Last data update: Jan 06, 2025. (Total: 48515 publications since 2009)
Records 1-22 (of 22 Records) |
Query Trace: Chase M[original query] |
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The diabetes technology society error grid and trend accuracy matrix for glucose monitors
Klonoff DC , Freckmann G , Pleus S , Kovatchev BP , Kerr D , Tse CC , Li C , Agus MSD , Dungan K , Voglová Hagerf B , Krouwer JS , Lee WA , Misra S , Rhee SY , Sabharwal A , Seley JJ , Shah VN , Tran NK , Waki K , Worth C , Tian T , Aaron RE , Rutledge K , Ho CN , Ayers AT , Adler A , Ahn DT , Aktürk HK , Al-Sofiani ME , Bailey TS , Baker M , Bally L , Bannuru RR , Bauer EM , Bee YM , Blanchette JE , Cengiz E , Chase JG , YChen K , Cherñavvsky D , Clements M , Cote GL , Dhatariya KK , Drincic A , Ejskjaer N , Espinoza J , Fabris C , Fleming GA , Gabbay MAL , Galindo RJ , Gómez-Medina AM , Heinemann L , Hermanns N , Hoang T , Hussain S , Jacobs PG , Jendle J , Joshi SR , Koliwad SK , Lal RA , Leiter LA , Lind M , Mader JK , Maran A , Masharani U , Mathioudakis N , McShane M , Mehta C , Moon SJ , Nichols JH , O'Neal DN , Pasquel FJ , Peters AL , Pfützner A , Pop-Busui R , Ranjitkar P , Rhee CM , Sacks DB , Schmidt S , Schwaighofer SM , Sheng B , Simonson GD , Sode K , Spanakis EK , Spartano NL , Umpierrez GE , Vareth M , Vesper HW , Wang J , Wright E , Wu AHB , Yeshiwas S , Zilbermint M , Kohn MA . J Diabetes Sci Technol 2024 19322968241275701 INTRODUCTION: An error grid compares measured versus reference glucose concentrations to assign clinical risk values to observed errors. Widely used error grids for blood glucose monitors (BGMs) have limited value because they do not also reflect clinical accuracy of continuous glucose monitors (CGMs). METHODS: Diabetes Technology Society (DTS) convened 89 international experts in glucose monitoring to (1) smooth the borders of the Surveillance Error Grid (SEG) zones and create a user-friendly tool-the DTS Error Grid; (2) define five risk zones of clinical point accuracy (A-E) to be identical for BGMs and CGMs; (3) determine a relationship between DTS Error Grid percent in Zone A and mean absolute relative difference (MARD) from analyzing 22 BGM and nine CGM accuracy studies; and (4) create trend risk categories (1-5) for CGM trend accuracy. RESULTS: The DTS Error Grid for point accuracy contains five risk zones (A-E) with straight-line borders that can be applied to both BGM and CGM accuracy data. In a data set combining point accuracy data from 18 BGMs, 2.6% of total data pairs equally moved from Zones A to B and vice versa (SEG compared with DTS Error Grid). For every 1% increase in percent data in Zone A, the MARD decreased by approximately 0.33%. We also created a DTS Trend Accuracy Matrix with five trend risk categories (1-5) for CGM-reported trend indicators compared with reference trends calculated from reference glucose. CONCLUSION: The DTS Error Grid combines contemporary clinician input regarding clinical point accuracy for BGMs and CGMs. The DTS Trend Accuracy Matrix assesses accuracy of CGM trend indicators. |
Notes from the field: Clinical and epidemiologic characteristics of mpox cases from the initial phase of the outbreak - New York city, May 19-July 15, 2022
