Miracle-dz/UniFAR-FTUs huggingface dataset:
The N-Terminal Region of Yeast Protein Phosphatase Ppz1 Is a Determinant for Its Toxicity

The Ppz enzymes are Ser/Thr protein phosphatases present only in fungi that are characterized by a highly conserved C-terminal catalytic region, related to PP1c phosphatases, and a more divergent N-terminal extension. In Saccharomyces cerevisiae, Ppz phosphatases are encoded by two paralog genes, PPZ1 and PPZ2. Ppz1 is the most toxic protein when overexpressed in budding yeast, halting cell proliferation, and this effect requires its phosphatase activity. We show here that, in spite of their conserved catalytic domain, Ppz2 was not toxic when tested under the same conditions as Ppz1, albeit Ppz2 levels were somewhat lower. Remarkably, a hybrid protein composed of the N-terminal extension of Ppz1 and the catalytic domain of Ppz2 was as toxic as Ppz1, even if its expression level was comparable to that of Ppz2. Similar amounts of yeast PP1c (Glc7) produced an intermediate effect on growth. Mutation of the Ppz1 myristoylable Gly2 to Ala avoided the localization of the phosphatase at the cell periphery but only slightly attenuated its toxicity. Therefore, the N-terminal extension of Ppz1 plays a key role in defining Ppz1 toxicity. This region is predicted to be intrinsically disordered and contains several putative folding-upon-binding regions which are absent in Ppz2 and might be relevant for toxicity.
Arachidonic acid metabolism controls macrophage alternative activation through regulating oxidative phosphorylation in PPARG dependent manner

Macrophages polarization is mainly controlled by metabolic reprogramming in microenvironment, thus leading to distinct outcomes of various diseases. However, the role of lipid metabolism in the regulation of macrophage alternative activation is incompletely understood. Using human THP-1 and mouse bone marrow derived macrophages polarization models, we revealed a pivotal role for arachidonic acid metabolism in controlling the polarization of M1 and M2 macrophages. We demonstrated that M2 macrophage polarization was inhibited by arachidonic acid, but inversely facilitated by its derived metabolite prostaglandin E2 (PGE2). Furthermore, PPARG bridges these two unconnected processes via modulating oxidative phosphorylation. These results highlight the critical role of arachidonic acid metabolism as an immune regulator in modulating metabolic homeostasis and pathological process.
Towards Multimodal Human-Like Characteristics and Expressive Visual Prosody in Virtual Agents

One of the key challenges in designing Embodied Conversational Agents (ECA) is to produce human-like gestural and visual prosody expressivity. Another major challenge is to maintain the interlocutor's attention by adapting the agent's behavior to the interlocutor's multimodal behavior. This paper outlines my PhD research plan that aims to develop convincing expressive and natural behavior in ECAs and to explore and model the mechanisms that govern human-agent multimodal interaction. Additionally, I describe in this paper my first PhD milestone which focuses on developing an end-to-end LSTM Neural Network model for upper-face gestures generation. The main task consists of building a model that can produce expressive and coherent upper-face gestures while considering multiple modalities: speech audio, text, and action units.
Embedding Partial Propagation Network for Fake News Early Detection

Detecting fake news as early as possible has attracted growing attention due to its fast-spreading nature and the significant harm it can cause. As demonstrated in recent studies, the propagation pattern of fake news on social media differs from that of real news, and a number of works have extracted different types of features from the propagation pattern for detection. However, a major limitation of this approach is that the propagation network is not fully available in the early stages, and may take a long time to complete. As a result, existing network-based fake news detection methods yield low accuracy during the early stages of propagation. To bridge the research gap, in this work we: (1) propose a novel network embedding algorithm, based on the investigation of a wide range of features obtained from the propagation network, which are not well studied in previous work; and (2) design an autoencoder-based neural architecture to predict the embedding of the complete propagation network using the partially available network in the early stages of propagation. Our experiments show that with the predicted embedding for the complete propagation network, our model can achieve state-of-the-art performance while only having access to the early stage propagation network.
Validation methods of nursing protocols: an integrative review.

