Life Sciences Commons^™

Large Scale Crowdsourced Radiotherapy Segmentations Across A Variety Of Cancer Anatomic Sites, Kareem A Wahid, Diana Lin, Onur Sahin, Michael Cislo, Benjamin E Nelms, Renjie He, Mohammed A Naser, Simon Duke, Michael V Sherer, John P Christodouleas, Abdallah S R Mohamed, James D Murphy, Clifton D Fuller, Erin F Gillespie

Faculty, Staff and Student Publications

Clinician generated segmentation of tumor and healthy tissue regions of interest (ROIs) on medical images is crucial for radiotherapy. However, interobserver segmentation variability has long been considered a significant detriment to the implementation of high-quality and consistent radiotherapy dose delivery. This has prompted the increasing development of automated segmentation approaches. However, extant segmentation datasets typically only provide segmentations generated by a limited number of annotators with varying, and often unspecified, levels of expertise. In this data descriptor, numerous clinician annotators manually generated segmentations for ROIs on computed tomography images across a variety of cancer sites (breast, sarcoma, head and neck, …

Potential Mitigation Of Environmental Impacts Of Intensive Plum Production In Southeast China With Maintenance Of High Yields: Evaluation Using Life Cycle Assessment, Xiaojun Yan, Delian Ye, Yafu Tang, Muhammad Atif Muneer, Peter Christie, Congyue Tou, Weidong Xu, Bingrong Shen, Jinxian Xu, Jiangzhou Zhang

Faculty, Staff and Student Publications

INTRODUCTION: Intensive plum production usually involves high yields but also high environmental costs due to excessive fertilizer inputs. Quantitative analysis of the environmental effects of plum production is thereby required in the development of optimum strategies to promote sustainable fruit production.

METHODS: We collected survey questionnaires from 254 plum production farms in Zhao'an county, Fujian province, southeast China to assess the environmental impacts by life cycle assessment (LCA) methodology. The farms were categorized into four groups based on yield and environmental impacts, i.e., LL (low yield and low environmental impact), LH (low yield but high environmental impact), HL (high yield …

Stellettin B Renders Glioblastoma Vulnerable To Poly (Adp-Ribose) Polymerase Inhibitors Via Suppressing Homology-Directed Repair, Xin Peng, Yingying Wang, Shaolu Zhang, Zhennan Tao, Yuxiang Dai, Francois X Claret, Moshe Elkabets, Hou-Wen Lin, Zhe-Sheng Chen, Dexin Kong

Faculty, Staff and Student Publications

No abstract provided.

Effect Of Type Of Mulch And Biological Soil Amendments Of Animal Origin (Bsaao) On Microbial Food Safety Risk On Cucumbers And Carrots Irrigated With Contaminated Or Chlorinated Water, Juan Fernando Moreira Calix

LSU Doctoral Dissertations

A comprehensive understanding of the effect biological soil amendments of animal origin and physical soil amendments have on produce contamination is important for developing strategies to mitigate this risk. Our studies investigated the persistence of generic E. coli, E. coli O157:H7 and Salmonella spp. in soil and produce surfaces with different BSAAO and mulch applications, as well as the effectiveness of chlorine treatments in reducing enteric bacteria in the field. Cucumbers harvested from plots with paper mulch had the highest levels of E. coli (3.76 Log CFU/cm²) while samples from maize mulch had the lowest levels (1.68 …

Tall Fescue Expressed Sequence Tag And Simple Sequence Repeats: Important Resources For Grass Species, Malay C. Saha, J. C. Zwonitzer, K. Chekhovskiy, M. A. R. Mian

IGC Proceedings (1977-2023)

