bluuebunny/crossref_metadata_2025 huggingface dataset:
Ungulate use of locally infectious zones in a re-emerging anthrax risk area
Authors: Walker Morgan A. , Uribasterra Maria , Asher Valpa , Ponciano José Miguel , Getz Wayne M. , Ryan Sadie J. , Blackburn Jason K.
Published: October 2020

Environmentally mediated indirect pathogen transmission is linked to host movement and foraging in areas where pathogens are maintained in the environment. In the case of anthrax, spores of the causative bacterium
Bacillus anthracis
are released into the environment following host death and create locally infectious zones (LIZs) around carcass sites; by grazing at LIZs, herbivores are potentially exposed to spores. Here, we used camera traps to assess how ungulate species use carcass sites in southwestern Montana and evaluated how these behaviours may promote indirect anthrax transmission, thus providing, to our knowledge, the first detailed documentation and study of the fine-scale mechanisms underlying foraging-based disease transmission in this ecosystem. We found that carcasses at LIZs significantly increased aboveground biomass of vegetation and concentrations of sodium and phosphorus, potentially making these sites more appealing to grazers. Host behavioural responses to LIZs varied depending on species, sex, season and carcass age; but, overall, our results demonstrated that carcasses or carcass sites serve as an attractant to herbivores in this system. Attraction to LIZs probably represents an increased risk of exposure to
B. anthracis
and, consequently, increased anthrax transmission rates. Accordingly, continued anthrax surveillance and control strategies are critical in this system.
An integrative machine learning approach to discovering multi-level molecular mechanisms of obesity using data from monozygotic twin pairs
Authors: Kibble Milla , Khan Suleiman A. , Ammad-ud-din Muhammad , Bollepalli Sailalitha , Palviainen Teemu , Kaprio Jaakko , Pietiläinen Kirsi H. , Ollikainen Miina
Published: October 2020

We combined clinical, cytokine, genomic, methylation and dietary data from 43 young adult monozygotic twin pairs (aged 22–36 years, 53% female), where 25 of the twin pairs were substantially weight discordant (delta body mass index > 3 kg m
−2
). These measurements were originally taken as part of the TwinFat study, a substudy of The Finnish Twin Cohort study. These five large multivariate datasets (comprising 42, 71, 1587, 1605 and 63 variables, respectively) were jointly analysed using an integrative machine learning method called group factor analysis (GFA) to offer new hypotheses into the multi-molecular-level interactions associated with the development of obesity. New potential links between cytokines and weight gain are identified, as well as associations between dietary, inflammatory and epigenetic factors. This encouraging case study aims to enthuse the research community to boldly attempt new machine learning approaches which have the potential to yield novel and unintuitive hypotheses. The source code of the GFA method is publically available as the R package GFA.
A new Devonian euthycarcinoid reveals the use of different respiratory strategies during the marine-to-terrestrial transition in the myriapod lineage
Authors: Gueriau Pierre , Lamsdell James C. , Wogelius Roy A. , Manning Phillip L. , Egerton Victoria M. , Bergmann Uwe , Bertrand Loïc , Denayer Julien
Published: October 2020

Myriapods were, together with arachnids, the earliest animals to occupy terrestrial ecosystems, by at least the Silurian. The origin of myriapods and their land colonization have long remained puzzling until euthycarcinoids, an extinct group of aquatic arthropods considered amphibious, were shown to be stem-group myriapods, extending the lineage to the Cambrian and evidencing a marine-to-terrestrial transition. Although possible respiratory structures comparable to the air-breathing tracheal system of myriapods are visible in several euthycarcinoids, little is known about the mechanism by which they respired. Here, we describe a new euthycarcinoid from Upper Devonian alluvio-lagoonal deposits of Belgium. Synchrotron-based elemental X-ray analyses were used to extract all available information from the only known specimen. Sulfur X-ray fluorescence (XRF) mapping and spectroscopy unveil sulfate evaporation stains, spread over the entire slab, suggestive of a very shallow-water to the terrestrial environment prior to burial consistent with an amphibious lifestyle. Trace metal XRF mapping reveals a pair of ventral spherical cavities or chambers on the second post-abdominal segment that do not compare to any known feature in aquatic arthropods, but might well play a part in air-breathing. Our data provide additional support for amphibious lifestyle in euthycarcinoids and show that different respiratory strategies were used during the marine-to-terrestrial transition in the myriapod lineage.
Learning agents in Black–Scholes financial markets
Authors: Vaidya Tushar , Murguia Carlos , Piliouras Georgios
Published: October 2020

