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Tigra Scientifica, Full Issue

Tigra scientifica

Tigra scientifica, showcasing the outstanding work by Clemson University students in the Creative Inquiry course Popular Science Journalism. Science and technology shape our world in profound ways — from the rise of space tourism to the rapid development of new medical treatments. In a democracy, communicating science is essential for informed debate and decision-making, a responsibility these students have embraced with energy and skill. The magazine began in Spring 2011 under Holly Tuten, Ph.D., who founded the CI course to pass along her passion for science writing. Since then, more than 200 students from 14 majors across five colleges have …

Synthesis Ago Nanoparticles By Nd:Yag Laser With Different Pulse Energies, Munaf S. Majeed, Shaymaa M. Mahmoud Mahmoud, Raghad Majeed Rasheed, Alaa Adnan Rashad

Baghdad Science Journal

One technique used to prepare nanoparticles material is Pulsed Laser Ablation in Liquid (PLAL), Silver Oxide nanoparticles (AgO) were prepared by using this technique, where silver target was submerged in ultra-pure water (UPW) at room temperature after that Nd:Yag laser which characteristics by 1064 nm wavelength, Q-switched, and 6ns pulse duration was used to irradiated silver target. This preparation method was used to study the effects of laser irradiation on Nanoparticles synthesized by used varying laser pulse energy 1000 mJ, 500 mJ, and 100 mJ, with 500 pulses each time on the particle size. Nanoparticles are characterized using XRD, SEM, …

A New Approach For Developing Spectrophotometric Determination Of Phenylephrine Drug In Pure, Pharmaceutics And Serum Samples Using Sodium Periodate As Oxidizing Agent Via A Green Method Of Cfia/Merging Zone Technique, Shahad L. Hamed, Bushra B. Qassim

Baghdad Science Journal

The research involved a rapid, automated and highly accurate developed CFIA/MZ technique for estimation of phenylephrine hydrochloride (PHE) in pure, dosage forms and biological sample. This method is based on oxidative coupling reaction of 2,4-dinitrophenylhydrazine (DNPH) with PHE in existence of sodium periodate as oxidizing agent in alkaline medium to form a red colored product at ʎmax (520 nm). A flow rate of 4.3 mL.min-1 using distilled water as a carrier, the method of FIA proved to be as a sensitive and economic analytical tool for estimation of PHE. Within the concentration range of 5-300 μg.mL-1, a calibration curve was …

Water Treatment Using Zinc Nanoparticles And Apricot Plant Extracts From Organic And Inorganic Pollution, Suzan Muslim Abdullah, Abbas Ali Salih Al-Hamdani, Labeeb Ahmed Al-Zubaidi

Baghdad Science Journal

The apricot plant was washed, dried, and powdered after harvesting to produce a fine powder that was used in water treatment. created an alcoholic extract from the apricot plant using ethanol, which was then analysed using GC-MS, Fourier transform infrared spectroscopy, and ultraviolet-visible spectroscopy to identify the active components. Zinc nanoparticles were created using an alcoholic extract. FTIR, UV-Vis, SEM, EDX, and TEM are used to characterize zinc nanoparticles. Using a continuous processing procedure, zinc nanoparticles with apricot extract and powder were employed to clean polluted water. Firstly, 2 g of zinc nanoparticles were used with 20 ml of polluted …

Study Of The Anticancer And Antimicrobial Biological Activity Of A New Series Of Thiohydantoin Derivatives, Qusay Hussein Hays, Dakhil Zughayir Mutlaq

Baghdad Science Journal

Recently, some prostate cancer patients have acquired resistance to the second -generation drugs (anzalutamide and apalutamide) prescribed for the treatment of this disease due to the emergence of the F876L mutation, which represents a challenge to modern medicine. In this study, a new series of 2-thiohydantoin derivatives were prepared through the reaction of different derivatives of maleimide (1c-4c) with isothiocyanate derivatives. The prepared compounds were diagnosed using FT-IR,1H-NMR ,13C-NMR, Mass spectra. The prepared series compounds has been studied against prostate cancer cells. The MTT assay was used to determine the activity of the prepared compounds against prostate cancer cells. The …

