Miracle-dz/UniFAR-FTUs huggingface dataset:
Latent Factors and Dynamics in Motor Cortex and Their Application to Brain–Machine Interfaces

In the 1960s, Evarts first recorded the activity of single neurons in motor cortex of behaving monkeys (Evarts, 1968). In the 50 years since, great effort has been devoted to understanding how single neuron activity relates to movement. Yet these single neurons exist within a vast network, the nature of which has been largely inaccessible. With advances in recording technologies, algorithms, and computational power, the ability to study these networks is increasing exponentially. Recent experimental results suggest that the dynamical properties of these networks are critical to movement planning and execution. Here we discuss this dynamical systems perspective and how it is reshaping our understanding of the motor cortices. Following an overview of key studies in motor cortex, we discuss techniques to uncover the “latent factors” underlying observed neural population activity. Finally, we discuss efforts to use these factors to improve the performance of brain–machine interfaces, promising to make these findings broadly relevant to neuroengineering as well as systems neuroscience.
Mosquitofish display differential left- and right-eye use during mirror image scrutiny and predator inspection responses

Previous work has shown that predator inspection in mosquitofish, Gambusia holbrooki, is more likely to occur when a mirror image of the test fish is visible on its left rather than on its right side. We investigated whether this is due to a preference for using the right eye when fixating the predator or the left eye when fixating the mirror image, or a combination of both eye preferences. We found that mosquitofish preferentially used the left eye during sustained scrutiny of their mirror image when tested in the absence of any predator. On the other hand, when tested in a swimway for predator inspection responses in the absence of any mirror image (or other social stimuli), mosquitofish explored the environment with the left eye when at a distance and the right eye when near the predator.
Consistent individual differences in early exploratory behaviour of male great tits

Individual differences in early exploratory behaviour were investigated in hand-reared juvenile male great tits, Parus major, during the first 18 weeks of their life. The juveniles differed consistently in their reaction to a novel object in a familiar environment, either when tested with different objects or when tested again after 9 weeks. Birds that approached a novel object more quickly were also quicker to visit all artificial trees present in a novel environment than birds that approached a novel object more slowly. These behavioural differences extended to the strength of foraging habits, built up during a training period in which food was always offered at the same place. After a change in the location of food, the quicker birds would keep going to the place where the food used to be. The slower birds tended to change their behaviour and stop going to the former place. The results show that juvenile male great tits differ consistently in various aspects of their exploratory behaviour at least during the first 18 weeks of life. The variation in behaviour was not likely to arise from differences in general activity or physical condition, but seems to refer to differences in the way in which information concerning the environment is collected and dealt with.
Ectoparasite affects choice and use of roost sites in the great tit, Parus major


Abstract Abstract. Many diurnal bird species roost at night in holes. As a regular visitor of a hole they are therefore a welcome host for several species of ectoparasites. The interactions of ectoparasites with the behaviour, life-history traits and population demography of their hosts are largely unknown. In the present study the effects of the haematophagous hen flea, Ceratophyllus gallinae , on the great tit's choice of winter roost site were investigated experimentally. Three experiments tested (1) whether great tits prefer a clean nestbox to one containing an old, but parasite-free nest, (2) whether they prefer a parasite-free nestbox to one infested with the haematophagous hen flea, and (3) whether they prefer not to use a nestbox when there is only an infested box available in their territory. In the first experiment there was no discrimination and both kinds of boxes were used equally often. In the second experiment the great tits clearly preferred to roost in the box without ectoparasites. In the third experiment a significantly higher proportion of the infested nestboxes were not used for roosting compared with the parasite-free boxes. Recently the validity of the conclusions drawn from nestbox studies where the naturally occurring detrimental ectoparasites are eliminated by the routine removal of old nests between breeding seasons has been questioned. This study shows that ectoparasites affect host behaviour and therefore lends support to that criticism.
Memory for inter-reinforcement interval variability and patch departure decisions in the starling,
 Sturnus vulgaris
 


