Miracle-dz/UniFAR-FTUs huggingface dataset:
Both Sides of the Story: Changing the "Pre-existing Culture of Dread" Surrounding Student Teamwork in Breakout Rooms

As universities transitioned in-person classrooms to virtual classrooms, instructors faced challenges and changes in how they conduct their classes and teaching style trying to keep virtual classrooms as similar to in-person as much as possible through the use of group work in breakout sessions. Within these breakout sessions, students are expected to work together to complete an assignment. Through 669 surveys and 19 interviews, our paper outlines the successes and challenges of breakout sessions and teamwork in virtual learning environments faced by professors, graduate teaching assistants, and students. Our findings show the importance of pedagogical research for online environments, the student need for persistent instructions and check-ins to facilitate teamwork in breakout sessions, and strong justification for the use of breakout sessions in online courses. Based on our findings, we propose design recommendations to address the challenges highlighted within the classroom and software used by instructors and students. Our work contributes and extends previous CSCW and HCI research in online distributed teamwork and education.
The Value of Activity Traces in Peer Evaluations: An Experimental Study

Peer evaluations are a well-established tool for evaluating individual and team performance in collaborative contexts, but are susceptible to social and cognitive biases. Current peer evaluation tools have also yet to address the unique opportunities that online collaborative technologies provide for addressing these biases. In this work, we explore the potential of one such opportunity for peer evaluations: data traces automatically generated by collaborative tools, which we refer to as "activity traces". We conduct a between-subjects experiment with 101 students and MTurk workers, investigating the effects of reviewing activity traces on peer evaluations of team members in an online collaborative task. Our findings show that the usage of activity traces led participants to make more and greater revisions to their evaluations compared to a control condition. These revisions also increased the consistency and participants' perceived accuracy of the evaluations that they received. Our findings demonstrate the value of activity traces as an approach for performing more reliable and objective peer evaluations of teamwork. Based on our findings as well as qualitative analysis of free-form responses in our study, we also identify and discuss key considerations and design recommendations for incorporating activity traces into real-world peer evaluation systems.
Method for estimating pulsatile wall shear stress from one‐dimensional velocity waveforms

Wall shear stress (WSS)—a key regulator of endothelial function—is commonly estimated in vivo using simplified mathematical models based on Poiseuille's flow, assuming a quasi‐steady parabolic velocity distribution, despite evidence that more rapidly time‐varying, pulsatile blood flow during each cardiac cycle modulates flow‐mediated dilation (FMD) in large arteries of healthy subjects. More exact and accurate models based on the well‐established Womersley solution for rapidly changing blood flow have not been adopted clinically, potentially because the Womersley solution relies on the local pressure gradient, which is difficult to measure non‐invasively. We have developed an open‐source method for automatic reconstruction of unsteady, Womersley‐derived velocity profiles, and WSS in conduit arteries. The proposed method (available online at https://doi.org/10.5281/zenodo.7576408) requires only the time‐averaged diameter of the vessel and time‐varying velocity data available from non‐invasive imaging such as Doppler ultrasound. Validation of the method with subject‐specific computational fluid dynamics and application to synthetic velocity waveforms in the common carotid, brachial, and femoral arteries reveals that the Poiseuille solution underestimates peak WSS 38.5%–55.1% during the acceleration and deceleration phases of systole and underestimates or neglects retrograde WSS. Following evidence that oscillatory shear significantly augments vasodilator production, it is plausible that mischaracterization of the shear stimulus by assuming parabolic flow leads to systematic underestimates of important biological effects of time‐varying blood velocity in conduit arteries.
Effect of disease prevalence and growth stage on symptoms severity in the Turnip mosaic virus - Arabidopsis thaliana pathosystem