OBJECTIVE to identify scientific production about validation methods of nursing care protocols. METHOD an integrative review with search at Scielo, Pubmed/MEDLINE, Virtual Health Library, Web of Science, Scopus, and EBSCOhost. The descriptors "validation studies", "validation studies as topic", "protocols", "clinical protocols", "practice guidelines as topic", "nursing" and "nursing assessment" and the uncontrolled descriptor "validation" were used. RESULTS thirty-two articles were selected, most of them Brazilian. Content validation by experts was the most frequent method, with no consensus on the number of participants for the process. The collection instruments were mostly created by the authors. Data analysis was performed using descriptive statistics and Content Validity Index, with a variable consensus rate in the analyzed articles. CONCLUSION protocols validated by experts are robust tools for use in clinical practice, with methodological rigor in development essential for its quality.
False News Classification and Dissemination: The case of the 2019 Indonesian Presidential Election

In this paper we investigate automated meth-ods for understanding false news dissemination on Twitter in relation to one particular event: the 2019 Indonesian presidential election. We collected a sample of 2,360 tweets related to topics addressed by fact-checking websites. The tweets were hand-labeled according to their trustworthiness. We trained several classiﬁcation models on the human-labelled data, using three groups of text features. The word n-gram features appeared to be the most eﬀective, reaching a recall of 85% for true news and 62% for false news. With this classiﬁer we labeled a larger sample of tweets related to fact-checking topics in the context of the 2019 Indonesian presidential elections. We then analysed the dissemination of true news and false news in the underlying Twitter network using community detection and centrality measures. The top inﬂuential users in the network disseminate more false news, including a government institution account and a veriﬁed politician’s account. Our results show that the combination of text features and social network analysis can provide valuable insights in detecting and preventing the dissemination of false news. Moreover, we make the dataset used in this research available for reuse by the community.
The Application of Brain Organoids: From Neuronal Development to Neurological Diseases

Brain organoids are derived from induced pluripotent stem cells and embryonic stem cells under three-dimensional culture condition. The generation of an organoid requires the self-assembly of stem cells, progenitor cells, and multiple types of differentiated cells. Organoids display structures that resemble defined brain regions and simulate specific changes of neurological disorders; thus, organoids have become an excellent model for investigating brain development and neurological diseases. In the present review, we have summarized recent advances of the methods of culturing brain organoids and the applications of brain organoids in investigating neurodevelopmental and neurodegenerative diseases.
Molecular identification and prevalence of Acidovorax avenae subsp. avenae causing red stripe of sugarcane in China

Red stripe caused by the bacterium Acidovorax avenae subsp. avenae (Aaa) is a disease of sugarcane that is distributed worldwide. In this study, 108 sugarcane leaf samples were collected in 2013–2016 from nine sugarcane‐growing regions in China. Aaa was detected by PCR with specific and novel primers from the 16S–23S rDNA internal transcribed spacer region in 81 of 84 (96%) leaves with red stripe symptoms and in 20 of 24 (83%) leaves without symptoms. Furthermore, Aaa was detected in all nine sampling locations representing six sugarcane‐producing provinces in China. The 101 amplified fragments were cloned and sequenced. The size of the nucleotide sequences varied from 436 to 454 bp and the sequence identity ranged from 89.2% to 100%, suggesting a significant genetic variation among Aaa strains from China. Five major restriction fragment length polymorphism (RFLP) profiles were obtained by in silico and polyacrylamide gel electrophoresis analyses of the PCR products digested with HindIII and EcoRI. The causal agent of sugarcane red stripe was also successfully isolated from a diseased plant and its pathogenicity confirmed by inoculation of healthy sugarcane plantlets and reproduction of disease symptoms. The data showed that Aaa is currently widespread in China, suggesting that control methods should be implemented to limit the impact of red stripe on sugarcane production.
NGF/TRKA Decrease miR-145-5p Levels in Epithelial Ovarian Cancer Cells

