Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid modelling of erythropoiesis and blood disorders

This dissertation is devoted to the development of new methods of mathematical modeling in biology and medicine, off-lattice discrete-continuous hybrid models, and their applications to modelling of hematopoiesis and blood disorders, such as leukemia and anemia. In this approach, biological cells are considered as discrete objects while intracellular and extracellular networks are described with continuous models, ordinary or partial differential equations. Cells interact mechanically and biochemically between each other and with the surrounding medium. They can divide, die by apoptosis or differentiate. Their fate is determined by intracellular regulation and influenced by local control from the surrounding cells or by global regulation from other organs. In the first part of the thesis, hybrid models with off-lattice cell dynamics are introduced. Model examples specific for biological processes and describing competition between cell proliferation and apoptosis, proliferation and differentiation and between cell cycling and quiescent state are investigated. Biological pattern formation with hybrid models is discussed. Application to bacteria filament is illustrated. In the next chapter, hybrid model are applied in order to model erythropoiesis, red blood cell production in the bone marrow. The model includes immature blood cells, erythroid progenitors, which can self-renew, differentiate or die by apoptosis, more mature cells, reticulocytes, which influence erythroid progenitors by means of growth factor Fas-ligand, and macrophages, which are present in erythroblastic islands in vivo. Intracellular and extracellular regulation by proteins and growth factors are specified and the feedback by the hormones erythropoietin and glucocorticoids is taken into account. The role of macrophages to stabilize erythroblastic islands is shown. Comparison of modelling with experiments on anemia in mice is carried out. The following chapter is devoted to leukemia modelling and treatment. Erythroleukemia, a subtype of Acute Myeloblastic Leukemia (AML), develops due to insufficient differentiation of erythroid progenitors and their excessive slef-renewal. A Physiologically Based Pharmacokinetics-Pharmacodynamics (PBPKPD) model of leukemia treatment with AraC drug and chronotherapeutic treatments of leukemia are examined. Comparison with clinical data on blast count in blood is carried out. The last chapter deals with the passage from a hybrid model to a continuous model in the 1D case. A convergence theorem is proved. Numerical simulations confirm a good agreement between these approaches.
Prospek Penggunaan Mikroba Antagonis sebagai agens pengendali hayati penyakit utama pada tanaman hias dan sayuran

Cultivation of ornamental plants and vegetables faces various problems that inhibit efforts to increase plant production. One of the most important constraints is disease incidences, i.e. wilt disease (Fusarium spp.) on carnation, damping off (Rhizoctonia spp.) on chrysanthemum, bacterial wilt (Ralstonia solanacearum) on Solanaceae, and club root (Plasmodiophora brassicae) on Barssicaceae. One of environmentally-friendly control methods is application of antagonistic microorganisms. The purpose of this paper is to inform prospects of the use of microbial antagonists as biological control agents of major diseases on ornamental plants and vegetables. Antagonistic microbes are the bacteria, fungi, actinomycetes or virus that can suppress other microbes. Antagonistic bacteria (Bacillus subtilis and Pseudomonas fluorescens), antagonistic fungi (Trichoderma harzianum, Gliocladium sp., and non-pathogenic Fusarium), actinomycetes (Streptomyces spp.), and virus (Carna-5 vaccine) are known to be effective as biological control agents. Their use as a biological control agent is proven to be prospective since their isolation techniques, propagation and biopesticide formulation are well known by inventors in Indonesia. Nowdays, the microbes have been formulated by various research institutes as microbial pesticides and licenced to private company and commercialized widely to the domestic market. This indicates that prospect of application of antagonistic microbe is very bright to control major diseases of ornamental plants and vegetables.
Enabling rapid cloud-based analysis of thousands of human genomes via Butler

We present Butler, a computational framework developed in the context of the international Pan-cancer Analysis of Whole Genomes (PCAWG)1 project to overcome the challenges of orchestrating analyses of thousands of human genomes on the cloud. Butler operates equally well on public and academic clouds. This highly flexible framework facilitates management of virtual cloud infrastructure, software configuration, genomics workflow development, and provides unique capabilities in workflow execution management. By comprehensively collecting and analysing metrics and logs, performing anomaly detection as well as notification and cluster self-healing, Butler enables large-scale analytical processing of human genomes with 43% increased throughput compared to prior setups. Butler was key for delivering the germline genetic variant call-sets in 2,834 cancer genomes analysed by PCAWG1.
Corresponding long-term shifts in stream temperature and invasive fish migration

