gebhart/patrepeval huggingface dataset:
Defining the cellular precursors to human breast cancer (2011)

Human breast cancers are broadly classified based on their gene-expression profiles into luminal- and basal-type tumors. These two major tumor subtypes express markers corresponding to the major differentiation states of epithelial cells in the breast: luminal (EpCAM(+)) and basal/myoepithelial (CD10(+)). However, there are also rare types of breast cancers, such as metaplastic carcinomas, where tumor cells exhibit features of alternate cell types that no longer resemble breast epithelium. Until now, it has been difficult to identify the cell type(s) in the human breast that gives rise to these various forms of breast cancer. Here we report that transformation of EpCAM(+) epithelial cells results in the formation of common forms of human breast cancer, including estrogen receptor-positive and estrogen receptor-negative tumors with luminal and basal-like characteristics, respectively, whereas transformation of CD10(+) cells results in the development of rare metaplastic tumors reminiscent of the claudin-low subtype. We also demonstrate the existence of CD10(+) breast cells with metaplastic traits that can give rise to skin and epidermal tissues. Furthermore, we show that the development of metaplastic breast cancer is attributable, in part, to the transformation of these metaplastic breast epithelial cells. These findings identify normal cellular precursors to human breast cancers and reveal the existence of a population of cells with epidermal progenitor activity within adult human breast tissues.
Roles of sexual cell agglutination in yeast mass mating (2003)

The agalpha1 mutant MAT alpha cells specifically lack the cell surface alpha-type sexual agglutination substance, which is also called alpha-agglutinin. Because the mutant cells (MATalpha agalpha1) can not form aggregates with MATa cells, MATalpha agalpha1 cells are unable to mate with MATa cells when they are co-inoculated in a liquid medium, and the mating is attenuated on solid medium. The attenuated mating ability shown in the previous studies gave us a vague idea about a physiological function of the sexual agglutinability. In order to solve the question, mating behavior of MATalpha agalpha1 cells was investigated here under conditions where the contact between MATa and MAT alpha cells is assisted by physical methods. A synthetic mutation agalpha1::URA3 was constructed and used as well as agalpha1-1 for this study to ensure the genetic defect. When a mixture of MATa and MAT alpha cells was kept on filter membrane placed on relatively dry agar medium, even agalpha1::URA3 mutant cells mated as efficiently as the wild type (AGalpha1) cells did. On filter membrane placed on moist agar medium, agalpha1 mutants mated 10-fold less efficiently than wild type cells did. The mutant cells mated 10000-time less efficiently than the wild type cells in a pellet formed by brief low speed centrifugation. In contrast, the wild type MATalpha cells mated well under all conditions tested. Under the pellet condition, a mixture of MATa and MATalpha AG alpha1 cells formed an extended and cotton-like pellet while a mixture of MATa and MATalpha agalpha1 cells formed a compact and tight pellet. These results suggest that sexual cell agglutination contributes not only to cell contact between MATa and MAT alpha cells thereby stabilizing a-alpha cell pairs, but also to construction of a uniquely organized ultra structure favorable for zygote formation and subsequent growth of diploid cells. The mating specific extended pellet formation was observed also in 4 pairs of a and alpha strains in ascosporogenous yeast genera Hansenula and Pichia.
Pathological airway remodelling in inflammation (2010)

It is clear that airway mesenchymal cells, including fibroblasts/myofibroblasts, are more dynamic in terms of differentiation and origin than has previously been recognised. Considering that these cells are key players in the remodelling process, it is of utmost importance to characterise specific markers for the various fibroblast phenotypes and to explore factors that drive the differentiation to develop future diagnostic and therapeutic tools for asthma patients.
The Stereochemistry of Allenic Enol Tautomerism – Independent Generation and Reactivity of the Enolates (2006)

