Digital Commons Network^™

Who Are Those “Risk-Taking Adolescents”? Individual Differences In Developmental Neuroimaging Research, James M. Bjork, Dustin A. Pardini

Psychiatry Publications

Functional magnetic resonance imaging (fMRI) has illuminated the development of human brain function. Some of this work in typically-developing youth has ostensibly captured neural underpinnings of adolescent behavior which is characterized by risk-seeking propensity, according to psychometric questionnaires and a wealth of anecdote. Notably, cross-sectional comparisons have revealed age-dependent differences between adolescents and other age groups in regional brain responsiveness to prospective or experienced rewards (usually greater in adolescents) or penalties (usually diminished in adolescents). These differences have been interpreted as reflecting an imbalance between motivational drive and behavioral control mechanisms, especially in mid-adolescence, thus promoting greater risk-taking. While intriguing, …

Role Of Interleukin-1 In Radiation-Induced Cardiomyopathy, Eleonora Mezzaroma, Ross B. Mikkelsen, Stefano Toldo, Adolfo G. Mauro, Khushboo Sharma, Carlo Marchetti, Asim Alam, Benjamin W. Van Tassell, David A. Gewirtz, Antonio Abbate

Pharmacotherapy and Outcomes Science Publications

Thoracic X-ray therapy (XRT), used in cancer treatment, is associated with increased risk of heart failure. XRT-mediated injury to the heart induces an inflammatory response leading to cardiomyopathy. The aim of this study was to determine the role of interleukin (IL)-1 in response to XRT injury to the heart and on the cardiomyopathy development in the mouse. Female mice with genetic deletion of the IL-1 receptor type I (IL-1R1 knockout mice [IL-1R1 KO]) and treatment with recombinant human IL-1 receptor antagonist anakinra, 10 mg/kg twice daily for 7 d, were used as independent approaches to determine the role of IL-1. …

Quality Control Material For The Detection Of Somatic Mutations In Fixed Clinical Specimens By Next-Generation Sequencing, Catherine I. Dumur, Jorge A. Almenara, Celeste N. Powers, Andrea Ferreira-Gonzalez

Pathology Publications

Background: Targeted next generation sequencing (NGS) technology to assess the mutational status of multiple genes on formalin-fixed, paraffin embedded (FFPE) tumors is rapidly being adopted in clinical settings, where quality control (QC) practices are required. Establishing reliable FFPE QC materials for NGS can be challenging and/or expensive. Here, we established a reliable and cost-effective FFPE QC material for routine utilization in the Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHP2) assay.

Methods: The performance characteristics of the CHP2 assay were determined by sequencing various cell line mixtures and 55 different FFPE tumors on the Ion Torrent PGM platform. A FFPE QC …

Quality Control Material For The Detection Of Somatic Mutations In Fixed Clinical Specimens By Next-Generation Sequencing, Catherine I. Dumur, Jorge A. Almenara, Celeste N. Powers, Andrea Ferreira-Gonzalez

Pathology Publications

Background

Targeted next generation sequencing (NGS) technology to assess the mutational status of multiple genes on formalin-fixed, paraffin embedded (FFPE) tumors is rapidly being adopted in clinical settings, where quality control (QC) practices are required. Establishing reliable FFPE QC materials for NGS can be challenging and/or expensive. Here, we established a reliable and cost-effective FFPE QC material for routine utilization in the Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHP2) assay.

Methods

The performance characteristics of the CHP2 assay were determined by sequencing various cell line mixtures and 55 different FFPE tumors on the Ion Torrent PGM platform. A FFPE QC …

Nosocomial Keratitis Caused By Methicillin-Resistant Staphylococcus Aureus: Case Report And Preventative Measures, Puneet S. Braich, Shruti Aggarwal, Sabrina Mukhtar, David Rp Almeida

Ophthalmology Publications

A 47-year-old African-American woman was admitted to the intensive care unit of our community hospital for respiratory failure secondary to severe decompensated heart failure, requiring intubation. In the ensuing days, she developed a methicillin-resistant Staphylococcus aureus (MRSA) infection of the cornea, despite no growth of MRSA in multiple blood, sputum, and urine cultures. This unexpected corneal infection complicated her hospital stay, and increased morbidity and disease-related cost. Risk factors, warning signs, and preventative measures for MRSA keratitis secondary to lagophthalmos (inability to completely close one's eyelids) are outlined in this case report. Implementing simple precautions such as taping eyelids shut …

Relocation Consequences On An Ophthalmology Consultation Service From An Inpatient To Outpatient Facility, Jorawer S. Singh, Vincent M. Imbrogno, Mary K. Howard, Amandip S. Cheema, Ausra D. Selvadurai, Surbhi Bansal

Ophthalmology Publications

Importance

This study shows that relocation of an academic ophthalmology residency program from an inpatient to an outpatient setting in western New York does not affect the consult volume but affects management patterns and follow-up rates.

