bluuebunny/crossref_metadata_2025 huggingface dataset:
No evidence for entrainment: endogenous gamma oscillations and rhythmic flicker responses coexist in visual cortex
Authors: Duecker Katharina , Gutteling Tjerk P. , Herrmann Christoph S. , Jensen Ole
Published: September 2020

Over the past decades, a plethora of studies have linked cortical gamma oscillations (∼30-100 Hz) to neuro-computational mechanisms. Their functional relevance, however, is still passionately debated. Here, we asked if endogenous gamma oscillations in the human brain can be entrained by a rhythmic photic drive>50 Hz. A noninvasive modulation of endogenous brain rhythms allows conclusions about their causal involvement in neurocognition. To this end, we systematically investigated oscillatory responses to a rapid sinusoidal flicker in the absence and presence of endogenous gamma oscillations using magnetoencephalography (MEG) in combination with a high-frequency projector. The photic drive produced a robust response over visual cortex to stimulation frequencies of up to 80 Hz. Strong, endogenous gamma oscillations were induced using moving grating stimuli as repeatedly done in previous research. When superimposing the flicker and the gratings, there was no evidence for phase or frequency entrainment of the endogenous gamma oscillations by the photic drive. Unexpectedly, we did not observe an amplification of the flicker response around participants’ individual gamma frequencies; rather, the magnitude of the response decreased monotonically with increasing frequency. Source reconstruction suggests that the flicker response and the gamma oscillations were produced by separate, coexistent generators in visual cortex. The presented findings challenge the notion that cortical gamma oscillations can be entrained by rhythmic visual stimulation. Instead, the mechanism generating endogenous gamma oscillations seems to be resilient to external perturbation.

Significance Statement

We aimed to investigate to what extent ongoing, high-frequency oscillations in the gamma band (30-100 Hz) in the human brain can be entrained by a visual flicker. Gamma oscillations have long been suggested to coordinate neuronal firing and enable inter-regional communication. Our results demonstrate that rhythmic visual stimulation cannot hijack the dynamics of ongoing gamma oscillations; rather, the flicker response and the endogenous gamma oscillations coexist in different visual areas. Therefore, while a visual flicker evokes a strong neuronal response even at high frequencies in the gamma-band, it does not entrain endogenous gamma oscillations in visual cortex. This has important implications for interpreting studies investigating the causal and neuroprotective effects of rhythmic sensory stimulation in the gamma band.
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir
Authors: Fellows Yates James A. , Valtueña Aida Andrades , Vågene Ashild J. , Cribdon Becky , Velsko Irina M. , Borry Maxime , Bravo-López Miriam J. , Fernandez-Guerra Antonio , Green Eleanor J. , Ramachandran Shreya L. , Heintzman Peter D. , Spyrou Maria A. , Hübner Alexander , Gancz Abigail S. , Hider Jessica , Allshouse Aurora F. , Warinner Christina
Published: September 2020

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived athttps://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.
Alternate models of acute dyslipidemia reveal divergent pathways upon atherosclerosis initiation
Authors: Hellberg Sanna , Shavva Vladimir S. , Metso Jari , Chen Guangchun , Li Quan-Zhen , Manfè Valentina , Olofsson Peder S. , Jauhiainen Matti , Binder Christoph J. , Malin Stephen G.
Published: September 2020

Atherosclerosis is thought to be initiated by the sub-intimal retention of apolipoprotein-B containing lipoproteins within susceptible sites of the vasculature. Understanding this initiation is not possible with current legacy mouse models of atherosclerosis. We created two mouse strains of inducible hypercholesterolemia based on conditional loss of apolipoprotein E or through inducible expression of a gain-of-function proprotein convertase subtilisin/kexin type 9 D374Y mutation. Both strains rapidly broke plasma-lipid homeostasis and converted to a state of atherogenic dyslipidemia, resulting in overt aortic-accumulation of lipoproteins within 10 days. RNA-sequencing revealed that the vascular response is completely dependent on the route taken to dyslipidemia, which nevertheless implicates known pathogenic pathways in the aetiology of atherosclerosis, and further implicates APOE as an inhibitor of inflammation. As atherosclerosis develops, a convergence of common mechanistic processes emerge in both strains with significant involvement of the immune system, and targeting of CD8 T cells can regulate a conserved aortic response. Our results define atherosclerosis initiation as highly heterogeneous process and identify multiple potential therapeutic targets that may influence disease onset.
White matter integrity requires continuous myelin synthesis at the inner tongue
Authors: Meschkat Martin , Steyer Anna M. , Weil Marie-Theres , Kusch Kathrin , Jahn Olaf , Piepkorn Lars , Agüi-Gonzalez Paola , Ngoc Phan Nhu Thi , Ruhwedel Torben , Sadowski Boguslawa , Rizzoli Silvio O. , Werner Hauke B. , Ehrenreich Hannelore , Nave Klaus-Armin , Möbius Wiebke
Published: September 2020

