bluuebunny/crossref_metadata_2025_split huggingface dataset:
How does the magnitude of genetic variation affect eco-evolutionary dynamics in character displacement?
Authors: Morita Keiichi , Yamamichi Masato 
Published: March 2021

AbstractWhile previous studies on character displacement tended to focus on trait divergence and convergence as a result of long-term evolution, recent studies suggest that character displacement can be a special case of evolutionary rescue, where rapid evolution prevents population extinction by weakening negative interspecific interactions. When the magnitude of genetic variation is small, however, the speed of trait divergence can be slow and populations may go extinct before the completion of character displacement. Here we analyzed a simple model to examine how the magnitude of genetic variation affects evolutionary rescue via ecological and reproductive character displacement that weakens resource competition and reproductive interference, respectively. We found that the large additive genetic variance is more important for preventing extinction in reproductive character displacement than in ecological character displacement. This is because reproductive interference produces a locally stable coexistence equilibrium with positive frequency-dependence (i.e., minority disadvantage) whereas ecological character displacement results in a globally stable coexistence equilibrium. Furthermore, population extinction becomes less likely when ecological and reproductive character displacement occur simultaneously due to positive covariance between ecological and reproductive traits. Our results suggest that while reproductive character displacement may be rarer than ecological character displacement, it is more likely to occur when there exists positive trait covariance, such as the case of a magic trait in reinforcement of speciation processes.
Healthcare utilisation survey as part of the Hybrid model of the Surveillance of Enteric Fever in India (SEFI) study: processes, results, and challenges
Authors: Raju Reshma , Angelin J Kezia , Karthikeyan Arun S , Kumar Dilesh , Kumar Ranjith R , Sahai Nikhil , Ramanujan Karthik , Murhekar Manoj , Elangovan A. , Samuel Prasanna , John Jacob , Kang Gagandeep 
Published: March 2021

AbstractBackgroundEnteric fever is a significant health challenge in low and middle-income countries. “Surveillance of Enteric Fever in India” (SEFI) network was set up to obtain reliable incidence data. Six sites utilised a hybrid surveillance model, a combination of facility-based surveillance and community-based healthcare utilisation survey (HCUS). HCUS was performed to determine the percentage of the catchment population utilising the study facilities for febrile episodes, and is described here.MethodsA two-stage sampling process was utilised for the HCUS to select 5000 households per site. Demographic data and healthcare-seeking behaviour were assessed.ResultsFebrile hospitalisation rate ranged from 2.5/1000 in Kullu to 9.6/1000 in Anantapur. The percentage of febrile admissions that sought care in the study hospital from the catchment area is 17% in Anantapur, 38% in Karimganj, 38% in Chandigarh, 10% in Nandurbar, 36% in Kullu and 24% in East Champaran respectively.ConclusionsThe variability in healthcare utilisation for fever admissions in the study hospitals underscores the importance of periodic healthcare utilisation surveys in hybrid surveillance. It is essential to adjust for those cases which have slipped out of the facility surveillance radar for obtaining an accurate estimate of the disease burden.
Modeling infection dynamics and mitigation strategies to support K-6 in-person instruction during the COVID-19 pandemic
Authors: Morrison Douglas E. , Nianogo Roch , Manuel Vladimir , Arah Onyebuchi A. , Anderson Nathaniel , Kuo Tony , Inkelas Moira 
Published: March 2021

AbstractObjectiveTo support safer in-person K-6 instruction during the coronavirus disease 2019 (COVID- 19) pandemic by providing public health authorities and school districts with a practical model of transmission dynamics and mitigation strategies.MethodsWe developed an agent-based model of infection dynamics and preventive mitigation strategies such as distancing, health behaviors, surveillance and symptomatic testing, daily symptom and exposure screening, quarantine policies, and vaccination. The model parameters can be updated as the science evolves and are adjustable via an online user interface, enabling users to explore the effects of interventions on outcomes of interest to states and localities, under a variety of plausible epidemiological and policy assumptions.ResultsUnder default assumptions, secondary infection rates and school attendance are substantially affected by surveillance testing protocols, vaccination rates, class sizes, and effectiveness of safety education.ConclusionsOur model helps policymakers consider how mitigation options and the dynamics of school infection risks affect outcomes of interest. The model’s parameters can be immediately updated in response to changes in epidemiological conditions, science of COVID-19 transmission dynamics, testing and vaccination resources, and reliability of mitigation strategies.
COVID-19 Vaccination Priority Evaluation
Authors: Dujmović Jozo , Tomasevich Daniel 
Published: March 2021

