GradDFT. A software library for machine learning enhanced density functional theory.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT: an endeavor with many open questions and technical challenges. In this work, we present GradDFT a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. GradDFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, GradDFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

Temporal compounding increases economic impacts of atmospheric rivers in California.

Temporally compounding atmospheric river (AR) events cause severe flooding and damage in California. However, the contribution of temporal compounding to AR-induced loss has yet to be systematically quantified. We show that the strongest ARs are more likely to be part of sequences, which are periods of elevated hydrologic hazard associated with temporally clustered ARs. Sequences increase the likelihood of flood-related impacts by 8.3% on AR days and 5.4% on non-AR days, and across two independent loss datasets, we find that ARs within sequences have over three times higher expected losses compared to ARs outside of sequences. Expected losses also increase when the preceding AR is higher intensity, when time since the preceding AR is shorter, and when an AR is the second or later event within a sequence. We conclude that temporal compounding is a critical source of information for predicting an AR's potential consequences.

Communicating computational workflows in a regulatory environment.

The volume of nucleic acid sequence data has exploded recently, amplifying the challenge of transforming data into meaningful information. Processing data can require an increasingly complex ecosystem of customized tools, which increases difficulty in communicating analyses in an understandable way yet is of sufficient detail to enable informed decisions or repeats. This can be of particular interest to institutions and companies communicating computations in a regulatory environment. BioCompute Objects (BCOs; an instance of pipeline documentation that conforms to the IEEE 2791-2020 standard) were developed as a standardized mechanism for analysis reporting. A suite of BCOs is presented, representing interconnected elements of a computation modeled after those that might be found in a regulatory submission but are shared publicly - in this case a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines.

Evidence from personal ornaments suggest nine distinct cultural groups between 34,000 and 24,000 years ago in Europe.

Mechanisms governing the relationship between genetic and cultural evolution are the subject of debate, data analysis and modelling efforts. Here we present a new georeferenced dataset of personal ornaments worn by European hunter-gatherers during the so-called Gravettian technocomplex (34,000-24,000 years ago), analyse it with multivariate and geospatial statistics, model the impact of distance on cultural diversity and contrast the outcome of our analyses with up-to-date palaeogenetic data. We demonstrate that Gravettian ornament variability cannot be explained solely by isolation-by-distance. Analysis of Gravettian ornaments identified nine geographically discrete cultural entities across Europe. While broadly in agreement with palaeogenetic data, our results highlight a more complex pattern, with cultural entities located in areas not yet sampled by palaeogenetics and distinctive entities in regions inhabited by populations of similar genetic ancestry. Integrating personal ornament and biological data from other Palaeolithic cultures will elucidate the complex narrative of population dynamics of Upper Palaeolithic Europe.

A methodology to estimate postdisaster unmet housing needs using limited data: Application to the 2017 California wildfires.

In the United States, assistance from the Department of Housing and Urban Development (HUD) plays an essential role in supporting the postdisaster recovery of states with unmet housing needs. HUD requires data on unmet needs to appropriate recovery funds. Ground truth data are not available for months after a disaster, however, so HUD uses a simplified approach to estimate unmet housing needs. State authorities argue that HUD's simplified approach underestimates the state's needs. This article presents a methodology to estimate postdisaster unmet housing needs that is accurate and relies only on data obtained shortly after a disaster. Data on the number of damaged buildings are combined with models for expected repair costs. Statistical models for aid distributed by the Federal Emergency Management Agency (FEMA) and the Small Business Administration (SBA) are then developed and used to forecast funding provided by those agencies. With these forecasts, the unmet need to be funded by HUD is estimated. The approach can be used for multiple states and hazard types. As validation, the proposed methodology is used to estimate the unmet housing needs following disasters that struck California in 2017. California authorities suggest that HUD's methodology underestimated the state's needs by a factor of 20. Conversely, the proposed methodology can replicate the estimates by the state authorities and provide accounts of losses, the amount of funding from FEMA and SBA, and the total unmet housing needs without requiring data unavailable shortly after a disaster. Thus, the proposed methodology can help improve HUD's funding appropriation without delays.

