bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual differences show that only some bats can cope with noise-induced masking and distraction
Authors: Gomes Dylan G.E. , Goerlitz Holger R. 
Published: July 2020

AbstractAnthropogenic noise is a widespread pollutant that has received considerable recent attention. While alarming effects on wildlife have been documented, we have limited understanding of the perceptual mechanisms of noise disturbance, which are required to understand potential mitigation measures. Likewise, individual differences in response to noise (especially via perceptual mechanisms) are likely widespread, but lacking in empirical data. Here we use echolocating bats, a trained discrimination task, and experimental noise playback to explicitly test perceptual mechanisms of noise disturbance. We demonstrate high individual variability in response to noise treatments and evidence for multiple perceptual mechanisms. Additionally, we highlight that only some individuals are able to cope with noise, while others are not. We tested for changes in echolocation call duration, amplitude, and peak frequency as possible ways of coping with noise. Although all bats strongly increased call amplitude and showed additional minor changes in call duration and frequency, these changes cannot explain the differences in coping and non-coping individuals. Our understanding of noise disturbance needs to become more mechanistic and individualistic as research knowledge is transformed into policy changes and conservation action.
Telomere lengths in plants are correlated with flowering time variation
Authors: Choi Jae Young , Purugganan Michael D. 
Published: July 2020

AbstractTelomeres are highly repetitive tandemly repeating DNA sequences found at chromosomal ends that protect chromosomes from deterioration during cell division. Using whole genome re-sequencing data, we found substantial natural intraspecific variation in telomere lengths in Arabidopsis thaliana, Oryza sativa (rice) and Zea mays (maize). Genome-wide association mapping in A. thaliana identifies a region that includes the telomerase reverse transcriptase (TERT) gene as underlying telomere length variation. TERT appears to exist in two haplotype groups (L and S), of which the L haplogroup allele shows evidence of a selective sweep in Arabidopsis. We find that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life history traits and chromosome integrity. We suggest that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier), and that chromosomal structure itself is an adaptive trait associated with plant life history strategies.
Evaluating the impacts of microbial activity and species interactions on passive bioremediation of a coastal acid sulfate soil (CASS) ecosystem
Authors: Ling Yu-Chen , Moreau John W. 
Published: July 2020

AbstractMicrobial iron and sulfate reduction are the primary drivers of coastal acid sulfate soil (CASS) passive bioremediation schemes. Microbial sulfate reduction is the limiting step for pyrite formation, a desirable endpoint for CASS remediation. Little is known, however, about the impacts of microbial activity or species interaction on long-term iron and sulfur cycling in CASS ecosystems. Using a combination of molecular biology, geochemical speciation and artificial intelligence-powered computational modeling, we deduced from microbial activity patterns (RNA-based) and geochemical measurements a best-fit equation for predicting biogeochemical pyrite formation in a model CASS ecosystem. In addition to the time-dependent activities of key sulfate-reducing prokaryotic taxa (e.g.Desulfobacteraceae), this equation required methylotrophs (Methylobacteriaceae) and bacterial predators (Bacteriovorax) for best-fitting, suggesting that specific microbial interactions exert meaningful influences on CASS bioremediation efficiency. Our findings confirmed that CASS microorganisms act as an assemblage in response to rewetting by tidewater. Accurate predictions of long-term CASS bioremediation efficiency require modelling of complex and interdependent relationships between geochemical speciation and microbial activity.HighlightsCoastal acid sulfate soil (CASS) is a global environmental issue.Microbial activity can be modelled quantitatively to predict CASS remediation.Sulfate-reducing prokaryotes (SRP) play a key role in CASS remediation.Predation on SRP with cultured representatives occurred during early wet-up.The above mechanism leads to increased activity among uncultured SRP.
Co-expressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplasts
Authors: Ramundo Silvia , Asakura Yukari , Salomé Patrice A. , Strenkert Daniela , Boone Morgane , Mackinder Luke C. M. , Takafuji Kazuaki , Dinc Emine , Rahire Michèle , Crèvecoeur Michèle , Magneschi Leonardo , Schaad Olivier , Hippler Michael , Jonikas Martin C. , Merchant Sabeeha , Nakai Masato , Rochaix Jean-David , Walter Peter 
Published: July 2020

