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2023

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Embeddable Soil Moisture Content Sensor Based On Open–End Microwave Coaxial Cable Resonator, Jing Guo, Yan Tang, Yongji Wu, Chen Zhu, Jie Huang Jan 2023

Embeddable Soil Moisture Content Sensor Based On Open–End Microwave Coaxial Cable Resonator, Jing Guo, Yan Tang, Yongji Wu, Chen Zhu, Jie Huang

Electrical and Computer Engineering Faculty Research & Creative Works

In This Paper, We Propose and Demonstrate a Novel Corrosion-Resistant, Embeddable Open-End Coaxial Cable Soil Moisture Sensor. This Microwave Resonator is Constructed using Two Reflectors Along the Coaxial Line. the First Reflector is a Metal Post at the Signal Input End, Short-Circuiting the Inner Conductor to the Outer Conductor. the Second Reflector Comprises a Welded Metal Plate Parallel to the Open-End of the Coaxial Line, Maintaining a Fixed Gap. a Moisture-Sensitive Polyvinyl Alcohol (PVA) Film is Inserted into This Gap. the Resonance Frequency of the Open-End Coaxial Cable Resonator is Highly Dependent on the Fringe Capacitance, Which Varies with Soil …


Chemical Classification By Monitoring Liquid Evaporation Using Extrinsic Fabry-Perot Interferometer With Microwave Photonics, Abhishek Prakash Hungund, Bohong Zhang, Anand Nambisan, Wassana Naku, Rex E. Gerald, Jie Huang Jan 2023

Chemical Classification By Monitoring Liquid Evaporation Using Extrinsic Fabry-Perot Interferometer With Microwave Photonics, Abhishek Prakash Hungund, Bohong Zhang, Anand Nambisan, Wassana Naku, Rex E. Gerald, Jie Huang

Electrical and Computer Engineering Faculty Research & Creative Works

Identification of liquids is essential in chemical analysis, safety, environmental protection, quality control, and research. A novel liquid identification system based on Microwave Photonics (MWP) measured time transient evaporation signals is investigated. An extrinsic Fabry-Perot Interferometer (EFPI) based optical probe using single-mode fiber (SMF) is proposed to monitor evaporation of different liquids. The MWP system is used to measure the optical path changes during liquid evaporation due to its high sensitivity, selectivity, and Signal-to-Noise Ratio (SNR). The measured S21 continuous wave (CW) time Magnitude and Phase signals were processed to extract features such as histogram and Fast Fourier Transform (FFT) …


Three-Dimensional Environmentally Sustainable Neuromorphic Computing System Based On Natural Organic Memristor, Jinhui Wang, Feng Zhao, Mohammed Rafeeq Khan, Md Mehedi Hasan Tanim, Zoe Templin Jan 2023

Three-Dimensional Environmentally Sustainable Neuromorphic Computing System Based On Natural Organic Memristor, Jinhui Wang, Feng Zhao, Mohammed Rafeeq Khan, Md Mehedi Hasan Tanim, Zoe Templin

Electrical and Computer Engineering Faculty Research & Creative Works

Three-dimensional environmentally sustainable neuromorphic computing system based on natural organic honey-memristor is proposed in this paper. The experimental results indicate the proposed systems have high inference accuracy over 90 % with device variation and nonlinearity. What is more, four conductance drift scenarios, ADC (Analog-to-Digital Converter) quantization effects, and different algorithms (VGG8 and DenseNet-40) are considered to further verify the proposed systems.


Symmetric Data-Driven Fusion Of Diffusion Tensor Mri: Age Differences In White Matter, Andrea Mendez Colmenares, Michelle B Hefner, Vince D Calhoun, Elizabeth A Salerno, Jason Fanning, Neha P Gothe, Edward Mcauley, Arthur F Kramer, Agnieszka Z Burzynska Jan 2023

Symmetric Data-Driven Fusion Of Diffusion Tensor Mri: Age Differences In White Matter, Andrea Mendez Colmenares, Michelle B Hefner, Vince D Calhoun, Elizabeth A Salerno, Jason Fanning, Neha P Gothe, Edward Mcauley, Arthur F Kramer, Agnieszka Z Burzynska

