bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal patterns inIxodes ricinusmicrobial communities: an insight into tick-borne microbe interactions
Authors: Lejal E , Chiquet J , Aubert J , Robin S , Estrada-Peña A , Rue O , Midoux C , Mariadassou M , Bailly X , Cougoul A , Gasqui P , Cosson JF , Chalvet-Monfray K , Vayssier-Taussat M , Pollet T 
Published: September 2020

AbstractBackgroundTicks transmit pathogens of medical and veterinary importance, and represent an increasing threat for human and animal health. Important steps in assessing disease risk and developing possible new future control strategies involve identifying tick-borne microbes, their temporal dynamics and interactions.MethodsUsing high throughput sequencing, we studied the microbiota dynamics ofIxodes ricinusfrom 371 nymphs collected monthly over three consecutive years in a peri-urban forest. After adjusting a Poisson Log Normal model to our data set, the implementation of a principal component analysis as well as sparse network reconstruction and differential analysis allowed us to assess inter-annual, seasonal and monthly variability ofI. ricinusmicrobial communities as well as their interactions.ResultsAround 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and potentially circulating in ticks: CandidatusMidichloria, Rickettsia, Spiroplasma, ArsenophonusandWolbachia. The structure of theI. ricinusmicrobiota was temporally variable with interannual recurrence and seemed to be mainly driven by OTUs belonging to environmental genera. The total network analysis revealed a majority of positive (partial) correlations. We identified strong relationships between OTUs belonging toWolbachiaandArsenophonus, betraying the presence of the parasitoid waspIxodiphagus hookeriin ticks, and the well known arthropod symbiontSpiroplasma, previously documented to be involved in the defense against parasitoid wasp inDrosophila melanogaster. Other associations were observed between the tick symbiont CandidatusMidichloriaand pathogens belonging toRickettsia, probablyRickettsia helvetica. More specific network analysis finally suggested that the presence of pathogens belonging to generaBorrelia, AnaplasmaandRickettsiamight disrupt microbial interactions inI. ricinus.ConclusionsHere, we identified theI. ricinusmicrobiota and documented for the first time the existence and recurrence of marked temporal shifts in the tick microbial community dynamics. We statistically showed strong relationships between the presence of some pathogens and the structure of theI. ricinusnon-pathogenic microbes. We interestingly detected close links between some tick symbionts and the potential presence of either pathogenicRickettsiaor a parasitoid in ticks. All these new findings might be very promising for the future development of new control strategies of ticks and tick-borne diseases.
Complex spike firing adapts to saliency of inputs and engages readiness to act
Authors: Bina Lorenzo , Romano Vincenzo , Hoogland Tycho M. , Bosman Laurens W.J. , De Zeeuw Chris I. 
Published: September 2020

AbstractThe cerebellum is involved in cognition next to motor coordination. During complex tasks, climbing fiber input to the cerebellum can deliver seemingly opposite signals, covering both motor and non-motor functions. To elucidate this ambiguity, we hypothesized that climbing fiber activity represents the saliency of inputs leading to action-readiness. We addressed this hypothesis by recording Purkinje cell activity in lateral cerebellum of awake mice learning go/no-go decisions based on entrained saliency of different sensory stimuli. As training progressed, the timing of climbing fiber signals switched in a coordinated fashion with that of Purkinje cell simple spikes towards the moment of occurrence of the salient stimulus that required action. Trial-by-trial analysis indicated that emerging climbing fiber activity is not linked to individual motor responses or rewards per se, but rather reflects the saliency of a particular sensory stimulus that engages a general readiness to act, bridging the non-motor with the motor functions.In briefMice were trained to identify the saliency of different sensory inputs in that they had to learn to ignore a prominent sound cue and respond to a light tactile cue in a Go/No-Go licking task. As the mice learned to discriminate the two inputs and respond to the proper signal, the Purkinje cells in the lateral cerebellum switched their climbing fiber activity (i.e., complex spike activity) towards the moment of occurrence of the salient stimulus that required a response, while concomitantly shifting the phase of their simple spike modulation. Trial-by-trial analysis indicates that the emerging climbing fiber activity is not linked to the occurrence of the motor response or reward per se, but rather reflects the saliency of a particular sensory stimulus engaging a general readiness to act.
GAMYB modulatesbHLH142and is homeostatically regulated by TDR during rice anther tapetal and pollen development
Authors: Ko Swee-Suak , Li Min-Jeng , Ho Yi-Cheng , Yu Chun-Ping , Yang Ting-Ting , Lin Yi-Jyun , Hsing Hung-Chien , Chen Tien-Kuan , Jhong Chung-Min , Li Wen-Hsiung , Ku Maurice Sun-Ben 
Published: September 2020

