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Acetylation Of Histone H3k27 Signals The Transcriptional Elongation For Estrogen Receptor Alpha, Yujing Gao, Lijia Chen, Yali Han, Fangrui Wu, Wen-Si Yang, Zheng Zhang, Tong Huo, Yingmin Zhu, Chengtai Yu, Hong Kim, Mark Lee, Zhen Tang, Kevin Phillips, Bin He, Sung Yun Jung, Yongcheng Song, Bokai Zhu, Rui-Ming Xu, Qin Feng Apr 2020

Acetylation Of Histone H3k27 Signals The Transcriptional Elongation For Estrogen Receptor Alpha, Yujing Gao, Lijia Chen, Yali Han, Fangrui Wu, Wen-Si Yang, Zheng Zhang, Tong Huo, Yingmin Zhu, Chengtai Yu, Hong Kim, Mark Lee, Zhen Tang, Kevin Phillips, Bin He, Sung Yun Jung, Yongcheng Song, Bokai Zhu, Rui-Ming Xu, Qin Feng

Faculty, Staff and Students Publications

As approximately 70% of human breast tumors are estrogen receptor α (ERα)-positive, estrogen and ERα play essential roles in breast cancer development. By interrupting the ERα signaling pathway, endocrine therapy has been proven to be an effective therapeutic strategy. In this study, we identified a mechanism by which Transcription Start Site (TSS)-associated histone H3K27 acetylation signals the Super Elongation Complex (SEC) to regulate transcriptional elongation of the ESR1 (ERα) gene. SEC interacts with H3K27ac on ESR1 TSS through its scaffold protein AFF4. Depletion of AFF4 by siRNA or CRISPR/Cas9 dramatically reduces expression of ESR1 and its target genes, consequently inhibiting …


Principles Of Rna Processing From Analysis Of Enhanced Clip Maps For 150 Rna Binding Proteins, Eric L Van Nostrand, Gabriel A Pratt, Brian A Yee, Emily C Wheeler, Steven M Blue, Jasmine Mueller, Samuel S Park, Keri E Garcia, Chelsea Gelboin-Burkhart, Thai B Nguyen, Ines Rabano, Rebecca Stanton, Balaji Sundararaman, Ruth Wang, Xiang-Dong Fu, Brenton R Graveley, Gene W Yeo Apr 2020

Principles Of Rna Processing From Analysis Of Enhanced Clip Maps For 150 Rna Binding Proteins, Eric L Van Nostrand, Gabriel A Pratt, Brian A Yee, Emily C Wheeler, Steven M Blue, Jasmine Mueller, Samuel S Park, Keri E Garcia, Chelsea Gelboin-Burkhart, Thai B Nguyen, Ines Rabano, Rebecca Stanton, Balaji Sundararaman, Ruth Wang, Xiang-Dong Fu, Brenton R Graveley, Gene W Yeo

Faculty, Staff and Students Publications

BACKGROUND: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types.

RESULTS: Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA …


Phosphoinositides In Retinal Function And Disease, Theodore G Wensel Apr 2020

Phosphoinositides In Retinal Function And Disease, Theodore G Wensel

Faculty, Staff and Students Publications

Phosphatidylinositol and its phosphorylated derivatives, the phosphoinositides, play many important roles in all eukaryotic cells. These include modulation of physical properties of membranes, activation or inhibition of membrane-associated proteins, recruitment of peripheral membrane proteins that act as effectors, and control of membrane trafficking. They also serve as precursors for important second messengers, inositol (1,4,5) trisphosphate and diacylglycerol. Animal models and human diseases involving defects in phosphoinositide regulatory pathways have revealed their importance for function in the mammalian retina and retinal pigmented epithelium. New technologies for localizing, measuring and genetically manipulating them are revealing new information about their importance for the …


Patient, Hospital And State-Level Policy Characteristics Associated With Prevalence Of Treating Opioid Use Disorder In United States Emergency Departments, Rafeek Adeyemi Yusuf Apr 2020

Patient, Hospital And State-Level Policy Characteristics Associated With Prevalence Of Treating Opioid Use Disorder In United States Emergency Departments, Rafeek Adeyemi Yusuf

Dissertations and Theses (Open Access)

The opioid crisis in the United States was declared a public health emergency due to escalating and untoward human, financial, and systemic consequences and effects on the nation. Opioid use disorder (OUD) comprising opioid abuse and dependence is devastating because of its associated chronic relapsing nature, overutilization of healthcare services, rising morbidity and mortality rates, and high cost of care. Efforts to address this have not made significant positive impacts. It is thus imperative to reassess the influence of factors associated with OUD. This study answered the question, what patient-, hospital-, and state-level policy factors were associated with prevalence of …