Black–Scholes (BS) is a remarkable quotation model for European option pricing in financial markets. Option prices are calculated using an analytical formula whose main inputs are strike (at which price to exercise) and volatility. The BS framework assumes that volatility remains constant across all strikes; however, in practice, it varies. How do traders come to learn these parameters? We introduce natural agent-based models, in which traders update their beliefs about the true implied volatility based on the opinions of other agents. We prove exponentially fast convergence of these opinion dynamics, using techniques from control theory and leader-follower models, thus providing a resolution between theory and market practices. We allow for two different models, one with feedback and one with an unknown leader.
Population dynamics with spatial structure and an Allee effect
Authors: Surendran Anudeep , Plank Michael J. , Simpson Matthew J.
Published: October 2020

Population dynamics including a strong Allee effect describe the situation where long-term population survival or extinction depends on the initial population density. A simple mathematical model of an Allee effect is one where initial densities below the threshold lead to extinction, whereas initial densities above the threshold lead to survival. Mean-field models of population dynamics neglect spatial structure that can arise through short-range interactions, such as competition and dispersal. The influence of non-mean-field effects has not been studied in the presence of an Allee effect. To address this, we develop an individual-based model that incorporates both short-range interactions and an Allee effect. To explore the role of spatial structure we derive a mathematically tractable continuum approximation of the IBM in terms of the dynamics of spatial moments. In the limit of long-range interactions where the mean-field approximation holds, our modelling framework recovers the mean-field Allee threshold. We show that the Allee threshold is sensitive to spatial structure neglected by mean-field models. For example, there are cases where the mean-field model predicts extinction but the population actually survives. Through simulations we show that our new spatial moment dynamics model accurately captures the modified Allee threshold in the presence of spatial structure.
Validity of Winkler’s mattress model for thin elastomeric layers: beyond Poisson’s ratio
Authors: Chandler Thomas G. J. , Vella Dominic
Published: October 2020

Winkler’s mattress model is often used as a simplified model to understand how a thin elastic layer, such as a coating, deforms when subject to a distributed normal load: the deformation of the layer is assumed proportional to the applied normal load. This simplicity means that the Winkler model has found a wide range of applications from soft matter to geophysics. However, in the limit of an incompressible elastic layer the model predicts infinite resistance to deformation, and hence breaks down. Since many of the thin layers used in applications are elastomeric, and hence close to incompressible, we consider the question of when the Winkler model is appropriate for such layers. We formally derive a model that interpolates between the Winkler and incompressible limits for thin elastic layers, and illustrate this model by detailed consideration of two example problems: the point-indentation of a coated elastomeric layer and self-sustained lift in soft elastohydrodynamic lubrication. We find that the applicability (or otherwise) of the Winkler model is not determined by the value of the Poisson ratio alone, but by a compressibility parameter that combines the Poisson ratio with a measure of the layer’s slenderness, which itself depends on the problem under consideration.
On the generation of periodic discrete structures with identical two-point correlation
Authors: Fernández M. , Fritzen F.
Published: October 2020

Strategies for the generation of periodic discrete structures with identical two-point correlation—called 2PC-equivalent—are developed. It is shown that starting from a set of 2PC-equivalent root structures, 2PC-equivalent child structures of arbitrary resolution and number of phases (e.g. material phases) can be generated based on phase extension through trivial embeddings, kernel-based extension and phase coalescence. Proofs are provided by means of discrete Fourier transform theory. A Python 3 implementation is offered for reproduction of examples and future applications.
Mitochondrial-Y chromosome epistasis inDrosophila melanogaster
Authors: Ågren J. Arvid , Munasinghe Manisha , Clark Andrew G.
Published: October 2020

The coordination between mitochondrial and nuclear genes is crucial to eukaryotic organisms. Predicting the nature of these epistatic interactions can be difficult because of the transmission asymmetry of the genes involved. While autosomes and X-linked genes are transmitted through both sexes, genes on the Y chromosome and in the mitochondrial genome are uniparentally transmitted through males and females, respectively. Here, we generate 36 otherwise isogenicDrosophila melanogasterstrains differing only in the geographical origin of their mitochondrial genome and Y chromosome, to experimentally examine the effects of the uniparentally inherited parts of the genome, as well as their interaction, in males. We assay longevity and gene expression through RNA-sequencing. We detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis. In particular, genes involved in male reproduction appear to be especially sensitive to such interactions, and variation on the Y chromosome is associated with differences in longevity. Despite these interactions, we find no evidence that the mitochondrial genome and Y chromosome are co-adapted within a geographical region. Overall, our study demonstrates a key role for the uniparentally inherited parts of the genome for male biology, but also that mito-nuclear interactions are complex and not easily predicted from simple transmission asymmetries.
Forest stratification shapes allometry and flight morphology of tropical butterflies
Authors: Mena Sebastián , Kozak Krzysztof M. , Cárdenas Rafael E. , Checa María F.
Published: October 2020