Density And Abundance Estimation Of West Indian Manatee, Trichechus Manatus, Between The States Of Ceará And Piauí, Northeast Brazil, Using Active Acoustics, Katherine Fiedler Choi Lima, Denis Moledo De Sousa Abessa, Daniel Gonzalez-Socoloske, Renata Sousa-Lima, Ana Carolina Oliveira De Meirelles, Cristine Pereira Negrão Silva

Faculty Publications

The West Indian manatee is one of the most threatened species in Brazil. The species has currently a patchy distribution from the state of Alagoas to the state of Amapá. The difficulty of observing manatees, especially in estuarine waters, is a challenge for conservation. Therefore, it is necessary to use new methodologies and technologies to solve manatee detection problems in their natural habitats. The goal of this study was to use an active acoustic method of detection to estimate manatee density and abundance in the estuarine complex of the Timonha and Ubatuba rivers, between the states of Ceará and Piauí, …

Can Large Language Models Discern Evidence For Scientific Hypotheses? Case Studies In The Social Sciences, Sai Koneru, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Hypothesis formulation and testing are central to empirical research. A strong hypothesis is a best guess based on existing evidence and informed by a comprehensive view of relevant literature. However, with exponential increase in the number of scientific articles published annually, manual aggregation and synthesis of evidence related to a given hypothesis is a challenge. Our work explores the ability of current large language models (LLMs) to discern evidence in support or refute of specific hypotheses based on the text of scientific abstracts. We share a novel dataset for the task of scientific hypothesis evidencing using community-driven annotations of studies …

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …

Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang

Computer Science Faculty Publications

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, …

The Combined Focal Loss And Dice Loss Function Improves The Segmentation Of Beta-Sheets In Medium-Resolution Cryo-Electron-Microscopy Density Maps, Yongcheng Mu, Thu Nguyen, Bryan Hawickhorst, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Although multiple neural networks have been proposed for detecting secondary structures from medium-resolution (5–10 Å) cryo-electron microscopy (cryo-EM) maps, the loss functions used in the existing deep learning networks are primarily based on cross-entropy loss, which is known to be sensitive to class imbalances. To monitor and tune the performance of various loss functions for the secondary structure detection problem, we investigated five loss functions: cross-entropy, Focal loss, Dice loss, and two combined loss functions. Using a U-Net architecture in our DeepSSETracer method and a dataset composed of 1,355 box-cropped atomic-structure/density-map pairs, we found that a newly designed loss function …

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Retrogressive Document Manipulation Of Us Federal Environmental Websites, Lesley Frew, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

Changes made to webpages can affect their retrievability. Often this is done with the intention of increasing the page's search engine ranking to improve overall access to information on the page. The Environmental Data and Governance Initiative (EDGI) created a dataset that describes changes on US federal environmental webpages between 2016 and 2020. EDGI noted that many environmental terms were deleted from the pages, but without user data, claims that page retrievability and public information access were lowered are only anecdotal. The Open Resource for Click Analysis in Search (ORCAS) dataset was created during the same time frame, from 2017 …

Identifying Patterns For Neurological Disabilities By Integrating Discrete Wavelet Transform And Visualization, Soo Yeon Ji, Sampath Jayarathna, Anne M. Perrotti, Katrina Kardiasmenos, Dong Hyun Jeong

Computer Science Faculty Publications

Neurological disabilities cause diverse health and mental challenges, impacting quality of life and imposing financial burdens on both the individuals diagnosed with these conditions and their caregivers. Abnormal brain activity, stemming from malfunctions in the human nervous system, characterizes neurological disorders. Therefore, the early identification of these abnormalities is crucial for devising suitable treatments and interventions aimed at promoting and sustaining quality of life. Electroencephalogram (EEG), a non-invasive method for monitoring brain activity, is frequently employed to detect abnormal brain activity in neurological and mental disorders. This study introduces an approach that extends the understanding and identification of neurological disabilities …

