Miracle-dz/UniFAR-FTUs huggingface dataset:
Experiments on the bacterial nucleoid of Escherichia coli viewed as a physical entity

In this thesis we focus on the compaction of DNA within Escherichia coli and aim to gain some understanding of the physical mechanism behind its spatial organization in the cell. Chapter I is a brief review of the current knowledge of nucleoid structure. We discuss a model for DNA compaction in the living Escherichia coli cell, for which this thesis has provided evidence. In this model the formation of the nucleoid is presented as the phase separation of supercoiled DNA in a suspension of proteins. Chapter II is a brief introduction to excluded-volume interactions and ends with an exposition of recent theoretical calculations that explain how the phase separation between DNA and proteins within E. coli may occur. In chapter III, a comparison between E. coli nucleoids isolated by the detergent and osmotic shock methods is presented. In chapter IV the presence of polyethylene glycol (PEG) was used to study the effect of polymeric depletion interactions on the dimensions of nucleoids isolated by osmotic shock. We derive the free energy of isolated nucleoids when compacted into the intracellular dimensions. A discussion of these results with reference to the phase separation theory developed by Odijk (1998) is given and we conclude that depletion can be the force behind the formation of the bacterial nucleoid. Based on dynamic light scattering (DLS) experiments we show that within isolated nucleoids the supercoil segments exhibit a fast dynamics. In chapter V the process of expansion of nucleoids released by osmotic shock is studied. In our experiments, nucleoids initially expanded quite fast, followed by a long intermediate period. The average exponent characterizing the dynamics of the intermediate phase is indicative of a process driven by excluded-volume. Nevertheless, there are substantial variations between the individual measurements, which are not fully understood. In Chapter VI we directly monitor the movement of DNA segments within isolated nucleoids. We conclude that the isolated nucleoid has a gel-like structure where supercoil segments show confined Brownian motion. The observed diffusion constant substantiates the DLS experiments preformed in Chapter IV.
A New Vehicle Arrival Prediction Model for Adaptive Signal Control in a Connected Vehicle Environment

With the development of connected vehicles (CVs) technology, it has become a new research topic to capture the dynamic traffic system by using CVs data. The traditional vehicle arrival prediction models are limited to the fixed detectors, which can only recognize the passing information of vehicles, but cannot identify the state of vehicles. This paper proposed a new vehicle arrival prediction model of traffic signal control in a connected vehicle environment. First, the vehicle’s identification number (ID), position, velocity, and acceleration were obtained in a CV environment. Second, a new vehicle arrival prediction model was developed by the joint probability distribution calibrated based on CV data. Then, the simulation experiment was designed for analyzing influence factors on model performance. The results show that the average relative error of each factor is less than 10%. Finally, the reliability of the proposed model was verified based on an adaptive signal control algorithm. Therefore, the proposed model can be used in the adaptive signal control system.
Do the multiple defense chemicals of visually distinct species enhance predator learning

Mullerian mimicry, where 2 unpalatable species share a warning pattern, is classically believed to be a form of mutualism, where the species involved share the cost of predator education. Birds learn to avoid a color signal faster when individual prey possesses 1 of 2 bitter-tasting chemicals rather than all having the same chemical, suggesting that Mullerian mimics that possess different defense chemicals are better protected than those that possess the same defense chemical. Using domestic chicks as predators and flavored, colored crumbs for prey, we investigated whether birds learn to avoid 2 visually distinct crumb types faster when each crumb type possesses a different defense chemical than when both crumb types share the same defense chemical. We found that birds learned to avoid 2 visually distinct color signals at a similar rate, irrespective of whether each color signal represented a different defense chemical or whether both color signals represented the same defense chemical. This experiment, therefore, indicates that in terms of predator avoidance learning, possessing 2 defense chemicals is more advantageous when prey look the same than when they look different. This suggests that Mullerian mimics with different defense chemicals not only are better protected than Mullerian mimics that share a single chemical but also benefit more from their mimetic resemblance. Copyright 2006.
Studies on floral phenology, fruit and seed maturation and harvest index based on fruit colour in Pongamia pinnata (L.) Pierre

