julilili42/papers huggingface dataset:
The Short antennae gene of Tribolium is required for limb development and encodes the orthologue of the Drosophila Distal-less protein
2001-01-15

ABSTRACT Insects bear a stereotyped set of limbs, or ventral body appendages. In the highly derived dipteran Drosophila melanogaster, the homeodomain transcription factor encoded by the Distal-less (Dll) gene plays a major role in establishing distal limb structures. We have isolated the Dll orthologue (TcDll) from the beetle Tribolium castaneum, which, unlike Drosophila, develops well-formed limbs during embryogenesis. TcDll is initially expressed at the sites of limb primordia formation in the young embryo and subsequently in the distal region of developing legs, antennae and mouthparts except the mandibles. Mutations in the Short antennae (Sa) gene of Tribolium delete distal limb structures, closely resembling the Dll phenotype in Drosophila. TcDll expression is severely reduced or absent in strong Sa alleles. Genetic mapping and molecular analysis of Sa alleles also support the conclusion that TcDll corresponds to the Sa gene. Our data indicate functional conservation of the Dll gene in evolutionarily distant insect species. Implications for evolutionary changes in limb development are discussed.
Accelerated telomere shortening in hematological lineages is limited to the first year following stem cell transplantation
2001-01-15

Abstract Using quantitative fluorescence in situ hybridization and flow cytometry, the telomere length of telomere repeat sequences after stem cell transplantation (SCT) were measured. The study included the telomeres of peripheral blood monocytes that should reflect the length of telomeres in stem cells and the telomeres of T lymphocytes that could shorten as a result of peripheral expansion. The loss of telomeres in monocytes and in memory T cells, although accelerated initially, became comparable to the loss of telomeres in healthy controls from the second year after transplantation. In addition, the telomere length in the naive T cells that were produced by the thymus was comparable to the telomere length in the naive T cells of the donor. Compared to the total length of telomeres available, the loss of telomere repeats in leukocytes after SCT resembles the accelerated shortening seen in early childhood and remains, therefore, relatively insignificant.
Analysis of Catabolite Control Protein A-Dependent Repression in Staphylococcus xylosus by a Genomic Reporter Gene System
2001-01-15

ABSTRACT A single-copy reporter system for Staphylococcus xylosus has been developed, that uses a promoterless version of the endogenous β-galactosidase gene lacH as a reporter gene and that allows integration of promoters cloned in front of lacH into the lactose utilization gene cluster by homologous recombination. The system was applied to analyze carbon catabolite repression of S. xylosus promoters by the catabolite control protein CcpA. To test if lacH is a suitable reporter gene, β-galactosidase activities directed by two promoters known to be subject to CcpA regulation were measured. In these experiments, repression of the malRA maltose utilization operon promoter and autoregulation of the ccpA promoters were confirmed, proving the applicability of the system. Subsequently, putative CcpA operators, termed catabolite-responsive elements ( cre s), from promoter regions of several S. xylosus genes were tested for their ability to confer CcpA regulation upon a constitutive promoter, P veg II . For that purpose, cre sequences were placed at position +3 or +4 within the transcribed region of P veg II . Measurements of β-galactosidase activities in the presence or absence of glucose yielded repression ratios between two- and eightfold. Inactivation of ccpA completely abolished glucose-dependent regulation. Therefore, the tested cre s functioned as operator sites for CcpA. With promoters exclusively regulated by CcpA, signal transduction leading to CcpA activation in S. xylosus was examined. Glucose-dependent regulation was measured in a set of isogenic mutants showing defects in genes encoding glucose kinase GlkA, glucose uptake protein GlcU, and HPr kinase HPrK. GlkA and GlcU deficiency diminished glucose-dependent CcpA-mediated repression, but loss of HPr kinase activity abolished regulation. These results clearly show that HPr kinase provides the essential signal to activate CcpA in S. xylosus . Glucose uptake protein GlcU and glucose kinase GlkA participate in activation, but they are not able to trigger CcpA-mediated regulation independently from HPr kinase.
Chromosomal imbalances associated with response to chemotherapy and cytotoxic cytokines in human malignant glioma cell lines
2001-01-15

