Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of contact algorithm for three‐dimensional numerical manifold method

This paper customizes a contact detection and enforcing scheme to fit the three‐dimensional (3‐D) numerical manifold method (NMM). A hierarchical contact system is established for efficient contact detection. The mathematical mesh, a unique component in the NMM, is utilized for global searching of possible contact blocks and elements, followed by the local searching to identify primitive hierarchies. All the potential contact pairs are then transformed into one of the two essential entrance modes: point‐to‐plane and crossing‐lines modes, among which real contact pairs are detected through a unified formula. The penalty method is selected to enforce the contact constraints, and a general contact solution procedure in the 3‐D NMM is established. Because of the implicit framework, an open‐close iteration is performed within each time step to determine the correct number of contact pairs among multi‐bodies and to achieve complete convergence of imposed contact force at corresponding position. The proposed contact algorithm extensively utilizes most of the original components of the NMM, namely, the mathematical mesh/cells and the manifold elements, as well as the external components associated with contacts, such as the contact body, the contact facet and the contact vertex. In particular, the utilization of two mutually approaching mathematical cells is efficient in detecting contacting territory, which makes this method particularly effective for both convex and non‐convex bodies. The validity and accuracy of the proposed contact algorithm are verified and demonstrated through three benchmark problems. Copyright © 2013 John Wiley & Sons, Ltd.
arXiv : Polarised target for Drell-Yan experiment in COMPASS at CERN, part I

In the polarised Drell-Yan experiment at the COMPASS facility in CERN pion beam with momentum of 190 GeV/c and intensity about $10^8$ pions/s interacted with transversely polarised NH$_3$ target. Muon pairs produced in Drel-Yan process were detected. The measurement was done in 2015 as the 1st ever polarised Drell-Yan fixed target experiment. The hydrogen nuclei in the solid-state NH$_3$ were polarised by dynamic nuclear polarisation in 2.5 T field of large-acceptance superconducting magnet. Large helium dilution cryostat was used to cool the target down below 100 mK. Polarisation of hydrogen nuclei reached during the data taking was about 80 %. Two oppositely polarised target cells, each 55 cm long and 4 cm in diameter were used. Overview of COMPASS facility and the polarised target with emphasis on the dilution cryostat and magnet is given. Results of the polarisation measurement in the Drell-Yan run and overviews of the target material, cell and dynamic nuclear polarisation system are given in the part II.
Long-term Photometric Variability in Kepler Full-frame Images: Magnetic Cycles of Sun–like Stars

Photometry from the Kepler mission is optimized to detect small, short-duration signals like planet transits at the expense of long-term trends. This long-term variability can be recovered in photometry from the full-frame images (FFIs), a set of calibration data collected approximately monthly during the Kepler mission. Here we present f3, an open-source package to perform photometry on the Kepler FFIs in order to detect changes in the brightness of stars in the Kepler field of view over long time baselines. We apply this package to a sample of 4000 Sun–like stars with measured rotation periods. We find that ≈10% of these targets have long-term variability in their observed flux. For the majority of targets, we find that the luminosity variations are either correlated or anticorrelated with the short-term variability due to starspots on the stellar surface. We find a transition between anticorrelated (starspot-dominated) variability and correlated (facula-dominated) variability between rotation periods of 15 and 25 days, suggesting the transition between the two modes is complete for stars at the age of the Sun. We also identify a sample of stars with apparently complete cycles, as well as a collection of short-period binaries with extreme photometric variation over the Kepler mission.
The effects of a specialized staff training on trauma-sensitivity in professionals working with patients with a psychotic disorder: A pilot study

ABSTRACT Background Studies show that the trauma-sensitivity of professionals working with patients with psychosis is insufficient. As a result, trauma-related problems remain undetected and untreated, which may impede recovery in this group. This study explored the effects of a specialised staff training on six trauma-sensitivity factors (i.e. knowledge, credibility, expected burden, harm expectancy, diagnostic competency and organizational support), self-reported trauma-sensitive behaviour and objective indicators of trauma-sensitive behaviour in medical files. Method Professionals (N = 56) rated the six trauma-sensitivity factors and their own trauma-sensitive behaviour at pre-training, post-training and at 6- and 12-months follow-up. Changes in indicators of trauma-sensitive behaviours were assessed by a review of medical files (N = 97). Results The specialized training increased knowledge, crediblity and experienced diagnostic compentence. The training decreased burden and harm expectancies, and enhanced self-reported trauma-sensitive behaviour. However, this positive change could not be objectified by indicators of trauma-sensitive behaviour in medical files. Discussion These findings support the notion that specialised training has a positive effect on increasing trauma-sensitivity and decreasing burden and harm expectancies, but not necessarily on observable trauma-sensitive behaviour. In addition to training staff, structural implementation and organisational support are argued to be essential to attain actual behaviour change.
Cultural values as policy directives: techniques, technologies and symbolic work