Glutathione affinity chromatography for the scalable purification of an oncolytic virus immunotherapy from microcarrier cell culture.

Therapeutic viral vectors are an emerging technology with several clinical applications in gene therapy, vaccines, and immunotherapy. Increased demand has required the redevelopment of conventional, low-throughput cell culture and purification manufacturing methods such as static cell stacks and ultracentrifugation. In this work, scalable methods were investigated for the manufacture of an oncolytic virus immunotherapy application consisting of a prototype strain of coxsackievirus A21 (CVA21) produced in adherent MRC-5 cells. Cell culture was established in stirred-tank microcarrier bioreactors, and an efficient affinity chromatography method was developed for the purification of harvested CVA21 through binding of the viral capsids to an immobilized glutathione (GSH) ligand. Bioreactor temperature during infection was investigated to maximize titer, and a decrease in temperature from 37°C to 34°C yielded a two-three-fold increase in infectivity. After purification of the 34°C harvests, the GSH affinity chromatography elution not only maintained a >two-fold increase in infectivity and viral genomes but also increased the proportion of empty capsids compared to 37°C harvests. Using material generated from both infection temperature setpoints, chromatographic parameters and mobile phase compositions were studied at the laboratory scale to maximize infectious particle yields and cell culture impurity clearance. Empty capsids that co-eluted with full capsids from 34°C infection temperature harvests were poorly resolved across the conditions tested, but subsequent polishing anion exchange and cation exchange chromatography steps were developed to clear residual empty capsids and other impurities. Oncolytic CVA21 production was scaled-up 75-fold from the laboratory scale and demonstrated across seven batches in 250 L single-use microcarrier bioreactors and purified with customized, prepacked, single-use 1.5 L GSH affinity chromatography columns. The large-scale bioreactors controlled at 34°C during infection maintained a three-fold increase in productivity in the GSH elution, and excellent clearance of host cell and media impurities was observed across all batches. This study presents a robust method for the manufacture of an oncolytic virus immunotherapy application that may be implemented for the scalable production of other viruses and viral vectors which interact with glutathione.

Outcomes After Liver Transplantation With Incidental Cholangiocarcinoma.

Cholangiocarcinoma (CCA) is currently a contraindication to liver transplantation (LT) in the United Kingdom (UK). Incidental CCA occurs rarely in some patients undergoing LT. We report on retrospective outcomes of patients with incidental CCA from six UK LT centres. Cases were identified from pathology records. Data regarding tumour characteristics and post-transplant survival were collected. CCA was classified by TNM staging and anatomical location. 95 patients who underwent LT between 1988-2020 were identified. Median follow-up after LT was 2.1 years (14 days-18.6 years). Most patients were male (68.4%), median age at LT was 53 (IQR 46-62), and the majority had underlying PSC (61%). Overall median survival after LT was 4.4 years. Survival differed by tumour site: 1-, 3-, and 5-year estimated survival was 82.1%, 68.7%, and 57.1%, respectively, in intrahepatic CCA (n = 40) and 58.5%, 42.6%, and 30.2% in perihilar CCA (n = 42; p = 0.06). 1-, 3-, and 5-year estimated survival was 95.8%, 86.5%, and 80.6%, respectively, in pT1 tumours (28.2% of cohort), and 65.8%, 44.7%, and 31.1%, respectively, in pT2-4 (p = 0.018). Survival after LT for recipients with incidental CCA is inferior compared to usual outcomes for LT in the United Kingdom. LT for earlier stage CCA has similar survival to LT for hepatocellular cancer, and intrahepatic CCAs have better survival compared to perihilar CCAs. These observations may support LT for CCA in selected cases.

Development and pilot test of criteria defining best practices for organizational sexual assault prevention.

