bluuebunny/crossref_metadata_2025 huggingface dataset:
Photoelectric studies of the transmembrane charge transfer reactions in photosystem I pigment‐protein complexes
Authors: Semenov Alexey Yu , Mamedov Mahir D , Chamorovsky Sergey K
Published: October 2003

The results of studies of charge transfer in cyanobacterial photosystem I (PS I) using the photoelectric method are reviewed. The electrogenicity in the PS I complex and its interaction with natural donors (plastocyanin, cytochrome c6
), natural acceptors (ferredoxin, flavodoxin), or artificial acceptors and donors (methyl viologen and other redox dyes) were studied. The operating dielectric constant values in the vicinity of the charge transfer carriers in situ were calculated. The profile of distribution of the dielectric constant along the PS I pigment–protein complex (from plastocyanin or cytochrome c6
through the chlorophyll dimer P700 to the acceptor complex) was estimated, and possible mechanisms of correlation between the local dielectric constant and electron transfer rate constant were discussed.
Interferon alpha inhibits the nuclear factor kappa B activation triggered by X gene product of hepatitis B virus in human hepatoma cells
Authors: Ohata Kazuyuki , Ichikawa Tatsuki , Nakao Kazuhiko , Shigeno Masaya , Nishimura Daisuke , Ishikawa Hiroki , Hamasaki Keisuke , Eguchi Katsumi
Published: October 2003

X gene product of hepatitis B virus (HBV) (HBx) regulates many transcription factors including nuclear factor kappa B (NF‐κB) and plays a key role in hepatocarcinogenesis. In this study, we demonstrated that the expression of full HBV genome and HBx gene similarly stimulated the transcriptional activity of NF‐κB in HuH‐7 human hepatoma cells, and that interferon (IFN)‐α as well as dominant negative mutant of IκB kinase‐α effectively inhibited the HBx‐mediated NF‐κB activation, but IFN‐γ did not. These results suggest that IFN‐α may have a function to block the NF‐κB activating pathway triggered by HBx in HBV hepatocytes.
A prokaryotic glutamate receptor: homology modelling and molecular dynamics simulations of GluR0
Authors: Arinaminpathy Yalini , Biggin Philip C. , Shrivastava Indira H. , Sansom Mark S.P.
Published: October 2003

GluR0 is a prokaryotic homologue of mammalian glutamate receptors that forms glutamate‐activated, potassium‐selective ion channels. The topology of its transmembrane (TM) domain is similar to that of simple potassium channels such as KcsA. Two plausible alignments of the sequence of the TM domain of GluR0 with KcsA are possible, differing in the region of the P helix. We have constructed homology models based on both alignments and evaluated them using 6 ns duration molecular dynamics simulations in a membrane‐mimetic environment. One model, in which an insertion in GluR0 relative to KcsA is located in the loop between the M1 and P helices, is preferred on the basis of lower structural drift and maintenance of the P helix conformation during simulation. This model also exhibits inter‐subunit salt bridges that help to stabilise the TM domain tetramer. During the simulation, concerted K+ ion–water movement along the selectivity filter is observed, as is the case in simulations of KcsA. K+ ion exit from the central cavity is associated with opening of the hydrophobic gate formed by the C‐termini of the M2 helices. In the intact receptor the opening of this gate will be controlled by interactions with the extramembranous ligand‐binding domains.
A statistical approach to evaluating distance metrics and analog assignments for pollen records
Authors: Gavin Daniel G , Oswald W.Wyatt , Wahl Eugene R , Williams John W
Published: October 2003

The modern analog technique typically uses a distance metric to determine the dissimilarity between fossil and modern biological assemblages. Despite this quantitative approach, interpretation of distance metrics is usually qualitative and rules for selection of analogs tend to bead hoc. We present a statistical tool, the receiver operating characteristic (ROC) curve, which provides a framework for identifying analogs from distance metrics. If modern assemblages are placed into groups (e.g., biomes), this method can (1) evaluate the ability of different distance metrics to distinguish among groups, (2) objectively identify thresholds of the distance metric for determining analogs, and (3) compute a likelihood ratio and a Bayesian probability that a modern group is an analog for an unknown (fossil) assemblage. Applied to a set of 1689 modern pollen assemblages from eastern North America classified into eight biomes, ROC analysis confirmed that the squared-chord distance (SCD) outperforms most other distance metrics. The optimal threshold increased when more dissimilar biomes were compared. The probability of an analog vs no-analog result (a likelihood ratio) increased sharply when SCD decreased below the optimal threshold, indicating a nonlinear relationship between SCD and the probability of analog. Probabilities of analog computed for a postglacial pollen record at Tannersville Bog (Pennsylvania, USA) identified transitions between biomes and periods of no analog.
Sensitivity of lysosomal enzymes to the plant alkaloid sanguinarine: comparison with other SH‐specific agents
Authors: Belyaeva T. , Leontieva E. , Shpakov A. , Mozhenok T. , Faddejeva M.
Published: October 2003

