Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid iIdentification of proteins by peptide-inass fingerprinting

Developments in ‘soft’ ionisation techniques have revolutionized mass-spectro- metric approaches for the analysis of protein structure. For more than a decade, such techniques have been used, in conjunction with digestion by specific pro- teases, to produce accurate peptide molecular weight ‘lingerprints’ of proteins. These linger-prints have com- monly been used to screen known proteins, in order to detect errors of translation, to characterize post-trans- lational mod&cations and to assign disulphide bonds. However, the extent to which peptide-mass information can be used alone to identify unknown sample proteins, independent of other analytical methods such as protein sequence analysis, has remained largely unexplored.
Development and reproduction of the predatory mite Amblyseius swirskii Athias-Henriot (Acari: Phytoseiidae) on Tetranychus urticae Koch (Acari: Tetranychidae) and Bemisia tabaci Gennadius (Heteroptera: Aleyrodidae)

ABSTRACT Amblyseius swirskii Athias-Henriot (Acari: Phytoseiidae) is an effective predator feeding on different insect and mite pests such as whiteflies, thrips and two-spotted spider mites. In this study, we documented the life table of A. swirskii on eggs of Tetranychus urticae and Bemisia tabaci under laboratory conditions (25 ± 1°C, 70 ± 5% RH and 16L: 8D). The results indicated that the developmental times of egg, larva, protonymph and deutonymph stages of A. swirskii were 1.36 ± 0.07, 1.23 ± 0.07, 1.43 ± 0.08 and 2.49 ± 0.14 days when fed on T. urticae and 0.95 ± 0.02, 0.96 ± 0.04, 1.25 ± 0.08 and 2.83 ± 0.1 days when fed on B. tabaci. The average of all immature stages on eggs of T. urticae and B. tabaci were 6.58 ± 0.12 and 6.01 ± 0.13 days, respectively. The average adult female longevities on the two different prey species were 25.58 ± 1.13 and 25.35 ± 0.81 days, respectively. The intrinsic rates of increase (r) and finite rates of increase (λ) on eggs of T. urticae and B. tabaci were 0.22 ± 0.01 and 0.12 ± 0.01 day−1 and 1.25 ± 0.02 and 1.13 ± 0.02 day−1, respectively. The net reproductive rates (R0) and mean generation times (T) on the two prey species were estimated as 12.14 ± 1.84 and 3.90 ± 0.63 offspring/individual and 11.08 ± 0.23 and 11.24 ± 0.2 days, respectively. These results indicate that A. swirskii can successfully survive and reproduce on T. urticae and B. tabaci and have the potential to be a more effective biological control agent of T. urticae than B. tabaci.
Réplication, dissémination et morphogénèse du virus de la maladie de Marek en cellules différenciées vers le lignage peau

Le virus de la maladie de Marek (MDV) est un alpha-herpesvirus responsable de lymphomes T mortels chez la poule. La peau et en particulier le follicule plumeux est considere comme le seul site de production de particules virales extracellulaires et est a l'origine de la dissemination horizontale du virus et de la contamination de l'environnement. Cependant, aucun systeme cellulaire ne permet de reproduire ce qui se passe dans ce tissu. Le but de ma these a donc ete de developper de nouveaux systemes de culture permettant de reproduire la replication, la morphogenese et l’excretion decrites in vivo. Pour cela, j’ai developpe deux systemes, des explants de peau d’embryons de poulet cultives ex vivo et des keratinocytes obtenus par differenciation de cellules souches embryonnaires de poule. J’ai egalement montre la permissivite au MDV de ces deux modeles de peau puis y ai etudie la replication et la morphogenese virale. Ces modeles permettront la recherche des determinants viraux et cellulaires impliques dans la production de virions extracellulaires et leur dissemination.
Hybrid power supplies for particle accelerators

A hybrid power supply topology is proposed for large particle accelerators/colliders. This topology combines the One-Cycle Controlled switching converter and the phase-controlled thyristor converter and it is suitable for two quadrant (rectifier and inverter) applications that require low ripple, high current, large dynamic range. <<ETX>>
Genome Composition Plasticity in Marine Organisms

