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Description
Dynamic software update (DSU) enables a program to update while it is running. DSU aims to minimize the loss due to program downtime for updates. Usually DSU is done in three steps: suspending the execution of an old program, mapping the execution state from the old program to a new

Dynamic software update (DSU) enables a program to update while it is running. DSU aims to minimize the loss due to program downtime for updates. Usually DSU is done in three steps: suspending the execution of an old program, mapping the execution state from the old program to a new one, and resuming execution of the new program with the mapped state. The semantic correctness of DSU depends largely on the state mapping which is mostly composed by developers manually nowadays. However, the manual construction of a state mapping does not necessarily ensure sound and dependable state mapping. This dissertation presents a methodology to assist developers by automating the construction of a partial state mapping with a guarantee of correctness.

This dissertation includes a detailed study of DSU correctness and automatic state mapping for server programs with an established user base. At first, the dissertation presents the formal treatment of DSU correctness and the state mapping problem. Then the dissertation presents an argument that for programs with an established user base, dynamic updates must be backward compatible. The dissertation next presents a general definition of backward compatibility that specifies the allowed changes in program interaction between an old version and a new version and identified patterns of code evolution that results in backward compatible behavior. Thereafter the dissertation presents formal definitions of these patterns together with proof that any changes to programs in these patterns will result in backward compatible update. To show the applicability of the results, the dissertation presents SitBack, a program analysis tool that has an old version program and a new one as input and computes a partial state mapping under the assumption that the new version is backward compatible with the old version.

SitBack does not handle all kinds of changes and it reports to the user in incomplete part of a state mapping. The dissertation presents a detailed evaluation of SitBack which shows that the methodology of automatic state mapping is promising in deal with real world program updates. For example, SitBack produces state mappings for 17-75% of the changed functions. Furthermore, SitBack generates automatic state mapping that leads to successful DSU. In conclusion, the study presented in this dissertation does assist developers in developing state mappings for DSU by automating the construction of state mappings with a correctness guarantee, which helps the adoption of DSU ultimately.
ContributorsShen, Jun (Author) / Bazzi, Rida A (Thesis advisor) / Fainekos, Georgios (Committee member) / Neamtiu, Iulian (Committee member) / Shrivastava, Aviral (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Compartmentalizing access to content, be it websites accessed in a browser or documents and applications accessed outside the browser, is an established method for protecting information integrity [12, 19, 21, 60]. Compartmentalization solutions change the user experience, introduce performance overhead and provide varying degrees of security. Striking a balance between

Compartmentalizing access to content, be it websites accessed in a browser or documents and applications accessed outside the browser, is an established method for protecting information integrity [12, 19, 21, 60]. Compartmentalization solutions change the user experience, introduce performance overhead and provide varying degrees of security. Striking a balance between usability and security is not an easy task. If the usability aspects are neglected or sacrificed in favor of more security, the resulting solution would have a hard time being adopted by end-users. The usability is affected by factors including (1) the generality of the solution in supporting various applications, (2) the type of changes required, (3) the performance overhead introduced by the solution, and (4) how much the user experience is preserved. The security is affected by factors including (1) the attack surface of the compartmentalization mechanism, and (2) the security decisions offloaded to the user. This dissertation evaluates existing solutions based on the above factors and presents two novel compartmentalization solutions that are arguably more practical than their existing counterparts.

The first solution, called FlexICon, is an attractive alternative in the design space of compartmentalization solutions on the desktop. FlexICon allows for the creation of a large number of containers with small memory footprint and low disk overhead. This is achieved by using lightweight virtualization based on Linux namespaces. FlexICon uses two mechanisms to reduce user mistakes: 1) a trusted file dialog for selecting files for opening and launching it in the appropriate containers, and 2) a secure URL redirection mechanism that detects the user’s intent and opens the URL in the proper container. FlexICon also provides a language to specify the access constraints that should be enforced by various containers.

The second solution called Auto-FBI, deals with web-based attacks by creating multiple instances of the browser and providing mechanisms for switching between the browser instances. The prototype implementation for Firefox and Chrome uses system call interposition to control the browser’s network access. Auto-FBI can be ported to other platforms easily due to simple design and the ubiquity of system call interposition methods on all major desktop platforms.
ContributorsZohrevandi, Mohsen (Author) / Bazzi, Rida A (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Doupe, Adam (Committee member) / Zhao, Ming (Committee member) / Arizona State University (Publisher)
Created2018
Description

Human Papillomavirus, or HPV, is a viral pathogen that most commonly spreads through sexual contact. HPV strains 6 and 11 normally cause genital warts, while HPV strains 16 and 18 commonly cause cervical cancer, which causes cancerous cells to spread in the cervix. Physicians can detect those HPV strains, using

Human Papillomavirus, or HPV, is a viral pathogen that most commonly spreads through sexual contact. HPV strains 6 and 11 normally cause genital warts, while HPV strains 16 and 18 commonly cause cervical cancer, which causes cancerous cells to spread in the cervix. Physicians can detect those HPV strains, using a Pap smear, which is a diagnostic test that collects cells from the female cervix.

