Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex structure of INAD PDZ45 and NORPA CC-PBM

INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. However, the molecular mechanism that governs the interaction between INAD and NORPA (phospholipase Cβ, PLCβ), a key step for the fast kinetics of the light signaling, is not known. Here, we show that the NORPA C-terminal coiled-coil domain and PDZ-binding motif (CC-PBM) synergistically bind to INAD PDZ45 tandem with an unexpected mode and unprecedented high affinity. Guided by the structure of the INAD-NORPA complex, we discover that INADL is probably a mammalian counterpart of INAD. The INADL PDZ89 tandem specifically binds to PLCβ4 with a mode that is strikingly similar to that of the INAD-NORPA complex, as revealed by the structure of the INADL PDZ89-PLCβ4 CC-PBM complex. Therefore, our study suggests that the highly specific PDZ tandem - PLCβ interactions are an evolutionarily conserved mechanism in PLCβ signaling in the animal kingdom.
Alumina-supported copper chloride: 3. Effect of exposure to ethylene

The effect of exposure to C2H4 of different CuCl2/Al2O3 catalysts characterized by a wide copper content (0.25 Al–OH groups; and (ii) >Al3+ coordinative unsaturated Lewis acidic sites are present on the catalyst. These results point out the possible determinant role of the support in side reactions and coking that are responsible for loss of selectivity and, respectively, catalyst decay during industrial runs.
Intérêts et validation de marqueurs précoces de génotoxicité environnementale

Le present projet propose de mettre au point des marqueurs biologiques de genotoxicite environnementale permettant une approche integree de la complexite des contaminations. Les preoccupations relatives aux pollutions des sols et des sediments sont recentes. La contamination metallique des sols par exemple, due aux activites anthropiques est cependant preoccupante. Ce, en termes de risques pour la sante humaine et environnementale, du fait de la persistance, de l’accumulation, et du transfert possible de ces metaux vers les nappes souterraines et vers les chaines trophiques. Le projet de recherche porte sur la validation au laboratoire de marqueurs de genotoxicite, mis en œuvre sur plusieurs especes representatives en ecotoxicologie terrestre, Eisenia fetida et Trifolium repens. Des travaux preliminaires, dans le cadre d’un programme « Ecotoxicite des sols contamines par les elements traces metalliques » soutenu par l’ANR et les FEDER, ont permis de mettre en evidence la pertinence du test des cometes avec Trifolium vis-a-vis des sols contaminees en elements traces metalliques ou a des hydrocarbures en melanges (lixiviats de dechet industriels). Le test des cometes (Single Cell Gel Electrophoresis Assay) permet la detection et la quantification des dommages a l’ADN (cassures double et simple brin, sites alcali-labiles) au sein d’une population cellulaire, induits par certains agents environnementaux. Il permet d’evaluer l’atteinte au genome d’organismes modeles exposes. Cette atteinte de l’ADN est une composante essentielle a estimer car elle contribue a l’origine des phenomenes de cancerogenese.
An ESCRT-LEM domain inner nuclear membrane protein surveillance system is poised to directly monitor the integrity of the nuclear envelope barrier and nuclear transport system

The integrity of the nuclear envelope membranes coupled to the diffusion barrier and selective transport properties of nuclear pore complexes (NPCs) are a prerequisite for the robust segregation of nucleoplasm and cytoplasm. Recent work supports that mechanical membrane disruption or perturbation to NPC assembly can trigger an ESCRT-dependent surveillance system that seals nuclear envelope pores: how these pores are sensed and sealed remains to be fully defined. Here, we show that the principal components of the nuclear envelope surveillance system in yeast, which includes the ESCRT Chm7 and the integral inner nuclear membrane (INM) protein Heh1, are spatially segregated by the nuclear transport system. Specifically, at steady state Chm7 is actively restricted from the nucleus by Crm1/Xpo1. Consistent with the idea that it is the exposure of the INM that triggers surveillance, the expression of a transmembrane anchor and the winged helix domain of Heh1 is sufficient to recruit and activate Chm7 at a membrane interface. Correlative light electron tomography under conditions of Chm7 hyper-activation further show the formation of an elaborate network of fenestrated sheets at the INM and suggest ER-membrane delivery at sites of nuclear envelope herniation. Our data point to a model in which exposure of Chm7 to Heh1, driven by any perturbation in the nuclear envelope barrier would lead to local nuclear envelope remodeling to promote membrane sealing. Our findings have implications for disease mechanisms associated with defects in NPC assembly and nuclear envelope integrity.
Binning microbial genomes using deep learning