Kyaw NTT , Kipperman N , Alroy KA , Baumgartner J , Crawley A , Peterson E , Ross A , Fowler RC , Ruiz VE , Leelawong M , Hughes S , Juste-Tranquille M , Lovingood K , Joe CD , Chase M , Shinall A , Ackelsberg J , Bergeron-Parent C , Badenhop B , Slavinski S , Reddy V , Lee EH . MMWR Morb Mortal Wkly Rep 2022 71 (5152) 1631-1633 Monkeypox virus (MPXV), an Orthopoxvirus that can cause monkeypox (mpox) disease in humans, was rarely seen outside Africa before 2022. Since May 2022, mpox has been reported in multiple countries and regions without endemic transmission, including the United States (1). New York City (NYC) quickly became one of the major foci of the 2022 outbreak after the first case in a NYC resident was diagnosed on May 19.* Epidemiologic profiles and clinical characteristics of mpox cases in the United States during this outbreak have been described (2,3), but previous summaries were limited by incomplete data or inclusion of only a subset of cases (2,3). Most case investigation data from mpox cases reported to the NYC Department of Health and Mental Hygiene (DOHMH) surveillance system have a high degree of completeness for gender, race or ethnicity, sexual orientation, and clinical signs and symptoms. To describe the characteristics of mpox in NYC, case investigation data for NYC residents with mpox diagnosed during May 19–July 15, 2022, were analyzed. Using a standardized form, DOHMH staff members attempted to interview all NYC residents with probable (a positive non-variola Orthopoxvirus polymerase chain reaction [PCR] test result)† or confirmed (a positive MPXV–specific PCR test result) mpox reported to DOHMH through mandated laboratory reporting. For patients who declined an interview or were unreachable, information obtained from medical care providers during DOHMH consultation calls was used. This activity was reviewed by CDC and conducted consistent with applicable federal law and CDC policy.§ |
The future of U.S. Agricultural injury surveillance needs collaboration
Scott E , Weichelt B , Lincoln J . J Agromedicine 2023 28 (1) 11-13 For injury epidemiologists, the hunt for data is an | ongoing detective story. While there is a thrill in the | chase, there is even more satisfaction in using those | data to drive important public health research and | programming. The size of the U.S. agriculture workforce and the declining number of work-related agricultural injuries made annual data collection costly. | Therefore, in 2015, the National Institute for | Occupational Safety and Health (NIOSH) discontinued | interagency agreements with Department of Labor | (DOL) and United States Department of Agriculture | (USDA) to collect national agricultural worker injury | data and developed a plan to seek alternative methods | to obtain quality agricultural injury surveillance data. | However, those means were not the only tool to gather | agricultural injury data, and many alternative efforts | persisted.1 The ethos of the new model seeks to engage | with extramural partners to fill the many identified | gaps in agricultural injury data. While some may long | for the “good old days” of the national injury surveys, | we recognize several factors make such endeavors | impractical. |
Detection of SARS-CoV-2 in Wastewater at Residential College, Maine, USA, August-November 2020.
Brooks YM , Gryskwicz B , Sheehan S , Piers S , Mahale P , McNeil S , Chase J , Webber D , Borys D , Hilton M , Robinson D , Sears S , Smith E , Lesher EK , Wilson R , Goodwin M , Pardales M . Emerg Infect Dis 2021 27 (12) 3111-3114 We used wastewater surveillance to identify 2 coronavirus disease outbreaks at a college in Maine, USA. Cumulative increases of >1 log(10) severe acute respiratory syndrome coronavirus 2 RNA in consecutive 24-hour composite samples preceded the outbreaks. For 76% of cases, RNA was identified in grab samples from residence halls <7 days before case discovery. |
Administration of Bamlanivimab to Skilled Nursing Facility Residents During a COVID-19 Outbreak, January-February 2021, Arizona.
