Miracle-dz/UniFAR-FTUs huggingface dataset:
Yeast [PSI+] Prion Aggregates Are Formed by Small Sup35 Polymers Fragmented by Hsp104*

The yeast [PSI+] determinant is related to formation of large prion-like aggregates of the conformationally altered Sup35 protein. Here, we show that these aggregates are composed of small Sup35 prion polymers and associated proteins. In contrast to other protein complexes of yeast lysates, but similarly to amyloid fibers, these polymers are insoluble in SDS at room temperature. The polymers on average are about 30-fold smaller than the aggregates and comprise from 8 to 50 Sup35 monomers. The size of polymers is characteristic of a given [PSI+] variant and differs between the variants. Blocked expression of Hsp104 chaperone causes gradual increase in the size of prion polymers, while inactivation of Hsp104 by guanidine HCl completely stops their fragmentation, which shows indispensability of Hsp104 for this process.
Intrinsic PID controller for a segway type mobile robot

The control of underactuated constrained systems have proven to be a challenging task. This paper extends an intrinsic geometric PID controller developed for fully actuated mechanical systems to a class of under actuated non-holonomic systems. As an illustration the results are applied to a self balancing Segway type mobile robot. The Segway is constrained to move under no slip conditions and has only two control inputs. We show that the geometric PID controller proposed in this paper ensures almost global locally exponential stability of the upright motion of the Segway even in the presence of large parameter uncertainties.
Concurrent Replication and Methylation at Mammalian Origins of Replication

ABSTRACT Observations made with Escherichia coli have suggested that a lag between replication and methylation regulates initiation of replication. To address the question of whether a similar mechanism operates in mammalian cells, we have determined the temporal relationship between initiation of replication and methylation in mammalian cells both at a comprehensive level and at specific sites. First, newly synthesized DNA containing origins of replication was isolated from primate-transformed and primary cell lines (HeLa cells, primary human fibroblasts, African green monkey kidney fibroblasts [CV-1], and primary African green monkey kidney cells) by the nascent-strand extrusion method followed by sucrose gradient sedimentation. By a modified nearest-neighbor analysis, the levels of cytosine methylation residing in all four possible dinucleotide sequences of both nascent and genomic DNAs were determined. The levels of cytosine methylation observed in the nascent and genomic DNAs were equivalent, suggesting that DNA replication and methylation are concomitant events. Okazaki fragments were also demonstrated to be methylated, suggesting that the rapid kinetics of methylation is a feature of both the leading and the lagging strands of nascent DNA. However, in contrast to previous observations, neither nascent nor genomic DNA contained detectable levels of methylated cytosines at dinucleotide contexts other than CpG (i.e., CpA, CpC, and CpT are not methylated). The nearest-neighbor analysis also shows that cancer cell lines are hypermethylated in both nascent and genomic DNAs relative to the primary cell lines. The extent of methylation in nascent and genomic DNAs at specific sites was determined as well by bisulfite mapping of CpG sites at the lamin B2, c-myc, and β-globin origins of replication. The methylation patterns of genomic and nascent clones are the same, confirming the hypothesis that methylation occurs concurrently with replication. Interestingly, the c-mycorigin was found to be unmethylated in all clones tested. These results show that, like genes, different origins of replication exhibit different patterns of methylation. In summary, our results demonstrate tight coordination of DNA methylation and replication, which is consistent with recent observations showing that DNA methyltransferase is associated with proliferating cell nuclear antigen in the replication fork.
Application of Stem Cells and iPS Cells in Toxicology

