Digital Commons Network^™

Integrative Multi-Omic Cancer Profiling Reveals Dna Methylation Patterns Associated With Therapeutic Vulnerability And Cell-Of-Origin, Wen-Wei Liang, Rita Jui-Hsien Lu, Reyka G Jayasinghe, Steven M Foltz, Eduard Porta-Pardo, Yifat Geffen, Michael C Wendl, Rossana Lazcano, Iga Kolodziejczak, Yizhe Song, Akshay Govindan, Elizabeth G Demicco, Xiang Li, Yize Li, Sunantha Sethuraman, Samuel H Payne, David Fenyö, Henry Rodriguez, Maciej Wiznerowicz, Hui Shen, D R Mani, Karin D Rodland, Alexander J Lazar, Ana I Robles, Li Ding, Clinical Proteomic Tumor Analysis Consortium

Faculty, Staff and Student Publications

DNA methylation plays a critical role in establishing and maintaining cellular identity. However, it is frequently dysregulated during tumor development and is closely intertwined with other genetic alterations. Here, we leveraged multi-omic profiling of 687 tumors and matched non-involved adjacent tissues from the kidney, brain, pancreas, lung, head and neck, and endometrium to identify aberrant methylation associated with RNA and protein abundance changes and build a Pan-Cancer catalog. We uncovered lineage-specific epigenetic drivers including hypomethylated FGFR2 in endometrial cancer. We showed that hypermethylated STAT5A is associated with pervasive regulon downregulation and immune cell depletion, suggesting that epigenetic regulation of STAT5A …

Krasg12d Inhibition Reprograms The Tumor Microenvironment Of Early And Advanced Pancreatic Cancer To Promote Fas-Mediated Killing By Cd8+ T Cells, Krishnan K Mahadevan, Kathleen M Mcandrews, Valerie S Lebleu, Sujuan Yang, Hengyu Lyu, Bingrui Li, Amari M Sockwell, Michelle L Kirtley, Sami J Morse, Barbara A Moreno Diaz, Michael P Kim, Ningping Feng, Anastasia M Lopez, Paola A Guerrero, Francesca Paradiso, Hikaru Sugimoto, Kent A Arian, Haoqiang Ying, Yasaman Barekatain, Lakshmi Kavitha Sthanam, Patience J Kelly, Anirban Maitra, Timothy P Heffernan, Raghu Kalluri

Faculty, Staff and Student Publications

The KRASG12D mutation is present in nearly half of pancreatic adenocarcinomas (PDAC). We investigated the effects of inhibiting the KRASG12D mutant protein with MRTX1133, a non-covalent small molecule inhibitor of KRASG12D, on early and advanced PDAC and its influence on the tumor microenvironment. Employing 16 different models of KRASG12D-driven PDAC, we demonstrate that MRTX1133 reverses early PDAC growth, increases intratumoral CD8+ effector T cells, decreases myeloid infiltration, and reprograms cancer associated fibroblasts. MRTX1133 leads to regression of both established PanINs and advanced PDAC. Regression of advanced PDAC requires CD8+ T cells and immune checkpoint blockade (ICB) synergizes with MRTX1133 …

Elimination Of Oncogenic Kras In Genetic Mouse Models Eradicates Pancreatic Cancer By Inducing Fas-Dependent Apoptosis By Cd8+ T Cells, Krishnan K Mahadevan, Valerie S Lebleu, Elena V Ramirez, Yang Chen, Bingrui Li, Amari M Sockwell, Mihai Gagea, Hikaru Sugimoto, Lakshmi Kavitha Sthanam, Desiree Tampe, Michael Zeisberg, Haoqiang Ying, Abhinav K Jain, Ronald A Depinho, Anirban Maitra, Kathleen M Mcandrews, Raghu Kalluri

Faculty, Staff and Student Publications

Oncogenic KrasG12D (Kras*) is critical for the initiation and maintenance of pancreatic ductal adenocarcinoma (PDAC), and a known repressor of tumor immunity. Conditional elimination of Kras* in genetic mouse models of PDAC leads to reactivation of Fas, CD8+ T cell mediated apoptosis, and complete eradication of tumors. Kras* elimination recruits activated CD4+ and CD8+ T cells and promotes the activation of antigen presenting cells. Mechanistically, Kras* mediated immune evasion involves epigenetic regulation of the Fas death receptor in cancer cells, via methylation of its promoter region. Further, analysis of human RNA sequencing identifies that high KRAS expressing PDAC tumors show …

