julilili42/papers huggingface dataset:
Experimental Gas Phase 1H NMR Spectra and Basis Set Dependence of ab initio GIAOMO Calculations of 1H and 13C NMR Absolute Shieldings and Chemical Shifts of Small Hydrocarbons
2004-10-01

Abstract High-resolution gas phase measurements of 1 H NMR spectra at 400 MHz and atmospheric pressure of seven small hydrocarbons are presented. The developed new method and the experimental set-up are described. Ab initio GIAO MO calculations of 1 H and 13 C NMR absolute shieldings on the HF, MP2 and B3LYP levels using 25 standard gaussian basis sets are reported for these hydrocarbons, based on experimental re distances. The measured gas phase 1 H chemical shifts have been converted to an absolute σ 0 shielding scale by use of the literature shielding of methane. These and gas phase 13 C literature values have been transferred with literature ZPV data to estimated σ e exp shieldings which are used to evaluate the basis set dependence of the calculated σ e shieldings utilizing linear least squares regressions. Exponential extrapolations of Dunning basis set calculations allow the determination of basis set limits for 1 H and 13 C shieldings. 1 H and 13 C chemical shifts have been derived from the HF calculated shieldings with shieldings of TMS which has been geometry optimized and GIAO calculated in each basis. Standard deviations (esd) as low as 0.09 ppm for 1 H and 0.76 ppm for 13 C calculations have been obtained. The statistically best basis set for simultaneous calculation of 1 H and 13 C absolute shieldings or relative shifts is 6-311G* within the HF and B3LYP methods. Aiming for highest accuracy and precision, 1 H and 13 C have to be treated separately. In this case, best results are obtained using MP2/6-311G** or higher for 1 H shieldings and MP2/cc-pVTZ for 13 C shieldings.
Automated Higher-Throughput Compound Screening on Ion Channel Targets Based on theXenopus laevisOocyte Expression System
2004-10-01

As numerous diseases have been shown to be related to dysfunction of ion channels and neurotransmitter receptors and to affect regulatory pathways, ion channels have attracted increasing attention as a target class for drug discovery. The concomitant demand of the pharmaceutical industry for adequate electrophysiological methods to investigate drug effects on specific ion channels in secondary and safety screening has resulted in the development of electrophysiological instrumentation that allows automated monitoring of ion channel function with a higher throughput. Here we tested a fully automated screening system based on the Xenopus laevis oocyte expression system. We addressed the questions of data quality and reproducibility obtained by automated oocyte injection and two-electrode voltage-clamp (TEVC) recording using the Roboocyte (Multi Channel Systems GmbH, Reutlingen, Germany) technology compared to conventional oocyte recording. A gamma-aminobutyric acid (GABA)A-receptor subtype (alpha(1)beta(2)) was chosen as an example for a ligand-gated ion channel, and the slowly activating potassium current I(Ks) as a voltage-activated ion channel. Oocytes were injected with cDNA or cRNA via the Roboocyte injection stage. Ion channel currents were successfully recorded after 2-7 days in about 40% of the oocytes injected with GABA(A) receptor cDNA, and after 2-4 days in about 60% of the oocytes injected with KCNE1 cRNA. EC(50) values for the GABA(A) receptor and IC(50) values for blockers of I(Ks) were comparable to values obtained with conventional TEVC recording techniques. In conclusion, our results show that the Roboocyte is a valuable automated tool for oocyte injection and TEVC recording that can be used in drug screening and target validation to enhance the number of compounds and oocytes tested per day.
Hydrogen Bonding in Imidazolium Nitrates [1]
2004-10-01

Abstract The imidazolium nitrates [ImH](NO 3 ) ( 1 ) and [ImBr](NO 3 ) ( 2 ) are obtained from the corresponding bromides [ImH]Br ( 3 ) and [ImBr]Br ( 4 ) and AgNO 3 in excellent yields (Im = 2, 3‐dihydro‐1, 3‐diisopropyl‐4, 5‐dimethylimidazol‐2‐ylidene). The crystal structures of 1 and 2 consist of infinite linear chains of ions linked by H···O and Br···O contacts. In addition, stacks consisting of imidazolium and nitrate ions in the sequence ImBr/NO 3 /ImBr/NO 3 ··· with parallel orientation of their plains are detected in 2 . The crystal structure of 3 is also reported.
THE LANGEVIN OR KRAMERS APPROACH TO BIOLOGICAL MODELING
2004-10-01

