bluuebunny/crossref_metadata_2025 huggingface dataset:
Population-scale testing can suppress the spread of COVID-19
Authors: Taipale Jussi , Romer Paul , Linnarsson Sten
Published: May 2020

We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) self-quarantine of infected individuals. Using a standard epidemiological model (SIR), we show here that by identification and isolation of the majority of infectious individuals, including those who may be asymptomatic, the reproduction number R0of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. We replicate these observations in a more complex stochastic dynamic model on a social network graph. We also find that the testing regime would be additive to other interventions, and be effective at any level of prevalence. If adopted as a policy, any industrial society could sustain the regime for as long as it takes to find a safe and effective cure or vaccine. Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Testing at the required scale would be feasible if existing qPCR-based methods are scaled up and multiplexed. A mass produced, low throughput field test kit could also be carried out at home. Economic analysis also supports the feasibility of the approach: current reagent costs for tests are in the range of a dollar or less, and the estimated benefits for population-scale testing are so large that the policy would be cost-effective even if the costs were larger by more than two orders of magnitude. To identify both active and previous infections, both viral RNA and antibodies could be tested. All technologies to build such test kits, and to produce them in the scale required to test the entire worlds’ population exist already. Integrating them, scaling up production, and implementing the testing regime will require resources and planning, but at a scale that is very small compared to the effort that every nation would devote to defending itself against a more traditional foe.
COVID-19 and depressive symptoms in students before and during lockdown
Authors: Meda Nicola , Pardini Susanna , Slongo Irene , Bodini Luca , Rigobello Paolo , Visioli Francesco , Novara Caterina
Published: May 2020

The lockdown due to coronavirus pandemic may exacerbate depressive symptoms, experts argue. Here we report that students, a high-risk category for mental disorders, report on average worse depressive symptoms than six months before isolation. The prospective data reported herein should alert clinician of a possible aggravation as well as new-onsets of depressive symptoms in students.
Media representation of spiders may exacerbate arachnophobic sentiments by framing a distorted perception of risk
Authors: Mammola Stefano , Nanni Veronica , Pantini Paolo , Isaia Marco
Published: May 2020

Spiders are able to arouse strong emotional reactions in humans. While spider bites are statistically rare events, our perception is skewed towards the potential harm spiders can cause to humans. We examined the human dimension of spiders through the lens of traditional media, by analysing more than 300 spider-related news published online in Italian newspapers between 2010 and 2020. We observed a recent, exponential increase in the frequency of the news, particularly those focused on medically important spiders – the Mediterranean black widow (Latrodectus tredecimguttatus) and the Mediterranean recluse (Loxosceles refescens). The news quality was generally poor: 70% contained different types of error, 32% were exaggerated, and in virtually none was an expert consulted. Overstated news referring to spider bites were significantly more shared on social media, thus contributing to frame a distorted perception of the risk associated with a spider bite and possibly reducing general public tolerance of spiders.
Atypical meiosis can be adaptive in outcrossedS. pombedue towtfmeiotic drivers
Authors: Bravo Núñez María Angélica , Sabbarini Ibrahim M. , Eide Lauren E. , Unckless Robert L. , Zanders Sarah E.
Published: May 2020

Killer meiotic drivers are genetic parasites that destroy ‘sibling’ gametes lacking the driver allele. The fitness costs of drive can lead to selection of unlinked suppressors. This suppression could involve evolutionary tradeoffs that compromise gametogenesis and contribute to infertility.Schizosaccharomyces pombe, an organism containing numerous gamete-killingwtfdrivers, offers a tractable system to test this hypothesis. Here, we demonstrate that in scenarios analogous to outcrossing,wtfdrivers generate a fitness landscape in which atypical gametes, such as aneuploids and diploids, are advantageous. In this context,wtfdrivers can decrease the fitness cost of mutations that disrupt meiotic fidelity and, in some circumstances, can even make such mutations beneficial. Moreover, we find thatS. pombeisolates vary greatly in their ability to make haploid gametes, with some isolates generating more than 25% aneuploid or diploid gametes. This work empirically demonstrates the potential for meiotic drivers to shape the evolution of gametogenesis.
Preparedness and response to Pediatric CoVID-19 in European Emergency Departments: a survey of the REPEM and PERUKI networks
Authors: Bressan Silvia , Buonsenso Danilo , Farrugia Ruth , Parri Niccolo’ , Oostenbrink Rianne , Titomanlio Luigi , Roland Damian , Nijman Ruud G. , Maconochie Ian , Da Dalt Liviana , Mintegi Santiago
Published: May 2020

Study objective

We aimed to describe the preparedness and response to the COVID-19 pandemic in referral EDs caring for children across Europe.

