Life Sciences Commons^™

Split Learning For Distributed Collaborative Training Of Deep Learning Models In Health Informatics, Zhijun Yin, Xiaoqian Jiang, Bradley A Malin

Faculty, Staff and Student Publications

Deep learning continues to rapidly evolve and is now demonstrating remarkable potential for numerous medical prediction tasks. However, realizing deep learning models that generalize across healthcare organizations is challenging. This is due, in part, to the inherent siloed nature of these organizations and patient privacy requirements. To address this problem, we illustrate how split learning can enable collaborative training of deep learning models across disparate and privately maintained health datasets, while keeping the original records and model parameters private. We introduce a new privacy-preserving distributed learning framework that offers a higher level of privacy compared to conventional federated learning. We …

Integrating Comorbidity Knowledge For Alzheimer's Disease Drug Repurposing Using Multi-Task Graph Neural Network

Faculty, Staff and Student Publications

Alzheimer's Disease (AD) is a multifactorial disease that shares common etiologies with its multiple comorbidities, especially vascular diseases. To predict repurposable drugs for AD utilizing the relatively well-investigated comorbidities' knowledge, we proposed a multi-task graph neural network (GNN)-based pipeline that incorporates the corresponding biomedical interactome of these diseases with their genetic markers and effective therapeutics. Our pipeline can accurately capture the interactions and disease classification in the network. Next, we predicted drugs that might interact with the AD module by the node embedding similarity. Our candidates are mostly BBB permeable, and literature evidence showed their potential for treating AD pathologies, …

Local Contrastive Learning For Medical Image Recognition, Xia Hu

Faculty, Staff and Student Publications

The proliferation of Deep Learning (DL)-based methods for radiographic image analysis has created a great demand for expert-labeled radiology data. Recent self-supervised frameworks have alleviated the need for expert labeling by obtaining supervision from associated radiology reports. These frameworks, however, struggle to distinguish the subtle differences between different pathologies in medical images. Additionally, many of them do not provide interpretation between image regions and text, making it difficult for radiologists to assess model predictions. In this work, we propose Local Region Contrastive Learning (LRCLR), a flexible fine-tuning framework that adds layers for significant image region selection as well as cross-modality …

The Kynurenine Pathway In Alzheimer’S Disease: A Meta-Analysis Of Central And Peripheral Levels, Zhongming Zhao

Faculty, Staff and Student Publications

OBJECTIVE: Changes in the kynurenine pathway are recognized in psychiatric disorders, but their role in Alzheimer's disease (AD) is less clear. We aimed to conduct a systematic review and meta-analysis to determine whether tryptophan and kynurenine pathway metabolites are altered in AD.

METHODS: We performed a systematic review and random-effects meta-analyses. Inclusion criteria were studies that compared AD and cognitively normal (CN) groups and assessed tryptophan or kynurenine pathway metabolites in cerebrospinal fluid or peripheral blood.

RESULTS: Twenty-two studies with a total of 1,356 participants (664 with AD and 692 CN individuals) were included. Tryptophan was decreased only in peripheral …

Federated Learning Based Futuristic Biomedical Big-Data Analysis And Standardization, Sukumar Rajendran, Saurav Mallik, Zhongming Zhao

Faculty, Staff and Student Publications

Medical data processing and analytics exert significant influence in furnishing dependable decision support for prospective biomedical applications. Given the sensitive nature of medical data, specialized techniques and frameworks tailored for application-centric processing are imperative. This article presents a conceptualization for the analysis and uniformitarian of datasets through the implementation of Federated Learning (FL). The realm of medical big data stems from diverse origins, necessitating the delineation of data provenance and attribute paradigms to facilitate feature extraction and dependency assessment. The architecture governing the data collection framework is intricately linked to remote data transmission, thereby engendering efficient customization oversight. The operational …

Phosphate2 And Pin-Likes7 Affect Symbiotic Nodule Phenotypes In Soybean, Bhawandeep Kaur