The influence of the benzo[c]phenanthridine alkaloid sanguinarine on some lysosomal enzyme activities was investigated. Sanguinarine inhibits lysosomal hydrolases in homogenates of cultured mouse fibroblasts. After incubation of mouse fibroblasts in culture with 100 μM sanguinarine an approximately 50% decrease in the activities of N‐acetyl‐β,d‐glucosaminidase (NAGA), β‐galactosidase (GAL), arylsulfatase and acid lipase was observed. Because the biological activity of sanguinarine might arise from the interaction of its iminium cation with enzyme thiol groups, we compared its effect on NAGA, GAL and acid phosphatase (AcP) activities with the effects of SH‐specific reagents p‐chloromercuribenzoic acid (CPMA) and N‐ethylmaleimide (NEM). Treatment of lysosomal fractions with millimolar concentrations of sanguinarine induces a dose‐dependent inhibition of the enzymes; for example, 0.6 mM sanguinarine causes approximately a 40% decrease in AcP and NAGA activities. NEM has similar effects, and increasing the preincubation temperature from 0 °C to 37 °C intensifies the inhibition due to both agents. CPMA also inhibits the activity of GAL (IC500.7 μM), AcP (IC5012.5 μM) and NAGA (IC506.8 μM) in a dose‐dependent manner but is more potent than sanguinarine or NEM. Comparative analysis of the primary structures of these enzymes using the program BLAST reveals the presence of highly conserved cysteine residues, which confirms the importance of thiol‐groups for their activities. Thus, both the experimental observations obtained in this study and the literature data imply a significant role of redox‐based mechanisms in regulating lysosomal functional activity.
The effects of acute afterload change on systolic ventricular function in conscious dogs with normal vs. failing hearts
Authors: Thompson Richard B. , van den Bos Ewout J. , Esposito David J. , Owen Clarence H. , Glower Donald D.
Published: October 2003

Background:

To date, no data exist on the linearity and, therefore, the usefulness of the preload recruitable stroke work (PRSW) and end‐systolic pressure–volume (ESPVR) relationships during acute afterload changes in heart failure.

Aims:

Our aim was, therefore, to characterize both relationships in a model of ventricular pacing induced heart failure at baseline and during acute changes in afterload.

Methods:

Dynamic left ventricular volume and transmural pressure were measured in 10 conscious dogs using sonomicrometry and micromanometry under control conditions and during heart failure produced by 3 weeks of rapid right ventricular pacing. Afterload was varied from baseline with intravenous infusions of nitroprusside and phenylephrine. Left ventricular function was assessed using the PRSW and ESPVR relationships.

Results:

Cardiac output demonstrated a linear inverse relationship with afterload in both normal and failing hearts (r2>0.5, P<0.001) with failure producing a parallel, downward shift of the afterload (x) vs. cardiac output (y) relationship (P<0.01). Yet, afterload variation did not affect PRSW or ESPVR relationships in either normal or failing hearts (r2<0.12, P>0.05).