AbstractIn photosynthetic eukaryotes, thousands of proteins are translated in the cytosol and imported into the chloroplast through the concerted action of two translocons — termed TOC and TIC — located in the outer and inner membranes of the chloroplast envelope, respectively. The degree to which the molecular composition of the TOC and TIC complexes is conserved over phylogenetic distances has remained controversial. Here, we combine transcriptomic, biochemical, and genetic tools in the green alga Chlamydomonas (Chlamydomonas reinhardtii) to demonstrate that, despite a lack of evident sequence conservation for some of its components, the algal TIC complex mirrors the molecular composition of a TIC complex fromArabidopsis thaliana.The Chlamydomonas TIC complex contains three nuclear-encoded subunits, Tic20, Tic56 and Tic100, and one chloroplast-encoded subunit, Tic214, and interacts with the TOC complex, as well as with several uncharacterized proteins to form a stable supercomplex (TicToc), indicating that protein import across both envelope membranes is mechanistically coupled. Expression of the nuclear and chloroplast genes encoding both known and the here newly identified TicToc components is highly coordinated, suggesting that a mechanism for regulating its biogenesis across compartmental boundaries must exist. Conditional repression of Tic214, the only chloroplast-encoded subunit in the TicToc complex, impairs the import of chloroplast proteins with essential roles in chloroplast ribosome biogenesis and protein folding and induces a pleiotropic stress response, including several proteins involved in the chloroplast unfolded protein response. These findings underscore the functional importance of the TicToc supercomplex in maintaining chloroplast proteostasis.
Semantic relatedness emerges in deep convolutional neural networks designed for object recognition
Authors: Huang Taicheng , Zhen Zonglei , Liu Jia 
Published: July 2020

AbstractHuman not only can effortlessly recognize objects, but also characterize object categories into semantic concepts and construct nested hierarchical structures. Similarly, deep convolutional neural networks (DCNNs) can learn to recognize objects as perfectly as human; yet it is unclear whether they can learn semantic relatedness among objects that is not provided in the learning dataset. This is important because it may shed light on how human acquire semantic knowledge on objects without top-down conceptual guidance. To do this, we explored the relation among object categories, indexed by representational similarity, in two typical DCNNs (AlexNet and VGG11). We found that representations of object categories were organized in a hierarchical fashion, suggesting that the relatedness among objects emerged automatically when learning to recognize them. Critically, the emerged relatedness of objects in the DCNNs was highly similar to the WordNet in human, implying that top-down conceptual guidance may not be a prerequisite for human learning the relatedness among objects. Finally, the developmental trajectory of the relatedness among objects during training revealed that the hierarchical structure was constructed in a coarse-to-fine fashion, and evolved into maturity before the establishment of object recognition ability. Taken together, our study provides the first empirical evidence that semantic relatedness of objects emerged as a by-product of object recognition, implying that human may acquire semantic knowledge on objects without explicit top-down conceptual guidance.Significance StatementThe origin of semantic concepts is in a long-standing debate, where top-down conceptual guidance is thought necessary to form the hierarchy structure of objects. Here we challenged this hypothesis by examining whether deep convolutional neural networks (DCNNs) for object recognition can emerge the semantic relatedness of objects with no relation information in training object datasets. We found that in the DCNNs representations of objects were organized in a hierarchical fashion, which was highly similar to WordNet in human. This finding suggests that top-down conceptual guidance may not be a prerequisite for human learning the relatedness among objects; rather, semantic relatedness of objects may emerge as a by-product of object recognition.
Dynamic transitions between neural states are associated with flexible task-switching during a memory task
Authors: Liu Wei , Kohn Nils , Fernández Guillén 
Published: July 2020