Dale AP , Hudson M , Cullen T , Ellingson K , Davis K , Armenta D , Friebus H , Currie C , Bhattarai R , Brady S , Komatsu K , Stone N , Uyeki T , Slifka KJ , Perez-Velez C , Keaton A . J Am Med Dir Assoc 2021 22 (7) 1357-1358 In November 2020, the Food and Drug Administration (FDA) issued an emergency use authorization (EUA) for bamlanivimab, a monoclonal antibody (mAb), for treatment of mild to moderate COVID-19 in nonhospitalized individuals at high risk for severe disease.1 Since that time, several other mAb therapies, either alone or in combination, have also been issued EUA for use in the treatment of mild-to-moderate COVID-19.2 Although COVID-19 poses a high morbidity and mortality risk among older adult residents of long-term care facilities, reports on mAb use in the management of COVID-19 in skilled nursing facilities (SNFs) are limited, and perceived logistical barriers to on-site infusion of the mAb therapy may reduce their use in these settings.3 , 4 This letter describes the use of bamlanivimab during a large SARS-CoV-2 outbreak at a 270-bed SNF (Facility A). |
Clinical decision support for worker health: A five-site qualitative needs assessment in primary care settings
Ash JS , Chase D , Baron S , Filios MS , Shiffman RN , Marovich S , Wiesen J , Luensman GB . Appl Clin Inform 2020 11 (4) 635-643 BACKGROUND: Although patients who work and have related health issues are usually first seen in primary care, providers in these settings do not routinely ask questions about work. Guidelines to help manage such patients are rarely used in primary care. Electronic health record (EHR) systems with worker health clinical decision support (CDS) tools have potential for assisting these practices. OBJECTIVE: This study aimed to identify the need for, and barriers and facilitators related to, implementation of CDS tools for the clinical management of working patients in a variety of primary care settings. METHODS: We used a qualitative design that included analysis of interview transcripts and observational field notes from 10 clinics in five organizations. RESULTS: We interviewed 83 providers, staff members, managers, informatics and information technology experts, and leaders and spent 35 hours observing. We identified eight themes in four categories related to CDS for worker health (operational issues, usefulness of proposed CDS, effort and time-related issues, and topic-specific issues). These categories were classified as facilitators or barriers to the use of the CDS tools. Facilitators related to operational issues include current technical feasibility and new work patterns associated with the coordinated care model. Facilitators concerning usefulness include users' need for awareness and evidence-based tools, appropriateness of the proposed CDS for their patients, and the benefits of population health data. Barriers that are effort-related include additional time this proposed CDS might take, and other pressing organizational priorities. Barriers that are topic-specific include sensitive issues related to health and work and the complexities of information about work. CONCLUSION: We discovered several themes not previously described that can guide future CDS development: technical feasibility of the proposed CDS within commercial EHRs, the sensitive nature of some CDS content, and the need to assist the entire health care team in managing worker health. |
Proliferation of Aedes aegypti in urban environments mediated by the availability of key aquatic habitats
Wilke ABB , Vasquez C , Carvajal A , Medina J , Chase C , Cardenas G , Mutebi JP , Petrie WD , Beier JC . Sci Rep 2020 10 (1) 12925 Aedes aegypti is the main vector of dengue, Zika, chikungunya, and yellow fever viruses. Controlling populations of vector mosquito species in urban environments is a major challenge and being able to determine what aquatic habitats should be prioritized for controlling Ae. aegypti populations is key to the development of more effective mosquito control strategies. Therefore, our objective was to leverage on the Miami-Dade County, Florida immature mosquito surveillance system based on requested by citizen complaints through 311 calls to determine what are the most important aquatic habitats in the proliferation of Ae. aegypti in Miami. We used a tobit model for Ae. aegypti larvae and pupae count data, type and count of aquatic habitats, and daily rainfall. Our results revealed that storm drains had 45% lower percentage of Ae. aegypti larvae over the total of larvae and pupae adjusted for daily rainfall when compared to tires, followed by bromeliads with 33% and garbage cans with 17%. These results are indicating that storm drains, bromeliads and garbage cans had significantly more pupae in relation to larvae when compared to tires, traditionally know as productive aquatic habitats for Ae. aegypti. Ultimately, the methodology and results from this study can be used by mosquito control agencies to identify habitats that should be prioritized in mosquito management and control actions, as well as to guide and improve policies and increase community awareness and engagement. Moreover, by targeting the most productive aquatic habitats this approach will allow the development of critical emergency outbreak responses by directing the control response efforts to the most productive aquatic habitats. |
Estimated Community Seroprevalence of SARS-CoV-2 Antibodies - Two Georgia Counties, April 28-May 3, 2020.
