Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of Biological Systems

Biological Systems and Dynamics In the Beginning The Hemodynamic System Cheyne-Stokes Respiration Population Dynamics of a Single Species Fibonacci, Malthus and Nicholsons Blowflies Fixed Points and Stability of a One-Dimensional First Order Difference Equation The Cobweb Diagram An Example: Hormone Secretion Higher Dimensional Maps Period Doubling Bifurcation in Infant Respiration Observability of Dynamic Variables Bioelectric Phenomena Measurement ECG, EEG, EMG, EOG and All That Measuring Movement Measuring Temperature Measuring Oxygen Concentration Biomedical Imaging The Importance of Measurement Biomedical Signal Processing Segmentation Error Measure and Automatic Analysis of EEGs ECG Signal Processing Vector Cardiography Embedology and State Space Representation Fractals, Chaos and Nonlinear Dynamics Prediction Computational Neurophysiology The Cell Action Potentials and Ion Channels Ficks Law, Ohms Law and the Einstein Relation Cellular Equilibrium: Nernst and Goldman Equivalent Circuits Dendrites Mathematical Neurodynamics Hodgkin, Huxley and the Squid Giant Axon FitzHugh-Nagumo Model Fixed Points and Stability of a One-Dimensional Differential Equation Nullclines and Phase Plane Pitchfork and Hopf Bifurcations in Two Dimensions Excitability Population Dynamics Predator-Prey Interactions Fixed Points and Stability of Two-Dimensional Differential Equations Disease Models: SIS, SIR and SEIR SARS in Hong Kong Action, Reaction and Diffusion Black Death and Spatial Disease Transmission Reaction-Diffusion Cardiac Dynamics Autonomous Agents Flocking Celluloid Penguins and Roosting Starlings Evaluating Crowd Simulations Complex Networks Human Networks: Growing Complex Networks Small World Networks of Spread of SARS Global Spread of Avian Influenza Complex Disease Transmission and Immunisation Complex Networks Constructed from Musical Composition Interaction of Grazing Herbivores Neuronal Networks and Complex Networks Conclusion Models Are a Reflection of Reality References A Summary appears at the end of each chapter.
Characterisation and modulation of drug resistance in lung cancer cell lines

Chemotherapy drug resistance is a major obstacle in the treatment of cancer. It can result from an increase in levels of cellular drug efflux pumps such as P-glycoprotein (P-gp). Using cellular models, this thesis aimed to investigate resistance in lung cancer cells while developing siRNA and membrane proteomic techniques and to increase our knowledge of the effect of lapatinib, a newly developed targeted therapy, in these resistant cells. Lapatinib, a growth factor receptor tyrosine kinase inhibitor synergised with P-gp substrate cytotoxics in P-gp over-expressing resistant cells. However, lapatinib treatment, at clinically relevant concentrations, also increased levels of the P-gp drug transporter in a dose-responsive manner. Conversely, exposure to the epidermal growth factor (EGF), an endogenous growth factor receptor ligand, resulted in a decrease in P-gp expression. Using drug accumulation, efflux and toxicity assays we determined that alteration in P-gp levels by either lapatinib or EGF had little functional significance. P-gp is not the only resistance mechanism so siRNA-mediated gene silencing was exploited to investigate the role of additional proteins with potential roles in resistance. Firstly, P-gp knockdown by siRNA was coupled with toxicity and accumulation assays to determine the impact of silencing this protein in the chosen resistant lung cells. Additional putative targets were chosen from microarray data identifying genes associated with the development of paclitaxel resistance. Of the three genes investigated, ID3, CRYZ and CRIP1, ID3 emerged as having a potential role in contributing to resistance in one of the resistant lung carcinoma cell lines investigated. Many of the proteins important in resistance are membrane expressed but due to their size and hydrophobic nature, can be difficult to characterise. A 2D-LC-MS method was designed and employed to examine membrane proteins from the resistant lung cell models. Suitable parameters important in optimal identification of the proteins were determined. Large numbers of proteins were identified and comparisons made, highlighting those that were differentially expressed.
Phylogeography of the Petunia integrifolia complex in southern Brazil

