Miracle-dz/UniFAR-FTUs huggingface dataset:
Stratification of bacterial concentrations, from upper to lower, in broiler litter

Primary Audience: Flock Supervisors, Researchers SUMMARY There have been numerous research studies concerning the different types of bacteria in broiler litter. However, very little is known about the spatial distribution of bacteria from the top to the bottom of the litter bed. Two experiments were conducted, one of a single flock in a pen trial, and the second on a commercial broiler farm for 8 consecutive flocks. Core litter samples were taken and 3 fractions of litter were removed from each core for bacterial analysis: the upper 5.08 cm of litter, the exact middle of the litter, and the lower section of litter directly on top of the dirt pad, being sure to include some dirt pad. Core litter samples were taken specifically at 7 d before placement then again at 1, 7, 14, 21, 35, and 49 d of age in experiment 1, and 14 and 35 d of age in experiment 2. Core samples were removed from 6 pens in the first experiment. In experiment 2, core litter samples were taken near the evaporative cooling cells, the environmental control room or middle of the house, and near the exhaust fans. Litter fractions were analyzed for Staphylococcus spp. , Clostridium perfringens, Escherichia coli, Salmonella spp. , total aerobes, and total anaerobes. A decrease was observed from the top to middle and from middle to bottom fractions of litter for all bacteria. From upper to lower, all bacteria concentrations were reduced by at least 99%. Therefore, the concentration of bacterial populations within broiler litter could shift dramatically within only a few inches of litter and the lower fraction of litter holds relatively less bacteria than the upper or middle fractions.
Characterisation of TPL-2 signalling pathways in innate immunity

The MAP 3-kinase TPL-2 is required for activation of ERK1/2 MAP kinases in macrophages after stimulation of Toll-like receptors and the receptors for TNF and IL-1β. TPL-2 drives inflammation in a number of autoimmune and inflammatory disease models, and consequently is considered a potential anti-inflammatory drug target. Recent evidence from the Ley laboratory has indicated that TPL-2 regulates the production of the critical pro-inflammatory cytokine TNFα in an ERK1/2-independent manner. The aim of this study was to use mass spectrometry-based phosphoproteomics to investigate the signalling pathways regulated by TPL-2 in an unbiased manner to more fully understand how TPL-2 regulates innate immunity. A method for SILAC labelling of bone marrow-derived macrophages was developed and used to quantify phosphorylation changes after genetic and pharmacological perturbation of TPL-2 signalling. Across 11 pair-wise comparisons, 31,457 unique phosphosites were identified, from which a shortlist of 37 potentially TPL-2-dependent, ERK1/2-independent phosphorylations was generated. The biological consequences of the majority of these TPL-2 regulated sites remain to be determined, although bioinformatic analysis suggest that they may have roles in regulation of gene expression and the cytoskeleton. The activating residues of the MAP 2-kinases, MKK3 and MKK6 were validated as novel TPL-2 targets in LPS-stimulated macrophages and MKK6 was shown to be a direct substrate by in vitro kinase assays using recombinant proteins. It was also demonstrated that TPL-2 controlled the phosphorylation of the activation loop of the MAP kinase p38γ, which is a direct target of MKK3/6. These data identified a novel signalling pathway downstream of TPL-2, increasing our understanding of how TPL-2 controls inflammatory responses.
Multi-Response Nanowire Grating-Coupled Surface Plasmon Resonance by Finite Element Method

In this paper, Surface Plasmon Resonance (SPR) has been applied for sensing acetone liquid by changing the refractive index based on nanowire grating. This sensor was proposed and numerically analysed using finite element method. The SPR sensor composed of multi-nanowires distributed in a parallel order at a specific distance. These wires were deposited onto the dielectric material and tested using laser light at wavelengths between 500 nm to 700 nm. Dual SPR dips emerged at two different SPR angles after further tuning the incident angle. The multi SPR dips are angularly wide but spectrally produced very sharp results. SPR sensor results were compared at four different plasmonic materials gold, silver, aluminium and copper using 532 nm wavelength. These plasmonic materials were tested using acetone at 100%, 50%, 10% concentrations. The sensitivity measurements of the sensor have shown that the dual SPR dips can be used effectively to increase the sensitivity of the designed sensor. Both dips were also used to increase the detection sensitivity of different types of liquids. The sensitivity of SPR causes a shift in dip or intensity due to any small change in refractive index. This shift varies according to the material and liquid concentration. The sensitivity of nanowire grating was measured by varying the refractive index with the resonance angle (θ°) at a single wavelength. The highest sensitivity has been discovered for gold which is 290.57°/RIU. This work is adopted for the improvement of the surface plasmon sensor using nanowire technology. The structure is easy and simple and can be applied to different applications.
Combining Ability for Disease Resistance, Yield, and Horticultural Traits of Cacao (Theobroma cacao L.) Clones

