bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploiting the Substrate Tolerance of Farnesyltransferase for Site‐Selective Protein Derivatization
Authors: Nguyen Uyen T. T. , Cramer Janina , Gomis Joaquin , Reents Reinhard , Gutierrez‐Rodriguez Marta , Goody Roger S. , Alexandrov Kirill , Waldmann Herbert 
Published: February 2007

AbstractThe site‐selective modification of proteins with a functional group is an important biochemical technique, but covalent attachment of a desired group to a chosen site is complicated by the reactivity of other amino acid side chains, often resulting in undesired side reactions. One potential solution to this problem involves exploiting the activity of protein‐modifying enzymes that recognize a defined protein sequence. Protein farnesyltransferase (FTase) covalently attaches an isoprenoid moiety to a cysteine unit in the context of a short C‐terminal sequence that can be easily grafted onto recombinant proteins. Here we describe the synthesis of four phosphoisoprenoids functionalized with biotin, azide, or diene groups. These phosphoisoprenoids bound to FTase with affinities comparable to that of the native substrate. With the exception of the biotin‐functionalized analogue, all the phosphoisoprenoids generated could be transferred to peptide and protein substrates by FTase. Unlike proteins modified with farnesyl moieties, Ypt7 prenylated with (2E,6E)‐8‐(azidoacetamido)‐3,7‐dimethylocta‐2,6‐dienyl groups did not oligomerize and showed no detectable increase in hydrophobicity. To assess the suitability of the functionalized isoprenoids for protein modifications they were further derivatized, both by Diels–Alder cycloaddition with 6‐maleimidohexanoic acid and by Staudinger ligation with a phosphine. We demonstrate that the Staudinger ligation proceeds more rapidly and is more efficient than the Diels–Alder cycloaddition. Our data validate the use of FTase as a protein‐modification tool for biochemical and biotechnological applications.
Sicherer Umgang mit gefährlichen Stoffen
Authors: Brock Thomas H. , Timm Kurt , Lewin‐Kretzschmar Uta 
Published: February 2007

AbstractBei Tätigkeiten mit Gefahrstoffen müssen die möglichen Gefährdungen sorgsam beurteilt werden. Dabei ist nicht nur die eher im Bewusstsein befindliche Brennbarkeit oder Toxizität von Stoffen relevant, sondern auch Gefahren, die von einer Anzahl weiterer Effekte, wie die Verwechslung von Stoffen oder Alterungsprozessen von Chemikalien, ausgehen können. Eine Reihe von Experimenten zeigt modellhaft solche Effekte. Mit Gefahrstoffen kann man sicher umgehen, jedoch muss man wissen, was man tut und die richtigen Maßnahmen konsequent ergreifen.
Opale: Photonische Kristalle
Authors: Fleischhaker Friederike , Zentel Rudolf 
Published: February 2007

AbstractOpale sind selbstorganisierte, kubisch dichtest gepackte Kolloidkristalle mit Kolloid‐Durchmessern im Nanometer‐ und Submikrometerbereich. Aufgrund der periodisch modulierten Dielektrizitätskonstante bilden sich photonische Bandlücken aus, so dass die Ausbreitung von Licht mit Wellenlängen in der Größenordnung der Gitterkonstanten unterdrückt wird. Dies erklärt u.a. den brillianten Farbeindruck. Opale können synthetisch aus Polymer‐ oder Metalloxidkolloiden in einem Bottom‐up‐Prozess hergestellt und auf vielfältige Weise chemisch funktionalisiert, strukturiert oder als Template für ihre invertierten Strukturen verwendet werden. Anwendungsgebiete reichen von optischen Chips, Farbdisplays und Effektpigmenten bis hin zu Biosensoren.
Ductular reaction is helpful in defining early stromal invasion, small hepatocellular carcinomas, and dysplastic nodules
Authors: Park Young Nyun , Kojiro Masamichi , Di Tommaso Luca , Dhillon Amar P. , Kondo Fukuo , Nakano Masayuki , Sakamoto Michiie , Theise Neil D. , Roncalli Massimo 
Published: February 2007