In this study, we evaluated the genetic diversity of the Petunia integrifolia species group using a phylogeographical approach, and attempted to understand better its diversification and taxonomy. Plants from five morphological groups were collected, covering a large part of the geographical distribution of most of the species. Two major clades were found in the phylogenetic tree, and an additional lineage, corresponding to P. inflata, was found in the haplotype network obtained for plastid markers. All three lineages are clearly delimited geographically, but, with the exception of P. inflata, the morphological groups were not genetically distinct. Our results suggest that a population expansion after a size reduction resulted in the establishment of two distinct and allopatric groups c. 0.5 Mya, one group occurring in a geologically ancient area, and the other occurring in areas that were under the influence of a series of marine transgressions/regressions at the end of the Pleistocene. These two clades are evolutionarily significant units with significantly different allele frequencies in their nuclear genome and reciprocal monophyly in maternal, uniparentally inherited markers. All our results suggest that the morphology-based taxonomy in this group does not reflect its evolutionary history, and revision of its species limits should incorporate the distribution of the genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 199–213.
Letna Dinamika Pojavljanja Vodnih Ptic Na Reki Dravi Med Mariborskim Jezerom In Jezom Melje (Sv Slovenija) / Yearly dynamics of waterbirds’ occurrence on the Drava River between Lake Maribor and Melje Dam (NE Slovenia)

Abstract Between April 2007 and April 2008, 40 systematic waterbird counts were conducted on the Drava River between Lake Maribor and the Melje Dam (length 8.5 km, area 155 ha) to determine the specific composition, abundance and seasonal dynamics of bird occurrence. Between October and May, counts were conducted every week, whereas between June and September they were carried out once every two weeks. In total, 26,803 individuals of 30 species were counted. The number of waterbirds and diversity of species were the highest from late December to late February, when more than 1,000 individuals were regularly present in the area. Waterbirds were distributed along the river unequally, with the highest number of birds present yearround in the city centre and in the first counting sector of Lake Maribor. The Mallard Anas platyrhynchos and Mute Swan Cygnus olor were recorded during every count, while occurrence frequency was greater than 50% in another 10 species. Dominant species in terms of percentage composition were Mallard, Black-headed Gull Chroicocephalus ridibundus, Coot Fulica atra, Mute Swan, Pochard Aythya ferina and Tufted Duck Ay. fuligula. Mute Swan and Mallard were the only breeding waterbirds in the study area. Both the total number of waterbirds and the highest daily total in the first two counting sectors were greater between October and March 1992/93 than in our study. The decline in numbers was the greatest for Mallard, Pochard and Tufted Duck, while an increase was noted in Mute Swan and Yellow-legged / Caspian Gull Larus michahellis / cachinnans. The total number of waterbirds and the number of some species in the study area were significantly higher than expected solely based on its length compared to the length of the lowland Drava in Slovenia (125.7 km). The study area is conservationally important for Pochard, Tufted Duck and Black-headed Gull
Estudo farmacognóstico das folhas de Alternanthera brasiliana (L.) Kuntze (Amaranthaceae)

SUMMARY. “Pharmacognostic Analysis of the Leaves of Alternanthera brasiliana (L.) Kuntze (Amaranthaceae)” . Alternanthera brasiliana, known in Brazilian traditional medicine as “ penicilina” , “ terramicina” and “ perpe tua-do-mato” , has proved anti-inflammatory, analgesic and antiviral activities. The leaves were morphoanatomically analyzed and the vegetal drug could be properly identified. It has simple, oval-lanceolate shaped, penninervate, oppositely crossed, membranaceous and pilose leaves, with different color standards, ranging from green to purple. Anatomy analysis showed amphistomatic leaves with ornamented non-glandular trichomes, dorsiventral mesophyll and eucamptodromous venation. Main vein showed changes in outlay and in the gauge of collateral vascular bundle, with sclerenchymatous tissue in the phloematic pole.
Feature Construction and Calibration for Clustering Daily Load Curves from Smart-Meter Data

