julilili42/papers huggingface dataset:
FhuA Barrel-Cork Hybrids Are Active Transporters and Receptors
2001-06-01

ABSTRACT The crystal structure of Escherichia coli FhuA reveals a β-barrel domain that is closed by a globular cork domain. It has been assumed that the proton motive force of the cytoplasmic membrane through the interaction of the TonB protein with the TonB box of the cork opens the FhuA channel. Yet, deletion of the cork results in an FhuA derivative, FhuAΔ5–160, that still displays TonB-dependent substrate transport and phage receptor activity. To investigate this unexpected finding further, we constructed FhuAΔ5–160 derivatives of FhuA proteins from Salmonella paratyphi B, Salmonella enterica serovar Typhimurium, and Pantoea agglomerans . The FhuAΔ5–160 proteins inserted correctly into the outer membrane, and with the exception of the P. agglomerans protein, transported ferrichrome and albomycin. FhuA hybrids consisting of the β-barrel of one strain and the cork of another strain were active and showed higher TonB-dependent ferrichrome transport rates than the corkless derivatives. Exceptions were the E. coli β-barrel/ Salmonella serovar Typhimurium cork hybrid protein and the Salmonella serovar Typhimurium β-barrel/ P. agglomerans cork hybrid protein, both of which were less active than the β-barrels alone. Each of the FhuA mutant proteins displayed activity for each of their ligands, except for phage T5, only when coupled to TonB. The hybrid FhuA proteins displayed a similar activity with the E. coli TonB protein as with their cognate TonB proteins. Sensitivity to phages T1, T5, and φ80, rifamycin CGP 4832, and colicin M was determined by the β-barrel, whereas sensitivity to phage ES18 and microcin J25 required both the β-barrel and cork domains. These results demonstrate that the β-barrel domain of FhuA confers activity and specificity and responds to TonB and that the cork domains of various FhuA proteins can be interchanged and contribute to the activities of the FhuA hybrids.
Limited Telomere Shortening in Hematopoietic Stem Cells after Transplantation
2001-06-01

A bstract : The number of cell divisions in hematopoietic stem cells (HSCs) following transplantation of bone marrow or mobilized peripheral blood into myelo‐ablated recipients is unknown. This number is expected to depend primarily on the number of transplanted stem cells, assuming that stem cells do not differ in engraftment potential and other functional properties. In a previous study, we found that the telomere length in circulating granulocytes in normal individuals shows a biphasic decline with age, most likely reflecting age‐related changes in the turnover of HSCs. In order to study HSCs' proliferation kinetics following stem cells transplantation, we analyzed the telomere length in donor‐derived nucleated blood cells in four HLA‐matched bone marrow transplant recipients relative to comparable cells from the sibling donors. In each case, the telomeres in granulocytes were shorter in the recipient than in the donor. This difference was established in the first year post transplantation and did not change after that. The telomere length in naïve and memory T cells showed marked differences after transplantation, complicating the interpretation of telomere length data using unseparated nucleated blood cells. Interestingly, the telomere length in naïve T cells that were first observed six months post transplantation was very similar in donor and recipient pairs. Our observations are compatible with a limited number of additional cell divisions in stem cell populations after bone marrow transplantations and support the idea that different populations of stem cells contribute to short‐term myeloid and long‐term lympho‐myeloid hematopoiesis.
Contralaterality of cortical auditory processing at the level of the M50/M100 complex and the mismatch field: A whole-head magnetoencephalography study
2001-06-01

Humans show a stronger cortical representation of auditory input at the opposite hemisphere each. To specify the temporal aspects of this contralaterality effect within the domain of speech stimuli, the present study recorded a series of evoked magnetic fields (M50, M100, mismatch field) subsequent to monaural application of stop consonant-vowel syllables using whole-head magnetoencephalography (MEG). The M50 components exhibited a skewed shape of cross-symmetrical distribution in terms of an initial maximum peak succeeded by a knot over the contralateral and a reversed pattern over the ipsilateral temporal lobe. Most presumably, this pattern of evoked fields reflects two distinct stages of central-auditory processing: (a) initial excitation of the larger contralateral and the smaller ipsilateral projection area of the stimulated ear; (b) subsequent transcallosal activation of the residual neurons, i.e. the targets of the non-stimulated ear, at either side. Previous studies using non-speech stimuli found contralaterality of central-auditory processing to extend to the M100 field. In contrast, a larger amplitude of ipsilateral M100 as compared to the respective opposite deflection emerged after stimulation of either ear. Finally, the computed magnetic analogues of mismatch negativity failed any significant laterality effects. These data provide first evidence for a distinct pattern of hemispheric differences at the level of the M50/M100 complex subsequent to monaural application of speech stimuli.
The Monoclonal Antibody W7C5 Defines a Novel Surface Antigen on Hematopoietic Stem Cells
2001-06-01

