Miracle-dz/UniFAR-FTUs huggingface dataset:
TGF-β1 increases sialidase 3 expression in human lung epithelial cells by decreasing its degradation and upregulating its translation

Abstract Purpose: We previously found extensive desialylation of glycoconjugates and upregulation of the sialidase enzyme NEU3 in fibrotic lesions in human and mouse lungs. However, studies using microarray analysis of whole lung tissue mRNA and single cell RNA-seq found no significant difference in levels of NEU3 mRNA between IPF patients and controls. This study aimed to elucidate how NEU3 was upregulated in fibrotic lungs. Materials and methods: Transforming growth factor-β1 (TGF-β1), a key driver of fibrosis, was added to A549 human alveolar basal epithelial adenocarcinoma cells and human small airway epithelial cells (HSAEpC). NEU3 expression in A549 cells and HSAEpC was detected by immunofluorescence staining. NEU3 translation and degradation were assessed by polysome profiling (polysomes efficiently translate mRNAs; monosomes poorly translate mRNAs) and cycloheximide chase after treating cells with or without TGF-β1 for 48 h. Results: TGF-β1 increased NEU3 expression and secretion in A549 cells and HSAEpC but did not change total (nuclear + cytosolic) NEU3 mRNA levels. TGF-β1 decreased the degradation rate of NEU3 in A549 cells. TGF-β1 decreased NEU3 mRNA levels in monosomes and increased NEU3 mRNA level in polysomes. Conclusion: TGF-β1 upregulates levels of NEU3 in epithelial cells by both decreasing NEU3 degradation and by increasing the translation of NEU3 mRNA, explaining the apparent paradox of high levels of NEU3 protein in pulmonary fibrosis without a concomitant increase in the expression of NEU3 mRNA.
Determining the critical thresholds for co-word network based on the theory of percolation transition

Purpose One of the chief purposes of bibliometric analysis is to reveal the intellectual structure of a knowledge domain. Yet due to the magnitude and the heterogeneous nature of bibliometric networks, some sorts of filtering procedures are often required to make the resulting network interpretable. A co-word analysis of more than 135,000 scholarly publications on Buddhism was conducted to compare the intellectual structure of Buddhist studies in three language communities, Chinese, English and Japanese, over two periods (1957–1986 and 1987–2016). Six co-word similarity networks were created so social network analysis-based community-detection algorithm can be identified to compare major research themes in different languages and eras. The paper aims to discuss this issue. Design/methodology/approach A series of filtering procedures was performed to exclude less discriminatory keywords and spurious relationships of a large, cross-language co-word network in Buddhist studies. Chief among the filtering heuristics was a percolation-transition based method to determine the similarity threshold that involves observing the relative decrease of nodes in the giant component with the increasing similarity threshold. Findings It was found that the topical patterns in the Chinese and Japanese scholarship of Buddhism are alike and observably distinct from that of the English scholarship. Furthermore, a far more drastic changes of research themes were observed in the English literature relative to the Chinese and Japanese literature. Originality/value The filtering procedures were shown to greatly enhance the modularity values and limited the number of modularity classes; thus, domain expert interpretation is feasible.
Diarrhea may be underestimated: a missing link in 2019 novel coronavirus

The outbreak of pneumonia caused by the 2019 Novel Coronavirus (2019-nCoV) was reported in Wuhan City, China. However, the clinical symptoms varied in different reports. Based on the results of inter-group difference test, we found that the incidence of diarrhea differed in three recent reports. As 2019-nCoV utilizes the same cell entry receptor ACE2 as severe acute respiratory syndrome coronavirus (SARS-CoV) and ACE2 tightly controls intestinal inflammation, to trace the route of infection mediated by 2019-nCoV, we used the single-cell RNA sequencing data for analysis. We found that the ACE2 mRNA was highly expressed in the healthy human small intestine rather than the lung. Besides, single-cell RNA sequencing data showed that ACE2 was significantly elevated in the proximal and distal enterocytes, where the small intestinal epithelium is exposed to the foreign pathogen. Thus, we suspect that ACE2-expressing small intestinal epithelium cells might be vulnerable to 2019-nCoV infection when people eat infected wild animals and diarrhea may serve as an indicator for infection, suggesting that clinicians should pay more attention to patients with diarrhea during the outbreak of pneumonia.
Porous Si Partially Filled with Water Molecules—Crystal Structure, Energy Bands and Optical Properties from First Principles