AbstractComputing the COVID-19 vaccination priority is an urgent and ubiquitous decision problem. In this paper we propose a solution of this problem using the LSP evaluation method. Our goal is to develop a justifiable and explainable quantitative criterion for computing a vaccination priority degree for each individual in a population. Performing vaccination in the order of the decreasing vaccination priority produces maximum positive medical, social, and ethical effects for the whole population. The presented method can be expanded and refined using additional medical and social conditions. In addition, the same methodology is suitable for solving other similar medical priority decision problems, such as priorities for organ transplants.
Household COVID-19 risk and in-person schooling
Authors: Lessler Justin , Grabowski M. Kate , Grantz Kyra H. , Badillo-Goicoechea Elena , Metcalf C. Jessica E. , Lupton-Smith Carly , Azman Andrew S. , Stuart Elizabeth A. 
Published: March 2021

AbstractIn-person schooling has proved contentious and difficult to study throughout the SARS-CoV-2 pandemic. Data from a massive online survey in the United States indicates an increased risk of COVID-19-related outcomes among respondents living with a child attending school in-person. School-based mitigation measures are associated with significant reductions in risk, particularly daily symptoms screens, teacher masking, and closure of extra-curricular activities. With seven or more mitigation measures, the association between in-person schooling and COVID-19-related outcomes all but disappears. Teachers working outside the home were more likely to report COVID-19-related outcomes, but this association is similar to other occupations (e.g., healthcare, office work). In-person schooling is associated with household COVID-19 risk, but this risk can likely be controlled with properly implemented school-based mitigation measures.One sentence summaryLiving with children attending in-person school is linked to a higher risk of COVID-19 outcomes, which school-based interventions can mitigate.
Increased region of surround stimulation enhances contextual feedback and feedforward processing in human V1
Authors: Revina Yulia , Petro Lucy S. , Denk-Florea Cristina B. , Rao Isa S. , Muckli Lars 
Published: March 2021

AbstractThe majority of synaptic inputs to the primary visual cortex (V1) are non-feedforward, instead originating from local and anatomical feedback connections. Animal electrophysiology experiments show that feedback signals originating from higher visual areas with larger receptive fields modulate the surround receptive fields of V1 neurons. Theories of cortical processing propose various roles for feedback and feedforward processing, but systematically investigating their independent contributions to cortical processing is challenging because feedback and feedforward processes coexist even in single neurons. Capitalising on the larger receptive fields of higher visual areas compared to primary visual cortex (V1), we used an occlusion paradigm that isolates top-down influences from feedforward processing. We utilised functional magnetic resonance imaging (fMRI) and multi-voxel pattern analysis methods in humans viewing natural scene images. We parametrically measured how the availability of contextual information determines the presence of detectable feedback information in non-stimulated V1, and how feedback information interacts with feedforward processing. We show that increasing the visibility of the contextual surround increases scene-specific feedback information, and that this contextual feedback enhances feedforward information. Our findings are in line with theories that cortical feedback signals transmit internal models of predicted inputs.Significance StatementThe visual system has circuit mechanisms for processing scene context. These circuits involve lateral and feedback inputs to neurons. These inputs interact with feedforward inputs and modulate neuronal responses to visual stimuli presented outside their receptive fields. Systematically investigating independent contributions of feedback and feedforward processes is challenging because they coexist even in single neurons. Here we use an occlusion paradigm to isolate feedback and lateral signals in human participants viewing natural scene images in fMRI. We show that increasing the visibility of the contextual surround increases scene-specific feedback information, which also enhances feedforward signals. Our findings are in line with theories that cortical feedback signals carry abstract internal models that combine with more detailed representations in primary visual cortex.
Mice immunized with the vaccine candidate HexaPro spike produce neutralizing antibodies against SARS-CoV-2
Authors: Seephetdee Chotiwat , Buasri Nattawut , Bhukhai Kanit , Srisanga Kitima , Manopwisedjaroen Suwimon , Lertjintanakit Sarat , Phueakphud Nut , Pakiranay Chatbenja , Kangwanrangsan Niwat , Srichatrapimuk Sirawat , Sungkanuparph Somnuek , Kirdlarp Suppachok , Chutipongtanate Somchai , Thitithanyanont Arunee , Hongeng Suradej , Wongtrakoongate Patompon 
Published: March 2021

