Miracle-dz/UniFAR-FTUs huggingface dataset:
Frontoparietal network dynamics impairments in juvenile myoclonic epilepsy revealed by MEG energy landscape

Juvenile myoclonic epilepsy (JME) is a form of idiopathic generalized epilepsy affecting brain activity. It is unclear to what extent JME leads to abnormal network dynamics across functional networks. Here, we proposed a method to characterise network dynamics in MEG resting-state data, combining a pairwise maximum entropy model (pMEM) and the associated energy landscape analysis. Fifty-two JME patients and healthy controls underwent a resting-state MEG recording session. We fitted the pMEM to the oscillatory power envelopes in theta (4-7 Hz), alpha (8-13 Hz), beta (15-25 Hz) and gamma (30-60 Hz) bands in three source-localised resting-state networks: the frontoparietal network (FPN), the default mode network (DMN), and the sensorimotor network (SMN). The pMEM provided an accurate fit to the MEG oscillatory activity in both patient and control groups, and allowed estimation of the occurrence probability of each network state, with its regional activity and pairwise regional co-activation constrained by empirical data. We used energy values derived from the pMEM to depict an energy landscape of each network, with a higher energy state corresponding to a lower occurrence probability. When comparing the energy landscapes between groups, JME patients showed fewer local energy minima than controls and had elevated energy values for the FPN within the theta, beta and gamma-bands. Furthermore, numerical simulation of the fitted pMEM showed that the proportion of time the FPN was occupied within the basins of characteristic energy minima was shortened in JME patients. These network alterations were confirmed by a significant leave-one-out classification of individual participants based on a support vector machine employing the energy values of pMEM as features. Our findings suggested that JME patients had altered multi-stability in selective functional networks and frequency bands in the frontoparietal cortices. Highlights An energy landscape analysis characterises the dynamics of MEG oscillatory activity Patients with JME exhibit fewer local minima of the energy in their energy landscapes JME affects the network dynamics in the frontoparietal network. Energy landscape measures allow good single-patient classification.
Simulation of shallow-water hydrodynamics using a high-resolution finite-volume technique on hierarchically-structured Cartesian grids

Progress on the development of new modelling methodologies to simulate environmental flows in two-dimensions is presented. First, a generalised Cartesian meshing methodology is developed whereby grids may be generated for two-dimensional multiply-connected regions of arbitrary complexity. The meshing technique is based on a hierarchical quadtree data structure and is also interactive, allowing the user considerable flexibility in the grid cell distribution through mesh refinement techniques. Of note, is that the grid generation procedure utilises a cut-cell approach which allows the domain to be cut out of the resulting quadtree Cartesian mesh, thus also providing a boundary-fitted capability. Secondly, a flow solver has been developed for the shallow water equations which is based on a fully conservative high-resolution finite-volume method similar to those used for shock-wave modelling in aerospace applications. The fluxes of mass and momentum across cell interfaces are calculated by solving a sequence of Riemann problems. Locally, this amounts to solving the governing partial differential equations exactly thus leading to highly accurate global solutions which are second-order in space and time and are valid for sub, transitional and supercritical flow regimes. The methods promise to be very versatile.
Hippocampal-amygdala interactions mediate uncertainty-dependent resistance to extinction following fear conditioning

The partial reinforcement extinction effect (PREE) is a paradoxical learning phenomenon in which omission of reinforcement during acquisition results in more persistent conditioned responding in extinction. Here, we report a significant PREE with an inverted-U, entropy-like distribution against reinforcement probability following tone foot shock fear conditioning in rats, which was associated with increased neural activity in hippocampus and amygdala as indexed by p-ERK and c-fos immunolabelling. In vivo electrophysiological recordings of local field potentials (LFPs) showed that 50% reinforcement was associated with increases in the frequency and power of tone-evoked theta oscillations in both the subiculum region of hippocampus and in basolateral amygdala (BLA) during both acquisition (Day 1) and extinction (Day 2) sessions. Tone-evoked LFPs in 50% reinforced animals also showed increases in coherence and bidirectional Granger Causality between hippocampus and amygdala. The results support a Bayesian interpretation of the PREE, in which the phenomenon is driven by increases in the entropy or uncertainty of stimulus contingencies, and indicate a crucial role for hippocampus in mediating this uncertainty-dependent effect.
Molecular and physiological analysis of drought stress responses in Zea mays treated with plant growth promoting rhizobacteria

