julilili42/papers huggingface dataset:
An upscaling method and a numerical analysis of swelling/shrinking processes in a compacted bentonite/sand mixture
2004-09-22

Abstract This paper presents an upscaling concept of swelling/shrinking processes of a compacted bentonite/sand mixture, which also applies to swelling of porous media in general. A constitutive approach for highly compacted bentonite/sand mixture is developed accordingly. The concept is based on the diffuse double layer theory and connects microstructural properties of the bentonite as well as chemical properties of the pore fluid with swelling potential. Main factors influencing the swelling potential of bentonite, i.e. variation of water content, dry density, chemical composition of pore fluid, as well as the microstructures and the amount of swelling minerals are taken into account. According to the proposed model, porosity is divided into interparticle and interlayer porosity. Swelling is the potential of interlayer porosity increase, which reveals itself as volume change in the case of free expansion, or turns to be swelling pressure in the case of constrained swelling. The constitutive equations for swelling/shrinking are implemented in the software GeoSys/RockFlow as a new chemo‐hydro‐mechanical model, which is able to simulate isothermal multiphase flow in bentonite. Details of the mathematical and numerical multiphase flow formulations, as well as the code implementation are described. The proposed model is verified using experimental data of tests on a highly compacted bentonite/sand mixture. Comparison of the 1D modelling results with the experimental data evidences the capability of the proposed model to satisfactorily predict free swelling of the material under investigation. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Regulation of renal adenosine excretion in humans--role of sodium and fluid homeostasis
2004-09-22

In summary, the physiological variability of EADO is remarkably small in humans. We demonstrate that even profound alterations in sodium and fluid homeostasis do not significantly affect EADO. These data provide a basis for evaluation of elevated EADO as a marker of renal injury in various clinical settings.
Progress in the preparation of peptide aldehydes via polymer supported IBX oxidation and scavenging by threonyl resin
2004-09-24

Peptide aldehydes are of interest due to their inhibitory properties toward numerous classes of proteolytic enzymes such as caspases or the proteasome. A novel access to peptide aldehydes is described using a combination of solid phase peptide synthesis with polymer-assisted solution phase synthesis based on the oxidation of peptide alcohols with a mild and selective polymer-bound IBX derivative. The oxidation is followed by selective purification via scavenging the peptide aldehyde in a capture-release procedure using threonine attached to an aminomethyl resin. Peptide aldehydes are obtained in excellent purity and satisfying yield. The optical integrity of the C-terminal residue is conserved in a high degree. The procedures are compatible with the use of common side-chain protecting groups. The potential for using the method in parallel approaches is very advantageous. A small collection of new and known peptide aldehydes has been tested for inhibitory activity against caspases 1 and 3.
AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis
2004-09-27

Summary For the efficient translocation of organic nitrogen, small peptides of two to three amino acids are posited as an important alternative to amino acids. A new transporter mediating the uptake of di‐ and tripeptides was isolated from Arabidopsis thaliana by heterologous complementation of a peptide transport‐deficient Saccharomyces cerevisiae mutant. AtPTR1 mediated growth of S. cerevisiae cells on different di‐ and tripeptides and caused sensitivity to the phytotoxin phaseolotoxin. The spectrum of substrates recognized by AtPTR1 was determined in Xenopus laevis oocytes injected with AtPTR1 cRNA under voltage clamp conditions. AtPTR1 not only recognized a broad spectrum of di‐ and tripeptides, but also substrates lacking a peptide bond. However, amino acids, ω ‐amino fatty acids or peptides with more than three amino acid residues did not interact with AtPTR1. At pH 5.5 AtPTR1 had an apparent lower affinity ( K 0.5 = 416 μ m ) for Ala‐Asp compared with Ala‐Ala ( K 0.5 = 54 μ m ) and Ala‐Lys ( K 0.5 = 112 μ m ). Transient expression of AtPTR1/GFP fusion proteins in tobacco protoplasts showed that AtPTR1 is localized at the plasma membrane. In addition, transgenic plants expressing the β ‐glucuronidase ( uidA ) gene under control of the AtPTR1 promoter demonstrated expression in the vascular tissue throughout the plant, indicative of a role in long‐distance transport of di‐ and tripeptides.
The prognostic value of progesterone receptor status in meningiomas
2004-09-27

