Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomic and Phylogenetic Analysis of the First Usutu Virus Isolate from a Human Patient Presenting with Neurological Symptoms

Usutu virus (USUV) is a mosquito-borne flavivirus, belonging to the Japanese encephalitis antigenic complex, that circulates among mosquitoes and birds. We describe and analyze the complete genome sequence of the first USUV strain isolated from an immunocompromised patient with neuroinvasive disease. This USUV isolate showed an overall nucleotide identity of 99% and 96%, respectively, with the genomes of isolates from Europe and Africa. Comparison of the human USUV complete polyprotein sequence with bird-derived strains, showed two unique amino acid substitutions. In particular, one substitution (S595G) was situated in the DIII domain of the viral Envelope protein that is recognized by flavivirus neutralizing antibodies. An additional amino acid substitution (D3425E) was identified in the RNA-dependent RNA polymerase (RdRp) domain of the NS5 protein. This substitution is remarkable since E3425 is highly conserved among the other USUV isolates that were not associated with human infection. However, a similar substitution was observed in Japanese encephalitis and in West Nile viruses isolated from humans. Phylogenetic analysis of the human USUV strain revealed a close relationship with an Italian strain isolated in 2009. Analysis of synonymous nucleotide substitutions (SNSs) among the different USUV genomes showed a specific evolutionary divergence among different countries. In addition, 15 SNSs were identified as unique in the human isolate. We also identified four specific nucleotide substitutions in the 5′ and 3′ untranslated regions (UTRs) in the human isolate that were not present in the other USUV sequences. Our analyses provide the basis for further experimental studies aimed at defining the effective role of these mutations in the USUV genome, their potential role in the development of viral variants pathogenic for humans and their evolution and dispersal out of Africa.
TIME, TEAMS, AND TASK PERFORMANCE: A LONGITUDINAL STUDY OF THE CHANGING EFFECTS OF DIVERSITY ON GROUP FUNCTIONING.

We hypothesize that as time passes and allows for greater collaboration among team members,the negative effects of surface-level (demographic) diversity are weakened, but the negative effects of deep-level (psychological) diversity are strengthened. We also propose that perceived diversity mediates the impact of "actual" demographic and psychological differences on team social integration and team task performance. These hypotheses were tested by tracking the development of 144 student project teams over 15 weeks. Theoretical constructs were measured at multiple times using a four-wave design. Data were collected prior to team formation (Time 1)and used to derive surface-level diversity measures for age, race, gender and marital status, as well as deep-level diversity measures for personality (conscientiousness), and values. Measures of collaboration, perceived diversity, and deep-level diversity were collected after teams had worked together for approximately one-third of their designated term (Time 2).
Green Synthesis of Gold Nanoparticles by a Metal Resistant Arthrobacter nitroguajacolicus Isolated From Gold Mine

Biosynthesis of gold nanoparticles would benefit from the development of clean, nontoxic and environmentally acceptable procedures concerning microorganisms from bacteria to fungi and even algae. Actinobacteria are soil bacteria which have the enormous ability as biotechnological tools. In this paper, we reported the biosynthesis of gold nanoparticles by a member of Arthrobacter genus isolated from Andaliyan gold mine in north-west of Iran. This metal resistance strain obtained from an acidophilic region ( ~ pH 5.6). The UV-vis and XRD spectra of the aqueous medium containing the strain and 1 mM HAuCl 4 for 24 h, demonstrated the formation of gold nanoparticles. TEM micrographs showed intra-extracellular production of gold nanoparticles with spherical shape and average size of 40 nm. The result of morphological and molecular tests revealed that the isolate was belonged to Atrhrobacter and has 100% similarity in 16SrRNA gene sequences to Arthrobacter nitroguajacolicus.
Pharmacokinetics of Quercetin-Loaded Methoxy Poly(ethylene glycol)-b-poly(L-lactic acid) Micelle after Oral Administration in Rats