AbstractBACKGROUND.Stromal invasion is 1 of the main features used to distinguish high‐grade dysplastic nodules (DNs) from well‐differentiated hepatocellular carcinomas (HCCs). The authors hypothesized that ductular reaction (DR) takes place around noninvasive hepatocellular nodules but not within the stroma contiguous to invasive HCC.METHODS.DR/cytokeratin 7 (CK7)‐positive patterns were evaluated in 105 resected small hepatic nodules according to the level of invasion. The nodules were classified histologically prior to immunostaining as noninvasive (large regenerative nodules, low‐grade DNs, and high‐grade DNs), minimally invasive (early HCCs with a vaguely nodular type), and overtly invasive (typical HCCs with a distinctly nodular type) in a review by expert pathologists, the current gold standard. Intranodular DR (inner DR) and DR around the nodule periphery (outer DR) were assessed separately on a semiquantitative scale from 0 to 4+.RESULTS.DR was 3 or 4+ in the majority of noninvasive nodules (inner DR, 81%; outer DR, 91%), whereas DR was 0 or 1+ in overtly invasive HCCs (inner DR, 96%; outer DR, 81%). Minimally invasive HCCs showed an intermediate DR pattern (2 or 3+ inner DR, 75%; 2+ outer DR, 67%). DR characteristically was absent at the stromal‐invasive, leading edge of tumor cells in both minimally invasive HCCs (focal loss of DR/CK7) and overtly invasive HCCs (diffuse loss of DR/CK7). The DR patterns in 41 needle‐biopsy samples were similar to the patterns observed in resected nodules.CONCLUSIONS.DR/CK7 immunostaining may help to identify small foci of invasion and to distinguish noninvasive, high‐grade DNs from both minimally invasive and overtly invasive HCCs. Cancer 2007 © 2007 American Cancer Society.
Recent improvement in the survival of patients with advanced nonsmall cell lung cancer enrolled in phase III trials of first‐line, systemic chemotherapy
Authors: Hotta Katsuyuki , Fujiwara Yoshiro , Matsuo Keitaro , Suzuki Takeshi , Kiura Katsuyuki , Tabata Masahiro , Takigawa Nagio , Ueoka Hiroshi , Tanimoto Mitsune 
Published: February 2007

AbstractBACKGROUND.Few studies have assessed formally whether treatment outcomes have improved substantially over the years for patients with advanced nonsmall cell lung cancer (NSCLC) enrolled in Phase III trials. The objective of the current investigation was to determine the time trends in outcomes for the patients in those trials.METHODS.The literature was searched to identify trials that addressed the role of chemotherapy regimens in the first‐line setting for the treatment of advanced NSCLC. Trends were tested by using multiple regression analysis.RESULTS.In total, 121 Phase III trials were identified that involved 42,768 patients with 263 chemotherapy arms and 11 best supportive care (BSC) arms, all of which were initiated between 1982 and 2002. Although the number of randomized patients and the proportion of patients with metastatic disease had increased over the years, the number of patients with a poor performance status who were accrued into the trials had decreased. Cisplatin‐based chemotherapy was been investigated most frequently during the period. The multiple regression analysis revealed a significant improvement in median survival and in the median time to disease progression over the years, with annual prolongations of 0.1203 months (3.609 days) and 0.0617 months (1.851 days), respectively (P< .0001 and P < .0130, respectively). In addition, the use of cisplatin and carboplatin was associated significantly with survival prolongation. The median survival for patients who received BSC also increased progressively over the years (P = .0487).CONCLUSIONS.The survival of patients with NSCLC in Phase III trials improved slowly but steadily over time, although the main factors responsible for this improvement remain unknown. Nonetheless, the current results also suggested that novel targets and new agents will be required in the future fight against advanced NSCLC. Cancer 2007 © 2007 American Cancer Society.
Expression levels and activation of a PXR variant are directly related to drug resistance in osteosarcoma cell lines
Authors: Mensah‐Osman Edith J. , Thomas Dafydd G. , Tabb Michelle M. , Larios Jose M. , Hughes Dennis P. , Giordano Thomas J. , Lizyness Michelle L. , Rae James M. , Blumberg Bruce , Hollenberg Paul F. , Baker Laurence H. 
Published: February 2007

AbstractBACKGROUND.Approximately 30% to 40% of all patients with osteosarcomas ultimately experience recurrence. The study investigated the hypothesis that the resistance of osteosarcoma to chemotherapy may be related to the expression of a pregnane xenobiotic receptor (PXR) variant protein and its role as the major inducer of P450 3A4 in these tumors.METHODS.Polymerase chain reaction (PCR) and Western blot analysis were used to determine PXR mRNA and protein expression, respectively. Real‐time PCR and CYP3A catalytic activity using 7‐benzyl‐trifluoromethyl coumarin (BFC) as the probe substrate were used to measure the induction of P450 3A4 or MDR1. siRNA transfections were performed for PXR and cytotoxicity determined by a colorimetric based assay or Annexin v‐Fitc staining.RESULTS.Differences were observed in the molecular size of the PXR protein expressed in sarcoma cell lines when compared with the wildtype PXR expressed in normal liver, kidney, or small intestine. A polyclonal PXR antibody raised against the N‐terminus of the wildtype PXR did not detect PXR expressed in these sarcoma cell lines. In the osteosarcoma cell lines, etoposide and doxorubicin were better inducers of P450 3A4 and MDR1 than rifampin. siRNA against PXR down‐regulated P450 3A4 expression only in the osteosarcoma cell line. Cytotoxicity assays showed that the resistance of the osteosarcoma cell lines to etoposide correlated with PXR protein expression levels and activation of P450 3A4 and could be prevented by ketoconazole.CONCLUSION.The results suggest that PXR plays a critical role in the regulation of P450 3A4 expression in osteosarcoma and that its expression and activation in these tumors may influence the effect of chemotherapeutic agents on the induction of target genes implicated in drug resistance. Cancer 2007. © 2007 American Cancer Society.
Hydrograph peakedness and basin area
Authors: Klein Micha 
Published: February 2007

AbstractThe peakedness of a basin and its variation with drainage area were analyzed for three areas. Peakedness of a basin is calculated as mean flow as a percentage of highest flow. A fitted power curve relating ‘Peakedness index’ (PI) to drainage area for each of the three areas indicates a break point in a basin of about 300 km2. This break point divides the basins into small basins which are more peaky and large basins which are less peaky. The break point is an outcome of a difference in order of magnitude between channel flow velocity from the headwater sources and hillside flow velocity. When the basin responds to hillslope flow the runoff from the head water sources has already flown about 30 km downstream.
The erosion of limestones under soil and the long term stability of soil vegetation systems on limestone
Authors: Trudgill Stephen T. 
Published: February 2007

AbstractData are presented on daily fluctuations of soil pH in organic soils overlying Carboniferous Limestone in Co. Clare, Eire. High rainfall leads to a drop in pH, as acid waters percolate through the soil, but after rainfall the solution of carbonates in the soil or the solution of the bedrock leads to a return of soil pH to alkalinity. Carbonates tend to remain in the soil on poorly drained sites but solutional removal of calcium occurs on freely drained sites and in the latter case the return to alkalinity is not so rapid. The presence of Calluna vulgaris is thought to be important as it appears to increase the acidity of percolating soil waters. On freely draining sites bedrock erosion may progress to such an extent that deep runnels form, down which soil may be lost.
A scree slope rockfall model
Authors: Statham Ian 
Published: February 2007

AbstractCertain observed characteristics of scree slopes; namely concavity of profile, straight slope angle less than the angle of repose, and good size sorting of particles, are not consistent with an angle of repose model for accumulation. An alternative model is proposed based upon rockfall and surface stone movement and is tested against experimental data of particle movement in the field. It is found that the mechanical model of stone movement generated adequately explains the motion of particles on scree slopes and that it is in keeping with the characteristics of many screes. The static features of some Isle of Skye screes were also measured and the straight‐concave slope form with good downslope sorting of material, characteristic of the rockfall process, was found to be present.
The morphology of riffle‐pool sequences
Authors: Richards K. S. 
Published: February 2007

