julilili42/papers huggingface dataset:
Case Isolation and Contact Tracing Can Prevent the Spread of Smallpox
2003-07-08

Fears that terrorist groups may have gained access to variola virus have led to widespread discussions on how to prevent the reintroduction of smallpox by vaccination and on the availability of sufficiently large amounts of vaccine. In this paper, the author examines how the spread of smallpox is affected by isolating overt cases and taking their contacts under close surveillance for up to 3 weeks. The author assumes that case detection gradually improves from initially 7 days to 3 days. This intervention should be accompanied by vaccination, but its outcome does not depend on the vaccine's efficacy. It may, therefore, be especially important in controlling outbreaks caused by pathogens whose immunologic properties have been modified by genetic engineering. Using stochastic computer simulations, the author demonstrates that contact tracing and case isolation can extinguish smallpox outbreaks in highly susceptible populations within less than half a year without causing totals of more than 550 secondary cases per 100 index cases. The author also derives simple approximate expressions that allow prognostication on how efficiently an outbreak can be controlled by the described measures alone and prediction of the expected number of cases in an outbreak and the number of people that must be taken under surveillance.
Patterns of circulating hepatitis B virus serum nucleic acids during lamivudine therapy
2003-07-08

Abstract We examined whether lamivudine treatment, in addition to the rapid decline of HBV serum DNA described in a large number of laboratories, causes changes in composition and amount of discernable circulating viral DNA and RNA. Nucleic acids were extracted from serial serum samples of a patient infected chronically and treated with lamivudine for 14 weeks. Three sequence segments of the HBV genome synthesized successively during replication, X, C, and X‐preC, were analyzed by competitive PCR and RT/PCR. In addition, RNA was examined for differential polyadenylation. Before treatment, identical DNA copy numbers (10 9 /ml) were found in all three segments. C segment DNA displayed the expected rapid decline. X‐preC, a target contiguous only on plus‐strand DNA behaved similarly. In contrast, the X segment DNA copy numbers showed a less pronounced decrease remaining at higher values (10 7 /ml) than the C and X‐preC segment (both about 2 × 10 5 /ml) at the end of therapy. X segment RNA displayed a persisting copy number of about 10 7 /ml, while C and X‐preC RNA decreased to about 10 5 copies/ml. Polyadenylated HBV RNA, full‐length and truncated, persisted initially at 10 5 but decreased to 10 4 to 10 3 copies/ml at the end of treatment. The major conclusions are the actual numbers of virus particles during lamivudine therapy can only be assessed via X segment DNA, since it is reverse transcribed first, and Lamivudine induced coexistence of DNA and RNA for the C and X segment at similar levels indicates drug‐arrested intermediates of reverse transcribed HBV DNA minus‐strand. Packaged RNA lacks a poly(A) tail whereas polyadenylated RNA is likely not packaged. J. Med. Virol. 71:24–30, 2003. © 2003 Wiley‐Liss, Inc.
Phase II trial of trofosfamide in patients with advanced pretreated soft tissue sarcomas.
2003-07-10

No objective remission was observed with oral low-dose trofosfamide in heavily pretreated soft tissue sarcoma patients, but almost half of the patients achieved disease stabilisation for half a year. The moderate toxicity profile observed in this study allows the consideration of trofosfamide as a reasonable palliative treatment option for patients with soft tissue sarcoma.
Ontogenesis of the scapula in marsupial mammals, with special emphasis on perinatal stages of didelphids and remarks on the origin of the therian scapula
2003-07-10

Abstract The development of the scapula was studied in embryonic and postnatal specimens of Monodelphis domestica and perinatal specimens of Philander opossum, Caluromys philander , and Sminthopsis virginiae using histological sections and 3D reconstructions. Additionally, macerated skeletons of postnatal M. domestica were examined. This study focused on the detachment of the scapulocoracoid from the sternum and on the acquisition of a supraspinous fossa, a supraspinatus muscle, and a scapular spine, all these events associated with the origin of the therian shoulder girdle. In none of the specimens is there a continuity of the cartilaginous scapulocoracoid with the sternum, even though the structures are in close proximity, especially in S. virginiae . At birth, the first rib laterally presents a pronounced boss that probably contacts the humerus during certain movements. Only the acromial portion of the scapular spine, which originates from the anterior margin of the scapular blade, is preformed in cartilage. The other portion is formed by appositional bone (“Zuwachsknochen”), which expands from the perichondral ossification of the scapula into an intermuscular aponeurosis between the supra‐ and infraspinous muscles. This intermuscular aponeurosis inserts more or less in the middle of the lateral surface of the developing scapula. Thus, the floor of the supraspinous fossa is present from the beginning of scapular development, simultaneously with the infraspinous fossa. The homology of the therian spine with the anterior border of the sauropsid and monotreme scapula is questioned. We consider the dorsal portion (as opposed to the ventral or acromial portion) of the scapular spine a neomorphic structure of therian mammals. J. Morphol. 258:115–129, 2003. © 2003 Wiley‐Liss, Inc.
Pion and sigma meson properties in a relativistic quark model
2003-07-11

