Miracle-dz/UniFAR-FTUs huggingface dataset:
Mathematical modelling of the core regulatory feedback mechanisms of p53 protein that decide cell fate

Cells defence against stresses that can cause DNA damage (single-strand breaks, double-strand breaks) is crucial in safeguarding the integrity of the genome and the survival of the organism as a whole. One of the genes that plays a pivotal role in maintaining the stability of the genome in humans is p53, which encodes its product p53 protein. The regulation of p53 activation is extremely complex, and molecular cell biology has gathered parts and pieces of the whole pathway. Mental intuition of this complex regulation is challenging; therefore, it requires a different method to quantitatively model and analyse to enhance the current understanding. This thesis has attempted to create two quantitative models of the mechanisms that regulate p53 basal levels and its appropriate activation as a stress response in deciding cell fate by either cell cycle arrest (to stop proliferation of DNA-damaged cells) or apoptosis (programmed cell death) to eliminate damaged cells. In the first part of the research, a modified and improved model from Sun et al. (2011) deterministic model is proposed to explain the p53 basal dynamics and its response to stress due to DNA double-strand breaks. This model in the form of delay differential equations incorporates the most recently found molecular interactions and hypothesis: the core regulators consist of ATM, Mdm2, MdmX, Wip1 and p53. ATM as a stress transducer, amplifies the stress signal and activates p53 and inhibits its regulators Mdm2 and MdmX. The network structure consists of two positive feedback loops (p53 auto-regulation and ATM auto-activation), three negative feedback loops (Mdm2, MdmX and Wip1) and the interplay of p53, Mdm2 and MdmX that have successfully captured the basal dynamics (spontaneous pulses under non-stressed conditions) and stress response (repeated pulses or oscillations under stressed conditions). The model simulation results show that p53 spontaneous pulses are due to intrinsic DNA damage involving low number of DNA double-strand breaks; and p53 auto-regulation is an important positive feedback contributing to a threshold activation of p53 in generating pulses whether spontaneous or repeated. It also shows that p53 dynamics are excitable, in that once initiated, it completes the pulse even if stress signal is inhibited. Bifurcation analysis revealed a spectrum of p53 behaviour under stressed and non-stressed conditions and characterised p53 dynamics as Type II excitability (oscillations arises from non-zero frequency). Most importantly, we reveal some novel findings on the mechanism of threshold activation of p53 pulsatile and oscillatory dynamics that are crucial for its physiological function as a transcription factor and guardian of the genome. The second model is an extension of the first model by incorporating the apoptosis initiation module structure from Zhang et al. (2009a) with modified parameter values for modelling the core regulatory mechanism of p53 protein that activates apoptotic switch in response to high DNA double-strand breaks. The…
Biohydrogenation of Unsaturated Fatty Acids IV. SUBSTRATE SPECIFICITY AND INHIBITION OF LINOLEATE Δ12-CIS, Δ11-TRANS-ISOMERASE FROM BUTYRIVIBRIO FIBRISOLVENS

Abstract Three parameters involved in the binding of substrate to linoleate isomerase of Butyrivibrio fibrisolvens have been identified from studies of inhibition by fatty acid isomers and analogues. They are (a) the π system of the substrate double bond, (b) hydrophobic interaction, and (c) hydrogen bonding of the substrate carboxyl group. Almost every unsaturated fatty acid tested inhibited the enzyme, regardless of configuration or double bond position between carbons 3 and 12. Superimposed on this contribution of unsaturation was the correlation of inhibition with chain length and with the presence of an active hydrogen on a C-1 substituent. Inhibition by unsaturated fatty acids or their derivatives in all cases examined was competitive. More restrictive requirements for isomerization were revealed by incubation of the enzyme with positional and configurational isomers and carboxyl derivatives of the substrate. An absolute requirement for a cis-9, cis-12-diene system and a free C-1 carboxyl group was shown. Two chelators, o-phenanthroline and EDTA, were identified as reversible inhibitors of the enzyme. Inhibition by o-phenanthroline was noncompetitive. The isomerase was also inhibited by the sulfhydryl reagents, p-hydroxymercuribenzoate, iodoacetamide, and N-ethylmaleimide.
Macrofaunal burrowing : The medium is the message