Fertilization of an oocyte by a spermatozoid, or in general terms, fertilization of the female gamete by the male gamete results in the genesis of the basic unit in the development of an organism, the embryo. The primordial unicellular embryo will, after several rounds of division, develop into a multicellular organism and ultimately into an offspring resembling its progenitors in structure and function. At the molecular level, embryonic development is governed by the expression and interaction of a specific set of genes, certain proteins and peptides, and the signaling of growth factors. In other words, embryonic development is a complex process, which involves a vast but specific genetic network corresponding to its different stages. Early observations made in the sea urchin (Driesch, 1892, 1893, 1894; Gilbert, 2000; Roux, 1888; Roux, 1894) demonstrated that splitting a two‐cell embryo into single cells resulted in the emergence of two fully developed organisms. Hans Spemann repeated these experiments in the salamander two‐cell embryo, ultimately obtaining two fully developed “twins” (Gilbert, 2000; Spemann, 1921). These early experiments demonstrated the totipotency of the early embryonic cells and the retention of certain “information,” which allows for the development of an organism. This information is progressively lost as the embryo develops and its cells differentiate and reach more specific roles (Gilbert, 2000; Spemann, 1921). However, the question remains, what is the stage at which cells lose this potential? Further experimentation revealed that cells derived from teratomas, or from mouse blastocysts inner cell mass (ICM) cultured upon a suitable fibroblast feeder layer, continue to proliferate without overt differentiation Application of Stem Cells and iPS Cells in Toxicology
Regulation of cell morphology and adhesion by the tuberous sclerosis complex (TSC1/2) gene products in human kidney epithelial cells through increased E‐cadherin/β‐catenin activity

We investigated the effects of overexpression of the tuberous sclerosis‐1 and ‐2 (TSC1/2) gene products (hamartin and tuberin, respectively) in the human kidney epithelial cell line 293 with an inducible expression system. As we had observed previously in fibroblasts, 293 cells overexpressing hamartin and/or tuberin grew more slowly in vitro. However, here we also observed that the 293 overexpressing cells underwent a dramatic morphological change in which groups of cells formed compact clusters. The overexpressing cells also displayed decreased dissociation and increased reaggregation in vitro. These changes were found to be associated with an increased level of E‐cadherin, which is known to regulate cell‐cell interactions in epithelial cells, and of its binding partner β‐catenin. Consistent with the role of E‐cadherin in these effects, we found that the observed changes in 293 cell morphology, dissociation, and adhesion were calcium‐dependent, and were reproduced by overexpression of E‐cadherin. In contrast, overexpression of TSC1 in rat embryo fibroblasts, which lack E‐cadherin, failed to elicit the same changes as in 293 cells. We conclude that the hamartin/tuberin complex exerted a direct effect on the morphology and adhesive properties of 293 cells through regulation of the level and/or activity of cellular E‐cadherin/β‐catenin. © 2003 Wiley‐Liss, Inc.
Zeroth Order Resonance Loop Antenna

A new type of low-profile omnidirectional antenna is proposed in this paper. The proposed antenna has the conceptual configuration of the horizontal magnetic loop current on perfect electric conductor plane, which has been realized by the zeroth-order resonator (ZOR) antenna using mushroom structure. The mushroom structure as a transmission line has negative, zero, and positive propagation constant depending on its operation frequency since mushroom structure is artificial composite right-left handed transmission line. Zeroth-order resonance, of which frequency is independent of physical length, is naturally presented. In particular, mushroom ZOR antenna generates a uniform vertical electric field against ground plane, so that it omnidirectionally radiates in a horizontal plane. Operation frequency, absolute gain, and gain variations for omnidirectional radiation of the designed prototype are 7.9 GHz, 2.6dBi, less than 1.5 dBi, respectively
Symmetry-Breaking of Interfacial Polygonal Patternsand Synchronization of Travelling Waves within aHollow-Core Vortex

A hollow vortex core in shallow liquid, produced inside a cylindrical reservoir using a rotating disk near the bottom of the container, exhibits interfacial polygonal patterns. These pattern formations are to some extent similar to those observed in various geophysical, astrophysical and industrial flows. In this study, the dynamics of rotating waves and polygonal patterns of symmetry-breaking generated in a laboratory model by rotating a flat disc near the bottom of a cylindrical tank is investigated experimentally. The goal of this paper is to describe in detail and to confirm previous conjecture on the generality of the transition process between polygonal patterns of the hollow vortex core under shallow water conditions. Based on the image processing and an analytical approach using power spectral analysis, we generalize in this work – using systematically different initial conditions of the working fluids – that the transition from any N-gon to (N+1)-gon pattern observed within a hollow core vortex of shallow rotating flows occurs in an universal two-step route: a quasi-periodic phase followed by frequency locking (synchronization). The present results also demonstrate, for the first time, that all possible experimentally observed transitions from N-gon into (N+1)-gon occur when the frequencies corresponding to N and N+1 waves lock at a ratio of (N-1)/N.
Recent Progresses on Self-incompatibility Research in Brassica Species