Our research intended to appraise the performance of two different Pseudomonas strains on Zea mays L. (cv. B73) under drought stress and non-stress conditions. Plants were inoculated with P. putida KT2440 (Pp) and P. fluorescens (Pf1) followed by sampling at 0, 3rd, and 6th day after imposition of drought stress (DAS). Both strains demonstrated significant improvement in root length, protein content, chlorophyll content, and root and shoot fresh masses as compared to un-inoculated drought stressed plants. Real-time quantitative PCR analysis revealed that drought stress responsive genes, i.e., the cold-related dehydrin 410 gene, WRKY18, and major facilitator superfamily were significantly down-regulated by Pf1 and Pp inoculation under drought stress condition on 6 DAS. Similarly, the down-regulated transcript abundance of lipoxygenase genes in inoculated plants on 6 DAS showed the role of Pf1 and Pp in scavenging reactive oxygen species under drought stress conditions. Among the selected jasmonic acid pathway responsive genes, maize protease inhibitor and 12-oxo-phytodienoatereductase 7 (OPR7) also revealed a potential role of these rhizobacteria under drought stress conditions. Seed inoculation of both strains significantly down-regulated the expression of OPR7 gene under stress conditions. Our results advocate the complex growth promotion effects of both selected rhizobacterial strains and amelioration of the drought by modulating the expression of drought stress responsive genes.
Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Abstract Larvae of the cosmopolitan family Limacodidae, commonly known as “slug” caterpillars, are well known because of the widespread occurrence of spines with urticating properties, a morpho‐chemical adaptive trait that has been demonstrated to protect the larvae from natural enemies. However, while most species are armed with rows of spines (“nettle” caterpillars), slug caterpillars are morphologically diverse with some species lacking spines and thus are nonstinging. It has been demonstrated that the evolution of spines in slug caterpillars may have a single origin and that this trait is possibly derived from nonstinging slug caterpillars, but these conclusions were based on limited sampling of mainly New World taxa; thus, the evolution of spines and other traits within the family remains unresolved. Here, we analyze morphological variation in slug caterpillars within an evolutionary framework to determine character evolution of spines with samples from Asia, Australia, North America, and South America. The phylogeny of the Limacodidae was reconstructed based on a multigene dataset comprising five molecular markers (5.6 Kbp: COI, 28S, 18S, EF‐1α, and wingless) representing 45 species from 40 genera and eight outgroups. Based on this phylogeny, we infer that limacodids evolved from a common ancestor in which the larval type possessed spines, and then slug caterpillars without spines evolved independently multiple times in different continents. While larvae with spines are well adapted to avoiding generalist predators, our results imply that larvae without spines may be suited to different ecological niches. Systematic relationships of our dataset indicate six major lineages, several of which have not previously been identified.
The Dietary Inclusion of Chickpea Seeds (Cicer Arietinum L.) Influences the Thermal Properties of Muscle Proteins, But Not the Texture of Drumstick Muscle in Broiler Chickens

I Department of Physics, Faculty of Production Engineering, University of Life Sciences in Lublin, Lublin, Poland. II Department of Animal Physiology, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland. III Institute of Animal Nutrition and Bromatology, Faculty of Biology, Animal Science and Bioeconomy, Faculty of University of Life Sciences in Lublin, Lublin, Poland. IV Department of Comparative Anatomy and Anthropology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland. V Department of Agricultural, Horticultural and Forest Machinery, Faculty of Production Engineering, University of Life Sciences in Lublin, Lublin, Poland. VI Department of Milk Technology and Hydrocolloids, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland.
Enhanced Population Control in Synthetic Bacterial Consortium by Interconnected Carbon Cross-Feeding