By investigating historic trapping records of invasive sea lamprey (Petromyzon marinus) throughout tributaries to the Laurentian Great Lakes, we found that upstream spawning migration timing was highly correlated with stream temperatures over large spatial and temporal scales. Furthermore, several streams in our study exceeded a critical spring thermal threshold (i.e., 15 °C) and experienced peak spawning migration up to 30 days earlier than in the 1980s, whereas others were relatively unchanged. Streams exhibiting warming trends and earlier migration were spatially clustered and generally found on the leeward side of the Great Lakes where the lakes most affect local climate. These findings highlight that all streams are not equally impacted by climate change and represent, to our knowledge, the first observation linking long-term changes in stream temperatures to shifts in migration timing of an invasive fish. Earlier sea lamprey migration in Great Lakes tributaries may improve young of the year growth a.
Whole Blood Transcriptional Profi ling Reveals Signifi cant Downregulation of HLA Class I and II Genes in Essential Thrombocythemia, Polycythemia Vera and Myelofi brosis

Gene expression profi ling studies in the Philadelphia-negative chronic myeloproliferative neoplasms have unraveled signifi cant deregulation of several immune and infl ammation genes that might be of importance for clonal evolution due to defective tumor immune surveillance. Other mechanisms might be downregulation of major histocompatibility (MHC) class I and II genes, which are used by tumor cells to escape antitumor T-cell-mediated immune responses. We have performed whole blood transcriptional profi ling of genes encoding human leukocyte antigen (HLA) class I and II molecules, beta2microglobulin and members of the antigen processing machinery of HLA class I molecules (LMP2, LMP7, TAP1, TAP2 and tapasin). The fi ndings of signifi cant downregulation of several of these genes may likely be of major importance for defective tumor immune surveillance. Since up-regulation of HLA-genes are recorded during treatment with epigenome modulating agents (DNA-hypometylators and DNA-hyperacetylators (histone deacetylase inhibitors)) and interferon-alpha2 our fi ndings call for prospective transcriptional studies of HLA-genes during treatment with these agents.
Drp1-dependent mitochondrial autophagy plays a protective role against pressure-overload-induced mitochondrial dysfunction and heart failure

heart failure after TAC. Injection of Tat-Beclin 1, a potent inducer of autophagy, but not control peptide, on day 7 after TAC, partially rescued mitochondrial autophagy and attenuated mitochondrial dysfunction and heart failure induced by overload. Haploinsufficiency of either drp1 or beclin 1 prevented the rescue by Tat-Beclin 1, suggesting that its effect is mediated in part through autophagy, including mitochondrial autophagy. Conclusions —Mitochondrial autophagy is transiently activated and then downregulated in the mouse heart in response to pressure overload. Downregulation of mitochondrial autophagy plays an important role in mediating the development of mitochondrial dysfunction and heart failure, whereas restoration of mitochondrial autophagy attenuates dysfunction in the heart during pressure overload. ( Circulation . 2016;133:1249-1263. DOI: 10.1161/CIRCULATIONAHA.115.020502.) rapidly through depolarization of the mitochondrial membrane potential and causes deterioration of the function of healthy mitochondria. Thus, cardiomyocytes possess robust quality control mechanisms, and autophagy, which degrades protein and organelles through lysosomes, is a major mechanism for the elimination of dysfunctional mitochondria. In this study, we show that both general autophagy and a mitochondria-specific form of autophagy (mitochondrial autophagy) are downregulated after pressure overload and that mitochondrial dysfunction develops only after mitochondrial autophagy is downregulated. Mitochondrial autophagy was induced in response to pressure overload through a mechanism dependent on Drp1, a protein known to mediate mitochondrial fission. Treatment of animals with Tat-Beclin 1 peptide, known to stimulate autophagy through mobilization of endogenous Beclin 1, a protein essential for autophagy, increased the level of mitochondrial autophagy in the heart and partially rescued the animals from the development of pressure overload–induced heart failure. These results suggest that interventions to restore the level of mitochondrial autophagy should be considered for potential treatment for patients with heart failure.
Differentiation between vaccinal and field strains of E. coli using phenotype and genotype characterization

Background: E. coli infection is considered as an important bacterial problem associated with significant economic losses and usually associated with a variety of disease conditions, including acute septicaemia, haemorrhagic enteritis, pericariditis, salpingitis and complicated air saculitis. These considerations suggest that control of E. coli by vaccination could be of great value especially live vaccine that based on defined mutations that impair and non-revering virulence. Material and Methods: Wild type O78 strain, Live O78 aroA gene deleted vaccine and Live O78 crp gene deleted vaccine were used to accomplish this study. Phenotypic characterization was adopted by studying the cultural, biochemical and serological properties. Also genotypic characterization was studied for 16S rRNA , aroA and crp genes. Results: Growth pattern on different media differed among the used strains as the wild type and Δ aroA mutant were nearly similar while the Δ crp mutant strain was greatly differed. Biochemically the difference between the wild-type and Δ aroA mutant was inability of mutant strain to produce arginine dihydrase (ADH) and fermentation of saccharose. On the other hand the Δ crp mutant failed to produce ADH and to ferment any of the carbohydrates except glucose. A successful amplification of the 16S rRNA gene at 585 bp was detected with the all tested strains while was 1206 bp with only wild type and Δ crp mutant strain when aroA gene primers were used. Regarding crp genes, the amplified products was at 1029 bp with the wild and Δ aroA mutant but not with Δ crp mutant strains. Conclusion: Findings of this study prove the use of methods based on molecular techniques like PCR to differentiate between different types of E. coli either wild or vaccinal mutant type strains. Also it may help in exclusion or proving the return back to virulence of the mutant vaccinal strains.
Conservation of saline patches in Central Otago needs better recognition of physical processes to secure future habitats

