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wiki | In computing, a directory structure is the way an operating system arranges files that are accessible to the user. Files are typically displayed in a hierarchical tree structure. |
wiki | Examples of this rule may be found in the structure of many file systems' directories (also known as folders): 0 – The topmost directory has zero parent directories; that is, there is no directory that contains the topmost directory. 1 – Each subdirectory has exactly one parent directory (not including shortcuts to the directory's location; while such files may have similar icons to the icons of the destination directories, they are not directories at all). Infinity – Each directory, whether the topmost directory or any of its subdirectories, according to the file system's rules, may contain any number of files or subdirectories. Practical limits to this number are caused by other factors, such as space available on storage media and how well the computer's operating system is maintained.In real-world software design, violations of this rule of thumb are common. For example, the FAT16 file system imposes a limit of 65,536 files to a directory. |
wiki | The terms hold-in range, pull-in range (acquisition range), and lock-in range are widely used by engineers for the concepts of frequency deviation ranges within which phase-locked loop-based circuits can achieve lock under various additional conditions. |
wiki | In theoretical computer science and cryptography, a trapdoor function is a function that is easy to compute in one direction, yet difficult to compute in the opposite direction (finding its inverse) without special information, called the "trapdoor". Trapdoor functions are a special case of one-way functions and are widely used in public-key cryptography.In mathematical terms, if f is a trapdoor function, then there exists some secret information t, such that given f(x) and t, it is easy to compute x. Consider a padlock and its key. It is trivial to change the padlock from open to closed without using the key, by pushing the shackle into the lock mechanism. Opening the padlock easily, however, requires the key to be used. |
wiki | Privilege escalation to root permissions by exploiting Shell Injection vulnerabilities in a setuid root binary on UNIX, or Local System by exploiting a service on Microsoft Windows. Attacking web users with HTML/script injection (Cross-site scripting).In 2008, 5.66% of all vulnerabilities reported that year were classified as Code Injection, the highest year on record. In 2015, this had decreased to 0.77%. |
wiki | The interrupt priority level (IPL) is a part of the current system interrupt state, which indicates the interrupt requests that will currently be accepted. The IPL may be indicated in hardware by the registers in a programmable interrupt controller, or in software by a bitmask or integer value and source code of threads. |
wiki | Other architectures have similar data structures, but may behave differently. Use of the IDT is triggered by three types of events: hardware interrupts, software interrupts, and processor exceptions, which together are referred to as interrupts. The IDT consists of 256 interrupt vectors–the first 32 (0–31 or 0x00–0x1F) of which are used for processor exceptions. |
wiki | Interrupts are assigned a number between 0 to 255. The interrupt vectors for each interrupt number are stored in the lower 1024 bytes of main memory. For example, interrupt 0 is stored from 0000:0000 to 0000:0003, interrupt 1 from 0000:0004 to 0000:0007, and so on. |
wiki | In computing, a directory is a file system cataloging structure which contains references to other computer files, and possibly other directories. On many computers, directories are known as folders, or drawers, analogous to a workbench or the traditional office filing cabinet. The name derives from books like a telephone directory that lists the phone numbers of all the people living in a certain area. Files are organized by storing related files in the same directory. |
wiki | The limit is created by the 32-bit integer limit (2,147,483,647), which is the largest possible integer that can be represented by 32 binary digits. In a computer with a 32-bit architecture, the memory address stored in one of the CPU registers will be limited to this number, thus the number of possible memory locations that can be addressed is limited to exactly 2 gibibytes, or roughly 2GB. While Linux, FreeBSD, and most Unix-like operating systems support PAE so long as the hardware does, Windows needs this boot option enabled manually. |
wiki | In computer architecture, 32-bit computing refers to computer systems with a processor, memory, and other major system components that operate on data in 32-bit units. Compared to smaller bit widths, 32-bit computers can perform large calculations more efficiently and process more data per clock cycle. Typical 32-bit personal computers also have a 32-bit address bus, permitting up to 4 GB of RAM to be accessed, far more than previous generations of system architecture allowed.32-bit designs have been used since the earliest days of electronic computing, in experimental systems and then in large mainframe and minicomputer systems. |
wiki | This attack works with file systems that have soft block size of 1024 or greater. At least ext2, ext3, reiserfs and minix have such property. |