2020-Current year OA Pubs

In the past 20 years, white matter (WM) microstructure has been studied predominantly using diffusion tensor imaging (DTI). Decreases in fractional anisotropy (FA) and increases in mean (MD) and radial diffusivity (RD) have been consistently reported in healthy aging and neurodegenerative diseases. To date, DTI parameters have been studied individually (e.g., only FA) and separately (i.e., without using the joint information across them). This approach gives limited insights into WM pathology, increases the number of multiple comparisons, and yields inconsistent correlations with cognition. To take full advantage of the information in a DTI dataset, we present the first application of …


A Universal Neocortical Mask For Centiloid Quantification, Pierrick Bourgeat, Vincent Doré, Christopher C Rowe, Tammie Benzinger, Duygu Tosun, Manu S Goyal, Pamela Lamontagne, Liang Jin, Michael W Weiner, Colin L Masters, Jurgen Fripp, Victor L Villemagne, Alzheimer's Disease Neuroimaging Initiative; Oasis3, Aibl Research Group Jan 2023

A Universal Neocortical Mask For Centiloid Quantification, Pierrick Bourgeat, Vincent Doré, Christopher C Rowe, Tammie Benzinger, Duygu Tosun, Manu S Goyal, Pamela Lamontagne, Liang Jin, Michael W Weiner, Colin L Masters, Jurgen Fripp, Victor L Villemagne, Alzheimer's Disease Neuroimaging Initiative; Oasis3, Aibl Research Group

2020-Current year OA Pubs

INTRODUCTION: The Centiloid (CL) project was developed to harmonize the quantification of amyloid beta (Aβ) positron emission tomography (PET) scans to a unified scale. The CL neocortical mask was defined using

METHODS: Using data from the Alzheimer's Dementia Onset and Progression in International Cohorts (ADOPIC) study (Australian Imaging Biomarkers and Lifestyle + Alzheimer's Disease Neuroimaging Initiative + Open Access Series of Imaging Studies), age-matched pairs of mild Alzheimer's disease (AD) and healthy controls (HC) were selected:

RESULTS: In the GAAIN dataset, the universal mask led to a small reduction in the variance of the YC, and a small increase in …


Multi-Omic Analysis Of The Tumor Microenvironment Shows Clinical Correlations In Ph1 Study Of Atezolizumab +/- Soc In Mm, Sandy Wong, Habib Hamidi, Luciano J Costa, Selma Bekri, Natalia Neparidze, Ravi Vij, Tina G Nielsen, Aparna Raval, Rajan Sareen, Elisabeth Wassner-Fritsch, Hearn J Cho Jan 2023

Multi-Omic Analysis Of The Tumor Microenvironment Shows Clinical Correlations In Ph1 Study Of Atezolizumab +/- Soc In Mm, Sandy Wong, Habib Hamidi, Luciano J Costa, Selma Bekri, Natalia Neparidze, Ravi Vij, Tina G Nielsen, Aparna Raval, Rajan Sareen, Elisabeth Wassner-Fritsch, Hearn J Cho

2020-Current year OA Pubs

Multiple myeloma (MM) remains incurable, and treatment of relapsed/refractory (R/R) disease is challenging. There is an unmet need for more targeted therapies in this setting; deep cellular and molecular phenotyping of the tumor and microenvironment in MM could help guide such therapies. This phase 1b study (NCT02431208) evaluated the safety and efficacy of the anti-programmed death-ligand 1 monoclonal antibody atezolizumab (Atezo) alone or in combination with the standard of care (SoC) treatments lenalidomide (Len) or pomalidomide (Pom) and/or daratumumab (Dara) in patients with R/R MM. Study endpoints included incidence of adverse events (AEs) and overall response rate (ORR). A novel …


Pregnancy Risk And Coerced Interventions After Dobbs, Elizabeth Kukura Jan 2023

Pregnancy Risk And Coerced Interventions After Dobbs, Elizabeth Kukura

SMU Law Review

Only nine months after the Supreme Court eliminated the federal constitutional right to abortion in Dobbs v. Jackson Women’s Health Organization, fourteen states had banned abortion entirely, and experts estimate the ultimate number of states imposing complete or near-complete restrictions on abortion care will likely rise to twenty-four. Millions of people with the capacity for pregnancy now (or will soon) live in places where getting pregnant means there is no choice other than to carry the pregnancy to term and give birth. One underappreciated, though critically important, impact of Dobbs is the extent to which newly enacted abortion restrictions will …