The Spatiotemporal Dynamics Of Semantic Integration In The Human Brain, Evan S Schaffer, Neeli Mishra, Matthew R Whiteway, Wenze Li, Michelle B Vancura, Jason Freedman, Kripa B Patel, Venkatakaushik Voleti, Liam Paninski, Elizabeth M C Hillman, L F Abbott, Richard Axel

Faculty, Staff and Student Publications

What are the spatial and temporal scales of brainwide neuronal activity? We used swept, confocally-aligned planar excitation (SCAPE) microscopy to image all cells in a large volume of the brain of adult Drosophila with high spatiotemporal resolution while flies engaged in a variety of spontaneous behaviors. This revealed neural representations of behavior on multiple spatial and temporal scales. The activity of most neurons correlated (or anticorrelated) with running and flailing over timescales that ranged from seconds to a minute. Grooming elicited a weaker global response. Significant residual activity not directly correlated with behavior was high dimensional and reflected the activity …

Lanthorn, Vol. 58, No. 03, September 11, 2023, Grand Valley State University

Volume 58, August 7, 2023 - April 15, 2024

Lanthorn is Grand Valley State's student newspaper, published from 1968 to the present.

Strawberry Enterprise Budget, Rebecca Sideman, Kaitlyn Orde, William Edwards

UNH Cooperative Extension

The worksheets in this resource were designed to track expenses and determine a profit/loss value for a strawberry planting. This workbook was designed to take specific planting through its lifecycle---from the preplant period to the final bearing year. Neither the activities or material listed in the worksheets are intended to be a step-by-step guide for strawberry production; depending on the production system and farm, only a subset will be relevant to each operation.

Determinants Of Hormonal Contraceptive Use Among Adolescent Females In The Republic Of Benin, Marlene Joannie Bewa

USF Tampa Graduate Theses and Dissertations

Introduction: Globally, 17 million adolescent girls—ages 15-19-- give birth every year, which affects educational and professional outcomes such as school completion, future employment, and economic empowerment. In Benin, adolescent girls have a substantial unmet need for sexual and reproductive health (SRH) information and services. More specifically, the need for hormonal contraceptive products and services, as well as accurate, age-appropriate, and comprehensive sexuality education, is not met universally.

Objective: This research objective is to understand personal, behavioral, and environmental barriers and facilitators to the access and uptake of modern contraceptive methods among adolescents in Benin. This will inform recommendations for improving …

Sex Hormone-Binding Globulin (Shbg) Mitigates Er Stress And Improves Viability And Insulin Sensitivity In Adipose-Derived Mesenchymal Stem Cells (Asc) Of Equine Metabolic Syndrome (Ems)-Affected Horses, Nabila Bourebaba, Mateusz Sikora, Badr Qasem, Lynda Bourebaba, Krzysztof Marycz

Faculty, Staff and Student Publications

BACKGROUND: Equine metabolic syndrome (EMS), which encompasses insulin resistance, low-grade inflammation and predisposition to laminitis is a critical endocrine disorder among the most prevalent conditions affecting horses from different breeds. According to the most recent research, low human sex hormone-binding globulin (SHBG) serum levels correlate with an increased risk of obesity, insulin resistance and diabetes, and may contribute to overall metabolic dysregulations. This study aimed to test whether exogenous SHBG could protect EMS affected adipose-derived stromal stem cells (EqASC

METHODS: EqASC

RESULTS: Obtained data demonstrated that exogenous SHBG treatment significantly promoted ASCs cells proliferation, cell cycle and survival with reduced …

Phasedancer: A Novel Targeted Assembler Of Segmental Duplications Unravels The Complexity Of The Human Chromosome 2 Fusion Going From 48 To 46 Chromosomes In Hominin Evolution, Barbara Poszewiecka, Krzysztof Gogolewski, Justyna A Karolak, Paweł Stankiewicz, Anna Gambin

Faculty, Staff and Students Publications

Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich regions of interest iteratively. We validate its robustness and efficiency using a golden-standard set of human BAC clones and in silico-generated SDs with predefined evolutionary scenarios. PhaseDancer enables extension of the incomplete complex SD-rich subtelomeric regions of Great Ape chromosomes orthologous to the human chromosome 2 (HSA2) fusion site, informing a model of HSA2 formation and unravelling the evolution of human and Great Ape genomes.

