Open Access. Powered by Scholars. Published by Universities.®

Digital Commons Network™

Open Access. Powered by Scholars. Published by Universities.®

Discipline
Institution
Keyword
Publication Year
Publication
Publication Type
File Type

Articles 54481 - 54510 of 824815

Full-Text Articles in Entire DC Network

Multi-Temporal Analysis Of Urbanization-Driven Slope And Ecological Impact Using Machine-Learning And Remote Sensing Techniques, Zhang Hao, Muhammad Haseeb, Zheng Xiangtian, Zainab Tahir, Syed Amer Mahmood, Aqil Tariq, Rana Waqar Aslam, M. Abdullah-Al-Wadud, Hesham El-Askary Nov 2024

Multi-Temporal Analysis Of Urbanization-Driven Slope And Ecological Impact Using Machine-Learning And Remote Sensing Techniques, Zhang Hao, Muhammad Haseeb, Zheng Xiangtian, Zainab Tahir, Syed Amer Mahmood, Aqil Tariq, Rana Waqar Aslam, M. Abdullah-Al-Wadud, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Rapid urbanization in Lahore, Pakistan, has led to significant ecological and thermal challenges, particularly the intensification of Urban Heat Island (UHI) effects and increased thermal stress as measured by the Urban Thermal Field Variance Index (UTFVI). This study employs a multi-temporal evaluation of Landsat satellite imagery and GIS-based analysis to investigate the Spatio-temporal trends in land-use and land-cover (LULC) changes from 1994 to 2024. We detected substantial changes in urban growth, vegetation cover, and barren areas using supervised classification (Random Forest) methods and remote sensing indices such as NDVI (Normalized Difference Vegetation Index), NDMI (Normalized Difference Moisture Index), NDBI (Normalized …


Id1 And Id3 Functions In The Modulation Of The Tumour Immune Microenvironment In Adult Patients With B-Cell Acute Lymphoblastic Leukaemia, Nathaly Poveda-Garavito, Carlos A. Orozco Castaño, Yulieth Torres-Llanos, Nataly Cruz-Rodriguez, Rafael Parra-Medina, Sandra Quijano, Jovanny Zabaleta, Alba Lucia Combita Nov 2024

Id1 And Id3 Functions In The Modulation Of The Tumour Immune Microenvironment In Adult Patients With B-Cell Acute Lymphoblastic Leukaemia, Nathaly Poveda-Garavito, Carlos A. Orozco Castaño, Yulieth Torres-Llanos, Nataly Cruz-Rodriguez, Rafael Parra-Medina, Sandra Quijano, Jovanny Zabaleta, Alba Lucia Combita

School of Medicine Faculty Publications

Introduction: B-cell acute lymphoblastic leukemia (B-ALL) in adults often presents a poor prognosis. ID1 and ID3 genes have been identified as predictors of poor response in Colombian adult B-ALL patients, contributing to cancer development. In various cancer models, these genes have been associated with immune regulatory populations within the tumor immune microenvironment (TIME). B-ALL progression alters immune cell composition and the bone marrow (BM) microenvironment, impacting disease progression and therapy response. This study investigates the relationship between ID1 and ID3 expression, TIME dynamics, and immune evasion mechanisms in adult B-ALL patients. Methods: This exploratory study analysed BM samples from 10 …


A Tetramer Of Bcl11a Is Required For Stable Protein Production And Fetal Hemoglobin Silencing, Ge Zheng, Maolu Yin, Stuti Mehta, I-Te Chu, Stacy Wang, Alia Alshaye, Kirstin Drainville, Altantsetseg Buyanbat, Frédérique Bienfait, Karin Tenglin, Qian Zhu, Stuart H Orkin Nov 2024

A Tetramer Of Bcl11a Is Required For Stable Protein Production And Fetal Hemoglobin Silencing, Ge Zheng, Maolu Yin, Stuti Mehta, I-Te Chu, Stacy Wang, Alia Alshaye, Kirstin Drainville, Altantsetseg Buyanbat, Frédérique Bienfait, Karin Tenglin, Qian Zhu, Stuart H Orkin

Faculty, Staff and Students Publications

Down-regulation of BCL11A protein reverses the fetal (HbF, α2γ2) to adult (HbA, α2β2) hemoglobin switch and is exploited in gene-based therapy for hemoglobin disorders. Due to reliance on ex vivo cell manipulation and marrow transplant, such therapies cannot lessen disease burden. To develop novel small molecule approaches, we interrogated the state of BCL11A protein in erythroid cells. We report that tetramer formation mediated by a single zinc-finger (ZnF0) is required for production of steady-state protein. Beyond its role in protein stability, the tetramer state is necessary for γ-globin gene repression, as an engineered monomer fails to engage a critical corepressor …