Plants emit volatile organic compounds (VOCs) in response to biotic and abiotic stimuli that provide information about their physiological status to other individuals in the community. Nearby receivers adjust their own defenses in response to these chemical cues. The majority of studies to date has concentrated on the communication of abiotic stressors (e.g. salinity or drought) or herbivory. Less attention had received the role of VOCs during microbial infections and almost nothing has been done for viruses. Here we investigated the function of VOCs during turnip mosaic virus infection of Arabidopsis thaliana. First, we looked at the influence of two factors on the kinetics of symptoms progression in receivers, namely the prevalence of infection in the population and the growth stage of the receiver plants at inoculation. We found that young plants were more sensitive to the protective effect of VOCs than older ones, and that high infection prevalence results in a slower disease progression in receivers. Second, we tested the possibility that jasmonates could be VOC candidates. To do this, we examined the kinetics of symptoms progression in jasmonate-insensitive and wild-type plants, and the results showed that the protective effect vanished in the mutant plants. Third, we investigated the possibility that root communication would be also relevant. We found that the kinetics of symptom progression across receivers was further slowed down in an age-dependent manner when plants were planted in the same pot. Together, these preliminary findings point to a potential function for disease prevalence in plant communities in regulating the severity of symptoms, this effect being mediated by VOCs.
Automatic Discovery of Cognitive Strategies with Tiny Recurrent Neural Networks

Normative modeling frameworks such as Bayesian inference and reward-based learning provide valuable insights into the fundamental principles of adaptive behavior. However, their ability to describe realistic animal behavior is limited by the typically small number of fitted parameters, leading to a cycle of handcrafted adjustments and model comparisons that are prone to research subjectivity. Here, we present a novel modeling approach leveraging recurrent neural networks to automatically discover the cognitive algorithms governing animal decision-making. We show that neural networks with only one or two units can predict choices of individual animals more accurately than classical cognitive models, and as accurately as larger neural networks, in three well-studied reward learning tasks. We then interpret the trained networks using dynamical systems concepts such as state-space and fixed-point attractors, leading to a unified comparison of different cognitive models and a detailed characterization of the cognitive mechanisms underlying the animal’s choices. Our approach also estimates behavior dimensionality and provides insights into the algorithms emerging in meta-reinforcement learning agents. Overall, we present a systematic approach for discovering interpretable cognitive strategies in decision-making, offering insights into neural mechanisms and a foundation for examining both healthy and dysfunctional cognition.
LOCC: a novel visualization and scoring of cutoffs for continuous variables

Objective There is a need for new methods to select and analyze cutoffs employed to define genes that are most prognostic significant and impactful. We designed LOCC (Luo’s Optimization Categorization Curve), a novel tool to visualize and score continuous variables for a dichotomous outcome. Methods To demonstrate LOCC with real world data, we analyzed TCGA hepatocellular carcinoma gene expression and patient data using LOCC. We compared LOCC visualization to receiver operating characteristic (ROC) curve for prognostic modeling to showcase its utility in understanding predictors in various TCGA datasets. Results Analysis of E2F1 expression in hepatocellular carcinoma using LOCC demonstrated appropriate cutoff selection and validation. In addition, we compared LOCC visualization and scoring to ROC curves and c-statistics, demonstrating that LOCC better described predictors. Analysis of a previously published gene signature showed large differences in LOCC scoring, and removing the lowest scoring genes did not affect prognostic modeling of the gene signature demonstrating LOCC scoring could distinguish which predictors were most critical. Conclusion Overall, LOCC is a novel visualization tool for understanding and selecting cutoffs, particularly for gene expression analysis in cancer. The LOCC score can be used to rank genes for prognostic potential and is more suitable than ROC curves for prognostic modeling. Graphical Abstract
New paradigms in actomyosin energy transduction: critical evaluation of non-traditional models for orthophosphate release

