Miracle-dz/UniFAR-FTUs huggingface dataset:
Imperfect synchrony in animal displays: why does it occur and what is the true role of leadership?

Synchrony can be defined as the precise coordination between independent individuals, and this behaviour is more enigmatic when it is imperfect. The traditional theoretical explanation for imperfect synchronous courtship is that it arises as a by-product of the competition between males to broadcast leading signals to attract female attention. This competition is considered an evolutionary stable strategy maintained through sexual selection. However, previous studies have revealed that leading signals are not honest indicators of male quality. We studied imperfect courtship synchrony in fiddler crabs to mainly test whether (i) signal leadership and rate are defined by male quality and (ii) signal leadership generates synchrony. Fiddler crab males wave their enlarged claws during courtship, and females prefer leading males—displaying ahead of their neighbour(s). We filmed groups of waving males in the field to detect how often individuals were leaders and if they engaged in synchrony. Overall, we found that courtship effort is not directly related to male size, a general proxy for quality. Contrary to the long-standing assumption, we also revealed that leadership is not directly related to group synchrony, but faster wave rate correlates with both leadership and synchrony. This article is part of the theme issue ‘Synchrony and rhythm interaction: from the brain to behavioural ecology’.
Parallel Minimum Cuts in Near-linear Work and Low Depth

We present the first near-linear work and poly-logarithmic depth algorithm for computing a minimum cut in an undirected graph. Previous parallel algorithms with poly-logarithmic depth required at least quadratic work in the number of vertices. In a graph with n vertices and m edges, our randomized algorithm computes the minimum cut with high probability in O(m log4 n) work and O(log3 n) depth. This result is obtained by parallelizing a data structure that aggregates weights along paths in a tree, in addition exploiting the connection between minimum cuts and approximate maximum packings of spanning trees. In addition, our algorithm improves upon bounds on the number of cache misses incurred to compute a minimum cut.
Virtual motionless photoacoustic microscopy for large-scale and high-resolution imaging based on K-Wave

Photoacoustic microscopy has high spatial resolution and unique high optical contrast, so it has attracted the attention of a large number of medical imaging researchers, and has made great progress in the past decade. At present, the most widely used photoacoustic microscopy uses point-by-point scanning imaging method. Although this system has high imaging accuracy, it has low imaging efficiency. Therefore, this paper proposes virtual photoacoustic microscopy based on single-pixel imaging using K-Wave to realize a wide-field imaging without motion. This method is based on the principles of photoacoustic imaging and Fourier single pixel imaging. According to the principle of Fourier single-pixel imaging, any image is a weighted superposition of a sequence of cosine stripes of different spatial frequencies, and the weight coefficients of these stripes can be obtained to reconstruct the image. Therefore, a series of spatial frequency stripes are used to illuminate the sample, and the photoacoustic signal obtained by a single ultrasonic transducer is the Fourier spectral coefficient of the sample corresponding to the spatial frequency, all the Fourier spectral coefficients are obtained, and finally the inverse Fourier transform to obtain high-resolution images. In order to verify the feasibility of this method, this paper uses the K-Wave simulation tool to build a single-pixel photoacoustic microscopic imaging simulation model, and uses this model to image blood vessels. The results show that the lateral resolution of large-scale imaging without point scanning can reach 17 microns, demonstrating that this method can achieve a wide-field imaging with high-resolution.
Exploration of PYP Practitioner Preschool Teachers’ Science Teaching Practices: The Effect of Pedagogical Beliefs

Abstract Introduction: The aim of this study was to investigate PYP practitioner preschool teachers’ science teaching practices in terms of their pedagogical beliefs. Methods: In this mixed method study, the quantitative data were first collected and analyzed, and then the qualitative data were collected and detailed. Accordingly, Pedagogical Belief Systems Scale (PBSS) was first implemented to 39 preschool teachers. Then, teachers were selected based on their scores from PBSS and included in the qualitative data processes. Data sources in this study are PBSS, Science Teaching Construction Task (STCT) and Classroom Observations. On the other hand, data analysis consisted of three steps. In the first step, quantitative data analysis was performed. Qualitative data analysis was performed in the second and third steps. In the first step of the qualitative data analysis, inductive content analysis was performed based on the constant comparative method on the responses of the teachers in the lower and upper groups to eight questions in STCT. Then, teachers’ science teaching practices in their own classrooms were analyzed through analytic rubric and enriched with field notes Results: The results revealed that PYP practitioner preschool teachers had child-centered pedagogical beliefs. They also performed science teaching activities based on question-answer and deliberative interactions representing child-centered orientation, independently of their pedagogical beliefs. Discussion: According to the results in this study, the quality of PYP practitioner preschool teachers’ theoretical orientations and practical applications for science teaching was independent of their pedagogical beliefs. However, preschool teachers with high pedagogical beliefs put more emphasis on inquiry in their theoretical conceptualizations about science teaching. Limitations: The most important limitation in this study is the population. The first limitation occurs because PYP practitioner preschool education institutions were very limited in Istanbul; PYP practitioner preschool teachers were difficult to reach. The second limitation is that this research relied on only teachers’ self-reported views and practices. Conclusion: Findings in this study is important in terms of describing the quality of preschool science teaching in the context of PYP and how teachers’ pedagogical beliefs serve it. Hence, based on the results obtained in the study, it was revealed that PYP practitioner preschool teachers were generally based on child-centered teaching and tended to use inquiry-based pedagogical strategies.
Blockade of retinal or cortical activity does not prevent the development of callosal patches normally associated with ocular dominance columns in primary visual cortex

