Miracle-dz/UniFAR-FTUs huggingface dataset:
How are Deep Learning Models Similar? An Empirical Study on Clone Analysis of Deep Learning Software

Deep learning (DL) has been successfully applied to many cuttingedge applications, e.g., image processing, speech recognition, and natural language processing. As more and more DL software is made open-sourced, publicly available, and organized in model repositories and stores (MODEL Zoo, Modeldepot), there comes a need to understand the relationships of these DL models regarding their maintenance and evolution tasks. Although clone analysis has been extensively studied for traditional software, up to the present, clone analysis has not been investigated for DL software. Since DL software adopts the data-driven development paradigm, it is still not clear whether and to what extent the clone analysis techniques of traditional software could be adapted to DL software. In this paper, we initiate the first step on the clone analysis of DL software at three different levels, i.e., source code level, model structural level, and input/output (I/O)-semantic level, which would be a key in DL software management, maintenance and evolution. We intend to investigate the similarity between these DL models from clone analysis perspective. Several tools and metrics are selected to conduct clone analysis of DL software at three different levels. Our study on two popular datasets (i.e., MNIST and CIFAR-10) and eight DL models of five architectural families (i.e., LeNet, ResNet, DenseNet, AlexNet, and VGG) shows that: 1). the three levels of similarity analysis are generally adequate to find clones between DL models ranging from structural to semantic; 2). different measures for clone analysis used at each level yield similar results; 3) clone analysis of one single level may not render a complete picture of the similarity of DL models. Our findings open up several research opportunities worth further exploration towards better understanding and more effective clone analysis of DL software.
ARDiff: scaling program equivalence checking via iterative abstraction and refinement of common code

Equivalence checking techniques help establish whether two versions of a program exhibit the same behavior. The majority of popular techniques for formally proving/refuting equivalence relies on symbolic execution – a static analysis approach that reasons about program behaviors in terms of symbolic input variables. Yet, symbolic execution is difficult to scale in practice due to complex programming constructs, such as loops and non-linear arithmetic. This paper proposes an approach, named ARDiff, for improving the scalability of symbolic-execution-based equivalence checking techniques when comparing syntactically-similar versions of a program, e.g., for verifying the correctness of code upgrades and refactoring. Our approach relies on a set of novel heuristics to determine which parts of the versions’ common code can be effectively pruned during the analysis, reducing the analysis complexity without sacrificing its effectiveness. Furthermore, we devise a new equivalence checking benchmark, extending existing benchmarks with a set of real-life methods containing complex math functions and loops. We evaluate the effectiveness and efficiency of ARDiff on this benchmark and show that it outperforms existing method-level equivalence checking techniques by solving 86% of all equivalent and 55% of non-equivalent cases, compared with 47% to 69% for equivalent and 38% to 52% for non-equivalent cases in related work.
Relating neural oscillations to laminar fMRI connectivity

Laminar fMRI can non-invasively study brain activation and potentially connectivity at the laminar level in humans. In a previous simultaneous laminar fMRI/EEG experiment, we observed that attention effects in alpha, beta and gamma band EEG power relate to attention effects in fMRI activation in V1/V2/V3 at distinct cortical depths: alpha and gamma band EEG attention effects related to fMRI effects in superficial layers, whereas beta attention effects related to deep layers. Here we reanalyzed these data to investigate how EEG-attention effects relate to changes in connectivity between regions. We computed the fMRI-based attention effect on laminar connectivity between regions within a hemisphere and connectivity between layers within brain regions. We observed that the beta band strongly relates to laminar specific changes in connectivity. Our results indicate that the attention-related decrease in beta power relates to an increase in deep-to-deep layer connectivity between regions and deep/middle to superficial layer connectivity within brain regions. The attention related alpha power increase predominantly relates to increases in connectivity between deep and superficial layers within brain regions. We observed no strong relation between laminar connectivity and gamma band oscillations. These results indicate that especially beta band oscillations, and to a lesser extent alpha band oscillations relate to laminar specific changes in connectivity as measured by laminar fMRI. Together, the effects for the alpha and beta bands suggest a complex picture of possibly co-occurring neural processes that can differentially affect laminar connectivity.
The Identity of Glochidion? cinerascens Miq. and of Rhamnus incanus Roxb.

Both these names are referable to Alphitonia as was already suggested by Kurz in Journ. Bot. 11: 207 (1873). Glochidion ? cinerascens was described by Miquel from a specimen collected in Sumatra. The type specimen in the Utrecht herbarium (36220), which was kindly put at my disposal, clearly represents an Alphitonia. It does not appear to agree with any of the species accepted by Braid in his 'Revision of the genus Alphitonia' in Kew Bull. 1925, I68-I86 (1925) and the following synonymy is suggested:-
CREB: the Mediator of Long Term Memory.