Release of the ATP hydrolysis product inorganic phosphate (Pi) from the active site of myosin is central in chemo-mechanical energy transduction and closely associated with the main force-generating structural change, the power-stroke. Despite intense investigations, the relative timing between Pi-release and the power-stroke remains poorly understood. This hampers in depth understanding of the production of force and motion by myosin in health and disease and also our understanding of myosin-active drugs. From the 1990s and up to today, models with the Pi-release either distinctly before or after the power-stroke, in unbranched kinetic schemes, have dominated the literature. However, in recent years, alternative models have emerged to explain apparently contradictory findings. Here, we first compare and critically analyze, three influential alternative models, either characterized by a branched kinetic scheme or by partial uncoupling of Pi-release and the power-stroke. Finally, we suggest critical tests of the models aiming for a unified picture.
Influence of goals on modular brain network organization during working memory

Introduction Top-down control underlies our ability to attend relevant stimuli while ignoring irrelevant, distracting stimuli and is a critical process for prioritizing information in working memory (WM). Prior work has demonstrated that top-down biasing signals modulate sensory-selective cortical areas during WM, and that the large-scale organization of the brain reconfigures due to WM demands alone; however, it is not yet understood how brain networks reconfigure between the processing of relevant versus irrelevant information in the service of WM. Methods Here, we investigated the effects of task goals on brain network organization while participants performed a WM task that required participants to detect repetitions (e.g., 0-back or 1-back) and had varying levels of visual interference (e.g., distracting, irrelevant stimuli). We quantified changes in network modularity–a measure of brain sub-network segregation–that occurred depending on overall WM task difficulty as well as trial-level task goals for each stimulus during the task conditions (e.g., relevant or irrelevant). Results First, we replicated prior work and found that whole-brain modularity was lower during the more demanding WM task conditions compared to a baseline condition. Further, during the WM conditions with varying task goals, brain modularity was selectively lower during goal-directed processing of task-relevant stimuli to be remembered for WM performance compared to processing of distracting, irrelevant stimuli. Follow-up analyses indicated that this effect of task goals was most pronounced in default mode and visual sub-networks. Finally, we examined the behavioral relevance of these changes in modularity and found that individuals with lower modularity for relevant trials had faster WM task performance. Discussion These results suggest that brain networks can dynamically reconfigure to adopt a more integrated organization with greater communication between sub-networks that supports the goal-directed processing of relevant information and guides WM.
Genetic diversity and antimicrobial resistance profiles of Staphylococcus pseudintermedius associated with skin and soft-tissue infections in companion animals in Lisbon, Portugal

Staphylococcus pseudintermedius is the main bacterial pathogen of skin and soft-tissue infections (SSTIs) in companion animals. Antimicrobial resistance in this species is a growing public health concern. This study aims to characterize a collection of S. pseudintermedius causing SSTIs in companion animals, establishing the main clonal lineages and antimicrobial resistance traits. The collection corresponded to all S. pseudintermedius (n = 155) causing SSTIs in companion animals (dogs, cats and one rabbit) collected between 2014 and 2018 at two laboratories in Lisbon, Portugal. Susceptibility patterns were established by disk diffusion for 28 antimicrobials (15 classes). For antimicrobials without clinical breakpoints available, a cut-off value (COWT) was estimated, based on the distribution of the zones of inhibition. The blaZ and mecA genes were screened for the entire collection. Other resistance genes (e.g., erm, tet, aadD, vga(C), dfrA(S1)) were searched only for those isolates showing an intermediate/resistance phenotype. For fluoroquinolone resistance, we determined the chromosomal mutations in the target genes grlA and gyrA. All the isolates were typed by PFGE following SmaI macrorestriction and isolates representative of each PFGE type were further typed by MLST. Forty-eight out of the 155 S. pseudintermedius isolates (31.0%) were methicillin-resistant (mecA+, MRSP). Multidrug-resistant (MDR) phenotypes were detected for 95.8% of the MRSP and 22.4% of the methicillin-susceptible (MSSP) isolates. Of particular concern, only 19 isolates (12.3%) were susceptible to all antimicrobials tested. In total, 43 different antimicrobial resistance profiles were detected, mostly associated with the carriage of blaZ, mecA, erm(B), aph3-IIIa, aacA-aphD, catpC221, tet(M) and dfr(G) genes. The 155 isolates were distributed within 129 PFGE clusters, grouped by MLST in 42 clonal lineages, 25 of which correspond to new sequence types (STs). While ST71 remains the most frequent S. pseudintermedius lineage, other lineages that have been replacing ST71 in other countries were detected, including ST258, described for the first time in Portugal. This study revealed a high frequency of MRSP and MDR profiles among S. pseudintermedius associated with SSTIs in companion animals in our setting. Additionally, several clonal lineages with different resistance profiles were described, evidencing the importance of a correct diagnosis and selection of the therapy.
Towards a psychological framework on time perception in patients with chronic tinnitus