Identifying Risk Factors For Chronic Kidney Disease Of Unknown Origin In Six Central American Countries And Houston, Texas, Erika Figueroa-Solis Apr 2020

Identifying Risk Factors For Chronic Kidney Disease Of Unknown Origin In Six Central American Countries And Houston, Texas, Erika Figueroa-Solis

Dissertations and Theses (Open Access)

Chronic kidney disease (CKD) is a public health problem that is recognized worldwide. The type of CKD in Central America does not fit the “usual” CKD encountered in countries with upper middle-income economies, and is also often referred to as CKD of undetermined cause (CKDu). Evidence suggests that CKDu is a disease of occupational origin that can be brought on by a combination of exposures: hot environments, high physical job demands, inadequate hydration protocols, and effects of other nephrotoxic agents. Many gaps remain in knowledge related to CKDu and its putative risk factors, geographic distribution, distributions of renal function in …


Diabetes And Cardiovascular Disease In Women: Current Challenges And New Hope, Efstratios Koutroumpakis, David Aguilar Apr 2020

Diabetes And Cardiovascular Disease In Women: Current Challenges And New Hope, Efstratios Koutroumpakis, David Aguilar

The Texas Heart Institute Journal

No abstract provided.


On The Estimation Of The Incidence And Prevalence In Two-Phase Longitudinal Sampling Design, Prithish Banerjee, Samiran Ghosh Apr 2020

On The Estimation Of The Incidence And Prevalence In Two-Phase Longitudinal Sampling Design, Prithish Banerjee, Samiran Ghosh

Faculty, Staff and Student Publications

Two-phase sampling design is a common practice in many medical studies. Generally, the first-phase classification is fallible but relatively cheap, while the accurate second phase state-of-the-art medical diagnosis is complex and rather expensive to perform. When constructed efficiently it offers great potential for higher true case detection as well as for higher precision at a limited cost. In this article, we consider epidemiological studies with two-phase sampling design. However, instead of a single two-phase study, we consider a scenario where a series of two-phase studies are done in a longitudinal fashion on a cohort of interest. Another major design issue …


Neurochemical Characterization Of Brainstem Pro-Opiomelanocortin Cells, Teodora Georgescu, David Lyons, Barbora Doslikova, Ana Paula Garcia, Oliver Marston, Luke K Burke, Raffaella Chianese, Brian Y H Lam, Giles S H Yeo, Justin J Rochford, Alastair S Garfield, Lora K Heisler Apr 2020

Neurochemical Characterization Of Brainstem Pro-Opiomelanocortin Cells, Teodora Georgescu, David Lyons, Barbora Doslikova, Ana Paula Garcia, Oliver Marston, Luke K Burke, Raffaella Chianese, Brian Y H Lam, Giles S H Yeo, Justin J Rochford, Alastair S Garfield, Lora K Heisler

Faculty, Staff and Student Publications

Genetic research has revealed pro-opiomelanocortin (POMC) to be a fundamental regulator of energy balance and body weight in mammals. Within the brain, POMC is primarily expressed in the arcuate nucleus of the hypothalamus (ARC), while a smaller population exists in the brainstem nucleus of the solitary tract (POMCNTS). We performed a neurochemical characterization of this understudied population of POMC cells using transgenic mice expressing green fluorescent protein (eGFP) under the control of a POMC promoter/enhancer (PomceGFP). Expression of endogenous Pomc mRNA in the nucleus of the solitary tract (NTS) PomceGFP cells was confirmed using fluorescence-activating cell sorting (FACS) followed by …


An In Vivo Genome-Wide Crispr Screen Identifies The Rna-Binding Protein Staufen2 As A Key Regulator Of Myeloid Leukemia, Jeevisha Bajaj, Michael Hamilton, Yutaka Shima, Kendall Chambers, Kyle Spinler, Eric L Van Nostrand, Brian A Yee, Steven M Blue, Michael Chen, David Rizzeri, Charles Chuah, Vivian G Oehler, H Elizabeth Broome, Roman Sasik, James Scott-Browne, Anjana Rao, Gene W Yeo, Tannishtha Reya Apr 2020