Many hermaphrodite plant species have evolved mechanisms to prevent self-fertilization. One such mechanism is self-incompatibility (SI), which is defined as the inability of a fertile hermaphrodite plant to produce zygotes after self-pollination. SI prevents self-fertilization by rejecting pollen from plants with the same genotype. The SI system in Brassica is controlled sporophytically by multiple alleles at a single locus, designated as S, and involves cell-cell communication between male and female. When the S phenotype of the pollen is the same as that of the stigma, pollen germination and/or pollen tube penetration are disturbed on the papilla cells. On the female side, two genes (SLG and SRK) located at the S locus, are involved in the SI reaction. SLG is a secreted glycoprotein expressed abundantly in the papilla cell, and SRK is a membrane-spanning receptor-like serine/threonine kinase whose extracellular domain is highly similar to SLG. Gain-of-function experiments have demonstrated that SRK solely determines S haplotype-specificity of the stigma, while SLG enhances the recognition reaction of SI. The sequence analysis of the S locus genomic region of Brassica campestris (syn. rapa) has led to the identification of an anther-specific gene, designated as SP11, which encodes a small cysteine-rich basic protein. Pollination bioassay and gain-of-function experiments have indicated that SP11 is the male S determinant. When the sequence of SP11 was aligned, six cysteine residues were found to be completely conserved among alleles. These conserved cysteine residues could be important for the tertiary structure of SP11. Recent biochemical analysis has suggested that SP11 operates as a sole ligand to activate its cognate SRK specifically. Because the activity of the S allele is controlled sporophytically, dominance relationships influence the ultimate phenotype of both the stigma and pollen. Molecular analysis has demonstrated that the dominance relationships between S alleles in the stigma were determined by SRK itself, but not by the relative expression level. In contrast, in the pollen, the expression of SP11 from the recessive S allele was specifically suppressed in the S heterozygote, suggesting that the dominance relationships in pollen were determined by the expression level of SP11.
A health monitoring system using multiple non-contact ECG sensors for automotive drivers

Health and alert-level monitoring of automotive driver is very important to reduce the number of vehicle accidents and associated fatalities. The proposed work focuses on the development of a reliable and low-cost health monitoring system for automotive drivers. It is based on non-contact electrocardiogram (ECG) principle. Multiple signal acquisition ECG electrodes are placed on the seat and seat-belt of the automotive. The signals from the different electrodes are interfaced to simple analog and digital signal processing units through a switching logic. The frequency domain-based digital processing and the switching logic ensures that best quality ECG signal is selected for heart rate (HR) estimation. A prototype of the proposed system is build and tested on several volunteers. These tests show that the accuracy is 2 bpm. Additional tests to determine the system performance in various conditions was conducted and results reported.
Test and repair of large embedded DRAMs. 2

For pt. 1 see ibid., p. 163-172 (2001). The era of embedded DRAM (eDRAM) in systems-on-silicon and in multimillion gate ASICs is upon us. As process developers and logic designers succeed in offering highly integrated functions to their customers, the test engineer is left with the seemingly impossible task of guaranteeing that the eDRAM utilized in these advanced chips has the same high test coverage and outgoing quality level as the customer has come to expect with discrete DRAM. Unfortunately, some of the very attributes that make eDRAM attractive to the ASIC designer i.e., high bandwidth with high I/O bus width and thus high macro pin count, make it very difficult to test when isolated from the chip terminals by various levels of logic and instantiated multiple times in the hierarchy. Several differing approaches have been taken to attempt to optimize the test of the embedded memory in these complex chips. This paper investigates two such approaches that have been developed: the ASIC-centric approach and the semi-custom, high volume solution, and discuss some details of their differing methodology and motivations for their varying directions.
EPIPOLAR IMAGE GENERATION AND CORRESPONDING POINT MATCHING FROM COAXIAL VEHICLE-BASED IMAGES

