around the second century BCE, Alexandria was a well-known center for learning. It earned renown as the intellectual capital of the Western world up through the third century CE. The librarians at Alexandria collected, copied, and organized scrolls from across the known world. According to a primary source, every ship that came to Alexandria was required to hand over their books to be copied, and the copies would be returned to the owner, the library keeping the original. The Library of Alexandria was damaged by various disasters over time, including fire, invasion, and earthquake. Scholars believe the collection slowly diminished over time due to theft and efforts to remove it ahead of invading armies. While there are popular stories about how the library was ultimately destroyed, most of these are more myth than fact. === Libraries in Rome === Julius Caesar and his successor Augustus were the first to establish public libraries in ancient Rome, including the library of Apollo on the Palatine Hill. Several emperors followed suit over the next four centuries, including Hadrian, Tiberius, and Vespasian. Roman aristocrats also had personal libraries, which usually contained works in both Greek and Latin. A valuable example of this has been found at Herculaneum near Pompeii. Papyrus manuscripts in Herculaneum's Villa of the Papyri were encased in ash after the eruption of Vesuvius in 79 CE. Modern archaeology is now able to scan these artifacts and discern their contents, including many writings from Philodemus. The average Roman would not have been familiar with books beyond what they might hear read aloud in the forum. Public figures would pay for particular passages to be read aloud to the public from the steps of a public library. === Libraries in the Middle Ages === In the European Middle Ages, libraries began to become more prevalent, despite a widespread reduction in new writing beyond religious themes. Most libraries were initially connected to monasteries or religious institutions. Scriptoriums copied Christian religious texts to share with other religious centers or to be read aloud to their own parishioners. The Holy Roman Emperor Charlemagne (r. 786-814) had a large impact on the advancement of written culture in the Medieval Christian world, acquiring as many written works as he could, and employing many scribes to copy and recirculate vernacular versions of religious works. Most of the text held in small personal libraries was still religious in nature. == Early modern libraries == === Libraries of the Renaissance === During the Renaissance era the merchant middle class grew, and more people found benefits in education. They relied on libraries as a place to study and gain knowledge. Libraries provided a valuable resource, enriching the culture of those who were educated. Universities that had been started in the Middle Ages, founded their own libraries. Books in these libraries could not be borrowed from these libraries and were generally chained to the shelves to prevent theft. As more of the population became literate, new ideas like Humanism and Natural Law spawned an increase personal libraries, although they remained small. Gutenberg's invention of the printing press in 1456 opened the door to the modern era for libraries. == Oldest working libraries == According to the German librarian Michael Knoche, it is not possible to determine which library is the “oldest”: "Precise year dates are a construct, especially in the case of very old libraries. When a collection of books deserves to be called a library depends very much on the point of view of the observer." Various libraries are referred to as the “oldest”: The library founded in the 6th century of the Saint Catherine's Monastery in Sinai is "reputedly the oldest continuously run library in existence today", according to the Library of Congress. Its collection of religious and secular manuscripts is ranging from Bibles, liturgies and prayer books to legal documents such as deeds, court cases and fatwahs (legal opinions). The Al Qarawiyyin Library was founded in 859 by Fatima al-Fihri and is often regarded as the oldest working library in the world. It is in Fez, Morocco and is part of the oldest continually operating university in the world, the University of al-Qarawiyyin. The library houses approximately 4,000 ancient Islamic manuscripts. These manuscripts include 9th century Qurans and the oldest known accounts of the Islamic prophet Muhammed. The Malatestiana Library (Italian: Biblioteca Malatestiana) is a public library in the city of Cesena in northern Italy. Opened in 1454 it is significant for being the first civic library in Europe open to the general public. == Library history reports and writings of the early 19th and 20th century == In the early 19th and 20th century, representative titles were created reporting library history in the United States and the United Kingdom. American titles include Public Libraries in the United States of America, Their History, Condition, and Management (1876), Memorial History of Boston (1881) by Justin Winsor, Public Libraries in America (1894) by William I. Fletcher, and History of the New York Public Library (1923) by Henry M. Lydenberg. British titles include Old English Libraries (1911) by Earnest A. Savage and The Chained Library: A Survey of Four Centuries in the Evolution of the English Library by Burnett Hillman Streeter. In the beginning of the 20th century, library historians began applying scientific research methodologies to examine the library as a social agency. Two works that demonstrate this argument are Geschichte der Bibliotheken (1925) by Alfred Hessel and the Library Quarterly article from 1931, “The Sociological Beginnings of the Library Movement in America” by Arnold Borden. With the establishment of library schools, master's theses and doctoral dissertations represented the shift in serious research regarding libraries and library history. Two published doctoral dissertations that mark this trend are Foundations of the Public Library: The Origins of the American Public Library Movement in Ne