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Turkish Journal of Agriculture and Forestry

No abstract provided.

Differential Binding Of Host Cell Proteins By Vpr Mutant R77q Compared With Wild Type Vpr, Madison C. Wagley

Theses and Dissertations

HIV Viral protein R (Vpr) is a multifunctional accessory protein which plays a role in nuclear import of the pre-integration complex, transactivation of HIV LTR promoter, cell cycle arrest, and apoptosis during HIV infection. R77Q is an HIV Vpr mutant which is associated with long-term non-progressor phenotypes, and which has previously been connected to higher levels of apoptosis compared to wild type Vpr in vitro. There are observable differences in host binding partners with HIV Vpr between wild type and R77Q strains as shown via coimmunoprecipitation and mass spectrometry. In one run R77Q samples showed binding to histone 1.2, 1.3, …

Development Of Raman Spectroscopic Methods To Analyze Chemical, Biological, And Physical Constituents For Food Safety And Quality, Hannah C. Broadbent

Theses and Dissertations

Ensuring food safety and quality is crucial for consumer health, satisfaction, and regulatory compliance. This study aims to develop rapid, reliable methods for detecting food constituents (i.e. lactose), pathogens (i.e. Listeria monocytogenes), and contaminants (i.e. micro- and nano-plastics) using Raman spectroscopy. With advantages like high specificity, minimal sample preparation, and fast analysis, Raman spectroscopy offers a promising alternative to traditional methods. This research explores its application in assessing chemical, biological, and physical properties of food to enhance safety and quality monitoring. Lactose-free products are increasingly popular due to the global prevalence of lactose intolerance, creating a need for effective verification …

Functional Protein Biomarkers Based On Distributions Of Expression Levels In Single-Cell Imaging Data, Misung Yi, Tingting Zhan, Hallgeir Rui, Inna Chervoneva

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

MOTIVATION: The intra-tumor heterogeneity of protein expression is well recognized and may provide important information for cancer prognosis and predicting treatment responses. Analytic methods that account for spatial heterogeneity remain methodologically complex and computationally demanding for single-cell protein expression. For many functional proteins, single-cell expressions vary independently of spatial localization in a substantial proportion of the tumor tissues, and incorporation of spatial information may not affect the prognostic value of such protein biomarkers.

RESULTS: We developed a new framework for using the distributions of functional single-cell protein expression levels as cancer biomarkers. The quantile functions of single-cell expressions are used …

Effects Of Pharmacologic And Genetic Manipulation Of Gaba-A Receptors On Network Activity, Peter Michael Lambert

Arts & Sciences Graduate Student Theses and Dissertations

GABAA receptors (GABAARs) are the primary inhibitory neurotransmitter receptors in the central nervous system. A rich diversity of receptor subtypes are produced by the combination of various GABA receptor subunits into a heteropentameric chloride channel. Inhibitory signaling through GABAARs occurs on timescales ranging from fast synaptic events lasting milliseconds to tonically active receptors providing standing inhibitory tone. GABAARs are modulated by many clinically important drugs including anesthetic, hypnotic, anxiolytic, and antidepressant agents. Of note, GABAARs are modulated by neurosteroids, which have recently been developed as novel therapeutic agents for psychiatric disease. The synchronized activation of GABAARs through coordinated activity of …

Roles Of Cpsa And Slamf1 In The Innate Immune Response To Mycobacterium Tuberculosis, Steven Grigsby

Arts & Sciences Graduate Student Theses and Dissertations

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), possesses an arsenal of virulence factors to evade host immunity. Not only is Mtb able to evade innate immunity, but adaptive immunity also often fails to adequately control Mtb infection. A mechanistic understanding of how Mtb establishes infection and evades immunity is critical to the development of a protective vaccine and novel therapeutics. The Mtb protein CpsA protects Mtb against the host NADPH oxidase and LC3-asociated phagocytosis of the innate immune system. Consequently, a ΔcpsA mutant is initially attenuated in vivo but eventually reaches the same bacterial burden in the lungs …

Early Islamic Bronze Weights From Ramla, Raz Kletter

'Atiqot

No abstract provided.

Fish Remains From ‘En Gedi, Omri Lernau

'Atiqot

No abstract provided.

Front Matter, The Editorial Board

'Atiqot

No abstract provided.

2025 Academic Conference Program

Holy Cross Undergraduate Academic Conference

No abstract provided.