An In Vivo Genome-Wide Crispr Screen Identifies The Rna-Binding Protein Staufen2 As A Key Regulator Of Myeloid Leukemia, Jeevisha Bajaj, Michael Hamilton, Yutaka Shima, Kendall Chambers, Kyle Spinler, Eric L Van Nostrand, Brian A Yee, Steven M Blue, Michael Chen, David Rizzeri, Charles Chuah, Vivian G Oehler, H Elizabeth Broome, Roman Sasik, James Scott-Browne, Anjana Rao, Gene W Yeo, Tannishtha Reya

Faculty, Staff and Students Publications

Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, and the double-stranded RBP Staufen2 (Stau2) in particular, emerged as critical regulators of myeloid leukemia. In a newly developed knockout mouse, loss of Stau2 led to a profound decrease in leukemia growth and improved survival in mouse models of the disease. Further, Stau2 was required for growth of primary human blast crisis chronic myeloid leukemia and acute myeloid leukemia. Finally, …


Provider Attitudes And Practice Patterns For Direct-Acting Antiviral Therapy For Patients With Hepatocellular Carcinoma, Nicole E Rich, Ju Dong Yang, Ponni V Perumalswami, Naim Alkhouri, Whitney Jackson, Neehar D Parikh, Neil Mehta, Reena Salgia, Andres Duarte-Rojo, Laura Kulik, Mina Rakoski, Adnan Said, Omobonike Oloruntoba, George N Ioannou, Maarouf A Hoteit, Andrew M Moon, Amol S Rangnekar, Sheila L Eswaran, Elizabeth Zheng, Janice H Jou, James Hanje, Anjana Pillai, Ruben Hernaez, Robert Wong, Steven Scaglione, Hrishikesh Samant, Devika Kapuria, Shaun Chandna, Russell Rosenblatt, Veeral Ajmera, Catherine T Frenette, Sanjaya K Satapathy, Parvez Mantry, Prasun Jalal, Binu V John, Oren K Fix, Michael Leise, Christina C Lindenmeyer, Avegail Flores, Nayan Patel, Z Gordon Jiang, Nyan Latt, Renumathy Dhanasekaran, Mobolaji Odewole, Sofia Kagan, Jorge A Marrero, Amit G Singal Apr 2020

Provider Attitudes And Practice Patterns For Direct-Acting Antiviral Therapy For Patients With Hepatocellular Carcinoma, Nicole E Rich, Ju Dong Yang, Ponni V Perumalswami, Naim Alkhouri, Whitney Jackson, Neehar D Parikh, Neil Mehta, Reena Salgia, Andres Duarte-Rojo, Laura Kulik, Mina Rakoski, Adnan Said, Omobonike Oloruntoba, George N Ioannou, Maarouf A Hoteit, Andrew M Moon, Amol S Rangnekar, Sheila L Eswaran, Elizabeth Zheng, Janice H Jou, James Hanje, Anjana Pillai, Ruben Hernaez, Robert Wong, Steven Scaglione, Hrishikesh Samant, Devika Kapuria, Shaun Chandna, Russell Rosenblatt, Veeral Ajmera, Catherine T Frenette, Sanjaya K Satapathy, Parvez Mantry, Prasun Jalal, Binu V John, Oren K Fix, Michael Leise, Christina C Lindenmeyer, Avegail Flores, Nayan Patel, Z Gordon Jiang, Nyan Latt, Renumathy Dhanasekaran, Mobolaji Odewole, Sofia Kagan, Jorge A Marrero, Amit G Singal

Faculty, Staff and Students Publications

BACKGROUND & AIMS: Direct-acting antivirals (DAAs) are effective against hepatitis C virus and sustained virologic response is associated with reduced incidence of hepatocellular carcinoma (HCC). However, there is controversy over the use of DAAs in patients with active or treated HCC and uncertainty about optimal management of these patients. We aimed to characterize attitudes and practice patterns of hepatology practitioners in the United States regarding the use of DAAs in patients with HCC.

METHODS: We conducted a survey of hepatology providers at 47 tertiary care centers in 25 states. Surveys were sent to 476 providers and we received 279 responses …


Comparison Of Surgical Versus Transcatheter Aortic Valve Replacement For Patients With Aortic Stenosis At Low-Intermediate Risk, Mahin R Khan, Waleed T Kayani, Malalai Manan, Ahmad Munir, Ihab Hamzeh, Salim S Virani, Yochai Birnbaum, Hani Jneid, Mahboob Alam Apr 2020

Comparison Of Surgical Versus Transcatheter Aortic Valve Replacement For Patients With Aortic Stenosis At Low-Intermediate Risk, Mahin R Khan, Waleed T Kayani, Malalai Manan, Ahmad Munir, Ihab Hamzeh, Salim S Virani, Yochai Birnbaum, Hani Jneid, Mahboob Alam

Faculty, Staff and Students Publications

BACKGROUND: To compare safety and efficacy of transcatheter aortic valve replacement (TAVR) with surgical aortic valve replacement (SAVR) in patients at low-intermediate risk, given the paucity of robust data.

