Life Sciences Commons^™

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Clinical Diagnosis Support With Convolutional Neural Network By Transfer Learning, Spencer Fogleman, Jeremy Otsap, Sangrae Cho

SMU Data Science Review

Breast cancer is prevalent among women in the United States. Breast cancer screening is standard but requires a radiologist to review screening images to make a diagnosis. Diagnosis through the traditional screening method of mammography currently has an accuracy of about 78% for women of all ages and demographics. A more recent and precise technique called Digital Breast Tomosynthesis (DBT) has shown to be more promising but is less well studied. A machine learning model trained on DBT images has the potential to increase the success of identifying breast cancer and reduce the time it takes to diagnose a patient, …

Identification And Characterization Of Forest Fire Risk Zones Leveraging Machine Learning Methods, Joshua Balson, Matt Chinchilla, Cam Lu, Jeff Washburn, Nibhrat Lohia

SMU Data Science Review

Across the United States, record numbers of wildfires are observed costing billions of dollars in property damage, polluting the environment, and putting lives at risk. The ability of emergency management professionals, city planners, and private entities such as insurance companies to determine if an area is at higher risk of a fire breaking out has never been greater. This paper proposes a novel methodology for identifying and characterizing zones with increased risks of forest fires. Methods involving machine learning techniques use the widely available and recorded data, thus making it possible to implement the tool quickly.

Stationary Exercise Classification Using Imus And Deep Learning, Andrew M. Heroy, Zackary Gill, Samantha Sprague, David Stroud, John Santerre

SMU Data Science Review

In the current market, successful fitness tracking devices utilize heart rate and GPS to determine performance. These devices are useful, but don't extensively classify stationary exercise. This paper proposes a modern approach for tuning and investigating optimal neural network types on stationary exercises using Inertial Measurement Units (IMUs). Using three IMUs located on the ankle, waist, and wrist, data is collected to map the body as it moves during the stationary physical activity. A novel five-stage deep learning tuning system was written and deployed to classify user movement as one of three classes: air squats, jumping jacks, and kettlebell swings. …

Using Machine Learning For Antimicrobial Resistant Dna Identification, Jason I. Lingle, John Santerre

SMU Data Science Review

In this paper, we present a novel machine learning-based methodology for identifying bacteria DNA sub-sequences that are associated with antimicrobial resistance. The dramatic rise in cases of antibiotic resistant bacteria has been an increasing threat across the globe as the existing treatments are rendered ineffective in treating most of these cases due to mutations of their DNA. Among the most recent bacteria to display antimicrobial resistance (AMR) is Neisseria Gonorrhea with the first global treatment failure taking place in 2016. In 2018, new cases of resistance to multiple, high levels of antibiotics were reported in the United Kingdom and Australia. …

Identification And Classification Of Poultry Eggs: A Case Study Utilizing Computer Vision And Machine Learning, Jeremy Lubich, Kyle Thomas, Daniel W. Engels

SMU Data Science Review

We developed a method to identify, count, and classify chickens and eggs inside nesting boxes of a chicken coop. Utilizing an IoT AWS Deep Lens Camera for data capture and inferences, we trained and deployed a custom single-shot multibox (SSD) object detection and classification model. This allows us to monitor a complex environment with multiple chickens and eggs moving and appearing simultaneously within the video frames. The models can label video frames with classifications for 8 breeds of chickens and/or 4 colors of eggs, with 98% accuracy on chickens or eggs alone and 82.5% accuracy while detecting both types of …

Investigating The Roles Of Rna Binding Protein Combinations In Neuronal Function And Organismal Behavior, Alexa Vandenburg

SMU Journal of Undergraduate Research

The Norris lab recently identified two RNA binding proteins required for proper neuron-specific splicing. The lab conducted touch- response behavioral assays to assess the function of these proteins in touch-sensing neurons. After isolating C. elegans worms with specific phenotypes, the lab used automated computer tracking and video analysis to record the worms’ behavior. The behavior of mutant worms differed from that of wild-type worms.

