bluuebunny/crossref_metadata_2025 huggingface dataset:
Bistability of somatic pattern memories: stochastic outcomes in bioelectric circuits underlying regeneration
Authors: Pezzulo Giovanni , LaPalme Joshua , Durant Fallon , Levin Michael
Published: February 2021

Nervous systems’ computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signalling originated in cells' communication with the outside world and with each other, enabling cooperation towards adaptive construction and repair of multicellular bodies. Here, we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering and even artificial intelligence. One of the predictions of this view is that regeneration and regulative development can restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states—in this case, pattern memories. We propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuitsin vivocan implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology and biomedicine of information processingin vivo.

This article is part of the theme issue ‘Basal cognition: multicellularity, neurons and the cognitive lens’.
Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil
Authors: Sakdapetsiri Chatsuda , Kuntaveesuk Aunchisa , Ngaemthao Wipaporn , Suriyachadkun Chanwit , Muangchinda Chanokporn , Chavanich Suchana , Viyakarn Voranop , Chen Bo , Pinyakong Onruthai
Published: February 2021

A novel bacterium, designated strain ANT13_2T, was isolated from a phenanthrene-degrading consortium enriched from a soil sample collected near the Great Wall Station located in the southwestern area of King George Island, Antarctica. Following a polyphasic taxonomic study, a novel species belonging to the genus

Paeniglutamicibacter

was described. The strain was a Gram-stain-positive bacterium that exhibited a rod–coccus growth cycle. Strain ANT13_2T grew aerobically at an optimum temperature of 20–25 °C and at pH 7.0–8.0. Ribose, arabinose and glucose were detected as whole-cell sugars. The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C15 : 0 (67.7 %) and anteiso-C17 : 0 (11.2 %). The DNA G+C content of the genomic DNA was 60.6 mol%. Based on 16S rRNA gene sequence analysis, strain ANT13_2T showed the highest similarities to

Paeniglutamicibacter antarcticus

SPC26T (98.9 %) followed by

Paeniglutamicibacter gangotriensis

Lz1yT (98.4 %),

Paeniglutamicibacter sulfureus

DSM 20167T (98.3%) and

Paeniglutamicibacter kerguelensis

KGN15T (97.9 %). The average nucleotide identity values between strain ANT13_2T and the type strains of

P. antarcticus

SPC26T and

P. gangotriensis

Lz1yT were 73.8 and 77.5 %, respectively, which are well below the 95–96 % species circumscription threshold. On the basis of this polyphasic taxonomic study, strain ANT13_2T is proposed to represent a novel species to be named Paeniglutamicibacter terrestris sp. nov. The type strain is ANT13_2T (=TBRC 11756T=NBRC 114615T).
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history
Authors: Coscolla Mireia , Gagneux Sebastien , Menardo Fabrizio , Loiseau Chloé , Ruiz-Rodriguez Paula , Borrell Sonia , Otchere Isaac Darko , Asante-Poku Adwoa , Asare Prince , Sánchez-Busó Leonor , Gehre Florian , Sanoussi C. N’Dira , Antonio Martin , Affolabi Dissou , Fyfe Janet , Beckert Patrick , Niemann Stefan , Alabi Abraham S. , Grobusch Martin P. , Kobbe Robin , Parkhill Julian , Beisel Christian , Fenner Lukas , Böttger Erik C. , Meehan Conor J. , Harris Simon R. , de Jong Bouke C. , Yeboah-Manu Dorothy , Brites Daniela
Published: February 2021

Human tuberculosis (TB) is caused by members of the

Mycobacterium tuberculosis

complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto, as well as two lineages (L5 and L6) traditionally referred to as

Mycobacterium africanum

. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known of their genomic diversity, phylogeography and evolution. Here, we analysed the genomes of 350 L5 and 320 L6 strains, isolated from patients from 21 African countries, plus 5 related genomes that had not been classified into any of the known MTBC lineages. Our population genomic and phylogeographical analyses showed that the unclassified genomes belonged to a new group that we propose to name MTBC lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure and genetic diversity. Finally, we could not confirm the previous association of drug-resistance markers with lineage and sublineages. Instead, our results indicate that the association of drug resistance with lineage is most likely driven by sample bias or geography. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of

M. africanum

, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of TB in Africa and globally.
West Nile virus in Portugal
Authors: Lourenço José , Barros Sílvia C , Zé-Zé Líbia , Damineli Daniel SC , Giovanetti Marta , Osório Hugo C , Amaro Fátima , Henriques Ana M , Ramos Fernanda , Luís Tiago , Duarte Margarida D , Fagulha Teresa , Alves Maria J , Obolski Uri
Published: February 2021

West Nile virus (WNV) causes outbreaks with sustained spillover to humans in many European countries. Despite Portugal’s Mediterranean climate being adequate for WNV transmission, only four human infections have been detected there so far. Here, we offer an historical account of past WNV circulation and develop new, climate-driven insights on the geo-temporal suitability for WNV transmission in Portugal. WNV and vector related literature and database reviews were performed in the context of Portugal covering the time period 1966-2020, and local climate data were used to estimate WNV transmission suitability for the period 1981-2019. Reviewed data demonstrate that WNV-compatible vectors are abundant across the entire country, while molecular and serological evidence for WNV circulation has mostly been associated with the southern districts. Our estimated WNV transmission suitability was found to support geographical differences in transmission potential that favour the southern districts, with an increasing trend over the past forty years due to climate change. Empirical and theoretical evidence supports WNV circulation in Portugal, but it remains unclear whether the virus is endemic or sporadically transmitted. Given the recent public health emergencies related to WNV in other European countries and the findings herein described in relation to Portugal, our study supports a timely change towards a local WNV active surveillance.