Abstract Callosal patches in primary visual cortex of Long Evans rats, normally associated with ocular dominance columns, emerge by postnatal day 10 (P10), but they do not form in rats monocularly enucleated a few days before P10. We investigated whether we could replicate the results of monocular enucleation by using tetrodotoxin (TTX) to block neural activity in one eye, or in primary visual cortex. Animals received daily intravitreal (P6–P9) or intracortical (P7–P9) injections of TTX, and our physiological evaluation of the efficacy of these injections indicated that the blockade induced by a single injection lasted at least 24 h. Four weeks later, the patterns of callosal connections in one hemisphere were revealed after multiple injections of horseradish peroxidase in the other hemisphere. We found that in rats receiving either intravitreal or cortical injections of TTX, the patterns of callosal patches analyzed in tangential sections from the flattened cortex were not significantly different from the pattern in normal rats. Our findings, therefore, suggest that the effects of monocular enucleation on the distribution of callosal connections are not due to the resulting imbalance of afferent ganglion cell activity, and that factors other than neural activity are likely involved.
Investigating the effect of idiosyncratic deals in Asian countries: A cross cultural analysis in Singapore, Thailand and Japan

The purpose of this study is to empirically compare and contrast the relationship between several dimensions of idiosyncratic deals (i-deals) and employee affective commitment among Asian countries. Data were collected from 909 employees in Singapore, Thailand and Japan. Results of the study show that there is a positive relationship between several i-deals and affective commitment. However, the effect size of i-deals on each dimension varies across the three countries. In particular, the effect size of task and work responsibilities i-deals on the affective commitment of Japanese employees is stronger than that of Thai employees. Simultaneously, the effect size of the i-deals on affective commitment of Singaporean employees is weaker than that of Thai employees. On the contrary, for the dimensions of schedule and location flexibility and financial incentives, the effect size of i-deals on affective commitment is weaker for Singaporean than for Japanese and Thai, and the effect sizes for Japanese and Thai are the same. The results of this study question the traditionally and universally naive conclusion that i-deals are effective. Although i-deals result in, to some extent, some positive consequences, the results of the study suggest that not in all cases do they increase employee affective commitment. Empirical evidence of the study also demonstrate that the effects i-deals had on employee affective commitment are inconsistent even across cultures with close cultural origin.
Experiencing organ failure in virtual reality: Effects of self- versus other-embodied perspective taking on empathy and prosocial outcomes

This study capitalizes on the unique capability of virtual reality (VR) to examine the efficacy of self- versus other-embodied perspective taking in promoting kidney donation in Singapore. The study used a 2 (self- vs other-embodied) × 2 (mirror vs photo presentation) between-subjects VR experiment (N = 128), wherein participants played the role of a patient needing a kidney donation, either as themselves or as a typical organ-failure patient. Our findings showed that self-embodied perspective taking triggered self-oriented emotions (i.e. personal distress) and subsequently egoistic motivations that resulted in alternative prosocial behaviors (e.g. monetary donation, volunteering) than kidney donation. We found that embodying the other, rather than the self, had the practical benefit of inducing other-oriented emotions (i.e. empathy) and hence altruistic motivations that promoted kidney donation. This study clarified the conditions under which embodied perspective taking promoted different prosocial outcomes, and the specific mechanisms through which it achieved those outcomes.
Before trilobite legs: Pygmaclypeatus daziensis reconsidered and the ancestral appendicular organization of Cambrian artiopods