Biggs HM , Harris JB , Breakwell L , Dahlgren FS , Abedi GR , Szablewski CM , Drobeniuc J , Bustamante ND , Almendares O , Schnall AH , Gilani Z , Smith T , Gieraltowski L , Johnson JA , Bajema KL , McDavid K , Schafer IJ , Sullivan V , Punkova L , Tejada-Strop A , Amiling R , Mattison CP , Cortese MM , Ford SE , Paxton LA , Drenzek C , Tate JE , CDC Field Surveyor Team , Brown Nicole , Chang Karen T , Deputy Nicholas P , Desamu-Thorpe Rodel , Gorishek Chase , Hanchey Arianna , Melgar Michael , Monroe Benjamin P , Nielsen Carrie F , Pellegrini Gerald JJr , Shamout Mays , Tison Laura I , Vagi Sara , Zacks Rachael . MMWR Morb Mortal Wkly Rep 2020 69 (29) 965-970 Transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is ongoing in many communities throughout the United States. Although case-based and syndromic surveillance are critical for monitoring the pandemic, these systems rely on persons obtaining testing or reporting a COVID-19-like illness. Using serologic tests to detect the presence of SARS-CoV-2 antibodies is an adjunctive strategy that estimates the prevalence of past infection in a population. During April 28-May 3, 2020, coinciding with the end of a statewide shelter-in-place order, CDC and the Georgia Department of Public Health conducted a serologic survey in DeKalb and Fulton counties in metropolitan Atlanta to estimate SARS-CoV-2 seroprevalence in the population. A two-stage cluster sampling design was used to randomly select 30 census blocks in each county, with a target of seven participating households per census block. Weighted estimates were calculated to account for the probability of selection and adjusted for age group, sex, and race/ethnicity. A total of 394 households and 696 persons participated and had a serology result; 19 (2.7%) of 696 persons had SARS-CoV-2 antibodies detected. The estimated weighted seroprevalence across these two metropolitan Atlanta counties was 2.5% (95% confidence interval [CI] = 1.4-4.5). Non-Hispanic black participants more commonly had SARS-CoV-2 antibodies than did participants of other racial/ethnic groups (p<0.01). Among persons with SARS-CoV-2 antibodies, 13 (weighted % = 49.9; 95% CI = 24.4-75.5) reported a COVID-19-compatible illness,* six (weighted % = 28.2; 95% CI = 11.9-53.3) sought medical care for a COVID-19-compatible illness, and five (weighted % = 15.7; 95% CI = 5.1-39.4) had been tested for SARS-CoV-2 infection, demonstrating that many of these infections would not have been identified through case-based or syndromic surveillance. The relatively low seroprevalence estimate in this report indicates that most persons in the catchment area had not been infected with SARS-CoV-2 at the time of the survey. Continued preventive measures, including social distancing, consistent and correct use of face coverings, and hand hygiene, remain critical in controlling community spread of SARS-CoV-2. |
Lessons learned from the implementation of HIV biological-behavioral surveys of key populations in the Caribbean
Volkmann T , Chase M , Lockard AM , Henningham D , Albalak R . AIDS Educ Prev 2018 30 (6) 528-541 In the Caribbean region, HIV prevalence is high among key population (KP) groups, such as sex workers and men who have sex with men. However, there is a lack of high-quality, population-level data estimating HIV prevalence and population sizes of KPs. The President's Emergency Plan for AIDS Relief has funded and completed five bio-behavioral surveillance (BBS) surveys using respondent-driven sampling methodology to target KP in the English-speaking Caribbean region. We describe the experience of implementing bio-behavioral surveys in the Caribbean region and document the context, processes, successes, and challenges, and make recommendations for future survey implementation. Successes include the provision of estimates of nationally representative HIV data and KP size estimates to improve HIV programming and provision of tools for routinization of BBS. Challenges include small KP sizes, the legal context, and the cost and speed of implementation. Future bio-behavioral surveys should include well-planned formative assessments and stakeholder involvement. |
Mumps outbreak in a Marshallese community - Denver Metropolitan Area, Colorado, 2016-2017
Marx GE , Burakoff A , Barnes M , Hite D , Metz A , Miller K , Davizon ES , Chase J , McDonald C , McClean M , Miller L , Albanese BA . MMWR Morb Mortal Wkly Rep 2018 67 (41) 1143-1146 In January 2017, the Colorado Department of Public Health and Environment (CDPHE) identified four epidemiologically linked cases of mumps among persons from a Marshallese community who were members of the same church in the Denver metropolitan area. During 2016-2017, sizable outbreaks of mumps reported in Arkansas, Hawaii, and Washington also affected the Marshallese population (1). CDPHE, the Tri-County Health Department (TCHD), and Denver Public Health collaborated to conduct an outbreak investigation during January-March 2017 using active and passive surveillance that identified 17 confirmed and 30 probable cases. Public health actions included conducting measles-mumps-rubella (MMR) vaccination clinics at local Marshallese churches; these resulted in the vaccination of 126 persons with >/=1 doses of MMR vaccine. Implementation of active surveillance and support from local Marshallese church leaders in promoting vaccination programs likely contributed to interruption of the outbreak. |
Capsule-Negative emm Types Are an Increasing Cause of Pediatric Group A Streptococcal Infections at a Large Pediatric Hospital in Texas.
