bluuebunny/crossref_metadata_2025_split huggingface dataset:
Out of sight: Surveillance strategies for emerging vectored plant pathogens
Authors: Mastin Alexander J. , van den Bosch Frank , Bourhis Yoann , Parnell Stephen 
Published: January 2022

AbstractEmerging pests and pathogens of plants are a major threat to natural and managed ecosystems worldwide. Whilst it is well accepted that surveillance activities are key to both the early detection of new incursions and the ability to identify pest-free areas, the performance of these activities must be evaluated to ensure they are fit for purpose. This requires consideration of the number of potential hosts inspected or tested as well as the epidemiology of the pathogen and the detection method used. In the case of plant pathogens, one particular concern is whether the visual inspection of plant hosts for signs of disease is able to detect the presence of these pathogens at low prevalences, given that it takes time for these symptoms to develop. One such pathogen is the ST53 strain of the vector-borne bacterial pathogen Xylella fastidiosa in olive hosts, which was first identified in southern Italy in 2013. Additionally, X. fastidiosa ST53 in olive has a rapid rate of spread, which could also have important implications for surveillance. In the current study, we evaluate how well visual surveillance would be expected to perform for this pathogen and investigate whether molecular testing of either tree hosts or insect vectors offer feasible alternatives. Our results identify the main constraints to each of these strategies and can be used to inform and improve both current and future surveillance activities.
Widespread transposon co-option in the Caenorhabditis germline regulatory network
Authors: Carelli Francesco , Cerrato Chiara , Dong Yan , Appert Alex , Dernburg Abby , Ahringer Julie 
Published: January 2022

AbstractThe movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. Here we show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one third of C. elegans germline-specific promoters have been co-opted from two related Miniature Inverted Repeat Transposable Elements (MITEs), CERP2 and CELE2. The promoters are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. Expansion of CERP2 occurred prior to radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in C. briggsae, we find evolutionary conservation of most CERP2 co-opted promoters, but a substantial fraction of events are species specific. Our work reveals the emergence of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.
Macrophage activation of cGAS and TRIM5 distinguish pandemic and non-pandemic HIV
Authors: Zuliani Alvarez Lorena , Govasli Morten L. , Rasaiyaah Jane , Monit Chris , Perry Stephen O. , Sumner Rebecca P. , McAlpine-Scott Simon , Dickson Claire , Faysal K. M. Rifat , Hilditch Laura , Miles Richard J. , Bibollet-Ruche Frederic , Hahn Beatrice H. , Boecking Till , Pinotsis Nikos , James Leo C. , Jacques David A. , Towers Greg J. 
Published: January 2022

SUMMARYPandemic viruses remain a global threat to health and economics but how they adapt to become pandemic remains poorly understood. Here we compare pandemic HIV-1(M) and non-pandemic HIV-(O) and HIV-2 strains finding that non-pandemic HIV replicate poorly in myeloid cell models due to activation of cGAS and TRIM5, and ensuing antiviral responses. We use phylogenetics and viral capsid structural biology to define specific differences between pandemic and non-pandemic HIV capsids and demonstrate that their genetic reversal in HIV-1(M) mutants causes TRIM5, cGAS and innate immune activation. We propose a model in which the parental lineage of pandemic HIV-1(M) has uniquely evolved a dynamic capsid that avoids activation of cGAS and TRIM5 to establish cloaked replication in myeloid cells. The unique adaptations of the pandemic virus lineage suggests a role in effective human-to-human transmissibility and highlight the importance of avoiding innate immune activation during pandemic human-to-human viral transmission.
The UBR box E3 ligases Poe and Hyd are required for efficient Pericentrin degradation
Authors: Varadarajan Ramya , Galletta Brian J. , Fagerstrom Carey J. , Haase Karen Plevock , Rusan Nasser M. 
Published: January 2022

AbstractCentrosomes are the major microtubule organizing centers (MTOC) of many cells and are composed of centrioles and the pericentriolar material (PCM). Centrosomes are an essential part of diverse cellular processes and require precise regulation of their protein levels. One protein whose levels must be regulated is Pericentrin – PCNT in humans and PLP in Drosophila. Increased PCNT expression and its protein accumulation is linked to clinical conditions including cancer, mental disorders, and ciliopathies. However, the mechanisms by which PCNT levels are regulated remains underexplored. Our previous study (Galletta, 2020) demonstrated that PLP levels are sharply downregulated during early spermatogenesis and this regulation is essential to spatially position PLP on the proximal end of centrioles. We hypothesized that the sharp drop in PLP protein was a result of a rapid protein degradation during the male pre-meiotic G2 phase. In this study we show that the N-terminal region of PLP is required for regulating its levels, which when elevated, extends PLP’s position distally on centrioles. Consequently, PCM was also mispositioned leading to defects in spermatids. We then performed a targeted screen where we identified the E2 ligases, Rad6 and UbcD1, and the UBR box family E3 ligases, Poe (UBR4) and Hyd (UBR5) as factors that promote PLP degradation in spermatocytes. Collectively, our study suggests that Poe and Hyd directly bind the N-terminus of PLP and target it for degradation, ensuring proper centriole/basal body assembly and male fertility.
Brain temperature affects quantitative features of hippocampal sharp wave ripples
Authors: Petersen Peter C. , Vöröslakos Mihály , Buzsáki György 
Published: January 2022

