julilili42/papers huggingface dataset:
Characterization of NovP and NovN: Completion of Novobiocin Biosynthesis by Sequential Tailoring of the Noviosyl Ring
2003-12-17

Two steps forward: The glycosylated aminocoumarin antibiotic novobiocin (1) is produced by Streptomyces spheroides and inhibits the bacterial type II topoisomerase DNA gyrase. The sugar-tailoring enzymes NovP and NovN that catalyze the final two steps in novobiocin biosynthesis were overproduced in Escherichia coli and characterized as a methyltransferase and carbamoyltransferase, respectively.
Establishing valid AIDS monitoring and research in countries with generalized epidemics
2003-12-17

The authors present guidelines for valid HIV/AIDS surveillance and epidemiologic research, and for clarification of uncertainties in transmission dynamics, particularly in countries with generalized epidemics. The consensus assumption that most HIV/AIDS cases in many developing regions, particularly sub-Saharan Africa, are explained by 'heterosexual' transmission (interpreted, by default, to mean penile-vaginal intercourse) has been challenged by recent reviews demonstrating an important contribution from unsafe health care practices. Resolution of existing uncertainties about the proportions of HIV transmission accounted for by specific parenteral exposures and sexual practices (e.g., vaginal and anal intercourse, considered separately) is crucial for the design and implementation of efficacious prevention strategies. Accurate risk-factor information is the best foundation upon which people living in countries with generalized epidemics can learn to protect themselves and their families. Multimethod approaches for developing sound HIV/AIDS research are presented.
Identification of an HLA-A*02 restricted immunogenic peptide derived from the cancer testis antigen HOM-MEL-40/SSX2.
2003-12-17

HOM-MEL-40/SSX2 is a SEREX-defined cancer testis antigen with frequent expression in various human neoplasms. To search for HLA-A*0201 restricted peptides that induce HOM-MEL-40/SSX2-specific CD8+ responses in breast cancer patients, we used the SYFPEITHI algorithm to identify three HOM-MEL-40/SSX2-derived nonamers with high binding affinity for HLA-A*0201, which has a prevalence of 40% in the Caucasian population. Of the three peptides, p41-49 and p103-111 but not p167-175 had been shown to be processed by the proteasome. Only stimulation with p103-111 induced HOM-MEL-40-specific CTLs in 5/7 patients with HOM-MEL-40/SSX2 positive breast cancers and in 6/11 healthy controls. HLA-A*0201 restriction of p103-111 was demonstrated by blocking with specific antibodies. The natural processing and presentation of p103-111 was demonstrated by the recognition of the HOM-MEL-40/SSX2 positive cell line SK-MEL-37 and of COS7/A2 cells transfected with HOM-MEL-40/SSX2 by p103-111 specific CD8+ cells. No correlation was found between CD8+ T-cell responses against p103-111 and anti-HOM-MEL-40/SSX2 antibody titers in the serum of patients, suggesting that CD8+ and B-cell responses against HOM-MEL-40/SSX2 are regulated independently. p103-111 holds promise as a broadly applicable peptide vaccine for patients with HOM-MEL-40/SSX2 positive neoplasms.
Characterization of NovP and NovN: Completion of Novobiocin Biosynthesis by Sequential Tailoring of the Noviosyl Ring
2003-12-17

Zwei Schritte vorwärts: Das glycosylierte Aminocumarin-Antibiotikum Novobiocin (1) wird von Streptomyces spheroides produziert. Es inhibiert die bakterielle Typ-II-Topoisomerase DNA-Gyrase. Die zuckerkonjugierten Enzyme NovP und NovN, die den finalen Schritt in der Novobiocin-Biosynthese katalysieren, wurden in Escherichia coli überexprimiert und als Methyltransferase bzw. Carbamoyltransferase charakterisiert.
The influence of deformation on secondary magnetic inclinations in the Nar/Phu valley (central Nepal).
2003-12-18