Abstract Figure
TOP-Plus is a Versatile Biosensor Platform for Monitoring SARS-CoV-2 Antibody Durability
Authors: Racine-Brzostek Sabrina E. , Karbaschi Mohsen , Gaebler Christian , Klasse P.J. , Yee Jim , Caskey Marina , Yang He S. , Hao Ying , Chadburn Amy , Shi Yuanyuan , Zuk Robert , Nussenzweig Michel C. , Cushing Melissa M. , Zhao Zhen
Published: February 2021

Background

There is a concern that low initial SARS-CoV-2 antibody titers in individuals may drop to undetectable levels within months after infection. Although this may raise concerns over long term immunity, both the antibody levels and avidity of the antibody-antigen interaction should be examined to understand the quality of the antibody response.

Methods

A testing-on-a-probe “plus” panel (TOP-Plus) was developed, which included a newly developed avidity assay built into the previously described SARS-CoV-2 TOP assays that measured total antibody (TAb), surrogate neutralizing antibody (SNAb), IgM and IgG on a versatile biosensor platform. TAb and SNAb levels were compared with avidity in previously infected individuals at 1.3 and 6.2 months post-infection in paired samples from 80 COVID-19 patients.

Results

The newly designed avidity assay in this TOP panel correlated well with a reference Bio-Layer Interferometry avidity assay (R=0.88). The imprecision of the TOP avidity assay was less than 9%. Although TAb and neutralization activity (by SNAb) decreased between 1.3 and 6.2 months post infection, the antibody avidity increased significantly (P < 0.0001).

Conclusion

This highly precise and versatile TOP-Plus panel with the ability to measure SARS-CoV-2 TAb, SNAb, IgG and IgM antibody levels and avidity of individual sera on one sensor can become a valuable asset in monitoring not only SARS-CoV-2-infected patients, but also the status of individuals’ COVID-19 vaccination response.
High-throughput splicing assays identify missense and silent splice-disruptivePOU1F1variants underlying pituitary hormone deficiency
Authors: Gergics Peter , Smith Cathy , Bando Hironori , Jorge Alexander A. L. , Rockstroh-Lippold Denise , Vishnopolska Sebastian , Castinetti Frederic , Maksutova Mariam , Carvalho Luciani Renata Silveira , Hoppmann Julia , Mayer Julian Martinez , Albarel Frédérique , Braslavsky Debora , Keselman Ana , Bergadá Ignacio , Martí Marcelo , Saveanu Alexandru , Barlier Anne , Jamra Rami Abou , Guo Michael H. , Dauber Andrew , Nakaguma Marilena , Mendonça Berenice B , Ozel A Bilge , Fang Qing , Ma Qianyi , Li Jun Z. , Brue Thierry , Millán María Ines Pérez , Kitzman Jacob O. , Arnhold Ivo JP , Pfaeffle Roland , Camper Sally A.
Published: February 2021

Pituitary hormone deficiency occurs in ∼1:4,000 live births. Approximately 3% of the cases are due to mutations in the alpha isoform of POU1F1, a pituitary-specific transcriptional activator. We found four separate heterozygous missense variants in unrelated hypopituitarism patients that were predicted to affect a minor isoform, POU1F1 beta, which can act as a transcriptional repressor. These variants retain repressor activity, but they shift splicing to favor the expression of the beta isoform, resulting in dominant negative loss of function. Using a high throughput splicing reporter assay, we tested 1,080 single nucleotide variants inPOU1F1. We identified 113 splice disruptive variants, including 23 synonymous variants. We evaluated separate cohorts of hypopituitarism patients and found two different synonymous splice disruptive variants that co-segregate with hypopituitarism. This study underlines the importance of evaluating the impact of variants on splicing and provides a catalog for interpretation of variants of unknown significance in thePOU1F1gene.
The successful introduction of a hand dermatitis clinic to reduce occupational dermatoses during the covid-19 pandemic
Authors: Walsh Sarah , Carey Siobhan
Published: February 2021

Background

The SARS-Co-V pandemic has necessitated strict hand hygiene practices in healthcare settings. An increased incidence of staff presentations of occupational dermatitis in our institutions prompted the establishment of a drop-in access daily hand dermatitis clinic.

Objective

to document the incidence and severity of cases of occupational dermatitis arising in healthcare workers during the first wave of the pandemic, and to reduce the impact of this with early assessment and treatment.