As a translator factor, CREB takes part in the transformation process from short term memory to long term memory, which has been evidenced in several different kinds of animals. In addition, its two forms as both activator and inhibitor with high conservation in their gene structures can mediate this transformation process in a more precise manner. Researches having been conducted so far and the recent progressed in this field were reviewed; the issues to be researched and addressed in future were also pointed out.
VAPYRIN attenuates defence by repressing PR gene induction and localized lignin accumulation during arbuscular mycorrhizal symbiosis of Petunia hybrida

The intimate association of host and fungus in arbuscular mycorrhizal (AM) symbiosis can potentially trigger induction of host defence mechanisms against the fungus, implying that successful symbiosis requires suppression of defence. We addressed this phenomenon by using AM-defective vapyrin (vpy) mutants in Petunia hybrida, including a new allele (vpy-3) with a transposon insertion close to the ATG start codon. We explore whether abortion of fungal infection in vpy mutants is associated with the induction of defence markers such as cell wall alterations, accumulation of reactive oxygen species (ROS), defence hormones, and induction of pathogenesis-related (PR) genes. We show that vpy mutants exhibit a strong resistance against intracellular colonization, which is associated with the generation of thick cell wall appositions (papillae) with lignin impregnation at fungal entry sites, while no accumulation of defence hormones, ROS, or callose was observed. Systematic analysis of PR gene expression revealed that several PR genes are induced in mycorrhizal roots of the wild type, and even more in vpy plants. Some PR genes are induced exclusively in vpy mutants. Taken together, these results suggest that VPY is involved in avoiding or suppressing the induction of a cellular defence syndrome that involves localized lignin deposition and PR gene induction.
Ligation bias is a major contributor to nonstoichiometric abundances of secondary siRNAs and impacts analyses of microRNAs

Plant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. High-throughput sequencing is used for the discovery and quantification of small RNAs. However, several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two stages of maize anthers to evaluate the performance of seven commercially-available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phasiRNAs, or tRNA-derived fragment. We also observed that ligation bias occurs at both ends of miRNAs and phasiRNAs, suggesting that the biased compositions observed in small RNA populations, including nonstoichiometric levels of phasiRNAs within a locus, may reflect a combination of biological and technical influences.
Assessing and Predicting Efficacy of Dance Intervention for Parkinson’s Disease

Parkinson’s disease (PD) is associated with a loss of internal cueing systems, affecting rhythmic motor tasks such as walking and speech production. Music and dance encourage spontaneous rhythmic coupling between sensory and motor systems; this has inspired the development of dance programs for PD. Here we assessed the therapeutic outcome and some underlying cognitive mechanisms of dance classes for PD, as measured by neuropsychological assessments of disease severity as well as quantitative assessments of rhythmic ability and sensorimotor experience. We assessed prior music and dance experience, beat perception (Beat Alignment Test), sensorimotor coupling (tapping to high- and low-groove songs), and disease severity (Unified Parkinson’s Disease Rating Scale in PD individuals) before and after four months of weekly dance classes. PD individuals performed better on UPDRS after four months of weekly dance classes, suggesting efficacy of dance intervention. Greater post-intervention improvements in UPDRS were associated with the presence of prior dance experience and with more accurate sensorimotor coupling. Prior dance experience was additionally associated with enhanced sensorimotor coupling during tapping to both high-groove and low-groove songs. These results show that dance classes for PD improve both qualitative and quantitative assessments of disease symptoms. The association between these improvements and dance experience suggests that rhythmic motor training, a mechanism underlying dance training, impacts improvements in parkinsonian symptoms following a dance intervention.
Affective Interfaces of Embodied Conversational Agents

: The visual representations of intelligent agents draw increasing attention recently. Additionally, the first impression of humans toward agents is the visual representations. How these man-made creatures’ looks determine users’ will to interact with. This research focuses on the appearances of embodied agents to investigate the affective interactions between users and agents. This study conducted one experiment to study the affective influences of embodied conversational agents (ECAs) on users in the learning tasks. A one-factor-at-three-levels counterbalanced by within-subjects design is employed in this study. This study asks whether there are significant experiential differences between ECAs when they are represented by different character classifications, such as character preference, user engagement and user-agent relationships. The main contributions of this study are summarised as follows: (1) character classifications can be related to human affective factors; and (2) there may be significant relations among character preference, engagement and user-agent relationships.
Why Are Deep Networks Fragile: Deformation of Intertwined Data