Expressed sequence tag (EST) databases have been growing exponentially. The simple sequence repeat (SSR) has become one of the most useful molecular marker systems in plant breeding and is widely used in cultivar fingerprinting, genetic diversity assessment, molecular mapping and marker-assisted selection. ESTs are a potential source for SSRs. The EST-SSR markers are of high quality and have versatile applications in molecular breeding (Bughrara et al., 2003; Saha et al., 2004 a, b, c). Here, we present an overview of our efforts to develop SSRs from tall fescue ESTs and their application for the genetic improvement of forage …

Repulsion-Phase Linkage Analysis Of Tetraploid Creeping Bentgrass (Agrostis Stolonifera L.), S. E. Warnke, N. Chakraborty, G. Jung

IGC Proceedings (1977-2023)

Creeping bentgrass is a cool-season grass species primarily used on golf course greens, tees, and fairways because of its tolerance of low mowing heights and recuperative ability. Creeping bentgrass is tetraploid and outcrossing and has been characterized as having bivalent chromosome pairing through cytogenetic analysis (Jones, 1956) and disomic inheritance based on the inheritance of isozyme markers (Warnke et al., 1998). The objective of this experiment was to evaluate the extent of repulsion-phase linkages of single dose AFLP type markers in a creeping bentgrass mapping population and to infer chromosome pairing behaviour based on the ratio of coupling to …

A Core Aflp Map Of Aposporic Tetraploid Paspalum Notatum (Bahiagrass), J. P. A. Ortiz, J. Stein, E. J. Martínez, S. C. Pessino, C. L. Quarin

IGC Proceedings (1977-2023)

Paspalum notatum (Bahiagrass) is a perennial rhizomatous species that reproduces by aposporous apomixis. Tetraploid races (2n=4x=40) are widely distributed from Central to South America and constitute one of the most valuable natural forage grasses for the subtropical areas of Paraguay, southern Brazil and north-eastern Argentina. Apospory in the species is controlled by a single locus, which exhibits a distorted segregation ratio. The objectives of this work were to develop a core genetic linkage map of the species by using AFLP markers and characterize the genomic region related to apospory.

Towards A Genetic Map In Creeping Bentgrass Based On Ssrs, Aflps And Rflps, H. Zhao, S. Bughrara

IGC Proceedings (1977-2023)

Creeping bentgrass (Agrostis palustris) (2n=4x=28) is commonly used in golf course, putting green, tees and fairways. In spite of the importance of the species in turfgrass industry, the genetic study of the creeping bentgrass has received relatively little attention. Genetic mapping, as a new tool, helps traditional turfgrass breeding methods through the construction of linkage, identification of quantitative trait loci linked to traits of interest, and application of marker assisted selection program. Molecular markers such as AFLPs, SSRs and RFLPs have been used extensively for the preparation of linkage maps of a number of crop species. The objective …

Integration Of Perennial Ryegrass (L. Perenne) Genetic Maps Using Gene-Associated Snps, A. C. Vecchies, R. C. Ponting, M. C. Drayton, N. O. I. Cogan, K. F. Smith, G. C. Spangenberg, J. W. Forster

IGC Proceedings (1977-2023)

The reference genetic map of perennial ryegrass was developed by the International Lolium Genome Initiative (ILGI), using the p150/112 one-way pseudo-testcross population. A selection of public domain genetic markers including RFLPs, detected by wheat, barley, oat and rice cDNA probes, and AFLPs were mapped, allowing studies of comparative relationships between perennial ryegrass and other Poaceae species. The map was enhanced through the addition of unique perennial ryegrass genomic DNA-derived SSR (LPSSR) markers, providing the basis of framework genetic mapping in other populations. In addition, a small number of RFLP loci detected by candidate genes involved in herbage quality traits were …

Construction And Comparison Of Genetic Linkage Maps Of Four F1 Populations Of Italian Ryegrass (Lolium Multiflorum Lam.), M. Vandewalle

IGC Proceedings (1977-2023)

The objective of this work was to integrate genetic maps and QTL-positions within 4 two-way pseudo-testcross F1 populations (each 110 genotypes) of Italian ryegrass (Lolium multiflorum) To integrate genetic maps and QTL-positions within the 4 populations and to the ILGI reference map, the maps used for initial QTL-analysis and marker assisted selection for yield and for different quality traits were further evaluated.

