Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterisation of the OTU domain deubiquitinase complement of Toxoplasma gondii

The OTU deubiquitinase family is expanded in Toxoplasma parasites, and members show preferences for Lys6-, Lys11-, Lys48-, and Lys63-linked ubiquitin chains, and additional specificity for NEDD8. AlphaFold-guided structural analysis reveals cryptic ubiquitin-binding domains with functional importance. The phylum Apicomplexa contains several parasitic species of medical and agricultural importance. The ubiquitination machinery remains, for the most part, uncharacterised in apicomplexan parasites, despite the important roles that it plays in eukaryotic biology. Bioinformatic analysis of the ubiquitination machinery in apicomplexan parasites revealed an expanded ovarian tumour domain–containing (OTU) deubiquitinase (DUB) family in Toxoplasma, potentially reflecting functional importance in apicomplexan parasites. This study presents comprehensive characterisation of Toxoplasma OTU DUBs. AlphaFold-guided structural analysis not only confirmed functional orthologues found across eukaryotes, but also identified apicomplexan-specific enzymes, subsequently enabling discovery of a cryptic OTU DUB in Plasmodium species. Comprehensive biochemical characterisation of 11 Toxoplasma OTU DUBs revealed activity against ubiquitin- and NEDD8-based substrates and revealed ubiquitin linkage preferences for Lys6-, Lys11-, Lys48-, and Lys63-linked chain types. We show that accessory domains in Toxoplasma OTU DUBs impose linkage preferences, and in case of apicomplexan-specific TgOTU9, we discover a cryptic ubiquitin-binding domain that is essential for TgOTU9 activity. Using the auxin-inducible degron (AID) to generate knockdown parasite lines, TgOTUD6B was found to be important for Toxoplasma growth.
Intraoperative Factors Modifying the Risk of Postoperative Pulmonary Complications After Living Donor Liver Transplantation

Background. The relationship between intraoperative anesthetic management and postoperative pulmonary complications (PPCs) after liver transplantation is not fully understood. We aimed to determine the intraoperative contributors to PPC. Methods. The retrospectively collected cohort included 605 patients who underwent living donor liver transplantation. PPCs comprised respiratory failure, respiratory infection, pulmonary edema, atelectasis (at least moderate degree), pneumothorax, and pleural effusion (at least moderate degree). The presence and type of PPC were evaluated by 2 pulmonary physicians. Logistic regression analysis was performed to determine the association between perioperative variables and PPC risk. Results. Of the 605 patients, 318 patients (52.6%) developed 486 PPCs. Multivariable analysis demonstrated that PPC risk decreased with low tidal volume ventilation (odds ratio [OR] 0.62 [0.41-0.94], P = 0.023) and increased with greater driving pressure at the end of surgery (OR 1.08 [1.01-1.14], P = 0.018), prolonged hypotension (OR 1.85 [1.27-2.70], P = 0.001), and blood albumin level ≤3.0 g/dL at the end of surgery (OR 2.43 [1.51-3.92], P < 0.001). Survival probability at 3, 6, and 12 mo after transplantation was 91.2%, 89.6%, and 86.5%, respectively, in patients with PPCs and 98.3%, 96.5%, and 93.4%, respectively, in patients without PPCs (hazard ratio 2.2 [1.3-3.6], P = 0.004). Graft survival probability at 3, 6, and 12 mo after transplantation was 89.3%, 87.1%, and 84.3%, respectively, in patients with PPCs and 97.6%, 95.8%, and 92.7%, respectively, in patients without PPCs (hazard ratio 2.3 [1.4-3.7], P = 0.001). Conclusions. We found that tidal volume, driving pressure, hypotension, and albumin level during living donor liver transplantation were significantly associated with PPC risk. These data may help determine patients at risk of PPC or develop an intraoperative lung-protective strategy for liver transplant recipients.
Generation of fuzzy decision trees by fuzzy ID3 with adjusting mechanism of AND/OR operators

An ability of adjusting the AND/OR operators is discussed in this paper to overcome the drawback of fuzzy ID3. The fuzzy ID3 has a mechanism to construct fuzzy rules. However, the fuzzy ID3 has a couple of problems, i.e., a lack of representation and an adjusting problem. In our fuzzy ID3, AND/OR operators are formulated using t-norm and t-conorm connectives with parameters and each parameter is adjusted using the golden section method. By using the golden section method, the proposed fuzzy ID3 gives accurate fuzzy rules. If the t-conorm connective is selected as AND/OR operator in the adjusting stage, the decision tree has more flexible representation.
Internalisation of stereotyped body appearance standards and body dissatisfaction in adolescent boys: Moderating role of sports participation