Abstract A priori, allenic enolates as reaction intermediates may be protonated to afford ( Z )‐ or ( E )‐α,β‐unsaturated carbonyl products. The allenic enolates are tautomeric with α‐vinylcarbanions. The literature on the behavior of these species on protonation is highly varied both in stereochemical outcome and in mechanistic interpretation. The current study has provided an independent mode of generation of the allenic enolates and has investigated the reaction stereochemistry of protonation to afford the stereoisomeric α,β‐unsaturated carbonyl products. Under kinetic conditions, these highly reactive species are protonated in the α,β‐π plane with preference ( E ) to the larger β group. Under thermodynamic conditions, addition/elimination equilibrates the two product stereoisomers. The kinetic protonation stereochemistry is a function of solvent, proton donor, and donor concentration. Computations serve to clarify the reaction mechanism. It was found that the stereochemistry of ketonization of allenic enolates follows the reaction course suggested as possible some decades earlier and common to less unique enolates. Additionally, the linear versus the bent enolate structure proves to depend on the countercation.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
NMDA receptor activation and respiratory chain complex V inhibition contribute to neurodegeneration in d‐2‐hydroxyglutaric aciduria (2002)

The inherited neurometabolic disease d-2-hydroxyglutaric aciduria is complicated by progressive neurodegeneration of vulnerable brain regions during infancy and early childhood, frequently presenting with hypotonia, epilepsy and psychomotor retardation. Here, we report that the pathogenetic role of the endogenously accumulating metabolite d-2-hydroxyglutarate (D-2), which is structurally similar to the excitatory amino acid glutamate, is mediated by at least three mechanisms. (i) D-2-induced excitotoxic cell damage in primary neuronal cultures from chick and rat involved N-methyl-d-aspartate (NMDA) receptor activation. Indeed, D-2 activated recombinant NMDA receptors (NR1/NR2A, NR1/NR2B) but not recombinant alpha-amino-3-hydroxy-5-methyl-4-isoxazole (AMPA) receptors in HEK293 cells. (ii) Fluorescence microscopy using fura-2 as a calcium indicator and the oxidant-sensitive dye dihydrorhodamine-123 revealed that D-2 disturbed intracellular calcium homeostasis and elicited the generation of reactive oxygen species. (iii) D-2 reduced complex V (ATP synthase) activity of the mitochondrial respiratory chain, reflecting an impaired energy metabolism due to inhibition of ATP synthesis but without affecting the electron-transferring complexes I-IV. Thus, D-2 stimulates neurodegeneration by mechanisms well-known for glutamate, NMDA or mitochondrial toxins. In conclusion, excitotoxicity contributes to the neuropathology of d-2-hydroxyglutaric aciduria, highlighting new neuroprotective strategies.
Scheduling of microfluidic operations for reconfigurable two-dimensional electrowetting arrays (2001)

We present an architectural design and optimization methodology for performing biochemical reactions using two-dimensional (2-D) electrowetting arrays. We define a set of basic microfluidic operations and leverage electronic design automation principles for system partitioning, resource allocation, and operation scheduling. Fluidic operations are carried out through the electrostatic configuration of a set of grid points. While concurrency is desirable to minimize processing time, the size of the 2-D array limits the number of concurrent operations of any type. Furthermore, functional dependencies between the operations also limit concurrency. We use integer linear programming to minimize the processing time by automatically extracting parallelism from a biochemical assay. As a case study, we apply our optimization method to the polymerase chain reaction, which is an important step in many lab-on-a-chip biochemical applications.
The 25 kDa synaptosomal-associated protein SNAP-25 is the major methionine-rich polypeptide in rapid axonal transport and a major substrate for palmitoylation in adult CNS (1992)

A conspicuous correlate of the developmental transformation of axonal growth cones to synaptic terminals is a marked increase in synthesis and axonal transport of a methionine-rich, acidic polypeptide of approximately 25 kDa. This polypeptide, designated "super protein" (SuP), is the most prominent species among methionine-labeled proteins conveyed by rapid axonal transport in mature CNS and PNS neurons of warm- and cold-blooded vertebrates. We show here that SuP is identical to SNAP-25, a highly conserved synaptic protein of known primary structure, by immunoprecipitation with anti-SNAP-25 antiserum of SuP labeled with 35S-methionine and transported by retinal ganglion cells of rat and cat. In addition, we show that SNAP-25/SuP is the most prominent species among retinal polypeptides that incorporate 3H-palmitate in vivo, that it is fatty acylated through a hydroxylamine-labile, thioester bond, and that palmitoylated SNAP-25/SuP is axonally transported. Thus, SNAP-25/SuP is a rapidly transported constituent of the presynaptic apparatus and a major neuronal substrate for long-chain fatty acylation.
Differentiation of Acute Myeloid Leukemia from B- and T-Lineage Acute Lymphoid Leukemias by Real-Time Quantitative Reverse Transcription-PCR of Lineage Marker mRNAs (2004)

