Miracle-dz/UniFAR-FTUs huggingface dataset:
Emotion regulation and cognitive function as mediating factors for the association between lifetime abuse and risk behaviors in women of color

Background: Lifetime abuse (i.e., childhood abuse, intimate partner violence) has been linked to risky behavioral outcomes (i.e., alcohol use, risky sex). Women who experience lifetime abuse have poor emotion regulation and may have problems with executive functioning, which could help explain the relationship between lifetime abuse and risky behaviors. However, research on executive functioning and emotion regulation as mediators of this relationship has been limited. In the present study, we examined this association. We hypothesized that lifetime abuse would be related to greater difficulty in emotion regulation and executive function, which would also be associated with greater alcohol use and risky sex. Methods:This cross-sectional study included 150 women with a history of lifetime abuse who were assessed for alcohol use using the AUDIT Score; emotion regulation was measured using the Difficulties with Emotion Regulation Scale (DERS); risky sex was measured using question: "in the last 90 days, how many people did you have anal or vaginal sex without using a condom? Executive function was assessed using the NIH Toolbox. Results: The mediation model followed the self-regulation theory, which proposes executive function as the higher-order cognitive process. Results showed that executive function deficit and poor emotion regulation significantly mediated the relationship between lifetime abuse and alcohol use severity (indirect effect = .097, SE .031, 95% CI = .035 to .158). Conclusion: Our findings suggest executive function and emotion regulation as a potential mechanism for alcohol use severity in women who experienced lifetime abuse (i.e., childhood abuse and intimate partner violence).
Studies of optical damage in lithium niobate in the presence of thermal gradients

Optical damage is studied at 100 K in thermal gradients from 5 × 102 to 1.3 × 103 K/cm. Gradients less than 5 × 102 K/cm have no effect upon the observed damage; however, gradients greater than 103 K are capable of eliminating the optical damage. This is interpreted as an effect due to thermoelectric current exactly cancelling the photovoltaic current. Our estimate of thermoelectric field in the illuminated spot ΔE = (dPs/dT)▿ TΔz agrees well with the photovoltaic field determined by Levanyuk et al. [Fiz. Tverd. Tela, 22 1161 (1980)], as well as with the d.c. experiments of Reznik et al. [J. Raman Spectry. , 15, 60 (1984)]. The present work substantiates our earlier hypothesis that spectral changes in optically damaged LiNbO3 arise from electric fields perpendicular to the optic c-axis [Chen, J. Appl. Phys., 40, 3389 (1969)], and are not due to photoexcited plasmons [Gorelik et al., Phys. Stat. Sol. , B105, K73 (1981)].
Aural vocabulary, orthographic vocabulary, and listening comprehension

Abstract Vocabulary is a key variable to successful listening comprehension. Research has explored the relationship between aural and orthographic vocabularies and listening comprehension. This current study examined the relationships among aural vocabulary, orthographic vocabulary, and listening comprehension within the same Japanese cohort in an integrated manner. The test data of 155 Japanese EFL students, who took identical aural and orthographic vocabulary tests (the listening vocabulary levels test [LVLT] and new vocabulary levels test [NVLT], respectively) and a high-stakes listening test (Test of English for International Communication (TOEIC) for Parts I and II), were analyzed. The results indicated that aural and orthographic vocabulary are closely related but not identical. Moreover, orthographic vocabulary is more connected to the word- and propositional-level understanding of extended texts than to aural vocabulary for the Japanese group. More specifically, the 2,000-word and 4,000-word level and the academic vocabulary of the orthographic vocabulary predicted 27% of the variance of the listening comprehension test performance, whereas only the academic words of the aural vocabulary predicted 8%.
A new technique for low-to-high altitude predictions of ablative hypersonic flowfields

A new coupled-chemistry PNS solution technique is developed for predicting finite-rate chemically reacting flows over a wide range of Mach numbers and for altitudes ranging from sea level to 250 kft. New diagonalized, two-step, and strongly implicit solution schemes are developed to efficiently and accurately solve the coupled species conservation equations. Furthermore, a new quasisteady ablation model is developed for Teflon that accounts for the material density variations. Numerical tests are conducted over the Mach number range of 6.89-20 and altitude range from sea level to 250 kft, and comparisons are made with available wind-tunnel and flight data on surface heat-transfer rates. The results show that the new two-step solution scheme provides a uniquely attractive combination of accuracy, stability, and computational efficiency over the entire range of conditions tested. Furthermore, nonablating low-altitude calculations show that finite-rate chemistry effects are still significant over a major portion of the shock layer. The classical Blottner-type linearization of the production terms is unstable for low-altitude high-Reynolds-number conditions. The results of Teflon ablation calculations show that, for the altitude range of 75-250 kft, the predicted surface ablation rates using our quasisteady ablation model are within 10% of the predictions of Scala's correlation based on flight data.
Storytelling and digitalization as opportunities for spa towns