The matching of corresponding points is the foundation of image-based 3D reconstruction. As coaxial vehicle-based images as concerned, however, since they are taken along the optical axis epipolar lines of coaxial stereo pair are arranged in the direction of radial in stead of nearly horizontal arrangement of stereo pair with horizontal baseline. Therefore, the generation of epipolar images and corresponding point matching on epipolar images are discussed in this paper. Although the straight lines in raw image become arcs in epipolar image, the point features are still apparently clear and possible for 1D corresponding point matching. Moreover, matching in the epipolar images can improve the success rate. Coaxial vehicle-based images are used to test the algorithms presented in this paper.
Beta emitters and radiation protection

Background. Beta emitters, such as 90Y, are increasingly being used for cancer treatment. However, beta emitters demand other precautions than gamma emitters during preparation and administration, especially concerning shielding. Aim. To discuss practical precautions for handling beta emitters in general, and specifically determine proper shielding for 90Y, while comparing to 177Lu and 131I. The aim is achieved through the application of physical principles combined with results from practical experience. Material and methods. Typical and maximal electron ranges were calculated for 131I, 177Lu, and 90Y, using data from a freely available database. Bremsstrahlung yields were calculated for 90Y shielded by lead, aluminium, or perspex. Bremsstrahlung spectrum from 90Y shielded by perspex was measured, and attenuation of spectrum by lead was calculated. Whole-body and finger doses to persons preparing 90Y-Zevalin were measured. Conclusions. Good laboratory practice is important to keep radiation doses low. To reduce bremsstrahlung, 90Y should not be shielded by lead but instead perspex (10 mm) or aluminium (5 mm). Bremsstrahlung radiation can be further reduced by adding a millimetre of lead on the outside of the primary shielding material. If suitable shielding is used and larger numbers of handlings are divided among several persons, then handling of beta emitters can be a safe procedure.
Research on the modeling and simulation of coordinate structure hybrid excitation synchronous generator with AC excitation

In order to improve the regulation difficulty of magnetic field and voltage of permanent-magnet synchronous machine (PMSM), a novel brushless coordinate structure hybrid excitation synchronous generator (HESG) with AC excitation is proposed in this paper. The output voltage of the HESG can be regulated through the control of the amplitude and phase of the AC excitation current. The structure and operation principle of the HESG are described. The mathematical model of the HESG with AC excitation is built. The simulation model of the HESG is established with S-function. The no-load characteristic, external behaviors and the regulation characteristic are simulated. The simulation results verify the feasibility of the proposed HESG and the correctness of the mathematical model.
Outbreaks of Hydropericardium Syndrome and Molecular Characterization of Korean Fowl Adenoviral Isolates