Conclusion:

Thus, the PRSW and ESPVR relationships are insensitive to acute afterload changes in both failing and normal hearts, and the failing left ventricle is no more afterload‐sensitive than the normal heart.
Palaeobiogeographic implications of Middle Permian brachiopods from Johore (Peninsular Malaysia)
Authors: SONE MASATOSHI , METCALFE IAN , LEMAN MOHD SHAFEEA
Published: October 2003

A new Middle Permian locality in northern Johore, Peninsular Malaysia, yields a small-sized, but compositionally unique, brachiopod fauna consisting of eight species: Pseudoleptodus sp., Caricula cf. salebrosa Grant, Neochonetes (Nongtaia) aff. arabicus (Hudson & Sudbury), Karavankina sp., Transennatia cf. insculpta (Grant), Hustedia sp., Orthothetina sp., and martiniid indet. The first four genera are new records for Malaysia; in particular, the rare taxa Pseudoleptodus and Caricula characterize the fauna. The brachiopods occur together with the ammonoid Agathiceras sp., the nautiloid Foordiceras? sp., bivalves, and crinoid stems. The locality belongs to the East Malaya terrane of the Cathaysian biotic region, but some affinities to species of the Sibumasu province are recognized. The Malaysian forms of Pseudoleptodus, Caricula and Transennatia are similar to those of the Ratburi Limestone (southern Thailand). A Roadian–early Wordian age is interpreted for the Johore fauna. The similarity of brachiopods reported here with those from the Ratburi Limestone suggests that there was species interchange or one-way migration between shallow waters of East Malaya and Sibumasu across the main Palaeo-Tethys. The Tethyan seaway between the two terranes must have been narrower than previously interpreted by some authors to allow such faunal traffic during the Roadian–Wordian time period.
Stratigraphical and palaeoecological importance of Caradoc (Upper Ordovician) graptolites from the Cardigan area, southwest Wales
Authors: WILLIAMS MARK , DAVIES JEREMY R. , WATERS RICHARD A. , RUSHTON ADRIAN W. A. , WILBY PHILIP R.
Published: October 2003

Graptolites from more than 60 horizons in the basinal Caradoc succession of southwest Wales, between Fishguard and Cardigan, allow recognition of the multidens, clingani and linearis biozones. The biostratigraphy permits recognition of major differences in the sedimentary rock-sequence north and south of structures associated with the Fishguard–Cardigan Fault Belt. The Penyraber Mudstone Formation, disconformably overlying the Fishguard Volcanic Group (Llanvirn), is partly of multidens Biozone age. It is succeeded south of the Newport Sands Fault by the Cwm yr Eglwys Mudstone Formation of clingani to linearis biozones age. North of the fault the Cwm yr Eglwys Mudstone Formation is replaced laterally by the northwards-thickening, sandstone turbidite-dominated Dinas Island Formation (clingani and linearis biozones). Graptolite stratigraphical distribution indicates that Dicranograptus clingani occurs only rarely within the caudatus Subzone of the clingani Biozone and that Climacograptus antiquuss.l. also does not range above the lower part of the clingani Biozone. The first occurrence of Dicellograptus morrisi, within the upper clingani Biozone, confirms its value as a marker for the morrisi Subzone, and is associated with the first occurrences of Diplacanthograptus dorotheus and Normalograptus minimus. Dicellograptus flexuosus, used to indicate the morrisi Subzone elsewhere, occurs throughout the clingani Biozone in the Cardigan area. The linearis Biozone is recognized by Climacograptus tubuliferus. Oxic bottom conditions in early and early mid-Caradoc times largely precluded the influx of, or preservation of, graptolite faunas in the Penyraber Mudstone Formation. Anoxic mudstones of the Cwm yr Eglwys Mudstone and Dinas Island formations preserve graptolite assemblages of 21 and 26 species, signalling strong open marine influences which persisted in this area until late Caradoc times. This contrasts with the shelfal faunas in the Whitland area (south Pembrokeshire), where the late Caradoc is dominated by low-diversity Normalograptus-dominated assemblages.
Age and tectonic setting of the Nesåa Batholith: implications for Ordovician arc development in the Caledonides of Central Norway
Authors: MEYER G. B. , GRENNE T. , PEDERSEN R. B.
Published: October 2003