An experiment with starlings was conducted to investigate the effect of variability in inter-reinforcement intervals on foraging decisions. The experimental design simulated an environment in which food was distributed in patches. Patches contained zero to four food items which could be collected by pecking at a key. All patches ended with sudden depletion. The time elapsed since the last reinforcement was the only way to detect the depletion of the patch. Once a patch was depleted, a new patch could be reached by completion of a travel requirement of 20 flights between two perches. Key pecks within a patch and the time of the last response in a patch (giving-in time) were recorded. The level of variability in the inter-reinforcement intervals was varied between different conditions. An increase in inter-reinforcement interval variability resulted in a flattening of response rate functions and giving-in time distributions, and in more asymmetry of the response functions, but not of the giving-in time distributions. Two theoretical models of decision making are presented, which differ in the assumptions about memory constraints. In one case, all inter-reinforcement intervals are remembered but in the other, only the intervals with extreme values are remembered. Both models accommodate response rates as a function of trial time, but only the second is compatible with the observed departure decision. Our results are compatible with net rate maximization.
The use of chemical cues in predator recognition by western toad tadpoles

Abstract Western toad, Bufo boreas , tadpoles were collected from a lake in the Cascade Mountains of central Oregon, where they occur in sympatry with backswimmers, Notonecta spp. , giant waterbugs, Lethocerus americanus , common garter snakes, Thamnophis sirtalis , roughskin newts, Taricha granulosa and rainbow trout, Oncorhynchus mykiss . Backswimmers, waterbugs and snakes prey on toad tadpoles. Newts and trout are potential tadpole predators, but they find toad tadpoles unpalatable. In laboratory tests, groups of tadpoles responded with anti-predator behaviour when exposed to live backswimmers, waterbugs and snakes, but not when exposed to either newts or trout. In subsequent tests, when only chemical cues from the stimulus animals were presented, the toad tadpoles again responded to backswimmers, waterbugs and snakes, but not to either newts or trout. When tests were conducted using only visual cues, tadpoles did not respond with anti-predator behaviour to any of the heterospecifics with the possible exception of garter snakes. These results show that western toad tadpoles can distinguish between predatory and non-predatory heterospecifics with which they co-occur, and that predator recognition by toad tadpoles is primarily based on chemical cues.
Effects of an endocrine disrupter on courtship and aggressive behaviour of male three-spined stickleback,Gasterosteus aculeatus


Oestrogenic endocrine-disrupting chemicals released into the environment have the potential to affect animal behaviour. This study examined the relationship between plasma levels of gonadal steroids and behaviour and the effects of exogenous hormonal perturbation on the behaviour of nesting male three-spined stickleback. Plasma gonadal steroid concentrations were related to levels of nesting and aggressive behaviours: levels of oestradiol were negatively related to courtship behaviours while levels of 11-ketotestosterone were negatively related to nesting behaviours. The behaviour of male three-spined stickleback exposed to environmentally relevant concentrations of an endocrine disrupter differed from the behaviour of control males. Control males increased their aggressive response to a live male conspecific over time, while males exposed to ethinyl oestradiol decreased their aggressive response. This study offers further evidence that low levels of endocrine-disrupting chemicals in the environment may exert subtle yet important effects on animal behaviour.
Semi-Quantification of Total Campylobacter and Salmonella During Egg Incubations Using a Combination of 16S rDNA and Specific Pathogen Primers for qPCR