The molar ratio of the nucleotides (GC%, i.e. the Guanine+Cytosine content) is well known to evolve through the genomes of all the organisms. Several hypotheses have been drawn out to explain the causes of the nucleotide composition variability among orgnisms. In the Thesis project major attention has been directed to the Metabolic Rate hypothesis (MRh). The main goal was to test if the MRh, first proposed to explain the nucleotide variability within mammalian genomes, could also explain the base composition variability among lower vertebrates and invertebrates. To this aim an extensive analysis of more than two hundred teleostean species has been carried out, followed by a pioneering study of annelid polychaete and tunicate genomes. Regarding teleosts, the results clearly highlighted that environment (i.e. salinity) and lifestyle (i.e. migration) both affect simultaneously the physiology (the metabolic rate), the morphology (the gill area) and the genome composition (GC%). Thus supporting a link between the metabolic rate (MR) and the genome base composition, as expected in the light of the MRh. Moreover, a comparative analysis of completely sequenced teleostean genomes showed that the metabolic rate was correlated not only with the GC content of the genome, but also with the intron structures. Indeed, at increasing metabolic rates introns were shorter and GC-richer. A preliminary analysis of annelids polychaetes showed that motile and sessile species were characterized by different MR and GC%, being both higher in the former than in the latter. The investigation was extended to the well known solitary tunicates, C. robusta and the congeneric C. savignyi. Our data revealed slight but significant morpho-physiological differences between the two species, consistent not only with an ecological niche differentiation, but also with their genomic GC content. All the above results converge towards the same conclusion, thus giving consistency to the MRh as major factor driving the genome base composition evolution of all living organisms.
Regulates Eye and Limb Development in Zebrafish

Uveal coloboma is a potentially blinding congenital ocular malformation caused by failure of the optic fissure to close during development. Although mutations in numerous genes have been described, these account for a minority of cases, complicating molecular diagnosis and genetic counseling. Here we describe a key role of aldh7a1 as a gene necessary for normal eye development. We show that morpholino knockdown of aldh7a1 in zebrafish causes uveal coloboma and misregulation of nlz1, another known contributor to the coloboma phenotype, as well as skeletal abnormalities. Knockdown of aldh7a1 leads to reduced cell proliferation in the optic cup of zebrafish, delaying the approximation of the edges of the optic fissure. The aldh7a1 morphant phenotype is partially rescued by co-injection of nlz1 mRNA suggesting that nlz1 is functionally downstream of aldh7a1 in regulating cell proliferation in the optic cup. These results support a role of aldh7a1 in ocular development and skeletal abnormalities in zebrafish.
A REVIEW ON DIMENSIONALITY REDUCTION TECHNIQUES IN DATA MINING

Data mining is a form of knowledge discovery essential for solving problems in a specific domain. Classification is a technique used for discovering classes of unknown data. Various methods for classification exists like Bayesian, Decision Trees and Rule based neural networks etc. Before applying any mining technique, irrelevantattributes needs to be filtered. Filtering is done using different feature selection techniques like wrapper, filter, and embedded technique. Feature selection plays an important role in data mining and machine learning. It helps to reduce the dimensionality of data and increase the performance of classification algorithms. A variety of feature selection methods have been presented in state-of-the-art literature to resolve feature selection problems such as large search space in high dimensional datasets like in microarray. However, it is a challenging task to identify the best feature selection method that suits a specific scenario or situation. Dimensionality reduction in data mining focuses on representing data with minimum number of dimensions such that its properties are not lost and hence reducing the underlying complexity in processing the data. Principal Component Analysis (PCA) is one of the prominent dimensionality reduction techniques widely used in network traffic analysis.
COMPUTATIONAL PREDICTION OF POTENT ANTIGENIC PEPTIDES FROM BORRELIA BURGDORFERI PROTEOME FOR VACCINE DESIGNING WITH STRUCTURAL VIEWPOINT FOR ITS INHIBITION.