The purpose of this study was to evaluate the potential of micelle to change the pharmacokinetics of quercetin (QUT), with a primary goal of enhancing its oral bioavailability. QUT-loaded methoxy poly(ethylene glycol)-b-poly(L-lactic acid) micelle (QUT-loaded MPEG-b-PLLA micelle) was prepared by a thin-film hydration method, resulting in a particle size of 88.5 nm. A liquid chromatography tandem-mass spectrometry (LC-MS/MS) method was developed and validated for determination of QUT in rat plasma. The chromatographic separation was performed on an Agilent Eclipse-C18 (4.6 mm × 50 mm, 3.5 μm) with an isocratic mobile phase system consisting of water and methanol (30 : 70, v/v) at a flow rate of 0.4 mL/min. Calibration curves were linear over the concentration ranges of 2.5–2000 ng/mL for QUT. The micelle was orally administered at a single does in rats, and the pharmacokinetic parameters were evaluated and compared with that administered with the QUT aqueous suspension. The results show that the micelle was able to increase the QUT's oral bioavailability 9-fold compared to the QUT aqueous suspension. These results suggest that methoxy poly(ethylene glycol)-b-poly(L-lactic acid) is a potential carrier for the oral delivery of QUT.
Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas

Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
Anti‐ganglioside autoantibodies in type 1 diabetes

Type 1 diabetes is an autoimmune disease that is accompanied by an immune response against pancreatic cells. As gangliosides are expressed in both peripheral nerves and pancreatic cells, we examined the possibility of correlation between type 1 diabetes, anti‐ganglioside autoantibodies, and neuropathy. Fifty diabetic patients and 30 controls with other autoimmune diseases underwent neurological examination and search for antibodies to gangliosides, glutamic acid decarboxylase (GAD65), and tyrosine phosphatase (IA2). Sixteen (32%) diabetic patients had neuropathy. Twelve diabetic sera were found to have anti‐ganglioside autoantibodies. Twenty sera were positive for anti‐GAD65 and nine for anti‐IA2 antibody. Sera from three control patients had anti‐ganglioside autoantibodies. No significant correlation was found between autoantibodies, neuropathy, and disease duration. Disease duration was shorter in patients with antibodies to GAD65 and IA2 and longer in neuropathic patients. The higher prevalence of antibodies in diabetic patients compared to controls may reflect the common pattern of antigens shared by peripheral nerve and pancreatic islet cells. Muscle Nerve, 2009
Inter- and intra-observer reliability of experienced and inexperienced observers for the Qualitative Behaviour Assessment in dairy cattle

Qualitative Behaviour Assessment (QBA) is part of the Welfare Quality® protocol for dairy cattle, although its inter- and intra-observer reliability have not been reported. This study evaluated inter- and intra-observer reliability of the QBA for dairy cattle in experienced and inexperienced observers using videos. Eight experienced observers performed the QBA (20 descriptors) twice for 16 video clips (60 s per clip; series 1) showing 4-17 animals. They assessed another 11 video clips showing herds (4 shots of 30 s per clip; series 2). Ten inexperienced observers performed the QBA on both video series one time. Inter-observer reliability of experienced observers ranged from slight to moderate (both assessments of series 1), and from low to high (series 2) for descriptors, and from slight to moderate for the QBA score. Inter-observer reliability of inexperienced observers ranged from low to moderate (series 1), and from low to high (series 2) for descriptors, and was moderate (both series) for the QBA score. Intra-observer correlations varied largely per descriptor and observer. They were both negative and positive, and ranged from low to very high. High correlations, however, were not necessarily associated with low paired differences. Values of half of the descriptors and the QBA score differed amongst experienced and inexperienced observers. The QBA appears insufficiently reliable as a tool for welfare assessment in dairy cattle.
Rapid, stable fluid dynamics for computer graphics

We present a new method for animating water based on a simple, rapid and stable solution of a set of partial differential equations resulting from an approximation to the shallow water equations. The approximation gives rise to a version of the wave equation on a height-field where the wave velocity is proportional to the square root of the depth of the water. The resulting wave equation is then solved with an alternating-direction implicit method on a uniform finite-difference grid. The computational work required for an iteration consists mainly of solving a simple tridiagonal linear system for each row and column of the height field. A single iteration per frame suffices in most cases for convincing animation.Like previous computer-graphics models of wave motion, the new method can generate the effects of wave refraction with depth. Unlike previous models, it also handles wave reflections, net transport of water and boundary conditions with changing topology. As a consequence, the model is suitable for animating phenomena such as flowing rivers, raindrops hitting surfaces and waves in a fish tank as well as the classic phenomenon of waves lapping on a beach. The height-field representation prevents it from easily simulating phenomena such as breaking waves, except perhaps in combination with particle-based fluid models. The water is rendered using a form of caustic shading which simulates the refraction of illuminating rays at the water surface. A wetness map is also used to compute the wetting and drying of sand as the water passes over it.
CS 224 W : Spamming PageRank-like Networks