A bstract : We recently raised a monoclonal antibody, termed W7C5, against a surface antigen that is expressed at low levels on bone marrow and peripheral blood CD34 + stem/progenitor cells but at high levels on fetal liver CD34 + cells. A reasonable staining intensity was achieved using magnetofluorescent liposome conjugates to analyze expression of W7C5 antigen on CD34 + CD38 − bone marrow (BM) cells. Flow cytometric analyses revealed that W7C5 detects about 50% of immature CD34 + CD38 − BM cells that coexpressed the differentiation antigens CD164, CD133, and CD172a (SIRPα). In addition, W7C5 also recognized a CD34 − BM fraction. These cells were negative for CD117 and CD133, but expressed CD45 and moderate levels of CD164. Injection of selected CD34 + W7C5 + and CD34 − W7C5 + cells into 55–60‐day‐old fetal sheep resulted in an engraftment of both fractions. Partial amino acid sequence analysis of affinity‐purified lysates of KU‐812 cells revealed that W7C5 detects a novel membrane protein. Together, W7C5 defines a novel molecule that is expressed on CD34 + as well as on CD34 − stem cell subsets.
Analysis of gene expression in arbuscular mycorrhizas: new approaches and challenges
2001-06-01

Summary This review summarizes the most recent results obtained using molecular biological techniques in the understanding of the arbuscular mycorrhizal symbiosis. On the plant side, cDNA libraries have been established from mycorrhizal RNA using several techniques, such as suppressive subtractive hybridization, and a large number of clones are being sequenced to obtain expressed sequence tags (ESTs). These ESTs can be transferred to solid supports (arrays) and hybridized with cDNA from different sources to obtain RNA accumulation profiles of genes expressed during the mycorrhizal symbiosis. On the fungal side, EST libraries are also being established, both using direct cloning and suppressive subtractive hybridization techniques. For both partners, the next steps are the detailed analysis of some relevant genes concerned with regulation and function, as well as the study of their role in the symbiosis. At the end of this review, we discuss how results about gene expression and functioning from molecular analyses can help in understanding the ecology of the symbiosis and the way in which it can be further exploited for application in plant production systems.
An efficient algorithm for finding short approximate non-tandem repeats
2001-06-01

Abstract We study the problem of approximate non-tandem repeat †extraction. Given a long subject string S of length N over a finite alphabet Σ and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact repeats) required by the algorithm, and prove a sublinear bound on their expected numbers. Using this result, we present a sub-quadratic algorithm for finding all short (i.e., of length O(log N)) approximate repeats. The running time of our algorithm is O(DN3pow(ε)−1log N), where ε = D/P and pow(ε) is an increasing, concave function that is 0 when ε = 0 and about 0.9 for DNA and protein sequences. Contact: adebiyi@informatik.uni-tuebingen.de †Throughout the paper we only consider non-tandem repeats.
Valsartan and candesartan can inhibit deteriorating effects of angiotensin II on coronary endothelial function
2001-06-01

The angiotensin II (Ang II) AT 1 -receptor antagonists, valsartan and candesartan, were compared with regard to their effect on Ang II-mediated changes in parameters of coronary endothelial function. Ang II (10 μM) induced increased concentrations of the vasoconstrictor endothelin, the procoagulatory substance plasminogen-activator-inhibitor-1 (PAI-1) and the precursor of the matrix-metalloproteinase 1 (MMP-1) in endothelial cell cultures from human coronary arteries. These increases were completely prevented by the addition of 10 μM valsartan or candesartan and partially by the addition of lower concentrations of these drugs, i.e. 1 μM and 0.1 μM. No significant difference between the effect of the two AT 1 -receptor antagonists was observed. These results suggest that AT 1 -receptor antagonists not only can reduce blood pressure by blocking the action of Ang II, but might also contribute to the prevention of atherogenesis and plaque instability.
The connectivity shapes video
2001-06-01