Methods

We did a cross-sectional point prevalence survey, which was developed and disseminated through the pediatric emergency medicine research networks for Europe (REPEM) and the United Kingdom and Ireland (PERUKI). We included a pre-determined number of centers based on each country population: five to ten EDs for countries with > 20 million inhabitants and one to five EDs for the other countries. ED directors or named delegates completed the survey between March 20th and 21st to report practice in use one month after the outbreak in Northern Italy. We used descriptive statistics to analyse data.

Results

Overall 102 centers from 18 countries completed the survey: 34% did not have an ED contingency plan for pandemics and 36% had never had simulations for such events. Wide variation on PPE items was shown for recommended PPE use at pre-triage and for patient assessment, with 62% of centers experiencing shortage in one or more PPE items. COVID-19 positive ED staff was reported in 25% of centers. Only 17% of EDs had negative pressure isolation rooms.

Conclusion

We identified variability and gaps in preparedness and response to the COVID-19 epidemic across European referral EDs for children. Early availability of a documented contingency plan, provision of simulation training, appropriate use of PPE, and appropriate isolation facilities emerged as key factors that should be optimized to improve preparedness and inform responses to future pandemics.
Deciphering the causal relationship between blood metabolites and Alzheimer’s Disease: a Mendelian Randomization study
Authors: Lord Jodie , Jermy Bradley , Green Rebecca , Wong Andrew , Xu Jin , Legido-Quigley Cristina , Dobson Richard , Richards Marcus , Proitsi Petroula
Published: May 2020

There are currently no disease modifying treatments for Alzheimer’s Disease (AD). Epidemiological studies have highlighted blood metabolites as potential biomarkers, but possible confounding and reverse causation prevent causal conclusions. Here, we investigated whether nineteen metabolites previously associated with midlife cognitive function, are on the causal pathway to AD.

Summary statistics from the largest Genome-Wide Association Studies (GWAS) for AD and for metabolites were used to perform bi-directional univariable Mendelian Randomisation (MR). Bayesian model averaging MR (MR-BMA) was additionally performed to address high correlation between metabolites and to identify metabolite combinations which may be on the AD causal pathway.

Univariable MR indicated three Extra-Large High-Density Lipoproteins (XL.HDL) to be on the causal pathway to AD: Free Cholesterol (XL.HDL.FC: OR=0.86, 95% CI=0.78-0.94), Total Lipids (XL.HDL.L: OR=0.88, 95% CI=0.80-0.97), and Phospholipids (XL.HDL.PL: OR=0.87, 95% CI=0.81-0.97); significant at an adjusted threshold of p<0.009. MR-BMA corroborated XL.HDL.FC to be amongst the top three causal metabolites, additionally to Total Cholesterol in XL.HDL (XL.HDL.C) and Glycoprotein Acetyls (GP) (posterior probabilities=0.112, 0.113, 0.287 respectively). Both XL.HDL.C and GP also demonstrated suggestive evidence of univariable causal associations (XL.HDL.C:OR=0.88, 95% CI=0.79-0.99; GP:OR=1.2, 95% CI=1.05-1.38); significant at the 5% level.

This study offers insight into the causal relationship between metabolites previously demonstrating association with mid-life cognition, and AD. It highlights GP in addition to several XL.HDLs as causal candidates which warrant further investigation. As the pathological changes underpinning AD are thought to develop decades prior to symptom onset, progressing these findings could hold special value in informing future risk reduction strategies.
Fractional SIR Epidemiological Models
Authors: Taghvaei Amirhossein , Georgiou Tryphon T. , Norton Larry , Tannenbaum Allen
Published: May 2020

The purpose of this work is to make a case for epidemiological models with fractional exponent in the contribution of sub-populations to the transmission rate. More specifically, we question the standard assumption in the literature on epidemiological models, where the transmission rate dictating propagation of infections is taken to be proportional to the product between the infected and susceptible sub-populations; a model that relies on strong mixing between the two groups and widespread contact between members of the groups. We content, that contact between infected and susceptible individuals, especially during the early phases of an epidemic, takes place over a (possibly diffused) boundary between the respective sub-populations. As a result, the rate of transmission depends on the product of fractional powers instead. The intuition relies on the fact that infection grows in geographically concentrated cells, in contrast to the standard product model that relies on complete mixing of the susceptible to infected sub-populations. We validate the hypothesis of fractional exponents i) by numerical simulation for disease propagation in graphs imposing a local structure to allowed disease transmissions and ii) by fitting the model to a COVID-19 data set provided by John Hopkins University (JHUCSSE) for the period Jan-31-20 to Mar-24-20, for the countries of Italy, Germany, Iran, and France.
Bayesian Inference of COVID-19 Spreading Rates in South Africa
Authors: Mbuvha Rendani , Marwala Tshilidzi
Published: May 2020