In the Langevin or Ornstein–Uhlenbeck approach to diffusion, stochastic increments are applied to the velocity rather than to the space variable. The density of this process satisfies a linear partial differential equation of the general form of a transport equation which is hyperbolic with respect to the space variable but parabolic with respect to the velocity variable, the Klein–Kramers or simply Kramers equation. This modeling approach allows for a more detailed description of individual movement and orientation dependent interaction than the frequently used reaction diffusion framework. For the Kramers equation, moments are computed, the infinite system of moment equations is closed at several levels, and telegraph and diffusion equations are derived as approximations. Then nonlinearities are introduced such that the semi-linear reaction Kramers equation describes particles which move and interact on the same time-scale. Also for these nonlinear problems a moment approach is feasible and yields nonlinear damped wave equations as limiting cases. We apply the moment method to the Kramers equation for chemotactic movement and obtain the classical Patlak–Keller–Segel model. We discuss similarities between chemotactic movement of bacteria and gravitational movement of physical particles.
Modelling transmission, immunity and disease of Haemophilus influenzae type b in a structured population
2004-10-01

An individual-based stochastic simulation model was constructed to study the epidemiology of Haemophilus influenzae type b (Hib) transmission, immunity and invasive disease. Embedded in a demographic model, the transmission model of Hib carriage employs the most important social mixing patterns with three types of contact sites (family, day-care group, and school class). The model includes immunity against invasive Hib disease, initiated and boosted by Hib carriage and cross-reactive bacterial encounters. The model reproduces the observed age patterns in Hib carriage and disease in Finland before large-scale use of the Hib conjugate vaccines. The model was used to investigate characteristics of Hib transmission. The analysis emphasizes transmission between children and adults in families while pointing out the importance of pre-school and school-aged children in maintaining Hib circulation. Carriage in these age groups is thus identified as being essential to target for sustained effects of interventions by vaccination.
IN SITU MEASUREMENTS OF THE H2O:CO2 RATIO IN FLUID INCLUSIONS BY INFRARED SPECTROSCOPY
2004-10-01

Synthetic H 2 O-CO 2 inclusions of variable molar volume and composition were analyzed above their homogenization temperature at 300°C by Fourier transform infrared spectroscopy.The ratio of the integrated absorbance of the antisymmetric stretching band of CO 2 near 2250 cm -1 and of the O-H stretching vibrations of H 2 O around 3700 cm -1 varies systematically with composition, whereas the effect of bulk-fluid molar volume on this ratio appears to be small.The following empirical equation reproduces the observed relationship between the ratio of integrated absorbances A of H 2 O over CO 2 and the molar H 2 O/CO 2 ratio: (H 2 O/CO 2 ) molar = 0.6978*(A H2O /A CO2 ) 1.378 .This relationship can be applied to fluid inclusions with molar volumes between 30 and 50 cm 3 /mole and for binary H 2 O-CO 2 fluid mixtures.It should be used with caution beyond the conditions stated.
Correlated nucleons in configuration space
2004-10-01

Several recent studies have dealt with the effects of short range\\ncorrelations on the momentum distribution of nucleons in nuclei. Here we\\ninvestigate the correlation effects on the density and spectral distribution in\\ncoordinate space. A combination of experimental data and spectral functions\\ncalculated from realistic N-N interactions allows us to resolve a recently\\nuncovered discrepancy with occupation of quasi-particle states derived from\\n(e,e'p) data.\\n
Hemodynamic changes with phenotype reversal during pregnancy in twin–twin transfusion syndrome
2004-10-01

Abstract Objectives We report an atypical case of twin–twin transfusion syndrome (TTTS) in monochorionic‐diamniotic twins with arterio‐arterial anastomoses in which the former donor became the recipient during pregnancy. Methods Serial sonographic monitoring was performed. Results There was a phenotype reversal in TTTS concerning growth and amniotic fluid ending at 27 weeks, with the dominance of the former smaller donor. Doppler sonography changed from absent enddiastolic flow of the donor to normal values in both twins. The new recipient showed transient ascites, the now smaller actual donor (former recipient) developed progressive cardiomegaly, hypertrophy of the myocardium and mitral and tricuspid insufficiency at 29 weeks. Doppler sonography in the new donor deteriorated to highly pathologic flow in the venous system, leading to cesarean section. The donor fetus died 12 h after delivery because of myocardial decompensation. The recipient did very well and was discharged 8 weeks later from the neonatology unit. Conclusion This atypical course shows the importance of serial sonographic monitoring in pregnancies with TTTS. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Lessons on Dermoscopy
2004-10-01