In this video we introduce a 3D shape representation that is based sol ely on mesh connectivity -- the {\\em connectivity shape}. Given a connectivity, we define its natural geometry as a smooth embedding in space with uniform edge lengths and describe efficient techniques to compute it. Furthermore, we show how to generate connectivity shapes that approximate given shapes. The details will soon be published in form of a full paper.
Frederick II of Hohenstaufen and Arabic Science
2001-06-01

The article argues that Frederick II of Hohenstaufen and his court played a unique role in the transfer and diffusion of Arabic science (with its Greek, Hebrew and Christian elements). Scientists at the court translated and elaborated upon it. Moreover, there existed a two-way traffic of scientific knowledge between Frederick and his court scholars, on the one hand, and several oriental courts and their scientists on the other hand. Thus the reader gains a view of Frederick's scientific activities from the Arab perspective, too. Frederick's contribution to the existing biological sciences of his time was his “Book of Falconry”, which was exceptional in the then contemporary approach and methods employed in those fields. Even in this treatise on falconry, Frederick drew upon the fund of knowledge of Arab practitioners. This chain of arguments concerning Arabic science is situated within the setup of Frederick's oriental political practice and sumptuous court life.
RXTE monitoring of Centaurus A
2001-06-01

\\n We report on the analysis from ~110 ks of X-ray\\n observations of Centaurus A carried out with the Proportional Counter\\n Array (PCA) and the High Energy X-ray Timing Experiment (HEXTE)\\n instruments on Rossi X-ray Timing Explorer (RXTE) during three monitoring\\n campaigns over the last 4 years (10 ks in 1996, 74 ks in 1998, and\\n 25 ks in 2000). The joint PCA/HEXTE X-ray spectrum can be well\\n described by a heavily absorbed power law with photon index 1.8 and a\\n narrow iron line due to fluorescence of cold matter. The measured column\\n depth decreased by about between 1996 and 2000, while the detected\\n 2-10 keV continuum flux remained constant between 1996 and 1998, but\\n increased by in 2000. Since in all three observations the iron line\\n flux did not vary, a corresponding decrease in equivalent width was\\n noted. No appreciable evidence for a reflection continuum in the\\n spectrum was detected. We present the interpretation of the iron line\\n strength through Monte Carlo computations of various geometries. No\\n significant temporal variability was found in Cen A at time scales from\\n days to tens of\\n minutes.\\n\\n \\n
Smut fungi (Ustilaginomycetes and Microbotryales, Basidiomycota) in Panama.
2001-06-01

This is the first publication dedicated to the diversity of smut fungi in Panama based on field work, the study of herbarium specimens, and references taken from literature. It includes smuts parasitizing cultivated and wild plants. The latter are mostly found in rural vegetation. Among the 24 species cited here, 14 species are recorded for the first time for Panama. One of them, Sporisorium ovarium, is observed for the first time in Central America. Entyloma spilanthis is found on the host species Acmella papposa var. macrophylla (Asteraceae) for the first time. Entyloma costaricense and Entyloma ecuadorense are considered synonyms of Entyloma compositarum and Entyloma spilanthis respectively. For the new combination Sponsorium panamensis see note at the end of this publication. Descriptions of the species are complemented by some illustrations, a checklist, and a key.
Cleavage of AML1/MTG8 by asymmetric hammerhead ribozymes
2001-06-01

The chromosomal translocation t(8;21) is one of the most frequent aberrations associated with acute myeloid leukaemia. It joins the 5′ section of the AML1 gene with the almost complete open reading frame of MTG8 (ETO) . The resulting fusion RNA represents a leukaemia‐specific target for antisense/ribozyme inhibition. We tested several asymmetric hammerhead ribozymes targeted against the fusion site for their ability to cleave the AML1 / MTG8 RNA at low magnesium concentrations. One ribozyme cleaves AML1 / MTG8 RNA with high catalytic efficiency without binding or cleaving the wild‐type AML1 transcript. The presence of cellular RNA does not affect the cleavage. Injection of AML1 / MTG8 RNA and ribozyme RNA into Xenopus eggs or oocytes causes a specific reduction of AML1/MTG8 protein expression. Asymmetric anti‐AML1/MTG8 ribozymes may be valuable modulators of AML1/MTG8 expression in leukaemic cells.
Mechanisms of MHC class I-restricted antigen presentation
2001-06-01