Studies of altitudinal and latitudinal gradients have identified links between the evolution of insect flight morphology, landscape structure and microclimate. Although lowland tropical rainforests offer steeper shifts in conditions between the canopy and the understorey, this vertical gradient has received far less attention. Butterflies, because of their great phenotypic plasticity, are excellent models to study selection pressures that mould flight morphology. We examined data collected over 5 years on 64 Nymphalidae butterflies in the Ecuadorian Chocó rainforest. We used phylogenetic methods to control for similarity resulting from common ancestry, and explore the relationships between species stratification and flight morphology. We hypothesized that species should show morphological adaptations related to differing micro-environments, associated with canopy and understorey. We found that butterfly species living in each stratum presented significantly different allometric slopes. Furthermore, a preference for the canopy was significantly associated with low wing area to thoracic volume ratios and high wing aspect ratios, but not with the relative distance to the wing centroid, consistent with extended use of fast flapping flight for canopy butterflies and slow gliding for the understorey. Our results suggest that microclimate differences in vertical gradients are a key factor in generating morphological diversity in flying insects.
Sex differences in moral judgements across 67 countries
Authors: Atari Mohammad , Lai Mark H. C. , Dehghani Morteza
Published: October 2020

Most of the empirical research on sex differences and cultural variations in morality has relied on within-culture analyses or small-scale cross-cultural data. To further broaden the scientific understanding of sex differences in morality, the current research relies on two international samples to provide the first large-scale examination of sex differences in moral judgements nested within cultures. Using a sample from 67 countries (Study 1;n= 336 691), we found culturally variable sex differences in moral judgements, as conceptualized by Moral Foundations Theory. Women consistently scored higher than men on Care, Fairness, and Purity. By contrast, sex differences in Loyalty and Authority were negligible and highly variable across cultures. Country-level sex differences in moral judgements were also examined in relation to cultural, socioeconomic, and gender-equality indicators revealing that sex differences in moral judgements are larger in individualist, Western, and gender-equal societies. In Study 2 (19 countries;n= 11 969), these results were largely replicated using Bayesian multi-level modelling in a distinct sample. The findings were robust when incorporating cultural non-independence of countries into the models. Specifically, women consistently showed higher concerns for Care, Fairness, and Purity in their moral judgements than did men. Sex differences in moral judgements were larger in individualist and gender-equal societies with more flexible social norms. We discuss the implications of these findings for the ongoing debate about the origin of sex differences and cultural variations in moral judgements as well as theoretical and pragmatic implications for moral and evolutionary psychology.
Mutation bias can shape adaptation in large asexual populations experiencing clonal interference
Authors: Gomez Kevin , Bertram Jason , Masel Joanna
Published: October 2020

The extended evolutionary synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behaviour of two simultaneously adapting traits, one with larger mutation rate
U
, the other with larger selection coefficient
s
, using asexual travelling wave models. We find that adaptation is dominated by whichever trait has the faster rate of adaptation
v
in isolation, with the other trait subject to evolutionary stalling. Reviewing empirical claims for mutation-biased adaptation, we find that not all occur in the ‘origin-fixation’ regime of population genetics where
v
is only twice as sensitive to
s
as to
U
. In some cases, differences in
U
are at least ten to twelve times larger than differences in
s
, as needed to cause mutation-biased adaptation even in the ‘multiple mutations’ regime. Surprisingly, when
U
>
s
in the ‘diffusive-mutation’ regime, the required sensitivity ratio is also only two, despite pervasive clonal interference. Given two traits with identical
v
, the benefit of having higher
s
is surprisingly small, occurring largely when one trait is at the boundary between the origin-fixation and multiple mutations regimes.
Captive-bred Atlantic salmon released into the wild have fewer offspring than wild-bred fish and decrease population productivity
Authors: O'Sullivan Ronan James , Aykanat Tutku , Johnston Susan E. , Rogan Ger , Poole Russell , Prodöhl Paulo A. , de Eyto Elvira , Primmer Craig R. , McGinnity Philip , Reed Thomas Eric
Published: October 2020