Burrowing by benthic infauna mixes both sediment grains and interstitial fluids, affect- ing sedimentary redox conditions and determining fates of organic matter and pollutants. Explicit, quantitative analyses of material properties of sediments, however, have been applied only recently to understand mechanisms of burrowing. Muds are elastic solids that fracture under small tensile forces exerted by burrowers, and are dominated by adhesive forces between sediment grains and the surrounding mucopolymeric gel and (or) by cohesion of this gel. By contrast, in clean sands behaving as granular materials, gravity is a much more significant force holding grains together than is adhesion or cohesion. Burrowers in muds have diverse structures that act as wedges to propagate cracks and elongate their burrows. In sands, increased rugosity on a small, and lique- faction on a larger scale, facilitate displacement of the grains that carry compressive forces along distinct force chains or arches. The classic dual-anchor system described for burrowers is reinter- preted as having several additional functions. The characteristic dilations or expansions function primarily as wedges that exert lateral tensile forces to propagate cracks forward, secondarily as double O-ring seals holding fluid pressure in the advancing burrow (maintaining tensile stresses needed to open a crack), and thirdly as anchors (to pull the shell along in bivalves in particular). Burrowing bivalves are wedges. In the case of burrowing gammarid amphipods, the dorsal exo- skeleton mirrors the shape of half a sedimentary bubble and constitutes a wedge. A great many anatomical features of burrowers can now be understood analogously. The identification of the mechanisms of burrowing by crack propagation suggests that a substantial revision of the previously described feeding guilds of polychaetes is required.
ANN model of stress-strain relationship for aluminium sponge in uniaxial compression

In this article, we present a proposition of a model of the compressive behaviour of open-cell aluminium with relation to the material apparent density. The research was based on experimental data from uniaxial compression tests conducted for two sample lots. These results were analysed with the use of neural networks in a specially designed algorithm. The main criterion for choosing a satisfactory approximation was mean absolute relative error MARE< 5%. As a result of the analysis, the sought relation was extracted and is presented as a proposition of a new ANN model of the compressive stress-strain relationship for aluminium sponge.
A Novel Trilateration Algorithm for RSSI-Based Indoor Localization

This paper proposed a novel trilateration algorithm for indoor localization based on received signal strength indication (RSSI). Firstly, all the raw measurement data are preprocessed by a Gaussian filter to reducing the influence of measurement noise. Secondly, the transmit power and the path loss exponent are estimated by a novel least-squares curve fitting (LSCF) method in the RSSI-based localization. Thirdly, a novel trilateration algorithm is proposed based on the extreme value theory, which constructs a nonlinear error function depending on distances and anchor nodes position. To minimize the function, a Taylor series approximation can be used for reduce the computational complexity. And, an iteration condition is designed to further improve the positioning accuracy. Afterward, Bayesian filtering is used to smoothing the localization error, and decrease the influence of the process noise. Both the simulation and experimental results demonstrate the effectiveness of the proposed methodology.
The handbook of New Zealand mammals

This book is the first comprehensive account of all 46 species of land-breeding mammals known in New Zealand, native and exotic, wild and feral, living and extinct. It describes their history, biology, and ecology, and brings together much information which has been gathered from widely scattered sources or was hitherto unpublished. The description of each species is arranged under conventional headings, and is standardized for easy reference. Because the only native land-breeding mammals in New Zealand are bats and seals, the great majority of the modern mammal fauna comprises introduced species, whose arrival has had profound effects, both for themselves and for the native fauna and flora. Each species account emphasizes the ecological effects of the introductions: for the natives, changes in numbers and distribution, and for the arrivals, changes in habitat, diet, numbers, and size in comparison with their ancestral stocks. The editor's introduction summarizes the general history and characteristics of the mammal fauna of New Zealand, and describes some of the problems that mammals present to resource managers in contemporary times. The twenty-nine contributors are all leading authorities in mammal science in New Zealand, and all have studied in the field the species they describe. This book will become the definitive work on the mammals of New Zealand, and a standard source of reference for mammal biologists both in New Zealand and elsewhere in the world. It will also be of considerable interest to ecologists interested in evolutionary adaptation in mammals.
Populasi kumbang Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) sebagai penyerbuk tanaman kelapa sawit (Elaeis guineensis Jacq.) di Kumai, Kalimantan Tengah

