Miracle-dz/UniFAR-FTUs huggingface dataset:
Wave-riding and wave-passing by ducklings in formation swimming

Abstract It has been commonly observed on open waters that ducklings/goslings follow their mothers in a highly organized formation. The questions arise: (1) why are they swimming in formation? (2) what is the best swimming formation? (3) how much energy can be preserved by each individual in formation swimming? To address these questions, we established a simplified mathematical and numerical model and calculated the wave drag on a group of waterfowl in a swimming formation. We observed two new and interesting findings: wave-riding and wave-passing. By riding the waves generated by a mother duck, a trailing duckling can obtain a significant wave-drag reduction. When a duckling swims at the ‘sweet point’ behind its mother, a destructive wave interference phenomenon occurs and the wave drag of the duckling turns positive, pushing the duckling forward. More interestingly, this wave-riding benefit could be sustained by the rest of the ducklings in a single-file line formation. Starting from the third one in a queue, the wave drag of individuals gradually tended towards zero, and a delicate dynamic equilibrium was achieved. Each individual under that equilibrium acted as a wave passer, passing the waves’ energy to its trailing one without any energy losses. Wave-riding and wave-passing are probably the principal reasons for the evolution of swimming formation by waterfowl. This study is the first to reveal the reasons why the formation movement of waterfowl can preserve individuals’ energy expenditure. Our calculations provide new insights into the mechanisms of formation swimming.
Got a Spark with Brook? Engaging Consumers in a Sexual Health Campaign through the Use of Creative (Metaphorical) Double Entendres

ABSTRACT This paper describes a study conducted in collaboration with a marketing agency and a nonprofit organization (NPO) providing regional sexual health services, which included advice on, and testing for, sexually transmitted infections (STIs). The study investigated the relative effectiveness of different formulations of double entendres on appeal, humor, the likelihood of social media engagement, and intention to seek more information about STIs. Advertisements containing double entendres were significantly more appealing and humorous if: (1) the grammatical formulation did not cue the intended meaning; (2) the double entendre involved a creative metaphorical expression; and (3) the double entendre referred to the middle part of the sexual scenario, referring to action rather than intent or result. Participants’ ratings varied very little according to their age, gender, and education. However, a qualitative investigation of the free-text responses revealed that there was some variation in the types of interpretations that were offered by participants depending on their age, gender, and education. The marketing agency incorporated our findings into their live campaign, which resulted in a notable increase in: (a) website traffic and social media engagement; (b) STI home-testing kits ordered; and (c) STI kits returned for testing, compared with previous campaigns.
Employers as educators: the role of work placement supervisors in facilitating the transfer of skills and knowledge

ABSTRACT Work-integrated learning (WIL) placements, undertaken as part of a higher education qualification, are recognised as a key opportunity for developing talent that is future-capable and can meet contemporary labour market demands. A workplace supervisor that can facilitate this learning is critical to the experience. The purpose of this study was to explore workplace supervisors’ views on their contributions as educators, and their role as facilitators for the transfer of skills and knowledge from university to the workplace. Semi-structured interviews were undertaken with 24 WIL host supervisors of students from Business, Sociology and Sports and Recreation in three universities across Australia and New Zealand. The findings confirm WIL supervisors do consider themselves as educators, moving beyond training students on how to complete tasks, to helping them develop the graduate capabilities needed for contemporary work. Further, they consider some skills to be transferable, rather than context-specific and particular to certain industries or workplace cultures. Yet, views on who should be responsible for transfer were mixed with disparities between the higher education curriculum and workplace tasks considered problematic. Key strategies and behaviours for facilitating transfer are identified to help workplace supervisors and educators create appropriate WIL experiences that integrate university and workplace learning.
Changes in reflexivity during existential supervision

ABSTRACT The goal of the current study was to uncover and describe the phenomenon of changes in reflexivity during existential supervision. We analyzed interviews with four female existential psychotherapy trainees utilizing Interpretative Phenomenological Analysis. The data yielded three themes: (1) The supervisory relationship: a basis for changes in reflexivity, (2) The influence of the nature of the supervisor’s presence and interventions used for expression of reflexivity, and (3) Changes in reflexivity: a subjective experience of internal transformations. Findings suggest supervision educators should be cognizant of the nature of the supervisory relationship and the supervisor’s presence and specific interventions used in supervision to enhance supervisee reflexivity. These findings add to an in-depth understanding of the supervision process and inform psychotherapy and supervision training programs aimed at improving trainee reflexivity.
The autonomous robotic environmental sensor (ARES)