Rapid molecular techniques that evaluate eggs for the presence of foodborne pathogens is an essential component to poultry food safety monitoring. Interestingly, it is not just table eggs that contribute to outbreaks of foodborne disease. Broiler layer production actively contributes to sustaining of foodborne pathogens within a flock. The surface contamination of production eggs with invasive pathogens such as Salmonella enterica, Campylobacter jejuni, and Listeria monocytogenes during embryogenesis results in gastrointestinal tract (GIT) colonization. Pathogens that secure a niche within the GIT during embryonic development are nearly impossible to eradicate from the food chain. Therefore, current monitoring paradigms are not comprehensive because they fail to capture the presence of invasive pathogens within the embryonic GIT rapidly. By developing tools to recognize the pathogens’ presence in the GIT during embryogenesis, producers are then able to spot evaluate broiler eggs for their potential risk as carriers of foodborne pathogens. In this study a novel qPCR assay was developed to semi-quantify pathogen load relative to total bacterial burden. Eggs sampled from three independent production broiler flocks of different ages were assayed for S. enterica (invA), C. jejuni (HipO), and L. monocytogenes (HlyA) against total microbial load (16s). The eggs were sampled at 1-day post-set within each flock, 2 weeks post-set, after vaccination (at 2.5 weeks) and 1-day post-hatch. The eggs were washed, and the yolk and embryonic chick GIT were collected. The DNA was extracted and subjected to a qPCR assay. The results confirm a novel technique for pathogen monitoring relative to total bacterial load and a unique method for monitoring the dynamics of foodborne pathogen invasion throughout broiler egg production.
Sexual incompatibility and geographical variation in mate recognition systems: tests in the salamander
 Desmognathus ochrophaeus
 


Abstract Behavioural differences that prevent between-population mating are evolutionarily important if they decrease gene flow and thus facilitate further differentiation. Sexual incompatibility and divergence of mate recognition systems were tested between three geographically isolated populations of the North American mountain dusky salamander, Desmognathus ochrophaeus (Amphibia: Plethodontidae). Significant sexual incompatibility was detected in all pair-wise comparisons between these populations; thus mating was assortative with respect to population. Ethological analyses of the contents of within-population courtship encounters revealed significant quantitative differences between populations in five of 10 behavioural scores. These results support the hypothesis that individuals from isolated populations of D. ochrophaeus do not recognize one another as potential mating partners. Quantitative differences in mate recognition systems may be responsible for this lack of compatibility, and may have evolved incidentally as responses to sexual selection acting differently in each population.
The functional role of serial dependence

The world tends to be stable from moment to moment, leading to strong serial correlations in natural scenes. As similar stimuli usually require similar behavioural responses, it is highly likely that the brain has developed strategies to leverage these regularities. A good deal of recent psychophysical evidence is beginning to show that the brain is sensitive to serial correlations, causing strong drifts in observer responses towards previously seen stimuli. However, it is still not clear that this tendency leads to a functional advantage. Here, we test a formal model of optimal serial dependence and show that as predicted, serial dependence in an orientation reproduction task is dependent on current stimulus reliability, with less precise stimuli, such as low spatial frequency oblique Gabors, exhibiting the strongest effects. We also show that serial dependence depends on the similarity between two successive stimuli, again consistent with the behaviour of an ideal observer aiming at minimizing reproduction errors. Lastly, we show that serial dependence leads to faster response times, indicating that the benefits of serial integration go beyond reproduction error. Overall our data show that serial dependence has a beneficial role at various levels of perception, consistent with the idea that the brain exploits the temporal redundancy of the visual scene as an optimization strategy.
Microenvironments Designed to Support Growth and Function of Neuronal Cells

Strategies for neural tissue repair heavily depend on our ability to temporally reconstruct the natural cellular microenvironment of neural cells. Biomaterials play a fundamental role in this context, as they provide the mechanical support for cells to attach and migrate to the injury site, as well as fundamental signals for differentiation. This review describes how different cellular processes (attachment, proliferation, and (directional) migration and differentiation) have been supported by different material parameters, in vitro and in vivo. Although incipient guidelines for biomaterial design become visible, literature in the field remains rather phenomenological. As in other fields of tissue regeneration, progress will depend on more systematic studies on cell-materials response, better understanding on how cells behave and understand signals in their natural milieu from neurobiology studies, and the translation of this knowledge into engineered microenvironments for clinical use.
Vascular dementia

