Miracle-dz/UniFAR-FTUs huggingface dataset:
A Review on the Effects of Biodiesel Blends on Compression Ignition Engine NOx Emissions

Biodiesels are produced by the transesterification of corresponding triglyceride feedstocks of vegetable (example: soybean, canola, palm, karanja) or animal fat sources. Currently, the leading feedstocks are soybean oil in the U.S., canola oil and rapeseed oil in Canada and Europe, and palm, karanja, jatropha and other oils in Asia. Due to the cost and production considerations of these biodiesels, blending biodiesels with the petroleum fuels appears to be a prudent option in the near-term. The use of biodiesels in compression ignition engines results generally in a reduction in the emissions of carbon monoxide (CO), hydrocarbons (HC), and particulate matter (PM), but a slight increase in the oxides of nitrogen (NOx) emission. The reported NOx emissions do not exhibit definitive trends and the results are significantly influenced by many factors, including engine type and design, test cycle, start of injection, ignition delay, fuel composition, adiabatic flame temperature, radiative heat transfer, fluid dynamics and combustion phasing. Due to appreciable variations in the physical properties and the highly nonlinear nature of the combustion process, the NOx emission with biodiesel blends does not vary monotonically with the percentage of biodiesel in the blend. Hence, the intricate dependence of NOx on biodiesel and its blending effect cannot be completely explained under all engine type and operating conditions. Although the literature contains several studies on the performance and emissions of compression ignition engines fueled with neat biodiesels, the information on the effects of blends is scattered and has not yet achieved a definitive status to explain the blending effect on NOx. Hence, this work was motivated to review the available data with respect to the NOx emission from engines fueled with the petroleum diesel/biodiesel blends.
DIAGNÓSTICO DE LEPTOSPIROSE POR PCR E CARACTERIZAÇÃO DE ISOLADOS DE Leptospira spp. POR SEQÜENCIAMENTO DO 16S rDNA E ANÁLISE DE VNTR

Leptospirosis is a widespread zoonosis caused by pathogenic members of the genus Leptospira that has a great impact on both human and veterinary public health. Early diagnosis of leptospirosis is important because severe leptospiral infection can have a fulminant course. The available serological techniques for the diagnosis of leptospirosis have low sensitivity during the early stage of the disease. Efforts are being made to develop simpler, effective, efficient and low cost diagnostic methods. In this work we first evaluate a PCR based method for diagnosis of leptospirosis. Primers were designed to amplify a 264 bp region within the lipL32 gene, which is conserved among pathogenic Leptospira and absent in non-pathogenic species. The sensitivity and specificity of the assay were evaluated using seven saprophytic serovars, 37 pathogenic serovars and fifteen other microorganisms. The method was very specific for pathogenic serovars, however lacked sensitivity. In order to enhance the sensitivity, another primer pair was designed which amplifies a 183 bp region within the 264 bp region of the lipL32 gene, and used in a nested PCR assay. This approach was much more sensitive than conventional PCR.
Correcting Ambiguous Base Labels in DNA Sequencing using Neural Networks and its Impact on DNA Barcoding Applications