Identification and reconstruction of microbial species from metagenomics wide genome sequencing data is an important and challenging task. Current existing approaches rely on gene or contig co-abundance information across multiple samples and k-mer composition information in the sequences. Here we use recent advances in deep learning to develop an algorithm that uses variational autoencoders to encode co-abundance and compositional information prior to clustering. We show that the deep network is able to integrate these two heterogeneous datasets without any prior knowledge and that our method outperforms existing state-of-the-art by reconstructing 1.8 - 8 times more highly precise and complete genome bins from three different benchmark datasets. Additionally, we apply our method to a gene catalogue of almost 10 million genes and 1,270 samples from the human gut microbiome. Here we are able to cluster 1.3 - 1.8 million extra genes and reconstruct 117 - 246 more highly precise and complete bins of which 70 bins were completely new compared to previous methods. Our method Variational Autoencoders for Metagenomic Binning (VAMB) is freely available at: https://github.com/jakobnissen/vamb
Extracting a Chinese learner corpus from the web: Grammatical error correction for Learning Chinese as a foreign language with statistical machine translation

In this paper, we describe the TMU system for the shared task of Grammatical Error Diagnosis for Learning Chinese as a Foreign Language (CFL) at NLP-TEA1. One of the main issues in grammatical error correction for CFL is a data bottleneck problem. The Chinese learner corpus at hand (NTNU learner corpus) contains only 1,208 sentences in total, which is obviously insufficient for training supervised techniques. To overcome this problem, we extracted a large-scale Chinese learner corpus from a language exchange site called Lang-8, which results in 95,706 sentences (two million words) after cleaning. We used it as a parallel corpus for a phrase-based statistical machine translation (SMT) system, which translates learner sentences into correct sentences.
Alignment symmetrisation optimization targeting phrase pivot statistical machine translation

An important step in mainstream statistical machine translation (SMT) is combining bidirectional alignments into one alignment model. This process is called sym-metrization. Most of the symmetrization heuristics and models are focused on direct translation (source-to-target). In this paper, we present symmetrization heuristic relaxation to improve the quality of phrase-pivot SMT (source-[pivot]-target). We show positive results (1.2 BLEU points) on Hebrew-to-Arabic SMT pivoting on English.
Physicochemical Characteristics of Korean Folk Sojues

In order to provide a quality index of Korean folk sojues, physicochemical properties of Korean folk sojues (Andong soju, Moonbaesul, Leekangju, Jindo Hongju, Chebiwon soju, Yethyang (rice) and Yethyang (barley)), Paekrosul, Chinese kaoliangchiews (Moutaichiew, Ergoutoutiu, Chuyehchingchiew, Zhikukaoliangchiew and Paigal), Japanese Senbatanuki shochu and two whiskies were determined. The pH of sojues () were mainly influenced by total acidity which was described as acetic acid. The conductivities of Paekrosul and Leekangju showed relatively high value of , respectively. Korean folk sojues and Paekrosul showed maximum absorption at 274 or in the spectrometric study. We performed principal components analysis (PCA) of physicochemical properties and spectrometric data to extract representative characteristics and to compare the similarity or the dissimilarity. The PCA plot showed the distinguished cluster of Korean folk sojues comparing with Chinese kaoliangchiew or Paekrosul etc.
Exercise-stimulated muscle ROS production and glucose uptake requires NADPH oxidase 2

1. Department of Nutrition, Exercise and Sports, University of Copenhagen, Denmark 2. Center of Exercise, Metabolism and Cancer, Biomedical Sciences Institute, Universidad de Chile. 3. Novo Nordisk Foundation Center for Basic Metabolic Research, Research Program in Integrative Metabolism and Environmental Influence, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark 4. Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
Dynamic Performance of Different Metal Foam Magnetorheological Fluid Materials