wiki | However, its use on small removable media is not advised, as the file-system headers consume from 600 KB to 2 MB, rendering floppy disks virtually useless. Like its predecessor, OFS (Old Be File System, written by Benoit Schillings - formerly BFS), it includes support for extended file attributes (metadata), with indexing and querying characteristics to provide functionality similar to that of a relational database. Whilst intended as a 64-bit-capable file system, the size of some on-disk structures mean that the practical size limit is approximately 2 exabytes. Similarly the extent-based file allocation reduces the maximum practical file size to approximately 260 gigabytes at best and as little as a few blocks in a pathological worst case, depending on the degree of fragmentation.Its design process, application programming interface, and internal workings are, for the most part, documented in the book Practical File System Design with the Be File System. |
wiki | A race condition or race hazard is the condition of an electronics, software, or other system where the system's substantive behavior is dependent on the sequence or timing of other uncontrollable events. It becomes a bug when one or more of the possible behaviors is undesirable. The term race condition was already in use by 1954, for example in David A. Huffman's doctoral thesis "The synthesis of sequential switching circuits".Race conditions can occur especially in logic circuits, multithreaded, or distributed software programs. |
wiki | High performance computing applications run on massively parallel supercomputers consist of concurrent programs designed using multi-threaded, multi-process models. The applications may consist of various constructs (threads, local processes, distributed processes, etc.) with varying degree of parallelism. Although high performance concurrent programs use similar design patterns, models and principles as that of sequential programs, unlike sequential programs, they typically demonstrate non-deterministic behavior. The probability of bugs increases with the number of interactions between the various parallel constructs. Race conditions, data races, deadlocks, missed signals and live lock are common error types. |
wiki | A translation lookaside buffer (TLB) is a memory cache that stores the recent translations of virtual memory to physical memory. It is used to reduce the time taken to access a user memory location. It can be called an address-translation cache. It is a part of the chip's memory-management unit (MMU). |
wiki | If the requested address is not in the TLB, it is a miss, and the translation proceeds by looking up the page table in a process called a page walk. The page walk is time-consuming when compared to the processor speed, as it involves reading the contents of multiple memory locations and using them to compute the physical address. After the physical address is determined by the page walk, the virtual address to physical address mapping is entered into the TLB. The PowerPC 604, for example, has a two-way set-associative TLB for data loads and stores. Some processors have different instruction and data address TLBs. |
wiki | The task state segment (TSS) is a structure on x86-based computers which holds information about a task. It is used by the operating system kernel for task management. Specifically, the following information is stored in the TSS: Processor register state I/O port permissions Inner-level stack pointers Previous TSS linkAll this information should be stored at specific locations within the TSS as specified in the IA-32 manuals. |
wiki | In digital computers, an interrupt (sometimes referred to as a trap) is a request for the processor to interrupt currently executing code (when permitted), so that the event can be processed in a timely manner. If the request is accepted, the processor will suspend its current activities, save its state, and execute a function called an interrupt handler (or an interrupt service routine, ISR) to deal with the event. This interruption is often temporary, allowing the software to resume normal activities after the interrupt handler finishes, although the interrupt could instead indicate a fatal error.Interrupts are commonly used by hardware devices to indicate electronic or physical state changes that require time-sensitive attention. Interrupts are also commonly used to implement computer multitasking, especially in real-time computing. Systems that use interrupts in these ways are said to be interrupt-driven. |
wiki | Instead of giving direct references to DOM objects, the host page typically gives references to wrappers that sanitize HTML, proxy URLs, and prevent redirecting the page; this allowed Caja to prevent certain phishing and cross-site scripting attacks, and prevent downloading malware. Also, since all rewritten programs ran in the same frame, the host page could allow one program to export an object reference to another program; then inter-frame communication was simply method invocation. The word "caja" is Spanish for "box" or "safe" (as in a bank), the idea being that Caja could safely contain JavaScript programs as well as being a capabilities-based JavaScript. |
wiki | Since the two windows may be handled by two different applications, these mechanisms require two different clients connected with the same X server to exchange data. The X Window System core protocol includes some requests and events that are specific to selection exchange, but the transfer is mainly done using event sending and window properties, which are not specific to selection transfer. Different types of data can be transferred: it is usually text, but can also be an image, a number, a list of objects, etc. In the following, only the case of text is considered. |
wiki | In computing, a system call (commonly abbreviated to syscall) is the programmatic way in which a computer program requests a service from the operating system on which it is executed. This may include hardware-related services (for example, accessing a hard disk drive or accessing the device's camera), creation and execution of new processes, and communication with integral kernel services such as process scheduling. System calls provide an essential interface between a process and the operating system. In most systems, system calls can only be made from userspace processes, while in some systems, OS/360 and successors for example, privileged system code also issues system calls. |
