Miracle-dz/UniFAR-FTUs huggingface dataset:
A psychological intervention strengthens students’ peer social networks and promotes persistence in STEM

A psychological intervention increased students’ persistence in biology by building their friendships in a gateway course. Retaining students in science, technology, engineering, and math (STEM) fields is critical as demand for STEM graduates increases. Whereas many approaches to improve persistence target individuals’ internal beliefs, skills, and traits, the intervention in this experiment strengthened students’ peer social networks to help them persevere. Students in a gateway biology course were randomly assigned to complete a control or values affirmation exercise, a psychological intervention hypothesized to have positive social effects. By the end of the term, affirmed students had an estimated 29% more friends in the course on average than controls. Affirmation also prompted structural changes in students’ network positions such that affirmed students were more central in the overall course friendship network. These differing social trajectories predicted STEM persistence: Affirmed students were 11.7 percentage points more likely than controls to take the next course in the bioscience sequence, an effect that was statistically mediated by students’ end-of-semester friendships.
Covid-19 Has Turned Home Advantage Into Home Disadvantage in the German Soccer Bundesliga

The main factors for home advantage (HA), quantified by the number of points won at home expressed as a percentage of all points, are believed to be crowd support, territoriality, familiarity, and travel fatigue. In 2020, the German Soccer Bundesliga interrupted its championship due to the Covid-19 pandemic after 25 rounds and the last nine rounds were played without audience. This unique situation allowed studying the effect of spectators on the team's performance and the referee's decisions. We hypothesized a decrease in HA and a more balanced distribution of fouls and disciplinary cards in the games without audience (GWOA) compared to the games with audience (GWA). We evaluated n = 223 GWA and n = 83 GWOA of the season 2019/20 and all games of the preceding season 2018/19 to analyze the distribution of game outcomes (wins, losses, and draws) and HA. We analyzed the number of fouls, disciplinary cards, and penalty kicks. We found significant differences in HA between GWA (HA = 54.35%) and GWOA (HA = 44.1%) as well as GWOA and games of 2018/19 (HA = 57.63%). The distribution of game outcomes in GWOA did not differ from GWA but differed significantly from 2018/19 (p = 0.031). The distribution of fouls showed a significant difference to equal distribution in GWA [home: 2,595 (48.56%); away: 2,749 (51.44%)] but not in GWOA [home: 1,067 (50.54%); away: 1,044 (49.46%)]. In the GWOA, we counted 178 (51.1%, home) and 170 (48.9%, away) cards, representing a significant difference in the distribution to GWA [home: 405 (44.85%); away: 498 (55.15%)]. The number of red cards differed significantly from an equal distribution for GWA (14 home and 28 away) but not for GWOA (eight home and seven away). In the last nine rounds without audience, we observed more home losses (36) than home wins (27). Hence, the Covid-19 lock-down led to a home disadvantage. One reason for this surprising result could be that the home team is missing an important familiar aspect when playing in their empty stadium without social support from their home audience. Furthermore, both teams know about the HA thus the away team could be more motivated in this unusual situation.
Bioinspired cilia arrays with programmable nonreciprocal motion and metachronal coordination

Programmable artificial cilia arrays enable metachronal coordination for enhanced fluid pumping at the low Reynolds number regime. Coordinated nonreciprocal dynamics in biological cilia is essential to many living systems, where the emergentmetachronal waves of cilia have been hypothesized to enhance net fluid flows at low Reynolds numbers (Re). Experimental investigation of this hypothesis is critical but remains challenging. Here, we report soft miniature devices with both ciliary nonreciprocal motion and metachronal coordination and use them to investigate the quantitative relationship between metachronal coordination and the induced fluid flow. We found that only antiplectic metachronal waves with specific wave vectors could enhance fluid flows compared with the synchronized case. These findings further enable various bioinspired cilia arrays with unique functionalities of pumping and mixing viscous synthetic and biological complex fluids at low Re. Our design method and developed soft miniature devices provide unprecedented opportunities for studying ciliary biomechanics and creating cilia-inspired wireless microfluidic pumping, object manipulation and lab- and organ-on-a-chip devices, mobile microrobots, and bioengineering systems.
The Effects of Limited Visual Acuity and Context on the Appearance of Anolis Lizard Dewlaps