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has highlighted the need for the development of prompt mitigating responses under conditions of high uncertainty. Fundamental to the design of rapid state reactions is the ability to perform epidemiological model parameter inference for localised trajectory predictions. In this work, we perform Bayesian parameter inference using Markov Chain Monte Carlo (MCMC) methods on the Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological models with time-varying spreading rates for South Africa. The results find two change points in the spreading rate of COVID-19 in South Africa as inferred from the confirmed cases. The first change point coincides with state enactment of a travel ban and the resultant containment of imported infections. The second change point coincides with the start of a state-led mass screening and testing programme which has highlighted community-level disease spread that was not well represented in the initial largely traveller based and private laboratory dominated testing data. The results further suggest that due to the likely effect of the national lockdown, community level transmissions are slower than the original imported case driven spread of the disease.
Assessment of the outbreak risk, mapping and infestation behavior of COVID-19: Application of the autoregressive and moving average (ARMA) and polynomial models
Authors: Pourghasemi Hamid Reza , Pouyan Soheila , Farajzadeh Zakariya , Sadhasivam Nitheshnirmal , Heidari Bahram , Babaei Sedigheh , Tiefenbacher John P.
Published: May 2020

Infectious disease outbreaks pose a significant threat to human health worldwide. The outbreak of pandemic coronavirus disease 2019 (COVID-2019) has caused a global health emergency. Identification of regions with high risk for COVID-19 outbreak is a major priority of the governmental organizations and epidemiologists worldwide. The aims of the present study were to analyze the risk factors of coronavirus outbreak and identify areas with a high risk of human infection with virus in Fars Province, Iran. A geographic information system (GIS)-based machine learning algorithm (MLA), support vector machine (SVM), was used for the assessment of the outbreak risk of COVID-19 in Fars Province, Iran. The daily observations of infected cases was tested in the third-degree polynomial and the autoregressive and moving average (ARMA) models to examine the patterns of virus infestation in the province and in Iran. The results of disease outbreak in Iran were compared with the data for Iran and the world. Sixteen effective factors including minimum temperature of coldest month (MTCM), maximum temperature of warmest month (MTWM), precipitation in wettest month (PWM), precipitation of driest month (PDM), distance from roads, distance from mosques, distance from hospitals, distance from fuel stations, human footprint, density of cities, distance from bus stations, distance from banks, distance from bakeries, distance from attraction sites, distance from automated teller machines (ATMs), and density of villages – were selected for spatial modelling. The predictive ability of an SVM model was assessed using the receiver operator characteristic – area under the curve (ROC-AUC) validation technique. The validation outcome reveals that SVM achieved an AUC value of 0.786 (March 20), 0.799 (March 29), and 86.6 (April 10) a good prediction of change detection. The growth rate (GR) average for active cases in Fars for a period of 41 days was 1.26, whilst it was 1.13 in country and the world. The results of the third-degree polynomial and ARMA models revealed an increasing trend for GR with an evidence of turning, demonstrating extensive quarantines has been effective. The general trends of virus infestation in Iran and Fars Province were similar, although an explosive growth of the infected cases is expected in the country. The results of this study might assist better programming COVID-19 disease prevention and control and gaining sorts of predictive capability would have wide-ranging benefits.
Visible implant elastomer (VIE) success in early larval stages of a tropical amphibian species
Authors: Fouilloux Chloe , Garcia-Costoya Guillermo , Rojas Bibiana
Published: May 2020

Animals are often difficult to distinguish at an individual level, but being able to identify individuals can be crucial in ecological or behavioral studies. In response to this challenge, biologists have developed a range of marking (tattoos, brands, toe-clips) and tagging (PIT, VIA, VIE) methods to identify individuals and cohorts. Animals with complex life cycles are notoriously hard to mark because of the distortion or loss of the tag across metamorphosis. In frogs, few studies have attempted larval tagging and none have been conducted on a tropical species. Here, we present the first successful account of VIE tagging in early larval stages (Gosner stage 25) of the dyeing poison frog (Dendrobates tinctorius) coupled with a novel anaesthetic (2-PHE) application for tadpoles that does not require buffering. Mean weight of individuals at time of tagging was 0.12g, which is the smallest and developmentally youngest anuran larvae tagged to date. We report 81% tag detection over the first month of development, as well as the persistence of tags across metamorphosis in this species. Cumulative tag retention versus tag observation differed by approximately 15% across larval development demonstrating that “lost” tags can be found later in development. Tagging had no effect on tadpole growth rate or survival. Successful application of VIE tags onD. tinctoriustadpoles introduces a new method that can be applied to better understand early life development and dispersal in various tropical species.
Single-cell analysis uncovers mechanisms of plasticity in leukemia initiating cells
Authors: Morris Vivian , Marion William , Hughes Travis , Sousa Patricia , Sensharma Prerana , Pikman Yana , Harris Marian , Shalek Alex K. , North Trista E. , Daley George Q. , da Rocha Edroaldo Lummertz , Rowe R. Grant
Published: May 2020