Link spam is been a serious problem in PageRankstyle systems. In this method of spamming, spammers create a collection of boosting pages in order to improve the PageRank of one or more target pages, artificially increasing its ranking and displacing high quality content pages in the overall ranking of web pages. In this paper, we look further into the problem of link spam and how we can remove it from the web. In particular, we analyze the process of generating spam farms and then characterize how we could detect them in real life. We propose a variety of spam farms from a purely theoretical basis, propose simple measure to counteract them and then show how spammers can easily thwart these efforts. By examining network properties of a 2009 snapshot of the Wikipedia graph, we propose a data-driven method to determine if a given page is a valid content page or a spam page. At the core of this method is out-degree distributions of in-neighbors of a given page. We show that this distribution is lognormal with parameters in a certain range for nearly all of the top 100 Wikipedia pages by PageRank, while none of the standard spam farms fit a lognormal distribution. Lastly, we show that, in order for a spammer to force a misclassification of one of their target pages, they must create a huge number of boosting pages, resulting in between a 1.7x and 3x increase in the number of boosting pages a spammer needs to create versus the number of pages that they would need to create in one of the ideal spam farms. When coupled with the existing Spam Mass Estimation algorithm, this forces spammers to hijack a significant amount of PageRank from trusted sources and then also generate several useless boosting pages, thereby doubling or tripling the operating costs.
Persuasion: From Single to Multiple to Metacognitive Processes

This article provides a brief overview of major developments in the history of contemporary persuasion theory. The first intuitive and empirical approaches to persuasion were guided by main-effect questions (e.g., are experts more persuasive than nonexperts? ). Furthermore, researchers focused on only one process by which variables (e.g., emotion, source credibility) would have an impact (e.g., emotion affected attitudes by classical conditioning). As data began to accumulate, so many new theories and effects were uncovered that the discipline faced collapse from the numerous inconsistencies evident. In response to the reigning confusion of the previous era, contemporary multiprocess theories were proposed (e.g., the elaboration likelihood model). According to these more integrative approaches, any one variable could affect attitudes by different processes in different situations and thereby sometimes produce opposite effects. Finally, we describe the role of a recently discovered new contributor to persuasion: self-validation. Unlike previous mechanisms that focus on primary cognition, this new process emphasizes secondary or meta-cognition.
Mini‐Mental State Exam Scores Vary with Education in Blacks and Whites

Previous studies have suggested that education and race may affect performance on standardized mental status tests. In order to more clearly define these relationships, a prospective longitudinal study was devised to answer two questions: (1) whether race or level of education affects scores on the Mini‐Mental State (MMS) exam in non‐demented people and (2) what numerical cutpoints maximize the sensitivity and specificity of utilizing the MMS to help diagnose dementia in blacks of varying educational attainment.
A Comparative Analysis of Feature Extraction Methods for Fruit Grading Classifications

Abstract: Fruit plays an important role in our life. India is exporting large number of fruits to abroad in that mosambi is one among. Before exporting the fruits, the fruits have to be graded according to their quality. This paper presents an evaluation and comparison of the performance of three different extraction methods for classification of defect and non defect fruits. Three different feature extraction methods are GLCM (Grey Level Co-occurrence Matrix), shape features and intensity based features. The performance of each feature extraction method is evaluated and compared based on PNN (Probabilistic Neural Network) classifier. The experimental results suggest that shape feature outperformed than other two methods.
Integrating Planning and Recognition to Close the Interaction Loop