Pongamia pinnata is a leguminous tree having enormous potential of producing high seed oil that could be as a source of biofuel. The collection of pods with higher seed quality characters is much important for production of elite seedlings at nursery and hence studies related to seed maturation were initiated as matured seed is the basic character of quality seed. To evaluate the steps in obtaining quality seed from the tree, studies were initiated on floral phenology, fruit and seed maturation and on evaluation of fresh fruit colour variation on seed and seedling quality characters. The results revealed that in pungam, the flowers per inflorescence ranged from 28.4 to 44.0, and only 3-4 per cent of the flowers set as pods. But the seed set was obtained with 80 per cent of the pods. The studies on pod maturation revealed that seeds of pods attained physiological maturation at 26 weeks after anthesis and it was accompanied with the change in colour of pods from green to dark brown and the seed from greenish white to dark brown, where the seeds had potential for higher germination (98 per cent). Evaluation on harvest index based on fresh fruits colour (yellow, light brown and dark brown) revealed that the seeds of light brown fruits recorded the higher germination (96 per cent), and seedling quality characters suggesting the collection of light brown fruits for obtaining good quality seed for sowing. The colour of pods also coincided with the colour obtained with maturation of pod studied with tagged flowers. Keywords: Pongamia pinnata, floral phenology, pod maturation, fruit colours, seed and seedling quality characters.
Simulation of Pentacene/Alq3 Bilayer OLET to Analyze the Effect of Alq3 Layer Thickness and Asymmetric Contacts on Device Performance

This study presents, device simulation of top contact bottom gate Pentacene/tris-(8-hydroxyquinolinato) aluminum (Alq3) bilayer Organic Light Emitting Transistor (OLET) on ATLAS 2-D device simulator. The electrical response of the device is successfully simulated and the effect of different thickness of Alq3 layer on device performance is also studied. During the simulation symmetrical source and drain contacts were considered. The device shows unipolar operation in p-type accumulation mode. However, no signs of light emission observed with symmetrical contacts. It has been demonstrated that the electrical behavior of the simulated device agree well with the experimental results. It is witnessed that the device current drops with increase in Alq3 thickness from 10nm to 20nm, thus degrading device field-effect performance. The dependence of emission on type of contacts and thickness of Alq3 layer has also been studied. It is found that the Langevin Recombination rate used for observing light emission, increases with increase in Alq3 thickness in a Pentacene/Alq3 bilayer OLET with asymmetric contacts, implying that optimisation of Alq3 thickness for light emission is essential.
Climate influence on Dinophysis spp. spatial and temporal distributions in Greek coastal water

Presence of Dinophysis spp. , the main phytoplankton genus responsible for the occurrence of lipophilic biotoxins of the okadaic acid group (Diarrhetic Shellfish Poisoning; DSP) in Greek mussels, was recorded in the pe- riod 2003-2008 in five major mussel culture areas of Greece. Dinophysis spp. abundances were simultaneously stud- ied with climatological parameters (air temperature, rainfall, wind direction and velocity) and the occurrence of DSP toxic episodes in mussels. Dinophysis spp. blooms occurred with a seasonal periodicity. Highest cell abundances of the bloom appeared steadily between late winter and spring, whereas occurrence of DSP toxicity in mussels followed a similar time pattern, with mouse bioassay-positive samples ranging between 10.2-28.1% of the total samples anal- ysed. Maximum mean Dinophysis spp. counts coincided with air temperatures in the range of 10-20°C; abundances higher than 1,000 cells L -1 were more frequently recorded at air temperatures in the range of 4-20°C in combination with low rainfall and low velocity winds (<Beaufort scale 4), blowing from the north (NW, N and NE) and south (SE and S). To our knowledge, this is the first report to correlate the occurrences and abundances of potentially toxic Dinophysis spp. and climatological data for the majority of the shellfish production areas studied. Such observations may contribute to the clarification of the occurrence patterns of DSP toxic episodes, hence bettering the economical management of mussel production.
Antibodies Reacting with Lipopolysaccharides from Bacteroides melaninogenicus, Bacteroides fragilis, and Fusobacterium nucleatum in Serum from Normal Human Subjects

Sera from 54 blood donors and 56 healthy children were examined for antibodies reacting with sheep erythrocytes sensitized with purified lipopolysaccharide from Bacteroides fragilis, Bacteroides melaninogenicus, and Fusobacterium nucleatum. Antibodies were detected in sera from most subjects within all age groups; the titers ranged from 10 to 320. The antibodies were sensitive to reductive cleavage by 2-mercaptoethanol and were specific for lipopolysaccharide from each of the three bacterial species. Antibodies were not found in samples of 10 umbilical cord sera.
The effects of anthropogenic food on the spatial behaviour of small Indian mongooses (Herpestes javanicus) in a subtropical rainforest

The aim of this study was to determine the extent to which mongooses Herpestes javanicus in the Caribbean National Forest use areas of high human use, and to compare space use patterns in these areas to those in areas of low human use. It was expected that the abundance of anthropogenic food in areas of high human use would lead to (1) higher population densities; (2) smaller home ranges; (3) more extensive range overlap and reduced territorial behaviour, than areas of low use. During the dry season, 14 mongooses were radio-collared and tracked in each of two areas: an area of high human use and an area of low human use. Six of these mongooses, one in an area of low human use and five in an area of high human use, were also tracked during the wet season. In both seasons, mongooses in the area of high human use used picnic areas more than expected based on availability. In the dry season, mongooses in the area of high human use had smaller home ranges than those in the area of low human use. Ranges overlapped extensively in both areas, and slightly more so in the area of low human use. However, individuals avoided each other spatially within the shared area of their ranges, and core home ranges overlapped little. In the wet (breeding) season, home-range size and overlap increased more for males than for females. Such differences in behaviour and population dynamics in these two areas have implications for rabies transmission rates and management throughout the forest.
A Novel Fault-Tolerant Control Method for Robot Manipulators Based on Non-Singular Fast Terminal Sliding Mode Control and Disturbance Observer

In this study, a novel Fault-Tolerant Control Methodology (FTCM) is developed for robot manipulators. First, to overcome singularity glitch and to enhance convergence time of conventional Terminal Sliding Mode Control (TSMC), a new Fast Terminal Sliding Mode Surface (FTSMS) is constructed. Next, to reduce the computation complexity and to provide requirements about undefined nonlinear functions for the control system, a Disturbance Observer (DO) to estimate uncertain dynamics, external disturbances, or faults. Besides, a Super-Twisting Reaching Control Law (STRCL) is designed to compensate for the estimated error of disturbance observer with chattering rejection. Final, a novel, robust, FTCM was developed for robot manipulators to obtain the stability goal of the system, to reach the prescribed performance, and to overcome the effects of disturbances, nonlinearities, or faults. Accordingly, the proposed FTCM has remarkable features, such as fast convergence speeds, robust precision, high tracking performance, significant alleviation of chattering behavior, and finite-time convergence. The position tracking computer simulations were implemented to exhibit the effectiveness and feasibility of the suggested FTCM compared with other control algorithms.
Long-term phytoplankton studies in the Bahía Blanca estuary, Argentina

Phytoplankton composition and abundance in the Bahia Blanca estuary, Argentina, have been studied from 1978 to 1993; also water temperature, salinity, transparency, and nutrient concentrations. The pattern of seasonal distribution showed a winter/early spring bloom of diatoms, dominated by Thalassiosira spp. , as the most important event in the annual cycle. Annual means of temperature and salinity showed relatively minor variations. Nutrient concentrations (nitrate, silicate, and phosphate) exhibited a positive trend with time. Chlorophyll a showed marked seasonal variations, with maximum values (up to 42 μg l −1 ) during the winter-early spring diatom bloom. The relationship between phytoplankton and environmental factors was investigated using multiple regression analysis. Chl a concentrations and total phytoplankton cell abundance were significantly negatively correlated with temperature, suggesting that temperature was the major source of temporal variability in phytoplankton in the area. Among the nutrients, the highest coefficient was for phosphate concentrations, indicating that this nutrient was more affected by phytoplankton uptake than were silicate and nitrate concentrations.
Induced Resistance – Orchestrating Defence Mechanisms through Crosstalk and Priming

In nature, plants interact with a wide range of microbial pathogens and herbivorous insects. During the evolutionary arms race between plants and their attackers, primary and secondary immune responses evolved to recognise common or highly specialised features of the attacker encountered, resulting in sophisticated mechanisms of induced defence. Induced resistance mechanisms are characterised by a broad-spectrum effectiveness and often act systemically in plant parts distant from the site of primary attack, thereby protecting the plant against subsequent invaders. Plant hormones are key players in the regulation of the defence signalling pathways involved. Because induced defence responses en- tail ecological fitness costs, plants must possess elaborate regulatory mechanisms that efficiently coordinate the activation of attacker-specific defences so that fitness costs are minimised while optimal resistance is attained. A major focus in plant defence signalling research is to uncover key mechanisms by which plants tailor their responses to different attackers, and to investigate how plants cope with si- multaneous interactions with multiple aggressors. Pathway crosstalk and priming for enhanced defence emerged as important regulatory mechanisms that enhance the efficiency of the plant's inducible defence arsenal. Here, we review the cur- rent knowledge on the signalling cascades involved in different types of induced pathogen and insect resistance, and the regulatory mechanisms by which plants are able to orchestrate their inducible defences in a cost-effective manner.
Constancy of bacterial abundance in surficial marine sediments

Controls on bacterial abundance in marine sediments remain poorly understood despite the importance to biogeochemical processes, benthic ecology, and in situ bioremediation. We report an analysis of direct microscopic counts of widely distributed surficial marine sediments, using a new approach of scaling abundance to the fluid volume of pore water within the sediments (bacteria FV−1). The analysis identified a greater constancy in benthic bacterial abundance than has been appreciated previously. Whether tested as a combined dataset or separately according to geographic region, less variance was observed when abundance was scaled to fluid volume rather than the traditional dimension of dry sediment mass. The decrease in variance suggests that the primary controls on abundance, such as nutrient acquisition or predator encounter rate, may also scale with porewater fluid volume. With values centered around 109 bacteria ml−1 FV, regulation must differ fundamentally from the water column, where values average 105–106 bacteria ml−1 FV.
Analyzing the Fullband E-Model and Extending it for Predicting Bursty Packet Loss

The E-model is the only recommended parametric tool for planning the quality of speech communication services, and its fullband version has recently been standardized by the International Telecommunication Union, ITU-T. In this paper, we analyze and extend the model by comparing its predictions for random and bursty packet loss as well as for delay to the results of a signal-based model, POLQA, as well as to the result of a subjective conversation test. The analysis shows that, by extending the fullband model to account for the burstiness, a reasonable prediction accuracy can be reached for random as well as bursty loss. The results are discussed and limitations of the current model are pointed out.
Effects of Supplementation Probiotic and Dried Yogurt Powder on Growth Performance, Carcass Characteristics, Intestinal Micro Flora and Immunity of Broiler Chickens

