julilili42/papers huggingface dataset:
Self‐reported changes in clinical behaviour by undergraduate dental students after video‐based teaching in paediatric dentistry
2005-06-27

Abstract Four cohorts of undergraduate students ( n = 113) were filmed on video tapes whilst performing paediatric treatments. Selected parts of these tapes were shown the day after. Thus, within one term each student was able to view his performance on a videotape as well as those of fellow students. After completion of the clinical course in paediatric dentistry students were asked by means of a questionnaire about behavioural changes in their clinical work regarding different topics. Considerable changes in behaviour were reported for various topics. Most of the students emphasised the viable role of the video for changing their behaviour. This was especially true for aspects of verbal and non‐verbal communication where mainly female students benefited. Moreover, video was thought to have been useful for improving capacities to deal with patients in fear or pain and for ergonomics. About two‐thirds of the students (64.6%) thought that watching the video had made it easier for them to put theoretical knowledge into action. Video does not seem to play an important role for confirmation and maintenance of behaviour patterns. In conclusion however, it can be stated that video has a high impact on the modification of behaviour patterns of undergraduate students for many aspects of clinical work. The use of video can thus attribute to dental education in an effective way.
High-Affinity Adaptors for Switchable Recognition of Histidine-Tagged Proteins
2005-06-28

We aspired to create chemical recognition units, which bind oligohistidine tags with high affinity and stability, as tools for selectively attaching spectroscopic probes and other functional elements to recombinant proteins. Several supramolecular entities containing 2-4 nitrilotriacetic acid (NTA) moieties were synthesized, which additionally contained an amino group, to which fluorescein was coupled as a sensitive reporter probe. These multivalent chelator heads (MCH) (termed bis-, tris-, and tetrakis-NTA) were characterized with respect to their interaction with hexahistidine (H6)- and decahistidine (H10)-tagged targets. Substantially increased binding stability with increasing number of NTA moieties was observed by analytical size exclusion chromatography. The binding enthalpies as determined by isothermal titration calorimetry increased nearly additively with the number of possible coordinative bonds between chelator heads and tags. Yet, a substantial excess of histidines in the oligohistidine tag was required for obtaining fully additive binding enthalpies. Dissociation kinetics of MCH/oligohistidine complexes measured by fluorescence dequenching showed an increase in stability by 4 orders of magnitude compared to that of mono-NTA, and subnanomolar affinity was reached for tris-NTA. The gain in free energy with increasing multivalency was accompanied by an increasing loss of entropy, which was ascribed to the high flexibility of the binding partners. Numerous applications of these MCHs for noncovalent, high affinity, yet reversible tethering of spectroscopic probes and other functional elements to the recombinant proteins can be envisioned.
Attentional modulation of auditory event-related potentials in a brain-computer interface
2005-06-28

Motivated by the particular problems involved in communicating with "locked-in" paralysed patients, we aim to develop a brain-computer interface that uses auditory stimuli. We describe a paradigm that allows a user to make a binary decision by focusing attention on one of two concurrent auditory stimulus sequences. Using support vector machine classification and recursive channel elimination on the independent components of averaged event-related potentials, we show that an untrained user's EEG data can be classified with an encouragingly high level of accuracy. This suggests that it is possible for users to modulate EEG signals in a single trial by the conscious direction of attention, well enough to be useful in BCI.
An auditory brain-computer communication device
2005-06-28

The thought-translation-device (TTD) is a brain-computer-interface (BCI) that enables completely paralyzed patients to communicate with their brain signals only. Voluntary self-regulation of brain signals (e.g. the slow cortical potentials) is achieved by a feedback training. Visual impairment of these patients requires an auditory feedback mode. The TTD can be entirely operated by listening and voluntary production of specific mental activity. It provides auditory (sonified) feedback of multiple EEG parameters for the training of self-regulation of brain signals which can operate a verbal spelling interface. The properties of the system are reported and the results of experiments with auditory feedback are presented.
Computational Study of Chronoamperometry at Rectangular Microelectrodes
2005-06-28