Abstract Outbreaks of hydropericardium syndrome (HPS), caused by fowl adenovirus serotype 4 (FAdV-4), have occurred in Korea and caused severe economic loss due to mortality and weight loss. From these outbreaks, several adenoviruses were isolated and identified in samples from broilers, layers, breeders, and native Korean fowl. In pathologic examinations, hydropericardium and multifocal hepatic necrosis, with an intranuclear inclusion body in hepatocytes, were observed. Specific adenovirus particles were also observed in the nucleus of hepatocytes, by electron microscopic examination. Polymerase chain reaction (PCR) analysis of the hexon gene identified all of the isolates as FAdV, serotype 4 and genotype C. To reproduce FAdV-4 field cases, 8- and 52-week-old specific pathogen free (SPF) chicks were infected intramuscularly with the field isolate CBU070244. The mortality rate of infected chicks ranged from 10%–40%, and specific pathologic lesions, such as swollen livers and hydropericardium, were observed. Further studies to determine the prevalence of infection, and analysis of the economic impact to the poultry industry, are needed in the near future. Reporte de Caso—Brote del síndrome de hidropericardio y caracterización molecular de aislados de adenovirus aviares de Corea. Brotes del síndrome hidropericardio causados por adenovirus aviar serotipo 4 han ocurrido en Corea causando graves pérdidas económicas debido a la mortalidad y a los bajos pesos corporales. A partir de pollos de engorde, ponedoras y gallinas nativas de Corea involucradas en estos brotes, se aislaron e identificaron varios adenovirus. En los exámenes patológicos se observó hidropericardio y necrosis hepática multifocal con presencia de cuerpos de inclusión intranucleares en los hepatocitos. Mediante el microscopio electrónico se observaron los adenovirus en el núcleo de los hepatocitos. El análisis de la reacción en cadena por la polimerasa del gen hexón identificó todos los virus aislados como pertenecientes al serotipo 4 y al genotipo C de los adenovirus aviares. Para reproducir la enfermedad, se utilizaron aves libres de patógenos de 8 y 52 semanas de edad, infectándolas por la vía intramuscular con el aislamiento de campo identificado como CBU070244. Los porcentajes de mortalidad de las aves infectadas varió del 10% al 40% y se observaron lesiones específicas como inflamación del hígado e hidropericardio. En el futuro cercano, se necesita realizar estudios adicionales para determinar la prevalencia de la infección y el análisis del impacto económico sobre la industria avícola. Abbreviations: bp = base pairs; CBNU = Chungbuk National University; CELiC = chicken embryo liver cells; CELO = chicken embryolethal orphan; CPE = cytopathic effect; FAdV = fowl adenovirus; FAdV-4 = fowl adenovirus serotype 4; HPS = hydropericardium syndrome; PCR = polymerase chain reaction; REA = restriction enzyme analysis; SPF = specific pathogen free
Contrast gain control in the primate retina: P cells are not X-like, some M cells are

Abstract Primate retinal ganglion cells that project to the magnocellular layers of the lateral geniculate nucleus (M) are much more sensitive to luminance contrast than those ganglion cells projecting to the parvocellular layers (P). We now report that increasing contrast modifies the temporal-frequency response of M cells, but not of P cells. With rising contrast, the M cells' responses to sinusoidal stimuli show an increasing attenuation at low temporal frequencies while the P cells' responses scale uniformly. The characteristic features of M-cell dynamics are well described by a model originally developed for the X and Y cells of the cat, where the hypothesized nonlinear feedback mechanism responsible for this behavior has been termed the contrast gain control (Shapley & Victor, 1978, 1981; Victor, 1987, 1988). These data provide further physiological evidence that the M-cell pathway differs from the P-cell pathway with regard to the functional elements in the retina. Furthermore, the similarity in dynamics between primate M cells and cat X and Y retinal ganglion cells suggests the possibility that P cells, being different from either group, are a primate specialization not found in the retinae of lower mammals.
Identification of a Family of Streptococcal Surface Proteins with Extremely Repetitive Structure*

The group B Streptococcus (GBS) causes the majority of life-threatening bacterial infections in newborn children. Most GBS strains isolated from such infections express a surface protein, designated Rib, that confers protective immunity and therefore is of interest for analysis of pathogenetic mechanisms. Sequence analysis demonstrated that Rib has an exceptionally long signal peptide (55 amino acid residues) and 12 repeats (79 amino acid residues each) that account for >80% of the sequence of the mature protein. The repeats are identical even at the DNA level, indicating that an efficient mechanism operates to maintain a highly repetitive structure in Rib. The structure of Rib is similar to that of α, a previously characterized surface protein that is common among GBS strains lacking Rib. However, highly purified preparations of Rib and α did not cross-react immunologically, although the two proteins show extensive amino acid residue identity (47% in the repeat region). When analyzed in Western blots, Rib and α give rise to a regularly spaced ladder pattern, apparently due to hydrolysis of acid-labile Asp-Pro bonds in the repeats. We conclude that Rib and α are members of a novel family of streptococcal surface proteins with unusual repetitive structure.