bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and Virulence Gene Profiles ofEscherichia coliO157 from Cattle Slaughtered in Buea, Cameroon
Authors: Akomoneh Elvis Achondou , Esemu Seraphine Nkie , Kfusi Achah Jerome , Ndip Roland N. , Ndip Lucy M. 
Published: June 2020

ABSTRACTBackgroundEscherichia coliO157 is an emerging foodborne pathogen of great public health concern. It has been associated with bloody diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome in humans. Most human infections have been traced to cattle and the consumption of contaminated cattle products. In order to understand the risk associated with the consumption of cattle products, this study sought to investigate the prevalence and identify virulence genes inE. coliO157 from cattle in Cameroon.MethodA total of 512 rectal samples were obtained and analysed using conventional bacteriological methods (enrichment on modified Tryptone Soy Broth and selective plating on Cefixime-Tellurite Sorbitol Mac-Conkey Agar) for the isolation ofE. coliO157. PresumptiveE. coliO157 isolates were confirmed serologically using E. COLIPRO™O157 latex agglutination test and molecularly using PCR targeting therfbgene in the isolates. Characterisation of the confirmedE. coliO157 strains was done by amplification ofstx1,stx2,eaeAandhlyAvirulence genes using both singleplex and multiplex PCR.ResultsE. coliO157 was detected in 56 (10.9%) of the 512 samples examined. The presence of the virulence genesstx2, eaeAandhylAwas demonstrated in 96.4% (54/56) of the isolates andstx1in 40 (71.4%) of the 54. The isolates exhibited three genetic profiles (I-III) with I (stx1, stx2, eaeAandhlyA) being the most prevalent (40/56; 71.4%) while two isolates had none of the virulence genes tested.ConclusionA proportion of cattle slaughtered in abattoirs in Buea are infected with pathogenicE. coliO157 and could be a potential source of human infections. We recommend proper animal food processing measures and proper hygiene be prescribed and implemented to reduce the risk of beef contamination.
Mechanotendography: description and evaluation of a new method for investigating the physiological mechanical oscillations of tendons using a piezo-based measurement system
Authors: Schaefer Laura V , Bittmann Frank N 
Published: June 2020

AbstractThe mechanotendography (MTG) analyzes mechanical oscillations of tendons during muscular actions. It can be assessed as equivalent to mechanomyography just applied for tendons. Since this method is unknown, the aim of this investigation was to evaluate the technical reliability of a piezo-based measurement system used for MTG.The reliability measurements were performed using audio files played by a subwoofer. The thereby generated mechanical pressure waves were recorded by a piezoelectric sensor based measurement system. The piezo sensor was fixed onto the subwoofer’s coverage. An audio of 40 Hz-sine oscillations and, to stay close to human applications, four different formerly in vivo recorded MTG-signals from Achilles and triceps brachii tendon were converted into audio files and were used as test signals. Five trials with each audio were performed. One audio was used for repetition trials on another day. The correlation of the recorded signals were estimated by the Spearman correlation coefficient (MCC), the intraclass-correlation-coefficient (ICC(3,1)), Cronbach’s alpha (CA) and by mean distances (MD) between the signals. They were compared between repetition and random matched signals.The repetition trials show high correlations (MCC: 0.86 ± 0.13, ICC: 0.89 ± 0.12, CA: 0.98 ± 0.03), low MD (0.03 ± 0.03V) and differ significantly from the random matched signals (MCC: 0.15 ± 0.10, ICC: 0.17 ± 0.09, CA: 0.37 ± 0.16, MD: 0.19 ± 0.01V) (p= 0.001 – 0.043).This speaks for an excellent reliability of the piezo-based measurement system in a technical setting. Since research showed that the skin above superficial tendons oscillates adequately, we estimate this tool as valid for the application in musculoskeletal systems. It might provide further insight into the functional behavior of tendons during muscular activity.
Genoprotective effects of Chaga mushroom (Inonotus obliquus) polysaccharides in UVB-exposed embryonic zebrafish (Danio rerio) through coordinated expression of DNA repair genes
Authors: Eid Jehane Ibrahim , Mohanty Swabhiman , Das Biswadeep 
Published: June 2020