Although disabling tinnitus is a chronic auditory phantom sensation, current knowledge on time perception (i.e., subjective time) in sufferers is limited and unsystematic. This theoretical analysis provides a first approach to this topic, highlighting the heterogeneity of time perception in humans as shown in various research areas. This heterogeneity is inherently related to goal attainment. Our immediate perception of time is restricted to present moment and recent past, whereas our sense of time is mostly future-oriented and represented as our past in a mental time line. The heterogeneity of time translates into a tension between anticipated changes one wants to see happen and full commitment that is required to goal attainment. Tinnitus sufferers are intensely aware of this tension in their self-perception. Their most compelling desire is that they no longer perceive tinnitus, but they get closer to this goal only by avoiding to put all their thoughts into it. Our analysis provides new perspectives on acceptance of tinnitus in relation to this time paradox. Building on the Tolerance model and the role of self-awareness in time perception, we contend that the main way for patients to gain long-term self-confidence is to engage in the present moment. Attention to this attitude is obscured in chronic sufferers by worries and ruminations associated with the ongoing presence of tinnitus. We provide arguments that time perception is a social perception, emphasizing the role of rewarding interactions in helping sufferers to overcome the feeling of being prevented from living in the moment. In the course of improvement towards acceptance, different changes in time perception are hypothesized that promote individuals’ disengagement from unattainable goal (i.e., tinnitus suppression). A framework for future research is proposed, which distinguishes individuals’ behaviors and associated emotions in relation to the time paradox.
Unraveling the mystery of canopy dieback caused by citrus disease Huanglongbing and its link to hypoxia stress

Devastating citrus disease Huanglongbing (HLB) is without existing cures. Herein, we present results demonstrating the possible mechanisms (hypoxia stress) behind HLB-triggered shoot dieback by comparing the transcriptomes, hormone profiles, and key enzyme activities in buds of severely and mildly symptomatic ‘Hamlin’ sweet orange (Citrus sinensis). Within six months (October – May) in field conditions, severe trees had 23% bud dieback, greater than mild trees (11%), with a concomitant reduction in canopy density. In February, differentially expressed genes (DEGs) associated with responses to osmotic stress, low oxygen levels, and cell death were upregulated, with those for photosynthesis and cell cycle downregulated in severe versus mild trees. For severe trees, not only were the key markers for hypoxia, including anaerobic fermentation, reactive oxygen species (ROS) production, and lipid oxidation, transcriptionally upregulated, but also alcohol dehydrogenase activity was significantly greater compared to mild trees, indicating a link between bud dieback and hypoxia. Tricarboxylic acid cycle revival, given the upregulation of glutamate dehydrogenase and alanine aminotransferase DEGs, suggests that ROS may also be generated during hypoxia-reoxygenation. Greater (hormonal) ratios of abscisic acid to cytokinins and jasmonates and upregulated DEGs encoding NADPH oxidases in severe versus mild trees indicate additional ROS production under limited oxygen availability due to stomata closure. Altogether, our results provided evidence that as HLB progresses, excessive ROS produced in response to hypoxia and during hypoxia-reoxygenation likely intensify the oxidative stress in buds leading to cell death, contributing to marked bud and shoot dieback and decline of the severely symptomatic sweet orange trees.
Biological therapy in systemic lupus erythematosus, antiphospholipid syndrome, and Sjögren’s syndrome: evidence- and practice-based guidance