Flores AR , Chase McNeil J , Shah B , Van Beneden C , Shelburne SA3rd . J Pediatric Infect Dis Soc 2018 8 (3) 244-250 Background: Bacterial infections caused by group A Streptococcus (GAS) are common in childhood. Few study reports have provided data on pediatric-specific trends in the epidemiology and bacterial strain characteristics of GAS infections. Methods: We prospectively collected GAS isolates from the clinical microbiology laboratory at Texas Children's Hospital between July 1, 2013, and June 30, 2017. Patient characteristics and GAS disease categories were determined through chart review. GAS isolates were obtained from patients in either the inpatient or outpatient setting, and cases were defined as pharyngeal disease, skin and soft-tissue infection (SSTI), or invasive disease on the basis of predefined criteria. All isolates were emm typed to determine trends over time. Results: We identified 930 cases over the 4-year period, including 432 (46.4%) pharyngeal, 235 (25.3%) SSTI, and 263 (28.3%) invasive disease types. The most frequently encountered emm types were emm1 (21.4%), emm12 (15.7%), emm89 (14.6%), emm4 (9.2%), and emm3 (8.2%). We observed significant changes over the 4-year period in the relative frequency of infections caused by emm1 (-17.7%; P = .046), emm4 (8.7%; P = .023), or emm6 (-7.9%; P = .024). Using bioinformatic analyses and targeted gene sequencing, we also discovered that all GAS emm28 and emm87 types harbored mutations that rendered them incapable of producing capsule. The relative frequency of GAS disease cases caused by capsule-negative GAS emm types (emm4, emm22, emm28, emm87, and emm89) increased over the 4-year period (32.2%-44.4%), although the difference was statistically significant for only nonpharyngeal disease types (27.1%-43.9%; P = .038). Conclusions: Our data suggest an evolving epidemiology of GAS in the Houston pediatric population characterized by an increase in the frequency of capsule-negative emm types. |
Public health economic burden associated with two single measles case investigations - Colorado, 2016-2017
Marx GE , Chase J , Jasperse J , Stinson K , McDonald CE , Runfola JK , Jaskunas J , Hite D , Barnes M , Askenazi M , Albanese B . MMWR Morb Mortal Wkly Rep 2017 66 (46) 1272-1275 During July 2016-January 2017, two unrelated measles cases were identified in the Denver, Colorado area after patients traveled to countries with endemic measles transmission. Each case resulted in multiple exposures at health care facilities and public venues, and activated an immediate and complex response by local and state public health agencies, with activities led by the Tri-County Health Department (TCHD), which serves Adams, Arapahoe, and Douglas counties. To track the economic burden associated with investigating and responding to single measles cases, personnel hours and supply costs incurred during each investigation were tracked prospectively. No secondary cases of measles were identified in either investigation. Postexposure prophylaxis (PEP) was administered to 31 contacts involving the first case; no contacts of the second case were eligible for PEP because of a delay in diagnosing measles disease. Public health costs of disease investigation in the first and second case were estimated at $49,769 and $18,423, respectively. Single measles cases prompted coordinated public health action and were costly and resource-intensive for local public health agencies. |
Recognition of the relationship between patients' work and health: A qualitative evaluation of the need for clinical decision support (CDS) for worker health in five primary care practices
Baron S , Filios MS , Marovich S , Chase D , Ash JS . J Occup Environ Med 2017 59 (11) e245-e250 OBJECTIVE: The aim of this study was to determine the perceived value and feasibility of increased access to information about workers' health for primary care providers (PCPs) by evaluating the need for clinical decision support (CDS) related to worker health in primary care settings. METHODS: Qualitative methods, including semi-structured interviews and observations, were used to evaluate the value and feasibility of three examples of CDS relating work and health in five primary care settings. RESULTS: PCPs and team members wanted help addressing patients' health in relation to their jobs; the proposed CDS examples were perceived as valuable because they provided useful information, promoted standardization of care, and were considered technically feasible. Barriers included time constraints and a perceived inability to act on the findings. CONCLUSION: PCPs recognize the importance and impact of work on their patients' health but often lack accessible knowledge at the right time. Occupational health providers can play an important role through contributions to the development of CDS that assists PCPs in recognizing and addressing patients' health, as well as through the provision of referral guidelines. |