This paper proposes and compares feature construction and calibration methods for clustering daily electricity load curves. Such load curves describe electricity demand over a period of time. A rich body of the literature has studied clustering of load curves, usually using temporal features. This limits the potential to discover new knowledge, which may not be best represented as models consisting of all time points on load curves. This paper presents three new methods to construct features: 1) conditional filters on time-resolution-based features; 2) calibration and normalization; and 3) using profile errors. These new features extend the potential of clustering load curves. Moreover, smart metering is now generating high-resolution time series, and so the dimensionality reduction offered by these features is welcome. The clustering results using the proposed new features are compared with clusterings obtained from temporal features, as well as clusterings with Fourier features, using household electricity consumption time series as test data. The experimental results suggest that the proposed feature construction methods offer new means for gaining insight in energy-consumption patterns.
Characterisation and UV inactivation of bacteriophages infecting human-specific Bacteroides strain GB-124

The pathogens contained in human faecal material can present a significant risk to human health, when discharged into surface waters. A recently isolated strain of Bacteroides spp. , (GB-124) has shown good ability to detect viruses (phages) in waters exclusively contaminated by human faecal material, with widespread geographical applicability, proving a low-cost microbial source tracking tool (MST). However, little is known about the morphology, ecology and inactivation of phages capable of infecting strain GB-124 during UV-B (representing the primary germicidal portion of sunlight) and UV-C radiation (a common tertiary disinfection stage in wastewater treatment). Therefore in order to address this knowledge gap, a total of twenty phages were isolated from municipal wastewater and characterised using transmission electron microscopy (TEM) and host range assessment. Ultraviolet radiation (UV) inactivation kinetics were determined using two phases of laboratorybased collimated beam experiments using UV-B and UV-C wavelengths.
Deciphering the transcriptional regulation and response of barley to obligate fungal biotroph invasion

Obligate fungal biotrophs have co-evolved with their plant hosts, a direct result of an intimate interaction that protects the integrity of the plant during pathogenesis, allowing it to obtain essential nutrients. To restrict the establishment of pathogen colonization, plants have evolved complex regulatory mechanisms to control the defense response, the most extreme of which involves Resistance (R) gene-mediated programmed cell death. While it is known that de novo gene expression and subsequent protein synthesis are required for several cell death programs, the primary transcriptional targets of R gene-mediated responses are unknown. Two alternative approaches were used to identify these transcriptional targets. The first approach uses a time-course microarray experiment that contrasts wild-type and loss-of-function mutant alleles of the Mla (powdery mildew) R gene to identify transcripts that distinguish incompatibility from compatibility. Earlier expression and stronger transcriptional responses were observed in compatible plants at 20 hours after inoculation, though this reaction diminished at later time points. In contrast, incompatible interactions exhibited a time-dependent strengthening of the transcriptional response, with increases in both fold change and total number of genes differentially expressed. These results implicate MLA as a repressor of early gene expression response and provides further evidence for a link between basal and R gene-mediated resistance. The second approach uses natural variation present in a doubled-haploid population to identify the regulatory hierarchy of gene expression during the interaction of barley and stem rust. A trans-eQTL hotspot is not associated with the R gene Rpg-TTKSK, but instead an inoculation-dependent expression polymorphism in Adf3 implicates it as a candidate susceptibility gene. In contrast, colocalization of a trans-eQTL hotspot with an enhancer of R gene-mediated resistance to stem rust associates the suppression of gene expression with enhanced resistance. Lastly, Blufensin1 (Bln1) is used as a case study for functional analysis using gene expression, structural features, and phenotype. Although greater expression of Bln1 was previously associated with incompatibility, virus-induced gene silencing and transient overexpression implicates that Bln1 negatively impacts defense. Collectively, these studies suggest that our understanding of gene expression and its phenotypic consequences is more complex than previously thought.
GENETICALLY MODIFIED TREES: PRODUCTION, PROPERTIES, AND POTENTIAL