Electronic Theses and Dissertations

Legumes and soil rhizobia share a symbiotic relationship, wherein rhizobia fix atmospheric dinitrogen in exchange for photosynthates from the host plant. This exchange of mutual benefits occurs in a specialized root structure called ‘nodule’. Soybean (Glycine max) nodules arise from root outer cortical cells. De novo cell differentiation of cortical cells during nodule development leads to the formation of two distinct nodule zones in the mature nodule: the central infection zone where nitrogen fixation occurs and the peripheral parenchyma zone that houses vascular bundles. Plant signaling mechanisms that dictate the development of these nodule zones are not known. To address …

Sustainable Utilisation And Management Of Food Waste For High-Value Products, Amit Jaiswal

Articles

Welcome to the Special Issue on “Sustainable Utilisation and Management of Food Waste for High-Value Products”. This Special Issue focuses on one of the most critical challenges facing our world today—the efficient management and utilisation of food waste. It presents a variety of scientific investigations from renowned scholars and researchers worldwide to address this challenge, covering an array of topics ranging from fundamental research to real-world applications. Food waste is a global dilemma that requires urgent attention. According to the Food and Agriculture Organization (FAO), approximately one-third of food produced for human consumption worldwide, or around 1.3 billion tons, is …

Summer Research Fellowship Project Descriptions 2023, Clark Science Center's Summer Research Fellows Program

SURF Abstracts (Women in Science)

A summary of research done by Smith College’s 2023 Summer Research Fellowship (SURF) Program participants. Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. Supervised by faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants were asked to summarize their research experiences for this publication.

Novel Reproductive Data On Blue Sucker, Cycleptus Elongatus (Cypriniformes: Catostomidae), From Northeastern Arkansas, C.T. Mcallister, D.G. Cloutman, E.M. Leis, H.W. Robison

Journal of the Arkansas Academy of Science

Nothing has been published in the scientific literature concerning the reproductive biology of the Blue Sucker, Cycleptus elongatus in Arkansas. We examined seven female C. elongatus collected in late February 2021 and 2022 and again in early March 2023 from the Black River, Lawrence County. Egg mass (g) averaged 15.8% of the total weight of these gravid females. It appears that this sucker can spawn as early as February in this population. This is the first time information on female reproduction in this species has been published from any population of C. elongatus in the state.

New Geographic Distributional Records For Two Lampreys (Petromyzontiformes: Petromyzontidae) In Arkansas, With Notes On Histopathology, C.T. Mcallister, H.W. Robison, E.M. Leis, D.G. Cloutman, A.C. Camus

Journal of the Arkansas Academy of Science

The recent update (2nd edition) of the Fishes of Arkansas includes what is known, to date, on the geographic distribution of five species of lampreys that occur in the state. Here, we provide new distributional records on two of those species, the chestnut lamprey (Ichthyomyzon castaneus) and southern brook lamprey (I. gagei), as well as documenting host-parasite information (histopathology) caused by the former species.

Updated Virophage Taxonomy And Distinction From Polinton-Like Viruses, Simon Roux, Matthias G. Fischer, Thomas Hackl, Laura A. Katz, Frederik Schulz, Natalya Yutin

Biological Sciences: Faculty Publications

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of “hyperparasitism” in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and …

Invasion Risk By Fruit Trees Mealybug Rastrococcus Invadens (Williams) (Homoptera: Pseudococcidae) Under Climate Warming, Abdelmutalab G.A. Azrag, Samira A. Mohamed, Shepard Ndlela, Sunday Ekesi

All Peer-Reviewed Publications

The mango mealybug Rastrococcus invadens (Williams) (Homoptera: Pseudococcidae) is a destructive and important insect pest of fruit trees in Africa and Asia, especially the mango. Females and nymphs feed on plant leaves and fruits and produce honeydew that causes sooty mold, leading to yield reduction. Although it is an important pest, the distribution of R. invadens under different climate change scenarios has not been established. In this study, we predicted the suitable habitat for R. invadens occurrence under current and future [two Shared Socioeconomic Pathways (SSPs) scenarios: (SSP2-4.5 and SSP5-8.5) for the years 2050s and 2070s], using environmental variables and …