The vertebrate immune system monitors whether an organism is invaded by pathogens. Therefore, each cell has to prove itself as healthy. This is achieved by presenting fragments of intracellular protein degradation products on the surface, i.e., each cell displays peptides on specialised proteins known as major histocompatibility complex (MHC) class I proteins. A displayed peptide has to pass certain constraints before its presentation: It has to be excised out of a protein, translocated into the endoplasmic reticulum (ER) and fit into the binding groove of a MHC molecule. In theory, alteration of the cellular protein profile by mutation or infection should force pathogen-specific T-cells to take action via recognition of foreign peptide bound to MHC class I molecules on the cell surface. Unfortunately, pathogens and tumours have evolved many ways to affect antigen presentation and to escape from immune response. Understanding the exact mechanisms of antigen presentation, i.e., protein cleavage and peptide binding by MHC molecules, would allow their manipulation by drugs and lead to the re-establishment of the correct antigen presentation pathway. This review will summarise current knowledge of the mechanisms of antigen presentation and discuss putative targets for therapeutic treatment as well as for vaccination strategies.
Penaeus monodon (Tiger Shrimp) Hemocyanin: Subunit Composition and Thermostability
2001-06-01

Penaeus monodon (class Crustacea, order Decapoda) is one of the largest shrimps of the Penaeidea family from the Indo - West Pacific region. The dioxygen-transporting protein hemocyanin, isolated from the hemolymph of this invertebrate, is composed of three 75 -76 kDa structural/functional subunits designated as Pm1, Pm2 and Pm3. The N-terminal sequences of the chains were determined and compared with those of other decapodan hemocyanin subunits. Pm2 and Pm3 are highly homologous and electrophoretically undistinguishable polypeptides. In comparison to Pm1, they have an extension of six residues. Pm1 is closely related to the subunit Pv2 of the Penaeus vannamei hemocyanin. Probably, subunits like Pm1 and Pv2 are family-specific for the Penaeidea hemocyanins and the other subunits are speciesspecific. Comparison of N-terminal sequences of respiratory proteins from the sub-orders Natantia and Reptantia demonstrated family- and sub-order-specific sequences. A melting point of 69 °C, lower than those for the di-hexameric decapodan hemocyanins, was determined from the temperature dependence of ellipticity of the mono-hexameric Penaeus monodon hemocyanin. Thermostability of decapodan hemocyanins depends on their aggregation state.
First-pass effect of an intravenous bolus of [13C]bicarbonate displayed breath-by-breath
2001-06-01

The dilution of an intravenous bolus dose of [ 13 C]bicarbonate is used as an estimate for the metabolic rate under certain conditions. It is a consistent finding in all studies that the total amount of intravenous [ 13 C]bicarbonate cannot be recovered as breath 13 CO 2 . In this study, we used a breath-by-breath analysis of 13 CO 2 to depict the washout of 13 CO 2 at a high temporal resolution to analyze the extent to which a probable first-pass effect is responsible for the reduced recovery. Eight healthy men were tested at seated rest and with bicycle exercise at a constant load relative to 40 and 75% maximal O 2 consumption (V ̇o 2 max ). [ 13 C]bicarbonate (0.0125 g/kg body wt) was administered as an intravenous bolus in each test. Respiratory mass spectrometry was used to derive the course of the end-tidal 13 CO 2 -to- 12 CO 2 ratio from the breath-by-breath data. Approximately 2 min after 13 C administration, the washout curve could be fitted well by a two-exponential curve describing a two-compartment mammillary model. Immediately after administration of the bolus dose, an excess peak in the end-tidal 13 CO 2 -to- 12 CO 2 ratio appeared. This peak could not be included in the two-exponential fitting. The area under the first peak resulted in 3.8 ± 1.3% of the total [ 13 C]bicarbonate dose at rest, 11.5 ± 2.9% at moderate exercise (40%V ̇o 2 max ), and 16.9 ± 4.0% at intensive exercise (75% V ̇o 2 max ). The first-pass effect had an increasing impact of up to about two-thirds of the lacking bicarbonate with higher exercise intensity. The “loss” of tracer via this first-pass effect must be considered when the results of studies with parenteral administration of [ 13 C]bicarbonate are considered, especially when it is given as a bolus dose and during exercise.
Euroscreen 2: Towards Community Policy on Insurance, Commercialization and Public Awareness
2001-06-01