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Vulnerable, Recalcitrant And Resilient: A Foucauldian Discourse Analysis Of Risk And Older People Within The Context Of Covid-19 News Media, Marjorie Skoss, Rachel Batten, Patricia Cain, Mandy Stanley

Research outputs 2022 to 2026

Risk is an innate and integral part of everyday life and is present in simple, everyday occupations and complex actions. Age-related stereotypes can mean older people have little opportunity to engage in activities that present some degree of risk. The present study explores the discourse around risk and older people in the context of the COVID-19 pandemic. We investigated news media as a reflection of the dominant public discourse around older people's behaviour to identify how risk is represented in relation to occupational engagement. Texts relating to older people and COVID-19 were sourced from the West Australian newspaper for a …

Ecu-Mss-2 Dataset, A New Multi-Species Seagrass, Md K. Noman, Syed M. S. Islam, Seyed M. Jalali, Jumana Abu-Khalaf, Paul Lavery

Research Datasets

The "ECU-MSS-2' dataset contains four different habitats, 'Amphibolis' spp (hereafter 'Amphibolis"), 'Halophila' spp (hereafter 'Halophila'), 'Posidonia' spp (hereafter 'Posidonia') and 'Background'. We compiled this image dataset from different sources. The 'Halophila' images were collected by the Centre for Marine Ecosystems Research, Edith Cowan University, Western Australia.

The 'Amphibolis' 'Background' and 'Posidonia' images were collected by the Department of Biodiversity, Conservation and Attractions (DBCA), Australia. The 'Amphibolis' class includes the seagrass species Amphibolis griffithii and Amphibolis Antarctica. The 'Halophila' class includes Halophila ovalis, while the 'Posidonia' class includes Posidonia sinuosa, Posidonia coriacea, and Posidonia Australis. The 'Background' class includes coral, sand, …

Is There A Relationship Between Parents' Screen Usage And Young Children’S Development?, Delphine Nguyen

School of Psychology Theses

There has been growing concern over the links between children's screen time use and cognitive development (Halton, 2020). However, researchers have generally overlooked the possible impact of parental screen time, which might decrease the opportunities of learning and social interactions for young children. To address this gap, we investigated the relationship between parental screen use and toddlers’ development. However, the start of this thesis coincided with the Covid-19 pandemic, and a few experimental tasks had to be adapted online. Thus, this thesis examined first whether online paradigms can provide valid data (word recognition, word learning and language assessment). Second, the …

Landscapes Of Play: An Exploration And Illumination Of Children’S Unsupervised Play Close To Home And A Researcher’S Journey To Becoming Posthuman., Mandy Andrews

School of Law, Humanities and Social Sciences Theses

Title: Landscapes of Play: An exploration and illumination of children’s unsupervised play close to home and a researcher’s journey to becoming posthuman. Author: Mandy Jo Andrews This thesis explores children’s play experiences and engagements out of doors close to home. Adopting a Deleuzian informed posthumanism the researcher’s journey towards immanence prompts re-thinking about play, childhood-nature entanglements, and play-space-place-player generation. Children’s unsupervised play outside of organised settings such as school or adventure playgrounds is less researched than that of organised settings. This thesis puts to work Deleuze’s process philosophy and Barad’s agential realism, together with Haraway’s biology informed multispecies manifesto, Bennett’s …

How Does Living In A Rural Location Affect Experiences Of Acquired Vision Impairment?, Rebecca Woods

School of Law, Humanities and Social Sciences Theses

This research explores the lived experiences of adults with acquired sight loss who live in rural areas in Southwest England. There is a scarcity of published academic research with this group. Vision impaired people who live in rural locations are therefore unrecognised sources of vision impairment rehabilitation knowledge. The research is conducted in an interpretivist paradigm. The research is guided by phenomenological understanding, rooted in Merleau-Ponty’s concepts of perception, the centrality of tool-use, and human embodiment. Attention is centred on the process of adapting to sight loss in a domestic setting, placing this research in an experiential, community-based educational context. …