AbstractGAMYB, UDT1, TIP2/bHLH142, TDR, and EAT1/DTD are important transcription factors (TFs) that play a crucial role during rice pollen development. This study demonstrates that bHLH142 acts downstream of UDT1 and GAMYB and works as a “hub” in these two pollen pathways. We show that GAMYB modulatesbHLH142expression through specific binding to the MYB motif ofbHLH142promoter during early stage of pollen development; while TDR acts as a transcriptional repressor of the GAMYB modulation ofbHLH142by binding to the E-box close to the MYB motif on the promoter. The up- and down-regulation of TFs highlights the importance that a tight, precise, and coordinated regulation among these TFs is essential for normal pollen development. Most notably, this study illustrates the regulatory pathways of GAMYB and UDT1 that rely onbHLH142in a direct and an indirect manner, respectively, and function in different tissues with distinct biological functions during pollen development. This study advances our understanding of the molecular mechanisms of rice pollen development.HighlightGAMYB can directly modulate the transactivation of thebHLH142, but the modulation is repressed by TDR to keep the homeostasis ofbHLH142gene expression to ensure normal pollen development.
Viscoelastic characteristics of the canine cranial cruciate ligament complex at slow strain rates
Authors: Readioff Rosti , Geraghty Brendan , Elsheikh Ahmed , Comerford Eithne 
Published: September 2020

AbstractLigaments including the cruciate ligaments support and transfer loads between bones applied to the knee joint organ. The functions of these ligaments can get compromised due to changes to their viscoelastic material properties. Currently there are discrepancies in the literature on the viscoelastic characteristics of knee ligaments which are thought to be due to tissue variability and different testing protocols.The aim of this study was to characterise the viscoelastic properties of healthy cranial cruciate ligaments (CCLs), from the canine knee (stifle) joint, with a focus on the toe region of the stress-strain properties where any alterations in the extracellular matrix which would affect viscoelastic properties would be seen.Six paired CCLs, from skeletally mature and disease-free Staffordshire bull terrier stifle joints were retrieved as a femur-CCL-tibia complex and mechanically tested under uniaxial cyclic loading up to 10 N at three strain rates, namely 0.1, 1 and 10 %/min, to assess the viscoelastic property of strain rate dependency. The effect of strain history was also investigated by subjecting contralateral CCLs to an ascending (0.1, 1 and 10 %/min) or descending (10, 1 and 0.1 %/min) strain rate protocol.The differences between strain rates were not statistically significant. However, hysteresis and recovery of ligament lengths showed some dependency on strain rate. Only hysteresis was affected by the test protocol and lower strain rates resulted in higher hysteresis and lower recovery. These findings could be explained by the slow process of uncrimping of collagen fibres and the contribution of proteoglycans in the ligament extracellular matrix to intra-fibrillar gliding, which results in more tissue elongations and higher energy dissipation. This study further expands our understanding of canine CCL behaviour, providing data for material models of femur-CCL-tibia complexes, and demonstrating the challenges for engineering complex biomaterials such as knee joint ligaments.
Association between COMT gene Val158Met heterozygote polymorphism and enhanced brain predicting processes
Authors: Bonetti L. , Sedghi N.A. , Bruzzone S.E.P. , Haumann N.T. , Paunio T. , Kantojärvi K. , Kliuchko M. , Vuust P. , Brattico E. 
Published: September 2020

