bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal glucocorticoids do not influence HPA axis activity or behavior of juvenile wild North American red squirrels
Authors: Westrick Sarah E , van Kesteren Freya , Boutin Stan , Lane Jeffrey E , McAdam Andrew G , Dantzer Ben 
Published: September 2020

AbstractEnvironmental factors experienced during development can affect the physiology and behavior of offspring. Maternal glucocorticoids (GCs) may convert environmental cues experienced by the mother into a cue triggering adaptive developmental plasticity in offspring. In North American red squirrels (Tamiasciurus hudsonicus), females exhibit increases in GCs when conspecific density is elevated, and selection favors more aggressive and perhaps more active mothers under high density conditions. We experimentally elevated maternal GCs during gestation or early lactation to test the hypothesis that elevated maternal GCs cause shifts in offspring aggression and activity that may prepare them for high density conditions. When offspring were weaned, we measured two behavioral traits (activity and aggression) using a standardized behavioral assay. Because maternal GCs may influence offspring hypothalamic-pituitary-adrenal (HPA) axis activity and HPA axis activity may in turn affect offspring behavior, we also measured the impact of our treatments on offspring HPA axis activity (adrenal reactivity and negative feedback) and the association between offspring HPA axis activity and behavior. Increased maternal GCs during lactation, but not gestation, only slightly elevated activity levels in offspring. Offspring aggression, adrenal reactivity, and negative feedback did not differ between GC-treated and control groups. Offspring with higher adrenal reactivity did exhibit lower aggression, but the relationship between adrenal reactivity and aggression was not affected by treatment with maternal GCs. These results suggest maternal GCs during gestation or early lactation alone may not be a sufficient cue to produce changes in behavioral and physiological stress responses in offspring in natural populations.Summary StatementWe found maternal glucocorticoid levels do not influence offspring personality or HPA axis dynamics in North American red squirrels. Regardless of maternal glucocorticoid treatment, more aggressive squirrels exhibited lower adrenal reactivity.
Effects of chondrogenic priming duration on mechanoregulation of engineered cartilage anlagen
Authors: McDermott Anna M. , Eastburn Emily A. , Kelly Daniel J. , Boerckel Joel D. 
Published: September 2020

AbstractBone development and repair occur by endochondral ossification of a cartilage anlage, or template. Endochondral ossification is regulated by mechanical cues. Recently, we found that in vivo mechanical loading promoted regeneration of large bone defects through endochondral ossification, in a manner dependent on the timing of load initiation. Here, we have developed an in vitro model of the cartilage anlage to test whether the chondrogenic differentiation state alters the response to dynamic mechanical compression. We cultured human bone marrow stromal cells (hMSCs) at high cell density in fibrin hydrogels under chondrogenic priming conditions for periods of 0, 2, 4, or 6 weeks prior to two weeks of dynamic mechanical loading. Samples were evaluated by biomechanical testing, biochemical analysis of collagen and glycosaminoglycan (GAG) deposition, gene expression analysis, and immunohistological analysis, in comparison to time-matched controls cultured under static conditions. We found that dynamic loading increased the mechanical stiffness of engineered anlagen in a manner dependent on the duration of chondrogenic priming prior to load initiation. For chondrogenic priming times of 2 weeks or greater, dynamic loading enhanced the expression of type II collagen and aggrecan, although no significant changes in overall levels of matrix deposition was observed. For priming periods less than 4 weeks, dynamic loading generally supressed markers of hypertrophy and osteogenesis, although this was not observed if the priming period was extended to 6 weeks, where loading instead enhanced the expression of type X collagen. Taken together, these data demonstrate that the duration of chondrogenic priming regulates the endochondral response to dynamic mechanical compression in vitro, which may contribute to the effects of mechanical loading on endochondral bone development, repair, and regeneration in vivo.
Esco2 and Cohesin Regulate CRL4 Ubiquitin Ligaseddb1Expression and Thalidomide Teratogenicity
Authors: Sanchez Annie C. , Thren Elise D. , Iovine M. Kathryn , Skibbens Robert V. 
Published: September 2020

ABSTRACTCornelia de Lange syndrome (CdLS) and Roberts syndrome (RBS) are severe developmental maladies that arise from mutation of cohesin (including SMC3, CdLS) and ESCO2 (RBS). Though ESCO2 activate cohesin, CdLS and RBS etiologies are currently considered non-synonymous and for which pharmacological treatments are unavailable. Here, we identify a unifying mechanism that integrates these genetic maladies to pharmacologically-induced teratogenicity via thalidomide. Our results reveal that Esco2 and cohesin co-regulate a component of CRL4 ubiquitin ligase through which thalidomide exerts teratogenic effects. These findings are the first to link RBS and CdLS to thalidomide teratogenicity and offers new insights into treatments.
Individual vocal signatures show reduced complexity following invasion
Authors: Smith-Vidaurre Grace , Perez Valeria , Wright Timothy F. 
Published: September 2020