Genetic modification using Agrobacterium- or biolistic- mediated gene transfer can overcome the limitations of conven- tional tree breeding. Alternatives to the use of antibiotic resistance selectable markers and how they might be used to overcome potential public concerns are described. Applications of genetic modifications to trees include altered wood properties, speeding up breeding cycles, forests as pharmaceutical factories, dendroremediation, and improved resistance to pests and diseases, as well as the restoration of sensitive landscapes.
Imazethapyr for Weed Control in Soybean (Glycine max)

Imazethapyr at 0.05 to 0.14 kg ai/ha applied preplant incorporated, preemergence, and postemergence was evaluated alone and with complementary herbicides in the field for weed control in soybean. Imazethapyr controlled 90% or more smooth pigweed regardless of application method or herbicide rate. Imazethapyr at 0.05 kg/ha controlled jimsonweed 30% better postemergence compared to soil applications. Imazethapyr at 0.10 kg/ha controlled 90% or more velvetleaf regardless of application method. The addition of alachlor to soil-applied imazethapyr enhanced giant foxtail, jimsonweed, and velvetleaf control. Adding acifluorfen or bentazon to postemergence imazethapyr antagonized weed control. Adding sethoxydim to postemergence imazethapyr was not beneficial.
The effects of replicative senescence and telomerase on contraction and motility of fibroblast cells

Fibroblast cells are important in wound healing as they differentiate into myofibroblasts that can migrate into a wound and create tension and aging skin seems to take longer to repair a wound. This study was designed to look at the migration and contraction ability of early (EP) and late (LP) passage cells as compared to cells with telomerase (hTERT), an enzyme that lengthens telomeres delaying senescence. To assess contraction, all cells were grown on coverslips with and without transforming growth factor beta, a wound healing agent, and stained for alpha smooth muscle actin (α‐sma) a myofibroblast marker. Collagen lattice assays were used to assess contraction by measuring lattice diameter as it contracted over time then stained for the presence of α‐sma. Finally, a scratch assay was used to measure the ability for each type of cell to migrate into a "wounded" area. Contraction by EP cells was greater than LP cells in a five day collagen lattice. Results on migration assays and α‐sma in coverslips and collagen lattice are still being analyzed; however expected results would show that EP and hTERT cells should migrate faster and have more α‐sma than LP cells. If these results are shown, they would suggest that the formation of α‐sma in EP and hTERT cells allows faster migration and better contraction than in LP cells. Funding provided by the University of Central Oklahoma.
Clarifying the Notion of Digital Transformation in IS Literature: A Comparison of Organizational Change Philosophies

The widespread availability of digital technologies led to a disruption of well-established business models in many industries. Digital Transformation (DT) is organizations’ strategy to prevent this disruption. However, in IS literature there exists no common understanding about what is exactly meant by DT, ranging from the transformation of whole industries to single processes of digitization. Hence, this conceptual paper aims to address this gap by comparing DT to prior organizational change philosophies. Based on the comparison, we clarify the notion of DT in IS literature by providing a definition and constructs that differentiate the content, order, and improvement goals of DT from other organizational change philosophies. Scholars and practitioners may find this conceptualization helpful to understand the different facets of DT. We hope that our suggestion for the use of consistent terminology will be embraced and will help to consolidate this research area and move it forward.
Localization of Type IV Collagen in the Myotome Cells during the Somite Differentiation in the Chick Embryo

Type IV collagen is a major structural component of basement membranes which play various roles upon their adjacent cells. In order to better understand roles of type IV collagen during the somite differentiation, we produced anti‐rat type IV collagen polyclonal antibodies and demonstrated spacial and temporal distribution of type IV collagen in somites of the chick embryo by immunohistochemical procedure. Type IV collagen was detected in the basal surface and the cytoplasm of epithelial dermatome cells at early stage of the somite differentiation, and then detected in myotome cells overlying apical surface of dermatomes, but not in migratory mesenchymal dermatome cells. With the appearance of type IV collagen‐expressing myotome cells, epithelial dermatome cells showed the decrease in immunoreaction with anti‐type IV collagen antibodies, the disappearance of their basal‐apical polarity and their epithelial shape. From these results, it was suggested that type IV collagen is an early marker for myotome cells, and that type IV collagen and/or other factors co‐expressed by myotome cells might provide an accelerative signal for epithelial/mesenchymal conversion of dermatome cells.
Sucessão entre cultivos orgânicos de milho e couve consorciados com leguminosas em plantio direto