Study of lineage markers at diagnosis by RTQ-PCR allows differentiation of AML from B-ALL or T-ALL without cell sorting, even when the bone marrow contains few blast cells.
Hemoglobinopathies (2011)

Hemoglobinopathies are a public health issue in today's multiethnic German population. Adequate care of the affected patients requires a wide variety of diagnostic and therapeutic measures.
Selecting Nucleic Acids for Biosensor Applications (2002)

In vitro selection can be used to generate nucleic acid binding species (aptamers) and catalysts (ribozymes) that can recognize a variety of molecules. Because nucleic acid function is largely derived from readily tabulated secondary structures, it has proven possible to engineer aptamers and ribozymes to function as biosensors. Labeling nucleic acids with reporter molecules has yielded simple antibody substitutes, but by relying on ligand-dependent conformational changes it has also proven possible to generate biosensors that can recognize and specifically report the presence of ligands in homogenous solution. It may prove possible to generate signaling aptamers and allosteric ribozymes (aptazymes) that are responsive to a large fraction of an organismal proteome or metabolome using automated methods. Nucleic acid biosensor arrays for non-nucleic acid targets could likely be generated with the same facility as DNA chips.
Myotonic Dystrophy Is Associated with a Reduced Level of RNA from the DMWD Allele Adjacent to the Expanded Repeat (1999)

Myotonic dystrophy is caused by the expansion of a CTG repeat sequence. The mechanism by which this expanded repeat produces the pathophysiology of myotonic dystrophy is not clear. It has been shown previously that expansion of the repeat produces allele-specific effects on transcripts from two genes, DMPK and SIX5. We have examined the effect of repeat expansion on the level of RNA from a third gene, DMWD. We have identified a polymorphism in this gene and developed a quantitative allele-specific assay for DMWD RNA levels, which we have applied to nuclear and cytoplasmic fractions of RNA from DM cell lines. We have found that the level of the DM-associated allele in the cytoplasm of DM cell lines is reduced by 20-50% compared with the wild-type allele, similar to the level of reduction found for SIX5 in allele-specific analysis. However, no such reduction is observed in RNA from the nuclear fraction of DM cell lines. This may reflect the complex nature of processing transcriptional units at the DM locus.
DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone (1998)

Despite extensive study, there is little experimental information available as to which of the deoxyribose hydrogen atoms of duplex DNA reacts most with the hydroxyl radical. To investigate this question, we prepared a set of double-stranded DNA molecules in which deuterium had been incorporated specifically at each position in the deoxyribose of one of the four nucleotides. We then measured deuterium kinetic isotope effects on the rate of cleavage of DNA by the hydroxyl radical. These experiments demonstrate that the hydroxyl radical reacts with the various hydrogen atoms of the deoxyribose in the order 5' H > 4' H > 3' H approximately 2' H approximately 1' H. This order of reactivity parallels the exposure to solvent of the deoxyribose hydrogens. Our work therefore reveals the structural basis of the reaction of the hydroxyl radical with DNA. These results also provide information on the mechanism of DNA damage caused by ionizing radiation as well as atomic-level detail for the interpretation of hydroxyl radical footprints of DNA-protein complexes and chemical probe experiments on the structure of RNA and DNA in solution.
3次元トーラス上のロッキングとカオス(低次元カオスII,カオスとその周辺,研究会報告) (1986)

この論文は国立情報学研究所の電子図書館事業により電子化されました。
Modification of the carbohydrate in ricin with metaperiodate — cyanoborohydride mixtures (1985)