ABSTRACT Cultural policies aim to respond to the widespread use of digital technologies in cultural practices by facilitating their application and addressing associated challenges. In arguing that policy positions emerge through the interface of digital technologies and culture and that they need to be negotiated in practice, this paper discusses how digital technologies are perceived and negotiated in traditional cultures of making. The immersive nature of cultural values is made explicit through symbolic work that embeds the digital as documentation of the life cycle of hand-woven materials. Applying the framework of cultural techniques, digital technologies are perceived as products of culture. They signify the interwoven complexities of values between people, cultural practice and materials recognising cultures of making as policy directives.
Diffusion and dispersion of passive tracers: Navier-Stokes vs. MHD turbulence

A comparison of turbulent diffusion and pair-dispersion in homogeneous, macroscopically isotropic Navier-Stokes (NS) and nonhelical magnetohydrodynamic (MHD) turbulence based on high-resolution direct numerical simulations is presented. Significant differences between MHD and NS systems are observed in the pair-dispersion properties, in particular a strong reduction of the separation velocity in MHD turbulence as compared to the NS case. It is shown that in MHD turbulence the average pair-dispersion is slowed down for τd ≲ t ≲ 10τd, τd being the Kolmogorov time, due to the alignment of the relative Lagrangian tracer velocity with the local magnetic field. Significant differences in turbulent single-particle diffusion in NS and MHD turbulence are not detected. The fluid particle trajectories in the vicinity of the smallest dissipative structures are found to be characteristically different although these comparably rare events have a negligible influence on the statistics investigated in this work.
The adenomatous polyposis coli protein 3o years on

Mutations in the gene encoding the Adenomatous polyposis coli protein (APC) were discovered as driver mutations in colorectal cancers almost 30 years ago. Since then, the importance of APC in normal tissue homeostasis has been confirmed in a plethora of other (model) organisms spanning a large evolutionary space. APC is a multifunctional protein, with roles as a key scaffold protein in complexes involved in diverse signalling pathways, most prominently the Wnt signalling pathway. APC is also a cytoskeletal regulator with direct and indirect links to and impacts on all three major cytoskeletal networks. Here, we interrogate the enormous depth of sequencing data now available to reveal the conservation of APC across taxonomy and relationships between different APC protein families.
Online decoding of covert speech based on the passive perception of speech

Background Brain-computer interfaces (BCIs) can offer solutions to communicative impairments induced by conditions such as locked-in syndrome. While covert speech-based BCIs have garnered interest, a major issue facing their clinical translation is the collection of sufficient volumes of high signal-to-noise ratio (SNR) examples of covert speech signals which can typically induce fatigue in users. Fortuitously, investigations into the linkage between covert speech and speech perception have revealed spatiotemporal similarities suggestive of shared encoding mechanisms. Here, we sought to demonstrate that an electroencephalographic cross-condition machine learning model of speech perception and covert speech can successfully decode neural speech patterns during online BCI scenarios. Methods In the current study, ten participants underwent a dyadic protocol whereby participants perceived the audio of a randomly chosen word and then subsequently mentally rehearsed it. Eight words were used during the offline sessions and subsequently narrowed down to three classes for the online session (two words, rest). The modelling was achieved by estimating a functional mapping derived from speech perception and covert speech signals of the same speech token (features were extracted via a Riemannian approach). Results While most covert speech BCIs deal with binary and offline classifications, we report an average ternary and online BCI accuracy of 75.3% (60% chance-level), reaching up to 93% in select participants. Moreover, we found that perception-covert modelling effectively enhanced the SNR of covert speech signals correlatively to their high-frequency correspondences. Conclusions These findings may pave the way to efficient and more user-friendly data collection for passively training such BCIs. Future iterations of this BCI can lead to a combination of audiobooks and unsupervised learning to train a non-trivial vocabulary that can support proto-naturalistic communication. Significance Statement Covert speech brain-computer interfaces (BCIs) provide new communication channels. However, these BCIs face practical challenges in collecting large volumes of high-quality covert speech data which can both induce fatigue and degrade BCI performance. This study leverages the reported spatiotemporal correspondences between covert speech and speech perception by deriving a functional mapping between them. While multiclass and online covert speech classification has previously been challenging, this study reports an average ternary and online classification accuracy of 75.3%, reaching up to 93% for select participants. Moreover, the current modelling approach augmented the signal-to-noise ratio of covert speech signals correlatively to their gamma-band correspondences. The proposed approach may pave the way toward a more efficient and user-friendly method of training covert speech BCIs.
Individual-specific functional connectivity shows improved performance in detecting and predicting individualized symptoms of Alzheimer’s disease in elderly people with/without APOE ε4 allele

