Miracle-dz/UniFAR-FTUs huggingface dataset:
CRISPR-Cas Systems - ReadingSample

This chapter describes the overall variability of CRISPR-Cas systems as observed in publicly available genomes and how this can be used to draw hypotheses on phylogenetic relationships between species and between strains of a given species. The fact that spacers are added sequentially at the leader end and that a given spacer is rarely acquired twice or duplicated are key elements for building hierarchical relationships between strains. Presence/absence of a given CRISPR locus and variability in the number of direct repeats and spacers in that locus between strains have been frequently reported, providing in some cases phylogenic information, but this polymorphism was extensively used for genotyping in only a few instances. The observation that not all strains possess a CRISPR locus in a given species precludes its use as a general typing tool. However, in some species, the degree of variability is a powerful marker of the species diversity and evolution. Through examples found among 1,434 published genomes of bacteria and archaea, different features of the CRISPR-Cas systems diversity will be highlighted.
The phloem mobility of glucosinolates

The transport properties of glucosinolates within Brassica napus are of interest as identification of the mechanism of transport could lead to lower levels Introduction being obtained in specific tissues such as the Oilseed rape (Brassica napus L.) is a major European seeds. The phloem mobility of 35S-gluconapin (butcrop, the most significant oil-producing crop of the tem3-enylglucosinolate) and 35S-desulphogluconapin in perate regions of central and northern Europe (Bones oilseed rape plants has been inferred from tissue disand Rossiter, 1996). The seed meal remaining after oil tribution patterns, as well as from observed coincident extraction is a valuable animal feed, high in protein, phloem mobility of 3H-gluconapin and 14C-sucrose.
Ether,dark Matter and Topology of the Universe(version 2)

In this article, we propose that a substance, called ether-substance, fills and constitutes all what is called “vacuum” in the Universe. We assume that it has a mass and consequently it could be the nature of dark matter. Modelling it as an ideal gas, we obtain the flat rotation curve of spiral galaxies. Using a very simple model of thermal transfer between baryonic particles and ether-substance, we obtain the baryonic Tully-Fisher’s law. So we introduce a new concept of ether, different from the pre-relativistic concept of ether, and we called “Cosmology based on ether” (CBE) Cosmology based on this new concept. In this CBE, topology of the Universe is much simpler and more attractive than topologies proposed by the Standard Cosmological model (SCM) (whose some fundamental aspects are kept in CBE). We propose 2 models in CBE. The first one does not need dark energy nor cosmological constant, and does not need the complex mathematics of General Relativity, contrary to SCM (and to the 2nd model of CBE). Nonetheless, we obtain in the 1st model of CBE a very simple Hubble’s constant, in 1/t, t age of the Universe, and many cosmological observations that were previously explained only by the SCM. Moreover we interpret in both models of CBE the Referential in which fossil radiation is isotropic. CBE is, as SCM, compatible with Special and General Relativity, despite that it is based on a new concept of ether
Do Parties Matter for Economic Outcomes? A Regression-Discontinuity Approach

A long-standing issue in political economics is to what extent party control makes a difference in determining fiscal and economics policies. This question is very difficult to answer empirically because parties are not randomly selected to govern political entities. This article uses a regression-discontinuity design, namely, party control changes discontinuously at 50% of the vote share, which can produce "near" experimental causal estimates of the effect of party control on economic outcomes. The method is applied to a large panel data set from Swedish local governments with a number of attractive features. The results show that there is an economically significant party effect: Left-wing governments spend and tax 2-3% more than right-wing governments. Left-wing governments also have 7% lower unemployment rates, which is partly due to that left-wing governments employ 4% more workers than right-wing governments. (JEL: C21, D72, D78, H71, H72) (c) 2008 by the European Economic Association.
The Effects of Early Feed Restriction on Growth Performance, Internal Organs and Blood Biochemical Indicators of Broilers

