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Dr. Benjamin  Johnson  Phd image

Dr. Benjamin Johnson Phd

1130 Ten Rod Rd Suite E305
North Kingstown RI 02852
401 940-0451
Medical School: Other - Unknown
Accepts Medicare: No
Participates In eRX: No
Participates In PQRS: No
Participates In EHR: No
License #: PS00654
NPI: 1205926219
Taxonomy Codes:
103TC0700X

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Publications

SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. - BMC bioinformatics
Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow includes quality control of reads, mapping to a reference, counting transcript abundance, and statistical tests for differentially expressed genes. In spite of the numerous tools developed for each component of an RNA-seq analysis workflow, easy-to-use bacterially oriented workflow applications to combine multiple tools and automate the process are lacking. With many tools to choose from for each step, the task of identifying a specific tool, adapting the input/output options to the specific use-case, and integrating the tools into a coherent analysis pipeline is not a trivial endeavor, particularly for microbiologists with limited bioinformatics experience.To make bacterial RNA-seq data analysis more accessible, we developed a Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis (SPARTA). SPARTA is a reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making bacterial RNA-seq analysis a routine process that can be undertaken on a personal computer or in the classroom. The easy-to-install, complete workflow processes whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping reads to a reference, counting gene features, calculating differential gene expression, and, importantly, checking for potential batch effects within the data set. SPARTA outputs quality analysis reports, gene feature counts and differential gene expression tables and scatterplots.SPARTA provides an easy-to-use bacterial RNA-seq transcriptional profiling workflow to identify differentially expressed genes between experimental conditions. This software will enable microbiologists with limited bioinformatics experience to analyze their data and integrate next generation sequencing (NGS) technologies into the classroom. The SPARTA software and tutorial are available at sparta.readthedocs.org.
On-chip preparation of nanoscale contrast agents towards high-resolution ultrasound imaging. - Lab on a chip
Micron-sized lipid-stabilised bubbles of heavy gas have been utilised as contrast agents for diagnostic ultrasound (US) imaging for many years. Typically bubbles between 1 and 8 μm in diameter are produced to enhance imaging in US by scattering sound waves more efficiently than surrounding tissue. A potential area of interest for Contrast Enhanced Ultrasound (CEUS) are bubbles with diameters <1 μm or 'nanobubbles.' As bubble diameter decreases, ultrasonic resonant frequency increases, which could lead to an improvement in resolution for high-frequency imaging applications when using nanobubbles. In addition, current US contrast agents are limited by their size to the vasculature in vivo. However, molecular-targeted nanobubbles could penetrate into the extra-vascular space of cancerous tissue providing contrast in regions inaccessible to traditional microbubbles. This paper reports a new microfluidic method for the generation of sub-micron sized lipid stabilised particles containing perfluorocarbon (PFC). The nanoparticles are produced in a unique atomisation-like flow regime at high production rates, in excess of 10(6) particles per s and at high concentration, typically >10(11) particles per mL. The average particle diameter appears to be around 100-200 nm. These particles, suspected of being a mix of liquid and gaseous C4F10 due to Laplace pressure, then phase convert into nanometer sized bubbles on the application of US. In vitro ultrasound characterisation from these nanoparticle populations showed strong backscattering compared to aqueous filled liposomes of a similar size. The nanoparticles were stable upon injection and gave excellent contrast enhancement when used for in vivo imaging, compared to microbubbles with an equivalent shell composition.