Background: Meningiomas are known to recur frequently, and their longterm management remains controversial. Previous studies indicate that progesterone and its receptors can play a role in the recurrence of meningiomas, but the correlation between the presence of these receptors and patients’ outcome is unclear. Aim: To conduct a retrospective analysis to investigate the prognostic relevance of progesterone receptor (PR) expression in meningiomas. Methods: Five hundred and eighty eight meningiomas operated on over a period of 10 years were examined immunohistochemically to determine the PR status using monoclonal antibodies. Several factors including recurrence (mean follow up of 65 month), sex, tumour tissue consistency, location, vascularity, and en plaque appearance were analysed. Results: PR status showed comparable values for men and women. World Health Organisation (WHO) grade II and III tumours had significantly fewer receptors than benign meningiomas. There was no significant correlation between PR status and recurrence rates in WHO grade I totally removed meningiomas. However, a combination of PR status and proliferation indices was shown to predict recurrence reliably. Conclusions: Together with routine histological evaluation, PR status can help to describe the biological behaviour of meningiomas. Only a combination of clinical and biological features can describe the behaviour of meningiomas, predict their recurrence, and help to devise more effective follow up strategies.
Identification of the Ca2+ Blocking Site of Acid-sensing Ion Channel (ASIC) 1
2004-09-27

Acid-sensing ion channels ASIC1a and ASIC1b are ligand-gated ion channels that are activated by H+ in the physiological range of pH. The apparent affinity for H+ of ASIC1a and 1b is modulated by extracellular Ca2+ through a competition between Ca2+ and H+. Here we show that, in addition to modulating the apparent H+ affinity, Ca2+ blocks ASIC1a in the open state (IC50 ∼ 3.9 mM at pH 5.5), whereas ASIC1b is blocked with reduced affinity (IC50 &amp;gt; 10 mM at pH 4.7). Moreover, we report the identification of the site that mediates this open channel block by Ca2+. ASICs have two transmembrane domains. The second transmembrane domain M2 has been shown to form the ion pore of the related epithelial Na+ channel. Conserved topology and high homology in M2 suggests that M2 forms the ion pore also of ASICs. Combined substitution of an aspartate and a glutamate residue at the beginning of M2 completely abolished block by Ca2+ of ASIC1a, showing that these two amino acids (E425 and D432) are crucial for Ca2+ block. It has previously been suggested that relief of Ca2+ block opens ASIC3 channels. However, substitutions of E425 or D432 individually or in combination did not open channels constitutively and did not abolish gating by H+ and modulation of H+ affinity by Ca2+. These results show that channel block by Ca2+ and H+ gating are not intrinsically linked.
Highly ordered phthalocyanine thin films on a technically relevant polymer substrate
2004-09-27

We have studied the molecular orientation of well-known representatives of organic semiconductors from the family of the phthalocyanines [copper phthalocyanine (CuPc) and its perfluorinated relative (CuPcF16)] on a conducting polymer thin film using polarization-dependent x-ray absorption spectroscopy. As a polymer substrate PEDOT:PSS [a mixture of poly-3,4-ethylenedioxy-thiophene (PEDOT) and polystyrenesulfonate (PSS), which is often applied as an electrode material in (all-)organic semiconductor devices] was spin coated onto indium-tin-oxide substrates. Even if the interfaces themselves are relatively ill defined (we found recently a mixing of the two organic materials and charge-transfer processes), a very high degree of molecular ordering is observed in the 20–50nm thick phthalocyanine films.
Evaluating a hybrid encoding and three crossover operators on the constrained portfolio selection problem
2004-09-28

In this paper we investigate the impact of different crossover operators for a real-valued evolutionary algorithm on the constrained portfolio selection problem based on the Markowitz mean-variance model. We also introduce an extension of a real-valued genotype, which increases the performance of the evolutionary algorithm significantly, independent of the crossover operator used. This extension is based on the effect that most efficient portfolios only consist of a selection of few assets. Therefore, the portfolio selection problem is actually a combination of a knapsack and continuous parameter problem. We also introduce a repair mechanism and examine the impact of Lamarckism on the performance of the evolutionary algorithm.
Long term variability of Cygnus X-1
2004-09-28