Image Analysis Of Pupal Sex Ratio In Honey Bee Hives, Anna Tattelman, Grace O’Brien

Biology Student Scholarship

Anna Tattelman ’27, Environmental Biology major

Grace O’Brien ’26, Biology major

Faculty mentor: Dr. Rachael Bonoan, Biology

Our project analyzes honey bee hive development over time. We are specifically looking at drone comb production over a four-week period with varying hive conditions and treatments. It has become more difficult to manage bee hives due to parasitic mites, such as Varroa Destructor. A common method beekeepers use to protect honey bees against these threats is adding drone comb to attract then remove mites. Through drone comb analysis we can determine how honey bees are responding to the treatments by evaluating their …

Scorpions Of The Horn Of Africa (Arachnida, Scorpiones). Part Xxxvii. The Genus Hemiscorpius (Hemiscorpiidae), František Kovařík, Hassan Sh A. Elmi, František Šťáhlavský

Euscorpius

Occurrence of the rare in the Horn of Africa genus Hemiscorpius Peters, 1861 (Scorpiones: Hemiscorpiidae) is summarized, including a distribution map. A male of Hemiscorpius lipsae Kovařík & Lowe, 2022 from Djibouti is described for the first time. A new species Hemiscorpius huluul sp. n. from Somaliland is described, fully complemented with color photographs.

Studies Evaluating Practices For Water Conservation: In-Situ Sensors For Determining Soil Field Capacity And Water Application Savings From Rebate-Driven Residential Landscape Transformations, Madison E. Martini

Theses and Dissertations

Water conservation is a critical issue that requires solutions to address growing water scarcity. In both agricultural and urban settings, targeting conservation efforts is essential for lasting progress as well as protection of communities and ecosystems. This research focuses on identifying practical means to reduce water use by studying separate conservation strategies in urban and agricultural contexts. Given their interdependence, addressing water use in both sectors is essential for achieving meaningful and lasting conservation outcomes. Agricultural water conservation relies on efficient irrigation practices, which depend on accurately determining soil field capacity (FC)--the amount of water soil can retain after excess …

Intervention Strategies To Overcome Hpv Vaccine Hesitancy Among Hispanic Immigrants In The Usa: A Video-Based Ap-Proach, Jamie Jensen

ScholarsArchive Data

These data come from a nationwide survey administered by Qualtrics testing a video intervention to help Hispanic Immigrants overcome barriers to HPV vaccination.

Associations Between Linguistic Factors And Vaccine Attitudes In A Hispanic Immigrant Population In The United States, Jamie Jensen

ScholarsArchive Data

Data are results of a nationwide survey administered by Qualtrics to Hispanic Immigrants concerning HPV vaccine uptake and hesitancy factors.

Rnase1-Driven Alk-Activation Is An Oncogenic Driver And Therapeutic Target In Non-Small Cell Lung Cancer, Zhengyu Zha, Chunxiao Liu, Meisi Yan, Cong Chen, Cheng Yu, Chenhao Zhou, Yi-Chuan Li, Hiro Yamaguchi, Leiguang Ye, Tong Liu, Ying-Nai Wang, Heng-Huan Lee, Wen-Hao Yang, Li-Chuan Chan, Baozhen Ke, Jennifer L Hsu, Lieming Ding, Dong Ji, Peng Pan, Yiran Meng, Yue Pu, Lunxu Liu, Mien-Chie Hung

Faculty, Staff and Student Publications

Targeted therapy has achieved significant success in the treatment of non-small cell lung cancer (NSCLC), particularly in patients harboring common oncogenic driver mutations such as EGFR, KRAS, and ALK rearrangement. However, ~35-50% of NSCLC patients without tyrosine kinase mutation or rearrangement (non-mutated) cannot benefit from these targeted treatments, highlighting the urgent need for novel therapeutic strategies for this patient population. In this study, we report a non-canonical role of human secretory ribonuclease 1 (RNase1), which binds to and activates wild-type ALK in lung cancer cells, thereby triggering its downstream signaling pathway. RNase1-driven ALK-activation (RDAA) cells exhibit enhanced cell proliferation, migration, …

Enriched Pathways In Gut Microbiome Predict Response To Immune Checkpoint Inhibitor Treatment Across Demographic Regions And Various Cancer Types, Xunhui Cai, Jennifer Y Cho, Lijun Chen, Yufeng Liu, Fenghu Ji, Siyi Ge, Hui Yu, Jianbo Shao, P Andrew Futreal, Boris Sepesi, Don Gibbons, Yaobing Chen, Guoping Wang, Chao Cheng, Meng Wu, Jianjun Zhang, Ansel Hsiao, Tian Xia