AbstractPredicting events in the ever-changing environment is a fundamental survival function intrinsic to the physiology of sensory systems, whose efficiency varies among the population. Even though it is established that a major source of such variations is genetic heritage, there are no studies tracking down auditory predicting processes to genetic mutations. Thus, we examined the neurophysiological responses to deviant stimuli recorded with magnetoencephalography (MEG) in 108 healthy participants carrying different variants of the Val158Met single-nucleotide polymorphism (SNP) within the catechol-O-methyltransferase (COMT) gene, which is responsible for the majority of catecholamines degradation in the prefrontal cortex. Our results showed significant amplitude enhancement of neural responses localized within inferior frontal gyrus, superior and middle temporal cortices to deviant auditory stimuli in heterozygote genotype carriers (Val/Met) vs homozygote (Val/Val and Met/Met) carriers. Integrating neurophysiology and genetics, this study provided new and broader insights into the brain mechanisms underlying optimal deviant detection.
Predictive Maps in Rats and Humans for Spatial Navigation
Authors: de Cothi William , Nyberg Nils , Griesbauer Eva-Maria , Ghanamé Carole , Zisch Fiona , Lefort Julie M. , Fletcher Lydia , Newton Coco , Renaudineau Sophie , Bendor Daniel , Grieves Roddy , Duvelle Éléonore , Barry Caswell , Spiers Hugo J. 
Published: September 2020

SummaryMuch of our understanding of navigation comes from the study of individual species, often with specific tasks tailored to those species. Here, we provide a novel experimental and analytic framework, integrating across humans, rats and simulated reinforcement learning (RL) agents to interrogate the dynamics of behaviour during spatial navigation. We developed a novel open-field navigation task (ʻTartarus Maze’) requiring dynamic adaptation (shortcuts and detours) to frequently changing obstructions in the path to a hidden goal. Humans and rats were remarkably similar in their trajectories. Both species showed the greatest similarity to RL agents utilising a ʻsuccessor representation’, which creates a predictive map. Humans also displayed trajectory features similar to model-based RL agents, which implemented an optimal tree-search planning procedure. Our results help refine models seeking to explain mammalian navigation in dynamic environments, and highlight the utility of modelling the behaviour of different species to uncover the shared mechanisms that support behaviour.
Image-based patch selection for deep learning to improve automated Gleason grading in histopathological slides
Authors: Speier William , Li Jiayun , Li Wenyuan , Sarma Karthik , Arnold Corey 
Published: September 2020

AbstractAutomated Gleason grading can be a valuable tool for physicians when assessing risk and planning treatment for prostate cancer patients. Semantic segmentation provides pixel-wise Gleason predictions across an entire slide, which can be more informative than classification of pre-selected homogeneous regions. Deep learning methods can automatically learn visual semantics to accomplish this task, but training models on whole slides is impractical due to large image sizes and scarcity of fully annotated data. Patch-based methods can alleviate these problems, and have been shown to produce significant results in histopathology segmentation. However, the irregular contours of biopsies on slides makes performance highly dependent on patch selection. In the traditional grid-based strategy, many patches lie on biopsy boundaries, reducing segmentation accuracy due to a reduction in contextual information. In this paper, we propose an automatic patch selection process based on image features. This algorithm segments the biopsy and aligns patches based on the tissue contour to maximize the amount of contextual information in each patch. This method was used to generate patches for a fully convolutional network to segment high grade, low grade, and benign tissue from a set of 59 histopathological slides, and results were compared against manual physician labels. We show that using our image-based patch selection algorithm results in a significant improvement in segmentation accuracy over the traditional grid-based approach. Our results suggest that informed patch selection can be a valuable addition to an automated histopathological analysis pipeline.
The vitamin A ester retinyl propionate has a unique metabolic profile and higher retinoid-related bioactivity over retinol and retinyl palmitate in human skin models
Authors: Bjerke Donald L. , Li Rui , Price Jason M. , Dobson Roy L.M. , Rodrigues MyriamRubecca , Tey ChingSiang , Vires Laura , Adams Rachel L. , Sherrill Joseph D. , Styczynski Peter B. , Goncalves Kirsty , Maltman Victoria , Przyborski Stefan , Oblong John E. 
Published: September 2020