Abstract Three (space) dimensional diffusion to a rectangular microelectrode of length l and width w , embedded in an infinite coplanar insulator is simulated with boundary conditions for a chronoamperometric experiment. An alternating direction implicit finite difference method (Douglas‐Gunn algorithm) utilizing a problem adapted grid is used to solve the diffusion equation. Current transients are computed for different values of the dimensionless length parameter L = l / w , starting with L =1, i.e., a square electrode. Edge effects at the four sides of the rectangular electrode as well as the vertex effect contribute to the total current. With increasing L the transients approach the behavior of a microband electrode transient, where diffusion is essentially two dimensional. The breakdown of the two dimensional diffusion approach with decreasing values of L is analyzed and quantified. This serves as a guideline for analyzing transients measured with electrodes where the condition l » w is not fulfilled.
Integrated modeling of the major events in the MHC class I antigen processing pathway
2005-06-30

Abstract Rational design of epitope‐driven vaccines is a key goal of immunoinformatics. Typically, candidate selection relies on the prediction of MHC–peptide binding only, as this is known to be the most selective step in the MHC class I antigen processing pathway. However, proteasomal cleavage and transport by the transporter associated with antigen processing (TAP) are essential steps in antigen processing as well. While prediction methods exist for the individual steps, no method has yet offered an integrated prediction of all three major processing events. Here we present WAPP, a method combining prediction of proteasomal cleavage, TAP transport, and MHC binding into a single prediction system. The proteasomal cleavage site prediction employs a new matrix‐based method that is based on experimentally verified proteasomal cleavage sites. Support vector regression is used for predicting peptides transported by TAP. MHC binding is the last step in the antigen processing pathway and was predicted using a support vector machine method, SVMHC. The individual methods are combined in a filtering approach mimicking the natural processing pathway. WAPP thus predicts peptides that are cleaved by the proteasome at the C terminus, transported by TAP, and show significant affinity to MHC class I molecules. This results in a decrease in false positive rates compared to MHC binding prediction alone. Compared to prediction of MHC binding only, we report an increased overall accuracy and a lower rate of false positive predictions for the HLA‐A*0201, HLA‐B*2705, HLA‐A*01, and HLA‐A*03 alleles using WAPP. The method is available online through our prediction server at http://www‐bs.informatik.uni‐tuebingen.de/WAPP .
Combined chips for atom optics
2005-06-30

We present experiments with Bose-Einstein condensates on a combined atom chip. The combined structure consists of a large-scale 'carrier chip' and smaller 'atom-optics chips,' containing micron-sized elements. This allows us to work with condensates very close to chip surfaces without suffering from fragmentation or losses due to thermally driven spin flips. Precise three-dimensional positioning and transport with constant trap frequencies are described. Bose-Einstein condensates were manipulated with submicron accuracy above atom-optics chips. As an application of atom chips, a direction sensitive magnetic-field microscope is demonstrated.
Interaction of Rv1625c, a mycobacterial class IIIa adenylyl cyclase, with a mammalian congener
2005-06-30

Summary The adenylyl cyclase Rv1625c from Mycobacterium tuberculosis codes for a protein with six transmembrane spans and a catalytic domain, i.e. it corresponds to one half of the pseudoheterodimeric mammalian adenylyl cyclases (ACs). Rv1625c is active as a homodimer. We investigated the role of the Rv1625c membrane domain and demonstrate that it efficiently dimerizes the protein resulting in a 7.5‐fold drop in K m for ATP. Next, we generated a duplicated Rv1625c AC dimer by a head‐to‐tail concatenation. This produced an AC with a domain order exactly as the mammalian pseudoheterodimers. It displayed positive cooperativity and a 60% increase of v max compared with the Rv1625c monomer. Further, we probed the compatibility of mycobacterial and mammalian membrane domains. The second membrane anchor in the Rv1625c concatamer was replaced with membrane domain I or II of rabbit type V AC. The mycobacterial and either mammalian membrane domains are compatible with each other and both recombinant proteins are active. A M. tuberculosis Rv1625c knockout strain was assayed in a mouse infection model. In vitro growth characteristics and in vivo organ infection and mortality were unaltered in the knockout strain indicating that AC Rv1625c alone is not a virulence factor.
Bap-dependent biofilm formation by pathogenic species of Staphylococcus: evidence of horizontal gene transfer?
2005-07-01