Objective

To investigate the effects on the ophthalmology consultation service of an academic program with relocation from a Regional Level-1 Trauma center to an outpatient facility.

Design

Consultation notes from 3 years before and 3 years after the University at Buffalo’s (UB) Department of Ophthalmology relocation from a Regional Level-1 Trauma center (Erie County Medical Center) to an outpatient facility (Ross Eye Institute) were …

Prevalence And Factors Predictive Of Intraocular Fungal Infection In Patients With Fungemia At An Academic Urban Tertiary Care Center, Elena Geraymovych, Joseph H. Conduff, Puneet S. Braich, Christopher T. Leffler, Vikram S. Brar

Ophthalmology Publications

Objective

To report the prevalence and to identify factors predictive of intraocular infection in patients with fungemia receiving prophylactic antifungal therapy.

Methods

A retrospective review of patients who received prophylactic antifungal therapy and a dilated fundus examination at an academic urban tertiary care center from 2000 to 2007. Basic demographic information, fungal species grown, antifungal agent(s) used, number of positive blood culture specimens, visual acuity, visual symptoms, and known risks of disseminated candidiasis were noted. Logistic regression analysis was used to determine the factors significantly associated with intraocular fungal infection.

Results

A total of 132 patients with positive fungemia culture …

Prevalence And Factors Predictive Of Intraocular Fungal Infection In Patients With Fungemia At An Academic Urban Tertiary Care Center, Elena Geraymovych, Joseph H. Conduff, Puneet S. Braich, Christopher T. Leffler, Vikram S. Brar

Ophthalmology Publications

Objective: To report the prevalence and to identify factors predictive of intraocular infection in patients with fungemia receiving prophylactic antifungal therapy.
Methods: A retrospective review of patients who received prophylactic antifungal therapy and a dilated fundus examination at an academic urban tertiary care center from 2000 to 2007. Basic demographic information, fungal species grown, antifungal agent(s) used, number of positive blood culture specimens, visual acuity, visual symptoms, and known risks of disseminated candidiasis were noted. Logistic regression analysis was used to determine the factors significantly associated with intraocular fungal infection.
Results: A total of 132 patients with positive fungemia culture …

Infrared Imaging Enhances Retinal Crystals In Bietti’S Crystalline Dystrophy, Vikram S. Brar, William H. Benson

Ophthalmology Publications

Infrared imaging dramatically increased the number of crystalline deposits visualized compared with clinical examination, standard color fundus photography, and red free imaging in patients with Bietti’s crystalline dystrophy. We believe that this imaging modality significantly improves the sensitivity with which these lesions are detected, facilitating earlier diagnosis and may potentially serve as a prognostic indicator when examined over time.

Progressive Cognitive Deficit, Motor Impairment And Striatal Pathology In A Transgenic Huntington Disease Monkey Model From Infancy To Adulthood, Anthony W. S. Chan, Jie Jiang, Yiju Chen, Chunxia Li, Melinda S. Prucha, Yijuan Hu, Tim Chi, Sean Moran, Tayeb Rahim, Shihua Li, Xiaojiang Li, Stuart M. Zola, Claudia M. Testa, Hui Mao, Rosa Villalba, Yoland Smith, Xiaodong Zhang, Jocelyne Bachevalier

Neurology Publications

One of the roadblocks to developing effective therapeutics for Huntington disease (HD) is the lack of animal models that develop progressive clinical traits comparable to those seen in patients. Here we report a longitudinal study that encompasses cognitive and motor assessment, and neuroimaging of a group of transgenic HD and control monkeys from infancy to adulthood. Along with progressive cognitive and motor impairment, neuroimaging revealed a progressive reduction in striatal volume. Magnetic resonance spectroscopy at 48 months of age revealed a decrease of N-acetylaspartate (NAA), further suggesting neuronal damage/loss in the striatum. Postmortem neuropathological analyses revealed significant neuronal loss in …

Plasmin Regulation Through Allosteric, Sulfated, Small Molecules, Rami A. Al-Horani, Rajesh Karuturi, Domonique T. White, Umesh R. Desai

