bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional analysis of sandstone ground stone tools: arguments for a qualitative and quantitative synergetic approach
Authors: Zupancich Andrea , Cristiani Emanuela 
Published: September 2020

AbstractIn the last few years, the application of quantitative methods in the field of use wear analysis has grown considerably, involving the use of different techniques. A development in surface measurements approaches has become necessary as standard assessments based upon qualitative functional analysis are often affected by a degree of subjectivity and a limited reproducibility. To advance the current methodological debate on functional analysis of ground stone technology, we present a combined methodological approach, including qualitative and quantitative analyses, applied to the study of experimental sandstone ground stone tools. We test surface quantification at a macro and micro-scale, paired with the observation and description of residue and use wear connected to the processing of plant, animal and mineral matters. Our results provide an exhaustive quantitative dataset concerning surface modifications associated with different uses and suggest an analytical workflow for the functional analysis of both experimental and archaeological ground stone assemblages. We also highlight the limitation and pitfalls of an exclusive adoption of quantitative methods in the study of ancient tool use demonstrating how a synergetic approach can enhance the quality, reproducibility and comparability of functional data.
Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology
Authors: Nikolic Natacha , Montes Iratxe , Lalire Maxime , Puech Alexis , Bodin Nathalie , Arnaud-Haond Sophie , Kerwath Sven , Corse Emmanuel , Gaspar Philippe , Hollanda Stéphanie , Bourjea Jérôme , West Wendy , Bonhommeau Sylvain 
Published: September 2020

AbstractAlbacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resource requires a robust understanding of the species’ biology and of the pattern of connectivity among oceanic regions, yet Indian Ocean albacore population dynamics remain poorly understood and its level of connectivity with the Atlantic Ocean population is uncertain. We analysed morphometrics and genetics of albacore (n = 1,874) in the southwest Indian (SWIO) and southeast Atlantic (SEAO) Oceans to investigate the connectivity and population structure. Furthermore, we examined the species’ dispersal potential by modelling particle drift through major oceanographic features. Males appear larger than females, except in South African waters, yet the length–weight relationship only showed significant male–female difference in one region (east of Madagascar and Reunion waters). The present study produced a genetic differentiation between the southeast Atlantic and southwest Indian Oceans, supporting their demographic independence. The particle drift models suggested dispersal potential of early life stages from SWIO to SEAO and adult or sub-adult migration from SEAO to SWIO.
Active open-loop control of elastic turbulence
Authors: van Buel Reinier , Stark Holger 
Published: September 2020

AbstractWe demonstrate through numerical solutions of the Oldroyd-B model in a two-dimensional Taylor–Couette geometry that the onset of elastic turbulence in a viscoelastic fluid can be controlled by imposed shear-rate modulations, one form of active open-loop control. Slow modulations display rich and complex behavior where elastic turbulence is still present, while it vanishes for fast modulations and a laminar response with the Taylor–Couette base flow is recovered. We find that the transition from the laminar to the turbulent state is supercritical and occurs at a critical Deborah number. In the state diagram of both control parameters, Weissenberg versus Deborah number, we identify the region of elastic turbulence. We also quantify the transition by the flow resistance, for which we derive an analytic expression in the laminar regime within the linear Oldroyd-B model. Finally, we provide an approximation for the transition line in the state diagram introducing an effective critical Weissenberg number in comparison to constant shear. Deviations from the numerical result indicate that the physics behind the observed laminar-to-turbulent transition is more complex under time-modulated shear flow.
Caries severity and socioeconomic inequalities in a nationwide setting: data from the Italian National pathfinder in 12-years children
Authors: Campus Guglielmo , Cocco Fabio , Strohmenger Laura , Cagetti Maria Grazia 
Published: September 2020