Methods

an open-access daily staff clinic run by dermatologists was established, and demographic and clinical data collected from each clinical encounter.

Results

532 staff attended the clinic over a 6 week period. This compared to 7 staff presenting to occupational health over the same period in 2019. The majority were females 81%,and ward based 51%. ITU and A&E staff represented 15%. The prevalence of occupational hand dermatitis was 88%. 52% were classed as mild, 26% as moderate 26% and 9% severe/very severe.

Conclusions

the pandemic and associated hand hygiene practices have led to a substantial increase in presentations of occupational hand dermatitis. A drop-in clinic proved an effective way of allowing staff to access treatment in a timely fashion.
Staff-Pupil SARS-CoV-2 Infection Pathways in Schools: A Population Level
Linked Data Approach
Authors: Thompson Daniel A , Abbasizanjani Hoda , Fry Richard , Marchant Emily , Griffiths Lucy , Akbari Ashley , Hollinghurst Joe , North Laura , Lyons Jane , Torabi Fatemeh , Davies Gareth , Gravenor Mike B , Lyons Ronan
Published: February 2021

Background

Better understanding of the role that children and school staff play in
the transmission of SARS-CoV-2 is essential to guide policy development on
controlling infection whilst minimising disruption to children’s education
and wellbeing.

Methods

Our national e-cohort (n=500,779) study used anonymised linked data for
pupils, staff and associated households linked via educational settings. We
estimated the risk of testing positive for SARS-CoV-2 infection for staff
and pupils over the period August - December 2020, dependent on measures of
recent exposure to known cases linked to their educational
settings.

Results

The total number of cases in a school was not associated with a
subsequent increase in the risk of testing positive (Staff OR per case 0.92,
95%CI 0.85, 1.00; Pupils OR per case 0.98, 95%CI 0.93, 1.02). Amongst
pupils, the number of recent cases within the same year group was
significantly associated with subsequent increased risk of testing positive
(OR per case 1.12, 95%CI 1.08 – 1.15). These effects were adjusted for a
range of demographic covariates, and in particular any known cases within
the same household, which had the strongest association with testing
positive (Staff OR 39.86, 95%CI 35.01, 45.38, pupil OR 9.39, 95%CI 8.94 –
9.88).

Conclusions

In a national school cohort, the odds of staff testing positive for
SARS-CoV-2 infection were not significantly increased in the 14-day period
after case detection in the school. However, pupils were found to be at
increased risk, following cases appearing within their own year group, where
most of their contacts occur. Strong mitigation measures over the whole of
the study period may have reduced wider spread within the school
environment.

What is known

Evidence of the role schools play in the transmission of
SARS-CoV-2 is limited

Higher positivity rates are observed in school staff
compared to pupils

Lack of evidence on transmission pathways transmission
into and within schools

What this study adds

First UK national level study of transmission between
pupils and staff in a school environment during the
SARS-CoV-2 pandemic.

Schools opening September-December 2020 was not
associated with an increased subsequent risk of testing
positive in staff

Pupils were found to be at increased risk of testing
positive, following cases appearing within their own year
group
SOUTH AMERICAN INDIGENOUS COMMUNITIES AND BODY MASS INDEX: A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Jara Carlos P , Mendes Natalia Ferreira , José Gomes Campos Claudinei , de Freitas Maria Isabel Pedreira , Oliveira Henrique Ceretta , Velloso Lício Augusto , de Araujo Eliana Pereira
Published: February 2021

Obesity is an increasing new pandemic. Currently more than 1.9 billion adults are overweight and at least 700 million of them are obese. Obesity is the result of a positive energy balance, which is conditioned by both environmental and genetic factors. Interestingly, individuals from similar ethnic-based ancestry communities, share both environmental and genetic features. Here, we described the relationship between indigenous Chilean groups and body mass Index. We conducted a Systematic review and Meta-analysis on Pubmed, LILACS, Scielo, Web of Science and Scopus databases. Our results showed that Indigenous Children present a lower BMI than Non-Indigenous Children. However, no difference within BMI was identified in adults. The gender affected the BMI as well. Aymara and Mapuche Women presented higher BMI than Indigenous Men. In the other hand, Indigenous people living in rural environment showed lower BMI than those whose live-in urban areas. Finally, Indigenous communities presented no difference in the risk to suffer Obesity when compared with Non-Indigenous communities. Here suggest that ethnicity could be a health determinant as well as a risk factor for obesity. Then, targeted prevention strategies with ethnic-based focus would be developed.
Mapping internet activity in Australian cities during COVID-19 lockdown: how occupational factors drive inequality
Authors: Zachreson Cameron , Martino Erika , Tomko Martin , Shearer Freya M. , Bentley Rebecca , Geard Nicholas
Published: February 2021