Faculty, Staff and Student Publications

Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore,

Association Between B-Cell Marker Expression And Runx1 Lesions In Acute Myeloid Leukemia, Beyond Runx1::Runx1t1 Fusion: Diagnostic Pitfalls With Mixed-Phenotype Acute Leukemia—B/Myeloid, Giby V George, Malgorzata Kajstura, Audrey N Jajosky, Hong Fang, Fatima Zahra Jelloul, W Richard Burack, L Jeffrey Medeiros, Wei Wang, Siba El Hussein

Faculty, Staff and Student Publications

Acute myeloid leukemia (AML) with RUNX1::RUNX1T1 fusion is well known to often demonstrate aberrant upregulation of CD19 expression. We studied the clinicopathologic and genetic features of 16 cases of AML with various RUNX1 lesions, including mutations, copy number gains, and translocations other than fusions with RUNX1T1. Most of these cases were classified as AML-myelodysplasia-related or AML-post-cytotoxic therapy based on the cytogenetic and molecular work-up. These neoplasms showed partial expression of one or more B-cell antigens by flow cytometry and/or immunohistochemistry, fulfilling the criteria for mixed-phenotype acute leukemia (MPAL)-B/myeloid (i.e., ≥20% blasts expressing B and myeloid lineage antigens) …

Senescent Cancer-Associated Fibroblasts Mediate Immunosuppression And Promote Breast Cancer Progression, Jiayu Ye

Arts & Sciences Graduate Student Theses and Dissertations

Breast cancer is the most frequently diagnosed cancer among women worldwide, and aging is the largest risk factor for breast cancer development. The process of aging is typically accompanied by a progressive accumulation of senescent cells, which are characterized by a series of markers such as p16INKA4 (p16) positivity and a distinctive profile of secretory factors including mitogens, cytokines, and extracellular matrix (ECM) proteins that are collectively recognized as senescence-associated secretory phenotype (SASP). Numerous data so far have shown that senescent stromal cells play critical roles in modulating tumor microenvironment and progression. For example, senescent fibroblasts induced in vitro could …

Novel Therapeutics For Myeloid Malignancies, Tim Kong

Arts & Sciences Graduate Student Theses and Dissertations

Myeloid malignancies are a group of heterogenous and clonal disorders that include myeloproliferative neoplasms (MPNs) and acute myeloid leukemia (AML). These blood cancers are driven by characteristic oncogenes and propagated by pro-inflammatory niches; MPNs demonstrate hyperactive JAK-STAT signaling and upregulate cytokines including TNF, IL-6, and IL-8. Current therapeutics such as ruxolitinib targeting JAK2 providing symptomatic benefit to MPN patients but are not curative and do not prevent disease transformation to acute myeloid leukemia (AML). As such, greater understanding of the underlying disease biology is still required with means of uncover cancer dependencies. Here, we utilize a series of multi-omic approaches …

Kras Mutation Detection By Liquid Biopsy For Pancreatic Ductal Adenocarcinoma, Mahmoud Yousef, Abdelrahman Yousef, Mark W Hurd, Ashwathy Pillai, Saikat Chowdhury, Mark Knafl, Paul M Roy, Mohammad Fanaeian, Sali Albarouki, Luca F Castelnovo, Jennifer Peterson, Brandon G Smaglo, Robert A Wolff, Shubham Pant, Jason Willis, Ryan Huey, Michael Overman, Ching-Wei Tzeng, Michael P Kim, Naruhiko Ikoma, Jess E Maxwell, Matthew H G Katz, Huamin Wang, Anirban Maitra, Eugene Koay, Ethan B Ludmir, Anthony Chen, Camila Lopez, Haoqiang Ying, John Paul Shen, Dan Zhao

Faculty, Staff and Student Publications

The clinical utility of liquid biopsy (LB) for pancreatic ductal adenocarcinoma (PDAC) remain understudied. Our single-institution cohort of 311 PDAC patients with non-tumor tissues informed LB found 81.2% positivity (N = 186) in metastatic cases and in 52.4% (N = 43) of localized disease. KRAS mutations were detected in 64.6% (N = 148) of metastatic cases and 16% (N = 13) for localized disease. Positive LB, especially KRAS mutation detection, is associated with worse overall survival (OS) in metastatic PDAC (median 14.5 vs. 31.3 months, HR = 2.7, 95%CI = 1.7-4.3, P <  0.0001). The positive concordance rates of KRAS and TP53 mutations were 63% and 68% in metastatic disease but only 7% (KRAS) and 33% (TP53) in localized disease, respectively. Among the 41 patients who underwent serial liquid biopsy testing, 25% tested positive after an initial negative result. LB detects therapeutically targetable mutations in 58.5% of PDAC patients and is associated with OS.