In many real-world domains, the presence of machines is becoming more ubiquitous to the point that they are usually more than simple automation tools. As part of the environment amongst human users, it is necessary for these computers and robots to be able to interact with them reasonably by either working independently around them or participating in a task, especially one with which a person needs help. This interactive procedure requires several steps: recognizing the user and environment from sensor data, interpreting the user’s activity and motives, determining a responsive behavior, performing the behavior, and then recognizing everything again to confirm the behavior choice and replan if necessary. At the moment, the research areas addressing these steps, activity recognition, plan recognition, intent recognition, and planning, have all been primarily studied independently. However, pipelining each independent process can be risky in real-time situations where there may be enough time to only run a few steps. This leads to a critical question: how do we perform everything under time constraints? In this thesis summary, I propose a framework that integrates these processes by taking advantage of features shared between them.
Adverse obstetrical and perinatal outcome in adolescent mothers associated with first birth: a hospital-based case-control study in a tertiary care hospital in North-East India

Purpose To analyze the adverse obstetrical and perinatal outcome of adolescent mothers associated with first birth. Patients and methods This prospective case-control study was conducted in a tertiary care teaching hospital of North-East India between January 2014 and December 2014. All adolescent primigravidae completing 28 weeks of gestation with singleton pregnancy and delivered at our institution were included in the study group. Primigravidae aged between 20 and 25 years were taken as a control group. Mothers having pregnancy complicated with diabetes mellitus, renal disorder, thyroid disorders, and cardiac diseases were excluded from the study. Demographic data, maternal complications like severe anemia, pre-eclampsia, eclampsia, gestational age at delivery, mode of delivery, and postpartum complications were compared. Among fetal complications, low-birth weight, preterm birth, neonatal intensive care unit admission, still birth, and early neonatal death were compared. All the patients were interviewed regarding contraceptive knowledge and its use preceding the pregnancy. Results Quality antenatal care was received by 80.6% of adolescent mothers. The adolescent mothers had a higher incidence of pre-eclampsia (odds ratio [OR] 2.017 95% confidence interval [CI]: 1.045–3.894, P=0.03), preterm deliveries (OR: 1.655, 95% CI: 1.039–2.636, P=0.03). Among fetal outcomes, the low- birth weight babies (OR: 1.59, 95% CI: 1.016–2.478), low mean birth weight (2,544.4±622.09 g versus 2,701.6±582.51 g), and higher admission to neonatal intensive care unit (OR: 1.957, 95% CI: 1.120–3.417) were significantly associated with adolescent mothers. There was no significant difference found regarding the mode of delivery, still birth, and early neonatal death. Moreover, contraceptive knowledge and its use were found to be poor among adolescent mothers. Conclusion With quality antenatal, intranatal, and postnatal care, the obstetric risk of childbirth in adolescent mothers may not be as serious as perceived to be.
Adaptive Delivery in Caching Networks

The problem of content delivery in caching networks is investigated for the scenarios where multiple users request identical files. An adaptive method is proposed for the delivery of redundant demands in caching networks. Based on the redundancy pattern in the current demand vector, the proposed method decides between the transmission of uncoded messages or the coded messages of Maddah-Ali and Niesen for delivery. Moreover, a lower bound on the delivery rate of redundant requests is derived. The performance of the adaptive method is investigated through numerical examples and Monte Carlo simulations. It is shown that the adaptive method considerably reduces the performance gap to the lower bound for the specific ranges of network parameters.
Question Answering over Freebase with Multi-Column Convolutional Neural Networks

Answering natural language questions over a knowledge base is an important and challenging task. Most of existing systems typically rely on hand-crafted features and rules to conduct question understanding and/or answer ranking. In this paper, we introduce multi-column convolutional neural networks (MCCNNs) to understand questions from three different aspects (namely, answer path, answer context, and answer type) and learn their distributed representations. Meanwhile, we jointly learn low-dimensional embeddings of entities and relations in the knowledge base. Question-answer pairs are used to train the model to rank candidate answers. We also leverage question paraphrases to train the column networks in a multi-task learning manner. We use FREEBASE as the knowledge base and conduct extensive experiments on the WEBQUESTIONS dataset. Experimental results show that our method achieves better or comparable performance compared with baseline systems. In addition, we develop a method to compute the salience scores of question words in different column networks. The results help us intuitively understand what MCCNNs learn.
FT overexpression induces precocious flowering and normal reproductive development in Eucalyptus.

Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1-5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.