Measurement of thermal comfort in the indoor environment enables making adjustments to building design and operations to improve building performance. Methods of measurement tend to be tedious and expensive, requiring several expensive sensors to be mounted in the building. In this paper, we propose the Autonomous Robotic Environmental Sensor (ARES), a custom-designed omniwheel mobile robot retrofitted with several sensors capable of autonomously taking measurements of the indoor environment at multiple positions, reducing the number of sensors, amount of labor required, and cost. A Sliding Mode Controller (SMC) is designed and applied to the robotic platform, and positional accuracy is verified, allowing for highly accurate movement to ensure environmental measurements occur at known positions. Wind velocity, air temperature, and relative humidity data collected by the ARES platform in a laboratory environment for 24 hours is analyzed, providing insight into the thermo-fluid variables in the room and the room’s predicted thermal comfort.
A fragment‐based approach to discovery of Receptor for Advanced Glycation End products inhibitors

The Receptor for Advanced Glycation End products (RAGE) is a pattern recognition receptor that signals for inflammation via the NF‐κB pathway. RAGE has been pursued as a potential target to suppress symptoms of diabetes and is of interest in a number of other diseases associated with chronic inflammation, such as inflammatory bowel disease and bronchopulmonary dysplasia. Screening and optimization have previously produced small molecules that inhibit the activity of RAGE in cell‐based assays, but efforts to develop a therapeutically viable direct‐binding RAGE inhibitor have yet to be successful. Here, we show that a fragment‐based approach can be applied to discover fundamentally new types of RAGE inhibitors that specifically target the ligand‐binding surface. A series of systematic assays of structural stability, solubility, and crystallization were performed to select constructs of the RAGE ligand‐binding domain and optimize conditions for NMR‐based screening and co‐crystallization of RAGE with hit fragments. An NMR‐based screen of a highly curated ~14 000‐member fragment library produced 21 fragment leads. Of these, three were selected for elaboration based on structure‐activity relationships generated through cycles of structural analysis by X‐ray crystallography, structure‐guided design principles, and synthetic chemistry. These results, combined with crystal structures of the first linked fragment compounds, demonstrate the applicability of the fragment‐based approach to the discovery of RAGE inhibitors.
Functional characterisation of single nucleotide variants of the psychiatric risk gene cacna1c in the zebrafish

Several genome-wide association studies have associated CACNA1C variants with psychiatric disorders. The molecular mechanisms involved are poorly understood. Taking advantage of the zebrafish larva as a model, we investigated how two different mutations in cacna1c – sa10930 (nonsense mutation) and sa15296 (splice site mutation), affect neuronal function. We characterized changes in cacna1c mRNA, neurotransmitter levels and behaviour, as well as whole-brain activity using single electrode local field potential recordings. Both point mutations resulted in a significant reduction in cacna1c mRNA, as well as social behaviour and prepulse inhibition deficits. Whereas sa15296 mutants displayed abnormal locomotor and open-field behaviour, we observed normal behaviour in the sa10930 mutants. Brain recordings from both mutants had lower spectral power while sa15296 displayed significant seizure-like activity. Finally, sa10930 homozygotes showed increased dopamine and serotonin levels, decreased gamma-aminobutyric acid (GABA) levels, and unchanged glutamate levels while homozygous sa15296 larvae showed increased levels of serotonin and glutamate, and unaffected levels of GABA and dopamine. Our work provides new insights into the functional role of CACNA1C in behavioural, electrophysiological and biochemical traits linked to psychiatric disorders. We show a functional role for the non-coding mutation (sa15296) in the cacna1c in vivo animal model. Consistent with existing hypotheses, our data suggest that disruption of gene expression, neurotransmission, and cortical excitability are involved in CACNA1C-related mechanisms of psychiatric disorders.
Plasticity in female timing may explain current shifts in breeding phenology of a North American songbird