The median survival for human malignant glioma patients treated with neurosurgery and postoperative radiotherapy does not exceed one year. Only a minority of patients benefit from adjuvant chemotherapy. It was the aim of our study to determine which genomic alterations in malignant gliomas modulate the sensitivity to chemotherapy or cytotoxic cytokines such as CD95 ligand (CD95L) or Apo2L/tumor necrosis factor-related apoptosis-inducing ligand (Apo2L/TRAIL). Therefore, we analyzed 12 human malignant glioma cell lines for chromosomal gains and losses by comparative genomic hybridization (CGH). The gains most commonly identified were on chromosomes 7q, 19, 1, and 20q, whereas the most frequent losses were on 13q, 11q, 18q, and 4q. By comparison with previously published data on this panel of glioma cell lines1112, we defined candidate regions which may carry genes responsible for sensitivity to chemotherapy or cytotoxic cytokines. All but one of the chromosomal regions associated with response to chemotherapy, i.e. 1p12, 3p21, 11p11.2-p13, 12q23, 17p11. 2-p13, were different from those associated with response to cytotoxic cytokines, i.e. lp12, 1q22, 12q12-q21. Genomic regions known to harbor major candidate genes, including genes encoding death ligands, death receptors, caspases and BCL-2 family proteins, were not found to be imbalanced. In addition, we identified 5q13-q14, 5q34, 10p11.2, 9q21-q34 as genomic regions associated with the proliferative activity of malignant glioma cell lines. Cell lines with gain on proximal 5q, where CCNB1 and CCNH reside, showed an increased growth rate, suggesting that cyclins activating cdc2, the dominant G2/M phase kinase, may play a role in glioma tumorigenes.
Ultraviolet and Visible Spectroscopy
2001-01-15

The article contains sections titled: 1. Introduction 1.1. Comparison with Other Spectroscopic Methods 1.2. Development and Uses 2. Theoretical Principles 2.1. Electronic States and Orbitals 2.2. Interaction Between Radiation and Matter 2.2.1. Dispersion 2.2.2. Absorption 2.2.3. Scattering 2.2.4. Reflection 2.2.5. Band Intensity 2.3. The Lambert - BeerLaw 2.3.1. Definitions 2.3.2. Deviations from the Lambert - Beer Law 2.4. Photophysics 2.4.1. Energy Level Diagram 2.4.2. Deactivation Processes 2.4.3. Transition Probability and Fine Structure of the Bands 2.5. Chromophores 2.6. Optical Rotatory Dispersion and Circular Dichroism 2.6.1. Generation of Polarized Radiation 2.6.2. Interaction with Polarized Radiation 2.6.3. Optical Rotatory Dispersion 2.6.4. CircularDichroism and the Cotton Effect 2.6.5. Magnetooptical Effects 3. Optical Components and Spectrometers 3.1. Principles of Spectrometer Construction 3.1.1. Sequential Measurement of Absorption 3.1.2. Multiplex Methods in Absorption Spectroscopy 3.2. Light Sources 3.2.1. Line Sources 3.2.2. Sources of Continuous Radiation 3.2.3. Lasers 3.3. Selection of Wavelengths 3.3.1. Prism Monochromators 3.3.2. Grating Monochromators 3.4. Polarizers and Analyzers 3.5. Sample Compartments and Cells 3.5.1. Closed Compartments 3.5.2. Modular Arrangements 3.5.3. Open Compartments 3.6. Detectors 3.7. Optical Paths for Special Measuring Requirements 3.7.1. FluorescenceMeasurement 3.7.2. Measuring Equipment for Polarimetry, ORD, and CD 3.7.3. Reflection Measurement 3.7.4. Ellipsometry 3.8. Effect of Equipment Parameters 3.9. Connection to Electronic Systems and Computers 4. Uses of UV - VIS Spectroscopy in Absorption, Fluorescence,and Reflection 4.1. Identification of Substances and Determination of Structures 4.2. Quantitative Analysis 4.2.1. Determination of Concentration by Calibration Curves 4.2.2. Classical Multicomponent Analysis 4.2.3. Multivariate Data Analysis 4.2.4. Use in Chromatography 4.3. Fluorimetry 4.3.1. Inner Filter Effects 4.3.2. Fluorescene and Scattering 4.3.3. Excitation Spectra 4.3.4. Applications 4.4. Reflectometry 4.4.1. Diffuse Reflection 4.4.2. Color Measurement 4.4.3. Regular Reflection 4.4.4. Determination of Film Thickness 4.4.5. Ellipsometry 4.5. Resonance Methods 4.5.1. SurfacePlasmon Resonance 4.5.2. Grating Couplers 4.6. On-Line Process Control 4.6.1. Process Analysis 4.6.2. Measurement of Film Thicknesses 4.6.3. Optical Sensors 4.7. Measuring Methods Based on Deviations from the Lambert - BeerLaw 5. Special Methods 5.1. Derivative Spectroscopy 5.2. Dual-Wavelength Spectroscopy 5.3. Scattering 5.3.1. Turbidimetry 5.3.2. Nephelometry 5.3.3. Photon Correlation Spectroscopy 5.4. Luminescence, Excitation, and Depolarization Spectroscopy, and Measurement of Lifetimes 5.5. Polarimetry 5.5.1. Sugar Analysis 5.5.2. Cellulose Determination 5.5.3. Stereochemical StructuralAnalysis 5.5.4. Use of Optical Activity Induced by a Magnetic Field 5.6. Photoacoustic Spectroscopy (PAS)
ChemInform Abstract: Simocyclinones, Novel Cytostatic Angucyclinone Antibiotics Produced by Streptomyces antibioticus Tue 6040. Part 1. Taxonomy, Fermentation, Isolation, and Biological Activities.
2001-01-16