Secondary magnetic remanences residing in pyrrhotite and anisotropy of magnetic susceptibility (AMS) were studied in low-grade metamorphic carbonates of the Tethyan Himalaya in Nar/Phu valley (central Nepal) and used for interpretation of tectonic deformations. The characteristic remanence (ChRM) is likely of thermomagnetic origin related to post-peak metamorphic cooling occurring after the Eohimalayan phase (35-32 Ma). The ChRM postdates small-scale folding (main Himalayan folding F1 and F2) as shown by a negative fold test of site mean directions at 99% confidence level, and has been probably acquired between 32 and 25 Ma. Late-orogenic long-wavelength folding associated with the Chako antiform (CA) is recorded by the spatial dispersion of ChRM directions and the distribution of the main axes of the AMS tensor. The mean tilting of the ChRM direction since remanence acquisition (≈20-30°) approximately coincides with the tilting of the CA (31°) at the study area indicating that the pyrrhotite remanence predates the CA (CA formed at <18 Ma according to preliminary U/Pb dating). However, comparison of tilt angles of remanence directions and AMS tensor axes suggests that remanence acquisition was not completed before the onset of the CA formation. This could imply a younger age (Early Miocene or even younger) of the ChRM. Using the distribution of remanence directions along a small-circle as well as the distribution of AMS tensor axes, a clockwise mean rotation of 16° is obtained for a remanence age of ≈30 Ma. An Early Miocene remanence age would not change this result substantially. Compilation of rotations in the Tethyan Himalaya deduced from secondary pyrrhotite remanences reveals an increasing clockwise rotation from the Hidden valley in the W to the Shiar valley in the E (≈150 km distance), incompatible with an oroclinal bending model.
Inter- and Intraobserver Agreement for Gastroesophageal Reflux Detection in Infants Using Multiple Intraluminal Impedance
2003-12-19

The multiple intraluminal impedance (MII) technique is a new method that allows pH-independent gastroesophageal reflux detection via changes in impedance caused by a liquid bolus inside the esophagus. We wanted to know whether this technique yields objective and reproducible results. Twenty 3- to 6-hour recordings of MII from 19 preterm infants (median gestational age at birth 30 weeks, range 24–34 weeks; age at study 26 days, range 13–93 days) were divided into 23-second segments and analyzed for reflux episodes by three investigators; one investigator analyzed the data set twice. Observer agreement was assessed using kappa statistics. Each investigator analyzed 16,627 23-second segments, with a median of 854 (range 486–979) segments per recording. Median kappa values for the 20 recordings were 0.79, 0.83, and 0.83 for the three pairs of investigators and 0.84 for the repeated scoring procedure. MII recordings could be analyzed with a high level of inter- and intraobserver agreement.
Photoemission study of Cu deposition on molecular-beam-epitaxy-grown ZnS(001)
2003-12-19

The formation, the chemical and electronic properties, and the thermal stability of the Cu/ZnS(001) interface were investigated by x-ray photoelectron spectroscopy, x-ray fluorescence spectroscopy, and low energy electron diffraction (LEED). ZnS(001) films with 16 ML thickness (4.3 nm), grown on bulk GaP(001) were used as a substrate for Cu deposition. During the room-temperature deposition of the Cu film, the initial submonolayer Cu atoms react with ZnS and the reaction is confined to the interface. Beyond 1 ML the Cu starts to display a metallic character. The Cu deposition induced a downward band bending of ZnS. In the S L2,3 emission spectrum, the Cu deposition results in a significant suppression of the Zn 3d-related doublet and creates a component at about 3.6 eV binding energy in the upper valence band. After annealing of room-temperature-deposited Cu films at temperatures higher than 220 °C, as well as Cu deposition at 320 °C, the signals of Ga 2p photoelectrons reappear, as a result of Cu atoms diffusing into the substrate and reacting with GaP. From LEED observation and attenuation of Zn 2p3/2 intensity, we may conclude that the Cu film grows in an island mode at room temperature, whereas a partially ordered arrangement is adopted at the ZnS(001) surface following Cu deposition at 320 °C.
Activation of Serratia marcescens Hemolysin through a Conformational Change
2003-12-20

ABSTRACT For Serratia marcescens , secreted hemolysin/cytotoxin is not only secreted but also activated by an outer membrane protein. Excluding posttranslational processing by mass spectrometry, the conformation of active and inactive ShlA derivatives strongly differed in electrophoretic mobilities, gel permeation chromatography, sensitivity to trypsin, circular dichroism, and intrinsic fluorescence. We concluded that ShlB interacts with ShlA during secretion and imposes a conformational change in ShlA to form the active hemolysin.
Immunoglobulin G Isotype Responses to Variant Surface Antigens ofPlasmodium falciparumin Healthy Gabonese Adults and Children during and after Successive Malaria Attacks
2003-12-20