Improving laboratory efficiency in the Caribbean to attain the World Health Organization HIV Treat All recommendations
Alemnji GA , Chase M , Branch S , Guevara G , Nkengasong JN , Albalak R . AIDS Res Hum Retroviruses 2017 34 (2) 132-139 Scientific evidence showing the benefits of early initiation of antiretroviral therapy (ART) prompted World Health organization (WHO) to recommend that all persons diagnosed HIV-positive should commence ART irrespective of CD4 count and disease progression. Based on this recommendation, countries should adopt and implement the HIV "Treat All" policy to achieve the UNAIDS 90-90-90 targets and ultimately reach epidemic control. Attaining this goal along the HIV treatment cascade depends on the laboratory to monitor progress and measure impact. The laboratory plays an important role in HIV diagnosis to attain the first 90 and in viral load (VL) and HIV drug resistance testing to reinforce adherence, improve viral suppression, and measure the third 90. Countries in the Caribbean region have endorsed the WHO HIV "Treat all" recommendation; however, they are faced with diminishing financial resources to support laboratory testing, seen as a rate-limiting factor to achieving this goal. To improve laboratory coverage with fewer resources in the Caribbean there is the need to optimise laboratory operations to ensure the implementation of high quality, less expensive, evidence-based approaches that will result in more efficient and effective service delivery. Suggested practical and innovative approaches to achieve this include: 1) targeted testing within HIV hotspots; 2) strengthening sample referral systems for VL; 3) better laboratory data collection systems; and 4) use of treatment cascade data for programmatic decision making. Furthermore, strengthening quality improvement and procurement systems will minimize diagnostic errors and guarantee a continuum of uninterrupted testing which is critical for routine monitoring of patients to meet the stated goal. |
Characteristics of fentanyl overdose - Massachusetts, 2014-2016
Somerville NJ , O'Donnell J , Gladden RM , Zibbell JE , Green TC , Younkin M , Ruiz S , Babakhanlou-Chase H , Chan M , Callis BP , Kuramoto-Crawford J , Nields HM , Walley AY . MMWR Morb Mortal Wkly Rep 2017 66 (14) 382-386 Opioid overdose deaths in Massachusetts increased 150% from 2012 to 2015 (1). The proportion of opioid overdose deaths in the state involving fentanyl, a synthetic, short-acting opioid with 50-100 times the potency of morphine, increased from 32% during 2013-2014 to 74% in the first half of 2016 (1-3). In April 2015, the Drug Enforcement Agency (DEA) and CDC reported an increase in law enforcement fentanyl seizures in Massachusetts, much of which was believed to be illicitly manufactured fentanyl (IMF) (4). To guide overdose prevention and response activities, in April 2016, the Massachusetts Department of Public Health and the Office of the Chief Medical Examiner collaborated with CDC to investigate the characteristics of fentanyl overdose in three Massachusetts counties with high opioid overdose death rates. In these counties, medical examiner charts of opioid overdose decedents who died during October 1, 2014-March 31, 2015 were reviewed, and during April 2016, interviews were conducted with persons who used illicit opioids and witnessed or experienced an opioid overdose. Approximately two thirds of opioid overdose decedents tested positive for fentanyl on postmortem toxicology. Evidence for rapid progression of fentanyl overdose was common among both fatal and nonfatal overdoses. A majority of interview respondents reported successfully using multiple doses of naloxone, the antidote to opioid overdose, to reverse suspected fentanyl overdoses. Expanding and enhancing existing opioid overdose education and prevention programs to include fentanyl-specific messaging and practices could help public health authorities mitigate adverse effects associated with overdoses, especially in communities affected by IMF. |
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.
