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An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald 2019 University of Massachusetts Medical School

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

Open Access Articles

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. In addition, our method enables state estimation on multivariate Gaussian signals. We validate our approach using simulated data, and benchmark the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We ...


Undergraduate Research And Teaching At Oak Lake Field Station, Lan Xu 2019 South Dakota State University

Undergraduate Research And Teaching At Oak Lake Field Station, Lan Xu

Oak Lake Field Station 30th Anniversary Retreat Presentations

No abstract provided.


Effects Of A Race Timer On The Three Minute All-Out Test For Critical Power, Paul K. Mandell 2019 Humboldt State University

Effects Of A Race Timer On The Three Minute All-Out Test For Critical Power, Paul K. Mandell

Theses and projects

Maximal exercise testing is commonly employed by exercise scientists in order to assess an athlete's’ capabilities and inform future training goals and tactics. The Critical Power (CP) concept provides a novel perspective on the physiological capacity of an individual to perform work. The 3 Minute All-Out Test (3MT) for critical power was developed by Vanhatalo, Doust, & Burnley in 2006. Concerns about pacing during the test lead to the development of protocol which blinds participants to time during the test. Twelve healthy active males were recruited to participate in the current study on the effects of a race timer on ...


Effects Of Acute Hypoxia On Danio Rerio, Karly Crail 2019 The University of Akron

Effects Of Acute Hypoxia On Danio Rerio, Karly Crail

Williams Honors College, Honors Research Projects

The purpose of this research experiment was to determine the effects of acute hypoxia on the embryonic zebrafish (Danio rerio) cardiovascular system and assess the critical oxygen level at which embryonic function is compromised. This goal was achieved by exposing embryos to decreasing oxygen concentrations, (6.0 mg/L-0 mg/L) and observing the heart under an inverted microscope. Data analysis was conducted to determine end systolic volume, end diastolic volume, stroke volume, heart rate, and cardiac output. It was hypothesized that hypoxia would stimulate cardiac activity, because in early developmental stages, tissues are supplied with oxygen through bulk diffusion ...


Suction Dredge Mining Impacts On Pacific Lamprey Populations And Habitat In Washington State: A Case Study Of The Entiat River, Jaime Liljegren 2019 Central Washington University

Suction Dredge Mining Impacts On Pacific Lamprey Populations And Habitat In Washington State: A Case Study Of The Entiat River, Jaime Liljegren

All Master's Theses

Suction dredge mining is a largely unregulated recreational activity in Washington State with potentially significant impacts to aquatic habitat. Although dredging has the potential to cause widespread ecological effects, only impacts to select species have been thoroughly assessed. Due to their reliance on freshwater habitat throughout multiple life stages, Pacific lamprey are significantly vulnerable to impacts from dredging practices. This thesis focuses on assessing the effects of dredging to lamprey habitat within state-owned aquatic lands of Washington. Pacific lamprey are anadromous, utilizing freshwater habitat throughout key life stages including spawning in substrate ranging from coarse gravel to fine sand, and ...


Mechanisms And Mitigation Of Skeletal Muscle Fatigue In Single Fibers From Older Adults, Aurora Foster 2019 University of Massachusetts Amherst

Mechanisms And Mitigation Of Skeletal Muscle Fatigue In Single Fibers From Older Adults, Aurora Foster

Masters Theses

Skeletal muscle fatigue is the contraction-induced decline in whole muscle force or power, and can be greater in older versus young adults. Fatigue primarily results from increased metabolism elevating phosphate (Pi) and hydrogen (H+), which alters myosin-actin interactions; however, which steps of the myosin-actin cross-bridge cycle are changed and their reversibility are unclear. PURPOSE: This study sought to: 1) Examine the effects of elevated Pi and H+ on molecular and cellular function, and 2) Test the ability of deoxyadenosine triphosphate (dATP), an alternative energy to adenosine triphosphate (ATP), to reverse the contractile changes induced with high Pi ...