Department of Dermatology, University of Tuebingen, Tuebingen, Germany Address correspondence and reprint requests to: Andreas Blum, MD, Department of Dermatology, University of Tuebingen, Liebermeisterstrasse 25, 72076 Tuebingen, Germany, or e-mail: [email protected]
A polynomial-time algorithm for the matching of crossing contact-map patterns
2004-10-01

Contact maps are a model to capture the core information in the structure of biological molecules, e.g., proteins. A contact map consists of an ordered set S of elements (representing a protein's sequence of amino acids), and a set A of element pairs of S, called arcs (representing amino acids which are closely neighbored in the structure). Given two contact maps (S, A) and (Sp, Ap) with /A/ > or = /Ap/, the CONTACT MAP PATTERN MATCHING (CMPM) problem asks whether the "pattern" (Sp, A,) "occurs" in (S, A), i.e., informally stated, whether there is a subset of /Ap/ arcs in A whose arc structure coincides with Ap. CMPM captures the biological question of finding structural motifs in protein structures. In general, CMPM is NP-hard. In this paper, we show that CMPM is solvable in O(/A/6/Ap/2) time when the pattern is {precedes, crosses}-structured, i.e., when each two arcs in the pattern are disjoint or crossing. Our algorithm extends to other closely related models. In particular, it answers an open question raised by Vialette that, rephrased in terms of contact maps, asked whether CMPM for {precedes, crosses}-structured patterns is NP-hard or solvable in polynomial time. Our result stands in sharp contrast to the NP-hardness of closely related problems. We provide experimental results which show that contact maps derived from real protein structures can be processed efficiently.
Enzymatic synthesis of a CCK‐8 tripeptide fragment
2004-10-01

Abstract A process for the synthesis of CCK‐8 tripeptide H‐Gly‐Trp‐Met‐OH catalyzed by immobilized enzyme was reported. Enzymes were used for the formation of peptide bonds and the removal of protecting group. starting with phenylacetyl (PhAc) glycin, N ‐protected dipeptide PhAc‐Gly‐TrpOMe was obtained by coupling PhAc‐protected glycine carboxamidomethyl ester (Ocam) with Trp‐OMe catalyzed by immobilized papain in buffered ethyl acetate. Then the condensation between PhAc‐Gly‐Trp‐OMe and Met‐OEt·HCl was carried out by immobilized α‐chymotrypsin catalysis in solvent free system. Basic hydrolysis was followed getting PhAc‐Gly‐Trp‐Met‐OH. The PhAc‐group was removed with penicillin G amidase and H‐Gly‐Trp‐Met‐OH was obtained in an overall yield of 43.9%. The reaction conversion of tripeptide in solvent free system was strongly affected by the system of basic salts added. The influence of the support materials used to deposit enzymes and structures of acyl donor and nucleophile on the reaction was also investigated.
Classification of natural landmark with biosonar
2004-10-01

Echolocating bats can make nocturnal flights in acoustically cluttered environments with the use of echolocation. Their marvelous ability to evaluate natural targets in complete darkness provides us an opportunity to learn target detection, classification, and identification with similar biomimetic platforms. In this work, natural landmark classification with a binaural system, a sequential sensing strategy, and a frequency after reconstruction algorithm are adopted to provide sequential acoustic images for target classification. Experimental results suggest that considerable improvements in classification accuracy can be achieved by the use of this sequential classification method.
Met326lle Aminoacid Polymorphism in the Human p85α Gene has no Major Impact on Early Insulin Signaling in Type 2 Diabetes
2004-10-01

Class I alpha phosphatidylinositol (PI) 3-kinase is an important enzyme in the early insulin signaling cascade, and plays a key role in insulin-mediated glucose transport. Despite extensive investigation, the genes responsible for the development of the common forms of type 2 diabetes remain unknown. This study was performed to identify variants in the coding region of p85 alpha, the regulatory subunit of PI 3-kinase. Fibroblasts from skin biopsies from type 2 diabetics and controls were established to address this issue. P85 alpha cDNA was sequenced, and a single point mutation at codon 326 was found. This mutation resulted in a homozygous missense amino acid change Met --> Ile in one subject with type 2 diabetes and heterozygous variant in two other diabetic patients and one with severe insulin resistance. Interestingly, those patients revealed an impaired insulin-mediated insulin receptor substrate (IRS)-1 binding to p85 alpha without any alteration in IRS-2/p85 alpha association. Furthermore, IRS-1, IRS-2, p85 alpha and MAPK protein contents were not significantly changed, and neither were MAPK or Akt phosphorylation. We conclude from our data that this variant may have only minor impact on signaling events; however, in combination with variants in other genes encoding signaling proteins, this may have a functional impact on early insulin signaling.
Assessment of Volume Depletion in Children with Malaria
2004-10-07