Climate change has driven changes in breeding phenology. Identifying the magnitude of phenological shifts and whether selection in response to climate change drives these shifts is key for determining species’ reproductive success and persistence in a changing world. We investigated reproductive timing in a primarily sedentary population of the dark-eyed junco (Junco hyemalis) over 32 years. We predicted that juncos would breed earlier in warmer springs in response to selection favouring earlier breeding. To test this prediction, we compared the annual median date for reproductive onset (i.e., egg one date) to monthly spring temperatures and examined evidence for selection favouring earlier breeding and for plasticity in timing. Egg one dates occurred earlier over time, with the timing of breeding advancing up to 24 days over the 32-year period. Breeding timing also strongly covaried with maximum April temperature. We found significant overall selection favouring earlier breeding (i.e., higher relative fitness with earlier egg one dates) that became stronger over time, but strength of selection was not predicted by temperature. Lastly, individual females exhibited plastic responses to temperature across years. Our findings provide further evidence that phenotypic plasticity plays a crucial role in driving phenological shifts in response to climate change. For multi-brooded bird populations, a warming climate might extend the breeding season and provide more opportunities to re-nest rather than drive earlier breeding in response to potential phenological mismatches. However, as plasticity will likely be insufficient for long-term survival in the face of climate change, further research in understanding the mechanisms of female reproductive timing will be essential for forecasting the effects of climate change on population persistence.
Sexual and temporal variation in New Zealand bellbird song repertoires

How song repertoires vary within species and change over time is well studied in male songbirds. However, variation in female song repertoires remains largely unstudied despite female song being much more common and complex than once assumed. We investigated the song syllable repertoire of the New Zealand bellbird (Anthornis melanura), a species where both sexes have complex but sexually dimorphic song. We compared songs at individual and population levels to investigate sex and temporal variation of syllable repertoires. We detected 96 syllable types in the population over four years, of which 58% were unique to males, 32% unique to females and 9% were shared between the sexes. The population syllable repertoire of both sexes changed substantially across years with similar turnover rates (Jaccard’s similarity coefficients; female 52.9–69.0%; male 58.6–73.7%). Furthermore, many syllable types, unique to each sex, varied in prevalence within the population across years. The syllable repertoire sizes of individuals were higher for males than females (13-32, n = 7 and 6-16, n = 8, respectively). Although these sample sizes were low, the temporal variation in syllable prevalence and turnover for individuals were similar to patterns at the population level. Overall, male and female bellbirds exhibited similarities in temporal patterns of yearly repertoire composition, with rapid changes in syllable prevalence, but females had fewer syllable types than males. We suggest that these similarities and differences are consistent with male and female song repertoires being driven by similar but not identical selection pressures.
Understanding the relationship between dispersal and range size

Understanding what drives the vast variability in species range size is still an outstanding question. Among the several processes potentially affecting species ranges, dispersal is one of the most prominent hypothesized predictors. However, the theoretical expectation of a positive dispersal-range size relationship has received mixed empirical support. Here, we synthesized results from 84 studies to investigate in which context dispersal is most important in driving species range size. We found that dispersal traits – proxies for dispersal ability – explain range sizes more often in temperate and subtropical regions than in tropical regions, when considering multiple components of dispersal, and when investigating a large number of species to capture dispersal and range size variation. In plants, positive effects of dispersal on range size were less often detected when examining broad taxonomic levels. In animals, dispersal is more important for range size increase in ectotherms than in endotherms. Our synthesis emphasizes the importance of considering different aspects of the dispersal process -departure, transfer, settlement-, niche aspects and evolutionary components, like time for range expansion and past geological-environmental dynamics. We therefore call for a more integrative view of the dispersal process and its causal relationship with range size.
Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers

Protein folding homeostasis in the endoplasmic reticulum (ER) is regulated by a signaling network, termed the unfolded protein response (UPR). Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident kinase/RNase that mediates signal transmission in the most evolutionarily conserved branch of the UPR. Dimerization and/or higher-order oligomerization of IRE1 are thought to be important for its activation mechanism, yet the actual oligomeric states of inactive, active, and attenuated mammalian IRE1 complexes remained unknown. We developed an automated two-color single-molecule tracking approach to dissect the oligomerization of tagged endogenous human IRE1 in live cells. In contrast to previous models, our data indicate that IRE1 exists as a constitutive homodimer at baseline and assembles into small oligomers upon ER stress. We demonstrate that the formation of inactive dimers and stress-dependent oligomers is fully governed by IRE1’s lumenal domain. Phosphorylation of IRE1’s kinase domain occurs more slowly than oligomerization and is retained after oligomers disassemble back into dimers. Our findings suggest that assembly of IRE1 dimers into larger oligomers specifically enables trans- autophosphorylation, which in turn drives IRE1’s RNase activity.
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