AbstractBackgroundChaga mushroom(Inonotus obliquus)is one of the most promising antioxidants with incredible health-promoting effects. Chaga polysaccharides (IOP) have been reported to enhance immune response and alleviate oxidative stress during development. However, the effects of IOP on the genotoxicity in model organisms are yet to be clarified.MethodsZebrafish embryos (12 hours post fertilization, hpf) were exposed to transient UVB (12 J/m2/s, 310 nm) for 10 secs using a UV hybridisation chamber, followed by IOP treatment (2.5 mg/mL) at 24 hpf for up to 7 days post fertilization (dpf). The genotoxic effects were assessed using acridine orange staining, alkaline comet assay, and qRT-PCR for screening DNA repair genes.ResultsWe found significant reduction in DNA damage and amelioration of the deformed structures in the IOP-treated zebrafish exposed to UVB (p < 0.05) at 5 dpf and thereafter. In addition, the relative mRNA expressions ofXRCC-5, XRCC-6, RAD51, P53,andGADD45were significantly upregulated in the IOP-treated UVB-exposed zebrafish. Pathway analysis demonstrated coordinated regulation of DNA repair genes, suggesting collective response during UVB exposure.ConclusionsOverall, IOP treatment ameliorated the genotoxic effects in UVB-exposed zebrafish embryos, which eventually assisted in normal development. The study suggested the efficacy of Chaga mushroom polysaccharides in mitigating UV-induced DNA damage.
Words in context: tracking context-processing during language comprehension using computational language models and MEG
Authors: Lopopolo Alessandro , Schoffelen Jan Mathijs , van den Bosch Antal , Willems Roel M. 
Published: June 2020

AbstractThe meaning of a word depends on its lexical semantics and on the context in which it is embedded. At the basis of this lays the distinction between lexical retrieval and integration, two basic operations supporting language comprehension. In this paper, we investigate how lexical retrieval and integration are implemented in the brain by comparing MEG activity to word representations generated by computational language models. We test both non-contextualized embeddings, representing words independently from their context, and contextualized embeddings, which instead integrate contextual information in their representations. Using representational similarity analysis over cortical regions and over time, we observed that brain activity in the left anterior temporal pole and inferior frontal regions shows higher similarity with contextualized word embeddings compared to non-contextualized embeddings, between 300 and 500 ms after word presentation. On the other hand, non-contextualized word embeddings show higher similarity with brain activity in the left lateral and anterior temporal lobe at earlier latencies – areas and latencies related to lexical retrieval. Our results highlight how lexical retrieval and context integration can be tracked in the brain using word embeddings obtained with computational models. These results also suggest that the distinction between lexical retrieval and integration might be framed in terms of context-independent and contextualized representations.
The Pleistocene-Holocene aquatic molluscs as indicators of the past ecosystem changes in Transbaikalia (Eastern Siberia, Russia)
Authors: Klishko Olga K. , Kovychev Evgeniy V. , Vinarski Maxim V. , Bogan Arthur E. , Jurgenson Georgiy. A. 
Published: June 2020

ABSTRACTData on historical change of the Transbaikalian malacofauna in the Neopleistocene and Holocene is presented. Fossil shells from archeological excavations of the ancient settlements dating from the Neolithic period to Medieval and also from a drill hole of the Neopleistocene alluvial deposits were collected. In total nine species of bivalve molluscs from the families Margaritiferidae, Unionidae, Limnocardiidae, Glycymerididae, including one marine species, and two gastropod species from families Viviparidae and Planorbidae were identified. The time of the existence of each fossil species was determined by radiocarbon dating. It was found that the species ranged in age from more 50,000 and 2,080–1,210 years ago. Five species inhabited the Transbaikal region and are locally extirpated in the present. Their disjunctive ranges in the past included southern Europe and Western and Eastern Siberia to Transbaikalia and in the east to Far East and Primorye of Russia. The time of existence and extirpation of the thermophilic species of generaAdacna, Planorbis, LanceolariaandAmuropaludinacorresponds to cycles of the warming and cooling in Pleistocene and Holocene according to regional climate chronological scales. It was possible to separate these species as indicators of paleoclimate. Change of the species composition of the malacofauna of region connected with natural cycles of climatochrons in the Pleistocene and Holocene is the appearance of the climatogenic succession. In the course of this succession the disappearance of the stenothermal species occurred on a regional level and decreasing their global ranges.
DReSS: A difference measurement based on reachability between state spaces of Boolean networks
Authors: Yin Ziqiao , Guo Binghui , Ma Shuangge Steven , Sun Yifan , Mi Zhilong , Zheng Zhiming 
Published: June 2020