This paper investigates the dynamic response of different metal foam magnetorheological (MR) fluid materials experimentally. Metal foam MR fluid materials can be used to manufacture the low-cost controllable damping devices without the need of a seal and provide a long service life. The MR fluid is stored in metal foam mainly by the capillary force. In the action of magnetic field, the MR fluid will be extracted out from metal foam and fill up the shear gap, and then, produce the MR effect. Three types of metal foams with different relative permeability, such as Fe, Ni, and Cu, are applied to store the MR fluid. A set of testing systems, including the plate-on-plate shear test rig, electromotor, and force sensor, is built to investigate the dynamic performance of these materials. In order to describe the dynamic response accurately, three parameters of response time are introduced and defined. The magnetic field, both in the shear gap and the pore of metal foam, is simulated by finite element method software. The experimental results show that the response time of metal foam MR fluid materials will change with different currents, which provides the theoretical and experimental basis for the further development of metal foam MR fluid dampers or actuators.
IDENTIFICAÇÃO E RASTREAMENTO DE VEÍCULOS UTILIZANDO FLUXO ÓPTICO

Controlar o trafego de veiculos e uma tarefa muito dificil de ser realizada. Essa atividade representa um grande desafio na busca por solucoes que possam ajudar o controle e a fiscalizacao de trafego de veiculos em vias terrestres. Neste trabalho considera-se o emprego do metodo diferencial, proposto por Lucas e Kanade, para estimacao do Fluxo Optico, como ferramenta computacional para rastrear e classificar veiculos a partir de frames de imagens de video. Os veiculos encontrados em cada frame sao classificados conforme o seu tamanho: pequeno, medio e grande porte. Os resultados deste trabalho podem ser aplicados, por exemplo, em sistemas de contagem de veiculos em rodovias. Outra aplicacao desse trabalho, que e de grande valia seria para a construcao de semaforos inteligentes, que controlam os tempos de bloqueio e liberacao da via baseados no fluxo de veiculos.
The study of the biodiversity in Mexico: a route with a course?

Mexico is a country with an extraordinary natural wealth; however, after 2 centuries of taxonomic work only a fraction of the total number of species that occur in the country is known. A major problem is that we are loosing this enormous biological wealth with increasing extinction rates that are now orders of magnitude larger than the natural rates. This supplement was edited considering that the continuous monitoring of Mexican biodiversity can be a useful tool to evaluate the balance between what we know and what we ignore about the number of species, and that the ongoing analysis could help directing future studies. Far from including all possible taxa, an analysis is presented of 56 biological groups that account for 94 412 species in Mexico which represent 8.59% of the world's total for those groups, with an average endemism of 39.7%. It is estimated from the data here published that Mexico's biota could be, on average, 3.3 times larger than what is now known.
A new surface gliding species of Chironomidae: An independent invasion of marine environments and its evolutionary implications

Insects have invaded marine habitats only rarely and secondarily. Recently, we discovered a flightless dipteran species skating rapidly on the surface of seawater ponds at the Pacific coast of eastern China. Morphological analyses initially suggested an isolated position of the non‐biting midge, suggesting the erection of a new genus within Chironomini (Diptera: Chironomidae). However, an analysis of molecular data revealed that the marine species is in fact nested within the species‐rich genus Dicrotendipes. The apparent conflict between molecular and morphological data can be easily explained. It is likely that the new species has evolved a series of autapomorphic adaptations. These traits clearly distinguish the taxon from other species of the genus but do not justify the erection of a new supraspecific taxon, which would render Dicrotendipes paraphyletic. The switch to marine environments was likely a trigger for various morphological modifications resulting from increased selective pressure. Molecular data suggest that the potential speciation event occurred around 19–29 Ma, linked with a migration from freshwater to seawater ponds along the Pacific Ocean. Considering the results of our analysis, we place the flightless marine skater in the genus Dicrotendipes. All life stages of Dicrotendipes sinicus Qi & Lin sp. n. are described and illustrated, associated with larvae obtained by rearing or confirmed through association with DNA barcodes. The biology and ecology of the species are outlined based on collection data and in situ observations. Evolutionary patterns linked with repeated invasions of marine habitats are discussed.
Application of NFC Technology for Cashless Payment System in Canteen