METHODS: We performed an aggregate data meta-analysis of 7 randomized controlled trials (RCTs) and 6,778 patients comparing TAVR with SAVR for aortic stenosis (AS) in low-intermediate risk patients (Society of Thoracic Surgeons risk-score ≤8%) using the random-effects model. Primary outcome was all-cause mortality at 30-day, 1-year and 2-year of follow-up. Secondary outcomes included cardiac-mortality, stroke, acute kidney injury (AKI), atrial fibrillation (AF), permanent pacemaker (PPM) implantation, major-bleeding, moderate-severe paravalvular regurgitation (PVR) …


Cofilin-1-Induced Actin Reorganization In Stored Platelets, Swapan K Dasgupta, Perumal Thiagarajan Apr 2020

Cofilin-1-Induced Actin Reorganization In Stored Platelets, Swapan K Dasgupta, Perumal Thiagarajan

Faculty, Staff and Students Publications

BACKGROUND: During platelet storage, there are extensive changes in cytoskeleton and phosphatidylserine exposure. The intrinsic mitochondrial pathway of apoptosis, activated in stored platelets, is a major mediator these changes. Cofilin-1 is an effector of actin reorganization. We examined the effect of cofilin-1 deficiency on cytoskeleton and phosphatidylserine exposure during storage and following activation of apoptosis.

METHODS AND RESULTS: We assessed actin filaments by Alexa-647-phalloidin and phosphatidylserine exposure by fluorescein isothiocyanate-lactadherin by fluorescence microscopy. In fresh platelets, actin filaments are distributed in the subcortical region, and they do not express phosphatidylserine in the outer surface. In stored platelets, there is retraction …


Defining A Taxonomy Of Intracranial Hypertension: Is Icp More Than Just A Number?, W Andrew Kofke, Swarna Rajagopalan, Diana Ayubcha, Ramani Balu, Jovany Cruz-Navarro, Panumart Manatpon, Elizabeth Mahanna-Gabrielli Apr 2020

Defining A Taxonomy Of Intracranial Hypertension: Is Icp More Than Just A Number?, W Andrew Kofke, Swarna Rajagopalan, Diana Ayubcha, Ramani Balu, Jovany Cruz-Navarro, Panumart Manatpon, Elizabeth Mahanna-Gabrielli

Faculty, Staff and Students Publications

Intracranial pressure (ICP) monitoring and control is a cornerstone of neuroanesthesia and neurocritical care. However, because elevated ICP can be due to multiple pathophysiological processes, its interpretation is not straightforward. We propose a formal taxonomy of intracranial hypertension, which defines ICP elevations into 3 major pathophysiological subsets: increased cerebral blood volume, masses and edema, and hydrocephalus. (1) Increased cerebral blood volume increases ICP and arises secondary to arterial or venous hypervolemia. Arterial hypervolemia is produced by autoregulated or dysregulated vasodilation, both of which are importantly and disparately affected by systemic blood pressure. Dysregulated vasodilation tends to be worsened by arterial …


Nr2f1 Heterozygous Knockout Mice Recapitulate Neurological Phenotypes Of Bosch-Boonstra-Schaaf Optic Atrophy Syndrome And Show Impaired Hippocampal Synaptic Plasticity, Chun-An Chen, Wei Wang, Steen E Pedersen, Ayush Raman, Michelle L Seymour, Fernanda R Ruiz, Anping Xia, Meike E Van Der Heijden, Li Wang, Jiani Yin, Joanna Lopez, Megan E Rech, Richard A Lewis, Samuel M Wu, Zhandong Liu, Fred A Pereira, Robia G Pautler, Huda Y Zoghbi, Christian P Schaaf Mar 2020

Nr2f1 Heterozygous Knockout Mice Recapitulate Neurological Phenotypes Of Bosch-Boonstra-Schaaf Optic Atrophy Syndrome And Show Impaired Hippocampal Synaptic Plasticity, Chun-An Chen, Wei Wang, Steen E Pedersen, Ayush Raman, Michelle L Seymour, Fernanda R Ruiz, Anping Xia, Meike E Van Der Heijden, Li Wang, Jiani Yin, Joanna Lopez, Megan E Rech, Richard A Lewis, Samuel M Wu, Zhandong Liu, Fred A Pereira, Robia G Pautler, Huda Y Zoghbi, Christian P Schaaf

