bluuebunny/crossref_metadata_2025 huggingface dataset:
Semiclassical approach for excitonic spectrum of Coulomb coupling between two Dirac particles
Authors: Zalipaev Victor V. , Kuidin Vladislav V.
Published: July 2021

The properties of the energy spectrum of excitons in monolayer transition metal dichalcogenides are investigated using a multiband model. In the multiband model, we use the excitonic Hamiltonian in the product base of the Dirac single-particle states at the conduction and valence band edges. Following the separation of variables, we decouple the corresponding energy eigenvalue system of the first-order ODE radial equations rigorously and solve the resulting second-order ODE self-consistently, using the finite difference method, thus we determine the energy eigenvalues of the discrete excitonic spectrum and the corresponding wave functions. We also developed a WKB approach to solve the same spectral problem in semiclassical approximation for the resulting ODE. We compare the results for the energy spectrum and the corresponding eigen-function forms for WS
2
and WSe
2
obtained by means of both methods. We also compare our results for the energy spectrum with other theoretical works for excitons, and with available experimental data.
Bits and pieces: understanding information decomposition from part-whole relationships and formal logic
Authors: Gutknecht A. J. , Wibral M. , Makkeh A.
Published: July 2021

Partial information decomposition (PID) seeks to decompose the multivariate mutual information that a set of source variables contains about a target variable into basic pieces, the so-called ‘atoms of information’. Each atom describes a distinct way in which the sources may contain information about the target. For instance, some information may be contained uniquely in a particular source, some information may be shared by multiple sources and some information may only become accessible synergistically if multiple sources are combined. In this paper, we show that the entire theory of PID can be derived, firstly, from considerations of part-whole relationships between information atoms and mutual information terms, and secondly, based on a hierarchy of logical constraints describing how a given information atom can be accessed. In this way, the idea of a PID is developed on the basis of two of the most elementary relationships in nature: the part-whole relationship and the relation of logical implication. This unifying perspective provides insights into pressing questions in the field such as the possibility of constructing a PID based on concepts other than redundant information in the general n-sources case. Additionally, it admits of a particularly accessible exposition of PID theory.
Classification of first strain-gradient elasticity tensors by symmetry planes
Authors: Le Quang Hung , He Qi-Chang , Auffray Nicolas
Published: July 2021

First strain-gradient elasticity is a generalized continuum theory capable of modelling size effects in materials. This extended capability comes from the inclusion in the mechanical energy density of terms related to the strain-gradient. In its linear formulation, the constitutive law is defined by three elasticity tensors whose orders range from four to six. In the present contribution, the symmetry properties of the sixth-order elasticity tensors involved in this model are investigated. If their classification with respect to the orthogonal symmetry group is known, their classification with respect to symmetry planes is still missing. This last classification is important since it is deeply connected with some identification procedures. The classification of sixth-order elasticity tensors in terms of invariance properties with respect to symmetry planes is given in the present contribution. Precisely, it is demonstrated that there exist 11 reflection symmetry classes. This classification is distinct from the one obtained with respect to the orthogonal group, according to which there exist 17 different symmetry classes. These results for the sixth-order elasticity tensor are very different from those obtained for the classical fourth-order elasticity tensor, since in the latter case the two classifications coincide. A few numerical examples are provided to illustrate how some different orthogonal classes merge into one reflection class.
Nearly constant
Q
dissipative models and wave equations for general viscoelastic anisotropy
Authors: Hao Qi , Greenhalgh Stewart
Published: July 2021

The quality factor (
Q
) links seismic wave energy dissipation to physical properties of the Earth’s interior, such as temperature, stress and composition. Frequency independence of
Q
, also called constant
Q
for brevity, is a common assumption in practice for seismic
Q
inversions. Although exactly and nearly constant
Q
dissipative models are proposed in the literature, it is inconvenient to obtain constant
Q
wave equations in differential form, which explicitly involve a specified
Q
parameter. In our recent research paper, we proposed a novel weighting function method to build the first- and second-order nearly constant
Q
dissipative models. Of importance is the fact that the wave equations in differential form for these two models explicitly involve a specified
Q
parameter. This behaviour is beneficial for time-domain seismic waveform inversion for
Q
, which requires the first derivative of wavefields with respect to
Q
parameters. In this paper, we extend the first- and second-order nearly constant
Q
models to the general viscoelastic anisotropic case. We also present a few formulations of the nearly constant
Q
viscoelastic anisotropic wave equations in differential form.
Beyond periodic revivals for linear dispersive PDEs
Authors: Boulton Lyonell , Farmakis George , Pelloni Beatrice
Published: July 2021