AbstractResearches on dynamical features of biological systems are mostly based on fixed network structure. However, both biological factors and data factors can cause structural perturbations to biological regulatory networks. There are researches focus on the influence of such structural perturbations to the systems’ dynamical features. Reachability is one of the most important dynamical features, which describe whether a state can automatically evolve into another state. However, there is still no method can quantitively describe the reachability differences of two state spaces caused by structural perturbations. DReSS, Difference based on Reachability between State Spaces, is proposed in this research to solve this problem. First, basic properties of DReSS such as non-negativity, symmetry and subadditivity are proved based on the definition. And two more indexes, diagDReSS and iDReSS are proposed based on the definition of DReSS. Second, typical examples likeDReSS= 0or1 are shown to explain the meaning of DReSS family, and the differences between DReSS and traditional graph distance are shown based on the calculation steps of DReSS. Finally, differences of DReSS distribution between real biological regulatory network and random networks are compared. Multiple interaction positions in real biological regulatory network show significant different DReSS value with those in random networks while none of them show significant different diagDReSS value, which illustrates that the structural perturbations tend to affect reachability inside and between attractor basins rather than to affect attractor set itself.Author summaryBoolean network is a kind of networks which is widely used to model biological regulatory systems. There are structural perturbations in biological systems based on both biological factors and data-related factors. We propose a measurement called DReSS to describe the difference between state spaces of Boolean networks, which can be used to evaluate the influence of specific structural perturbations of a network to its state space quantitively. We can use DReSS to detect the sensitive interactions in a regulatory network, where structural perturbations can influence its state space significantly. We proved properties of DReSS including non-negativity, symmetry and subadditivity, and gave examples to explain the meaning of some special DReSS values. Finally, we present an example of using DReSS to detect sensitive vertexes in yeast cell cycle regulatory network. DReSS can provide a new perspective on how different interactions affect the state space of a specific regulatory network differently.
A forward genetic screen identifies Dolk as a regulator of startle magnitude through the potassium channel subunit Kv1.1
Authors: Meserve Joy H. , Nelson Jessica C. , Marsden Kurt C. , Hsu Jerry , Echeverry Fabio A. , Jain Roshan A. , Wolman Marc A. , Pereda Alberto E. , Granato Michael 
Published: June 2020

AbstractThe acoustic startle response is an evolutionary conserved avoidance behavior. Disruptions in startle behavior, in particular startle magnitude, are a hallmark of several human neurological disorders. While the neural circuitry underlying startle behavior has been studied extensively, the repertoire of genes and genetic pathways that regulate this locomotor behavior has not been explored using an unbiased genetic approach. To identify such genes, we took advantage of the stereotypic startle behavior in zebrafish larvae and performed a forward genetic screen coupled with whole genome analysis. This identified mutants in eight genes critical for startle behavior, including two genes encoding proteins associated with human neurological disorders, Dolichol kinase (Dolk), a broadly expressed regulator of the glycoprotein biosynthesis pathway, and the potassium Shaker-like channel subunit Kv1.1. We demonstrate that Kv1.1 acts independently of supraspinal inputs to regulate locomotion, suggesting its site of action is within spinal circuitry. Moreover, we show that Kv1.1 protein is mis-localized indolkmutants, suggesting they act in a common genetic pathway to regulate movement magnitude. Combined, our results identify a diverse set of eight genes all associated with human disorders that regulate zebrafish startle behavior and reveal a previously unappreciated role for Dolk and Kv1.1 in regulating movement magnitude via a common genetic pathway.Author summaryUnderlying all animal behaviors are neural circuits, which are controlled by numerous molecular pathways that direct neuron development and activity. To identify and study these molecular pathways that control behavior, we use a simple vertebrate behavior, the acoustic startle response, in the larval zebrafish. In response to an intense noise, larval zebrafish will quickly turn and swim away to escape. From a genetic screen, we have identified a number of mutants that behave in abnormal ways in response to an acoustic stimulus. We cloned these mutants and identified eight genes that regulate startle behavior. All eight genes are associated with human disorders, and here we focus on two genes,dolkandkcna1a, encoding Dolk, a key regulator of protein glycosylation, and the potassium channel Kv1.1, respectively. We demonstrate that loss ofdolkorkcna1acauses larval zebrafish to perform exaggerated swim movements and that Dolk is required for Kv1.1 protein localization to axons of neurons throughout the nervous system, providing strong evidence thatdolkandkcna1aact in a common molecular pathway. Combined, our studies provide new insights into the genetic regulation of startle behavior.
Structures of FHOD1-Nesprin1/2 complexes reveal alternate binding modes for the FH3 domain of formins
Authors: Lim Sing Mei , Cruz Victor E. , Antoku Susumu , Gundersen Gregg G. , Schwartz Thomas U. 
Published: June 2020