A variety of strong and electroweak interaction properties of the pion and\\nthe light scalar sigma meson are computed in a relativistic quark model. Under\\nthe assumption that the resulting coupling of these mesons to the constituent\\nquarks is identical, the sigma meson mass is determined as M_sigma=385.4 MeV.\\nWe discuss in detail the gauging of the non-local meson-quark interaction and\\ncalculate the electromagnetic form factor of the pion and the form factors of\\nthe pi(0) -&gt; gamma gamma and sigma -&gt; gamma gamma processes. We obtain explicit\\nexpressions for the relevant form factors and evaluate the leading and\\nnext-to-leading orders for large Euclidean photon virtualities. Turning to the\\ndecay properties of the sigma we determine the width of the electromagnetic\\nsigma -&gt; gamma gamma transition and discuss the strong decay sigma -&gt; pi pi. In\\na final step we compute the nonleptonic decays D -&gt; sigma pi and B -&gt; sigma pi\\nrelevant for the possible observation of the sigma meson. All our results are\\ncompared to available experimental data and to results of other theoretical\\nstudies.\\n
1,3-Bis(4-nitrophenyl)triazene
2003-07-12

The structure of the title compound, C(12)H(9)N(5)O(4), reveals an almost planar molecule (r.m.s. deviation = 0.061 A), in which the interplanar angle between the phenyl rings is 5.7 (1) degrees and the largest interplanar angle is that between the phenyl ring and the nitro group of one of the 4-nitrophenyl substituents [8.8 (3) degrees ]. The observed molecular conformation suggests a delocalization of pi-electrons extended over the diazoamine group and the terminal aryl substituents. Intermolecular N-H.O interactions between the twofold screw-related molecules give rise to helical chains along the [010] direction. Intermolecular C-H.O interactions then generate sheets of molecules in the (10-1) plane, and these sheets are held together by N.C and O.O pi-pi interactions.
Amoeboid shape change and contact guidance: T-lymphocyte crawling through fibrillar collagen is independent of matrix remodeling by MMPs and other proteases
2003-07-15

Abstract The passage of leukocytes through basement membranes involves proteolytic degradation of extracellular matrix (ECM) components executed by focalized proteolysis. We have investigated whether the migration of leukocytes through 3-dimensional collagenous tissue scaffolds requires similar ECM breakdown. Human T blasts and SupT1 lymphoma cells expressed mRNA of MMP-9, MT1-MMP, MT4-MMP, cathepsin L, uPA, and uPAR as well as ADAM-9, -10, -11, -15, and -17. Upon long-term migration within 3-dimensional collagen matrices, however, no in situ collagenolysis was obtained by sensitive fluorescein isothiocyanate–collagen fragmentation analysis and confocal fluorescence/backscatter microscopy. Consistent with nonproteolytic migration, T-cell crawling and path generation were not impaired by protease inhibitor cocktail targeting MMPs, serine proteases, cysteine proteases, and cathepsins. Dynamic imaging of cell-ECM interactions showed T-cell migration as an amoeba-like process driven by adaptive morphology, crawling along collagen fibrils (contact guidance) and squeezing through pre-existing matrix gaps by vigorous shape change. The concept of nonproteolytic amoeboid migration was confirmed for multicomponent collagen lattices containing hyaluronan and chondroitin sulfate and for other migrating leukocytes including CD8+ T blasts, monocyte-derived dendritic cells, and U937 monocytic cells. Together, amoeboid shape change and contact guidance provide constitutive protease-independent mechanisms for leukocyte trafficking through interstitial tissues that are insensitive toward pharmacologic protease inhibitors.
Inhibitors of DNA methylation and histone deacetylation activate cytomegalovirus promoter-controlled reporter gene expression in human glioblastoma cell line U87
2003-07-17