The growth rate of broiler chickens has increased greatly due to enhancement in genetics, nutrition and management. However, the high growth rate of broilers has caused many health problems, To avoid those problems, feed restriction was used as a management strategy to prevent excessive growth during early period. This study accessed the effects of early feed restricted on growth performance, internal organs and blood biochemical indicators of broilers. A total of 180 male Arbor Acres broilers were obtained and randomly assigned to 2 treatment groups. The treatments included control group (basal diet and feed restricted group (dietary energy and protein levels were diluted by 10%). At 14 d, two birds of each replicate were randomly chosen, wing vein blood samples were taken for blood biochemical indicators determination, then slaughtered to measure internal organs. The result showed that birds fed diluted feed had lower ( P ) body weight at 14 days. There was no significant difference in body weight between restricted and control groups at 42 days. No changes were observed in feed intake and feed conversion ratio between groups. Feed restriction also had no significant effects on internal organs, intestine and serum biochemical indicators. Taken together, this study suggested that dietary protein and energy diluted by 10% from 8 to 14 d is a suitable feeding program.
Calling for more accurate information in aquarium trade: analysis of live-fish import permits in Costa Rica

Ornamental fish trade is a growing business around the world, but also a major pathway for the introduction of potentially invasive species. Trade patterns and policies have been evaluated in high-income countries while developing countries in tropical regions have been overlooked, even when they are especially vulnerable to invasions by aquarium fishes. We analyzed the live fish import data and regulations in Costa Rica as a study case for a tropical country that regularly trades with many countries. We evaluated the quality of the taxonomic information given in live fish import permits issued by the Costa Rican Ministry of Environment between 1998 and 2004. We used FishBase to extract information about geographical distribution, habitat, historical introduction records, and taxonomic information on all the species we cataloged. A total of 834,624 live individuals were imported into Costa Rica from six countries with the scientific name absent for many individuals (40.6%) and correctly written in only 29.6% of the cases. We estimated that 352 different species were imported into the country. Most species imported were freshwater fishes and South America natives. We found that regulations of ornamental fish imports in Costa Rica are usually not enforced. The lack of accurate information in the live fish permits does not allow the full understanding and scope of live animal imports and their potential impacts. We call for more accurate information in the global aquarium trade by aiming to have much better tools to regulate the traffic of ornamental fishes.
Multitarget Tracking by Improved Particle Filter Based onH

This paper considers the problem of multitarget tracking in cluttered environment. To reduce the dependency on the noise priori knowledge, an improved particle filtering (PF) data association approach is presented based on theH ∞ filter (HF). This approach can achieve higher robustness in the condition that the measurement noise prior is unknown. Because of the limitations of the HF in nonlinear tracking, we first present the H ∞ unscented filter (HUF) by embedding the unscented transform (UT) into the
Explaining access to citizenship in Europe: How citizenship policies affect naturalization rates

In Europe, a variety of national policies regulate access to citizenship. This article analyses how citizenship policies affect naturalization rates among immigrants. Our analysis confirms that favourable citizenship policies positively affect naturalization rates, especially among first-generation immigrants with more than 5 but fewer than 20 years of residence. However, most variation is explained by other factors. Immigrants from poor, politically unstable, and non-EU countries are more likely to be a citizen of their European country of residence. Other important predictors of the citizenship status of immigrants are language, years of residence (first generation), and age (second generation). Explanations of naturalization rates in Europe should not only take into account institutional conditions but also include other destination and origin country factors and individual characteristics of immigrants.
EPP in EMAC, Solar Proton Events

Energetic particle precipitation in ECHAM5/MESSy – Part 2: Solar Proton Events A. J. G. Baumgaertner, P. Jöckel, H. Riede, G. Stiller, and B. Funke Max Planck Institute for Chemistry, 55020 Mainz, Germany now at Deutsches Zentrum für Luft-und Raumfahrt (DLR), Institut für Physik der Atmosphäre, Oberpfaffenhofen, 82234 Weßling, Germany Institute for Meteorology and Climate Research, Forschungszentrum Karlsruhe, Germany Instituto de Astrofisica de Andalucia, Granada, Spain Received: 1 January 2010 – Accepted: 9 February 2010 – Published: 15 February 2010 Correspondence to: A. J. G. Baumgaertner (work@andreas-baumgaertner.net) Published by Copernicus Publications on behalf of the European Geosciences Union.
Phylogeography of the Neotropical catfish Pimelodus albicans (Siluriformes: Pimelodidae) from río de la Plata basin, South America, and conservation remarks

