GPU-accelerated on-the-fly nonadiabatic semiclassical dynamics.

GPU-accelerated on-the-fly nonadiabatic dynamics is enabled by interfacing the linearized semiclassical dynamics approach with the TeraChem electronic structure program. We describe the computational workflow of the "PySCES" code interface, a Python code for semiclassical dynamics with on-the-fly electronic structure, including parallelization over multiple GPU nodes. We showcase the abilities of this code and present timings for two benchmark systems: fulvene solvated in acetonitrile and a charge transfer system in which a photoexcited zinc-phthalocyanine donor transfers charge to a fullerene acceptor through multiple electronic states on an ultrafast timescale.

Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol.

The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes.

Determination of the cycle threshold value of the Xpert Xpress SARS-CoV-2/Flu/RSV test that corresponds to the presence of infectious SARS-CoV-2 in anterior nasal swabs.

Despite having high analytical sensitivities and specificities, qualitative SARS-CoV-2 nucleic acid amplification tests (NAATs) cannot distinguish infectious from non-infectious virus in clinical samples. In this study, we determined the highest cycle threshold (Ct) value of the SARS-CoV-2 targets in the Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4plex) test that corresponded to the presence of detectable infectious SARS-CoV-2 in anterior nasal swab samples. A total of 111 individuals with nasopharyngeal swab specimens that were initially tested by the Xpert Xpress SARS-CoV-2 test were enrolled.

Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ-sulfanyl-ethan-1-ol (CFSF-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments.

2-Tetrafluoro(trifluoromethyl)-λ-sulfanylethan-1-ol (CFSF-ethanol) combines the polar hydrophobicity of tetrafluoro(trifluoromethyl)-λ-sulfanyl (CFSF) group with the polarity of simple alcohols. The properties of aqueous solutions of the well-known fluorinated alcohols 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) were compared with those of aqueous solutions of the novel CFSF-ethanol. Those properties were computed using all atom molecular dynamics simulations with OPLS-compatible parameters.

Two novel recombinant human mastadenovirus D genotypes associated with acute respiratory illness.

Two novel genotypes of species human mastadenovirus D designated 109 and 110 were isolated from three epidemiologically unrelated cases of acute respiratory disease detected in January 2018 by surveillance efforts at the California/Mexico border. Both genotypes represent examples of intertypic recombination. Genotype D109 is most closely related to genotype D56 (97.

Assessing the use of a micro-sampling device for measuring blood protein levels in healthy subjects and COVID-19 patients.

Background: Venous phlebotomy performed by trained personnel is critical for patient diagnosis and monitoring of chronic disease, but has limitations in resource-constrained settings, and represents an infection control challenge during outbreaks. Self-collection devices have the potential to shift phlebotomy closer to the point of care, supporting telemedicine strategies and virtual clinical trials. Here we assess a capillary blood micro-sampling device, the Tasso Serum Separator Tube (SST), for measuring blood protein levels in healthy subjects and non-hospitalized COVID-19 patients.

Clinical evaluation of the BioFire Global Fever Panel for the identification of malaria, leptospirosis, chikungunya, and dengue from whole blood: a prospective, multicentre, cross-sectional diagnostic accuracy study.

Background: Acute febrile illness is a common presentation for patients at hospitals globally. Assays that can diagnose a variety of common pathogens in blood could help to establish a diagnosis for targeted disease management. We aimed to evaluate the performance of the BioFire Global Fever Panel (GF Panel), a multiplex nucleic acid amplification test performed on whole blood specimens run on the BioFire FilmArray System, in the diagnosis of several pathogens that cause acute febrile illness.

Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches.

RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights.

Department of Defense mid-season vaccine effectiveness estimates for the 2019-2020 influenza season.

This report provides mid-season vaccine effectiveness (VE) estimates from the Armed Forces Health Surveillance Division (AFHSD), the DoD Global Respiratory Pathogen Surveillance (DoDGRS) program, and the Naval Health Research Center (NHRC) for the 2019-2020 influenza season. Using a test negative case-control study design, the AFHSD performed a VE analysis for active component service members while the DoDGRS program and NHRC collaborated to perform a VE analysis for DoD beneficiaries and U.S.

Duration of seropositivity following yellow fever vaccination in U.S. military service members.

Background: The United States military regularly deploys thousands of service members throughout areas of South America and Africa that are endemic for yellow fever (YF) virus. To determine if booster doses might be needed for service members who are repetitively or continually deployed to YF endemic areas, we evaluated seropositivity among US military personnel receiving a single dose of YF vaccine based on time post-vaccination.

Methods: Serum antibodies were measured using a plaque reduction neutralization test with 50% cutoff in 682 military personnel at 5-39 years post-vaccination.

Live Oral Adenovirus Type 4 and Type 7 Vaccine Induces Durable Antibody Response.

Human adenoviruses (AdV) are mostly associated with minimal pathology. However, more severe respiratory tract infections and acute respiratory diseases, most often caused by AdV-4 and AdV-7, have been reported. The only licensed vaccine in the United States, live oral AdV-4 and AdV-7 vaccine, is indicated for use in the military, nearly exclusively in recruit populations.