Attempts to target antibody-ricin conjugates (immunotoxins) to designated cell types in vivo may be thwarted by their rapid clearance by hepatic reticuloendothelial cells which have receptors that recognise oligosaccharide side chains on the toxin. The B-chain of ricin contains high mannose type oligosaccharides and the A-chain contains a complex unit (GlcNAc)2-Fuc-Xyl-(Man)4-6, all of which potentially could be recognised by the reticuloendothelial system. Treatment of ricin with a mixture of sodium metaperiodate and sodium cyanoborohydride at pH 3.5 resulted in oxidative cleavage of the carbohydrates and reduction of the aldehyde groups thus formed to primary alcohols. By conducting the modification procedure at acidic pH, both the possibility of Schiff's base formation between the aldehyde groups and amino groups in the protein and the possibility of non-specific oxidation of amino acids were minimised. The extent of the carbohydrate modification depended on the duration of treatment, resulting maximally in the destruction of 13 of the 18 mannose residues and of all xylose and fucose. The toxicity of the modified toxin to cells in culture declined by up to 90% as the carbohydrate was destroyed. This was not due to a reduced ability of the B-chain to bind to cells or of the A-chain to inactivate ribosomes. In contrast to the in vitro results, the toxicity of the modified toxin to mice and rats was elevated by up to fourfold. The modification greatly reduced the clearance of the toxin by non-parenchymal cells in the liver and prevented the damage to hepatic Kupffer and sinusoidal cells and to the red pulp of the spleen that is inflicted by the native toxin. The elevated toxicity to animals appears to be because the modified toxin evades the reticuloendothelial system and persists in the bloodstream for longer periods, thus resulting in lethal damage to vital tissues in the animal at lower dosage. The results suggest that immunotoxins prepared from modified ricin would not be readily cleared by the reticuloendothelial system and so be more effective at killing their target cells.
Interleukin 13: novel role in direct regulation of proliferation and differentiation of primitive hematopoietic progenitor cells. (1994)

The recently cloned interleukin 13 (IL-13) shares most investigated biological activities on B lymphocytes and monocytes with IL-4. In this study we investigated for the first time the potential role of IL-13 in the regulation of the growth of hematopoietic progenitor cells. IL-13 enhanced stem cell factor (SCF)-induced proliferation of Lin-Sca-1+ bone marrow progenitor cells more potently than IL-4. The effect of IL-13 was purely synergistic, since IL-13 alone stimulated no colony formation. Single cell experiments suggested that the synergistic effect of IL-13 on Lin-Sca-1+ progenitors was directly mediated. In contrast, IL-13 had no synergistic activity on SCF-induced proliferation of the more mature Lin-Sca-1- progenitor cells. Thus, the cloning frequency in response to SCF + IL-13 was at least 20-fold higher in the Lin-Sca-1+ than the Lin-Sca-1- progenitor cell population. Furthermore, IL-13 but not IL-4 synergistically enhanced colony formation of Lin-Sca-1+ progenitors in response to granulocyte/macrophage colony-stimulating factor (GM-CSF) (threefold), whereas both IL-4 and IL-13 enhanced G-CSF-induced colony formation (threefold), and neither of the two significantly affected CSF-1 and IL-3-induced proliferation. Finally, whereas stimulation of Lin-Sca-1+ progenitors by SCF + G-CSF resulted in the formation of 90% granulocytes, the addition of IL-13 resulted in the production of macrophages exclusively. This novel effect on differentiation was directly mediated, shared with IL-4, and could not be observed on Lin-Sca-1- progenitor cells. Collectively, these findings indicate a novel role of IL-13 in early myelopoiesis, partially overlapping but also different from that of IL-4.
RPL: IPv6 Routing Protocol for Low-Power and Lossy Networks (2012)

Low-Power and Lossy Networks (LLNs) are a class of network in which
both the routers and their interconnect are constrained. LLN routers
typically operate with constraints on processing power, memory, and
energy (battery power). Their interconnects are characterized by high
loss rates, low data rates, and instability. LLNs are comprised of
anything from a few dozen to thousands of routers. Supported traffic
flows include point-to-point (between devices inside the LLN), point-
to-multipoint (from a central control point to a subset of devices
inside the LLN), and multipoint-to-point (from devices inside the LLN
towards a central control point). This document specifies the IPv6
Routing Protocol for Low-Power and Lossy Networks (RPL), which
provides a mechanism whereby multipoint-to-point traffic from devices
inside the LLN towards a central control point as well as point-to-
multipoint traffic from the central control point to the devices
inside the LLN are supported. Support for point-to-point traffic is
also available. [STANDARDS-TRACK]
A dynamical model for generating synthetic electrocardiogram signals (2003)