ABSTRACT Saline soils are scattered within multiple inland basins in the semi-arid, rain shadow areas of the South Island, New Zealand. Competing land use activities in agriculture, mining, viticulture and human habitation have led to a strong decline in saline soils to an estimated < 1% of their original distribution. Small areas of ‘new’ (decades old) salinity have arisen at some highly modified sites but these are poorly understood in relation to older saline soils. Recent information from fine-scale geological surveys and geochemical analysis of substrates at two Department of Conservation scientific reserves in Central Otago, with specialist saline flora, is presented in a short synthesis. The goal is to amend existing viewpoints on plant–substrate interactions at what are abandoned gold mine sites. The current surface conditions at Springvale Reserve and Chapman Road Reserve, near Alexandra, which have developed acute salinity during the last 100 years since mining ceased, are outlined. The process of salt accumulation at each site is also clarified and seeks to rectify previous views on local salt source. The new geological data can inform conservation management of the sites, to better address the overall decline of saline habitat for indigenous plant species. A new adaptive management approach is proposed for each reserve that essentially harnesses effects of physical processes, to secure botanical values in the near future.
Mechanisms regulating GABAergic neurogenesis in the developing mouse midbrain

In this study, we provide molecular, genetic and phenotypic evidence for the unique, overlapping and synergistic interaction between the hairy Enhancer of split-related [h/E(spl)] transcription factor (TF) MEGANE (MGN, HELT, HESLIKE) and the proneural TF MASH1 (ASCL1) for the acquisition of midbrain GABAergic identity. By combination of gain- and loss-of-function experiments in the developing mouse midbrain, we discovered a novel dorsal/ventral specification mechanism by which MGN and MASH1 cooperation induces GABAergic identity. These results provide a novel paradigm how [h/E(spl)] and proneural families can cooperate for the acquisition of midbrain GABAergic neuronal identity.
Male tree weta are attracted to cuticular scent cues but do not discriminate according to sex or among two closely related species

Recognition of conspecifics is an essential precursor of successful mating. Where related species coexist, species discrimination might be important, but because related species are similar, species signal recognition may actually be low. Chemical cues such as cuticular hydrocarbons (CHCs) are frequently used by insects to identify suitable sexual partners. We predicted that New Zealand tree weta (Hemideina spp.), a genus of nocturnal ensiferan Orthoptera that live both allopatrically and sympatrically, use chemical signals from either frass or CHCs to find mates. In a series of six laboratory trials using both H. thoracica and H. crassidens, we found that male tree weta, but not female tree weta, occupied cavities primed with female cuticular cues more often than cavities without. However, males did not discriminate between chemical cues of male and female conspecifics, or between conspecifics and heterospecifics. In field trials, tree weta did not occupy artificial cavities primed with either female frass or female cuticular cues more often than unscented cavities. However, in both trials weta preferentially returned to cavities that had already been occupied earlier in the trials. A final field trial confirmed the presence of mixed species harems during the mating season in one region of sympatry. Our results suggest that selection on sex and species specific chemical cues that could be used to find conspecific mates is weak. Mixed species aggregations suggest that identification of conspecific mating cues has not evolved to be species specific. We infer that for male tree weta, the cost of mating with heterospecifics is likely less than not mating at all.
Point-to-Point Positioning Control Performance of a 2-DOF Robotic Finger

This paper investigated the positioning control performance of a two-degree-of-freedom (2-DOF) robotic finger mechanism to achieve precision motion control as an initial study towards developing a multi-fingered robotic hand system. Previous research has shown that behaviours such as instability, large steady-state error and poor transient performance often occur in the robotic hand mechanism. Therefore, this paper described the design of a 2-DOF robotic finger mechanism, which was then compared with the performance of several controllers by Point-to-Point (PTP) positioning control. The proposed controllers relied on the angular position control of each motor joint, (i.e. the position control of the 2-DOF robotic finger mechanism). The closed-loop system for an uncompensated and compensated system were used in this study with several reference angles. Three different control strategies namely; (i) Proportional Integral Derivative (PID) controller (ii) Fuzzy Logic controller (FLC) and (iii) Linear Quadratic Regulator (LQR) controller were selected for comparison via simulation and in performing the experimental work. The controller results were validated by Point-to-Point (PTP) positioning control at different reference amplitudes. From the results, the FLC was found to provide optimal performance with a higher level of adaptability for the PTP positioning control with improvements in both response time by 97.9% (0.075 s) and steady-state error by 99.5% (0.01°) compared to the uncompensated system. Index Term— point-to-point, robotic finger, controller,
Hemagglutinin assay for influenza virus