AbstractThe riffle‐pool sequence has not been subjected to the same level of intensive research as the meandering planform, although riffles and pools may be a fundamental prerequisite for meandering. The pseudo‐cyclic oscillation of the bed in a riffle‐pool stream suggests the application of a variety of techniques of spatial series analysis, which provide objective measures of riffle wavelength, and suggest processes capable of explaining riffles and pools and their relationship with meanders.The second‐order autoregressive process is suggested as a stochastic process which models the bed‐profile oscillation. Velocity pulsations associated with large scale turbulent eddies are probably responsible for accretions and erosions which interact with the flow to maintain these perturbations, so that sections lagged by distances of 2πw are positively correlated.The effect of the riffle‐pool sequence on flow geometry is far more significant than the effects of plan geometry or of downstream variations, which supports the view that this feature is a fundamental aspect of channel morphometry. There is a tendency, however, for curved reaches to exhibit reduced variance of roughness, velocity, and water surface slope, which reinforces the minimization hypothesis. The extreme temporal variation between riffle and pool flow characteristics demands that any classificatory scheme uses scale‐free and stable measures, and a discriminant analysis using hydraulic exponents represents a convenient summary of the field data.
Lateral translocation of soil plasma through a small valley basin in the Northaw Great Wood, Hertfordshire
Authors: Huggett R. J. 
Published: February 2007

AbstractThe paper looks at the process of lateral translocation in a small valley basin from the Northaw Great Wood, Hertfordshire. The valley basin comprises four lithostratigraphic units (London Clay and Pebble Gravel, and the others a mixture of these two), which were initially established in the field by a rough assessment of texture. Particle size analysis validated the lithostratigraphic units as delineated in the field; it was found unnecessary to alter the boundaries of the units. Patterns of lateral translocation of silt and clay (measured by the hydrometer method) and the amorphous colloidal hydrous oxides and hydroxides of Al, Fe, Mn and Si (measured in oxalate solution by atomic absorption spectrophotometry) are inferred from balance sheets of the relative gains and losses of the materials. Materials from horizons formed in lithostratigraphic units derived from London Clay are balanced against a clay dilution factor; those from the lithostratigraphic unit of Pebble Gravel against the dilution of sand on a clay‐free basis. The results lead to the following conclusions about the process of lateral translocation: it has been a significant contributor to soil development; larger amounts of material have moved down‐slope towards the hollow than over the nose because there has, theoretically, been more throughflow in the hollow; for some materials there has been less down‐slope transport in lower horizons owing to less throughflow in them.
Adaptive adjustment of channel geometry
Authors: Bennett R. J. 
Published: February 2007

AbstractThis paper constructs a model of channel geometry composed of three subsections: a steady‐state submodel, a gradedstate submodel, and a stochastic error submodel. With the aid of this representation of the morphology of channels, the at‐a‐point changes in geometry can be reproduced by a simple recursive equation of autoregressive, moving‐average form which is derived from methods used in the statistical analysis of time series. A set of height loss data for three Japanese rivers derived from Yatsu's (1955) paper is used to determine the effect of bed material changes on adaptations within the graded‐state submodel of the channel. The results of analyzing the autocorrelation function, spectrum, and adaptive parameter shifts within this model can be used to infer that significant changes in the amplitude of height change variation, and a shift to higher frequency oscillations of bed forms are associated with the shift in bed material conditions.
The differential impact of some soil loss factors on flow, runoff creep and rainwash
Authors: de Ploey J. , Savat J. , Moeyersons J. 
Published: February 2007

AbstractThe Hortonian model of runoff flow which had been thought to be applicable in arid areas has previously been shown not to be valid, notably in Israel, where inverse relations have been observed between slope angle, and runoff discharge and slope erosion. The paper discusses laboratory experiments on simulated slope conditions in a rather arid environment. It is shown by rain simulation on granite grus that infiltration capacity is a function of rainfall intensity, slope angle and runoff discharge. The infiltration capacity f can equal the rainfall intensity beyond a critical distance x(m) so that discharge becomes constant. Debris covers affect runoff hydraulics, especially on poorly cohesive soils, and both slow downslope and upslope movements which correspond to the process of so‐called runoff creep can occur. Coarse debris and grass covers, as roughness factors, induce hydraulic discontinuities and activate local turbulent flow and slope erosion. Instead of being merely protective elements these factors tend to catalyze the slope wash, in comparison with naked surfaces, if the Reynolds number of the flow exceeds a certain critical value.
Debris flows on vegetated screes in the black mountain, Carmarthenshire
Authors: Statham Ian 
Published: February 2007