The Cambrian Stage 3 Chengjiang biota in South China is one of the most influential Konservat-Lagerstätten worldwide thanks to the fossilization of diverse non-biomineralizing organisms through pyritization. Despite their contributions to understanding the evolution of early animals, several Chengjiang species remain poorly known due to their scarcity and/or incomplete preservation. Here, we use micro-computed tomography to reveal in detail the ventral appendage organization of the enigmatic non-trilobite artiopod Pygmaclypeatus daziensis – one of the rarest euarthropods in Chengjiang – and explore its functional ecology and broader evolutionary significance. Pygmaclypeatus daziensis possesses a set of uniramous antennae and 14 pairs of post-antennal biramous appendages, the latter of which show an unexpectedly high degree of heteronomy based on the localized differentiation of the protopodite, endopodite and exopodite along the antero-posterior body axis. The small body size (less than 2 cm), presence of delicate spinose endites, and well-developed exopodites with multiple paddle-shaped lamellae on the appendages of P. daziensis indicate a nekto-benthic mode of life, and a scavenging/detritus feeding strategy. Pygmaclypeatus daziensis shows that appendage heteronomy is phylogenetically widespread within Artiopoda – the megadiverse clade that includes trilobites and their relatives with non-biomineralizing exoskeletons – and suggests that a single exopodite lobe with paddle-like lamellae is ancestral for this clade. Cover image: Morphological reconstruction of the non-trilobite artiopod Pygmaclypeatus daziensis from the early Cambrian (Stage 3) Chengjiang biota in south China. Artwork by Holly Sullivan (https://www.sulscientific.com/).
Fatty acid-binding proteins and fatty acid synthase influence glial reactivity and promote the formation of Müller glia-derived progenitor cells in the avian retina

The capacity for retinal regeneration varies greatly across vertebrates species. A recent comparative epigenetic and transcriptomic investigation of Müller glial (MG) in the retinas of fish, birds and mice revealed that Fatty Acid Binding Proteins (FABPs) are among the most highly up-regulated genes in activated chick MG (Hoang et al., 2020). Herein we provide an in-depth follow-up investigation to describe patterns of expression and how FABPs and fatty acid synthase (FASN) influence glial cells in the chick retina. During development, FABP7 is highly expressed by embryonic retinal progenitor cells (eRPCs) and maturing MG, whereas FABP5 is gradually up-regulated in maturing MG and remains elevated in mature glial cells. PMP2 (FABP8) is expressed by oligodendrocytes and FABP5 is expressed by non-astrocytic inner retinal glial cells, and both of these FABPs are significantly up-regulated in activated MG in damaged or growth factor-treated retinas. In addition to suppressing the formation of MGPCs, we find that FABP-inhibition suppressed the accumulation of proliferating microglia, although the microglia appeared highly reactive. scRNA-seq analyses of cells treated with FABP-inhibitor revealed distinct changes in patterns of expression suggesting that FABPs are involved in the transitions of MG from a resting state to a reactive state and conversion from reactive MG to MGPCs. Inhibition of FABPs in undamaged retinas had a significant impact upon the transcriptomic profiles of MG, with up-regulation of genes associated with gliogenesis, decreases in genes associated with neurogenesis, and suppression of the ability of MG to become MGPCs. scRNA-seq analyses of microglia indicated that FABP inhibition enhances gene modules related to reactivity, proliferation and cytokine signaling. We find that the proliferation of retinal progenitors in the circumferential marginal zone (CMZ) is unaffected by FABP-inhibitor. Upstream of FABP activity, we inhibited FASN in damaged retinas, which reduced numbers of dying cells, increased the proliferation of microglia, and potently suppressed the formation MGPCs in damaged retinas. We conclude that the activity of FASN and FABPs are required early during the formation of proliferating MGPCs. Fatty acid metabolism and cell signaling involving fatty acids are important in regulating glial homeostasis in the retina, and the dedifferentiation and proliferation of microglia and MGPCs.
A human stem cell resource to decipher the biochemical and cellular basis of neurodevelopmental defects in Lowe syndrome

Human brain development is a complex process where multiple cellular and developmental events are co-ordinated to generate normal structure and function. Alteration in any of these events can impact brain development, manifesting clinically as neurodevelopmental disorders. Human genetic disorders of lipid metabolism often present with features of altered brain function. Lowe syndrome (LS), is a X-linked recessive disease with features of altered brain function. LS results from mutations in OCRL1 that encodes a phosphoinositide 5-phosphatase enzyme. However, the cellular mechanisms by which loss of OCRL1 leads to brain defects remain unknown. Human brain development involves several cellular and developmental features not conserved in other species and understanding such mechanisms remains a challenge. Rodent models of LS have been generated, but failed to recapitulate features of the human disease. Here we describe the generation of human stem cell lines from LS patients. Further, we present biochemical characterization of lipid metabolism in patient cell lines and demonstrate their use as a “disease-in-a-dish” model for understanding the mechanism by which loss of OCRL1 leads to altered cellular and physiological brain development.
The transcriptional response to oxidative stress is independent of stress-granule formation

Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded-protein, and viral stress responses, whether and how SGs contribute to stress-induced transcription has not been rigorously examined. To address this issue, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Sodium-arsenite stress for 3 hours predominantly resulted in the induction or upregulation of stress-responsive mRNAs whose levels peaked during cell recovery after stress cessation. The stress-transcriptome is enriched in mRNAs coding for protein chaperones, including HSP70 and low molecular-weight heat shock proteins, glutathione transferases, and several non-coding RNAs. Oxidative stress also induced prominent cytoplasmic stress granules that disassembled 3-hours after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/ Rasputin protein inhibited stress-granule assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus, SG assembly and stress-induced effects on gene expression appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.
Emerging harmful algal blooms caused by distinct seasonal assemblages of the toxic diatom Pseudo-nitzschia in Narragansett Bay, RI, USA

The diatom Pseudo-nitzschia produces the neurotoxin domoic acid (DA) that bioaccumulates in shellfish, causing illness in humans and marine animals upon ingestion. In 2017, high levels of DA in shellfish meat closed shellfish harvest in Narragansett Bay (NBay), Rhode Island for the first time in history, although abundant Pseudo-nitzschia have been observed for over 50 years. What caused these events is unknown: whether an environmental factor altered endemic Pseudo-nitzschia physiology or new DA-producing strain(s) were introduced. To investigate, we conducted weekly sampling from 2017-2019 to compare with 2016 precautionary closure and 2017 closure samples. Particulate DA was quantified by highly sensitive LC-MS/MS and correlated with environmental metadata. Pseudo-nitzschia were identified using high-throughput rDNA sequencing, yielding a detailed understanding of distinct seasonal multi-species assemblages. Low DA was detected throughout 2017-2019, except in recurring peaks in the fall and early summer. Fall DA peaks contained toxigenic species (P. pungens var. pungens, P. multiseries, P. calliantha, and P. subpacifica) as well as a novel P. americana taxon. Fewer species were present during summer DA peaks including toxigenic P. multiseries, P. plurisecta, and P. delicatissima. Most 2017 closure samples contained P. australis. Our data showed P. australis as infrequent but particularly concerning. Recurring Pseudo-nitzschia assemblages were driven by seasonal temperature changes and DA correlated with low dissolved inorganic nitrogen. Thus, the NBay closures were likely caused by resident assemblages dependent on nutrient status as well as the episodic introductions of species that may be a result of oceanographic and climactic shifts.
Deep Bayesian networks for uncertainty estimation and adversarial resistance of white matter hyperintensity segmentation

White matter hyperintensities (WMH) are frequently observed on structural neuroimaging of elderly populations and are associated with cognitive decline and increased risk of dementia. Many existing WMH segmentation algorithms produce suboptimal results in populations with vascular lesions or brain atrophy, or require parameter tuning and are computationally expensive. Additionally, most algorithms do not generate a confidence estimate of segmentation quality, limiting their interpretation. MRI-based segmentation methods are often sensitive to acquisition protocols, scanners, noise-level, and image contrast, failing to generalize to other populations and out-of-distribution datasets. Given these concerns, we propose a novel Bayesian 3D Convolutional Neural Network (CNN) with a U-Net architecture that automatically segments WMH, provides uncertainty estimates of the segmentation output for quality control and is robust to changes in acquisition protocols. We also provide a second model to differentiate deep and periventricular WMH. 432 subjects were recruited to train the CNNs from four multi-site imaging studies. A separate test set of 158 subjects was used for evaluation, including an unseen multi-site study. We compared our model to two established state-of-the-art techniques (BIANCA and DeepMedic), highlighting its accuracy and efficiency. Our Bayesian 3D U-Net achieved the highest Dice similarity coefficient of 0.89 ± 0.08 and the lowest modified Hausdorff distance of 2.98 ± 4.40 mm. We further validated our models highlighting their robustness on ‘clinical adversarial cases’ simulating data with low signal-to-noise ratio, low resolution, and different contrast (stemming from MRI sequences with different parameters). Our pipeline and models are available at: https://hypermapp3r.readthedocs. io