A method for analyzing a vaccine consisting of the following steps: (a) detect the hemagglutinin of influenza virus in the vaccine, or one of its samples with the following steps: (i) contacting the sample with a lectin that is immobilized on a solid support, for supplying the captured hemagglutinin; and (ii) detecting the hemagglutinin captured by an immunoassay; and (b) use the results of step (a) to calculate the concentration of hemagglutinin in the vaccine.
Constructionsofpairsoforthogonal latincubes

Funding information Russian Science Foundation, Grant/Award Number: 18‐11‐00136 Abstract A pair of orthogonal latin cubes of order q is equivalent to a maximum distance separable code with distance 3 or to an OA q (3, 5, ) 1 orthogonal array. We construct pairs of orthogonal latin cubes for sequences of previously unknown orders q i = 16(18 − 1) + 4 i and q i = 16(18 + 5) + 4 ′ i . The minimal new obtained parameters of orthogonal arrays are OA (3, 5, 84) 1 .
Reproductive biology of two species of Hyalella Smith, 1874 (Crustacea: Amphipoda: Hyalellidae) from southern Brazil

ABSTRACT Reproduction is a critical event in the life cycle of animals, and a high amount of energy is allocated to it. The aim of this study was to characterize the reproductive biology of two recently described species of Hyalella from the north-east region of state of Rio Grande do Sul in southern Brazil. The specimens were collected during 12 months from a stream source (Hyalella georginae) and from a water reservoir (H. gauchensis), in Palmeira das Missões municipality, state of Rio Grande do Sul. Upon sampling, ovigerous females and pairs in precopulatory behaviour were separated into microtubes. In the laboratory, the cephalothorax length (CL in mm) of all specimens was measured. Male size at onset of sexual maturity was larger than that of the females, in both species. There was a correlation between the size of paired males and females: larger males carried larger females, in both Hyalella species. Precopulatory pairs were found throughout the year; however, H. georginae had a higher frequency in spring, and H. gauchensis in autumn. There was a positive correlation between the CL of ovigerous females and the number of eggs/juveniles. A reduction in the number of eggs throughout the embryonic development was observed in H. georginae. The average fecundity of H. georginae was significantly higher than H. gauchensis. The differences between the reproductive biology of these species may be related to the physical and environmental conditions at which they are exposed in their habitats.
Optical Aberrations of Guinea Pig Eyes

Purpose The guinea pig is widely used in studies of refractive error development and myopia which often involve experimental optical manipulations. The study described here investigated the optical quality of the guinea pig eye, for which there are limited data, despite its fundamental importance to understanding visually guided eye growth. Methods The ocular aberrations of eight adolescent New Zealand pigmented guinea pigs (6–11 weeks old) were measured after cycloplegia using a custom-built Shack–Hartmann aberrometer and fit with a Zernike polynomial function to the 10th order (65 terms). The optical quality of their eyes was assessed in terms of individual Zernike coefficients, and data were further analyzed to derive root-mean-square (RMS) wavefront errors, modulation transfer functions (MTFs), point spread functions (PSFs), Strehl ratios, and depth of focus. A 4-mm pupil was used in all computations. The derived data are compared with equivalent data from normal young adult human eyes. Results The guinea pigs exhibited low hyperopia and a small amount of positive spherical aberration, with other aberration terms decreasing with increasing order. Their average depth of focus, estimated from through-focus modulation, was 3.75 diopters. The RMS wavefront error of the guinea pig eye was found to be larger than that of the human eye for the same pupil size, reflecting a higher degree of aberrations, although the PSF (area) on the retina was smaller and sharper due to its shorter focal length. The radial average best-focus MTF derived for the guinea pig eye showed good performance at very low spatial frequencies, with a steeper decline with increasing frequency than for the human eye, dropping below 0.3 at 9 cpd. When converted to linear units (cycles/mm), the guinea pig eye had a higher spatial frequency cutoff and a slight contrast advantage for low spatial frequencies compared to the human eye. Conclusions The optical quality of the guinea pig eye is far superior to their reported behavioral visual acuity. This implies a neuroanatomical limit to their vision, which contrasts with the close match of optical and neural limits to spatial resolution in human eyes. The significance for eye growth regulation of the relative optical advantages exhibited by guinea pig eyes, when optical quality is expressed in linear rather than angular retinal units, warrants further consideration.