julilili42/papers huggingface dataset:
Tailoring Ultraresins Based on the Cross-Linking of Polyethylene Imines. Comparative Investigation of the Chemical Composition, the Swelling, the Mobility, the Chemical Accessibility, and the Performance in Solid-Phase Synthesis of Very High Loaded Resins
2004-03-13

Ultraresins have been prepared from polyethyleneimines and cross-linking molecules and have been provided with various degrees of cross-linking. The total nitrogen loading and the loading with secondary and with tertiary amines have been determined in all products. Nitrogen loadings of the novel resins were up to 15 mmol/g, reactive secondary amines up to 13.8 mmol/g. In addition to the exceptionally high loading, the novel resins displayed efficient swelling volumes in polar and nonpolar solvents. The mobility of resin-bound species as determined by EPR-spectroscopy, depending on the amount of cross-linker, indicated good flexibility and reactivity of this resin type. The novel, high-loaded resins have been investigated subsequently in solid-phase synthesis. The Rink amide linker and two different hydroxy linkers (hydroxyacetamide, HMPB) have been attached to the resin. Despite the high loadings, the secondary amines were easily accessible and could be functionalized exhaustively. Reactivity of the linker-coupled resins was found to be closely related to the resin composition. Increased resin cross-linking led to reduced swelling, reduced mobility, and reduced reactivity in the synthesis of a medium-sized model peptide. As the result of the systematic investigation of structure-property relations in Ultraresins, a support material was identified that combined high reactivity and a mobility in the range of the extremely flexible Tentagel supports. In the optimized Ultraresin, >95% of all available secondary nitrogens could be coupled with Rink linker or with the small 2-hydroxyacetamide anchor, resulting in loadings from 2.7 to 6.8 mmol/g, respectively. A resin with an attached HMPB linker and spacer delivered analytically pure peptides in solid-phase synthesis, fully exploiting the exceptionally high loadings.
IL-4 and IL-13 Up-Regulate Intestinal Trefoil Factor Expression: Requirement for STAT6 and De Novo Protein Synthesis
2004-03-15

Abstract The development of intestinal goblet cell hyperplasia/hypertrophy during nematode infection involves the Th2 cytokines IL-4 and IL-13 via STAT6 activation. This is thought to play an important role in host protective immunity against the infection. In this study we demonstrate that IL-4 and IL-13 up-regulate the specific goblet cell product trefoil factor-3 (TFF3) from the mucus-producing HT-29 CL.16E and HT-29 cells selected by adaptation to methotrexate. Up-regulation of TFF3 mRNA and protein levels occurred in a time- and dose-dependent fashion and was accompanied by up-regulation of the goblet cell product mucin 2 (MUC2). Addition of actinomycin D before IL-4/IL-13 stimulation led to decreases in TFF3 mRNA levels similar to those observed in controls without IL-4/IL-13. Furthermore, IL-4-mediated increased TFF3 transcription required de novo protein synthesis. Stable transfection of HT-29 CL.16E cells with a truncated dominant-negative form of STAT6 produced a cell line that was unresponsive to IL-4/IL-13. Although only one consensus STAT6 binding site is contained in the TFF3 gene, located in the intron 1, it did not operate as an enhancer in the context of an SV40 promoter/luciferase construct. Thus, STAT6 activation mediates a transcriptional enhancement of TFF3 by induction of de novo synthesized protein in goblet cells.
Patterns of variation in the phalangeal formulae of land tortoises (Testudinidae): Developmental constraint, size, and phylogenetic history
2004-03-15