Knowledge of genetic differences among commonly cultivated cacao clones, as well as the type of gene ac- tion involved for disease resistance, yield, quality, and horticultural traits, are essential for cacao breeders to select parental clones effi ciently and effectively. This information is also critical for quantitative geneticists in designing and improving quantitative trait loci (QTL) localization strategies using breeding populations, whether they involve analysis of multiple populations crossed to one common parent or association genetic analysis. The objectives of this research were to 1) verify the genetic identity of parental cacao clones used to produce hybrids for fi eld evaluation at the Centro Agronomico Tropical de Investigacion y Enzenanza (CATIE), Turrialba, Costa Rica, using molecular marker analysis, and 2) estimate general and specifi c combining ability (GCA and SCA) of the parental clones for resistance to frosty pod (Moniliophthora roreri Cif. and Par.) and black pod (Phytophthora palmivora (Butl.) Butl. ) diseases, total number of pods, vigor (as measured by trunk diameter), and measures of maturity (months to fifl owering and pod production). Misidentifi cation of cacao clones was found at three levels. Molecular marker analysis revealed that six parental clones differed in identity to supposedly identical accessions from other germplasm collections. Trees of the parental clone UF 273 consisted of two clearly different genotypes, resulting in two types of progeny, requiring separate designation for correct statistical analysis. Out-crossed progeny, presumably from foreign pollen, and selfed progeny were also found. Two of the traits measured, percent healthy pods and percent pods with frosty pod, showed predominantly additive gene action, while the traits total number of pods and trunk diameter, demonstrated regulation by both additive and nonadditive gene action. Number of months to fi rst fl owering and fi rst fruit both showed evidence of predominant regulation by nonadditive gene effects. Crosses of two parental clones, UF 712 and UF 273 Type I, were identifi ed as potential candidates for QTL analysis as breeding populations, given their favorable GCA estimates for frosty pod resistance and total pod production, respectively. Cacao is a perennial species widely cultivated in America,
Bardet-Biedl Syndrome Gene Variants Are Associated With Both Childhood and Adult Common Obesity in

Bardet-Biedl syndrome (BBS) is a rare developmental disorder with the cardinal features of abdominal obesity, retinopathy, polydactyly, cognitive impairment, renal and cardiac anomalies, hypertension, and diabetes. BBS is genetically heterogeneous, with nine genes identified to date and evidence for additional loci. In this study, we performed mutation analysis of the coding and conserved regions of BBS1, BBS2, BBS4, and BBS6 in 48 French Caucasian individuals. Among the 36 variants identified, 12 were selected and genotyped in 1,943 French-Caucasian case subjects and 1,299 French-Caucasian nonobese nondiabetic control subjects. Variants in BBS2, BBS4, and BBS6 showed evidence of association with common obesity in an age-dependent manner, the BBS2 single nucleotide polymorphism (SNP) being associated with common adult obesity (P 0.0005) and the BBS4 and BBS6 SNPs being associated with common early-onset childhood obesity (P 0.0003) and common adult morbid obesity (0.0003 < P < 0.007). The association of the BBS4 rs7178130 variant was found to be supported by transmission disequilibrium testing (P 0.006). The BBS6 variants also showed nominal evidence of association with quantitative components of the metabolic syndrome (e.g., dyslipidemia, hyperglycemia), a complication previously described in BBS patients. In summary, our preliminary data suggest that variations at BBS genes are associated with risk of common obesity. Diabetes 55:2876 –2882, 2006
Isolation and Characterization of Viruses Present in Four Clones of Garlic (Allium sativum) in Venezuela