Further Investigation Of Lead Exposure As A Potential Threatening Process For A Scavenging Marsupial Species, D. J. Hutchinson, E. M. Jones, J. M. Pay, J. R. Clarke, Michael T. Lohr, J. O. Hampton

Research outputs 2022 to 2026

There is a growing recognition of the harmful effects of lead exposure on avian and mammalian scavengers. This can lead to both lethal and non-lethal effects which may negatively impact wildlife populations. Our objective was to assess medium-term lead exposure in wild Tasmanian devils (Sarcophilus harrisii). Frozen liver samples (n = 41), opportunistically collected in 2017–2022, were analysed using inductively coupled plasma mass spectrometry (ICP-MS) to determine liver lead concentrations. These results were then used to calculate the proportion of animals with elevated lead levels ( > 5 mg/kg dry weight) and examine the role of explanatory variables that may have …

The Relationship Between Alpha-Defensin 1 And Gut Microbiome Composition In A Population Of Bhutanese Refugee Adults With A High Prevalence Of Type 2 Diabetes, Daisha Alana Drake

Honors Theses and Capstones

The New Hampshire Bhutanese refugee population is disproportionately affected by obesity and metabolic disorders such as type 2 diabetes. The gut microbiome is important for overall human health, with high microbial richness and diversity being associated with reduced chronic inflammation and type 2 diabetes risk. Microbial richness and diversity have been shown to decrease in United States (U.S.) immigrant populations, but have not been measured in refugee populations. One of the anti-inflammatory functions of the gut microbiome is related to the production of short-chain fatty acids (SCFAs), which regulate pro-inflammatory cytokine production. Alpha-defensin 1 is an antimicrobial peptide that is …

Neuronal Primary Cilia In Postnatal Brains & Alzheimer’S Disease Mice Eeg Patterns Under Fear Conditioning, Sierra Rose Mae Walsh

Honors Theses and Capstones

Alzheimer’s Disease (AD) is a neurodegenerative condition caused by the abnormal accumulation of amyloid β plaque. While small amounts of amyloid β plaque is to be expected with increased age, AD presents amyloid precursor protein (APP), a gene promoting inappropriate plaque formation, causing early neuronal death and tissue depreciation. APP23 transgenic mouse models contain the human mutation in the neocortical and hippocampal positions, areas revealing of plaque accumulation and memory loss. Within the hippocampal cortices, the primary cilia, which regulate higher cognition and neurodevelopment can be studied along with burst suppressions, or moments of high focal activity, to target potential …

Revolutionary Advances In The Treatment Of Genetic Disease, Emma Kaitlyn Carrigan

Honors Theses and Capstones

No abstract provided.

Meta-Analytic Connectivity Modelling Of Healthy Swallowing, Chris R. Tilton

Honors Theses and Capstones

A quantitative, voxel-wise meta-analysis was performed to investigate the brain regions involved in healthy human swallowing. Studies included in the meta-analysis (1) examined water swallowing, saliva swallowing, or both, (2) included healthy, normal subjects, and (3) reported stereotaxic brain activation coordinates in standard space. Following these criteria, a systematic literature review identified 8 studies that met the criteria. An activation likelihood estimation (ALE) meta-analysis and meta-analytic connectivity modelling (MACM) analysis were performed with BrainMap software. Ten clusters with high activation likelihood were found in the bilateral precentral gyri, right insula, left declive, right medial frontal gyrus, right dorsal nucleus of …

Cutaneous Microbiome Of Red Fox (Vulpes Vulpes) Infected With Sarcoptic Mange (Sarcoptes Scabiei), Jacqueline C. Robidoux

Honors Theses and Capstones

Sarcoptic mange is a parasitic skin disease that affects countless mammals worldwide, including red foxes (Vulpes vulpes). The symptoms, such as hair loss, crusting, and the number of mites, vary between individual foxes. Sarcoptic mange damages the skin barrier, which in turn disrupts the biodiversity of bacteria in the microbiome. It is unknown what the biodiversity of bacteria is at each stage of the disease. This experiment will compare the microbiomes of different samples with and without mange; in hopes to reveal a connection between the different severities of sarcoptic mange and the biodiversity of bacteria and fungi …

Investigating The Relationship Between Sea Ice Extent And Erignathus Barbatus Breeding Phenology In The Alaskan Arctic, Rachel E. Lewis

Honors Theses and Capstones

No abstract provided.