wiki | Java Optimized Processor (JOP) is a Java processor, an implementation of Java virtual machine (JVM) in hardware. JOP is free hardware under the GNU General Public License, version 3. The intention of JOP is to provide a small hardware JVM for embedded real-time systems. The main feature is the predictability of the execution time of Java bytecodes. JOP is implemented over an FPGA. |
wiki | A journaling file system is a file system that keeps track of changes not yet committed to the file system's main part by recording the goal of such changes in a data structure known as a "journal", which is usually a circular log. In the event of a system crash or power failure, such file systems can be brought back online more quickly with a lower likelihood of becoming corrupted.Depending on the actual implementation, a journaling file system may only keep track of stored metadata, resulting in improved performance at the expense of increased possibility for data corruption. Alternatively, a journaling file system may track both stored data and related metadata, while some implementations allow selectable behavior in this regard. |
wiki | Journaled File System (JFS) is a 64-bit journaling file system created by IBM. There are versions for AIX, OS/2, eComStation, ArcaOS and Linux operating systems. The latter is available as free software under the terms of the GNU General Public License (GPL). HP-UX has another, different filesystem named JFS that is actually an OEM version of Veritas Software's VxFS. |
wiki | Most file systems are based on a block device, which is a level of abstraction for the hardware responsible for storing and retrieving specified blocks of data, though the block size in file systems may be a multiple of the physical block size. This leads to space inefficiency due to internal fragmentation, since file lengths are often not integer multiples of block size, and thus the last block of a file may remain partially empty. This will create slack space. |
wiki | Some newer file systems, such as Btrfs and FreeBSD UFS2, attempt to solve this through techniques called block suballocation and tail merging. Other file systems such as ZFS support variable block sizes.Block storage is normally abstracted by a file system or database management system (DBMS) for use by applications and end users. |
wiki | A process can also receive capabilities via Unix sockets. These file descriptors not only control access to the file system, but also to other devices like the network sockets. Flags are also used to control more fine-grained access like reads and writes. |
wiki | Enforcing restrictions on file permissions can also close gaps in W^X enforcement caused by memory mapped files. Outright forbidding the usage of arbitrary native code can also mitigate kernel and CPU vulnerabilities not exposed via the existing code on the computer. A less intrusive approach is to lock a file for the duration of any mapping into executable memory, which suffices to prevent post-inspection bypasses. |
wiki | Processes can in some cases install a custom signal handler, allowing them to recover on their own, but otherwise the OS default signal handler is used, generally causing abnormal termination of the process (a program crash), and sometimes a core dump. Segmentation faults are a common class of error in programs written in languages like C that provide low-level memory access and few to no safety checks. They arise primarily due to errors in use of pointers for virtual memory addressing, particularly illegal access. |
wiki | In such cases, an NMI can execute an interrupt handler that transfers control to a special monitor program. From this program, a developer can inspect the machine's memory and examine the internal state of the program at the instant of its interruption. This also allows the debugging or diagnosing of computers which appear hung. |
wiki | Modern block storage devices do not require interleaving. Data is now commonly stored as clusters (groups of sectors), and the data buffer is sufficiently large to allow all sectors in a block to be read at once without any delay between sectors. == References == |
wiki | Free-space bitmaps are one method used to track allocated sectors by some file systems. While the most simplistic design is highly inefficient, advanced or hybrid implementations of free-space bitmaps are used by some modern file systems. |
wiki | In some other instruction sets, such as the ARM architectures, SPARC, and OpenRISC, subroutine call instructions put the return address into a specific general-purpose register, so that register is designated by the instruction set architecture as the link register. In some others, such as PA-RISC, RISC-V, and the IBM System/360 and its successors, including z/Architecture, the subroutine call instruction can store the return address in any general-purpose register; a particular register is usually chosen, by convention, to be used as the link register. The ARMv7 architecture uses general-purpose register R14 as the link register, OpenRISC uses register r9, and SPARC uses "output register 7" or o7.Some architectures have two link registers: a standard "branch link register" for most subroutine calls, and a special "interrupt link register" for interrupts. |