The expression of many cellular genes is modulated by DNA methylation and histone acetylation. These processes can influence malignant cell transformation and are also responsible for the silencing of DNA constructs introduced into mammalian cells for therapeutic or research purposes. As a better understanding of these biological processes may contribute to the development of novel cancer treatments and to study the complex mechanisms regulating gene silencing, we established a cellular system suitable to dissect the mechanisms regulating DNA methylation and histone acetylation. For this purpose, we stably transfected the neuroblastoma cell line U87 with a cytomegalovirus promoter-driven reporter gene construct whose expression was analyzed following treatment with the DNA methylation inhibitor 5'-aza-2'-deoxycytidine or histone deacetylation inhibitor trichostatin A. Both substances reactivated the silenced cytomegalovirus promoter, but with different reaction kinetics. Furthermore, whereas the kinetics of reactivation by trichostatin A did not substantially change over the time range considered (5 days), reactivation induced by 5'-aza-2'-deoxycytidine showed profound differences between day 1 and longer time points. We showed that this effect is related to the down-regulation of DNA replication by 5'-aza-2'-deoxycytidine. Finally, we have shown that the simultaneous administration of trichostatin A and 5'-aza-2'-deoxycytidine results in reactivation of the CMV promoter according to a cooperative, not synergistic or additive, mechanism. In conclusion, our cellular system should represent a powerful tool to investigate the complex mechanisms regulating gene silencing and to identify new anticancer drugs.
Generation of dominant‐negative effects on the heat shock response in Arabidopsis thaliana by transgenic expression of a chimaeric HSF1 protein fusion construct
2003-07-17

Summary Upon heat stress, heat shock factors (HSFs) control the expression of heat shock protein (HSP) genes by transcriptional activation. The perplexing multiplicity of HSF genes in Arabidopsis – 21 potential genes have been identified – renders it difficult to identify mutant phenotypes. In this study, we have attempted to generate a transdominant‐negative mutant of HSF by transgenic expression of a protein fusion construct, EN‐HSF1, consisting of the Drosophila engrailed repressor domain (EN) and the complete Arabidopsis AtHSF1. Transgenic lines were screened for impaired ability to induce high levels of low‐molecular‐weight heat shock proteins (sHSPs). Two lines, EH14‐6 and EH16‐3, which showed quantitative differences in the expression of EN‐HSF1, were further analysed for induction of thermotolerance and heat‐stress‐dependent mRNAs of a number of different HSF target genes encoding different HSP and HSF. The mRNA levels of all genes tested were moderately downregulated in EH14‐6 but strongly reduced in EH16‐3 plants compared to wild‐type (Wt) and HSF1 ‐overexpressing control plants. The inhibition of the induction of heat shock response correlated with impaired basal and acquired thermotolerance of the EH16‐3 line. The kinetics of HSP expression suggest that the negative effect of EN‐HSF1 is stronger in the early phase of the heat shock response, and that the reduction in mRNA levels is partially compensated at the translational level.
Predictors of successful self control during brain-computer communication
2003-07-21

Initial performance in the self regulation of SCP is positively correlated with later performance in severely paralysed patients, and thus represents a useful predictor for efficient brain-computer communication.
Melatonin Receptor Signaling in Pregnant and Nonpregnant Rat Uterine Myocytes as Probed by Large Conductance Ca2+-Activated K+ Channel Activity
2003-07-22

The mRNAs of MT1 and MT2 melatonin receptors are present in cells from nonpregnant (NPM) and pregnant (PM) rat myometrium. To investigate the coupling of melatonin receptors to Gq- and Gi-type of heterotrimeric G proteins, we analyzed the activity of large-conductance Ca2+-activated K+ (BKCa) channels, the expression of which in the uterus is confined to smooth muscle cells. The melatonin receptor agonist 2-iodomelatonin induced a pertussis toxin (PTX)-insensitive increase in channel open probability that was blocked by the nonselective antagonist luzindole. The 2-iodomelatonin effect on channel open probability was suppressed by overexpression of the Gqalpha-inactivating protein RGS16 and the phospholipase C inhibitor U-73122. The activity of BKCa channels is differentially regulated by protein kinase A (PKA) in NPM and PM cells. Thus, the beta-adrenoceptor agonist isoprenaline inhibited the BKCa channel conducted whole-cell outward current (Iout) in NPM cells and enhanced Iout in PM cells. Additional application of 2-iodomelatonin antagonized the isoprenaline effect on Iout in NPM cells but enhanced Iout in PM cells. All 2-iodomelatonin effects on Iout were sensitive to PTX treatment and the PKA inhibitor H-89. We therefore conclude that melatonin activates both the PTX-insensitive Gq/phospholipase C/Ca2+ and the PTX-sensitive Gi/cAMP/PKA signaling pathway in rat myometrium.
Structure of MrsD, an FAD-binding protein of the HFCD family
2003-07-22

