Miracle-dz/UniFAR-FTUs huggingface dataset:
Transfer of Spatial Contact Information Among Limbs and the Notion of Peripersonal Space in Insects

Internal representation of far-range space in insects is well established, as it is necessary for navigation behavior. Although it is likely that insects also have an internal representation of near-range space, the behavioral evidence for the latter is much less evident. Here, we estimate the size and shape of the spatial equivalent of a near-range representation that is constituted by somatosensory sampling events. To do so, we use a large set of experimental whole-body motion capture data on unrestrained walking, climbing and searching behavior in stick insects of the species Carausius morosus to delineate ‘action volumes’ and ‘contact volumes’ for both antennae and all six legs. As these volumes are derived from recorded sampling events, they comprise a volume equivalent to a representation of coinciding somatosensory and motor activity. Accordingly, we define this volume as the peripersonal space of an insect. It is of immediate behavioral relevance, because it comprises all potential external object locations within the action range of the body. In a next step, we introduce the notion of an affordance space as that part of peripersonal space within which contact-induced spatial estimates lie within the action ranges of more than one limb. Because the action volumes of limbs overlap in this affordance space, spatial information from one limb can be used to control the movement of another limb. Thus, it gives rise to an affordance as known for contact-induced reaching movements and spatial coordination of footfall patterns in stick insects. Finally, we probe the computational properties of the experimentally derived affordance space for pairs of neighboring legs. This is done by use of artificial neural networks that map the posture of one leg into a target posture of another leg with identical foot position.
Effect of Genotype and Maternal Affective Disorder on Intronic Methylation of FK506 Binding Protein 5 in Cord Blood DNA

A single nucleotide polymorphism (SNP: rs1360780) in FKBP5 (FK506 Binding Protein 5) has been shown to interact with exposure to childhood adversity to promote loss of methylation and increase in gene expression in adults. We asked whether rs1360780 can influence FKBP5 intronic methylation in the context of exposure to maternal affective disorders in utero. Sixty cord blood DNA samples from the Boston Birth Cohort were genotyped at rs1360780 and studied for methylation changes as they relate to genotype and exposure to affective disorders during pregnancy. Linear regression was employed to contrast the risk (TT) genotype to the heterozygous (CT) and homozygous (CC) genotypes with adjustment for potential confounders. The recessive genotype (TT) was associated with increased methylation at multiple CpGs in the FKBP5 intron 5 region (p < 0.01). These findings were enhanced among cases exposed to maternal affective disorders (p = 0.02). A human cell line treated with cortisol showed that changes in intron 5 CpG methylation and FKBP5 expression were inversely associated. These findings suggest that rs1360780 can influence FKBP5 intronic methylation by acting in cis as a methylation quantitative locus and highlight the impact of genotypic risk on methylation in utero. Additionally, prenatal stress exposure compounded with the risk genotype may lead to a compensatory increase in methylation.
Microexpressions Differentiate Truths From Lies About Future Malicious Intent

The few previous studies testing whether or not microexpressions are indicators of deception have produced equivocal findings, which may have resulted from restrictive operationalizations of microexpression duration. In this study, facial expressions of emotion produced by community participants in an initial screening interview in a mock crime experiment were coded for occurrence and duration. Various expression durations were tested concerning whether they differentiated between truthtellers and liars concerning their intent to commit a malicious act in the future. We operationalized microexpressions as expressions occurring less than the duration of spontaneously occurring, non-concealed, non-repressed facial expressions of emotion based on empirically documented findings, that is ≤0.50 s, and then more systematically ≤0.40, ≤0.30, and ≤0.20 s. We also compared expressions occurring between 0.50 and 6.00 s and all expressions ≤6.00 s. Microexpressions of negative emotions occurring ≤0.40 and ≤0.50 s differentiated truthtellers and liars. Expressions of negative emotions occurring ≤6.00 s also differentiated truthtellers from liars but this finding did not survive when expressions ≤1.00 s were filtered from the data. These findings provided the first systematic evidence for the existence of microexpressions at various durations and their possible ability to differentiate truthtellers from liars about their intent to commit an act of malfeasance in the future.
We12BFit!—Improving Physical Fitness in 7–12-Year-Old Children With Developmental Coordination Disorder: Protocol of a Multicenter Single-Arm Mixed-Method Study

