Digital Commons Network^™

Classification Of Colon Cancer Patients Into Consensus Molecular Subtypes Using Support Vector Machines, Necla Koçhan, Baris Emre Dayanc

Turkish Journal of Biology

Background/aim: The molecular heterogeneity of colon cancer has made classification of tumors a requirement for effective treatment. One of the approaches for molecular subtyping of colon cancer patients is the Consensus Molecular Subtypes (CMS) developed by the Colorectal Cancer Subtyping Consortium (CRCSC). CMS-specific RNA-Seq dependent classification approaches are recent with relatively low sensitivity and specificity. In this study, we aimed to classify patients into CMS groups using RNA-seq profiles. Materials and methods: We first identified subtype specific and survival associated genes using Fuzzy C-Means (FCM) algorithm and log-rank test. Then we classified patients using Support Vector Machines with Backward Elimination …

Genomic Loci Influence Patterns Of Structural Covariance In The Human Brain, Junhao Wen, Aristeidis Sotiras, Daniel S Marcus, Pamela Lamontagne, John C Morris, Et Al.

2020-Current year OA Pubs

Normal and pathologic neurobiological processes influence brain morphology in coordinated ways that give rise to patterns of structural covariance (PSC) across brain regions and individuals during brain aging and diseases. The genetic underpinnings of these patterns remain largely unknown. We apply a stochastic multivariate factorization method to a diverse population of 50,699 individuals (12 studies and 130 sites) and derive data-driven, multi-scale PSCs of regional brain size. PSCs were significantly correlated with 915 genomic loci in the discovery set, 617 of which are newly identified, and 72% were independently replicated. Key pathways influencing PSCs involve reelin signaling, apoptosis, neurogenesis, and …

A Computational Exploration: Docking Analysis Of Compounds From Foeniculum Vulgare As Potential Aromatase Inhibitors For Endometriosis Candidate Therapy, Dwi Anita Suryandari, Puji Sari, Hadi Sunaryo, Khaerunissa Anbar Istiadi

Indonesian Journal of Medical Chemistry and Bioinformatics

Aromatase inhibitors (AI) have controlling symptoms and size of endometriotic implants, making them a promising second-line therapy for endometriosis treatment.pretreatment with letrozole, an AI, combined with leuprolide acetate and resveratrol has been found to improve in vitro fertilization (IVF) outcomes in women mild endometriosis.in this study we screening and analysis of ten phenolic compounds from Foeniculum vulgare using molecular docking with Mcole server.from this results showed that three phenolic trans resveratrol (TR), caempherol coumaril (CC) have low gibbs energy compare with resveratrol (R). The binding modalities of compound TR and compound R were hydrogen-bonding between the hydroxyl and oxygen atom …

Cerulean Warbler (Setophaga Cerulea) Response To Changes In Forest Structure In Indiana., Kamal Islam, Jennifer Wagner, Ryan Dibala, Margaret Macneil, Kyle Kaminski, Lila (Prichard) Young

Ornitología Neotropical

No abstract provided.

Book Reviews—ReseñAs De Libros—Resenhas De Livros, John G. Blake

Ornitología Neotropical

No abstract provided.

The Breeding Biology Of The Fork-Tailed Flycatcher (Tyrannus Savana) In Lowland Pine Savanna Habitats In Belize, Mario Teul, Victoria D. Piaskowski, Kari M. Williams

Ornitología Neotropical

No abstract provided.

Robin A Hughes, 1934-1991, Oscar Gonzalez M.

Ornitología Neotropical

No abstract provided.

Feminist Pedagogy In Stem: The Intersection Of Stem Pedagogy And Feminist Theory, Lesley-Ann Giddings, Candice R. Price

Feminist Pedagogy

No abstract provided.