Sexual violence affects millions of Americans, and approximately one out of every three women and one out of every four men have experienced sexual violence during their lifetime. While prevention efforts have focused on implementing specific programmatic approaches, there has been relatively little focus on developing comprehensive and effective approaches to reduce sexual assault prevention across an organization. This study describes the development of the Prevention Evaluation Framework, an assessment targeting organizational best practices for comprehensive sexual assault prevention across multiple domains including human resources, collaborative relationships and infrastructure, use of evidence-informed approaches, quality implementation and continuous evaluation of programs/policies. Using the structured RAND/University of California, Los Angeles appropriateness method to develop the assessment, we conducted a literature review and solicited expert feedback about what a comprehensive organizational approach to sexual assault prevention should entail. We then pilot tested the assessment with 3 United States military service academies; and continued to improve and adapt the assessment to a range of organizations with input from 6 Department of Defense headquarters organizations, and 9 universities across the country. Given the nascent state of the evidence about what makes an effective organizational approach to sexual assault prevention, the assessment reflects one way of promoting quality in this evolving field. The consistency between the experts' ratings and the literature, and the relevance of the items across organizations suggest that the assessment provides important guidance to inform the development of comprehensive organizational approaches to sexual assault prevention and to the evaluation of ongoing efforts.

SEC coupled with in-line multiple detectors for the characterization of an oncolytic Coxsackievirus.

V937 is an oncolytic virus immunotherapy clinical drug candidate consisting of a proprietary formulation of Coxsackievirus A21 (CVA21). V937 specifically binds to and lyses cells with over-expressed ICAM-1 receptors in a range of tumor cell types and is currently in phase I and II clinical trials. Infectious V937 particles consist of a ∼30 nm icosahedral capsid assembled from four structural viral proteins that encapsidate a viral RNA genome. Rapid and robust analytical methods to quantify and characterize CVA21 virus particles are important to support the process development, regulatory requirements, and validation of new manufacturing platforms. Herein, we describe a size-exclusion chromatography (SEC) method that was developed to characterize the V937 drug substance and process intermediates. Using a 4-in-1 combination of multi-detectors (UV, refractive index, dynamic and static light scattering), we demonstrate the use of SEC for the quantification of the virus particle count, the determination of virus size (molecular weight and hydrodynamic diameter), and the characterization of virus purity by assessing empty-to-full capsid ratios. Through a SEC analysis of stressed V937 samples, we propose CVA21 thermal degradation pathways that result in genome release and particle aggregation.

Origin of Ferroelectric Domain Wall Alignment with Surface Trenches in Ultrathin Films.

Engraving trenches on the surfaces of ultrathin ferroelectric (FE) films and superlattices promises control over the orientation and direction of FE domain walls (DWs). Through exploiting the phenomenon of DW-surface trench (ST) parallel alignment, systems where DWs are known for becoming electrical conductors could now become useful nanocircuits using only standard lithographical techniques. Despite this clear application, the microscopic mechanism responsible for the alignment phenomenon has remained elusive. Using ultrathin PbTiO_{3} films as a model system, we explore this mechanism with large scale density functional theory simulations on as many as 5,136 atoms. Although we expect multiple contributing factors, we show that parallel DW-ST alignment can be well explained by this configuration giving rise to an arrangement of electric dipole moments which best restore polar continuity to the film. These moments preserve the polar texture of the pristine film, thus minimizing ST-induced depolarizing fields. Given the generality of this mechanism, we suggest that STs could be used to engineer other exotic polar textures in a variety of FE nanostructures as supported by the appearance of ST-induced polar cycloidal modulations in this Letter. Our simulations also support experimental observations of ST-induced negative strains which have been suggested to play a role in the alignment mechanism.

Psychosocial aspects of Historical and Cultural Learning: Historical Trauma and Resilience among Indigenous Young Adults.

PURPOSE: The purpose of this manuscript is to evaluate the impact of the Remember the Removal (RTR) program, with specific emphasis on participants' experiences learning about and reacting to Cherokee history, including historical trauma. METHODS: Two cohorts of intervention participants (1984 and 2015) participated in focus groups. An exploratory analysis was performed to categorize themes around the effects of historical training. RESULTS: Results yielded two themes and subsequent sub-themes: 1) Reactions to Historical Learning: confronting misrepresentation and erasure, mixed emotions, looking backwards, looking forwards, strengthening Cherokee identity; and 2) The Effects of Colonization: emotional sides of historical loss, empowerment, resilience, and belonging, and addressing contemporary discrimination. CONCLUSION: Teaching tribally-specific historical events was related to increased thoughts about historical loss, an increased awareness of non-Native people's lack of historical knowledge about Native people and subsequent experiences of discrimination, but also an increased sense of tribal identity, resilience, and belonging.