The project Euroscreen 2 has examined genetic screening and testing with particular reference to implications for insurance, commercialization through marketing of genetic tests direct to the public, and issues surrounding raising public awareness of these and other developments in genetics, including the practical experiment of a Gene Shop. This paper provides a snapshot of the three year project. The study group's work included monitoring developments in different European countries and exploring possibilities for regulation in insurance and commercialization together with public attitudes to regulation. The success or failure of different strategies is not independent of public awareness. Exploration of policy, however, also requires examination of fundamental concepts such as solidarity and geneticization.
Cryostripping of the Long Saphenous Vein with a Percutaneously Guided Probe
2001-06-01

BACKGROUND Although the technique of vein removal with a cryoprobe is both simple and well known, it has not yet been widely accepted. A modified probe now eliminates difficulties in its use. OBJECTIVE The original probe has a tip that can be cooled with NO2 or CO2 to −85°C to permit stripping by freezing the vein to the probe from inside the vein. This tip has now been provided with an anatomic curvature and a flexible guide tip, making it easier to introduce the probe into the incision and guide it distally with percutaneous support. WE report on the use of this modified instrument to strip 325 long saphenous veins. RESULTS The modified probe has permitted us to increase the percentage of complete stripping procedures without further distal incisions from 67% to 91%. The procedure was successful in 62% of veins that had already undergone previous sclerosing procedures. Incomplete removal or duplicated long saphenous veins were easily remedied by subsequent stripping starting proximally from a small, distal incision. CONCLUSION Stripping of the long saphenous vein with this modified and easily guided cryoprobe is rapid, uncomplicated, highly effective, and leaves fewer scars.
Dendritic Cell‐Based Vaccines in Patients with Hematological Malignancies
2001-06-01

A bstract : The epithelial mucin MUC1 is overexpressed on many epithelial malignancies as well as on some B‐cell lymphomas and multiple myelomas. In the present study, we describe MUC1 expression also on primary AML blasts. To analyze the presentation of MUC1‐derived HLA‐A2 restricted peptides by primary AML blasts, we induced MUC1‐specific cytotoxic T‐lymphocytes (CTLs) in vitro using peptide pulsed dendritic cells from HLA‐A2 + healthy donors as antigen‐presenting cells. These CTLs efficiently lysed primary AML blasts that constitutively expressed both MUC1 and HLA‐A2. The specificity of the CTLs was confirmed in a cold target inhibition assay. Our data demonstrate that MUC1‐derived peptides are tumor antigens in AML which could potentially be used for immunotherapeutic approaches.
A new device for percutaneous suture-mediated closure of arterial puncture sites using exteriorized needles: initial experience.
2001-06-01

Percutaneous suture with this new device is an acceptably safe and effective method to achieve immediate hemostasis of the arterial access site after interventional procedures with minimized manipulation of the puncture track.
Confined tissue ablation for vitrectomy: a study at FELIX
2001-06-01

The Free Electron Laser for Infrared EXperiments (FELIX) Free Electron Laser Facility provides a continuously tunable source ranging continuously through the 4.5 to 200 micron region. The infrared beam consists of short micropulses, which have a nominal duration of 5 ps and are separated by intervals of either 1 ns or 40 ns of zero intensity. The micropulses form a macropulse train with a duration of up to 15 microseconds. The macropulses are repeated every few hundred ms, with a maximum repetition rate of 10 Hz. Previous studies have shown that the combination of this macro / micro pulse structure, coupled with energy output tuned to the vibrational mode of the Amide- band (? = 6.45 ?m), gives a source well suited to precise tissue ablation. Here the thermal, mechanical and molecular behavior of the ablation was studied. Unlike previous studies, which have concentrated on unconstrained ablation where particles could be ejected from the system at the tissue - air boundary, this experiment simulated the confined ablation necessary during a vitrectomy. It is thought that this is the first study where this has been done, and also the first to study vitreous, which consists of only 2% protein rather than the 20% present in corneal tissue for example.