Medicinal Chemistry Publications

Plasmin, a key serine protease, plays a major role in clot lysis and extracellular matrix remodeling. Heparin, a natural polydisperse sulfated glycosaminoglycan, is known to allosterically modulate plasmin activity. No small allosteric inhibitor of plasmin has been discovered to date. We screened an in-house library of 55 sulfated, small glycosaminoglycan mimetics based on nine distinct scaffolds and varying number and positions of sulfate groups to discover several promising hits. Of these, a pentasulfated flavonoid-quinazolinone dimer 32 was found to be the most potent sulfated small inhibitor of plasmin (IC50 = 45 μM, efficacy = 100%). Michaelis-Menten kinetic studies revealed …

Structural Studies Of Aav2 Rep68 Reveal A Partially Structured Linker And Compact Domain Conformation, Faik N. Musayev, Francisco Zarate-Perez, Martino Bardelli, Clayton Bishop, Emil F. Saniev, R. Michael Linden, Els Henckaerts, Carlos R. Escalante

Medicinal Chemistry Publications

Adeno-associated virus (AAV) nonstructural proteins Rep78 and Rep68 carry out all DNA transactions that regulate the AAV life cycle. They share two multifunctional domains: an N-terminal origin binding/nicking domain (OBD) from the HUH superfamily and a SF3 helicase domain. A short linker of ~20 amino acids that is critical for oligomerization and function connects the two domains. Although X-ray structures of the AAV5 OBD and AAV2 helicase domains have been determined, information about the full-length protein and linker conformation is not known. This article presents the solution structure of AAV2 Rep68 using small-angle X-ray scattering (SAXS). We first determined the …

A Simple Method For Discovering Druggable, Specific Glycosaminoglycan-Protein Systems. Elucidation Of Key Principles From Heparin/Heparan Sulfate-Binding Proteins, Aurijit Sarkar, Umesh R. Desai

Medicinal Chemistry Publications

Glycosaminoglycans (GAGs) affect human physiology and pathology by modulating more than 500 proteins. GAG-protein interactions are generally assumed to be ionic and nonspecific, but specific interactions do exist. Here, we present a simple method to identify the GAG-binding site (GBS) on proteins that in turn helps predict high specific GAG–protein systems. Contrary to contemporary thinking, we found that the electrostatic potential at basic arginine and lysine residues neither identifies the GBS consistently, nor its specificity. GBSs are better identified by considering the potential at neutral hydrogen bond donors such as asparagine or glutamine sidechains. Our studies also reveal that an …

Dismira: Prioritization Of Disease Candidates In Mirna-Disease Associations Based On Maximum Weighted Matching Inference Model And Motif-Based Analysis, Joseph J. Nalluri, Bhanu K. Kamapantula, Debmalya Barh, Neha Jain, Antaripa Bhattacharya, Sintia Silva De Almeida, Rommel Thiago Juca Ramos, Artur Silva, Vasco Azevedo, Preetam Ghosh

Computer Science Publications

Background

MicroRNAs (miRNAs) have increasingly been found to regulate diseases at a significant level. The interaction of miRNA and diseases is a complex web of multilevel interactions, given the fact that a miRNA regulates upto 50 or more diseases and miRNAs/diseases work in clusters. The clear patterns of miRNA regulations in a disease are still elusive.

Methods

In this work, we approach the miRNA-disease interactions from a network scientific perspective and devise two approaches - maximum weighted matching model (a graph theoretical algorithm which provides the result by solving an optimization equation of selecting the most prominent set of diseases) …

Use Of A Green Familiar Faces Paradigm Improves P300-Speller Brain-Computer Interface Performance, Qi Li, Shuai Lu, Jian Li, Ou Bai

Computer Science Publications

Background

A recent study showed improved performance of the P300-speller when the flashing row or column was overlaid with translucent pictures of familiar faces (FF spelling paradigm). However, the performance of the P300-speller is not yet satisfactory due to its low classification accuracy and information transfer rate.

Objective

To investigate whether P300-speller performance is further improved when the chromatic property and the FF spelling paradigm are combined.