A dynamical model based on three coupled ordinary differential equations is introduced which is capable of generating realistic synthetic electrocardiogram (ECG) signals. The operator can specify the mean and standard deviation of the heart rate, the morphology of the PQRST cycle, and the power spectrum of the RR tachogram. In particular, both respiratory sinus arrhythmia at the high frequencies (HFs) and Mayer waves at the low frequencies (LFs) together with the LF/HF ratio are incorporated in the model. Much of the beat-to-beat variation in morphology and timing of the human ECG, including QT dispersion and R-peak amplitude modulation are shown to result. This model may be employed to assess biomedical signal processing techniques which are used to compute clinical statistics from the ECG.
Performance Modeling for Packet Networks with Satellite Overflow Channels (1981)

In a packet network using medium speed terrestrial connectivity, average end-to-end delay can be reduced by using highspeed satellite overflow channels despite their propagation delay. To investigate networks of this type analytically, we derive a new basic queueing model for overflow systems with buffered traffic. The simple, closed-form expressions facilitate analysis. Approximations are developed for multiple primary systems with a single overflow channel; these agree with simulation. Using the overflow model analysis indicated the following. The reduced queueing delay to the high capacity overflow channel more than compensated for propagation delay. Inherent, broadcast transmission capabilities of satellite channels reduced overall network delay. The high capacity overflow channels permit networks to withstand substantial nodal imbalance and overloads.
Toxicity Review of Ethylene Glycol Monomethyl Ether and its Acetate Ester (2000)

Ethylene glycol monomethyl ether (EGME) and its acetate ester (EGMEA) are highly flammable, colorless, moderately volatile liquids with very good solubility properties. They are used in paints, lacquers, stains, inks and surface coatings, silk-screen printing, photographic and photo lithographic processes, for example, in the semiconductor industry, textile and leather finishing, production of food-contact plastics, and as an antiicing additive in hydraulic fluids and jet fuel. EGME and EGMEA are efficiently absorbed by inhalation as well as via dermal penetration. Dermal absorption may contribute substantially to the total uptake following skin contact with liquids or vapours containing EGME or EGMEA. EGMEA is rapidly converted to EGME in the body and the two substances are equally toxic in animals. Therefore, the two substances should be considered as equally hazardous to man. Effects on peripheral blood, testes, and sperm have been reported at occupational exposure levels ranging between 0.4 and 10 ppm EGME in air, and with additional, possibly substantial, dermal exposure. Severe malformations and disturbed hematopoiesis have been linked with exposure to EGME and EGMEA at unknown, probably high, levels. Embryonic deaths in monkeys and impaired spermatogenesis in rabbits have been reported after daily oral doses of 12 and 25 mg per kg body weight, respectively. In several studies, increased frequency of spontaneous abortions, disturbed menstrual cycle, and subfertility have been demonstrated in women working in the semiconductor industry. The contribution of EGME in relation to other exposure factors in the semiconductor industry is unclear.
New approach of fabrication and dispensing of micromachined cesium vapor cell (2008)

We describe the fabrication of wafer-scale alkali vapor cells based on silicon micromachining and anodic bonding. The principle of the proposed micromachined alkali cell is based on an extremely compact sealed vacuum cavity of a few cubic millimeters containing caesium vapors, illuminated by a high-frequency modulated laser beam. The alkali cells are formed by sealing an etched silicon wafer between two glass wafers. The technique of cell filling involves the use of an alkali dispenser. The activation of cesium vapors is made by local heating of the dispenser below temperature range causing degradations of cesium vapor purity. Thus, the procedure avoids negative effects of cesium chemistry on the quality of cell surfaces and sealing procedure. To demonstrate the clock operation, cesium absorption as well as coherent population trapping resonance was measured in the cells.