Human Adenovirus Type 55 Distribution, Regional Persistence, and Genetic Variability.

Human adenovirus type 55 (HAdV-55) causes acute respiratory disease of variable severity and has become an emergent threat in both civilian and military populations. HAdV-55 infection is endemic to China and South Korea, but data from other regions and time periods are needed for comprehensive assessment of HAdV-55 prevalence from a global perspective. In this study, we subjected HAdV-55 isolates from various countries collected during 1969-2018 to whole-genome sequencing, genomic and proteomic comparison, and phylogenetic analyses.

Neutralizing and Neuraminidase Antibodies Correlate With Protection Against Influenza During a Late Season A/H3N2 Outbreak Among Unvaccinated Military Recruits.

Background: Antibodies that inhibit hemagglutination have long been considered a correlate of protection against influenza, but these antibodies are only a subset of potentially protective antibodies. Neutralizing and neuraminidase antibodies may also contribute to protection, but data on their associations with protection are limited.

Methods: We measured preoutbreak hemagglutinin pseudovirus neutralization (PVN) and neuraminidase inhibition (NAI) antibody titers in unvaccinated military recruits who experienced an H3N2 influenza outbreak during training.

Effect of Oral Oseltamivir on Virological Outcomes in Low-risk Adults With Influenza: A Randomized Clinical Trial.

Background: Duration of viral shedding is a determinant of infectivity and transmissibility, but few data exist about oseltamivir's ability to alter viral shedding.

Methods: From January 2012 through October 2017, a randomized, double-blinded multicenter clinical trial was conducted in adults aged 18-64 years at 42 sites in Thailand, the United States, and Argentina. Participants with influenza A or B and without risk factors for complications of influenza were screened for the study.

Department of Defense end-of-season influenza vaccine effectiveness estimates for the 2017-2018 season.

The Department of Defense (DoD) generates influenza vaccine effectiveness (VE) estimates each season. The Armed Forces Health Surveillance Branch Air Force (AFHSB-AF) satellite, Naval Health Research Center Operational Infectious Disease Directorate at the Naval Health Research Center (NHRCOID), and the Armed Forces Health Surveillance Branch (AFHSB) all conduct influenza surveillance and perform test-negative case-control analyses to estimate seasonal influenza VE for DoD populations. The mid-season estimates contribute to the aggregate data utilized by the Food and Drug Administration's Vaccine and Related Biological Products Advisory Committee to select the composition of the influenza vaccine for the next influenza season.

CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry.

A new, multithreaded, trajectory method based software platform, CoSIMS, is revealed and compared to reference MOBCAL collision cross sections (CCS). CoSIMS employs various molecular mechanics algorithms to lessen the computational resources required to simulate thousands of buffer gas-ion collisions, including the neglect of London dispersion interactions at long distances and the removal of trajectories that insignificantly contribute to the total CCS via an ellipsoidal projection approximation. The showcased program is used to calculate the collision cross sections of carbon fullerenes, proteins, and DNA strands of various lengths, sizes, and molecular weights, and these are compared against the CCSs calculated by MOBCAL.

Outbreak of Chlamydia pneumoniae Infections and X-ray-Confirmed Pneumonia in Army Trainees at Fort Leonard Wood, Missouri, 2014.

Introduction: Chlamydia pneumoniae (Cp) is a bacterium that causes pneumonia and other respiratory diseases. Fever may be present early but absent by time of presentation to clinic. Increases in X-ray-confirmed pneumonia (XCP) and laboratory-confirmed Cp infections were observed in new soldiers in training at Fort Leonard Wood (FLW), Missouri, early in 2014.

Surveillance for norovirus and enteric bacterial pathogens as etiologies of acute gastroenteritis at U.S. military recruit training centers, 2011-2016.

An estimated 179 million cases of acute gastroenteritis (AGE) occur each year in the U.S. and AGE is commonly reported within both training and deployed U.

Outbreak of influenza and rhinovirus co-circulation among unvaccinated recruits, U.S. Coast Guard Training Center Cape May, NJ, 24 July-21 August 2016.

Military and Coast Guard recruits are particularly susceptible to respiratory infections. Although seasonal influenza vaccinations are mandatory for recruits, the vaccine expires annually in June. On 29 July 2016, the U.

Influenza vaccine effectiveness: Maintained protection throughout the duration of influenza seasons 2010-2011 through 2013-2014.

Background: Factors, such as age, comorbidities, vaccine type, herd immunity, previous influenza exposure, and antigenic shift may impact the immune response to the influenza vaccine, protection against circulating strains, and antibody waning. Evaluating vaccine effectiveness (VE) is important for informing timing of vaccine administration and evaluating overall vaccine benefit.

Methods: VE was assessed using febrile respiratory illness surveillance among Department of Defense non-active duty beneficiaries from influenza seasons 2010-2011 through 2013-2014.

Respiratory Infections in the U.S. Military: Recent Experience and Control.

This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures.