Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Model of Calcium/Calmodulin- Dependent Protein Kinase II Activation

Calcium/calmodulin-dependent protein kinase II (CaMKII) is a key element in the calcium second messenger cascades that lead to long term potentiation (LTP) of synaptic strength. In this thesis, I have constructed kinetic models of activation of CaMKII and measured some of the unknown parameters of the model. I used the models to elucidate mechanisms of activation of CaMKII and to study the kinetics of its activation under conditions similar to those in dendritic spines. In chapter 2, I developed a new experimental method to rapidly stop the autophosphorylation reaction. I used this method to measure the catalytic turnover number of CaMKII. To quantitatively characterize CaMKII atophosphorylation in nonsaturating calcium, I also measured the autophosphorylation turnover number when CaMKII is activated by calmodulin mutants that can bind calcium ions only in either the amino or the carboxyl lobes. Previous models of CaMKII activation assumed that binding of calmodulins to individual CaMKII subunits is independent and that autophosphorylation occurs within a ring of 6 subunits. However, a recent structure of CaMKII suggests that pairs of subunits cooperate in binding calmodulin and raises the possibility that the autophosphorylation occurs within pairs of subunits. In chapter 3, I constructed a model in which CaMKII subunits cooperate in binding calmodulin. This model reconciled previous experimental results from the literature that appeared contradictory. In chapter 4, I constructed two models for CaMKII autophosphorylation, in which autophosphorylation can occur either in rings or pairs, and used them to design experiments aimed at differentiating between these possibilities. Previously published measurements and the measurements that I performed are more consistent with autophosphorylation occurring within pairs. In chapter 5, I constructed a model for simultaneous interactions among calcium, calmodulin, and CaMKII, and I used an automatic parameter search algorithm to fit the parameters for this model. I used it to characterize which of the parameters of calcium transients are critical for CaMKII activation. This modeling work is part of a continuing effort to realistically model the spatial and temporal aspects of calcium second messenger signaling in dendritic spines.
Cases of External Myiasis Caused by Diptera (Sarcophaga sp.) on Three Cyprinid Species

Sarcophaga sp. caused external myiases on three cyprinid species caught from Atatürk Dam Lake, Turkey) in July 2006. A total of 130 live dipteran larvae were collected from the body surfaces of Cyprinus carpio L. , 1758, Barbus grypus Heckel, 1843, and Capoeta trutta Heckel, 1843. There was 100% infestation of all three species of fish, with a mean intensity of 13.6 for C. carpio , 5.6 for B. grypus , and 4.3 for C. trutta . The myiases were probably accidental infections on stressed and immobilized fishes.
Suppression of Phytophthora Infection in Citrus Infected with Viroids

Citrus viroid-induced resistance to Phytophthora infection in citrus was measured by the number of Phytophthora sporangia in 'Rio Red' grapefruit (Citrus paradisi Macf.) bait tissue infected with citrus viroids compared with non-inoculated controls. Different viroid isolates containing mixtures of viroids (Citrus exocortis viroid (CEVd), Hop stunt viroid (HSVd), Citrus viroid III (CVd-III), Citrus viroid IV (CVd-IV)) were designated by plant numbers and sources. Source 13E was associated with the lowest number of sporangia in bark, leaves, and roots used as baits, whereas CEVd E9, a known severe CEVd isolate, significantly reduced the number of sporangia in leaves and bark. Sources 1A, 2E, 3E, 4D, and 6E showed a significantly reduced number of sporangia on bark, leaves, and roots compared with healthy plants and 44A; however, their effect was not as pronounced as that of E9 and 13E. Sources 12E and 44A did not suppress sporangia production. Previous reverse transcriptase-polymerase chain re- action analysis showed that all source plants had mixed infections with several viroids, whereas 12E and 44A contained no viroids. In addition to confirming the earlier reports on the suppression of Phytophthora infection in general, our study showed significantly reduced Phytophthora sporangia development resulting from a number of viroids in mixed infection, but there did not appear to be any effect related to viroid species. To determine if concentration affected resistance to Phytophthora, phenolic acids were extracted. Extraction of phenolic acids with 80% ethanol was more efficient compared with 100% methanol and an acetonitrile-water mixture. High-performance liquid chromatography revealed no notable detection of salicylic acid in healthy and viroid- infected plants, but there was a small peak corresponding to salicylic acid in Phytoph- thora-infected and both viroid and Phytophthora-infected plants. Flavone was detected in all the source plants with a slight increase in Phytophthora-infected and both viroid and Phytophthora-infected plants. A peak corresponding to quercetin dehydrate was detected in Phytophthora-infected plants. Efficient use of the right viroid isolate(s) can result in suppression of Phytophthora infection of citrus.
Morphology and allometry suggest multiple origins of rostral appendages in Sri Lankan agamid lizards

Rostral appendages occur in a very small number of species spread across the entire clade of iguanian lizards. The five species of Sri Lankan agamid lizards of the poorly known endemic genus Ceratophora show remarkable variation in the morphology and development of rostral appendages, which are absent in two species and present in the other three. Parsimony and Bayesian comparative methods do not robustly resolve whether the appendage evolved once (with two losses), twice (with one loss) or thrice independently. The appendage in C. tennentii is leaf-shaped, present in juveniles and monomorphic in adults. It is quite dissimilar to the appendages in C. aspera and C. stoddartii which are horn-shaped, absent in juveniles and dimorphic in adults. Ceratophora stoddartii is more closely related to C. erdeleni, which lacks the rostral appendage, than it is to C. aspera. The combined morphological, allometric and phylogenetic evidence suggests rostral appendages evolved three times within Ceratophora: perhaps once as a result of natural selection for crypsis (in C. tennentii) and twice as a result of sexual selection (in C. aspera and C. stoddartii). Our results suggest that these unusual ornaments can evolve by more than one mechanism and more readily than is suggested by their low frequency among iguanian lizards.
Diversity of Life through Time

Global diversity is the total number of taxa living in the present day or at any time in the geological past. Reconstructing the trajectory of global diversity by compiling data from the fossil record has been a major research agenda for palaeontologists for decades. The goal is to produce an accurate reconstruction of the pattern of global diversity that will ultimately allow us to understand the causes of diversity increases, decreases and transitions in the composition of the biota. The Paleobiology Database, a new large-scale database based on individual collections of fossil taxa, allows palaeontologists to standardise sampling, thereby controlling for vagaries of the fossil record. Collection-level data also allows researchers to identify any asynchrony of changes in diversity among regions of the globe, with the ultimate goal of identifying the habitats or environments that support biodiversity growth. Key Concepts: Biodiversity is the number of taxa alive in any interval of time. Given that not all taxa are readily preserved in the fossil record and not all taxa can be counted, trajectories of interpolated changes in biodiversity are more relevant than estimates of extrapolated diversity. Ancient biodiversity patterns are biased in multiple ways; extreme care must be taken to adjust for biases. Diversification can be positive and negative; mass depletions of biodiversity are caused by severe and rapid environmental changes, whereas major increases of diversity are more gradual being governed by recoveries from mass extinctions and evolutionary innovations. Evidence for limits of diversity is increasing in the fossil and molecular records. Different taxa dominated at different times. New taxa tend to originate in shallow tropical reef environments. Keywords: biodiversity; diversification; extinction; macroevolution; fossils
Improving Mathematics Learning and Teaching through Syllabus Change in a South African University Campus: ICT Leverage

Abstract This paper presents the investigated effect of curriculum change on student performance in first-year Mathematics (Math-1) modules at the Medunsa Campus of the University of Limpopo, South Africa. The change increased the syllabus scope intensely. However, when student examination marks in the old modules were compared with those of other students in the new modules, the latter showed improvements in average marks. However, larger variances were indicated, which is diverse performance. Exploration as to why higher performance was achieved showed that speed in lecturer facilitation and student practice by using technology was one reason. It was then left to improve uniformity in performance, which was thus recommended by the study.
Non‐starch polysaccharides of canola meal: Quantification, digestibility in poultry and potential benefit of dietary enzyme supplementation

The non-starch polysaccharide (NSP) content as determined by gas chromatography (component neutral sugars) and colorimetry (uronic acids) was shown to be 16–22% in ten different samples of defatted canola (low glucosinolate rapeseed) seed. The non-cellulosic components of NSP accounted for 13–16% of the meal and on average consisted of arabinose (33%), xylose (13%), galactose (13%), glucose (5%), mannose (3%), rhamnose (2%), fucose (2%) and uronic acids (30%). Yellow-seeded and brown-seeded samples of canola contained similar contents of total dietary fibre although the composition of the fibre components tended to differ with the former showing a low content of lignin and associated polyphenols and a high content of NSP as compared with the latter type. NDF values tended to be lower for yellow-seeded than for brown-seeded canola due to the relatively high content of NSP in neutral detergent solubles of yellow-seeded canola. An initial balance study with laying hens showed low (<3%) digestibility of the polysaccharide components, and further studies were conducted with a commercial enzyme preparation (SP249, Novo Laboratories Ltd, Lachine, Quebec) to enhance the in-vivo hydrolysis of the NSP fraction of the meal. Laying hens were fed a semipurified diet containing 40% commercial canola meal with and without enzyme (1%). NSP digestibility was increased to 37% by the enzyme supplementation.
The Effect of Commercial Additive (Toxic-Chec) and Propionic Acid on the Fermentation and Aerobic Stability of Silage with Pig Excreta

ABSTRACT The experiment was carried out to evaluate the effect of Toxic-chec commercial additive and propionic acid on the fermentation and aerobic Stability of silage made with pig excreta, corn stover, molasses and urea; during fermentation. The growth of microorganisms in the silage and aerobic stability of the silage were tested. Microsilos were conducted in the laboratory with the following treatments made in triplicate (T): T1 = silage without additive; T2 = silage + 0.05% commercial additive; T3 = silage + 0.05% propionic acid. Three microsilos were realized by treatment in a complete randomized design. The study was carried out in the laboratories of Rumen Microbiology and Animal Nutrition, Graduate College, Montecillo State Campus, Mexico, between June and November 2012. The results showed that the additives tested affected the pH in treatments, but did not affect the concentration of volatile fatty acids, acetic, propionic and Original Research Article
Effects of fenugreek seeds and its extracts on plasma lipid profile: a study on rabbits

In this study the effect of varying levels of fenugreek were examined on the plasma lipids of animals pretreated with either a control diet or a high‐fat diet for 9 weeks. Although the plasma cholesterol was significantly reduced in both groups, triglyceride levels were only reduced in animals pretreated with the high‐fat diet. HDL‐cholesterol levels were not significantly altered in and case. In addition, the effect of fenugreek seed powder and some of its extracts were investigated for the determination of the active fraction. Fenugreek seed powder and its extracts at 30% of the animals' diet were observed to greatly affect the plasma lipids when added to animals pretreated with a high‐fat. Fenugreek and its extracts reduced the levels of cholesterol, triglyceride and LDL‐cholesterol with no effect on the HDL‐cholesterol. This selective reduction in LDL‐cholesterol results in the improvement of the ratio of HDL‐cholesterol to LDL‐cholesterol which is beneficial in the prevention of atherosclerosis. In addition, the ratio of total cholesterol to HDL‐cholesterol was reduced. This hypolipidaemic effect of fenugreek was associated with the defatted fraction of the seed powder, and among the extracts analysed, the crude saponin extract was the most effective fraction with respect to the fenugreek seeds. The improvement of the plasma lipid profile by fenugreek treatment further supports the use of fenugreek seeds as a hypolipidaemic agent in the improvement of lipid disorders. Copyright © 1998 John Wiley & Sons, Ltd.
Increased photosynthetic performance in holly trees infested by scale insects

Summary 1Changes in plant physiological features after herbivory may alleviate the adverse effects of herbivores. We examined the ability of Ilex aquifolium L. (European Holly) plants to compensate for scale insect herbivory through increased photosynthesis. Based on assumptions of the source–sink hypothesis, we predicted that scale insects, by inducing supplementary sinks for photosynthates, would increase photosynthesis. 2Photosynthetic performance was evaluated by measuring chlorophyll fluorescence parameters in plants growing under natural light and temperature at the field station of the University of Santiago (north-west Spain). We measured photosynthesis on infested leaves of infested trees; scale-free leaves of infested trees; and scale-free leaves of scale-free trees. 3Insect infestation significantly increased photosynthetic efficiency. Effects of scale insects on photosynthesis were particularly enhanced by high temperature and light. Scale insects also altered the photosynthesis of leaves not directly affected by the insects. 4Our study showed that changes in the balance between source and sink tissues, induced by scale insects, may partly explain host plant photosynthesis. We suggest that increased feeding rates of scale insects promoted by high temperature and light conditions would increase the carbon demand of infested plants, resulting in greater compensatory photosynthesis.
Catálogo dos Erotylidae (Coleoptera) Neotropicais

The present catalog is an inventory of names proposed in Erotylidae (from family through subspecies) ocurring in the Neotropical Region, up to the present date (1988). It updates the nomenclature of included taxa, adds taxonomic units proposed after the Kuhnt's Genera Insectorum (Kuhnt, 1909) and includes abbreviated references to the literature, which are fully cited at the end of this catalogue. The systematic order follows Kuhnt, 1909, and afterwards, the position given to each taxa by the original author.
Estimating shrub biomass from basal stem diameters

For 25 northern Rocky Mountain shrub species, linear regressions are presented for total aboveground weight on basal stem diameter (average r2 of 0.91) and for leaf weight on basal stem diameter (average r2 of 0.74). The percentage of stem-wood weight in diameter classes of 0 to 0.5 cm, 0.5 to 2 cm, and 2 to 5 cm varies with basal stem diameter and species growth characteristics (as shown in figures). For these classes, diameters of stem wood averaged 0.21 cm, 0.76 cm, and 2.37 cm, respectively; however, some species differed significantly from these averages. Coefficients of variation ranged from 60 to 340 for shrub weight per unit area sampled in 12 stands. Some distributions were positively skewed. Implications for sampling are discussed.
Formation of Conjugated Δ8,Δ10-Double Bonds by Δ12-Oleic-acid Desaturase-related Enzymes

Divergent forms of the plant Δ12-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Δ11,Δ13-double bonds by modification of an existing Δ12-double bond in C18 fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Δ9-double bond to produce the conjugatedtrans-Δ8,trans-Δ10-double bonds found in calendic acid (18:3Δ8 trans ,10 trans ,12 cis ), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40–50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Δ9 cis ,12 cis ). These results are thus consistent with a route of calendic acid synthesis involving modification of the Δ9-double bond of linoleic acid. Regiospecificity for Δ9-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.
Estado actual del conocimiento sobre el yamú, Brycon amazonicus

Se presenta y se discute la informacion disponible sobre el yamu Brycon amazonicus, en aspectos de su historia natural, escala de maduracion gonadal, establecimiento y manejo de reproductores, reproduccion inducida, criopreservacion de gametos, larvicultura, alevinaje, nutricion, cultivo y otros topicos. El objetivo del autor es presentar esta revision como una ayuda para fortalecer la creacion de un paquete tecnologico que permita la explotacion sostenible de esta especie nativa con ventajas para la piscicultura de Colombia.
The Role of Nutrients in a Dietary Intervention in Improving Blood Cholesterol Profile and Lowering Cardiovascular Risk