Nerve Growth Factor (NGF) and its high-affinity receptor tropomyosin receptor kinase A (TRKA) increase their expression during the progression of epithelial ovarian cancer (EOC), promoting cell proliferation and angiogenesis through several oncogenic proteins, such as c-MYC and vascular endothelial growth factor (VEGF). The expression of these proteins is controlled by microRNAs (miRs), such as miR-145, whose dysregulation has been related to cancer. The aims of this work were to evaluate in EOC cells whether NGF/TRKA decreases miR-145 levels, and the effect of miR-145 upregulation. The levels of miR-145-5p were assessed by qPCR in ovarian biopsies and ovarian cell lines (human ovarian surface epithelial cells (HOSE), A2780 and SKOV3) stimulated with NGF. Overexpression of miR-145 in ovarian cells was used to evaluate cell proliferation, migration, invasion, c-MYC and VEGF protein levels, as well as tumor formation and metastasis in vivo. In EOC samples, miR-145-5p levels were lower than in epithelial ovarian tumors. Overexpression of miR-145 decreased cell proliferation, migration and invasion of EOC cells, changes that were concomitant with the decrease in c-MYC and VEGF protein levels. We observed decreased tumor formation and suppressed metastasis behavior in mice injected with EOC cells that overexpressed miR-145. As expected, ovarian cell lines stimulated with NGF diminished miR-145-5p transcription and abundance. These results suggest that the tumoral effects of NGF/TRKA depend on the regulation of miR-145-5p levels in EOC cells, and that its upregulation could be used as a possible therapeutic strategy for EOC.
Thin-Slice Magnetic Resonance Imaging-Based Radiomics Signature Predicts Chromosomal 1p/19q Co-deletion Status in Grade II and III Gliomas

Objective: Chromosomal 1p/19q co-deletion is recognized as a diagnostic, prognostic, and predictive biomarker in lower grade glioma (LGG). This study aims to construct a radiomics signature to non-invasively predict the 1p/19q co-deletion status in LGG. Methods: Ninety-six patients with pathology-confirmed LGG were retrospectively included and randomly assigned into training (n = 78) and validation (n = 18) dataset. Three-dimensional contrast-enhanced T1 (3D-CE-T1)-weighted magnetic resonance (MR) images and T2-weighted MR images were acquired, and simulated-conventional contrast-enhanced T1 (SC-CE-T1)-weighted images were generated. One hundred and seven shape, first-order, and texture radiomics features were extracted from each imaging modality and selected using the least absolute shrinkage and selection operator on the training dataset. A 3D-radiomics signature based on 3D-CE-T1 and T2-weighted features and a simulated-conventional (SC) radiomics signature based on SC-CE-T1 and T2-weighted features were established using random forest. The radiomics signatures were validated independently and evaluated using receiver operating characteristic (ROC) curves. Tumors with IDH mutations were also separately assessed. Results: Four radiomics features were selected to construct the 3D-radiomics signature and displayed accuracies of 0.897 and 0.833, areas under the ROC curves (AUCs) of 0.940 and 0.889 in the training and validation datasets, respectively. The SC-radiomics signature was constructed with 4 features, but the AUC values were lower than that of the 3D signature. In the IDH-mutated subgroup, the 3D-radiomics signature presented AUCs of 0.950–1.000. Conclusions: The MRI-based radiomics signature can differentiate 1p/19q co-deletion status in LGG with or without predetermined IDH status. 3D-CE-T1-weighted radiomics features are more favorable than SC-CE-T1-weighted features in the establishment of radiomics signatures.
Group Level Audio-Video Emotion Recognition Using Hybrid Networks

This paper presents a hybrid network for audio-video group Emo-tion Recognition. The proposed architecture includes audio stream,facial emotion stream, environmental object statistics stream (EOS)and video stream. We adopted this method at the 8th EmotionRecognition in the Wild Challenge (EmotiW2020). According to thefeedback of our submissions, the best result achieved 76.85% in theVideo level Group AFfect (VGAF) Test Database, 26.89% higherthan the baseline. Such improvements prove that our method isstate-of-the-art.
Landscape correlates of bushmeat consumption and hunting in a post-frontier Amazonian region