To date, no reliable biomarkers are available that link individual-specific functional connectivity and patients’ individualized symptoms for early detection and prediction of Alzheimer’s disease (AD) in elderly people with specific genotypes. Meanwhile, functional magnetic resonance imaging (MRI) and machine learning are promising tools that can reveal the relationships between brain and behavior at individual level towards predicting the transition to AD. In this study, individual-specific functional connectivity was constructed in elderly participants with Apolipoprotein E (APOE) ε4 allele (N = 120) and without APOE ε4 allele (N = 115), respectively. In particular, machine learning based on a recursive feature selection technique was carried out to track multiple clinical symptoms among differing genotypes at individual level from normal aging (NA) and AD. It was found that the captured neuroimaging features in both APOE genotyping groups were able to distinguish the changes of clinical symptoms from NA to AD. Besides, our findings illustrated that the connections between individual-specific functional regions exhibited significantly higher correlation between estimated and observed scores in multiple clinical symptoms than those from atlas-based functional connectivity for both APOE genotyping groups, while no significant performance was detected when the data of two APOE genotyping groups were combined for the estimation models. Further, individual-specific between-network connectivity constitutes a major contributor for accessing cognitive symptoms in both APOE genotyping groups. Therefore, this study demonstrated the essential role of individual variation in cortical functional anatomy and the significance in combining brain and behavior for improving the accuracy in detection and prediction of AD in elderly people with specific genotypes.
Interpreting phytoliths assemblages at chimpanzee (Pan troglodytes verus) nut-cracking sites in Bossou Forest, Guinea

The nut-cracking behaviour of the chimpanzees of Bossou Forest has been long documented and studied in order to understand ultimate drivers for this form of durophagy by these apes. At sites in which they break open the nuts of the oil palm (Elaeis guineaeensis) on stone anvils with stone hammers, fragments of the tools as well as remnants of the nuts may be deposited into local sediments; however, they may become less visible at the macroscopic level as these sites are no longer used (become dormant). We build upon work that has been done to document this unique cultural heritage in West African chimpanzees by interpreting phytolith assemblages in sediments at active nut-cracking sites (used within the last two months). We compare these assemblages with those found in sediments of sites that have been dormant for ~10 years and sites where chimpanzees have not been observed to access and crack open oil palm nuts with stone tools. We predicted that larger assemblages of spheroid echinates, a phytolith associated with palms, would be found at active nut-cracking sites, however we found no statistical difference between total spheroid echinates (measured as total number found per gram of dry sediment) assemblages produced across active nut-cracking, dormant, or non-nut-cracking sites. This may have been due to small sample size (N≤6 sediment samples for each of the three sites) and so further sample collection and analyses are needed for inter-site comparisons. We also measured 2D area (μm2), perimeter and maximum diameter of spheroid echinates found in nut endocarps (shells) and leaflets from an oil palm frond. Intra-specific differences from all three measurements were found with these phytoliths being larger in the nut endocarp than the leaflet. This has implications for (re)interpreting the assemblages of spheroid echinate phytoliths at the three sites to determine if there is a greater productivity larger-sized spheroid echinates that fall within the size range of those measured for the nut endocarp (mean maximum diameter of 14.9 μm versus 7.8 μm for those found in oil palm leaflet). Finally, we argue for the importance of initialising and continuing the interpretation of phytolith assemblages in local sediments that are located near sites where directed plant input by non-human taxa has occurred, in this case, chimpanzees cracking open oil palm nuts using stone tools. This is important to refine our interpretation of phytolith assemblages where human and non-human taxa who use complex foraging strategies share ecological spaces.
Tau polarizes an aging transcriptional signature to excitatory neurons and glia

Aging is a major risk factor for Alzheimer’s disease (AD), and cell-type vulnerability underlies its characteristic clinical manifestations. We have performed longitudinal, single-cell RNA-sequencing in Drosophila with pan-neuronal expression of human tau, which forms AD neurofibrillary tangle pathology. Whereas tau- and aging-induced gene expression strongly overlap (93%), they differ in the affected cell types. In contrast to the broad impact of aging, tau-triggered changes are strongly polarized to excitatory neurons and glia. Further, tau can either activate or suppress innate immune gene expression signatures in a cell type-specific manner. Integration of cellular abundance and gene expression pinpoints Nuclear Factor Kappa B signaling as a potential marker for neuronal vulnerability. We also highlight the conservation of cell type-specific transcriptional patterns between Drosophila and human postmortem brain tissue. Overall, our results create a resource for dissection of dynamic, age-dependent gene expression changes at cellular resolution in a genetically tractable model of tauopathy.
Peptidyl tRNA Hydrolase Is Required for Robust Prolyl-tRNA Turnover in Mycobacterium tuberculosis