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …

Effects Of Aging On The Reproductive Success Of Female Saltmarsh Sparrows (Ammospiza Caudacutus) In Maine And New Hampshire, Isabella Rose Collamati

Honors Theses and Capstones

The saltmarsh sparrow (Ammospiza caudacutus) is a ground-nesting specialist in coastal salt marshes of the Northeast. Rising sea-levels increase the loss of offspring due to tidal flooding, reducing nest success and resulting in a sharp population decline. In other avian species, age has been shown to affect nest success through altering fertility, behavior, and the number of young produced, favoring older individuals. I investigated age effects on nest success of female saltmarsh sparrows using nest monitoring data collected at four sites of a long-term demographic monitoring project: Chapman's Landing (Stratham, NH), Eldridge Marsh (Wells, ME), Popham Beach (Phippsburg, …

Odd Bedfellows & Marriage Of Necessity: Public Health And Politics In American Federalism, Gabriella Victoria Chianese

Honors Theses and Capstones

In the wake of the coronavirus disease 2019 (COVID-19) pandemic, while the public disagrees over mask mandates, required vaccinations, and social distancing, it seems like one common sentiment exists – a distaste for the odd bedfellows of politics and public health. There are those who cry for the compartmentalization of the science of public health and the art of politics to rectify this situation. In the wake of so much confusion and chaos, it is not unjustified to demand the depoliticization of public health; however, this response is unrealistic given the modern political climate, demonstrates a narrow understanding of the …

Contralateral Acl Rupture Is More Common Than Acl Graft Rupture In Australian Netballers After Acl Reconstruction, Conor Honeywill

Theses

Background: Netball is a popular sport worldwide, particularly in females. The nature of the sport makes it high-risk for anterior cruciate ligament (ACL) injury.

Purpose: The primary outcome was to determine the prevalence of ACL graft rupture and contralateral ACL (CACL) rupture in Australian female netballers following ACL Reconstruction (ACLR). Additionally, this study aimed to determine the rate of return to sport and psychological readiness.

Study Design: Cross-Sectional Study

Methods: From a prospective database, 332 consecutive ACLR with hamstring autograft conducted between the years 2007-2015 performed by 2 surgeons in female netball players were identified. Patients were retrospectively surveyed at …

Sustaining Development Through Biodiversity Offsets, Linda Abdo

Theses

Biodiversity offsets, also called “environmental offsets”, are actions used to compensate for the loss of biodiversity and social values associated with development projects. They are commonly used by governments to contribute to ecologically sustainable development (ESD); however, offsets have been criticised for inappropriate use, poor implementation, and inadequate monitoring, reporting and enforcement. Regardless, use of offsets is likely to increase due to regulatory convenience in easing community discomfort with development impacts. This thesis investigated how biodiversity offsets in Australia can be enhanced to align with ESD principles. Analyses of peer-reviewed journal articles, published reports, media articles and legislative instruments for …

Population Genetic Structure Associated With A Landscape Barrier In The Western Grasswren (Amytornis Textilis Textilis), Aline Gibson Vega, Michelle L. Hall, Amanda Ridley, Saul J. Cowen, Amy L. Slender, Allan H. Burbidge, Marina Louter, W. Jason Kennington

Research outputs 2022 to 2026

Dispersal patterns can dictate genetic population structure and, ultimately, population resilience, through maintaining gene flow and genetic diversity. However, geographical landforms, such as peninsulas, can impact dispersal patterns and thus be a barrier to gene flow. Here, we use 13 375 genome-wide single-nucleotide polymorphisms (SNPs) to evaluate genetic population structure and infer dispersal patterns of the Western Grasswren Amytornis textilis textilis (WGW, n = 140) in the Shark Bay region of Western Australia. We found high levels of genetic divergence between subpopulations on the mainland (Hamelin) and narrow peninsula (Peron). In addition, we found evidence of further genetic sub-structuring within …