Lyme disease is the most common tick-borne infectious disease found in North America and in Europe. Lyme is a Multi-Systemic Disease caused by the bacteria called Borrelia burgdorferi (Bb) which normally is a bacterial spirochete (spiral shape). It is zoonotic disease, which is also known as Lyme boreliosis. The scope of the current work is to predict and design a potent antigenic peptide of the bacteria Borrelia burgdorferi to develop a potential vaccine. The bacterial proteome is collected from HAMAP and processed for screening purpose based on the similarity against Human CDS using TFastaY. The proteins were subjected to fourfold screening process for the identification of most antigenic sites within them by using different servers like EMBOSS Antigen and Protein Variability Server. The selected antigenic peptides were designed using Chimera followed by the geometry optimization and energy evaluation. Since many commercial drugs have been available the molecular docking studies has been carried out to know the inhibitory efficiency of drugs to inhibit the disease causing protein. Targeting the surface antigenic peptides of Borrelia burgdorferi the In-silico studies has been carried out to identify the best antigenic peptides responsible for this. Based on the energy values the best antigenic peptides were selected, Protein-peptide docking was carried out to analyze the antigenic propensity with the protein
EFFECT OF ORGANIC AMENDMENTS ON DISTRIBUTION, STABILITY AND CARBON CONCENTRATION OF SOIL AGGREGATES

A good soil structure is indicated by the abundance of soil aggregates which has an important role in sustainable agricultural management and soil productivity. As it affects hydraulic conductivity, gases transport within the soil and seed germination, root respiration and eventually plant growth. The different sized fractions of soil aggregates are influenced significantly by both the amount and the composition of organic matter present in the soil (Piccolo, 1996). The degree of soil aggregation and aggregate stability is the result of the interaction between organic and inorganic soil components. Soil structure degradation occurs mostly due to the decrease in soil organic carbon caused by excessive soil cultivation and soil erosion. Eroded soils have consistently shown lower soil organic carbon and nutrient concentrations in upper profiles than cultivated soils, this is also true for other physical properties such as soil texture and saturated hydraulic conductivity (Heckrath et al., 2005). Soil organic carbon (SOC), includes soil organisms (e.g. microbial biomass), simple organic compounds (e.g. polysaccharides), large and complex humic substances, as well as relatively fresh residue at various stages of decomposition (Weil and Magdoff, 2004). The effect of different composted and un composted products on soil aggregate stability across time scales vary from weeks, months to years after the incorporation (Monnier, 1965). The various components of organic carbon such as microbial biomass carbon, polysaccharides and humic substances play very important role in the aggregate formation mechanism. The polysaccharides are highly complex polymers, consisting of many structural units, and are naturally resistant to decomposition or become resistant through reaction with other soil constituents and serve as binding agents. Microbial biomass carbon is an active form of carbon and it influences aggregate formation and stability. Humic substances account for the largest and most decomposed proportion of soil organic matter (SOM) with chemically complex and ill-defined structure, and act as persistent binding agent for stabilization of aggregates. Stabilization of aggregates by organic matter (Six et al., 2004) and interactions between aggregative factors and aggregate structures is well documented. In most studies, the organic matter additions were characterized by their elemental composition but additional information such as contents of humic and non-humic substances were seldom provided. In this study we hypothesized that addition of organic sources on equivalent carbon level basis affect the soil aggregate formation differently as composition of materials vary. The objectives of the present study were, to examine the quality (fundamental characteristics) of the traditional organic manures and their direct effect upon formation, Pak. J. Agri. Sci., Vol. 53(4), xxx-xxx; 2016 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/16.4205 http://www.pakjas. com.pk
Fire history along environmental gradients in the Sacramento Mountains, New Mexico: Influences of local patterns and regional processes

Abstract Patterning in fire regimes occurs at multiple spatiotemporal scales owing to differences in scaling of local and regional influences. Local fire occurrence and behavior may be controlled largely by site factors, while regional climate and changes in human land use can synchronize fire timing across large areas. We examined historical patterns in fires during the past five centuries across gradients in forest types and physiography and in relation to regional climate variability and land use change in the Sacramento Mountains in southern New Mexico. Forest stand-level chronologies of fires were reconstructed for 19 pinyon-juniper, ponderosa pine, and mixed-conifer stands using fire-scar records in crossdated tree-ring series. The fire history documents both local and regional factors effected fire occurrences in stands. Lower-elevation stands recorded more frequent fire than higher-elevation stands, although there were not significant differences between means of fire frequencies from clusters of ponderosa pine and mixed-conifer stands. Mean fire intervals ranged from approximately 3 to 11 years in ponderosa pine sites to 4 to 14 years in mixed-conifer sites. Sites on the steeper west side of the range, where fire spread more readily between forest types, recorded significantly more frequent fire than sites on the more physiographically heterogeneous east side. Fires were also synchronized by regional factors. Fire occurrences and fire-free years are related to variability in both annual Palmer Drought Severity Indices and El Niño-Southern Oscillation events. Fire regimes in the stands were also profoundly effected by changes in human land use patterns, with fire cessation in all sites following intensive Euro-American settlement beginning in the 1880s.
Genetic Relationship of Iranian Pear Genotypes with European and Asian Pears as Revealed by Random Amplified Polymorphic DNA Markers