AbstractUpdated and revised versions of COVID-19 vaccines are vital due to genetic variations of the SARS-CoV-2 spike antigen. Furthermore, vaccines that are safe, cost-effective, and logistically friendly are critically needed for global equity, especially for middle to low income countries. Recombinant protein-based subunit vaccines against SARS-CoV-2 have been reported with the use of the receptor binding domain (RBD) and the prefusion spike trimers (S-2P). Recently, a new version of prefusion spike trimers, so called “HexaPro”, has been shown for its physical property to possess two RBD in the “up” conformation, as opposed to just one exposed RBD found in S-2P. Importantly, this HexaPro spike antigen is more stable than S-2P, raising its feasibility for global logistics and supply chain. Here, we report that the spike protein HexaPro offers a promising candidate for SARS-CoV-2 vaccine. Mice immunized by the recombinant HexaPro adjuvanted with aluminium hydroxide using a prime-boost regimen produced high-titer neutralizing antibodies for up to 56 days after initial immunization against live SARS-CoV-2 infection. In addition, the level of neutralization activity is comparable to that of convalescence sera. Our results indicate that the HexaPro subunit vaccine confers neutralization activity in sera collected from mice receiving the prime-boost regimen.
Beyond colour gamuts: Novel metrics for the reproduction of photoreceptor signals
Authors: Hexley Allie C. , Morimoto Takuma , Smithson Hannah E. , Spitschan Manuel 
Published: March 2021

AbstractColour gamuts describe the chromaticity reproduction capabilities of a display, i.e. its ability to reproduce the relative cone excitations from real-world radiance spectra. While the cones dominate “canonical” visual function (i.e. perception of colour, space, and motion) under photopic light levels, they are not the only photoreceptors in the human retina. Rods and melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) also respond to light and contribute to both visual and non-visual light responses, including circadian rhythms, sleep-wake control, mood, pupil size, and alertness. Three-primary display technologies, with their focus on reproducing colour, are not designed to reproduce the rod and melanopsin excitations. Moreover, conventional display metrics used to characterize three-primary displays fail to describe the display’s ability (or inability) to reproduce rod and melanopsin excitations, and thus do not capture the display’s ability to reproduce the full human physiological response to light. In this paper, three novel physiologically relevant metrics are proposed for quantifying the reproduction and distortion of the photoreceptor signals by visual displays. A novel equal-luminance photoreceptor excitation diagram is proposed, extending the well-known MacLeod-Boynton chromaticity diagram, to allow visualizations of the five-dimensional photoreceptor signal space in a three-dimensional projection.
A BCI-based vibrotactile neurofeedback training improves motor cortical excitability during motor imagery
Authors: Grigorev N. , Savosenkov A. , Lukoyanov M. , Udoratina A. , Shusharina N. , Kaplan A. , Hramov A. , Kazantsev V. , Gordleeva S. 
Published: March 2021

