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. Our implementation paves the way for an efficient semiclassical approach to model the nonadiabatic excited state dynamics of complex molecules, materials, and condensed phase systems.

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. 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 force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. The strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.

Introduction to the Emerging Cognitive Science of Distributed Human-Autonomy Teams.

Teams are a fundamental aspect of life-from sports to business, to defense, to science, to education. While the cognitive sciences tend to focus on information processing within individuals, others have argued that teams are also capable of demonstrating cognitive capacities similar to humans, such as skill acquisition and forgetting (cf., Cooke, Gorman, Myers, & Duran, 2013; Fiore et al., 2010). As artificially intelligent and autonomous systems improve in their ability to learn, reason, interact, and coordinate with human teammates combined with the observation that teams can express cognitive capacities typically seen in individuals, a cognitive science of teams is emerging. Consequently, new questions are being asked about teams regarding teamness, trust, the introduction and effects of autonomous systems on teams, and how best to measure team behavior and phenomena. In this topic, four facets of human-autonomy team cognition are introduced with leaders in the field providing in-depth articles associated with one or more of the facets: (1) defining teams; (2) how trust is established, maintained, and repaired when broken; (3) autonomous systems operating as teammates; and (4) metrics for evaluating team cognition across communication, coordination, and performance.

Characteristics of healthcare personnel with SARS-CoV-2 infection: 10 emerging infections program sites in the United States, April 2020-December 2021.

BACKGROUND: Understanding characteristics of healthcare personnel (HCP) with SARS-CoV-2 infection supports the development and prioritization of interventions to protect this important workforce. We report detailed characteristics of HCP who tested positive for SARS-CoV-2 from April 20, 2020 through December 31, 2021. METHODS: CDC collaborated with Emerging Infections Program sites in 10 states to interview HCP with SARS-CoV-2 infection (case-HCP) about their demographics, underlying medical conditions, healthcare roles, exposures, personal protective equipment (PPE) use, and COVID-19 vaccination status. We grouped case-HCP by healthcare role. To describe residential social vulnerability, we merged geocoded HCP residential addresses with CDC/ATSDR Social Vulnerability Index (SVI) values at the census tract level. We defined highest and lowest SVI quartiles as high and low social vulnerability, respectively. RESULTS: Our analysis included 7,531 case-HCP. Most case-HCP with roles as certified nursing assistant (CNA) (444, 61.3%), medical assistant (252, 65.3%), or home healthcare worker (HHW) (225, 59.5%) reported their race and ethnicity as either non-Hispanic Black or Hispanic. More than one third of HHWs (166, 45.2%), CNAs (283, 41.7%), and medical assistants (138, 37.9%) reported a residential address in the high social vulnerability category. The proportion of case-HCP who reported using recommended PPE at all times when caring for patients with COVID-19 was lowest among HHWs compared with other roles. CONCLUSIONS: To mitigate SARS-CoV-2 infection risk in healthcare settings, infection prevention, and control interventions should be specific to HCP roles and educational backgrounds. Additional interventions are needed to address high social vulnerability among HHWs, CNAs, and medical assistants.

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. A healthcare worker subsequently collected anterior nasal swabs from all SARS-CoV-2-positive individuals, and those specimens were tested by the Xpert 4plex test, viral culture, and laboratory-developed assays for SARS-CoV-2 replication intermediates. SARS-CoV-2 Ct values from the Xpert 4plex test were correlated with data from culture and replication intermediate testing to determine the Xpert 4plex assay Ct value that corresponded to the presence of infectious virus. Ninety-eight of the 111 (88.3%) individuals initially tested positive by the Xpert Xpress SARS-CoV-2 test. An anterior nasal swab specimen collected from positive individuals a median of 2 days later (range, 0-9 days) tested positive for SARS-CoV-2 by the Xpert 4plex test in 39.8% (39/98) of cases. Of these samples, 13 (33.3%) were considered to contain infectious virus based on the presence of cultivable virus and replication intermediates, and the highest Ct value observed for the Xpert 4plex test in these instances was 26.3. Specimens that yielded Ct values of ≤26.3 when tested by the Xpert 4plex test had a likelihood of containing infectious SARS-CoV-2; however, no infectious virus was detected in specimens with higher Ct values.IMPORTANCEUnderstanding the correlation between real-time PCR test results and the presence of infectious SARS-CoV-2 may be useful for informing patient management and workforce return-to-work or -duty. Further studies in different patient populations are needed to correlate Ct values or other biomarkers of viral replication along with the presence of infectious virus in clinical samples.

Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters.

Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases. If a metric of interest directly compares infected and uninfected populations, calculated detection probabilities for both groups may be useful in identifying bias. Here, we use an individual-based simulation to test whether changes in capture rate due to infection can alter estimates of three key metrics: 1) reduction in the reproductive success of infected parents relative to uninfected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) changes in allele frequencies between generations. We explore the direction and underlying causes of the biases that emerge from these simulations. Finally, we argue that short series of mark-recapture sampling bouts, potentially implemented in under a week, can yield key data on detection bias due to infection while not adding a significantly higher burden to disease ecology studies.

Sociodemographic and Occupational Characteristics Associated with Early and Continued COVID-19 Vaccine Uptake Among Healthcare Personnel: Monroe County, NY.

OBJECTIVE: Identify characteristics of healthcare personnel (HCP) who did not have timely initiation of the COVID-19 primary series, as well as HCP who did not receive a booster vaccine. METHODS: Characteristics of HCP enrolled in a COVID-19 vaccine effectiveness study between 12/28/2020-12/01/2022 were compared by timing of receipt of 1st mRNA dose, and by receipt of a booster dose. Data for this retrospective cohort analysis came from HCP working at a large healthcare system in Monroe County, New York, and included standardized questionnaires and verified vaccination status. HCP were categorized by whether they received their 1stmRNA COVID-19 vaccine between 12/14/2020-03/30/2021 (earlier) or 04/01/2021-09/28/2021 (later) based on timing of local vaccine eligibility and mandates, and by whether they received a 3rdmRNA booster dose by 12/01/22. Logistic regression models were run to identify characteristics of HCP who had later 1stdose receipt or did not receive a booster. RESULTS: 3,375 HCP were enrolled. Of these, 86.8 % had early initiation of their 1stCOVID-19 vaccine, and 85.0 % received a booster dose. Low education, low household income, younger age (<50), non-White race and public health insurance were all significant predictors of later receipt of 1stdose and lack of uptake of a booster. However, advanced professional role was only found to be a significant predictor of early 1stdose receipt. CONCLUSIONS: Continual monitoring of COVID-19 vaccine uptake among HCP to identify those less likely to receive new booster doses will be crucial to support targeted vaccine campaigns in this important population.

Residential social vulnerability among healthcare personnel with and without severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection in Five US states, May-December 2020.

OBJECTIVE: To characterize residential social vulnerability among healthcare personnel (HCP) and evaluate its association with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection. DESIGN: Case-control study. SETTING: This study analyzed data collected in May-December 2020 through sentinel and population-based surveillance in healthcare facilities in Colorado, Minnesota, New Mexico, New York, and Oregon. PARTICIPANTS: Data from 2,168 HCP (1,571 cases and 597 controls from the same facilities) were analyzed. METHODS: HCP residential addresses were linked to the social vulnerability index (SVI) at the census tract level, which represents a ranking of community vulnerability to emergencies based on 15 US Census variables. The primary outcome was SARS-CoV-2 infection, confirmed by positive antigen or real-time reverse-transcriptase- polymerase chain reaction (RT-PCR) test on nasopharyngeal swab. Significant differences by SVI in participant characteristics were assessed using the Fisher exact test. Adjusted odds ratios (aOR) with 95% confidence intervals (CIs) for associations between case status and SVI, controlling for HCP role and patient care activities, were estimated using logistic regression. RESULTS: Significantly higher proportions of certified nursing assistants (48.0%) and medical assistants (44.1%) resided in high SVI census tracts, compared to registered nurses (15.9%) and physicians (11.6%). HCP cases were more likely than controls to live in high SVI census tracts (aOR, 1.76; 95% CI, 1.37-2.26). CONCLUSIONS: These findings suggest that residing in more socially vulnerable census tracts may be associated with SARS-CoV-2 infection risk among HCP and that residential vulnerability differs by HCP role. Efforts to safeguard the US healthcare workforce and advance health equity should address the social determinants that drive racial, ethnic, and socioeconomic health disparities.

Effectiveness of a bivalent mRNA vaccine dose against symptomatic SARS-CoV-2 infection among U.S. Healthcare personnel, September 2022-May 2023.