SUMMARY Identifying the drivers of bushmeat consumption and hunting is important for informing conservation strategies and recognizing challenges to human food security. However, studies often neglect the importance of landscape context, which can influence bushmeat supply and demand. Here, by quantifying bushmeat consumption and hunting in 262 households in a post-frontier region in Amazonia, we tested the hypotheses that bushmeat consumption and hunting are positively associated with two landscape characteristics: (1) forest cover, which has been shown to define game availability; and (2) remoteness, which is related to limited access to marketed meat. Bushmeat consumption was widespread but more likely in remote forested areas. Hunting was more likely in more forested areas, especially nearer to urban centres. Our findings suggest that bushmeat remains an important food source even in heavily altered forest regions and that landscape context is an important determinant of bushmeat consumption and hunting. Although people living in remote, forested areas are likely to be the most dependent on bushmeat, those living in more populous, peri-urban areas are likely the actors contributing most to total hunting effort, due to a higher probability of hunting combined with higher human population densities. This finding undermines the assumption that rural–urban migration in the tropics will deliver a much-needed reprieve for many overhunted species.
Conversational Interfaces for Search As Learning

Searching the web to learn new things or gain knowledge has become a common activity. Recent advances in conversa- tional user interfaces have led to a new research opportunity – that of analyzing the potential of conversational interfaces in improving the effectiveness of search as learning (SAL). Addressing this knowledge gap, in this position paper we present conversational interfaces to support search as learning and novel methods to measure user performance and learning. Our experimental results reveal that conversational interfaces can improve user engagement, augment user long-term memora- bility, and alleviate user cognitive load. These findings have important implications on designing effective SAL systems.
Extracellular Matrix Signaling Regulates Definitive Endoderm Differentiation in Embryonic Stem Cells

During development embryonic stem cells use a variety of external cues to direct their differentiation. In particular, definitive endoderm specification coincides with signaling from soluble factors and the extracellular matrix. By contrast, in vitro differentiation methods often rely exclusively on growth factors to direct cell fate and so the role of extracellular matrix signaling is not well understood. Thus this dissertation examines how extracellular matrix enhances soluble factor signaling during definitive endoderm differentiation. Soluble factors used to direct definitive endoderm specification (e.g. Activin A) are shown to induce embryonic stem cells to activate traction forces and assemble a lineage- specific extracellular matrix that is rich in fibronectin and laminin. By contrast, pluripotent embryonic stem cells do not assemble substantial extracellular matrix or activate contractility. Traction forces are shown to be required for definitive endoderm specification and laminin is shown to improve differentiation in a dose-dependent manner. Extracellular laminin and contractility promote Activin A signaling by inhibiting SMAD7 expression and allowing nuclear accumulation of phosphorylated-SMAD2, respectively. This work demonstrates a role for extracellular matrix in regulating the signaling pathways that guide early embryonic stem cell fate
Integrity Analysis for GPS-Based Navigation of UAVs in Urban Environment

The increasing use of Unmanned Aerial Vehicles (UAVs) in safety-critical missions in both civilian and military areas demands accurate and reliable navigation, where one of the key sources of navigation information is presented by Global Navigation Satellite Systems (GNSS). In challenging conditions, for example, in urban areas, the accuracy of GNSS-based navigation may degrade significantly due to user-satellite geometry and obscuration issues without being noticed by the user. Therefore, considering the essentially dynamic rate of change in this type of environment, integrity monitoring is of critical importance for understanding the level of trust we have in positioning and timing data. In this paper, the dilution of precision (DOP) coefficients under nominal and challenging conditions were investigated for the purpose of integrity monitoring in urban environments. By analyzing positioning information in a simulated urban environment using a software-based GNSS receiver, the integrity monitoring approach based on joint consideration of GNSS observables and environmental parameters has been proposed. It was shown that DOP coefficients, when considered together with a number of visible satellites and cut-off elevations specific to the urban environment carry valuable integrity information that is difficult to get using existing integrity monitoring approaches. This has allowed generating indirect integrity measures based on cut-off elevation and satellite visibility that can be used for UAV path planning and guidance in urban environments.
The Mediator Subunit, Med23 Is Required for Embryonic Survival and Regulation of Canonical WNT Signaling During Cranial Ganglia Development