Leukemia initiating cells (LICs) fuel leukemic growth and spark relapse. Previously thought to be primitive and rare, the LIC state may actually be heterogeneous and dynamic, enabling evasion of therapies. Here, we use single-cell transcriptomics to track LIC multipotency within the cellular ontogeny ofMLL-rearranged B-lymphoblastic leukemia (MLL-r B-ALL). Although we identify rare transcriptionally and phenotypically primitive LICs, we also observe LICs emerging from more differentiated populations with the capability to replenish the full leukemic cellular diversity. We find that activation of MYC-driven oxidative phosphorylation controls this process of facultative state conversion in LICs.
The habenula clock influences prediction of danger
Authors: Basnakova Adriana , Cheng Ruey-Kuang , Ming Joanne Chia Shu , D’Agostino Giuseppe , Suryadi  , Hui Germaine Tan Jia , Langley Sarah R. , Jesuthasan Suresh
Published: May 2020

The response of an animal to a sensory stimulus depends on the nature of the stimulus and on predictions mediated by spontaneous activity in neurons. Here, we ask how circadian variation in the prediction of danger, and thus the response to a potential threat, is controlled. We focus on the habenula, a mediator of threat response that functions by regulating neuromodulator release, and use zebrafish as the experimental system. Single cell transcriptomics indicates that multiple clock genes are expressed throughout the habenula, while quantitative in situ hybridization confirms that the clock oscillates. Two-photon calcium imaging indicates a circadian change in spontaneous activity of habenula neurons. To assess the role of this clock, a truncated clocka gene was specifically expressed in the habenula. This partially inhibited the clock, as shown by changes in per3 expression as well as altered day-night variation in dopamine, serotonin and acetylcholine levels. Behaviourally, anxiety-like responses evoked by an alarm pheromone were reduced. Circadian effects of the pheromone were disrupted, such that responses in the day resembled those at night. Behaviours that are regulated by the pineal clock and not triggered by stressors were unaffected. These findings establish that the habenula clock regulates the expectation of danger, thus identifying one mechanism for circadian change in the response to a stressor.
Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s
Authors: Joshi Jaya , Beaudoin Guillaume A.W. , Patterson Jenelle A. , García-García Jorge D. , Belisle Catherine E. , Chang Lan-Yen , Li Lei , Duncan Owen , Millar A. Harvey , Hanson Andrew D.
Published: May 2020

Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mech-anismin planta. Unexpectedly, transcriptome datamining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in devel-oping grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiaminde novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thia-zole auxotrophy inEscherichia coli. There is thus aprima faciecase that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain filling period.

Abbreviations

DHAla, dehydroalanine; EST, expressed sequence tag; FDR, false discovery rate; IPTG, β-D-1-thiogalactopyranoside
Why species richness of plants and herbivorous insects do or do not correlate
Authors: Shinohara Naoto , Yoshida Takehito
Published: May 2020

Unraveling the determinants of herbivorous insect diversity has been a major challenge in ecology. Despite the strong association between insect and plant species, previous studies conducted in natural systems have shown great variation in the strength of the correlation between their species richness. Such variation can be attributed to the proportion of generalist insect species (generality), though both higher and lower generality may weaken the correlation because 1) generalist insect species are less dependent on the number of plant species and 2) specialist insect species utilize only a part of the total plant species. To explore these opposing effects, we studied plant and herbivorous insect communities in semi-natural grasslands in Japan. Plant–insect interactions were evaluated in a unique way with a particular focus on the staying and herbivory behaviors of insects, which reflect their habitat use as well as host use. We fousnd that generality of insect communities negatively affected the correlation between species richness of plants and insects. However, such negative effect was significant only when the insect species richness was related with the number of plant species interacted with some insect species, instead of with that of total plant species. The results suggest that considering either of the opposing effects of insect generality is insufficient and they should be inclusively interpreted to understand the relationship between plant and insect species richness.
PCNA has specific functions in regulation of metabolism in haematological cells
Authors: Røst Lisa M. , Olaisen Camilla , Sharma Animesh , Nedal Aina , Petrovic Voin , Kvitvang Hans Fredrik N. , Bruheim Per , Otterlei Marit
Published: May 2020