AbstractBiochemical mechanisms are temperature-dependent. Brain temperature shows wide variations across brain states, and such changes may explain quantitative changes in network oscillations. Here we report on the coupling of various hippocampal sharp wave ripple features to brain temperature. Ripple frequency, occurrence rate and duration correlated with temperature dynamics. By focal manipulation of the brain temperature in the hippocampal CA1 region, we show that ripple frequency can be increased and decreased by local heating and cooling, respectively. Changes of other parameters, such as the rate of SPW-R and ripple duration were not consistently affected. Our findings suggest that brain temperature in the CA1 region plays a leading role in affecting the ripple frequency, whereas other parameters of SPW-Rs may be determined by mechanisms upstream from the CA1 region. These findings illustrate that physiological variations of brain temperature exert important effects on hippocampal circuit operations.
Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment
Authors: Sutherland Ben J. G. , Finke Jan F. , Saunders Robert , Warne Snehal , Schulze Angela D. , Strohm Jeff H. T. , Chan Amy M. , Suttle Curtis A. , Miller Kristina M. 
Published: January 2022

AbstractTemperate coastal marine waters are often thermally stratified from spring through fall but can be dynamic and disrupted by tidal currents and wind-driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO2 (pCO2), and its associated microbial communities to the surface. Anecdotally, these events impact shellfish hatcheries and farms, warranting improved understanding of changes in composition and activity of marine microbial communities in relation to environmental processes. To characterize both compositional and functional changes associated with abiotic factors, here we generate a reference metatranscriptome from the Strait of Georgia over representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO2 levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite and pCO2. Community composition changes were observed to occur at broad taxonomic levels, and most notably to vary with temperature and pCO2. Functional gene expression profiles indicated a strong difference between early (June-July) and late summer (August-October) associated with viral activity. The taxonomic data suggests this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO2) than with the temporal effect. Microbial composition and activity in these waters varies with both short-term effects observed alongside abiotic variation as well as long-term effects observed across seasons. The analysis of both taxonomy and functional gene expression simultaneously in the same samples by environmental RNA (eRNA metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.
Evaluation of the effects of vaccination regimes on the transmission dynamics of COVID-19 pandemic
Authors: Nakamoto Ichiro 
Published: January 2022

AbstractThe COVID-19 pandemic has yet to be eliminated globally despite the advancement of immunization programs. Evaluation of the effects of the vaccination regimes of COVID-19 is critical for understanding the potential capacity of countermeasures and informing subsequent prioritization strategies of responses. Research and observational data provide broad support regarding the importance of effective vaccines, in contrast, debates remain on the timing and priority of booster vaccination under the assumption of resource constraint. This study aims to evaluate the effect of vaccination regimes on the trajectory of the COVID-19 pandemic from the medium-term perspective. We employ a mathematical model to infer critical epidemiological characteristics associated with COVID-19, thereafter perform simulation on the transmission dynamics of the epidemic up to 3 years. The outcomes imply that in the absence of severe variants of the pathogen, administration of booster vaccination curtails the peak size of total cases and share of severe infections at later waves. Nevertheless, it can be better off by prioritizing the primary doses to unvaccinated individuals when vaccine shortage is challenged. The effects of priority categories are consistent across a broad range of profiles. Increasing the rollout capacity (i.e., administration rate) of doses can render the reproduction number lower than one and hence contain the transmission of pandemic ultimately controlling for other factors. The timing of rollout of primary doses is pivotal in reducing the magnitude of transmission saturation. It is of importance to prioritize the administration of primary vaccination series to vulnerable individuals efficiently and thereafter increment of administration capacity when the supply of vaccine increases over time to scale down the size of an epidemic.
Targeted photothrombotic stroke leads to disruptions in neurovascular coupling
Authors: Sunil Smrithi , Jiang John , Shah Shashwat , Kura Sreekanth , Kilic Kivilcim , Erdener Sefik Evren , Ayata Cenk , Devor Anna , Boas David A. 
Published: January 2022