CORRECTING AMBIGUOUS BASE LABELS IN DNA SEQUENCING USING NEURAL NETWORKS AND ITS IMPACT ON DNA BARCODING APPLICATIONS Eddie Yee Tak Ma University of Guelph, 2018 Advisor: Professor Stefan C Kremer Obtaining DNA sequences relies on software algorithms, sequencing technology, and human effort. Advancement in algorithms and technology improves the rate in obtaining sequences. In this thesis, an artificial neural network based method improves the number of bases obtained from Sanger sequencing, by post-processing DNA sequences and replacing ambiguous N-labels with DNA base labels. The existing KB basecalling algorithm produces the initial sequence that is post-processed by the presented method. DNA Barcoding is a platform that depends on highly accurate sequences. In DNA Barcoding, species are identified by short reads of a standardized gene region (e.g. 600-700 bases for COI). Barcode of Life Datasystems (BOLD) is the largest repository and analytics platform serving the International Barcode of Life (iBOL) project. In this thesis, a novel machine learned error correction system is developed, the System-3 N-label Editor (S3). S3 is developed and validated on DNA Barcoding data, using 850,000 ambiguous base labels across 160,000 sequences. S3 internally represents uncertainty to estimate error and commits an N-label replacement when predicted error is sufficiently low. S3 maintains an observed error rate lower than 1%, while disambiguating 79% of N-labels in animal barcodes, 80% of N-labels from plant barcodes, and 58% of N-labels in nonprotein-coding markers. S3 is tested for its impact in bioinformatics applications on 90,000 sequences from Canadian National Parks Malaise Project. Bioinformatics analyses are run using the KB, S3, and BOLD sequences as three treatment groups. Three applications are used for the comparison: Barcode Gap, Species Identification and Discovery, and Tree Building. The barcode gap refers to the difference in the between-and-within species distances; S3 improves the difference in two-thirds of species as compared with KB. For species identification/discovery, S3 did not improve over KB in resolving species. When phylogenetic trees are constructed using an overlapping region between KB, S3, and BOLD sequences – S3 trees are significantly more similar to to BOLD trees. The success in N-label replacement performance validation of S3, and encouraging results in DNA Barcoding applications point the way to future works that work on modern sequencing technologies and cover other error correction modes.
The End of Science: Facing the Limits of Knowledge in the Twilight of the Scientific Age

As a writer for SCIENTIFIC AMERICAN, John Horgan has an unsurpassed window on contemporary science, routinely interviewing the scientific geniuses of our times, scientists such as Richard Dawkins, Murray Gell-Mann, Stephen Hawking, Karl Popper and Noam Chomsky. In THE END OF SCIENCE, Horgan displays his genius for getting these larger-than-life figures to be human, whilst also encouraging them to confront the very limits of knowledge. Have the big questions all been answered? Has all the knowledge worth pursuing become known? Will there be a final 'theory of everything' that signals the end? Horgan extracts surprisingly candid answers to these and other delicate questions as he discusses God, Star Trek, superstrings, quarks, consciousness and numerous other topics. In a time where scientific rationality is under fire from every quarter, THE END OF SCIENCE is a witty, thoughtful, profound and entertaining narrative which serves as both a critique of and a homage to modern science.
Implication de la protéine de biogenèse des ribosomes Rsl24d1 dans l'homéostasie de cellules souches embryonnaires murines

Le controle de l'expression des programmes geniques orchestrant le developpement precoce et l'homeostasie des cellules souches fait l'objet de recherches intenses. En effet, les cellules souches embryonnaires (CSE) sont caracterisees par des proprietes comme leur clonogenicite (la capacite a proliferer dans le meme etat indifferencie) et leur pluripotence (la capacite a se differencier et a former les tissus embryonnaires et adultes). Au niveau moleculaire, l'identite des CSE est orchestree par le controle de l'expression genique aux niveaux epigenetique, transcriptionnel, post- transcriptionnel et traductionnel en reponse a l'activation de voies de signalisation specifiques. Dans ce contexte, des donnees recentes suggerent un role de la machinerie traductionnelle les ribosomes et de la regulation de leur biogenese, dans le maintien de l'homeostasie de cellules souches de differentes especes. A partir de l'analyse de donnees transcriptomiques a haut debit (RNAseq), mon equipe d'accueil a ainsi identifie un ensemble de proteines associees aux ribosomes (PaR) significativement enrichies dans les cellules souches embryonnaires murines (CSEm) en comparaison a des lignees cellulaires murines differenciees et a des tissus. Parmi ces candidats, mes travaux de these ont consiste a la caracterisation d'une PaR particulierement enrichie : Rsl24d1. Rsl24d1 est une proteine de biogenese des ribosomes decrites exclusivement chez la levure. Son profil d'expression dans differentes lignees de CSEm suggere une fonction specifique: enrichissement au niveau transcriptionnel et proteique dans les CSE a l'etat de pluripotence naif et diminution importante au cours de la differenciation. En effet, des approches de perte d'expression de Rsl24d1 m'ont permis d'etablir l'importance de cette PaR dans l'homeostasie des CSEm. Rsl24d1 contribue au maintien de la proliferation cellulaire des CSE, de leur clonogenicite et plus moderement a leur pluripotence. Rsl24d1 semble etre une proteine majoritairement nucleaire mais egalement associee aux sous- unites 60S libres des ribosomes cytoplasmiques. D'autre part, la perte d'expression de Rsl24d1 affecte specifiquement la biogenese des particules ribosomiques 60S. Ainsi, comme chez la levure, dans les CSEm, Rsl24d1 est un facteur navette orchestrant la maturation des particules ribosomiques pre-60S. Par ailleurs, Rsl24d1 semble permettre le maintien d'un taux de synthese proteique eleve permettant notamment le renouvellement des proteines ayant une demi-vie courte parmi lesquels on recense des facteurs de transcription de la pluripotence comme Oct4 (Oct3/4), Nanog et Esrrb. Mes travaux de these ont donc permis d'identifier et de caracteriser un facteur de biogenese de la sous-unite 60S, Rsl24d1, implique dans l'homeostasie des CSEm
Liberating Reformed Tradition: The Challenge of Christian Vocation in a Twenty-First Century World