In a campus community, mostly is younger people andstay in University hostel without cooking facilities then have to getfrom canteen for foods and beverages. In office hour with limitedbreak time either breakfast or lunch everyone is rushing to get foodand crowded situation are happen. One of the issues is paymentsystem use manually (cash) and queue at the cashier to pay foods,sometime need to wait a few minute until to get the turn. Cashlesspayment such as token or credit system is implementing in some ofrestaurant and food courts but does not applicable in Universitycanteen that most of customers are students with small transaction,only a few dollars and cents. Nowadays, mobile phone or smartphone is not a luxury thing and most of student carries it for phonecall, message, email, or browsing internet. Most of smart phone alsoembedded with Near Field Communication (NFC) reader inside thephone, thus by using this phone with NFC enable to do paymentsystem at the canteen. The credit is deducted from mobile phonebalance for pre-paid system or billed in monthly for postpaid andthis system have working together to the cellular phone operator.Confirmation on payment system is shows whether customerapprove payment or not then a notification is sent to user.With thissystem be able to overcome several issues such as queue at cashierfor payment and risk of student to carry cash money while buyingfoods.
Effect of Nitrate on Iron Reduction and Phosphorus Release in Flooded Paddy Soil

The increase in P availability to rice under flooded soil conditions involves the reductive dissolution of iron phosphate and iron (hydr)oxide phosphate. However, since is a more favourable electron acceptor in anaerobic soils than Fe, high loads function as a redox buffer limiting the reduction of Fe. The effect of adding on Fe reduction and P release in paddy soil was investigated. Pot experiment was conducted where was added to flooded soil and changes of redox potential and , and concentrations in soil solution at 10 cm depth were monitored as a function of time. Redox potential decreased with time to -96 mV, but it was temporarily poised at about 330360 mV when was present. Nitrate addition to soil led to reduced release of and prevented the solubilization of P. Phosphate in pore water began to rise soon after incubation and reached final concentrations about 0.82 mg P/L in the soil without addition. But, in the soil with addition, in pore water was maintained in the range of 0.20. 3 mg P/L. The duration of inhibition in release was closely related to the presence of , and the timing of release was inversely related to the concentration in soil solution. The results suggest that preferential use of as an electron acceptor in anaerobic soil condition can strongly limit Fe reduction and P solubilization.
The “Gene Cube”: A Novel Approach to Three-dimensional Clustering of Gene Expression Data

A very popular technique for isolating significant genes from cancerous tissues is the application of various clustering algorithms on data obtained by DNA microarray experiments. The objective of the present work is to take into consideration the chromosomal identity of every gene before the clustering, by creating a three-dimensional structure of the form Chromosomes×Genes×Samples. Further on, the k-Means algorithm and a triclustering technique called δ- TRIMAX, are applied independently on the structure. The present algorithm was developed using the Python programming language (v. 3.5.1). For this work, we used two distinct public datasets containing healthy control samples and tissue samples from bladder cancer patients. Background correction was performed by subtracting the median global background from the median local Background from the signal intensity. The quantile normalization method has been applied for sample normalization. Three known algorithms have been applied for testing the “gene cube”, a classical k-means, a transformed 3D k-means and the δ-TRIMAX. Our proposed data structure consists of a 3D matrix of the form Chromosomes×Genes×Samples. Clustering analysis of that structure manifested very good results as we were able to identify gene expression patterns among samples, genes and chromosomes. Discussion: to the best of our knowledge, this is the first time that such a structure is reported and it consists of a useful tool towards gene classification from high-throughput gene expression experiments. Such approaches could prove useful towards the understanding of disease mechanics and tumors in particular.
Rôle du fer sur Legionella pneumophila et sur sa persistance dans les biofilms naturels