Adapting Shift Work Schedules For Sleep Quality, Sleep Duration, And Sleepiness In Shift Workers., Gerben Hulsegge, Pieter Coenen, Gregg M Gascon, Manisha Pahwa, Birgit Greiner, Ciarán Bohane, Imelda S Wong, Juha Liira, Rachel Riera, Daniela V Pachito

Ambulatory and Primary Care Articles

BACKGROUND: Shift work is associated with insufficient sleep, which can compromise worker alertness with ultimate effects on occupational health and safety. Adapting shift work schedules may reduce adverse occupational outcomes.

OBJECTIVES: To assess the effects of shift schedule adaptation on sleep quality, sleep duration, and sleepiness among shift workers.

SEARCH METHODS: We searched CENTRAL, PubMed, Embase, and eight other databases on 13 December 2020, and again on 20 April 2022, applying no language restrictions.

SELECTION CRITERIA: We included randomised controlled trials (RCTs) and non-RCTs, including controlled before-after (CBA) trials, interrupted time series, and cross-over trials. Eligible trials evaluated any of …

A Magneto-Activated Nanoscale Cytometry Platform For Molecular Profiling Of Small Extracellular Vesicles, Kangfu Chen, Bill T.V. Duong, Sharif U. Ahmed, Piriththiv Dhavarasa, Z Wang, Mahmoud Labib, Connor Flynn, Jingya Xu, Yi Y. Zhang, H Wang, Xiaolong Yang, Jagotamoy Das, Hossein Zargartalebi, Yuan Ma, Shana O. Kelley

Peninsula Medical School

Exosomal PD-L1 (exoPD-L1) has recently received significant attention as a biomarker predicting immunotherapeutic responses involving the PD1/PD-L1 pathway. However, current technologies for exosomal analysis rely primarily on bulk measurements that do not consider the heterogeneity found within exosomal subpopulations. Here, we present a nanoscale cytometry platform NanoEPIC, enabling phenotypic sorting and exoPD-L1 profiling from blood plasma. We highlight the efficacy of NanoEPIC in monitoring anti-PD-1 immunotherapy through the interrogation of exoPD-L1. NanoEPIC generates signature exoPD-L1 patterns in responders and non-responders. In mice treated with PD1-targeted immunotherapy, exoPD-L1 is correlated with tumor growth, PD-L1 burden in tumors, and the immune suppression …

A Split And Inducible Adenine Base Editor For Precise In Vivo Base Editing, Hongzhi Zeng, Qichen Yuan, Fei Peng, Dacheng Ma, Ananya Lingineni, Kelly Chee, Peretz Gilberd, Emmanuel C Osikpa, Zheng Sun, Xue Gao

Faculty, Staff and Students Publications

DNA base editors use deaminases fused to a programmable DNA-binding protein for targeted nucleotide conversion. However, the most widely used TadA deaminases lack post-translational control in living cells. Here, we present a split adenine base editor (sABE) that utilizes chemically induced dimerization (CID) to control the catalytic activity of the deoxyadenosine deaminase TadA-8e. sABE shows high on-target editing activity comparable to the original ABE with TadA-8e (ABE8e) upon rapamycin induction while maintaining low background activity without induction. Importantly, sABE exhibits a narrower activity window on DNA and higher precision than ABE8e, with an improved single-to-double ratio of adenine editing and …

Guardians Of The Past: Safeguarding A Nation's Heritage Through Manuscripts And Rare Collections, Parbati Pandey Ms, Madhusudhan Margam Prof.