Eligibility and utilization of implantable cardioverter-defibrillators in a regional STEMI system. - Heart rhythm : the official journal of the Heart Rhythm Society
Studies have shown mortality benefit for implantable cardioverter-defibrillators (ICDs) in ST-elevation myocardial infarction (STEMI) patients with reduced left ventricular ejection fraction (LVEF), but contemporary eligibility and appropriate utilization of ICDs is unknown.The purpose of this study was to determine the contemporary eligibility and appropriate utilization of ICDs post-STEMI.Using the prospective Minneapolis Heart Institute regional STEMI registry, LVEF before discharge and at follow-up were stratified into 3 groups: normal (LVEF ≥50%), mildly reduced (LVEF 35%-49%), and severely reduced (LVEF <35%).From March 2003 to June 2012, 3626 patients were treated. Patients with in-hospital death (n = 187), ICD in place (n = 21), negative cardiac biomarkers (n = 337), and undocumented in-hospital LVEF (n = 9) were excluded, leaving 3072 patients in the final analysis, including 1833 (59.7%) with LVEF ≥50%, 875 (28.5%) with LVEF between 35% and 49%, and 364 (11.8%) with LVEF <35% before hospital discharge. Overall, 1029 patients (33.5%) underwent follow-up echocardiography ≥40 days post-STEMI, including 140 of the 364 patients (38.5%) discharged with LVEF <35%. In total, 73 patients (7.1%) with follow-up echocardiography ≥40 days post-STEMI met criteria for an ICD (68 LVEF ≤30%, 5 LVEF 30%-35%, and New York Heart Association class II or greater). Only 26 of these patients (35.6%) underwent ICD placement within 1 year post-STEMI. Overall, only 10% to 15% of potentially eligible patients had an ICD implemented.Rates of ICD implantation in appropriate STEMI patients after 40 days are low. Strategies are needed to identify and expand access to these high-risk patients.Copyright © 2016 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.
Resensitizing daclatasvir-resistant hepatitis C variants by allosteric modulation of NS5A. - Nature
It is estimated that more than 170 million people are infected with hepatitis C virus (HCV) worldwide. Clinical trials have demonstrated that, for the first time in human history, the potential exists to eradicate a chronic viral disease using combination therapies that contain only direct-acting antiviral agents. HCV non-structural protein 5A (NS5A) is a multifunctional protein required for several stages of the virus replication cycle. NS5A replication complex inhibitors, exemplified by daclatasvir (DCV; also known as BMS-790052 and Daklinza), belong to the most potent class of direct-acting anti-HCV agents described so far, with in vitro activity in the picomolar (pM) to low nanomolar (nM) range. The potency observed in vitro has translated into clinical efficacy, with HCV RNA declining by ~3-4 log10 in infected patients after administration of single oral doses of DCV. Understanding the exceptional potency of DCV was a key objective of this study. Here we show that although DCV and an NS5A inhibitor analogue (Syn-395) are inactive against certain NS5A resistance variants, combinations of the pair enhance DCV potency by >1,000-fold, restoring activity to the pM range. This synergistic effect was validated in vivo using an HCV-infected chimaeric mouse model. The cooperative interaction of a pair of compounds suggests that NS5A protein molecules communicate with each other: one inhibitor binds to resistant NS5A, causing a conformational change that is transmitted to adjacent NS5As, resensitizing resistant NS5A so that the second inhibitor can act to restore inhibition. This unprecedented synergistic anti-HCV activity also enhances the resistance barrier of DCV, providing additional options for HCV combination therapy and new insight into the role of NS5A in the HCV replication cycle.
The Effect of Body Mass Index on Pelvic Floor Support 1 Year Postpartum. - Reproductive sciences (Thousand Oaks, Calif.)
Elevated body mass index (BMI) is associated with the incidence, prevalence, and progression of pelvic organ prolapse (POP). This study investigated the effect of peripartum BMI on pelvic floor support 1 year postpartum (PP1y). One hundred eight nulliparous women had their BMI recorded and underwent POP assessments using the Pelvic Organ Prolapse Quantification System at baseline, third trimester (36th to 38th week of pregnancy [G36-38w]), and PP1y. Pelvic organ prolapse was defined as ≥stage II. Women gained on average 1.9 kg between baseline and PP1y. After adjustment, increasing BMI PP1y was associated with increasing anterior wall descent (P < .0001) and higher odds of having POP PP1y (odds ratio: 1.41, 95% confidence interval: 1.01-1.97, P = .045). Trial of labor compared to unlabored cesarean delivery, POP G36-38w, and decreased fetal weight were independently associated with anterior vaginal wall laxity PP1y. Our finding suggests that postpartum BMI influences pelvic floor laxity 1 year after delivery. Postpartum weight reduction may serve as a strategy for POP prevention in some women.© The Author(s) 2015.