Flygare S , Simmon K , Miller C , Qiao Y , Kennedy B , Di Sera T , Graf EH , Tardif KD , Kapusta A , Rynearson S , Stockmann C , Queen K , Tong S , Voelkerding KV , Blaschke A , Byington CL , Jain S , Pavia A , Ampofo K , Eilbeck K , Marth G , Yandell M , Schlaberg R . Genome Biol 2016 17 (1) 111 BACKGROUND: High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption. RESULTS: We present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface. CONCLUSIONS: Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices. |
Comparative dissolution of electrospun Al2O3 nanofibres in artificial human lung fluids
Shin HU , Stefaniak AB , Stojilovic N , Chase GG . Environ Sci Nano 2015 2 (3) 251-261 Sub-micron sized alumina fibres were fabricated by electrospinning and calcination of a polymer template fibre. In the calcination step, different controlled temperature heating cycles were conducted to obtain fibres of different crystalline structures. Their biodurabilities were tested at pH 7.4 with lung airway epithelial lining fluid or serum ultrafiltrate (SUF) and at pH 4.5 with macrophage phagolysosomal simulant fluid (PSF). Potential to generate free radicals was tested in vitro. Through the variation in the soak temperature from 650 [degree]C to 950 [degree]C (experiments S650-S950), the heating protocol affected the morphological characteristics, crystal structure, surface area, and density of the alumina fibres while their dissolution half-times were not significantly affected in SUF or PSF. Fibre samples formed at different heating ramp rates (experiments R93-R600) showed significant variation in the dissolution rates with the highest ramp rate corresponding to the highest dissolution rate. Thus, by increasing the calcination temperature ramp rate the alumina fibres may be produced that have reduced biodurability and lower inflammogenic potential. The fibres with the highest dissolution rated had the least aluminium content. The solubility half-times of the alumina fibres were shortest for fibres calcined at the fastest temperature ramp rate (though soak temperature did not have an effect). The ramp rates also affected the aluminium content of the fibres suggesting that the content may affect the structural strength of the fibres and control the dissolution. |
Differences in type I interferon signaling antagonism by dengue viruses in human and non-human primate cell lines
Medina FA , Torres-Malave G , Chase AJ , Santiago GA , Medina JF , Santiago LM , Munoz-Jordan JL . PLoS Negl Trop Dis 2015 9 (3) e0003468 BACKGROUND/OBJECTIVES: In vitro studies have shown that dengue virus (DENV) can thwart the actions of interferon (IFN)-alpha/beta and prevent the development of an antiviral state in infected cells. Clinical studies looking at gene expression in patients with severe dengue show a reduced expression of interferon stimulated genes compared to patients with dengue fever. Interestingly, there are conflicting reports as to the ability of DENV or other flaviviruses to inhibit IFN-alpha/beta signaling. METHODOLOGY/PRINCIPAL FINDINGS: In order to determine the relative inhibition of IFN-alpha/beta signaling by DENVs, a method combining flow cytometry and a four-parameter logistic regression model was established. A representative isolate from DENV-1, -3 and -4 and seventeen representative isolates encompassing all DENV-2 genotypes were evaluated. All of the DENVs evaluated in this study were capable of inhibiting IFN-alpha/beta signaling. Most of the strains were able to inhibit IFN-alpha/beta to a degree similar to DENV strain 16681; however, DENV-2 sylvatic strains demonstrated an increased inhibition of phosphorylated signal transducer and activator of transcription (pSTAT1). Surprisingly, we were unable to observe inhibition of pSTAT1 by DENV-2 sylvatic strains or the Asian strain 16681 in non-human primate (NHP) cell lines. Analysis in primary Rhesus macaque dendritic cells suggests that DENVs are capable of inhibiting IFN signaling in these cells. However, contrary to human dendritic cells, production of IFN-alpha was detected in the supernatant of DENV-infected Rhesus macaque dendritic cells. CONCLUSIONS: The ability of DENVs to inhibit IFN-alpha/beta signaling is conserved. Although some variation in the inhibition was observed, the moderate differences may be difficult to correlate with clinical outcomes. DENVs were unable to inhibit pSTAT1 in NHP cell lines, but their ability to inhibit pSTAT1 in primary Rhesus macaque dendritic cells suggests that this may be a cell specific phenomena or due to the transformed nature of the cell lines. |
Placental malaria is rare among Zanzibari pregnant women who did not receive intermittent preventive treatment in pregnancy