AbstractThis study presents the result of the second National pathfinder conducted in Italy on children’s oral health, reporting the prevalence and severity of caries in 12-year old children and describing the caries figure related to the socioeconomic inequalities, both at individual level and macroeconomic level. The two-digit codes related to ICDAS (International Caries Detection and Assessment System) for each tooth and the gingival bleeding score were recorded at school on 7,064 children (48.97% males and 51.03% females). The Gross National Product (GNP) per capita, the Gini Index and Unemployment rate in each Italian section, parents’ educational levels, working status, smoking habit and their ethnic background were recorded. Zero-inflated-negative-binomial (ZINB) models were run, using caries-free teeth, teeth with enamel lesions, cavitated lesions and restorations as functions of socioeconomic explanatory variables, to evaluate the effects of justifiable economic factors of geographical distribution. The mean number of enamel lesions, cavitated lesions and filled per teeth were statistically significant (p < 0.01) dissimilar among the Italian section. GNP per capita, Gini Index and Unemployment rate were significantly correlated to ICDAS scores and filled teeth. Important differences in ICDAS score values remain among children from different socioeconomic backgrounds. Efforts should be made to improve awareness and knowledge regarding oral health practice and to implement preventive programs and access to dental services in Southern Italy where the disease is still unresolved.
The neuropathic phenotype of the K/BxN transgenic mouse with spontaneous arthritis: pain, nerve sprouting and joint remodeling
Authors: Gonçalves dos Santos Gilson , Jimenéz-Andrade Juan Miguel , Woller Sarah A. , Muñoz-Islas Enriqueta , Ramírez-Rosas Martha Beatriz , Ohashi Nobuko , Ferreira Catroli Glaucilene , Fujita Yuya , Yaksh Tony L. , Corr Maripat 
Published: September 2020

AbstractThe adult K/BxN transgenic mouse develops spontaneous autoimmune arthritis with joint remodeling and profound bone loss. We report that both males and females display a severe sustained tactile allodynia which is reduced by gabapentin but not the potent cyclooxygenase inhibitor ketorolac. In dorsal horn, males and females show increased GFAP+ astrocytic cells; however, only males demonstrate an increase in Iba1+ microglia. In dorsal root ganglia (DRG), there is an increase in CGRP+, TH+, and Iba1+ (macrophage) labeling, but no increase in ATF3+ cells. At the ankle there is increased CGRP+, TH+, and GAP-43+ fiber synovial innervation. Thus, based on the changes in dorsal horn, DRG and peripheral innervation, we suggest that the adult K/BxN transgenic arthritic mice display a neuropathic phenotype, an assertion consistent with the analgesic pharmacology seen in this animal. These results indicate the relevance of this model to our understanding of the nociceptive processing which underlies the chronic pain state that evolves secondary to persistent joint inflammation.
Asymmetry induced suppression of chaos
Authors: Biswas Animesh , Chaurasia Sudhanshu Shekhar , Parmananda P. , Sinha Sudeshna 
Published: September 2020

AbstractWe explore the dynamics of a group of unconnected chaotic relaxation oscillators realized by mercury beating heart systems, coupled to a markedly different common external chaotic system realized by an electronic circuit. Counter-intuitively, we find that this single dissimilar chaotic oscillator manages to effectively steer the group of oscillators on to steady states, when the coupling is sufficiently strong. We further verify this unusual observation in numerical simulations of model relaxation oscillator systems mimicking this interaction through coupled differential equations. Interestingly, the ensemble of oscillators is suppressed most efficiently when coupled to a completely dissimilar chaotic external system, rather than to a regular external system or an external system identical to those of the group. So this experimentally demonstrable controllability of groups of oscillators via a distinct external system indicates a potent control strategy. It also illustrates the general principle that symmetry in the emergent dynamics may arise from asymmetry in the constituent systems, suggesting that diversity or heterogeneity may have a crucial role in aiding regularity in interactive systems.
Honey-inspired antimicrobial hydrogels resist bacterial colonization through twin synergistic mechanisms
Authors: Zhang Tiffany , Qu Yue , Gunatillake Pathiraja A. , Cass Peter , Locock Katherine E. S. , Blackman Lewis D. 
Published: September 2020