PCNA’s essential roles in DNA replication and repair are well established, while its recently discovered cytosolic roles are less explored. Here we show that impairing PCNA’s cytosolic scaffold functions led to massive changes in cellular signaling, and most strikingly, a strong reduction in glycolytic metabolite and nucleoside phosphate pools in haematological cancer cells. This was not detected in cells from solid tissues nor in primary monocytes from healthy donors. However, lipopolysaccharide stimulated monocytes responded to targeting PCNA’s scaffold function similarly to haematological cancer cells, suggesting that cellular stress is an important factor for the observed response. Integrated transcriptome, proteome and metabolome analysis revealed that pathways involved in protein stability/folding and immune responses were affected in haematopoietic cancer cells. Altogether, our data suggests that PCNA has an important role in regulation of cytoplasmic stress via regulation of central carbon metabolism in haematological cells, which potentially can be targeted in cancer treatment.

Highlight

A strong reduction in glycolytic metabolites and the nucleoside phosphate pools was detected in haematological cancer cells upon inhibiting PCNA scaffold functions. These metabolic changes were not found in cancer cells from other tissues, indicating a special role of PCNA in regulation of metabolism in cells of haematological origin.
Does hippocampal volume explain performance differences on hippocampal-dependent tasks?
Authors: Clark Ian A. , Monk Anna M. , Hotchin Victoria , Pizzamiglio Gloria , Liefgreen Alice , Callaghan Martina F. , Maguire Eleanor A.
Published: May 2020

Marked disparities exist across healthy individuals in their ability to imagine scenes, recall autobiographical memories, think about the future and navigate in the world. The importance of the hippocampus in supporting these critical cognitive functions has prompted the question of whether differences in hippocampal grey matter volume could be one source of performance variability. Evidence to date has been somewhat mixed. In this study we sought to mitigate issues that commonly affect these types of studies. Data were collected from a large sample of 217 young, healthy adult participants, including whole brain structural MRI data (0.8mm isotropic voxels) and widely-varying performance on scene imagination, autobiographical memory, future thinking and navigation tasks. We found little evidence that hippocampal grey matter volume was related to task performance in this healthy sample. This was the case using different analysis methods (voxel-based morphometry, partial correlations), when whole brain or hippocampal regions of interest were examined, when comparing different sub-groups (divided by gender, task performance, self-reported ability), and when using latent variables derived from across the cognitive tasks. Hippocampal grey matter volume may not, therefore, significantly influence performance on tasks known to require the hippocampus in healthy people. Perhaps only in extreme situations, as in the case of licensed London taxi drivers, are measurable ability-related hippocampus volume changes consistently exhibited.

Highlights

Evidence is mixed about whether hippocampal volume affects cognitive task performance

This is particularly the case concerning individual differences in healthy people

We collected structural MRI data from 217 healthy people

They also had widely-varying performance on cognitive tasks linked to the hippocampus

In-depth analyses showed little evidence hippocampal volume affected task performance
Nano-analytical Characterization of Breast Tissue Biopsies Reveals an Association between Spherical Nano and Micro Particles and Invasive Malignant Breast Tumours
Authors: Tsolaki Elena , Doran William , Overbeck Jan , Magnani Luca , Olivo Alessandro , Herrmann Inge K. , Bertazzo Sergio
Published: May 2020

The presence of calcifications on mammograms is a widely used diagnostic marker for breast cancer. While the clinicopathological analysis of breast tissue is well-developed, an in-depth characterisation of the properties of calcifications at the micro and nano scale remained elusive. In this work, we use nano-analytical methods to investigate the calcification present in healthy breast tissue, as well as in benign and malignant breast tumour tissue biopsies. While polycrystalline apatite with lower crystallinity can be found in all breast tissue samples, we show that magnesium-containing nano and micro spherical particles are found only in malignant invasive breast cancers. These particles concentration increases with cancer progression. The discovery of these spherical particles provides new insights into the characteristics of breast calcification associated with malignant tumours and opens new research pathways to a better understanding of breast tumours and their microenvironment in general.
Cortical and subcortical hemodynamic changes during human sleep slow waves
Authors: Betta Monica , Handjaras Giacomo , Leo Andrea , Federici Alessandra , Farinelli Valentina , Ricciardi Emiliano , Siclari Francesca , Meletti Stefano , Ballotta Daniela , Benuzzi Francesca , Bernardi Giulio
Published: May 2020