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Aspirin promotes TFF2 gene activation in human gastric cancer cell lines
2001-01-19

Trefoil factor family (TFF) peptides promote cell migration, heal the mucosa and may suppress tumor growth. In reporter gene assays we show that aspirin (1–12 mM) evokes a six‐fold up‐regulation of TFF2 , but not TFF1 and TFF3 transcription in human gastrointestinal cell lines. 6 h after application up‐regulation of endogenous TFF2 mRNA was observed. TFF2 transcription was enhanced by indomethacin and arachidonic acid but repressed by staurosporine, suggesting mediation via protein kinase C. We mapped an aspirin responding element −546 to −758 bp upstream of TFF2 . Up‐regulation of TFF2 by aspirin may partially explain the chemopreventive potential of low dose aspirin in gastrointestinal carcinogenesis.
Alkylating Polymers: Resin-Released Carbenium Ions as Versatile Reactive Intermediates in Polymer-Assisted Solution-Phase Synthesis
2001-01-19

Solid-supported diazoalkane analogues for the smooth and clean esterifications of carboxylic acids [Eq. (1)] as well as of complex compound mixtures: the alkylating polymers presented here were synthesized as solid-supported 3-alkyl-1-aryltriazenes and are capable of releasing carbenium ions following acidic activation.
Alkylating Polymers: Resin-Released Carbenium Ions as Versatile Reactive Intermediates in Polymer-Assisted Solution-Phase Synthesis
2001-01-19

Solid-supported diazoalkane analogues for the smooth and clean esterifications of carboxylic acids [Eq. (1)] as well as of complex compound mixtures: the alkylating polymers presented here were synthesized as solid-supported 3-alkyl-1-aryltriazenes and are capable of releasing carbenium ions following acidic activation. Supporting information for this article is available on the WWW under http://www.angewandte.com or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Three‐dimensional Simulations of a Planet Embedded in a Protoplanetary Disk
2001-01-20

The dynamical influence of Jupiter-sized planets still embedded in protostellar disks is studied by means of numerical simulations. The three-dimensional structure of the disk is fully taken into account. Assuming a disk mass of 3.5 × 10-3 M☉ within 2 and 13 AU, typical values for the vertical thickness H/r = 0.05 and viscosity of the disk α ≈ 4 × 10-3, we find for the mass accretion rate onto the planet a value of 6 × 10-5 MJ yr-1 and for the migration timescale a value of 105 yr. These results are in excellent agreement with previously obtained results from two-dimensional calculations of infinitesimally thin disks. We argue that this agreement is to be expected if the vertical height of the disk is similar or smaller than the size of the Roche lobe of the embedded planet. Three-dimensional models having a lower planetary mass or different H/r values display small deviations from two-dimensional results.
A representation of an NTCP function for local complication mechanisms
2001-01-22