AbstractIn this study, we address the issue of whether vibrotactile feedback can enhance the motor cortex excitability translated into the plastic changes in local cortical areas during motor imagery (MI) BCI-based training. For this purpose, we focused on two of the most notable neurophysiological effects of MI – the event-related-desynchronization (ERD) level and the increase in cortical excitability assessed with navigated transcranial magnetic stimulation (nTMS). For TMS navigation, we used individual high-resolution 3D brain MRIs. Ten BCI-naive and healthy adults participated in this study. The MI (rest or left/right hand imagery using Graz-BCI paradigm) tasks were performed separately in the presence and absence of feedback. To investigate how much the presence/absence of vibrotactile feedback in MI BCI-based training could contribute to the sensorimotor cortical activations, we compared the MEPs amplitude during MI after training with and without feedback. In addition, the ERD levels during MI BCI-based training were investigated. Our findings provide evidence that applying vibrotactile feedback during MI training leads to (i) an enhancement of the desynchronization level of mu-rhythm EEG patterns over the contralateral motor cortex area corresponding to the MI of the non-dominant hand; (ii) an increase in motor cortical excitability in hand muscle representation corresponding to a muscle engaged by the MI.
Synergistic positive feedback underlying seizure initiation
Authors: Graham Robert T. , Parrish R. Ryley , Alberio Laura , Johnson Emily L. , Owens Laura J. , Trevelyan Andrew J. 
Published: March 2021

AbstractSeizure onset is a critically important brain state transition that has proved very difficult to predict accurately from recordings of brain activity. Here we show that an intermittent, optogenetic, stimulation paradigm reveals a latent change in dendritic excitability that is tightly correlated to the onset of seizure activity. Our data show how the precipitous nature of the transition can be understood in terms of multiple, synergistic positive feedback mechanisms: raised intracellular Cl-and extracellular K+, coupled to a reduced threshold for dendritic plateau potentials, and which in turn leads to a switch to pyramidal burst firing. Notably, the stimulation paradigm also delays the evolving epileptic activity, meaning that not only can one monitor seizure risk safely, it may even have an additional anti-epileptic benefit.One Sentence SummaryRapid transitions into seizures arise from mutually accelerating feedback loops, involving changes in dendritic excitability
VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
Authors: Poulose Ninu , Forsythe Nicholas , Polonski Adam , Gregg Gemma , Maguire Sarah , Fuchs Marc , Minner Sarah , Sauter Guido , McDade Simon S. , Mills Ian G. 
Published: March 2021

AbstractA comprehensive understanding of androgen receptor (AR) signalling mechanisms during prostate carcinogenesis is instrumental in developing novel therapies. Studies have shown glycosylation as a key androgen regulated process and that O-GlcNAc transferase (OGT), the enzyme that catalyses the covalent addition of UDP-N-acetylglucosamine (UDP-GlcNAc) to serine and threonine residues of proteins, is often up-regulated in prostate cancer (PCa) with its expression correlated with high Gleason score. In this study we have identified an AR and OGT co-regulated factor, VPRBP also known as DCAF1. We show that VPRBP is regulated by the AR at the transcript level, and stabilized by OGT at the protein level. VPRBP knockdown in PCa cells led to a significant decrease in cell proliferation, p53 stabilization, nucleolar fragmentation and increased p53 recruitment to the chromatin. In human prostate tumor samples, VPRBP protein overexpression correlated with AR amplification, OGT overexpression, early biochemical relapse and poor clinical outcome. Analysis of TCGA datasets found a positive correlation of VPRBP with AR mRNA expression. Furthermore, AR activity gene signature analysis revealed a positive correlation of VPRBP with a subset of AR target genes implying that VPRBP has a preferential regulatory impact on part of the AR regulome. In conclusion, we have shown that VPRBP/DCAF1 promotes PCa cell proliferation by restraining p53 activation under the influence of the AR and OGT as well as uncovered a unique subset of AR activity gene signature that correlates with VPRBP expression with the potential for new avenues for patient stratification and treatment.
The component parts of bacteriophage virions accurately defined by a machine-learning approach built on evolutionary features
Authors: Thung Tze Y. , White Murray E. , Dai Wei , Wilksch Jonathan J. , Bamert Rebecca S. , Rocker Andrea , Stubenrauch Christopher J , Williams Daniel , Huang Cheng , Schittelhelm Ralf , Barr Jeremy J. , Jameson Eleanor , McGowan Sheena , Zhang Yanju , Wang Jiawei , Dunstan Rhys A. , Lithgow Trevor 
Published: March 2021