Faculty, Staff and Students Publications

Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS) has been identified as an autosomal-dominant disorder characterized by a complex neurological phenotype, with high prevalence of intellectual disability and optic nerve atrophy/hypoplasia. The syndrome is caused by loss-of-function mutations in NR2F1, which encodes a highly conserved nuclear receptor that serves as a transcriptional regulator. Previous investigations to understand the protein's role in neurodevelopment have mostly used mouse models with constitutive and tissue-specific homozygous knockout of Nr2f1. In order to represent the human disease more accurately, which is caused by heterozygous NR2F1 mutations, we investigated a heterozygous knockout mouse model and found that this model …


Cutting The Cord: A Case Of Late Presenting Driveline Infection, Brian Laughey, Lauren Eyadiel, Barbara Pisani Mar 2020

Cutting The Cord: A Case Of Late Presenting Driveline Infection, Brian Laughey, Lauren Eyadiel, Barbara Pisani

The VAD Journal

Ventricular assist device (VAD) related infection, specifically driveline infection, is a common complication after VAD implantation. A 45-year old patient with a delayed skin infection at the site of the original driveline nearly one year after VAD inactivation and surgical driveline burial was treated with antibiotics and surgical debridement for approximately six months. Continued discharge at driveline site and growth of methicillin susceptible Staphylococcus aureus resulted in the recommendation of explantation of the VAD. Post-VAD explantation, the patient remains symptom free and without infection 21 months following explant.


Modeling Hospital-Wide Extracorporeal Cardiopulmonary Resuscitation: Pros And Cons, Shiksha Joshi, Sandipan Shringi, Manpreet Sira, Maya Guglin Mar 2020

Modeling Hospital-Wide Extracorporeal Cardiopulmonary Resuscitation: Pros And Cons, Shiksha Joshi, Sandipan Shringi, Manpreet Sira, Maya Guglin

The VAD Journal

Background: We aimed to analyze the potential benefits of implementing a hospital-wide extracorporeal cardiopulmonary resuscitation (ECPR) protocol.

Methods: We analyzed in-hospital cardiac arrests in a large, academic hospital for two consecutive years. For this model, we assumed that ECPR would be started in all adults, with no upper age limit, who have a full code status. We excluded codes lastingminutes, arrests with asystole as an initial rhythm, and patients with hemorrhagic shock or who coded due to new stroke (contraindications for anticoagulation). We calculated how many extra lives could be saved per year if ECPR was initiated during each code …


Heart Rate Variability: A Possible Machine Learning Biomarker For Mechanical Circulatory Device Complications And Heart Recovery, Theodore Lin, Zain Khalpey, Shravan Aras Mar 2020

Heart Rate Variability: A Possible Machine Learning Biomarker For Mechanical Circulatory Device Complications And Heart Recovery, Theodore Lin, Zain Khalpey, Shravan Aras

The VAD Journal

Cardiovascular disease continues to be the number one cause of death in the United States, with heart failure patients expected to increase to >8 million by 2030. Mechanical circulatory support (MCS) devices are now better able to manage acute and chronic heart failure refractory to medical therapy, both as bridge to transplant or as bridge to destination. Despite significant advances in MCS device design and surgical implantation technique, it remains difficult to predict response to device therapy. Heart rate variability (HRV), measuring the variation in time interval between adjacent heartbeats, is an objective device diagnostic regularly recorded by various MCS …


Predicting Bleeding And Thrombosis Complications In Patients With Continuous Flow Left Ventricular Assist Devices, Kyle Zacholski, William Kuan, Justin Mccann Mccann, Aric Schadler, Aaron Cook, Sara Parli, Adam Sieg Mar 2020

Predicting Bleeding And Thrombosis Complications In Patients With Continuous Flow Left Ventricular Assist Devices, Kyle Zacholski, William Kuan, Justin Mccann Mccann, Aric Schadler, Aaron Cook, Sara Parli, Adam Sieg

The VAD Journal

Background: Left ventricular assist device (LVAD) therapy has been proven to relieve heart failure symptoms and improve survival, but is not devoid of bleeding and/or thrombotic complications. Risk stratification tools have been utilized in other cardiovascular disease populations to estimate the risk of bleeding and thrombosis with and without anticoagulation, including the HAS-BLED, HEMORR2HAGES, CHADS2 and CHA2DS2-VASc models. The study objective was to evaluate the predictive value of available risk models for bleeding and thrombotic complications in patients with an LVAD within one year of implantation.