A chimeric influenza hemagglutinin delivered by parainfluenza virus 5 vector induces broadly protective immunity against genetically divergent influenza a H1 viruses in swine.

Pigs are an important reservoir for human influenza viruses, and influenza causes significant economic loss to the swine industry. As demonstrated during the 2009 H1N1 pandemic, control of swine influenza virus infection is a critical step toward blocking emergence of human influenza virus. An effective vaccine that can induce broadly protective immunity against heterologous influenza virus strains is critically needed. In our previous studies [McCormick et al., 2015; PLoS One, 10(6):e0127649], we used molecular breeding (DNA shuffling) strategies to increase the breadth of the variable and conserved epitopes expressed within a single influenza A virus chimeric hemagglutinin (HA) protein. Chimeric HAs were constructed using parental HAs from the 2009 pandemic virus and swine influenza viruses that had a history of zoonotic transmission to humans. In the current study, we used parainfluenza virus 5 (PIV-5) as a vector to express one of these chimeric HA antigens, HA-113. Recombinant PIV-5 expressing HA-113 (PIV5-113) were rescued, and immunogenicity and protective efficacy were tested in both mouse and pig models. The results showed that PIV5-113 can protect mice and pigs against challenge with viruses expressing parental HAs. The protective immunity was extended against other genetically diversified influenza H1-expressing viruses. Our work demonstrates that PIV5-based influenza vaccines are efficacious as vaccines for pigs. The PIV5 vaccine vector and chimeric HA-113 antigen are discussed in the context of the development of universal influenza vaccines and the potential contribution of PIV5-113 as a candidate universal vaccine.

Characteristics and outcomes of patients with COVID-19 at a district general hospital in Surrey, UK.

BACKGROUND: This retrospective cohort study aims to define the clinical findings and outcomes of every patient admitted to a district general hospital in Surrey with COVID-19 in March 2020, providing a snapshot of the first wave of infection in the UK. This study is the first detailed insight into the impact of frailty markers on patient outcomes and provides the infection rate among healthcare workers. METHODS: Data were obtained from medical records. Outcome measures were level of oxygen therapy, discharge and death. Patients were followed up until 21 April 2020. RESULTS: 108 patients were included. 34 (31%) died in hospital or were discharged for palliative care. 43% of patients aged over 65 died. The commonest comorbidities were hypertension (49; 45%) and diabetes (25; 23%). Patients who died were older (mean difference ±SEM, 13.76±3.12 years; p<0.0001) with a higher NEWS2 score (median 6, IQR 2.5-7.5 vs median 2, IQR 2-6) and worse renal function (median differences: urea 2.7 mmol/L, p<0.01; creatinine 4 µmol/L, p<0.05; eGFR 14 mL/min, p<0.05) on admission compared with survivors. Frailty markers were identified as risk factors for death. Clinical Frailty Scale (CFS) was higher in patients over 65 who died than in survivors (median 5, IQR 4-6 vs 3.5, IQR 2-5; p<0.01). Troponin and creatine kinase levels were higher in patients who died than in those who recovered (p<0.0001). Lymphopenia was common (median 0.8, IQR 0.6-1.2; p<0.005). Every patient with heart failure died (8). 26 (24%) were treated with continuous positive airway pressure (CPAP; median 3 days, IQR 2-7.3) and 9 (8%) were intubated (median 14 days, IQR 7-21). All patients who died after discharge (4; 6%) were care home residents. 276 of 699 hospital staff tested were positive for COVID-19. CONCLUSIONS: This study identifies older patients with frailty as being particularly vulnerable and reinforces government policy to protect this group at all costs.

Large scale and linear scaling DFT with the CONQUEST code.