A mathematical formalism was tailored for the description of mechanisms complicating radiation therapy with a predominantly local component. The functional representation of an NTCP function was developed based on the notion that it has to be robust against population averages in order to be applicable to experimental data. The model was required to be invariant under scaling operations of the dose and the irradiated volume. The NTCP function was derived from the model assumptions that the complication is a consequence of local tissue damage and that the probability of local damage in a small reference volume is independent of the neighbouring volumes. The performance of the model was demonstrated with an animal model which has been published previously (Powers et al 1998 Radiother. Oncol. 46 297-306).
Critical Analysis of Dual-Chamber Implantable Cardioverter-Defibrillator Arrhythmia Detection
2001-01-23

Background —One of the perceived benefits of dual-chamber implantable cardioverter-defibrillators (ICDs) is the reduction in inappropriate therapy due to new detection algorithms. It was the purpose of the present investigation to propose methods to minimize bias during such comparisons and to report the arrhythmia detection clinical results of the PR Logic dual-chamber detection algorithm in the GEM DR ICD in the context of these methods. Methods and Results —Between November 1997 and October 1998, 933 patients received the GEM DR ICD in this prospective multicenter study. A total of 4856 sustained arrhythmia episodes (n=311) with stored electrogram and marker channel were classified by the investigators; 3488 episodes (n=232) were ventricular tachycardia (VT)/ventricular fibrillation (VF), and 1368 episodes (n=149) were supraventricular tachycardia (SVT). The overall detection results were corrected for multiple episodes within a patient with the generalized estimating equations (GEE) method with an exchangeable correlation structure between episodes. The relative sensitivity for detection of sustained VT and/or VF was 100.0% (3488 of 3488, n=232; 95% CI 98.3% to 100%), the VT/VF positive predictivity was 88.4% uncorrected (3488 of 3945, n=278) and 78.1% corrected (95% CI 73.3% to 82.3%) with the GEE method, and the SVT positive predictivity was 100.0% (911 of 911, n=101; 95% CI 96% to 100%). Conclusions —A structured approach to analysis limits the bias inherent in the evaluation of tachycardia discrimination algorithms through the use of relative VT/VF sensitivity, VT/VF positive predictivity, and SVT positive predictivity along with corrections for multiple tachycardia episodes in a single patient.
Relativistic description of constituent quarks
2001-01-23

In this paper we propose a formalism to remove the center of mass motion of the relativistic three-quark system in order to calculate not only one-body operators, but also two-body interactions. We employ various methods used in the past to remove the center of mass motion. We then calculate the masses of the nucleon and \\ensuremath{\\Delta} resonance with residual one-gluon, sigma meson, and pseudoscalar pion and eta meson exchange potentials. Magnetic moments, root mean square radii, pion-nucleon coupling constant, and the axial vector coupling constant are also calculated. The main purpose of the calculation is to study the effect of the removal of the center of mass motion and investigate the similarities and differences between a relativistic and nonrelativistic description of constituent quarks. The method projecting onto the total momentum is found to give results consistent with experiments. It is also found that light quark mass and strong confinement are appropriate to reproduce the nucleon and \\ensuremath{\\Delta} masses in the relativistic approach.
ChemInform Abstract: Luminescence of New 2,6‐ and 1,5‐Naphthalene‐Based PPV‐Type Trimers and Polymers.
2001-01-23

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Syntheses and Cytotoxic, Antimicrobial, Antifungal, and Cardiovascular Activity of New Quinoline Derivatives.
2001-01-23

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enhanced absorption Hanle effect on theFg=F→Fe=F+ 1 closed transitions
2001-01-25

We analyse the Hanle effect on a closed transition. Two configurations are examined, for linear- and circular-polarized laser radiation, with the applied magnetic field collinear to the laser light wavevector. We describe the peculiarities of the Hanle signal for linearly-polarized laser excitation, characterized by narrow bright resonances at low laser intensities. The mechanism behind this effect is identified, and numerical solutions for the optical Bloch equations are presented for different transitions.
Both subtelomeric regions are required and sufficient for specific DNA fragmentation during macronuclear development in Stylonychia lemnae
2001-01-25

