julilili42/papers huggingface dataset:
Lipoconjugates for the Noncovalent Generation of Microarrays in Biochemical and Cellular Assays
2002-12-02

The generation of microarrays by functionalization of hydrophobic glass surfaces with conjugates of triacylated lipophilic end-groups and with a peptide or hapten as a test substance is presented. Immobilization on the hydrophobic surfaces through the triacylated anchor group is fully orthogonal to the reactivity of functional groups within the test substances. The technique is therefore free of risk that reactions of these functional groups may influence the biological activity of the test compounds in screening applications. In addition, no preactivation of either the surface or the compounds is required. Reagents and substrates may be stored at ambient conditions for long periods of time. The lipoconjugates are administered from aqueous solution enabling automated nanopipetting down to spot dimensions of 100 microm across. The microstructures are stable with respect to the conditions of biochemical assays and applications in cell biology. Due to the hydrophobicity of the nonfunctionalized surfaces, standard blocking protocols used in microtiter-plate testing can be employed, thereby inhibiting nonspecific binding of assay reagents. Generation of these microstructures on hydrophobic glass slides or coverslips enables highly sensitive multichannel read-outs with high-resolution fluorescence microscopy.
Comparison of TG-43 dose calculations to pinpoint ion chamber and diamond detector measurements
2002-12-03

Brachytherapy is an area of radiation therapy where the availability of high-resolution detectors with a low energy-dependence is of great importance. The suitability of two detectors is investigated in this study. Measurements in the proximity of an Ir-192 source were performed with a diamond detector type 60003 and a pinpoint chamber type 31006 (both PTW-Freiburg). For comparison, dose values were calculated with the dose calculation formalism recommended by the task group 43 (Nath et al 1995 Med. Phys. 22 209-34).
Cardiac energetics correlates to myocardial hypertrophy in Friedreich's ataxia
2002-12-04

Abstract Friedreich's ataxia is a neurodegenerative disease frequently associated with hypertrophic cardiomyopathy. We have determined mitochondrial ATP, phosphocreatine, and intracellular inorganic phosphate levels by 31 P nuclear magnetic resonance spectroscopy in the heart of 11 Friedreich's ataxia patients and 11 healthy controls. For the first time, to our knowledge, we showed a significant correlation between the extent of myocardial energy deficiency and the degree of myocardial hypertrophy. When combining our results with previous works on Friedreich's ataxia, these novel findings suggest that energy metabolism is most likely the cause and hypertrophy the effect in Friedreich's ataxia. Ann Neurol 2003;53:000–000
Evolution of Urticaria Pigmentosa into Indolent Systemic Mastocytosis: Abnormal Immunophenotype of Mast Cells without Evidence of c-kit Mutation ASP-816-VAL
2002-12-05

Mastocytosis comprises a heterogeneous group of hematological disorders which are morphologically defined by proliferation and accumulation of tissue mast cells in one or more organs. Clinical manifestations of mastocytosis range from disseminated maculopapular skin lesions (= urticaria pigmentosa [UP]) that may spontaneously regress to highly aggressive neoplasms like mast cell leukemia or mast cell sarcoma. Recently, it could be shown that systemic mastocytosis (SM) is a clonal disorder often exhibiting mutations of c-kit, a protooncogene encoding the tyrosine kinase receptor for stem cell factor (SCF). Mutations of c-kit are considered to play a key role in the pathogenesis of mastocytosis. Therefore, we investigated the unique case of a 36 year-old male patient with indolent systemic mastocytosis (ISM) evolving from UP (cutaneous mastocytosis) by means of histology, immunophenotyping and molecular biology. At the time of initial diagnosis the bone marrow showed only a mild diffuse increase in mast cells but compact infiltrates were missing. The serum tryptase levels were normal. Five years later, however, the bone marrow histology displayed patchycompact mast cell infiltrates, which now allowed to establish the diagnosis of an ISM. The serum tryptase levels at this time were markedly elevated. At both time points, mast cells were analyzed by immunohistochemistry using anti-tryptase antibody AA1, by flow cytometry using antibodies against CD2 and CD25, and nested polymerase chain reaction (PCR) on laser-microdissected, single pooled mast cells. Immunohistochemistry revealed strong tryptase-positivity of mast cells in both cutaneous and bone marrow infiltrates. Flow cytometry yielded an aberrant expression of CD2 and CD25 on bone marrow mast cells. However, repeated thorough PCR analysis failed to unveil c-kit mutation in atypical mast cells of skin and bone marrow samples of both dates. These findings clearly show that ISM can evolve from UP. Moreover, our study provides further evidence that the c-kit mutation Asp-816-Val is not invariably present in ISM.
Continuous long‐term monitoring of UV radiation in professional mountain guides reveals extremely high exposure
2002-12-06