AMIN KRISTIANTO SAPUTRA. Population of Weevil Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) as Oil Palm Pollinator (Elaeis guineensis Jacq.) in Kumai, Central Borneo. Supervised by TRI ATMOWIDI and TARUNI SRI PRAWASTI. Elaeidobius kamerunicus is the effective pollinators of oil palm plants. The weevil is monophagous and complete their life cycle in male inflorescences of oil palm. Pollinating by the weevils increase oil palm productivity. This research aimed to observe weevil population and the relationship between environment factors and the weevil population. This research consist of observing morphological of weevil, estimating the population with counting the weevil on male inflorescences, and measuring the environment factors in the field. Relationship between environment factors and the weevil population were analyzed by CANOCO 4.0. High population of the weevil occurred in July and low in October. Population size of the weevil was above the minimum population for effective pollination. Weevil population on the field related to the number of spikelet of male inflorescences. Rainfall and temperature were negatively affect to the weevil population. Keyword: pollination, oil palm, Elaeidobius kamerunicus, environmental factors POPULASI KUMBANG Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) SEBAGAI PENYERBUK TANAMAN KELAPA SAWIT (Elaeis guineensis Jacq.) DI KUMAI, KALIMANTAN TENGAH AMIN KRISTIANTO SAPUTRA
The Bacteriological Risk Transported to Seas by Rivers; the Example of Çırpıcı River, the Sea of Marmara, Istanbul, Turkey

The identification of bacteriologically characters of coastal areas is important due to the fact that bacteriological pollution, transported to seas via rivers is a potential threat for ecosystem, animal and human health. In this study, bacteriological load of Cirpici River transporting to the Sea of Marmara from Zeytinburnu location in Istanbul and its relationship with primary hydrographic parameters investigated. The levels of fecal coliform (FC), total coliform (TC), fecal streptococci (FS) and total heterotrophic aerobic bacteria (HPC) tested using Membrane Filtration Technique in the surface water samples. Seawater temperature, pH, salinity, dissolved oxygen were recorded in-situ using multiparameter (YSI556 MPS). While the highest TC detected to be 13x107 CFU/100 ml, the highest FC was 14x106 CFU/100 ml. The lowest FC recorded as 25x10 CFU/100 ml. While the highest FS level was determined to be 73x105 CFU/100 ml, the highest HPC was 14x106 CFU / ml. Variable environmental parameters recorded for seawater temperature between 10.3-29.5˚C; pH 6.0-8.38; dissolved oxygen 0.34- 10.71 mg /l and salinity 16.50-26.57 psu during the study period. Significant correlation between the temperature and FC, FS and THAB detected. The levels of bacteria detected at the spot where the Cirpici River poured into the Sea of Marmara were found higher than the station at the 800 m open of the Sea of Marmara. It was determined that the Cirpici River carried 103 CFU bacterial loads at 100 ml for TC to the Sea of Marmara. The FC and FS counts carried to the Marmara Sea from Cirpici River recorded to be 102/100 ml and 103/100 ml, respectively. The fact that FC and TC levels were above the limit values during the study indicate the stability of pollution sources in the region and that the Cirpici Stream carries a bacteriological risk in terms of human, animal, and environmental health.
Work System Framework: Analisis Inmagic Presto dan Zendesk