The release of captive-bred animals into the wild is commonly practised to restore or supplement wild populations but comes with a suite of ecological and genetic consequences. Vast numbers of hatchery-reared fish are released annually, ostensibly to restore/enhance wild populations or provide greater angling returns. While previous studies have shown that captive-bred fish perform poorly in the wild relative to wild-bred conspecifics, few have measured individual lifetime reproductive success (LRS) and how this affects population productivity. Here, we analyse data on Atlantic salmon from an intensely studied catchment into which varying numbers of captive-bred fish have escaped/been released and potentially bred over several decades. Using a molecular pedigree, we demonstrate that, on average, the LRS of captive-bred individuals was only 36% that of wild-bred individuals. A significant LRS difference remained after excluding individuals that left no surviving offspring, some of which might have simply failed to spawn, consistent with transgenerational effects on offspring survival. The annual productivity of the mixed population (wild-bred plus captive-bred) was lower in years where captive-bred fish comprised a greater fraction of potential spawners. These results bolster previous empirical and theoretical findings that intentional stocking, or non-intentional escapees, threaten, rather than enhance, recipient natural populations.
Evidence of sperm removal behaviour in an externally fertilizing species and compensatory behaviour for the risk of self-sperm removal
Authors: Takegaki Takeshi , Nakanishi Ayako , Kanatani Yosuke , Kawase Shoma , Yoshida Masa-aki , Sato Noriyosi
Published: October 2020

The removal of rival sperm from a female's sperm storage organ acts as a strong sperm competition avoidance mechanism, which has been reported only in internally fertilizing species and not at all in externally fertilizing species. This study demonstrated for the first time that nest-holding males of
Bathygobius fuscus
, an externally fertilizing marine fish, remove the sperm of rival sneaker males from the spawning nest by exhibiting tail-fanning behaviour within the nest. Males showed tail-fanning behaviour when semen was artificially injected into the nest but not when seawater was injected, and in open nests this behaviour resulted in higher paternity rates for the focal male. The sperm removal behaviour entails the risk of removing their own sperm; therefore, additional sperm release behaviour is likely necessary to benefit from the sperm removal effect. Consistent with this, males increased post-fanning sperm release behaviour more in the semen than in the seawater injection treatment. Moreover, males who had removed sperm for a longer time spent more time releasing sperm after the removal, suggesting that the additional sperm release behaviour compensated for the loss of their own sperm. These results suggest that sperm removal behaviour is not restricted to internally fertilizing organisms and deserves further investigation in this and other species.
Komodo-dragon cathelicidin-inspired peptides are antibacterial against carbapenem-resistant Klebsiella pneumoniae
Authors: Hitt Samantha J. , Bishop Barney M. , van Hoek Monique L.
Published: October 2020

Introduction.The rise of carbapenem-resistant enterobacteriaceae (CRE) is a growing crisis that requires development of novel therapeutics.

Hypothesis.To this end, cationic antimicrobial peptides (CAMPs) represent a possible source of new potential therapeutics to treat difficult pathogens such as carbapenem-resistantKlebsiella pneumoniae(CRKP), which has gained resistance to many if not all currently approved antibiotics, making treatment difficult.

Aim.To examine the anti-CRKP antimicrobial activity of the predicted cathelicidins derived fromVaranus komodoensis(Komodo dragon) as well as synthetic antimicrobial peptides that we created.

Methodology.We determined the minimum inhibitory concentrations of the peptides against CRKP. We also characterized the abilities of these peptides to disrupt the hyperpolarization of the bacterial membrane as well as their ability to form pores in the membrane.

Results.We did not observe significant anti-CRKP activity for the predicted native Komodo cathelicidin peptides. We found that the novel peptides DRGN-6,-7 and -8 displayed significant antimicrobial activity against CRKP with MICs of 4–8 µg ml−1. DRGN-6 peptide was the most effective peptide against CRKP. Unfortunately, these peptides showed higher than desired levels of hemolysis, althoughin vivotesting in the waxwormGalleria mellonellashowed no mortality associated with treatment by the peptide; however, CRKP-infected waxworms treated with peptide did not show an improvement in survival.

Conclusion.Given the challenges of treating CRKP, identification of peptides with activity against it represents a promising avenue for further research. Given DRGN-6′s similar level of activity to colistin, DRGN-6 is a promising template for the development of novel antimicrobial peptide-based therapeutics.
Prevalence of antibodies against sars-cov-2 in professionals of a public health laboratory at são paulo, sp, brazil
Authors: Silva Valéria Oliveira , de Oliveira Elaine Lopes , Castejon Marcia Jorge , Yamashiro Rosemeire , Ahagon Cintia Mayumi , López-Lopes Giselle Ibette , da Silveira Edilene Peres Real , Hong Marisa Ailin , Carmo Timenetsky Maria do , Freitas Carmem Aparecida , Brígido Luís Fernando de Macedo
Published: October 2020

Background

Covid-19 Serology may document exposure and perhaps protection to the virus and serological test may help understand epidemic dynamics. We tested health workers form a public laboratory to evaluate previous exposure to the virus and estimate the prevalence of antibodies against-SARS-CoV-2 in Adolfo Lutz Institute, State of São Paulo, Brazil.