AbstractInspired by the interesting natural antimicrobial properties of honey, biohybrid composite materials containing a low-fouling polymer hydrogel network and an encapsulated antimicrobial peroxide-producing enzyme have been developed. These synergistically combine both passive and active mechanisms for reducing microbial bacterial colonization. The mechanical properties of these materials were assessed using compressive mechanical analysis, which revealed these hydrogels possessed tunable mechanical properties with Young’s moduli ranging from 5 to 500 kPa. The long-term enzymatic activities of these materials were also assessed over a 1-month period using colorimetric assays. Finally, the passive low-fouling properties and active antimicrobial activity against a leading opportunistic pathogen, Staphylococcus epidermidis, were confirmed using bacterial cell counting and bacterial adhesion assays. This study resulted in non-adhesive substrate-permeable antimicrobial materials, which could reduce the viability of planktonic bacteria by greater than 7 logs. It is envisaged these new biohybrid materials will be important for reducing bacterial adherence in a range of industrial applications.
In vivo 31P magnetic resonance spectroscopy study of mouse cerebral NAD content and redox state during neurodevelopment
Authors: Skupienski Radek , Do Kim Q. , Xin Lijing 
Published: September 2020

AbstractNicotinamide adenine dinucleotide (NAD) is an important cofactor of energy-producing pathways. The redox ratio (NAD+/NADH) reflects the cellular oxidoreductive state. Oxidative stress and redox dysregulation have been suggested to contribute to various neurological diseases. The assessment of NAD content has been recently demonstrated in large animals and human brains by 31P magnetic resonance spectroscopy. However, its measurement in small rodents has never been attempted. The purpose of this study was to investigate, in vivo, the NAD content during mouse brain neurodevelopment. 31P-MR-spectra were acquired in the mouse brain at postnatal days P20, P40, P90 and P250 at 14.1 T using a 3D-localization sequence. High spectral quality was achieved at 14.1 T. NAD+ and NADH were quantified with mean Cramér-Rao lower bound of 10% and 14%, respectively. An increase in NAD+/NADH was observed from P20 to P250 due to a decrease in [NADH]. The intracellular pH was significantly reduced with age, while the free [Mg2+] in the brain was significantly increased. This study demonstrates for the first time the feasibility of the measurement of NAD content in vivo in mouse brains during development, which opens the prospect of longitudinally studying energy metabolism and redox dysfunction in mouse models of brain pathology.
Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST
Authors: Chekli Yankel , Peron-Cane Caroline , Dell’Arciprete Dario , Allemand Jean-François , Li Chenge , Ghigo Jean-Marc , Gautier Arnaud , Lebreton Alice , Desprat Nicolas , Beloin Christophe 
Published: September 2020

AbstractBacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localisation of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and used to specifically tag the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study the organization and dynamics of the bacterial cell surface proteins.
Improvements and inter-laboratory implementation and optimization of blood-based single-locus age prediction models using DNA methylation of the ELOVL2 promoter
Authors: Garali Imene , Sahbatou Mourad , Daunay Antoine , Baudrin Laura G. , Renault Victor , Bouyacoub Yosra , Deleuze Jean-François , How-Kit Alexandre 
Published: September 2020

AbstractSeveral blood-based age prediction models have been developed using less than a dozen to more than a hundred DNA methylation biomarkers. Only one model (Z-P1) based on pyrosequencing has been developed using DNA methylation of a single locus located in the ELOVL2 promoter, which is considered as one of the best age-prediction biomarker. Although multi-locus models generally present better performances compared to the single-locus model, they require more DNA and present more inter-laboratory variations impacting the predictions. Here we developed 17,018 single-locus age prediction models based on DNA methylation of the ELOVL2 promoter from pooled data of four different studies (training set of 1,028 individuals aged from 0 and 91 years) using six different statistical approaches and testing every combination of the 7 CpGs, aiming to improve the prediction performances and reduce the effects of inter-laboratory variations. Compared to Z-P1 model, three statistical models with the optimal combinations of CpGs presented improved performances (MAD of 4.41–4.77 in the testing set of 385 individuals) and no age-dependent bias. In an independent testing set of 100 individuals (19–65 years), we showed that the prediction accuracy could be further improved by using different CpG combinations and increasing the number of technical replicates (MAD of 4.17).
A novel isoform of cryptochrome 4 (Cry4b) is expressed in the retina of a night-migratory songbird
Authors: Einwich Angelika , Dedek Karin , Seth Pranav Kumar , Laubinger Sascha , Mouritsen Henrik 
Published: September 2020