ABSTRACTAntimicrobial resistance (AMR) continues to evolve as a major threat to human health and new strategies are required for the treatment of AMR infections. Bacteriophages (phages) that kill bacterial pathogens are being identified for use in phage therapies, with the intention to apply these bactericidal viruses directly into the infection sites in bespoke phage cocktails. Despite the great unsampled phage diversity for this purpose, an issue hampering the roll out of phage therapy is the poor quality annotation of many of the phage genomes, particularly for those from infrequently sampled environmental sources. We developed a computational tool called STEP3to use the “evolutionary features” that can be recognized in genome sequences of diverse phages. These features, when integrated into an ensemble framework, achieved a stable and robust prediction performance when benchmarked against other prediction tools using phages from diverse sources. Validation of the prediction accuracy of STEP3was conducted with high-resolution mass spectrometry analysis of two novel phages, isolated from a watercourse in the Southern Hemisphere. STEP3provides a robust computational approach to distinguish specific and universal features in phages to improve the quality of phage cocktails, and is available for use athttp://step3.erc.monash.edu/.IMPORTANCEIn response to the global problem of antimicrobial resistance there are moves to use bacteriophages (phages) as therapeutic agents. Selecting which phages will be effective therapeutics relies on interpreting features contributing to shelf-life and applicability to diagnosed infections. However, the protein components of the phage virions that dictate these properties vary so much in sequence that best estimates suggest failure to recognize up to 90% of them. We have utilised this diversity in evolutionary features as an advantage, to apply machine learning for prediction accuracy for diverse components in phage virions. We benchmark this new tool showing the accurate recognition and evaluation of phage components parts using genome sequence data of phages from under-sampled environments, where the richest diversity of phage still lies.
Selective attention and decision-making have separable neural bases in space and time
Authors: Moerel Denise , Rich Anina N. , Woolgar Alexandra 
Published: March 2021

ABSTRACTAttention and decision-making processes are fundamental to cognition. However, they are usually experimentally confounded, making it difficult to link neural observations to specific processes. Here we separated the effects of selective attention from the effects of decision-making on human brain activity, using a two-stage task where the attended stimulus and decision were orthogonal and separated in time. Multivariate pattern analyses of multimodal neuroimaging data revealed the dynamics of perceptual and decision-related information coding through time (magnetoencephalography (MEG)), space (functional Magnetic Resonance Imaging (fMRI)), and their combination (MEG-fMRI fusion). Our MEG results showed an effect of attention before decision-making could begin, and fMRI results showed an attention effect in early visual and frontoparietal regions. Model-based MEG-fMRI fusion suggested that attention boosted stimulus information in frontoparietal and early visual regions before decision-making was possible. Together, our results suggest that attention affects neural stimulus representations in frontoparietal regions independent of decision-making.
Episodic memory in aspects of brain information transfer by resting-state network topology
Authors: Yan Tianyi , Wang Gongshu , Wang Li , Liu Tiantian , Li Ting , Wang Luyao , Suo Dingjie , Funahashi Shintaro , Chen Duanduan , Wang Bin , Wu Jinglong 
Published: March 2021

AbstractStudies suggest that resting-state functional connectivity conveys cognitive information; also, activity flow mediates cognitive information transfer. However, the exact mechanism of interregional interactions underlying episodic memory remains unclear. We performed a combined analysis of task-evoked activity and resting-state functional connectivity by activity flow mapping to estimate the information transfer mechanism of episodic memory. We found that the cognitive control and attentional networks were the most recruited structures in information transfers during both encoding and retrieval processes; these networks were correlated with task-evoked activation. Differences in information transfer intensity between encoding and retrieval mainly existed in the visual, somatomotor and hippocampal systems. Furthermore, information transfer showed high predictive power for episodic memory ability and mediated relationships between task-evoked activation and memory performance. Additional analysis indicated that structural connectivity had a transportive role in information transfer. Finally, our study presented the information transfer mechanism of episodic memory from multiple neural perspectives.