Examination Of The Role Of Neuroimmune Signaling In Drug Addiction, Catherine Levy 2019 University of Colorado, Boulder

Examination Of The Role Of Neuroimmune Signaling In Drug Addiction, Catherine Levy

Undergraduate Honors Theses

Cocaine and oxycodone addictions are chronic, relapsing disorders characterized by maladaptive patterns of drug seeking that create significant impairment for the user. While the homeostatic functions of neuroimmune cells such as microglia and astrocytes have been well characterized, little work has examined the structural and functional alterations of these neuroglial cells following repeated drug intake. The first experiment of this study used male and female Sprague-Dawley rats to examine sex differences in microglial cells following repeated cocaine intake. The second experiment used a rodent model of oxycodone self-administration to test the ability of ibudilast, a non-selective anti-inflammatory drug, to reduce ...


Relación Entre La Grasa Subcutánea Y Desempeño Maternal En Vacas Angus Primerizas, Esteban Mendoza de la Pava, Adel David Kalil Rey 2019 Universidad de La Salle, Bogotá

Relación Entre La Grasa Subcutánea Y Desempeño Maternal En Vacas Angus Primerizas, Esteban Mendoza De La Pava, Adel David Kalil Rey

Zootecnia

El objetivo del presente estudio, tuvo como finalidad lograr identificar el porcentaje de grasa dorsal que se moviliza en vacas Angus primerizas posterior al parto y cómo este podría verse relacionado con el desempeño maternal y el peso al destete del ternero. Para poder lograr este objetivo, se evaluaron doce vacas primerizas de la raza Angus del CIC (centro de investigación y capacitación) San Miguel en Facatativa, Cundinamarca, con diversos parámetros productivos como: peso corporal, puntaje de condición corporal del preparto y al destete, espesor de grasa dorsal (preparto y destete), espesor de grasa en el anca (preparto y destete ...


Smart Sheep Need More Protection, Michael L. Woodruff 2019 East Tennessee State University

Smart Sheep Need More Protection, Michael L. Woodruff

Animal Sentience

The target article unequivocally establishes that sheep are far more intelligent and cognitively sophisticated than is generally acknowledged. For this reason, the authors advocate for significantly more stringent regulation of agricultural and research practices when sheep are used. I briefly review the existing US regulations governing the use of sheep in research and discuss the extent to which they are applied to sheep. I then discuss weaknesses in the current regulations, concluding that they should be changed to mandate housing all research animals in environments that accommodate the psychosocial needs of each species.


Modified Open-Field Test With Odor Search Stimulus: Anticipated Canine Motivation And Behavioral Outcomes Between Anxious And Non-Anxious Dogs, Savanna Bergeron 2019 Iowa State University

Modified Open-Field Test With Odor Search Stimulus: Anticipated Canine Motivation And Behavioral Outcomes Between Anxious And Non-Anxious Dogs, Savanna Bergeron

Creative Components

Fear is an emotion that is necessary to survive, but when it’s prolonged and frequent, it can cause suffering in both animals and humans. Fear and anxiety are interrelated; therefore, fear can cause anxiety and anxiety can cause fear. Treatments for anxiety behaviors are currently an ongoing process, in order to improve the mental health of the animal. This review is focused on trying to understand anxiety behaviors through the use of a modified open-field test. More specifically, an odor search stimulus is used in conjunction with dogs on L-DOPA treatments. Previous animal models, particularly the mouse and rat ...


The Effect Of Manipulating Vertical Motion On Running Economy, Claire Copriviza 2019 Humboldt State University

The Effect Of Manipulating Vertical Motion On Running Economy, Claire Copriviza

Theses and projects

While several biomechanical factors have been identified as key determinants of running economy (i.e. metabolic cost), the influence of individual mechanical factors such as center of mass vertical motion (ΔCoMz) remains unclear. The purpose of this study was to determine how manipulating ΔCoMz effects running economy. Twelve runners used a visual biofeedback system to control their ΔCoMz during running as we measured the metabolic, kinematic, and muscle activation responses to the different levels of ΔCoMz. Running economy was strongly correlated to ΔCoMz and was optimized at an intermediate center of mass vertical motion of ...