SCN5A variant that blocks fibroblast growth factor homologous factor regulation causes human arrhythmia. - Proceedings of the National Academy of Sciences of the United States of America
Nav channels are essential for metazoan membrane depolarization, and Nav channel dysfunction is directly linked with epilepsy, ataxia, pain, arrhythmia, myotonia, and irritable bowel syndrome. Human Nav channelopathies are primarily caused by variants that directly affect Nav channel permeability or gating. However, a new class of human Nav channelopathies has emerged based on channel variants that alter regulation by intracellular signaling or cytoskeletal proteins. Fibroblast growth factor homologous factors (FHFs) are a family of intracellular signaling proteins linked with Nav channel regulation in neurons and myocytes. However, to date, there is surprisingly little evidence linking Nav channel gene variants with FHFs and human disease. Here, we provide, to our knowledge, the first evidence that mutations in SCN5A (encodes primary cardiac Nav channel Nav1.5) that alter FHF binding result in human cardiovascular disease. We describe a five*generation kindred with a history of atrial and ventricular arrhythmias, cardiac arrest, and sudden cardiac death. Affected family members harbor a novel SCN5A variant resulting in p.H1849R. p.H1849R is localized in the central binding core on Nav1.5 for FHFs. Consistent with these data, Nav1.5 p.H1849R affected interaction with FHFs. Further, electrophysiological analysis identified Nav1.5 p.H1849R as a gain-of-function for INa by altering steady-state inactivation and slowing the rate of Nav1.5 inactivation. In line with these data and consistent with human cardiac phenotypes, myocytes expressing Nav1.5 p.H1849R displayed prolonged action potential duration and arrhythmogenic afterdepolarizations. Together, these findings identify a previously unexplored mechanism for human Nav channelopathy based on altered Nav1.5 association with FHF proteins.
Internal medicine point-of-care ultrasound assessment of left ventricular function correlates with formal echocardiography. - Journal of clinical ultrasound : JCU
Although focused cardiac ultrasonographic (FoCUS) examination has been evaluated in emergency departments and intensive care units with good correlation to formal echocardiography, accuracy for the assessment of left ventricular systolic function (LVSF) when performed by internal medicine physicians still needs independent evaluation.This prospective observational study in a 640-bed, academic, quaternary care center, included 178 inpatients examined by 10 internal medicine physicians who had completed our internal medicine bedside ultrasound training program. The ability to estimate LVSF with FoCUS as "normal," "mild to moderately decreased," or "severely decreased" was compared with left ventricular ejection fraction (>50%, 31-49%, and <31%, respectively) from formal echocardiography interpreted by a cardiologist.Sensitivity and specificity of FoCUS for any degree of LVSF impairment were 0.91 (95% confidence interval [CI] 0.80, 0.97) and 0.88 (95% CI 0.81, 0.93), respectively. The interrater agreement between internal medicine physician-performed FoCUS and formal echocardiography for any LVSF impairment was "good/substantial" with κ = 0.77 (p < 0.001), 95% CI (0.67, 0.87). Formal echocardiography was classified as "technically limited due to patient factors" in 20% of patients; however, echogenicity was sufficient in 100% of FoCUS exams to classify LVSF.Internal medicine physicians using FoCUS identify normal versus decreased LVSF with high sensitivity, specificity, and "good/substantial" interrater agreement when compared with formal echocardiography. These results support the role of cardiac FoCUS by properly trained internal medicine physicians for discriminating normal from reduced LVSF. © 2015 Wiley Periodicals, Inc. J Clin Ultrasound 44:92-99, 2016.© 2015 Wiley Periodicals, Inc.