AbstractThe primary sensory molecule underlying light-dependent magnetic compass orientation in migratory birds has still not been identified. The cryptochromes are the only known class of vertebrate proteins which could mediate this mechanism in the avian retina. Cryptochrome 4 of the night-migratory songbird the European robin (Erithacus rubecula; erCry4) has several of the properties needed to be the primary magnetoreceptor in the avian eye. Here, we report on the identification of a novel isoform of erCry4, which we named erCry4b. Cry4b includes an additional exon of 29 amino acids compared to the previously described form of Cry4, now called Cry4a. When comparing the retinal circadian mRNA expression pattern of the already known isoform erCry4a and the novel erCry4b isoform, we find that erCry4a is stably expressed throughout day and night, whereas erCry4b shows a diurnal mRNA oscillation. The differential characteristics of the two erCry4 isoforms regarding their 24-h rhythmicity in mRNA expression leads us to suggest that they might have different functions. Based on the 24-h expression pattern, erCry4a remains the more likely cryptochrome to be involved in radical-pair-based magnetoreception, but at the present time, an involvement of erCry4b cannot be excluded.
Comparative genomics of Alexander Fleming’s original Penicillium isolate (IMI 15378) reveals sequence divergence of penicillin synthesis genes
Authors: Pathak Ayush , Nowell Reuben W. , Wilson Christopher G. , Ryan Matthew J. , Barraclough Timothy G. 
Published: September 2020

AbstractAntibiotics were derived originally from wild organisms and therefore understanding how these compounds evolve among different lineages might help with the design of new antimicrobial drugs. We report the draft genome sequence of Alexander Fleming’s original fungal isolate behind the discovery of penicillin, now classified as Penicillium rubens Biourge (1923) (IMI 15378). We compare the structure of the genome and genes involved in penicillin synthesis with those in two ‘high producing’ industrial strains of P. rubens and the closely related species P. nalgiovense. The main effector genes for producing penicillin G (pcbAB, pcbC and penDE) show amino acid divergence between the Fleming strain and both industrial strains, whereas a suite of regulatory genes are conserved. Homologs of penicillin N effector genes cefD1 and cefD2 were also found and the latter displayed amino acid divergence between the Fleming strain and industrial strains. The draft assemblies contain several partial duplications of penicillin-pathway genes in all three P. rubens strains, to differing degrees, which we hypothesise might be involved in regulation of the pathway. The two industrial strains are identical in sequence across all effector and regulatory genes but differ in duplication of the pcbAB–pcbC–penDE complex and partial duplication of fragments of regulatory genes. We conclude that evolution in the wild encompassed both sequence changes of the effector genes and gene duplication, whereas human-mediated changes through mutagenesis and artificial selection led to duplication of the penicillin pathway genes.
Utility of red cell distribution width as a diagnostic and prognostic marker in non-small cell lung cancer
Authors: Song Bin , Shi Pengchong , Xiao Jianhong , Song Yanfang , Zeng Menglu , Cao Yingping , Zhu Xianjin 
Published: September 2020