EEG slow waves, the hallmarks of NREM sleep, are closely linked to the restorative function of sleep and their regional cortical distribution reflects plasticity- and learning-related processes. Here we took advantage of simultaneous EEG-fMRI recordings to map cortical and subcortical hemodynamic (BOLD) fluctuations time-locked to sleep slow waves. Recordings were performed in twenty healthy adults during an afternoon nap. Slow waves were associated with BOLD-signal increases in the brainstem and in portions of thalamus and cerebellum characterized by preferential functional connectivity with limbic and somatomotor areas, respectively. At the cortical level, significant BOLD-signal decreases were found in several areas, including insula and somatomotor cortex, and were preceded by slow signal increases that peaked around slow-wave onset. EEG slow waves and BOLD fluctuations showed similar cortical propagation patterns, from centro-frontal to temporo-occipital cortices. These regional patterns of hemodynamic-electrical coupling are consistent with theoretical accounts of the functions of sleep slow waves.
Is a long hygroscopic awn an advantage forThemeda triandrain drier areas?
Authors: Morris Craig D
Published: May 2020

Themeda triandrahas bigeniculate hygroscopic lemma seed awns that twist when wet and drying, thereby transporting the caryopsis across the soil surface into suitable germination microsites. The prediction that awns would be longer in drier grassland and have greater motility to enable them to move quickly and further to find scarce germination sites was tested in KwaZulu-Natal. Awns (n = 100) were collected from 16 sites across a mean annual precipitation gradient (575-1223 mm), ranging from 271-2097 m a.s.l. The daily movement of hydrated long and short awns (n = 10) across blotting paper was tracked for five days, and the rotational speed of anchored awns was measured. Awn length varied considerably (mean: 41.4-63.2 mm; sd: 3.44-8.99) but tended to increase (r = 0.426, p = 0.099) not decline, with increasing MAP. Awn length was unrelated to elevation, temperature and aridity indices. Long awns rotated at the same rate (2 min 48 sec) but moved twice as fast (46.3 vs. 22.1 mm day-1) and much further (maximum: 82.1 vs. 38.6 mm day-1) than short awns. Whether moisture limits awn development, the benefit of longer awns to negotiate densely tufted mesic grassland, and the multifunctionality of awns require investigation.
Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models
Authors: Weiss Michael N. , Franks Daniel W. , Brent Lauren J. N. , Ellis Samuel , Silk Matthew J. , Croft Darren P.
Published: May 2020

Social network methods have become a key tool for describing, modelling, and testing hypotheses about the social structures of animals. However, due to the non-independence of network data and the presence of confounds, specialized statistical techniques are often needed to test hypotheses in these networks. Datastream permutations, originally developed to test the null hypothesis of random social structure, have become a popular tool for testing a wide array of null hypotheses. In particular, they have been used to test whether exogenous factors are related to network structure by interfacing these permutations with regression models.

Here, we show that these datastream permutations typically do not represent the null hypothesis of interest to researchers interfacing animal social network analysis with regression modelling, and use simulations to demonstrate the potential pitfalls of using this methodology.

Our simulations show that utilizing common datastream permutations to test the coefficients of regression models can lead to extremely high type I (false-positive) error rates (> 30%) in the presence of non-random social structure. The magnitude of this problem is primarily dependent on the degree of non-randomness within the social structure and the intensity of sampling

We strongly recommend against utilizing datastream permutations to test regression models in animal social networks. We suggest that a potential solution may be found in regarding the problems of non-independence of network data and unreliability of observations as separate problems with distinct solutions.
New Music System Reveals Spectral Contribution to Statistical Learning
Authors: Loui Psyche
Published: May 2020

1

Knowledge of speech and music depends upon the ability to perceive relationships between sounds in order to form a stable mental representation of statistical structure. Although evidence exists for the learning of musical scale structure from the statistical properties of sound events, little research has been able to observe how specific acoustic features contribute to statistical learning independent of the effects of long-term exposure. Here, using a new musical system, we show that spectral content is an important cue for acquiring musical scale structure. In two experiments, participants completed probe-tone ratings before and after a half-hour period of exposure to melodies in a novel musical scale with a predefined statistical structure. In Experiment 1, participants were randomly assigned to either a no-exposure control group, or to exposure groups who heard pure tone or complex tone sequences. In Experiment 2, participants were randomly assigned to exposure groups who heard complex tones constructed with odd harmonics or even harmonics. Learning outcome was assessed by correlating pre/post-exposure ratings and the statistical structure of tones within the exposure period. Spectral information significantly affected sensitivity to statistical structure: participants were able to learn after exposure to all tested timbres, but did best at learning with timbres with odd harmonics, which were congruent with scale structure. Results show that spectral amplitude distribution is a useful cue for statistical learning, and suggest that musical scale structure might be acquired through exposure to spectral distribution in sounds.
Continuous Reports of Sensed Hand Position During Sensorimotor Adaptation
Authors: Tsay Jonathan S. , Parvin Darius E. , Ivry Richard B.
Published: May 2020