The paper reports the results on first-principles investigation of energy band spectrum and optical properties of bulk and nanoporous silicon. We present the evolution of energy band-gap, refractive indices and extinction coefficients going from the bulk Si of cubic symmetry to porous Si with periodically ordered square-shaped pores of 7.34, 11.26 and 15.40 Å width. We consider two natural processes observed in practice, the hydroxylation of Si pores (introduction of OH groups into pores) and the penetration of water molecules into Si pores, as well as their impact on the electronic spectrum and optical properties of Si superstructures. The penetration of OH groups into the pores of the smallest 7.34 Å width causes a disintegration of hydroxyl groups and forms non-bonded protons which might be a reason for proton conductivity of porous Si. The porosity of silicon increases the extinction coefficient, k, in the visible range of the spectrum. The water structuring in pores of various diameters is analysed in detail. By using the bond valence sum approach we demonstrate that the types and geometry of most of hydrogen bonds created within the pores manifest a structural evolution from distorted hydrogen bonds inherent to small pores (∼7 Å) to typical hydrogen bonds observed by us in larger pores (∼15 Å) which are consistent with those observed in a wide database of inorganic crystals.
Distribution, number, and certain neurochemical identities of infracortical white matter neurons in the brains of three megachiropteran bat species

A large population of infracortical white matter neurons, or white matter interstitial cells (WMICs), are found within the subcortical white matter of the mammalian telencephalon. We examined WMICs in three species of megachiropterans, Megaloglossus woermanni, Casinycteris argynnis, and Rousettus aegyptiacus, using immunohistochemical and stereological techniques. Immunostaining for neuronal nuclear marker (NeuN) revealed substantial numbers of WMICs in each species—M. woermanni 124,496 WMICs, C. argynnis 138,458 WMICs, and the larger brained R. aegyptiacus having an estimated WMIC population of 360,503. To examine the range of inhibitory neurochemical types we used antibodies against parvalbumin, calbindin, calretinin, and neural nitric oxide synthase (nNOS). The calbindin and nNOS immunostained neurons were the most commonly observed, while those immunoreactive for calretinin and parvalbumin were sparse. The proportion of WMICs exhibiting inhibitory neurochemical profiles was ~26%, similar to that observed in previously studied primates. While for the most part the WMIC population in the megachiropterans studied was similar to that observed in other mammals, the one feature that differed was the high proportion of WMICs immunoreactive to calbindin, whereas in primates (macaque monkey, lar gibbon and human) the highest proportion of inhibitory WMICs contain calretinin. Interestingly, there appears to be an allometric scaling of WMIC numbers with brain mass. Further quantitative comparative work across more mammalian species will reveal the developmental and evolutionary trends associated with this infrequently studied neuronal population.
Surface Modifications of Poly(Ether Ether Ketone) via Polymerization Methods—Current Status and Future Prospects

Surface modification of poly(ether ether ketone) (PEEK) aimed at applying it as a bone implant material aroused the unflagging interest of the research community. In view of the development of implantology and the growing demand for new biomaterials, increasing biocompatibility and improving osseointegration are becoming the primary goals of PEEK surface modifications. The main aim of this review is to summarize the use of polymerization methods and various monomers applied for surface modification of PEEK to increase its bioactivity, which is a critical factor for successful applications of biomedical materials. In addition, the future directions of PEEK surface modifications are suggested, pointing to low-ppm surface-initiated atom transfer radical polymerization (SI-ATRP) as a method with unexplored capacity for flat surface modifications.
Hardware Trojan Mitigation in Pipelined MPSoCs

Multiprocessor System-on-Chip (MPSoC) has become necessary due to the the billions of transistors available to the designer, the need for fast design turnaround times, and the power wall. Thus, present embedded systems are designed with MPSoCs, and one possible way MPSoCs can be realized is through Pipelined MPSoC (PMPSoC) architectures, which are used in applications from video surveillance to cryptosystems. Hardware Trojans (HTs) on PMPSoCs are a significant concern due to the damage caused by their stealth. An adversary could use HTs to extract secret information (data leakage) to modify functionality/data (functional modification) or make PMPSoCs deny service. In this article, we present PMPGuard, a mechanism that (1) detects the presence of hardware Trojans in Third Party Intellectual Property (3PIP) cores of PMPSoCs by continuous monitoring and testing and (2) recovers the system by switching the infected processor core with another one. We designed, implemented, and tested the system on a commercial cycle accurate multiprocessor simulation environment. Compared to the state-of-the-art system-level techniques that use Triple Modular Redundancy (TMR) and therefore incur at least 3× area and power overheads, our proposed system incurs about 2× area and 1.5× power overheads without any adverse impact on throughput.
Construction rapide, performante et mutualisée de systèmes de reconnaissance et de synthèse de la parole pour de nouvelles langues. (Rapid, efficient and joint construction of speech recognition and synthesis systems for new languages)

