Miracle-dz/UniFAR-FTUs huggingface dataset:
Inter-institutional Resource Sharing in Undergraduate HPC Education: Interviews with University Administrators

High performance computing (HPC), typically used only in research until recently, is being integrated more into undergraduate curricula across disciplines. HPC resources are expensive but lend themselves easily to sharing among institutions. However, in the context of undergraduate education, inter-institutional sharing of such resources is still relatively rare. The authors hold the belief that generating administrator support early in system-wide initiatives for sharing resources is crucial for long term success. Taking the case of a specific HPC cluster at the University of Wisconsin-Eau Claire, part of the University of Wisconsin System (UW-System) of higher educational institutions, the authors asked 15 administrators from the system about the barriers as well as the path forward for better cluster sharing in undergraduate education. The responses to the interview questions were analyzed qualitatively for themes and sentiments. Five themes arose from this analysis, related to awareness of and access to HPC, cost-sharing structures, industry needs, institutional factors, and variations in benefits depending on the field. The sentiments were overwhelmingly positive, but with variations depending on the questions asked and approaches taken by the interviewees. Overall, the responses indicated a positive attitude and willingness to incorporate HPC in undergraduate education as well as the importance of awareness of such resources. They also indicate that cost-sharing structures and institutional factors are both the biggest barriers and the keys to better sharing practices and industry partnerships. At the end, the authors make recommendations for anyone looking to establish a framework to share HPC resources across institutions.
Investigating Reflection in Undergraduate Software Development Teams: An Analysis of Online Chat Transcripts

Metacognition is widely acknowledged as a key soft skill in collaborative software development. The ability to plan, monitor, and reflect on cognitive and team processes is crucial to the efficient and effective functioning of a software team. To explore students' use of reflection--one aspect of metacognition--in undergraduate team software projects, we analyzed the online chat channels of teams participating in agile software development projects in two undergraduate courses that took place exclusively online (n = 23 teams, 117 students, and 4,915 chat messages). Teams' online chats were dominated by discussions of work completed and to be done; just two percent of all chat messages showed evidence of reflection. A follow-up analysis of chat vignettes centered around reflection messages (n = 63) indicates that three-fourths of the those messages were prompted by a course requirement; just 14% arose organically within the context of teams' ongoing project work. Based on our findings, we identify opportunities for computing educators to increase, through pedagogical and technological interventions, teams' use of reflection in team software projects.
Challenges and opportunities of using a cooperative digital educational plan. Evaluation of the implementation

Abstract The virtual school board (VSB) offers teachers a browser-based platform to support a multilevel, evidence-based educational plan. The present study examines teachers’ use of the VSB. Based on technology acceptance model (TAM), 17 teachers from nine schools were interviewed about their use of the VSB. The evaluation was based on qualitative content analysis (QCA). For seven categories the intercoder reliabilities were acceptable. After 24 months, the users said that they used the VSB for support planning, diagnostics, discussions with parents and other documentation. They rated the overview gained and the interdisciplinary exchange as beneficial. However, a lack of technical expertise within the staff, the technical equipment and the user interface hindered teachers, such that almost a fifth never used the software completely. The challenges are complex. Needless to say, missing, little or old technical hardware is likely to decrease the usage of a digital tool; the implementation also faces the challenges of recontextualisation, and additionally faces the resource-labelling dilemma. Therefore, these challenges must be dealt with in the mutual interaction between school practice, educational research and professional information and communication technology (ICT) development.
Observation of femtosecond light pulse propagation by using digital light-in-flight recording by holography

We demonstrate motion pictures of femtosecond light pulse propagation. We adopted digital light-in-flight recording by holography as a technique for observation of femtosecond light pulse propagation. We recorded and reconstructed a moving picture of femtosecond light pulse propagating on a diffuser plate on which a test chart pattern was printed. The center wavelength and the duration of the light pulse were 800 nm and 96 fs, respectively. We successfully observed femtosecond light pulse propagation for 530 fs by the technique.
Current crowding effect on the ideality factor and efficiency droop in blue lateral InGaN/GaN light emitting diodes

By examining two types of lateral InGaN/GaN light emitting diodes with different contact patterns, we demonstrate that in the intermediate range of current where the space-charge region dominates in the device performance, the ideality factor (β) increases from 1.9 (current spreading design) up to 2.4 (current crowding design). This modification of β-factor could be erroneously treated as the change of free carrier recombination nature. The current crowding design is also responsible for the local overheating and heavier efficiency droop that occurs at the characteristic current 2.3 times smaller in comparison with the current spreading design.
Registration of 3D Point Cloud of Human Body Based on the Range Images and RGB Images