Early Detection Of Risk Factor For Suicidal Ideation Among Senior High School Students In Jakarta: Updated Measurement, Nova R. Yusuf, Sabarinah Prasetyo, Byron J. Good Nov 2024

Early Detection Of Risk Factor For Suicidal Ideation Among Senior High School Students In Jakarta: Updated Measurement, Nova R. Yusuf, Sabarinah Prasetyo, Byron J. Good

Kesmas

The key strategy to address suicide in adolescents is school-based suicidal prevention by adapting a screening instrument to the local culture and policymakers’ perception of suicide. This study aimed to develop an instrument for the early detection of risk for suicidal ideation and identify influential risk factors for suicidal ideation among high school students in Jakarta, Indonesia. This study was conducted in 2018 with a mixed-method design (quantitative and qualitative approaches). It was found that 5% of students had suicidal ideation in July–November 2018, and 13.8% had a high-risk factor for suicidal ideation. The instrument developed in this study consisted …


Assessment Of Free Drinking Water Facilities And Its Potential Health Risks: A Study In The University X, Indah Actry Zane Lumbantobing, Bambang Wispriyono, Fitri Kurniasari, Sifa Fauzia, Muhammad Nur Ihsan Ayyasy, Alissa Siti Haura, Ghina Labibah, Muhammad Abiyyu Akmal, Kirana Mahadewi Heryadi, Firda Alfianti, Nuranida Fauziyah Nov 2024

Assessment Of Free Drinking Water Facilities And Its Potential Health Risks: A Study In The University X, Indah Actry Zane Lumbantobing, Bambang Wispriyono, Fitri Kurniasari, Sifa Fauzia, Muhammad Nur Ihsan Ayyasy, Alissa Siti Haura, Ghina Labibah, Muhammad Abiyyu Akmal, Kirana Mahadewi Heryadi, Firda Alfianti, Nuranida Fauziyah

Kesmas

University X offers free drinking water facilities. However, it has a significant problem in accessing safe drinking water. This study aimed to examine the microbial and chemical parameters of the free drinking water facilities at University X. The microbial quality was assessed by evaluating the total coliform bacteria, and the chemical parameter assessment, substances such as nitrate, iron, manganese, hexavalent chromium, and fluoride were analyzed across 12 water samples from various locations within the university. Among these, only total coliform and fluoride levels exceeded the guidelines of the World Health Organization (WHO) and the Indonesian Ministry of Health. An Environmental …


Social Determinants Of Neonatal Health Outcomes In Indonesia: A Multilevel Regression Analysis, Rooswanti Soeharno, Amal Chalik Sjaaf Nov 2024

Social Determinants Of Neonatal Health Outcomes In Indonesia: A Multilevel Regression Analysis, Rooswanti Soeharno, Amal Chalik Sjaaf

Kesmas

Indonesia’s neonatal mortality rate remains alarmingly high. This study addressed the determinants of neonatal outcomes in Indonesia, including the effects of a decentralized health system, socioeconomic disparities, and geographic variations. The analysis used 2018 national survey data across 34 provinces, 513 cities/districts, and 300,000 households, with a sample of 73,864 women aged 10-54 years who have given birth in the preceding five years. The multilevel regression was used to assess the impact of social determinants and systemic inequalities on neonatal health. Key findings revealed a neonatal mortality rate that, despite being preventable in many cases, remained high with significant disparities. …


Human Capital Assessment In Indigenous Regions To Enable Sustainable Futures, Victoria N. Sharakhmatova, Elena G. Mikhailova Nov 2024

Human Capital Assessment In Indigenous Regions To Enable Sustainable Futures, Victoria N. Sharakhmatova, Elena G. Mikhailova

Faculty Publications

This study is dedicated to the economic valuation of human capital (HC) in the regions where the Indigenous peoples of Kamchatka reside. The entire Kamchatksky Krai is considered an Indigenous people’s ancestral territory. However, in this study, only municipalities whose population is more than one-third Indigenous were chosen for the assessment. This includes six municipal districts and one urban district (Aleytsky, Bystrinsky, Karaginsky, Olyutorsky, Penzhinsky, and Tigilsky municipal districts and Palana urban district). The study employs statistical analysis and integrated, situational approaches: the investment approach was deemed the most appropriate tool for the economic assessment of HC in Indigenous territories. …


