Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystals structure of Classical swine fever virus NS5B (residues 1-682)

Typically not assisted by proofreading, the RNA-dependent RNA polymerases (RdRPs) encoded by the RNA viruses may need to independently control its fidelity to fulfill virus viability and fitness. However, the precise mechanism by which the RdRP maintains its optimal fidelity level remains largely elusive. By solving 2.1–2.5 A resolution crystal structures of the classical swine fever virus (CSFV) NS5B, an RdRP with a unique naturally fused N-terminal domain (NTD), we identified high-resolution intra-molecular interactions between the NTD and the RdRP palm domain. In order to dissect possible regulatory functions of NTD, we designed mutations at residues Y471 and E472 to perturb key interactions at the NTD–RdRP interface. When crystallized, some of these NS5B interface mutants maintained the interface, while the others adopted an ‘open’ conformation that no longer retained the intra-molecular interactions. Data from multiple in vitro RdRP assays indicated that the perturbation of the NTD–RdRP interactions clearly reduced the fidelity level of the RNA synthesis, while the processivity of the NS5B elongation complex was not affected. Collectively, our work demonstrates an explicit and unique mode of polymerase fidelity modulation and provides a vivid example of co-evolution in multi-domain enzymes.
Report of first isolation of the zoonotic Arcobacter species from swine fecal samples in Ecuador

Arcobacter butzleri , A . cryaerophilus , A . skirrowii and A . thereius are recognised as emerging zoonotic agents, recovered from animals and human beings. The information available about Arcobacter species in Latin America is scarce. Among domestic animals, swine are considered important reservoir and source of contamination of different Arcobacter species. This communication reports the first simultaneous isolation of the four zoonotic Arcobacter species in Ecuador. Preliminary identification was done by phenotypic characteristics and definitive species identification was made by multiplex PCR method. Further investigation about the prevalence, distribution, ecology and interactions with human beings of these species is required. Key words : Arcobacter, zoonotic species, reservoir, Ecuador.
Brucella periplasmic protein EipB is a molecular determinant of cell envelope integrity and virulence

The Gram-negative cell envelope is a remarkable structure with core components that include an inner membrane, an outer membrane, and a peptidoglycan layer in the periplasmic space between. Multiple molecular systems function to maintain integrity of this essential barrier between the interior of the cell and its surrounding environment. We show that a conserved DUF1849-family protein, EipB, is secreted to the periplasmic space of Brucella, a monophyletic group of intracellular pathogens. In the periplasm, EipB folds into an unusual fourteen-stranded β-spiral structure that resembles the LolA and LolB lipoprotein delivery system, though the overall fold of EipB is distinct from LolA/LolB. Deletion of eipB results in defects in Brucella cell envelope integrity in vitro and in maintenance of spleen colonization in a mouse model of B. abortus infection. Transposon disruption of ttpA, which encodes a periplasmic protein containing tetratricopeptide repeats, is synthetically lethal with eipB deletion. ttpA is a reported virulence determinant in Brucella, and our studies of ttpA deletion and overexpression strains provide evidence that this gene also contributes to cell envelope function. We conclude that eipB and ttpA function in the Brucella periplasmic space to maintain cell envelope integrity, which facilitates survival in a mammalian host. Importance Brucella species cause brucellosis, a global zoonosis. A gene encoding a conserved DUF1849-family protein, which we have named EipB, is present in all sequenced Brucella and several other genera in the class Alphaproteobacteria. This manuscript provides the first functional and structural characterization of a DUF1849 protein. We show that EipB is secreted to the periplasm where it forms a spiral-shaped antiparallel-β protein that is a determinant of cell envelope integrity in vitro and virulence in an animal model of disease. eipB genetically interacts with ttpA, which also encodes a periplasmic protein. We propose that EipB and TtpA function as part of a system required for cell envelope homeostasis in select Alphaproteobacteria.
Texture and phase variation of ALD PbTiO3 films crystallized by rapid thermal anneal