Saat ini informasi dan pengetahuan sangat berharga terutama dengan adanya persaingan, sulit bagi organisasi untuk mengelola pengetahuan di dalam organisasi. Pengetahuan setiap orang dalam organisasi atau perusahaan tentu berbeda, dalam pelaksanaan proses pengolahan Pengetahuan tidak berjalan maksimal di lingkungannya. Pemrosesan berbasis Manajemen Pengetahuan menjadi salah satu solusi untuk membantu pemrosesan pengetahuan dalam organisasi. Saat ini telah ada pengembangan Aplikasi TI berdasarkan Manajemen Pengetahuan yang diharapkan memiliki dampak positif dalam membantu dan membangun organisasi atau perusahaan. Dalam tulisan ini, akan dianalisis dan membandingkan dua Aplikasi TI berdasarkan Manajemen Pengetahuan, pertama Inmagic Presto dan kedua Zendesk. Penelitian ini dilakukan untuk melihat kelebihan dan perbandingan yang ada pada kedua aplikasi dalam menggunakan Kerangka Kerja Sistem. Hasil analisis akan menjadi kesimpulan untuk merekomendasikan Aplikasi IT berdasarkan Manajemen Pengetahuan sesuai dengan kebutuhan perusahaan, yang didasarkan pada kemampuan yang ada di setiap aplikasi dan area implementasi aplikasi. Kata kunci —Work System Framework, Manajemen Pengetahuan, Inmagic Presto, Zendesk
Soluções variacionais e numéricas da Equação de Schrödinger 1D submetida ao potencial de Pöschl-Teller

This paper presents the numerical and variational solutions of the 1D Schrödinger Equation submitted to the Pöschl-Teller potential. The methods used were the Variational Method and the Finite Difference Method. They were presented in a didactic and detailed way with the purpose of instructing both undergraduate and graduate students, about the applicability and effectiveness of the aforementioned methods. We use the Pöschl-Teller potential due to the fact that it is little explored in the books of Quantum Mechanics used in undergraduation courses and also because of its diverse applications, such as in Bose-Einstein condensates, waveguides, topological defects in field theory and so on. We conclude this paper comparing the variational and numerical solutions with the analytical solution and present the advantages of each method.
Bioecological study of parasitic complexes of aphids in North-West Algeria

Received 26.08. 2019; accepted 25.10. 2019; published online 30.12. 2019 Myzus persicae (Sulzer, 1776) (Hemiptera Aphididae) is the most significant aphid pest of peach trees. Chemical control of this species is a quick and simple method to prevent the development of this pest, however, the massive use of these chemicals poses potential health and environmental risks. This study proposes an alternative biological control approach based on the use of parasitoids to reduce aphidian populations. The study, which we undertook over the course of three years, allowed us to observe almost the same species of parasitoid (Hymenoptera Braconidae) on the vegetable crops taken into exam in the study. However, some species were considered to be absent in the region. Others appeared only during the second and last year of study as Aphidius funebris Mackauer, 1961, Trioxys angelicae Haliday, 1833 and Praon exsoletum Nees, 1811. This study showed total dominance of A. matricarae Haliday, 1834 with very high parasitism (values of 61%, 54% and 78% during 2012, 2013 and 2014, respectively) followed by Lysephlebus testaceipes Cresson, 1880.
Structural and biochemical studies of MCM proteins