First Records Of The Spider Wasp Entypus Ochrocerus Dahlbom (Hymenoptera: Pompilidae: Pepsinae) From The Continental United States, Jamaica, And The Bahamas, Frank E. Kurczewski, Rick C. West, Dionne Newell, Scott Johnson Nov 2024

First Records Of The Spider Wasp Entypus Ochrocerus Dahlbom (Hymenoptera: Pompilidae: Pepsinae) From The Continental United States, Jamaica, And The Bahamas, Frank E. Kurczewski, Rick C. West, Dionne Newell, Scott Johnson

Insecta Mundi

A small population of Entypus ochrocerus Dahlbom, a predominantly Greater Antilles spider wasp (Hymenoptera: Pompilidae: Pepsinae), is reported for the first time from the continental United States based on photographs and associated information from iNaturalist.org. The species was initially misidentified online as E. unifasciatus unifasciatus (Say) or Entypus sp. However, Entypus u. unifasciatus individuals from east of the 100th Meridian in the United States typically have melanochromatic (dark) wings with a subapical xanthochromatic (orange-amber) patch. Entypus ochrocerus from Miami-Dade County, Florida is differentiated from E. u. unifasciatus by its black body with dark greenish blue reflections …


New Country Records For Macroscython Granulosus Otto, 2016 (Coleoptera: Eucnemidae: Dromaeolinae: Dromaeolini), With Redescription Of The Female, Robert L. Otto, Jiří Háva Nov 2024

New Country Records For Macroscython Granulosus Otto, 2016 (Coleoptera: Eucnemidae: Dromaeolinae: Dromaeolini), With Redescription Of The Female, Robert L. Otto, Jiří Háva

Insecta Mundi

New country records for Macroscython granulosus Otto, 2016 (Coleoptera: Eucnemidae: Dromaeolinae: Dromaeolini), a eucnemid known only from Laos and Thailand, are reported from China and Nepal. A redescription and images of the female are provided.


Review Of Nealyda Dietz (Lepidoptera: Gelechiidae: Apatetrinae) With Description Of A New Species From The Florida Keys, Sidney V. Bennett, James E. Hayden Nov 2024

Review Of Nealyda Dietz (Lepidoptera: Gelechiidae: Apatetrinae) With Description Of A New Species From The Florida Keys, Sidney V. Bennett, James E. Hayden

Insecta Mundi

Nealyda grandipinella Bennett and Hayden, new species, is described from Big Pine Key, Florida, USA. Photographs of the adult and of male and female genitalia are provided for N. grandipinella and its congeners within the state of Florida. Nealyda Dietz (Lepidoptera: Gelechiidae) is provisionally transferred from Anomologinae to Apatetrinae based on characters of the genitalia. The homology and terminology of the processes arising from the vinculum of gelechiid genitalia are explored. The potential host plant of the new species is discussed, along with other undescribed species of Nealyda.


First Record Of The Camphor Shot Borer, Cnestus Mutilatus (Blandford) (Coleoptera: Curculionidae: Scolytinae), In Massachusetts, Lawrence E. Barringer Nov 2024

First Record Of The Camphor Shot Borer, Cnestus Mutilatus (Blandford) (Coleoptera: Curculionidae: Scolytinae), In Massachusetts, Lawrence E. Barringer

Insecta Mundi

Cnestus mutilatus (Blandford) (Coleoptera: Curculionidae: Scolytinae) is reported from Massachusetts, United States for the first time. Brief trapping information is provided.


Accumbal Plasticity And Associated Behavioral Adaptations In The Spared Nerve Injury Model Of Chronic Neuropathic Pain, Yu-Hsuan Chang Nov 2024

Accumbal Plasticity And Associated Behavioral Adaptations In The Spared Nerve Injury Model Of Chronic Neuropathic Pain, Yu-Hsuan Chang

Arts & Sciences Graduate Student Theses and Dissertations

Chronic pain is a debilitating neurological disorder that affects hundreds of millions of individuals worldwide. It is associated with cognitive symptoms such as cognitive inflexibility, which is defined as the inability to adaptively update behavior in response to changing environmental conditions. To date, there are no effective treatments for these symptoms, even though they substantially contribute to the decreased quality of life of chronic pain patients and are associated with reduced efficacy of pain management strategies. Therefore, understanding the neural circuit adaptations that drive cognitive symptoms of chronic pain, like cognitive inflexibility, is essential for improving existing treatments for this …


An Evaluation Of A Multidisciplinary Care Planning Tool For People With Intellectual Disabilities And Behaviours Of Concern, Rohit Shankar Nov 2024

An Evaluation Of A Multidisciplinary Care Planning Tool For People With Intellectual Disabilities And Behaviours Of Concern, Rohit Shankar

Peninsula Medical School

No abstract provided.