AbstractFlexible behavior requires switching between different task conditions. It is known that such task- switching is associated with costs in terms of slowed reaction time, reduced accuracy, or both. The neural correlates of task-switching have usually been studied by requiring participants to switch between distinct task demands that recruit different brain networks. Here, we investigated the transition of neural states underlying switching between two opposite memory-related processes (i.e.,memory retrieval and memory suppression) in a memory task. We investigated 26 healthy participants who performed a Think/No-Think task while being in the fMRI scanner. Behaviorally, we show that it was more difficult for participants to suppress unwanted memories when a No-Think was preceded by a Think trial instead of another No- Think trial. Neurally, we demonstrate that Think-to-No-Think switches were associated with an increase in control-related and a decrease in memory-related brain activity. Neural representations of task demand, assessed by decoding accuracy, were lower immediately after task switching compared to the non-switch transitions, suggesting a switch-induced delay in the neural transition towards the required task condition. This suggestion is corroborated by an association between condition-specific representational strength and condition-specific performance in switch trials. Taken together, we provided neural evidence from the time-resolved decoding approach to support the notion that carry-over of the previous task-set activation is associated with the switching cost leading to less successful memory suppression.Significance statementOur brain can switch between multiple tasks but at the cost of less optimal performance during transition. One possible neuroscientific explanation is that the representation of the task condition is not easy to be updated immediately after switching. Thus, weak representations for the task at hand explain performance costs. To test this, we applied brain decoding approaches to human fMRI data when participants switched between successive trials of memory retrieval and suppression. We found that switching leads to a weaker representation of the current task. The remaining representation of the previous, opposite task is associated with inferior performance in the current task. Therefore, timely updating of task representations is critical for task switching in the service of flexible behaviors.
Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)
Authors: Gruber Conor , Patel Roosheel , Trachman Rebecca , Lepow Lauren , Amanat Fatima , Krammer Florian , Wilson Karen M. , Onel Kenan , Geanon Daniel , Tuballes Kevin , Patel Manishkumar , Mouskas Konstantinos , Simons Nicole , Barcessat Vanessa , Del Valle Diane , Udondem Samantha , Kang Gurpawan , Gangadharan Sandeep , Ofori-Amanfo George , Rahman Adeeb , Kim-Schulze Seunghee , Charney Alexander , Gnjatic Sacha , Gelb Bruce D. , Merad Miriam , Bogunovic Dusan 
Published: July 2020

SummaryInitially, the global outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spared children from severe disease. However, after the initial wave of infections, clusters of a novel hyperinflammatory disease have been reported in regions with ongoing SARS-CoV-2 epidemics. While the characteristic clinical features are becoming clear, the pathophysiology remains unknown. Herein, we report on the immune profiles of eight Multisystem Inflammatory Syndrome in Children (MIS-C) cases. We document that all MIS-C patients had evidence of prior SARS-CoV-2 exposure, mounting an antibody response with normal isotype-switching and neutralization capability. We further profiled the secreted immune response by high-dimensional cytokine assays, which identified elevated signatures of inflammation (IL-18 and IL-6), lymphocytic and myeloid chemotaxis and activation (CCL3, CCL4, and CDCP1) and mucosal immune dysregulation (IL-17A, CCL20, CCL28). Mass cytometry immunophenotyping of peripheral blood revealed reductions of mDC1 and non-classical monocytes, as well as both NK- and T-lymphocytes, suggesting extravasation to affected tissues. Markers of activated myeloid function were also evident, including upregulation of ICAM1 and FcγR1 in neutrophil and non-classical monocytes, well-documented markers in autoinflammation and autoimmunity that indicate enhanced antigen presentation and Fc-mediated responses. Finally, to assess the role for autoimmunity secondary to infection, we profiled the auto-antigen reactivity of MIS-C plasma, which revealed both known disease-associated autoantibodies (anti-La) and novel candidates that recognize endothelial, gastrointestinal and immune-cell antigens. All patients were treated with anti-IL6R antibody or IVIG, which led to rapid disease resolution tracking with normalization of inflammatory markers.One Sentence SummaryThis study maps the cellular and serological immune dysfunction underlying a novel pediatric inflammatory syndrome associated with SARS-CoV-2.
Objective sensory testing methods reveal a higher prevalence of olfactory loss in COVID-19–positive patients compared to subjective methods: A systematic review and meta-analysis
Authors: Hannum Mackenzie E. , Ramirez Vicente A. , Lipson Sarah J. , Herriman Riley D. , Toskala Aurora K. , Lin Cailu , Joseph Paule V. , Reed Danielle R. 
Published: July 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has currently infected over 6.5 million people worldwide. In response to the pandemic, numerous studies have tried to identify causes and symptoms of the disease. Emerging evidence supports recently acquired anosmia (complete loss of smell) and hyposmia (partial loss of smell) as symptoms of COVID-19, but studies of olfactory dysfunction show a wide range of prevalence, from 5% to 98%. We undertook a search of Pubmed/Medline and Google Scholar with the keywords “COVID-19,” “smell,” and/or “olfaction.” We included any study that quantified olfactory loss as a symptom of COVID-19. Studies were grouped and compared based on the type of method used to measure smell loss—subjective measures such as self-reported smell loss versus objective measures using rated stimuli—to determine if prevalence rate differed by method type. For each study, 95% confidence intervals (CIs) were calculated from point estimates of olfactory disturbance rates. We identified 34 articles quantifying anosmia as a symptom of COVID-19, collected from cases identified from January 16 to April 30, 2020. The pooled prevalence estimate of smell loss was 77% when assessed through objective measurements (95% CI of 61.4-89.2%) and 45% with subjective measurements (95% CI of 31.1-58.5%). Objective measures are a more sensitive method to identify smell loss as a result of infection with SARS-CoV-2; the use of subjective measures, while expedient during the early stages of the pandemic, underestimates the true prevalence of smell loss.
Sample Pooling as an efficient strategy for SARS-COV-2 RT-PCR screening: a multicenter study in Spain
Authors: de Salazar Adolfo , Aguilera Antonio , Trastoy Rocio , Fuentes Ana , Alados Juan Carlos , Causse Manuel , Galán Juan Carlos , Moreno Antonio , Trigo Matilde , Pérez Mercedes , Roldán Carolina , Pena Ma José , Bernal Samuel , Serrano-Conde Esther , Barbeito Gema , Torres Eva , Riazzo Cristina , Cortes-Cuevas Jose Luis , Chueca Natalia , Coira Amparo , Sanchez-Calvo Juan M , Marfil Eduardo , Becerra Federico , Gude María José , Pallarés Ángeles , Del Molino María Luisa Pérez , García Federico 
Published: July 2020

AbstractImportanceThe actual demand on SARS-CoV-2 diagnosis is a current challenge for clinical laboratories. Sample pooling may help to ameliorate workload in clinical laboratories.Objectiveto evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of CoVID-19, by using different commercial platforms for nucleic acid extraction and amplification.Design and settingsobservational, prospective, multicentre study across 9 Spanish clinical microbiology laboratories including SARS-CoV-2 RNA testing performed in April 2020, during the first three days after acceptance to participate.Participants and Methods3519 naso-oro-pharyngeal samples received at the participating laboratories were processed individually and in pools (351 pools) according to the existing methodology in each of the centres.ResultsWe found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 24/29 pools (30 samples), minor discordances were found; for five pools (5 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.93%, 100%, 100% and 99.85% respectively; accuracy was 99.86% and kappa concordant coefficient was 0.988. As a result of the sample dilution effect of pooling, a loss of 2-3 Cts was observed for E, N or RdRP genes.Conclusionwe show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. We believe that our results may help clinical laboratories to respond to the actual demand and clinical need on SARS-CoV-2 testing, especially for the screening of low prevalence populations.Key pointsQuestionMay clinical laboratories implement sample pooling as an efficient and safe strategy for SARS-COV-2 RT-PCR screening?FindingsSensitivity, specificity, positive and negative predictive values for pooling were 97.93%, 100%, 100% and 99.85% respectively; accuracy was 99.86% and kappa concordant coefficient was 0.988.MeaningSample pooling can be used safely at clinical laboratories, especially for the screening of low prevalence populations.
DETECTION OF AUTOLOGOUS BLOOD DOPING
Authors: Malm Christer , Granlund Irene , Hall Michael , Lindén Pernilla , Ericsson Magnus , Langridge James I. , Gethings Lee A. , Hughes Chris , Khoo Nelson 
Published: July 2020