Qtls For Morphogenetic Traits In Medicago Truncatula, B. Julier, T. Huguet, J. M. Prosperi, P. Barre, Christian Huyghe, G. Cardinet

IGC Proceedings (1977-2023)

Plant morphogenesis that includes growth, development and flowering date, drives a large number of agronomical important traits in both grain and forage crops. Quantitative trait locus (QTL) mapping is a way to locate zones of the genome that are involved in the variations observed in a segregating population. Co-location of QTLs and candidate genes is an indication of the involvement of the genes in the variation. The objective of this study was to analyse segregation of aerial morphogenetic traits in a mapping population of recombinant inbred lines of the model legume species M. truncatula , to locate QTLs and candidate …

A Comprehensive Analysis Of Gene Expression And Genomic Alterations In A Newly Formed Autotetraploid Of Paspalum Notatum, L. G. Martelotto, J. P. A. Ortiz, F. Espinoza, C. L. Quarin, S. C. Pessino

IGC Proceedings (1977-2023)

The proportion of angiosperms that have experienced one or more episodes of chromosome doubling is estimated to be of the order of 50-70%. This prominence of polyploidy probably implies some adaptive significance. The emergence of novel phenotypes could allow polyploids to enter new niches or enhance their chances of being selected for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through dosage-regulation, altered regulatory interactions and rapid genetic/epigenetic changes. The objective of this work was to carry out an extensive transcript profiling and genome analysis of …

Effects Of Sowing Date And Phosphorus Fertiliser Application On Winter Survival Of Lucerne Cv. Aohan In The Northern Semi-Arid Region Of China, Z. L. Wang, Q. Zh. Sun, Y. W. Wang, Zh. Y. Li, Sh. F. Zhao

IGC Proceedings (1977-2023)

In the northern semi-arid region of China, winter survival is always a limiting factor for lucerne production, because low temperatures and a dry climate in winter (Zhou et al., 1993; Ma, 2000; Sun & Gui, 2001; Sun et al., 2003). An experiment was conducted to find an appropriate sowing date and P application rate in order to improve lucerne winter survival.

The Top 50 Most Cited Articles On The Medial Patellofemoral Ligament (Mpfl): A Bibliometric Analysis, Varag Abed, Alex Duvall, Jonathan D. Rexroth, Alyssa Goodwin, Joseph Liu, Austin Stone

Medical Student Research Symposium

Objectives: To determine which original articles on the topic of the medial patellofemoral ligament (MPFL) have been cited the most in the literature utilizing a bibliometric approach. Secondarily, to determine temporal trends between article types.

Methods: Articles on the topic of the MPFL were identified by utilizing the Web of Science Database. The search yielded 1,596 results and the top 50 cited original articles were collected for further analysis. The following information was gathered for all included articles: title, first author's name, journal name, year of publication, impact factor of the journal in 2021, total number of citations of the …

Thymic Stromal Lymphopoietin Participates In The Host Response To Intra-Amniotic Inflammation Leading To Preterm Labor And Birth, Tomi Kanninen, Li Tao, Roberto Romero, Yi Xu, Marcia Arenas-Hernandez, Jose Galaz, Zhenjie Liu, Derek Miller, Dustyn Levenson, Jonathan M. Greenberg, Jonathan Panzer, Justin Padron, Kevin Theis, Nardhy Gomez-Lopez Phd

Medical Student Research Symposium

Objective: To determine if bacteria (Ureaplasma parvum and Sneathia spp.) associated with intra-amniotic infection can trigger the induction of cytokine Thymic stromal lymphopoietin (TSLP) in human amnion epithelial cells (hAECs) in vitro.