Methods

This study was an open, prospective evaluation among professionals of Adolfo Lutz Institute some administrative personnel from the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay. SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants.

Results

A total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity.

Conclusions

We documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, higher among outsourced workers and those residing with COVID-19 patients. COVID related work did not increased seropositivity. Some symptoms show strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings.
Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App
Authors: Sudre Carole H. , Murray Benjamin , Varsavsky Thomas , Graham Mark S. , Penfold Rose S. , Bowyer Ruth C. , Pujol Joan Capdevila , Klaser Kerstin , Antonelli Michela , Canas Liane S. , Molteni Erika , Modat Marc , Cardoso M. Jorge , May Anna , Ganesh Sajaysurya , Davies Richard , Nguyen Long H , Drew David A. , Astley Christina M. , Joshi Amit D. , Merino Jordi , Tsereteli Neli , Fall Tove , Gomez Maria F. , Duncan Emma L. , Menni Cristina , Williams Frances M.K. , Franks Paul W. , Chan Andrew T. , Wolf Jonathan , Ourselin Sebastien , Spector Tim , Steves Claire J.
Published: October 2020

Reports of “Long-COVID”, are rising but little is known about prevalence, risk factors, or whether it is possible to predict a protracted course early in the disease. We analysed data from 4182 incident cases of COVID-19 who logged their symptoms prospectively in the COVID Symptom Study app. 558 (13.3%) had symptoms lasting >=28 days, 189 (4.5%) for >=8 weeks and 95 (2.3%) for >=12 weeks. Long-COVID was characterised by symptoms of fatigue, headache, dyspnoea and anosmia and was more likely with increasing age, BMI and female sex. Experiencing more than five symptoms during the first week of illness was associated with Long-COVID, OR=3.53 [2.76;4.50]. A simple model to distinguish between short and long-COVID at 7 days, which gained a ROC-AUC of 76%, was replicated in an independent sample of 2472 antibody positive individuals. This model could be used to identify individuals for clinical trials to reduce long-term symptoms and target education and rehabilitation services.
SI epidemic model applied to COVID-19 data in mainland China
Authors: Demongeot J. , Griette Q. , Magal P.
Published: October 2020

The article is devoted to the parameters identification in the SI model. We consider several methods, starting with an exponential fit of the early cumulative data of Sars-CoV2 in mainland China. The present methodology provides a way to compute the parameters at the early stage of the epidemic. Next, we establish an identifiability result. Then we use the Bernoulli-Verhulst model as a phenomenological model to fit the data and derive some results on the parameters identification. The last part of the paper is devoted to some numerical algorithms to fit a daily piecewise constant rate of transmission.
Modelling the dispersion of SARS-CoV-2 on a dynamic network graph
Authors: Bryant Patrick , Elofsson Arne
Published: October 2020

Background

When modelling the dispersion of an epidemic using R0, one only considers the average number of individuals each infected individual will infect. However, we know from extensive studies of social networks that there is significant variation in the number of connections and thus social contacts each individual has. Individuals with more social contacts are more likely to attract and spread infection. These individuals are likely the drivers of the epidemic, so-called superspreaders. When many superspreaders are immune, it becomes more difficult for the disease to spread, as the connectedness of the social network dramatically decreases. If one assumes all individuals being equally connected and thus as likely to spread disease as in a SIR model, this is not true.

Methods

To account for the impact of social network structure on epidemic development, we model the dispersion of SARS-CoV-2 on a dynamic preferential attachment graph which changes appearance proportional to observed mobility changes. We sample a serial interval distribution that determines the probability of dispersion for all infected nodes each day. We model the dispersion in different age groups using age-specific infection fatality rates. We vary the infection probabilities in different age groups and analyse the outcome.

Results

The impact of movement on network dynamics plays a crucial role in the spread of infections. We find that higher movement results in higher spread due to an increased probability of new connections being made within a social network. We show that saturation in the dispersion can be reached much earlier on a preferential attachment graph compared to spread on a random graph, which is more similar to estimations using R0.

Conclusions

We provide a novel method for modelling epidemics by using a dynamic network structure related to observed mobility changes. The social network structure plays a crucial role in epidemic development, something that is often overlooked.
Epidemic Curve of Contamination in a Hospital That Served as Sentinel of the Spread of the SARS-Cov-2 Epidemic in the City of Rio de Janeiro
Authors: Santos Marisa , Felippe Guimarães Tereza Cristina , Cramer Helena , Mucillo Fabiana , Silva Bezerra Izabella Pereira da , Quintanilha Barbosa Raiana Andrade , Kasai Brunswick Tais Hanae , Carvalho Adriana Bastos , Dias Glauber Monteiro , Issa Aurora , Carvalho Adriana Bastos , Carvalho Antonio Carlos Campos de
Published: October 2020