Significant hypovolaemia does not exacerbate complications of severe or moderate malaria. As rapid rehydration of children with malaria may have risks, we suggest that fluid replacement regimens should aim to correct fluid losses over 12-24 h.
Aspects of Dentinogenesis: A Model for Biomineralization
2004-10-07

This chapter contains sections titled: Introduction Basic Odontogenesis Dentinogenesis Pre-conditions for Dentinogenesis as Model for Biomineralization Processes Methods and Results Acknowledgments References
MEMBRANE TRAFFICKING IN PLANTS
2004-10-08

▪ Abstract Plant membrane trafficking shares many features with other eukaryotic organisms, including the machinery for vesicle formation and fusion. However, the plant endomembrane system lacks an ER-Golgi intermediate compartment, has numerous Golgi stacks and several types of vacuoles, and forms a transient compartment during cell division. ER-Golgi trafficking involves bulk flow and efficient recycling of H/KDEL-bearing proteins. Sorting in the Golgi stacks separates bulk flow to the plasma membrane from receptor-mediated trafficking to the lytic vacuole. Cargo for the protein storage vacuole is delivered from the endoplasmic reticulum (ER), cis-Golgi, and trans-Golgi. Endocytosis includes recycling of plasma membrane proteins from early endosomes. Late endosomes appear identical with the multivesiculate prevacuolar compartment that lies on the Golgi-vacuole trafficking pathway. In dividing cells, homotypic fusion of Golgi-derived vesicles forms the cell plate, which expands laterally by targeted vesicle fusion at its margin, eventually fusing with the plasma membrane.
Fosmidomycin‐Clindamycin for the Treatment ofPlasmodium falciparumMalaria
2004-10-08

It has been demonstrated that fosmidomycin has good tolerability and rapid onset of action, but late recrudescences preclude its use alone; in vitro, clindamycin has been shown to act synergistically with fosmidomycin against Plasmodium falciparum. We conducted a study in pediatric outpatients with P. falciparum malaria in Gabon to evaluate the efficacy and safety of an oral combination of fosmidomycin-clindamycin of 30 mg/kg and 10 mg/kg of body weight, respectively, every 12 h. Patients 7-14 years old were recruited in cohorts of 10. The first 10 patients were treated for 5 days. The duration of treatment was then incrementally shortened in intervals of 1 day if >85% of the patients in a cohort were cured by day 14. All dosing regimens were well tolerated, and no serious adverse events occurred. Asexual parasites and fever rapidly cleared in all patients. Cure ratios of 100% on day 14 were achieved with treatment durations of 5 (10/10 patients), 4 (10/10 patients), 3 (10/10 patients), and 2 days (10/10 patients); 1 day of treatment led to a cure ratio of 50% (5/10 patients). Fosmidomycin-clindamycin is safe and well tolerated, and short-course regimens achieved high efficacy in children with P. falciparum malaria. Fosmidomycin-clindamycin is a promising novel treatment option for malaria.
Serologic Assay Based on Gliadin-Related Nonapeptides as a Highly Sensitive and Specific Diagnostic Aid in Celiac Disease
2004-10-08

Abstract Background: Celiac disease (CD) is induced by wheat gliadins and related cereal proteins. Anti-gliadin antibodies (AGAs) are present in the serum of CD patients, but these antibodies have lower diagnostic specificity and sensitivity than autoantibodies [anti-endomysium antibodies (AEmAs) and anti-tissue transglutaminase antibodies (AtTGAs)]. Recently, AGAs from CD patients were found to recognize deamidated gliadin peptides, probably formed by the action of tissue transglutaminase. Methods: We synthesized several gliadin peptides and their glutamine-glutamic acid-substituted counterparts on cellulose membranes and tested their recognition by IgA in sera of 52 AEmA-positive CD patients and 76 AEmA-negative controls in a luminescence assay. For comparison, we assayed IgA concentrations of AGAs, AtTGAs, and AEmAs. For measurement of AtTGAs, we used the human recombinant antigen. Results: We identified several nonapeptides that were detected with high specificity by IgA in CD patients. Diagnostic accuracy of the peptide antibody assay was highest when peptide PLQPEQPFP was used in combination with peptide PEQLPQFEE within one assay. AGAs were above the cutoff in 14 of the controls, but only 5 of the controls were positive for peptide antibodies. For comparison, 82% and 94% of samples were correctly classified by AGAs and the combination nonapeptide assay, respectively (P = 0.007), and the AtTGAs correctly classified 98%. Conclusion: The peptide antibody assay has higher diagnostic accuracy than AGAs for distinguishing patients with CD from controls, and has diagnostic accuracy similar to that of AtTGAs.
Heteromeric KCNE2/KCNQ1 potassium channels in the luminal membrane of gastric parietal cells
2004-10-08