Organic crop succession of maize and collard greens intercropped with legumes in no-tillage system New farming practices have been developed to reduce the application of fertilizer and pesticides and minimize the aggression to the environment, producing healthy foods and environmentally correct. We evaluated the performance of the succession of collard greens (Brassica oleracea L. var. acephala) and corn (Zea mays L.) intercropped with green manure legumes under no-tillage organic system. The study was conducted in Seropedica, Rio de Janeiro State, during two years. We utilized dwarf velvet bean (Mucuna deeringiana) and showy crotalaria (Crotalaria spectabilis) as green manure intercropped with collard greens and in succession sunn hemp (Crotalaria juncea) and velvet bean (Mucuna pruriens) intercropped with corn. As a control, there was a single crop system of corn and collard greens. The experimental design was of randomized complete blocks, a factorial 3 (crop system) x 2 (doses of poultry bed manure), with four replications, in plots of 20 m 2 . For the collard greens we applied 0 and 5.4 t ha -1 of poultry bed manure (2.7 t ha -1
Thermodynamic quantities of two-dimensional Ising models obtained by noisy mean-field annealing and a coherent Ising machine

Noisy mean field annealing (NMFA) is an algorithm that mimics a coherent Ising machine (CIM), which is an optical system for solving Ising problems. The NMFA has reproduced the solver performance of the CIM for systems of limited size even though it simplifies the interaction between spins with a mean-field approximation. However, recent experiments observing various thermodynamic quantities have revealed that the CIM can capture the phase transitions of the two-dimensional Ising models that the mean field cannot capture. This situation leads to a fundamental question as to how well the NMFA can capture the features of the thermodynamic quantities around the phase transition. This paper answers that the NMFA reproduces the thermodynamic features of the mean field, but cannot reproduce the CIM results. This suggests that, in terms of sampling, the level of performance of the CIM is beyond that of the NMFA.
Multiplier Bootstrap-based Exploration

Despite the great interest in the bandit problem, designing efficient algorithms for complex models remains challenging, as there is typically no analytical way to quantify uncertainty. In this paper, we propose Multiplier Bootstrap-based Exploration (MBE), a novel exploration strategy that is applicable to any reward model amenable to weighted loss minimization. We prove both instance-dependent and instance-independent rate-optimal regret bounds for MBE in sub-Gaussian multi-armed bandits. With extensive simulation and real data experiments, we show the generality and adaptivity of MBE.
Occurrence of Colletotrichum dematium on selected herbs species and preparations inhibiting pathogen’s growth and development in vitro

The studies investigated the occurrence of little known in Poland fungus Colletotrichum dematium, found in 2005-2010 on the plants of caraway and angelica in 2008-2010, cultivated in the Lublin region. The effectiveness of some preparations in inhabiting the growth and development of the pathogenic strain K 426 C. dematium was studied. The effect of biotechnical preparations Biochikol 020 PC (chitosan 20 g/dm) and Biosept 33 SL (33% of grapefruit extract) and 11 fungicides from different chemical groups was examined. The method consisted of adding the preparation in use form to sterile culture medium and inoculation of the pathogen inoculum. The colonies of C. dematium growing on the medium without preparations constituted the control. The percentage of growth inhibition after 4 and 8 days of growth, the type of toxic activity, inhibition of morphological structures formation and causing degeneration of pathogens mycelium were adopted as the criteria to assess the activity of preparations. Biosept 33 SL, and fungicides Dithane Neo Tec 75 WG and Helm-Cymi 72.5 WP were recognized as the most effective in reducing the growth and development of the pathogen.