Created2021-04-06
Description

Johann Gregor Mendel studied patterns of trait inheritance in plants during the nineteenth century. Mendel, an Augustinian monk, conducted experiments on pea plants at St. Thomas’ Abbey in what is now Brno, Czech Republic. Twentieth century scientists used Mendel’s recorded observations to create theories about genetics.

Created2022-01-13
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Description

In the 1930s, George Beadle and Boris Ephrussi discovered factors that affect eye colors in developing fruit flies. They did so while working at the California Institute of Technology in Pasadena, California. (1) They took optic discs (colored fuchsia in the image) from fruit fly larvae in the third instar

In the 1930s, George Beadle and Boris Ephrussi discovered factors that affect eye colors in developing fruit flies. They did so while working at the California Institute of Technology in Pasadena, California. (1) They took optic discs (colored fuchsia in the image) from fruit fly larvae in the third instar stage of development. Had the flies not been manipulated, they would have developed into adults with vermilion eyes. (2) Beadle and Ephrussi transplanted the donor optic discs into the bodies of several types of larvae, including those that would develop with normal colored eyes (brick red), and those that would develop eyes with other shades of red, such as claret, carmine, peach, and ruby (grouped together and colored black in the image). (3a) When implanted into normal hosts that would develop brick red eyes, the transplanted optic disc developed into an eye that also was brick red. (3b) When implanted into abnormal hosts that would develop eyes of some other shade of red, the transplanted optic discs developed into eyes that were vermilion. Beadle and Ephrussi concluded that there was a factor, such as an enzyme or some other protein, produced outside of the optic disc that influenced the color of the eye that developed from the disc.

Created2016-10-11
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Description

This illustration shows George Beadle and Edward Tatum's experiments with Neurospora crassa that indicated that single genes produce single enzymes. The pair conducted the experiments at Stanford University in Palo Alto, California. Enzymes are types of proteins that can catalyze reactions inside cells, reactions that produce a number of things,

This illustration shows George Beadle and Edward Tatum's experiments with Neurospora crassa that indicated that single genes produce single enzymes. The pair conducted the experiments at Stanford University in Palo Alto, California. Enzymes are types of proteins that can catalyze reactions inside cells, reactions that produce a number of things, including nutrients that the cell needs. Neurospora crassa is a species of mold that grows on bread. In the early 1940s, Beadle and Tatum conducted an experiment to discover the abnormal genes in Neurospora mutants, which failed to produce specific nutrients needed to survive. (1) Beadle and Tatum used X-rays to cause mutations in the DNA of Neurospora, and then they grew the mutated Neurospora cells in glassware. (2) They grew several strains, represented in four groups of paired test tubes. For each group, Neurospora was grown in one of two types of growth media. One medium contained all the essential nutrients that the Neurospora needed to survive, which Beadle and Tatum called a complete medium. The second medium was a minimal medium and lacked nutrients that Neurospora needed to survive. If functioning normally and in the right conditions, however, Neurospora can produce these absent nutrients. (3) When Beadle and Tatum grew the mutated mold strains on both the complete and on the minimal media, all of the molds survived on the complete media, but not all of the molds survived on the minimal media (strain highlighted in yellow). (4) For the next step, the researchers added nutrients to the minimal media such that some glassware received an amino acid mixture (represented as colored squares) and other glassware received a vitamin mixture (represented as colored triangles) in an attempt to figure out which kind of nutrients the mutated molds needed. The researchers then took mold from the mutant mold strain that had survived on a complete medium and added that mold to the supplemented minimal media. They found that in some cases the mutated mold grew on media supplemented only with vitamins but not on media supplemented only with amino acids. (5) To discover which vitamins the mutant molds needed, Beadle and Tatum used several tubes with the minimal media, supplementing each one with a different vitamin, and then they attempted to grow the mutant mold in each tube. They found that different mutant strains of the mold grew only on media supplemented with different kinds of vitamins, for instance vitamin B6 for one strain, and vitamin B1 for another. In experiments not pictured, Beadle and Tatum found in step (4) that other strains of mutant mold grew on minimal media supplemented only with amino acids but not on minimal media supplemented only with vitamins. When they repeated step (5) on those strains and with specific kinds of amino acids in the different test tubes, they found that the some mutated mold strains grew on minimal media supplemented solely with one kind of amino acid, and others strains grew only on minimal media supplemented with other kinds of amino acids. For both the vitamins and amino acid cases, Beadle and Tatum concluded that the X-rays had mutated different genes in Neurospora, resulting in different mutant strains of Neurospora cells. In a cell of a given strain, the X-rays had changed the gene normally responsible for producing an enzyme that catalyzed a vitamin or an amino acid. As a result, the Neurospora cell could no longer produce that enzyme, and thus couldn't catalyze a specific nutrient.