'Man's Forgotten Friend': Dogs Appointed As Domesticated Companions And The Coronavirus Pandemic, Rebekah Gregory

School of Law, Humanities and Social Sciences Theses

The metaphorical confinement of national lockdowns saw the egocentric adoption of dogs appointed as domesticated companions. While public approval of ‘animal’ welfare legislation and the growing popularity of ‘green’ theory and industry has grown, ‘animals’ are still victim to the consumer and the anthropocentric cultures which promote individual, economic, social, and specifically ‘human’ advancement at all costs. Even though the reasons why ‘animals’ are victimised has been researched, how the pandemic has impacted upon this treatment and consumer culture’s/anthropocentrism’s influence has been somewhat absent within academic discussion. In fact, how the global events of COVID-19 have impacted upon dog treatment, …

Developing A Strategy For Synergy Between Home And Church To Increase Youth Engagement And Faith Formation At Barriere Adventist Church, Timoteus Nagy

Doctor of Ministry Projects

Problem

There was no intentional synergistic relationship between the home and the church at the Barriere Adventist Church. As a result, church leaders often expressed discouragement when they saw teens become disengaged with church and spirituality. They suggested that the root problem of this symptom was the lack of cooperation between the two faith-forming institutions in keeping young people engaged and growing in their faith. As a pastor, I saw this deficiency and our urgent need for change.

Method

A six-month action research strategy was designed and delivered at the Barriere Adventist Church. Twenty members from every generational cohort were …

Inactive Metallopeptidase Homologs: The Secret Lives Of Pseudopeptidases, Peter Lyons

Faculty Publications

Inactive enzyme homologs, or pseudoenzymes, are proteins, found within most enzyme families, that are incapable of performing catalysis. Rather than catalysis, they are involved in protein-protein interactions, sometimes regulating the activity of their active enzyme cousins, or scaffolding protein complexes. Pseudoenzymes found within metallopeptidase families likewise perform these functions. Pseudoenzymes within the M14 carboxypeptidase family interact with collagens within the extracellular space, while pseudopeptidase members of the M12 "a disintegrin and metalloprotease" (ADAM) family either discard their pseudopeptidase domains as unnecessary for their roles in sperm maturation or utilize surface loops to enable assembly of key complexes at neuronal synapses. …

Taking Sides? Aspect Has Limited Influence On Soil Environment Or Litter Decomposition In Pan-European Study Of Roadside Verges, A. Amstutz, L. B. Firth, J. I. Spicer, P. De Frenne, L. Gómez-Aparicio, B. J. Graae, S. Kuś, S. Lindmo, A. Orczewska, F. Rodríguez-Sánchez, P. Vangansbeke, T. Vanneste, M. E. Hanley

School of Biological and Marine Sciences

In addition to well-known effects on species ecophysiology, phenology, and distributions, climate change is widely predicted to impact essential ecosystem services such as decomposition and nutrient cycling. While temperature and soil moisture are thought to influence litter decomposition, elucidating consistent soil process responses to observed or predicted shifts in climate have proven difficult to evidence. Here we investigated how aspect (i.e., north-south orientation), a natural model for variation in soil temperature, influenced soil physico-chemical conditions and decomposition of two standardised litter types (Green tea and Rooibos teabags) in Pole-facing (PF) and Equator-facing (EF) roadside verges spanning a 3000 km and …

The North–South Divide? Macroalgal Functional Trait Diversity And Redundancy Varies With Intertidal Aspect, Axelle Amstutz, Louise B. Firth, Andy Foggo, John I. Spicer, Mick E. Hanley

School of Biological and Marine Sciences

Background and Aims Marine macroalgae (‘seaweeds’) are critical to coastal ecosystem structure and function, but also vulnerable to the many environmental changes associated with anthropogenic climate change (ACC). The local habitat conditions underpinning observed and predicted ACC-driven changes in intertidal macroalgal communities are complex and probably site-specific and operate in addition to more commonly reported regional factors such as sea surface temperatures. Methods We examined how the composition and functional trait expression of macroalgal communities in SW England varied with aspect (i.e. north–south orientation) at four sites with opposing Equator- (EF) and Pole-facing (PF) surfaces. Previous work at these sites …