ABSTRACT This study explores how thermal spa towns use storytelling and digitalization to create a tourist experience capable of attracting new, younger clientele who are searching for well-being. An exploratory study investigated a French association of spa towns (La Route des Villes d'Eaux) in the Massif Central that included a series of interviews, non-participant observation, and data analysis. The results highlight how storytelling and digitalization enhance the personality of the destination, a result of the differentiating, authentic, and emotionally engaging offbeat stories that are a product of the region’s heritage and culture. This article sheds new light on possible pitfalls that can arise when spa towns use storytelling coupled with digitalization. A differentiating storyline is recommended here in accordance with the chosen target. It should also be tested beforehand, especially if the storyline contains offbeat humour. It is also necessary to adopt an appropriate mode and channel of communication, as well as an appropriate rhythm, form, and length of video and audio content that meets the expectations of all stakeholders. Moreover, if storytelling and digitalization intend to develop and animate a community that includes socio-professionals, tourists, and locals, sufficient human and financial resources must be devoted to it.
Primary care trainee nursing associates in England: a qualitative study of higher education institution perspectives

Abstract Aim: To explore higher education institution (HEI) perspectives on the development and implementation of trainee nursing associates (NAs) in the primary care workforce in England. Background: Current shortages of primary health care staff have led to innovative skill mix approaches in attempts to maintain safe and effective care. In England, a new level of nursing practice, NAs, was introduced and joined the workforce in 2019. This role was envisaged as a way of bridging the skills gap between health care assistants and registered nurses and as an alternative route into registered nursing. However, there is limited evidence on programme development and implementation of trainee NAs within primary care settings and HEI perspectives on this. Methods: This paper draws from a larger qualitative study of HEI perspectives on the trainee NA programme. Twenty-seven staff involved in training NAs, from five HEIs across England, were interviewed from June to September 2021. The interview schedule specifically included questions relating to primary care. Data relating to primary care were extracted and analysed using a combined framework and thematic analysis approach. Findings: Three themes were developed: ‘Understanding the trainee role and requirements’, ‘Trainee support in primary care’ and ‘Skills and scope of practice’. It is apparent that a more limited understanding of the NA programme requirements can lead to difficulties in accessing the right support for trainees in primary care. This can create challenges for trainees in gaining the required competencies and uncertainty in understanding what constitutes a safe scope of practice within the role for both employers and trainees. It might be anticipated that as this new programme becomes more embedded in primary care, a greater understanding will develop, support will improve and the nature and scope of this new level of practice will become clearer.
The stability of inviscid Beltrami flow between parallel free-slip impermeable boundaries

Abstract We present a family of exact inviscid three-dimensional Beltrami flows in a horizontally periodic domain lying between two parallel free-slip boundaries. Significantly, these flows are not stress free: the horizontal vorticity varies on each boundary. Using direct numerical simulations (employing horizontal hyperdiffusion only for numerical stability), we find that the largest-scale member of the family is unstable and breaks down into anisotropic turbulence, with relatively large horizontal vorticity at and near each boundary, and associated surface frontal features. We conjecture that all members of the family are similarly unstable. The free-slip boundaries play an important role in the late stages of the instability by constraining the deformation of vortex lines near the boundaries. This study appears to be the first to consider the role of boundary horizontal vorticity in an inviscid context.
Three-dimensional numerical simulation of turbulent mixing by Rayleigh-Taylor instability

Three‐dimensional simulation of the mixing of miscible fluids by Rayleigh–Taylor instability is described for density ratios, ρ1/ρ2, in the range 1.5 to 20. Significant dissipation of density fluctuations and kinetic energy occurs via the cascade to high wave numbers. Comparison is made with experimental measurements of the overall growth of the mixing zone and of the magnitude of density fluctuations. The differences between 2‐D and 3‐D simulation are discussed.
Somatostatin-expressing neurons in the ventral tegmental area innervate specific forebrain regions and are involved in the stress response