ABSTRACT Genetic variation within specific fruit tree germplasms is an important tool in fruit tree breeding programs. In the present work, the genetic relationship of 31 European and Iranian (Pyrus communis L.) and Asian (Pyrus serotina Rehd) genotypes of pear were studied using 19 randomly amplified polymorphic DNA (RAPD) primers. Fifteen out of the 19 primers used in this study amplified 3373 clear and reproducible bands associated with 150 loci and many of them were polymorphic. The dendrogram resulting from the unweighted pair-group method of arithmetic cluster analysis separated the cultivars into eight groups. The correlation coefficient between the cophenetic matrix and the similarity matrix was 0.82 (r = 0.82). There was a significant difference between populations and most studied genotypes clustered closely together based on their geographic origin and Iranian pears placed between two groups of pears. Results showed the suitability of RAPD analysis in genetic diversity study of pear.
Efficient Gene Transfer and Expression in Islets by an Adenoviral Vector that Lacks All Viral Genes

Although adenoviral vector-mediated gene transfer has significant potential for gene therapy, host immune responses to virally expressed proteins and small insert capacity may limit its clinical application. In order to overcome these disadvantages, a new adenoviral vector that lacks all viral genes has been developed. Using the green fluorescent (GFP) gene as a reporter gene, we investigated the efficiency of gene transfer by this all-viral-genes-deleted and minimal cis-element remaining adenoviral vector (miniAd-GFP) in islets in vitro and ex vivo, and compared it with the E1-deleted adenoviral vector (E1-GFP). One day after in vitro infection, GFP was expressed in both miniAd-GFP- and E1-GFP-infected islets. The percentage of GFP-positive single cells was not significantly different between miniAd-GFP-infected islets and E1-GFP-infected islets. When these islets were transplanted into syngeneic diabetic mice, both miniAd-GFP- and E1-GFP-infected islet grafts reversed diabetes, and normal blood glucose levels were maintained for over 20 weeks posttransplantation. Mild lymphocyte infiltration was found in all E1-GFP-infected islet grafts at all time points. However, this was not seen in most miniAd-GFP-infected islet grafts. Our results indicate that gene transfer by an adenoviral vector that lacks all viral genes is as efficient as E1-deleted adenoviral vector-mediated gene transfer in islets. Furthermore, this adenoviral vector might be less immunogeneic than the E1-deleted adenoviral vector.
Does increased connectivity with the Mediterranean Sea improve the ecological status of the macroinvertebrates in the lagoon of Boughrara (SW Mediterranean)

The lagoon of Boughrara is an almost closed system, with limited hydrological connections with the sea. Over the past several decades, the lagoon has been exposed to increased pollution due to growing human activities in the surrounding area. From 2004–2007, the channel “El-Kantra” connecting the lagoon to the sea has been extended with increased mixing with marine waters. In this work, we monitored the ecosystem of the lagoon after its rapid exposure to development and associated pollution. Two marine surveys were carried out in winter 2010 and then in winter 2013; the sediment was sampled and the principal physical and chemical parameters were measured at 13 stations. Results show that aspects of the environmental quality of the lagoon have improved from 2010 to 2013, most likely due to the extension of the channel whereby lagoon waters are better mixed resulting in improved physico-chemical conditions over this timeframe. Nevertheless, the study of the macrobenthic community did not show any improvement. On the contrary, the species richness and the abundance of the macrofauna have decreased, and some tolerant species such as bivalves (Abra alba and Cerastoderma edule) have increased in abundance. This demonstrates continued impacts on the lagoon ecosystem.
Differences in size, pigmentation, and fluctuating asymmetry in stressed and nonstressed northern leopard frogs (Rana pipiens)