PbTiO3 (lead titanate) thin films were deposited by atomic layer deposition (ALD) and crystallized via rapid thermal anneal. The films were grown using lead bis(3-N,N-dimethyl-2-methyl-2-propanoxide) and tetrakis dimethylamino titanium as cation precursors. A combination of H2O and ozone was used as oxidizers. Phase-pure, stoichiometric PbTiO3 was confirmed using x-ray diffraction, Rutherford backscattering spectroscopy, and scanning transmission electron microscopy. Ferroelectric hysteresis loops obtained by patterning circular capacitors with areas of 4.92 × 10−4 cm2 indicate a Pmax = 48 μC/cm2, 2Pr = 60 μC/cm2, Ec1 = −73 kV/cm, Ec2 = 125 kV/cm, and a leakage current density of 15 μA/cm2 at 138 kV/cm. Capacitance versus voltage measurements were used to obtain a maximum dielectric constant of 290 at 85 kV/cm and loss tangent under 4% tested in the range of ±275 kV/cm. ALD PbTiO3 grown with near-ideal cation ratios crystallized into randomly oriented perovskite grains when grown on a sputtered Pt-coated Si substrate. A variation of rapid thermal anneal temperatures, ramp rates, and nucleation layers was investigated and did not have a significant effect on perovskite grain orientation.PbTiO3 (lead titanate) thin films were deposited by atomic layer deposition (ALD) and crystallized via rapid thermal anneal. The films were grown using lead bis(3-N,N-dimethyl-2-methyl-2-propanoxide) and tetrakis dimethylamino titanium as cation precursors. A combination of H2O and ozone was used as oxidizers. Phase-pure, stoichiometric PbTiO3 was confirmed using x-ray diffraction, Rutherford backscattering spectroscopy, and scanning transmission electron microscopy. Ferroelectric hysteresis loops obtained by patterning circular capacitors with areas of 4.92 × 10−4 cm2 indicate a Pmax = 48 μC/cm2, 2Pr = 60 μC/cm2, Ec1 = −73 kV/cm, Ec2 = 125 kV/cm, and a leakage current density of 15 μA/cm2 at 138 kV/cm. Capacitance versus voltage measurements were used to obtain a maximum dielectric constant of 290 at 85 kV/cm and loss tangent under 4% tested in the range of ±275 kV/cm. ALD PbTiO3 grown with near-ideal cation ratios crystallized into randomly oriented perovskite grains when grown on a sputtered Pt-coated .
Natural Preservatives for Extending the Shelf-Life of Seafood: A Revisit.

Consumer demand for minimally processed seafood that retains its sensory and nutritional properties after handling and storage is increasing. Nevertheless, quality loss in seafood occurs immediately after death, during processing and storage, and is associated with enzymatic, microbiological, and chemical reactions. To maintain the quality, several synthetic additives (preservatives) are promising for preventing the changes in texture and color, development of unpleasant flavor and rancid odor, and loss of nutrients of seafood during storage at low temperature. However, the use of these preservatives has been linked to potential health hazards. In this regard, natural preservatives with excellent antioxidant and antimicrobial properties have been extensively searched and implemented as safe alternatives in seafood processing, with the sole purpose of extending shelf-life. Natural preservatives commonly used include plants extracts, chitosan and chitooligosaccharide, bacteriocins, bioactive peptides, and essential oils, among others. This review provides updated information about the production, mode of action, applications, and limitations of these natural preservatives in seafood preservation.
SF6 decomposition components under different metallic free‐conducting wire‐type particles in positive DC partial discharge

This study aimed to explore the common free‐conducting wire‐type particles that can produce severe partial discharge (PD) in DC gas‐insulated equipment. The experiment was conducted on the SF6 positive DC PD experimental system to determine the influence of the free‐conducting wire‐type particles of three kinds of metal materials (aluminum, 18/8 stainless steel, and copper) on SF6 decomposition. The change rules of five main characteristic decomposition components, namely, CF4, CO2, SOF2, SO2F2, and SO2, under different free‐conducting metal particles were obtained using gas chromatography–mass spectrometry quantitative detection. No significant correlation was observed between the formation of CO2 and the kinds of metal materials; however, the kinds of metal materials significantly influenced the formation of the other four kinds of characteristic gases. The differences in the physical and chemical properties of the metal materials caused the different characteristics of SF6 positive DC PD decomposition under different free‐conducting metal wire‐type particles. Findings provide an experimental basis for the diagnosis of fault‐type positive DC SF6 gas‐insulated equipment. © 2018 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Effects on the Motor Cortex in Gamma Rhythm in Terms of Central Pattern Generator