Myelin, the electrically insulating axonal sheath, is composed of lipids and proteins with exceptionally long lifetime. This raises the question how myelin function is affected by myelin turnover. We have studied the integrity of myelinated tracts after experimentally preventing the formation of new myelin in the CNS of adult mice, using an inducibleMbpnull allele. Oligodendrocytes survived recombination, continued expressing myelin genes, but failed to maintain compacted myelin sheaths. Using 3D electron microscopy and mass spectrometry imaging we visualized myelin-like membranes that failed to incorporate adaxonally, most prominently at juxta-paranodes. Myelinoid body formation indicated degradation of existing myelin at the abaxonal side and at the inner tongue of the sheath. Compacted myelin thinning and shortening of internodes, with about 50% myelin lost after 20 weeks (=5 months), ultimately led to axonal pathology and neurological disease. These data reveal that functional axon-myelin units require the continuous incorporation of new myelin membranes.
A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures
Authors: Schinn Song-Min , Morrison Carly , Wei Wei , Zhang Lin , Lewis Nathan E.
Published: September 2020

The control of nutrient availability is critical to large-scale manufacturing of biotherapeutics. However, the quantification of proteinogenic amino acids is time-consuming and thus is difficult to implement for real-timein situbioprocess control. Genome-scale metabolic models describe the metabolic conversion from media nutrients to proliferation and recombinant protein production, and therefore are a promising platform forin silicomonitoring and prediction of amino acid concentrations. This potential has not been realized due to unresolved challenges: (1) the models assume an optimal and highly efficient metabolism, and therefore tend to underestimate amino acid consumption, and (2) the models assume a steady state, and therefore have a short forecast range. We address these challenges by integrating machine learning with the metabolic models. Through this we demonstrate accurate and time-course dependent prediction of individual amino acid concentration in culture medium throughout the production process. Thus, these models can be deployed to control nutrient feeding to avoid premature nutrient depletion or provide early predictions of failed bioreactor runs.
Single-cell profiling of histone modifications in the mouse brain
Authors: Bartosovic Marek , Kabbe Mukund , Castelo-Branco Gonçalo
Published: September 2020

The development of the mouse central nervous system (CNS) involves coordinated execution of transcriptional and epigenetic programs. These programs have been extensively studied through single-cell technologies in a pursuit to characterize the underlying cell heterogeneity. However, histone modifications pose additional layers of both positive and negative regulation that defines cellular identity. Here we show that the Cut&Tag technology can be coupled with a droplet-based single cell library preparation platform to produce high quality chromatin modifications data at a single cell resolution in tens of thousands of cells. We apply single-cell Cut&Tag (scC&T) to probe histone modifications characteristic of active promoters (H3K4me3), active promoters and enhancers (H3K27ac), active gene bodies (H3K36me3) and inactive regions (H3K27me3) and generate scC&T profiles for almost 50,000 cells. scC&T profiles of each of these histone modifications were sufficient to determine cell identity and deconvolute at single cell level regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. Moreover, we used scC&T to investigate the single-cell chromatin occupancy of transcription factor Olig2 and the cohesin complex component Rad21. Our results indicate that analysis of histone modifications and transcription factor occupancy at a single cell resolution can provide unique insights of epigenomic landscapes in the CNS. We also provide an online resource that can be used to interactively explore the data athttps://castelobranco.shinyapps.io/BrainCutAndTag2020/.
Intracellular stiffening competes with cortical softening in glioblastoma cells
Authors: Alibert Charlotte , Pereira David , Lardier Nathan , Etienne-Manneville Sandrine , Goud Bruno , Asnacios Atef , Manneville Jean-Baptiste
Published: September 2020

Cancer cell softening increases with the progression of the disease, suggesting that mechanical phenotyping could be used as a diagnostic or prognostic method. Here we investigate the cell mechanics of gliomas, brain tumors that originate from glial cells or glial progenitors. We use two microrheology techniques, a single cell parallel plates rheometer to probe whole cell mechanics and optical-tweezers to probe intracellular rheology. We show that cell mechanics discriminates human glioma cells of different grades. When probed globally, grade IV glioblastoma cells are softer than grade III astrocytoma cells, while they are surprisingly stiffer at the intracellular level. We explain this difference between global and local intracellular behaviours by changes in the composition and spatial organization of the cytoskeleton and by changes in nuclear mechanics. Our study highlights the need to combine rheology techniques for potential diagnostic or prognostic methods based on cancer cell mechanophenotyping.
Analyses of Biomarker Traits in Diverse UK Biobank Participants Identify Associations Missed by European-centric Analysis Strategies
Authors: Sun Quan , Graff Misa , Rowland Bryce , Wen Jia , Huang Le , Lee Moa P. , Avery Christy L. , Franceschini Nora , North Kari E. , Li Yun , Raffield Laura M.
Published: September 2020