The COVID-19 pandemic had a profound impact on the operation of Brazilian hospital units, even those dedicated to non-infectious diseases. This study aims to describe the Covid-19 epidemic curve from a cardiovascular specialized nosocomial unit. All symptomatic employees were submitted to RT-qPCR. A total of 613 tests were performed on 548 employees between March 23, 2020, and June 4, 2020; with 45.7% positivity from the samples, representing 11.9% of the total employees. The epidemic curve showed a profound drop after first week of May. The data showed a high contamination rate despite widespread availability of personal protective equipment and employees’ training.
An NIH Investment in Health Equity - The Economic Impact of the Flint Center for Health Equity Solutions
Authors: Meghea Cristian I. , Montgomery Barrett Wallace , Ellington Roni , Wang Ling , Barajas Clara , Lewis E. Yvonne , Yeary Sheridan T. , Van Egeren Laurie A. , Furr-Holden Debra
Published: October 2020

Background

Health disparities are pervasive and are linked to economic losses in the United States of up to $135 billion per year. The Flint Center for Health Equity Solutions (FCHES) is a Transdisciplinary Collaborative Center for health disparities research funded by the National Institute of Minority Health and Health Disparities (NIMHD). The purpose of this study was to estimate the economic impact of the 5-year NIH investment in FCHES in Genesee County, Michigan.

Methods

The estimated impacts of FCHES were calculated using a U.S.-specific input/output (I/O) model, IMPLAN, from IMPLAN Group, LLC., which provides a software system to access geographic specific data regarding economic sector interactions from a variety of sources. This allowed us to model the cross-sector economic activity that occurred throughout Genesee County, Michigan, as a result of the FCHES investment. The overall economic impacts were estimated as the sum of three impact types: 1. Direct (the specific expenditures impact of FCHES and the Scientific Research and Development Services sector); 2. Indirect (the impact on suppliers to FCHES and the Scientific Research and Development Services sector); and 3. Induced (the additional economic impact of the spending of these suppliers and employees in the county economy).

Results

The total FCHES investment amounted to approximately $11 million between 2016-2020. Overall, combined direct, indirect, and induced impacts of the total FCHES federal investment in Genesee County included over 161 job-years, over $7.6 million in personal income, and more than $19.2 million in economic output. In addition, this combined economic activity generated close to $2.3 million in state/local and federal tax revenue. The impact multipliers show the ripple effect of the FCHES investment. For example, the overall output of over $19.2 million led to an impact multiplier of 1.75 – every $1 of federal FCHES investment led to an additional $.75 of economic output in Genesee County.

Conclusions

The FCHES research funding yields significant U.S. direct economic impacts above and beyond the direct NIH investment of $11 million. The economic impact estimation method may be relevant and generalizable to other TCCs or other large research centers such as FCHES.
The Causal Effect of Air Pollution on COVID-19 Transmission: Evidence from China
Authors: He Guojun , Pan Yuhang , Tanaka Takanao
Published: October 2020

There is increasing concern that ambient air pollution could exacerbate COVID-19 transmission. However, estimating the relationship is challenging because it requires one to account for epidemiological characteristics, to isolate the impact of air pollution from potential confounders, and to capture the dynamic impact. We propose a new econometric framework to address these challenges: we rely on the epidemiological Susceptible-Infectious-Recovered-Deceased (SIRD) model to construct the outcome of interest, the Instrument Variable (IV) model to estimate the causal relationship, and the Flexible-Distributed-Lag (FDL) model to understand the dynamics. Using data covering all prefectural Chinese cities, we find that a 10-point (14.3%) increase in the Air Quality Index would lead to a 2.80 percentage point increase in the daily COVID-19 growth rate with 2 to 13 days of delay (0.14 ∼ 0.22 increase in the reproduction number: R0). These results imply that improving air quality can be a powerful tool to contain the spread of COVID-19.
GLIOBLASTOMA MULTIFORME: A META-ANALYSIS OF DRIVER GENES, CURRENT DIAGNOSIS, AND TUMOR HETEROGENEITY
Authors: Herrera-Oropeza Gabriel Emilio , Angulo-Rojo Carla , Gástelum-López Santos Alberto , Varela-Echavarría Alfredo , Hernández-Rosales Maribel , Aviña-Padilla Katia
Published: October 2020