ABSTRACT We assessed immunoglobulin G (IgG) isotype responses with specificity for the variant surface antigens (VSA) of heterologous Plasmodium falciparum isolates by using flow cytometry and plasma from healthy Gabonese adults and from children during and after two consecutive malaria episodes. The individual isolate-specific antibody profiles differed markedly in terms of their isotype content but were similar for healthy adults and healthy uninfected children. In healthy adults, IgG3 and IgG2 responses were the highest, while in healthy children, IgG3 and IgG4 predominated. A transiently elevated IgG1 response was observed during the second of two successive malaria episodes in children, signaling P. falciparum infection-induced cross-reactive anti-VSA responses. Our findings highlight the prominence of IgG3 in the overall profile of these responses but also indicate a marked age-related increase in the prevalence of anti-VSA antibodies of the classically noncytophilic IgG2 isotype, possibly reflecting the high frequency of the histidine-131 variant of FcγRIIA in the Gabonese population.
Histological Findings in Experimental Macular Surgery with Indocyanine Green
2003-12-22

Previously described severe damage to the inner retina of human donor eyes could not be found with even higher doses of ICG in this porcine model. Although differences within the species may contribute to these contradictory results, it is conceivable that the postmortem time and the vitality of the tissue influence the outcome in this ex vivo system.
A comprehensive robotic model for neural & acoustic signal processing in bats
2003-12-22

A scale-accurate robotic model of a bat biosonar head which reproduces all known functional characteristics of its biological paragon is being build in the CIRCE project. The heads of bats are a set of intelligent, adaptively controlled sonar antennae, where signal processing is carried out both in the acoustic and in the neural domain. The primary project goal is to identify hypotheses of high explanatory power for the function of these biological systems. The progress report given here outlines involved engineering challenges and explains design decisions in the areas of ultrasonic transducers, antennae shapes, actuation and neuromimetic signal processing.
Higher order prediction for geometry compression
2003-12-22

A lot of techniques have been developed for the encoding of triangular meshes as this is a widely used representation for the description of surface models. Although methods for the encoding of the neighbor information, the connectivity, are near optimal, there is still room for better en-codings of vertex locations, the geometry. Our geometry encoding strategy follows the predictive coding paradigm, which is based on a region growing encoding order. Only the delta vectors between original and predicted locations are encoded in a local coordinate system, which splits into two tangential and one normal component. In this paper we introduce so-called higher order prediction for an improved encoding of the normal component. We first encode the tangential components with parallelogram prediction. Then we fit a higher order surface to the so far encoded geometry. As we encode the normal component as a bending angle, it is found by intersecting the higher order surface with the circle defined by the tangential components. Experimental results show that our strategy allows saving one bit per vertex for the normal component independent of the tangential prediction rule used.
Instruction set emulation for rapid prototyping of SoCs
2003-12-22

In this paper the application of Instruction Set Emulation (ISE) for rapid prototyping of SoCs is presented. The emulation works in a way that both the software and the hardware behaviour of the emulated processor core is reproduced cycle accurately. This requires the use of hardware and software components. The hardware component consists of a board containing a VLIW processor and FPGAs. The software component is an instruction set simulator of the core running on the VLIW processor. The FPGAs are used for emulating the SoC bus of this processor core. This way the simulation of an instruction set of a processor core has been extended to a real emulation of this core that can be used for rapid prototyping.
Partial loss-of-function alleles reveal a role forGNOMin auxin transport-related, post-embryonic development ofArabidopsis
2003-12-23

The Arabidopsis GNOM gene encodes an ARF GDP/GTP exchange factor involved in embryonic axis formation and polar localisation of the auxin efflux regulator PIN1. To examine whether GNOM also plays a role in post-embryonic development and to clarify its involvement in auxin transport,we have characterised newly isolated weak gnom alleles as well as trans-heterozygotes of complementing strong alleles. These genotypes form a phenotypic series of GNOM activity in post-embryonic development,with auxin-related defects, especially in the maintenance of primary root meristem activity and in the initiation and organisation of lateral root primordia. Our results suggest a model for GNOM action mediating auxin transport in both embryogenesis and post-embryonic organ development.
Effect of Treatment with Dornase Alpha on Airway Inflammation in Patients with Cystic Fibrosis
2003-12-23