During the COVID-19 pandemic, evidence has accumulated that movement restrictions enacted to combat virus spread produce disparate consequences along socioeconomic lines. We investigate the hypothesis that people engaged in financially secure employment are better able to adhere to mobility restrictions, due to occupational factors that link the capacity for flexible work arrangements to income security. We use high-resolution spatial data on household internet traffic as a surrogate for adaptation to home-based work, together with the geographical clustering of occupation types, to investigate the relationship between occupational factors and increased internet traffic during work hours under lockdown in two Australian cities. By testing our hypothesis based on the observed trends, and exploring demographic factors associated with divergences from our hypothesis, we are left with a picture of unequal impact dominated by two major influences: the types of occupations in which people are engaged, and the composition of households and families. During lockdown, increased internet traffic was correlated with income security and, when school activity was conducted remotely, to the proportion of families with children. Our findings suggest that response planning and provision of social and economic support for residents within lockdown areas should explicitly account for income security and household structure. Overall, the results we present contribute to the emerging picture of the impacts of COVID-19 on human behaviour, and will help policy makers to understand the balance between public health and social impact in making decisions about mitigation policies.
Engagement with COVID-19 Public Health Measures in the United States: A Cross-Sectional Social Media Analysis from June to November 2020
Authors: Massey Daisy , Huang Chenxi , Lu Yuan , Cohen Alina , Oren Yahel , Moed Tali , Matzner Pini , Mahajan Shiwani , Caraballo César , Kumar Navin , Xue Yuchen , Ding Qinglan , Dreyer Rachel P. , Roy Brita , Krumholz Harlan M.
Published: February 2021

Background

The coronavirus disease 2019 (COVID-19) has continued to spread in the US and globally. Closely monitoring public engagement and perception of COVID-19 and preventive measures using social media data could provide important information for understanding the progress of current interventions and planning future programs.

Objective

To measure the public’s behaviors and perceptions regarding COVID-19 and its daily life effects during the recent 5 months of the pandemic.

Methods

Natural language processing (NLP) algorithms were used to identify COVID-19 related and unrelated topics in over 300 million online data sources from June 15 to November 15, 2020. Posts in the sample were geotagged, and sensitivity and specificity were both calculated to validate the classification of posts. The prevalence of discussion regarding these topics was measured over this time period and compared to daily case rates in the US.

Results

The final sample size included 9,065,733 posts, 70% of which were sourced from the US. In October and November, discussion including mentions of COVID-19 and related health behaviors did not increase as it had from June to September, despite an increase in COVID-19 daily cases in the US beginning in October. Additionally, counter to reports from March and April, discussion was more focused on daily life topics (69%), compared with COVID-19 in general (37%) and COVID-19 public health measures (20%).

Conclusions

There was a decline in COVID-19-related social media discussion sourced mainly from the US, even as COVID-19 cases in the US have increased to the highest rate since the beginning of the pandemic. Targeted public health messaging may be needed to ensure engagement in public health prevention measures until a vaccine is widely available to the public.
Immune cell residency in the nasal mucosa and COVID-19 severity across the age range
Authors: Winkley Konner , Banerjee Dithi , Louiselle Daniel , Biswell Rebecca , Posey Nyshele , Fatheree Kelly , McDanel Stephanie , Bradley Todd , Moffatt Mary E. , Koseva Boryana , Cheung Warren A , Johnston Jeffrey J , Selvarangan Rangaraj , Pastinen Tomi , Grundberg Elin
Published: February 2021

Severe coronavirus disease of 2019 (COVID-19) positively correlates with age (Centers for Disease Control), develops after progression of infection from the upper airway to the lower respiratory tract (LRT), and can worsen into acute respiratory distress syndrome (ARDS) (Shi et al., 2020). Why children seem to be less likely to develop severe disease remains unclear. As the nasal mucosa (NM) is the first site of contact and defense for respiratory pathogens such as SARS-CoV-2 before dissemination to the LRT (Casadei and Salinas, 2019), we hypothesized that differences in this tissue across the age range may help explain the disparity in COVID-19 severity. To this end, we profiled NM samples across the lifespan in health and disease. We find that global transcriptomic changes including the expression of SARS-CoV-2 and coronavirus-associated receptors and factors are not correlated with age or the novel virus type, since pediatric NM cells mount similar antiviral response to both SARS-CoV-2 or Influenza B. Rather, we find immune cell residency in NM decreases dramatically with age especially cells of the innate immune system. This includes a resident-memory-like T cell subset with antiviral properties. These observations give plausible biological explanation to the observed clinical differences in disease spectrum and provide a foundation for future experimental studies.
Molecular Mechanism of Parosmia
Authors: Parker Jane K. , Kelly Christine E. , Gane Simon B.
Published: February 2021

The molecular stimuli that trigger a parosmic response have been identified. Parosmia is a debilitating disease in which familiar smells become distorted and unpleasant. Often a result of post infectious smell loss, incidences are increasing as the number of COVID-19 cases escalates worldwide. Little is understood of its pathophysiology, but the prevailing hypothesis for the underlying mechanism is a mis-wiring of olfactory sensory neurons. We identified 15 different molecular triggers in coffee using GC-Olfactometry as a relatively rapid screening tool for assessment of both quantitative olfactory loss and parosmia. This provides evidence for peripheral causation, but places constraints on the mis-wiring theory.
Modeling fractional order dynamics of Syphilis via Mittag-Leffler law
Authors: Bonyah E. , Chukwu C.W. , Juga M.L. , Fatmawati
Published: February 2021