Neurobridge: A Prototype Platform For Discovery Of The Long-Tail Neuroimaging Data, Lei Wang, Janine Bijsterbosch, Rick Herrick, Daniel Marcus, Stephen M Moore, Et Al. Jan 2023

Neurobridge: A Prototype Platform For Discovery Of The Long-Tail Neuroimaging Data, Lei Wang, Janine Bijsterbosch, Rick Herrick, Daniel Marcus, Stephen M Moore, Et Al.

2020-Current year OA Pubs

INTRODUCTION: Open science initiatives have enabled sharing of large amounts of already collected data. However, significant gaps remain regarding how to find appropriate data, including underutilized data that exist in the long tail of science. We demonstrate the NeuroBridge prototype and its ability to search PubMed Central full-text papers for information relevant to neuroimaging data collected from schizophrenia and addiction studies.

METHODS: The NeuroBridge architecture contained the following components: (1) Extensible ontology for modeling study metadata: subject population, imaging techniques, and relevant behavioral, cognitive, or clinical data. Details are described in the companion paper in this special issue; (2) A …


The Role Of Vaccination Route With An Adenovirus-Vectored Vaccine In Protection, Viral Control, And Transmission In The Sars-Cov-2/K18-Hace2 Mouse Infection Model, Alexandria Dickson, Elizabeth Geerling, E Taylor Stone, Mariah Hassert, Tara L Steffen, Taneesh Makkena, Madeleine Smither, Katherine E Schwetye, Jianfeng Zhang, Bertrand Georges, M Scot Roberts, John J Suschak, Amelia K Pinto, James D Brien Jan 2023

The Role Of Vaccination Route With An Adenovirus-Vectored Vaccine In Protection, Viral Control, And Transmission In The Sars-Cov-2/K18-Hace2 Mouse Infection Model, Alexandria Dickson, Elizabeth Geerling, E Taylor Stone, Mariah Hassert, Tara L Steffen, Taneesh Makkena, Madeleine Smither, Katherine E Schwetye, Jianfeng Zhang, Bertrand Georges, M Scot Roberts, John J Suschak, Amelia K Pinto, James D Brien

2020-Current year OA Pubs

INTRODUCTION: Vaccination is the most effective mechanism to prevent severe COVID-19. However, breakthrough infections and subsequent transmission of SARS-CoV-2 remain a significant problem. Intranasal vaccination has the potential to be more effective in preventing disease and limiting transmission between individuals as it induces potent responses at mucosal sites.

METHODS: Utilizing a replication-deficient adenovirus serotype 5-vectored vaccine expressing the SARS-CoV-2 RBD (AdCOVID) in homozygous and heterozygous transgenic K18-hACE2, we investigated the impact of the route of administration on vaccine immunogenicity, SARS-CoV-2 transmission, and survival.

RESULTS: Mice vaccinated with AdCOVID via the intramuscular or intranasal route and subsequently challenged with SARS-CoV-2 showed …


Winter Dynamics Of Storm Water Management Ponds And Winter Tolerance In Three Aquatic Plant Species, Patrick Strzalkowski Jan 2023

Winter Dynamics Of Storm Water Management Ponds And Winter Tolerance In Three Aquatic Plant Species, Patrick Strzalkowski

Theses and Dissertations (Comprehensive)

The vast majority of the research into the performance of stormwater management ponds (SWMPs) has been performed in warm regions or during the warmer seasons in temperate regions. It is presumed that SWMPs are inactive in the winter as any potential stormwater is trapped in snow and ice. The main goal of this thesis was to test this presumption and to study the dynamics and performance of three SWMPs during the winter. Remote water level loggers were installed into the three SWMPs and daily grab samples from the influents and effluents were taken and analyzed for total phosphorus (TP), chloride, …


Contrasting Seasonal Cycling Of Arsenic In A Series Of Subarctic Shield Lakes With Different Morphometric Properties, Jeremy Harbinson Jan 2023

Contrasting Seasonal Cycling Of Arsenic In A Series Of Subarctic Shield Lakes With Different Morphometric Properties, Jeremy Harbinson