Created2016-10-12
Description

The Southern Gastric Brooding Frog (Rheobotrahcus silus) was a frog species that lived in Australia. It was declared extinct in 2002. Once adult males fertilized the eggs of females, the females swallowed their eggs. The stomachs of the females then functioned somewhat like wombs, protecting the eggs while they gestated.

The Southern Gastric Brooding Frog (Rheobotrahcus silus) was a frog species that lived in Australia. It was declared extinct in 2002. Once adult males fertilized the eggs of females, the females swallowed their eggs. The stomachs of the females then functioned somewhat like wombs, protecting the eggs while they gestated. Once the eggs developed into juveniles, female frogs performed oral birth and regurgitated their young.

Created2017-02-06
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Description

Mechanism of Notch Signaling: The image depicts a type of cell signaling, in which two animal cells interact and transmit a molecular signal from one to the other. The process results in the production of proteins, which influence the cells as they differentiate, move, and contribute to embryological development. In

Mechanism of Notch Signaling: The image depicts a type of cell signaling, in which two animal cells interact and transmit a molecular signal from one to the other. The process results in the production of proteins, which influence the cells as they differentiate, move, and contribute to embryological development. In the membrane of the signaling cell, there is a ligand (represented by a green oval). The ligand functions to activate a change in a receptor molecule. In the receiving cell, there are receptors; in this case, Notch proteins (represented by orange forks). The Notch proteins are embedded in the receiving cell membrane, and they have at least two parts: an intracellular domain (inside the cell) and the receptor (outside the cell). Once the ligand and receptor bind to each other, a protease (represented by the dark red triangle) can sever the intracellular domain from the rest of the Notch receptor. Inside the nucleus of the receiving cell (represented by the gray area) are the cellês DNA (represented by the multi-colored helices) and its transcription factors (blue rectangles). Transcription factors are proteins that bind to DNA to regulate transcription, the first step in gene expression, which eventually yields proteins or other products. Initially, repressor proteins (represented by a red irregular hexagon) prevent transcription factors from allowing transcription. When the severed Notch receptor intracellular domain reaches the nucleus, it displaces the repressor. The transcription factor can then signal for transcription to occur. 1) There is a Notch receptor protein in the membrane of a receiving cell, and a ligand for this receptor (for example, Delta) in the membrane of the signaling cell. When the ligand binds to the receptor, the intracellular domain of the receptor changes shape. 2) Inside the receiving cell, there are proteases. Once the intracellular domain of the receptor changes shape, the protease can bind to it and shear the intracellular domain away from the rest of the receptor molecule. 3) The severed intracellular domain is shuttled to the receiving cell nucleus. Here, the intracellular domain displaces a repressor protein. This allows a transcription factor to initiate DNA transcription. During transcription, DNA is used as a template to create RNA. Following transcription, the process of translation occurs, which uses RNA as a template to create proteins. These proteins influence the behavior, fate, and differentiation of cells, which contribute to normal embryonic development

Created2014-08-21
Description

Fruit flies of the species Drosophila melanogaster develop from eggs to adults in eight to ten days at 25 degrees Celsius. They develop through four primary stages: egg, larva, pupa, and adult. When in the wild, female flies lay their fertilized eggs in rotting fruit or other decomposing material that

Fruit flies of the species Drosophila melanogaster develop from eggs to adults in eight to ten days at 25 degrees Celsius. They develop through four primary stages: egg, larva, pupa, and adult. When in the wild, female flies lay their fertilized eggs in rotting fruit or other decomposing material that can serve as food for the larvae. In the lab, fruit flies lay their fertilized eggs in a mixture of agar, molasses, cornmeal, and yeast. After roughly a day, each egg hatches into a larva. The larva eats the material it finds itself in, and for four days it grows into stages of increasing size, called first-, second-, and third-instar stages. This figure shows a third-instar larva. Each larva has sections of tissue called imaginal discs, from which various parts of the adult anatomy develop. This figure shows the imaginal discs that will develop into antennae (colored purple), eyes (colored red), brain (colored blue), and wings (colored green). After four days, the larva turns into a pupa by making a casing, similar to caterpillars, and grows within the casing. After a four-day metamorphosis, the adult fly then emerges from its pupal casing. Adult males look somewhat different from adult females, as the males have darker rear abdomen segments than do females. The warmer the temperature around the eggs, the faster the flies develop to adults.

Created2016-10-11