The locomotion is one of the basic skills essential for animals’ survival. It is a key research field where the locomotion is modulated by the motor cortex. It is shown by the investigation that the neural oscillations have key roles in neural communication. To assess the impacts on the motor cortex in gamma rhythm based on different frequencies central pattern generator (CPG), it is attempted to establish the model between the motor cortex and the CPG. The primary motor cortex and the primary somatosensory cortex are included in the motor cortex. The effects level is qualified using the power spectrum, spiking time histogram, rastergram, spectrogram in terms of the wavelet analysis and coherence between neural populations. The main findings include (1) The CPG with various frequencies under the gamma rhythm frequency can be embedded in gamma oscillation and the gamma power is modified by the CPG phase. (2) There is an optimal CPG with appreciate frequency and amplitude making the neural populations oscillate for the best action in the gamma band. Therefore, to process the neural population the appropriate stimulus is suitable. (3) When CPGs with different parameters are sent into the neural populations, the coherence difference mainly takes place in the gamma band. Therefore, there is an interaction between the internal dynamics with incoming stimuli providing a substrate for processing the complex information. A beneficial exploration can be provided by the investigation on the information process mechanisms in the motor cortex.
Reconstructing the human first trimester fetal–maternal interface using single cell transcriptomics

During the early weeks of human pregnancy, the fetal placenta implants into the uterine mucosa (decidua) where placental trophoblast cells intermingle and communicate with maternal cells. Here, we profile transcriptomes of ∼50,000 single cells from this unique microenvironment, sampling matched first trimester maternal blood and decidua, and fetal cells from the placenta itself. We define the cellular composition of human decidua, revealing five distinct subsets of decidual fibroblasts with differing growth factors and hormone production profiles, and show that fibroblast states define two distinct decidual layers. Among decidual NK cells, we resolve three subsets, each with a different immunomodulatory and chemokine profile. We develop a repository of ligand-receptor pairs (www.CellPhoneDB.org) and a statistical tool to predict the probability of cell-cell interactions via these pairs, highlighting specific interactions between decidual NK cells and invading fetal extravillous trophoblast cells, maternal immune and stromal cells. Our single cell atlas of the maternal-fetal interface reveals the cellular organization and interactions critical for placentation and reproductive success.
Optogenetic entrainment of the septo-hippocampal circuit is state conditional and attenuates spatial accuracy

Acknowledgements: We are very appreciative of the thoughts on analysis and the interpretation of our results provided by Dr. Kamran Diba, Dr. Colin Lever, Dr. Matt Wilson, Dr. Nathan Insel, Dr. Andre Fenton, Dr. Allan Gulledge and the assigned anonymous reviewers. We thank Andrew Alvarenga (GMW) for assistance with the custom design and manufacture of optical and electrophysiological implants. We thank Bruno Rivard, Rhys Niedecker for assistance with components of Figure 1. We are grateful for COBRE support from Sheryl White who greatly assisted with immunohistochemistry and from Todd Classon who assisted with imaging. We thank Pierre-Pascal Lenck-Santini, Sylvain Barriere and Sophie Sakkaki for assistance with Matlab code used for signal processing. We thank Mr. Daniel Mills for editing. We also acknowledge Neuralynx (Montana, USA) for dedicated technical support and Karl Deisseroth for supplying the adenovirus used in the study. This work would not have been possible without the advice of Dr. John Kubie during development and implementation of the spatial accuracy task. We declare no conflicts of interest. This work was supported by startup funds to JMB by UVM and by the NIH Grants NS108765 (GLH/JMB); NS108296 (GLH/JMB).
Inventory of Lowland-Breeding Birds on the Alaska Peninsula