Long time scale radio–X-ray correlations in black holes during the hard state have been found in many sources and there seems to emerge a universal underlying relationship which quantitatively describes this behavior. Although it would appear only natural to detect short term emission patterns in the X-ray and – with a certain time lag – in the radio, there has been little evidence for this up to now. The most prominent source for radio–X-ray correlations on short time scales (minutes) so far remains GRS 1915+105 where a single mass ejection could be detected successively in X-ray, IR, and radio wavebands. We analyze a database of more than 4 years of simultaneous radio–X-ray data for Cygnus X-1 from the Ryle Telescope and RXTE PCA/HEXTE. We confirm the existence of a radio–X-ray correlation on long time scales, especially at hard energies. We show that apparent correlations on short time scales in the lightcurves of Cygnus X-1 are most likely the coincidental outcome of white noise statistics. Interpreting this result as a breakdown of radio–X-ray correlations on shorter time scales, this sets a limit to the speed of the jet.
Sporadic rapid‐onset dystonia–parkinsonism syndrome: Failure of bilateral pallidal stimulation
2004-09-28

Abstract We report on a woman who had a severe sporadic nonprogressive dystonia–parkinsonism syndrome with rapid onset of symptoms at age 21. Secondary causes for dystonia were ruled out. No response to levodopa/carbidopa was seen. The patient fulfilled all diagnostic criteria of rapid‐onset dystonia–parkinsonism, except for autosomal‐dominant inheritance. Bilateral deep brain stimulation of the globus pallidus failed to alleviate her symptoms. © 2004 Movement Disorder Society
Enzymatic reactions in anaerobic 2-methylnaphthalene degradation by the sulphate-reducing enrichment culture N 47
2004-09-28

The upper pathway of anaerobic degradation of 2-methylnaphthalene was studied with a sulphate-reducing enrichment culture, which is able to grow with naphthalene or 2-methylnaphthalene as sole carbon source and electron donor. Anaerobic degradation of 2-methylnaphthalene is initiated by an addition of fumarate to the methyl-group producing the first intermediate, naphthyl-2-methyl-succinate. In a subsequent beta-oxidation of the original methyl atom, the central metabolite 2-naphthoic acid is generated. In the following pathway, the aromatic ring system is reduced, cleaved, and finally oxidised to CO(2). Here, we present two new enzymatic reactions of the 2-methylnaphthalene degradation pathway that were measured in crude cell extracts. All metabolites were identified with HPLC by co-elution with synthesised reference substances. The first enzyme, succinyl-CoA:naphthyl-2-methyl-succinate CoA-transferase, catalyses the activation of naphthyl-2-methyl-succinic acid to the corresponding CoA ester. The average specific activity of this enzyme was 19.6 nmol x min(-1) x mg of protein(-1). The CoA-transfer was not inhibited by sodium borohydride and only partially by hydroxylamine, indicating that this enzyme belongs to the family III of CoA-transferases like the corresponding enzyme in the anaerobic toluene degradation pathway. The product of this CoA-transfer reaction, naphthyl-2-methyl-succinyl-CoA is then oxidised in a reaction to naphthyl-2-methylene-succinyl-CoA by the enzyme naphthyl-2-methyl-succinyl-CoA dehydrogenase. The specific activity of this enzyme was 0.115 nmol x min(-1) x mg of protein(-1). The enzymatic activity could only be detected using phenazine methosulphate as electron acceptor. No activity was observed with natural electron acceptors such as nicotinamide adenine dinucleotide or flavin adenine dinucleotide. The two novel reactions presented here demonstrate that the original methyl-group of 2-methylnaphthalene is oxidised to the carboxyl group of 2-naphthoic acid in the upper part of the anaerobic degradation pathway.
Energetic Instability Unjams Sand and Suspension
2004-09-28

Jamming is a phenomenon occurring in systems as diverse as traffic, colloidal suspensions, and granular materials. A theory on the reversible elastic deformation of jammed states is presented. First, an explicit granular stress-strain relation is derived that captures many relevant features of sand, including especially the Coulomb yield surface and a third-order jamming transition. Then this approach is generalized, and employed to consider jammed magnetorheological and electrorheological fluids, again producing results that compare well to experiments and simulations.
A memetic inference method for gene regulatory networks based on S-Systems
2004-09-28