The eukaryotic MCM2-7 replicative helicase is a hetero-complex composed by 6 homologues belonging to the AAA+ ATPase superfamily. These proteins form a ring-like structure which is essential for the initiation and the progression of the replication fork. In order to better understand the cellular role and mechanism of action of these proteins, I carried out structural and functional studies on two different systems: the archaeal MCM proteins, that forms a homomeric ring representing a simplified model of the eukaryotic complex, and the less well studied human MCM8, whose exact role in eukaryotic cells has not been elucidated. MCM interacts in two ways with the DNA: the canonical "loaded" mode where the MCM protein is encircling the DNA, and a "associated" mode where the DNA is wrapped around the enzyme. Using the protein from the archaeon Methanothermobacter thermautotrophicum, I biochemically shown that binding of MCM proteins affect the degree of supercoiling of dsDNA and that subdomain A is crucial for this interaction. To determine the structure of the C-terminal domain of the MCM proteins, the less studied region, I produced three different constructs corresponding to the C terminus of the MCM proteins from M. thermoautotrophicum and Sulfolobus solfataricus. Despite a large effort using “high throughput” crystallisation techniques, no well diffracting crystals could be reproducibly obtained. An alternative structural biology approach has been adopted, using NMR analysis. Preliminary data are compatible with the bioinformatics prediction of a winged helix domain, but further work on isotope-labelled proteins is necessary for a full 3D characterisation. Two other MCM proteins have been more recently described (MCM8 and MCM9): they are present in a variety of eukaryotic organisms, do not interact with the MCM2-7 complex and their function in the cell is still unknown. These protein are co-evolutionary related and it is conceivable that they have a functional link. I cloned and expressed in E. coli cells a large number of hMCM8 fragments: two of them (the N-terminus and the AAA+ domain) can be successfully expressed in soluble form and have been purified and used for biochemical assays. Both proteins forms dimers, bind ssDNA and the AAA+ catalytic domain displays ATPase activity. Further effort will be done to optimise the purification protocol to obtain proteins suitable for structural studies. In order to assess the hypothesis of a functional relationship between MCM8 and MCM9 proteins, a similarly extensive cloning strategy was applied to human MCM9, with the aim of obtaining constructs expressing a variety of fragments, to be co-expressed with the equivalent hMCM8 domains, and to test the formation of functional complexes.
The Least Common Denominator: Species or Operational Taxonomic Units?

Molecular techniques have given microbial ecologists an entirely new dimension for understanding natural ecosystems. This chapter discusses the common terms used by microbial ecologists to describe diversity, and attempts to explain their virtues and pitfalls. The first classification system was devised by Aristotle at least 2,400 years ago who generated the first hierarchy based on creationist and essential tenets. This system was based on only the two categories "species" and "genus," which were motivated by recurrent observations about the world. The current prokaryotic species concept fulfils the requisites of being universally applicable to the cellular nuclei-less microorganisms. In this chapter, the different terms used by microbial ecologists to name the units that they observe, their suitability, and which of them may (from our point of view) have an optimal applicability, are discussed. It is possible that a single observed band contains up to three different sequences or viceversa where an identical sequence can appear in different bands. There is a growing group of scientists who prefer the use of operational taxonomic unit (OTU) to name their units of comparison.
Extending Movable Surfaces with Touch Interaction Using the VirtualTablet: An Extended View

Immersive output and natural input are two core aspects of a virtual reality experience. Current systems are frequently operated by a controller or gesture-based approach. However, these techniques are either very accurate but require an effort to learn, or very natural but miss haptic feedback for optimal precision. We transfer ubiquitous touch interaction with haptic feedback into a virtual environment. To validate the performance of our im- plementation, we performed a user study with 28 participants. As the results show, the movable and cheap real world object supplies an accurate touch detection that is equal to a laserpointer-based interaction with a controller. Moreover, the virtual tablet can extend the functionality of a real world tablet. Additional information can be displayed in mid-air around the touchable area and the tablet can be turned over to interact with both sides. Therefore, touch interaction in virtual environments allows easy to learn and precise system interaction and can even augment the established touch metaphor with new paradigms.
The Effect of Supramalleolar Orthotic Use on Activity and Participation Skills in Children with Down Syndrome

ABSTRACT Introduction This study aimed to determine if supramalleolar orthosis (SMO) use improved activity level skill and participation levels in children with Down syndrome (DS) who have been walking for at least 1 year. Methods Twenty children with DS (aged 2–10 years) wore no orthoses for 4 weeks followed by SMOs for 4 weeks. At the initial visit, using goal attainment scaling (GAS), families determined two participation goals and expected outcomes. After both the no-orthoses and orthoses phases, goal attainment, Gross Motor Function Measure-Scale E, single-limb stance time, and shuttle run time were measured. Results SMO use led to improvements in Gross Motor Function Measure-Scale E (P = 0.01) and GAS scores (P ≥ 0.001), as well as a time by condition interaction for shuttle run time (P = 0.049). Conclusions The use of SMOs led to improvements in activity level outcomes in family-selected participation goals.