We conducted the first systematic inventory of birds in the lowlands (areas ≤100 m above sea level) of the Alaska Peninsula during summers of 2004–2007 to determine their breeding distributions and habitat associations in this remote region. Using a stratified random survey design, we allocated sample plots by elevation and land cover with a preference for wetland cover types used by shorebirds, a group of particular interest to land managers. We surveyed birds during 10-min counts at 792 points across 52, 5 km × 5 km sample plots distributed from south of the Naknek River (58.70°N,157.00°W) to north of Port Moller (56.00°N,160.52°W). We detected 95 bird species including 19 species of shorebirds and 34 species (36% of total) considered at the time to be of conservation concern for the land managers in the region. The most numerous shorebirds on point counts were dunlin Calidris alpina, short-billed dowitcher Limnodromus griseus, and Wilson's snipe Gallinago delicata. We found the breeding-season endemic marbled godwit Limosa fedoa beringiae at 20 plots within a 3,000-km2 area from north of Ugashik Bay to just north of Port Heiden and east to the headwaters of the Dog Salmon and Ugashik rivers. The most abundant passerines on point counts were American tree sparrow Spizelloides arborea, Lapland longspur Calcarius lapponicus, and savannah sparrow Passerculus sandwichensis. Sandhill crane Antigone canadensis, glaucous-winged gull Larus glaucescens, and greater scaup Aythya marila were also relatively abundant. We categorized habitat associations for 30 common species and found that lowland herbaceous vegetation supported wetland-focused species including sandhill crane, marbled godwit, short-billed dowitcher, and dunlin; whereas, dwarf shrub-ericaceous vegetation supported tundra-associated species such as willow ptarmigan Lagopus lagopus, rock sandpiper Calidris ptilocnemis, and American pipit Anthus rubescens. Tall shrub vegetation was important to several species of warblers and sparrows, as well as one species of shorebird (greater yellowlegs Tringa melanoleuca). We found that point counts augmented with incidental observations provided an almost complete inventory of lowland-breeding species on the study area. These data form a baseline to monitor any future changes in bird distribution and abundance on the Alaska Peninsula.
A Review on Phytochemical Analysis and Ethnobotanical Uses of Haloxylon stocksii

Haloxylon stocksii (family: Chenopodiaceae) is a succulent halophyte shrub tolerant to environmental stresses making it suitable for cultivation in saline land of arid and semi-arid regions because it is tolerant to abiotic stresses such as drought and high temperature. It has useful applications that contain fruiting tops and stem as animal feed, different plant parts for medicine, and re-establishment of tarnished lands. One major factor hindering its successful development and promotion is the inadequate and scattered knowledge available on these species. The purpose of this article is to highlight the importance of H. stocksii by summarizing information on occurrence, ecology, medicinal and other uses, cultivation and ethnobotany to stimulate interest to promote its domestication and commercialization for regional and global markets. Moreover, it also summarized reported phytochemistry and pharmacological activities.
Nutrient deposition enhances post-fire survival in non-N-fixing savanna tree seedlings

Nutrient deposition can modify plant growth rates and potentially alter the susceptibility of plants to disturbance events, while also influencing properties of disturbance regimes. In mixed tree-grass ecosystems, such as savannas and tropical dry forests, tree seedling growth rates strongly influence the ability of seedlings to survive fire (i.e. post-fire seedling survival), and hence, vegetation structure and tree community composition. However the effects of nutrient deposition on the susceptibility of recruiting trees to fire are poorly quantified. In a field experiment, seedlings of multiple N-fixing and non-N-fixing tropical dry forest tree species were exposed to nitrogen (N) and phosphorus (P) fertilisation, and fire. We quantified nutrient-mediated changes in a) mean seedling growth rates; b) growth rates of the fastest growing individuals and c) post-fire seedling survival. N-fixers had substantially higher baseline post-fire seedling survival, that was unaffected by nutrient addition. Fertilisation, especially with N, increased post-fire survival probabilities in non-N-fixers by increasing the growth rates of the fastest growing individuals. These results suggest that fertilisation can lead to an increase in the relative abundance of non-N-fixers in the resprout community, and thereby, alter the community composition of tropical savanna and dry forest tree communities in the long-term.
Mitigating selfish primary user emulation attack in multi-channel context : a game-theoretic approach