Engineered microbial consortia can provide several advantages over monocultures in terms of utilization of mixed substrates, resistance to perturbations, and division of labor in complex tasks. However, maintaining stability, reproducibility, and control over population levels in variable conditions can be challenging in multi-species cultures. In our study, we modeled and constructed a synthetic symbiotic consortium with a genetically encoded carbon cross-feeding system. The system is based on strains of Escherichia coli and Acinetobacter baylyi ADP1, both engineered to be incapable of growing on glucose on their own. In a culture supplemented with glucose as the sole carbon source, growth of the two strains is afforded by the exchange of gluconate and acetate, resulting in inherent control over carbon availability and population balance. We investigated the system robustness in terms of stability and population control under different inoculum ratios, substrate concentrations, and cultivation scales, both experimentally and by modeling. To illustrate how the system might facilitate division of genetic circuits among synthetic microbial consortia, a green fluorescent protein sensitive to pH and a slowly-maturing red fluorescent protein were expressed in the consortium as measures of a circuit’s susceptibility to external and internal variability, respectively. The symbiotic consortium maintained stable and linear growth and circuit performance regardless of the initial substrate concentration or inoculum ratios. The developed cross-feeding system provides simple and reliable means for population control without expression of non-native elements or external inducer addition, being potentially exploitable in consortia applications involving precisely defined cell tasks or division of labor.
Erliquiose no Brasil

Erliquiose e uma doenca causada por rickettsias pertencentes ao genero Ehrlichia. No Brasil, estudos sorologicos e moleculares tem avaliado a ocorrencia de especies de Ehrlichia em caes, gatos, animais selvagens e seres humanos. Ehrlichia canis e a principal especie em caes no Brasil, embora a infeccao por E. ewingii tenha, recentemente, despertado suspeita em cinco caes. O DNA de E. chaffeensis foi detectado e caracterizado em cervo-do-pantanal, enquanto que E. muris e E. ruminantium ainda nao foram identificadas no Brasil. A erliquiose monocitica canina causada pela E. canis parece ser altamente endemica em muitas regioes do Brasil, embora dados de prevalencia nao estejam disponiveis em muitas delas. O DNA de E. canis tambem foi detectado e caracterizado em tres gatos domesticos, enquanto anticorpos contra E. canis foram detectados em felideos neotropicais de vida livre. Evidencias sorologicas sugerem a ocorrencia de erliquiose humana no Brasil, entretanto, o agente etiologico ainda nao foi identificado. A melhoria do diagnostico molecular promovera a identificacao e caracterizacao de especies associadas a erliquiose humana no Brasil.
Mesenchymal stem cell therapy assisted by nanotechnology: a possible combinational treatment for brain tumor and central nerve regeneration

Abstract Mesenchymal stem cells (MSCs) intrinsically possess unique features that not only help in their migration towards the tumor-rich environment but they also secrete versatile types of secretomes to induce nerve regeneration and analgesic effects at inflammatory sites. As a matter of course, engineering MSCs to enhance their intrinsic abilities is growing in interest in the oncology and regenerative field. However, the concern of possible tumorigenesis of genetically modified MSCs prompted the development of non-viral transfected MSCs armed with nanotechnology for more effective cancer and regenerative treatment. Despite the fact that a large number of successful studies have expanded our current knowledge in tumor-specific targeting, targeting damaged brain site remains enigmatic due to the presence of a blood–brain barrier (BBB). A BBB is a barrier that separates blood from brain, but MSCs with intrinsic features of transmigration across the BBB can efficiently deliver desired drugs to target sites. Importantly, MSCs, when mediated by nanoparticles, can further enhance tumor tropism and can regenerate the damaged neurons in the central nervous system through the promotion of axon growth. This review highlights the homing and nerve regenerative abilities of MSCs in order to provide a better understanding of potential cell therapeutic applications of non-genetically engineered MSCs with the aid of nanotechnology.
New approaches for the design and the fabrication of pixelated filters

Multispectral or hyperspectral images allow acquiring new information that could not be acquired using colored images and, for example, identifying chemical species on an observed scene using specific highly selective thin film filters. Those images are commonly used in numerous fields, e.g. in agriculture or homeland security and are of prime interest for imaging systems for onboard scientific applications (e.g. for planetology).
Evolution of barrier loci at an intermediate stage of speciation with gene flow

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of differentiation; however, the underlying mechanisms are not well understood. We used an integrated approach to investigate evolutionary processes governing genetic differentiation between the hybridizing campions (Silene dioica (L.) Clairv. and S. latifolia Poiret). Demographic modeling indicated that the two species diverged with continuous gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that 5% of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection and differentiation was significantly elevated around previously identified QTLs associated with assortative mating. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that the interplay of background selection and conserved genomic features is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection drove the evolution of barrier loci played and the genomic landscape of differentiation between the two species, consistent with predictions for speciation in the face of gene flow.
Flow cytometry in assessment of sperm integrity and functionality – a review