AbstractAn increasing number of studies have indicated that red blood cell distribution width (RDW) may be a novel biomarker for the diagnosis and prognosis of various malignancies. However, to date, data on the association of RDW with non-small cell lung cancer (NSCLC) are unclear. Our present study aimed to explore the value of RDW in NSCLC patients. A total of 338 NSCLC patients, 109 small cell lung cancer (SCLC) patients, and 302 healthy participants were retrospectively analyzed between January 2016 and December 2018. In the present study, we found that RDW was significantly increased in NSCLC patients. Receiver-operating characteristic (ROC) analysis showed that the area under the ROC curve (AUC) of RDW was 0.753 in discriminating NSCLC patients from healthy participants, the optimal cut-off value of RDW was 12.95, and the specificity and sensitivity were 76.33% and 76.16%, respectively. Further analysis found that RDW can enhance the diagnostic performance of Cyfra21-1 and NSE in discriminating NSCLC patients from healthy participants or SCLC patients. Among NSCLC patients, RDW was significantly correlated with TNM stage, T stage, N stage, M stage, and Cyfra21-1, indicating that RDW may be helpful for predicting the prognosis of NSCLC patients. Our findings suggest that RDW can be used as an auxiliary marker for the diagnosis and prognosis of NSCLC.
Accelerating the experimental responses on cell behaviors: a long-term prediction of cell trajectories using Social Generative Adversarial Network
Authors: Comes Maria Colomba , Filippi J. , Mencattini A. , Corsi F. , Casti P. , De Ninno A. , Di Giuseppe D. , D’Orazio M. , Ghibelli L. , Mattei F. , Schiavoni G. , Businaro L. , Di Natale C. , Martinelli E. 
Published: September 2020

AbstractThe incremented uptake provided by time-lapse microscopy in Organ-on-a-Chip (OoC) devices allowed increased attention to the dynamics of the co-cultured systems. However, the amount of information stored in long-time experiments may constitute a serious bottleneck of the experimental pipeline. Forward long-term prediction of cell trajectories may reduce the spatial–temporal burden of video sequences storage. Cell trajectory prediction becomes crucial especially to increase the trustworthiness in software tools designed to conduct a massive analysis of cell behavior under chemical stimuli. To address this task, we transpose here the exploitation of the presence of “social forces” from the human to the cellular level for motion prediction at microscale by adapting the potential of Social Generative Adversarial Network predictors to cell motility. To demonstrate the effectiveness of the approach, we consider here two case studies: one related to PC-3 prostate cancer cells cultured in 2D Petri dishes under control and treated conditions and one related to an OoC experiment of tumor-immune interaction in fibrosarcoma cells. The goodness of the proposed strategy has been verified by successfully comparing the distributions of common descriptors (kinematic descriptors and mean interaction time for the two scenarios respectively) from the trajectories obtained by video analysis and the predicted counterparts.
Factors influencing riverine utilization patterns in two sympatric macaques
Authors: Otani Yosuke , Bernard Henry , Wong Anna , Tangah Joseph , Tuuga Augustine , Hanya Goro , Matsuda Ikki 
Published: September 2020

AbstractMany species of terrestrial animals, including primates, live in varied association with the aquatic (e.g., riverine or coastal) environment. However, the benefits that each species receive from the aquatic environment are thought to vary depending on their social and ecological characteristics, and thus, elucidating those benefits to each species is important for understanding the principles of wild animal behaviour. In the present study, to gain a more complete picture of aquatic environment use, including social and ecological factors in primates, factors affecting riverine habitat utilization of two macaque species (Macaca nemestrina and M. fascicularis) were identified and qualitative comparisons were made with sympatric proboscis monkeys (Nasalis larvatus), which have different social and ecological characteristics. Temporal variation in sighting frequency of macaques at the riverbanks was positively related to the fruit availability of a dominant riparian plant species and negatively related to the river water level which affects the extent of predation pressure. Riverine utilization of macaques was greatly influenced by distribution and abundance of food (especially fruit) resources, possibly in association with predation pressure. Additionally, qualitative ecological comparisons with sympatric proboscis monkeys suggest that the drivers of riverine utilization depend on the feeding niches of the species, and different anti-predator strategies resulting from their differing social structures.