New U–Pb zircon dating yields a crystallization age of 458±3 Ma for the largely gabbroic Grøndalsfjell Intrusive Complex in the Gjersvik Nappe of the Caledonian Upper Allochthon in Scandinavia. This is identical, within error, to the age of the adjacent Møklevatnet Complex that is dominated by quartz monzodiorite (456±2 Ma), and the two intrusive suites may be regarded as members of a composite intrusion here referred to as the Nesåa Batholith. Mafic members of this calc-alkaline batholith are characterized by slightly positive εNd–εSr values, marked enrichment of the light rare earth elements and high Th/Yb ratios suggestive of a subduction-modified mantle source. The I-type granitoids have similar isotope values and highly fractionated rare earth element patterns, and are interpreted as products from partial melting of garnet-bearing mafic rocks. The Nesåa Batholith intruded a previously deformed, 483 Ma or older, metavolcanic sequence of oceanic arc affinity. The margins of the pluton show evidence for synkinematic emplacement, which is tentatively interpreted in terms of magma ascent controlled by deep-seated shear zones. Further uplift and exhumation of the crystallized plutons was followed by rapid deposition of batholith-derived conglomerates and arkoses in a marginal basin represented by the Limingen Group. The age of the Nesåa Batholith fills the gap in reported ages for Caledonian magmatism, between the Early to Middle Ordovician, oceanic to continental margin type, arc sequences of Laurentian palaeotectonic affinity, and the Late Ordovician–Early Silurian batholith complexes of interpreted Laurentian margin affinity. It is interpreted as an early phase of the more extensive plutonism recorded in the Bindal Batholith of the Uppermost Allochthon to the west. Our model implies that the Early Ordovician oceanic arc sequences of the Gjersvik Nappe were deformed and accreted on to Laurentian margin lithologies prior to Late Ordovician times. This composite crustal assemblage was the source for the voluminous quartz monzodioritic intrusions of the Nesåa Batholith, which formed by partial melting due to ponding of subduction-related mantle derived mafic magmas either within or at the base of the active continental margin.
Polymetamorphism and ductile deformation of staurolite–cordierite schist of the Bossòst dome: indication for Variscan extension in the Axial Zone of the central Pyrenees
Authors: MEZGER JOCHEN E. , PASSCHIER CEES W.
Published: October 2003

The Bossòst dome is an E–W-trending elongated structural and metamorphic dome developed in Cambro-Ordovician metasedimentary rocks in the Variscan Axial Zone of the central Pyrenees. A steep fault separates a northern half-dome, cored by massif granite, from an E–W-trending doubly plunging antiform with granitic sills and dykes in the core to the south. The main foliation is a flat-lying S1/2 schistosity that grades into a steeper-dipping slaty cleavage at the dome margins. Three major deformational and two metamorphic phases can be differentiated. S1/2 schistosity is an axial planar cleavage to W-vergent recumbent folding that probably occurred in mid-Westphalian time. Peak regional metamorphism M1 is characterized by static growth of staurolite and garnet following thermal relaxation of the previously thickened crust. Strong non-coaxial deformation recording uniform top-to-the-SE extension during D2a is preserved in staurolite–garnet schists in a 1.5 km thick, shallowly SE-dipping zone in the southeastern dome. A 500 m thick contact aureole (M2) was imprinted on the regionally metamorphosed rocks following the intrusion the Bossòst granite during D2b. More coaxial deformation prevailed during synkinematic growth of M2 phases in the inner part of the contact aureole around the northern part of the dome, where it obliterated D2a fabrics. Progressive non-coaxial deformation continued in the southeastern antiform and is recorded by late-synkinematic growth of cordierite. Successive overprinting of the M1 staurolite–garnet assemblage by andalusite and cordierite of M2 is preserved in the southern part. The assemblage muscovite+cordierite+staurolite+biotite is considered metastable, given the low Mn and Zn contents of staurolite and cordierite, and interpreted as the result of prograde metamorphism during decompression. P–T conditions during M2 were approximately 3 kbar and 600 °C. Pervasive crenulations and mesoscopic to regional southerly verging folds are the result of D3 NNE–SSW compression post-dating ductile deformation and contact metamorphism. Polymetamorphic assemblages of the Bossòst dome preserve a regionally confined zone of ESE-directed extensional shearing within an overall N–S compressional setting. Exact timing of extensional shearing is not known, but can be constrained by recumbent folding during the mid-Westphalian and granitic intrusions, which confine it to Late Carboniferous time (c. 305 Ma). Crustal-scale flat-lying extensional shear zones with similar orientation and time frame are observed in the Hospitalêt massif of the eastern Axial Zone. This suggests that crustal extension, though probably restricted by regional strain partitioning over orthogneiss or intruding granitic bodies within an overall compressive setting, was not uncommon in Late Carboniferous time in the Axial Zone of the Pyrenees.
The Lessons of Defeat: Transforming the Qing State after the Boxer War
Authors: Thompson Roger R.
Published: October 2003