Methods: This was a retrospective, single-center analysis …


A Case Of Heartmate 3 Outflow Graft Twisting With Extraluminal Thrombosis: Is Computed Tomography Angiography Helpful?, Karim Saleb, Marianna Zagurovskaya, Michael Sekela, Maya Guglin Mar 2020

A Case Of Heartmate 3 Outflow Graft Twisting With Extraluminal Thrombosis: Is Computed Tomography Angiography Helpful?, Karim Saleb, Marianna Zagurovskaya, Michael Sekela, Maya Guglin

The VAD Journal

Twists in the outflow graft of the HeartMateTM 3 device (Abbott) have recently been described as a sporadic, late complication. We present a case with a unique combination of external compression of the HeartMate 3 outflow graft by a surgical scar compounded by thrombus formation in the space between the band relief and the outflow graft with associated twist of the outflow graft and severe flow limitation. Computed tomography angiogram (CTA) of the chest was suggestive of outflow graft thrombosis. Our case sheds additional light on the limited specificity of gated CTA in distinguishing the outflow graft twisting from …


Gut Microbial Protein Expression In Response To Dietary Patterns In A Controlled Feeding Study: A Metaproteomic Approach, Sheng Pan, Meredith A J Hullar, Lisa A Lai, Hong Peng, Damon H May, William S Noble, Daniel Raftery, Sandi L Navarro, Marian L Neuhouser, Paul D Lampe, Johanna W Lampe, Ru Chen Mar 2020

Gut Microbial Protein Expression In Response To Dietary Patterns In A Controlled Feeding Study: A Metaproteomic Approach, Sheng Pan, Meredith A J Hullar, Lisa A Lai, Hong Peng, Damon H May, William S Noble, Daniel Raftery, Sandi L Navarro, Marian L Neuhouser, Paul D Lampe, Johanna W Lampe, Ru Chen

Faculty, Staff and Students Publications

Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period (


Cell Type Composition And Circuit Organization Of Clonally Related Excitatory Neurons In The Juvenile Mouse Neocortex, Cathryn R Cadwell, Federico Scala, Paul G Fahey, Dmitry Kobak, Shalaka Mulherkar, Fabian H Sinz, Stelios Papadopoulos, Zheng H Tan, Per Johnsson, Leonard Hartmanis, Shuang Li, Ronald J Cotton, Kimberley F Tolias, Rickard Sandberg, Philipp Berens, Xiaolong Jiang, Andreas Savas Tolias Mar 2020

Cell Type Composition And Circuit Organization Of Clonally Related Excitatory Neurons In The Juvenile Mouse Neocortex, Cathryn R Cadwell, Federico Scala, Paul G Fahey, Dmitry Kobak, Shalaka Mulherkar, Fabian H Sinz, Stelios Papadopoulos, Zheng H Tan, Per Johnsson, Leonard Hartmanis, Shuang Li, Ronald J Cotton, Kimberley F Tolias, Rickard Sandberg, Philipp Berens, Xiaolong Jiang, Andreas Savas Tolias

Faculty, Staff and Students Publications

Clones of excitatory neurons derived from a common progenitor have been proposed to serve as elementary information processing modules in the neocortex. To characterize the cell types and circuit diagram of clonally related excitatory neurons, we performed multi-cell patch clamp recordings and Patch-seq on neurons derived from Nestin-positive progenitors labeled by tamoxifen induction at embryonic day 10.5. The resulting clones are derived from two radial glia on average, span cortical layers 2–6, and are composed of a random sampling of transcriptomic cell types. We find an interaction between shared lineage and connection type: related neurons are more likely to …


Survey Of Latino/Hispanic Adult Immigrants Living In The Colonias Of Hidalgo County, Texas Evaluating Reported Food Insecurity And Immigration-Related Fear, Julia Rosenberg, Sindhu Sudanagunta, Marsha Griffin Mar 2020

Survey Of Latino/Hispanic Adult Immigrants Living In The Colonias Of Hidalgo County, Texas Evaluating Reported Food Insecurity And Immigration-Related Fear, Julia Rosenberg, Sindhu Sudanagunta, Marsha Griffin

Journal of Applied Research on Children: Informing Policy for Children at Risk

Background:

Colonias in Hidalgo County, Texas are residential communities near the Texas-Mexico border which often lack basic living necessities with high rates of poverty. Due to complex socioeconomic/geopolitical stressors (factors ranging from income inequality to access to transportation to concern regarding safety and legal status), colonia residents have limited access to fresh produce, while processed foods are more readily available, resulting in significant food insecurity.