Library Philosophy and Practice (e-journal)

Preserving a nation's traditional and cultural heritage is imperative to transcending generations. Manuscripts and rare collections serve as invaluable windows into the past, allowing us to connect with our ancestors, understand our roots, and appreciate the rich tapestry of our cultural diversity. In this ever-changing world, exploring innovative approaches to conserve, digitize, and promote access to these treasures for the benefit of present and future generations is crucial. Libraries must preserve these rare collections, which are essential for future generations. This paper mainly focuses on the important deterioration factors for paper objects and book materials. It provides various methods, tools, …

Usa Archaeology Museum Newsletter - September 2023, Archaeology Museum

Archaeology Museum Newsletters

In this edition of the Archaeology Museum's newsletter:

• Unwritten: Archaeology & Oral History of Jim Crow Mobile Exhibit
• Unwritten: Archaeology & Oral History of Jim Crow Mobile Exhibit Speaker Series Schedule
• Alabama Archaeological Society Southwest Chapter Fall Speaker Series
• Alabama Archaeology Day
• Halloween at the Museum
• Native Plants Garden Update
• Giving to the Archaeology Museum

Front Matter Vol.59 No.3 [9/2023], Folia Medica Indonesiana

Folia Medica Indonesiana

No abstract provided.

Toxicity Test On The Combination Of Caesalpinia Sappan And Zingiber Officinale In Rattus Norvegicus Induced By Complete Freund's Adjuvant, Nadiah Armadanti Salma, Tukiran, Suyatno Sutoyo, Fauzia Indah Sabila

Folia Medica Indonesiana

Highlights: 1. This study determined the toxic effects of combining Caesalpinia sappan and Zingiber officinale extracts, as people need to be aware of the potential side effects of these common herbal remedies for the treatment of rheumatoid arthritis. 2. The combination of Caesalpinia sappan and Zingiber officinale extracts is efficacious and non-toxic as an antiarthritis treatment, hence, the ingredients can be upgraded to standardized herbal medicines and phytopharmaceuticals. Abstract Sappanwood (Caesalpinia sappan) and red ginger (Zingiber officinale) are plant species that have been studied for their efficacy in treating inflammation related to rheumatoid arthritis. This study aimed to examine the …

Physical Activity Levels And Total Food Intake Among Preclinical Students At A School Of Medicine And Health Sciences, Lydia Esterlita Halim, Francisca Tjhay, Nawanto Agung Prastowo, Vetinly, Nelly Tina Widjaja

Folia Medica Indonesiana

Highlights: 1. This is the first cross-sectional study in Indonesia that was conducted specifically to find a correlation between physical activity levels and food intake. 2. As lower physical activity was found to be associated with higher food intake, this study suggests that physical activity might be taken into consideration to manipulate one's food consumption Abstract One of the most crucial things a person can do to enhance the well-being of their body is to engage in regular physical activity. However, currently, there are still many people who have low physical activity levels. It is stated that habitual physical activity …

Biology Teachers’ Perspective On Change Of Curriculum Policy: A Case For Implementation Of “Independent” Curriculum, Kintan Limiansi, Suranto Aw, Paidi Paidi, Caly Setiawan

The Qualitative Report

Curriculum change is one way of adapting education in the face of various scientific and technological developments. These changes lead to different views from numerous educational actors, one of which is teachers. This study aims to explore biology teachers' perspectives on curriculum change in Indonesia. A qualitative phenomenological study with semi-structured interviews explored the biology teachers' perspectives. The interview results were analyzed using the thematic analysis method with ATLAS.ti 22 software to determine themes. The results showed four themes from biology teachers' perspectives on curriculum change, which are (1) the factors affecting independent curriculum implementation; (2) the teachers' concerns; (3) …

Out Of The Palaearctic: The Helophorus Water Beetles Of The Afrotropical Region (Coleoptera: Helophoridae), David T. Bilton

School of Biological and Marine Sciences

Helophorus Fabricius, 1775 (Coleoptera: Hydrophiloidea: Helophoridae) is an old and largely Holarctic genus of beetles, with most extant diversity concentrated in the Palae­arctic. As with a number of primarily northern temperate lineages, the genus has colonised the Afrotropical Region, with species described from the Ethiopian Highlands and southern Africa. Here, the Afrotropical Helophorus fauna is revised, based on a study of all primary types and additional material, including extensive recent collections from South Africa. The known Afrotropical fauna is shown to be comprised of six species, only three of which were previously described: H. aethiopicus Régimbart, 1907, from southern highland …