Isolation and characterization of viruses infecting garlic in Venezuela indicate the presence of onion yellow dwarf virus [OYDV] in most field-grown plants of the clones Criollo venezolano, Morado peruano and Blanco, while 14% of the Criollo venezolano plants showed co-infection of leek yellow stripe virus [LYSV] and OYDV. In leaf tissues OYDV showed an average concentration of 165 μg/g fresh wt. , the value being similar among clones. In Criollo venezolano plants co-infected by LYSV and OYDV the concentration of the former was three fold lower than that of OYDV. Serological tests on leaf extracts of garlic plants indicated the absence of the garlic yellow streak virus [GYSV], shallot latent virus [SLV] and garlic latent virus [GLV] in the clones Criollo venezolano, Morado peruano and Blanco. GLV was found to infect plants of the clone Gigante. Physicochemical analysis of purified GLV strongly supports the inclusion of this virus as a definitive member of the carlavirus group. Zusammenfassung Isolierung und Charakterisierung von Viren, die in vier Knoblauchklonen (Allium sativum) in Venezuela vorkommen Die Isolierung und Charakterisierung der Viren, die Knoblauch in Venezuela infizieren, zeigen die Anwesenheit des onion [Kuchenzwiebel] yellow dwarf virus [OYDV] in den meisten der im Freiland wachsenden Knoblauchpflanzen der Klonalen Typen criollo venezolano, morado peruano und bianco. 14% der criollo venezolano Pflanzen wiesen eine gleichzeitige Infektion mit leek [Lauch] yellow stripe virus [LYSV] und OYDV auf. OYDV lag im Blattgewebe in einer durchschittlichen Konzentration von 165 μg/g Frischgewicht vor; der Wert war innerhalb der klonalen Typen ahnlich. In criollo venezolano Pflanzen, die mit LYSV und OYDV koinfiziert waren, war die Konzentration des esteren etwa ein Drittel des OYDV. Serologische Tests von Blattextraten von Knoblauchpflanzen zeigten die Abwesenheit des garlic [Knoblauch] yellow streak virus [GYSV], shallot [Schalotte] latent virus [SLV] und garlic [Knoblauch] latent virus [GLV] in den klonalen Typen criollo venezolano, morado peruano und bianco. Es wurde beobachtet, das GLV Pflanzen des klonalen Knoblauchtyps gigante infiziert. Die physikochemische Analyse von gereinigtem GLV unterstiitzt die Eingruppierung dieses Virus als definitives Mitglied den Carlavirus Gruppe.
Microbial and geohelminthes population in different parts of Daucus carota L. (Carrot)

Daucus carota (Carrot) is a common vegetable often consumed for its enormous nutritional benefits but without thoughts of its possible contamination with disease causing microorganisms. The different parts namely eyes, between buds, leaf stump and body of Daucus carota obtained from different spots in Owerri were analyzed using standard microbiological and parasitological methods. The mean heterotrophic bacteria count ranges from 1.28 x 10 9 cfu/g in between buds to > 10 10 cfu/g in the leaf stump. Mean coliform count ranges from 1.55 x 10 7 in the body to > 10 10 in the eyes, leaf stump and between buds. The mean fungal count was 1.54 x 10 7 in the body and > 10 10 cfu/g in the leaf stump and between buds. There was no significant difference at P = 0.05 in mean microbial counts in the different parts of Daucus carota and from the different sampling spots. Organisms isolated include spp of Staphylococcus, Corynebacterium, Bacillus, Pseudomonas, Micrococcus, Serratia, Escherichia, Enterococcus, Penicillium, Rhizopus, Saccharomyces, Geotrichium, Mucor, and Aspergillus. Geohelminthes detected include Ascaris lumbricoides, Hookworms and Strongyliodes stercoralis. The level of contamination of the carrots calls for urgent need to create awareness on proper hygiene practices, GMP and HACCP application.
From nucleus to axon: Spatial regulation of bclw mRNA promotes neurotrophin-dependent axon survival

