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Biomedical Engineering and Bioengineering Commons™
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Articles 1 - 16 of 16
Full-Text Articles in Biomedical Engineering and Bioengineering
Fast And Accurate Autofocus Control Using Guassian Standard Deviation And Gradient-Based Binning, Peter Dimeo, Lu Sun, Xian Du
Fast And Accurate Autofocus Control Using Guassian Standard Deviation And Gradient-Based Binning, Peter Dimeo, Lu Sun, Xian Du
Mechanical and Industrial Engineering Faculty Publication Series
We propose a fast and accurate autofbcus algorithm using Gaussian standard deviation and gradient-based binning. Rather than iteratively searching for the optimal focus using an optimization process, the proposed algorithm directly calculates the mean of the Gaussian shaped focus measure (FM) curve to find the optimal focus location and uses the FM curve standard deviation to adapt the motion step size. The calculation only requires 3-4 defocused images to identify the center location of the FM curve. Furthermore, by assigning motion step sizes based on the FM curve standard deviation, the magnitude of the motion step is adaptively controlled according …
From Soap Bubbles To Cell Membranes, Peter Beltramo
From Soap Bubbles To Cell Membranes, Peter Beltramo
Science and Engineering Saturday Seminars
Have you ever blown a soap bubble and wondered - what causes the bubble to be so stable and produces those colorful reflections of light? The answer lies in a class of molecules known as surfactants, and they have remarkable similarities with the molecules that comprise the cell membrane of all living organisms. In this workshop, we will use the analogy of a soap bubble to describe cellular membrane properties such as chemistry, structure, membrane transport, and ion channel formation. The goals of this workshop are to 1) link initially intractable concepts in biology like intracellular transport to the intuitive …
Bubble Lab Exercise, Peter Beltramo
Bubble Lab Exercise, Peter Beltramo
Science and Engineering Saturday Seminars
The cell membrane is a ubiquitous component in mammalian cells which control many vital biological functions. It consists of a phospholipid bilayer with embedded protein molecules which serve to transport molecules between the interior and exterior of the cell. Understanding what makes cell membranes so important and how they function requires concepts from physics, chemistry, and of course biology, but it is difficult to learn and conceptualize the structure and function of membranes due to their nanoscopic size and dynamic nature which can’t be properly appreciated in a static textbook. This activity draws analogies between the chemistry and structure of …
Generating Optimal Control Simulations Of Musculoskeletal Movement Using Opensim And Matlab, Leng-Feng Lee, Brian R. Umberger
Generating Optimal Control Simulations Of Musculoskeletal Movement Using Opensim And Matlab, Leng-Feng Lee, Brian R. Umberger
Kinesiology Department Faculty Publication Series
Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting …
Nanotechnology Overview Powerpoint, Mark Tuominen
Nanotechnology Overview Powerpoint, Mark Tuominen
Nanotechnology Teacher Summer Institutes
Nanotechnology is the understanding and control of matter at dimensions of roughly 1 to 100 nanometers, where unique phenomena enable novel applications. This PowerPoint gives an overview of the field and introduces the teacher summer institute.
Identification Of A New Class Of Antifungals Targeting The Synthesis Of Fungal Sphingolipids, Patrick Flaherty, Et. Al.
Identification Of A New Class Of Antifungals Targeting The Synthesis Of Fungal Sphingolipids, Patrick Flaherty, Et. Al.
Mathematics and Statistics Department Faculty Publication Series
Recent estimates suggest that>300 million people are afflicted by serious fungal infections worldwide. Current antifungal drugs are static and toxic and/or have a narrow spectrum of activity. Thus, there is an urgent need for the development of new antifungal drugs. The fungal sphingolipid glucosylceramide (GlcCer) is critical in promoting virulence of a variety of human-pathogenic fungi. In this study, we screened a synthetic drug library for compounds that target the synthesis of fungal, but not mammalian, GlcCer and found two compounds [N=-(3-bromo-4-hydroxybenzylidene)-2-methylbenzohydrazide (BHBM) and its derivative, 3-bromo-N=-(3-bromo-4-hydroxybenzylidene) benzohydrazide (D0)] that were highly effective in vitro and in vivo against …
Metastatic Tumor Evolution In Diuse Gastric Cancer And Cancer Organoid Modeling Implicate Tgfbr2 As A Potential Driver, Patrick Flaherty
Metastatic Tumor Evolution In Diuse Gastric Cancer And Cancer Organoid Modeling Implicate Tgfbr2 As A Potential Driver, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
Background: Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis. Results: Both the primary tumor and ovarian metastasis have common biallelic loss-of-function of both the CDH1 and TP53 tumor suppressors, indicating a common genetic origin. While the primary tumor exhibits amplification of …
Activity Intent Recognition Of The Torso Based On Surface Electromyography And Inertial Measurement Units, Zhe Zhang
Masters Theses 1911 - February 2014
This thesis presents an activity mode intent recognition approach for safe, robust and reliable control of powered backbone exoskeleton. The thesis presents the background and a concept for a powered backbone exoskeleton that would work in parallel with a user. The necessary prerequisites for the thesis are presented, including the collection and processing of surface electromyography signals and inertial sensor data to recognize the user’s activity. The development of activity mode intent recognizer was described based on decision tree classification in order to leverage its computational efficiency. The intent recognizer is a high-level supervisory controller that belongs to a three-level …
Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Hojoon Lee, Patrick Flaherty, Hanlee P. Ji