Methods

We proposed a new spelling paradigm in which the flashing row or column is overlaid with translucent green pictures of familiar faces (GFF spelling paradigm). We analyzed the ERP waveforms elicited by …

Transcriptional Network Growing Models Using Motif-Based Preferential Attachment, Ahmed F. Abdelzaher, Ahmad F. Al-Musawi, Preetam Ghosh, Michael L. Mayo, Edward J. Perkins

Computer Science Publications

Understanding relationships between architectural properties of gene-regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics, as it can provide insights into, e.g., disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs – i.e., small-node subgraphs that occur more abundantly in GRNs than expected from chance alone. Because these transcriptional modules represent “building blocks” of complex networks and exhibit a wide range of functional and dynamical properties, they may contribute to the remarkable robustness and dynamical stability associated with the whole of GRNs. Here, we …

Miregulome: A Knowledge-Base Of Mirna Regulomics And Analysis, Debmalya Barh, Bhanu Kamapantula, Neha Jain, Joseph Nalluri, Antaripa Bhattacharya, Lucky Juneja, Neha Barve, Sandeep Tiwari, Anderson Miyoshi, Vasco Azevedo, Kenneth Blum, Anil Kumar, Artur Silva, Preetam Ghosh

Computer Science Publications

miRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes, and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics. miRegulome attempts to bridge this gap. The current version of miRegulome v1.0 provides details on the entire regulatory modules of miRNAs altered in response to …

Maprepeat: An Approach For Effective Assembly Of Repetitive Regions In Prokaryotic Genomes, Diego Cb Mariano, Felipe L. Pereira, Preetam Ghosh, Debmalya Barh, Henrique Cp Figueiredo, Artur Silva, Rommel Tj Ramos, Vasco Ac Azevedo

Computer Science Publications

The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology …

Self-Organizing Feature Maps Identify Proteins Critical To Learning In A Mouse Model Of Down Syndrome, Clara Higuera, Katheleen J. Gardiner, Krzysztof J. Cios

Computer Science Publications

Down syndrome (DS) is a chromosomal abnormality (trisomy of human chromosome 21) associated with intellectual disability and affecting approximately one in 1000 live births worldwide. The overexpression of genes encoded by the extra copy of a normal chromosome in DS is believed to be sufficient to perturb normal pathways and normal responses to stimulation, causing learning and memory deficits. In this work, we have designed a strategy based on the unsupervised clustering method, Self Organizing Maps (SOM), to identify biologically important differences in protein levels in mice exposed to context fear conditioning (CFC). We analyzed expression levels of 77 proteins …

Self-Organizing Feature Maps Identify Proteins Critical To Learning In A Mouse Model Of Down Syndrome, Clara Higuera, Katheleen J. Gardiner, Kryzysztof Cios

Computer Science Publications

Down syndrome (DS) is a chromosomal abnormality (trisomy of human chromosome 21) associated with intellectual disability and affecting approximately one in 1000 live births worldwide. The overexpression of genes encoded by the extra copy of a normal chromosome in DS is believed to be sufficient to perturb normal pathways and normal responses to stimulation, causing learning and memory deficits. In this work, we have designed a strategy based on the unsupervised clustering method, Self Organizing Maps (SOM), to identify biologically important differences in protein levels in mice exposed to context fear conditioning (CFC). We analyzed expression levels of 77 proteins …

Enabling Smartphone-Based Hd Video Chats By Cooperative Transmissions In Crns, Tao Jing, Xuewei Cui, Wei Cheng, Shixiang Zhu, Yan Huo, Xiuzhen Cheng

Computer Science Publications

Smartphones have been equipped with the cameras that can shoot HD videos, and the video chat apps such as Skype are becoming popular. We can, therefore, intuitively predict the trend that users are expecting to enjoy HD video chats via utilizing their smartphones. Most of the current Internet services, however, cannot support the live HD video transmissions because of their low uplink rate. In order to overcome this limit, we propose to offload the uplink transmissions to cooperative users via cognitive radio networks. Specifically, we first divide the video stream into several substreams according to the H.264/SVC standard and the …

Self-Organizing Feature Maps Identify Proteins Critical To Learning In A Mouse Model Of Down Syndrome, Clara Higuera, Kathleen J. Gardiner, Kryzysztof Cios

Computer Science Publications

Down syndrome (DS) is a chromosomal abnormality (trisomy of human chromosome 21) associated with intellectual disability and affecting approximately one in 1000 live births worldwide. The overexpression of genes encoded by the extra copy of a normal chromosome in DS is believed to be sufficient to perturb normal pathways and normal responses to stimulation, causing learning and memory deficits. In this work, we have designed a strategy based on the unsupervised clustering method, Self Organizing Maps (SOM), to identify biologically important differences in protein levels in mice exposed to context fear conditioning (CFC). We analyzed expression levels of 77 proteins …

Identifying Influential Nodes In A Wound Healing-Related Network Of Biological Processes Using Mean First-Passage Time, Tomasz Jakub Arodz, Danail Bonchev