Sensorimotor learning entails multiple learning processes, some volitional and explicit, and others automatic and implicit. A new method to isolate implicit adaptation involves the use of a “clamped” visual perturbation in which, during a reaching movement, visual feedback is limited to a cursor that follows an invariant trajectory, offset from the target by a fixed angle. Despite full awareness that the cursor movement is not contingent on their behavior, as well as explicit instructions to ignore the cursor, systematic changes in motor behavior are observed, and these changes have the signatures of implicit adaptation observed in studies using classic visuomotor perturbations. While it is clear that the response to clamped feedback occurs automatically, it remains unknown if the adjustments in behavior remain outside the participant’s awareness. To address this question, we used the clamp method and directly probed awareness by asking participants to report their hand position after each reach. As expected, we observed robust deviations in hand angle away from the target (average of ∼18°). The hand reports also showed systematic deviations over the course of adaptation, initially attracted towards the visual feedback and then in the opposite direction, paralleling the shift in hand position. However, these effects were subtle (∼2° at asymptote), with the hand reports dominated by a feedforward signal associated with the motor intent yet modulated in a limited way by feedback sources. These results confirm that adaptation in response to a visual perturbation is not only automatic, but also largely implicit.

NEWS AND NOTEWORTHY

Sensorimotor adaptation operates in an obligatory manner. Qualitatively, subjective reports obtained after adaptation demonstrate that, in many conditions, participants are unaware of significant changes in behavior. In the present study, we quantified participants’ awareness of adaptation by obtaining reports of hand position on a trial-by-trial basis. The results confirm that participants are largely unaware of adaptation, but also reveal the subtle influence of feedback on their subjective experience.
How repeated outbreaks drive the evolution of bacteriophage communication: Insights from a mathematical model
Authors: Doekes Hilje M. , Mulder Glenn A. , Hermsen Rutger
Published: May 2020

Communication based on small signalling molecules is widespread among bacteria. Recently, such communication was also described in bacteriophages. Upon infection of a host cell, temperate phages of theBacillus subtilis-infecting SPbeta group induce the secretion of a phage-encoded signalling peptide, which is used to inform the lysis-lysogeny decision in subsequent infections: the phages produce new virions and lyse their host cell when the signal concentration is low, but favour a latent infection strategy, lysogenising the host cell, when the signal concentration is high. Here, we present a mathematical model to study the ecological and evolutionary dynamics of such viral communication. We show that a communication strategy in which phages use the lytic cycle early in an outbreak (when susceptible host cells are abundant) but switch to the lysogenic cycle later (when susceptible cells become scarce) is favoured over a bet-hedging strategy in which cells are lysogenised with constant probability. However, such phage communication can evolve only if phage-bacteria populations are regularly perturbed away from their equilibrium state, so that acute outbreaks of phage infections in pools of susceptible cells continue to occur. Our model then predicts the selection of phages that switch infection strategy when half of the available susceptible cells have been infected.
FromATOMtoGradiATOM: Cortical gradients support time and space processing as revealed by a meta-analysis of neuroimaging studies
Authors: Cona Giorgia , Wiener Martin , Scarpazza Cristina
Published: May 2020

According to the ATOM (A Theory Of Magnitude), formulated by Walsh more than fifteen years ago, there is a general system of magnitude in the brain that comprises regions, such as the parietal cortex, shared by space, time and other magnitudes (Walsh, 2003).

The present meta-analysis of neuroimaging studies used the Activation Likelihood Estimation (ALE) method in order to determine the set of regions commonly activated in space and time processing and to establish the neural activations specific to each magnitude domain. Following PRISMA guidelines, we included in the analysis a total of 112 and 114 experiments, exploring space and time processing, respectively.

We clearly identified the presence of a system of brain regions commonly recruited in both space and time and that includes: bilateral insula, the pre-supplementary motor area (SMA), the right frontal operculum and the intraparietal sulci. These regions might be the best candidates to form the core magnitude neural system. Surprisingly, along each of these regions but the insula, ALE values progressed in a cortical gradient from time to space. The SMA exhibited an anterior-posterior gradient, with space activating more-anterior regions (i.e., pre-SMA) and time activating more-posterior regions (i.e., SMA-proper). Frontal and parietal regions showed a dorsal-ventral gradient: space is mediated by dorsal frontal and parietal regions, and time recruits ventral frontal and parietal regions.