Recently, we and others have shown that luminal K + recycling via KCNQ1 K + channels is required for gastric H + secretion. Inhibition of KCNQ1 by the chromanol 293B strongly diminished H + secretion. The present study aims at clarifying KCNQ1 subunit composition, subcellular localization, regulation and pharmacology in parietal cells. Using in situ hybridization and immunofluorescence techniques, we identified KCNE2 as the β subunit of KCNQ1 in the luminal membrane compartment of parietal cells. Expressed in COS cells, hKCNE2/hKCNQ1 channels were activated by acidic pH, PIP 2 , cAMP and purinergic receptor stimulation. Qualitatively similar results were obtained in mouse parietal cells. Confocal microscopy revealed stimulation‐induced translocation of H + ,K + ‐ATPase from tubulovesicles towards the luminal pole of parietal cells, whereas distribution of KCNQ1 K + channels did not change to the same extent. In COS cells the 293B‐related substance IKs124 blocked hKCNE2/hKCNQ1 with an IC 50 of 8 n m . Inhibition of hKCNE1‐ and hKCNE3‐containing channels was weaker with IC 50 values of 370 and 440 n m , respectively. In conclusion, KCNQ1 coassembles with KCNE2 to form acid‐activated luminal K + channels of parietal cells. KCNQ1/KCNE2 is activated during acid secretion via several pathways but probably not by targeting of the channel to the membrane. IKs124 could serve as a leading compound in the development of subunit‐specific KCNE2/KCNQ1 blockers to treat peptic ulcers.
Screening for Mutations Related to Atovaquone/Proguanil Resistance in Treatment Failures and Other Imported Isolates ofPlasmodium falciparumin Europe
2004-10-08

Tyr268Ser seems to be a sufficient, but not a necessary, cause for atovaquone/proguanil treatment failure. The prevalence of both codon-268 mutations is currently unlikely to be >1% in the European patient pool.
Reliability of data in structured peer-to-peer systems
2004-10-08

Peer-to-peer (P2P) systems are very useful for managing large amounts of widely distributed data. For this purpose distributed hash tables (DHT) offer a highly scalable and self-organizing paradigm for efficient distribution and retrieval of data. Thereby a common assumption of P2P systems is, that the participating nodes are unreliable and may fail at any time. Since many of research goes into the design of DHT lookup services, these systems aim to provide a stable global addressing structure. But to storage data reliable in a DHT only few techniques were already developed. However since data has to be stored persistent in the network, it should be retrieved anytime, even if nodes fail. In this work we discuss possibilities to store data fault tolerant in a structured peer-to-peer system.
EChem++An Object-Oriented Problem Solving Environment for Electrochemistry. 2. The Kinetic Facilities of EccoA Compiler for (Electro-)Chemistry
2004-10-09

We describe a modeling software component Ecco, implemented in the C++ programming language. It assists in the formulation of physicochemical systems including, in particular, electrochemical processes within general geometries. Ecco's kinetic part then translates any user defined reaction mechanism into an object-oriented representation and generates the according mathematical model equations. The input language, its grammar, the object-oriented design of Ecco, based on design patterns, and its integration into the open source software project EChem++ are discussed. Application Strategies are given.
Support for service composition in i3
2004-10-10

We consider the problem of service composition in a wide area network, where an end-user can send its packets through intermediate processing points (middleboxes) which can perform a variety of services. Example of such services are filtering, intrusion detection, anonymization, transcoding, and caching. In this paper, we argue that the Internet Indirection Infrastructure (i3)--an overlay network architecture that enables users to locate services and control the path followed by their packets--provides a natural platform for service composition. We discuss the challenges in implementing service compositions on top of i3, and suggest several approaches to address these challenges.