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Spike sorting is a critical step for single-unit-based analysis of neural activities extracellularly and simultaneously recorded using multi-channel electrodes. When dealing with recordings from very large numbers of neurons, existing methods, which are mostly semiautomatic in nature, become inadequate.

This dissertation aims at automating the spike sorting process. A high performance,

Spike sorting is a critical step for single-unit-based analysis of neural activities extracellularly and simultaneously recorded using multi-channel electrodes. When dealing with recordings from very large numbers of neurons, existing methods, which are mostly semiautomatic in nature, become inadequate.

This dissertation aims at automating the spike sorting process. A high performance, automatic and computationally efficient spike detection and clustering system, namely, the M-Sorter2 is presented. The M-Sorter2 employs the modified multiscale correlation of wavelet coefficients (MCWC) for neural spike detection. At the center of the proposed M-Sorter2 are two automatic spike clustering methods. They share a common hierarchical agglomerative modeling (HAM) model search procedure to strategically form a sequence of mixture models, and a new model selection criterion called difference of model evidence (DoME) to automatically determine the number of clusters. The M-Sorter2 employs two methods differing by how they perform clustering to infer model parameters: one uses robust variational Bayes (RVB) and the other uses robust Expectation-Maximization (REM) for Student’s 𝑡-mixture modeling. The M-Sorter2 is thus a significantly improved approach to sorting as an automatic procedure.

M-Sorter2 was evaluated and benchmarked with popular algorithms using simulated, artificial and real data with truth that are openly available to researchers. Simulated datasets with known statistical distributions were first used to illustrate how the clustering algorithms, namely REMHAM and RVBHAM, provide robust clustering results under commonly experienced performance degrading conditions, such as random initialization of parameters, high dimensionality of data, low signal-to-noise ratio (SNR), ambiguous clusters, and asymmetry in cluster sizes. For the artificial dataset from single-channel recordings, the proposed sorter outperformed Wave_Clus, Plexon’s Offline Sorter and Klusta in most of the comparison cases. For the real dataset from multi-channel electrodes, tetrodes and polytrodes, the proposed sorter outperformed all comparison algorithms in terms of false positive and false negative rates. The software package presented in this dissertation is available for open access.
ContributorsMa, Weichao (Author) / Si, Jennie (Thesis advisor) / Papandreou-Suppappola, Antonia (Committee member) / He, Jingrui (Committee member) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2019
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Description
In this paper, it is determined that learning retention decreases with age and there is a linear rate of decrease. In this study, four male Long-Evans Rats were used. The rats were each trained in 4 different tasks throughout their lifetime, using a food reward as motivation to work. Rats

In this paper, it is determined that learning retention decreases with age and there is a linear rate of decrease. In this study, four male Long-Evans Rats were used. The rats were each trained in 4 different tasks throughout their lifetime, using a food reward as motivation to work. Rats were said to have learned a task at the age when they received the highest accuracy during a task. A regression of learning retention was created for the set of studied rats: Learning Retention = 112.9 \u2014 0.085919 x (Age at End of Task), indicating that learning retention decreases at a linear rate, although rats have different rates of decrease of learning retention. The presence of behavioral training was determined not to have a positive impact on this rate. In behavioral studies, there were statistically significant differences between timid/outgoing and large ball ability between W12 and Z12. Rat W12 had overall better learning retention and also was more compliant, did not resist being picked up and traveled more frequently at high speeds (in the large ball) than Z12. Further potential studies include implanting an electrode into the frontal cortex in order to compare neuro feedback with learning retention, and using human subjects to find the rate of decrease in learning retention. The implication of this study, if also true for human subjects, is that older persons may need enhanced training or additional refresher training in order to retain information that is learned at a later age.
ContributorsSpinrad, Amelia (Author) / Si, Jennie (Thesis director) / Thompson, Patrick (Committee member) / Ma, Weichao (Committee member) / Barrett, The Honors College (Contributor)
Created2014-05
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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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 cellĂŞs 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