Theses and Dissertations (Comprehensive)

The subarctic shield near Yellowknife, Northwest Territories (NWT), is populated with thousands of small lakes (<1.5 km2) and several large lakes. Historic mining activities in the region have left a legacy of environmental impacts and widespread arsenic (As) contamination in both aquatic and terrestrial environments. In particular, several small subarctic lakes near Yellowknife have been previously documented to be contaminated with high levels of As. Subarctic lakes are characterized by seasonal ice-cover that can persist for more than half of the year, yet little is known about the under-ice spatial and seasonal dynamics of As cycling. The objective of …


Food And Drug Regulation: Statutory And Regulatory Supplement (2023), Adam I. Muchmore Jan 2023

Food And Drug Regulation: Statutory And Regulatory Supplement (2023), Adam I. Muchmore

Faculty Scholarship

This Statutory and Regulatory Supplement is intended for use with its companion casebook, Food and Drug Regulation: A Statutory Approach (2021). This is not a traditional statutory supplement. Instead, it contains selected, aggressively edited provisions of the Federal Food, Drug and Cosmetic Act (FFDCA), related statutes, and the Code of Federal Regulations. The Supplement includes all provisions assigned as reading in the casebook, as well as a few additional provisions that some professors may wish to cover. The excerpts are designed to be teachable rather than


From Perception To Behavior: The Neural Circuits Underlying Prey Hunting In Larval Zebrafish, Shuyu I Zhu, Geoffrey J Goodhill Jan 2023

From Perception To Behavior: The Neural Circuits Underlying Prey Hunting In Larval Zebrafish, Shuyu I Zhu, Geoffrey J Goodhill

2020-Current year OA Pubs

A key challenge for neural systems is to extract relevant information from the environment and make appropriate behavioral responses. The larval zebrafish offers an exciting opportunity for studying these sensing processes and sensory-motor transformations. Prey hunting is an instinctual behavior of zebrafish that requires the brain to extract and combine different attributes of the sensory input and form appropriate motor outputs. Due to its small size and transparency the larval zebrafish brain allows optical recording of whole-brain activity to reveal the neural mechanisms involved in prey hunting and capture. In this review we discuss how the larval zebrafish brain processes …


Abundance Of Acvr1b Transcript Is Elevated During Septic Conditions: Perspectives Obtained From A Hands-On Reductionist Investigation, Anucha Preechanukul, Thatcha Yimthin, Sarunporn Tandhavanant, Tobias Brummaier, Chalita Chomkatekaew, Sukanta Das, Basirudeen Syed Ahamed Kabeer, Mohammed Toufiq, Darawan Rinchai, T Eoin West, Damien Chaussabel, Narisara Chantratita, Mathieu Garand Jan 2023

Abundance Of Acvr1b Transcript Is Elevated During Septic Conditions: Perspectives Obtained From A Hands-On Reductionist Investigation, Anucha Preechanukul, Thatcha Yimthin, Sarunporn Tandhavanant, Tobias Brummaier, Chalita Chomkatekaew, Sukanta Das, Basirudeen Syed Ahamed Kabeer, Mohammed Toufiq, Darawan Rinchai, T Eoin West, Damien Chaussabel, Narisara Chantratita, Mathieu Garand

2020-Current year OA Pubs

Sepsis is a complex heterogeneous condition, and the current lack of effective risk and outcome predictors hinders the improvement of its management. Using a reductionist approach leveraging publicly available transcriptomic data, we describe a knowledge gap for the role of ACVR1B (activin A receptor type 1B) in sepsis. ACVR1B, a member of the transforming growth factor-beta (TGF-beta) superfamily, was selected based on the following: 1) induction upon


Learning A Healthy Rhythm: An Intervention To Increase Children’S Resources For Stress Management, Kristin Haglund, Amanda L. King, Abir K. Bekhet, Mauricio Garnier-Villarreal, Karen Olson, Rashs Atshan, Angela Ortiz, Johanna De Los Santos, Ruth Ann Belknap Jan 2023

Learning A Healthy Rhythm: An Intervention To Increase Children’S Resources For Stress Management, Kristin Haglund, Amanda L. King, Abir K. Bekhet, Mauricio Garnier-Villarreal, Karen Olson, Rashs Atshan, Angela Ortiz, Johanna De Los Santos, Ruth Ann Belknap