The existing 3D reconstruction techniques rarely can be easily used in people's daily life, and the traditional registration algorithms have the drawback of massive calculation. In this paper it presented a registration algorithm of body point cloud based on RGB images and Range images. First, it used kinect to obtain the RGB images and Range images from different perspectives. Then it extracted the pairs of 2D feature points on RGB images using scale-invariant feature transform (SIFT) and random sample consensus (RANSAC) algorithm application for the coarse registration and used the improved iterative closest point (ICP) algorithm for the fine registration. Second, it eliminated the background information and the noise points of the model edges. Finally it completed the registration process. Experimental results show that the algorithm can accurately accomplish the body point clouds registration using the low-cost instrument and has a relatively high efficiency.
Specific heat in high magnetic fields and non-Fermi-liquid behavior inCeMIn5(M=Ir,Co)

The low-temperature specific heat, in magnetic fields to 32 T, and the magnetic susceptibility are reported on single crystals of the new heavy-fermion superconductors $\mathrm{Ce}M{\mathrm{In}}_{5},$ $M=\mathrm{Ir}$ and Co, as well as the new heavy-fermion antiferromagnet ${\mathrm{CeRhIn}}_{5}. $ The absence of a pronounced field dependence to the specific heat of the Ir and Co systems suggests that the large Sommerfeld coefficients of these compounds are due to correspondingly large effective electron masses. In addition, the indicated non-Fermi-liquid behavior previously suggested from the temperature dependence of the resistivity of ${\mathrm{CeIrIn}}_{5}$ has been confirmed in our measurements of the susceptibility and specific heat for this compound, as well as in the susceptibility and specific heat of ${\mathrm{CeCoIn}}_{5}. $ The existence of superconductivity in these systems that appears, based on their non-Fermi-liquid behavior, to develop near a quantum critical point is further support for this superconductivity being of unconventional nature.
ORF3c is expressed in SARS-CoV-2 infected cells and suppresses immune activation by inhibiting innate sensing

SARS-CoV-2 proteins are translated from subgenomic RNAs (sgRNAs). While most of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. For example, the ORF3a sgRNA also encodes ORF3c, an enigmatic 4l-amino acid peptide. Here, we show that ORF3c is expressed in SARS-CoV-2 infected cells and suppresses RIG-I- and MDA5-mediated immune activation and IFN-β induction. Mechanistic analyses revealed that ORF3c interacts with the signaling adaptor MAVS, induces its C-terminal cleavage and inhibits the interaction of RIG-I with MAVS. The immunosuppressive activity of ORF3c is conserved among members of the subgenus sarbecovirus, including SARS-CoV and coronaviruses isolated from bats. Notably, however, the SARS-CoV-2 delta and kappa variants harbor premature stop codons in ORF3c demonstrating that this reading frame is not essential for efficient viral replication in vivo and likely compensated by other viral proteins. In agreement with this, disruption of ORF3c did not significantly affect SARS-CoV-2 replication in CaCo-2 or CaLu-3 cells. In summary, we here identify ORF3c as an immune evasion factor of SARS-CoV-2 that suppresses innate sensing in infected cells.
Activation of prefrontal parvalbumin interneurons ameliorates treatment-resistant working memory deficit even under continuous antipsychotic treatment in a mouse model of schizophrenia

BACKGROUND One of the critical unmet medical needs in schizophrenia is a remedy for cognitive deficits. However, the neural circuit mechanisms of them remain unresolved. In addition, despite the patients with schizophrenia cannot stop taking antipsychotics due to a high rate of discontinuation-induced relapse, previous studies using animal models of schizophrenia have not considered these clinical situations. METHODS Here, we employ multi-dimensional approaches, including histological analysis in the prelimbic cortex, LC-MS/MS-based in vivo dopamine D2 receptor occupancy analysis for antipsychotic drugs, in vivo calcium imaging and behavioral analyses of mice using chemogenetic manipulation, to investigate neural mechanisms and potential therapeutic interventions for working memory deficit in a mouse model with chronic phencyclidine (PCP) administration that resembles the schizophrenia symptomatology. RESULTS Chronic PCP administration led to abnormalities in excitatory and inhibitory synapses, including dendritic spines of pyramidal neurons, vesicular glutamate transporter 1 (VGLUT1) positive terminals, and parvalbumin (PV) positive GABAergic interneurons, in layer 2–3 of the prelimbic cortex. Continuous olanzapine, which achieved a sustained therapeutic window of dopamine D2 receptor occupancy (60–80%) in the striatum, did not affect these synaptic abnormalities and working memory deficit in the PCP-treated mice. We found that the selective prelimbic PV activation, using hM3D(Gq)-DREADD system confirmed by in vivo calcium imaging, restored working memory deficit, even under continuous olanzapine treatment. CONCLUSIONS Our study raises a possibility that intervention in prefrontal PV neurons leads to an add-on therapy to antipsychotics targeting amelioration of treatment-resistant cognitive deficits in schizophrenia.
High-speed measurement of axial grain transport in a rotating drum