Background: Children with developmental coordination disorder (DCD) are less physically fit than their typically developing peers. No substantiated treatments are available for children with DCD to address this issue. Aims: This study aims to describe 1. the design and rationale of We12BFit! -PF, a training to increase cardiorespiratory fitness, muscle strength and anaerobic power in 7-12-year-old children with DCD and 2. the methods to examine its preliminary effectiveness and feasibility. Methods: We12BFit! -PF was developed using the steps of defining a treatment theory as proposed by Whyte et al. This includes the definition of targets, mechanisms of action, and essential ingredients. We12BFit! -PF will be evaluated in children diagnosed with DCD according to the criteria of the Diagnostic and Statistical Manual of mental disorders (DSM-V) aged 7–12, recruited from rehabilitation centers and physical therapy clinics. Indication for participation will be a need related to enhancing PF, for example tiring quickly, being quickly out of breath or being unable to keep up with peers during PA. During the treatment the participants will be engaged in a group training (2 × 60 min/week, 10 weeks) targeting cardiorespiratory fitness using high intensity interval training, muscle strength using exercises without weights and anaerobic power using plyometrics. Training intensity during high intensity interval training will be monitored with heart rate monitors, if necessary the intensity will be adjusted. Using a single-arm mixed-method design, the preliminary effectiveness will be determined using the 20 meter Shuttle Run Test, hand held dynamometry (JAMAR and MicroFET) and the Muscle Power Sprint Test, which will be assessed in week 0, 11, and 23. Feasibility will be assessed by interviewing parents and children and by organizing a focus group session with the trainers at the end of We12BFit! -PF. Based on a 5% improvement in VO2peak the minimum sample size is 19 children. Ethics and dissemination: The University of Groningen, University Medical Center Groningen medical ethics committee approved the study (METC 2015.216). Final results will be disseminated via scientific publications, presentations and congress proceedings. Funding organizations will receive a final study report. Trial Registration: This study was registered with Netherlands Trial Registry (NTR6334, www.trialregister.nl).
Exploration of the Rate of Forgetting as a Domain-Specific Individual Differences Measure

Learners differ in their learning aptitude. Modern computerized fact-learning systems take these individual differences into account by adapting repetition schedules to the learner’s characteristics. Adaptation is based on monitoring responses during learning and using these responses to inform the model’s decisions about when to introduce and repeat material by updating the model’s internal parameters. Typically, adaptive systems start a learning session with a set of default parameters, with these parameters being updated and adapted to the learner’s characteristics when responses are collected. Here we explore whether domain-general individual differences such as working-memory capacity or measures of general intelligence, which can be assessed prior to learning sessions, can inform the choice of initial model parameters. Such an approach is viable if the domain-general individual differences are related to the model parameters estimated during learning. In the current study, we asked participants to learn factual information, and assessed whether their learning performance, operationalized as (1) a model-parameter that captures the rate of forgetting, and (2) the results on an immediate and delayed post-test, was related to two common measures of individual differences: working memory capacity and general cognitive ability. We failed to find evidence in favor for such relations, suggesting that, at least in this relatively small and homogeneous sample, executive functioning and attentional control did not play important roles in predicting delayed recall. The model parameters estimated during learning, on the other hand, are highly correlated with delayed recall of the studied material.
Predicting Gleason Score of Prostate Cancer Patients Using Radiomic Analysis

Purpose: Use of quantitative imaging features and encoding the intra-tumoral heterogeneity from multi-parametric magnetic resonance imaging (mpMRI) for the prediction of Gleason score is gaining attention as a non-invasive biomarker for prostate cancer (PCa). This study tested the hypothesis that radiomic features, extracted from mpMRI, could predict the Gleason score pattern of patients with PCa. Methods: This analysis included T2-weighted (T2-WI) and apparent diffusion coefficient (ADC, computed from diffusion-weighted imaging) scans of 99 PCa patients from The Cancer Imaging Archive (TCIA). A total of 41 radiomic features were calculated from a local tumor sub-volume (i.e., regions of interest) that is determined by a centroid coordinate of PCa volume, grouped based on their Gleason score patterns. Kruskal-Wallis and Spearman's rank correlation tests were used to identify features related to Gleason score groups. Random forest (RF) classifier model was used to predict Gleason score groups and identify the most important signature among the 41 radiomic features. Results: Gleason score groups could be discriminated based on zone size percentage, large zone size emphasis and zone size non-uniformity values (p < 0.05). These features also showed a significant correlation between radiomic features and Gleason score groups with a correlation value of −0.35, 0.32, 0.42 for the large zone size emphasis, zone size non-uniformity and zone size percentage, respectively (corrected p < 0.05). RF classifier model achieved an average of the area under the curves of the receiver operating characteristic (ROC) of 83.40, 72.71, and 77.35% to predict Gleason score groups (G1) = 6; 6 < (G2) < (3 + 4) and (G3) ≥ 4 + 3, respectively. Conclusion: Our results suggest that the radiomic features can be used as a non-invasive biomarker to predict the Gleason score of the PCa patients.
A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus

Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.
Harvest of the Oleaginous Microalgae Scenedesmus obtusiusculus by Flocculation From Culture Based on Natural Water Sources

Harvest and dewatering poses a significant economical burden for industrial algae biomass production. To mitigate these effects, energy efficient techniques for these process steps have to be developed. Flocculation of the microalgae Scenedesmus obtusiusculus in salt based medium was induced by pH-shift and alternatively by addition of two biological flocculants, chitosan, and the commercial tannin CFL-PT. This is the first time that CFL-PT is used as an algae flocculant particularly focusing on harvesting of halophilic strains. The method was characterized and subsequently optimized. In comparison to biological flocculants, induction by pH shift is far cheaper, but due to buffering effects of the brackish cultivation medium infeasible amounts of base are required to raise the pH-value. tannin appears to be superior compared to chitosan not only in the absence of algae organic matter (AOM), but tannin-based harvest is also more robust regarding culture pH in presence of AOM. A higher flocculant-demand for modified tannin compared to chitosan is offset by the lower price. Given the employed strain and cultivation conditions, cultivation time had no pronounced effect on flocculation efficiencies (FE) while algae zeta-potential and bacterial communities also remained stable.
Production of the Neurotoxin Salsolinol by a Gut-Associated Bacterium and Its Modulation by Alcohol

Utilizing a simulated gastrointestinal medium which approximates physiological conditions within the mammalian GI tract, experiments aimed at isolating and identifying unique microbial metabolites were conducted. These efforts led to the finding that Escherichia coli, a common member of the gut microbiota, is capable of producing significant quantities of salsolinol. Salsolinol is a neuroactive compound which has been investigated as a potential contributor to the development of neurodegenerative diseases such as Parkinson’s disease (PD). However the origin of salsolinol within the body has remained highly contested. We herein report the first demonstration that salsolinol can be made in vitro in response to microbial activity. We detail the isolation and identification of salsolinol produced by E. coli, which is capable of producing salsolinol in the presence of dopamine with production enhanced in the presence of alcohol. That this discovery was found in a medium that approximates gut conditions suggests that microbial salsolinol production could exist in the gut. This discovery lays the ground work for follow up in vivo investigations to explore whether salsolinol production is a mechanism by which the microbiota may influence the host. As salsolinol has been implicated in the pathogenesis of PD, this work may be relevant, for example, to investigators who have suggested that the development of PD may have a gut origin. This report suggests, but does not establish, an alternative microbiota-based mechanism to explain how the gut may play a critical role in the development of PD as well other conditions involving altered neuronal function due to salsolinol-induced neurotoxicity.
A Calcium Mediated Mechanism Coordinating Vascular Smooth Muscle Cell Adhesion During KCl Activation

Efficient mechanotransduction in vascular smooth muscle cells (VSMCs) is intimately coupled to physical coupling of the cell to extracellular matrix proteins (ECM) by integrins. Integrin adhesion receptors are essential for normal vascular function and defective integrin signaling is associated with cardiovascular disease. However, less is known about the mechanism of integrin activation in VSMCs in relation to vasoregulation. Our laboratory previously demonstrated that the vasoconstrictor Angiotensin II increases VSMC stiffness in concert with enhanced adhesion to fibronectin (FN), indicating an important role for adhesion in contraction. However, the mechanism of this coordination remains to be clarified. In this study, intracellular Ca2+ ([Ca2+]i) was hypothesized to link integrin activation through inside-out signaling pathways leading to enhanced adhesion in response to AII. By using atomic force microscopy (AFM) with an anti-α5 antibody coated AFM probe, we confirmed that cell stiffness was increased by AII, while we observed no change in adhesion to an α5 integrin antibody. This indicated that increases in cell adhesion to FN induced by AII were occurring through an integrin activation process, as increased membrane integrin expression/receptor density would have been accompanied by increased adhesion to the anti-α5 antibody. Further studies were performed using either KCl or BAPTA-AM to modulate the level of [Ca2+]i. After KCl, VSMCs showed a rapid transient increase in cell stiffness as well as cell adhesion to FN, and these two events were synchronized with superimposed transient increases in the level of [Ca2+]i, which was measured using the Ca2+ indicator, fluo-4. These relationships were unaffected in VSMCs pretreated with the myosin light chain kinase inhibitor, ML-7. In contrast, unstimulated VSMCs incubated with an intracellular calcium chelator, BAPTA-AM, showed reduced cell adhesion to FN as well the expected decrease in [Ca2+]i. These data suggest that in VSMCs, integrin activation is linked to signaling events tied to levels of [Ca2+]i while being less dependent on events at the level of contractile protein activation. These findings provide additional evidence to support a role for adhesion in VSMC contraction and suggest that following cell contractile activation, that adhesion may be regulated in tandem with the contractile event.
High-Throughput Screening for Bacterial Glycosyltransferase Inhibitors