We study the phenomenon of revivals for the linear Schrödinger and Airy equations over a finite interval, by considering several types of non-periodic boundary conditions. In contrast to the case of the linear Schrödinger equation examined recently (which we develop further), we prove that, remarkably, the Airy equation does not generally exhibit revivals even for boundary conditions very close to periodic. We also describe a new, weaker form of revival phenomena, present in the case of certain Robin-type boundary conditions for the linear Schrödinger equation. In this weak revival, the dichotomy between the behaviour of the solution at rational and irrational times persists, but in contrast to the classical periodic case, the solution is not given by a finite superposition of copies of the initial condition.
The eigenbuckling analysis of hexagonal lattices: closed-form solutions
Authors: Adhikari S.
Published: July 2021

Elastic instability such as the buckling of cellular materials plays a pivotal role in their analysis and design. Despite extensive research, the quantifi- cation of critical stresses leading to elastic instabi- lities remains challenging due to the inherent nonlinearities. We develop an analytical approach considering the spectral decomposition of the elasticity matrix of two-dimensional hexagonal lattice materials. The necessary and sufficient condition for the buckling is established through the zeros of the eigenvalues of the elasticity matrix. Through the analytical solution of the eigenvalues, the conditions involving equivalent elastic properties of the lattice were directly connected to the mathematical requirement of buckling. The equivalent elastic properties are expressed in closed form using geometric properties of the lattice and trigonometric functions of a non-dimensional axial force parameter. The axial force parameter was identified for four different stress cases, namely, compressive stress in the longitudinal and transverse directions separately and together and torsional stress. By solving the resulting nonlinear equations, we derive exact analytical expressions of critical eigenbuckling stresses for these four cases. Crucial parameter combinations leading to minimum buckling stresses are derived analytically. The exact closed-form analytical expressions derived in the paper can be used for quick engineering design calculations and benchmarking related experimental and numerical studies.
Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle
Authors: Álvarez-Varas Rocío , Rojas-Hernández Noemi , Heidemeyer Maike , Riginos Cynthia , Benítez Hugo A. , Araya-Donoso Raúl , Reséndiz Eduardo , Lara-Uc Mónica , Godoy Daniel A. , Muñoz-Pérez Juan Pablo , Alarcón-Ruales Daniela E. , Alfaro-Shigueto Joanna , Ortiz-Alvarez Clara , Mangel Jeffrey C. , Vianna Juliana A. , Véliz David
Published: July 2021

Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle (Chelonia mydas) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq; 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds (n= 158). Our results support genetic divergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation ofC. mydasto the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.
Temporal niche partitioning as a novel mechanism promoting co-existence of sympatric predators in marine systems
Authors: Lear Karissa O. , Whitney Nicholas M. , Morris John J. , Gleiss Adrian C.
Published: July 2021

Niche partitioning of time, space or resources is considered the key to allowing the coexistence of competitor species, and particularly guilds of predators. However, the extent to which these processes occur in marine systems is poorly understood due to the difficulty in studying fine-scale movements and activity patterns in mobile underwater species. Here, we used acceleration data-loggers to investigate temporal partitioning in a guild of marine predators. Six species of co-occurring large coastal sharks demonstrated distinct diel patterns of activity, providing evidence of strong temporal partitioning of foraging times. This is the first instance of diel temporal niche partitioning described in a marine predator guild, and is probably driven by a combination of physiological constraints in diel timing of activity (e.g. sensory adaptations) and interference competition (hierarchical predation within the guild), which may force less dominant predators to suboptimal foraging times to avoid agonistic interactions. Temporal partitioning is often thought to be rare compared to other partitioning mechanisms, but the occurrence of temporal partitioning here and similar characteristics in many other marine ecosystems (multiple predators simultaneously present in the same space with dietary overlap) introduces the question of whether this is a common mechanism of resource division in marine systems.
Harsh is large: nonlinear vocal phenomena lower voice pitch and exaggerate body size
Authors: Anikin Andrey , Pisanski Katarzyna , Massenet Mathilde , Reby David
Published: July 2021

A lion's roar, a dog's bark, an angry yell in a pub brawl: what do these vocalizations have in common? They all sound harsh due to nonlinear vocal phenomena (NLP)—deviations from regular voice production, hypothesized to lower perceived voice pitch and thereby exaggerate the apparent body size of the vocalizer. To test this yet uncorroborated hypothesis, we synthesized human nonverbal vocalizations, such as roars, groans and screams, with and without NLP (amplitude modulation, subharmonics and chaos). We then measured their effects on nearly 700 listeners' perceptions of three psychoacoustic (pitch, timbre, roughness) and three ecological (body size, formidability, aggression) characteristics. In an explicit rating task, all NLP lowered perceived voice pitch, increased voice darkness and roughness, and caused vocalizers to sound larger, more formidable and more aggressive. Key results were replicated in an implicit associations test, suggesting that the ‘harsh is large’ bias will arise in ecologically relevant confrontational contexts that involve a rapid, and largely implicit, evaluation of the opponent's size. In sum, nonlinearities in human vocalizations can flexibly communicate both formidability and intention to attack, suggesting they are not a mere byproduct of loud vocalizing, but rather an informative acoustic signal well suited for intimidating potential opponents.
A shared mechanism for facial expression in human faces and face pareidolia
Authors: Alais David , Xu Yiben , Wardle Susan G. , Taubert Jessica
Published: July 2021