Expanding knowledge about the cellular composition of subcortical brain regions demonstrates large heterogeneity and differences from the cortical architecture. Recently, we described three subtypes of somatostatin-expressing (Sst) neurons in the mouse ventral tegmental area (VTA) and showed their local inhibitory action on the neighbouring dopaminergic neurons (Nagaeva et al., 2020). Here, we report that VTA Sst neurons especially from the anterolateral part also project far outside the VTA and innervate several forebrain regions that are mainly involved in the regulation of emotional behaviour. Deletion of these VTA Sst neurons affected several behaviours and drug responses, such as home cage activity, sensitization of locomotor activity to morphine, fear conditioning responses, and reactions to inescapable stress of forced swimming, often in a sex-dependent manner. Together, these data demonstrate that VTA Sst neurons have selective projection targets, which are distinct from the main targets of VTA dopamine neurons and involved in the regulation of a variety of behaviours mostly associated with the stress response. This, makes Sst neurons a meaningful addition to the remote VTA circuit and stress-related neuronal network.
Stimulus-specific prediction error neurons in mouse auditory cortex

Comparing expectation with experience is an important neural computation performed throughout the brain and is a hallmark of predictive processing. Experiments that alter the sensory outcome of an animal's behavior reveal enhanced neural responses to unexpected self-generated stimuli, indicating that populations of neurons in sensory cortex may reflect prediction errors (PEs), mismatches between expectation and experience. However, enhanced neural responses to self-generated stimuli could also arise through nonpredictive mechanisms, such as the movement-based facilitation of a neuron's inherent sound responses. If sensory prediction error neurons exist in sensory cortex, it is unknown whether they manifest as general error responses, or respond with specificity to errors in distinct stimulus dimensions. To answer these questions, we trained mice of either sex to expect the outcome of a simple sound-generating behavior and recorded auditory cortex activity as mice heard either the expected sound or sounds that deviated from expectation in one of multiple distinct dimensions. Our data reveal that the auditory cortex learns to suppress responses to self-generated sounds along multiple acoustic dimensions simultaneously. We identify a distinct population of auditory cortex neurons that are not responsive to passive sounds or to the expected sound but that encode prediction errors. These prediction error neurons are abundant only in animals with a learned motor-sensory expectation, and encode one or two specific violations rather than a generic error signal. Together, these findings reveal that cortical predictions about self-generated sounds have specificity in multiple simultaneous dimensions and that cortical prediction error neurons encode specific violations from expectation. SIGNIFICANCE STATEMENT Audette et. al record neural activity in the auditory cortex while mice perform a sound-generating forelimb movement and measure neural responses to sounds that violate an animal's expectation in different ways. They find that predictions about self-generated sounds are highly specific across multiple stimulus dimensions and that a population of typically nonsound-responsive neurons respond to sounds that violate an animal's expectation in a specific way. These results identify specific prediction error (PE) signals in the mouse auditory cortex and suggest that errors may be calculated early in sensory processing.
APOBEC3F is the main source of editing identified during the 2022 outbreak of human monkeypox virus

On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the two different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5’GpA context, indicative of APOBEC3 cytosine deaminase activity. By using a sensitive PCR (3D-PCR) method allowing differential amplification of AT-rich DNA, we demonstrate that G->A hypermutated MPXV genomes can be recovered experimentally from APOBEC3 transfection followed by MPXV infection. Here, among the 7 human APOBEC3 cytidine deaminases (A3A-A3C, A3DE, A3F-A3H), only APOBEC3F was capable of extensively deaminating cytidine residues in MPXV genomes. Hyperedited genomes were also recovered in ~42% of analyzed patients, indicating that editing is part of the natural cycle of MPXV infection. Moreover, we demonstrate that substantial repair of these mutations occurs. Upon selection, corrected G->A mutations escaping drift loss contribute to the MPXV evolution observed in the current epidemics. Thus, stochastic or transient overexpression of APOBEC3F gene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.
Translation rate prediction and regulatory motif discovery with multi-task learning

Many studies have found that sequence in the 5’ untranslated regions (UTRs) impacts the translation rate of an mRNA, but the regulatory grammar that underpins this translation regulation remains elusive. Deep learning methods deployed to analyse massive sequencing datasets offer new solutions to motif discovery. However, existing works focused on extracting sequence motifs in individual datasets, which may not be generalisable to other datasets from the same cell type. We hypothesise that motifs that are genuinely involved in controlling translation rate are the ones that can be extracted from diverse datasets generated by different experimental techniques. In order to reveal more generalised cis-regulatory motifs for RNA translation, we develop a multi-task translation rate predictor, MTtrans, to integrate information from multiple datasets. Compared to single-task models, MTtrans reaches a higher prediction accuracy in all the benchmarked datasets generated by various experimental techniques. We show that features learnt in human samples are directly transferable to another dataset in yeast systems, demonstrating its robustness in identifying evolutionarily conserved sequence motifs. Furthermore, our newly generated experimental data corroborated the effect of most of the identified motifs based on MTtrans trained using multiple public datasets, further demonstrating the utility of MTtrans for discovering generalisable motifs. MTtrans effectively integrates biological insights from diverse experiments and allows robust extraction of translation-associated sequence motifs in 5’UTR.
Resilience of genetic diversity in forest trees over the Quaternary