During development, dorsal root ganglion (DRG) neurons depend on target-derived neurotrophins to establish a functional circuit capable of conveying sensory information to the central nervous system. Neurotrophins signal from the periphery via dyneindependent retrograde transport of signaling endosomes to activate a nuclear transcriptional response critical for neuronal survival. Importantly, neurotrophins support the health of the entire DRG neuron, but it is not well understood how neurotrophins specifically function to promote survival of axons. Previous research demonstrated that target-derived neurotrophins induce expression of the anti-apoptotic Bcl2 family member, Bclw, and in vivo studies demonstrate that Bclw is a critical survival factor for sensory axons. Here we describe multi-step regulation of bclw mRNA from the nucleus to the axon to support the health and long-term maintenance of axons. We find that neurotrophins induce transcription of bclw mRNA, which is rapidly transported to axons. There it is locally translated to prevent caspase-dependent apoptosis and axon degeneration. We identify the RNA-binding protein splicing factor proline-glutamine rich (SFPQ) as a critical regulator that specifically interacts with bclw mRNA. SFPQ is required for nuclear export of bclw mRNA and for generating an axonal pool of bclw mRNA. Interestingly, we find that SFPQ binds and regulates additional mRNAs also
Classification system for rain fed wheat grain cultivars using artificial neural network

Artificial neural network (ANN) models have found wide applications, including prediction, classification, system modeling and image processing. Image analysis based on texture, morphology and color features of grains is essential for various applications as wheat grain industry and cultivation. In order to classify the rain fed wheat cultivars using artificial neural network with different neurons number of hidden layers, this study was done in Islamic Azad University, Shahr-e-Rey Branch, during 2010 on 6 main rain fed wheat cultivars grown in different environments of Iran. Firstly, data on 6 colors, 11 morphological features and 4 shape factors were extracted, then these candidated features fed Multilayer Perceptron (MLP) neural network. The topological structure of this MLP model consisted of 21 neurons in the input layer, 6 neurons (Sardari, Sardari 39, Zardak, Azar 2, ABR1 and Ohadi) in the output layer and two hidden layers with different neurons number (21-30-10-6, 21-30-20-6 and 21-30-30-6). Finally, accuracy average for classification of rain fed wheat grains cultivars computed 86.48% and after feature selection application with UTA algorithm increased to 87.22% in 21-30-20-6 structure. The results indicate that the combination of ANN, image analysis and the optimum model architecture 21-30-20-6 had excellent potential for cultivars classification. Key words: Rain fed wheat, grain, artificial neural networks (ANNs), multilayer perceptron (MLP), feature selection.
Waterbird Response to Changes in Habitat Area and Diversity Generated by Rainfall in a SW Atlantic Coastal Lagoon

Abstract The rainfall regime of the Pampas region of Argentina shows a long-term cyclic behavior that has increased in intensity over the historical mean during the last four decades. In this paper we explored the effects of changes in monthly cumulative rainfall on lagoon and riparian habitat, and, in turn on the wetland waterbird community. We also explored the responses of waterbird morphofunctional groups to fluctuation in water level and habitat diversity caused by the change in rainfall at the Mar Chiquita Coastal Lagoon, Argentina (37°32’ to 37°45’S, 57°19’ to 57°26’W). Analysis of satellite images shows that increases in rainfall increased wetland water surface, but reduced riparian habitat area and habitat diversity. Increases in water surface negatively affected the abundances and species richness of waterbirds; habitat diversity did not explain a significant portion of total waterbird variability. Shorebirds (i.e., yellowlegs, plover, sandpiper) were the most affected by reduction in mudflats and habitat diversity. Other waterbirds (i.e., long-legged wading birds, waterfowls) were affected by increases in water surface (ducks, swans, long-legged waterbirds and gulls), decrease in mudflat availability (long-legged waterbirds and gulls), and decrease in habitat diversity (ducks). Our results show that the inter-annual variability in the rainfall pattern influenced the presence and abundance of most waterbirds, and species richness and composition. Fluctuation in water depth per se is known to be a key factor for habitat use of many waterbirds, but habitat diversity also needs to be considered.
ASSESSMENT OF MOLECULAR DIVERSITY IN WHEAT (TRITICUM AESTIVUM L. AND TRITICUM DURUM L.) GENOTYPES CULTIVATED IN SEMI-ARID REGION OF GUJARAT