Shift In Algal Blooms From Micro‐ To Macroalgae Around China With Increasing Eutrophication And Climate Change, Yuan Feng, Yonglong Xiong, Jm Hall‐Spencer, Kailin Liu, John Beardall, K Gao, Jingke Ge, Juntian Xu, G Gao

School of Biological and Marine Sciences

Blooms of microalgal red tides and macroalgae (e.g., green and golden tides caused by Ulva and Sargassum) have caused widespread problems around China in recent years, but there is uncertainty around what triggers these blooms and how they interact. Here, we use 30 years of monitoring data to help answer these questions, focusing on the four main species of microalgae Prorocentrum donghaiense, Karenia mikimotoi, Noctiluca scintillans, and Skeletonema costatum) associated with red tides in the region. The frequency of red tides increased from 1991 to 2003 and then decreased until 2020, with S. costatum red tides exhibiting the highest rate …

Perioperative Oxygenation—What's The Stress?, Joseph Larvin, Mark Edwards, Daniel S. Martin, Martin Feelisch, Michael P.W. Grocott, Andrew F. Cumpstey

Peninsula Medical School

Oxygen is the most used drug in anaesthesia. Despite such widespread use, optimal perioperative oxygen administration remains highly controversial because of concerns about the competing harms of both hyperoxia and hypoxia. Notwithstanding a Cochrane review concluding that routinely administering a fractional inspired oxygen concentration (FiO₂) >0.6 intraoperatively might increase postoperative morbidity and mortality, the World Health Organization (WHO) currently recommends all anaesthetised patients receive 0.8 FiO₂ during and immediately after surgery to reduce surgical site infections. Results from the largest trial available at the time of these two reviews (suggesting long-term survival may be worse with high …

Emigration Of Post-Spawned Twaite Shad Alosa Fallax, An Anadromous And Iteroparous Fish, In A Highly Fragmented River, Mark I.A. Yeldham, J. Robert Britton, Charles Crundwell, Peter Davies, Jamie R. Dodd, Andrew D. Nunn, Randolph Velterop, Jonathan D. Bolland

School of Biological and Marine Sciences

Anthropogenic barriers are widely known to negatively impact the spawning migrations of anadromous fishes, by delaying or preventing passage upstream. Although the impacts of barriers on emigrating post-spawned adults are less well studied, they could potentially impact the fitness and subsequent return rates of iteroparous species. In this study, passive acoustic telemetry was used to track the emigrations of 53 twaite shad Alosa fallax in the River Severn basin in their first spawning migration a year after being tagged, giving insights into their emigration movements and the impacts of anthropogenic weirs on these movements. A. fallax began their emigrations after …

Inconsistent Bioreceptivity Of Three Mortar Mixes In Subtidal Sites, Jessica R. Bone, Alice E. Hall, Rick Stafford, Roger J.H. Herbert

School of Biological and Marine Sciences

Concrete is extensively used in coastal engineering and development which, in addition to its high carbon footprint, threatens intertidal habitats and ecosystems. Eco-engineering addresses this by designing habitat features into coastal infrastructure. The chemical bioreceptivity of cement has been shown to vary, but ordinary Portland cement is generally considered to be the least bioreceptive. In this study, we compare two low carbon mortars (a natural, single source cement (VP), and an ordinary Portland cement/ ground granulated blast furnace slag blend (GGBS)) with an ordinary Portland cement-based control mix (OPC). The three mortars were made into smooth blocks which were secured …

Transgressive Gene Expression And Expression Plasticity Under Thermal Stress In A Stable Hybrid Zone, Lindsey C. Schwartz, Vanessa L. González, Ellen E. Strong, Manuela Truebano, Thomas J. Hilbish

School of Biological and Marine Sciences

Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene …