Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering plant–pathogen interactions applying metabolomics: principles and applications

Abstract The in-depth study of plant metabolic networks and their changes in response to biotic stimuli is an emerging field of metabolomics which has a great potential to provide new insights into plant physiology, plant–pathogen interactions, crop protection and breeding. In spite of the development of metabolomics in numerous applications, its application to the study of plant–pathogen interactions is still in its infancy. Here we describe an integrated methodology for the study of plant–pathogen interactions, ranging from experimental design and execution, to analyses of samples and data, and their biological interpretation. As a study case, the investigation of interactions in the pathosystem potato (Solanum tuberosum L.) and Rhizoctonia solani using metabolomics is presented. Chemical analyses were performed by integrating Fourier transform-ion cyclotron resonance/mass spectrometry (FT-ICR/MS) with gas chromatography/mass spectrometry (GC/MS). The use of two analytical platforms enabled the study of alterations in the content of infected plants for a large number of metabolites belonging to chemical groups with diverse physicochemical properties, such as amino acids, fatty acids, and carboxylic acids, as well as carbohydrates, and terpenoid and steroidal glycoalkaloids. The biological interpretation of data was performed using the powerful software Cytoscape whose role in metabolomics will be highlighted, and BioCyc databases. The principle behind such an approach is to reveal changes in the global metabolic network of the plant in response to pathogen invasion and subsequently to correlate those changes to gene expression.
Survey of flooding attack mobile Adhoc network

Mobile ad hoc networks will appear in environments where the nodes of the networks are absent and have little or no physical protection against tampering. The wireless nodes of MANET are thus susceptible to compromise and are particularly vulnerable to denial of service (DoS) attacks launched by malicious nodes or intruders. Flooding attack is one such type of DoS attack, in which a compromised node floods the entire network by sending a large number of fake RREQs to nonexistent nodes in the network, thus resulting in network congestion. In this paper, the security of MANET AODV routing protocol is investigated by identifying the impact of flooding attack on it. A simulation study of the effects of flooding attack on the performance of the AODV routing protocol is presented using random waypoint mobility model The simulation environment is implemented by using the NS-2 network simulator. It is observed that due to the presence of such malicious nodes, average percentage of packet loss in the network, average routing overhead and average bandwidth requirement− all increases, thus degrading the performance of MANET significantly.
Inoptimality losses in forest management decisions caused by errors in an inventory based on airborne laser scanning and aerial photographs

Errors in inventory data may lead to inoptimal decisions that ultimately result in financial losses for forest owners. We estimated the expected monetary losses resulting from data errors that are similar to errors in laser-based forest inventory. The mean loss was estimated for 67 stands by simulating 100 realizations of inventory data for each stand with errors that mimic those in airborne laser scanning (ALS) based inventory. These realizations were used as input data in stand management optimization, which maximized the present value of all future net incomes (NPV). The inoptimality loss was calculated as the difference between the NPV of the optimal solution and the true NPV of the solution obtained with erroneous input data. The results showed that the mean loss exceeded €300·ha–1 (US$425·ha–1) in 84% of the stands. On average, the losses increased with decreasing stand age and mean diameter. Furthermore, increasing errors in the basal area weighted mean diameter and basal area of spruce were found .
Sequence Polymorphism and Expression Analysis of Genes Encoding Gibberellin 20-oxidase from Dasypyrus villosum

Based on the known GA20-oxidase (GA20ox) cDNAs of barley and wheat, oligonucleotide primers were designed to isolate GA20ox genes from genomic DNA of Dasypyrum villosum. A total of 19 clones were obtained. Each of them contained an open reading frame encoding a putative 40-KDa protein of 359 amino acid residues. Twenty-one SNPs and 4 InDels were found and could divide the 19 sequences into 2 classes, designated as DvGA20ox-1 and DvGA20ox-2, respectively. Q-PCR analyses showed that both DvGA20ox-1 and DvGA20ox-2 were in leaf blade, leaf sheath, stem, eustipes, root and developing spike. Similar expression levels were found between DvGA20ox-1 and DvGA20ox-2 in three stages. The total expression levels of DvGA20ox-1 and DvGA20ox-2 presented downtrend in leaf blade and ascend in stem, eustipes and developing spike along with the development of plants, respectively. However, they were firstly increased and then decreased in root from seeding stage to heading stage. These results revealed that the gene expression profile of DvGA20ox-1 and DvGA20ox-2 closely related to the growth and development of D. villosum.
Critical importance of large native trees for conservation of a rare Neotropical epiphyte

The distribution of rare plants may be limited by environmental or density‐dependent factors that reduce population growth and persistence. The relative importance of environmental limitations vs. the degree to which conspecifics influence recruitment may determine optimal management strategies for plants of conservation concern. We sowed seeds of a rare epiphytic orchid in trees from agricultural Costa Rican landscapes to ask how recruitment is influenced by established conspecific plants and the environment. We hypothesized that recruitment is positively influenced by conspecific plants. Conspecific adults were expected to be associated with favourable microhabitats and mycorrhizal fungi for germinating seeds, without creating unfavourably competitive conditions. Alternatively, we hypothesized that recruitment varies due to environmental differences among study sites or host trees, irrespective of adult proximity. We experimentally added 240 packets of seeds from 2 source populations into four naturally established populations. Germination was evaluated after five months. We used mixed models and conditional inference trees to evaluate results. Proximity to conspecific adults neither increased nor decreased germination. Instead, large native trees and microsites with more closed canopies supported significantly greater germination than smaller cultivated trees and microsites with more open canopies. Synthesis. Landscape changes that replace large native trees with a more homogenous array of cultivated species may not only reduce rare epiphyte populations directly, but also limit their ability to colonize disturbed secondary habitats. Because the habitat is the prime determinant of recruitment, large and often isolated native trees that act as refuges for rare epiphytes in disturbed landscapes should be a top priority for local conservation efforts.
The Antioxidant Status in Rheumatoid Arthritis

In the present work, we studied the antioxidant status in the blood of a group (n=29) of rheumatoid arthritis (RA) patients and compared it with that of a control group (n=30). There was a significant increase (p<0.001) in the plasma lipid peroxide level, but no change in the plasma ascorbic acid level, when the RA group was compared with the control group. There was a significant decrease in reduced glutathione (GSH, p<0.01) and in glutathione peroxidase (GPX, p<0.05) and superoxide dismutase (SOD, p<0.001) activities in the hemolysate of RA patients when compared with the control group values. A good correlation was obtained between the parameters estimated in the hemolysate. This study reflects the oxidative stress as a result of altered antioxidant status in the blood of RA patients, which findings may have implications in the pathogenesis of the disease.
Molecular Phylogenetics of Bromeliaceae: Evidence from trnL(UAA) Intron Sequences of the Chloroplast Genome

: Phylogenetic relationships within Bromeliaceae were assessed by comparative sequencing of chloroplast trnL(UAA) intronic DNA. Sixty-seven taxa were analyzed, encompassing 62 species, two subspecies and two varieties from 32 bromeliad genera. One representative of Rapateaceae and two of Velloziaceae were used as outgroups. Introns were amplified by the polymerase chain reaction and conserved flanking primers. Amplification products were sequenced directly. Of 700 base pairs total trnL (UAA) intron size, 551 bp could be unambiguously aligned. Sequence divergence among ingroup taxa ranged from zero to 4.6 %. Phylogenetic reconstruction by parsimony analysis of 73 informative base substitutions yielded 1092 most parsimonious trees. The topology of the resulting strict consensus tree was only partially consistent with current classification schemes. Brocchinia and Ayensua grouped close together and formed a well-supported basal clade, suggesting a sister group relationship of both to the remainder of the family. The remaining ingroup species were divided into an unresolved polytomy of three lineages, comprising (1) all members of subfamily Tillandsioideae, (2) the three investigated Hechtia species, and (3) all Bromelioideae and the remaining Pitcairnioideae (except Brocchinia, Ayensua and Hechtia). The latter clade was split into another polytomy of five sublineages, one of which comprised all Bromelioideae. Whereas monophyly of Tillandsioideae and Bromelioideae was supported by trnL intron data, Pitcairnioideae as traditionally circumscribed are clearly polyphyletic. There is evidence that the genera Tillandsia, Vriesea, Guzmania, Abromeitiella, Deuterocohnia, Dyckia, Pitcairnia and Aechmea in the present circumscription are not monophyletic.
A REVIEW PAPER ON WIRELESS SENSOR NETWORK AND GPRS MODULE FOR AUTOMATED IRRIGATION