College of Nursing Faculty Research and Publications

This article describes a pilot test of a community engaged, culturally relevant, arts-based intervention. The purpose was to increase children’s personal protective buffering resources. Protective buffering resources help children cope with stressful stimuli, reduce activation of their systemic stress response, mitigate allostatic load, and promote optimal health. The “Learning a Healthy Rhythm” intervention included a stress management component and an ongoing Afro-Latino percussion program for 18 children ages 9–11. The stress management component included educational content about stress, self-assessment of stress symptoms, and stress management techniques. A mixed-method intervention evaluation design was used. Qualitative data, quantitative data, and biometrics including …


Gene-Educational Attainment Interactions In A Multi-Population Genome-Wide Meta-Analysis Identify Novel Lipid Loci, Lisa De Las Fuentes, Karen L. Schwander, Yun Ju Sung, Mary F. Feitosa, Ahn Do, C. Charles Gu, Treva K. Rice, Mary K. Wojczynski, Michael M. Province, Dabeeru C. Rao, Et Al. Jan 2023

Gene-Educational Attainment Interactions In A Multi-Population Genome-Wide Meta-Analysis Identify Novel Lipid Loci, Lisa De Las Fuentes, Karen L. Schwander, Yun Ju Sung, Mary F. Feitosa, Ahn Do, C. Charles Gu, Treva K. Rice, Mary K. Wojczynski, Michael M. Province, Dabeeru C. Rao, Et Al.

2020-Current year OA Pubs

No abstract provided.


Intra-Articular Aav9 Α-L-Iduronidase Gene Replacement In The Canine Model Of Mucopolysaccharidosis Type I, Raymond Yu-Jeang Wang, Shih-Hsin Kan, Haoyue Zhang, Jodi D Smith, Afshin Aminian, Elizabeth Snella, Jackie K Jens, Sarah P Young, Patricia I Dickson, N Matthew Ellinwood Jan 2023

Intra-Articular Aav9 Α-L-Iduronidase Gene Replacement In The Canine Model Of Mucopolysaccharidosis Type I, Raymond Yu-Jeang Wang, Shih-Hsin Kan, Haoyue Zhang, Jodi D Smith, Afshin Aminian, Elizabeth Snella, Jackie K Jens, Sarah P Young, Patricia I Dickson, N Matthew Ellinwood

2020-Current year OA Pubs

Mucopolysaccharidosis type I (MPS I), an inherited lysosomal storage disorder characterized by deficiency of


Philoponus And Forms, Owen Goldin Jan 2023

Philoponus And Forms, Owen Goldin

Philosophy Faculty Research and Publications

This chapter examines Philoponus’ stance in regard to positing Platonic forms. He rejects separately existing universals. But Philoponus never decisively rejects Platonic forms, as understood in as logoi in the mind of God, identified with the Platonic Demiurge. So understood, these forms are particulars that are such as can cause a multiplicity of particulars to exist. He attributes such causal principles to Aristotle, and to Plato as interpreted by Aristotle, without correction. He does however take issue with Forms subsisting prior to the demiurgic intellect, and accordingly follows his teacher Ammonius in rejecting the Proclean interpretation of Plato’s metaphysics. In …


Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang Jan 2023

Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose …


Intergenic Transcription In In Vivo Developed Bovine Oocytes And Pre-Implantation Embryos, Saurav Ranjitkar, Mohammad Shiri, Jiangwen Sun, Xiuchun Tian Jan 2023

Intergenic Transcription In In Vivo Developed Bovine Oocytes And Pre-Implantation Embryos, Saurav Ranjitkar, Mohammad Shiri, Jiangwen Sun, Xiuchun Tian

Computer Science Faculty Publications

Background

Intergenic transcription, either failure to terminate at the transcription end site (TES), or transcription initiation at other intergenic regions, is present in cultured cells and enhanced in the presence of stressors such as viral infection. Transcription termination failure has not been characterized in natural biological samples such as pre-implantation embryos which express more than 10,000 genes and undergo drastic changes in DNA methylation.