Recombinant human deoxyribonuclease (rhDNase) has been shown to improve lung function and reduce the number of pulmonary exacerbations in patients with cystic fibrosis (CF), but its long-term effect on airway inflammation remains unknown. In this study, we used bronchoalveolar lavage (BAL) to investigate the long-term effect of rhDNase on inflammation in patients with CF having mild lung disease. A total of 105 patients with CF (> or =5 years of age) having normal lung function were randomized to receive rhDNase (2.5 mg/day) or no rhDNase. Patients with a normal percentage of neutrophils in BAL fluid at baseline were not randomized and served as the control group. The percentage of neutrophils in the pooled BAL sample was similar in both randomized groups at baseline. A significant increase in neutrophils was observed over the 3-year study period in both untreated patients and control subjects, whereas neutrophils remained unchanged in patients treated with rhDNase. Elastase activities and interleukin-8 concentrations also increased in untreated patients and remained stable in patients on rhDNase. We conclude that in patients with CF, an increase in neutrophilic airway inflammation is found that is positively influenced by rhDNase treatment.
Molecular diversity of arbuscular mycorrhizal fungi in Prunus africana, an endangered medicinal tree species in dry Afromontane forests of Ethiopia
2003-12-23

• The molecular diversity of arbuscular mycorrhizal (AM) fungi colonizing roots of Prunus africana and of AM fungal spores obtained from baiting cultures of indigenous soils from two dry afromontane forests of Ethiopia was investigated. • The internal transcribed spacer (ITS) rDNA region from colonized roots and single spores of three AM fungal spore types was amplified, cloned and sequenced using AM fungal specific primers. • Phylogenetic analysis using the 5.8S rDNA data set revealed that 109 of the sequences obtained belong to members of the Glomeromycota. Subsequent 5.8S/ITS2 rDNA sequence analysis indicated high AM fungal diversity and dominance of Glomus types. Twenty sequence types belonged to the Glomeraceae and one each to the Diversisporaceae and Archaeosporaceae. Two of the three spore types were identified as Glomus etunicatum and Glomus mosseae. • Twenty of the AM fungal types identified are new to Ethiopia and to science. The AM fungal community differed between the two sites studied.
MprF-mediated biosynthesis of lysylphosphatidylglycerol, an important determinant in staphylococcal defensin resistance
2003-12-24

Frequently bacteria are exposed to membrane-damaging cationic antimicrobial molecules (CAMs) produced by the host's immune system (defensins, cathelicidins) or by competing microorganisms (bacteriocins). Staphylococcus aureus achieves CAM resistance by modifying anionic phosphatidylglycerol with positively charged L-lysine, resulting in repulsion of the peptides. Inactivation of the novel S. aureus gene, mprF, which is found in many bacterial pathogens, has resulted in the loss of lysylphosphatidylglycerol (L-PG), increased inactivation by CAM-containing neutrophils, and attenuated virulence. We demonstrate here that expression of mprF is sufficient to confer L-PG production in Escherichia coli, which indicates that MprF represents the L-PG synthase. L-PG biosynthesis was studied in vitro and found to be dependent on phosphatidylglycerol and lysyl-tRNA, two putative substrate molecules. Further addition of cadaverin, a competitive inhibitor of the lysyl-tRNA synthetases, or of RNase A abolished L-PG biosynthesis, thereby confirming the involvement of lysyl-tRNA. This study forms the basis for further detailed analyses of L-PG biosynthesis and its role in bacterial infections.
Larval ontogeny ofMicromelerpeton credneri(Temnospondyli, Dissorophoidea)
2003-12-24

ABSTRACT A growth series of 97 specimens of the dissorophoid temnospondyl Micromelerpeton credneri from the Permo-Carboniferous of Central Europe is taken as a basis for ontogenetic investigations. Whereas the dermal skull roof is already ossified and sutured in the smallest specimen with a skull length of 6 mm, the ossification sequence of the postcranium can be reconstructed. Compared to branchiosaurids and Recent urodeles, the ossification of the postcranial skeleton is delayed. For the first time, external gills are described in Micromelerpeton credneri. Their three pairs of branches shorten proportionally during ontogeny. A Cartesian transformation and biometric analyses show allometric changes in the dermal skull roof. Whereas the preorbital region elongates slightly (due to positive allometric growth of nasal length and negative allometric growth of orbits) and grows in width isometrically, the postorbital skull table shows isometry in length (due to positive allometry of frontal length and negative allometry of parietal length) and distinct negative allometry in width (due to negative allometry of parietal and supratemporal width). The interorbital width relatively decreases. The cheek region shows positive allometry both in length and in width, shifting the jaw articulation posteriorly. In this way proportionally more space and attachment area for the adductor musculature are provided and the gape enlarges proportionally. The positive allometric growth of the diameter of the sclerotic ring indicates increased importance of the optical sense. Transformation into the adult stage took place gradually and in a longer period of time during ontogeny than in extant amphibians.
Bone Marrow Mastocytosis Associated with IgM Kappa Plasma Cell Myeloma
2003-12-30