The biofilm-associated protein (Bap) is a surface protein implicated in biofilm formation by Staphylococcus aureus isolated from chronic mastitis infections. The bap gene is carried in a putative composite transposon inserted in SaPIbov2, a mobile staphylococcal pathogenicity island. In this study, bap orthologue genes from several staphylococcal species, including Staphylococcus epidermidis , Staphylococcus chromogenes , Staphylococcus xylosus , Staphylococcus simulans and Staphylococcus hyicus , were identified, cloned and sequenced. Sequence analysis comparison of the bap gene from these species revealed a very high sequence similarity, suggesting the horizontal gene transfer of SaPIbov2 amongst them. However, sequence analyses of the flanking region revealed that the bap gene of these species was not contained in the SaPIbov2 pathogenicity island. Although they did not contain the icaADBC operon, all the coagulase-negative staphylococcal isolates harbouring bap were strong biofilm producers. Disruption of the bap gene in S. epidermidis abolished its capacity to form a biofilm, whereas heterologous complementation of a biofilm-negative strain of S. aureus with the Bap protein from S. epidermidis bestowed the capacity to form a biofilm on a polystyrene surface. Altogether, these results demonstrate that Bap orthologues from coagulase-negative staphylococci induce an alternative mechanism of biofilm formation that is independent of the PIA/PNAG exopolysaccharide.
The potential significance of microbial Fe(III) reduction during deposition of Precambrian banded iron formations
2005-07-01

ABSTRACT During deposition of late Archean–early Palaeoproterozoic Precambrian banded iron formations (BIFs) the downward flux of ferric hydroxide (Fe(OH) 3 ) and phytoplankton biomass should have facilitated microbial Fe(III) reduction. However, quantifying the significance of such a metabolic pathway in the Precambrian is extremely difficult, considering the post‐depositional alteration of the rocks and the lack of ideal modern analogues. Consequently, we have very few constraints on the Fe cycle at that time, namely (i) the concentration of dissolved Fe(II) in the ocean waters; (ii) by what mechanisms Fe(II) was oxidized (chemical, photochemical or biological, the latter using either O 2 or light); (iii) where the ferric hydroxide was precipitated (over the shelf vs. open ocean); (iv) the amount of phytoplankton biomass, which relates to the nutrient status of the surface waters; (v) the relative importance of Fe(III) reduction vs. the other types of metabolic pathways utilized by sea floor microbial communities; and (vi) the proportion of primary vs. diagenetic Fe(II) in BIF. Furthermore, although estimates can be made regarding the quantity of reducing equivalents necessary to account for the diagenetic Fe(II) component in Fe‐rich BIF layers, those same estimates do not offer any insights into the magnitude of Fe(III) actually generated within the water column, and hence, the efficiency of Fe and C recycling prior to burial. Accordingly, in this study, we have attempted to model the ancient Fe cycle, based simply on conservative experimental rates of photosynthetic Fe(II) oxidation in the euphotic zone. We estimate here that under ideal growth conditions, as much as 70% of the biologically formed Fe(III) could have been recycled back into the water column via fermentation and organic carbon oxidation coupled to microbial Fe(III) reduction. By comparing the potential amount of biomass generated phototrophically with the reducing equivalents required for Fe(III) reduction and magnetite formation, we also hypothesize that another anaerobic metabolic pathway might have been utilized in the surface sediment to oxidize the fermentation by‐products. Based on the premise that the deep ocean waters were anoxic, this role could have been fulfilled by methanogens, and maybe even methanotrophs that employed Fe(III) reduction.
Refining the Rules of Gliadin T Cell Epitope Binding to the Disease-Associated DQ2 Molecule in Celiac Disease: Importance of Proline Spacing and Glutamine Deamidation
2005-07-01