Facial expressions are vital for social communication, yet the underlying mechanisms are still being discovered. Illusory faces perceived in objects (face pareidolia) are errors of face detection that share some neural mechanisms with human face processing. However, it is unknown whether expression in illusory faces engages the same mechanisms as human faces. Here, using a serial dependence paradigm, we investigated whether illusory and human faces share a common expression mechanism. First, we found that images of face pareidolia are reliably rated for expression, within and between observers, despite varying greatly in visual features. Second, they exhibit positive serial dependence for perceived facial expression, meaning an illusory face (happy or angry) is perceived as more similar in expression to the preceding one, just as seen for human faces. This suggests illusory and human faces engage similar mechanisms of temporal continuity. Third, we found robust cross-domain serial dependence of perceived expression between illusory and human faces when they were interleaved, with serial effects larger when illusory faces preceded human faces than the reverse. Together, the results support a shared mechanism for facial expression between human faces and illusory faces and suggest that expression processing is not tightly bound to human facial features.
Insects use lubricants to minimize friction and wear in leg joints
Authors: Nadein Konstantin , Kovalev Alexander , Thøgersen Jan , Weidner Tobias , Gorb Stanislav
Published: July 2021

A protein-based lubricating substance is discovered in the femoro-tibial joint of the darkling beetleZophobas morio(Insecta). The substance extrudes to the contacting areas within the joint and appears in a form of filiform flows and short cylindrical fragments. The extruded lubricating substance effectively reduces the coefficient of sliding friction to the value of 0.13 in the tribosystemglass/lubricant/glass. This value is significantly lower than 0.35 in the control tribosystemglass/glassand comparable to the value of 0.14 for the tribosystemglass/dry PTFE(polytetrafluoroethylene or Teflon). The study shows for the first time that the friction-reducing mechanism found inZ. moriofemoro-tibial joints is based on the lubricant spreading over the contacting surfaces rolling or moving at low loads and deforming at higher loads, preventing direct contact of joint counterparts. BesidesZ. morio, the lubricant has been found in the leg joints of the Argentinian wood roachBlaptica dubia.
Direct and indirect effects of male genital elaboration in female seed beetles
Authors: Arnqvist Göran , Grieshop Karl , Hotzy Cosima , Rönn Johanna , Polak Michal , Rowe Locke
Published: July 2021

Our understanding of coevolution between male genitalia and female traits remains incomplete. This is perhaps especially true for genital traits that cause internal injuries in females, such as the spiny genitalia of seed beetles where males with relatively long spines enjoy a high relative fertilization success. We report on a new set of experiments, based on extant selection lines, aimed at assessing the effects of long male spines on females in
Callosobruchus maculatus
. We first draw on an earlier study using microscale laser surgery, and demonstrate that genital spines have a direct negative (sexually antagonistic) effect on female fecundity. We then ask whether artificial selection for long versus short spines resulted in direct or indirect effects on female lifetime offspring production. Reference females mating with males from long-spine lines had higher offspring production, presumably due to an elevated allocation in males to those ejaculate components that are beneficial to females. Remarkably, selection for long male genital spines also resulted in an evolutionary increase in female offspring production as a correlated response. Our findings thus suggest that female traits that affect their response to male spines are both under direct selection to minimize harm but are also under indirect selection (a good genes effect), consistent with the evolution of mating and fertilization biases being affected by several simultaneous processes.
Food talk: 40-Hz fin whale calls are associated with prey biomass
Authors: Romagosa Miriam , Pérez-Jorge Sergi , Cascão Irma , Mouriño Helena , Lehodey Patrick , Pereira Andreia , Marques Tiago A. , Matias Luís , Silva Mónica A.
Published: July 2021

Animals use varied acoustic signals that play critical roles in their lives. Understanding the function of these signals may inform about key life-history processes relevant for conservation. In the case of fin whales (Balaenoptera physalus), that produce different call types associated with different behaviours, several hypotheses have emerged regarding call function, but the topic still remains in its infancy. Here, we investigate the potential function of two fin whale vocalizations, the song-forming 20-Hz call and the 40-Hz call, by examining their production in relation to season, year and prey biomass. Our results showed that the production of 20-Hz calls was strongly influenced by season, with a clear peak during the breeding months, and secondarily by year, likely due to changes in whale abundance. These results support the reproductive function of the 20-Hz song used as an acoustic display. Conversely, season and year had no effect on variation in 40-Hz calling rates, but prey biomass did. This is the first study linking 40-Hz call activity to prey biomass, supporting the previously suggested food-associated function of this call. Understanding the functions of animal signals can help identifying functional habitats and predict the negative effects of human activities with important implications for conservation.
Achromobacter spp. genetic adaptation in cystic fibrosis
Authors: Gabrielaite Migle , Nielsen Finn C. , Johansen Helle K. , Marvig Rasmus L.
Published: July 2021