Abstract We compared a range of anatomical features of northern leopard frogs (Rana pipiens Schreber) collected from areas where deformity rates were low (-2% in nonstressed regions) and high (-40% in the stressed region) to determine if one or more of these characters might be useful in detecting developmental stress. Deformed individuals from the stressed region were significantly lighter than normal frogs both from the same region and from nonstressed regions. Body length, head width, femur length, and forelimb length were also significantly shorter in deformed and normal individuals from the stressed region than in individuals from nonstressed regions. Despite being smaller, deformed individuals had significantly larger pigment spots. Fluctuating asymmetry in femur length, femur spot area, femur spot number, and tibio-fibula length was significantly greater in deformed frogs than in normal frogs from the stressed population and the nonstressed group. Of these characters, however, only femur spot number provided a data set suitable for fluctuating asymmetry analysis (R - L values have a normal distribution, no directional asymmetry, no size-dependent asymmetry). There were no significant differences found among the three groups for fluctuating asymmetry in forelimb length, eyespot area, lateral spot number, and lateral spot area.
Tissue specificity of cytosolic `K^+` retention, `Na^+` extrusion, and vacuolar `Na^+` sequestration traits in the context of differential salinity stress tolerance in barley and wheat

Wheat and barley are ranked the second and fifth most important crops in terms of dry matter production. Both of them are classified as glycophytes, and their production is strongly affected by soil salinity. Thus, given the extent of land salinization in the world and predicted population growth to 9.3 billion by 2050, creating salt tolerant wheat and barley germplasm remains one of highest priorities for breeders. Salinity tolerance is a complex physiological trait composed of numerous sub-traits controlled by multiple regulatory pathways. Until now, most studies were focused on traits related to sodium, such as `Na^+` exclusion from uptake, control of xylem `Na^+` loading, `Na^+` retrieval from the shoot or vacuolar Na+ sequestration. However, it is not `Na^+` but the `K^+``/Na^+` ratio in the cytosol that ultimately determines plant performance under saline conditions. In recent years, `K^+` retention in root mature zone has emerged as an important component of salt tolerance mechanisms in many plant species. However, whether the importance of cell’s ability to maintain `K^+` in plant overall salt tolerance can be extrapolated to other root zones or tissues (e.g. leaves) remained obscure prior to this work. Also elusive remained the essentiality of root `Na^+` exclusion and vacuolar `Na^+` sequestration in various root tissues. Furthermore, the relative contribution of each of the above salt tolerant mechanisms towards the overall salinity tolerance remained unclear, especially at the tissue specific level.
ASSOCIATION ANALYSIS OF GENES CSRP3, EDG4 A PRKAG3 WITH MEAT QUALITY IN CZECH LARGE WHITE PIGS

In this part of our project we focused on pH and me at colour and three actual candidate genes (CSPR3, EDG4 and PRKAG3 ). Their mutations were chosen for investigating th e effect and influence of these three markers on pork quality in commercial breed population of Czech Large White pigs. The blood and tissue samples ( m.longissimus lumborum et thoracis ) were collected from a purebred population of 86 Czech Large White sows. All animals were from one breed, fed using standard commercial protocol and slaughtered at average 91.2 kg of live weight in the same abattoir. Genotypes in actual candidate genes for meat qualit y EDG4 , CSPR3 and PRKAG3 were detremined by previously reported PCR-RFLP assays. The measured phenotypes were pH ultimate and meat colour characteristics L* (lightness), a* (redness) , b* (yellowness). The statistical analysis was performed by the general linear model (GLM) by SAS for Windows 9.1. 4. All markers were polymorphic in our Czech large White population but for CSRP3 and PRKAG3 markers only two genotypes were observed, homozygous animals TT and GG in CSRP3 and PRKAG3 , respectively, were not observed. We revealed no s ignificant associations between EDG4, CSPR3, PRKAG3 and meat colour or pH ultimate. These results can b e influenced by limited number of animals included in this preliminary stud y. In next part of our project we focus on another meat quality traits in larger number of ani mals to confirm previously reported asscociation of mentioned genes.