julilili42/papers huggingface dataset:
In Vivo Evidence for TonB Dimerization
2003-09-16

ABSTRACT TonB, in complex with ExbB and ExbD, is required for the energy-dependent transport of ferric siderophores across the outer membrane of Escherichia coli , the killing of cells by group B colicins, and infection by phages T1 and φ80. To gain insights into the protein complex, TonB dimerization was studied by constructing hybrid proteins from complete TonB (containing amino acids 1 to 239) [TonB(1-239)] and the cytoplasmic fragment of ToxR which, when dimerized, activates the transcription of the cholera toxin gene ctx . ToxR(1-182)-TonB(1-239) activated the transcription of lacZ under the control of the ctx promoter (P ctx :: lacZ ). Replacement of the TonB transmembrane region by the ToxR transmembrane region resulted in the hybrid proteins ToxR(1-210)-TonB(33-239) and ToxR(1-210)-TonB(164-239), of which only the latter activated P ctx :: lacZ transcription. Dimer formation was reduced but not abolished in a mutant lacking ExbB and ExbD, suggesting that these complex components may influence dimerization but are not strictly required and that the N-terminal cytoplasmic membrane anchor and the C-terminal region are important for dimer formation. The periplasmic TonB fragment, TonB(33-239), inhibits ferrichrome and ferric citrate transport and induction of the ferric citrate transport system. This competition provided a means to positively screen for TonB(33-239) mutants which displayed no inhibition. Single point mutations of inactive fragments selected in this manner were introduced into complete TonB, and the phenotypes of the TonB mutant strains were determined. The mutations located in the C-terminal half of TonB, three of which (Y163C, V188E, and R204C) were obtained separately by site-directed mutagenesis, as was the isolated F230V mutation, were studied in more detail. They displayed different activity levels for various TonB-dependent functions, suggesting function-related specificities which reflect differences in the interactions of TonB with various transporters and receptors.
The Anatomy of the World's Largest Extinct Rodent
2003-09-18

Phoberomys is reported to be the largest rodent that ever existed, although it has been known only from isolated teeth and fragmentary postcranial bones. An exceptionally complete skeleton of Phoberomys pattersoni was discovered in a rich locality of fossil vertebrates in the Upper Miocene of Venezuela. Reliable body mass estimates yield ∼700 kilograms, more than 10 times the mass of the largest living rodent, the capybara. With Phoberomys , Rodentia becomes one of the mammalian orders with the largest size range, second only to diprotodontian marsupials. Several postcranial features support an evolutionary relationship of Phoberomys with pakaranas from the South American rodent radiation. The associated fossil fauna is diverse and suggests that Phoberomys lived in marginal lagoons and wetlands.
Chronobiological aspects of primate research
2003-09-18

Terrestrial animals live in an environment that undergoes regular variations, ultimately induced by the geophysical conditions prevailing in our solar/earth system. Solar radiation and gravity, in combination with the earth's rotation around its inclined axis and its orbit around the sun, and the moon's revolution around earth, produce marked diurnal, seasonal and lunar as well as tidal periodicities in important physical environmental factors, such as light intensity, ambient temperature, humidity, precipitation, day and night length, and duration of twilight. As a consequence of these periodicities being superimposed on one another, many relevant biotic environmental factors, such as food availability and predator pressure, as well as social contact, communication and competition with conspecifics, and intra- and interspecific competition for food may also vary diurnally, seasonally, lunar periodically or tidally. In this way each animal's environment has a highly complex time structure, is highly repetitive in time and thus highly predictive. Reliable predictivity provides a good substrate for genetically fixed adaptations. Hence, in addition to other general or specific physiological, ecological and/or behavioural adaptations, animals have also evolved endogenous diurnal (circadian), annual (circannual), lunar (circalunar) and/or tidal (circatidal) rhythms.
Studies in organic archaeometry VI. Fat analysis sheds light on everyday life in prehistoric Anatolia: traces of lipids identified in chalcolithic potsherds excavated near Boğazkale, Central Turkey
2003-09-18