Granular mixtures segregate radially by size when tumbled in a partially filled horizontal drum on short timescales. The smaller component moves towards the axis of rotation and forms a buried core, which then forms undulations that grow into axial bands. Experimental and simulational studies have provided differing accounts of the type of transport taking place in radially segregated and self-diffusing grains. We investigate the bulk axial transport of small quantities of tracer particles travelling amongst glass spheres using non-invasive high-speed synchrotron x-ray particle tracking, which allows us to access timescales not explored previously. The mixtures used have varying propensity to axially segregate based on the glass sphere sizes when the tracers are present in larger proportions; we found that the single-particle dynamics of these mixtures when the tracer concentration is low do not appreciably depend on the relative particle sizes, implying that the potential for a mixture to axially segregate cannot be inferred from the microscopic dynamics of individual small particles. From the single-particle dynamics, we also found that while the standard measure of diffusive behaviour, the slope of the mean-squared displacement, is close to that expected from diffusive transport, more detailed analyses indicate anomalous transport.
Atypical cell death in the growth plate chondrocytes of Tric-b-knockout mice

TRIC-A and TRIC-B proteins form homotrimeric cation-permeable channels in the sarco/endoplasmic reticulum (SR/ER) and nuclear membranes and are thought to contribute to counterionic flux coupled with store Ca2+ release in various cell types. Serious mutations in the TRIC-B locus cause autosomal recessive osteogenesis imperfecta (OI), which is characterized by insufficient bone mineralization. We have reported that Tric-b-knockout mice can be used as an OI model. Here we report irregular cell death in proliferating growth plate chondrocytes in developing Tric-b-knockout bones. In the knockout chondrocytes, excess pro-collagen fibers were occasionally accumulated in severely dilated ER elements. Of the major ER stress pathways, the PERK pathway was preferentially hyperactivated in the knockout chondrocytes, and most likely altered gene expression to induce apoptosis-related proteins including CHOP and caspase 12. In Ca2+ imaging experiments, the knockout chondrocytes exhibited aberrant Ca2+ handling; ER Ca2+ release was impaired, and intracellular Ca2+ concentration was elevated. Our data suggest that Tric-b deficiency directs growth plate chondrocytes to pro-apoptotic stages by compromising cellular Ca2+-handling and exacerbating ER stress, leading to atypical apoptotic cell death.
Gene essentiality in cancer is better predicted by mRNA abundance than by gene regulatory network-inferred activity

Gene regulatory networks (GRNs) are often deregulated in tumor cells, resulting in altered transcriptional programs that facilitate tumor growth. These altered networks may make tumor cells vulnerable to the inhibition of specific regulatory proteins. Consequently, the reconstruction of GRNs in tumors is often proposed as a means to identify therapeutic targets. While there are examples of individual targets identified using GRNs, the extent to which GRNs can be used to predict sensitivity to targeted intervention in general remains unknown. Here we use the results of genome-wide CRISPR screens to systematically assess the ability of GRNs to predict sensitivity to gene inhibition in cancer cell lines. Using GRNs derived from multiple sources, including GRNs reconstructed from tumor transcriptomes and from curated databases, we infer regulatory gene activity in cancer cell lines from ten cancer types. We then ask, in each cancer type, if the inferred regulatory activity of each gene is predictive of sensitivity to CRISPR perturbation of that gene. We observe slight variation in the correlation between gene regulatory activity and gene sensitivity depending on the source of the GRN and the activity estimation method used. However, we find that there is consistently a stronger relationship between mRNA abundance and gene sensitivity than there is between regulatory gene activity and gene sensitivity. This is true both when gene sensitivity is treated as a binary and a quantitative property. Overall, our results suggest that gene sensitivity is better predicted by measured expression than by GRN-inferred activity.
Topology recapitulates ontogeny of dendritic arbors

Branching of dendrites and axons allows neurons to make synaptic contacts with large numbers of other neurons, facilitating the high connectivity of the nervous system. Neurons have geometric properties, such as the lengths and diameters of their branches, that change systematically throughout the arbor in ways that are thought to minimize construction costs and to optimize the transmission of electrical signals and the intracellular transport of materials. In this work, we investigated whether neuronal arbors also have topological properties that reflect the growth and/or functional properties of their dendritic arbors. In our efforts to uncover possible topological rules, we discovered a function that depends only on the topology of bifurcating trees such as dendritic arbors: the tip-support distribution, which is the average number of branches that support n dendrite tips. We found that for many, but not all, neurons from a wide range of invertebrate and vertebrate species, the tip-support distribution follows a power law with slopes ranging from -1.4 and -1.8 on a log-log plot. The slope is invariant under iterative trimming of terminal branches and under random ablation of internal branches. We found that power laws with similar slopes emerge from a variety of iterative growth processes including the Galton-Watson (GW) process, where the power-law behavior occurs after the percolation threshold. Through simulation, we show the slope of the power-law increases with the branching probability of a GW process, which corresponds to a more regular tree. Furthermore, the inclusion of postsynaptic spines and other terminal processes on branches causes a characteristic deviation of the tip-support distribution from a power law. Therefore, the tip-support function is a topological property that reflects the underlying branching morphogenesis of dendritic trees.
Global transcriptional analysis of Geobacter sulfurreducens gsu1771 mutant biofilm grown on two different support structures

Electroactive biofilms formation by the metal-reducing bacterium Geobacter sulfurreducens is a crucial for bioelectricity generation and bioremediation. The transcriptional regulator GSU1771 controls the expression of essential genes involved in electron transfer and biofilm formation in G. sulfurreducens, with GSU1771-deficient producing thicker and more electroactive biofilms. Here, RNA-seq analyses were conducted to compare the global gene expression patterns of wild-type and Δgsu1771 mutant biofilms grown on non-conductive (glass) and conductive (graphite electrode) materials. The Δgsu1771 biofilm grown on the glass surface exhibited 467 differentially expressed (DE) genes (167 upregulated and 300 downregulated) versus the wild-type biofilm. In contrast, the Δgsu1771 biofilm grown on the graphite electrode exhibited 119 DE genes (79 upregulated and 40 downregulated) versus the wild-type biofilm. Among these DE genes, 67 were also differentially expressed in the Δgsu1771 biofilm grown on glass (56 with the same regulation and 11 exhibiting counter-regulation). Among the upregulated genes in the Δgsu1771 biofilms, we identified potential target genes involved in exopolysaccharide synthesis (gsu1961-63, gsu1959, gsu1972-73, gsu1976-77). RT-qPCR analyses were then conducted to confirm the differential expression of a selection of genes of interest. DNA-protein binding assays demonstrated the direct binding of the GSU1771 regulator to the promoter region of pgcA, pulF, relA, and gsu3356. Furthermore, heme-staining and western blotting revealed an increase in c-type cytochromes including OmcS and OmcZ in Δgsu1771 biofilms. Collectively, our findings demonstrated that GSU1771 is a global regulator that controls extracellular electron transfer and exopolysaccharide synthesis in G. sulfurreducens, which is crucial for electroconductive biofilm development. Importance Biofilm formation is a multi-stage process that is finely coordinated by signal transduction and complex gene regulation mechanisms. Given the importance of biofilms and their biotechnological applications, understanding these processes in G. sulfurreducens is of great significance. Here, we studied the transcriptional profile of the Δgsu1771 strain biofilms formed on two different supporting materials: (1) glass, a non-conductive surface and (2) a graphite electrode-based microbial fuel cell (MFC), which enabled us to assess the transcriptional responses of this strain during current production. By analyzing these two conditions, our study elucidated genes of interest that could be essential for biofilm production and extracellular electron transfer (EET) and provides new insights into the mechanisms that control these complex processes in G. sulfurreducens.
Mechanism of barotaxis in marine zooplankton

Hydrostatic pressure is a dominant environmental cue for vertically migrating marine organisms but the physiological mechanisms of responding to pressure changes remain unclear. Here we uncovered the cellular and circuit bases of a barokinetic response in the planktonic larva of the marine annelid Platynereis dumerilii. Increases in pressure induced a rapid, graded and adapting upward swimming response due to faster ciliary beating. By calcium imaging, we found that brain ciliary photoreceptors showed a graded response to pressure changes. The photoreceptors in animals mutant for ciliary opsin-1 had a smaller ciliary compartment and mutant larvae showed diminished pressure responses. The ciliary photoreceptors synaptically connect to the head multiciliary band that propels swimming via serotonergic motoneurons. Genetic inhibition of the serotonergic cells blocked pressure-dependent increases in ciliary beating. We conclude that ciliary photoreceptors function as pressure sensors and activate ciliary beating through serotonergic signalling during barokinesis.
Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning

Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) – Cas technology has revolutionized many fields in biology. Beyond Cas9 nucleases, Cas12a (formerly Cpf1) has emerged as a promising alternative to Cas9 for editing AT-rich genomes. Despite the promises, guide RNA efficiency prediction through computational tools search still lacks accuracy. Through a computational meta-analysis, here we report that Cas12a target and off-target cleavage behaviour are factor of nucleotide bias combined with nucleotide mismatches relative to the protospacer adjacent motif (PAM) site. These features helped to train a machine learning random forest algorithm to improve the accuracy by at least 15% to existing algorithms to predict guide RNA efficiency for Cas12a enzyme. Despite the progresses, our report underscores the need for more representative datasets and further benchmarking to reliably and accurately predict guide RNA efficiency and off-target effects for Cas12a enzymes.