AbstractObjectivesAutologous blood transfusion (ABT) enhances athlete’s performance, is banned as doping by the World Anti-Doping Agency (WADA). Currently, there is no implemented detection method for ABT. Transfusion of one’s own, long-term cryopreserved red blood cells (cryo-RBC) immediately increases circulating RBC count, hemoglobin mass, blood volume and oxygen carrying capacity, resulting in enhanced physical performance. Functional viablity of cryo-RBC are maintained for decades, but storage lesions lead to removal of damaged RBC from circulation days after transfusion, with remaining circulating cryo-RBC displaying normal half-life.MethodsThe cytosolic RBC peptidome from 22 human subjects (12 men and 10 women) was analyzed by UHPLC-MS/MS before and after ABT with cryo-RBC. As a control group and for investigation of confounders, 14 elite athletes and 5 recreational subjects were sampled multiple times, also at high altitude.ResultsHere we report alteration in the cytosolic peptidome of circulating RBC weeks after ABT, discriminating doped from non-doped human subjects. A valid discriminating multivariate model (OPLS-DA) based on <200 peptides was accomplished (R2/Q2= 0.88/0.59, P CV-ANOVA < 0.0001, ROC AUC = 0.97). Models did not show bias for sex, high altitude or elite endurance training and racing.ConclusionIdentified peptides with low intra- and inter-individual variation, and high multivariate model weight and probability scores, create a direct method for the detection of autologous blood doping.
The UK Covid-19 lockdown weakened in April and May 2020: implications for the size of the epidemic and for outcomes had lockdown been earlier
Authors: Lander Anthony 
Published: July 2020

AbstractThe number of active cases in the UK Covid-19 epidemic, the case fatality rate, the susceptible proportion of the population, and how well the lockdown was maintained during April–May 2020 are unknown. These four have a relationship with the shape of the daily mortality curve once one considers the intervals from infection to death or recovery. Without an understanding of this relationship we cannot say that an earlier lockdown would have saved lives. Using a small stochastic model, the lockdown had to be weakened, in April and May, for simulated deaths to match ongoing actual daily deaths. Google mobility data was found to be consistent with the weakening required in the model with similar changes from baseline in time and magnitude. If in an earlier lockdown, mobility and interactions would have followed a similar course, then with a large epidemic curve an earlier lockdown might be associated with many more deaths than some currently believe. This was confirmed in the stochastic model and in two modified SIR models of epidemics of various sizes. The first SIR model had a fixed period to recovery and the second used random periods, both models had random periods to death. Weakening of the mitigations was required to tune the output in large but not in small epidemics. This gives weight to the epidemic having affected many more individuals than some reports currently suggest. In both one and two-week earlier lockdowns, total deaths were found to depend on the size of the epidemic and to vary from 2,000–49,000 deaths. There was a linear relationship between the peak proportion of the population infected and the reciprocal of the case fatality rate. This work questions the low prevalence of < 0.1%, reported by the Office for National Statistics in May and June 2020, since to accommodate a weakening lockdown, the shape of the daily mortality curve, and an acceptable case fatality rate a much larger epidemic curve is required.