Abstract As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here, we present PEPATAC, an ATAC-seq pipeline that is easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also demonstrate the advantage of aligning to the mitochondrial genome serially, which improves the accuracy of alignment statistics and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project. BSD2-licensed code and documentation are available at https://pepatac.databio. org.
BinChecker: a new algorithm for quality assessment of microbial draft genomes

In the reconstruction of microbial genomes from metagenomic sequence data, the estimation of the final completeness and possible contamination is crucial for quality control. In metagenomics candidate genomes are usually obtained from a metagenome assembly and a subsequent binning of the assembled contigs. BinChecker provides a novel approach to quality assessment that is based on a fast protein domain search and a clustering approach for identification of marker domain (“feature”) sets. The feature sets that are used for estimation are not pre-computed for a given database of reference genomes, but are individually found for each bin by adaptive clustering and feature selection. In particular, the adaptivity facilitates the creation and extension of the underlying database, which just requires to add protein feature profiles of reference genomes. Tests with simulated bins indicate that the prediction accuracy of BinChecker meets the current state of the art while providing significant advantages in terms of speed and flexibility.
Real-time Noise-suppressed Wide-Dynamic-Range Compression in Ultrahigh-Resolution Neuronal Imaging

With a limited dynamic range of an imaging system, there are always regions with signal intensities comparable to the noise level, if the signal intensity distribution is close to or even wider than the available dynamic range. Optical brain/neuronal imaging is such a case where weak-intensity ultrafine structures, such as, nerve fibers, dendrites and dendritic spines, often coexist with ultrabright structures, such as, somas. A high fluorescence-protein concentration makes the soma order-of-magnitude brighter than the adjacent ultrafine structures resulting in an ultra-wide dynamic range. A straightforward enhancement of the weak-intensity structures often leads to saturation of the brighter ones, and might further result in amplification of high-frequency background noises. An adaptive illumination strategy to real-time-compress the dynamic range demands a dedicated hardware to operate and owing to electronic limitations, might encounter a poor effective bandwidth especially when each digitized pixel is required to be illumination optimized. Furthermore, such a method is often not immune to noise-amplification while locally enhancing a weak-intensity structure. We report a dedicated-hardware-free method for rapid noise-suppressed wide-dynamic-range compression so as to enhance visibility of such weak-intensity structures in terms of both contrast-ratio and signal-to-noise ratio while minimizing saturation of the brightest ones. With large-FOV aliasing-free two-photon fluorescence neuronal imaging, we validate its effectiveness by retrieving weak-intensity ultrafine structures amidst a strong noisy background. With compute-unified-device-architecture (CUDA)-acceleration, a time-complexity of <3 ms for a 1000×1000-sized 16-bit data-set is secured, enabling a real-time applicability of the same.
Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity

Nucleotide-based signaling molecules (NSMs) are widespread in bacteria and eukaryotes, where they control important physiological and behavioral processes. In bacteria, NSM-based regulatory networks are highly complex, entailing large numbers of enzymes involved in the synthesis and degradation of active signaling molecules. How the converging input from multiple enzymes is transformed into robust and unambiguous cellular responses has remained unclear. Here we show that Escherichia coli converts dynamic changes of c-di-GMP into discrete binary signaling states, thereby generating heterogeneous populations with either high or low c-di-GMP. This is mediated by an ultrasensitive switch protein, PdeL, which senses the prevailing cellular concentration of the signaling molecule and couples this information to c-di-GMP degradation and transcription feedback boosting its own expression. We demonstrate that PdeL acts as a digital filter that facilitates precise developmental transitions, confers cellular memory, and generates functional heterogeneity in bacterial populations to evade phage predation. Based on our findings, we propose that bacteria apply ultrasensitive regulatory switches to convert dynamic changes of NSMs into binary signaling modes to allow robust decision-making and bet-hedging for improved overall population fitness.