Closing Pit Lakes As Aquatic Ecosystems: Risk, Reality, And Future Uses, Mark A. Lund, Melanie L. Blanchette

Research outputs 2022 to 2026

Mine pit lakes are formed when open-cut pits flood with water, and these lakes occur by the thousands on every inhabited continent. The remediation and closure of pit lakes is a pressing issue for sustainable development and provision of freshwater ecosystem services. While pit lakes can be spectacular examples of recreation and renewal, pit lakes may be better known for their poor water qualities and risks to communities and the environment. Often the public wants to simply “fill the pits in” to restore a terrestrial landscape, but this is not always possible. Therefore, planning for remediation and future uses is …

Mitoq Alleviates Hippocampal Damage After Cerebral Ischemia: The Potential Role Of Sirt6 In Regulating Mitochondrial Dysfunction And Neuroinflammation, Ayman A. Ibrahim, Sherif S. Abdel Mageed Dr, Marwa M. Safar Prof.Dr, Mohammed F. El-Yamany Prof.Dr., Mamdouh A. Oraby Dr.

Pharmacy

Aims: Mitochondrial perturbations are the major culprit of the inflammatory response during the initial phase of cerebral ischemia. The present study explored the neuroprotective effect of the mitochondrial-targeted antioxidant, Mitoquinol (MitoQ), against hippocampal neuronal loss in an experimental model of brain ischemia/ reperfusion (I/R) injury. Main methods: Rats were subjected to common carotid artery occlusion for 45 min, followed by reperfusion for 24 h. MitoQ (2 mg/kg; i.p daily) was administered for 7 successive days prior to the induction of brain ischemia. Key findings: I/R rats exhibited hippocampal damage evidenced by aggravated mitochondrial oxidative stress, thereby enhancing mtROS and oxidized …

Investigating Bzip Recognition Of Dna Sequences Through A Knob-Socket Perspective, Aaron Tran

University of the Pacific Theses and Dissertations

To investigate whether higher order packing interactions confer protein-DNA specificity, a modified Knob-Socket (KS) model was used to analyze the interface of bZIP-DNA crystal structures. The KS analysis identified a nine-residue quadripartite recognition core consisting of four contiguous KS pockets P1, P2, N3, and N4 that each pack one of the four DNA half-site bases in the target sequence. Only one base per base pair packs, and these interactions are split across the DNA strands: the first two positive strand positions 1p and 2p pack into P1 and P2 while the last two negative strand positions 3n and 4n pack …

Development Of Multivalent Dna-Peptide Nucleosome Mimetics And Multi-Domain Protein Inhibitors That Directly Or Indirectly Target The E3 Ligase Uhrf1, Li Gu

University of the Pacific Theses and Dissertations

UHRF1 is an E3 ubiquitin ligase and a key epigenetic regulator establishing a crosstalk between DNA methylation and histone modification. Despite the important biochemical role of UHRF1 in cells, its overexpression has been found in almost all primary cancer types including breast cancer, lung cancer and so on. Numerous evidence indicates a strong link between tumorigenesis and UHRF1 overexpression, supporting its potential as a universal biomarker for cancer. However, UHRF1 is “yet-to-be drugged” and no highly potent chemical probes have been developed to target UHRF1 to date. In this study, we proposed two drug design approaches for UHRF1. The first …

A Dnak Chaperone System Connects Type Iv Pilus Activity To Polysaccharide Secretion In The Cyanobacterium Nostoc Punctiforme, Heather J. Mcdonald

University of the Pacific Theses and Dissertations

Type IV pili (T4P) systems are widely utilized among bacteria to power and direct surface motility. The production and secretion of a viscous polysaccharide to provide friction and resistance to the extended pilus structure is seen in several species of cyanobacteria including Nostoc punctiforme. The complex coregulation of polysaccharide secretion and T4P motor activity is not fully understood, although studies indicate a consistent relationship between functional motility and intact pathways of polysaccharide secretion and pilus extension in cyanobacteria. Using a combination of protein-protein interaction analysis, cytological studies, and comparative genomics this study proposes a theoretical mechanism for T4P motor influenced …