The aim of this work was to investigate the efficacy of local Probiotic and dried Yogurt powder on productive performance, Carcass Characteristics and intestinal micro flora of Broiler chickens (Cobb-500). A total of two hundred twenty five (225) one-day old broiler chicks were randomly divided to three experimental groups (75) chick/treatment, which divided to (3) replicates ( 25 Chicks / replicate ). The dietary treatments were: (T1) basal diet as control; (T2) basal diet plus (1 kg ) of the Iraqi probiotic containing of ( Lactobacillus acidophilus 10 8 , Bacillus subtilus 10 9 , Bifidobacterium 10 8 and Saccharomyces cerevesiae 10 9 / gm) to (100 kg) diet . (T3) basal diet plus (1 kg) dry Yogurt powder to (100 kg) diet The experiment was lasted for (42 days. Live body weight (BW), Weight Gain (WG), Feed Intake (FI), and Feed Conversion Ratio (FCR), were measured on 21, 35 and 42 days of age. At the end of experiment (dressing %, breast% and giblets% immune organ) and mortality rate were measured. The groups fed the probiotic and dried yogurt powder showed significantly (p<0.05) higher value for body weight (BW) as compared with the control treatments at the period of (21-35). No significant difference was observed in feed conversion ratio among treatments in any of the evaluated age intervals. Feed intake differences were detected in all evaluated age intervals, with the group fed the dried yogurt powder caused significantly (p<0.05) higher feed intake in the first and second intervals as compared with the groups that fed the probiotic and control group. At the end of the period (42 days of age), the results showed that the dietary supplementation with powder of dried yogurt led to a significant improvement (p<0.05) in body weight, feed intake and total Mortality decreased significantly (p<0.05) in all periods of age for the treatment( T3), compared with those birds fed the probiotic(T2) product and those fed control group(T1). The relative weights of lymphoid organs (spleen, bursa of fabrecius) as an indicator of the immune system condition. The highest weight of spleen observed at the (treatment T3) with addition of yogurt powder mean while their was not significant (P<0.05) differences of the weight of bursa of fabrecius, in all treatments but their was improvement in the weight of immune organ in (T2, T3). The result shows the treatments were lead to significantly (p<0.05) decreased of total counts of aerobic bacterial in jejunum micro flora compared with control group. Key words: Probiotic, dried yogurt powder, productive performance, immunity, mortality.
Analysis of Electronic and Optical Properties of Pristine LiNbO3 Using First-Principle Calculations

The electronic-optical properties of lithium niobate (LiNbO3) are identified by utilizing the first principle calculation based on density function theory (DFT) executed in the ATK VNL. The exchange-correlation function of generalized-gradient-approximation utilizing density functional theory is performed to extract the electronic-optical properties of lithium niobate crystal. The lattice constants and unit cell volume are investigated from the optimized structure, that is in good resemblance with the previous reported research work. Electronic band structure and density of states (DOS) exhibited its semiconducting nature demonstrating a bandgap equal to 3.56eV. Optical properties, like absorption coefficient, complex dielectric function, refractive index is also determined and matched to the practical values. The optical spectrum of LiNbO3 is analyzed and found appropriate for applications such as optical waveguides, piezoelectric sensors, and optical modulators.
Seed Dispersal of the Palm Attalea oleifera in a Remnant of the Brazilian Atlantic Forest1

ABSTRACT This study investigated the seed dispersal of the canopy palm Attalea oleifera in a 3500 ha fragment of the Brazilian Atlantic Forest. We monitored ten fruiting palms during six months, when the following mammals were recorded feeding on Attalea fruits and/or seeds: (1) Brazilian squirrels (Sciurus aestuans, 78 diurnal records); (2) white-eared opossums (Didelphis albiventris, 8 nocturnal records); (3) black-humped agoutis (Dasyprocta prymnolopha, 3 diurnal records); (4) pacas (Agouti paca, 1 nocturnal record); (5) rice rats (Oryzomys capito, 11 nocturnal records); and (6) short-tailed opossums (Monodelphis americana, 4 diurnal records). Fruit removal on the ground reached 71.9 ± 21.9 percent after a three-month period, and most fruits were moved less than 5 m from parental palms. Squirrels generally moved fruits and endocarps 5–10 m from parents, whereas opossums, pacas, and agoutis moved 91.7, 78, and 74.1 percent of fruits less than 5 m, respectively. Oviposition on endocarps by the bruchid Pachymeros cardo ranged between 62.1 and 84.3 percent of endocarps previously manipulated by white-eared opossums, squirrels, and rice rats, whereas 57.9 percent of old endocarps collected around reproductive palms were attacked by bruchids. Moreover, oviposition on endocarps varied from 42.3 percent in the case of single endocarps to 70.9 percent of endocarps in piles. Attalea seeds abundantly germinated beneath parental palms despite the high levels of predation, and distribution of both seedlings and adults suggested that squirrels played an important role in palm recruitment at the study site.