Spermatozoa must possess many attributes to fertilize an egg but few laboratory methods can assess all of these attributes simultaneously and objectively. Most laboratory methods used to assess the quality of semen in veterinary andrology can be inaccurate and time-consuming. Laboratory techniques which evaluate only one sperm attribute, often provide results that have a weak correlation with fertility. Therefore, semen used for artificial insemination should not be assessed based on the results of one method only but rather on the comprehensive results of several laboratory tests. Flow cytometry is a modern method of analysing diJ169fferent types of cells, including sperm cells. It is based on the scattering of light and fluorescence, the outcome of which yields results that are recorded and evaluated by computer technology which makes an objective assessment. Flow cytometry in combination with fluorescence microscopy and fluorescent probes provides a comprehensive, accurate, objective, and rapid analysis of the ejaculate. In a short time frame it allows us to test thousands of sperm for their structure and properties, even with a minimal amount of semen. This method enables the evaluation of several indicators simultaneously in a population of sperm as a whole or for each sperm individually. It informs us about the selected indicators of sperm quality in the sample by examining the membrane integrity, DNA, mitochondria, acrosome, oxidative stress, and other properties. Flow cytometry has become an important method of evaluating the functional and morphological properties of sperm and is used for research in veterinary science as well as for a routine assessment of the semen quality.
Postfire deciduous canopies drive patterns in snowshoe hare herbivory of regenerating black spruce

The future of boreal forests in Alaska, United States, will likely consist of more deciduous-dominant stands because larger and more severe fires facilitate the establishment of deciduous species such as trembling aspen (Populus tremuloides Michx.) and Alaska birch (Betula neoalaskana Sarg.). Whether stands transition to a deciduous-dominant system or mixed-wood forest or return to being dominated by black spruce (Picea mariana (Mill.) Britton, Sterns & Poggenb. ) depends on the capacity of regenerating black spruce to grow and produce seed before the next fire. We hypothesized that winter herbivory by snowshoe hares (Lepus americanus Erxleben, 1777) can suppress black spruce under deciduous canopies. We addressed this question by measuring changes in spruce height and herbivory across 54 plots in Interior Alaska that burned 8–88 years ago and related these data to plot-level data collected by the Bonanza Creek Long-Term Ecological Research program. Spruce were more likely browsed at deciduous-dominant sites with dense canopies, and this browsing likely reduced their height growth. Although we found more subtle effects of browsing on height at the individual level, browsing was an important variable in a confirmatory path analysis at the plot level. These observations affirm our broader hypothesis of the selectivity of hare browsing, in that snowshoe hares prefer to browse spruce that are taller and faster growing, effectively “leveling” regenerating seedlings and saplings so that browsed and unbrowsed individuals within a site are the same height.
Urban Area Division and Function Discovery Based on Trajectory Data

Urban functional area identification can not only help city managers to carry out urban planning effectively, but also have important significance in policy making and resource allocation. In this paper, we propose a method of urban functional area identification based on data mining of human large-scale spatiotemporal trajectory and the semantic analysis of POIs, and construct the analytic model UADAFIM (urban area Division and Function identification model). Adaptive density clustering through trajectory data, by clustering each class cluster and producing the central point of each cluster, we use the central point as the discrete points to produce the Voronoi Diagram, and through our algorithm we divide the city into different areas, effectively avoiding the restriction of dividing city by the urban road network. In addition, we make the regional functional theme documents by the POIs data, the LDA model is used to effectively excavate the main functions of each area. Our study takes the Beijing city as the analysis, the research object, as well as the verification object.
Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking

Synthetic transcriptional networks built from CRISPR-based repressors (CRISPRi) rely on shared use of a core dCas9 protein. In E. coli, CRISPRi cannot support more than about a dozen simultaneous gRNAs before the fold repression of any individual gRNA drops below 10x. We show with a simple model based on previous characterization of competition in CRISPRi that activation by CRISPR-based activators (CRISPRa) is much less sensitive to dCas9 bottle-necking than CRISPRi. We predict that E. coli should be able to support dozens to hundreds of CRISPRa gRNAs at >10-fold activation.
Polymorphisms in DNA repair genes modify lymphoma risk

Introduction: The high risk of lymphoma among individuals affected by hereditary syndromes associated with aberrant repair of DNA double-strand breaks points towards an important role of this pathway in lymphomagenesis. Single nucleotide polymorphisms (SNPs) that affect DNA repair mechanisms can increase[for full text, please go to the a.m. URL]