wiki | It handles the rest of startup as well as memory, peripherals, and input/output (I/O) requests from software, translating them into data-processing instructions for the central processing unit. The critical code of the kernel is usually loaded into a separate area of memory, which is protected from access by application software or other less critical parts of the operating system. The kernel performs its tasks, such as running processes, managing hardware devices such as the hard disk, and handling interrupts, in this protected kernel space. |
wiki | In computer operating system design, kernel preemption is a property possessed by some kernels (the cores of operating systems), in which the CPU can be interrupted in the middle of executing kernel code and assigned other tasks (from which it later returns to finish its kernel tasks). |
wiki | In computing, Physical Address Extension (PAE), sometimes referred to as Page Address Extension, is a memory management feature for the x86 architecture. PAE was first introduced by Intel in the Pentium Pro, and later by AMD in the Athlon processor. It defines a page table hierarchy of three levels (instead of two), with table entries of 64 bits each instead of 32, allowing these CPUs to directly access a physical address space larger than 4 gigabytes (232 bytes). The page table structure used by x86-64 CPUs when operating in long mode further extends the page table hierarchy to four or more levels, extending the virtual address space, and uses additional physical address bits at all levels of the page table, extending the physical address space. It also uses the topmost bit of the 64-bit page table entry as a no-execute or "NX" bit, indicating that code cannot be executed from the associated page. The NX feature is also available in protected mode when these CPUs are running a 32-bit operating system, provided that the operating system enables PAE. |
wiki | A page table is the data structure used by a virtual memory system in a computer operating system to store the mapping between virtual addresses and physical addresses. Virtual addresses are used by the program executed by the accessing process, while physical addresses are used by the hardware, or more specifically, by the random-access memory (RAM) subsystem. The page table is a key component of virtual address translation that is necessary to access data in memory. |
wiki | In computing, a page fault (sometimes called PF or hard fault) is an exception that the memory management unit (MMU) raises when a process accesses a memory page without proper preparations. Accessing the page requires a mapping to be added to the process's virtual address space. Besides, the actual page contents may need to be loaded from a backing store, such as a disk. The MMU detects the page fault, but the operating system's kernel handles the exception by making the required page accessible in the physical memory or denying an illegal memory access. Valid page faults are common and necessary to increase the amount of memory available to programs in any operating system that uses virtual memory, such as Windows, macOS, and the Linux kernel. |
wiki | The pages most frequently accessed at any point are called the working set, which may change over time. When the working set is not significantly greater than the system's total number of real storage page frames, virtual memory systems work most efficiently and an insignificant amount of computing is spent resolving page faults. As the total of the working sets grows, resolving page faults remains manageable until the growth reaches a critical point. |
wiki | A single-core processor is a microprocessor with a single core on its die. It performs the fetch-decode-execute cycle once per clock-cycle, as it only runs on one thread. A computer using a single core CPU is generally slower than a multi-core system. |
wiki | A multi-core processor implements multiprocessing in a single physical package. Designers may couple cores in a multi-core device tightly or loosely. |
wiki | For each of C, E, and F, it is 20, 12, and 10 respectively. The lowest is F with 10. Since Activity A's duration is 20 which is higher than F's drag-plus-lag of 10, A's drag is 10. |
wiki | Activities A and E have nothing in parallel and therefore have drags of 10 days and 20 days respectively. Activities B and C are both parallel to F (float of 15) and H (float of 20). B has a duration of 20 and drag of 15 (equal to F's float), while C has a duration of only 5 days and thus drag of only 5. |
wiki | Systems Tool Kit (formerly Satellite Tool Kit), often referred to by its initials STK, is a multi-physics software application from Analytical Graphics, Inc. (an Ansys company) that enables engineers and scientists to perform complex analyses of ground, sea, air, and space platforms, and to share results in one integrated environment. At the core of STK is a geometry engine for determining the time-dynamic position and attitude of objects ("assets"), and the spatial relationships among the objects under consideration including their relationships or accesses given a number of complex, simultaneous constraining conditions. STK has been developed since 1989 as a commercial off the shelf software tool. |
wiki | STK is free software, but a number of its classes, particularly some physical modelling algorithms, are covered by patents held by Stanford University and Yamaha.The STK is used widely in creating software synthesis applications. Versions of the STK instrument classes have been integrated into ChucK, Csound, Real-Time Cmix, Max/MSP (as part of PeRColate), SuperCollider and FAUST. It has been ported to SymbianOS and iOS as well. |
wiki | This limitation is because with only one GB reserved for the kernel, there isn't enough memory for the page table entries to map more than 16 GB of memory. Additional restrictions on the maximum amount of memory addressable thorough AWE are imposed by the Windows licensing scheme. For example, Windows 2000 Advanced Server was limited to 8 GB, while Windows 2000 Data Center Server supported 64 GB.An article published in Dr. Dobb's Journal in 2004 noted that memory allocated using Address Windowing Extensions will not be written to the pagefile, and suggested that AWE regions could therefore be used as a way of protecting sensitive application data such as encryption keys. |