Abstract Celiac disease is driven by intestinal T cells responsive to proline-rich gluten peptides that often harbor glutamate residues formed by tissue transglutaminase-mediated glutamine conversion. The disease is strongly associated with the HLA variant DQ2.5 (DQA1*05, DQB1*02), and intestinal gluten-reactive T cells from DQ2.5-positive patients are uniquely restricted by this HLA molecule. In this study, we describe the mapping of two novel T cell epitopes of γ-gliadin and the experimental identification of the DQ2.5 binding register of these and three other γ-gliadin epitopes. The new data extend the knowledge base for understanding the binding of gluten peptides to DQ2.5. The alignment of the experimentally determined binding registers of nine gluten epitopes reveal positioning of proline residues in positions P1, P3, P6, and P8 but never in positions P2, P4, P7, and P9. Glutamate residues formed by tissue transglutaminase-mediated deamidation are found in position P1, P4, P6, P7, or P9, but only deamidations in positions P4 and P6, and rarely in P7, seem to be crucial for T cell recognition. The majority of these nine epitopes are recognized by celiac lesion T cells when presented by the related but nonassociated DQ2.2 (DQA1*0201, DQB1*02) molecule. Interestingly, the DQ2.2 presentation for most epitopes is less efficient than presentation by the DQ2.5 molecule, and this is particularly prominent for the α-gliadin epitopes. Contrary to previous findings, our data do not show selective presentation of DQ2.5 over DQ2.2 for gluten epitopes that carry proline residues at the P3 position.
Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus
2005-07-01

A putative prenyltransferase gene, ftmPT1 , was identified in the genome sequence of Aspergillus fumigatus . ftmPT1 was cloned and expressed in Escherichia coli , and the protein FtmPT1 was purified to near homogeneity and characterized biochemically. This enzyme was found to catalyse the prenylation of cyclo - l -trp- l -Pro (brevianamide F) at the C-2 position of the indole nucleus. FtmPT1 is a soluble monomeric protein, which does not contain the usual prenyl diphosphate binding site (N/D)DXXD found in most prenyltransferases, and which does not require divalent metal ions for its enzymic activity. K m values for brevianamide F and dimethylallyl diphosphate were determined as 55 and 74 μM, respectively. The turnover number was 5·57 s −1 . FtmPT1 showed a high substrate specificity towards dimethylallyl diphosphate, but accepted different tryptophan-containing cyclic dipeptides. Together with dimethylallyltryptophan synthase of ergot alkaloid biosynthesis, FtmPT1 belongs to a new group of prenyltransferases with aromatic substrates.
Pressure and temperature-dependence of water solubility in Fe-free wadsleyite
2005-07-01

The effects of temperature and pressure on water solubility in wadsleyite in the system MgO-SiO2- H2O were investigated. Experiments were carried out using a 1000 ton multi-anvil press. One series of experiments was performed at a fixed pressure of 15 GPa and at various temperatures and in a second series the temperature was fixed at 1200 °C and pressure was varied from 13 to 18 GPa. The starting material was a mixture of oxides and hydroxides equivalent to the composition Mg2SiO4 + 5 wt% H2O. Run products consisted of wadsleyite, quenched hydrous melt, and minor amounts of clinoenstatite. The water content of wadsleyite was quantified by ion probe. Results show that at 15 GPa, the water solubility in wadsleyite decreases significantly with increasing temperature from ~2.2 wt% H2O at 900 °C down to ~0.9 wt% H2O at 1400 °C; the corresponding Mg/Si ratios increase from 1.80 to 1.91 over this temperature range. This effect appears to be largely due to changes in the water activity in the coexisting melt. The partition coefficient of water between wadsleyite and coexisting melt is nearly independent of temperature with Dwaterwadsleyite/melt ≈ 0.08. No significant effect of pressure on water solubility was observed at 1200 °C. Our data suggest that the water storage capacity of wadsleyite in the transition zone is much lower than previously suggested. Together with previous results on ringwoodite, our data imply a strong decrease of the water partition coefficient between wadsleyite and ringwoodite with temperature. This decrease could have two important consequences: (1) The width of the 520 km discontinuity may vary strongly as a function of temperature. (2) During cooling of the Earth's mantle since the Hadean, water may have increasingly partitioned from the lower into the upper part of the transition zone.
Induction of a chemoattractive proinflammatory cytokine response after stimulation of keratinocytes with Propionibacterium acnes and coproporphyrin III
2005-07-01