The enteropathogenic and enterohemorrhagic Escherichia coli NleB proteins as well as the Salmonella enterica SseK proteins are type III secretion system effectors that function as glycosyltransferase enzymes to post-translationally modify host substrates on arginine residues. This modification is unusual because it occurs on the guanidinium groups of arginines, which are poor nucleophiles, and is distinct from the activity of the mammalian O-linked N-acetylglucosaminyltransferase. We conducted high-throughput screening assays to identify small molecules that inhibit NleB/SseK activity. Two compounds, 100066N and 102644N, both significantly inhibited NleB1, SseK1, and SseK2 activities. Addition of these compounds to cultured mammalian cells was sufficient to inhibit NleB1 glycosylation of the tumor necrosis factor receptor type 1-associated DEATH domain protein. These compounds were also capable of inhibiting Salmonella enterica strain ATCC 14028 replication in mouse macrophage-like cells. Neither inhibitor was significantly toxic to mammalian cells, nor showed in vitro cross-reactivity with the mammalian O-linked N-acetylglucosaminyltransferase. These compounds or derivatives generated from medicinal chemistry refinements may have utility as a potential alternative therapeutic strategy to antibiotics or as reagents to further the study of bacterial glycosyltransferases.
Trajectory-Based Skill Learning Using Generalized Cylinders

In this article, we introduce Trajectory Learning using Generalized Cylinders (TLGC), a novel trajectory-based skill learning approach from human demonstrations. To model a demonstrated skill, TLGC uses a Generalized Cylinder—a geometric representation composed of an arbitrary space curve called the spine and a surface with smoothly varying cross-sections. Our approach is the first application of Generalized Cylinders to manipulation, and its geometric representation offers several key features: it identifies and extracts the implicit characteristics and boundaries of the skill by encoding the demonstration space, it supports for generation of multiple skill reproductions maintaining those characteristics, the constructed model can generalize the skill to unforeseen situations through trajectory editing techniques, our approach also allows for obstacle avoidance and interactive human refinement of the resulting model through kinesthetic correction. We validate our approach through a set of real-world experiments with both a Jaco 6-DOF and a Sawyer 7-DOF robotic arm.
From Evolutionary Aspects of Zoophytophagy to Biological Control

Zoophytophagy (true omnivory) is a ubiquitous behaviour. It allows plant-feeding predators to maximize their development by finding essential nutrients, and to survive when animal resources are scarce. In agroecosystems, some zoophytophagous predators are highly efficient biological control agents. However, when feeding on plants, they can generate crop damage that reduce grower’s interest in these predators. Artificial selection on behavioural traits of candidate zoophytophagous predators could improve the ecosystem services they provide. Thus, a zoophytophagous species considered as noxious may become an adequate biocontrol agent, following a selection process. Numerous theoretical and applied aspects should be considered during the selection process for the breeding of desired individuals. This review focuses on the potential of the evolutionary approach to optimize the biological control services provided by plant-feeding predators – or zoophytophagous predators – and discuss some ecological and biological control consequences as well as the limitations of the approach.
Automatic Caption Generation for Medical Images

With the increasing availability of medical images coming from different modalities (X-Ray, CT, PET, MRI, ultrasound, etc.), and the huge advances in the development of incredibly fast, accurate and enhanced computing power with the current graphics processing units. The task of automatic caption generation from medical images became a new way to improve healthcare and the key method for getting better results at lower costs. In this paper, we give a comprehensive overview of the task of image captioning in the medical domain, covering: existing models, the benchmark medical image-caption datasets, and evaluation metrics that have been used to measure the quality of the generated captions.