wiki | A page, memory page, or virtual page is a fixed-length contiguous block of virtual memory, described by a single entry in the page table. It is the smallest unit of data for memory management in a virtual memory operating system. Similarly, a page frame is the smallest fixed-length contiguous block of physical memory into which memory pages are mapped by the operating system.A transfer of pages between main memory and an auxiliary store, such as a hard disk drive, is referred to as paging or swapping. |
wiki | ("until completely extinguished, repeat the last third of Des — F once or twice. In no case, however, conclude to Des!") Presumably an expression of unrequited love (Santos 2014: 35). |
wiki | Subversive affirmation is not to be confused with transgression, parody, deception or masquerade. It does not emerge from a place of aggression or as what the French philosopher Michel Foucault defines as a counter-discourse. In this sense Léger compares over-identification to Lacan's Discourse of the Analyst, as opposed to the Discourse of the Master or the Discourse of the Hysteric. |
wiki | The genomic DNA of eukaryotes associates with histones to form chromatin. The level of chromatin compaction depends heavily on histone methylation and other post-translational modifications of histones. Histone methylation is a principal epigenetic modification of chromatin that determines gene expression, genomic stability, stem cell maturation, cell lineage development, genetic imprinting, DNA methylation, and cell mitosis. |
wiki | Histone-modifying enzymes are enzymes involved in the modification of histone substrates after protein translation and affect cellular processes including gene expression. To safely store the eukaryotic genome, DNA is wrapped around four core histone proteins (H3, H4, H2A, H2B), which then join to form nucleosomes. These nucleosomes further fold together into highly condensed chromatin, which renders the organism's genetic material far less accessible to the factors required for gene transcription, DNA replication, recombination and repair. Subsequently, eukaryotic organisms have developed intricate mechanisms to overcome this repressive barrier imposed by the chromatin through histone modification, a type of post-translational modification which typically involves covalently attaching certain groups to histone residues. |
wiki | Discourse on the Method of Rightly Conducting One's Reason and of Seeking Truth in the Sciences (French: Discours de la Méthode Pour bien conduire sa raison, et chercher la vérité dans les sciences) is a philosophical and autobiographical treatise published by René Descartes in 1637. It is best known as the source of the famous quotation "Je pense, donc je suis" ("I think, therefore I am", or "I am thinking, therefore I exist"), which occurs in Part IV of the work. A similar argument, without this precise wording, is found in Meditations on First Philosophy (1641), and a Latin version of the same statement Cogito, ergo sum is found in Principles of Philosophy (1644). Discourse on the Method is one of the most influential works in the history of modern philosophy, and important to the development of natural sciences. |
wiki | A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. |
wiki | In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. |
wiki | In queueing theory, a discipline within the mathematical theory of probability, the M/M/c queue (or Erlang–C model: 495 ) is a multi-server queueing model. In Kendall's notation it describes a system where arrivals form a single queue and are governed by a Poisson process, there are c servers, and job service times are exponentially distributed. It is a generalisation of the M/M/1 queue which considers only a single server. The model with infinitely many servers is the M/M/∞ queue. |
wiki | PolyQ is a biological database of polyglutamine repeats in disease and non-disease associated proteins. |
wiki | For subversive affirmation to be effective, its address must be anonymous rather than targeted. In contrast to film theories that give a specific gender identification to Lacan's notion of the gaze, subversive affirmation emphasizes the inconsistency of symbolic mandates and the fact that there is no Big Other. This is why Laibach avoid both irony as well as the category of art. |
wiki | In enzymology, a L-fucose isomerase (EC 5.3.1.25) is an enzyme that catalyzes the chemical reaction L-fucose ⇌ {\displaystyle \rightleftharpoons } L-fuculoseHence, this enzyme has one substrate, L-fucose, and one product, L-fuculose. This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The systematic name of this enzyme class is L-fucose aldose-ketose-isomerase. This enzyme participates in fructose and mannose metabolism. |
wiki | Peptide:N-glycosidase F, commonly referred to as PNGase F, is an amidase of the peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase class. PNGase F works by cleaving between the innermost GlcNAc and asparagine residues of high mannose, hybrid, and complex oligosaccharides from N-linked glycoproteins and glycopeptides. This results in a deaminated protein or peptide and a free glycan.PNGase F has a molecular weight of 35,500 and consists of a polypeptide chain of 314 amino acids. The optimal pH for enzyme activity is 8.6. |
wiki | Histone H3.1 is a protein in humans that is encoded by the H3C1 gene.Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. |