sk a Reformed person to talk about tradition, and their first response probably will be a blank stare. As a cradle Calvinist, I was taught that tradition was basically an add-on. Tradition was that endless adiaphora of scholastic speculation and papal pronouncements that the medieval Church had piled onto the simple honest truths of the Bible. We, the true heirs of John Calvin and his iconoclastic followers in Geneva, Scotland, the Netherlands, and Massachusetts Bay, preferred our religion straight up and unadorned, dispensed directly from the word of God itself. Reformed worship, architecture, and spirituality became notoriously spare and plain. I am often asked at the Congregational Library for an old “order of worship” or “communion service” so that present-day heirs of the Puritans can put on an historically-accurate Sunday program. But of course, these were people who constitutionally despised set forms and written rules. They left behind a lot of paper, but not much of the kind that my callers are looking for. Within the Reformed churches more generally, anything that smacked of ritual or, even worse, a rule imposed by some external authority became anathema. Church sanctuaries avoided all representations of God, the communion elements grew smaller and smaller, and the Bible on that large central pulpit loomed ever larger. But of course, most sensible Reformed Christians recognize that they do indeed have a “tradition. ” There is no such thing as a faith based on the Bible only. All Protestants recognize the Bible as their central authority, but they also realize that it always comes within an interpretive framework. Especially in those churches that originated in the Calvinist wing of the Protestant Reformation—the Dutch, German, and Hungarian Reformed, the New England Congregationalists, the Scotch Covenanters, and Presbyterians of many hues and stripes—the “tradition” really means the Easter 2006
Analog Simulation

The distinction between analog and digital representation is reexamined; it emerges that a more fundamental distinction is that between symbolic and analog simulation. Analog simulation is analyzed in terms of a (near) isomorphism of causal structures between a simulating and a simulated process. It is then argued that a core concept, naturalistic analog simulation, may play a role in a bottom-up theory of adaptive behavior which provides an alternative to representational analyses. The appendix discusses some formal conditions for naturalistic analog simulation.
SpoT and GppA hydrolases prevent the gratuitous activation of RelA by pppGpp in Escherichia coli

Stringent response, a conserved regulation seen in bacteria, is effected through the modified nucleotides (p)ppGpp. The metabolic cycle of these molecules is driven by the synthase activity of RelA and SpoT and the hydrolase activity of SpoT and GppA which together sets the basal (p)ppGpp pool. Growth arrest due to (p)ppGpp accumulation from basal RelA activity apparently explained the essentiality of SpoT hydrolase function. We found, pppGpp degradation was enhanced when the SpoT hydrolase activity was lowered or eliminated and when this was alleviated by inactivation of the GppA hydrolase, gratuitous synthesis of (p)ppGpp by RelA was activated, leading to growth arrest. The RelA-ribosome interaction was not mandatory for these phenotypes. Our results show, for the first time, elevated pppGpp promoted the amplification of RelA-mediated stringent response in the absence of established RelA activating signals in the cell and the SpoT and GppA hydrolases prevented this. The accumulation of pppGpp inhibited the SpoT hydrolase activity. We propose this autocatalytic activation of RelA by pppGpp is likely to be an allosteric regulation and can result in a bistable switch.
Reply to referee comments on “Dimensional analysis of a landscape evolution model with incision threshold” by Theodoratos and Kirchner