Abstract Ultraviolet radiation (UVR) is estimated to be one of the most important risk factors for nonmelanoma and melanoma skin cancers. High occupational UV exposure is assumed to be associated with skin cancer. Mountain guides receive considerable UV doses due to altitude‐related increase of UVR and reflection from snow‐ and ice‐covered surfaces. The aim of our study was to assess the annual occupational UV exposure of mountain guides. Spore film test chambers containing spores of Bacillus subtilis (VioSpor) were used as UV dosimeters with a spectral sensitivity profile similar to erythema‐weighted data calculated from spectroradiometric measurements. Nine mountain guide instructors carried dosimeters on the sides of their heads on a total of 1,406 working days during one year (July 1999–June 2000). Dosimeters were changed monthly. Measurements of 92 months could be evaluated (4–12 months/mountain guide). The mean individual monthly UV exposure was 107 standard erythema doses (SED) (median 71 SED; range 10–505 SED). The mean annual cumulative UV exposure was 1,097 SED (median 1,273 SED; range 312–1,770 SED) per mountain guide. The mean UV dose per day (4–10 hr) was 6.6 SED (median 5.7 SED; range 0.6–24.2 SED). This is the second study of continuous annual UV dosimetry in a cohort of outdoor workers. Our study showed that it is not sufficient to interpolate annual UV exposure from a few days' measurements. Only long‐term dosimetry can give reliable yearly information of UVR load. Median daily UV exposure exceeded limits for UV radiation ( e.g. , ACGIH effective dose 30 J/m 2 per 8 hr period corresponding to 1.08 SED/day) 6‐fold; maximal exposure exceeded these limits 23‐fold. These extremely high exposure values are suggestive for an increased risk of skin cancer and thorough epidemiologic studies in the collectives of professional and recreational mountaineering are required. © 2002 Wiley‐Liss, Inc.
Territory formation in mobile robots
2002-12-09

Animals navigate through their environment using diverse strategies. These navigation strategies might be highly dependent on the animal's ecological niche. Though a lot of work is focused on biological navigation mechanisms, the cognitive ecology of spatial memory is poorly understood. The performances of different navigation mechanisms in the context of a biologically relevant behavior can be assessed by using mobile robots. For this task, territorial behavior was built on Khepera miniature robots. Territoriality is strongly dependent on spatial learning and thus provides a powerful context for testing of sensory and computational complexity needed by animals solving special tasks. Simultaneously, the principles underlying the establishment of territories in a previously uninhabited area and how it is dependent on environmental parameters can be investigated. In the present paper, territoriality in robots is introduced. The robots navigate by relying on poor sensor input anda representation of the environment of a low complexity. Qualitative results show that territories form. Subsequently, the consequences of the introduction of a newcomer in already established territories are presented.
Hand‐Held and Palm‐Top Chemical Microsensor Systems for Gas Analysis
2002-12-09

This chapter contains sections titled: Introduction Conventional Hand-held Systems Hardware Setup Fundamentals of the Sensing Process Commercially Available Instruments Based on Conventional Technology Silicon-Based Microsensors Micromachining Techniques Microstructured Chemocapacitors Micromachined Resonating Cantilevers Micromachined Calorimetric Sensors Single-Chip Multisensor System Operation Modes for CMOS Microsystems Summary and Outlook
Screening for biologically active metabolites with endosymbiotic bacilli isolated from arthropods
2002-12-10