We survey the underlying theory behind the large-scale and linear scaling density functional theory code, conquest, which shows excellent parallel scaling and can be applied to thousands of atoms with diagonalization and millions of atoms with linear scaling. We give details of the representation of the density matrix and the approach to finding the electronic ground state and discuss the implementation of molecular dynamics with linear scaling. We give an overview of the performance of the code, focusing in particular on the parallel scaling, and provide examples of recent developments and applications.

Birth weight predicted baseline muscular efficiency, but not response of energy expenditure to calorie restriction: An empirical test of the predictive adaptive response hypothesis.

OBJECTIVES: Aiming to test the evolutionary significance of relationships linking prenatal growth conditions to adult phenotypes, this study examined whether birth size predicts energetic savings during fasting. We specifically tested a Predictive Adaptive Response (PAR) model that predicts greater energetic saving among adults who were born small. METHODS: Data were collected from a convenience sample of young adults living in Albuquerque, NM (n = 34). Indirect calorimetry quantified changes in resting energy expenditure (REE) and active muscular efficiency that occurred in response to a 29-h fast. Multiple regression analyses linked birth weight to baseline and postfast metabolic values while controlling for appropriate confounders (e.g., sex, body mass). RESULTS: Birth weight did not moderate the relationship between body size and energy expenditure, nor did it predict the magnitude change in REE or muscular efficiency observed from baseline to after fasting. Alternative indicators of birth size were also examined (e.g., low v. normal birth weight, comparison of tertiles), with no effects found. However, baseline muscular efficiency improved by 1.1% per 725 g (S.D.) increase in birth weight (P = 0.037). CONCLUSIONS: Birth size did not influence the sensitivity of metabolic demands to fasting-neither at rest nor during activity. Moreover, small birth size predicted a reduction in the efficiency with which muscles convert energy expended into work accomplished. These results do not support the ascription of adaptive function to phenotypes associated with small birth size. © 2015 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:484-492, 2016. © 2015 Wiley Periodicals, Inc.

Microdemographic Determinants of Population Recovery among the Northern Aché.

A pattern of population crash and rapid recovery is a common feature of the pacification and settlement experience of the indigenous peoples of tropical South America. Despite the obvious importance of these events to the demographic and anthropological sciences as a whole, as well as their significant practical implications, little is known about the microdemographic determinants of these paired phenomena. Using methods of asymptotic and stochastic demographic analysis, we reconstructed the microdemographic drivers of this history among one indigenous population: the Northern Aché of eastern Paraguay. This article explores the implications of these relationships for understanding the overall demographic turnaround observed within similar groups, as well as for the future trajectory of the Northern Aché in particular.

Social and clinical predictors of drug-resistant tuberculosis in a public hospital, Monterrey, Mexico.

PURPOSE: Drug-resistant tuberculosis (DRTB) is steadily increasing in Mexico, but little is known of patient risk factors in the Mexico-United States border region. This preliminary case-control study included 95 patients with active pulmonary TB with drug susceptibility results attending the José E. González University Hospital in the urban hub of Nuevo León-the Monterrey Metropolitan Area. We report potential social and clinical risk factors of DRTB among this hospital-based sample. METHODS: We collected data through face-to-face interviews and medical record reviews from 25 cases with DRTB and 70 drug-sensitive controls. DNA was collected to assess an effect of genetic ancestry on DRTB by using a panel of 291,917 genomic markers. We calculated crude and multivariate logistic regression. RESULTS: After adjusting for potential confounding factors, we found that prior TB treatment (odds ratio, 4.5; 95% confidence interval, 0.9-21.1) and use of crack cocaine (odds ratio, 4.6; 95% confidence interval, 1.1-18.7) were associated with DRTB. No other variables, including genetic ancestry and comorbidities, were predictive. CONCLUSIONS: Health care providers may benefit from recognizing predictors of DRTB in regions where routine drug susceptibility testing is limited. Prior TB treatment and illicit drug use, specifically crack cocaine, may be important risk factors for DRTB in this region.

The effects of socioeconomic status, clinical factors, and genetic ancestry on pulmonary tuberculosis disease in northeastern Mexico.