Asymmetric Introgression in a Spotted Salamander Hybrid Zone. - The Journal of heredity
Before the establishment of reproductive isolation, deeply diverged intraspecific lineages can experience complex genetic and behavioral interactions as they come into secondary contact. Divergent selective and demographic processes mediate gene flow among lineages, resulting in hybrid zones with complex biogeographic structure. Discordance in the biogeographic patterns of autosomal and maternally inherited loci provides a useful window to infer the processes mediating admixture and introgression across hybrid zones. Here, we sampled 489 genotypes across a hybrid zone between 2 phylogeographic lineages of the spotted salamander, Ambystoma maculatum, and characterize discordant patterns of nuclear and mitochondrial introgression across the contact boundary. Our results indicate asymmetric introgression of nuclear DNA beyond the contact boundary from the western to eastern lineage, with introgression of eastern mitochondrial DNA into the western lineage. We discuss alternative mechanisms for this pattern and attribute this result to neutral patterns of population expansion of the western lineage into the east in combination with female mate choice for larger-bodied western males. Our results underscore the complexity of interacting mechanisms that give rise to reproductive asymmetries in the earliest stages of the speciation process.© The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Use of whole exome sequencing for the identification of Ito-based arrhythmia mechanism and therapy. - Journal of the American Heart Association
Identified genetic variants are insufficient to explain all cases of inherited arrhythmia. We tested whether the integration of whole exome sequencing with well-established clinical, translational, and basic science platforms could provide rapid and novel insight into human arrhythmia pathophysiology and disease treatment.We report a proband with recurrent ventricular fibrillation, resistant to standard therapeutic interventions. Using whole-exome sequencing, we identified a variant in a previously unidentified exon of the dipeptidyl aminopeptidase-like protein-6 (DPP6) gene. This variant is the first identified coding mutation in DPP6 and augments cardiac repolarizing current (Ito) causing pathological changes in Ito and action potential morphology. We designed a therapeutic regimen incorporating dalfampridine to target Ito. Dalfampridine, approved for multiple sclerosis, normalized the ECG and reduced arrhythmia burden in the proband by >90-fold. This was combined with cilostazol to accelerate the heart rate to minimize the reverse-rate dependence of augmented Ito.We describe a novel arrhythmia mechanism and therapeutic approach to ameliorate the disease. Specifically, we identify the first coding variant of DPP6 in human ventricular fibrillation. These findings illustrate the power of genetic approaches for the elucidation and treatment of disease when carefully integrated with clinical and basic/translational research teams.© 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.
The Carbonic Anhydrase Inhibitor Ethoxzolamide Inhibits the Mycobacterium tuberculosis PhoPR Regulon and Esx-1 Secretion and Attenuates Virulence. - Antimicrobial agents and chemotherapy
Mycobacterium tuberculosis must sense and adapt to host environmental cues to establish and maintain an infection. The two-component regulatory system PhoPR plays a central role in sensing and responding to acidic pH within the macrophage and is required for M. tuberculosis intracellular replication and growth in vivo. Therefore, the isolation of compounds that inhibit PhoPR-dependent adaptation may identify new antivirulence therapies to treat tuberculosis. Here, we report that the carbonic anhydrase inhibitor ethoxzolamide inhibits the PhoPR regulon and reduces pathogen virulence. We show that treatment of M. tuberculosis with ethoxzolamide recapitulates phoPR mutant phenotypes, including downregulation of the core PhoPR regulon, altered accumulation of virulence-associated lipids, and inhibition of Esx-1 protein secretion. Quantitative single-cell imaging of a PhoPR-dependent fluorescent reporter strain demonstrates that ethoxzolamide inhibits PhoPR-regulated genes in infected macrophages and mouse lungs. Moreover, ethoxzolamide reduces M. tuberculosis growth in both macrophages and infected mice. Ethoxzolamide inhibits M. tuberculosis carbonic anhydrase activity, supporting a previously unrecognized link between carbonic anhydrase activity and PhoPR signaling. We propose that ethoxzolamide may be pursued as a new class of antivirulence therapy that functions by modulating expression of the PhoPR regulon and Esx-1-dependent virulence.Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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