In this paper, we address the problem of finding gene regulatory networks from experimental DNA microarray data. As underlying mathematical model we used S-Systems, a quantitative model, which recently has found increased attention in the literature. Due to the complexity of the inference problem some researchers suggested evolutionary algorithms for this purpose. We introduce enhancements to this optimization process to infer the parameters of sparsely connected non-linear systems given by the observed data more reliably and precisely. Due to the limited number of available data the inferring problem is under-determined and ambiguous. Further on, the problem often is multi-modal and therefore appropriate optimization strategies become necessary. In this paper, we propose a new method, which evolves the topology as well as the parameters of the mathematical model to find the correct network. This method is compared to standard algorithms found in the literature.
High throughput functional genomics: Identification of novel genes with tumor suppressor phenotypes
2004-09-28

Abstract We have used a combination of high throughput functional genomics, computerized database mining and expression analyses to discover novel human tumor suppressor genes (TSGs). A genome‐wide high throughput cDNA phenotype screen was established to identify genes that induce apoptosis or reduce cell viability. TSGs are expressed in normal tissue and frequently act by reduction of growth of transformed cells or induce apoptosis. In agreement with that and thus serving as platform validation, our pro‐apoptotic hits included genes for which tumor suppressing activities were known, such as kangai1 and CD81 antigen. Additional genes that so far have been claimed as putative TSGs or associated with tumor inhibitory activities (prostate differentiation factor, hRAS‐like suppressor 3, DPH2L1‐like and the metastasis inhibitor Kiss1) were confirmed in their proposed TSG‐like phenotype by functionally defining their growth inhibitory or pro‐apoptotic function towards cancer cells. Finally, novel genes were identified for which neither association with cell growth nor with apoptosis were previously described. A subset of these genes show characteristics of TSGs because they (i) reduce the growth or induce apoptosis in tumor cells; (ii) show reduced expression in tumor vs. normal tissue; and (iii) are located on chromosomal (LOH‐) loci for which cancer‐associated deletions are described. The pro‐apoptotic phenotype and differential expression of these genes in normal and malignant tissue make them promising target candidates for the diagnosis and therapy of various tumors.
Some Reactions of Magnesium Arylporphyrazines: Evidence of Dehydroporphyrazine Formation
2004-09-28

Abstract The reactivity of the 2,3‐dibromobenzo‐annulated 2,3,7,8,12,13‐hexakis( m ‐trifluoromethylphenyl)porphyrazine magnesium complex 1 towards butyllithium and tert ‐butylmagnesium chloride in the presence of metallic magnesium was studied. It was found that n ‐butyllithium reacts mainly with the porphyrazine macrocycle to give tetraazachlorins and other reduction products, similarly to porphyrins. On treatment of 1 with t BuMgCl and Mg, dehydroporphyrazine 4 (arynoporphyrazine) was generated and trapped with furan, confirming the possibility of the formation of a dehydrophthalocyanine. The structures of the products were verified by UV/Vis and NMR spectroscopy, and also mass spectrometry (MALDI‐TOF). Utilization of the tetrapyrrolic macrocycle 1 for this type of reaction may become a new synthetic strategy for unsymmetrical peripheral derivatization of phthalocyanines and related compounds. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
Utilizing an island model for EA to preserve solution diversity for inferring gene regulatory networks
2004-09-28

In this paper we address the problem of finding gene regulatory networks from artificial data sets of DNA microarray experiments. Some researchers suggested evolutionary algorithms for this purpose. We suggest to use an enhancement for evolutionary algorithms to infer the parameters of the nonlinear system given by the observed data more reliably and precisely. At present, we use S-Systems because they are a general mathematical model for simulating the complex interactions of gene regulatory networks. Due to the limited number of available data, the inferring problem is highly under-determined and ambiguous. Further on, the problem often is highly multi-modal and therefore appropriate optimization strategies become necessary. We propose to use an island model to maintain diversity in the EA population to prevent premature convergence and to raise the probability of finding the global optimum.
Lessons on Dermoscopy: Dermoscopic Pattern of Hemosiderotic Dermatofibroma
2004-09-29