Systemic lupus erythematosus (SLE), antiphospholipid syndrome (APS), and Sjögren’s syndrome (SS) are heterogeneous autoimmune diseases. Severe manifestations and refractory/intolerance to conventional immunosuppressants demand other options, namely biological drugs, and small molecules. We aimed to define evidence and practice-based guidance for the off-label use of biologics in SLE, APS, and SS. Recommendations were made by an independent expert panel, following a comprehensive literature review and two consensus rounds. The panel included 17 internal medicine experts with recognized practice in autoimmune disease management. The literature review was systematic from 2014 until 2019 and later updated by cross-reference checking and experts’ input until 2021. Preliminary recommendations were drafted by working groups for each disease. A revision meeting with all experts anticipated the consensus meeting held in June 2021. All experts voted (agree, disagree, neither agree nor disagree) during two rounds, and recommendations with at least 75% agreement were approved. A total of 32 final recommendations (20 for SLE treatment, 5 for APS, and 7 for SS) were approved by the experts. These recommendations consider organ involvement, manifestations, severity, and response to previous treatments. In these three autoimmune diseases, most recommendations refer to rituximab, which aligns with the higher number of studies and clinical experience with this biological agent. Belimumab sequential treatment after rituximab may also be used in severe cases of SLE and SS. Second-line therapy with baricitinib, bortezomib, eculizumab, secukinumab, or tocilizumab can be considered in SLE-specific manifestations. These evidence and practice-based recommendations may support treatment decision and, ultimately, improve the outcome of patients living with SLE, APS, or SS.
The relation between college students’ neuroticism and loneliness: The chain mediating roles of self-efficacy, social avoidance and distress

Background Recently, identifying the psychological mechanism of college students’ loneliness has attracted wide attention because the maladjustment caused by college students’ loneliness is increasingly common. This study explored the relationship and potential mechanism between college students’ neuroticism and loneliness in a large sample. Methods A total of 4,600 college students completed the Big Five Personality Scale, Loneliness Scale, Self-efficacy Scale and Social Avoidance and Distress Scale. Results By examining the chain mediating roles of self-efficacy, social avoidance and distress (SAD) in the relation between neuroticism and loneliness, the present study found that college students’ neuroticism was positively associated with loneliness via self-efficacy and SAD, respectively, and sequentially. Conclusions The results suggest a significant positive association between neuroticism and loneliness, which is influenced by the mediating effects of both self-efficacy and social avoidance and distress (SAD), as well as the chained mediating effects of self-efficacy and SAD.
Reduced C9orf72 expression exacerbates polyGR toxicity in patient iPSC-derived motor neurons and a Type I protein arginine methyltransferase inhibitor reduces that toxicity

Introduction Intronic repeat expansions in the C9orf72 gene are the most frequent known single genetic causes of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These repeat expansions are believed to result in both loss-of-function and toxic gain-of-function. Gain-of-function results in the production of toxic arginine-rich dipeptide repeat proteins (DPRs), namely polyGR and polyPR. Small-molecule inhibition of Type I protein arginine methyltransferases (PRMTs) has been shown to protect against toxicity resulting from polyGR and polyPR challenge in NSC-34 cells and primary mouse-derived spinal neurons, but the effect in human motor neurons (MNs) has not yet been explored. Methods To study this, we generated a panel of C9orf72 homozygous and hemizygous knockout iPSCs to examine the contribution of C9orf72 loss-of-function toward disease pathogenesis. We differentiated these iPSCs into spinal motor neurons (sMNs). Results We found that reduced levels of C9orf72 exacerbate polyGR15 toxicity in a dose-dependent manner. Type I PRMT inhibition was able to partially rescue polyGR15 toxicity in both wild-type and C9orf72-expanded sMNs. Discussion This study explores the interplay of loss-of-function and gain-of-function toxicity in C9orf72 ALS. It also implicates type I PRMT inhibitors as a possible modulator of polyGR toxicity.