Syphilis is one the most dangerous sexually transmitted disease which is common in the world. In this work, a mathematical model is formulated with an emphasis on treatment. The reproduction number which presents information on the spread of the disease is determined. The model’s steady states are established, and the disease free state’s local and global stability are studied. The existence and uniqueness of solutions for both Caputo-Fabrizio and Atangana-Baleanu derivative in the Caputo sense are established. Numerical simulations were carried out to support the analytical solution, which indicates that the fractional order derivatives influence the dynamics of the spread of the Syphilis in the community.

2010 MSC: 00-01, 99-00
Loss of Factor H family proteins associates with meningococcal disease severity
Authors: van Beek Anna E. , Pouw Richard B. , Wright Victoria J. , Sallah Neneh , Inwald David , Hoggart Clive , Brouwer Mieke C. , Galassini Rachel , Thomas John , Calvo-Bado Leo , Fink Colin , Jongerius Ilse , Hibberd Martin , Wouters Diana , Levin Michael , Kuijpers Taco W.
Published: February 2021

Neisseria meningitidis, the causative agent of meningococcal disease (MD), evades complement-mediated clearance upon infection by ‘hijacking’ the human complement regulator factor H (FH). The FH protein family also comprises the homologous FH-related (FHR) proteins, hypothesized to act as antagonists of FH, and FHR-3 has recently been implicated to play a major role in MD susceptibility. Here, we show that, next to FH and FHR-3, the circulating levels of all FH family proteins are equally decreased during pediatric MD. We did not observe a specific consumption of FH or FHR-3 byN. meningitidisduring the first days of infection and the levels recovered over time. MD severity associated predominantly with a loss of FH. Strikingly, loss of FH and FHRs associated strongly with renal failure, suggesting insufficient protection of host tissue by the FH protein family. Retaining higher levels of FH family proteins may thus limit tissue injury during MD.
How effective was Newfoundland & Labrador’s travel ban to prevent the spread of COVID-19? An agent-based analysis
Authors: Aleman Dionne M. , Tham Benjamin Z. , Wagner Sean J. , Semelhago Justin , Mohammadi Asghar , Price Paul , Giffen Randy , Rahman Proton
Published: February 2021

Background

To prevent the spread of COVID-19 in Newfoundland & Labrador (NL), NL implemented a wide travel ban in May 2020. We estimate the effectiveness of this travel ban using a customized agent-based simulation (ABS).

Methods

We built an individual-level ABS to simulate the movements and behaviors of every member of the NL population, including arriving and departing travellers. The model considers individual properties (spatial location, age, comorbidities) and movements between environments, as well as age-based disease transmission with pre-symptomatic, symptomatic, and asymptomatic transmission rates. We examine low, medium, and high travel volume, traveller infection rates, and traveller quarantine compliance rates to determine the effect of travellers on COVID spread, and the ability of contact tracing to contain outbreaks.

Results

Infected travellers increased COVID cases by 2-52x (8-96x) times and peak hospitalizations by 2-49x (8-94x), with (without) contact tracing. Although contact tracing was highly effective at reducing spread, it was insufficient to stop outbreaks caused by travellers in even the best-case scenario, and the likelihood of exceeding contact tracing capacity was a concern in most scenarios. Quarantine compliance had only a small impact on COVID spread; travel volume and infection rate drove spread.

Interpretation

NL’s travel ban was likely a critically important intervention to prevent COVID spread. Even a small number of infected travellers can play a significant role in introducing new chains of transmission, resulting in exponential community spread and significant increases in hospitalizations, while outpacing contact tracing capabilities. With the presence of more transmissible variants, e.g., the UK variant, prevention of imported cases is even more critical.
INCLUSIVE HEALTH: MODELING COVID-19 IN CORRECTIONAL FACILITIES AND COMMUNITIES
Authors: Greenhalgh Scott , Provencher Ashley
Published: February 2021

Mass incarceration, commonly associated with overcrowding and inadequate health resources for incarcerated people, creates a fertile environment for the spread of the coronavirus disease 2019 (COVID-19) in U.S. correctional facilities. The exact role that correctional facilities play in enhancing COVID-19 spread and enabling community re-emergence of COVID-19 is unknown. We constructed a novel stochastic model of COVID-19 transmission to estimate the impact of correctional facilities, specifically jails and state prisons, for enhancing disease transmission and enabling disease re-emergence in local communities. Using our model, we evaluated scenarios of testing and quarantining infected incarcerated people at 0.0, 0.5, and 1.0 times the rate that occurs for infected people in the local community for population sizes of 5, 10, and 20 thousand people. Our results illustrate testing and quarantining an incarcerated population of 800 would reduce the probability of a major community outbreak by 6% and also prevent between 250 to 730 incidences of COVID-19 per year, depending on local community size. These findings illustrate that managing COVID-19 in correctional facilities is essential to mitigate risks to community health, and thereby stresses the importance of improving the health standards of incarcerated people.
A wind speed threshold for increased outdoor transmission of coronavirus: An ecological study
Authors: Clouston Sean A. P. , Morozova Olga , Meliker Jaymie R.
Published: February 2021

Background

To examine whether outdoor transmission may contribute to the COVID-19 epidemic, we hypothesized that slower outdoor wind speed is associated with increased risk of transmission when individuals socialize outside.