ABSTRACT The aim of this study was to test the moderating role of sport participation in the mediation model of media pressures, internalisation of appearance ideals and body dissatisfaction in adolescent boys. Five hundred and seventy adolescent boys (mean age 17.2 ± 0.45; range 15–19 years) participated in the cross-sectional study. Adolescents completed a questionnaire consisting of measures of attitudes towards sociocultural pressures on appearance, body dissatisfaction and sport participation (participation in achievement sport, leisure exercising and non-participation in any sports). Sports participation moderated the associations between the internalisation of stereotyped appearance ideals and body dissatisfaction. In athletes, the effect of internalisation of thin body ideals on body dissatisfaction was not significant, while the effect of internalisation of muscular/athletic body ideals was negative. In leisure exercisers, the effect of internalisation of muscular body ideals on body dissatisfaction was not significant, yet internalisation of thin body ideals had a significant effect on body dissatisfaction. The strongest associations between appearance ideals internalisation and body dissatisfaction were found in adolescent boys who reported no participation in sports. Sports participation might be an effective tool in decreasing the negative effect of internalisation of stereotyped appearance ideals on adolescent boys’ body image.
Type Inference with Selftype

The metavariable self is fundamental in object-oriented languages. Typing self in the presence of inheritance has been studied by Abadi and Cardelli, Bruce, and others. A key concept in these developments is the notion of selftype, which enables flexible type annotations that are impossible with recursive types and subtyping. Bruce et al. demonstrated that, for the language TOOPLE, type checking is decidable. Open until now is the problem of type inference with selftype. In this paper we present a type inference algorithm for a type system with selftype, recursive types, and subtyping. The example language is the object calculus of Abadi and Cardelli, and the type inference algorithm runs in nondeterministic polynomial time.
The psychometric properties and clinical utility of neural measures of reward processing

Abstract Reward processing is implicated in the etiology of several psychological conditions including depressive disorders. In the current paper, we examined the psychometric properties of a neural measure of reward processing, the reward positivity (RewP), in 279 adult women at baseline and 187 women 8 weeks later. The RewP demonstrated excellent internal consistency at both timepoints and good test–retest reliability using estimates from both classical test theory and generalizability theory. Additionally, the difference between RewP following reward and loss feedback was marginally associated with depressive symptoms in a subsample of participants. We also examined the relationship between subject-level dependability estimates and depression severity, finding that depressive symptoms may contribute to lower dependability on reward trials. However, this finding did not survive correction for multiple comparisons and should be replicated in future studies. These findings support RewP as a useful measure of individual differences of reward processing and point to the potential utility of this measure for various forms of psychopathology.
Negotiating the Kin-State Citizenship: The Case of Croats from Herzegovina

Abstract This article explores how the meanings individuals ascribed to kin-state citizenship change in the long term. Previous research has looked at the real-time acquisition of citizenship and established three dimensions of meanings individuals ascribe to citizenship: identity, instrumental, and legitimacy. Building on the case of Croats from Herzegovina (BiH), who acquired citizenship back in the 1990s, the article demonstrates how meanings individuals ascribe to citizenship change over time across each dimension—subject to the perception of inclusion into the kin-state, type and the extent of opportunities kin-states provide, as well as the routinization of citizenship practices. By disaggregating each dimension further, the article extends the understanding of kin-state citizenship and shows how individuals respond to the policy implementation’s overall dynamics by aligning the meanings they ascribe to citizenship. Therefore, future work should look more closely at the interplay between state policy dynamics and its impact on individuals.
Islands in the Stream: The Effect of Plasma Flow on Tearing Stability

Reducing plasma flow clearly decreases the stability of tearing modes in multiple regimes (sawtooth, hybrid) in both highand low-aspect-ratio tokamaks (DIII-D, JET, NSTX, each with distinct means of lessening rotation). Further, reducing flow makes preexisting “saturated” islands larger at the same beta. Thus lower plasma flow impairs high-beta operation owing both to the destabilization and to the impact of tearing-mode islands. The physics is that flow shear (not flow) at the tearing rational surface is classically stabilizing, making the tearing stability index more negative (more stable). In this picture, with profiles and all else the same, the critical beta at which neoclassical tearing modes (NTMs) destabilize is proportional to and hence lower flow and flow shear lead to destabilization at lower beta. Similarly, if destabilized, the saturated NTM island width is proportional to and thus increases as flow and flow shear are reduced. A working model for a significant level of stabilizing shear in the plasma toroidal angular flow d dr at a given rational surface is of order of the inverse of the product of the local values of the parallel magnetic shear length Ls and the Alfvén time A . Experimental data are fitted for the effect of this normalization of flow shear in a simple empirical model for both onset and saturation of tearing modes. Most theoretical literature is on the consequence of flow shear on classical tearing stability at zero beta; tokamaks at high beta have large magnetic Prandtl number (an issue for the sign of the flow effect) and very large Lundquist number. It is in this regime that theory will be compared to experimentally based empirical models. The consequence for future tokamaks with low rotation may be lower tearing stability than now expected.
Feeding black holes: tracing gas flows from the outskirts to the centers of galaxies