MrsD from Bacillus sp. HIL-Y85/54728 is a member of the HFCD (homo-oligomeric flavin-containing Cys decarboxylases) family of flavoproteins and is involved in the biosynthesis of the lantibiotic mersacidin. It catalyses the oxidative decarboxylation of the C-terminal cysteine residue of the MrsA precursor peptide of mersacidin, yielding a (Z)-enethiol intermediate as the first step in the formation of the unusual amino acid S-[(Z)-2-aminovinyl]-methyl-D-cysteine. Surprisingly, MrsD was found to bind FAD, in contrast to the three other characterized members of the HFCD family, which bind FMN. To determine the molecular discriminators of FAD binding within the HFCD family, the crystal structure of MrsD was analyzed at a resolution of 2.54 A. Crystals of space group F432 contain one MrsD monomer in the asymmetric unit. However, a Patterson search with EpiD-derived models failed. Based on the consideration that the dodecameric MrsD particle of tetrahedral symmetry resembles the quaternary structure of EpiD, rotational and translational parameters were derived from the geometric consideration that the MrsD dodecamer is generated from a monomer by crystallographic symmetry around the position (1/4, 1/4, 1/4) of the unit cell. A structural comparison with the FMN-binding members of the HFCD family EpiD and AtHAL3a shows conserved sequence motifs in contact with the flavin's pyrimidine ring but divergent environments for the dimethylbenzene ring of the isoalloxazine moiety. The position of the ribityl chain differs in MrsD from that found in EpiD and AtHAL3a. However, the FMN-phosphate binding sites are also highly conserved in their exact positions. In all three cases, the flavin cofactor is bound to a structurally conserved region of the Rossmann-fold monomer, exposing its Re side for catalysis. The adenosyl phosphate of FAD is anchored in a well defined binding site and the adenosine moieties are oriented towards the interior of the hollow particle, where three of them pack against each other around the threefold axis of a trimeric facet.
Peripheral blood cell telomere length measurements indicate that hematopoietic stem cell turnover is not significantly increased in whole blood and apheresis PLT donors
2003-07-22

BACKGROUND: The telomere length (TEL) of peripheral blood leukocytes (PBLs) can be used to estimate hematopoietic stem cell turnover. The current study investigated whether the repetitive stimulation of the hematopoietic system caused by regular whole blood (WB) and PLT donations would affect PBL TEL. STUDY DESIGN AND METHODS: PBLs were obtained from healthy donors (n=94) with a history of at least 3 years of WB donation (median, 7.7 years; range, 3.0‐43.0 years) plus additional apheresis PLT donations. The median (range) numbers of WB and PLT donations were 22.0 (6.0‐194.0) and 42.0 (7.0‐336.0), respectively. Additionally, samples were obtained from healthy nondonors (n=47). PBL TEL was measured with fluorescence in situ hybridization and flow cytometry (flow‐FISH). Flow‐FISH results were expressed in molecular equivalents of soluble fluorochrome units (MESF; 1000 MESF=1 kMESF) either as absolute (TEL) or as age‐adjusted TEL (ΔTEL). RESULTS: Donor granulocyte and lymphocyte TELs were 12.6 ± 0.3 (mean ± SEM) and 13.2 ± 0.3 kMESF, respectively. No differences were observed when compared with corresponding nondonor data (granulocytes, 12.5 ± 0.4 kMESF; lymphocytes, 13.6 ± 0.5 kMESF). Furthermore, ΔTEL values did not differ between the two groups and were not different from previously established reference values. In addition, neither donor data for age‐adjusted TEL for granulocytes nor ΔTEL for lymphocytes were correlated with either total years or total numbers of WB and/or PLT donations. CONCLUSION: Long‐term WB and PLT donation does not affect PBW TEL as measured by flow‐FISH, arguing against a significantly increased stem cell turnover.
On the Velo–Zwanziger phenomenon
2003-07-22