Ca 7500 years old potsherds stemming from a special type of jar were excavated in Central Anatolia.Upon chemical analysis traces of still remaining lipids were found: some fatty acids were identified, permitting the interpretation that the ancient content was a fat of animal origin, which can be considered as milk from ruminants or a dairy produce thereof.This result supports the archaeological hypothesis that such jars were used for the production of dairy produces, thus also giving some indication of the economic basis of chalcolithic life in this area.
Developmental Outcome of Levetiracetam, Its Major Metabolite in Humans, 2‐Pyrrolidinone N‐Butyric Acid, and Its Enantiomer (R)‐α‐ethyl‐oxo‐pyrrolidine Acetamide in a Mouse Model of Teratogenicity
2003-09-22

Summary: Purpose: The purpose of this study was to test the teratogenic potential of the antiepileptic drug (AED) levetiracetam (LEV), its major metabolite in humans, 2‐pyrrolidone‐ N ‐butyric acid (PBA), and enantiomer, ( R )‐α‐ethyl‐oxo‐pyrrolidine acetamide (REV), in a well‐established mouse model. Methods: All compounds were administered by intraperitoneal injections once daily to SWV/Fnn mice on gestational days 81⁄2 to 121⁄2. LEV was administered at doses of 600, 1,200, and 2,000 mg/kg/day, piracetam (PIR) and PBA, at 600 and 1,200 mg/kg/day, and REV, at 600 mg/kg/day. On gestational day 181⁄2, fetuses were examined for gross external malformations and prepared for skeletal analysis by using Alizarin Red S staining. Results: No significant gross external malformations were observed in any of the study groups. Fetal weights were significantly reduced in most study groups. Resorption rates were significantly increased only in the 2,000‐mg/kg/day LEV group. The overall incidence of skeletal abnormalities and specifically of hypoplastic phalanges was significantly increased in both PBA treatments and in the intermediate 1,200‐mg/kg/day LEV group. In contrast to that in humans, 24‐h urinary excretion analysis in mice showed that 65–100% of the LEV doses were excreted unchanged, whereas only 4% was excreted as the metabolite PBA. Conclusions: Results of this study demonstrate that both LEV and its major metabolite in humans, PBA, do not induce major structural malformations in developing SWV/Fnn embryos and suggest that they provide a margin of reproductive safety for the pregnant epileptic population when compared with other AEDs tested in this mouse model.
Three-dimensional photoionization modelling of the hydrogen-deficient knots in the planetary nebula Abell 30
2003-09-22

We have constructed a photoionization model, using the 3-D Monte Carlo code MOCASSIN for one of the hydrogen-deficient knots (J3) of the born-again planetary nebula Abell 30. The model consists of spherical knots, comprising a cold, dense, hydrogen-deficient core with very high metal abundances. The inner core is surrounded by a less dense hydrogen-deficient and metal-enriched gas envelope, with less extreme abundances. The envelope of the knot might have been formed by the mixing of the knot material with the surrounding nebular gas. This bi-chemistry, bi-density model did not produce enough heating to match the fluxes of the collisionally excited emission lines (CELs) and of the optical recombination lines (ORLs) observed in the spectrum of the knot. We therefore included heating by photoelectric emission from dust grains in the thermal equilibrium calculations, and found that dust-to-gas ratios of 0.077 and 0.107 by mass for the central core and the envelope of the knot, respectively, are sufficient to fit the spectrum. Surprisingly, photoelectric emission from grains is the dominant source of heating in the hot envelope of the knot, while heating by photoionization of helium and heavy elements dominates in the cold core. The chemical abundances inferred from our modelling indicate, in agreement with the empirical analysis of Wesson et al. (2003), that the C/O ratio in the two regions of the knot is less than unity, contrary to theoretical predictions for born-again nebulae.
Imatinib mesylate affects the development and function of dendritic cells generated from CD34+ peripheral blood progenitor cells
2003-09-23