Endosymbiotic bacteria from the genus Bacillus were isolated from different compartments of the gut of various members of insects (Hexapoda) and millipedes (Diplopoda). They were grown in submerged culture and investigated by biological assays and HPLC-diode array analysis regarding their production of bioactive metabolites, which were isolated and determined in structure. Known compounds and yet unknown derivatives from the primary metabolism were detected, as well as antibacterially and antifungally acting peptide antibiotics.
The non-classical MHC molecule HLA-G protects human muscle cells from immune-mediated lysis: implications for myoblast transplantation and gene therapy
2002-12-11

HLA-G is a non-classical MHC class I molecule with highly limited tissue distribution which has been attributed chiefly immune-regulatory functions. We previously have reported that HLA-G is expressed in inflamed muscle in vivo and by cultured myoblasts in vitro. Here, we used the in vitro models of human myoblasts or TE671 muscle rhabdomyosarcoma cells to characterize the functional role of HLA-G for muscle immune cell interactions. Gene transfer of the two major isoforms of HLA-G (transmembranous HLA-G1 and soluble HLA-G5) into TE671 rendered these cells resistant to alloreactive lysis by direct inhibition of natural killer (NK) cells, and CD4 and CD8 T cells. Further, HLA-G reduced alloproliferation, interfered with effective priming of antigen-specific cytotoxic T cells and reduced antigen-specific alloreactive lysis. HLA-G pre-induced on cultured myoblasts inhibited lysis by alloreactive peripheral blood mononuclear cells. This protection was reversed by a neutralizing HLA-G antibody. Interestingly, a few HLA-G-positive cells within a population of HLA-G-negative muscle target cells conveyed significant inhibitory effects on alloreactive lysis. Our results reveal further insights into the immunobiology of muscle and suggest that ectopic expression of HLA-G may promote the survival of transplanted myoblasts in the future treatment of hereditary muscle diseases. Further, HLA-G could represent a novel self-derived anti-inflammatory principle applicable in strategies against inflammatory aggression.
Haploinsufficiency at the -synuclein gene underlies phenotypic severity in familial Parkinson's disease
2002-12-11

To date, two point mutations, G209A and G88C, have been reported in the coding region of the alpha-synuclein gene in autosomal dominant familial Parkinson's disease. When translated, these lead to the missense mutations Ala53Thr and Ala30Pro, respectively. Reduced mRNA expression of the G209A allele was reported recently in a Greek-American family. Here, we show that alpha-synuclein mRNA is normally expressed in blood cells and report the results of an analysis of alpha-synuclein mRNA and protein expression in lymphoblastoid cell lines established from kindreds with the G209A and G88C mutations. mRNA expression was characterized using a TaqMan real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assay. We assessed five affected and three unaffected members of a German family with the G88C mutation and two affected members in different, unrelated Greek families with the G209A mutation. The ratio of wild-type to mutant alpha-synuclein allele expression ranged from 2.2 to 9.2 in the affected individuals with a severe clinical phenotype. The ratios of the expression levels of the wild-type to mutant alleles were only slightly decreased in mild cases and were less than 1.0 in two asymptomatic heterozygotes. Sequence analysis of the RT-PCR products showed only the presence of G in position 88 and G in position 209 in severely affected heterozygotes of the German and Greek families, respectively. High performance liquid chromatography/mass spectrometry demonstrated that, relative to wild-type alpha-synuclein, there is a reduction of Ala30Pro alpha-synuclein in lymphoblastoid cell lines originating from severely affected, but not mildly affected G88C/+ heterozygotes. Taken together, these data indicate that there is haploinsufficiency at the alpha-synuclein gene and that the ratio of expression of the wild-type to mutant alleles correlates with the severity of the clinical phenotype. Furthermore, these findings suggest that haploinsufficiency of alpha-synuclein mutations may contribute to disease progression in these forms of familial Parkinson's disease.
Identification of anArabidopsismitochondrial succinate–fumarate translocator
2002-12-12