Diverse socioeconomic and clinical factors influence susceptibility to tuberculosis (TB) disease in Mexico. The role of genetic factors, particularly those that differ between the parental groups that admixed in Mexico, is unclear. The objectives of this study are to identify the socioeconomic and clinical predictors of the transition from latent TB infection (LTBI) to pulmonary TB disease in an urban population in northeastern Mexico, and to examine whether genetic ancestry plays an independent role in this transition. We recruited 97 pulmonary TB disease patients and 97 LTBI individuals from a public hospital in Monterrey, Nuevo León. Socioeconomic and clinical variables were collected from interviews and medical records, and genetic ancestry was estimated for a subset of 142 study participants from 291,917 single nucleotide polymorphisms (SNPs). We examined crude associations between the variables and TB disease status. Significant predictors from crude association tests were analyzed using multivariable logistic regression. We also compared genetic ancestry between LTBI individuals and TB disease patients at 1,314 SNPs in 273 genes from the TB biosystem in the NCBI BioSystems database. In crude association tests, 12 socioeconomic and clinical variables were associated with TB disease. Multivariable logistic regression analyses indicated that marital status, diabetes, and smoking were independently associated with TB status. Genetic ancestry was not associated with TB disease in either crude or multivariable analyses. Separate analyses showed that LTBI individuals recruited from hospital staff had significantly higher European genetic ancestry than LTBI individuals recruited from the clinics and waiting rooms. Genetic ancestry differed between individuals with LTBI and TB disease at SNPs located in two genes in the TB biosystem. These results indicate that Monterrey may be structured with respect to genetic ancestry, and that genetic differences in TB susceptibility in parental populations may contribute to variation in disease susceptibility in the region.

An evaluation of the accuracy of small-area demographic estimates of population at risk and its effect on prevalence statistics.

Demographic estimates of population at risk often underpin epidemiologic research and public health surveillance efforts. In spite of their central importance to epidemiology and public-health practice, little previous attention has been paid to evaluating the magnitude of errors associated with such estimates or the sensitivity of epidemiologic statistics to these effects. In spite of the well-known observation that accuracy in demographic estimates declines as the size of the population to be estimated decreases, demographers continue to face pressure to produce estimates for increasingly fine-grained population characteristics at ever-smaller geographic scales. Unfortunately, little guidance on the magnitude of errors that can be expected in such estimates is currently available in the literature and available for consideration in small-area epidemiology. This paper attempts to fill this current gap by producing a Vintage 2010 set of single-year-of-age estimates for census tracts, then evaluating their accuracy and precision in light of the results of the 2010 Census. These estimates are produced and evaluated for 499 census tracts in New Mexico for single-years of age from 0 to 21 and for each sex individually. The error distributions associated with these estimates are characterized statistically using non-parametric statistics including the median and 2.5th and 97.5th percentiles. The impact of these errors are considered through simulations in which observed and estimated 2010 population counts are used as alternative denominators and simulated event counts are used to compute a realistic range fo prevalence values. The implications of the results of this study for small-area epidemiologic research in cancer and environmental health are considered.

Indirect estimates of total fertility rate using child woman/ratio: a comparison with the Bogue-Palmore method.

Indirect estimation methodologies of the total fertility rate (TFR) have a long history within demography and have provided important techniques applied demographers can use when data is sparse or lacking. However new methodologies for approximating the total fertility rate have not been proposed in nearly 30 years. This study presents a novel method for indirectly approximating the total fertility rate using an algebraic rearrangement of the general fertility rate (GFR) through the known relationship between GFR and TFR. It then compares the proposed method to the well-known Bogue-Palmore method. These methods are compared in 196 countries and include overall errors as well as characteristics of the countries that contribute to fertility behavior. Additionally, these methods were compared geographically to find any geographical patterns. We find this novel method is not only simpler than the Bogue-Palmore method, requiring fewer data inputs, but also has reduced algebraic and absolute errors when compared with the Bogue-Palmore method and specifically outperforms the Bogue-Palmore method in developing countries. We find that our novel method may be useful estimation procedure for demographers.