The Rarita-Schwinger equation in a curved background and an external electromagnetic field is discussed. We analyse the equation in the 2-component spinor formalism and derive Buchdahl conditions for them. The result is that the equation can consistently be imposed only on Einstein manifolds with vanishing electromagnetic field.
The allograft inflammatory factor‐1 in Creutzfeldt–Jakob disease brains
2003-07-23

The allograft inflammatory factor‐1 (AIF‐1) is a 17‐kDa IFN‐γ inducible Ca 2+ ‐binding EF‐hand protein that is encoded within the HLA class III genomic region and is involved in immune dysfunction and smooth muscle cell activation. We used immunohistochemistry double labelling experiments to analyse the spatial distribution and cell‐type‐specific localization of AIF‐1 in the brains of patients who died as a result of sporadic Creutzfeldt–Jakob disease (CJD) and neuropathologically unaltered controls. Significantly more AIF‐1 immunoreactive macrophages/microglial cells and, interestingly, neurones were observed in CJD patients compared to controls. Western blotting confirmed more prominent AIF‐1 immunoreactive bands of approximately 50 kDa in four CJD patients compared to three controls. Chaotropic SDS‐PAGE of the recombinant AIF‐1 resulted in almost complete reduction of the 50 kDa band and mass spectrometry revealed only AIF‐1‐specific tryptic protein fragments suggesting that trimerized AIF‐1 is the predominant form in vivo . Finally, we analysed mechanisms of neuronal AIF‐1 induction. Following H 2 O 2 challenge, a model of general cell stress, we observed the gradual induction of AIF‐1 and, more interestingly, release to the supernatant of SKNSH neurones. Parallel reverse transcriptase polymerase chain reaction and sequencing was used to confirm AIF‐1 mRNA expression.
Nonlinear Dynamics of a Bose-Einstein Condensate in a Magnetic Waveguide
2003-07-24

We have studied the internal and external dynamics of a Bose-Einstein condensate in an anharmonic magnetic waveguide. An oscillating condensate experiences a strong coupling between the center of mass motion and the internal collective modes. Because of the anharmonicity of the magnetic potential, not only the center of mass motion shows harmonic frequency generation, but also the internal dynamics exhibit nonlinear frequency mixing. Thereby, the condensate shows shape oscillations with an extremely large change in the aspect ratio of up to a factor of 10. We describe the data with a theoretical model to high accuracy. For strong excitations we test the experimental data for indications of a chaotic behavior.
Simulation of Elution Profiles for Two-Dimensional Dynamic Gas Chromatographic Experiments
2003-07-24

The interconversion of E and Z isomers of acetaldoxime 1 and butyraldoxime 2 have been investigated by comprehensive two-dimensional dynamic gas chromatography (DGCxDGC) and computer simulation. Time-resolved cryogenic modulation is capable of revealing the precise isomeric ratio as a fine structure under the dynamic elution profile, which is characterized in one-dimensional experiments by a plateau formation or peak coalescence caused by interconversion of the isomers during the separation process. The chromatographic theoretical plate model has been extended for the computer simulation of comprehensive two-dimensional dynamic chromatographic experiments. A novel program, ChromWin 2D, based on the new algorithm has been developed for computer simulation to evaluate and predict the elution profiles of DGCxDGC experiments. ChromWin 2D allows the determination of rate constants and barriers of isomerization, epimerization, and enantiomerization processes occurring during chromatographic separations. The Eyring activation parameters of the E/Z and Z/E isomerization barriers in the presence of the stationary phase BP21 (poly(ethylene glycol) terephthalate terminated) were determined by temperature-dependent experiments between 80 and 90 degrees C for 1 and 70 and 130 degrees C for 2. The thermodynamic Gibbs free energy of the E/Z equilibrium of the isomers has been determined from the time-resolved chromatograms by cryogenic modulation. The method described here constitutes a new and important tool for the determination of isomerization barriers, which are of great interest, for example, for the quantitative determination of derivatized aldehydes, such as dinitrophenylhydrazine derivatives, in trace analysis.