Abstract Documentation of variation in phalangeal formulae in land tortoises combined with ontogenetic information from turtles in general were used, in a phylogenetic context, to infer the potential effect of size and developmental constraints upon patterns of morphological variation. A sample of 201 specimens and published illustrations of 37 tortoise species were examined, representing all but one living genera and most species of the Testudinidae. Specimens were either articulated dry skeletons or preserved animals that were x‐rayed. The patterns of digital and phalangeal loss in tortoises were predicted from developmental studies of the manus and pes in other turtles. If a digit is lost, it is the first digit, which is the last one to develop. If a digit has a single phalanx, it is usually the fifth digit. The primitive phalangeal formula for land tortoises is probably 2–2–2–2–1, the most common pattern found in living testudinid species. The presence of a second phalanx in the fifth digit evolved independently many times and usually in large tortoises. Such additions were interpreted as instances of peramorphosis. Many small tortoises have a full complement of digits (five) and phalanges (two in each digit); nevertheless, phalangeal and digital loss is associated with small size. Small and medium size tortoises exhibit greater variation in phalangeal number than do large tortoises. We hypothesize that epigenetic processes, and not simply adaptation, played a major role in the evolution of the variation in phalangeal formulae in tortoises. J. Exp. Zool. (Mol. Dev. Evol.) 302B:134–146, 2004 . © 2004 Wiley‐Liss, Inc.
Biological aspects of radiation and drug-eluting stents for the prevention of restenosis
2004-03-16

Based on recent advances, this article aims to review the biological basis for the use of either radiation or drug-eluting stents for the prevention of restenosis, and to elucidate the complementary role that they may play in the future. Vascular restenosis is a multifactorial process primarily driven by the remodeling of the arterial wall, as well as by the hyperproliferation of smooth muscle cells (SMC). These pathophysiological features are the target of therapeutic strategies aimed at inhibiting constrictive remodeling as well as inhibiting SMC proliferation. The success of radiation as well as anti-proliferative drugs such as paclitaxel and sirolimus lies in the primary and/or multifactorial inhibition of cell proliferation. Radiation has the additional feature of preventing constrictive remodeling while sirolimus has the potential property of being anti-inflammatory, which may be a desirable feature. The effects of radiation are not reliant on any uptake and "metabolism" by the target cells, as in the case with drugs, and thus radiation potentially may be more effective as a result of its more-direct action. However, radiation does have some significant drawbacks compared to drug-eluting stents, including a much delayed re-endothelialization resulting in the need for prolonged anti-platelet therapy. Based on recent clinical data, drug-eluting stents have been shown to markedly reduce the likelihood of restenosis, which actually favors this approach for the prevention of restenosis. From a biological perspective, drug-eluting stents and radiation have certain differences, which are reviewed in this article.
Iron‐Containing Nucleoside Analogues with Pronounced Apoptosis‐Inducing Activity
2004-03-17

Bioactive organometallic compounds: Iron-containing nucleoside analogues, which can be stereoselectively synthesized in a few steps starting from simple carbohydrates, cause tumor cells to undergo apoptosis (programmed cell death; see picture for the typical morphological characteristics of BJAB tumor cells after apoptosis). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z53132_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A Mechanistic Study of Enantiomeric Separation with Vancomycin and Balhimycin as Chiral Selectors by Capillary Electrophoresis. Dimerization and Enantioselectivity
2004-03-20

The role of the sugar moiety of glycopeptide antibiotics in chiral recognition was investigated with capillary electrophoresis. Two glycopeptide antibiotics, vancomycin and balhimycin, were employed as models since they possess the same aglycon and almost identical sugar moieties, however, with different attachment sites to the aglycon. The observed enantioselectivity of balhimycin for dansylated alpha-amino acids is 2.6 times higher than that of vancomycin. Blocking of the sugar amino group of balhimycin by N-carbamoylation reaction with KOCN led to a significantly decreased enantioselectivity compared to vancomycin, which remained almost the same upon carbamoylation. These results suggest a major role of the amino sugar together with its site of attachment to the aglycon. A dimerization-based mechanism is proposed to explain this phenomenon due to the fact that the dimerization properties of glycopeptides are similarly related to their glycosylation patterns; e.g., the dimerization constant of balhimycin is 78 times higher than that of vancomycin. Furthermore, the dimerization of glycopeptides promotes their affinity to carboxyl-containing ligands via cooperativity effects between the dimerization and the formation of glycopeptide-ligand complexes. The higher dimer stability probably leads to a more favorable conformation for chiral recognition. Thus, it is concluded that a weakened dimerization of N-carbamoylated balhimycin results in a decreased enantioselectivity.
UCHL1 is a Parkinson's disease susceptibility gene
2004-03-21