Alpina Nov 2024

Alpina

Appalachia

No abstract provided.


Alone With Wolves: Gudrun Pflueger Believes That A Buried Instinct To Handle Predators Saved Her In A Wilderness Meadow, Christine Woodside Nov 2024

Alone With Wolves: Gudrun Pflueger Believes That A Buried Instinct To Handle Predators Saved Her In A Wilderness Meadow, Christine Woodside

Appalachia

No abstract provided.


The Significance Of Cannibalism, Panic, And Sanctuary In The Interactions Between Prey And Predator With A Stage Structure, Ahmed Sami Abdulghafour, Raid Kamel Naji Nov 2024

The Significance Of Cannibalism, Panic, And Sanctuary In The Interactions Between Prey And Predator With A Stage Structure, Ahmed Sami Abdulghafour, Raid Kamel Naji

Iraqi Journal for Computer Science and Mathematics

This paper analyzes a novel prey-predator model that takes into account the predator's stage structure, cannibalism within the predator population, panicky behavior, and the existence of a sanctuary where the prey might hide from the predator. The Holling type II functional response is used in the predation process. The behavior of the identified fixed points of the proposed system has been closely analyzed. The analysis focuses on the local stability and potential bifurcations that could happen close to the system's fixed points. The Lyapunov function approach is used to investigate the fixed-point stability zone globally. Numerical simulations were run to …


Soil Biogeography And Community Assembly In Polar Regions, Jesse Jorna Nov 2024

Soil Biogeography And Community Assembly In Polar Regions, Jesse Jorna

Theses and Dissertations

The polar regions provide community ecologists with natural microcosms, that include reduced species diversity, steep environmental gradients and limited human perturbance. Soil biodiversity in the polar regions is poorly understood, and the driving forces behind community compositions can range in scale from glacial forces 20,000 years ago to the impact of a researcher's footstep. Here, we present the results of an investigation of the driving factors behind biodiversity in Arctic and Antarctic soils, with specific attention to the role of community assembly processes. We suggest a framework for investigating the effects of inter-bacterial community processes like facilitation and argue for …


Strprofiler: Efficient Comparisons Of Short Tandem Repeat Profiles For Biomedical Model Authentication., Jared M Andrews, Michael W Lloyd, Steven Neuhauser, Margaret Bundy, Emily L Jocoy, Susan Airhart, Carol J Bult, Yvonne A Evrard, Jeffrey Chuang, Suzanne Baker Nov 2024

Strprofiler: Efficient Comparisons Of Short Tandem Repeat Profiles For Biomedical Model Authentication., Jared M Andrews, Michael W Lloyd, Steven Neuhauser, Margaret Bundy, Emily L Jocoy, Susan Airhart, Carol J Bult, Yvonne A Evrard, Jeffrey Chuang, Suzanne Baker

Faculty Research 2024

SUMMARY: Short tandem repeat (STR) profiling is commonly performed for authentication of biomedical models of human origin, yet no tools exist to easily compare sets of STR profiles to each other or an existing database in a high-throughput manner. Here, we present STRprofiler, a Python package, command line tool, and Shiny application providing methods for STR profile comparison and cross-contamination detection. STRprofiler can be run with custom databases or used to query against the Cellosaurus cell line database.

AVAILABILITY AND IMPLEMENTATION: STRprofiler is freely available as a Python package with a rich CLI from PyPI https://pypi.org/project/strprofiler/ with source code available …


Hypertonic Saline Induces Host Protective Immune Responses Against, Tran Xuan Ngoc Huy, Trang Thi Nguyen, Said Abdi Salad, Ched Nicole Turbela Aguilar, Alisha Wehdnesday Bernardo Reyes, Lauren Togonon Arayan, Wongi Min, Hu Jang Lee, Huynh Tan Hop, Suk Kim Nov 2024