This cytokine pattern may favour a chemotactic response and implicates P. acnes and coproporphyrin III in the recruitment of inflammatory cells to the site of infection and in the development of acne lesions.
Functions of the siderophore esterases IroD and IroE in iron-salmochelin utilization
2005-07-01

The siderophore salmochelin is produced under iron-poor conditions by Salmonella and many uropathogenic Escherichia coli strains. The production of salmochelin, a C-glucosylated enterobactin, is dependent on the synthesis of enterobactin and the iroBCDEN gene cluster. An E. coli IroD protein with an N-terminal His-tag cleaved cyclic salmochelin S4 to the linear trimer salmochelin S2, the dimer salmochelin S1, and the monomers dihydroxybenzoylserine and C-glucosylated dihydroxybenzoylserine (salmochelin SX, pacifarinic acid). The periplasmic IroE protein was purified as a MalE–IroE fusion protein. This enzyme degraded salmochelin S4 and ferric-salmochelin S4 to salmochelin S2 and ferric-salmochelin S2, respectively. In E. coli , uptake of ferric-salmochelin S4 was dependent on the cleavage by IroE, and independent of the FepBDGC ABC transporter in the cytoplasmic membrane. IroC, which has similarities to ABC-multidrug-resistance proteins, was necessary for the uptake of salmochelin S2 from the periplasm into the cytoplasm. IroE did not function as a classical binding protein since salmochelin S2 was taken up in the absence of a functional IroE protein. IroC mediated the uptake of iron via enterobactin in a fepB mutant. IroE was also necessary in this case for the uptake of ferric-enterobactin, which indicated that only the linear degradation products of enterobactin were taken up via IroC. PfeE, the Pseudomonas aeruginosa IroE homologue, was cloned, and its enzymic activity was shown to be very similar to that of IroE. It is suggested that homologues in other bacteria are also periplasmic IroE-type esterases of siderophores.
Aptamer-based capture molecules as a novel coating strategy to promote cell adhesion
2005-07-01

The improvement of the cytocompatibility of medical implants is a major goal in biomaterials research. During the last years many researchers worked on the fascinating approach to seed the respective cell types on various artificial substrates before implantation. For instance, cell-seeded implants are supposed to be better candidates for transplantable bone substitutes than conventional artificial bone grafts. To improve cell seeding efficiency and cytocompatibility, we designed a new coating material for medical implants. We used aptamers, highly specific cell binding nucleic acids generated by combinatorial chemistry with an in vitro selection called systematic evolution of exponential enrichment (SELEX). Aptamers do have high binding affinity and selectivity to their target. In our study, human osteoblasts from osteosarcoma tissue were used as a target to create the aptamer. Single aptamer mediated cell sorting assays showed the binding affinity with osteoblasts. Additionally, the aptamers immobilized on tissue culture plates could capture osteoblasts directly and rapidly from the cell solution. This model proves that aptamer coated artificial surfaces can greatly enhance cell adhesion. We assume that this strategy is capable to improve the clinical application of tissue engineered implants.
A 20‐ka climate record from Central Himalayan loess deposits
2005-07-01

Abstract The southwest monsoon that dominated Central Himalaya has preserved loessic silt deposits preserved in patches that are proximal to periglacial areas. The occurrence of such silts suggests contemporary prevalence of cold and dry northwesterly winds. Field stratigraphy, geochemistry, mineral magnetism, infrared stimulated luminescence (IRSL) and radiocarbon dating has enabled reconstruction of an event chronology during the past 20 ka. Three events of loess accretion could be identified. The first two events of loess deposition occurred betweem 20 and 9 ka and were separated by a phase of moderate weathering. Pedogenesis at the end of this event gave rise to a well‐developed soil that was bracketed around 9 to &gt; 4 ka. This was followed by the third phase of loess accretion that occurred around 4 to &gt; 1 ka. Episodes of loess deposition and soil formation are interpreted in terms of changes in the strength of the Indian southwest monsoon. Copyright © 2005 John Wiley &amp; Sons, Ltd.