Objectives:

The aim of this study is to assess levels of food insecurity, current eating habits, barriers of access, and interest in more readily affordable and accessible produce options in colonias of Hidalgo County, Texas. …


Deep Learning In Clinical Natural Language Processing: A Methodical Review, Stephen Wu, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, Hua Xu Mar 2020

Deep Learning In Clinical Natural Language Processing: A Methodical Review, Stephen Wu, Kirk Roberts, Surabhi Datta, Jingcheng Du, Zongcheng Ji, Yuqi Si, Sarvesh Soni, Qiong Wang, Qiang Wei, Yang Xiang, Bo Zhao, Hua Xu

Faculty, Staff and Student Publications

OBJECTIVE: This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research.

MATERIALS AND METHODS: We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers.

RESULTS: DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) …


Ms 220 Guide To The Sister Agnes Mary Joy Papers (1970-2013), Agnes Mary Joy (1931-2020) Mar 2020

Ms 220 Guide To The Sister Agnes Mary Joy Papers (1970-2013), Agnes Mary Joy (1931-2020)

Manuscript Finding Aids

Sister Agnes Mary Joy papers include ephemera, photographs, handwritten detailed patient notes, lectures, administrative material, correspondence, and professional material. The bulk of the material in this collection is linked to her work at the director of chaplaincy services for the Institute of Religion. See more at MS 220.


Evidence For Gene-Smoking Interactions For Hearing Loss And Deafness In Japanese American Families, Jia Y Wan, Christina Cataby, Andrew Liem, Emily Jeffrey, Trina M Norden-Krichmar, Deborah Goodman, Stephanie A Santorico, Karen L Edwards Mar 2020

Evidence For Gene-Smoking Interactions For Hearing Loss And Deafness In Japanese American Families, Jia Y Wan, Christina Cataby, Andrew Liem, Emily Jeffrey, Trina M Norden-Krichmar, Deborah Goodman, Stephanie A Santorico, Karen L Edwards

Faculty, Staff and Student Publications

BACKGROUND: This study investigated the relationship between smoking and hearing loss and deafness (HLD) and whether the relationship is modified by genetic variation. Data for these analyses was from the subset of Japanese American families collected as part of the American Diabetes Association Genetics of Non-insulin Dependent Diabetes Mellitus study. Logistic regression with generalized estimating equations assessed the relationship between HLD and smoking. Nonparametric linkage analysis identified genetic regions harboring HLD susceptibility genes and ordered subset analysis was used to identify regions showing evidence for gene-smoking interactions. Genetic variants within these candidate regions were then each tested for interaction with …


Examining Measurement Reactivity In Daily Diary Data On Substance Use: Results From A Randomized Experiment, Anne Buu, Songshan Yang, Runze Li, Marc A Zimmerman, Rebecca M Cunningham, Maureen A Walton Mar 2020

Examining Measurement Reactivity In Daily Diary Data On Substance Use: Results From A Randomized Experiment, Anne Buu, Songshan Yang, Runze Li, Marc A Zimmerman, Rebecca M Cunningham, Maureen A Walton

Faculty, Staff and Student Publications

The debate about whether measurement reactivity exists in daily diary research on substance use is still unsettled due to the issues of study design and statistical methodology. This study proposes a time-varying effect model (TVEM) that characterizes the trajectory of substance use behaviors with nonparametric functions determined by the data rather than imposes presumed parametric functions. It also allows researchers to investigate the effect of measurement reactivity on not only the likelihood of using substances but also the amount of substance use. The TVEM was applied to analyze diary data on alcohol and marijuana use collected from an experiment, which …


Coaction Between Physical Activity And Fruit And Vegetable Intake In Racially Diverse, Obese Adults, Natalia I Heredia, Maria E Fernandez, Alexandra E Van Den Berg, Casey P Durand, Harold W Kohl, Belinda M Reininger, Kevin O Hwang, Lorna H Mcneill Mar 2020

Coaction Between Physical Activity And Fruit And Vegetable Intake In Racially Diverse, Obese Adults, Natalia I Heredia, Maria E Fernandez, Alexandra E Van Den Berg, Casey P Durand, Harold W Kohl, Belinda M Reininger, Kevin O Hwang, Lorna H Mcneill

Faculty, Staff and Student Publications

PURPOSE: There is minimal understanding of the potential for coaction, defined as action on one behavior increasing the likelihood of taking action on another behavior, between physical activity (PA) and fruit and vegetable (FV) intake. The purpose of this study was to assess the bidirectional coaction between FV intake and PA, as well as self-efficacy for these behaviors, in a racially diverse sample of obese adults.