Achromobacter

spp. are emerging pathogens in patients with cystic fibrosis (CF) and

Achromobacter

spp. caused infections are associated with more severe disease outcomes and high intrinsic antibiotic resistance. While conventional CF pathogens are studied extensively, little is known about the genetic determinants leading to antibiotic resistance and the genetic adaptation in

Achromobacter

spp. infections. Here, we analysed 101

Achromobacter

spp. genomes from 51 patients with CF isolated during the course of up to 20 years of infection to identify within-host adaptation, mutational signatures and genetic variation associated with increased antibiotic resistance. We found that the same regulatory and inorganic ion transport genes were frequently mutated in persisting clone types within and between

Achromobacter

species, indicating convergent genetic adaptation. Genome-wide association study of six antibiotic resistance phenotypes revealed the enrichment of associated genes involved in inorganic ion transport, transcription gene enrichment in β-lactams, and energy production and translation gene enrichment in the trimethoprim/sulfonamide group. Overall, we provide insights into the pathogenomics of

Achromobacter

spp. infections in patients with CF airways. Since emerging pathogens are increasingly recognized as an important healthcare issue, our findings on evolution of antibiotic resistance and genetic adaptation can facilitate better understanding of disease progression and how mutational changes have implications for patients with CF.
Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study
Authors: Agoti Charles N. , Ochola-Oyier Lynette Isabella , Mohammed Khadija Said , Lambisia Arnold W. , de Laurent Zaydah R. , Morobe John M. , Mburu Maureen W. , Omuoyo Donwilliams O. , Ongera Edidah M. , Ndwiga Leonard , Maitha Eric , Kitole Benson , Suleiman Thani , Mwakinangu Mohamed , Nyambu John , Otieno John , Salim Barke , Musyoki Jennifer , Murunga Nickson , Otieno Edward , Kiiru John , Kasera Kadondi , Amoth Patrick , Mwangangi Mercy , Aman Rashid , Kinyanjui Samson , Warimwe George , Phan My , Agweyu Ambrose , Cotten Matthew , Barasa Edwine , Tsofa Benjamin , Nokes D. James , Bejon Philip , Githinji George
Published: July 2021

Background

The transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood.

Methods

We undertook phylogenetic analysis of 747 SARS-CoV-2 positive samples collected across six counties in coastal Kenya during the first two waves (March 2020 - February 2021). Viral imports and exports from the region were inferred using ancestral state reconstruction (ASR) approach.

Results

The genomes were classified into 35 Pango lineages, six of which accounted for 79% of the sequenced infections: B.1 (49%), B.1.535 (11%), B.1.530 (6%), B.1.549 (4%), B.1.333 (4%) and B.1.1 (4%). Four identified lineages were Kenya specific. In a contemporaneous global subsample, 990 lineages were documented, 261 for Africa and 97 for Eastern Africa. ASR analysis identified >300 virus location transition events during the period, these comprising: 69 viral imports into Coastal Kenya; 93 viral exports from coastal Kenya; and 191 inter-county import/export events. Most international viral imports (58%) and exports (92%) occurred through Mombasa City, a key touristic and commercial Coastal Kenya center; and many occurred prior to June 2020, when stringent local COVID-19 restriction measures were enforced. After this period, local virus transmission dominated, and distinct local phylogenies were seen.

Conclusions

Our analysis supports moving control strategies from a focus on international travel to local transmission.

Funding

This work was funded by Wellcome (grant#: 220985) and the National Institute for Health Research (NIHR), project references: 17/63/and 16/136/33 using UK aid from the UK Government to support global health research, The UK Foreign, Commonwealth and Development Office.
Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics
Authors: Selvan Myvizhi Esai , Onel Kenan , Gnjatic Sacha , Klein Robert J. , Gümüş Zeynep H.
Published: July 2021

Background

Inherited genetic variants play an important role in cancer susceptibility. Recent studies show that rare, deleterious variants (RDVs) in a few genes are critical determinants of heritable cancer risk. Better understanding of germline RDVs will contribute to improved precision prevention, screening and treatment.