Low-density lipoprotein cholesterol has been positively associated to an increase of cardiovascular risk by a large number of epidemiological studies. On the contrary, high-density lipoprotein cholesterol results inversely related to cardiovascular risk. In this contest plasma total cholesterol and low-density lipoprotein cholesterol concentration, and the total cholesterol - high-density lipoprotein cholesterol ratio seems to be able to predict cardiovascular risk. Diet and its composition affects various plasma cholesterol concentration and their ratios. Particularly, a reduction of saturated fat acids dietary intake is strictly related to both improve of blood lipid profile and reduction of cardiovascular events incidence. On the other hand, the evidences from epidemiologic and clinical studies are consistent in finding that the reduction of cardiovascular risk depends by nutrients used for replacing saturated fat acids. Specifically it has been demonstrated that replacement of saturated fat acids with unsaturated fat acids, either monounsaturated or polyunsaturated ones, is effective in improving cardiovascular risk. On the contrary, saturated fat acids replacement with high glycemic index refined carbohydrate actually increases cardiovascular risk. Despite that, many dietary guidelines do not give any tips about nutrients to use in replacement of saturated fat acids, underestimating the significance. In this perspective Mediterranean diet, represents an attractive dietary pattern for the improvement of blood lipid profile and the reduction of the cardiovascular risk.
SURFACE PLASMON RESONANCE – A PROMISING METHOD FOR ESTIMATING THE QUALITY OF MOTOR OIL

Shown in this paper is the possibility to diagnose quality of motor oil by using the method of surface plasmon resonance (SPR) Investigated in this work were four samples of the motor oil Genuine 5w-30 dexos 2, namely: the fresh one and three ones taken after car mileages 180, 430 and 712 km. When measuring the kinetics of refraction indexes for the studied samples of used oil, the authors observed a characteristic “shoulder” caused by sedimentation of oxidation and wear particles on the surface of SPR device sensitive element, while in the case of fresh oil there took place only the temperature drift of the refraction index. It has been experimentally shown that using the SPR method improves more than one order (from Δfmin = 0.17 vol.% down to Δfmin = 0.0107 vol.%) the detection limit and enhances sensitivity of measuring the wear particles concentration in motor oil as compared with the refractometric method. Thus, it is experimentally proved that the SPR method can be offered to control quality of motor oils as well as the degree of wear inherent to interacting parts of machinery.
What is Allium paniculatum? Establishing taxonomic and molecular phylogenetic relationships within A. sect. Codonoprasum

Allium paniculatum L. is commonly recorded from the Euro‐Mediterranean and Irano‐Turanian regions. Evidence from literature and herbarium collections revealed that many different taxa of A. sect. Codonoprasum Rchb. , all characterized by big size, diffuse and densely flowered umbrella, very long spathe valves, long pedicels, and cylindrical‐campanulate perigon, have been wrongly attributed to this species thus affecting records on its geographic distribution and morphological characterization. In order to define the true identity of A. paniculatum, we analyzed specimens coming from the type locality (Don River), and provided details on morphology, ecology, karyology, leaf anatomy, seed morphology and seed coat micro‐sculpturing. Taxonomic and phylogenetic relationships with related species of sect. Codonoprasum and with other taxa of different sections were investigated by means of morphological characters and molecular data from the internal transcribed spacers (ITS) nrDNA and the trnH‐psbA cpDNA region. Maximum parsimony and Bayesian inference analyses of molecular data recovered two main clades in A. sect. Codonoprasum and clearly separated A. paniculatum from related taxa. The taxonomic implications of these patterns of relationships are discussed. To our knowledge, this is the first study documenting in‐depth phylogenetic relationships within A. sect. Codonoprasum.
Electrochemical reactivation of granular activated carbon: pH dependence

The objectives of this paper were to verify and to quantify the dependence of granular activated carbon (GAC) electrochemical reactivation efficiency on the extreme pH values that occur at the electrodes. Phenol-loaded GAC was reactivated using a bench-scale electrochemical reactor. The pH values in the cathode and anode compartments during reactivation were 12 and 2, respectively. The pH of the electrolyte controlled the reactivation efficiency, and cathodic reactivation efficiencies were about 30% higher at pH 12 than at pH 2. Cathodic reactivation was about 20% more efficient than the anodic reactivation. The cathode, the reducing electrode, generates OH– ions, which increase the local pH at the cathode. Reduced phenol adsorbability at high pH promotes desorption from previously loaded GAC, thus increasing the reactivation efficiency. Greater phenol desorption was observed at pH 12 when the GAC was subjected to a 50-mA current than in the absence of a current. Thus, electrochemical reactivation is more.