Results

Using Automatic Readthrough Transcription Detection (ARTDeco) and data of in vivo developed bovine oocytes and embryos, we found abundant intergenic transcripts that we termed as read-outs (transcribed from 5 to 15 kb after TES) and …


Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang Jan 2023

Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang

Computer Science Faculty Publications

Motivation

Single-cell RNA sequencing (scRNA-seq) offers a powerful tool to dissect the complexity of biological tissues through cell sub-population identification in combination with clustering approaches. Feature selection is a critical step for improving the accuracy and interpretability of single-cell clustering. Existing feature selection methods underutilize the discriminatory potential of genes across distinct cell types. We hypothesize that incorporating such information could further boost the performance of single cell clustering. Results

We develop CellBRF, a feature selection method that considers genes’ relevance to cell types for single-cell clustering. The key idea is to identify genes that are most important for discriminating …


A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyang Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu Jan 2023

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyang Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background

Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods

Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …


An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He Jan 2023

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …


A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyag Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu Jan 2023

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyag Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background: Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods: Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …


The Protective Impact Of Growth Hormone Against Rotenone-Induced Apoptotic Cell Death Via Acting On Endoplasmic Reticulum Stress And Autophagy Axis, Özge Rencüzoğullari, Selay Tornaci, Yağmur Çeli̇k, Nayat Narot Taş, Pinar Obakan Yerli̇kaya, Eli̇f Damla Arisan, Ajda Çoker Gürkan Jan 2023

The Protective Impact Of Growth Hormone Against Rotenone-Induced Apoptotic Cell Death Via Acting On Endoplasmic Reticulum Stress And Autophagy Axis, Özge Rencüzoğullari, Selay Tornaci, Yağmur Çeli̇k, Nayat Narot Taş, Pinar Obakan Yerli̇kaya, Eli̇f Damla Arisan, Ajda Çoker Gürkan

Turkish Journal of Biology

Human growth hormone (GH) is crucial modulator of cellular metabolisms, including cell proliferation and organ development, by stimulating insulin-like growth factor-1 (IGF-1), which has various functions such as cell proliferation, tissue growth, survival, or neuroprotection. Therefore, GH is implicated as a critical player in the cell and can enhance neurogenesis and provide neuroprotection during the treatment of neurological diseases such as Parkinson's disease (PD). In this study, the neuroprotective role of GH was investigated in rotenone-induced PD models for the first time. Both SH-SY5Y and SK-N-AS neuroblastoma cells were exposed to rotenone to mimic PD pathogenesis as stated in previous …


Functional Enhancement Of Acute Infracted Heart By Coinjection Of Autologous Adipose-Derived Stem Cells With Matrigel, Baozhu Wang, Mengmeng Wang, Yan Li, Meihua Shao, Dan Zhan, Shiqi Yan, Xiang Ma, Yitong Ma Jan 2023

Functional Enhancement Of Acute Infracted Heart By Coinjection Of Autologous Adipose-Derived Stem Cells With Matrigel, Baozhu Wang, Mengmeng Wang, Yan Li, Meihua Shao, Dan Zhan, Shiqi Yan, Xiang Ma, Yitong Ma

Turkish Journal of Biology

Recent clinical developments in tissue bioengineering have applications in acute cardiac ischemia and infarction and include the use of stem cells that combine injectable scaffold material. This study aimed to evaluate the effects of adipose-derived stem cells (ADSCs) that combine the Matrigel scaffold on cardiac morphology/functions. The autologous ADSCs myocardial infarction (MI) model was induced by the permanent ligation method of the left anterior descending coronary artery (LAD). MI-operated rats were randomly divided into PBS group, Matrigel group, PBS plus ADSCs group (PBS+ADSCs), and Matrigel plus ADSCs group (Matrigel+ADSCs). Matrigel was used as an injectable scaffold. Rats with a 1-week-old …


Tsrna-15797-Modified Bmsc-Derived Exosomes Mediate Lfng To Induce Angiogenesis In Osteonecrosis Of The Femoral Head, Shanhong Fang, Mengqiang You, Jie Wei, Peng Chen Jan 2023

Tsrna-15797-Modified Bmsc-Derived Exosomes Mediate Lfng To Induce Angiogenesis In Osteonecrosis Of The Femoral Head, Shanhong Fang, Mengqiang You, Jie Wei, Peng Chen