Methods

Daily COVID-19 incidence reported in Suffolk County, NY, between March 16th– December 31st, 2020, was the outcome. Average wind speed and maximal daily temperature were collated by the National Oceanic and Atmospheric Administration. Negative binomial regression was used to model incidence rates while adjusting for susceptible population size.

Results

Cases were very high in the initial wave but diminished once lockdown procedures were enacted. Most days between May 1st, 2020, and October 24th, 2020, had temperatures 16-28°C and wind speed diminished slowly over the year and began to increase again in December 2020. Unadjusted and multivariable-adjusted analyses revealed that days with temperatures ranging between 16-28°C where wind speed was <8.85 kilometers per hour (KPH) had increased COVID-19 incidence (aIRR=1.45, 95% C.I.=[1.28-1.64], P<0.001) as compared to days with average wind speed ≥8.85 KPH.

Conclusion

Throughout the U.S. epidemic, the role of outdoor shared spaces such as parks and beaches has been a topic of considerable interest. This study suggests that outdoor transmission of COVID-19 may occur by noting that the risk of transmission of COVID-19 in the summer was higher on days with low wind speed. Outdoor use of increased physical distance between individuals, improved air circulation, and use of masks may be helpful in some outdoor environments where airflow is limited.
PesTrapp mobile app: A trap setting application for real-time entomological field and laboratory study
Authors: Ling Cheong Yoon , Rasli Rosilawati , Che Ibrahim Mohd Khairuddin , Farahininajua Fikri Siti Futri , Nazarudin Nur Ayuni , Hock Lim Kuang , Muhamed Khairul Asuad , Tajul Hassan Mohd Zahari , Yahya Umpong Mohd Izral , Taib Mohd Zainuldin , Ahmad Nazni Wasi , Lim Lee Han
Published: February 2021

Zoonotic diseases such as malaria, dengue, Zika and chikungunya remain endemic in many countries. Setting and deploying trap to capture the host/vector species are fundamental to understand their density and distribution. Human effort to manage the trap data accurately and timely is an exhaustive endeavour when the study area expands and study period prolongs. One stop mobile app to manage and monitor the process of animal trapping, from field to laboratory level is still scarce. We developed a new mobile app named “PesTrapp” especially for medical entomologists to acquire the vector density index based on the mobile updates of ovitraps and species information in field and laboratory. This study aimed to highlight the mobile app’s development and design, describe the user experience and evaluate the preliminary user assessment of the mobile app. The mobile app was developed using mobile framework and database. User evaluation of the mobile app was based on the adjusted Mobile App Rating Scale and Standardized User Experience Percentile Rank Questionnaire. The process flows of system design and detailed screen layouts were described. The user experiences of using the app in a project to study Aedes surveillance in six study sites in Selangor, Malaysia were described. The overall mean user evaluation score of the mobile app was 4.0 (SD=0.6), which showed its acceptability by the users. The PesTrapp, a one-stop solution, is anticipated to improve the entomological surveillance work processes. This new mobile app can contribute as a tool in the vector control countermeasure strategies.
The kinetic variations of anti-nucleocapsid antibody in SARS-CoV-2 infection
Authors: Kawada Shoji , Ogata Atsushi , Kato Yasuhiro , Okamoto Masashi , Yamaguchi Yuta , Morita Takayoshi , Kumanogoh Atsushi
Published: February 2021

The humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in controlling coronavirus disease 2019 (COVID-19) infections. However, little is known about the persistence of the antibody response.

We evaluated that the kinetics of anti-nucleocapsid protein antibody of SARS-CoV2 infected healthcare workers in COVID-19 cluster occurred hospital. The long-term kinetics of anti-N antibody was classified high and keep pattern, high and decay pattern, and low and keep pattern. COVID-19 contact and symptomaticity was not related to kinetic patterns.

The reason of kinetic difference was still unclear. However natural anti-SARS-CoV-2 antibody persistence was not uniform, suggesting inter-individual difference of SARS-CoV2 vaccine efficacy.
ADHD in adults with recurrent depression
Authors: Powell Victoria , Agha Sharifah Shameem , Jones Rhys Bevan , Eyre Olga , Thapar Anita , Rice Frances
Published: February 2021

Background

Depression is highly heterogeneous in its clinical presentation. Those with attention deficit/hyperactivity disorder (ADHD) may be at risk of a more chronic and impairing depression compared to those with depression alone according to studies of young people. However, no studies to date have examined ADHD in recurrently depressed adults in mid-life.