Elucidating Immune Signaling Of Influenza A Virus And Aspergillus Fumigatus Co-Infections Through Pioneered Model Development, Meagan Danyelle Rippee-Brooks 2019 Missouri State University

Elucidating Immune Signaling Of Influenza A Virus And Aspergillus Fumigatus Co-Infections Through Pioneered Model Development, Meagan Danyelle Rippee-Brooks

MSU Graduate Theses

Bacterial co-infections with influenza A virus (IAV) are extremely serious and life-threatening. However, there exists limited understanding about the importance of fungal infections with IAV. Clinical case reports indicate that fungal co-infections do occur and suggest the IAV pandemic of 2009 had a propensity to predispose patients to secondary fungal infections more than previous IAV strains. IAV-fungal co-infections are marked by high mortality rates of 47 to 61% in previously healthy individuals between the ages of 20 and 60. Yet, the variables involved in this co-infection remain undetermined. I achieved effective recapitulation of this co-infection using a C57Bl/6 murine ...


Neuronal And Glial Expression Of Glun2c And Glun2d Nmda Receptor Subunit Mrna In Different Regions Of The Mouse Forebrain, Hassan Alsaad 2018 University of Nebraska Medical Center

Neuronal And Glial Expression Of Glun2c And Glun2d Nmda Receptor Subunit Mrna In Different Regions Of The Mouse Forebrain, Hassan Alsaad

Theses & Dissertations

N-methyl-D-aspartate (NMDA) receptors are a subtype of glutamate receptors that are widely expressed in the brain, where they mediate critical functions. While the actions of the predominate GluN2 NMDAR subunits, GluN2A and GluN2B are relatively well understood, the function of GluN2C and GluN2D in the telencephalon is largely unknown. To better understand the possible role of GluN2C and GluN2D subunits, we used fluorescence in situ hybridization together with multiple cell markers to define the distribution and type of cells expressing GluN2C and GluN2D mRNA. Also, a GluN2C-KO mouse was used as a negative control.

GluN2C mRNA expression was only found ...


Alternatives To Laboratory Animals: Definition And Discussion, Andrew N. Rowan 2018 The Institute for the Study of Animal Problems

Alternatives To Laboratory Animals: Definition And Discussion, Andrew N. Rowan

Andrew N. Rowan, DPhil

The origins of the concept of "alternatives" to the use of animals in research may be traced back to the 1800's and the furore about using live animals in surgical and other experiments. Some of the animal protection societies in England were prepared to accept animal experimentation provided it was performed under anesthesia. Even Dr. Marshall Hall, who championed the spread of experimental medicine in 19th century England, considered it necessary to control and prevent unwarranted, inept and cruel experimentation (French, 1975). The concept of alternatives has developed in the 20th century to encompass not only the reduction (prevention ...


Behavioral Insights Into Nociceptor Function: A Systematic Approach To Understanding Postsurgical And Neuropathic Pain Mechanisms In Rats, Max Odem 2018 The Univesity of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Behavioral Insights Into Nociceptor Function: A Systematic Approach To Understanding Postsurgical And Neuropathic Pain Mechanisms In Rats, Max Odem

UT GSBS Dissertations and Theses (Open Access)

Postsurgical and neuropathic pain are each clinically common, and often associated with ongoing pain. Ongoing pain has been linked to ongoing activity (OA) in human C-fiber nociceptors. Preclinical studies using rodent neuropathic models have concentrated on allodynia driven by OA generated in non-nociceptive Aβ fibers, but little attention has been paid to postsurgical pain in sham controls or to C-fiber nociceptor OA promoting ongoing pain.

Operant assays that reveal negative motivational and cognitive aspects of voluntary pain-related behavior may be particularly sensitive to pain-related alterations. In the mechanical conflict (MC) test, rodents can freely choose to escape from a brightly ...