—Primary User Emulation Attack (PUEA), in which attackers emulate primary user signals causing restriction of secondary access on the attacked channels, is a serious security problem in Cognitive Radio Networks (CRNs). If the attacker performs a PUEA for occupying the attacked channel selﬁshly, it is called a selﬁsh attacker. Network managers could adopt a surveillance process on disallowed channels for identifying illegal channel occupation of selﬁsh PUEA attackers and hence mitigating selﬁsh PUEA. Determining surveillance strategies, particularly in multi-channel context, is necessary for ensuring network operation fairness. In this paper, we adopt a sequence-form representation of the game between the selﬁsh attack and the surveillance process, called surveillance game, to formulate the relation between the selﬁsh attack and the surveillance process in multi-channel CRNs and explore the Nash Equilibrium (NE). We show that performing the obtained NE surveillance strategy signiﬁcantly mitigates PUEA.
Determinants of Preferences for Advertisement and Communication in the Promotion of Anti-Malaria Products in Ibadan, Southwestern Nigeria

One of the strategies for promoting malaria prevention and control globally is advertisement of anti-malaria products. This study was designed to determine users’ preferences for style of advertisement and communication of anti-malaria products in Ibadan. Data collection involved twelve Key Informant Interviews and 500 copies of a questionnaire. Radio was the most preferred and most accessible medium of advert in both rural and urban areas. A large majority (86.4%) of rural dwellers preferred advertisements in form of speeches, house-to-house campaigns, face-to-face counselling and rallies. Whereas, advertisement in forms of drama (44.0%) and music (16.0%) were preferred by the urban dwellers. Results show that advertisements and communication programs on anti-malaria products do not relay messages on drug reaction and its treatment, and cost of anti-malaria products. Hence, advertisements and communicative programmes for controlling malaria would be more effective if the social and environmental factors influencing preferences for advertisement are put into consideration.
Photoexcitation de la fluorescence de recombinaison differee dans l'ultra-violet lointain et relaxation des etats super-excites dans les cristaux moleculaires organiques

Ce travail est une contribution a l'etude, dans la matiere moleculaire dense, des processus specifiques de relaxation electronique induits par des interactions intermoleculaires avec transfert d'excitation ou de charge. L'essentiel de nos resultats porte sur les cristaux d'anthracene et de p-terphenyle excites par des photons d'energie jusqu'a 40 ev. La these comporte trois parties. La premiere regroupe (chapitres i a iv) l'essentiel des notions fondamentales sur les proprietes photodynamiques des etats excites dans ces cristaux. La seconde partie concerne notre contribution experimentale qui vise a detecter des transitions impliquant un transfert de charge avec formation de paires electron-trou. Pour cela, nous utilisons la mesure de l'intensite, resolue en temps (ns), de la fluorescence de recombinaison geminee sensible a un champ magnetique; nous en rappelons les fondements theoriques (chapitre v). Les resultats experimentaux (chapitre vi) concluent a l'apparition, au-dessus d'un seuil caracteristique, d'une composante de fluorescence differee due a la presence de paires electron-trou, de grande duree de vie, dans un etat triplet. La derniere partie est consacree a l'interpretation de nos observations. La nature du phenomene detecte conduit (chapitre vii) a une analyse cinetique de la recombinaison de paires geminees. On propose un mecanisme intrinseque qui permet ensuite (chapitre viii) de rendre compte du spectre d'excitation mesure et de le comparer a ceux, des processus de fission en singulets et en triplets et du rendement quantique de fluorescence prompte. Nous discutons l'ensemble des precisions nouvelles obtenues sur la nature des phenomenes de relaxation electronique des excitations d'energie elevee
Uso de Mineração de Dados para Identificação de Atos Suspeitos na Prova de Direção da CNH

U ma das principais causas de perda de receita e a fraude. E com o crescente volume e armazenamento de dados varias empresas torna-se inviavel a analise manual de todos os dados. O uso do KDD e ( Knowledge Discovery in Database - Descoberta de conhecimento em base de dados) e um dos recursos no auxilio de gestao de grande quantidade de dados e transforma-los em informacoes. Este trabalho descreve uma das etapas do KDD, a mineracao de dados, para extrair informacoes sobre indice de aprovacao de exame de direcao para obtencao da CNH, de uma base de dados real, para identificar possiveis casos de fraudes nesse exame. Foi utilizado deteccao de outlier utilizando o boxplot e cluster com algoritmo k-means. Atraves dessas aplicacoes foi possivel identificar os indices de aprovacao atipicos e extrair informacoes sobre esses casos encontrados.