The Norris lab also discovered two possible RNA binding protein sites in SAD-1, a neuronal gene implicated in the neuronal development of C. elegans1. These two binding sites may control the splicing of SAD-1. The lab …

Combinatorial Genetics Of Rna Binding Proteins For Lifespan Regulation In C. Elegans, Nikita Tapiawala

SMU Journal of Undergraduate Research

RNA binding proteins control post-transcriptional aspects of gene regulation. While transcriptional control over the aging process has been well-established, less is known about post-transcriptional control over the aging process. We have used CRISPR/Cas9 genetics to study combinations of RNA binding proteins in C. elegan, a transparent nematode or roundworm one millimeter in length, and their role in aging. The manner in which the research was conducted was through experimental laboratory work in which the lifespan of the nematodes was monitored until their death. The three mutations affecting RNA binding proteins that assays were performed with are exc-7, fox-1, and mbl-1. …

Investigating Peroxiredoxins Impact On Amps, Noah Earland

SMU Journal of Undergraduate Research

The Orr-Radyuk lab is interested in understanding the link between aging and genetic influences controlling the cell’s redox state, as determined by enzymes involved in reducing and oxidizing (redox) reactions. They have observed that Drosophila normally exhibit a shift towards a pro-oxidizing cellular environment and spikes in AMP levels, independent of infections, when they reach old age. Additionally, peroxiredoxins (PRXs), a family of thiol-dependent peroxidases, have been shown to impact lifespan, and regulate the same pro-oxidizing shift seen in advanced age. Beyond their peroxidase functions, RXRs can also interact with signaling pathways related to immunity. Previous data showed that PRXs …

The Systematic Position Of The Avian Species Metopothrix Aurantiacus, J. Alan Feduccia

Journal of the Graduate Research Center

The Orange-fronted Softtail, Metopotlzrix aurantiacus, now known to occur in the upper Amazon in southeastern Colombia, eastern Equador, eastern Peru, western Brazil, and northeastern Bolivia (Peters, 1951: 115) was described by Sclater and Salvin (1866: 190-191), who placed it in the Pipridae. Sclater (1888: 292) retained Metopothrix in the Pipridae without comment, placing it between Masius and Pipra. Berlepsch (1903: 108), in reviewing the systemic position of the genus stated that "this bird is not a Piprine [sic] form, as was believed by its describers, but a Dendrocolaptine [sic], closely allied to Xenerpestes, and agreeing with it in general characters …

Adrenal Corticosteroidogenesis And Hypothyroidsm: Effect Of Long-Term Treatment With P-Aminobenzoic Acid, John L. Mccarthy, Linda W. Laury

Journal of the Graduate Research Center

The relationship between induced hypothyroidism and adrenal involution has been studied by a variety of approaches in an attempt to elucidate the physiological basis between the events. McCarthy et al. (1959) reported on an investigation of feeding several antithyroidal agents to rats to study adrenal gland involution. While adrenal involution did occur following treatment with several of the goitrogens, only in one case was there a difference in peripheral plasma adrenal corticoid levels. In rats fed p-aminobenzoic acid (PABA) for 12 weeks, peripheral levels of corticosterone (B) decreased and levels of a Porter-Silber positive chromogen increased markedly. Work from the …

Preface, Joe P. Harris

Journal of the Graduate Research Center

When classes started in the Fall, 1969, at Southern Methodist University, it was the first time in forty-two years that Mayne Longnecker was not present to greet the new students on campus.

Natural History Of The Avian Families Dendrocolaptidae (Woodhewers) And Furnariiae (Ovenbirds), J. Alan Feduccia

Journal of the Graduate Research Center

During my investigations of the evolution of the woodhewers and ovenbirds I attempted to gather together data on the natural history of the groups and synthesize it into a meaningful form. In this summary I have stressed habitat, food, foraging behavior, and nidification. Although it should be realized that the present generic limits (Peters, 1951) are at best tentative, I thought it best to summarize the natural history according to the present classification. As most of the future changes in the classification of these groups will very likely involve lumping of genera, the information contained herein should remain separable to …

Fine Structure Of The Fibrillar Flight Muscles In The Housefly, Musca Domestica (Diptera), R. S. Sohal, V. F. Allison

Journal of the Graduate Research Center

Insects of the orders Hemiptera, Hymenoptera, Coleoptera and Diptera have developed an asynchronous flight mechanism. The frequency of the muscle contraction is not directly related to the rate of nervous stimulation (Pringle 1965). An initial nervous stimulus produces an active state in the flight muscle during which a variable number of oscillatory contractions take place. Consequently, insects like the house-fly can maintain a very high frequency of wing beat (180-200 per second). Asynchronous flight muscles differ from the vertebrate skeletal muscles and insect synchronous flight muscles; in the latter each nerve impulse produces a single contraction of the innervated fibres. …

A New Shorebird From The Upper Pliocene, J. Alan Feduccia

Journal of the Graduate Research Center

One of the avian fossils recovered from the Saw Rock Canyon local fauna of the Upper Pliocene of Seward County, Kansas, is the humerus of a scolopacine shorebird which closely resembles the Recent Tringa solitaria. Present evidence favors a late Hemphillian age for the fauna (Hibbard, 1964. Pap. Michigan Acad. Sci., Arts, and Letters, 49: 115-127), and the fauna is taken from a lower section of the Rexroad formation than are the Fox Canyon and Rexroad local faunas of the Rexroad formation of Meade County, Kansas. Many of the mammals in the Saw Rock Canyon local fauna are considered to …

Fine Structure Of Nucleoli In Cells Of Encysted Hymenolepis Diminuta, John E. Ubelaker

Journal of the Graduate Research Center

Studies of the fine structure of 5 day old cysticercoids of H. diminuta revealed nucleoli with well-formed lamellae in germinal cells within the body of the encysted worm. The nucleoli were located centrally in the nucleus and appeared not to be attached to the chromosomes, chromatin, or to the nuclear envelope.