Peptidyl tRNA hydrolase (Pth) is an enzyme that cuts unfinished peptides off tRNA that has been prematurely released from a stalled ribosome. Pth is essential in nearly all bacteria, including the pathogen Mycobacterium tuberculosis (Mtb), but it has not been clear why. ABSTRACT Enzymes involved in rescuing stalled ribosomes and recycling translation machinery are ubiquitous in bacteria and required for growth. Peptidyl tRNA drop-off is a type of abortive translation that results in the release of a truncated peptide that is still bound to tRNA (peptidyl tRNA) into the cytoplasm. Peptidyl tRNA hydrolase (Pth) recycles the released tRNA by cleaving off the unfinished peptide and is essential in most bacteria. We developed a sequencing-based strategy called copper sulfate-based tRNA sequencing (Cu-tRNAseq) to study the physiological role of Pth in Mycobacterium tuberculosis (Mtb). While most peptidyl tRNA species accumulated in a strain with impaired Pth expression, peptidyl prolyl-tRNA was particularly enriched, suggesting that Pth is required for robust peptidyl prolyl-tRNA turnover. Reducing Pth levels increased Mtb’s susceptibility to tRNA synthetase inhibitors that are in development to treat tuberculosis (TB) and rendered this pathogen highly susceptible to macrolides, drugs that are ordinarily ineffective against Mtb. Collectively, our findings reveal the potency of Cu-tRNAseq for profiling peptidyl tRNAs and suggest that targeting Pth would open new therapeutic approaches for TB. IMPORTANCE Peptidyl tRNA hydrolase (Pth) is an enzyme that cuts unfinished peptides off tRNA that has been prematurely released from a stalled ribosome. Pth is essential in nearly all bacteria, including the pathogen Mycobacterium tuberculosis (Mtb), but it has not been clear why. We have used genetic and novel biochemical approaches to show that when Pth levels decline in Mtb, peptidyl tRNA accumulates to such an extent that usable tRNA pools drop. Thus, Pth is needed to maintain normal tRNA levels, most strikingly for prolyl-tRNAs. Many antibiotics act on protein synthesis and could be affected by altering the availability of tRNA. This is certainly true for tRNA synthetase inhibitors, several of which are drug candidates for tuberculosis. We find that their action is potentiated by Pth depletion. Furthermore, Pth depletion results in hypersensitivity to macrolides, drugs that are not active enough under ordinary circumstances to be useful for tuberculosis.
The CUT&RUN Blacklist of Problematic Regions of the Genome

Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors and co-factors. The ENCODE project and others have compiled blacklists for ChIP-seq which have been widely adopted: these lists contain regions of high and unstructured signal, regardless of cell type or protein target. While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions. For this reason, we have compiled blacklists based on CUT&RUN data for the human and mouse genomes, identifying regions consistently called as peaks in negative controls by the CUT&RUN peak caller SEACR. Using published CUT&RUN data from our and other labs, we show that the CUT&RUN blacklist regions can persist even when peak calling is performed with SEACR against a negative control, and after ENCODE blacklist removal. Moreover, we experimentally validated the CUT&RUN Blacklists by performing reiterative negative control experiments in which no specific protein is targeted, showing that they capture >80% of the peaks identified. We propose that removing these problematic regions prior to peak calling can substantially improve the performance of SEACR-based peak calling in CUT&RUN experiments, resulting in more reliable peak datasets.
Study of galaxies in the Eridanus void. Sample and oxygen abundances

We present a sample of 66 galaxies belonging to the equatorial part (Dec.= -7$^o$, +7$^o$) of the large so called Eridanus void (after Fairall 1998). The void galaxies are selected as to be separated from the luminous galaxies ($M_{\rm B} < M_{\rm B}^{*} +1$), delineating the void, by more than 2 Mpc. Our main goal is to study systematically the evolutionary parameters of the void sample (metallicity and gas content) and to compare the void galaxy properties with their counterparts residing in denser environments. Besides the general galaxy parameters, compiled mainly from the literature, we present the results of dedicated observations to measure the oxygen abundance O/H in HII-regions of 23 void galaxies obtained with the 11-m SALT telescope (SAAO) and the 6-m BTA telescope (SAO), as well as the O/H estimates derived from the analysis of the SDSS DR12 spectra for 3 objects. We compiled all available data on O/H in 36 these void galaxies, including those for 11 galaxies available in the literature (for one object both SDSS and SALT spectra were used), and analyze this data in relation to galaxy luminosity ($\log$(O/H) versus $M_{\rm B}$). Comparing them with the control sample of similar type galaxies from the Local Volume, we find clear evidence for a substantially lower average metallicity of the Eridanus void galaxies. This result matches well the conclusions of our recent similar study for galaxies in the Lynx-Cancer void.