Nous etudions dans cette these la construction mutualisee de systemes de reconnaissance et de synthese de la parole pour de nouvelles langues, avec un objectif de performance et de rapidite de developpement. Le developpement rapide des technologies vocales pour de nouvelles langues anime des ambitions scientifiques et est aujourd’hui considere comme strategique par les acteurs industriels. Cependant, le developpement des langues est conduit de maniere morcelee par quelques centres de recherche travaillant chacun sur un nombre reduit de langues. Or, ces technologies partagent de nombreux points communs. Notre etude se concentre sur la construction et la mutualisation d'outils pour la creation de lexiques, l’apprentissage de regles de phonetisation et l’exploitation de donnees imparfaites. Nos contributions portent sur la selection de donnees pertinentes pour l’apprentissage de modeles acoustiques, le developpement conjoint de phonetiseurs et de lexiques de prononciation pour la reconnaissance et la synthese de la parole, et l’exploitation de modeles neuronaux pour la transcription phonetique a partir du texte et du signal de parole. De plus, nous presentons une approche de detection automatique des erreurs de transcriptions phonetiques dans les bases de donnees annotees de signal de parole. Cette etude a montre qu’il etait possible de reduire de maniere importante la quantite de donnees a annoter manuellement lors du developpement de nouveaux systemes de synthese de la parole. Cela contribue naturellement a reduire le temps de collecte de donnees pour la creation de nouveaux systemes. Finalement, nous etudions un cas applicatif.
Incidence and risk of proteinuria associated with newly approved vascular endothelial growth factor receptor tyrosine kinase inhibitors in cancer patients: an up-to-date meta-analysis of randomized controlled trials

ABSTRACT Objective: We performed a meta-analysis to quantify the overall incidence and risk of proteinuria associated with five newly approved VEGFR-TKIs (regorafenib, vandetanib, cabozantinib, lenvatinib, axitinib) in cancer patients. Methods: Pubmed, Embase, ASCO abstracts, and ESMO abstracts were searched to identify relevant studies. Overall incidence rates, relative risk (RR), and 95% confidence intervals (CI) were estimated using random or fixed effects models according to the heterogeneity of included studies. Results: A total of 9,446 patients from 20 RCTs were included for the meta-analysis. The use of newly approved VEGFR-TKIs was associated with an increased risk of all-grade (RR 2.35, 95% CI 1.69–3.27, P < 0.001) and high-grade (RR 3.70, 95% CI 2.09–6.54, P < 0.001) proteinuria. On subgroup analysis, lenvatinib, axitinib, and vandetanib significantly increased the risk of all-grade proteinuria, and lenvatinib was associated with an increased risk of high-grade proteinuria. In addition, the risk of developing high-grade proteinuria events was significant for patients with hepatocellular carcinoma (HCC) and renal cell carcinoma (RCC), but not for patients with colorectal cancer (CRC) and thyroid cancer (TC). Conclusion: Treatment with newly approved VEGFR-TKIs significantly increases the risk of developing proteinuria events in cancer patients, especially for patients treated with lenvatinib.
Control of crystal symmetry breaking with halogen substituted benzylammonium in layered hybrid metal-halide perovskites.

Layered hybrid metal-halide perovskites with non-centrosymmetric crystal structure are predicted to show spin-selective band splitting from Rashba effects. Thus, fabrication of metal-halide perovskites with defined crystal symmetry is desired to control the spin-splitting in their electronic states. Here, we report the influence of halogen para-substituents on the crystal structure of benzylammonium lead iodide perovskites (4-XC6H4CH2NH3)2PbI4 (X = H, F, Cl, Br). Using X-ray diffraction and second-harmonic generation, we study structure and symmetry of single crystal and thin film samples. We report that introduction of a halogen atom lowers the crystal symmetry such that the chlorine- and bromine-substituted structures are non-centrosymmetric. The differences can be attributed to the nature of the intermolecular interactions between the organic molecules. We calculate electronic band structures and find good control of Rashba splittings. Our results present a facile approach to tailor hybrid layered metal halide perovskites with potential for spintronic and non-linear optical applications.
Isolation of singlet carbene derived 2-arsa-1,3-butadiene radical cations and dications.