An association between mastocytosis and monoclonal gammopathy is a relatively rare but well recognized clinical finding. In the majority of cases, however, overt myeloma or lymphoma is not detectable morphologically. Here we describe the case of a 51 year-old male patient first presenting with paresis of the right facial nerve and the serological finding of IgM kappa paraproteinemia. The patient did not have organomegaly, lytic bone lesions, or urticaria pigmentosa-type skin lesions. Histological examination of a trephine biopsy specimen revealed the unusual coexistence of plasma cell myeloma and mastocytosis. Immunohistochemically, plasma cells were found to exhibit a monotypic staining for Ig heavy chain mu and Ig light chain kappa, thus confirming their neoplastic nature. Mast cells showed prominent spindling and formed dense multifocal infiltrates, thus enabling the diagnosis of bone marrow mastocytosis. Immunohistochemically, mast cells expressed tryptase, chymase, and KIT (CD117). In addition, aberrant expression of CD25 on mast cells was detected, confirming the coexistence of a neoplastic mast cell-proliferative disorder. According to the WHO proposal for classification of hematopoietic malignancies, this unique case, showing the association of two very rare haematologic neoplasms, can therefore best be referred to as bone marrow mastocytosis associated with IgM kappa plasma cell myeloma (SM-AHNMD).
Splenic Mastocytosis: Report of Two Cases and Detection of the Transforming SomaticC-KITMutation D816V
2003-12-30

In the vast majority of patients with systemic mastocytosis (SM), the bone marrow is the primary extracutaneous site of disease. In addition to bone marrow involvement, other visceral organs such as the spleen, liver or the gastrointestinal tract, may also be affected. However, isolated involvement of a single extramedullary organ is rarely seen in SM. We report on two patients with SM with splenic involvement, lack of 'diagnostic' mast cell (MC) infiltrates in the bone marrow, and absence of skin lesions. In one patient, a myelodysplastic syndrome was diagnosed prior to the detection of SM. Both patients presented with massive splenomegaly and multifocal MC infiltrates in splenic tissues. These MCs also expressed CD25 as well as the C-KIT mutation D816V. In consecutive examinations, the mutation was also detected in the bone marrow in both patients suggesting diffuse infiltration with neoplastic cells. In summary, our data show that the spleen can be a primary site of disease in rare cases of SM. Mastocytosis should therefore be considered as a (rare) differential diagnosis in patients with splenomegaly of unknown etiology.
Dissociable Cortical Processing of Recognizable and Non-recognizable Biological Movement: Analysing Gamma MEG Activity
2003-12-31

Recognition of biological motion is one of the essential ingredients of human evolutionary survival. When biological motion is revealed solely by a set of light dots on the joints of an invisible human figure, the perceptual system reliably distinguishes it from similar configurations. Here, we assessed the changes in neuromagnetic cortical responses during visual perception of biological motion. Healthy humans saw a randomized set of stimuli consisting of a point-light canonical walker and a scrambled configuration in which the spatial positions of dots were randomly rearranged on the screen. In separate runs, configurations were presented either within an upright or inverted (180 degrees ) orientation in the image plane. Participants performed a one-back repetition task lifting a forefinger in response to the second of two consecutive identical stimuli of each type. Both recognizable upright and non-recognizable inverted walkers evoke enhancements in oscillatory gamma brain activity (25-30 Hz) over the left occipital cortices as early as 100 ms from stimulus onset. Only a recognizable upright walker, however, yields further consecutive peaks over the parietal (130 ms) and right temporal (170 ms) lobes. Scrambled displays do not elicit any increases in the gamma response. The stimulus-specific time course and topographic dynamics of cortical oscillatory activity indicate that the brain rapidly dissociates spatial coherence and meaning revealed through biological movement.