Glioblastoma (GBM) is the most aggressive and common brain cancer in adults with the lowest life expectancy. The current neuro-oncology practice has incorporated genes involved in key molecular events that drive GBM tumorigenesis as biomarkers to guide diagnosis and design treatment. This study summarizes findings describing the significant heterogeneity of GBM at the transcriptional and genomic levels, emphasizing eighteen driver genes with clinical relevance. A pattern was identified fitting the stem cell model for GBM ontogenesis, with an up-regulation profile forMGMTand down-regulation forATRX, H3F3A, TP53, andEGFRin the mesenchymal subtype. We also detected overexpression ofEGFR, NES, VIM, andTP53in the classical subtype and ofMKi67andOLIG2genes in the proneural subtype. In keeping with this, we found a panel of nine biomarkers with a strong potential to determine the GBM molecular subtype. A unique distribution of somatic mutations was found for the young and adult population, particularly for genes related to DNA repair and chromatin remodeling, highlightingATRX, MGMT, andIDH1. Our results also revealed that highly lesioned genes undergo differential regulation with particular biological pathways for young patients. This meta-analysis will help delineate future strategies related to the use of these molecular markers for clinical decision-making in the medical routine.
Deep learning segmentation model for automated detection of the opacity regions in the chest X-rays of the Covid-19 positive patients and the application for disease severity
Authors: Tang Haiming , Sun Nanfei , Li Yi , Xia Haoran
Published: October 2020

Purpose

The pandemic of Covid-19 has caused tremendous losses to lives and economy in the entire world. The machine learning models have been applied to the radiological images of the Covid-19 positive patients for disease prediction and severity assessment. However, a segmentation model for detecting the opacity regions like haziness, ground-glass opacity and lung consolidation from the Covid-19 positive chest X-rays is still lacking.

Methods

The recently published collection of the radiological images for a rural population in United States had made the development of such a model a possibility, for the high quality images and consistent clinical measurements. We manually annotated 221 chest X-ray images with the lung fields and the opacity regions and trained a segmentation model for the opacity region using the Unet framework and the Resnet18 backbone. In addition, we applied the percentage of the opacity region over the area of the total lung fields for predicting the severity of patients.

Results

The model has a good performance regarding the overlap between the predicted and the manually labelled opacity regions. The performance is comparable for both the testing data set and the validation data set which comes from very diverse sources. However, careful manual examinations by experienced radiologists show mistakes in the predictions, which could be caused by the anatomical complexities. Nevertheless, the percentage of the opacity region can predict the severity of the patients well in regards to the ICU admissions and mortality.

Conclusion

In view of the above, our model is a successful first try in the development of a segmentation model for the opacity regions for the Covid-19 positive chest X-rays. However, additional work is needed before a robust model can be developed for the ultimate goal of the implementations in the clinical setting.

Model and supporting materials can be found in https://github.com/haimingt/opacity_segmentation_covid_chest_X_ray.
Prevalence of SARS-CoV-2 IgG antibodies in a population from Veracruz (Southeastern Mexico)
Authors: Remes-Troche Jose María , Ramos-De-la-Medina Antonio , Manríquez-Reyes Marisol , Martínez-Pérez Maldonado Laura , Solis-Gonzalez María Antonieta , Hernández Flores Karina Guadalupe , Cid Héctor Vivanco
Published: October 2020

Introduction/Aim

Recent studies have shown that seroprevalence is quite variable depending on the country, the population and the time of the pandemic in which the serological tests are performed. Here, we investigated the prevalence of IgG antibodies against SARS-CoV-2 in a population living in Veracruz City, México.

Methods

From of June 1 to July 31, 2020, the consecutive adult patients (age ≥18 years) that attended 2 ambulatory diagnostic private practice centers for testing were included. Samples were run on the Abbott Architect instrument using the commercial Abbott SARS-CoV-2 IgG assay. The main outcome was seroprevalence. Demographics, previous infection to SARS-CoV-2 (according to a previous positive polymerase-chain reaction nasopharyngeal swab), self-suspicious of virus of infection (according to have in the previous 4 weeks either fever, headache, respiratory symptoms but not a confirmatory PCR) or no having symptoms were also evaluated.

Results

A total of 2174 subjects were tested, included 53.6% women (mean age 41.8±15.17 years, range 18-98 years). One thousand and forty-one (52.5%) subjects were asymptomatic, 722 (33.2%) had suspicious of infection and 311 (14.3%) had previous infection. Overall, 642 of 2174 (29.5% [95% CI 27.59%-31.47%]) of our population were seropositive. Seropositivity among groups was 21.3% in asymptomatic, 23.4% in self-suspicious patients and 73.9% in previous infection patients.