Vascular dementia (VaD) is more common than appreciated and increases in incidence with advancing age. VaD is heterogeneous and consists of several syndromes: strategic single infarcts in locations such as medial thalamus, hippocampus, caudate nucleus, and parietal lobe; multiple large infarcts; multiple lacunar infarcts; predominantly subcortical white matter infarcts; and various infarct types combined with Alzheimer's disease. The diagnosis of VaD is based on several features, the most important of which are the occurrence of a stroke temporally related to dementia onset and the presence of bilateral cortical or subcortical infarcts on imaging. Treatment of VaD with cholinesterase inhibitors provides symptomatic benefits. Significant challenges to research in VaD are defining the importance of microvascular disease and learning how to recognize it clinically.
Helical Piezoelectric Energy Harvester and Its Application to Energy Harvesting Garments

In this paper, we propose a helical piezoelectric energy harvester, examine its application to clothes in the form of an energy harvesting garment, and analyze its design and characteristics. The helical harvester is composed of an elastic core and a polymer piezoelectric strap twining the core. The fabricated harvester is highly elastic and can be stretched up to 158% of its initial length. Following the experiments using three different designs, the maximum output power is measured as 1.42 mW at a 3 MΩ load resistance and 1 Hz motional frequency. The proposed helical harvesters are applied at four positions of stretchable tight-fitting sportswear, namely shoulder, arm joint, knee, and hip. The maximum output voltage is measured as more than 20 V from the harvester at the knee position during intended body motions. In addition, electric power is also generated from this energy harvesting garment during daily human motions, which is about 3.9 V at the elbow, 3.1 V at the knee, and 4.4 V at the knee during push-up, walking, and squatting motions, respectively.
Production of Bioactive Peptides by Lactobacillus Species: From Gene to Application

To compensate for their amino acid auxotrophy, lactobacilli have developed the ability to hydrolyze proteins present in their environment. This proteolytic activity not only generates the free amino acids needed by the bacteria, but also a large variety of peptides, some of which are endowed with biological activities. These so-called “bioactive peptides” (BAPs) are interesting from a nutrition and healthcare perspective. The use of lactic acid bacteria (LAB) such as lactobacilli is an effective strategy for production and valorization of new BAPs. The proteolytic activity of lactobacilli is exerted in a strain- and species-dependent manner: each species exhibits different proteinase content, leading to a large variety of proteolytic activities. This underlines the high potential of Lactobacillus strains to produce novel hydrolysates and BAPs of major interest. This review aims at discussing the potential of different Lactobacillus species to release BAPs from fermentation media and processes. Strategies used for peptide production are presented. Additionally, we propose a methodology to select the most promising Lactobacillus strains as sources of BAPs. This methodology combines conventional approaches and in silico analyses.
Vascular Calcification Markers and Hemodialysis Vascular Access Complications

Background: Arteriovenous (AV) access dysfunction is a common complication in hemodialysis patients. Markers of vascular calcification are associated with cardiovascular outcomes and mortality in this population, but their association with vascular access outcomes is unknown. In this study, we aimed to evaluate the association between selected vascular calcification makers and vascular access complications in a cohort of hemodialysis patients. Method: Fetuin-A, osteopontin (OPN), osteoprotegerin (OPG), and bone morphogenetic protein-7 (BMP-7) were measured in blood samples from 219 dialysis patients in the Choice for Healthy Outcomes in Caring for end-stage renal disease study; these patients were using a permanent vascular access. Participants were followed for up to 1 year or until the occurrence of a vascular access intervention or replacement. Associations with AV fistula (AVF) and AV graft (AVG) intervention-free survival were assessed in models adjusted for demographic characteristics, comorbidities, and inflammation. Results: A total of 24 out 103 participants with an AVF and 43 out of 116 participants with an AVG had an intervention during follow-up. Lower fetuin-A, higher OPN, and higher BMP-7 were associated with a higher risk of AVF intervention (adjusted hazard ratios [aHR] for highest versus lowest tertile = 0.30 [95% CI 0.10–0.94]) for fetuin-A, 3.84 (95% CI 1.16–12.74) for OPN, and 3.49 (95% CI 1.16–10.52) for BMP-7. OPG was not significantly associated with the risk of AVF intervention. The associations of OPN and BMP-7 with AVF intervention appeared stronger among participants without diabetes (aHR 8.06; 95% CI 1.11–58.57 for OPN and aHR 2.55; 95% CI 1.08–6.08 for BMP-7, respectively) than among their counterparts with diabetes (p interaction = 0.06). None of the markers studied were significantly associated with AVG interventions. Conclusion: Lower fetuin-A and higher OPN and BMP-7 are associated with complications in AVF but not in AVG, suggesting a role for calcification in the pathogenesis AVF failure.
MOHONE: Modeling Higher Order Network Effects in KnowledgeGraphs via Network Infused Embeddings