AbstractThe manner in which vocal learning is used for social recognition may be sensitive to the social environment. Biological invaders capable of vocal learning are useful for testing this possibility, as invasion alters population size. If vocal learning is used for individual recognition, then individual identity should be encoded in frequency modulation patterns of acoustic signals. Furthermore, frequency modulation patterns should be more complex in larger social groups, reflecting greater selection for individual distinctiveness. We compared social group sizes and used supervised machine learning and frequency contours to compare contact call structure between native range monk parakeets (Myiopsitta monachus) in Uruguay and invasive range populations in the U.S. Invasive range sites exhibited fewer nests and simpler frequency modulation patterns. Beecher’s statistic revealed reduced individual identity content and fewer possible unique individual signatures in invasive range calls. Lower estimated social densities and simpler individual signatures are consistent with relaxed selection on the complexity of calls learned for individual recognition in smaller social groups. These findings run counter to the traditional view that vocal learning is used for imitation, and suggest that vocal learning can be employed to produce individual vocal signatures in a manner sensitive to local population size.
Antibody Upstream Sequence Diversity and Its Biological Implications Revealed by Repertoire Sequencing
Authors: Zhu Yan , Yang Xiujia , Wu Jiaqi , Tang Haipei , Wang Qilong , Guan Junjie , Xie Wenxi , Chen Sen , Chen Yuan , Wang Minhui , Lan Chunhong , Wei Lai , Sun Caijun , Zhang Zhenhai 
Published: September 2020

AbstractThe sequence upstream of antibody variable region (Antibody Upstream Sequence, or AUS) consists of 5’ untranslated region (5’ UTR) and two leader regions, L-PART1 and L-PART2. The sequence variations in AUS affect the efficiency of PCR amplification, mRNA translation, and subsequent PCR-based antibody quantification as well as antibody engineering. Despite their importance, the diversity of AUSs has long been neglected. Utilizing the rapid amplification of cDNA ends (5’RACE) and high-throughput antibody repertoire sequencing (Rep-Seq) technique, we acquired full-length AUSs for human, rhesus macaque (RM), cynomolgus macaque (CM), mouse, and rat. We designed a bioinformatics pipeline and discovered 2,957 unique AUSs, corresponding to 2,786 and 1,159 unique sequences for 5’ UTR and leader, respectively. Comparing with the leader records in the international ImMunoGeneTics (IMGT), while 529 were identical, 313 were with single nucleotide polymorphisms (SNPs), 280 were totally new, and 37 updated the incomplete records. The diversity of AUSs’ impact on related antibody biology was also probed. Taken together, our findings would facilitate Rep-Seq primer design for capturing antibodies comprehensively and efficiently as well as provide a valuable resource for antibody engineering and the studies of antibody at the molecular level.
Virome-wide serological profiling reveals association of herpesviruses with obesity
Authors: Hasan Mohammad Rubayet , Rahman Mahbuba , Khan Taushif , Saeed Amira , Sundaraju Sathyavathi , Flores Annaliza , Hawken Philip , Rawat Arun , Elkum Naser , Hussain Khalid , Tan Rusung , Tang Patrick , Marr Nico 
Published: September 2020

AbstractThe relationship between viral infection and obesity has been known for several decades but epidemiological data related to obesity is limited to only a few viral pathogens. To identify associations between viral infections and obesity, a high-throughput virome-wide serological profiling tool, VirScan, was used to measure antibody responses to a wide range of viruses. Serum specimens from 457 Qatari adults (lean=184;obese=273) and 231 Qatari children (lean=111;obese=120) were assessed by VirScan. Pediatric specimens were simultaneously tested by conventional serology for several herpesviruses to validate VirScan results. Viral association with obesity was determined by calculation of odds ratio (OR) andp-values from Fisher test, and by multivariate regression analysis to adjust for age and gender, with Bonferroni correction for multiple testing. Comprehensive serological profiling of Qatari adult population with VirScan revealed positive and negative associations (p<0.05) of antibody responses to members of Herpesviridae and Picornaviridae families, respectively, with obesity. After adjustingp-values for multiple comparisons, only herpes simplex virus 1 (HSV-1) and Rhinovirus A were positively (OR=3.3; 95%CI 2.15-4.99;p=2.787E-08) and negatively (OR=0.4; 95%CI 0.26-0.65;p=1.175E-03) associated with obesity. At the peptide level, higher prevalence of antibodies against several peptide epitopes of HSV-1/2 was positively (OR=2.35-3.82;p≤3.981E-05) associated with obesity. No such associations were seen at the species or peptide levels in the pediatric population. By multivariate regression analysis, HSV-1 was independently associated with obesity irrespective of age and gender. These findings are in agreement with limited data on the adipogenic properties of HSV-1 observed in vitro.ImportanceThe state of Qatar has one of the highest rates of obesity and associated morbidities in the world. Although obesity is predominantly caused by the intake of high calorie diet and reduced physical activities, other factors including infections with certain viruses have been reported. Among these viruses, human adenoviruses were widely studied but epidemiological data for other viruses in relation to human obesity are limited. Here, we studied the association of obesity in Qatari adults and children with a wide range of viral pathogens using VirScan, a virome-wide serological profiling tool. Our results indicate significant association HSV-1 with obesity in the adult population only. Furthermore, we have identified a set of HSV peptides as candidate obesogenic factors for future studies.
Online modification of goal-directed control in human reaching movements
Authors: De Comite Antoine , Crevecoeur Frédéric , Lefèvre Philippe 
Published: September 2020