Tiny Machine Learning For Underwater Image Enhancement: Pruning And Quantizaition Approach, Dr Khaled Nagaty, The British University In Egypt, Andreas Pester Dr

Computer Science

Many people have expressed an interest in underwater image processing in a variety of fields, including underwater vehicle control, archaeology, marine biological studies, etc. Underwater exploration is becoming an increasingly important element of our lives, with applications ranging from underwater marine and creature research to pipeline and communication logistics, military use, touristic and entertainment use. Underwater images suffer from poor visibility, distortion, and poor quality for a variety of causes, including light propagation. The major issue arises when these images must be captured at depths greater than 500 feet and artificial lighting needs to be provided. Efficient algorithms and models …

Deep Learning For Microbiome-Based Integrative Modeling And Microbial Biomarkers Identification, Sen Yang

Statistical Science Theses and Dissertations

The human microbiome, comprising trillions of microorganisms, plays a pivotal role in modulating host physiology via molecular and metabolite exchanges. One of the major challenges in this field lies in the effective integration of microbiome and metabolomics data, an achievement that holds the promise of substantially enhancing the precision of disease prediction. However, many datasets prioritize microbiome data while neglecting paired metabolome information. Additionally, the prevalent analytical tools face challenges in effectively merging these intricate datasets, leading to possible misinterpretations and reduced prediction accuracies.

To address these challenges, the first part of this research introduces the Microbiome-based Supervised Contrastive Learning …

Protocol To Build A Drug-Testing Pipeline Using Large Populations Of Drosophila Melanogaster, Jay Deloriea, Cassandra Millet-Boureima, Chiara Gamberi

Biology

As a small animal that recapitulates many fundamental aspects of human disease, Drosophila lends itself to probing the biological activity of molecules and drug candidates. Here, we present a protocol to build a drug-testing pipeline in Drosophila. We describe steps for generating synchronous populations of Bicaudal C mutants by genetic crossing and wild-type fly culturing for controlled compound administration and exemplary phenotypic assays. For complete details on the use and execution of this protocol, please refer to Millet-Boureima et al.,¹ Millet-Boureima et al.,² and Gamberi et al.³

Plants As Vectors For Environmental Prion Transmission, Christina M Carlson, Samuel Thomas, Matthew W Keating, Paulina Soto, Nicole M Gibbs, Haeyoon Chang, Jamie K Wiepz, Annabel G Austin, Jay R Schneider, Rodrigo Morales, Christopher J Johnson, Joel A Pedersen

Faculty, Staff and Student Publications

Prions cause fatal neurodegenerative diseases and exhibit remarkable durability, which engenders a wide array of potential exposure scenarios. In chronic wasting disease of deer, elk, moose, and reindeer and in scrapie of sheep and goats, prions are transmitted via environmental routes and the ability of plants to accumulate and subsequently transmit prions has been hypothesized, but not previously demonstrated. Here, we establish the ability of several crop and other plant species to take up prions via their roots and translocate them to above-ground tissues from various growth media including soils. We demonstrate that plants can accumulate prions in above-ground tissues …

Enhancing The Anticancer Potential Of Metformin: Fabrication Of Efficient Nanospanlastics, In Vitro Cytotoxic Studies On Hep-2 Cells And Reactome Enhanced Pathway Analysis, Shereen Nader, Sara El Wahed, Noha Badawy, Mona Saber, Maha Abdollah

Pharmacy

Metformin (MET), an oral antidiabetic drug, was reported to possess promising anticancer effects. We hypothesized that MET encapsulation in unique nanospanlastics would enhance its anticancer potential against HEP-2 cells. Our results showed the successful fabrication of Nano-MET spanlastics (d = 232.10 ± 0.20 nm; PDI = 0.25 ± 0.11; zeta potential = (−) 44.50 ± 0.96; drug content = 99.90 ± 0.11 and entrapment efficiency = 88.01 ± 2.50%). MTT assay revealed the enhanced Nano-MET cytotoxicity over MET with a calculated IC50 of 50 μg/mL and > 500 μg/mL, respectively. Annexin V/PI apoptosis assay showed that Nano-MET significantly decreased …