BACKGROUND: Bivalent mRNA vaccines were recommended since September 2022. However, coverage with a recent vaccine dose has been limited, and there are few robust estimates of bivalent VE against symptomatic SARS-CoV-2 infection (COVID-19). We estimated VE of a bivalent mRNA vaccine dose against COVID-19 among eligible U.S. healthcare personnel who had previously received monovalent mRNA vaccine doses. METHODS: We conducted a case-control study in 22 U.S. states, and enrolled healthcare personnel with COVID-19 (case-participants) or without COVID-19 (control-participants) during September 2022-May 2023. Participants were considered eligible for a bivalent mRNA dose if they had received 2-4 monovalent (ancestral-strain) mRNA vaccine doses, and were ≥67 days after the most recent vaccine dose. We estimated VE of a bivalent mRNA dose using conditional logistic regression, accounting for matching by region and four-week calendar period. We adjusted estimates for age group, sex, race and ethnicity, educational level, underlying health conditions, community COVID-19 exposure, prior SARS-CoV-2 infection, and days since the last monovalent mRNA dose. RESULTS: Among 3,647 healthcare personnel, 1,528 were included as case-participants and 2,119 as control-participants. Participants received their last monovalent mRNA dose a median of 404 days previously; 1,234 (33.8%) also received a bivalent mRNA dose a median of 93 days previously. Overall, VE of a bivalent dose was 34.1% (95% CI, 22.6%-43.9%) against COVID-19 and was similar by product, days since last monovalent dose, number of prior doses, age group, and presence of underlying health conditions. However, VE declined from 54.8% (95% CI, 40.7%-65.6%) after 7-59 days to 21.6% (95% CI 5.6%-34.9%) after ≥60 days. CONCLUSIONS: Bivalent mRNA COVID-19 vaccines initially conferred approximately 55% protection against COVID-19 among U.S. healthcare personnel. However, protection waned after two months. These findings indicate moderate initial protection against symptomatic SARS-CoV-2 infection by remaining up-to-date with COVID-19 vaccines.

A Time for Every Purpose: Using Time-Dependent Sensitivity Analysis to Help Understand and Manage Dynamic Ecological Systems.

AbstractSensitivity analysis is often used to help understand and manage ecological systems by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time-for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act on. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life history events, and endogenously driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.

Profiling cognitive workload in an unmanned vehicle control task with cognitive models and physiological metrics.

In the present study, we use Cognitive Metrics Profiling (CMP) to capture variance in cognitive load within a complex unmanned vehicle control task. We aim to demonstrate convergent validity with existing workload measurement methods, and to decompose workload into constituent cognitive resources to aid in diagnosing causes of workload. A cognitive model of the task was developed and examined to determine the extent to which it could predict behavioral performance, subjective workload, and validated physiological workload metrics. We also examined model activity to draw insights regarding loaded cognitive capacities. We found that composite workload from the model predicted physiological metrics, performance, and subjective workload. Moreover, the model indicates that differences in workload were driven largely by procedural, declarative, and temporal memory demands. We have found preliminary evidence of correspondence between workload predictions of a CMP model and physiological measures of workload. This suggests our approach captures interesting aspects of workload in a complex task environment and may provide a theoretical link between behavioral, physiological, and subjective metrics. This approach may provide a means to design effective workload mitigation interventions and improve decision-making about personnel tasking and automation.

Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ6-sulfanyl-ethan-1-ol (CF3SF4-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments.

2-Tetrafluoro(trifluoromethyl)-λ6-sulfanylethan-1-ol (CF3SF4-ethanol) combines the polar hydrophobicity of tetrafluoro(trifluoromethyl)-λ6-sulfanyl (CF3SF4) 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 CF3SF4-ethanol. Those properties were computed using all atom molecular dynamics simulations with OPLS-compatible parameters. DFT ab initio calculations were used to accurately describe the nonsymmetrical, hypervalent sulfur in CF3SF4-ethanol. Although the molecular and conformational characteristics of CF3SF4-ethanol are like those of both TFE and HFIP, the greater hydrophobicity and lower polarity of CF3SF4-ethanol resulted in solution phase aggregation at a much lower concentration. The properties computed for TFE and HFIP in this work were consistent with published computational and experimental studies. CF3SF4-ethanol is predicted to be environmentally benign and hence an excellent green solvent candidate while possessing many of the same properties as TFE or HFIP.

Defining a Relationship Between Postoperative Antibiotic Use and Wound Complications in the Setting of an Uncomplicated Laparoscopic Appendectomy.