In “Dimensional analysis of a landscape evolution model with incision threshold”, the authors extend a previous analysis of the classic advection-diffusion landscape evolution equation with a constant source term to include a threshold for erosion. Though the neither the idea of erosion thresholds nor the advection-diffusion equation themselves are new, I have not seen them combined in this way before. This novel connection, together with the authors very thoughtful and insightful analysis of the equations produces some valuable and widely applicable conclusions. In particular, the fact that introducing a threshold adds a parameter to the nondimensionalized equations that distinguishes landscapes with different relative threshold magnitudes from one another fundamentally is very interesting.
Effect of Dietary Incorporation of Azolla Meal on Production Performance and Egg Quality of Vanaraja Laying Hens

An experiment was conducted to evaluate the effect of dietary incorporation of Azolla meal on production performance and egg quality of Vanaraja laying hens. Seventy two, 48-weeks old Vanaraja laying hens were randomly distributed into three dietary treatment groups of 24 hens each and were reared in deep litter system. Each treatment contained 4 replicates of 6 hens each. Three experimental diets were formulated by incorporating Azolla meal (AZM) at 0, 5% and 10% levels. A measured quantity of feed (150 g/day) was offered to each bird everyday during the experimental period. Egg production was recorded daily on individual pen basis and percent hen housed egg production (HHEP) was calculated. The average feed consumption was recorded as g/hen/day and feed efficiency was calculated on the basis of feed consumed per unit egg mass production. All the eggs laid during the last five consecutive days of each 28 days period were collected to measure the egg weight. Twelve eggs were randomly chosen in each treatment from the eggs laid during the last three consecutive days of each 28-day period to determine the egg quality. Dietary incorporation of AZM at either 5 or 10% level reduced the body weight of laying hens. The egg production, egg weight, egg mass per day and feed conversion efficiency (g feed/g egg) was comparable among the 0% (control), 5% and 10% AZM incorporated diets. The egg quality indices like albumen, yolk and egg shell percentage observed were similar across the different dietary treatment groups. Similarly, Dietary incorporation of AZM upto 10% in the diet had no influence on Haugh unit and shell thickness.
Multiple element of miniaturized printed log-periodic second series koch dipole array antenna for wideband chipless RFID tag reader

This paper aims to produce a low profile, wideband, and high gain antenna for chipless RFID tag readers. A miniaturized and wideband printed Log-Periodic Second Series Koch Dipole Array (LPSSKDA) with eleven elements operating over 0.8 GHz-3.2 GHz is designed using the FR4 board. The single LPSSKDA antenna, which acts as the chipless RFID reader antenna having gain between 5.2 and 6.1 dBi and frequency range from 1-3 GHz. A double element of the LPSSKDA antenna is proposed for improving the antenna gain to 6.9-7.9 dBi over the frequency range. The antenna is fabricated to validate the simulation and measurement results in terms of reflection coefficient, radiation pattern, and surface current distribution.
Pancreas Neuroendocrine Tumors: An Introduction

Neuroendocrine tumors are rare, however their incidence is increasing. Details of the clinical aspects of these unusual tumors are gradually being revealed all over the world. Pancreas neuroendocrine tumors are a heterogeneous group of tumors with diverse morphologies and behaviors. However, as their character is being revealed, new treatment options have been developed in recent years. This introduction presents an overview of Pancreas Neuroendocrine Tumors, with a focus on their origin, character, epidemiology and biology
Infinite Renormalization

In quantum field theory divergent expressions are "discarded", leaving finite expressions which provide the best predictions anywhere in science. In fact, this "renormalization procedure" involves no mystery or illegitimate operations. This paper explains, in terms accessible to non-experts, how the procedure really works and explores some different ways in which physicists have suggested that one understand it.
Bird Diversity Patterns along Urbanization Gradients: Some Recommendations for Landscape Planner