L. pneumophila est une bacterie ubiquitaire des environnements aquatiques, responsable de la legionellose. Elle est principalement retrouvee au sein de protozoaires, mais aussi dans les biofilms. Il est admit que le fer est l'un des elements indispensable a la croissance de ce pathogene. En 2008, une etude a ete realisee au sein de notre equipe montrant une modulation de l'expression des genes entre L. pneumophila a l'etat planctonique, et a l'etat de biofilm. Dans cette meme etude, l'ajout de forte concentration en fer (1,25 g/l), dans le milieu de culture des biofilms, a revele une inhibition de leur developpement. Le fer presente donc un role dans l'etablissement de biofilms mono especes de L. pneumophila. Nous avons developpe un modele de biofilms naturels, formes a partir d'eau de riviere, afin de tester l'etablissement de L. pneumophila, dans des conditions ou l'eau de riviere est supplementee en fer ou au contraire appauvrit, par l'ajout de chelateurs, le deferoxamine mesylate (DFX) ou le dipyridyl (DIP). Les ajouts de fer et de DFX n'ont eu aucun impact sur l'etablissement de L. pneumophila contrairement au DIP, qui a induit une augmentation de l'implantation de ces bacteries.Par ailleurs, nous avons effectue une analyse transcriptomique sur L. pneumophila cultivees en milieu liquide supplemente en DFX. L'ajout du chelateur a entraine une induction de l'expression de 113 genes et la repression de 246 genes. Parmi les genes induits, certains sont deja connus comme etant impliques dans le metabolisme du fer ou controles par le fer. Parmi eux, un gene a ete surexprime, il n'a jamais ete associe au fer et sa fonction est encore inconnue a ce jour. Il s'agit du gene lpp2867. Des investigations ont ete realisees afin de caracteriser et de comprendre le role de la proteine pour laquelle il code. Elle est notamment impliquee dans l'infection des amibes et des macrophages. Son role dans le transport du fer ferreux a egalement ete mis en avant. Cette proteine a ete nommee IroT pour « iron transporter ».
Etude comparative de deux cupules cimentées dans une croix de Kerboull au cours des reprises de prothèse totale de hanche : cotyle full PE versus double mobilité. A propos de 95 cas

Introduction Le descellement et l'instabilite sont les principales causes de revisionsacetabulaires. Les reprises iteratives imposent une reconstruction cotyloidienne. Les cotyles a double mobilite (DM) previennent l'instabilite, mais leurs resultats au cours des revisions avec reconstruction acetabulaire sont peu evalues.Materiel et methode Cette etude retrospective de 95 reprises acetabulaires avec anneau de soutien compare 60 cotyles en polyethylene a 35 cotyles a DM scelles dans une croix de Kerboull. L'âge moyen etait de 68 ans, le nombre de reprises acetabulaires allait de 1 a 6 et les destructions osseuses etaient severes (58% de stade 3a de Paprosky). Une greffe osseuse etait associee dans 76% des cas. Au recul de 45 mois, les evenements luxation et reprise chirurgicale pour descellement iteratif etaient etudies. Une etude radiologique jugeait la survie radiologique et l'osteointegration des greffes.Resultats La prevalence des luxations etait de 25% dans le groupe full PE contre 3% dans le groupe DM. Les taux de reprise pour descellement aseptique etaient respectivement de 14 et 13% dans les groupes full PE et DM. Un descellement radiologique etait retrouve dans 39% des cas du groupe full PE et 29% des cas du groupe DM. L'osteointegration des greffes etait respectivement de 54 et 52% dans ces deux populations.Conclusion La superiorite des cotyles a DM en prevention de l'instabilite est confirmee. Si dans la population generale il n'a pas ete mis en evidence de difference significative en terme de survie entre ces deux concepts, l'etude des sous groupe d'âge permet de« generaliser » l'utilisation des cotyles a DM chez le plus de 70 ans. Son utilisation doit rester prudente chez les moins de 70 ans ou les resultats semblent pencher vers les cotyles full PE. Cependant a compter de la 5eme reprise acetabulaire au vu du risque d'instabilite il semble raisonnable de proposer l'utilisation d'un implant a DM en faisant abstraction de l'âge