ABSTRACTThe nuclear position in eukaryotic cells is controlled by a nucleo-cytoskeletal network, with important roles in cell differentiation, division and movement. Forces are transmitted through conserved linker of nucleoskeleton and cytoskeleton (LINC) complexes that traverse the nuclear envelope and engage on either side of the membrane with diverse binding partners. Nesprin-2 giant (Nes2G), a LINC element in the outer nuclear membrane, connects to the actin network directly as well as through FHOD1, a formin whose major activity is bundling actin. Much of the molecular details of this process remain poorly understood. Here, we report the crystal structure of Nes2G bound to FHOD1. We show that the G-binding domain of FHOD1 is rather a spectrin repeat binding enhancer for the neighboring FH3 domain, possibly establishing a common binding mode among this subclass of formins. The FHOD1-Nes2G complex structure suggests that spectrin repeat binding by FHOD1 is likely not regulated by the DAD helix of FHOD1. Finally, we establish that Nes1G also has one FHOD1 binding spectrin repeat, indicating that these abundant, giant Nesprins have overlapping functions in actin-bundle recruitment for nuclear movement.
Gradient analysis of landscape variation in Norway
Authors: Simensen Trond , Halvorsen Rune , Erikstad Lars 
Published: June 2020

SUMMARYA multitude of landscape characterisation and mapping methods exist, but few methods take into account that landscapes properties vary in a gradual, continuous manner along multiple directions of variation. In this study, we used gradient analytic methods, rooted in ecological continuum theory, to analyse landscape variation throughout Norway. The aim is to explain differences in landscape properties in the simplest possible way, by identifying ‘complex landscape gradients’ (CLGs), i.e. composite gradients of co-occurring landscape elements and properties.We collected data by stratified sampling of 100 test areas (20×20 km), in which we delineated a total of 3966 observation units (landscape polygons 4–30 km²) based on geomorphological criteria. For each observation unit, 85 landscape variables were recorded. We identified patterns of variation in landscape element composition by parallel use of two multivariate statistical methods, detrended correspondence analysis (DCA) and global nonmetric multidimensional scaling (GNMDS).The analyses revealed that the most important properties explaining differences in total landscape elements composition was location of the landscape relative to the coastline and coarse-scale landform variation. Most landscape elements had distinct optima within specific segments along broad-scale complex-gradients in landscape properties. A tentative landscape-type hierarchy was built by an iterative procedure by which the amount of compositional turnover in landscape-element composition between adjacent types was standardised. Six ‘major landscape types’ were identified based on geomorphological criteria. Within each major type, we identified a unique set of 2–5 important CLGs, representing geo-ecological, bio-ecological, and land use-related landscape variation. Minor landscape types were obtained by combining segments along two or more CLGs.The study shows that geological diversity, biological diversity and human land-use are tightly intertwined at the landscape level of ecological complexity, and that predominantly abiotic processes control and constrain both biotic processes and human land use.
Plant Genotype Influences Physicochemical Properties of Substrate as well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar
Authors: Rheault Karelle , Lachance Denis , Morency Marie-Josée , Thiffault Évelyne , Guittonny Marie , Isabel Nathalie , Martineau Christine , Séguin Armand 
Published: June 2020

AbstractAbandoned unrestored mines are an important environmental issue since they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic conditions and unfavorable biotic conditions. However, some pioneer tree species having high level of genetic diversity, such as balsam poplar (Populus balsamifera), are able to naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, two contrasting mine waste storage facilities (waste rock versus tailings) from the Abitibi region of Quebec (Canada), on which poplars have grown naturally, were selected. First, we assessedin situthe impact of vegetation presence on each type of mine wastes. The presence of balsam poplars improved soil health locally by improving physicochemical properties (e.g. higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment, ten genotypes ofP. balsamiferacollected on both mine sites and from a natural forest nearby were grown in these mine wastes. Tree growth was monitored during two growing seasons, after which the effect of genotype-by-environment interactions was assessed by measuring the physicochemical properties of the substrates and the changes in microbial communities, using a metabarcoding approach. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect of tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.
A simple canonical circuitry for non-stationary normalization by inhibition to explain and predict change detection in monkey area MT
Authors: Ernst Udo , Chen Xiao , Bohnenkamp Lisa , Galashan Fingal Orlando , Wegener Detlef 
Published: June 2020

AbstractSudden changes in visual scenes often indicate important events for behavior. For their quick and reliable detection, the brain must be capable to process these changes as independent as possible from its current activation state. In motion-selective area MT, neurons respond to instantaneous speed changes with pronounced transients, often far exceeding the expected response as derived from their speed tuning profile. We here show that this complex, non-linear behavior emerges from the combined temporal dynamics of excitation and divisive inhibition, and provide a comprehensive formal analysis. A central prediction derived from this investigation is that attention increases the steepness of the transient response irrespective of the activation state prior to a stimulus change, and irrespective of the sign of the change. Extracellular recordings of attention-dependent representation of both speed increments and decrements confirmed this prediction and suggest that improved change detection derives from basic computations in a canonical cortical circuitry.