Hypertonic Saline Induces Host Protective Immune Responses Against, Tran Xuan Ngoc Huy, Trang Thi Nguyen, Said Abdi Salad, Ched Nicole Turbela Aguilar, Alisha Wehdnesday Bernardo Reyes, Lauren Togonon Arayan, Wongi Min, Hu Jang Lee, Huynh Tan Hop, Suk Kim

Faculty Research 2024

Hypertonic saline (HTS) resuscitation can enhance immune responses against various pathogens, however, the effect of HTS on brucellosis is yet to be defined. In this study, we found that HTS inhibited Brucella infection in mice by augmenting Th1 immunity. HTS treatment enhanced the serum cytokines production and the expression of nitric oxide synthase (NOS2) and nuclear factor kappa B (NF-ĸB) p50 and p65, crucial anti-Brucella effectors in splenocytes. In addition, HTS treatment also inhibited the phosphorylation of MAPK signaling, accompanied by the down-regulation of the autophagy marker LC3B-II. Due to directing an appropriate immune response, HTS treatment substantially decreased bacterial …


Effective Nutrient Management Of Surface Waters In The United States Requires Expanded Water Quality Monitoring In Agriculturally Intensive Areas, Christopher Oates, Hactor Fajardo, Khara Grieger, Daniel Obenaur, Rebecca Muenich, Natalie G. Nelson Nov 2024

Effective Nutrient Management Of Surface Waters In The United States Requires Expanded Water Quality Monitoring In Agriculturally Intensive Areas, Christopher Oates, Hactor Fajardo, Khara Grieger, Daniel Obenaur, Rebecca Muenich, Natalie G. Nelson

Biological and Agricultural Engineering Faculty Publications and Presentations

The U.S. Clean Water Act is believed to have driven widespread decreases in pollutants from point sources and developed areas, but has not substantially affected nutrient pollution from agriculture. Today, the highest nutrient concentrations in surface waters are often associated with agricultural production. In this Perspective, we explore whether challenges stemming from the Clean Water Act’s inability to mitigate agricultural nutrient pollution are also exacerbated by coarse nutrient monitoring. We evaluate the current state of nutrient monitoring in surface waters of the contiguous U.S. relative to agricultural nutrient inputs to assess how monitoring effort varies across agriculturally intensive areas. The …


The Laboratory Opossum (Monodelphis Domestica) Is A Unique Model For Research On Zika Virus: Robust Immune Response, Widespread Dissemination, And Long-Term Persistence, André Filipe Pastor, Susan M. Mahaney, Juan Garcia Jr., Marisol Morales, Oscar Quintanilla, Marco Arriaga, John M. Thomas, John L. Vandeberg Nov 2024

The Laboratory Opossum (Monodelphis Domestica) Is A Unique Model For Research On Zika Virus: Robust Immune Response, Widespread Dissemination, And Long-Term Persistence, André Filipe Pastor, Susan M. Mahaney, Juan Garcia Jr., Marisol Morales, Oscar Quintanilla, Marco Arriaga, John M. Thomas, John L. Vandeberg

School of Medicine Publications

The Zika virus (ZIKV) epidemic elicited a rapid commitment to the development of animal models for ZIKV research. Non-human primates (NHPs) and mice have made significant contributions to this research, but NHPs are expensive, have a long gestation period, and are available only in small numbers; non-genetically modified mice are resistant to infection. To address these deficiencies, we have established the laboratory opossum, Monodelphis domestica, as a small animal model that complements the mouse and monkey models. We developed and validated an indirect ELISA for measuring antibodies to ZIKV in opossums, as well as an immunohistochemistry (IHC) method to detect …


Multi-Scale Thermal Mapping Of Submarine Groundwater Discharge In Coastal Ecosystems Of A Volcanic Area, Ebony L. Williams, Christopher B. Kratt, Raymond S. Rodolfo, Mark R. Lapus, Ryan R. Lardizabal, Aya S. Bangun, Amber T. Nguyen, Scott W. Tyler, M. Bayani Cardenas Nov 2024

Multi-Scale Thermal Mapping Of Submarine Groundwater Discharge In Coastal Ecosystems Of A Volcanic Area, Ebony L. Williams, Christopher B. Kratt, Raymond S. Rodolfo, Mark R. Lapus, Ryan R. Lardizabal, Aya S. Bangun, Amber T. Nguyen, Scott W. Tyler, M. Bayani Cardenas