Despite the dramatic underrepresentation of non-European populations in human genetics studies, researchers continue to exclude participants of non-European ancestry, even when these data are available. This practice perpetuates existing research disparities and can lead to important and large effect size associations being missed. Here, we conducted genome-wide association studies (GWAS) of 31 serum and urine biomarker quantitative traits in African (n=9354), East Asian (n=2559) and South Asian (n=9823) UK Biobank participants ancestry. We adjusted for all known GWAS catalog variants for each trait, as well as novel signals identified in European ancestry UK Biobank participants alone. We identify 12 novel signals in African ancestry and 3 novel signals in South Asian participants (p<1.61 × 10−10). Many of these signals are highly plausible and rare in Europeans (1% or lower minor allele frequency), includingcispQTLs for the genes encoding serum biomarkers like gamma-glutamyl transferase and apolipoprotein A,PIEZ01andG6PDvariants with impacts on HbA1c through likely erythocytic mechanisms, and a coding variant inGPLD1, a gene which cleaves GPI-anchors, associated with normally GPI-anchored protein alkaline phosphatase in serum. This work illustrates the importance of using the genetic data we already have in diverse populations, with many novel discoveries possible in even modest sample sizes.
Tractable models of ecological assembly
Authors: Serván Carlos A. , Allesina Stefano
Published: September 2020

Ecological assembly, the way natural communities form under ecological time-scales, is a fundamental and yet poorly understood process. Recent theoretical and empirical approaches to assembly consider systems in which a group of species is introduced in a new environment, and dynamics prune the system down to a sub-community of coexisting species. This “top-down” assembly approach contrasts with the well-studied “bottom-up”, or sequential, assembly, in which species from a pool enter the system one at a time, giving rise to priority effects and complex dynamics. Here we determine under which conditions the two approaches are equivalent, i.e., lead asymptotically to the same exact set of coexisting species. To achieve this result, we represent the assembly process as a network in which nodes are sub-communities and edges stand for invasions shifting the composition of the ecological community from a stable configuration to another. This abstraction makes it easy to determine which states the community can occupy, as well as highlight the potential for priority effects or cyclic species composition. We discuss how the equivalence between bottom-up and top-down assembly can advance our understanding of this challenging process from an empirical and theoretical point of view, informing the study of ecological restoration and the design and control of ecological communities.
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

Environmental 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 Statement

We 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

Bone 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

Cornelia 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

The 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

The 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

The 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.

Importance

The 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

Humans 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 & Noteworthy

The 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

Motivation

Increasing 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.

Results

We 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

Brain 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

The 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

Olfaction 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

Purpose

In 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/approach

A 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.

Findings

The 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/implications

Perfect 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 implications

AUVs 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 implications

The proposed controller can be useful for military missions for carrying warfare and hydrographic surveys for deploying instruments.

Originality/value

A 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.
Supply chain management in the era of circular economy: the moderating effect of big data
Authors: Del Giudice Manlio , Chierici Roberto , Mazzucchelli Alice , Fiano Fabio
Published: September 2020

Purpose

This paper analyzes the effect of circular economy practices on firm performance for a circular supply chain and explores the moderating role that big-data-driven supply chain plays within these relationships.

Design/methodology/approach

This study uses data collected through an online survey distributed to managers of 378 Italian firms that have adopted circular economy principles. The data are processed using multiple regression analysis.

Findings

The results indicate that the three categories of circular economy practices investigated – namely circular economy supply chain management design, circular economy supply chain relationship management and circular economy HR management – play a crucial role in enhancing firm performance from a circular economy perspective. A big-data-driven supply chain acts as a moderator of the relationship between circular economy HR management and firm performance for a circular economy supply chain.

Originality/value

This study makes a number of original contributions to research on circular economy practices in a big-data-driven supply chain and provides useful insights for practitioners. First, it answers the call to capture digital transformation trends and to extend research on sustainability in supply chain management. Second, it enhances the literature by investigating the relationships between three different kinds of circular economy supply chain practices and firm performance. Finally, it clarifies the moderating role of big data in making decisions and implementing circular supply chain solutions to achieve better environmental, social and economic benefits.
The effect of green HRM on employee green behaviors in higher education: the mediating mechanism of green work engagement
Authors: Aboramadan Mohammed
Published: September 2020

Purpose

Building on the social exchange theory (SET), this study aims to propose a model of the effects of green human resource management on employee in-role, extra-role and green innovative work behavior (GIWB). This study proposes, building on both the job demands-resources model and SET, that the aforementioned links can be explained through the mediating role of green work engagement (GWE).