Abstract. Male Anolis lizards display their colorful dewlaps in a variety of contexts, ranging from long-distance territorial displays to close-range agonistic and courtship displays. Anoles have eyes of high optical quality and a retina that contains tightly spaced, small-diameter photoreceptors. Highest visual acuity is associated with the center of the retina (=12.5 cycles o -1), whereas acuity is much lower in the periphery. Anoles possess a small eye that creates a small retinal image, which limits their maximum visual spatial acuity to approximately 1/10 that of humans. In animal visual systems spatial resolution falls rapidly with distance from the stimulus. In some species, dewlap color patterns are fairly complex and may transmit various kinds of information. To gain insight into the visual information that conspecifics can potentially extract from dewlap color patterns, we modified high-resolution digital photographs reflecting the limits imposed by the acuity of the Anolis eye. For central retinal vision, from a distance of 0.5 m or less, the finest levels of dewlap pattern spatial detail were visible. At greater distances, and/or for peripheral vision, much less detail could be resolved. When viewed from 1 m away with peripheral vision, only the average color of the large patches could be detected, and all pattern detail was lost. The potential information content of the dewlap patterns changes dramatically with the context in which it is viewed. We show that a clear knowledge of an animal's sensory limitations can lead to greatly improved hypotheses about signal function.
A neural mechanism for affective well-being: Subgenual cingulate cortex mediates real-life effects of nonexercise activity on energy

A neural mechanism underlying the real-life effects of nonexercise activity on well-being promises novel intervention targets. Physical activity substantially improves well-being and mental health, but the underlying brain processes remain unclear. Most research concerns exercise, although the majority of everyday human behaviors, such as walking or stair climbing, are nonexercise activities. Combining neuroimaging with ecological assessment of activity and GPS-triggered smartphone diaries, we show a specific association of nonexercise activity with energy in two independent samples mediated by the subgenual part of the anterior cingulate cortex (sgACC), a key emotion regulatory site. Furthermore, energy predicted a range of mental health metrics. sgACC volume moderated humans’ emotional gain from nonexercise activity in real life: Individuals with low sgACC volume, a risk factor for depression, felt less energized when inactive but benefited more from periods of high nonexercise activity. This suggests an everyday life mechanism affecting affective well-being in the general population and, if substantiated in patient samples, a risk and resilience process for mood disorders.
Singling the odd ones out: a novelty detection approach to find defects in infrastructure-as-code

Infrastructure-as-Code (IaC) is increasingly adopted. However, little is known about how to best maintain and evolve it. Previous studies focused on defining Machine-Learning models to predict defect-prone blueprints using supervised binary classification. This class of techniques uses both defective and non-defective instances in the training phase. Furthermore, the high imbalance between defective and non-defective samples makes the training more difficult and leads to unreliable classifiers. In this work, we tackle the defect-prediction problem from a different perspective using novelty detection and evaluate the performance of three techniques, namely OneClassSVM, LocalOutlierFactor, and IsolationForest, and compare their performance with a baseline RandomForest binary classifier. Such models are trained using only non-defective samples: defective data points are treated as novelty because the number of defective samples is too little compared to defective ones. We conduct an empirical study on an extremely-imbalanced dataset consisting of 85 real-world Ansible projects containing only small amounts of defective instances. We found that novelty detection techniques can recognize defects with a high level of precision and recall, an AUC-PR up to 0.86, and an MCC up to 0.31. We deem our results can influence the current trends in defect detection and put forward a new research path toward dealing with this problem.
MirageManager: enabling stateful migration for unikernels

Unikernels are a new lightweight virtualization technology born as an alternative to virtual machines and containers. Geared towards service provisioning for the Internet of Things (IoT) and edge computing, they offer extremely small memory footprint and strong isolation properties. However, the unikernels ecosystem is still in its infancy and lacks quintessential functionalities found in more well-established virtualization technologies. For example, stateful migration is a highly desired feature for mobile edge services in distributed environments which is not yet supported by unikernels. This is one of the shortcomings preventing us from reaping the full benefits of unikernels outside of stateless applications. In this work, we aim bridging this gap with MirageManager: a ready-to-deploy unikernel migration system enabling lossless migration supported by a function-level, application logic check-pointing library of our design. Our evaluation results show that MirageManager is able to lower the service downtime by ~80%, and drastically reduce the state transfer data by almost ~100% when comparing against Podman. Additionally, MirageManager also beats Podman, a container-based engine, in parallel service migration across constrained edge networks reducing the overall migration time by up to ~6x.
Apicobasal Surfaceome Architecture Encodes for Polarized Epithelial Functionality and Depends on Tumor Suppressor PTEN