Environmental Science Faculty Publications

Submarine groundwater discharge (SGD) in volcanic areas commonly exhibits high temperatures, concentrations of metals and CO2, and acidity, all of which could affect sensitive coastal ecosystems. Identifying and quantifying volcanic SGD is crucial yet challenging because the SGD might be both discrete, through fractured volcanic rock, and diffuse. At a volcanic area in the Philippines, the novel combination of satellite and drone-based thermal infrared remote sensing, ground-based fiber-optic distributed temperature sensing, and in situ thermal profiling in coastal sediment identified the multi-scale nature of SGD and quantified fluxes. We identified SGD across ∼30 km of coastline. The different approaches revealed …


Association Of Acute Rejection And De Novo Renal Cell Carcinoma In Kidney Transplant Patients: An Optn Data Analysis, Molly Casey, Emmalie Yanacek, Hitesh Kaul, John Knorr, Kamran Khanmoradi, Afshin Parsikia, Nikolaos Chandolias, Kevin Zarrabi, Radi Zaki Nov 2024

Association Of Acute Rejection And De Novo Renal Cell Carcinoma In Kidney Transplant Patients: An Optn Data Analysis, Molly Casey, Emmalie Yanacek, Hitesh Kaul, John Knorr, Kamran Khanmoradi, Afshin Parsikia, Nikolaos Chandolias, Kevin Zarrabi, Radi Zaki

Einstein Health Papers

Background: Kidney Transplant Recipients (KTRs) are at risk of renal cell carcinoma (RCC). The risk of RCC in KTRs is approximated to be 5–10 times higher compared with the general population. A relation between kidney rejection and renal malignancy has been described and relates to the effect of immunosuppression at the genomic level. We decided to investigate any suggestive clinical evidence of this in the OPTN database. Methods: KTRs with de novo RCC between July 2004 and June 2022 were identified. Demographics, baseline characteristics, virology, and immunology data were compared between patients with and without RCC. Our follow-up period was …


Complement Immune System In Pulmonary Hypertension-Cooperating Roles Of Circadian Rhythmicity In Complement-Mediated Vascular Pathology, Hunter Devaughn, Haydn E Rich, Anthony Shadid, Priyanka K Vaidya, Marie-Francoise Doursout, Pooja Shivshankar Nov 2024

Complement Immune System In Pulmonary Hypertension-Cooperating Roles Of Circadian Rhythmicity In Complement-Mediated Vascular Pathology, Hunter Devaughn, Haydn E Rich, Anthony Shadid, Priyanka K Vaidya, Marie-Francoise Doursout, Pooja Shivshankar

The Brown Foundation: Institute of Molecular Medicine

Originally discovered in the 1890s, the complement system has traditionally been viewed as a "compliment" to the body's innate and adaptive immune response. However, emerging data have shown that the complement system is a much more complex mechanism within the body involved in regulating inflammation, gene transcription, attraction of macrophages, and many more processes. Sustained complement activation contributes to autoimmunity and chronic inflammation. Pulmonary hypertension is a disease with a poor prognosis and an average life expectancy of 2-3 years that leads to vascular remodeling of the pulmonary arteries; the pulmonary arteries are essential to host homeostasis, as they divert …


Host Dna Depletion On Frozen Human Respiratory Samples Enables Successful Metagenomic Sequencing For Microbiome Studies, Minsik Kim, Raymond C Parrish, Michael J Tisza, Viral S Shah, Thi Tran, Matthew Ross, Juwan Cormier, Aribah Baig, Ching-Ying Huang, Laura Brenner, Isabel Neuringer, Katrine Whiteson, J Kirk Harris, Amy D Willis, Peggy S Lai Nov 2024

Host Dna Depletion On Frozen Human Respiratory Samples Enables Successful Metagenomic Sequencing For Microbiome Studies, Minsik Kim, Raymond C Parrish, Michael J Tisza, Viral S Shah, Thi Tran, Matthew Ross, Juwan Cormier, Aribah Baig, Ching-Ying Huang, Laura Brenner, Isabel Neuringer, Katrine Whiteson, J Kirk Harris, Amy D Willis, Peggy S Lai

Faculty, Staff and Students Publications

Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed …


Strategies To Enhance Diagnostic Capabilities For The New Drug-Resistant Tuberculosis (Dr-Tb) Drugs, Antonia Morita Iswari Saktiawati, Anca Vasiliu, Francesca Saluzzo, Onno W Akkerman Nov 2024

Strategies To Enhance Diagnostic Capabilities For The New Drug-Resistant Tuberculosis (Dr-Tb) Drugs, Antonia Morita Iswari Saktiawati, Anca Vasiliu, Francesca Saluzzo, Onno W Akkerman