Interactive Effects Of Sublethal Concentrations Of Fracking Biocides And Abandoned Mine Drainage On Amphipod Behavior, Kelly Lenhart

Electronic Theses and Dissertations

This thesis examined the sublethal effects of three pollutants, namely glutaraldehyde, 4,4-dimethyloxazolidine (DMO), and abandoned mine drainage (AMD), on amphipods. The primary objective was to investigate their combined effects on amphipods. The three pollutants, despite having the potential to combine in the environment, have not been studied to determine their potential for detrimental interactive effects which could result in unexpected environmental damage.

The research employed a series of experimental setups involving controlled exposure of amphipods to varying, putatively sublethal, concentrations of the chemicals of interest. Subsequently, effects were assessed via both behavioral and feeding assessments. To facilitate this analysis, novel …

Stem's Missing Women: Why Biology's Undergraduate Pipeline Is Diverging From Career Paths, Rosemary Roberto

Graduate Student and Postdoctoral Fellow Symposium

No abstract provided.

Histological Study Of The Restorative Effect Of Roselle (Hibiscus Sabdariffa Linn.) Tea On The Digestive Organs Of Monosodium Glutamate-Induced Mice (Mus Musculus Linn.), Kanigara Anupama Sistra, Ngurah Intan Wiratmini, A. A.S.A. Sukmaningsih

Folia Medica Indonesiana

Highlights: • This original study examined the antioxidant compounds derived from naturally sourced Hibiscus sabdariffa calyx. • The findings demonstrated that roselle tea offers a viable and cost-effective solution for repairing histological damage to the digestive organs induced by monosodium glutamate. Abstract Monosodium glutamate (MSG) is a commonly used synthetic additive for enhancing food flavor. Excessive use of MSG can cause cytotoxic effects, which disrupt the balance of oxidative stress and free radicals in the body, particularly in the human digestive system. Roselle (Hibiscus sabdariffa) is a plant with red petals renowned for its abundance of beneficial compounds, including polyphenols, …

Investigating The Effects Of A Southward Flow In The Southeastern Florida Shelf Using Robotic Instruments, Alfredo Quezada

All HCAS Student Capstones, Theses, and Dissertations

We deployed a Slocum G3 glider fitted with an acoustic Doppler current profiler (ADCP), a Conductivity-Temperature-Depth sensor (CTD), optics sensor channels, and a propeller on the Southeastern Florida shelf. The ADCP and CTD provide continuous measurements of Northern and Eastern current velocity components, salinity, temperature, and density, throughout the water column in a high-current environment. The optics sensor channels are able to provide measurements of chlorophyll concentrations, colored dissolved organic matter (CDOM), and backscatter particle counts. Additionally, for one of the glider deployments, we deployed a Wirewalker wave-powered profiling platform system also fitted with an ADCP and a CTD in …

Synthesis And Antibacterial Evaluation For Some New Schiff-Bases Derived From P-Aminoacetanilide, Eman M. Hussain

Baghdad Science Journal

Derivatives of Schiff-bases possess a great importance in pharmaceutical chemistry. They can be used for synthesizing different types of bioactive compounds. In this paper, derivatives of new Schiff bases have been synthesized from several serial steps. The acid (I) was synthesized from the reaction of dichloroethanoic acid with 2 moles of p-aminoacetanilide. New acid (I) converted to its ester (II) via the reaction of (I) with dimethyl sulphate in the present of anhydrous of sodium carbonate and dry acetone. Acid hydrazide (III) has been synthesized by adding 80% of hydrazine hydrate to the new ester using ethanol as a solvent. …

Ru(Ii) Polypyridyl Photosensitizers For Phototherapy, Houston Cole

Chemistry & Biochemistry Dissertations - Archive

This dissertation describes the design, synthesis, and photobiological characterization of key target molecules that modify the 1) length of the IP-nT “PDT” ligand, 2) electronic nature of the bipyridine or phenanthroline type ancillary ligands, and 3) chirality of the coordination complex. The targets and subsequent studies will test the hypothesis that molecules with low-lying and long-lived 3ILCT states are responsible for this unusually high photocytotoxic potency and seeks to further understand what structural features (aside from the IP-nT ligand) lead to more favorable photobiological properties.