Material or subjects: Amniotic fluid and chorioamniotic membrane (CAM) were collected from women with sPTL who delivered at term (n=30) or preterm without intra-amniotic inflammation (n=34), with sterile intra-amniotic inflammation (SIAI, n=27), or with intra-amniotic infection (IAI, n=17). Amnion epithelial cells (AECs), Ureaplasma parvum, and Sneathia spp. were also utilized.

Methods: The expression of TSLP, TSLPR, and IL-7Rα was evaluated in amniotic fluid or CAM by …

Functional Analysis Provides Insight Into Missing Heritability, Scott L. Baughan, Michael A. Tainsky, Fatima Darwiche

Medical Student Research Symposium

Accurate ascertainment of genetic risk can be potentially lifesaving for patients who inherit cancer promoting mutations. However, even with the most extensive panel testing clinically available, a large number of patients will test negative despite family history of cancer or test positive for a variant of unknown significance (VUS). For these patients, clinical management is complicated; patients want to know their risk, and may fear disease they are not at great risk for (benign VUS) or they may not be given access to potentially lifesaving early screening procedures (pathogenic VUS). ATM has proven a challenge to clinicians due to its …

Glutamate, And Its Relationship To Task-Induced Functional Connectivity In The Human Brain: A Focus On Schizophrenia, Kathleen Liu Young, John Kopchick, Jeffrey Stanley, Vaibhav Diwadkar

Medical Student Research Symposium

Glutamate is the brain’s major excitatory neurotransmitter mediating both neuroplasticity and network function (Zhou & Danbolt, 2014). Basal glutamate (Glu) measured using proton magnetic resonance spectroscopy (1H-MRS) provides insight into a region’s density of neuropil related to the glutamatergic system. Moreover, given the role of glutamate in mediating brain network function, Glu levels may play a role in the brain’s functional connectivity (FC), which is typically estimated from functional magnetic resonance imaging (fMRI) time series data. These questions converge when considering the clinical syndrome of schizophrenia (SCZ). Patients with SCZ show abnormalities in basal Glu in the hippocampus and prefrontal …

Creating Habitat Suitability Models For Restoration Of Sesbania Tomentosa And Chenopodium Oahuense On Molokai, Hawaii, Bronwyn Meldrum

Undergraduate Honors Theses

Hawaii is home to incredible diversity in both plant and animal life. Nearly 90% of Hawaii’s 1,400 plant taxa are found nowhere else in the world, and in an ecosystem threatened by invasive species and terrain alteration, this puts them at risk of extinction. As pressures on global biodiversity intensify, conservation efforts and restoration of endangered species are of the utmost importance. The Molokai Land Trust is actively working to eradicate invasive kiawe (Prosopis pallida) forests and to restore endemic species and other native vegetation on the Mokio Preserve. These vital efforts are made more difficult because the …

Gabaergic Interneurons And Prenatal Ethanol Exposure: From Development To Aging, Adelaide R. Tousley

Dartmouth College Ph.D Dissertations

Fetal Alcohol Spectrum Disorders are the most common non-genetic cause of neurodevelopmental disability worldwide. Individuals with Fetal Alcohol Spectrum Disorder experience clinical symptoms including differences in physical, cognitive and behavioral development beginning in early childhood, but continue to face challenges into adulthood. There is a critical need to examine the effects of prenatal ethanol exposure across early development, and to establish how the developmental effects of prenatal ethanol exposure may or may not progress in aging individuals. To contribute to these two areas, I asked how a binge-type prenatal ethanol exposure might affect: (1) early postnatal development of striatal neurons …

An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali

All Works

Plants play a crucial role in supplying food globally. Various environmental factors lead to plant diseases which results in significant production losses. However, manual detection of plant diseases is a time-consuming and error-prone process. It can be an unreliable method of identifying and preventing the spread of plant diseases. Adopting advanced technologies such as Machine Learning (ML) and Deep Learning (DL) can help to overcome these challenges by enabling early identification of plant diseases. In this paper, the recent advancements in the use of ML and DL techniques for the identification of plant diseases are explored. The research focuses on …