Faculty, Staff and Students Publications

The global burden of drug-resistant tuberculosis (DR-TB) continues to challenge healthcare systems worldwide. There is a critical need to tackle DR-TB by enhancing diagnostics and drug susceptibility testing (DST) capabilities, particularly for emerging DR-TB drugs. This endeavor is crucial to optimize the efficacy of new therapeutic regimens and prevent the resistance and overuse of these invaluable weapons. Despite this urgency, there remains a lack of comprehensive review of public health measures aimed at improving the diagnostics and DST capabilities. In this review, we outline strategies to enhance the capabilities, especially tailored to address the challenges posed by resistance to new …


An Annotated Biobank Of Triple Negative Breast Cancer Patient-Derived Xenografts Featuring Treatment-Naïve And Longitudinal Samples Throughout Neoadjuvant Chemotherapy, Amanda L Rinkenbaugh, Yuan Qi, Shirong Cai, Jiansu Shao, Faiza Hancock, Sabrina Jeter-Jones, Xiaomei Zhang, Emily Powell, Lei Huo, Rosanna Lau, Chunxiao Fu, Rebekah Gould, Petra Den Hollander, Elizabeth E Ravenberg, Jason B White, Gaiane M Rauch, Banu Arun, Clinton Yam, Alastair M Thompson, Gloria V Echeverria, Stacy L Moulder, W Fraser Symmans, Jeffrey T Chang, Helen Piwnica-Worms Nov 2024

An Annotated Biobank Of Triple Negative Breast Cancer Patient-Derived Xenografts Featuring Treatment-Naïve And Longitudinal Samples Throughout Neoadjuvant Chemotherapy, Amanda L Rinkenbaugh, Yuan Qi, Shirong Cai, Jiansu Shao, Faiza Hancock, Sabrina Jeter-Jones, Xiaomei Zhang, Emily Powell, Lei Huo, Rosanna Lau, Chunxiao Fu, Rebekah Gould, Petra Den Hollander, Elizabeth E Ravenberg, Jason B White, Gaiane M Rauch, Banu Arun, Clinton Yam, Alastair M Thompson, Gloria V Echeverria, Stacy L Moulder, W Fraser Symmans, Jeffrey T Chang, Helen Piwnica-Worms

Faculty, Staff and Students Publications

Triple negative breast cancer (TNBC) that fails to respond to neoadjuvant chemotherapy (NACT) can be lethal. Developing effective strategies to eradicate chemoresistant disease requires experimental models that recapitulate the heterogeneity characteristic of TNBC. To that end, we established a biobank of 92 orthotopic patient-derived xenograft (PDX) models of TNBC from the tumors of 75 patients enrolled in the ARTEMIS clinical trial ( NCT02276443 ) at MD Anderson Cancer Center, including 12 longitudinal sets generated from serial patient biopsies collected throughout NACT and from metastatic disease. Models were established from both chemosensitive and chemoresistant tumors, and nearly 30% of PDX models …


Focal Deletions Of A Promoter Tether Activate The Irx3 Oncogene In T-Cell Acute Lymphoblastic Leukemia, Sunniyat Rahman, Gianna Bloye, Nadine Farah, Jonas Demeulemeester, Joana R Costa, David O'Connor, Rachael Pocock, Tanya Rapoz-D'Silva, Adam Turna, Lingyi Wang, Soowah Lee, Adele K Fielding, Juliette Roels, Roman Jaksik, Małgorzata Dawidowska, Pieter Van Vlierberghe, Suzana Hadjur, Jim R Hughes, James O J Davies, Alejandro Gutierrez, Michelle A Kelliher, Peter Van Loo, Mark A Dawson, Marc R Mansour Nov 2024

Focal Deletions Of A Promoter Tether Activate The Irx3 Oncogene In T-Cell Acute Lymphoblastic Leukemia, Sunniyat Rahman, Gianna Bloye, Nadine Farah, Jonas Demeulemeester, Joana R Costa, David O'Connor, Rachael Pocock, Tanya Rapoz-D'Silva, Adam Turna, Lingyi Wang, Soowah Lee, Adele K Fielding, Juliette Roels, Roman Jaksik, Małgorzata Dawidowska, Pieter Van Vlierberghe, Suzana Hadjur, Jim R Hughes, James O J Davies, Alejandro Gutierrez, Michelle A Kelliher, Peter Van Loo, Mark A Dawson, Marc R Mansour