INTRODUCTION: Appendicitis is a very common diagnosis that surgeons manage daily. Some surgeons are still giving antibiotics to patients suffering from uncomplicated appendicitis in the postoperative setting, despite an abundance of evidence to support a single preoperative dose of antibiotics. In this paper, we will describe the management of post-operative antibiotics at our institutions following uncomplicated appendicitis with regard to the use of antibiotics in the post-operative setting. METHODS: A retrospective chart review was performed analyzing post-operative antibiotic use and postoperative complications in 179 patients undergoing laparoscopic appendectomy for uncomplicated appendicitis. We retrospectively examined the patients to change our future practices as we perform appendectomies routinely, and there is practice variation at our centers. Current Procedural Terminology (CPT) codes for 'laparoscopic appendectomy' were used to identify the patients within our inclusion criteria. Twenty-four patients were excluded from the analysis as they had complicated appendicitis or met other exclusion criteria. We only studied the patient with uncomplicated appendicitis, as those with complicated appendicitis have a different clinical course that involves post-operative antibiotic administration or prolonged antibiotic administration with or without drain placement. Both arms of the study were homogeneous regarding patient characteristics. An independent test of the development of wound infection for those patients receiving post-operative antibiotics versus those not receiving post-operative antibiotics was conducted using the SPC XL 2010 Microsoft Excel (Redmond, USA) add-in. A p-value of <0.05 was considered statistically significant. This included the odds ratio for the development of complications.  Results: There was no difference in the risk of infection rate in patients given post-operative antibiotics; however, given the odds ratio of 6.53, there is an association between an increased wound infection rate and patients who received post-operative antibiotics.  Discussion: An appendectomy is a standard surgical procedure for acute appendicitis. The guidelines for using pre-operative antibiotics in uncomplicated appendicitis are well established; however, there is no specific recommendation on whether to continue antibiotics post-operatively. However, there is significant provider variability on this topic. Antibiotic use post-operatively in clean-contaminated cases, such as uncomplicated acute appendicitis, has been associated with higher risks of surgical site infections.  Conclusion: The use of antibiotics post-operatively may not be indicated for uncomplicated laparoscopic appendectomy and may increase wound infections. A large-scale study including a larger population and extending it to other hospitals may increase statistical significance and help guide physician management.

Predicting and Controlling Spillover in Multispecies Disease Transmission Networks: Steady-State Analysis.

AbstractIn multispecies disease systems, pathogen spillover from a "reservoir community" can maintain disease in a "sink community" where it would otherwise die out. We develop and analyze models for spillover and disease spread in sink communities, focusing on questions of control: which species or transmission links are the most important to target to reduce the disease impact on a species of concern? Our analysis focuses on steady-state disease prevalence, assuming that the timescale of interest is long compared with that of disease introduction and establishment in the sink community. We identify three regimes as the sink community R0 scales from 0 to 1. Up to R0≈0.3, overall infection patterns are dominated by direct exogenous infections and one-step subsequent transmission. For R0≈1, infection patterns are characterized by dominant eigenvectors of a force-of-infection matrix. In between, additional network details can be important; we derive and apply general sensitivity formulas that identify particularly important links and species.

Sleep, Immune Function, and Vaccinations in Military Personnel: Challenges and Future Directions.

The U.S. military invests substantial resources to vaccinate all personnel, including recruits, against operationally important infectious disease threats. However, research suggests that vaccine immune response and, therefore, vaccine effectiveness may be inadvertently reduced because of chronic and/or acute sleep deficiency experienced by recipients around the time of vaccination. Because sleep deficiency is expected and even necessary in deployed and training contexts, research investigations of the impacts of sleep and related physiological systems such as circadian rhythms on vaccine effectiveness in military settings are needed. Specifically, research should be aimed at understanding the effects of sleep deficiency, as well as vaccine administration schedules, on response to vaccination and clinical protection. Furthermore, knowledge gaps among military medical leadership on sleep, vaccines, and immune health should be assessed. This area of research may benefit the health and readiness of service members while also decreasing health care utilization and associated costs from illness.

A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems.

Sensitivity analysis is often used to help understand and manage ecological systems, by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time-for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act upon. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life-history events, and endogenously-driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.

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 (97.68% genomic similarity) and features a type D22-like penton base, a type D19-like hexon gene, and a type D9-like fiber [P22/H19/F9]. On the other hand, genotype D110 is most closely related to type D22 (96.94% genomic similarity) and features a type D67-like penton base, a novel hexon gene, and a type D9-like fiber [P67/H110/F9]. Importantly, the fibers of both novel genotypes are highly similar to those of genotypes D56 and D59, which have also been isolated from a few cases of respiratory infections. The present report shows data contributing to the understanding of the molecular determinants of the expanded tissue tropism of certain members of species HAdV-D.

Recurrent activity in neuronal avalanches.

A new statistical analysis of large neuronal avalanches observed in mouse and rat brain tissues reveals a substantial degree of recurrent activity and cyclic patterns of activation not seen in smaller avalanches. To explain these observations, we adapted a model of structural weakening in materials. In this model, dynamical weakening of neuron firing thresholds closely replicates experimental avalanche size distributions, firing number distributions, and patterns of cyclic activity. This agreement between model and data suggests that a mechanism like dynamical weakening plays a key role in recurrent activity found in large neuronal avalanches. We expect these results to illuminate the causes and dynamics of large avalanches, like those seen in seizures.