ABSTRACTHuman skin is exposed daily to environmental stressors, which cause acute damage and inflammation. Over time this leads to morphological and visual appearance changes associated with premature aging. Topical vitamin A derivatives such as retinol (ROL), retinyl palmitate (RPalm), and retinyl propionate (RP) have been used to reverse these changes and improve the appearance of skin. This study investigated a stoichiometric comparison of these retinoids usingin vitroandex vivoskin models. Skin biopsies were treated topically to compare skin penetration and metabolism. Treated keratinocytes were evaluated for transcriptomics profiling and hyaluronic acid (HA) synthesis and treated 3D epidermal skin equivalents were stained for epidermal thickness, Ki67, and filaggrin. A retinoic acid receptor-alpha (RARα) reporter cell line was used to compare retinoid activation levels. Results fromex vivoskin found that RP and ROL have higher penetration levels compared to RPalm. RP is metabolized primarily into ROL in the viable epidermis and dermis whereas ROL is esterified into RPalm and metabolized into the inactive retinoid 14-hydroxy-4,14-retro-retinol (14-HRR). RP treatment yielded higher RARα activation and HA synthesis levels than ROL whereas RPalm had a null effect. In keratinocytes, RP and ROL stimulated similar gene expression patterns and pathway theme profiles. In conclusion, RP and ROL show a similar response directionality whereas RPalm response was inconsistent. Additionally, RP has a consistently higher magnitude of response compared with ROL or RPalm.
Fine tuning of Piezo1 Expression and Activity Ensures Efficient Myoblast Fusion during Skeletal Myogenesis
Authors: Ortuste Quiroga Huascar Pedro , Ganassi Massimo , Yokoyama Shingo , Nakamura Kodai , Yamashita Tomohiro , Raimbach Daniel , Hagiwara Arisa , Harrington Oscar , Breach-Teji Jodie , Asakura Atsushi , Suzuki Yoshiro , Tominaga Makoto , Zammit Peter S. , Goto Katsumasa 
Published: September 2020

AbstractMechanical stimuli such as stretch and resistance training are essential to regulate growth and function of skeletal muscle. However, the molecular mechanisms involved in sensing mechanical stress during muscle formation remain unclear. Here, we investigate the role of the mechano-sensitive ion channel Piezo1 during myogenic progression. Direct manipulation of Piezo1 in muscle stem cells alters their myogenic progression. Indeed,Piezo1knockdown suppresses myoblast fusion leading to smaller myotubes. Such event is accompanied by significant downregulation of the fusogenic proteinMyomaker. In parallel, whilePiezo1knockdown also lowers Ca2+influx in response to stretch, Piezo1 activation increases Ca2+influx in response to stretch and enhances myoblasts fusion. We believe these findings may help understand molecular defects present in some muscle diseases. Altogether our study shows that Piezo1 is essential for terminal muscle differentiation acting on myoblast fusion, suggesting that Piezo1 deregulation may have implications in muscle aging and degenerative diseases including muscular dystrophies.
Testing multiple drivers of the temperature‐size rule with nonlinear temperature increase
Authors: Tabi Andrea , Garnier Aurélie , Pennekamp Frank 
Published: September 2020

Abstract

The temperature‐size rule (TSR) describes the inverse relationship between organism size and environmental temperature in uni‐ and multicellular species. Despite the TSR being widespread, the mechanisms for shrinking body size with warming remain elusive.

Here, we experimentally test three hypotheses (differential development and growth [DDG], maintain aerobic scope and regulate oxygen supply [MASROS] and the supply–demand [SD] hypothesis) potentially explaining the TSR using the aquatic protist Colpidium striatum in three gradually changing and one constant temperature environment crossed with three different nutrient levels.