Abstract An Erratum has been published for this article in Ann Neurol 2004;55:899 . The reported inverse association between the S18Y variant of the ubiquitin carboxy‐terminal hydrolase L1 ( UCHL1 ) gene and Parkinson's disease (PD) has strong biological plausibility. If confirmed, genetic association of this variant with PD may support molecular targeting of the UCHL1 gene and its product as a therapeutic strategy for PD. In this light, we performed a collaborative pooled analysis of individual‐level data from all 11 published studies of the UCHL1 S18Y gene variant and PD. There were 1,970 cases and 2,224 unrelated controls. We found a statistically significant inverse association of S18Y with PD. Carriers of the variant allele (Y/Y plus Y/S vs S/S) had an odds ratio (OR) of 0.84 (95% confidence interval [CI], 0.73–0.95) and homozygotes for the variant allele (Y/Y vs S/S plus Y/S) had an OR of 0.71 (95% CI, 0.57–0.88). There was a linear trend in the log OR consistent with a gene dose effect ( p = 0.01). The inverse association was most apparent for young cases compared with young controls. There was no evidence for publication bias and the associations remained significant after excluding the first published, hypothesis‐generating study. These findings confirm that UCHL1 is a susceptibility gene for PD and a potential target for disease‐modifying therapies. Ann Neurol 2004
Observer dependence for the phonon content of the sound field living on the effective curved space-time background of a Bose-Einstein condensate
2004-03-22

We demonstrate that the ambiguity of the particle content for quantum fields\\nin a generally curved space-time can be experimentally investigated in an\\nultracold gas of atoms forming a Bose-Einstein condensate. We explicitly\\nevaluate the response of a suitable condensed matter detector, an ``Atomic\\nQuantum Dot,'' which can be tuned to measure time intervals associated to\\ndifferent effective acoustic space-times. It is found that the detector\\nresponse related to laboratory, ``adiabatic,'' and de Sitter time intervals is\\nfinite in time and nonstationary, vanishing, and thermal, respectively.\\n
An Abundance of Escherichia coli Is Harbored by the Mucosa- Associated Bacterial Flora of Interleukin-2-Deficient Mice
2004-03-23

ABSTRACT Mice deficient in interleukin-2 are well suited for use as an animal model for inflammatory bowel disease. Raised under specific-pathogen-free conditions, interleukin-2-deficient mice develop an inflammatory bowel disease resembling ulcerative colitis in humans. The finding that colitis was attenuated when the mice were kept under germfree conditions implies that the resident intestinal flora is involved in the pathogenesis of colitis. The present study addresses the composition of the mucosa-associated bacterial flora in colon samples from interleukin-2-deficient mice that developed colitis. This was investigated by comparative 16S ribosomal DNA (rDNA) sequence analysis and fluorescence in situ hybridization using rRNA-targeted fluorescent probes to quantify the bacterial populations of the mucosa-associated flora. The investigations revealed distinct differences in the bacterial composition of the mucosa-associated flora between interleukin-2-deficient mice and healthy controls. Fluorescence in situ hybridization identified up to 10% of the mucosa-associated flora in interleukin-2-deficient mice as Escherichia coli , whereas no E. coli was detected in the mucosa from healthy wild-type mice. This finding was consistent with the results from comparative 16S rDNA analysis. About one-third of the clones analyzed from 16S rDNA libraries of interleukin-2-deficient mice represented Enterobacteriaceae , whereas none of the clones analyzed from the healthy controls harbored 16S rDNA from Enterobacteriaceae . The abundance of E. coli in the colonic mucosa of interleukin-2-deficient mice strongly suggests a participation in the pathogenesis of colitis in the interleukin-2-deficient mouse model for inflammatory bowel disease.
Proton MR spectroscopy in succinic semialdehyde dehydrogenase deficiency
2004-03-23