Faculty, Staff and Student Publications

Oncogenes can be activated in cis through multiple mechanisms including enhancer hijacking events and noncoding mutations that create enhancers or promoters de novo. These paradigms have helped parse somatic variation of noncoding cancer genomes, thereby providing a rationale to identify noncanonical mechanisms of gene activation. Here we describe a novel mechanism of oncogene activation whereby focal copy number loss of an intronic element within the FTO gene leads to aberrant expression of IRX3, an oncogene in T-cell acute lymphoblastic leukemia (T-ALL). Loss of this CTCF-bound element downstream to IRX3 (+224 kb) leads to enhancer hijack of an upstream developmentally active …


Blood Matters: The Hematological Signatures Of Coronavirus Infection, Ayelen Toro, Ana P Arévalo, Marianoel Pereira-Gómez, Agustina Sabater, Eric A Zizzi, Paula Perbolianachis, Gaston Pascual, Sofia Lage-Vickers, Jorge L Pórfido, Ines Achinelli, Rocio Seniuk, Juan Bizzotto, Pablo Sanchis, Alvaro Olivera, Alejandro Leyva, Pilar Moreno, Alicia Costábile, Alvaro Fajardo, Federico Carrión, Martín Fló, Natalia Olivero-Deibe, Fernando Rodriguez, Nicolas Nin, Nicolas Anselmino, Estefania Labanca, Elba Vazquez, Javier Cotignola, Daniel F Alonso, Maria P Valacco, Marcelo Marti, Francesco Gentile, Artem Cherkasov, Martina Crispo, Gonzalo Moratorio, Geraldine Gueron Nov 2024

Blood Matters: The Hematological Signatures Of Coronavirus Infection, Ayelen Toro, Ana P Arévalo, Marianoel Pereira-Gómez, Agustina Sabater, Eric A Zizzi, Paula Perbolianachis, Gaston Pascual, Sofia Lage-Vickers, Jorge L Pórfido, Ines Achinelli, Rocio Seniuk, Juan Bizzotto, Pablo Sanchis, Alvaro Olivera, Alejandro Leyva, Pilar Moreno, Alicia Costábile, Alvaro Fajardo, Federico Carrión, Martín Fló, Natalia Olivero-Deibe, Fernando Rodriguez, Nicolas Nin, Nicolas Anselmino, Estefania Labanca, Elba Vazquez, Javier Cotignola, Daniel F Alonso, Maria P Valacco, Marcelo Marti, Francesco Gentile, Artem Cherkasov, Martina Crispo, Gonzalo Moratorio, Geraldine Gueron

Faculty, Staff and Student Publications

Recent developments have broadened our perception of SARS-CoV-2, indicating its capability to affect the body systemically beyond its initial recognition as a mere respiratory pathogen. However, the pathways of its widespread are not well understood. Employing a dual-modality approach, we integrated findings from a Murine Hepatitis Virus (MHV) infection model with corroborative clinical data to investigate the pervasive reach of Coronaviruses. The novel presence of viral particles within red blood cells (RBCs) was demonstrated via high-resolution transmission electron microscopy, with computational modeling elucidating a potential heme-mediated viral entry mechanism via Spike protein affinity. Our data affirm viral localization in RBCs, …


The Pharmacogenomic And Immune Landscape Of Snornas In Human Cancers, Runhao Wang, Chengxuan Chen, Yuan Liu, Mei Luo, Jingwen Yang, Yamei Chen, Lifei Ma, Liuqing Yang, Chunru Lin, Lixia Diao, Leng Han Nov 2024

The Pharmacogenomic And Immune Landscape Of Snornas In Human Cancers, Runhao Wang, Chengxuan Chen, Yuan Liu, Mei Luo, Jingwen Yang, Yamei Chen, Lifei Ma, Liuqing Yang, Chunru Lin, Lixia Diao, Leng Han

Faculty, Staff and Student Publications

Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs primarily known for their role in the chemical modification of other RNAs. Recent studies suggested that snoRNAs may play a broader role in anti-cancer treatments such as targeted therapies and immunotherapies. Despite these insights, the comprehensive landscape of snoRNA associations with drug response and immunotherapy outcomes remains unexplored. In this study, we identified 79,448 and 75,185 associations between snoRNAs and drug response using data from VAEN and CancerRxTissue, respectively. Additionally, we discovered 29,199 associations between snoRNAs and immune checkpoint genes and 47,194 associations between snoRNAs and immune cell infiltrations. Sixteen …