Abstract We analyzed the distribution and kinematics of the atomic gas (HI) in 16 nearby spiral galaxies. Our results indicate that the morphology of the atomic gas and dynamically disturbed outer disks correlate with the AGN type present (Seyfert, LINER). From the combined HI and CO data (from the NUGA project), 2-dimensional maps of the gas flow are computed and gas inflow rates are derived as a function of radius within the disks.
Multi-generational workforce job retention: Coping strategy influences among South African engineers

This study investigated the relationship between generational cohorts and job retention as influenced by coping strategies. Participants were a convenience sample of 151 full-time South African engineers (Generation X: 1961 to 1980 = 47.7%; white = 66.9%; male = 89.4%). Participants completed the Positive Coping Behaviour Inventory (PCBI) as well as the Retention Factors Behaviour Inventory (RFBI). A stepwise regression analysis revealed no age cohort differences in terms of job retention. However, affective positive (emotion-focused) coping significantly predicted satisfaction with retention factors. No differences were found in term of the demographic variables. Human resource practitioners should prioritise innovative work coping mechanisms that will guide retention strategies within the engineering sector in South Africa.
Subjective socioeconomic status and envy in Chinese collectivist culture: The role of sense of control

This study explored the relationship between subjective socioeconomic status (SSS) and envy, as well as the role that sense of control plays in this relationship in the Chinese collectivist culture. Participants were 927 Chinese adults (female = 64.8%; mean age = 24.52 years, SD = 4.935 years) who completed a series of questionnaires. Structural equation modelling showed that having a lower SSS was associated with a higher level of dispositional, benign, and malicious envy. Sense of control negatively mediated the relationship between SSS and dispositional, benign, and malicious envy. Multigroup analyses revealed no sex differences in either main or indirect effects. These results are related to the Chinese collectivist culture. The mediating role of sense of control is partially consistent with the social cognitive theory of social class. We propose that interventions focusing on sense of control could help reduce debilitating envy and its negative effects among lower SSS individuals.
Relational importance in early and middle adulthood age groups in South Africa

We explored the relational importance in early and middle adulthood in a South African setting. Informants were 52 participants (female = 58%, African language speaking = 31%, age range = 18–65; younger adults = 50%). Data on the types of important relationships and the reasons behind the importance for the different age groups were collected through semi-structured, open-ended questions. Thematic analysis indicated family, friends, and spiritual relationships as the most important relationships across the age groups. Other relationships important to both groups, were relationships pertaining to work, pet/s, and self. The middle adulthood age group emphasised the importance of work relationships above those with friends and further indicated relationships with their spouse, success, and neighbours. Younger adults indicated relationships with romantic partners, academics, and society as a whole. The findings suggest a convoy effect on relationship preferences for these age groups in that they highlight the importance of social relationships and how they vary in different developmental phases or stages of life. Implications for consideration of developmental phases in the design of interventions are indicated.
Purpose in life and academic performance: Grit mediation among Chinese college students

This study explored the mediating effect of grit (consistency of interest, perseverance of effort) on the association between purpose in life (meaningfulness, goal orientation, and beyond-the-self) and academic performance. Data were collected from 493 students from two universities in Hunan province, China (male = 21.5 %, female = 78.5%; mean age = 20.86 years, SD = 1.69 years). They completed the scales of purpose in life, grit, and academic performance. Following structural equation model analyses, the results showed that higher purpose in life (specifically goal orientation) associated with superior academic performance. Grit (specifically perseverance of effort) mediated the association between purpose in life (specifically goal orientation) and academic performance, increasing the likelihood of high academic achievment. Similarly, grit (specifically perseverance of effort) mediated the relationship between higher purpose in life (specifically beyond-the-self) and academic performance, also increasing the likelihood of high academic achieving. The findings highlight the importance of grit defined by perseverance of effort, goal orientation, as well as belief in beyond the personal self to college achievement in a long-term oriented culture.
The classroom environment and college students’ being silent/hidden dropouts: The chain of mediating effects of college identification and academic achievement