In many classiﬁcation tasks, the training samples are highly intertwined in the original input space. In image datasets, for example, a large fraction of training samples near each training point belong to different classes. The neural network seeks to learn a new representation of data—the last layer of the network—in which the training samples are linearly separable. Going from intertwined training data to such separable representation necessarily introduces severe deformation to the representation space, whereby points close to each other in the input space are mapped to be far apart in the new representation. In this work, we develop metrics to rigorously quantify how intertwined the input data is and how much space deformation the neural network produces during its training. Such deformation is a fundamental reason why these neural networks are fragile to adversarial perturbations. Our experiments quantify how ﬁtting an intertwined dataset requires the model to deform the original space of the datasets in a way that small perturbations can result in big changes in the model’s output.
Extracellular DJ-1 induces sterile inflammation in the ischemic brain

Inflammation is implicated in the onset and progression of various diseases, including cerebral pathologies. Here we report that DJ-1, which plays a role within cells as an antioxidant protein, functions as a damage-associated molecular pattern (DAMP), and triggers inflammation if released from dead cells into the extracellular space. We first found that recombinant DJ-1 protein induces the production of various inflammatory cytokines in bone marrow-derived macrophages (BMMs). We further identified a unique peptide sequence in the αG and αH helices of DJ-1 that activates Toll-like receptor 2 (TLR2) and TLR4. In the ischemic brain, DJ-1 is released into the extracellular space from necrotic neurons within 24 hours after stroke onset and makes direct contact with the surfaces of infiltrating myeloid cells. Administration of an antibody against DJ-1 suppresses the expression of inflammatory cytokines in infiltrating immune cells and attenuates ischemic neuronal damage. Our results demonstrate a previously unknown function of DJ-1 as a DAMP and suggest that extracellular DJ-1 could be a therapeutic target to prevent inflammation in tissue injuries and neurodegenerative diseases. Significance statement DJ-1 has been thoroughly investigated as a cytoprotective antioxidant protein in neurons. However, here we demonstrate that extracellularly released DJ-1 triggers neurotoxic inflammation after ischemic stroke. Intracellular DJ-1 increases in response to oxidative stress in ischemic neurons, but if ischemic stresses result in necrotic cell death, DJ-1 is released extracellularly. Released DJ-1 interacts with TLR2 and TLR4 on the surface of infiltrating myeloid cells and triggers post-ischemic inflammation, leading to the exacerbated pathologies of ischemic stroke. Thus, extracellular DJ-1 is a previously unknown inflammatogenic DAMP, and may be a putative target for therapeutic intervention to prevent progression of inflammatory and neurodegenerative diseases.
Understanding the photophysics and structural organization of photosynthetic proteins using model lipid membranes assembled from natural plant thylakoids

The light-harvesting (LH) biomembranes from photosynthetic organisms perform solar energy absorption and transfer with high efficiency. There is great interest in the nanoscale biophysics of photosynthesis, however, natural membranes are complex and highly curved so can be challenging to study. Here we present model photosynthetic “hybrid membranes” assembled from a combination of natural LH membranes and synthetic lipids deposited into a patterned polymerized lipid template on glass. This arrangement offers many advantages over previous model systems including: a sufficiently complex mixture of natural proteins to mimic the biological processes, a modular self-assembly mechanism, and a stabilizing template promoting the formation of supported lipid bilayers from complex natural membranes with high protein content (that would not otherwise form). These hybrid membranes can be used as a platform to delineate the complex relationship between LH energy pathways and membrane organization. Atomic force microscopy and fluorescence lifetime microscopy revealed that hybrid membranes have an elongated fluorescence lifetime (∼4 ns) compared to native membranes (∼0.5 ns), a direct consequence of reduced protein density and an uncoupling of protein-protein interactions. We observed the real time self-assembly and migration of LH proteins from natural membrane extracts into the hybrid membranes and monitored the photophysical state of the membranes at each stage. Finally, experiments utilizing our hybrid membranes suggest that assays currently used in the photosynthesis community to test the electron transfer activity of Photosystem II may have non-specific interactions with other proteins, implying that new methods are needed for reliable quantification of electron transfers in photosynthesis.
F-domain valency determines outcome of signaling through the angiopoietin pathway

Angiopoietin 1 and 2 (Ang1 and Ang2) modulate angiogenesis and vascular homeostasis through engagement of their very similar F-domain modules with the Tie2 receptor tyrosine kinase on endothelial cells. Despite this similarity in the underlying receptor binding interaction, the two angiopoietins have opposite effects: Ang1 induces phosphorylation of protein kinase B (AKT), strengthens cell-cell junctions and enhances endothelial cell survival while Ang2 antagonizes these effects1–4. To investigate the molecular basis for the opposing effects, we examined the protein kinase activation and morphological phenotypes produced by a series of computationally designed protein scaffolds presenting the Ang1 F-domain in a wide range of valencies and geometries. We find two broad phenotypic classes distinguished by the number of presented F-domains: scaffolds presenting 4 F-domains have Ang2 like activity, upregulating pFAK and pERK but not pAKT, and failing to induce cell migration and tube formation, while scaffolds presenting 6 or more F-domains have Ang1 like activity, upregulating pAKT and inducing migration and tube formation. The scaffolds with 8 or more F-domains display superagonist activity, producing stronger phenotypes at lower concentrations than Ang1. When examined in vivo, superagonist icosahedral self-assembling nanoparticles caused significant revascularization in hemorrhagic brains after a controlled cortical impact injury.
Anterior Nucleus of Thalamus Gates Progression of Mesial Temporal Seizures by Modulating Thalamocortical Synchrony

The anterior nucleus of the thalamus (ANT) mediates cortical-subcortical interactions between the limbic system and is hypothesized to facilitate the early organization of temporal lobe seizures. We set out to investigate the dynamic changes in synchronization parameters between the seizure onset zone (SOZ) and ANT during seizure stages (pre-onset to post-termination) in seven patients (n=26 seizures) with drug-resistant nonlesional temporal lobe epilepsy. Using local field potentials recorded directly from the limbic system and the ANT during stereoelectroencephalography, we confirm that the onset of mesial temporal lobe seizure is associated with increased thalamocortical network excitability and phase-amplitude coupling. The increase in thalamocortical phase synchronization preceded seizure onset, thereby suggesting that the early organization of temporal lobe seizures involves the integration of the ANT within the epileptic network. Towards seizure termination, there is a significant decrease in thalamic excitability, thalamocortical synchronization, and decoupling, thereby suggesting a breakdown in thalamocortical connectivity. A higher disease burden is significantly correlated with increased synchronization between the ANT and epileptic networks. Collectively, the results elucidate mechanistic insights and provide the temporal architecture of thalamocortical interactions that can be targeted in the rational designing of closed-loop seizure abortive interventions. Highlights Anterior nucleus of thalamus is coactivated at the onset of temporal lobe seizures Increase thalamocortical synchronization and excitability is observed at seizure onset Seizure termination is characterized by a breakdown in thalamocortical connectivity Increased seizure burden affects thalamocortical synchronization
Studies on Regulation of Cholesterol Metabolism Induced by Dietary Food Constituents or Xenobiotics.

protein peptic hydrolyzate or β-lactoglobulin tryptic hydrolyzate in suppressing the increase in the serum cholesterol level exceeded that of soy protein. In the case of high cholesterol feeding, dietary proteins affected serum cholesterol levels and inhibited cholesterol absorption through changes of micellar cholesterol solubility in the intestine, accompanied by an increase of fecal steroid excretion. Dietary peptides derived from β-lactoglobulin or soy protein inhibited cholesterol absorption in CaCo-2 cells. Dietary proteins affect the nature of bile acid micelles in the intestine, confirming observations by freeze-fracture transmission electron microscopy. Dietary proteins regulates the expression of the hepatic apolipoprotein gene. Dietary excess tyrosine or xenobiotics caused hypercholesterolemia characterized by an increase of both HDLcholesterol and LDL+VLDL-cholesterol. The stimulated synthesis of cholesterol in the liver is the main reason for this. The causal interrelationship between the hypercholesterolemia induced by dietary xenobiotics and the secretion of catecholamines or thyroid hormones was observed. These results indicate that the changes in cholesterol metabolism induced by dietary proteins, xenobiotics or excess tyrosine are expressed through intestinal and hepatic events.
Cryo-EM structure of yeast 90S preribosome at 3.4 Å resolution

Previously, we determined a cryo-EM structure of Saccharomyces cerevisiae 90S preribosome obtained after depletion of the RNA helicase Mtr4 at 4.5 Å resolution (Sun et al., 2017). The 90S preribosome is an early assembly intermediate of small ribosomal subunit. Here, the structure was improved to 3.4 Å resolution and reveals many previously unresolved structures and interactions, in particular around the central domain of 18S rRNA. The central domain adopts a closed conformation in our structure, in contrast to an open conformation in another high-resolution structure of S. cerevisiae 90S. The new model of 90S would serve as a better reference for investigation of the assembly mechanism of small ribosomal subunit.