2-Arsa-1,3-butadienes (L)As(cAACR) (L = PhC[double bond, length as m-dash]C{(NDipp)CH}2, Dipp = 2,6-iPr2C6H3; cAACR = C{(NDipp)CMe2CH2C(R)}, R = Me2 2a, R = cyclohexyl (Cy) 2b) and the corresponding radical cations [(L)As(cAACR)]GaCl4 (R = Me2 3a, Cy 3b) and dications [(L)As(cAACR)](GaCl4)2 (R = Me 4a, Cy 4b) featuring a C[double bond, length as m-dash]C-As[double bond, length as m-dash]C π-conjugated framework are reported.
(R)-Salbutamol Improves Imiquimod-Induced Psoriasis-Like Skin Dermatitis by Regulating the Th17/Tregs Balance and Glycerophospholipid Metabolism

Psoriasis is a skin disease that is characterized by a high degree of inflammation caused by immune dysfunction. (R)-salbutamol is a bronchodilator for asthma and was reported to alleviate immune system reactions in several diseases. In this study, using imiquimod (IMQ)-induced mouse psoriasis-like dermatitis model, we evaluated the therapeutic effects of (R)-salbutamol in psoriasis in vivo, and explored the metabolic pathway involved. The results showed that, compared with IMQ group, (R)-salbutamol treatment significantly ameliorated psoriasis, reversed the suppressive effects of IMQ on differentiation, excessive keratinocyte proliferation, and infiltration of inflammatory cells. Enzyme-linked immunosorbent assays (ELISA) showed that (R)-salbutamol markedly reduced the plasma levels of IL-17. Cell analysis using flow cytometry showed that (R)-salbutamol decreased the proportion of CD4+ Th17+ T cells (Th17), whereas it increased the percentage of CD25+ Foxp3+ regulatory T cells (Tregs) in the spleens. (R)-salbutamol also reduced the increased weight ratio of spleen to body. Furthermore, untargeted metabolomics showed that (R)-salbutamol affected three metabolic pathways, including (i) arachidonic acid metabolism, (ii) sphingolipid metabolism, and (iii) glycerophospholipid metabolism. These results demonstrated that (R)-salbutamol can alleviate IMQ-induced psoriasis through regulating Th17/Tregs cell response and glycerophospholipid metabolism. It may provide a new use of (R)-salbutamol in the management of psoriasis.
Apprentissage neuronal profond pour l'analyse de contenus multimodaux et temporels. (Deep learning for multimodal and temporal contents analysis)

Notre perception est par nature multimodale, i.e. fait appel a plusieurs de nos sens. Pour resoudre certaines tâches, il est donc pertinent d’utiliser differentes modalites, telles que le son ou l’image.Cette these s’interesse a cette notion dans le cadre de l’apprentissage neuronal profond. Pour cela, elle cherche a repondre a une problematique en particulier : comment fusionner les differentes modalites au sein d’un reseau de neurones ? Nous proposons tout d’abord d’etudier un probleme d’application concret : la reconnaissance automatique des emotions dans des contenus audio-visuels.Cela nous conduit a differentes considerations concernant la modelisation des emotions et plus particulierement des expressions faciales. Nous proposons ainsi une analyse des representations de l’expression faciale apprises par un reseau de neurones profonds.De plus, cela permet d’observer que chaque probleme multimodal semble necessiter l’utilisation d’une strategie de fusion differente.C’est pourquoi nous proposons et validons ensuite deux methodes pour obtenir automatiquement une architecture neuronale de fusion efficace pour un probleme multimodal donne, la premiere se basant sur un modele central de fusion et ayant pour visee de conserver une certaine interpretation de la strategie de fusion adoptee, tandis que la seconde adapte une methode de recherche d'architecture neuronale au cas de la fusion, explorant un plus grand nombre de strategies et atteignant ainsi de meilleures performances.Enfin, nous nous interessons a une vision multimodale du transfert de connaissances. En effet, nous detaillons une methode non traditionnelle pour effectuer un transfert de connaissances a partir de plusieurs sources, i.e. plusieurs modeles pre-entraines. Pour cela, une representation neuronale plus generale est obtenue a partir d’un modele unique, qui rassemble la connaissance contenue dans les modeles pre-entraines et conduit a des performances a l'etat de l'art sur une variete de tâches d'analyse de visages.
Interaction analysis under misspecification of main effects: Some common mistakes and simple solutions