Succinic semialdehyde dehydrogenase (SSADH) deficiency is a rare hereditary disorder of the CNS catabolism of gamma-aminobutyric acid (GABA), leading to accumulation of the metabolite 4-hydroxybutyrate (GHB). Here the authors report on 1.5 and 3.0 T proton MR spectroscopy in a patient with SSADH deficiency. A characteristic pattern with clearly elevated GABA levels and traces of GHB was found in both the white and the gray matter of the brain. In vivo spectroscopy may be useful for diagnosis and monitoring SSADH deficiency.
A FhuA mutant of Escherichia coli is infected by phage T1-independent of TonB
2004-03-23

Infection of Escherichia coli K-12 by phages T1 and phi 80 requires the FhuA outer membrane protein and the TonB protein. Mutations in the N-terminal globular domain close to the predicted channel in the beta-barrel of FhuA were created. The FhuA Delta 107-111 N104K K110D L111P mutant and the FhuA(L(109)DPNGLK(110)) insertion mutant were sensitive to phage T1, but nearly resistant to phage phi 80. FhuA Delta 107-111 N104K K110D L111P mediated phage T1 infection in a tonB mutant without formation of TonB-independent phage T1 host-range mutants. The FhuA mutants showed no altered sensitivity to phage T5. Although the phages share overlapping binding sites in FhuA, the structural alterations elicited by the mutations resulted in very different phage sensitivities. In the FhuA deletion mutant, the TonB requirement for phage T1 infection was partially bypassed.
Comprehending and visualizing software based on XML-representations and call graphs
2004-03-23

We have implemented a package VISUR/RAR in XPCE/SWI-PROLOG, which provides some further functionality of an integrated development environments (IDE): it allows for the visualization of rules (VISUR) together with the reasoning about rule structures (RAR). VISUR/RAR is part of the toolbox DISLOG, which is also developed under XPCE/SWI-PROLOG; the functionality of DISLOG ranges from reasoning in disjunctive deductive databases to applications such as the management and visualization of stock information. The deductive database of RAR manages rules for analyzing PROLOG-code based on suitable dependency graphs and rules for recovering the design of PROLOG- and JAVA-software using a query language FNQUERY for XML-representations, which we have developed. It can be applied for improving the design of rule-based systems, for computing certain software metrics, and for supporting refactoring techniques. The obtained results can be visualized using graphs and tables in VISUR.
Time Is an Important Factor when Processing Samples for the Detection of Disseminated Tumor Cells in Blood/Bone Marrow by Reverse Transcription-PCR
2004-03-24

Despite histopathologic evidence of tumor-free margins, many breast cancer patients suffer from recurrence of their disease. This may reflect the presence of disseminated, premetastatic tumor cells at the time of initial diagnosis and therapy. The detection of disseminated tumor cells in bone marrow/blood has been associated with increased mortality in breast cancer patients (1). Reverse transcription-PCR (RT-PCR) for cytokeratin 19 (CK19) may be a useful alternative or complement to immunocytochemical detection (2). Unfortunately, results of RT-PCR studies vary widely. The reasons for this are conceptual as well as technical. Because RNAses in samples can degrade RNA before analysis, we measured mRNA by RT-PCR in 15 sets of four samples each that were processed at different time points after collection and addition of a known amount of MCF-7 ...
Vortex liquids and vortex quantum Hall states in trapped rotating Bose gases
2004-03-24

We discuss the feasibility of quantum Hall states of vortices in trapped low-density two-dimensional Bose gases with large particle interactions. For interaction strengths larger than a critical dimensionless 2D coupling constant , upon increasing the rotation frequency, the system is shown to spatially separate into vortex lattice and melted vortex lattice (vortex liquid) phases. At a first critical frequency, the lattice melts completely, and strongly correlated vortex and particle quantum Hall liquids coexist in inner respectively outer regions of the gas cloud. Finally, at a second critical frequency, the vortex liquid disappears and the strongly correlated particle quantum Hall state fills the whole sample.
Phylogenetic trees based on gene content
2004-03-25

Abstract Summary: Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known ‘fact’ that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method. Availability: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html
Covariant kaon dynamics and kaon flow in heavy ion collisions
2004-03-25