Conclusions

We found one of the highest seroprevalences reported for SARS-CoV-2 worldwide in asymptomatic subjects (21.3%) as well in subjects with self-suspicious of COVID-19 (23.4%). The number of infected subjects in our population is not encouraging and it should be interpreted with caution.
On nonlinear incidence rate of Covid-19
Authors: Paul Swarna Kamal , Jana Saikat , Bhaumik Parama
Published: October 2020

Classical Susceptible-Infected-Removed model with constant transmission rate and removal rate may not capture real world dynamics of epidemic due to complex influence of multiple external factors on the spread. On top of that transmission rate may vary widely in a large region due to non-stationarity of spatial features which poses difficulty in creating a global model. We modified discrete global Susceptible-Infected-Removed model by using time varying transmission rate, recovery rate and multiple spatially local models. No specific functional form of transmission rate has been assumed. We have derived the criteria for disease-free equilibrium within a specific time period. A single Convolutional LSTM model is created and trained to map multiple spatiotemporal features to transmission rate. The model achieved 8.39% mean absolute percent error in terms of cumulative infection cases in each locality in a 10-day prediction period. Local interpretations of the model using perturbation method reveals local influence of different features on transmission rate which in turn is used to generate a set of generalized global interpretations. A what-if scenario with modified recovery rate illustrates rapid dampening of the spread when forecasted with the trained model. A comparative study with current normal scenario reveals key necessary steps to reach baseline.
White matter brain aging In Relationship to Schizophrenia and Its Cognitive Deficit
Authors: Wang Jingtao , Kochunov Peter , Sampath Hemalatha , Hatch Kathryn S. , Ryan Meghann C. , Xue Fuzhong , Neda Jahanshad , Paul Thompson , Hahn Britta , Gold James , Waltz James , Hong L. Elliot , Chen Shuo
Published: October 2020

We hypothesized that cerebral white matter deficits in schizophrenia (SZ) are driven in part by accelerated white matter aging and are associated with cognitive deficits. We used machine learning model to predict individual age from diffusion tensor imaging features and calculated the delta age (Δage) as the difference between predicted and chronological age. Through this approach, we translated multivariate white matter imaging features into an age-scaled metric and used it to test the temporal trends of accelerated aging-related white matter deficit in SZ and its association with the cognition. Followed feature selection, a machine learning model was trained with fractional anisotropy values in 34 of 43 tracts on a training set consisted of 107 healthy controls (HC). The brain age of 166 SZs and 107 HCs in the testing set were calculated using this model. Then, we examined the SZ-HC group effect on Δage and whether this effect was moderated by chronological age using the regression spline model. The results showed that Δage was significantly elevated in the age >30 group in patients(p< 0.001) but not in age ⩽ 30 group(p= 0.364). Δage in patients was significantly and negatively associated with both working memory(β= −0.176,p= 0.007) and processing speed(β= −0.519,p= 0.035) while adjusting sex and chronological age. Overall, these findings indicate that the Δage is elevated in SZs and become significantly from middle life stage; the increase of Δage in SZs is associated with the decline neurocognitive performance.
Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw
Authors: Haan Tracie J. , Drown Devin M.
Published: October 2020

Understanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antibiotic resistance. In permafrost associated soils, climate and human driven forces augment near-surface thaw altering the overlying active layer. Physiochemical changes shift bacterial community composition and metabolic functioning, however, it is unknown if permafrost thaw will affect ARGs comprising the boreal soil resistome. To assess how thaw shifts the resistome, we performed susceptibility testing and whole genome sequencing on soil isolates from a disturbance-induced thaw gradient in Interior Alaska. We found resistance was widespread in the Alaskan isolates, with 87% of the 90 isolates resistant to at least one of the five antibiotics. We also observed positive trends in both the proportion of resistant isolates and the abundance of ARGs with permafrost thaw. However, the number of ARGs per genome and types of genes present were shown to cluster more strongly by bacterial taxa rather than thaw emphasizing the evolutionary origins of resistance and the role vertical gene transfer has in shaping the predominantly chromosomally encoded ARGs. The observed higher proportion of plasmid-borne and distinct ARGs in our isolates compared to RefSoil+ suggests local conditions affect the composition of the resistome along with selection for ARG mobility. Overall taxonomy and geography shape the resistome, suggesting that as microbial communities shift in response to permafrost thaw so will the ARGs in the boreal active layer.

IMPORTANCE

As antibiotic resistance continues to emerge and rapidly spread in clinical settings, it is imperative to generate studies that build insight into the ecology of environmental resistance genes that pose a threat to human health. This study provides insight into the occurrence of diverse ARGs found in Alaskan soil bacteria which is suggestive of the potential to compromise health. The observed differences in ARG abundance with increasing permafrost thaw suggest the role of soil disturbance in driving the distribution of resistant determinants and the predominant taxa that shape the resistome. Moreover, the high-quality whole genome assemblies generated in this study are an extensive resource for microbial researchers interested in permafrost thaw and will provide a steppingstone for future research into ARG mobility and transmission risks.