The Role Of Tumor Suppressor Dear1 In The Acquisition Of Mammary Stem/Progenitor Cell Properties, Uyen Le 2018 The University of Texas M D Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

The Role Of Tumor Suppressor Dear1 In The Acquisition Of Mammary Stem/Progenitor Cell Properties, Uyen Le

UT GSBS Dissertations and Theses (Open Access)

Breast cancer is the most commonly diagnosed cancer in women in America. Ductal carcinoma in situ (DCIS), one of the earliest pre-invasive forms of invasive ductal carcinoma (IDC), has a 30-50% risk of progressing to IDC. Understanding the mechanisms regulating progression from DCIS to IDC would help identify biomarkers to stratify patients at higher risk of progression or metastasis. Cumulative literature suggests the earliest phase of dissemination from the primary tumor is driven by the epithelial-mesenchymal transition (EMT) program. DEAR1 is a tumor suppressor gene which is mutated, undergoes loss of heterozygosity in breast cancer, and is downregulated in DCIS ...


22 - Bugs In Bugs, Josemaria Garcia 2018 University of North Georgia

22 - Bugs In Bugs, Josemaria Garcia

Georgia Undergraduate Research Conference (GURC)

The primary purpose of the Bugs in Bugs project is to measure a student’s ability to go complete a research report and to observe demonstrations of key fundamental research aspects such as understanding scientific works, collecting and entering data, analyzing and creating graphs, and overall how to write a lab report. Working with Principles of Biology II and Microbiology classes, students were provided with a topic and methodology respective to their class; however, groups within the classes had the freedom to create their own hypotheses and theses, choose how to collect and interpret data, make charts and graphs, and ...


Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza 2018 California State University, Los Angeles

Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza

STAR (STEM Teacher and Researcher) Presentations

Cell-free protein synthesis (CFPS) has emerged as an enabling biotechnology for research and biomanufacturing as it allows for the production of protein without the need for a living cell. Applications of CFPS include the construction of libraries for functional genomics and structural biology, the production of personalized medicine, and the expression of virus-like particles. The absence of a cell wall provides an open platform for direct manipulation of the reaction conditions and biological machinery. This project focuses on adapting the CFPS biotechnology to the classroom, making a hands-on bioengineering approach to learning protein synthesis accessible to students grades K-16 through ...


A Forest To Shore Celebration, 2018 Selected Works

A Forest To Shore Celebration

Jennifer Mattei

Mattei’s lecture and walk on the Living Shoreline was a highlight of Stratford’s Forest to Shore Day, which took place Saturday, Sept 22, throughout the town. The family-oriented program consisted of a variety of free events highlighting the town’s natural, cultural and recreational resources.


Personal Safety Culture: A New Measure For General Aviation Pilots, Bradley S. Baugh, Kimberly M. Bracewell, Urara Takano, Mattie N. Milner, Emily C. Anania, Nadine K. Ragbir, Mudhur Bharat Gupta, Diego M. Garcia, Drishti O. Valecha, Daniel A. Marte, Scott R. Winter, Stephen Rice 2018 Embry-Riddle Aeronautical University

Personal Safety Culture: A New Measure For General Aviation Pilots, Bradley S. Baugh, Kimberly M. Bracewell, Urara Takano, Mattie N. Milner, Emily C. Anania, Nadine K. Ragbir, Mudhur Bharat Gupta, Diego M. Garcia, Drishti O. Valecha, Daniel A. Marte, Scott R. Winter, Stephen Rice

National Training Aircraft Symposium (NTAS)

Safety culture has been a subject of research for over three decades and is now widely accepted as a critical component of organizational safety programs both domestically and internationally. Through the development of a healthy safety culture, aviation organizations can improve safety processes, reduce mishaps, and mitigate risk more effectively. This is done through the holistic team efforts of an organization’s members and the organization’s leadership. How about aviators who are not part of an organization? Is it possible to identify a personal safety culture defined outside of the traditional organization? And, is it possible to create an ...


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