Our results indicate that an inverted repeat with the core sequence 5'-TGAA present in both subtelomeric regions acts as a Cbs in Stylonychia. The results allow us to propose a mechanistic model for DNA processing in this ciliate.
The Role of Heat Shock Proteins and Their Receptors in the Activation of the Immune System
2001-01-27

Heat shock proteins (HSPs) have been described as potent tumor vaccines in animal models and are currently studied in clinical trials. The underlying immune response relies on immunogenic peptides that the HSPs have acquired intracellularly by interfering with the classical antigen processing pathways. There have been numerous reports shedding light on how HSPs are able to gain this function and a number of important requirements for HSP-mediated specific immunity have been described: first, the ability of HSPs to bind immunogenic peptides. Second, the acquisition of HSPs by specialized antigen presenting cells with efficient antigen processing pathways capable of inducing cellular immune responses. Third, the existence of specific receptors on the surfaces of antigen presenting cells, allowing efficient and rapid uptake of HSP-peptide complexes from the extracellular fluid. And fourth, the ability of heat shock proteins to activate antigen presenting cells, enabling the latter to prime cytotoxic T cell responses against the peptides associated to HSPs.
Proteome Analysis by Three-Dimensional Protein Separation: Turnover of Cytosolic Proteins in Hepatocytes
2001-01-27

We performed a three-dimensional separation of pulse-chase dual-labelled rat liver cytosolic proteins using hydrophobic interaction chromatography, isoelectric focusing, and SDS gel electrophoresis. Due to very different expression rates but similar size and pI of rat liver cytosolic proteins, we demonstrate the impossibility of successful two-dimensional separations of such complex protein mixtures. A pre-fractionation of proteins by hydrophobic interaction chromatography is therefore recommended prior to two-dimensional gel electrophoresis. Our studies confirmed the correlation between protein turnover rates and surface hydrophobicity.
THE VORTEX BLOB METHOD AS A SECOND-GRADE NON-NEWTONIAN FLUID
2001-01-31

We show that a certain class of vortex blob approximations for ideal hydrodynamics in two dimensions can be rigorously understood as solutions to the equations of second-grade non-Newtonian fluids with zero viscosity and initial data in the space of Radon measures M (R 2). The solutions of this regularized PDE, also known as the isotropic Lagrangian averaged Euler or Euler-α equations, are geodesics on the volume preserving diffeomorphism group with respect to a new weak right invariant metric. We prove global existence of unique weak solutions (geodesics) for initial vorticity in M (R 2) such as point-vortex data, and show that the associated coadjoint orbit is preserved by the flow. Moreover, solutions of this particular vortex blob method converge to solutions of the Euler equations with bounded initial vorticity, provided that the initial data is approximated weakly in measure, and the total variation of the approximation also converges. In particular, this includes grid-based approximation schemes as are common in practical vortex computations.
SUBGROUPS WHICH ARE THE UNION OF FOUR CONJUGACY CLASSES
2001-01-31

Subgroups which are the union of two and three conjugacy classes were studied previously in Sharyari and Shahabi (Bull. of Iranian Math. Soc. 1999, 25 (1), 55–66; J. Algebra 1998, 207 (1), 326–332). In this article we will determine the structure of subgroups which are the union of four conjugacy classes.
Nonadiabatic contribution to the quasiparticle self-energy in systems with strong electron-phonon interaction
2001-01-31

We investigate effects of a nonadiabatic electron-phonon(boson) interaction\\non the quasiparticle self-energy in the lowest order in the coupling constant.\\nExisting approaches either overestimate, or underestimate these effects because\\nof different approximations for momentum and frequency dependences of the\\nvertex corrections. The connection between the nonadiabaticity and a possible\\ninstability of the interacting Fermi system is discussed as well.\\n
Renal Gluconeogenesis
2001-02-01

Studies conducted over the last 60 years in animals and in vitro have provided considerable evidence that the mammalian kidney can make glucose and release it under various conditions. Until quite recently, however, it was generally believed that the human kidney was not an important source of glucose except during acidosis and after prolonged fasting. This review will summarize early work in animals and humans, discuss methodological problems in assessing renal glucose release in vivo, and present results of recent human studies that provide evidence that the kidney may play a significant role in carbohydrate metabolism under both physiological and pathological conditions.