Reduced Venetoclax Exposure To 7 Days Vs Standard Exposure With Hypomethylating Agents In Newly Diagnosed Aml Patients, Christophe Willekens, Alexandre Bazinet, Samy Chraibi, Alex Bataller, Justine Decroocq, Benjamin Carpentier, Delphine Lebon, Abhishek Maiti, Nicolas Gauthier, Nicholas Short, Sarah Bonnet, Koji Sasaki, Sabine Khalife-Hachem, Mahesh Swaminathan, Jean-Baptiste Micol, Florence Pasquier, Christophe Marzac, Damien Roos-Weil, Laurent Pascal, Naval Daver, Tapan Kadia, Didier Bouscary, Farhad Ravandi, Arnaud Pages, Hagop Kantarjian, Stéphane De Botton, Courtney Dinardo

Faculty, Staff and Student Publications

Hypomethylating agent (HMA) plus venetoclax (VEN) regimens are standard of care in patients with acute myeloid leukemia (AML) ineligible for intensive chemotherapy. While the VEN label recommends continuous 28-day cycles, shortened VEN durations may induce similar response rates and improve tolerability. It is unknown how a VEN exposure reduced to 7 days during cycles compares to standard HMA + VEN. We retrospectively compared newly diagnosed AML patients treated with azacitidine (AZA) x 7 days plus VEN x 7 days ("7 + 7" regimen) from the first cycle (n = 82) vs patients treated with standard dose HMA + VEN (std-HMA/VEN) …

Multimeric Transcription Factor Bcl11a Utilizes Two Zinc-Finger Tandem Arrays To Bind Clustered Short Sequence Motifs, John R Horton, Meigen Yu, Jujun Zhou, Melody Tran, Rithvi R Anakal, Robert M Blumenthal, Yun Huang, Xing Zhang, Xiaodong Cheng

Faculty, Staff and Student Publications

BCL11A, a transcription factor, is vital for hematopoiesis, including B and T cell maturation and the fetal-to-adult hemoglobin switch. Mutations in BCL11A are linked to neurodevelopmental disorders. BCL11A contains two DNA-binding zinc-finger arrays, low-affinity ZF2-3 and high-affinity ZF4-6, separated by a 300-amino-acid linker. ZF2-3 and ZF4-5 share 73% identity, including five out of six DNA base-interacting residues. These arrays bind similar short sequence motifs in clusters, with the linker enabling a broader binding span. Crystallographic structures of ZF4-6, in complex with oligonucleotides from the β-globin locus region, reveal DNA sequence recognition by residues Asn756 (ZF4), Lys784 and Arg787 (ZF5). A …

Humanized Saccharomyces Cerevisiae Provides A Facile And Effective Tool To Identify Damaging Human Variants That Cause Exosomopathies, Khondakar Sayef Ahammed, Milo B Fasken, Anita H Corbett, Ambro Van Hoof

Faculty, Staff and Student Publications

The RNA exosome is an evolutionarily conserved, multiprotein complex that is the major RNase in 3' processing and degradation of a wide range of RNAs in eukaryotes. Single amino acid changes in RNA exosome subunits cause rare genetic diseases collectively called exosomopathies. However, distinguishing disease-causing variants from nonpathogenic ones remains challenging, and the mechanism by which these variants cause disease is largely unknown. Previous studies have employed a budding yeast model of RNA exosome-linked diseases that relies on mutating the orthologous yeast genes. Here, we develop a humanized yeast model of exosomopathies that allows us to unambiguously assess damaging effects …

First Record Of Corella Japonica In California, Lauren M. Stefaniak, Marie L. Nydam, Susanna López-Legentil

Marine Science

Many ascidian (sea squirt) species are common members of fouling communities, particularly on floating substrates such as docks and pilings and through maritime transport, have been introduced worldwide. For the past 30 years, marinas in Southern California have been regularly monitored for introduced species due to their proximity to the international shipping terminals in Los Angeles and Long Beach Harbors. Here, we report on the first record in the eastern Pacific of an ascidian in the family Corellidae (O. Phlebobranchia), Corella japonica, found at the Newmarks Yacht Centre in Los Angeles Harbor. This study further highlights the importance of continuously …