Molecular diversity was assessed among wheat genotypes cultivated in semi-arid region of Gujarat employing molecular markers. In total, 18 RAPD and eight SSR markers amplified 5554 fragments with 66.83 % polymorphism and 343 fragments with 90.32% polymorphism respectively. Unweighted pair group method with arithmetic mean (UPGMA) analysis generated by RAPD, SSR and combined RAPD and SSR based on genetic distance estimates displayed two major clusters consisting of irrigated aestivum (I), irrigated and rainfed durum (II) wheat genotypes. A Jaccard’s similarity coefficient of all genotypes derived from RAPD data ranged from 0.65 to 0.90 and that of SSR ranged from 0.45 to 0.94. Marker data subjected to analysis of molecular variances revealed more diversity within population. The PIC value for RAPD and SSR markers ranged from 0.91 to 0.96 and 0.57 to 0.76 respectively, with marker indexes of 11.35 and 5.35, demonstrating its utility in genetic diversity analysis. The results of PCoA analysis were comparable to dendrograms. Analysis of molecular variance (AMOVA) for combined RAPD and SSR displayed more variance within and among population than RAPD and SSR. These molecular markers can be put to use for characterization and selection of wheat genotypes suitable for cultivation in irrigated and rainfed conditions.
Multigene differences between Microdochium nivale and Microdochium majus

Microdochium nivale (Fr.) Samuels & Hallett and Microdochium majus (Wollenw.) Glynn & S.G. Edwards are sister species that cause diseases on grasses and cereals at low temperatures. The DNA sequences of RPB2 (RNA polymerase II), β-tubulin, EF-1α (elongation factor), and ITS (rDNA internal transcribed spacer) from these groups were analysed to compare the extent of differences between these species, among isolates from Europe compared with those from North America, and among isolates of M. nivale originally collected from Agrostis spp. compared with isolates from wheat (Triticum aestivum). All of the regions studied except for ITS resolved M. nivale and M. majus isolates into separate clades. The RPB2 sequences also resolved both the North American and European M. majus isolates and M. nivale isolates from either turfgrasses or wheat into separate clades. These results support the recent elevation of M. nivale and M.majus to sister species and also provide some support for the assertion that there may be h.
Modeling Influence with Semantics in Social Networks: a Survey

The discovery of influential entities in all kinds of networks (e.g. social, digital, or computer) has always been an important field of study. In recent years, Online Social Networks (OSNs) have been established as a basic means of communication and often influencers and opinion makers promote politics, events, brands or products through viral content. In this work, we present a systematic review across i) online social influence metrics, properties, and applications and ii) the role of semantic in modeling OSNs information. We end up with the conclusion that both areas can jointly provide useful insights towards the qualitative assessment of viral user-generated content, as well as for modeling the dynamic properties of influential content and its flow dynamics.
Response of fruit fly, Bactrocera dorsalis complex on methyl eugenol derived from basil plant, Ocimum sanctum L.

Fruit fly is one of the major pests that attack horticultural commodities, as well as the insect becomes a major pest in mango plantation all over the world. The objective of this research was to study the response of fruit fly on methyl eugenol (ME) derived from basil plant used as attractant. The response test was conducted on 5 concentrations of ME (0.1 mL; 0.2 mL; 0.,3 mL; 0.4 mL; and control treatment/commercial eugenol = Petrogenol 0.2 mL) as laboratory test using Olfactometer, semi field trial using screencage (2m x 2m x 2 m), and field treatment. The semi field trial was conducted by placing a mango tree with ± 1 m of heigh and placing a sticky trap inside. Each of the screencage was infested by 50 male fruit flies. Those two experiments were arranged in Completely Randomized Design consisted of 5 treatments and 5 replications. The field experiment was conducted in mango plantation at Panyingkiran, Majalengka which was arranged in the Randomized Block Design with 5 treatments and 5 replications. The plastic bottle trap was used in the field test that was placed on the height of ± 1.5–2 m above soil surface. The result of laboratory test on Olfactometer showed that all of fruit fly gave response to the ME concentrations where the highest concentration the lowest of male insect were caught. On the concentration of 0.1 mL and 0.2 ml, the insect was more responsive compare to control treatment. In the semi field trial, the concentration of 0.2 mL showed the highest response with the highest number of insect trapped (30%). Field treatment indicated that the highest captured was on the concentration of 0.2 mL with the average of insect captured of 226 fruit flies. Titer Analysis of methyl eugenol from basil plant with Gas Kromatografi (GC) it's 82.29%, whereas level of methyl eugenol from commercial attractant as high as 94.09%.