Complementation of a yeast acr1 mutant carrying a deletion of the succinate/fumarate carrier gene enabled functional identification of a mitochondrial succinate translocator from Arabidopsis thaliana (AtmSFC1). Thus complementation of yeast mutants is applicable also for identification and characterization of organellar transporters. Reverse transcription polymerase chain reaction and promoter‐GUS fusion showed expression of AtmSFC1 in 2 day old dark grown seedlings, which declined in cotyledons during further development, consistent with a role in export of fumarate for gluconeogenesis during lipid mobilization at early germination of Arabidopsis seeds. In mature plants, expression was found in developing and germinating pollen, suggesting a role in ethanolic fermentation.
Acetal−Vinyl Sulfide Cyclization on Sugar Substrates:  Effect of Structure and Substituent
2002-12-13

A range of 2-deoxyfuranoside and -pyranoside derivatives were fashioned into derivatives that carry a vinyl or propenyl side chain. Extension of the alkene by a Suzuki cross-coupling reaction with 1-bromo-1-(phenylthio)ethene gave thioenol ethers as the cyclization substrates. The treatment of these substrates with BF(3).Et(2)O in tert-butylmethyl ether below 0 degrees C induced cyclization to optically active bicyclic ethers. If the cyclizations are carried out in toluene as the solvent, the isomerization of the terminal thioenol ether to the inner thioenol ether can take place prior to the cyclization. The cyclization reactions can be impeded by steric and electronic factors. The opening of the bicyclic ethers could be illustrated with the base-induced conversion of the ketone 53 to the cyclooctenone 54.
Cellularisation in the endosperm ofArabidopsis thalianais coupled to mitosis and shares multiple components with cytokinesis
2002-12-15

Distinct forms of cytokinesis characterise specific phases of development in plants. In Arabidopsis, as in many other species, the endosperm that nurtures the embryo in the seed initially develops as a syncytium. This syncytial phase ends with simultaneous partitioning of the multinucleate cytoplasm into individual cells, a process referred to as cellularisation. Our in vivo observations show that, as in cytokinesis, cellularisation of theArabidopsis endosperm is coupled to nuclear division. A genetic analysis reveals that most Arabidopsis mutations affecting cytokinesis in the embryo also impair endosperm cellularisation. These results imply that cellularisation and cytokinesis share multiple components of the same basic machinery. We further report the identification of mutations in a novel gene, SPÄTZLE, that specifically interfere with cellularisation of the endosperm, but not with cytokinesis in the embryo. The analysis of this mutant might identify a specific checkpoint for the onset of cellularisation.
Methyl pyruvate stimulates pancreatic β-cells by a direct effect on KATP channels, and not as a mitochondrial substrate
2002-12-15

In pancreatic β-cells, methyl pyruvate is a potent secretagogue and is widely used to study stimulus—secretion coupling. In contrast with pyruvate, which barely stimulates insulin secretion, methyl pyruvate was suggested to act as an effective mitochondrial substrate. We show that methyl pyruvate elicited electrical activity in the presence of 0.5mM glucose, in contrast with pyruvate. Accordingly, methyl pyruvate increased the cytosolic free Ca2+ concentration after an initial decrease, similar to glucose. The initial decrease was inhibited by thapsigargin, suggesting that methyl pyruvate stimulates ATP production. This assumption is supported by the observation that methyl pyruvate hyperpolarized the mitochondrial membrane potential, similar to glucose. However, in contrast with glucose, methyl pyruvate even slightly decreased NAD(P)H autofluorescence and did not influence ATP production or the ATP/ADP ratio. This observation questions the suggestion that methyl pyruvate acts as a powerful mitochondrial substrate. The finding that methyl pyruvate directly inhibited a cation current across the inner membrane of Jurkat T-lymphocyte mitochondria suggests that this metabolite may increase ATP production in β-cells by activating the respiratory chains without providing reduction equivalents. We conclude that this mechanism may account for a slight and transient increase in ATP production. We further show that methyl pyruvate inhibited the KATP current measured in the standard whole-cell configuration, an effect that was at least partly antagonized by diazoxide. Accordingly, single-channel currents in inside-out patches were blocked by methyl pyruvate. We conclude that inhibition of KATP channels, and not activation of metabolism, mediates the induction of electrical activity in pancreatic β-cells by methyl pyruvate.
The gyromagnetic factor in electrodynamics, quantum theory and general relativity
2002-12-16