Design/methodology/approach

Data were collected from employees (n. 208) working in Palestinian higher education organizations using a self-administered questionnaire. The partial least squares-structural equation modeling was the primary statistical technique adopted to examine the study’s hypotheses.

Findings

The results suggest that green human resources management (GHRM) was a significant predictor of employee in-role green behavior, extra-role green behavior and GIWB. Furthermore, GWE demonstrated to be a significant intervening mechanism to explain the above-mentioned relationships.

Practical implications

The results provide useful insights for higher education policymakers on how GHRM may positively contribute to employee green outcomes.

Originality/value

This paper is novel for several reasons. First, it contributes to the general literature of GHRM. Second, it contributes to the limited body of knowledge on GHRM in the context of higher education. Third, the distinct contribution of this study is the introduction of GIWB as an outcome of GHRM, and GWE as a mediating variable in the relationship between GHRM and employee green behaviors.
Development of a soft cable-driven hand exoskeleton for assisted rehabilitation training
Authors: Xu Dawen , Wu Qingcong , Zhu Yanghui
Published: September 2020

Purpose

Hand motor dysfunction has seriously reduced people’s quality of life. The purpose of this paper is to solve this problem; different soft exoskeleton robots have been developed because of their good application prospects in assistance. In this paper, a new soft hand exoskeleton is designed to help people conduct rehabilitation training.

Design/methodology/approach

The proposed soft exoskeleton is an under-actuated cable-driven mechanism, which optimizes the force transmission path and many local structures. Specifically, the path of force transmission is optimized and cables are wound around cam-shaped spools to prevent cables lose during fingers movement. Besides, a pre-tightening system is presented to adjust the preload force of the cable-tube. Moreover, a passive brake mechanism is proposed to prevent the cables from falling off the spools when the remote side is relaxed.

Findings

Finally, three control strategies are proposed to assist in rehabilitation training. Results show that the average correlation coefficient of trajectory tracking is 90.99% and this exoskeleton could provide steady clamping force up to 35 N, which could meet the demands of activities in daily living. Surface electromyography (sEMG)-based intention recognition method is presented to complete assistance and experiments are conducted to prove the effectiveness of the assisted grasping method by monitoring muscle activation, finger angle and interactive force.

Research limitations/implications

However, the system should be further optimized in terms of hardware and control to reduce delays. In addition, more clinical trials should be conducted to evaluate the effect of the proposed rehabilitation strategies.

Social implications

May improve the ability of hemiplegic patients to live independently.

Originality/value

A novel under-actuated soft hand exoskeleton structure is proposed, and an sEMG-based auxiliary grasping control strategy is presented to help hemiplegic patients conduct rehabilitation training.
Mixing data analytics with intuition: Liverpool Football Club scores with integrated intelligence
Authors: Lichtenthaler Ulrich
Published: September 2020

Purpose

The paper aims to present key insights for achieving a sustainable competitive advantage from implementing data analytics solutions and artificial intelligence (AI).

Design/methodology/approach

This conceptual paper builds on prior empirical and conceptual research, and it offers anecdotal evidence from a best-practice case study of Liverpool Football Club.

Findings

Beyond the well-known companies in profiting from AI, such as Amazon, this paper presents a surprising best-practice example for achieving a competitive advantage from combining data analytics and AI with human expertise. Liverpool Football Club is a leading soccer club from England, and it has experienced a major revival in terms of sporting success and financial performance in recent years. The club’s emphasis on data analytics and AI only contributed to this impressive evolution when it was complemented with the emotional intelligence and people skills of its present manager Juergen Klopp. Along with new conceptual arguments, this example of integrated intelligence offers important insights for managers and executives in companies from many industries – far beyond sports management.

Originality/value

The conceptual arguments and case example illustrate that the competitive benefits of implementing standardized AI solutions in an isolated way will often be relatively limited. Many AI solutions will be standardized in the near future, and they may easily be applied by many firms. Thus, even those companies that are considered as AI pioneers may not be able to sustain their competitive advantage unless they develop an integrated intelligence architecture, which combines human and AI. This integration of data analytics and AI with the human intelligence and expertise of a firm’s employees offers the basis for a sustainable advantage because it is difficult to match for competitors. Thus, the paper offers new theoretical insights and direct managerial implications with regard to profiting from AI and data analytics.