Development of the vertebrate head is a complex and dynamic process, which requires integration of all three germ layers and their derivatives. Of special importance are ectoderm-derived cells that form the cranial placodes, which then differentiate into the cranial ganglia and sensory organs. Critical to a fully functioning head, defects in cranial placode and sensory organ development can result in congenital craniofacial anomalies. In a forward genetic screen aimed at identifying novel regulators of craniofacial development, we discovered an embryonically lethal mouse mutant, snouty, which exhibits malformation of the facial prominences, cranial nerves and vasculature. The snouty mutation was mapped to a single nucleotide change in a ubiquitously expressed gene, Med23, which encodes a subunit of the global transcription co-factor complex, Mediator. Phenotypic analyses revealed that the craniofacial anomalies, particularly of the cranial ganglia, were caused by a failure in the proper specification of cranial placode neuronal precursors. Molecular analyses determined that defects in cranial placode neuronal differentiation in Med23sn/sn mutants were associated with elevated WNT/β-catenin signaling, which can be partially rescued through combined Lrp6 and Wise loss-of-function. Our work therefore reveals a surprisingly tissue specific role for the ubiquitously expressed mediator complex protein Med23 in placode differentiation during cranial ganglia development. This highlights the importance of coupling general transcription to the regulation of WNT signaling during embryogenesis.
Multiscale Entropy Analysis: Application to Cardio-Respiratory Coupling

It is known that in pathological conditions, physiological systems develop changes in the multiscale properties of physiological signals. However, in real life, little is known about how changes in the function of one of the two coupled physiological systems induce changes in function of the other one, especially on their multiscale behavior. Hence, in this work we aimed to examine the complexity of cardio-respiratory coupled systems control using multiscale entropy (MSE) analysis of cardiac intervals MSE (RR), respiratory time series MSE (Resp), and synchrony of these rhythms by cross multiscale entropy (CMSE) analysis, in the heart failure (HF) patients and healthy subjects. We analyzed 20 min of synchronously recorded RR intervals and respiratory signal during relaxation in the supine position in 42 heart failure patients and 14 control healthy subjects. Heart failure group was divided into three subgroups, according to the RR interval time series characteristics (atrial fibrillation (HFAF), sinus rhythm (HFSin), and sinus rhythm with ventricular extrasystoles (HFVES)). Compared with healthy control subjects, alterations in respiratory signal properties were observed in patients from the HFSin and HFVES groups. Further, mean MSE curves of RR intervals and respiratory signal were not statistically different only in the HFSin group (p = 0.43). The level of synchrony between these time series was significantly higher in HFSin and HFVES patients than in control subjects and HFAF patients (p < 0.01). In conclusion, depending on the specific pathologies, primary alterations in the regularity of cardiac rhythm resulted in changes in the regularity of the respiratory rhythm, as well as in the level of their asynchrony.
Cerebrospinal fluid closing pressure-guided tap test for the diagnosis of idiopathic normal pressure hydrocephalus: A descriptive cross-sectional study

Background: Tap test improves symptoms of idiopathic normal pressure hydrocephalus (iNPH); hence, it is widely used as a diagnostic procedure. However, it has a low sensitivity and there is no consensus on the parameters that should be used nor the volume to be extracted. We propose draining cerebrospinal fluid (CSF) during tap test until a closing pressure of 0 cm H2O is reached as a standard practice. We use this method with all our patients at our clinic. Methods: This is a descriptive cross-sectional study where all patients with presumptive diagnosis of iNPH from January 2014 to December 2019 were included in the study. We used a univariate descriptive analysis and stratified analysis to compare the opening pressure and the volume of CSF extracted during the lumbar puncture, between patients in whom a diagnosis of iNPH was confirmed and those in which it was discarded. Results: A total of 92 patients were included in the study. The mean age at the time of presentation was 79.4 years and 63 patients were male. The diagnosis of iNPH was confirmed in 73.9% patients. The mean opening pressure was 14.4 cm H2O mean volume of CSF extracted was 43.4 mL. Conclusion: CSF extraction guided by a closing pressure of 0 cm H2O instead of tap test with a fixed volume of CSF alone may be an effective method of optimizing iNPH symptomatic improvement and diagnosis.