Methods

We have performed the largest to date jointly processed germline pan-cancer case-control association study from whole-exome sequencing (WES) data of 20,789 participants, split into discovery and validation cohorts. We focused on high-penetrance RDVs based on ClinVar database. To increase the statistical power, we pursued a collapsing approach and compared the cumulative RDV burden at gene and gene-set levels using penalized logistic regression. Next, we investigated how the accumulation of RDVs in an individual (RDV load) is associated with cancer risk. Finally, we studied how personal RDV load in specific gene-sets affected i) age of diagnosis; ii) tumor immune microenvironment; and iii) tumor mutational burden using Mann-Whitney U test and Kruskal-Wallis test.

Results

Our results confirm known associations between cancer risk and germline RDVs in BRCA1/2 genes, and show associations with risk for RDVs in Fanconi Anemia (FA), DNA damage repair (DDR), cancer predisposition (CPD) and somatic cancer driver gene-sets in two independent cohorts. Furthermore, increased personal germline RDV load in these gene-sets increased cancer risk, and once cancer developed, tumor characteristics. Notably, we show that the personal RDV load of an individual in FA, DDR or CPD genes is a potential marker for younger age of onset, M1 macrophage fraction in tumor microenvironment, and, in specific cancers, increased tumor mutation burden.

Conclusions

Our findings will help better stratification of individuals at high cancer risk, as well as the characterization of the influence of their personal germline RDV load on age of diagnosis, tumor microenvironment and mutational burden. These high-risk individuals may benefit from increased surveillance, earlier screening and prevention efforts, and treatments that exploit their tumor characteristics, improving prognosis.
Aetiology of Lobar Pneumonia Determined by Multiplex Molecular Analyses of Lung and Pleural Aspirate Specimens in The Gambia
Authors: Mackenzie Grant A , McLellan Jessica , Machuka Eunice , Ndiaye Malick , Pathirana Jayani , Fombah Augustin , Abatan Baderinwa , Hossain Ilias , Manjang Ahmed , Greenwood Brian , Hill Philip C
Published: July 2021

Background

Pneumonia aetiology generally relies on insensitive blood cultures or an assumption that organisms in the pharynx are causal. We determined the causes of lobar pneumonia in rural Gambia using lung aspiration.

Methods

Pneumonia surveillance was undertaken among all ages. Blood culture and chest radiographs were performed routinely while lung or pleural aspirates were collected from selected patients. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in August 2009 and replaced by PCV13 from May 2011. We used conventional microbiology, and from April 8, 2011 to July 17, 2012, utilized a multiplex PCR assay on lung aspirates. We calculated proportions with pathogens, associations between co-infecting pathogens, and PCV effectiveness.

Results

2,550 patients were admitted with clinical pneumonia; 741 with lobar pneumonia or pleural effusion. We performed multiplex PCR on 156 lung and 4 pleural aspirates. Pathogens were detected in 116 specimens, Streptococcus pneumoniae (n=68), Staphylococcus aureus (n=26), and Haemophilus influenzae type b (n=11). Bacteria (n=97) were more common than viruses (n=49). Common viruses were bocavirus (n=11) and influenza (n=11). Co-infections were frequent (n=55). M. catarrhalis was detected in eight patients and in every case there was co-infection with S. pneumoniae. The odds ratio of vaccine-type pneumococcal pneumonia in patients with two or three compared to zero doses of PCV was 0.17 (95% CI 0.06, 0.51).

Conclusions

Lobar pneumonia in rural Gambia was caused primarily by bacteria, particularly S. pneumoniae and S. aureus. Co-infection was common and M. catarrhalis always co-infected with S. pneumoniae. PCV was highly efficacious against vaccine-type pneumococcal pneumonia.

Key Messages

What is the key question?

Using specimens directly from the infected lung, what is the aetiology of lobar pneumonia in rural West Africa?

What is the bottom line?

Using specimens directly from the infected lung, Streptococcus pneumoniae and Staphylococcus aureus were the predominant causes of lobar pneumonia in rural West Africa and pneumococcal conjugate vaccine effectively prevented pneumococcal pneumonia.

Why read on?

Learn about the certain aetiology of lobar pneumonia in 160 Gambian patients with specimens directly from the lung.
Neurological, neuropsychiatric and psychiatric symptoms during COVID-19 infection and after recovery: a systematic review of observational studies
Authors: Stavrou Maria , Solomou Solomis , Kythreotou Anthousa , Ioannou Antreas , Lioutas Eva , Lioutas Joanna , Karayiannis Peter
Published: July 2021

Background

The SARS-CoV-2 virus causes a wide spectrum of disease severity. Initial manifestations include fever, dry cough, and constitutional symptoms, which may progress to respiratory disease. There may also be neurological and psychiatric manifestations, involving both the central and peripheral nervous system.

Methods

We performed a literature search of the databases PubMed, EMBASE, The Cochrane Library and Web of Science for observational studies reporting neurological, psychiatric, and neuropsychiatric effects of COVID-19. This was followed by a narrative synthesis to summarise the data and discuss neuropsychiatric associations, symptom severity, management, and recovery.