Our study supports but also expands the ATOM theory. Therefore, we here re-named it the ‘GradiATOM’ theory (Gradient Theory of Magnitude), proposing that gradient organization can facilitate the transformations and integrations of magnitude representations by allowing space- and time-related neural populations to interact with each other over minimal distances.
Modern Machine Learning: Partition & Vote
Authors: Priebe Carey E. , Vogelstein Joshua T. , Engert Florian , White Christopher M.
Published: May 2020

We present modern machine learning, focusing on the state-of-the-art classification methods of decision forests and deep networks, as partition and vote schemes. This illustrative presentation allows for both a unified basic understanding of how these methods work from the perspective of classical statistical pattern recognition as well as useful basic insight into their relationship with each other … and potentially with brain functioning.
anTraX: high throughput video tracking of color-tagged insects
Authors: Gal Asaf , Saragosti Jonathan , Kronauer Daniel J. C.
Published: May 2020

Recent years have seen a surge in methods to track and analyze animal behavior. Nevertheless, tracking individuals in closely interacting, group-living organisms remains a challenge. Here we present anTraX, an algorithm and software package for high-throughput video tracking of color-tagged insects. anTraX combines neural network classification of animals with a novel approach for representing tracking data as a graph, enabling individual tracking even in cases where it is difficult to segment animals from one another, or where tags are obscured. The use of color tags, a well-established and robust method for marking individual insects in groups, relaxes requirements for image size and quality, and makes the software broadly applicable. anTraX is readily integrated into existing tools and methods for automated image analysis of behavior to further augment its output. anTraX can handle large-scale experiments with minimal human involvement, allowing researchers to simultaneously monitor many social groups over long time periods.
A novel single-domain Na+-selective voltage-gated channel in photosynthetic eukaryotes
Authors: Helliwell Katherine E. , Chrachri Abdul , Koester Julie , Wharam Susan , Taylor Alison R. , Wheeler Glen L. , Brownlee Colin
Published: May 2020

The evolution of Na+-selective four-domain voltage-gated channels (4D-Navs) in animals allowed rapid Na+-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signalling. Whilst bacteria encode single-domain Na+-selective voltage-gated channels (BacNav), they typically exhibit much slower kinetics than 4D-Navs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na+-selective signalling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus Flytrap where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na+-selective single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores. The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and sensitivity to the highly selective 4D-Nav blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na+-based signalling in eukaryotes is not restricted to animals or to the presence of 4D-Navs. The EukCatB channels therefore represent an independent evolution of fast Na+-based electrical signalling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae.

One Sentence Summary

The capacity for rapid Na+-based signalling has evolved in ecologically important coccolithophore species via a novel class of voltage-gated Na+ channels, EukCatBs.
Synthesis runs counter to directional folding of a nascent protein domain
Authors: Chen Xiuqi , Rajasekaran Nandakumar , Liu Kaixian , Kaiser Christian M.
Published: May 2020

Folding of individual domains in large proteins during translation helps to avoid otherwise prevalent inter-domain misfolding. How folding intermediates observedin vitrofor the majority of proteins relate to co-translational folding remains unclear. Combiningin vivoand single-molecule experiments, we followed the co-translational folding of the G-domain, encompassing the first 293 amino acids of elongation factor G. Surprisingly, the domain remains unfolded until it is fully synthesized, without collapsing into molten globule-like states or forming stable intermediates. Upon fully emerging from the ribosome, the G-domain transitions to its stable native structure via folding intermediates. Our results suggest a strictly sequential folding pathway initiating from the C-terminus. Folding and synthesis thus proceed in opposite directions. The folding mechanism is likely imposed by the final structure and might have evolved to ensure efficient, timely folding of a highly abundant and essential protein.
Hugin+neurons link the sleep homeostat to circadian clock neurons
Authors: Schwarz Jessica E. , King Anna N. , Hsu Cynthia T. , Barber Annika F. , Sehgal Amita
Published: May 2020

Sleep is controlled by homeostatic mechanisms, which drive sleep after wakefulness, and a circadian clock, which confers the 24-hour rhythm of sleep. These processes interact with each other to control the timing of sleep in a daily cycle as well as following sleep deprivation. However, the mechanisms by which they interact are poorly understood. We show here thathugin+ neurons, previously identified as neurons that function downstream of the clock to regulate rhythms of locomotor activity, are also targets of the sleep homeostat. Sleep deprivation decreases activity ofhugin+ neurons, likely to suppress circadian-driven activity during recovery sleep, and manipulations ofhugin+ neurons affect sleep increases generated by activation of the homeostatic sleep locus, the dorsal fanshaped body (dFB). Also, mutations in peptides produced by thehugin+ locus increase recovery sleep following deprivation. Trans-synaptic mapping reveals thathugin+ neurons feed-back onto central clock neurons, which also show decreased activity upon sleep loss, in a Hugin-peptide dependent fashion. We propose thathugin+ neurons integrate circadian and sleep signals to modulate circadian circuitry and regulate the timing of sleep.