Biocargos: Capture And Release Gels For Optimized Storage Of Biologics., Chinmay Shashank Potnis

Electronic Theses and Dissertations

No abstract provided.

Conserved And Divergent Gene Regulatory Programs Of The Mammalian Neocortex, Nathan R Zemke, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Ting Wang, Et Al.

2020-Current year OA Pubs

Divergence of cis-regulatory elements drives species-specific traits

Single-Cell Analysis Of Chromatin Accessibility In The Adult Mouse Brain, Songpeng Zu, Yang Eric Li, Et Al.

2020-Current year OA Pubs

Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete

Telomeric Regulation Of Chromosomal Instability In Colorectal Cancer, Kyle Labella, Kyle A Labella

Dissertations and Theses (Open Access)

Telomere dysfunction drives chromosomal instability (CIN) during the transition from benign adenoma to malignant adenocarcinoma. While CIN provides a mutator mechanism for cancer-relevant genomic events, its role in shaping tumor biology during carcinogenesis is not well understood. Here, we explored the molecular and biological impact of telomere dysfunction and associated CIN in vivo in a faithful model of CRC. In vivo lineage tracing revealed that CIN increased neoplastic cell competition and clonal expansion through accelerated differentiation of neighboring stem cells, resulting in increased number of adenomas and decreased survival in CIN-high Apc^min mice. Mechanistically, CIN represses EZH2 leading to …

Understanding The Kinetics Of Laser-Induced Nanowelding Of Nanoparticles And The Motility Of Bacteria When Faced With Obstacles, Ariel Rogers

Graduate Theses and Dissertations

This dissertation has two focus areas: nanoparticle nanowelding and bacteria motility in the presence of micrometer sized structures. There are two main projects for the nanoparticle nanowelding studies: “Real-time imaging of laser-induced nanowelding in solution” and “Two-color laser-induced nanostructure shape modulation.” For the real-time imaging project, I used a fluorescence microscope, a 405 nm laser, and various python packages to quantify the average size of nanowelded nanostructures as a function of time and found that the average nanostructure growth over time fit the parameters of A¯(t) ∝ c0(1−e−t/τ), where c0 represents the initial concentration of nanoparticles in the solution and …

Electrodeposition Studies Of Gold Nanoparticles And Alginate Hydrogel Films., Harikrishnan Nambiathan Nambiar

Electronic Theses and Dissertations

This dissertation investigates the electrochemical deposition (ECD) and electrophoretic deposition (EPD) processes involving citrate (cit)-stabilized Au nanoparticles (NPs) and calcium alginate (Ca-Alg-Au NP) hydrogel films. The first part of the dissertation investigates the influence of NP size, surface area (SA) coverage, and ligand stabilizers on the electrochemical growth of Au on Au NPs, aiming to enhance our understanding of the growth process during the nucleation and growth of metal NPs. The growth kinetics depend on Au NP size (4 nm > 15 nm > 50 nm) for a constant SA coverage, as determined by the overpotentials for ECD. The growth rate increases …

“Be Sustainable”: Eosc-Life Recommendations For Implementation Of Fair Principles In Life Science Data Handling, Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Katrina Exter, Sven Fahrner, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Björn Grüning, Kim Tamara Gurwitz, John M Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, Allyson L Lister, Dario Livio Longo, Rebecca Ludwig, Bénédicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Michaela Th Mayrhofer, Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S Richard, Paolo Romano, Antonio Rosato, Alex Sánchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon

Faculty, Staff and Student Publications

The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from …

Ni2+, Pt4+, Pd2+, And Mn2+ Metal Ions Complexes With Azo Derived From Quinolin-2-Ol And 3-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide: Synthesis, Characterization, Thermal Study ,And Antioxidant Activity, Adhraa Ghazi Abdulrazzaq, Abbas Ali Salih Al-Hamdani

Baghdad Science Journal

Diazotization reaction between quinolin-2-ol and (2-chloro-1-(4-(N-(5-methylisoxazol-3-yl)sulfamoyl)phenyl)-2l4-diazyn-1-ium was carried out resulting in ligand-HL, this in turn reacted with the next metal ions (Ni2+, Pt4+, Pd2+, and Mn2+) forming stable complexes with unique geometries such as (tetrahedral for both Ni2+ and Mn2+, octahedral for Pt4+ and square planer for Pd2+ ). The creation of such complexes was detected by employing spectroscopic means involving ultraviolet-visible which proved the obtained geometries, fourier transfer proved the formation of azo group and the coordination with metal ion through it. Pyrolysis (TGA & DSC) studies proved the coordination of water residues with metal ions inside the coordination …

Single-Cell Analysis Of Chromatin Accessibility In The Adult Mouse Brain, Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, Antonio Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M Margarita Behrens, Joseph R Ecker, Allen Wang, Sebastian Preissl, Bing Ren

Faculty, Staff and Student Publications

Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are …

Brain-Wide Correspondence Of Neuronal Epigenomics And Distant Projections, Jingtian Zhou, Zhuzhu Zhang, May Wu, Hanqing Liu, Yan Pang, Anna Bartlett, Zihao Peng, Wubin Ding, Angeline Rivkin, Will N Lagos, Elora Williams, Cheng-Ta Lee, Paula Assakura Miyazaki, Andrew Aldridge, Qiurui Zeng, J L Angelo Salinda, Naomi Claffey, Michelle Liem, Conor Fitzpatrick, Lara Boggeman, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Jordan Altshul, Mia A Kenworthy, Cynthia Valadon, Joseph R Nery, Rosa G Castanon, Neelakshi S Patne, Minh Vu, Mohammad Rashid, Matthew Jacobs, Tony Ito, Julia Osteen, Nora Emerson, Jasper Lee, Silvia Cho, Jon Rink, Hsiang-Hsuan Huang, António Pinto-Duartec, Bertha Dominguez, Jared B Smith, Carolyn O'Connor, Hongkui Zeng, Shengbo Chen, Kuo-Fen Lee, Eran A Mukamel, Xin Jin, M Margarita Behrens, Joseph R Ecker, Edward M Callaway

Faculty, Staff and Student Publications

Single-cell analyses parse the brain’s billions of neurons into thousands of ‘cell-type’ clusters residing in different brain structures1. Many cell types mediate their functions through targeted long-distance projections allowing interactions between specific cell types. Here we used epi-retro-seq2 to link single-cell epigenomes and cell types to long-distance projections for 33,034 neurons dissected from 32 different regions projecting to 24 different targets (225 source-to-target combinations) across the whole mouse brain. We highlight uses of these data for interrogating principles relating projection types to transcriptomics and epigenomics, and for addressing hypotheses about cell types and connections related to genetics. …

Single-Cell Dna Methylome And 3d Multi-Omic Atlas Of The Adult Mouse Brain, Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa G Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, Antonio Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zhanghao Wu, Ion Stoica, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Chongyuan Luo, Jesse R Dixon, Hongkui Zeng, Bing Ren, M Margarita Behrens, Joseph R Ecker

Faculty, Staff and Student Publications

Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular atlas of brain cell types and their gene regulatory landscapes. Here we used single-nucleus methylome sequencing (snmC-seq3) and multi-omic sequencing (snm3C-seq)1 technologies to generate 301,626 methylomes and 176,003 chromatin conformation–methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell taxonomy with 4,673 cell groups and 274 …