Findings

The most frequently reported neurological symptoms were ageusia, hyposmia/anosmia, dizziness, headache, and loss of consciousness. Statistically significant relationships were noted between Asian ethnicity and peripheral neuropathy (p=0.0001) and neuro-syndromic symptoms (p=0.001). ITU admission was found to have a statistically significant relationship with male sex (p=0.024). Depression and anxiety were also identified both during and after infection. The most frequent treatments used were intravenous immunoglobulins, followed by antibiotics, antivirals, and hydroxychloroquine; with mean treatment duration of 6 days.

Interpretation

Various neuropsychiatric symptoms have been associated with COVID-19 infection. More studies are required to further our knowledge in the management of neurological and psychiatric symptoms during and after COVID-19 infection
Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets
Authors: Ramos Jairo , Caywood Laura J. , Prough Michael B. , Clouse Jason E. , Herington Sharlene D. , Slifer Susan H. , Fuzzell M. Denise , Fuzzell Sarada L. , Hochstetler Sherri D. , Miskimen Kristy L. , Main Leighanne R. , Osterman Michael D. , Laframboise Owen , Zaman Andrew F. , Whitehead Patrice L. , Adams Larry D. , Laux Renee A. , Song Yeunjoo E. , Foroud Tatiana M. , Mayeux Richard P. , George-Hyslop Peter St. , Ogrocki Paula K. , Lerner Alan J. , Vance Jeffery M. , Cuccaro Michael L. , Haines Jonathan L. , Pericak-Vance Margaret A. , Scott William K.
Published: July 2021

Background

Studies of cognitive impairment (CI) in Amish communities have identified sibships containing multiple CI and cognitively unimpaired (CU; unaffected after age 75) individuals. We hypothesize that these CU individuals may carry protective alleles delaying age at onset (AAO) of CI, preserving cognition in older age despite increased genetic risk. As well, the genetic and cultural isolation in the Amish since the early 1800s may have reduced the complexity of the genetic architecture of CI, increasing the power to detect protective alleles in this population. With this in mind we conducted a genome-wide study (GWAS) to identify loci associated with AAO of CI in a sample of Amish adults over age 75.

Methods

1,522 individuals aged 43-99 (mean age 73.1, 42% men) screened at least once for CI using the Modified Mini-Mental State exam (3MS) were genotyped using Illumina chipsets. Genotypes were imputed for 7,815,951 single nucleotide variants (SNV) with minor allele frequency (MAF) > 1%. The outcome studied was age, defined as 1) age at the first 3MS result indicating impairment (AAO; 3MS <87; 362 CI individuals) or 2) age at last normal exam (3MS >=87, 1,160 CU individuals). Cox mixed-effects models examined association between age and each SNV, adjusting for sex and familial relationships. To replicate genome-wide significant findings, SNVs in a 1 Megabase region centered on the peak SNV were examined for association with age using these same methods in the NIA-LOAD family study dataset (1,785 AD cases, 1,565 unaffected controls, mean age 73.5.

Results

Three SNV were significantly associated (p<5 x 10-8) with AAO in the Amish, on chromosomes 6 (rs14538074; HR=3.35), 9 (rs534551495; HR=2.82), and 17 (rs146729640; Hazard Ratio (HR)=6.38). Each region found the common allele associated with later AAO. Replication analysis detected association at rs146729640, with nominal statistical significance (HR=1.49, p=0.02).

Conclusions

The replicated genome-wide significant association with AAO on chromosome 17 suggest this may be novel locus associated with delayed onset of AD. The associated SNP is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for AD.
The protocol for a scoping review analyzing the association between physical activity interventions after a genitourinary cancer diagnosis and incidences of depression and anxiety
Authors: Grob Sydney , Mucci Lorelei , McGrath Colleen
Published: July 2021

The following is a protocol for a planned scoping review of the effect of physical activity interventions on incidences of depression and anxiety incidences in men diagnosed with a genitourinary cancer. If exercise interventions are found to correlate with lower incidences of depression and anxiety, physical activity interventions offer a potentially modifiable, low-cost, accessible, and natural intervention to improve quality of life outcomes in men with genitourinary cancers. We plan to screen literature from publicly available databases, PubMed and Embase, for intervention studies in this area by implementing abstract/title and full-text screening by two independent reviewers followed by data extraction performed by two independent reviewers. Results will be synthesized in narrative format accompanied by relevant tabulated findings. We anticipate no ethical risks while completing this scoping review. Upon completion of this scoping review, results will be disseminated via publication.

Article Summary (Strengths and Limitations)

This scoping review will address a critical area of potentially-modifiable interventions to improve quality-of-life indicators in genitourinary cancer survivorship research.