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we performed comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasted European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Hence, surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity, over time. Altogether, our results indicate that forest trees were able to retain their evolutionary potential over very long periods of time despite strong environmental changes. One-Sentence Summary Population genomic analyses reveal that forest trees retained their evolutionary potential over the Quaternary.
Leafhopper transmits soybean stay-green associated virus to legume plants

A novel geminivirus, soybean stay-green associated virus (SoSGV), was previously shown to cause soybean delayed senescence and is associated with the incidences of soybean stay-green syndrome. The transmission methods of SoSGV were not yet understood. We captured insects belonging to 24 distinct species in a soybean field with the SoSGV outbreak and detected the presence of SoSGV only in leafhoppers and bean bugs (Riptortus pedestris). Caged feeding experiments using captured leafhoppers and bean bugs from soybean fields showed that leafhoppers, but not bean bugs, are vectors transmitting SoSGV. The common brown leafhopper (Orosius orientalis) is identified as the dominant leafhopper species and can establish colonies feeding on soybean plants in experimental conditions. An investigation of SoSGV defective DNA revealed that soybean genomic DNA could be inserted into the SoSGV genome, while sequences from wild soybean, red bean, and cowpea were also identified. We further showed that the common brown leafhopper could transmit SoSGV to wild soybean and red bean plants, emphasizing the vector role of the leafhopper in the transmission of SoSGV in the field.
New method for shape recognition based on dynamic programming

In this paper we present a new method for shape recognition based on dynamic programming. First, each contour of shape is represented by a set of points. After alignment and matching between two shapes, the outline of the shape is divided into parts according to N angular and M radial sectors , Each Sector contains a portion of the contour; this portion is divided at the inflexion points into convex and concave sections, and the information about sections are extracted in order to provide a semantic content to the outline shape, then this information are coded and transformed into a string of symbols. Finally we find the best alignment of two complete strings and compute the optimal cost of similarity. The algorithm has been tested on a large set of shape databases and real images (MPEG-7, natural silhouette database).
Efficient, robust, and versatile fluctuation data analysis using MLE MUtation Rate calculator (mlemur)

Almost 80 years since the publication of the seminal work by Salvador Luria and Max Delbrück, the fluctuation assay has remained an important tool for analysing the levels of mutagenesis in microbial populations. The mutant counts originating from some average number of mutations are usually assumed to obey the Luria–Delbrück distribution. While several tools for estimating mutation rates are available, they sometimes lack accuracy or versatility under non-standard conditions. In this work we developed extensions to the Luria– Delbrück protocol to account for phenotypic lag and cellular death with either perfect or partial plating. Hence, our novel MLE MUtation Rate calculator, or mlemur, is the first tool that provides a user-friendly graphical interface allowing the researchers to model their data with consideration for partial plating, differential growth of mutants and non-mutants, phenotypic lag, cellular death, variability of the final number of cells, post-exponential-phase mutations, and the size of inoculum. Additionally, mlemur allows the users to incorporate most of these special conditions at the same time to obtain highly accurate estimates of mutation rates and p values, confidence intervals for an arbitrary function of data (such as fold) and perform power analysis and sample size determination for the likelihood ratio test. We assess the accuracy of point and interval estimates produced by mlemur against historical and simulated fluctuation experiments. We believe both mlemur and the analyses in this work might be of great help when evaluating fluctuation experiments and increase the awareness of the limitations of the widely-used Lea–Coulson formulation of the Luria-Delbrück distribution in the more realistic biological contexts. Author Summary Despite many recent developments in the department of fluctuation data analysis, geneticists are often limited to either a very strict classical Luria–Delbrück protocol, or possibly a modified one with relaxation of just one assumption (e.g., differential fitness of mutants and wild-type cells). In some cases, such as partial plating, researchers use historical methods whose accuracy strictly depends on the conditions of the experiment and thus are not optimal in a wide range of parameters. A novel tool for fluctuation data analysis, mlemur (MLE MUtation Rate calculator), alleviates these problems and provides new extensions that allow to account for phenotypic lag and cellular death. Additionally, we find that the failure to properly account for these additional parameters might lead to inaccurate point and interval estimates of the mutation rate. Our results underline the importance of careful examination of the fluctuation assay to ensure that the chosen statistical model reflects the biological and technical conditions of the experiment.