AbstractThe Black Mountain Scarp in Carmarthenshire is currently being modified by debris‐flow activity along gullies cut into the vegetated scree, which is a persistent feature of the scarp‐front. Low angled, concave debris flow cones are accumulating at the mouths of the gullies.Mean rate of sediment yield from the sides of one gully was estimated to be 8·4 m3 in one year, and 9·8 m3 was shifted out of the gully by a single debris‐flow in the same year. Movement by other transport processes, such as streamflow, was negligible in the gullies. No new gullies are being initiated at the present and all of them appear to be in a similar state of development. Consequently, it appears that some marked environmental change was responsible for initiating gully erosion. If present rates of gully‐erosion are representative of the past, the gullies are only about 540–700 years old and may possibly have been initiated by sheep‐grazing in the area.
An inexpensive circuit design for the acoustic detection of oscillations in bedload transport in natural streams
Authors: Anderson M. G. 
Published: February 2007

AbstractA circuit design is reported which is demonstrated to be capable of receiving and recording the underwater sound of inter‐particle collisions on natural stream beds during the process of bedload transport. Field trials were undertaken in a natural stream with sand‐sized bedload particles. The results obtained, for a constant stream stage, give support to the idea of the occurrence of short period oscillations in the rate of bedload transport.
Flow and sedimentary processes in the meandering river South Esk, Glen Clova, Scotland
Authors: Bridge John S. , Jarvis Jack 
Published: February 2007

AbstractChannel geometry, flow and sedimentation in a meander bend of the River South Esk were studied from bankfull stages (January–February) to low water stages (May) in 1974. Bed topography varied little over the study period, showing a typical pool and ripple geometry. Variation of mean depth and velocity with discharge differed from section to section around the bend, due primarily to locally varying flow resistance with stage.The flow pattern for all stages was dominated by a single spiral over the point bar, with a development zone at the bend entrance. Deviation of bed shear stress from the mean flow direction was in general accord with theory, especially for high stages. The use of a uniform longitudinal water surface slope in the calculation of bed shear stress is not justified because of a complicated water surface topography, also such calculated shear may not represent effective bed shear on grains, as it accounts also for energy losses associated with secondary flows.Dunes covered much of the bar at high stages, with increasing proportions of ripples, sand ribbons and lower phase plane beds at low stages. Local flow resistance generally decreases from dunes, diminished and ripple‐backed dunes, ripples, sand ribbons to plane beds, and bed forms are predicted quite well by the stream power‐grain size scheme.Mean size, sorting and skewness of sediment over the bed changes little with stage. In general, size decreases, sorting improves and skewness changes from positive to negative from the talweg to the inner bank, and in the downstream direction. Allen's (1970a, b) force balance equation for moving bed load particles is supported for bankfull stage, with some reservations, and textural characteristics are explained by progressive sorting in the direction of sediment transport.Large‐scale trough cross stratification (with some flat bedding) formed at high stage by dunes (and lower phase plane beds) dominates the point bar sediments. Alternations of fine‐medium sand (often cross‐laminated) and vegetation‐rich layers result from periodic deposition on the grassed upper bar surface.Fining upwards sequences produced by lateral channel migration are modified by a coarsening upward subsequence in the upstream bar region where spiral flow is developing from the bend upstream.
Disturbed periodic model for river meanders
Authors: Ferguson R. I. 
Published: February 2007

AbstractAlthough river meanders are not perfectly regular their serial statistics show periodic tendencies which cannot be explained by previous stochastic models. The regular and random approaches to meander geometry can be reconciled in a disturbed periodic model with separate scale, sinuosity, and irregularity parameters. Meandering is viewed as a deterministic oscillation but irregularity is introduced by quasi‐random variability in valley‐floor topography and materials. For stability such a model needs either a Bagnold type limit on bend curvature or frictional damping of the oscillatory response to individual disturbances. Realistic statistical properties are derived for the second case. The differential equation for direction can be approximated by a second‐order autoregression, which generates realistic simulated patterns and gives a good fit to natural direction series.