The loss of apicobasal polarity during the epithelial-to-mesenchymal transition (EMT) is a hallmark of cancer and metastasis. The key feature of this polarity in epithelial cells is the subdivision of the plasma membrane into apical and basolateral domains, with each orchestrating specific intra- and extracellular functions. Epithelial transport and signaling capacities are thought to be determined largely by the quality, quantity and nanoscale organization of proteins residing in these membrane domains, the apicobasal surfaceomes. Despite its implications for cancer, drug uptake and infection, our current knowledge of how the polarized surfaceome is organized and maintained is limited. Here we used chemoproteomic surfaceome scanning to establish proteotype maps of apicobasal surfaceomes and reveal quantitative distributions of i.a. surface proteases, phosphatases and tetraspanins as potential key regulators of polarized cell functionality. We show further that tumor-suppressor PTEN regulates polarized surfaceome architecture and uncover a potential role in collective cell migration. Our differential surfaceome analysis provides a molecular framework to elucidate polarized protein networks regulating epithelial functions and PTEN-associated cancer progression. Summary One cell, two functionally different surfaceomes: Chemoproteomic surfaceome scanning reveals quantitative polarization of protein networks across the epithelial cell membrane and unrecognized roles of tumor suppressor PTEN in surfaceome organization associated with cancer progression.
A Two-Step Bioreactor for Lung Recellularization

Bioreactors for reseeding of decellularized lung scaffolds have evolved with a wide variety of advancements. These include biomimetic mechanical stimulation, constant nutrient flow, multi-output monitoring, and large mammal scaling. Although dynamic bioreactors are not new to the field of bioengineered lungs, ideal conditions during cell seeding have not been extensively studied or controlled. To address the lack of cell dispersal in traditional seeding methods, we have designed a two-step bioreactor. The first step rotates a seeded lung every 20 minutes at different angles to ensure 20 percent of cells are anchored to a particular location based on the known rate of attachment. The second step involves perfusion culture to ensure nutrient dispersion and cellular growth. Compared to statically seeded lungs followed by conventional perfusion, rotationally seeded lungs followed by perfusion had significantly increased dsDNA content and more uniform cellular distribution. This new bioreactor system will aid in recellularizing the lung and other geometrically complex organs for tissue engineering.
Structural basis for repurpose and design of nucleoside drugs for treating COVID-19

SARS-CoV-2 has caused a global pandemic of COVID-19 that urgently needs an effective treatment. Nucleoside analog drugs including favipiravir have been repurposed for COVID-19 despite of unclear mechanism of their inhibition of the viral RNA polymerase (RdRp). Here we report the cryo-EM structures of the viral RdRp in complex with favipiravir and two other nucleoside inhibitor drugs ribavirin and penciclovir. Ribavirin and the ribosylated form of favipiravir share a similar ribose scaffold that is distinct from penciclovir. However, the structures reveal that all three inhibitors are covalently linked to the primer strand in a monophosphate form despite the different chemical scaffolds between favipiravir and penciclovir. Surprisingly, the base moieties of these inhibitors can form mismatched pairs with the template strand. Moreover, in view of the clinical disadvantages of remdesivir mainly associated with its prodrug form, we designed several orally-available remdesivir parent nucleoside derivatives, including VV16 that showed 5-fold more potent than remdesivir in inhibition of viral replication. Together, these results demonstrate an unexpected promiscuity of the viral RNA polymerase and provide a basis for repurpose and design of nucleotide analog drugs for COVID-19. One Sentence Summary Cryo-EM structures of the RNA polymerase of SARS-CoV-2 reveals the basis for repurposing of old nucleotide drugs to treat COVID-19.
Neutrophils Encompass a Regulatory Subset Suppressing T Cells in Apparently Healthy Cattle and Mice

Neutrophils that reside in the bone marrow are switly recruited from circulating blood to fight infections. For a long time, these first line defenders were considered as microbe killers. However their role is far more complex as cross talk with T cells or dendritic cells have been described for human or mouse neutrophils. In cattle, these new roles are not documented yet. We identified a new subset of regulatory neutrophils that is present in the mouse bone marrow or circulate in cattle blood under steady state conditions. These regulatory neutrophils that display MHC-II on the surface are morphologically indistinguishable from classical MHC-IIneg neutrophils. However MHC-IIpos and MHC-IIneg neutrophils display distinct transcriptomic profiles. While MHC-IIneg and MHC-IIpos neutrophils display similar bacterial phagocytosis or killing activity, MHC-IIpos only are able to suppress T cell proliferation under contact-dependent mechanisms. Regulatory neutrophils are highly enriched in lymphoid organs as compared to their MHC-IIneg counterparts and in the mouse they express PDL-1, an immune checkpoint involved in T-cell blockade. Our results emphasize neutrophils as true partners of the adaptive immune response, including in domestic species. They open the way for discovery of new biomarkers and therapeutic interventions to better control cattle diseases.
Molecular and morphological analyses clarify species delimitation and reveal a new Betula species in section Costatae