Systematic Genomic Identification Of Colorectal Cancer Genes Delineating Advanced From Early Clinical Stage, Hojoon Lee, Patrick Flaherty, Hanlee P. Ji
Mathematics and Statistics Department Faculty Publication Series
Background: Colorectal cancer is the third leading cause of cancer deaths in the United States. The initial assessment of colorectal cancer involves clinical staging that takes into account the extent of primary tumor invasion, determining the number of lymph nodes with metastatic cancer and the identification of metastatic sites in other organs. Advanced clinical stage indicates metastatic cancer, either in regional lymph nodes or in distant organs. While the genomic and genetic basis of colorectal cancer has been elucidated to some degree, less is known about the identity of specific cancer genes that are associated with advanced clinical stage and …
Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Anna Cushing, Patrick Flaherty, Erik Hopmans, John M. Bell, Hanlee P. Ji
Rvd: A Command-Line Program For Ultrasensitive Rare Single Nucleotide Variant Detection Using Targeted Next-Generation Dna Resequencing, Anna Cushing, Patrick Flaherty, Erik Hopmans, John M. Bell, Hanlee P. Ji
Mathematics and Statistics Department Faculty Publication Series
Background: Rare single nucleotide variants play an important role in genetic diversity and heterogeneity of specific human disease. For example, an individual clinical sample can harbor rare mutations at minor frequencies. Genetic diversity within an individual clinical sample is oftentimes reflected in rare mutations. Therefore, detecting rare variants prior to treatment may prove to be a useful predictor for therapeutic response. Current rare variant detection algorithms using next generation DNA sequencing are limited by inherent sequencing error rate and platform availability. Findings: Here we describe an optimized implementation of a rare variant detection algorithm called RVD for use in targeted …
Terahertz Imaging For Cancer Detection, Benjamin A. St. Peter
Terahertz Imaging For Cancer Detection, Benjamin A. St. Peter
Masters Theses 1911 - February 2014
This project evaluates the ability of terahertz (THz) radiation to differentiate cancerous from non-cancerous human breast lumpectomy and mastectomy tissue. This is done by aiming a narrow-band THz beam at medical samples and measuring reflected power. THz images of specimens from Breast Conservation Surgery (BCS) were created using a gas laser source and mechanical scanning. The design and characterization of this system is discussed in detail. The images were correlated with optical histological micrographs of the same specimens and discrimination values of more than 70% were found for five of the six samples using Receiver Operating Characteristic (ROC) analysis.
Ultrasensitive Detection Of Rare Mutations Using Next-Generation Targeted Resequencing, Patrick Flaherty, Georges Natsoulis, Omkar Muralidharan, Mark Winters, Jason Buenrostro, John Bell, Sheldon Brown, Mark Holodniy, Nancy Zhang, Hanlee P. Ji
Ultrasensitive Detection Of Rare Mutations Using Next-Generation Targeted Resequencing, Patrick Flaherty, Georges Natsoulis, Omkar Muralidharan, Mark Winters, Jason Buenrostro, John Bell, Sheldon Brown, Mark Holodniy, Nancy Zhang, Hanlee P. Ji
Mathematics and Statistics Department Faculty Publication Series
With next-generation DNA sequencing technologies, one can interrogate a specific genomic region of interest at very high depth of coverage and identify less prevalent, rare mutations in heterogeneous clinical samples. However, the mutation detection levels are limited by the error rate of the sequencing technology as well as by the availability of variant-calling algorithms with high statistical power and low false positive rates. We demonstrate that we can robustly detect mutations at 0.1% fractional representation. This represents accurate detection of one mutant per every 1000 wild-type alleles. To achieve this sensitive level of mutation detection, we integrate a high accuracy …
Genome-Wide Requirements For Resistance To Functionally Distinct Dna-Damaging Agents, Patrick Flaherty
Genome-Wide Requirements For Resistance To Functionally Distinct Dna-Damaging Agents, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of ;4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNAdamage-response pathways as well as genes whose role in the DNA-damage …
A Latent Variable Model For Chemogenomic Profiling, Patrick Flaherty
A Latent Variable Model For Chemogenomic Profiling, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
Motivation: In haploinsufficiency profiling data, pleiotropic genes are often misclassified by clustering algorithms that impose the constraint that a gene or experiment belong to only one cluster. We have developed a general probabilistic model that clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure. Results: We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that …
Chemogenomic Profiling: Identifying The Functional Interactions Of Small Molecules In Yeast, Patrick Flaherty
Chemogenomic Profiling: Identifying The Functional Interactions Of Small Molecules In Yeast, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
We demonstrate the efficacy of a genome-wide protocol in yeast that allows the identification of those gene products that functionally interact with small molecules and result in the inhibition of cellular proliferation. Here we present results from screening 10 diverse compounds in 80 genome-wide experiments against the complete collection of heterozygous yeast deletion strains. These compounds include anticancer and antifungal agents, statins, alverine citrate, and dyclonine. In several cases, we identified previously known interactions; furthermore, in each case, our analysis revealed novel cellular interactions, even when the relationship between a compound and its cellular target had been well established. In …
Functional Profiling Of The Saccharomyces Cerevisiae Genome, Patrick Flaherty
Functional Profiling Of The Saccharomyces Cerevisiae Genome, Patrick Flaherty
Mathematics and Statistics Department Faculty Publication Series
Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth …