Miracle-dz/UniFAR-FTUs huggingface dataset:
Variational Template Machine for Data-to-Text Generation

How to generate descriptions from structured data organized in tables? Existing approaches using neural encoder-decoder models often suffer from lacking diversity. We claim that an open set of templates is crucial for enriching the phrase constructions and realizing varied generations. Learning such templates is prohibitive since it often requires a large paired corpus, which is seldom available. This paper explores the problem of automatically learning reusable "templates" from paired and non-paired data. We propose the variational template machine (VTM), a novel method to generate text descriptions from data tables. Our contributions include: a) we carefully devise a specific model architecture and losses to explicitly disentangle text template and semantic content information, in the latent spaces, and b)we utilize both small parallel data and large raw text without aligned tables to enrich the template learning. Experiments on datasets from a variety of different domains show that VTM is able to generate more diversely while keeping a good fluency and quality.
GTC: Guided Training of CTC Towards Efficient and Accurate Scene Text Recognition

Connectionist Temporal Classification (CTC) and attention mechanism are two main approaches used in recent scene text recognition works. Compared with attention-based methods, CTC decoder has a much shorter inference time, yet a lower accuracy. To design an efficient and effective model, we propose the guided training of CTC (GTC), where CTC model learns a better alignment and feature representations from a more powerful attentional guidance. With the benefit of guided training, CTC model achieves robust and accurate prediction for both regular and irregular scene text while maintaining a fast inference speed. Moreover, to further leverage the potential of CTC decoder, a graph convolutional network (GCN) is proposed to learn the local correlations of extracted features. Extensive experiments on standard benchmarks demonstrate that our end-to-end model achieves a new state-of-the-art for regular and irregular scene text recognition and needs 6 times shorter inference time than attention-based methods.
Molecular alignment echoes probing collision-induced rotational-speed changes

We show that the decays with pressure of the alignment echoes induced in N2O-He gas mixtures by two laser pulses with various delays bring detailed information on collision-induced changes of the rotational speed. Measurements and calculations demonstrate that collisions reduce the echo amplitude all the more efficiently when the echo appears late. We quantitatively explain this behavior by the filamentation of the classical rotational phase space induced by the first pulse and the progressive narrowing of the filaments with time. The variation of the echo decay thus reflects the ability of collisions to change the molecules' rotational speed by various amounts, enabling refined tests of models for the dissipation induced by intermolecular forces.
A bright, high rotation-measure FRB that skewers the M33 halo

We report the detection of a bright fast radio burst, FRB\,191108, with Apertif on the Westerbork Synthesis Radio Telescope (WSRT). The interferometer allows us to localise the FRB to a narrow $5\arcsec\times7\arcmin$ ellipse by employing both multibeam information within the Apertif phased-array feed (PAF) beam pattern, and across different tied-array beams. The resulting sight line passes close to Local Group galaxy M33, with an impact parameter of only 18\,kpc with respect to the core. It also traverses the much larger circumgalactic medium of M31, the Andromeda Galaxy. We find that the shared plasma of the Local Group galaxies could contribute $\sim$10\% of its dispersion measure of 588\,pc\,cm$^{-3}$. FRB\,191108 has a Faraday rotation measure of +474\,$\pm\,3$\,rad\,m$^{-2}$, which is too large to be explained by either the Milky Way or the intergalactic medium. Based on the more moderate RMs of other extragalactic sources that traverse the halo of M33, we conclude that the dense magnetised plasma resides in the host galaxy. The FRB exhibits frequency structure on two scales, one that is consistent with quenched Galactic scintillation and broader spectral structure with $\Delta\nu\approx40$\,MHz. If the latter is due to scattering in the shared M33/M31 CGM, our results constrain the Local Group plasma environment. We found no accompanying persistent radio sources in the Apertif imaging survey data.
The M31/M33 tidal interaction: a hydrodynamic simulation of the extended gas distribution

We revisit the orbital history of the Triangulum galaxy (M33) around the Andromeda galaxy (M31) in view of the recent Gaia Data Release 2 proper motion measurements for both Local Group galaxies. Earlier studies consider highly idealized dynamical friction, but neglect the effects of dynamical mass loss. We show the latter process to be important using mutually consistent orbit integration and N-body simulations. Following this approach, we find an orbital solution that brings these galaxies to within ∼50 kpc of each other in the past, ∼6.5 Gyr ago. We explore the implications of their interaction using an N-body/hydrodynamical simulation with a focus on the origin of two prominent features: (1) M31’s Giant Stellar Stream; and (2) the M31–M33 H i filament. We find that the tidal interaction does not produce a structure reminiscent of the stellar stream that survives up to the present day. In contrast, the M31–M33 H i filament is likely a fossil structure dating back to the time of the ancient encounter between these galaxies. Similarly, the observed outer disc warp in M33 may well be a relic of this past event. Our model suggests the presence of a tidally induced gas envelope around these galaxies, and the existence of a diffuse gas stream, the ‘Triangulum stream’, stretching for tens of kpc from M33 away from M31. We anticipate upcoming observations with the recently commissioned, Five-hundred-metre Aperture Spherical radio Telescope that will target the putative stream in its first years of operation.
Efficient 2D neuron boundary segmentation with local topological constraints

We present a method for segmenting neuron membranes in 2D electron microscopy imagery. This segmentation task has been a bottleneck to reconstruction efforts of the brain's synaptic circuits. One common problem is the misclassification of blurry membrane fragments as cell interior, which leads to merging of two adjacent neuron sections into one via the blurry membrane region. Human annotators can easily avoid such errors by implicitly performing gap completion, taking into account the continuity of membranes. Drawing inspiration from these human strategies, we formulate the segmentation task as an edge labeling problem on a graph with local topological constraints. We derive an integer linear program (ILP) that enforces membrane continuity, i.e. the absence of gaps. The cost function of the ILP is the pixel-wise deviation of the segmentation from a priori membrane probabilities derived from the data. Based on membrane probability maps obtained using random forest classifiers and convolutional neural networks, our method improves the neuron boundary segmentation accuracy compared to a variety of standard segmentation approaches. Our method successfully performs gap completion and leads to fewer topological errors. The method could potentially also be incorporated into other image segmentation pipelines with known topological constraints.
Unsupervised Multiple Person Tracking using AutoEncoder-Based Lifted Multicuts

Multiple Object Tracking (MOT) is a long-standing task in computer vision. Current approaches based on the tracking by detection paradigm either require some sort of domain knowledge or supervision to associate data correctly into tracks. In this work, we present an unsupervised multiple object tracking approach based on visual features and minimum cost lifted multicuts. Our method is based on straight-forward spatio-temporal cues that can be extracted from neighboring frames in an image sequences without superivison. Clustering based on these cues enables us to learn the required appearance invariances for the tracking task at hand and train an autoencoder to generate suitable latent representation. Thus, the resulting latent representations can serve as robust appearance cues for tracking even over large temporal distances where no reliable spatio-temporal features could be extracted. We show that, despite being trained without using the provided annotations, our model provides competitive results on the challenging MOT Benchmark for pedestrian tracking.
A Word to the WISE: Confusion is Unavoidable for WISE-selected Infrared Excesses

Stars with excess infrared radiation from circumstellar dust are invaluable for studies of exoplanetary systems, informing our understanding of processes of planet formation and destruction alike. All-sky photometric surveys have made the identification of dusty infrared excess candidates trivial, however, samples that rely on data from Wise Infrared Survey Explorer (WISE) are plagued with source confusion, leading to high false-positive rates. Techniques to limit its contribution to WISE-selected samples have been developed, and their effectiveness is even more important as we near the end-of-life of Spitzer, the only facility capable of confirming the excess. Here, we present a Spitzer follow-up of a sample of 22 WISE-selected infrared excess candidates near the faint-end of the WISE detection limits. Eight of the 22 excesses are deemed the result of source confusion, with the remaining candidates all confirmed by the Spitzer data. We consider the efficacy of ground-based near-infrared imaging and astrometric filtering of samples to limit confusion among the sample. We find that both techniques are worthwhile for vetting candidates, but fail to identify all of the confused excesses, indicating that they cannot be used to confirm WISE-selected infrared excess candidates, but only to rule them out. This result confirms the expectation that WISE-selected infrared excess samples will always suffer from appreciable levels of contamination, and that care should be taken in their interpretation regardless of the filters applied.
Clinical techniques to prevent cough at emergence from general anaesthesia: A meta-analysis

Brief summary: Various techniques can reduce the incidence of cough at tracheal extubation. Whilst effect size differs between treatments, homogeneity was identified within each subgroup of treatments. This meta-analysis allows anaesthesiologists to make informed choices on the use of techniques to prevent emergence cough. Background: Cough at extubation increases the risk of morbidity following surgical procedures. So, prevention of cough may aid perioperative risk management. Several techniques have been described for prevention of cough at or immediately after tracheal extubation. This meta-analysis compares various pharmacological methods for prevention of cough at emergence from general anaesthesia and aims to establish an evidence base for the rational use of these techniques. Methods: Several electronic databases (1966-2018) were searched systematically for randomised controlled trials that reported the incidence of cough at extubation. The quality of the studies identified was assessed using the Jadad methodology. Six techniques to prevent cough were analysed using the Mantel-Haenszel fixed-effects model. The odds ratio (OR) and number needed to treat (NNT) were used as the summary efficacy measures. Results: Of 1114 articles screened, 22 comparisons in 17 studies (1007 patients) were included in the final analysis. Significant heterogeneity of effect was observed when all studies were analysed together. However, there was homogeneity within each treatment subgroup. This reflected significant effect-size differences between techniques. The largest effect-sizes were seen with endotracheal tube cuff inflation with alkalinised lignocaine (pooled OR 0.052; 95% CI 0.027-0.102; NNT 1.67) and topical lignocaine (pooled OR 0.065; 95% CI 0.015-0.274; NNT 2.35). Conclusion: The incidence of cough at extubation of the trachea can be reduced. The overall effect size of the studied strategies was useful (pooled OR 0.149; 95% CI 0.13-0.18; NNT 2.62). No single technique prevented cough in all patients but cuff inflation with alkalinised lignocaine and topical 4% lignocaine were most effective.
Cell Line-, Protein-, and Sialoglycosite-Specific Control of Flux-Based Sialylation in Human Breast Cells: Implications for Cancer Progression

Sialylation, a post-translational modification that impacts the structure, activity, and longevity of glycoproteins has been thought to be controlled primarily by the expression of sialyltransferases (STs). In this report we explore the complementary impact of metabolic flux on sialylation using a glycoengineering approach. Specifically, we treated three human breast cell lines (MCF10A, T-47D, and MDA-MB-231) with 1,3,4-O-Bu3ManNAc, a “high flux” metabolic precursor for the sialic acid biosynthetic pathway. We then analyzed N-glycan sialylation using solid phase extraction of glycopeptides (SPEG) mass spectrometry-based proteomics under conditions that selectively captured sialic acid-containing glycopeptides, referred to as “sialoglycosites. ” Gene ontology (GO) analysis showed that flux-based changes to sialylation were broadly distributed across classes of proteins in 1,3,4-O-Bu3ManNAc-treated cells. Only three categories of proteins, however, were “highly responsive” to flux (defined as two or more sialylation changes of 10-fold or greater). Two of these categories were cell signaling and cell adhesion, which reflect well-known roles of sialic acid in oncogenesis. A third category—protein folding chaperones—was unexpected because little precedent exists for the role of glycosylation in the activity of these proteins. The highly flux-responsive proteins were all linked to cancer but sometimes as tumor suppressors, other times as proto-oncogenes, or sometimes both depending on sialylation status. A notable aspect of our analysis of metabolically glycoengineered breast cells was decreased sialylation of a subset of glycosites, which was unexpected because of the increased intracellular levels of sialometabolite “building blocks” in the 1,3,4-O-Bu3ManNAc-treated cells. Sites of decreased sialylation were minor in the MCF10A (<25% of all glycosites) and T-47D (<15%) cells but dominated in the MDA-MB-231 line (~60%) suggesting that excess sialic acid could be detrimental in advanced cancer and cancer cells can evolve mechanisms to guard against hypersialylation. In summary, flux-driven changes to sialylation offer an intriguing and novel mechanism to switch between context-dependent pro- or anti-cancer activities of the several oncoproteins identified in this study. These findings illustrate how metabolic glycoengineering can uncover novel roles of sialic acid in oncogenesis.
“The Italian Study on Recovery 2” Phase 1: Psychometric Properties of the Recovery Assessment Scale (RAS), Italian Validation of the Recovery Assessment Scale

Background The achievement of recovery is related to the notion of developing personal potential and restoring a legitimate social role, even against the backdrop of mental illness limitations. It is still difficult to fully understand this highly subjective and dynamic process. Therefore, in order to test the recovery process, specific tools, still only marginally used in our country, are needed. Aims The Italian Study on Recovery is the first study aimed at confirming the validity of the Italian version of the Recovery Assessment Scale (RAS), an instrument developed with the goal of detecting recovery among patients. Method This multicentric research involved several Mental Health Services from various parts of Italy. The first phase of the study consisted in the administration of the Italian translation of RAS, previously used in a pilot study conducted in 2009. RAS was administered to 219 patients diagnosed with psychosis, whose mental disorder lasted for at least 5 years. Results Findings supported the good psychometric properties of the Italian version of RAS, demonstrating its capability of identifying patients matching the “in recovery” operational criteria. Conclusions In consideration of the results highlighting the good psychometric properties of RAS, the present study may contribute to the diffusion of instruments to be included in Mental Health Service planning in the Italian context, in order to start a recovery-oriented transformation.
Abnormal Anatomical Rich-Club Organization and Structural–Functional Coupling in Mild Cognitive Impairment and Alzheimer's Disease

Emerging research indicates interruptions in the wiring organization of the brain network in Mild cognitive impairment (MCI) and Alzheimer's disease (AD). Due to the important role of rich-club organization in distinguishing abnormalities of AD patients and the close relationship between structural connectivity (SC) and functional connectivity (FC), our study examined whether changes in SC-FC coupling and the relationship with abnormal rich-club organizations during the development of diseases may contribute to the pathophysiology of AD. Structural diffusion-tensor imaging (DTI) and resting-state functional magnetic resonance imaging (fMRI) were performed in 38 normal controls (NCs), 40 MCI patients and 19 AD patients. Measures of the rich-club structure and its role in global structural–functional coupling were administered. Our study found decreased levels of feeder and local connectivity in MCI and AD patients, which were the main contributing factors to the lower efficiency of the brain structural network. Another important finding was that we have more accurately characterized the changing pattern of functional brain dynamics. The enhanced coupling between SC and FC in MCI and AD patients might be due to disruptions in optimal structural organization. More interestingly, we also found increases in the SC-FC coupling for feeder and local connections in MCI and AD patients. SC-FC coupling also showed significant differences between MCI and AD patients, mainly between the abnormal feeder connections. The connection density and coupling strength were significantly correlated with clinical metrics in patients. The present findings enhanced our understanding of the neurophysiologic mechanisms associated with MCI and AD.
Molecular and Functional Characterization of CaNAC035, an NAC Transcription Factor From Pepper (Capsicum annuum L.)

NAC (NAM, ATAF1/2, and CUC2) proteins are the plant-specific transcription factors (TFs) which are important in plant response to abiotic stresses. However, knowledge about the functional role that NACs play in pepper abiotic stress tolerance is limited. In this study, we isolated a NAC TF gene, CaNAC035, from pepper (Capsicum annuum L.), where the protein is localized in the nucleus and functions as a transcriptional activator. CaNAC035 expression is induced by low and high temperatures, osmotic stress, salt, gibberellic acid (GA), methyl-jasmonic acid (MeJA), salicylic acid (SA), and abscisic acid (ABA). To understand the function of CaNAC035 in the abiotic stress responsep, we used virus-induced gene silencing in pepper to knockdown the CaNAC035 and overexpressed the CaNAC035 in Arabidopsis. The results showed that pepper seedlings in which CaNAC035 was silenced, showed more damage than the control pepper plants after cold, NaCl, and mannitol treatments. Correspondingly increased electrolyte leakage, a higher level of malondialdehyde (MDA), H2O2, and superoxide radicals were found after cold treatments. CaNAC035-silenced seedlings exhibited lower chlorophyll content while CaNAC035-overexpressed Arabidopsis plants had higher germination rate and fresh weight after mannitol and NaCl treatments. We also reported 18 proteins that potentially interact with CaNAC035 and may participate in processes such as the stress response, resistance, and photosynthesis. Our results suggest that CaNAC035 is a positive regulator of abiotic stress tolerance in pepper which acts through multiple signaling pathways.
Molecular Dynamics of Lipopolysaccharide-Induced Lung Injury in Rodents

Acute respiratory distress syndrome (ARDS) is a common disease entity in critical care medicine and is still associated with a high mortality. Because of the heterogeneous character of ARDS, animal models are an insturment to study pathology in relatively standardized conditions. Rodent models can bridge the gap from in vitro investigations to large animal and clinical trials by facilitating large sample sizes under physiological conditions at comparatively low costs. One of the most commonly used rodent models of acute lung inflammation and ARDS is administration of lipopolysaccharide (LPS), either into the airways (direct, pulmonary insult) or systemically (indirect, extra-pulmonary insult). This narrative review discusses the dynamics of important pathophysiological pathways contributing to the physiological response to LPS-induced injury. Pathophysiological pathways of LPS-induced lung injury are not only influenced by the type of the primary insult (e.g., pulmonary or extra-pulmonary) and presence of additional stimuli (e.g., mechanical ventilation), but also by time. As such, findings in animal models of LPS-induced lung injury may depend on the time point at which samples are obtained and physiological data are captured. This review summarizes the current evidence and highlights uncertainties on the molecular dynamics of LPS-induced lung injury in rodent models, encouraging researchers to take accurate timing of LPS-induced injury into account when designing experimental trials.
Asparaginyl-tRNA Synthetase, a Novel Component of Hippo Signaling, Binds to Salvador and Enhances Yorkie-Mediated Tumorigenesis

Aminoacyl-tRNA synthetases (ARSs), which are essential for protein translation, were recently shown to have non-translational functions in various pathological conditions including cancer. However, the molecular mechanism underlying the role of ARSs in cancer remains unknown. Here, we demonstrate that asparaginyl-tRNA synthetase (NRS) regulates Yorkie-mediated tumorigenesis by binding to the Hippo pathway component Salvador. NRS-RNAi and the NRS inhibitor tirandamycin B (TirB) suppressed Yorkie-mediated tumor phenotypes in Drosophila. Genetic analysis showed that NRS interacted with Salvador, and NRS activated Hippo target genes by regulating Yorkie phosphorylation. Biochemical analyses showed that NRS blocked Salvador-Hippo binding by interacting directly with Salvador, and TirB treatment inhibited NRS-Salvador binding. YAP target genes were upregulated in a mammalian cancer cell line with high expression of NRS, whereas TirB treatment suppressed cancer cell proliferation. These results indicate that NRS regulates tumor growth by interacting with Salvador in the Hippo signaling pathway.