AbstractFunctional neuroimaging, which measures hemodynamic responses to brain activity, has great potential for monitoring stroke patients. However, the neurophysiological interpretations of these hemodynamic signals remain a challenge as the stroke is likely to alter both neural activity and neurovascular coupling. To address this challenge, we simultaneously captured neural activity, through fluorescence calcium imaging, and hemodynamics, through intrinsic optical signal imaging, during longitudinal stroke recovery. We found that photothrombotic stroke to somatosensory forelimb region altered neurovascular coupling in the acute phase (2 days and 1 week post-stroke) within the affected forelimb and peri-infarct regions. Neurovascular coupling was reestablished in the chronic phase (4 weeks post-stroke), and acute recovery of neurovascular coupling predicted sensorimotor function. Stroke also resulted in increases in the power of global brain oscillations, which showed distinct patterns between calcium and hemodynamics. Increased calcium excitability in the contralesional hemisphere was associated with increased intrahemispheric connectivity. Additionally, acute increases in hemodynamic oscillations were associated with improved sensorimotor outcomes.TeaserAcute ischemic stroke leads to neurovascular uncoupling and the extent of early recoupling predicts sensorimotor recovery.
Common synaptic inputs are not distributed homogeneously among the motor neurons that innervate synergistic muscles
Authors: Del Vecchio A. , Germer C. , Kinfe T. M. , Nuccio S. , Hug F. , Eskofier B. , Farina D. , Enoka R. M. 
Published: January 2022

AbstractThe force generated by the muscles involved in an action is produced by common synaptic inputs received by the engaged motor neurons. The purpose of our study was to identify the low-dimensional latent components, defined hereafter as neural modules, underlying the discharge rates of the motor units from two knee extensors (vastus medialis and lateralis) and two hand muscles (index and thumb muscles) during isometric contractions. The neural modules were extracted by factor analysis from the pooled motor units and no assumptions were made regarding the orthogonality of the modules or the association between the modules and each muscle. Factor analysis identified two independent neural modules that captured most of the covariance in the discharge rates of the motor units in the synergistic muscles. Although the neural modules were strongly correlated with the discharge rates of motor units in each of the synergistic pair of muscles, not all motor units in a muscle were correlated with the neural module for that muscle. The distribution of motor units across the pair of neural modules differed for each muscle: 80% of the motor units in first dorsal interosseous were more strongly correlated with the neural module for that muscle, whereas the proportion was 70%, 60%, and 45% for the thenar, vastus medialis, and vastus lateralis muscles. All other motor units either belonged to both modules or to the module for the other muscle (15% for vastus lateralis). Based on a simulation of 480 integrate-and-fire neurons receiving independent and common inputs, we demonstrate that factor analysis identifies the three neural modules with high levels of accuracy. Our results indicate that the correlated discharge rates of motor units arise from at least two sources of common synaptic input that are not distributed homogeneously among the motor neurons innervating synergistic muscles.
Genomic estimation of quantitative genetic parameters in wild admixed populations
Authors: Aase Kenneth , Jensen Henrik , Muff Stefanie 
Published: January 2022

Abstract

Heritable genetic variation among free‐living animals or plants is essential for populations to respond to selection and adapt. It is therefore important to be able to estimate additive genetic variance VA, which can be obtained using a GLMM known as the animal model. An underlying assumption of the standard animal model is that the study population is genetically unstructured, which is often unrealistic. In fact, admixture might be the norm rather than the exception in the wild, like in geographically structured populations, in the presence of (im)migration or in reintroduction and conservation contexts. Unfortunately, animal model estimators may be biased in such cases. The so‐called genetic group animal models that account for genetically differentiated subpopulations have recently become popular, but methodology is currently only available for cases where relatedness among individuals can be estimated from pedigrees.

To ensure that genetic group animal models with heterogeneous VA remain applicable to populations with genomic data but no pedigrees, there is a clear need to generalize these models to the case when exclusively genomic data are available. We therefore introduce such methodology for wild admixed systems by extending methods that were recently suggested in the context of plant breeding. Our extension relaxes the limiting assumptions that currently restrict their use to artificial breeding set‐ups.

We illustrate the usefulness of the extended genomic genetic group animal model on a wild admixed population of house sparrows resident in an island system in Northern Norway, where genome‐wide data on more than 180,000 single nucleotide polymorphisms (SNPs) are available to derive genomic relatedness. We compare our estimates of quantitative genetic parameters to those derived from a corresponding pedigree‐based genetic group animal model. The satisfactory agreement indicates that the new method works as expected.