Pimelodus albicans Valenciennes, 1840 (common name "moncholo" or "bagre blanco") is an endemic species of the family Pimelodidae in the rio de la Plata basin. Phylogenetic approach based on cytochrome b sequences was performed to test the existence of a unique evolutionary lineage in P. albicans and to discriminate populations units or subpopulations related to a migration behavior of this taxon in the rio de la Plata basin. This study included 34 samples of P. albicans of different collecting sites in the rio de la Plata estuary and in the rio Arrecifes belonging to the rio Parana basin. Among 614 base pairs in the cytochrome b sequence data set, 203 were variable and 120 were phylogenetically informative sites in P. albicans. A total of twenty haplotypes, nucleotide diversity (p) = 0.032 and haplotype diversity = 0.941 were found. Tajima's test showed significant value D= -1.88 (p<0.05) rejecting the neutral mutation hypothesis for the P. albicans data set. All phylogenetic approaches showed that P. albicans included four monophyletic assemblages that were supported by high bootstrap and Bayesian posterior probability values. Minimum spanning network corroborated these groups for P. albicans haplotypes. High genetic structure was found in P. albicans by means of AMOVA analysis showing that the rio Arrecifes samples constitute an isolated lineage. Moreover, the high value of genetic divergence (10%) between the rio de la Plata and the rio Arrecifes populations could suggest that P. albicans may be conformed by a sibling species complex. On the other hand, a degree of genetic structuring was detected among different sites of the rio de la Plata. A partial isolation of the 760 site may suggest that P. albicans could migrates to different tributaries for reproduction, generating different schools of haplotypes which could mix in the rio de la Plata estuary. The high nucleotide diversity found in the 765 site and the existence of gene flow with the remaining collecting sites would be concordant with the outlined hypothetic scenarios of the mixing populations in the middle of the rio de la Plata estuary.
IN SEARCH FOR A VIABLE PEDAGOGICAL AGENT IN ASSISTIVE APPLICATIONS FOR DYSLEXIC CHILDREN

TO attend to dyslexia, many studies have been conducted, and in the frontline is the design of assistive applications for dyslexic children. However, studies have not been focused on the nature and appearance of these pedagogical agents used in assistive applications, especially considering children’s preferences and their users’ experiences. Hence, this study employs Systematic Literature Review (SLR) methodology to collate and analyse the research-based and publicly-available assistive applications designed for dyslexic children. The findings present two categories of virtual assistants used in the analysed assistive applications, which are girl-like and animal-like objects. This girl-like object is used by 83.3% of the analysed works. We then proceed with and on-site experiment to collect the dyslexic children’s preferences. The result showed that boy-like objects are much more preferable, depending on their gender, which contradicts with previous works that present girl-like objects as avatar most of the time.
Nurse staffing, patient turnover and safety climate and their association with in-patient falls and injurious falls on medical acute care units: a cross-sectional study

Objective: Falls and related injuries remain a considerable health risk for in-patients. Numerous studies link falls with nurse staffing levels, but the results are inconsistent. The purpose of this study was to explore the associations between fall prevalence and injurious falls on medical wards and three unit-level system factors: daily nurse staffing, patient turnover, and safety climate. Methods: Using a cross-sectional design, we conducted a secondary data analysis of data from the Patient Safety and Falls Project. Five medical units in a Swiss university hospital were included, resulting in a data set of 949 days, with daily measures of nurse staffing, patient turnover and falls. The safety climate was measured using a subscale of the Safety Attitudes Questionnaire and analyzed at the unit level including data from 154 nurses. Robust multivariate logistic regression was used to explore nurse staffing, patient turnover, and safety climate’s associations with in-patient falls and fall injuries. Results: After controlling for patient age, length of stay and nursing fulltime equivalents, registered nurse experience showed a significant negative relationship with falls (OR = .83, p < .0001). Patient turnover and safety climate were not significantly associated to falls or fall injuries. Conclusions: By linking nurse staffing variables to in-patient falls and fall injuries, the current study’s findings partly confirm those of previous research. Further investigation will be necessary to isolate key factors influencing the association at the unit level between safety climate and in-patient falls.
Build and Travel KD-Tree with CUDA