The statistical practice of modeling interaction with two linear main effects and a product term is ubiquitous in the statistical and epidemiological literature. Most data modelers are aware that the misspecification of main effects can potentially cause severe type I error inflation in tests for interactions, leading to spurious detection of interactions. However, modeling practice has not changed. In this article, we focus on the specific situation where the main effects in the model are misspecified as linear terms and characterize its impact on common tests for statistical interaction. We then propose some simple alternatives that fix the issue of potential type I error inflation in testing interaction due to main effect misspecification. We show that when using the sandwich variance estimator for a linear regression model with a quantitative outcome and two independent factors, both the Wald and score tests asymptotically maintain the correct type I error rate. However, if the independence assumption does not hold or the outcome is binary, using the sandwich estimator does not fix the problem. We further demonstrate that flexibly modeling the main effect under a generalized additive model can largely reduce or often remove bias in the estimates and maintain the correct type I error rate for both quantitative and binary outcomes regardless of the independence assumption. We show, under the independence assumption and for a continuous outcome, overfitting and flexibly modeling the main effects does not lead to power loss asymptotically relative to a correctly specified main effect model. Our simulation study further demonstrates the empirical fact that using flexible models for the main effects does not result in a significant loss of power for testing interaction in general. Our results provide an improved understanding of the strengths and limitations for tests of interaction in the presence of main effect misspecification. Using data from a large biobank study “The Michigan Genomics Initiative”, we present two examples of interaction analysis in support of our results.
Swine multifocal ulcerative colitis and crypt abscesses associated with Entamoeba polecki subtype 3 and Salmonella Typhimurium

Piglets aged approximately 50 days exhibited diarrhea and wasting. Multiple white foci were detected in the colon of a dead piglet; histopathological findings revealed multifocal ulcers and crypt abscesses with Entamoeba trophozoites and gram-negative bacilli in the piglet. These pathogens were identified as Entamoeba polecki subtype 3 and Salmonella enterica serovar Typhimurium, respectively. Numerous E. polecki subtype 3 trophozoites were located on the edge of the ulcerative and necrotic lesions in the lamina propria. Crypt abscesses were associated with S. Typhimurium. These results suggest that E. polecki subtype 3 caused multifocal ulcerative colitis accompanied by crypt abscesses with S. Typhimurium in the piglet. This study is the first report of colitis with E. polecki subtype 3 and S. Typhimurium coinfection.
A microRNA Expression Profile as Non-Invasive Biomarker in a Large Arrhythmogenic Cardiomyopathy Cohort

Arrhythmogenic Cardiomyopathy (AC) is a clinically and genetically heterogeneous myocardial disease. Half of AC patients harbour private desmosomal gene variants. Although microRNAs (miRNAs) have emerged as key regulator molecules in cardiovascular diseases and their involvement, correlated to phenotypic variability or to non-invasive biomarkers, has been advanced also in AC, no data are available in larger disease cohorts. Here, we propose the largest AC cohort unbiased by technical and biological factors. MiRNA profiling on nine right ventricular tissue, nine blood samples of AC patients, and four controls highlighted 10 differentially expressed miRNAs in common. Six of these were validated in a 90-AC patient cohort independent from genetic status: miR-122-5p, miR-133a-3p, miR-133b, miR-142-3p, miR-182-5p, and miR-183-5p. This six-miRNA set showed high discriminatory diagnostic power in AC patients when compared to controls (AUC-0.995), non-affected family members of AC probands carrying a desmosomal pathogenic variant (AUC-0.825), and other cardiomyopathy groups (Hypertrophic Cardiomyopathy: AUC-0.804, Dilated Cardiomyopathy: AUC-0.917, Brugada Syndrome: AUC-0.981, myocarditis: AUC-0.978). AC-related signalling pathways were targeted by this set of miRNAs. A unique set of six-miRNAs was found both in heart-tissue and blood samples of AC probands, supporting its involvement in disease pathogenesis and its possible role as a non-invasive AC diagnostic biomarker.