Sex Differences In Paternal Arsenic-Induced Intergenerational Metabolic Effects Are Mediated By Estrogen, Yanfeng Xue, Yingyun Gong, Xin Li, Fei Peng, Guolian Ding, Zhao Zhang, Junchao Shi, Ilma Saleh Savul, Yong Xu, Qi Chen, Leng Han, Shengyong Mao, Zheng Sun

Faculty, Staff and Students Publications

BACKGROUND: Gene-environment interactions contribute to metabolic disorders such as diabetes and dyslipidemia. In addition to affecting metabolic homeostasis directly, drugs and environmental chemicals can cause persistent alterations in metabolic portfolios across generations in a sex-specific manner. Here, we use inorganic arsenic (iAs) as a prototype drug and chemical to dissect such sex differences.

METHODS: After weaning, C57BL/6 WT male mice were treated with 250 ppb iAs in drinking water (iAsF0) or normal water (conF0) for 6 weeks and then bred with 15-week-old, non-exposed females for 3 days in cages with only normal water (without iAs), to generate iAsF1 or conF1 …

Effects Of Moringa Oleifera Extract As An Immunomodulator Of Lymphocyte Cells And Macrophages In Balb/C Mice Infected With Plasmodium Berghei, Putu Khrisna Dharma Jaya, Putu Indah Budi Apsari, Pande Made Alitta Cantika Putri Nadya Dewi, Dewa Ayu Agus Sri Laksemi, I Ketut Cahyadi Adi Winata Sutarta

Folia Medica Indonesiana

Highlights: 1. This study assessed the immunomodulatory potential of Moringa oleifera, which may serve as a natural source for antimalarial treatment. 2. Moringa oleifera extract can act as an immunomodulator due to its suppressive effect on Plasmodium berghei infection. Abstract Malaria is an infectious disease caused by protozoa of the genus Plasmodium. In Indonesia, this disease remains a health concern that must be resolved. Due to its high prevalence in eastern Indonesia, it is a challenge to eradicate this disease. Moringa oleifera contains various substances that are believed to have antimalarial activity. This study aimed to determine the effectiveness of …

Antibiotic-Producing Streptomyces Sp. Isolated From The Soil Of A Mangrove Ecosystem, Wiwin Retnowati, Ni Made Mertaniasih, Marijam Purwanta, Nurul Wiqoyah, Atika, Sekar Maharani, Wilda Mahdani

Folia Medica Indonesiana

Highlights: 1. The unexplored soil of mangrove ecosystems in Surabaya, Indonesia, has the potential to be home to biodiversity, including Streptomyces sp. that can produce antibiotics. 2. Streptomyces sp. has antibacterial properties against Gram-positive and Gram-negative bacteria, and the duration of incubation plays a critical role in regulating the antibacterial activity. Abstract A mangrove ecosystem in Surabaya, Indonesia, has a high salinity, pH, potassium, phosphorus, and nitrate contents. This ecosystem comprises a mixture of sand, dust, mud, and clay, which has the potential to be a conducive environment for the isolation of Streptomyces. The importance of Streptomyces in biotechnology lies …

Metformin Effectiveness In Reducing Mortality Among Covid-19 Patients With Type 2 Diabetes Mellitus At A Tertiary Hospital In Indonesia, Yudivaniel Zihono, Hany Yusmaini, Uswatun Hasanah, Erna Harfiani, Md Ikhsan Mokoagow, Dicky Budiman

Folia Medica Indonesiana

Highlights: 1. As there is a scarcity of publications on the use of metformin for COVID-19 in Indonesia, the findings of this present study may contribute more insight to the existing body of research and provide data specific to the Southeast Asian population. 2. This study revealed a decreased mortality rate associated with metformin use in diabetic patients with mild to moderate COVID-19 infection. 3. This study suggests that diabetic patients may continue metformin treatment during a COVID-19 infection as the medication has sustained therapeutic effects. Abstract COVID-19 patients with comorbidities, such as type 2 diabetes (T2DM), have a higher …

Antifungal Activity Of Endophytic Bacteria Isolated From Miana Plants (Coleus Scutellarioides (L.) Benth.) Against Candida Albicans, Melda Yunita, Ruth Magdalena Lumbantobing, Ritha Tahitu