Computer Science Publications

In this study we offer an approach to network physiology, which proceeds from transcriptomic data and uses gene ontology analysis to identify the biological processes most enriched in several critical time points of wound healing process (days 0, 3 and 7). The top-ranking differentially expressed genes for each process were used to build two networks: one with all proteins regulating the transcription of selected genes, and a second one involving the proteins from the signaling pathways that activate the transcription factors. The information from these networks is used to build a network of the most enriched processes with undirected links …

Assessment Of Residential History Generation Using A Public-Record Database, David C. Wheeler, Aobo Wang

Biostatistics Publications

In studies of disease with potential environmental risk factors, residential location is often used as a surrogate for unknown environmental exposures or as a basis for assigning environmental exposures. These studies most typically use the residential location at the time of diagnosis due to ease of collection. However, previous residential locations may be more useful for risk analysis because of population mobility and disease latency. When residential histories have not been collected in a study, it may be possible to generate them through public-record databases. In this study, we evaluated the ability of a public-records database from LexisNexis to provide …

Proceedings Of The 2015 Midsouth Computational Biology And Bioinformatics Society (Mcbios) Conference, Jonathan D. Wren, Shraddha Thakkar, Ramin Homayouni, Donald J. Johann, Mikhail G. Dozmorov

Biostatistics Publications

No abstract provided.

What Was Glaucoma Called Before The 20th Century?, Christopher T. Leffler, Stephen G. Schwartz, Francesca M. Giliberti, Matthew T. Young, Dennis Bermudez

Biostatistics Publications

Glaucoma involves a characteristic optic neuropathy, often with elevated intraocular pressure. Before 1850, poor vision with a normal eye appearance, as occurs in primary open-angle glaucoma, was termed amaurosis, gutta serena, or black cataract. Few observers noted palpable hardness of the eye in amaurosis. On the other hand, angle-closure glaucoma can produce a green or gray pupil, and therefore was called, variously, glaucoma (derived from the Greek for glaucous, a nonspecific term connoting blue, green, or light gray) and viriditate oculi. Angle closure, with palpable hardness of the eye, mydriasis, and anterior prominence of the lens, was described in greater …

Penalized Ordinal Regression Methods For Predicting Stage Of Cancer In High-Dimensional Covariate Spaces, Amanda Elswick Gentry, Colleen K. Jackson-Cook, Debra E. Lyon, Kellie J. Archer

Biostatistics Publications

The pathological description of the stage of a tumor is an important clinical designation and is considered, like many other forms of biomedical data, an ordinal outcome. Currently, statistical methods for predicting an ordinal outcome using clinical, demographic, and high-dimensional correlated features are lacking. In this paper, we propose a method that fits an ordinal response model to predict an ordinal outcome for high-dimensional covariate spaces. Our method penalizes some covariates (high-throughput genomic features) without penalizing others (such as demographic and/or clinical covariates). We demonstrate the application of our method to predict the stage of breast cancer. In our model, …

Assessment Of Weighted Quantile Sum Regression For Modeling Chemical Mixtures And Cancer Risk, Jenna Czarnota, Chris Gennings, David C. Wheeler

Biostatistics Publications

In evaluation of cancer risk related to environmental chemical exposures, the effect of many chemicals on disease is ultimately of interest. However, because of potentially strong correlations among chemicals that occur together, traditional regression methods suffer from collinearity effects, including regression coefficient sign reversal and variance inflation. In addition, penalized regression methods designed to remediate collinearity may have limitations in selecting the truly bad actors among many correlated components. The recently proposed method of weighted quantile sum (WQS) regression attempts to overcome these problems by estimating a body burden index, which identifies important chemicals in a mixture of correlated environmental …

Identifying Molecular Features Associated With Psychoneurological Symptoms In Women With Breast Cancer Using Multivariate Mixed Models, Qing Zhou, Colleen Jackson-Cook, Debra Lyon, Robert Perera, Kellie Archer

Biostatistics Publications

Breast cancer (BC) is the second most common cancer among women. Research shows many women with BC experience anxiety, depression, and stress (ADS). Epigenetics has recently emerged as a potential mechanism for the development of depression.1 Although there are growing numbers of research studies indicating that epigenetic changes are associated with ADS, there is currently no evidence that this association is present in women with BC. The goal of this study was to identify high-throughput methylation sites (CpG sites) that are associated with three psychoneurological symptoms (ADS) in women with BC. Traditionally, univariate models have been used to examine …

Computer Simulation, Bioinformatics, And Statistical Analysis Of Cancer Data And Processes, Kellie J. Archer, Kevin Dobbin, Swati Biswas, Roger S. Day, David C. Wheeler, Hao Wu

Biostatistics Publications

No abstract provided.