Plotkin M , Said K , Msellem MI , Chase RP , Hendler N , Khamis AR , Roman E , Kitojo C , Schwartz AC , Gutman J , McElroy PD . Am J Trop Med Hyg 2014 91 (2) 367-373 Zanzibar has transitioned from malaria control to the pre-elimination phase, and the continued need for intermittent preventive treatment during pregnancy (IPTp) has been questioned. We conducted a prospective observational study to estimate placental malaria positivity rate among women who did not receive IPTp with sulfadoxine-pyrimethamine. A convenience sample of pregnant women was enrolled from six clinics on the day of delivery from August of 2011 to September of 2012. Dried placental blood spot specimens were analyzed by polymerase chain reaction (PCR); 9 of 1,349 specimens (0.7%; precision estimate = 0.2-1.1%) were PCR-positive for Plasmodium falciparum. Placental infection was detected on both Pemba (N = 3) and Unguja (N = 6). Placental malaria positivity in Zanzibar was low, even in the absence of IPTp. It may be reasonable for the Ministry of Health to consider discontinuing IPTp, intensifying surveillance efforts, and promoting insecticide-treated nets and effective case management of malaria in pregnancy. |
Impairment of CD4+ T cell polarization by dengue virus-infected dendritic cells
Chase AJ , Medina FA , Munoz-Jordan JL . J Infect Dis 2011 203 (12) 1763-74 BACKGROUND: The production of type I interferon alpha/beta (IFN-alpha/beta) is crucial to viral clearance during dengue virus (DENV) infection; however, in vitro-infected dendritic cells (DCs) exhibit a decreased capacity to respond to IFN-alpha/beta stimulation, and antigen-presenting cells (APCs) isolated from patients with acute DENV infection exhibit defects in T cell priming. METHODS: In order to ascertain the stimulatory capacity of primary human monocyte-derived DCs infected with wild-type DENV isolates, representing a range of genotypes and disease outcomes, we cocultured infected DCs with allogeneic-naive CD4(+) T cells. The gene expression patterns of IFN-alpha/beta sensitive genes were quantitated to determine if the infected DCs displayed a blunted IFN-alpha/beta response. RESULTS: DENV-infected DCs induced the initial proliferation of naive CD4(+) T cells but they remained nonpolarized in effector function. The expression of IFN-alpha/beta-stimulated genes was downregulated, revealing that the inhibition of IFN-alpha/beta signaling is conserved among endemic DENV serotype 2 strains. CONCLUSIONS: The failure of naive CD4(+) T cells to differentiate into IFN gamma-producing effector T cells when primed by DENV-infected DCs cannot be explained solely by a block in IFN-alpha/beta signaling, suggesting that the ability of DENV to evade the early host response is multifaceted. |
Transforming strategies for the prevention of chronic HBV and HCV infections
Ward JW , Hu DJ , Alter MJ , Kanwal F , Taylor C , Block JM , Caballero JB , Chase D , Saly M , Sandt L , Swan T . J Fam Pract 2010 59 S23-8 The article focuses on the prevention of chronic hepatitis B and C virus (HBV and HCV) infections in the U.S. It discusses the global implication of the pandemic chronic viral infections, prevention strategies for HBV infection using the framework of the Centers for Disease Control and Prevention (CDC), and the HCV in quality indicators which include confirmation of HCV viremia, hepatitis A and HBV vaccinations, counseling, and treatment with the Department of Health and Human Services Centers. |
Revival and emended description of 'Mycobacterium paraffinicum' (Davis, Chase and Raymond 1956) as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev
Toney NC , Adekambi T , Toney S , Yakrus M , Butler WR . Int J Syst Evol Microbiol 2009 60 (10) 2307-2313 The omission of the name 'Mycobacterium paraffinicum' from the 1980 Approved List of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly 'M. paraffinicum' strains grew slowly in >7 days, stained acid-alcohol fast, produced yellow-pigmented smooth waxy colonies in the dark at an optimal temperature of 35 degrees C. However 'M. paraffinicum' strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase, and lacked growth at 42 degrees C as compared to M. scrofulaceum. The mycolic acid pattern as determined by high performance liquid chromatography (HPLC) clustered 'M. paraffinicum' with M. scrofulaceum, Mycobacterium avium, and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of 'M. paraffinicum' ATCC 12670 and five additional isolates using comparative gene studies with 16S rRNA, hsp65, rpoB and concatenated sequences demonstrated separate, monophyletic tree branching that was distinct from similar nontuberculous mycobacteria and formed a tight taxonomical group with the classical reference strain of 'M. paraffinicum'. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of 'M. paraffinicum' with a genetic distance of 0.12 and was distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of the slow-growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain located in the worldwide collections as the type strain ATCC 12670T =DSM 44181T =NCIMB10420T. |
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