Evidences Of Diurnal Feeding Activity In Trichoptera Larvae, John O. Mecom

Journal of the Graduate Research Center

The literature of the aquatic insect order Trichoptera (caddisflies) is extensive. Ross (1944), Denning (1950a, 1950b, 1954, 1956), Banks (1944) and Betten (1934), among others, have been major contributors to the taxonomy and zoogeography of North American species. Important studies of the general ecology of both adult and larval forms have been made by Lloyd (1921), Scott (1958), and Hynes (1961) but Mecom and Cummins (1964) have commented on the limited knowledge of the trophic relationships of Trichoptera. Hanna (1957), Jones (1950), Chapman and Demory (1963) studied the food ingested by Trichoptera larvae, but except for the very limited experiments …

Dialysis Studies Of The K+ Binding Capacity Of Physarum Polycephalum, Claude Nations

Journal of the Graduate Research Center

Anderson (1964) has observed that migrating plasmodia of the slime mold, Physarum polycephalum, maintain a higher concentration of K+ in the region of the advancing front than in the posterior trailing region. He has also found that most of the Na- but little of the K+ in the posterior region can be removed by flushing water over the organism. Previous work by Anderson (1962) had revealed that alcohol precipitates prepared from plasmodial homogenates contain considerable quantities of K- which cannot be removed by washing. Based on these discoveries he has suggested that K+, but not Na+ is closely associated with …

Morphological Variation In Cephalogonimus Americanus (Trematoda: Cephalogonimidae) From Amphibians In Colorado, John E. Ubelaker, John D. Kimbrough

Journal of the Graduate Research Center

A collection of western toads, Bufo boreas Baird and Girard, 1852, and neotenic tiger salamanders, Ambystoma tigrinum (Green) from Sheep Lake, Horseshoe Park, Rocky Mountain National Park, Colorado, were examined for helminths in the spring of 1966. Oswaldo-Cruzia subauricularis (Rudolphi, 1819) was found in Bufo boreas and Ophiotaenia filarioides (LaRue, 1909) in Ambystoma tigrinum. In addition, both hosts harbored Spironoura pretiosa Ingles, 1936, Phylloclistomum bufonis Frandsen, 1957 and Cephalogonimus americanus. The last species differed greatly in appearance in the two hosts and these differences are reported herein.

Zoogeography Of Bats, Karl F. Koopman

Fondren Science Series

The Order Chiroptera is the second largest order of mammals, with, according to my most recent revised figure, 846 species. Inasmuch as the group is world-wide, reaching many distant islands, and inasmuch as many species and higher groups are quite localized and some very distinctive, one might expect that a good deal of work on bat zoogeography would have been undertaken. However, such is not the case. Darlington (1957, pp. 320-410) does discuss the general geographical patterns of bats, and Tate (1946) gives a useful analysis of the bats of the Malay archipelago. However, many writers on zoogeography have given …

Bats: Carriers Of Human Disease-Producing Agents, Robert J. Baker

Fondren Science Series

For many years bats have been known to be harbingers of various agents which produce disease in man. Elsewhere in this volume certain parasites of bats are discussed including the association of these animals with Trypanosoma cruzi in South America and Texas (Ubelaker, 1970). Little is known concerning the association of bats with bacteria which cause disease in man. Four serotypes of Salmonella known to cause salmonellosis have been isolated from bats, one from bats collected in the Canal Zone (Klite & Kourany, 1965) and the other three from bats collected in southwestern Colombia, South America (Arata et al., 1968). …

Classification Of Bats, F. Koopman, J. Knox Jones Jr.