Aims

To investigate ADHD in women in mid-life with a history of recurrent depression.

Method

In a sample of women in mid-life (n=148) taken from a UK based prospective cohort of adults with a history of recurrent depression, we investigated the prevalence of ADHD and the association of ADHD with clinical features of depression.

Results

12.8% of the recurrently depressed women had elevated ADHD symptoms and 3.4% met DSM-5 diagnostic criteria for ADHD. None of the women reported having a diagnosis of ADHD from a medical professional. ADHD was associated with earlier age of depression onset, higher depression associated impairment, a greater recurrence of depressive episodes and increased persistence of subthreshold depression symptoms over the study period, higher levels of irritability and increased risk of self-harm or suicide attempt. ADHD symptoms were associated with increased risk of hospitalisation and receiving non-first line antidepressant medication.

Conclusions

Higher ADHD symptoms appear to index a worse clinical presentation for depression. Findings suggest that in women with early onset, impairing and recurrent depression, the possibility of underlying ADHD masked by depression needs to be considered.
The antibody response to SARS-CoV-2 infection persists over at least 8 months in symptomatic patients
Authors: Levi Riccardo , Ubaldi Leonardo , Pozzi Chiara , Angelotti Giovanni , Sandri Maria Teresa , Azzolini Elena , Salvatici Michela , Savevski Victor , Mantovani Alberto , Rescigno Maria
Published: February 2021

The factors involved in the persistence of antibodies to SARS-CoV-2 are unknown. We evaluated the antibody response to SARS-CoV-2 in personnel from 10 healthcare facilities and its association with individuals’ characteristics and COVID-19 symptoms in an observational study. We enrolled 4735 subjects (corresponding to 80% of all personnel) for three time points over a period of 8-10 months. For each participant, we determined the rate of antibody increase or decrease over time in relation to 93 features analyzed in univariate and multivariate analyses through a machine learning approach. In individuals positive for IgG (≥ 12 AU/mL) at the beginning of the study, we found an increase [p= 0.0002] in antibody response in symptomatic subjects, particularly with anosmia/dysgeusia (OR 2.75, 95% CI 1.753 – 4.301), in a multivariate logistic regression analysis. This may be linked to the lingering of SARS-CoV-2 in the olfactory bulb.
Disparities After Discharge: The Association of Limited English Proficiency and Post-Discharge Patient Reported Issues
Authors: Malevanchik Lev , Wheeler Margaret , Gagliardi Kristin , Karliner Leah , Shah Sachin J.
Published: February 2021

Background

Patients with limited English proficiency (LEP) experience worse outcomes following hospital discharge. Care transition programs are common, yet little is known about the disparities in quality (process and outcome measures) experienced by patients with LEP.

Methods

We conducted a retrospective cohort study to determine the association of LEP and care transition quality at an urban, US academic hospital. We examined all adults discharge home from the hospital from May 2018 through April 2019. All patients received a multilingual, automated telephone call three days after discharge to assess and address patient-reported issues. We determined care transition quality using process measures (reach rate, time to resolve reported issue) and outcome measures (discharge instructions questions, difficulty obtaining prescriptions, medication concerns, follow up care questions, new or worsening symptoms, any other clinical issues). All results were adjusted for measured confounders; we used predicted probabilities and average marginal effect (AME) to describe associations.

Results

13,860 patients were included in the study; 11% had LEP. The program reached most patients regardless of LEP status but was less likely to reach patients with LEP (AME 3.3%; 95% CI, 1.4% to 5.1%). After adjustment, patients with LEP reported high rates of all measured patient-reported outcomes: discharge instruction (AME 4.8%; 95% CI, 2.7% to 6.9%), obtaining prescriptions (AME 2.9%; 95% CI, 0.6% to 5.1%), medications concerns (AME 2.3%; 95% CI, 0.0% to 4.6%), follow up questions (AME 2.8%; 95% CI, 0.3% to 5.3%), new or worsening symptoms (AME 3.2%; 95% CI, 0.7% to 5.8%), and any other clinical issues (AME 3.6%; 95% CI, 1.1% to 6.1%). When issues were identified, the association between LEP and time to resolution of an issue was statistically, but not clinically, significant.

Conclusion and Relevance

Among patients with LEP, substantial disparities exist in patient-reported post-discharge outcome measures indicating a need for better discharge processes that focus on quality and health equity. Following discharge, relatively minor disparities were observed in the processes of a care transitions program that supports non-English languages.
Predicted distribution of a rare and understudied forest carnivore: Humboldt martens (Martes caurina humboldtensis)
Authors: Moriarty Katie , Thompson Joel , Delheimer Matthew , Barry Brent , Linnell Mark , Levi Taal , Hamm Keith , Early Desiree , Gamblin Holly , Gunther Micaela Szykman , Ellison Jordan , Prevéy Janet S. , Hartman Jennifer , Davis Ray
Published: February 2021

Background

A suite of mammalian species have experienced range contractions following European settlement and post-settlement development of the North American continent. For example, while North American martens (American marten,Martes americana; Pacific marten,M. caurina) generally have a broad range across northern latitudes, local populations have experienced substantial reductions in distribution and some extant populations are small and geographically isolated. The Humboldt marten (M. c. humboldtensis), a subspecies of Pacific marten that occurs in coastal Oregon and northern California, was recently designated as federally threatened in part due to its reduced distribution. To inform strategic conservation actions, we assessed Humboldt marten occurrence by compiling all known records from their range.