Neural Mechanisms Of Language Development In Infancy, Scott Huberty, Christian O'Reilly, Virginia Carter Leno, Mandy Steiman, Sara J. Webb, Mayada Elsabbagh, The Basis Team

Publications

Understanding the neural processes underpinning individual differences in early language development is of increasing interest, as it is known to vary in typical development and to be quite heterogeneous in neurodevelopmental conditions. However, few studies to date have tested whether early brain measures are indicative of the developmental trajectory of language, as opposed to language outcomes at specific ages. We combined recordings from two longitudinal studies, including typically developing infants without a family history of autism, and infants with increased likelihood of developing autism (infant-siblings) (N = 191). Electroencephalograms (EEG) were recorded at 6 months, and behavioral assessments at …

Potassium-Selective Channelrhodopsins, Elena G Govorunova, Oleg A Sineshchekov, John L Spudich

Faculty, Staff and Student Publications

Since their discovery 21 years ago, channelrhodopsins have come of age and have become indispensable tools for optogenetic control of excitable cells such as neurons and myocytes. Potential therapeutic utility of channelrhodopsins has been proven by partial vision restoration in a human patient. Previously known channelrhodopsins are either proton channels, non-selective cation channels almost equally permeable to Na+ and K+ besides protons, or anion channels. Two years ago, we discovered a group of channelrhodopsins that exhibit over an order of magnitude higher selectivity for K+ than for Na+. These proteins, known as “kalium channelrhodopsins” or KCRs, lack the canonical tetrameric …

Movement, Behavior, And Trophic Ecology Of A Pelagic Predator Guild In The Eastern Tropical Pacific Ocean, Ryan Keith Logan

All HCAS Student Capstones, Theses, and Dissertations

Pelagic apex predators exert strong influences on ecological communities, and often support valuable commercial or recreational fisheries worldwide. Yet, due to their rarity and pelagic lifestyle, many species, such as billfishes, have proven particularly difficult to study at resolutions necessary to define dynamics of recovery from fishery interaction, physical interaction with environmental features and prey exploitation, and competitive interactions among other billfish predators. This leads to a paucity of knowledge on billfish ecology and habitat use, and hinders management efforts. With the ever-improving and miniaturization of technology and oceanographic datasets, the ability to define and quantify these interactions of fish …

Inland Dry Season Saline Intrusion In The Vietnamese Mekong River Delta Is Driving The Identification And Implementation Of Alternative Crops To Rice, Brooke Kaveney, Edward Barrett-Lennard, Khoi Chau Minh, Minh Dang Duy, Kim Phuong Nguyen Thi, Paul Kristiansen, Susan Orgill, Ben Stewart-Koster, Jason Condon

Grain and Other Field Crops Research Articles

CONTEXT
Inland saline intrusion is occurring during the dry season in the Mekong River Delta (MRD), Vietnam. Rising sea levels, tidal fluctuations, drought, and changes to upstream flow contribute to extensive salinisation of rice producing areas of the MRD, leading to substantial rice crop losses.

OBJECTIVE
The identification, evaluation and implementation of alternative crop and soil management solutions are required to complement on-going rice production in the region.

METHODS
A review of scientific and grey literature was conducted regarding the nature and extent of salinisation in the MRD and the adoption and management of alternative crops to rice.