Many knowledge graph embedding methods operate on triples and are therefore implicitly limited by a very local view of the entire knowledge graph. We present a new framework MOHONE to effectively model higher order network effects in knowledge-graphs, thus enabling one to capture varying degrees of network connectivity (from the local to the global). Our framework is generic, explicitly models the network scale, and captures two different aspects of similarity in networks: (a) shared local neighborhood and (b) structural role-based similarity. First, we introduce methods that learn network representations of entities in the knowledge graph capturing these varied aspects of similarity. We then propose a fast, efficient method to incorporate the information captured by these network representations into existing knowledge graph embeddings. We show that our method consistently and significantly improves the performance on link prediction of several different knowledge-graph embedding methods including TRANSE, TRANSD, DISTMULT, and COMPLEX(by at least 4 points or 17% in some cases).
Drop-catch behaviour is play in herring gulls, Larus argentatus


Behaviours with no apparent adaptive function are sometimes described as play without rigorous testing of alternative explanations. One such behaviour is the repeated dropping and catching of objects by birds. We observed drop-catch behaviour by herring gulls over 3 years at a site where the birds frequently dropped clams to break them on hard surfaces below. We tested unique suites of predictions from three hypotheses, that the drop-catch behaviour is play, that it functions to expose potential kleptoparasites, or that it serves to reposition clams before foraging drops. We tested data from 72 drop-catch series and 504 typical foraging drop series to determine which suite of predictions most closely matched our observations. As predicted if the behaviour were play, drop-catches were performed more by younger birds, not necessarily over a hard substrate, and sometimes with nonfood objects. Clams that were subjected to drop-catches were generally not repositioned or eaten. These results suggest a motivation for drop-catching that is distinct from foraging. Finally, drop-catches were more frequent when it was warm and when there were high winds, also consistent with the play hypothesis. Drop-catch behaviour closely matched the predictions of the play hypothesis and we were able to reject the two alternative explanations.
Micro-Fabricated Resonator Based on Inscribing a Meandered-Line Coupling Capacitor in an Air-Bridged Circular Spiral Inductor

This letter presents a high-performance micro-fabricated resonator based on inscribing a meandered-line square coupling capacitor in an air-bridged circular spiral inductor on the GaAs-integrated passive device (IPD) technology. The main advantages of the proposed method, which inserts a highly effective coupling capacitor between the two halves of a circular spiral inductor, are the miniaturized size, enhanced coupling coefficient, and improved selectivity. Moreover, using an air-bridge structure utilizes the enhanced mutual inductance in which it maximizes the self-inductance by a stacking inductor layout to obtain a high coupling effect. The simulated and measured S-parameters of a prototype resonator with an effective overall circuit size of 1000 µm × 800 µm are in good agreement. The measured insertion and return losses of 0.41 and 24.21 dB, respectively, at a measured central frequency of 1.627 GHz, as well as an upper band transmission zero with a suppression level of 38.7 dB, indicate the excellent selectivity of the developed resonator.