Abstract Imatinib mesylate (STI571) is a competitive Bcr-Abl tyrosine kinase inhibitor and has yielded encouraging results in treatment of chronic myelogenous leukemia (CML) and gastrointestinal stroma tumors (GISTs). Apart from inhibition of the Abl protein tyrosine kinases, it also shows activity against platelet-derived growth factor receptor (PDGF-R), c-Kit, Abl-related gene (ARG), and their fusion proteins while sparing other kinases. In vitro studies have revealed that imatinib mesylate can inhibit growth of cell lines and primitive malignant progenitor cells in CML expressing Bcr-Abl. However, little is known about the effects of imatinib mesylate on nonmalignant hematopoietic cells. In the current study we demonstrate that in vitro exposure of mobilized human CD34+ progenitors to therapeutic concentrations of imatinib mesylate (1-5 μM) inhibits their differentiation into dendritic cells (DCs). DCs obtained after 10 to 16 days of culture in the presence of imatinib mesylate showed concentration-dependent reduced expression levels of CD1a and costimulatory molecules such as CD80 and CD40. Furthermore, exposure to imatinib mesylate inhibited the induction of primary cytotoxic T-lymphocyte (CTL) responses. The inhibitory effects of imatinib mesylate were accompanied by down-regulation of nuclear localized RelB protein. Our results demonstrate that imatinib mesylate can act on normal hematopoietic cells and inhibits the differentiation and function of DCs, which is in part mediated via the nuclear factor κB signal transduction pathway.
A Formal Total Synthesis of the Salicylihalamides
2003-09-23

The synthesis of the macrolactone 23 is described. The synthesis features a diastereoselective hydroboration of the chiral alkene 17 followed by a Suzuki cross-coupling reaction with the benzoate 5. The resulting seco acid 21 was converted to the macrolactone 23 by a Mitsunobu lactonization using immobilized triphenylphosphine. The stereogenic centers in the alkene 17 were established by a Noyori reduction of the beta-keto ester 8 and an Evans aldol reaction. The synthesis illustrates the conversion of a syn aldol product to the corresponding anti product by inversion of the methyl-bearing center.
Breast cancer in young women (≤35 years): Genomic aberrations detected by comparative genomic hybridization
2003-09-24

Abstract Sporadic breast cancer in young women is different from the one in older patients regarding pathological features and aggressiveness of the tumors, but the spectrum of genetic alterations are largely unknown. We used comparative genomic hybridization (CGH) to analyze DNA copy number changes in 88 tumor samples from women ≤35 years of age. Findings were compared to histopathological data including tumor type, grading, lymph nodes and metastasis. Genomic gains clustered to chromosome arms 1q (64.8%), 8q (61.4%), 17q (50.0%), 20q (33.0%), 3q (20.5%), 1p (17.0%), 5p (17.0%) and 15q (17%). Losses were commonly located on 8p (19.3 %), 11q (11.4%), 16q (11.4%), 17p (11.4%) and 18q (10.2%). A comparison with published CGH data from breast carcinomas of similar type and grade showed the following differences: (1) gains were much more frequent than losses, and (2) losses on 8p22–p23 were more prevalent in patients with positive lymph node metastasis ( p = 0.02), and Grade III tumors were associated with gains on the long arm of chromosome 8 ( p = 0.01). Therefore, alterations in these genomic regions may be responsible for the reduced survival of patients with early onset breast cancer. © 2003 Wiley‐Liss, Inc.
Cognitive Stimulation and Interference in Idea-Generating Groups
2003-09-25

This chapter builds on some 15 years of research on group idea generation carried out at the University of Tübingen, Germany, and Utrecht University, The Netherlands. During these years, three questions have been the primary focus of attention: How can the productivity loss of brainstorming groups be explained? How can productivity of these groups be improved? Why do people think that group brainstorming is more effective than individual brainstorming, whereas the opposite is true? However, the research program has increasingly shifted toward a cognitive approach. The chapter is organized as follows. The first section describes some early research pertaining to the productivity loss of groups, possibilities for improving group performance, and the illusory belief that group brainstorming is more effective than individual brainstorming. It then outlines a cognitive approach to these issues and argues that earlier findings can be interpreted as either cognitive interference or cognitive stimulation effects. The third section discusses recent studies aimed at testing these ideas. The final section draws some conclusions and suggests practical implications and future directions for research.
Structure–property correlation over five phases and four transitions in Pb5Al3F19
2003-09-25