We find that the constant and slowly warming environments show similar responses in terms of population dynamics, whereas populations with linear and fast warming quickly decline and show a stronger temperature‐size response.

Our analyses suggest that acclimation may have played a role in observing these differences among treatments. The SD hypothesis is most parsimonious with the data, however, neither the DDG nor the MASROS hypothesis can be firmly dismissed. We conclude that the TSR is driven by multiple ecological and acclimatory responses, hence multicausal.

A free Plain Language Summary can be found within the Supporting Information of this article.
The importance of individual‐to‐society feedbacks in animal ecology and evolution
Authors: Cantor Maurício , Maldonado‐Chaparro Adriana A. , Beck Kristina B. , Brandl Hanja B. , Carter Gerald G. , He Peng , Hillemann Friederike , Klarevas‐Irby James A. , Ogino Mina , Papageorgiou Danai , Prox Lea , Farine Damien R. 
Published: September 2020

Abstract

The social decisions that individuals make—who to interact with and how frequently—give rise to social structure. The resulting social structure then determines how individuals interact with their surroundings—resources and risks, pathogens and predators, competitors and cooperators.

However, despite intensive research on (a) how individuals make social decisions and (b) how social structure shapes social processes (e.g. cooperation, competition and conflict), there are still few studies linking these two perspectives. These perspectives represent two halves of a feedback loop: individual behaviour scales up to define the social environment, and this environment, in turn, feeds back by shaping the selective agents that drive individual behaviour.

We first review well‐established research areas that have captured both elements of this feedback loop—host–pathogen dynamics and cultural transmission. We then highlight areas where social structure is well studied but the two perspectives remain largely disconnected. Finally, we synthesise existing research on 14 distinct research topics to identify new prospects where the interplay between social structure and social processes are likely to be important but remain largely unexplored.

Our review shows that the inherent links between individuals’ traits, their social decisions, social structure and social evolution, warrant more consideration. By mapping the existing and missing connections among many research areas, our review highlights where explicitly considering social structure and the individual‐to‐society feedbacks can reveal new dimensions to old questions in ecology and evolution.
Decoupling the effects of food and density on life‐history plasticity of wild animals using field experiments: Insights from the steward who sits in the shadow of its tail, the North American red squirrel
Authors: Dantzer Ben , McAdam Andrew G. , Humphries Murray M. , Lane Jeffrey E. , Boutin Stan 
Published: September 2020

AbstractLong‐term studies of wild animals provide the opportunity to investigate how phenotypic plasticity is used to cope with environmental fluctuations and how the relationships between phenotypes and fitness can be dependent upon the ecological context.Many previous studies have only investigated life‐history plasticity in response to changes in temperature, yet wild animals often experience multiple environmental fluctuations simultaneously. This requires field experiments to decouple which ecological factor induces plasticity in fitness‐relevant traits to better understand their population‐level responses to those environmental fluctuations.For the past 32 years, we have conducted a long‐term integrative study of individually marked North American red squirrelsTamiasciurus hudsonicusErxleben in the Yukon, Canada. We have used multi‐year field experiments to examine the physiological and life‐history responses of individual red squirrels to fluctuations in food abundance and conspecific density.Our long‐term observational study and field experiments show that squirrels can anticipate increases in food availability and density, thereby decoupling the usual pattern where animals respond to, rather than anticipate, an ecological change.As in many other study systems, ecological factors that can induce plasticity (such as food and density) covary. However, our field experiments that manipulate food availability and social cues of density (frequency of territorial vocalizations) indicate that increases in social (acoustic) cues of density in the absence of additional food can induce similar life‐history plasticity, as does experimental food supplementation.Changes in the levels of metabolic hormones (glucocorticoids) in response to variation in food and density are one mechanism that seems to induce this adaptive life‐history plasticity.Although we have not yet investigated the energetic response of squirrels to elevated density or its association with life‐history plasticity, energetics research in red squirrels has overturned several standard pillars of knowledge in physiological ecology.We show how a tractable model species combined with integrative studies can reveal how animals cope with resource fluctuations through life‐history plasticity.