Starting with some basic facts about the gyromagnetic factor g in Maxwell's theory, we review the special role played by a g factor g = 2 in quantum mechanics and elementary particle physics, and we draw attention to the same value g = 2 for the black holes and many other (electro-)vacuum solutions of general relativity. We strengthen and extend this special role of g = 2 in general relativity by considering a class of slowly rotating, charged mass shells, showing that the black-hole value g = 2 is extremely robust. Therefrom, we advance the hypothesis that the coincidence between these preferred g values signifies a deep common root of quantum theory and general relativity.
Numerical evolution of axisymmetric, isolated systems in general relativity
2002-12-17

We describe in this article a new code for evolving axisymmetric isolated systems in general relativity. Such systems are described by asymptotically flat space-times which have the property that they admit a conformal extension. We are working directly in the extended `conformal' manifold and solve numerically Friedrich's conformal field equations, which state that Einstein's equations hold in the physical space-time. Because of the compactness of the conformal space-time the entire space-time can be calculated on a finite numerical grid. We describe in detail the numerical scheme, especially the treatment of the axisymmetry and the boundary.
A fast logarithm converter
2002-12-17

Divisions, square and square root operations or, in general, exponentiations are performed frequently in computer graphics algorithms, but are either slow if done by software or expensive if implemented in hardware. An elegant way to solve this problem is to transform the operands into the logarithm, turning divisions into subtractions and exponentiations into multiplications, and the results back into the number domain. However, significant gains in performance and costs can only be achieved if the converters are compact and fast. We describe the design principles of a pipelined logarithm converter, which is scalable with respect to speed, precision and chip space.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A prototyping environment for hardware/software codesign in the COBRA project
2002-12-17

We present a prototyping environment with special benefit for hardware/software codesign which we use as target architecture in the COBRA project. This architecture is very flexible, easy extensible, and provides a high gate complexity. It supports standard processor integration as well as processor emulation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Kobold: a neural coprocessor for backpropagation with online learning
2002-12-17

In this paper we propose an architecture of a neural coprocessor for on-board learning standard backpropagation. The hardware implementation works as a neural coprocessor connected to a personal computer by a special asynchronous interface. The coprocessor consists of several equal submodules representing one column of the neural net. So the architecture allows to compose any size of neural net depending on the specific application and, additionally, recurrency is allowed. Kobold speeds up the performance in contrast to earlier hardware implementations because of its new specialized control and communication structure. The subprocessors communicate asynchronously and locally with their nearest neighbours and synchronously by a global bus. The operations are controlled by dataflow. This means, a neuron calculates its weighted sum as soon as all inputs are available.
Design flow for hardware/software cosynthesis of a video compression system
2002-12-17

The implementation of a cosynthesis design flow in the CASTLE (Codesign And Synthesis Tool Environment) system is presented. The design flow generates a synthesizable hardware description and a C, C++, or Fortran compiler for an application-oriented processor. The approach is illustrated by the design of an embedded video compression system which can be integrated into the video card of a PC. The design flow is structured as follows. First, the requirements of the application programs are analyzed. Based on these analysis results, the designer decides on the appropriate processor structure. The processor structure is entered on a block diagram level into the CASTLE system by using a schematic entry. The CASTLE system performs the processor cosynthesis based on a VHDL library of processor components. Several processor datapaths for the video compression system were synthesized to illustrate the trade-offs between flexibility and performance when designing application-oriented processors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Specification of interface components for synchronous data paths
2002-12-17

The simulation semantics of VHDL necessitates the specification of the interface signal transitions at bit level with exact timing which is not well suited for abstract specification and synthesis. The paper shows a methodology to model the interface of a behavioural description suited for high level synthesis where different abstraction levels are separated. It shows the transformations to generate a RT data path while holding the exact simulation semantics at the interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>