The calorimetric and dielectric properties of Pb 5 Al 3 F 19 in the five phases stable under ambient pressure are correlated with structure for fuller characterization of each phase. The first-order transition between ferroelectric phase V and antiferroelectric phase IV at T V,IV = 260 (5) K exhibits a thermal hysteresis of 135 (5) K on heating, with a maximum atomic displacement Δ( xyz ) max = 1.21 (6) Å; the transition from phase IV to ferroelastic phase III at 315 (5) K is also first order but with a thermal hysteresis of 10 (5) K and Δ( xyz ) max = 0.92 (7) Å; that from phase III to paraelastic phase II at 360 (5) K is second order without hysteresis and has Δ( xyz ) max = 0.69 (4) Å; and the transition from phase II to paraelectric phase I at 670 (5) K is second or higher order, with Δ( xyz ) max = 0.7 (4) Å. The measured entropy change Δ S at T V,IV agrees well with Δ S as derived from the increased configurational energy by Stirling's approximation. For all other phase transitions, 0.5 ≥ Δ S &gt; 0 J mol −1 K −1 is consistent with an entropy change caused primarily by the changes in the vibrational energy. The structure of phase III is determined both by group theoretical/normal mode analysis and by consideration of the structures of phases II, IV and V reported previously; refinement is by simultaneous Rietveld analysis of the X-ray and neutron diffraction powder profiles. The structure of prototypic phase I is predicted on the basis of the atomic arrangement in phases II, III, IV and V. The introduction of 3 d electrons into the Pb 5 Al 3 F 19 lattice disturbs the structural equilibrium, the addition of 0.04% Cr 3+ causing significant changes in atomic positions and increasing T IV,III by ∼15 K. Substitution of Al 3+ by 20% or more Cr 3+ eliminates the potential minima that otherwise stabilize phases IV, III and II.
Adapting inverse planning to patient and organ geometrical variation: algorithm and implementation
2003-09-26

Image guided radiotherapy has the potential to improve both tumour control and normal tissue sparing by including temporal patient specific geometry information into the adaptive planning process. In this study we present a practical method of image guided adaptive inverse planning based on computed tomography (CT) and portal image feedback during the treatment course. The method is based on a general description of the radiotherapy optimization problem subject to dynamic geometrical variations of the patient/organs. We will demonstrate the feasibility of off-line image feedback into the inverse planning process with the example of three prostate cancer patients. CT and portal images acquired during the early course of the treatment are used to predict the geometrical variation distribution of a patient and to re-optimize the treatment plan accordingly. We will study the convergence of the optimization problem with respect to the number of image measurements and adaptive feedback loops.
4′-Phosphopantetheine and Coenzyme A Biosynthesis in Plants
2003-09-26

Coenzyme A is required for many synthetic and degradative reactions in intermediary metabolism and is the principal acyl carrier in prokaryotic and eukaryotic cells. Coenzyme A is synthesized in five steps from pantothenate, and recently the CoaA biosynthetic genes in bacteria and human have all been identified and characterized. Coenzyme A biosynthesis in plants is not fully understood, and to date only the AtHAL3a (AtCoaC) gene of Arabidopsis thaliana has been cloned and identified as 4'-phosphopantothenoylcysteine (PPC) decarboxylase (Kupke, T., Hernández-Acosta, P., Steinbacher, S., and Culiáñez-Macià, F. A. (2001) J. Biol. Chem. 276, 19190-19196). Here, we demonstrate the cloning of the four missing genes, purification of the enzymes, and identification of their functions. In contrast to bacterial PPC synthetases, the plant synthetase is not CTP-but ATP-dependent. The complete biosynthetic pathway from pantothenate to coenzyme A was reconstituted in vitro by adding the enzymes pantothenate kinase (AtCoaA), 4'-phosphopantothenoylcysteine synthetase (AtCoaB), 4'-phosphopantothenoylcysteine decarboxylase (AtCoaC), 4'-phosphopantetheine adenylyltransferase (AtCoaD), and dephospho-coenzyme A kinase (AtCoaE) to a mixture containing pantothenate, cysteine, ATP, dithiothreitol, and Mg2+.
Compromised interferon gamma (IFN-gamma) production in the elderly to both acute and latent viral antigen stimulation: contribution to the immune risk phenotype?
2003-09-26