Birds in an urban area often being used to indicate the quality of the city. The objective of this study was to analyze the response of birds to different intensities of urban-rural change. The high variation of house size and arrangement within housing clusters in the residential area of Sentul City (Bogor, West Java) was used as a model to mimic urbanization gradients in a city landscape. Five housing clusters were selected to represent the degree of urbanization gradients. Build to unbuild land ratio and density of mature trees were used to designate urbanization gradients in the chosen observation sites. Birds were observed using a standard point count method. Bird diversity was the highest in low urbanization (33 species) and diminishing in the higher urbanization grades (15 species). Sites with the highest urbanization rate still able to function as bird habitat, although the species number was low. The persistent bird species against urban-rural were mostly insectivores, nectarivores, and granivores (seed-eaters), while species that we’re unable to cope with urbanization were generally raptors, bush dependent species (e.g. babbler group) and thick canopy dependent species (e.g. green pigeon). The results indicate that (i) there is a negative relationship between degree of urbanization and bird species persistence in urban areas; (ii) efforts for bird conservation should not only focus on regreening but also be directed toward plant functional diversity to accommodate more diverse birds; (iii) urban landscape planner should consider maintaining or creating patch(es) of semi-nature areas as a refuge habitat for birds and other city-persistent species.
Development of two stable green nanoformulations with potent anticancer properties

Breast cancer is the most common cause of cancer death among women; thus, developing new drugs is crucial. Essential oils (EO)s with a wide range of bioactivities, such as anticancer effects, have provided a valuable source for this purpose. In this study, components of two medicinally important EOs were identified using GC-MS analysis. Moreover, antioxidant effects, as well as anti-cancer properties, were evaluated.The EOs formulated into nanoemulsion using the spontaneous emulsification approach, separately. Comprehensive stability tests were performed to select the optimum nanoemulsions of each EO. Anticancer effect of the most stable nanoemulsion of Zataria multiflora with a particle size of 43 ± 4 nm (PDI 0.4 ± 0.2 and SPAN 0.6 ± 0.1) was significantly better non-formulated form against four human breast cancer cell lines, MCF-7, MDA-MB-175, MDA-MB-231, and MDA-MB-468. Interestingly, the anticancer effect of Artemisia dracunculus nanoemulsion (16 ± 4 nm, 0.2 ± 0.1, and 0.4 ± 0.1) was also significantly improved in compassion to the essential oil. Considering the results, prepared nanoemulsions could be used as supplementary drugs or food additives.
Assessing Clivia taxonomy using the core DNA barcode regions, matK and rbcLa

Background: Clivia is a genus of the family Amaryllidaceae endemic to South Africa and Swaziland. Six species and one natural hybrid have been described. Some morphological traits overlap between some species, thus causing taxonomic confusion. Objectives: The discriminatory power of the core DNA barcodes ( matK and rbcLa ) was evaluated, and the current taxonomy of Clivia was assessed. Method: Seventy-four two-locus DNA barcodes from 4 to 18 specimens per species were generated. Results: The matK region had a higher mean intraspecific variation of 0.21 compared with the 0.02 of rbcLa . The two-locus barcodes have an aligned length of 1335 base pairs. Three species, Clivia mirabilis, Clivia nobilis and Clivia caulescens , are monophyletic in the Bayesian Inference (BI) cladogram. The remaining Clivia species ( Clivia miniata, Clivia gardenii, Clivia robusta and their affinities) are paraphyletic. Clivia is divided into 17 haplogroups with those of C. mirabilis and C. nobilis being unique. Clivia caulescens has three haplotypes. The Clivia species from the north-eastern distribution range of the Eastern Cape and KwaZulu-Natal provinces have 11 haplogroups and no species-specific DNA barcodes. These groups have no correlation with the current taxonomy or geographical distribution. Conclusions: Only 37.33% of the species can be correctly identified with the ‘best match’ option in SpeciesIdentifier. Clivia mirabilis, C. nobilis and C. caulescens have unique DNA barcodes to identify them. Specimens from the Ngome area in KwaZulu-Natal have a unique DNA barcode, separating them from the rest of C. gardenii . A taxonomic revision is suggested.