Our extension of the very popular animal model ensures that the upcoming challenges with increasing availability of genomic data for quantitative genetic studies of wild admixed populations can be handled. To make the method widely available to the scientific community, we offer guidance in the form of a tutorial including step‐by‐step instructions to facilitate implementation.
Selective attention to lesson‐relevant contextual information promotes 3‐ to 5‐year‐old children's learning
Authors: King Jill , Markant Julie 
Published: January 2022

AbstractAttending to distracting or competing information is typically considered detrimental to learning, but the presence of competing information can also facilitate learning when it is relevant to ongoing task goals. Educational settings often contain contextual elements such as classroom decorations or visual aids to enhance student learning. Despite this, most research examining effects of contextual information on children's learning has only utilized lesson‐irrelevant stimuli. While this research has shown that increased looking to task‐irrelevant information hinders learning, the extent to which looking to lesson‐relevant information can benefit children's learning is unknown. We addressed this question by examining 3‐ to 5‐year‐old children's attention to and learning from lesson‐relevant contextual information. We recorded children's eye movements as they viewed video science lessons while lesson‐relevant and ‐irrelevant images appeared in the periphery. We assessed learning based on improvements in content knowledge following the video lessons and separately measured selective attention skills using the Track‐It task. Children overall spent more time looking at lesson‐relevant versus ‐irrelevant images, and those with more initial knowledge of the lesson topics or more advanced selective attention skills showed increased preferential looking to the relevant images. This increased preferential looking to lesson‐relevant images related to more effective learning during trials in which both relevant and irrelevant images were present. These results suggest that the effects of competing contextual information on early learning depend on the relationship between information content and task goals, as well as children's ability to actively select task‐relevant information from their environment.
Paradoxical changes of coronary computed tomography derived fractional flow reserve
Authors: Tsugu Toshimitsu , Tanaka Kaoru , Nagatomo Yuji , Belsack Dries , De Maeseneer Michel , De Mey Johan 
Published: January 2022

AbstractA total of 1335 outpatients with suspected coronary artery disease and who underwent computed tomography derived fractional flow reserve (FFRCT) analysis were examined. Only four patients showed reverse increase of FFRCT from the proximal to the distal vessel and all of them had a large ramus artery (RAM). Of all parameters (vessel length, lumen volume, plaque volume, and left ventricular mass), only the bifurcation angle was significantly higher in reverse increase of FFRCT with RAM group (106.0 ± 15.8°) than normal FFRCT with RAM group (82.6 ± 21.7°) and normal FFRCT without RAM group (66.9 ± 21.1°).
Frailty and mortality associations in patients with COVID‐19: a systematic review and meta‐analysis
Authors: Subramaniam Ashwin , Shekar Kiran , Afroz Afsana , Ashwin Sushma , Billah Baki , Brown Hamish , Kundi Harun , Lim Zheng Jie , Ponnapa Reddy Mallikarjuna , Curtis J. Randall 
Published: January 2022

AbstractBackgroundObservational data during the pandemic have demonstrated mixed associations between frailty and mortality.AimTo examine associations between frailty and short‐term mortality in patients hospitalised with coronavirus disease 2019 (COVID‐19).MethodsIn this systematic review and meta‐analysis, we searched PubMed, Embase and the COVID‐19 living systematic review from 1 December 2019 to 15 July 2021. Studies reporting mortality and frailty scores in hospitalised patients with COVID‐19 (age ≥18 years) were included. Data on patient demographics, short‐term mortality (in hospital or within 30 days), intensive care unit (ICU) admission and need for invasive mechanical ventilation (IMV) were extracted. The quality of studies was assessed using the Newcastle−Ottawa Scale.ResultsTwenty‐five studies reporting 34 628 patients were included. Overall, 26.2% (n = 9061) died. Patients who died were older (76.7 ± 9.6 vs 69.2 ± 13.4), more likely male (risk ratio (RR) = 1.08; 95% confidence interval (CI): 1.06–1.11) and had more comorbidities. Fifty‐eight percent of patients were frail. Adjusting for age, there was no difference in short‐term mortality between frail and non‐frail patients (RR = 1.04; 95% CI: 0.84–1.28). The non‐frail patients were commonly admitted to ICU (27.2% (4256/15639) vs 29.1% (3567/12274); P = 0.011) and had a higher mortality risk (RR = 1.63; 95% CI: 1.30–2.03) than frail patients. Among patients receiving IMV, there was no difference in mortality between frail and non‐frail (RR = 1.62; 95% CI 0.93–2.77).ConclusionThis systematic review did not demonstrate an independent association between frailty status and short‐term mortality in patients with COVID‐19. Patients with frailty were less commonly admitted to ICU and non‐frail patients were more likely to receive IMV and had higher mortality risk. This finding may be related to allocation decisions for patients with frailty amidst the pandemic.