Fondren Science Series

In the 10th edition of Systema Naturae, published in 1758 and the starting point of the binomial system of nomenclature currently employed in zoology, Linnaeus recognized seven species of bats, which he placed in a single genus (Vespertilio) and grouped with the primates and dermopterans. All of Linnaeus's seven species are recognized today, but as they now are classified each represents a distinctive genus, and the genera are arranged taxonomically in five different families of two suborders. In contrast to Linnaeus's scheme, the present classification of bats (long ago placed in a distinct order, Chiroptera) lists 847 Recent species, belonging …

Adaptations For Flight In Bats, Terry A. Vaughan

Fondren Science Series

Flight developed independently in three groups of vertebrates. From reptilian ancestry arose the pterosaurs and the birds, and bats evolved from primitive mammals. Pterosaurs became extinct, together with their relatives the dinosaurs, more than 75 million years ago, whereas both birds and bats are still remarkably successful today. Pterosaurs probably used mostly gliding flight, but birds and bats use primarily flapping flight. Birds and bats use different styles of flight, probably as a result of the different ways in which these animals perceive their environments. Vision, which is used by birds for orientation, allows the recognition of obstacles at considerable …

Feed Mechanisms Of Bats, Bryan P. Glass

Fondren Science Series

It is a fair generalization that in food habits bats may be divided into two major categories, those which are carnivores, and those which are not. Since the molariform dentition of carnivorous species more nearly resembles that of other Mesozoic mammals than the dentition of non-carnivorous bats, it is generally agreed that the carnivorous dentition is primitive, and the more specialized dentitions are derived therefrom. Being carnivorous therefore restricts the freedom of the dentition to evolve. Structural differences between kinds of carnivores are found in means of apprehension of prey rather than in dentition, and often involve specialization of other …

Chiropteran Reproduction, Dilford C. Carter

Fondren Science Series

Knowledge of chiropteran reproduction increased sufficiently after Allen's (1939) review of this subject so that Asdell (1964) could present a systematic and somewhat comparative account of breeding periods and number of young produced. Brosset (1966) briefly discussed some general and secondary aspects of bat reproduction. A continued accumulation of reproductive data strengthens some of our concepts and necessitates our alteration of some views. Fragmentary information from a reasonable variety of species indicates greater variability in chiropteran reproduction than would seem the case from the few detailed studies published.

Bat Conservation, Edwin Gould

Fondren Science Series

Since we know that some bat populations attain astronomical size, bat conservation may seem inconsequential. However, during the past 10 to 20 years, some bat-banders and other mammalogists have reported a decrease of bats in hibernating cave colonies. In general, summer colonies of most species of bats are dispersed; from these sites migrating bats converge on relatively few caves in which they hibernate. Some species are probably most vulnerable in at least the following four situations. 1. Hibernating bats that roost in caves or mines may be destroyed by teenagers or adults who have no concern for the bats. 2. …

Thermoregulation In Bats, Robert E. Henshaw

Fondren Science Series

Much controversy surrounds the ability of bats to thermoregulate, especially within the hibernating state. The general conception is that all bats become poikilothermic daily and also over-winter in deep hibernation. In fact, as much diversity exists in thermoregulatory patterns in the Order Chiroptera as exists in all of the rest of the mammals. Some species maintain their body temperature with a precision of + or - 1 ° C, whether active or asleep; while other species can remain in deep torpidity with the body temperature near 0°C for several months without arousal. The intent of the present paper is to …

Chiropteran Mortality, David D. Gillette, John D. Kimbrough

Fondren Science Series

The study of chiropteran mortality is a difficult one because observations concerning mass mortality, predation, and fatal accidents are sporadic and unexpected. Almost every known predaceous animal preys on bats from time to time; but (with one or two rare exceptions) do so only when an occasional opportunity presents itself, and do not specialize in bat predation. Our knowledge of bat pathology is meager. Mass-mortalities have been reported only from sight observations, and the causative organisms rarely ascertained, because of the unexpected encounter. The relationships between human and chiropteran diseases are becoming much better understood; this study is mostly oriented …

The Role Of Karyotypes In Phylogenetic Studies Of Bats, Edwin Gould

Fondren Science Series

There are several reasons for using chromosome form and number (the karyotype) in phylogenetic studies. Since the material of the genotype forms part of the chromosomes, the karyotype is less influenced by external factors than are other morphological and physiological characteristics (John and Lewis, 1966). There are, however, two obvious ways natural selection can act on changes in the karyotype. The first involves the ability of the karyotype to proceed through the mechanics of mitosis or meiosis. If mitosis is blocked the cell line would die. If the rearrangement interferes with proper functioning of meiosis the result is reduced or …

Preface, Bob H. Slaughter

Fondren Science Series

Madison Avenue has been using the "think tank" or "Brain storming" approach for decades in the solution of difficult problems. Although the discussion of the same or similar problems by specialists in different disciplines works equally as well in science, the technique has not been in wide use. The symposium can stimulate this type of cross-fertilization of ideas and is gaining popularity, especially in Quaternary studies.