The influence of the chiral mean field on the transverse flow in heavy ion collisions at SIS energy is investigated within covariant kaon dynamics. For the kaon mesons inside the nuclear medium a quasi-particle picture including scalar and vector fields is adopted and compared to the standard treatment with a static potential. It is confirmed that a Lorentz force from spatial component of the vector field provides an important contribution to the in-medium kaon dynamics and strongly counterbalances the influence of the vector potential on the in-plane flow. The calculated results show that the new FOPI data can be reasonably described using the Brown Rho parameterization, which partly takes into account the correction of higher order contributions in the chiral expansion. This indicates that one can abstract the information on the kaon potential in a nuclear medium from the analysis of the transverse flow.
A new species ofXinpusaurus(Thalattosauria) from the Upper Triassic of China
2004-03-25

ABSTRACT A new species of Xinpusaurus Yin in Yin et al., 2000 (Thalattosauria, Thalattosauridae), is described from the Wayao Member of the Falang Formation (Tuvalian, Carnian, Upper Triassic) of Guanling County in Guizhou, southwestern China. It is the third thalattosaur species known from the Guanling faunal assemblage of marine reptiles. The type and only specimen consists of an entire skeleton, including a complete skull. It differs from the type species, X. suni, by its smaller adult size, the larger nasal, the more slender angular and low retroarticular process, the shape of the cervical neural spines, the number of presacral vertebrae, the large size of the scapula, the shape of the radius, the presence of a well ossified carpus, the more slender femur, the smaller hindfin, the presence of a complete row of distal tarsal ossifications, and the proportions of the metatarsals. It is consequently referred to a new species, Xinpusaurus kohi. A new analysis of thalattosaur interrelationships based on 30 cranial and postcranial characters corroborates a sister-group relationship between Xinpusaurus and Nectosaurus from the Carnian of California.
Tyramine functions as a toxin in honey bee larvae during Varroa-transmitted infection by Melissococcus pluton
2004-03-25

From wounds of honey bee pupae, caused by the mite Varroa destructor, coccoid bacteria were isolated and identified as Melissococcus pluton. The bacterial isolate was grown anaerobically in sorbitol medium to produce a toxic compound that was purified on XAD columns, gelfiltration and preparative HPLC. The toxic agent was identified by GC-MS and FTICR-MS as tyramine. The toxicity of the isolated tyramine was tested by a novel mobility test using the protozoon Stylonychia lemnae. A concentration of 0.2 mg/ml led to immediate inhibition of mobility. In addition the toxicity was studied on honey bee larvae by feeding tyramine/water mixtures added to the larval jelly. The lethal dosis of tyramine on 4-5 days old bee larvae was determined as 0.3 mg/larvae when added as a volume of 20 microl to the larval food in brood cells. Several other biogenic amines, such as phenylethylamine, histamine, spermine, cadaverine, putrescine and trimethylamine, were tested as their hydrochloric salts for comparison and were found to be inhibitory in the Stylonychia mobility test at similar concentrations. A quantitative hemolysis test with human red blood cells revealed that tyramine and histamine showed the highest membranolytic activity, followed by the phenylethylamine, trimethylamine and spermine, while the linear diamines, cadaverine and putrescine, showed a significantly lower hemolysis when calculated on a molar amine basis. The results indicate that tyramine which is a characteristic amine produced by M. pluton in culture, is the causative agent of the observed toxic symptoms in bee larvae. Thus this disease, known as European foulbrood, is possibly an infection transmitted by the Varroa destructor mite.
Double‐chamber right ventricle associated with severe fetal cardiac failure
2004-03-26

Abstract Fetal cardiac defects leading to intrauterine cardiac failure and subsequent fetal hydrops are rare. We report an unusual case of a double‐chamber right ventricle leading to progressive fetal cardiac insufficiency and hydrops. The patient was first managed conservatively. Delivery by Cesarean section was performed for a pathological fetal heart‐rate tracing at 28 weeks of gestation. The newborn died 4 h postpartum due to generalized cardiac insufficiency. Copyright © 2004 ISUOG. Published by John Wiley &amp; Sons, Ltd.