wiki | Histone H1 is one of the five main histone protein families which are components of chromatin in eukaryotic cells. Though highly conserved, it is nevertheless the most variable histone in sequence across species. |
wiki | These phosphorylations play important and well-characterized roles in signaling pathways and metabolism. However, other amino acids can also be phosphorylated post-translationally, including arginine, lysine, aspartic acid, glutamic acid and cysteine, and these phosphorylated amino acids have recently been identified to be present in human cell extracts and fixed human cells using a combination of antibody-based analysis (for pHis) and mass spectrometry (for all other amino acids).Protein phosphorylation was first reported in 1906 by Phoebus Levene at the Rockefeller Institute for Medical Research with the discovery of phosphorylated vitellin. However, it was nearly 50 years until the enzymatic phosphorylation of proteins by protein kinases was discovered. |
wiki | Protein phosphorylation is a reversible post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become either activated or deactivated, or otherwise modifying its function. Approximately 13000 human proteins have sites that are phosphorylated.The reverse reaction of phosphorylation is called dephosphorylation, and is catalyzed by protein phosphatases. Protein kinases and phosphatases work independently and in a balance to regulate the function of proteins.The amino acids most commonly phosphorylated are serine, threonine, tyrosine in eukaryotes, and also histidine in prokaryotes and plants (though it is now known to be common in humans). |
wiki | In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. Each human cell contains about 30 million nucleosomes.Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosome positions in the genome are not random, and it is important to know where each nucleosome is located because this determines the accessibility of the DNA to regulatory proteins.Nucleosomes were first observed as particles in the electron microscope by Don and Ada Olins in 1974, and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg. |
wiki | They can cause replication fork stalling and are bypassed by translesion synthesis. In E. coli, adenine is preferentially inserted across from AP sites, known as the "A rule". The situation is more complex in higher eukaryotes, with different nucleotides showing a preference depending on the organism and experimental conditions. |
wiki | Escherichia coli (AIEC) NC101 is a mouse isolate, serotype O2:H6/41, that is pro-carcinogenic, adherent-invasive (AIEC), probiotic strain of Escherichia coli, a species of bacteria that thrives in the intestines of mammals. NC101 has also been identified as a nicotinic acid (NA) auxotroph, a pathobiont, which is an organism that is harmful under certain circumstances, and is an important, relevant model organism that demonstrates how susceptible individuals may produce inappropriate immune responses to seemingly benign intestinal E. coli. |
wiki | D-loop replication is a proposed process by which circular DNA like chloroplasts and mitochondria replicate their genetic material. An important component of understanding D-loop replication is that many chloroplasts and mitochondria have a single circular chromosome like bacteria instead of the linear chromosomes found in eukaryotes. However, many chloroplasts and mitochondria have a linear chromosome, and D-loop replication is not important in these organelles. Also, not all circular genomes use D-loop replication as the process of replicating its genome.In many organisms, one strand of DNA in the plasmid comprises heavier nucleotides (relatively more purines: adenine and guanine). |
wiki | The Mesodinium nuclear code (translation table 29) is a genetic code used by the nuclear genome of the ciliates Mesodinium and Myrionecta. |
wiki | During oxidative phosphorylation, electrons are transferred from the electron donors to a series of electron acceptors in a series of redox reactions ending in oxygen, whose reaction releases half of the total energy.In eukaryotes, these redox reactions are catalyzed by a series of protein complexes within the inner membrane of the cell's mitochondria, whereas, in prokaryotes, these proteins are located in the cell's outer membrane. These linked sets of proteins are called the electron transport chain. In eukaryotes, five main protein complexes are involved, whereas in prokaryotes many different enzymes are present, using a variety of electron donors and acceptors. |
wiki | The coenzyme Q: cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain (EC 1.10.2.2), playing a critical role in biochemical generation of ATP (oxidative phosphorylation). Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial (cytochrome b) and the nuclear genomes (all other subunits). Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most eubacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. |
wiki | RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription. |
wiki | A more realistic model of a mediator complex without the CDK module is shown in the second figure.The mediator complex is required for the successful transcription by RNA polymerase II. Mediator has been shown to make contacts with the polymerase in the transcription preinitiation complex. A recent model showing the association of the polymerase with mediator in the absence of DNA is shown in the figure to the left. |
wiki | Under physiological conditions (pH 7.4) in proteins the side chain usually occurs as the negatively charged aspartate form, −COO−. It is a non-essential amino acid in humans, meaning the body can synthesize it as needed. |
wiki | Analysis of phosphopeptides can provide information about which amino acids are phosphorylated and how many sites on the primary sequence are phosphorylated.Phosphorylation of serine and threonine residues is conserved during MHC class I and MHC class II antigen processing. Phosphopeptides are thus displayed on the surface of cells. |