Folia Medica Indonesiana

Highlights: 1.Due to the adverse effects associated with current antifungal drugs, research on traditional medicine is necessary to explore other options for candidiasis treatment. 2.Following the findings of this study, it is recommended to conduct further research by incorporating Coleus scuttellarioides filtrate into the growth medium, since this may improve bacterial growth by producing optimal secondary metabolites. Abstract Candida albicans is the most common organism responsible for both mucosal and systemic infections, accounting for approximately 70% of fungal infections worldwide. Miana, scientifically known as Coleus scuttellarioides (L.) Benth., is recognized for its use in traditional medicinal practices. Miana plants contain …

Development Of Formulae To Determine Living Stature Using Handprint Anthropometry Of Tagalog People In The Philippines, Tharmar Nataraja Moorthy, Ivan Nikkimor Lao Dinglasa, Myrtati Dyah Artaria

Folia Medica Indonesiana

Highlights: 1. This is the first-ever anthropological study on Tagalog people in the Philippines that has established formulae for determining stature using handprint length measurements. 2. This study has generated formulae that are applicable for personal identification purposes within real crime scenes. Abstract Forensic science plays a crucial role in the pursuit of justice, particularly through the identification of physical evidence found at crime scenes, such as human fingerprints and handprints. This study aimed to develop formulae for determining living stature using the handprint anthropometry of Tagalog people, an indigenous ethnic group in the Philippines. A total of 360 Tagalog …

Antifungal Activity Of Selaginella Plana (Desv. Ex Poir.) Hieron Extract Against Candida Albicans In Vitro, Juen Carla Warella, Khairunnida Rahma, Agung Dwi Wahyu Widodo, Rebekah Juniati Setiabudi

Folia Medica Indonesiana

Highlights: 1. A study on the medical benefits of Selaginella plana has significant academic value due to its extensive traditional usage among the Moluccan people as a medicinal remedy, especially for its antifungal properties. 2. The findings of this study will allow further screening to determine the mechanism of action of bioactive compounds in inhibiting the growth of Candida albicans Abstract Candidiasis is an opportunistic infection caused by Candida albicans. This infection commonly affects the skin, oral mucosa, vagina, and gastrointestinal tract. Excessive use of azole antifungals in the treatment of Candida albicans infections can lead to the development of …

Back Matter Vol.59 No.3 [9/2023], Folia Medica Indonesiana

Folia Medica Indonesiana

No abstract provided.

Multiple Structural And Functional Annotations Based In-Silico Characterization Of Q9brx8 Protein, Eiman Zahid, Muhammad Farhan Sarwar

Karbala International Journal of Modern Science

Numerous proteins found in humans are poorly understood because there is a dearth of experimental evidence. Hypothetical proteins (HPs) or uncharacterized proteins are the terms used to describe these proteins. In this work, one of these proteins, Q9BRX8, is investigated using in-silico or bioinformatics tools to reveal its significant properties. In this regard, NCBI for the sequence retrieval, ProtParam tool for analysis of physiochemical properties, SOPMA for secondary structure prediction, SWISS-Model for homology modelling, STRING for protein-protein interaction and HDOCK for protein-protein docking analysis among other tools, were incorporated. The physiochemical characteristics indicated that Q9BRX8, which has an instability score …

Postpartum Depression, Danny Masterson, Christina Butigian, Arlinda Kubati, Emily Ramdeholl, Leticia Sanchez

Discovery Day

Background: Postpartum depression (PPD) affects 10-20% of women in the US. It is a condition in which mothers’ experience depression during pregnancy or within 4 weeks postpartum. Numerous physiological, socio-economic, and psychological factors have been linked to postpartum depression. Mothers with postpartum depression can experience feelings of (a) extreme sadness, (b) anxiety, and (c) exhaustion that may make it difficult for them to complete activities of daily living for themselves or for others. PPD in its severest form can lead to suicide and acts of harming the newborn.

Methodology: Information was gathered using the search engines: (a) Pubmed, (b) PubMed …

Influence Of Salinity On The Biometric Traits Of Striped Catfish (Pangasianodon Hypophthalmus) And Barley (Hordeum Vulgare) Cultivated Under An Integrated Aquaculture-Agriculture System, Muziri Mugwanya, Fahad Kimera, Khaled Madkour, Mahmoud A. O. Dawood

Faculty Journal Articles

No abstract provided.