Background and Aims Delineating closely related and morphologically similar species with overlapping ranges can be difficult. Here, we use section Costatae (genus Betula) as a model to resolve species and subspecies boundaries in four morphologically similar trees: Betula ashburneri, Betula costata, Betula ermanii and Betula utilis (including ssp. utilis, and diploid and tetraploid races of ssp. albosinensis). Methods We genotyped 298 individuals (20-80 per species) from 38 populations at 15 microsatellite markers and a subset of 34 individuals from 21 populations using restriction-site associated DNA sequencing (RAD-seq). Morphometric analysis was conducted to characterise leaf variation for a subset of 89 individuals. Key Results Molecular analyses and leaf morphology found little differentiation between B. ashburneri, diploid B. utilis ssp. albosinensis and some samples of B. utilis ssp. utilis suggesting that these should be treated as a single species. By contrast, tetraploid Betula utilis ssp. albosinensis was divided into two groups with group I genetically similar to B. utilis ssp. utilis based on SNPs and group II, a very distinct cluster, which we propose as a new species, namely, Betula buggsii. Phylogenomic analysis based on 2,285,620 SNPs show a well-supported monophyletic clade of B. buggsii, forming a sister with a well-supported clade of B. ashburneri, diploid B. albosinensis and some samples of B. utilis ssp. utilis. Morphologically, Betula buggsii is characterised by elongated lenticels and a distinct pattern of bark peeling. Betula buggsii is geographically restricted to the Qinling-Daba Mountains. Conclusions Our study reveals six genetically distinguishable species: B. ashburneri, B. buggsii, B. costata, B. utilis ssp. utilis, B. utilis ssp. albosinensis and B. ermanii. Our research demonstrates an integrative approach in delimitating species using morphological and genetic samples from their nearly entire distributions. Analyses based on subsets of species’ distributions may lead to erroneous species or subspecies delineation.
A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data and species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 protein-coding sequences of plastome data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the group using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggest putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 69.38 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we herein recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity to use a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and chloroplast genomes to reconstruct deep and shallow phylogenies of plants.
Adipose Triglyceride Lipase is needed for homeostatic control of Sterol Element-Binding Protein-1c driven hepatic lipogenesis

Sterol Regulatory Element-Binding Protein-1c (SREBP-1c) is translated as an inactive precursor-protein that is proteolytically activated to promote fatty-acid (FA) biosynthesis, when unsaturated (u)FAs are scarce. During fasting, however, lipogenesis is low, and adipose-tissue lipolysis supplies the organism with FAs. Adipose TriGlyceride Lipase (ATGL) is the rate-limiting enzyme for lipolysis, and it preferentially hydrolyzes uFAs. Therefore, we hypothesized that ATGL-derived FAs may suppress the proteolytic activation of SREBP-1c in the liver. Here we show that (i) SREBP-1c is inactive during fasting but active after refeeding, (ii) uFA species liberated by ATGL suppress SREBP-1c activation in vitro, (iii) SREBP-1c is hyper-activated in livers of mice lacking ATGL, and (iv) pharmacological inhibition of ATGL selectively activates SREBP-1c in hepatocytes. Our findings highlight an ATGL/SREBP-1c axis, instrumental to coordinate lipogenesis and lipolysis, whose homeostatic regulation is crucial to avoid severe diseases including diabetes, cardiomyopathy, and even cancer.
The epithelial splicing regulator ESRP2 is epigenetically repressed by DNA hypermethylation in Wilms tumour and acts as a tumour suppressor

Wilms tumour (WT), a childhood kidney cancer with embryonal origins, has been extensively characterised for genetic and epigenetic alterations, but a proportion of WTs still lack identifiable abnormalities. To uncover DNA methylation changes critical for WT pathogenesis, we compared the epigenome of fetal kidney with two WT cell lines, using methyl-CpG immunoprecipitation. We filtered our results to remove common cancer-associated epigenetic changes, and to enrich for genes involved in early kidney development. This identified four candidate genes that were hypermethylated in WT cell lines compared to fetal kidney, of which ESRP2 (epithelial splicing regulatory protein 2), was the most promising gene for further study. ESRP2 was commonly repressed by DNA methylation early in WT development (in nephrogenic rests) and could be reactivated by DNA methyltransferase inhibition in WT cell lines. When ESRP2 was expressed in WT cell lines, it acted as an inhibitor of cellular proliferation in vitro and in vivo it suppressed tumour growth of orthotopic xenografts in nude mice. RNA-seq of the ESRP2-expressing WT cell lines identified several novel splicing targets, in addition to well-characterised targets of ESRP2. One of these targets, LEF1, is a component of the Wnt signalling pathway that is essential for kidney development and commonly disrupted in WT. We propose a model in which the Wnt pathway can be disrupted in early kidney development to generate WT, either by genetic abnormalities such as WT1 mutations, or by epigenetic defects, such as ESRP2 methylation.