AbstractHumans are able to perform very sophisticated reaching movements in a myriad of contexts based on flexible control strategies influenced by the task goal and environmental constraints such as obstacles. However, it remains unknown whether these control strategies can be adjusted online. The objective of this study was to determine whether the factors which determine control strategies during planning also modify the execution of an ongoing movement following sudden changes in task demand. More precisely, we investigated whether, and at which latency, feedback responses to perturbation loads followed the change in the structure of the goal target or environment. We changed the target width (square or rectangle) to alter the task redundancy, or the presence of obstacles to induce different constraints on the reach path, and assessed based on surface recordings when the change in visual display altered the feedback response to mechanical perturbations. Task-related EMG responses were detected within 150 ms of a change in target shape. Considering visuomotor delays of ∼ 100 ms, these results suggest that it takes 50 ms to change control policy within a trial. An additional 30 ms delay was observed when the change in context involved sudden appearance or disappearance of obstacles. Overall, our results demonstrate that the control policy within a reaching movement is not static: contextual factors which influence movement planning also influence movement execution at surprisingly short latencies. Moreover, the additional 30 ms associated with obstacles suggest that these two types of changes may be mediated via distinct processes.New & NoteworthyThe present work demonstrates that the control strategies used to perform reaching movements are adjusted online when the structure of the target or the presence of obstacles are altered during movements. Thus, the properties of goal-directed reaching control are not simply selected during the planning stage of a movement prior to execution. Rather, they are dynamically and rapidly adjusted online, within ∼150ms, according to changes in environment.
Detecting High Scoring Local Alignments in Pangenome Graphs
Authors: Schulz Tizian , Wittler Roland , Rahmann Sven , Hach Faraz , Stoye Jens 
Published: September 2020

AbstractMotivationIncreasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.ResultsWe present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.
Metabolic changes in brain slices over time: a multiplatform metabolomics approach
Authors: Gonzalez-Riano Carolina , Tapia-González Silvia , Perea Gertrudis , González-Arias Candela , DeFelipe Javier , Barbas Coral 
Published: September 2020

ABSTRACTBrain slice preparations are widely used for research in neuroscience. However, a high-quality preparation is essential and there is no consensus regarding stable parameters that can be used to define the status of the brain slice preparation after its collection at different time points. Thus, it is critical to establish the best experimental conditions forex-vivostudies using brain slices for electrophysiological recording. In this study, we used a multiplatform (LC-MS and GC-MS) untargeted metabolomics-based approach to shed light on the metabolome and lipidome changes induced by the brain slice preparation process. We have found significant modifications in the levels of 300 compounds, including several lipid classes and their derivatives, as well as metabolites involved in the GABAergic pathway and the TCA cycle. All these preparation-dependent changes in the brain biochemistry should be taken into consideration for future studies to facilitate non-biased interpretations of the experimental results.
Bioarchaeological analysis of one of the earliest Islamic burials in the Levant
Authors: Srigyan Megha , Bolívar Héctor , Ureña Irene , Santana Jonathan , Petersen Andrew , Iriarte Eneko , Jakobsson Mattias , Smith Colin , Ibañez Juan José , Götherström Anders , Günther Torsten , Valdiosera Cristina 
Published: September 2020

AbstractThe Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here, we present for the first time, a multidisciplinary bioarchaeological analysis of two individuals dated to late 7th and early 8th centuries from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates, religious and cultural burial evidence indicate that this site represents one of the earliest Islamic Arab burials in the Levant during the Late Antiquity period. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This is highlighted through substantial Neolithic Levant ancestry in our samples, inviting an alternative scenario of long-term continuity in this region. This raises questions about the influence of ancient populations and historical migrations to genetic structure in the Middle East. As our study represents the first genomic analysis of an early Islamic burial in the Levant, we discuss our findings and possible historic scenarios in light of forces such as genetic drift and their possible interaction with religious and cultural processes.
Effects of an odor background on moth pheromone communication: constituent identity matters more than blend complexity
Authors: Conchou Lucie , Lucas Philippe , Deisig Nina , Demondion Elodie , Renou Michel 
Published: September 2020