DESIGN: This is a secondary analysis using data collected from the Path to Health study, a randomized controlled trial. ClinicalTrials.gov Identifier: NCT03674229.

SAMPLE: Obese adults who completed baseline and 6-month follow-up assessments.

MEASURES: For …


Fibrin Clots Maintain The Viability And Proliferative Capacity Of Human Mesenchymal Stem Cells: An In Vitro Study, Ryan J Warth, Paul G Shupe, Xueqin Gao, Mohammad Syed, Walter R Lowe, Johnny Huard, Christopher D Harner Mar 2020

Fibrin Clots Maintain The Viability And Proliferative Capacity Of Human Mesenchymal Stem Cells: An In Vitro Study, Ryan J Warth, Paul G Shupe, Xueqin Gao, Mohammad Syed, Walter R Lowe, Johnny Huard, Christopher D Harner

Faculty, Staff and Student Publications

BACKGROUND: Augmentation of soft-tissue repairs with an autologous fibrin clot has been used clinically for nearly four decades; however, fibrin clots tend to produce an abundance of scar tissue, which is known to inhibit soft-tissue regeneration. Mesenchymal stem cells (MSCs) embedded in fibrin clots before repair could reduce scar tissue deposition and facilitate soft-tissue regeneration. To our knowledge, no published studies have directly evaluated the viability or bioactivity of MSCs in fresh human fibrin clots over time. The purpose of this study was to evaluate the viability and bioactivity of human MSCs inside human fibrin clots over time in nutritive …


Temporal Trends And Geographic Variations In Mortality Rates From Prescription Opioids: Lessons From Florida And West Virginia, Sarah A Palumbo, Charles H Hennekens, Janet D Robishaw, Robert S Levine Mar 2020

Temporal Trends And Geographic Variations In Mortality Rates From Prescription Opioids: Lessons From Florida And West Virginia, Sarah A Palumbo, Charles H Hennekens, Janet D Robishaw, Robert S Levine

Faculty, Staff and Students Publications

OBJECTIVES: To explore temporal trends and geographic variations in mortality from prescription opioids from 1999 to 2016.

METHODS: Centers for Disease Control and Prevention Wide-ranging Online Data for Epidemiologic Research Multiple Cause of Death files were used to calculate age-adjusted rates and 95% confidence intervals (CIs) and create spatial cluster maps.

RESULTS: From 1999 to 2016, counties in West Virginia experienced the highest overall mortality rates in the United States from prescription opioids. Specifically, from 1999 to 2004, the highest rate in West Virginia of 24.87/100,000 (95% CI 17.84-33.73) was the fourth highest in the United States. From 2005 to …


The Impact Of Diabetic Foot Ulcers And Unilateral Offloading Footwear On Gait In People With Diabetes, Erica Ling, Brian Lepow, He Zhou, Ana Enriquez, Ashley Mullen, Bijan Najafi Mar 2020

The Impact Of Diabetic Foot Ulcers And Unilateral Offloading Footwear On Gait In People With Diabetes, Erica Ling, Brian Lepow, He Zhou, Ana Enriquez, Ashley Mullen, Bijan Najafi

Faculty, Staff and Students Publications

BACKGROUND: Unilateral offloading footwear prescribed to patients with diabetic foot ulcers elevates one limb relative to the other, which may lead to limp and abnormal gait. This study investigated whether the unilateral foot ulcer and offloading combination negatively impacts gait function beyond diabetic peripheral neuropathy.

METHODS: Eighty-six participants were recruited in 3 groups: 12 with diabetic peripheral neuropathy and unilateral foot ulcers wearing offloading footwear (offloading group, age = 55.6 ± 9.5 years, BMI = 30.9 ± 4.5 kg/m

FINDINGS: The offloading group exhibited deteriorated gait function compared to the non-diabetic group (p < 0.005, Cohen's effect size d = 0.90-2.61). They also had decreased gait speed (p < 0.001, d = 1.79) and stride length (p < 0.001, d = 1.76), as well as increased gait cycle time (p < 0.001, d = 1.67) and limp (p < 0.050, d = 0.72-1.49) compared to the neuropathy group. The offloading group showed increased gait unsteadiness compared to the neuropathy group, but the difference did not reach statistical significance in our samples.

INTERPRETATION: This study demonstrated that while diabetic …