Ray tracing is an important and widely used tool in computer graphic. Entertainment and game industry have already benefit a lot from ray tracing. However, designers and end-users are forced to use off-line ray tracing tools for a long time due to the high computation load. In ray tracing, most of the computation is concentrated on whether hundreds of millions of rays hit objects in a scene. The naive algorithm calculate intersection between every ray and every triangle in the scene, which yields O(nm) computation time with n rays and m triangles. Inspired by binary search in one dimension space, one of the most popular and efficient improvement is partition the scene and build a tree to represent it. With this tree we have algorithm with O(nlog(m)). Travelling kd-tree with n rays is a natural parallel problem with each ray independent to each other. Thus if we have a kd-tree for a scene, the intersection problem can be calculated with O(log(m)) on n processors, which is an optimal algorithm with nm/log(m) accelerator. In practice, the accelerator is much lower due to hardware limitation, which we will discuss later. In this case kd-tree(k-dimensional tree)is developed with many other spacial partition algorithms. Despite animation with dynamic scene, kd-tree has been proved to be the most efficient data structure for static scene[2][16]. There are two tasks for us to use kd-tree in ray tracing: 1.Build kd-tree with triangle soup; 2.Travel kd-tree to find intersection points. This paper will first review state-of-the-art algorithms to build and travel kd-tree, both serial and parallel. Then implement an algorithm to build kd-tree with CUDA. Finally analyse this algorithm and try to make it faster and more memory efficient.
Genetic and phenotypic characterisation of animal, carcass, and meat quality traits from temperate and tropically adapted beef breeds. 1. Animal measures

A total of 7622 cattle were measured for several weight and body composition traits in temperate and tropically adapted breeds. Traits included: liveweight, hip height, body fat score, muscle score, flight time, ultrasound scanned fatness, and eye muscle area. Measurements were taken at 3 stages during the project: post-weaning, start of finishing, and end of finishing (i.e. pre-slaughter). Animals were finished to 3 target market-weight end-points (220, 280, or 340 kg carcass weight), either on pasture or in a feedlot, and in 2 different geographic regions for tropically adapted breeds. These data were used to estimate genetic parameters for the traits at each stage, and also to estimate the effect of market weight and finishing regimes on the phenotypic and genetic expression of each trait measured at the end of finishing stage. Results showed, for all traits, that the magnitude of the phenotypic expression increased across the stages and market-weight end-points for the end of finishing measures. Feedlot finishing decreased the age at slaughter, and increased fatness and muscling compared with pasture-finished animals. Heritabilities ranged from 0.13 to 0.58, with subjectively scored traits generally being lower than objectively measured traits. Additive genetic variances generally increased with stage of measurement, and with increasing market weight. Genetic correlations of the same measure across stages or market weights were all close to unity. Additive genetic variances of the various traits were similar for feedlot versus pasture finish groups, and the genetic correlation between each measure for feedlot and pasture finish was generally greater than 0.80. The effect of finishing geographic region (i.e. temperate versus subtropical environments) for the tropically adapted breeds had little effect on the size of the additive genetic variances or genetic correlations between traits across geographic regions. The results imply that changing the production system had a significant impact on the phenotypic expression of growth and body composition traits but little effect on the underlying genetic expression and subsequent ranking of sires (i.e. no evidence of genotype by production environment interactions). Therefore, these live animal measures could be used as selection criteria in genetic evaluation programs and may also be genetically correlated with abattoir carcass and meat quality traits.
Proposed Integrated Bicycle Feeder Mode Service Analysis for Bus Rapid Transit SystemA Multinomial Logit Model Approach PROPOSED INTEGRATED BICYCLE FEEDER MODE SERVICE ANALYSIS FOR BUS RAPID TRANSIT SYSTEMA MULTINOMIAL LOGIT MODEL APPROACH