Models And Mechanisms Of Chemotherapy-Induced Side Effects, Junwei Du

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cancer is among the leading causes of death worldwide. Chemotherapy remains a cornerstone in the treatment of various cancers; however, it often leads to a range of debilitating side effects that compromise its efficacy and profoundly impact patients' quality of life and psychosocial well-being. These side effects can be broadly categorized into short-term effects, such as nausea, vomiting, fatigue, hair loss, and neutropenia, and long-term effects which can persist months or even years after treatment, including peripheral neuropathies, cognitive impairment, cardiotoxicity, nephrotoxicity and ototoxicity. Among the most common and dose-limiting side effects are chemotherapy-induced peripheral neuropathy (CIPN) and cardiotoxicity (CTX). …

Exploring The Acute Effects Of Sedentary Behaviors On Cardiometabolic Risk In Hispanic Adolescents With Obesity: A Randomized Crossover Study, Erica G Soltero, Osamah Salim, Yiming Mirabile, Salma M Musaad

Children’s Nutrition Research Center Staff Publications

Background/Objectives: Time spent in sedentary pursuits is associated with adverse metabolic profiles. Adolescents spend 65-75% of their day in sedentary pursuits; however, evidence among youth is less conclusive. This study examined the effects of an acute 4 h bout of sedentary behaviors on cardiometabolic outcomes and energy expenditure in Hispanic adolescents (12-16 years old) with obesity (BMI% ≥ 95th).

Methods: This study used a randomized cross-over design to engage participants (N = 12) in two sedentary conditions, an active condition where youth were engaged in two hours of 'active' sitting activities (e.g., reading and puzzles) and two hours …

Deep Learning-Based Automatic Segmentation Of Cerebral Infarcts On Diffusion Mri, Wi-Sun Ryu, Dawid Schellingerhout, Jonghyeok Park, Jinyong Chung, Sang-Wuk Jeong, Beom Joon Kim, Keun-Sik Hong, Kyung Bok Lee, Tai Hwan Park, Sang-Soon Park, Jong-Moo Park, Kyusik Kang, Yong-Jin Cho, Hong-Kyun Park, Byung-Chul Lee, Kyung-Ho Yu, Mi Sun Oh, Soo Joo Lee, Jae Guk Kim, Jae-Kwan Cha, Dae-Hyun Kim, Jun Lee, Man Seok Park, Dongmin Kim, Oh Young Bang, Eung Yeop Kim, Chul-Ho Sohn, Hosung Kim, Hee-Joon Bae, Dong-Eog Kim

Faculty, Staff and Student Publications

We explored effects of (1) training with various sample sizes of multi-site vs. single-site training data, (2) cross-site domain adaptation, and (3) data sources and features on the performance of algorithms segmenting cerebral infarcts on Magnetic Resonance Imaging (MRI). We used 10,820 annotated diffusion-weighted images (DWIs) from 10 university hospitals. Algorithms based on 3D U-net were trained using progressively larger subsamples (ranging from 217 to 8661), while internal testing employed a distinct set of 2159 DWIs. External validation was conducted using three unrelated datasets (n = 2777, 50, and 250). For domain adaptation, we utilized 50 to 1000 subsamples from …

Contribution To The Knowledge Of Cave-Dwelling Fauna From The Prokletije Mountains, Joanna Kocot-Zalewska, Iwona Słowińska, Paweł Domagała, Jakub Bienias, Dominik Szymański, Dawid Szymański, Hubert Szymański, Paweł Sienkiewicz, Andrzej Józef Woźnica

International Journal of Speleology

The article presents the results of the study on invertebrate fauna inhabiting caves in the Prokletije Mountains. This mountain range is located on the border of Montenegro, Albania, and Kosovo. During the expeditions to Albania in 2021 and to Montenegro in 2022–2023, 17 caves and one bauxite mine were visited altogether. All the studied caves are located very high, above 1,700 m a.s.l., where the temperature inside is low, and several are filled with ice or snow. During the Albanian expedition 102 arthropods have been collected altogether. Among these were 19 beetles (Coleoptera), 44 flies (Diptera), three crickets (Orthoptera), five …

Development Of A Qualitative Spot Assay For Zinc Detection In Fortified Cereal Grain Matrices, Ashley L. Lamborn

Theses and Dissertations

The present thesis is a compilation of a literature review, journal manuscript, and two standard operating procedures (SOP) on the qualitative determination of zinc in fortified cereal grain products and matrices. The literature review addresses the premise of the research as well as potential solutions for the development of a rapid qualitative spot assay for zinc determination. Quality assurance assays affirm the presence of micronutrients in food fortification initiatives, but no rapid qualitative spot methods for the assessment of zinc currently exist. Chromogenic reagents that may perform a key role in the rapid determination of zinc are identified. The journal …