Turkish Journal of Biology

Background: Osteonecrosis of the femoral head (ONFH) is an ischemic disease characterized by the impairment of angiogenesis. We have previously elucidated the role of tsRNAs and BMSC exosomes in ONFH, but whether tsRNA-modified BMSC exosomes promote angiogenesis in ONFH remains unclear. Methods: The expression of angiogenesis-related tsRNA in plasma exosomes from ONFH patients was examined by q-PCR. The function of tsRNA in HUVECs was identified by CCK-8 and angiogenesis assay. Exosomes purified from tsRNA-15797 overexpressed BMSCs were cocultured with HUVECs to examine their role in angiogenesis. The molecule mechanism of tsRNA-15797-modified exosomes was explored by RNA sequencing, dual-luciferase assay, and …


Mir-216b-5p Promotes Late Apoptosis/Necroptosis In Trastuzumab-Resistant Sk-Br-3 Cells, İştar Burcu Dolapçi, Senem Noyan, Ayşegül Yücel Polat, Hakan Gürdal, Bala Gür Dedeoğlu Jan 2023

Mir-216b-5p Promotes Late Apoptosis/Necroptosis In Trastuzumab-Resistant Sk-Br-3 Cells, İştar Burcu Dolapçi, Senem Noyan, Ayşegül Yücel Polat, Hakan Gürdal, Bala Gür Dedeoğlu

Turkish Journal of Biology

Breast cancer is the most common cancer in women. The human epidermal growth factor receptor 2 (HER2) overexpressing subtype is related to poor prognosis with an aggressive phenotype and is reported as one of the most commonly seen subtypes. Trastuzumab is prevalently used as a treatment method for HER2+ breast cancer however, resistance to the drug frequently occurs following the treatment. MicroRNAs (miRNAs) are 19-23 nucleotide long small RNAs, which regulate gene expression at posttranscriptional level and studies show that there are differentially expressed miRNAs between drug sensitive and resistant groups, indicating that they might have some key roles in …


Analysis Of Morphological And Pomological Features Of Apricot In The Nakhchivan Autonomous Republic Of Azerbaijan, Ami̇na Raki̇da Jan 2023

Analysis Of Morphological And Pomological Features Of Apricot In The Nakhchivan Autonomous Republic Of Azerbaijan, Ami̇na Raki̇da

Turkish Journal of Agriculture and Forestry

Apricot (Prunus armeniaca L.) is grown across a wide geographical area and has been cultivated in Azerbaijan for more than three thousand years. The purpose of the study was to characterize the apricot varieties and forms collected from the Nakhchivan Autonomous Republic of Azerbaijan. Fourty-four apricot varieties and forms were studied according to 10 (phenological, pomological, morphological) parameters. A wide variation was found between yield, total soluble solids and fruit weight among varieties and forms. Fruits of the most of apricot varieties and forms were small, only two of them-Hampa and Limon Erik 2-had a fruit weight more than …


Screening Of Sunflower (Helianthus Annuus L.) Cultivars/Hybrids For Heat Stress Tolerance Using Growth And Physiobiochemical Indicators, Mobeen ., Abida Parveen, Abdullah Ahmed Al-Ghamdi, Fahad M. Al-Hemaid, Mohamed Ragab Abdelgawwad Jan 2023

Screening Of Sunflower (Helianthus Annuus L.) Cultivars/Hybrids For Heat Stress Tolerance Using Growth And Physiobiochemical Indicators, Mobeen ., Abida Parveen, Abdullah Ahmed Al-Ghamdi, Fahad M. Al-Hemaid, Mohamed Ragab Abdelgawwad

Turkish Journal of Agriculture and Forestry

High temperatures may cause scorching of the twigs and leaves along with visual symptoms of sunburn, leaf senescence, growth inhibition, and ultimately decreased plant growth and biomass. Sunflower (Helianthus annuus L.) is one of the important oil seed crops and it potentially fits in agricultural system and oil production sector of Pakistan. Hence, it is important to get the best variety which may able to tolerate high temperatures in hot and humid environments. For this purpose, we have conducted the present study using ten different cultivars of (Hysin-33, T-40, H-OI, Hysin-39, Suncross, Gulshin, FH-825, FH-797, FH-784, AGSUN-5270) of H. …