This scoping review could inform the use of readily available, low-cost, and low-barrier, treatment options to men suffering from depression and anxiety.

This review is limited to information from interventional studies only as a preliminary review of available research.

This review is limited to interventional studies in male cancer patients of specific genitourinary cancers (prostate, bladder, kidney, testicular).
High resolution linear epitope mapping of the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 mRNA vaccine recipients
Authors: Nitahara Yuko , Nakagama Yu , Kaku Natsuko , Candray Katherine , Michimuko Yu , Tshibangu-Kabamba Evariste , Kaneko Akira , Yamamoto Hiromasa , Mizobata Yasumitsu , Kakeya Hiroshi , Yasugi Mayo , Kido Yasutoshi
Published: July 2021

The prompt rollout of the coronavirus disease (COVID-19) messenger RNA (mRNA) vaccine is facilitating population immunity, which shall become more dominant than natural infection-induced immunity. At the beginning of the vaccine era, understanding the epitope profiles of vaccine-elicited antibodies will be the first step in assessing functionality of vaccine-induced immunity. In this study, the high-resolution linear epitope profiles of Pfizer-BioNTech COVID-19 mRNA vaccine recipients and COVID-19 patients were delineated by using microarrays mapped with overlapping peptides of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. The vaccine-induced antibodies targeting RBD had broader distribution across the RBD than that induced by the natural infection. Thus, relatively lower neutralizability was observed when a half-maximal neutralization titer measured in vitro by live virus neutralization assays was normalized to a total anti-RBD IgG titer. However, mutation panel assays targeting the SARS-CoV-2 variants of concern have shown that the vaccine-induced epitope variety, rich in breadth, may grant resistance against future viral evolutionary escapes, serving as an advantage of vaccine-induced immunity.

Importance

Establishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of messenger RNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable. The next debate is regarding the coverage of SARS-CoV-2 variants. At the beginning of this vaccine era, it is of importance to describe the similarities and differences between the immune responses of COVID-19 vaccine recipients and naturally infected individuals. In this study, we demonstrated that the antibody profiles of vaccine recipients are richer in variety, targeting a key protein of the invading virus, than those of naturally infected individuals. Yet vaccine-elicited antibodies included more non-neutralizing antibodies than infection-elicited, their breadth in antibody variations suggested possible resilience against future SARS-CoV-2 variants. The antibody profile achieved by vaccinations in naive individuals pose important insight into the first step towards vaccine-based population immunity.
Modelling, Simulations and Analysis of the First and Second COVID-19 Epidemics in Beijing
Authors: Min Lequan
Published: July 2021

Background

In December 2019, a novel coronavirus-induced pneumonia (COVID-19) broke out in Wuhan, China. On 19 January and on 8 June 2020, there were two wave COVID-19 epidemics happened in Beijing. Modelling, simulations and analysis for the two wave epidemics are important issues.

Methods

This study introduces a symptomatic-asymptomatic-recoverer-death differential equation model (SARDDE). It presents the conditions of the asymptotical stability on the disease-free equilibrium of the SARDDE. It proposes the necessary conditions of disease spreading for the SARDDE. Based on the reported data of the first and the second COVID-19 epidemics in Beijing and numerical simulations, it determines the parameters of the SARDDE, respectively.

Results

Numerical simulations of the SARDDE describe well the outcomes of the current symptomatic and asymptomatic individuals, the recovered symptomatic and asymptomatic individuals, and the died infected individuals, respectively. The numerical simulations obtain the following results.

The transmission rate of the symptomatic infections caused by the symptomatic individuals in the second Beijing epidemic is about two times higher than the one in the first Beijing epidemic.

Both the symptomatic and the asymptomatic individuals cause lesser asymptomatic spread than symptomatic spread.

The blocking rates of 89.32% and 97.48% (reaching the infection turning points) to the symptomatic infections cannot prevent the spreads of the first and the second COVID-19 epidemics in Beijing, respectively.

That on the day 28, the symptomatic infection blocking rates reached to 100% has made the second Beijing epidemics epidemic end on day 56.

That on the day 98, the symptomatic infection blocking rates reached to 100% has made the the first Beijing epidemics epidemic end on day 140.

Keeping the blocking rates, the recovery rates and the death rates reaching the infection turning points would make the numbers of current hospitalized infected individuals reach, on day 140, 208958 individuals and 25017 individuals for the two Beijing epidemics, respectively.