wiki | Self-affirmation theory is a psychological theory that focuses on how individuals adapt to information or experiences that are threatening to their self-concept. Claude Steele originally popularized self-affirmation theory in the late 1980s, and it remains a well-studied theory in social psychological research.Self-affirmation theory contends that if individuals reflect on values that are personally relevant to them, they are less likely to experience distress and react defensively when confronted with information that contradicts or threatens their sense of self. Experimental investigations of self-affirmation theory suggest that self-affirmation can help individuals cope with threat or stress and that it might be beneficial for improving academic performance, health, and reducing defensiveness. |
wiki | The Shine–Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon. Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start site. The Shine–Dalgarno sequence is common in bacteria, but rarer in archaea. It is also present in some chloroplast and mitochondrial transcripts. The six-base consensus sequence is AGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while the shorter GAGG dominates in E. coli virus T4 early genes.The Shine–Dalgarno sequence was proposed by Australian scientists John Shine and Lynn Dalgarno in 1973. |
wiki | It also specifies a Shine–Dalgarno sequence flanked by two unique restriction sites (portable Shine–Dalgarno sequence). The tacI and the tacII promoters respectively direct transcription approximately 11 and 7 times more efficiently than the derepressed parental lac UV5 promoter and approximately 3 and 2 times more efficiently than the trp promoter in the absence of the trp repressor. Both hybrid promoters can be repressed by the lac repressor and both can be derepressed with isopropyl-beta-D-thiogalactoside. |
wiki | Cholera toxin (also known as choleragen and sometimes abbreviated to CTX, Ctx or CT) is an AB5 multimeric protein complex secreted by the bacterium Vibrio cholerae. CTX is responsible for the massive, watery diarrhea characteristic of cholera infection. It is a member of the heat-labile enterotoxin family. |
wiki | The Pseudomonas exotoxin (or exotoxin A) is an exotoxin produced by Pseudomonas aeruginosa. Vibrio cholerae produces a similar protein called the Cholix toxin (Q5EK40).It inhibits elongation factor-2. It does so by ADP-ribosylation of EF2 using NAD+. This then causes the elongation of polypeptides to cease. This mechanism is similar to that of diphtheria toxin.It has been investigated as a treatment for hepatitis B and cancer. |
wiki | In biochemistry, a glycolytic oscillation is the repetitive fluctuation of in the concentrations of metabolites, classically observed experimentally in yeast and muscle. The first observations of oscillatory behaviour in glycolysis were made by Duysens and Amesz in 1957.The problem of modelling glycolytic oscillation has been studied in control theory and dynamical systems since the 1960s since the behaviour depends on the rate of substrate injection. Early models used two variables, but the most complex behaviour they could demonstrate was period oscillations due to the Poincaré–Bendixson theorem, so later models introduced further variables. == References == |
wiki | In enzymology, a glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) (EC 1.2.1.12) is an enzyme that catalyzes the chemical reaction D-glyceraldehyde 3-phosphate + phosphate + NAD+ ⇌ {\displaystyle \rightleftharpoons } 3-phospho-D-glyceroyl phosphate + NADH + H+The 3 substrates of this enzyme are D-glyceraldehyde 3-phosphate, phosphate, and NAD+, whereas its 3 products are 3-phospho-D-glyceroyl phosphate, NADH, and H+. This enzyme participates in glycolysis / gluconeogenesis. |
wiki | Nietzschean affirmation (German: Bejahung) is a concept that has been scholarly identified in the philosophy of Friedrich Nietzsche. An example used to describe the concept is a fragment in Nietzsche's The Will to Power: Suppose that we said yes to a single moment, then we have not only said yes to ourselves, but to the whole of existence. For nothing stands alone, either in ourselves or in things; and if our soul did but once vibrate and resound with a chord of happiness, then all of eternity was necessary to bring forth this one occurrence—and in this single moment when we said yes, all of eternity was embraced, redeemed, justified and affirmed. |
wiki | Histone H2A is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells. The other histone proteins are: H1, H2B, H3 and H4. |
wiki | Histone H4 is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and a long N-terminal tail, H4 is involved with the structure of the nucleosome of the 'beads on a string' organization. Histone proteins are highly post-translationally modified. |
wiki | Each had come from a frozen embryo that, rather than being destroyed for research, was implanted in an adoptive mother. (pp. 111-123) |
wiki | In serious cases, the condition can be life-threatening.The dermoid sinus gene is believed by some to be recessive, meaning that the animal must receive one defective gene from each parent in order to develop the condition. Where one parent carries the gene and the other does not, the offspring remain carriers and can continue to pass the defective gene on to their offspring in turn. Others believe that the dermoid sinus condition is more appropriately characterized as polygenic, involving multiple genes. |