In India 60 -70% economy depends on the farming. Irrigation system in India has given a high priority in money making. Many new technology are being urbanized to permit agricultural automation to increase and carry its complete potential . To get whole benefit of these technologies, we would not just think the suggestion of developing a new single technology but should appear at the wider issues for entire development of a system. In our country, crop growing are depends on the climatic condition which is not sufficient source of water. Use of excessive amount of water use there is damage of soil. In Irrigation system, depending upon the soil strategy, water is provided to plant . An automated irrigation system was developed to optimize water use for agricultural crops. The system has a wireless distributed sensor network of soil-moisture, humidity and temperature sensors placed in the root of the plants. In previous, automatic irrigation system based on ARMs and RF module are used. The system were powered by photovoltaic panels and have at a time transmit and receive communication link base on a cellularInternet boundary that allowed for data examination. The aim of our paper is to modernizing agriculture technology by programming components and built the necessary component for the system.
THE SALIVARY GLAND CHROMOSOMES OF TWO SIBLING SPECIES OF BLACK FLIES INCLUDED IN EUSIMULIUM AUREUM FRIES

Two closely related dichromosomic sibling species of Eusimulium "aureum" were segregated cytologically in populations sampled from the Toronto area. The known range of these two so far included southern Ontario and Quebec, and New York State. Both siblings have extremely similar salivary gland chromosomes but they differ by four homozygously rearranged regions, all in the first chromosome, and in the degree of chromosomal polymorphism. Although sympatric over a wide range, the two siblings do not interbreed as evidenced by the failure to find critical heterozygous loops for the interspecific inversions, and the absence of common intraspecific inversions. Therefore the siblings represent two biologically distinct species.
Avian collisions at two wind farms in Tasmania, Australia: taxonomic and ecological characteristics of colliders versus non-colliders

Abstract Data obtained during carcass and bird utilisation surveys conducted over an approximately 10-year period at two wind farms in northwest Tasmania (Bluff Point Wind Farm [BPWF] and Studland Bay Wind Farm [SBWF]) were compared. Of the species present onsite only 21% at the BPWF and 18% at the SBWF were found to collide with turbines, indicating that presence onsite was a poor indicator of collision risk. Furthermore, there was a poor relationship between abundance onsite and collisions with turbines. A classification and regression tree classified species into the groups that collided or did not collide, based on two classifiers. Specific families/superfamilies and foraging strategies/zones were associated with collision risk and indicated that particular morphological, ecological and behavioural factors were associated with a species' vulnerability to colliding with wind turbines. Future studies should investigate whether the patterns found at these sites are consistent across other habitats and sites.
Impact of drilling date on Apera spica‐venti L. and Alopecurus myosuroides Huds, in winter cereals

Summary The impact of drilling date on Apera spica-venti and Alopecurus myosuroides in winter cereals was investigated in field trials in 1991 and 1992. Two drilling dates were considered with an inter val of 14 to 16 days between dates. Generally, drilling date had an inconsistent effect on weed plant populations in spring, but seedling emerg ence of both species appeared to be delayed at the later drilling compared with the earlier date. This delay may partly explain the reduced com petitive ability of A. myosuroides in wheat in 1991 and 1992 and of A. spica-venti in wheat in 1991 at the later drilling date. The seed popula tion per plant of both species was lower at the later date in some instances, whereas in others drilling date had no effect. Reduced seed produc tion was mainly caused by a reduction of the number of inflorescences per plant. The poten tial of utilizing drilling dates as a cultural control measure against grass weeds is discussed.
Morphological Divergence of Continental and Island Populations of Canada Lynx

Abstract Lynx canadensis (Canada Lynx) mostly occurs in the continental area of North America. Two populations in Atlantic Canada on Newfoundland and Cape Breton Island are geographically isolated. Past studies have revealed geographical and environmental barriers that have significantly impacted processes that ultimately influence the ecology, genetics, evolution, and conservation of the species' populations. However, equivocal results were obtained as to the morphological and genetic characteristics of the species, and very little is known in this regard on the island populations. The aim of this study was to investigate skull morphometric variation between the species' populations. We examined and measured 18 craniodental characters on 171 specimens spanning the species' Canadian range, including most of its boreal forest range and the 2 island populations. Univariate and multivariate analyses provided evidence for significant morphological differentiation among the species' populations. Factors pertaining to geographical isolation of populations accounted for the bulk of the craniometric variation for both males and females. Principal component analysis (PCA) identified 3 geographical groups: mainland Canada, Newfoundland, and Cape Breton Island. Consistent with the “island rule”, analysis of variance with the Sheffé significant difference post hoc test and PCA results indicated that continental individuals were significantly larger than those from Cape Breton Island, whereas those from Newfoundland, which is significantly larger than Cape Breton Island, exhibited intermediate size. Shape-related variations in the frontal bone among the 3 geographical groups were detected. Six out of the 18 craniodental characters, i.e., postorbital constriction, mastoid, mandible, upper tooth row, mandibular molar row, and upper canine to canine segment, can be used in discriminant function analysis to distinguish between these 3 groups and correctly classify more than 90% of the individuals from the insular populations. We showed for the first time differentiation between Canada Lynx populations on Cape Breton Island and those in the rest of Canada. Individuals from Cape Breton Island appeared the smallest. Contrary to expectations, the Rocky Mountains did not prove to be a significant geographical barrier, resulting in no morphological differentiation of the British Columbia populations. The morphological variations we reported in this study should benefit conservation and management programs in Atlantic Canada, where the levels of the Canada Lynx population are critically low. Conservation plans that strive to maintain the genetic variation documented in the present study should help ensure the preservation of sufficient variability for adaptation to changing environmental conditions required for the long-term viability of populations of Canada Lynx.
Higher-order integration schemes for jump-diﬀusion models of biomolecular reaction networks

The work of this master thesis revolves around jump-diﬀusion approximations of pure Markovian jump processes used to model biomolecular interaction networks if molecule counts are low. Recently error bounds for such an approximations were derived and based on them an adaptive simulation algorithm was developed that dynamically partitions reactions into fast and slow ones and applies the diﬀusion approximation to the fast ones as the stochastic simulation unfolds [1]. In order to obtain noticeable speed-up between the simulation of the pure jump process and of that hybrid model, eﬃcient higher-order integrators need to be employed for the diﬀusion part. A potential candidate solver is S-ROCK2, a second weak order explicit integrator [2]. Goal of the master thesis project is to obtain a fast and robust integrator for jump-diﬀusion models with adaptive reaction partitioning. It involves reimplementing S-ROCK2 in Matlab and later on scaling it up using C++ on parallel architecture using openMP, or equivalent. The incorporation into the jump-diﬀusion simulation requires a clever re-initialization procedure of the integrator after a re-partitioning event. The algorithm will be benchmarked on large kinetic models from the systems and synthetic biology domain. Good programming skills are required and a certain willingness to absorb the underlying mathematics will be necessary.
The Gauss2++ Model – A Consistent Risk Neutral and Real World Calibration

Especially in the insurance industry interest rate models play a crucial role e.g. to calculate the insurance company’s liabilities, performance scenarios or risk measures. A prominant candidate is the 2-Additive-Factor Gaussian Model (Gauss2++ model) – in a different representation also known as the 2-Factor Hull-White model. In each application a distinction must be made whether the model is regarded under the risk neutral or the real world measure. In this paper, we propose a framework to estimate the model such that it can be applied under both measures in a consistent manner. For this the change of measure needs to be specified. We first show that any progressive and square-integrable function can be used to specify the change of measure without loosing the analytic tractability of e.g. zero-coupon bond prices. We then propose and analyse three candidates, which are easy to calibrate: a constant, a step and a linear function. The constant function can lead to extreme interest rates in the long forecasting horizon and the result depends highly on the chosen valuation date. Following the economic view that current market fluctuations should not influence long term predictions much, the latter two candidates distinguish between a short and a long term risk premium to regularize the interest rates in the long horizon. We apply all variants to historic data and show that the variants of the framework with the latter two functions indeed produce realistic and much more stable long term interest rate forecasts than the constant case. This stability over time would translate to performance scenarios of e.g. interest rate sensitive fonds and risk measures.
Characterisation of pumpkin yellow vein mosaic virus from India

Yellow vein mosaic disease symptoms occur frequently in pumpkin in India. Diseased plants show vein yellowing, which sometimes coalesces to form chlorotic patches. Infected plants are stunted and flowers drop prematurely, greatly reducing yields. Diseased plants are infected by a begomovirus, designated pumpkin yellow vein mosaic virus (PYVMV), which is transmitted readily and in a persistent manner by the whitefly, Bemisia tabaci. Transmission of PYVMV requires minimum acquisition and inoculation access periods of 30 min and 10 min, respectively. The minimum latent period in the insect is 6 h and the virus persists in the vector for at least 8 days. PYVMV has a narrow host range consisting of a small number of cucurbit species and some tobacco cultivars. It was detected serologically in diseased plants and in viruliferous B. tabaci using polyclonal antibodies in a double-antibody sandwich enzyme-linked immunosorbent assay. Reactions with monoclonal antibodies in a triple-antibody sandwich ELISA showed that PYVMV has an epitope profile distinct from those of other begomoviruses from the Indian sub-continent. Polymerase chain reaction amplified fragments from the putative viral coat and movement protein genes. Based on comparative phylogeny of complete coat protein gene sequences, PYVMV was most similar to to the bipartite Tomato leaf curl New Delhi virus from India and appears to be a new strain of this virus.