Public transit plays a vital role in economic development for access to the commuters/ travelers to the city centers of metropolitan cities of developing countries. Accessibility of public transit system is a prime factor faced by developing countries due to the lack of feeder services. Therefore, an attempt to improve the feeder services (with different modes i.e. as walking, bicycle, mini bus) is major importance. The present research focuses on new innovative ideas of bicycle as feeder mode with its three services i.e. Exclusive Bicycle Lane, Bicycle operation in mixed traffic with park & ride facility and Bicycle Sharing Service for Bus Rapid Transit System (BRTS) corridor of Ahmedabad city. The multinomial logit model was applied to develop the models. The findings from the study revealed that as income increases the preference to BMT-PR service increases over BSS and EBL service for their commuting purpose. The observations of age distribution shows with increase in age, the choice of EBL service over BSS and decrease BMT-PR service over BSS. Gender wise distribution indicated that preference to EBL service as well as BMT-PR service are higher among male groups compared with female groups. The observation of the study revealed that with increase in travel time, the respondents are more preferring BSS service over both EBL service and BMTPR service. Same as travel distance increases will be more preference of BSS over EBL service and BMT-PR service by commuters. The output of this research can be extremely useful to increase ridership of public transit by integrating feeder service.
Expanding Field of Strawberry Viruses Which Are Important in North America

Strawberry production is increasing annually, with the world production exceeding 4 million tons. Virus diseases of strawberry are also increasing as the crop is planted in new regions and exposed to new viruses. A decade ago there were about a dozen viruses known to infect strawberry. There are now seven known aphid transmitted viruses—Strawberry crinkle, Latent C, Mottle, Mild yellow edge, Pseudo mild yellow edge, Vein banding, and Chlorotic fleck. Whitefly transmitted viruses have become more important; four criniviruses and one geminivirus have emerged as new threats to strawberry in areas where vectors are present. The ilarviruses that infect strawberry include Strawberry necrotic shock (previously misdiagnosed as Tobacco streak), Tobacco streak, Fragaria chiloensis latent, and Apple mosaic viruses. Strawberry necrotic shock is the predominant ilarvirus in the United States, whereas Fragaria chiloensis latent has significant presence in Chile. Modern strawberry cultivation has minimized the impact of nematode transmitted viruses but the elimination of methyl bromide may lead to the reemergence of this virus group in the future. With the knowledge we have acquired over the last decade, it is now possible to have robust certification systems, the cornerstone for minimizing the impact and spread of strawberry viruses.
Comparison of Different Interpolation Techniques For Modelling Temperatures In Middle Blacksea Region

Objective of this study is to determine the best method for modeling and mapping monthly and annual temperatures (minimum, maximum, mean) of northern Turkey by using geographical information systems (GIS). Temperature data of 72 different meteorological observation stations were used for modeling and mapping purposes. Inverse Distance Weighting (IDW), Thin-plate smoothing spline (TPS), Simple Kriging (SK), Cokriging (CK) and Linear Regression Model (LR) were used to analyze spatial distribution of temperature data. The correlation coefficients were used to compare the methods. The data was divided in two different groups for validation procedure. The first group of data from 58 stations was used for analysis and the second group of data from 14 stations was used for testing purposes. Correlation coefficients among the estimated and measured monthly mean temperatures varied between 0.80 and 0.95. Correlation coefficients for all months were found to be significant (P < 0.01). In general, LR yielded the best results for monthly mean temperatures. While TPS was identified as the best method for monthly minimum temperatures for most of the months, LR, IDW, and CK methods yielded best results for other months. All methods yielded unsatisfactory results for maximum temperatures, especially for summer months.