A randomized, double-blind study was performed in 50 patients to compare the transthecal and traditional subcutaneous infiltration techniques of digital block anesthesia regarding the onset of time to achieve anesthesia and pain during the infiltration. All the patients had sustained injury involving two or four fingers of the hand. Each patient served as his or her own control, having one finger infiltrated with the transthecal technique and the other with the subcutaneous infiltration technique. Time to loss of pinprick sensation and pain (at the time of the infiltration and 24 hours postoperatively) were assessed using a visual analogue scale and verbal response score. A total of 104 blocks (52 transthecal and 52 subcutaneous infiltration) were performed. All of these blocks were successful. Mean time to achieve anesthesia with the transthecal block was 165 seconds, compared with 100 seconds for the subcutaneous infiltration block. The mean analogue pain score was higher for transthecal blocks than for subcutaneous infiltration blocks (3.2 ± 0.19 versus 1.6 ± 0.14). Twenty-four hours postoperatively, 24 patients who had the transthecal block experienced pain at the injection site of the digit. However, none of the patients who received the subcutaneous infiltration block complained of pain at the digit. The technique of anesthesia preferred by patients for their finger was the subcutaneous infiltration block, because it causes less pain. Our results confirm the efficacy of the transthecal block for achieving anesthesia of the finger; however, because it is a more painful procedure, it is not recommended.
Iron supply to tobacco plants through foliar application of iron citrate and ferric dimerum acid
2004-09-29

Experiments to assess the re‐greening and the distribution of leaf‐applied iron (Fe) within the aerial organs were developed with tobacco ( Nicotiana tabacum L.) plants. Fe (III)‐citrate and Fe‐dimerum acid were applied to a part of the leaf and plant re‐greening was monitored for 6 weeks after treatment. Fluid Fe increments associated with foliar Fe application were measured within 3 days after application. Fe distribution from the site of application within the leaf and the untreated above‐ground plant parts was evaluated. Leaf fluid Fe concentration was determined by a novel procedure based on Fe chelation by desferrioxamine E and high performance liquid chromatography separation on a reversed‐phase column. The ferrioxamine E method enabled accurate determination of small amounts of Fe present in leaf fluid. Foliar Fe‐dimerum acid and Fe (III)‐citrate treatment to chlorotic tobacco plants induced new growth re‐greening. It was concluded that the applied Fe‐containing compounds penetrated the leaf, were distributed within the plant and that Fe supplied as both complexes could be utilized by the plant cell.
Simultaneous measurement of saturation and relaxation in human brain by repetitive magnetization transfer pulses
2004-09-29

Abstract Magnetization transfer (MT) by equidistant pulse trains can be described as being analogous to progressive partial saturation, where ‘direct’ saturation of water is amplified by MT contributions that are dependent on macromolecular content and differential saturation. This concept was applied to study the transition to steady state in the human brain using similar MT‐pulses as in imaging. Up to 41 bell‐shaped MT‐pulses of 12 ms duration were applied at frequency offsets between 0.5 and 15 kHz with flip angles between 1080 and 1440°. Central white and parietal gray matter was studied in human subjects using STEAM for localized read‐out ( TE = 30 ms, TM = 13.7 ms). The apparent degree of saturation, δ app , and the longitudinal relaxation of the water pool during the pulse repetition period (PR) were fitted to the transient behavior after signal correction for cerebro‐spinal fluid. PR was varied between 15 and 100 ms to assess the PR‐dependence of the fitted parameters. The MT‐term in δ app exceeded the direct saturation and attained its maximum at PR &gt; 100 ms. The macromolecular pool was only partially saturated by a single MT‐pulse. The offset may be increased to 2.5 kHz to reduce direct saturation without sacrificing MT in white matter. The estimated relaxation rates (1.04 ± 0.11 s −1 in WM; 0.76 ± 0.13 s −1 in GM) were faster than are commonly observed at 1.5 T. The apparent saturation is a measure for MT that is not confounded by relaxation. To maximize MT in brain tissue, MT‐pulses should be applied at PR = 100 ms or longer. At shorter PR, a larger steady state satuation is obtained at the cost of increased contributions from direct saturation. Since this accelerates the convergence, PR should be decreased to reach the steady state within a specified time. A faster transition can always be achieved at a reduced frequency offset via increased direct saturation. Copyright © 2004 John Wiley &amp; Sons, Ltd.