The elderly suffer from an increased incidence of infectious disease, accompanied by increased morbidity and mortality. Interferon-gamma plays an important role in defense against intracellular pathogens such as mycobacteria and viruses. A reduced capacity to produce this cytokine in the elderly, as demonstrated by our findings of significant decreases in IFN-gamma production in vitro on stimulation with bacterial products (LPS) or viral antigens (influenza vaccine), might therefore contribute to disease susceptibility. Moreover, accumulating data suggest that persistent infection with EBV and particularly CMV impacts upon the immune system in aging and may contribute to the immune risk phenotype (IRP), which predicts remaining longevity in the very elderly. Using tetramer technology and IFN-gamma ELISPOT assays, we found that the commonly-observed clonal expansions of CD8+ T-cells in the elderly were for the most part poorly-functional CMV- and EBV-specific cells, expressing little CD28. The resulting accumulation of dysfunctional cells may lead to a reduction of the repertoire of functional T-cells available for responses to novel antigens. Further longitudinal studies are needed to demonstrate whether cytokines such as IFN-g are also part of the IRP. Improving the definition of the IRP will help to understand and thus prevent or reverse age-associated immune dysfunction.
In Vivo Efficiency of Four Commercial Monopolar Radiofrequency Ablation Systems
2003-09-26

Under physiological liver perfusion the open perfused system and the internally cooled system provided the best efficiency values with lowest standard deviations. The energy efficiency was increased markedly for all systems after occlusion of the portal vein either alone or in combination with arterial occlusion. Occlusion of the hepatic artery did not improve the efficiency.
Vestibular Schwann cells are a distinct subpopulation of peripheral glia with specific sensitivity to growth factors and extracellular matrix components
2003-09-26

Abstract Vestibular nerve Schwann cells are predisposed to develop schwannoma. While knowledge concerning this condition has greatly improved, little is known about properties of normal vestibular Schwann cells. In an attempt to understand this predisposition, we evaluated cell density regulation and proliferative features of these cells taken from 6‐day‐old rats. Data were compared to those obtained with sciatic Schwann cells. In both vestibular and sciatic 7‐day‐old cultures, Schwann cells appear as bipolar or flattened cells. However, sciatic and vestibular cells greatly differ in other aspects: on poly‐ L ‐lysine coating, sciatic cells specifically synthesize myelin basic protein, while expression of P0 mRNAs is restricted to some vestibular cells. Laminin increases sciatic cell density but not that of vestibular cells. Fibronectin selectively enhances the proliferation of vestibular Schwann cells and lacks an effect on sciatic ones. Comparison of cell density changes between sciatic and vestibular cells shows that they are sensitive to two different sets of growth factors. Progesterone and FGF‐2 combined with forskolin selectively enhance the cell density of sciatic glia, while IGF‐1 and GDNF specifically increase vestibular cell density. Furthermore, BrdU incorporation assays indicate that GDNF is also a mitogen for vestibular cells. Altogether, vestibular Schwann cells display phenotypic features and responsiveness to exogenous signals that are significantly different from sciatic Schwann cells, suggesting that vestibular glia form a subpopulation of Schwann cells. © 2003 Wiley Periodicals, Inc. J Neurobiol 57: 270–290, 2003
Senescence: the cost of being young and healthy?
2003-09-26

The fitness of youth has to be paid for in later life by an increased incidence of age-associated diseases. Such a concept of antagonistic pleiotropy was defined by Georg Wick (Institute of Biomedical Ageing Research, Austrian Academy of Sciences, Innsbruck), who opened the immunosenescence session of the 4th Symposium on Cytokine and Apoptosis in the Cardiovascular System. This well-established argument runs as follows: [...]
The Conformational Preference of the Methyl Group in 1‐Methyl‐1‐Silacyclohexane
2003-09-26

The conformational equilibrium of the title compound has been investigated experimentally in the gas phase by gas electron diffraction and in solution at low temperatures by 13C NMR, and theoretically by quantum chemical calculations. Both experimental methods result in a preference of the equatorial position of the methyl group, 68(7)% in the gas phase at 298 K and 74(1)% in solution at 110K. The calculations predict 66% equatorial conformer at room temperature.
Granular Elasticity without the Coulomb Condition
2003-09-29

A self-contained elastic theory is derived which accounts both for mechanical yield and shear-induced volume dilatancy. Its two essential ingredients are thermodynamic instability and the dependence of the elastic moduli on compression.
Assessment of peripheral arterial occlusive disease: comparison of multislice-CT angiography (MS-CTA) and intraarterial digital subtraction angiography (IA-DSA).
2003-09-29

In patients with peripheral arterial occlusive disease, MS-CTA of the lower extremity is a promising minimal-invasive method for detection of relevant arterial stenoses. However, the technique was limited to routine diagnostic purposes due to severe calcifications and time consuming reconstruction procedures.