wiki | == Strains == Innocuous: Laboratory: E. coli K-12, one of two laboratory strains (innocuous) Clifton wild type (!) W3110 DH5α Dam dcm strain HB101 Escherichia coli B, the other of the two lab strains from which all lab substrains originate Escherichia coli BL21(DE3)Pathogenic: Enterotoxigenic E. coli (ETEC) Enteropathogenic E. coli (EPEC) Enteroinvasive E. coli (EIEC) Enterohemorrhagic E. coli (EHEC) Enteroaggregative E. coli (EAEC) Uropathogenic E. coli (UPEC) Verotoxin-producing E. coli E. coli O157:H7 is an enterohemorrhagic strain also 2006 North American E. coli outbreak E. coli O104:H4, also 2011 E. coli O104:H4 outbreak Escherichia coli O121 Escherichia coli O104:H21 Escherichia coli K1, meningitis Adherent Invasive Escherichia coli (AIEC), morbus Crohn Escherichia coli NC101 Shigella Shigella flexneri Shigella dysenteriae Shigella boydii Shigella sonnei == References == |
wiki | Bacteriovoracales is an order of bacteria. == References == |
wiki | An example of this is Actrapid. Receptors for steroid hormones are usually found within the protoplasm and are referred to as intracellular or nuclear receptors, such as testosterone. |
wiki | Lipid soluble hormones, (such as steroids) generally pass through the plasma membranes of target cells (both cytoplasmic and nuclear) to act within their nuclei. Brassinosteroids, a type of polyhydroxysteroids, are a sixth class of plant hormones and may be useful as an anticancer drug for endocrine-responsive tumors to cause apoptosis and limit plant growth. |
wiki | Insulin (, from Latin insula, 'island') is a peptide hormone produced by beta cells of the pancreatic islets encoded in humans by the INS gene. It is considered to be the main anabolic hormone of the body. It regulates the metabolism of carbohydrates, fats and protein by promoting the absorption of glucose from the blood into liver, fat and skeletal muscle cells. In these tissues the absorbed glucose is converted into either glycogen via glycogenesis or fats (triglycerides) via lipogenesis, or, in the case of the liver, into both. |
wiki | Insulin degludec is a modified insulin that has one single amino acid deleted in comparison to human insulin, and is conjugated to hexadecanedioic acid via gamma-L-glutamyl spacer at the amino acid lysine at position B29. It is included in the World Health Organization's List of Essential Medicines as an equivalent to insulin glargine. In 2020, it was the 136th most commonly prescribed medication in the United States, with more than 4 million prescriptions. |
wiki | In the process of breaking down glucose, a net yield of 1 ATP is formed per every one glucose molecule processed, as well as 1 NADH and 1 NADPH. In comparison, glycolysis has a net yield of 2 ATP molecules and 2 NADH molecules per every one glucose molecule metabolized. This difference in energy production may be offset by the difference in protein amount needed per pathway. |
wiki | Glycolysis is the metabolic pathway that converts glucose (C6H12O6) into pyruvate, and in most organisms, occurs in the liquid part of cells, the cytosol. The free energy released in this process is used to form the high-energy molecules adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide (NADH). Glycolysis is a sequence of ten reactions catalyzed by enzymes. |
wiki | In molecular biology, a histone octamer is the eight-protein complex found at the center of a nucleosome core particle. It consists of two copies of each of the four core histone proteins (H2A, H2B, H3, and H4). The octamer assembles when a tetramer, containing two copies of H3 and two of H4, complexes with two H2A/H2B dimers. Each histone has both an N-terminal tail and a C-terminal histone-fold. Each of these key components interacts with DNA in its own way through a series of weak interactions, including hydrogen bonds and salt bridges. These interactions keep the DNA and the histone octamer loosely associated, and ultimately allow the two to re-position or to separate entirely. |
wiki | The primary protein components of chromatin are histones. An octamer of two sets of four histone cores (Histone H2A, Histone H2B, Histone H3, and Histone H4) bind to DNA and function as "anchors" around which the strands are wound. In general, there are three levels of chromatin organization: DNA wraps around histone proteins, forming nucleosomes and the so-called beads on a string structure (euchromatin). |
wiki | Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, is a metabolite that occurs as an intermediate in several central pathways of all organisms. With the chemical formula H(O)CCH(OH)CH2OPO32-, this anion is a monophosphate ester of glyceraldehyde. |
wiki | In combinatorial mathematics, a de Bruijn sequence of order n on a size-k alphabet A is a cyclic sequence in which every possible length-n string on A occurs exactly once as a substring (i.e., as a contiguous subsequence). Such a sequence is denoted by B(k, n) and has length kn, which is also the number of distinct strings of length n on A. Each of these distinct strings, when taken as a substring of B(k, n), must start at a different position, because substrings starting at the same position are not distinct. Therefore, B(k, n) must have at least kn symbols. And since B(k, n) has exactly kn symbols, De Bruijn sequences are optimally short with respect to the property of containing every string of length n at least once. |
wiki | The sequences are named after the Dutch mathematician Nicolaas Govert de Bruijn, who wrote about them in 1946. As he later wrote, the existence of de Bruijn sequences for each order together with the above properties were first proved, for the case of alphabets with two elements, by Camille Flye Sainte-Marie (1894). The generalization to larger alphabets is due to Tatyana van Aardenne-Ehrenfest and de Bruijn (1951). Automata for recognizing these sequences are denoted as de Bruijn automata. In most applications, A = {0,1}. |
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