RESULTS
Familiar …

Acupuncture Treatment For Post-Stroke Depression: Intestinal Microbiota And Its Role, Hailun Jiang, Shizhe Deng, Jieying Zhang, Junjie Chen, Boxuan Li, Weiming Zhu, Menglong Zhang, Chao Zhang, Zhihong Meng

Faculty, Staff and Student Publications

Stroke-induced depression is a common complication and an important risk factor for disability. Besides psychiatric symptoms, depressed patients may also exhibit a variety of gastrointestinal symptoms, and even take gastrointestinal symptoms as the primary reason for medical treatment. It is well documented that stress may disrupt the balance of the gut microbiome in patients suffering from post-stroke depression (PSD), and that disruption of the gut microbiome is closely related to the severity of the condition in depressed patients. Therefore, maintaining the balance of intestinal microbiota can be the focus of research on the mechanism of acupuncture in the treatment of …

Pasture Pig Basics, Jacob Hadfield, Jessie Hadfield, Joshua Dallin, Lorie Millward

All Current Publications

With an increasing push for more sustainable agriculture practices, raising pigs on pasture has gained much attention over recent years. Although it is possible to raise pigs on pasture, and this production method may support some sustainability goals, there are some important considerations. This fact sheet provides insight and answers to aspiring pig farmers so that they can make better-informed decisions before purchasing their pigs.

Characterisation Of Perennial Ryegrass Parental Inbred Lines For Generating Recombinant Inbred Lines For Fine Mapping And Gene Cloning, U. C. M. Anhalt, S. Barth, T. Schwarzacher, J. S. Heslop-Harrison

IGC Proceedings (1977-2023)

Intermated recombinant inbred lines (IRIs) are a powerful tool for fine mapping and cloning of genes. Such population structures have been particularly helpful for cloning of genes in the model genetic plant Arabidopsis thaliana. IRIs or recombinant inbred lines (RILs) would be valuable for perennial ryegrass (Lolium perenne), but its allogamous character means that the construction of RILs is a difficult task. The international Lolium community would benefit from the development of such lines. The aims of the projects are to characterise the parental lines and initial generations at the (1) phenotypic, (2) molecular and (3) molecular …

A High-Density Ssr Linkage Map Of Red Clover And Its Transferability To Other Legumes, S. Isobe, S. Sato, E. Asamizu, I. Klimenko, N. N. Kozlov, K. Okumura, S. Tabata

IGC Proceedings (1977-2023)

A high-density linkage map of red clover was constructed based on SSR and RFLP markers. In order to construct a linkage map with user (breeder) friendly markers; i.e. informative and easy detection, two policies were adopted for marker development. One was that the markers should be derived from cDNA or gene-rich regions, and the other was that the SSR markers should be detected polymorphisms on agarose gels. We also discuss the transferability of the markers on the map to other red clover germplasm and legumes. Such highly transferable markers could be used to screen anchor markers for both on a …

Development Of Est And Aflp Markers Linked To A Gene For Resistance To Ryegrass Blast (Pyricularia Sp.) In Italian Ryegrass (Lolium Multiflorum Lam.), Y. Miura, C. Ding, R. Ozaki, M. Hirata, M. Fujimori, H. Cai, K. Mizuno

IGC Proceedings (1977-2023)

Ryegrass blast, caused by the fungus Pyricularia sp. is one of the most serious diseases of Italian ryegrass (Lolium multiflorum Lam.). However, in Italian ryegrass, except for a new cultivar ‘Sachiaoba’, no resistant cultivars were found in Japan (Mizuno et al., 2003). For these reasons, improving the disease resistance of Italian ryegrass is one of the most important goals in the breeding programs. The aim of this study was to identify genes for resistance to ryegrass blast and to develop EST and AFLP markers linked tightly to the resistance genes.

Qtl Analysis And Trait Dissection In Ryegrass (Lolium Spp.), T. Yamada, J. W. Forster

IGC Proceedings (1977-2023)

Key points

1. Molecular marker-based genetic analysis permits the dissection of complex phenotypes through resolution of the locations of pleiotropic and interacting genetic factors.
2. Several QTLs for agronomically important characters such as flowering time, winter hardiness and forage quality have been identified in perennial ryegrass by molecular marker-based map analysis.
3. Some QTLs were putatively orthologous to those for equivalent traits in cereals.
4. The identification of co-location between QTLs and functionally-associated genetic markers is critical for the future implementation of marker-assisted selection programs.