Conclusions

Virtual simulations suggest that the strict prevention and control strategies implemented by Beijing government are effective and necessary; using the data from the beginning to the days after about two weeks after the turning points can estimate well and approximately the following outcomes of the two COVID-19 epidemics, respectively. To avoid multiple epidemic outbreaks, a recommendation is that the authorities need to have maintained the prevention and control measures implemented, at least, 7 days after reaching the turning point until new current infection cases disappear. It is expected that the research can provide better understanding, explaining, and dominating for epidemic spreads, prevention and control measures.
Durable Humoral and Cellular Immune Responses Following Ad26.COV2.S Vaccination for COVID-19
Authors: Barouch Dan H. , Stephenson Kathryn E. , Sadoff Jerald , Yu Jingyou , Chang Aiquan , Gebre Makda , McMahan Katherine , Liu Jinyan , Chandrashekar Abishek , Patel Shivani , Gars Mathieu Le , de Groot Anne Marit , Heerwegh Dirk , Struyf Frank , Douoguih Macaya , van Hoof Johan , Schuitemaker Hanneke
Published: July 2021

Interim immunogenicity and efficacy data for the Ad26.COV2.S vaccine for COVID-19 have recently been reported1-3. We describe here the 8-month durability of humoral and cellular immune responses in 20 individuals who received one or two doses of 5×1010 vp or 1011 vp Ad26.COV2.S and in 5 participants who received placebo2. We evaluated antibody and T cell responses on day 239, which was 8 months after the single-shot vaccine regimen (N=10) or 6 months after the two-shot vaccine regimen (N=10), although the present study was not powered to compare these regimens3. We also report neutralizing antibody responses against the parental SARS-CoV-2 WA1/2020 strain as well as against the SARS-CoV-2 variants D614G, B.1.1.7 (alpha), B.1.617.1 (kappa), B.1.617.2 (delta), P.1 (gamma), B.1.429 (epsilon), and B.1.351 (beta).
An Autoantigen Profile from Jurkat T-Lymphoblasts Provides a Molecular Guide for Investigating Autoimmune Sequelae of COVID-19
Authors: Wang Julia Y. , Zhang Wei , Roehrl Michael W. , Roehrl Victor B. , Roehrl Michael H.
Published: July 2021

In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoantigens (autoAgs) and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) of DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation in the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs such as LCP1 and NACA that are altered in the T cells of COVID patients may provide insight into T-cell responses in the viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2.
Does prior healthcare experience predict success on clinical courses and add value to admissions processes?
Authors: Darling-Pomranz Claire , Gray James , Spencer David
Published: July 2021

Objectives

This work sought to assess whether prior clinical experience provided any guide to likely course achievement from three completed cohorts of Physician Associates at the University of Sheffield.

Methods

Sixty students who entered the PA course at TUoS since it began in 2016 were included in the study. Each students’ original course application was reviewed for healthcare experience and mapped against first sit examination scores. Statistical analysis was undertaken with a two-tailed t-test.

Results

No correlation was found between previous healthcare experience and performance in examinations. Students with previous healthcare experience performed slightly worse than those without in the OSCE examination but not at a level of statistical significance.

Conclusions

The use of clinical experience as part of the criteria of entry does not predict success on a Physician Associate course. We support the position of the 2010 Ottawa conference that quality assured methodologies along with objective cut offs for previous academic attainment are the most appropriate way to select students for clinical courses.
Navigating uncertain illness trajectories for young children with serious infectious illness: a mixed-methods modified grounded theory study
Authors: Neill Sarah , Bray Lucy , Carter Bernie , Roland Damian , Carrol Enitan D , Bayes Natasha , Riches Lucie , Hughes Joanne , Pandey Poornima , O’Donnell Jennifer , Palmer-Hill Sue
Published: July 2021

Infectious illness is the biggest cause of death in children due to a physical illness, particularly in children under five years. If mortality is to be reduced for this group of children, it is important to understand factors affecting their pathways to hospital.

The aim of this study was to retrospectively identify organisational and environmental factors, and individual child, family, and professional factors affecting timing of admission to hospital for children under five years of age with a serious infectious illness (SII).

Methods

An explanatory modified grounded theory mixed methods design was used in collaboration with parents. Two stages of data collection were conducted: Stage 1, interviews with 22 parents whose child had recently been hospitalised with a SII and 14 health professionals (HPs) involved in their pre-admission trajectories; Stage 2, focus groups with 18 parents and 16 HPs with past experience of SII in young children. Constant comparative analysis generated the explanatory theory.

Findings

The core category was ‘navigating uncertain illness trajectories for young children with serious infectious illness’. Uncertainty was prevalent throughout the parents’ and HPs’ stories about their experiences of navigating social rules and overburdened health services for these children. The complexity of and lack of continuity within services, family lives, social expectations and hierarchies provided the context and conditions for children’s, often complex, illness trajectories. Parents reported powerlessness and perceived criticism leading to delayed help-seeking. Importantly, parents and professionals missed symptoms of serious illness. Risk averse services were found to refer more children to emergency departments.

Conclusions

Parents and professionals have difficulties recognising signs of SII in young children and can feel socially constrained from seeking help. The increased burden on services has made it more difficult for professionals to spot the seriously ill child.