AbstractOlfaction allows insects to communicate with pheromones even in complex olfactory landscapes. It is generally admitted that, due to the binding selectivity of the receptors, general odorants should weakly interfere with pheromone detection. However, laboratory studies show that volatile plant compounds (VPCs) modulate responses to the pheromone in male moths. We used extracellular electrophysiology and calcium imaging to measure the responses to the pheromone of receptor and central neurons in malesAgrotis ipsilonwhile exposed to simple or composite backgrounds of VPCs. Maps of activities were built using calcium-imaging to visualize which areas in antennal lobes (ALs) were affected by VPCs. To mimic a natural olfactory landscape short pheromone puffs were delivered over VPC backgrounds. We chose a panel of VPCs with different chemical structures and physicochemical properties representative of the odorant variety encountered by a moth. We evaluated the intrinsic activity of each VPC and compared the impact of VPC backgrounds at antenna and antennal lobe levels. Then, we prepared binary, ternary and quaternary combinations to determine whether blend activity could be deduced from that of its components. Our data confirm that a VPC background interfere with the moth pheromone system in a dose-dependent manner. Interference with the neuronal coding of pheromone signal starts at the periphery. VPCs showed differences in their capacity to elicit Phe-ORN firing response that cannot be explained by differences in stimulus intensities because we adjusted the source concentrations to vapor pressures. Thus, these differences must be attributed to the selectivity of ORs or any other olfactory proteins. The neuronal network in the ALs, which reformats the ORN-input, did not improve pheromone salience. We postulate that the AL network might have evolved to increase sensitivity and encode for fast changes over a wide range of concentrations, possibly at some cost for selectivity. Comparing three- or four-component blends to binary blends or single compound indicated that a blend showed the activity of its most active compound. Thus, although the diversity of a background might increase the probability of including a VPC interacting with the pheromone system, chemical diversity does not seem to be a prominent factor per se. Global warming is significantly affecting plant metabolism so that the emissions of VPCs and resulting odorscapes are modified. Increase in atmospheric mixing rates of VPCs will change olfactory landscapes which, as confirmed in our study, might impact pheromone communication.
Adaptive fuzzy sliding mode formation controller for autonomous underwater vehicles with variable payload
Authors: Panda Madhusmita , Das Bikramaditya , Subudhi Bidyadhar , Pati Bibhuti Bhusan 
Published: September 2020

PurposeIn this paper, an adaptive fuzzy sliding mode controller (AFSMC) is developed for the formation control of a team of autonomous underwater vehicles (AUVs) subjected to unknown payload mass variations during their mission.Design/methodology/approachA sliding mode controller (SMC) is designed to drive the state trajectories of the AUVs to a switching surface in the state space. The payload mass variation results in parameter variation in AUV dynamics leading to actuator failure. This further leads to loss of communication among the members of the team. Hence, an adaptive SMC based on fuzzy logic is developed to maintain the coordinated motion of AUVs with payload mass variation.FindingsThe results are obtained by employing adaptive SMC for AUVs with and without payload variations and are compared. It is observed that the proposed adaptive SMC exhibits improved performance and tracks the desired trajectory in less time even with variation in the payload. The adaptive fuzzy control algorithm is developed to handle variation in payload mass variation. Lyapunov theory is used to establish stability of AFSMC controller.Research limitations/implicationsPerfect alignment is assumed between centres of gravity (OG) and buoyancy (OB), thus AUVs maintaining horizontal stability during motion. The AUVs’ body centres are aligned with centres of gravity (OG), thus the distance vector being rg = [0,0,0]T. As it is a tracking problem, sway motion cannot be neglected as the AUVs are travelling in a curved locus, hence susceptible to Coriolis and centripetal forces. The AUV is underactuated as only two thrusters at the stern plate that are employed for the surge and yaw controls and error in Y- direction are controlled by adjusting control input in surge and heave direction. Control inputs to the thruster are constants, and depth control is achieved by adjusting the rudder angle.Practical implicationsAUVs are employed in military mission or surveys, and they carry heavy weapons or instrument to be deployed at or picked from specific locations. Such tasks lead to variation in payload, causing overall mass variation during an AUV’s motion. A sudden change in the mass after an AUV release or pick load results in variation in depth and average velocity.Social implicationsThe proposed controller can be useful for military missions for carrying warfare and hydrographic surveys for deploying instruments.Originality/valueA proposed non-linear SMC has been designed, and its performances have been verified in terms of tracking error in X, Y and Z directions. An adaptive fuzzy SMC has been modelled using quantized state information to compensate payload variation. The stability of AFSMC controller is established by using Lyapunov theorem, and reachability of the sliding surface is ensured.