The present study investigated the relationship between the classroom environment (CE) and hidden dropout (HD), and the chain mediating role of college identification (CI) and academic achievement (AA) in that relationship. A total of 1 214 Chinese college students were participants. Specifically, 63.43% were female students, 15.90% were junior students, 35.17% were sophomore students, and 37.40% were freshmen students. The students completed the hidden dropout scale, as well as measures of the classroom environment and the college identification. Students’ academic record of the previous semester served as the academic achievement measures. Road path analysis was used to examine the relationships between variables and to test the hypothesized mediating effects. Results indicated that a lower sense of CE was associated with higher HD dropout. The CE not only directly affected college students’ HD but also indirectly affected their HD level through the chain intermediary role of college identification and AA. CI significantly mediated CE and DP, so that DP was lower. Similarly, higher AA mediated the CE and HD relationship so that HD was lower in students who were happier with the college environment and who had higher grades. Path road analysis revealed a chain mediating effect of CI and AA on the relationship between CE and HD because their joint effect was 0.23% higher than the mediating effect of CI, and 6.24% higher than the AA’s mediating effect. These findings suggest a need for college student development offices to pay attention to college students, particularly male students, in terms of the importance of creating a positive classroom environment and supporting college identification and academic achievement to reduce the likelihood of college students becoming silent/hidden dropouts. Additionally, college student development offices should address the different mechanisms that may influence their reason for dropping out silently.
Agricultural crop-type classification of multi-polarization SAR images using a hybrid entropy decomposition and support vector machine technique

This article presents the application of a hybrid classification technique of entropy decomposition and support vector machine (EDSVM) for crop-type categorization. It takes the advantage of the desired parameters from the entropy decomposition (ED) method and the statistical learning method based on the support vector machine (SVM) method that determines the optimal separation between classes in a higher dimensional feature space to improve on the existing classification results. ED is capable of extracting valuable decomposed parameters of entropy H and alpha α for image interpretation with analysis of the underlying scattering mechanisms. H demonstrates the randomness of the underlying scattering mechanisms and α is used to define the type of scattering mechanisms. However, in the application of agricultural crops where the scattering mechanisms of the crops are quite similar to each other, the distribution of the H and α in the H–α feature space overlaps from one class to another. Moreover, the drawback of ED is the arbitrariness of the boundaries for each class. To overcome this issue, SVM classifier is deployed to determine the decision boundaries by projecting the training sets of the classes into higher dimensional feature space. Hence, the hybrid EDSVM is developed to provide an alternative solution to improve the classification accuracy. In this article, EDSVM classifier is applied on a multi-crop field Airborne Synthetic Aperture Radar (AIRSAR) image of Flevoland in the Netherlands and the robustness of the classifier is evaluated. The classification is done with the purpose of separating the different types of crops with the characteristics of the scattering mechanism. At the same time, a hybrid entropy decomposition and neural network (EDNN) classifier method is developed to validate the effectiveness of the EDSVM classifier. As a result, EDSVM is proved to be robust and to yield a superior result compared with neural network (NN), SVM and EDNN classifiers.
Dynamic Phase‐Field Fracture in Viscoelastic Materials using a First‐Order Formulation

In this contribution we present analytical results on a model for dynamic fracture in viscoelastic materials at small strains that have been obtained in full depth in [1]. In the model, the sharp crack interface is regularized with a phase‐field approximation, and for the phase‐field variable a viscous evolution with a quadratic dissipation potential is employed. A non‐smooth penalization prevents material healing. The viscoelastic momentum balance is formulated as a first order system and coupled in a nonlinear way to the non‐smooth evolution equation of the phase field. We give a full discretization in time and space using a discontinuous Galerkin method for the first‐order system. We discuss the existence of discrete solutions and, with the step size in space and time tending to zero, their convergence to a suitable notion of weak solution of the system. Eventually, we provide a numerical benchmark and compare it with simulation results found in [2].
Nonlinear dynamics of inclined films under low-frequency forcing

The evolution of an inclined liquid film, subjected to regular inlet disturbances of small frequency, f, is studied experimentally and computationally. The fluorescence imaging method is used to quantitatively document film thickness at a downstream window of the flow channel, and a Galerkin finite-element solution of the Navier–Stokes equation of motion is invoked to predict the entire spatio-temporal dynamics of the free surface. Experiments confirm that, below a certain frequency, fp, the regular wave train is destroyed by the appearance of one or more parasitic crests behind each major wave. Experiments and simulations indicate that parasitic crests are not the result of spatially unlocalized instabilities in the substrate, but originate in a regular way from a depression developing at the tails of growing solitary waves. Their downstream fate is dictated by the proximity of the next major wave, and thus different scenarios are predicted and observed for f≈fp and f≪fp. A theoretical explanation of the.
Generative adversarial networks for three‐dimensional microstructure generation

Multiscale simulations are demanding in terms of computational resources. In the context of continuum micromechanics, the multiscale problem arises from the need of inferring macroscopic material parameters from the microscale. If the underlying microstructure is explicitly given by means of µCT‐scans, convolutional neural networks can be used to learn the microstructure‐property mapping, which is usually obtained from computational homogenization. The convolutional neural network (CNN) approach provides a significant speedup, especially in the context of heterogeneous or functionally graded materials. Another application is uncertainty quantification, where many expensive evaluations are required. However, one bottleneck of this approach is the large number of training microstructures needed.