Methods

We compiled Humboldt marten locations since their rediscover to present (1,692 marten locations, 1996-2020). We spatially-thinned locations to 500-m to assess correlations with variables across contemporary Humboldt marten distribution (n=384). Using maximum entropy modeling (Maxent), we created distribution models with variables optimized for spatial scale; pre-selected scales were associated with marten ecology (50 to 1170 m radius). Marten locations were most correlated with abiotic factors (e.g., precipitation), which are unalterable and therefore uninformative within the context of restoration or management actions. Thus, we created variables to focus on hypothesized marten habitat relationships, including understory conditions such as predicted suitability of shrub species.

Results

Humboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon), mast producing trees), increased pine (Pinus sp) overstory cover and precipitation at home-range spatial scales, areas with low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature on the species, we found little evidence that Humboldt marten locations were associated with old growth structural indices, perhaps because of a potential mismatch in the association between this index and shrub cover. As with any species distribution model, there were gaps in predicted distribution where Humboldt martens have been located during more recent surveys, for instance the southeastern portion of Oregon’s coast range. Conservation efforts and our assessment of potential risks to Humboldt marten populations would benefit from additional information on range extent, population sizes, and fine-scale habitat use. Like many rare and lesser-known species, this case study provides an example of how limited information can provide differing interpretations, emphasizing the need for study-level replication in ecology.
Intraspecific trait changes have large impacts on community functional composition but do not affect ecosystem function
Authors: Pichon Noémie A. , Cappelli Seraina L. , Allan Eric
Published: February 2021

Plant functional traits can provide a more mechanistic understanding of community responses to global change and effects on ecosystem functions. In particular, nitrogen enrichment shifts trait composition by promoting dominance of fast growing, acquisitive plants (with high specific leaf area [SLA] and low leaf dry matter content [LDMC]), and such fast species have higher aboveground biomass production. Changes in mean trait values can be due to a shift in species identity, a shift in species relative abundance and/or a shift in intraspecific trait values. However, we do not know the relative importance of these three shifts in determining responses to global change and effects on function.

We quantified the relative importance of composition, abundance and intraspecific shifts in driving variation in SLA and LDMC. We collected leaf samples in a large grassland experiment, which factorially manipulates functional composition (slow vs. fast species), plant species richness, nitrogen enrichment and foliar fungal pathogen removal. We fitted structural equation models to test the relative importance of abundance shifts, intraspecific shifts and sown trait composition in contributing to overall variation in community weighted mean traits and aboveground and belowground biomass production.

We found that intraspecific shifts were as important as abundance shifts in determining community weighted mean traits, and even had large effects relative to a wide initial gradient in trait composition. Intraspecific trait shifts resulted in convergence towards intermediate SLA, in diverse communities, although convergence was reduced by nitrogen addition and enhanced by pathogen removal. In contrast, large intraspecific shifts in LDMC were not influenced by the treatments. Belowground biomass was reduced by SLA and increased by LDMC, while aboveground biomass increased in communities dominated by high SLA species. However, despite large intraspecific trait shifts, intraspecific variation in these traits had no effect on above or belowground biomass production.

Our results add to a growing body of literature showing large intraspecific trait variation and emphasise the importance of using field sampled data to determine community composition. However, they also show that intraspecific variation does not affect ecosystem functioning and therefore trait response-effect relationships may differ between vs. within species.
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees
Authors: Almodaresi Fatemeh , Khan Jamshed , Madaminov Sergey , Pandey Prashant , Ferdman Michael , Johnson Rob , Patro Rob
Published: February 2021

Motivation

In the past few years, researchers have proposed numerous indexing schemes for searching large databases of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes—Mantis, VariMerge, and Bifrost—that can serve as colored de Bruijn graph representations in addition to serving ask-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data.

Results

In this paper, we show how to build a scalable and updatable exact sequence-search index. Specifically, we extend Mantis using the Bentley-Saxe transformation to support efficient updates. We demonstrate Mantis’s scalability by constructing an index of≈40K samples from SRA by adding samples one at a time to an initial index of 10K samples.

Compared to VariMerge and Bifrost, Mantis is more efficient in terms of index-construction time and memory, query time and memory, and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Mantis scaled to more than 39K samples. Queries were over 24×faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Mantis indexes were about 2.5×smaller than Bifrost’s indexes and about half as big as VariMerge’s indexes.

Availability

The updatable Mantis implementation is available athttps://github.com/splatlab/mantis/tree/mergeMSTs.

Contact

rob@cs.umd.edu

Supplementary information

Supplementary data are available online.