These four essays were first presented to an audience in Washington, D.C. in April 2002 at the Annual Meeting of the Association for Asian Studies. Richard Horowitz, the panel organizer, argued that:

the roots of China's modern state can be found in the Xinzheng or ‘new policy’ reforms during the last decade of the Qing dynasty. These reforms marked a radical departure for the Chinese state, involving a sustained effort to import foreign models and adapt them to Chinese realities. Although scholarship on reforms to provincial and local state institutions in this period is substantial, the transformation of the central government in Beijing has received little attention.
‘The Redemption of the Rascals’: The Xinzheng Reforms and the Transformation of the Status of Lower-Level Central Administration Personnel
Authors: Gabbiani Luca
Published: October 2003

Two of the main practical problems which confronted the Xinzheng reforms (1901–1911) were, on the one hand, financial issues, and on the other, personnel issues. In this paper, I will concentrate on the latter. When one thinks of the reforms in relation to administrative personnel, the main aspects generally brought up are centered upon innovations introduced at that time. Among other things, we could mention the new schools or, to be more general, the new educational system that was built up around the empire—mostly after 1900—to prepare a new generation of officials trained in specific fields of ‘modern’ knowledge. They, in turn, were expected to fill in the positions in the newly set up administrative institutions at the central and local levels. Their new training was to allow them to be in charge of the new responsibilities the reformed Qing bureaucratic apparatus had set out to perform in such fields as justice, fiscality and finances, the military and police, education or public health, to name but a few. To summarize, the search for talented men, a Chinese age-old principle for sound government, was trusted to that for new talents. The 1905 disbanding of the traditional examination system did much to reinforce this trend. During the first decade of the 20th century, the steady increase in the number of Chinese young men going abroad to study—especially to Japan—can serve as a testimony to this `new knowledge and new talent fever' of the late Qing. The fights against one another to which some of the central and provincial administrative offices resorted in order to secure for themselves the services of those deemed of talent are but another exemplary illustration of this aspect.
Searching for statistically significant regulatory modules
Authors: Bailey Timothy L. , Noble William Stafford
Published: October 2003

Motivation: The regulatory machinery controlling gene expression is complex, frequently requiring multiple, simultaneous DNA-protein interactions. The rate at which a gene is transcribed may depend upon the presence or absence of a collection of transcription factors bound to the DNA near the gene. Locating transcription factor binding sites in genomic DNA is difficult because the individual sites are small and tend to occur frequently by chance. True binding sites may be identified by their tendency to occur in clusters, sometimes known as regulatory modules.

Results: We describe an algorithm for detecting occurrences of regulatory modules in genomic DNA. The algorithm, called mcast, takes as input a DNA database and a collection of binding site motifs that are known to operate in concert. mcast uses a motif-based hidden Markov model with several novel features. The model incorporates motif-specific p-values, thereby allowing scores from motifs of different widths and specificities to be compared directly. The p-value scoring also allows mcast to only accept motif occurrences with significance below a user-specified threshold, while still assigning better scores to motif occurrences with lower p-values. mcast can search long DNA sequences, modeling length distributions between motifs within a regulatory module, but ignoring length distributions between modules. The algorithm produces a list of predicted regulatory modules, ranked by E-value. We validate the algorithm using simulated data as well as real data sets from fruitfly and human.

Availability: http://meme.sdsc.edu/MCAST/paper

Contact: tlb@maths.uq.edu.au

*To whom correspondence should be addressed.

†Formerly William Noble Grundy, see www.gs.washington.edu/noble/name-change.html
HMM sampling and applications to gene finding and alternative
splicing
Authors: Cawley Simon L. , Pachter Lior
Published: October 2003

The standard method of applying hidden Markov models to biological problems is to find a Viterbi (maximal weight) path through the HMM graph. The Viterbi algorithm reduces the problem of finding the most likely hidden state sequence that explains given observations, to a dynamic programming problem for corresponding directed acyclic graphs. For example, in the gene finding application, the HMM is used to find the most likely underlying gene structure given a DNA sequence. In this note we discuss the applications of sampling methods for HMMs. The standard sampling algorithm for HMMs is a variant of the common forward-backward and backtrack algorithms, and has already been applied in the context of Gibbs sampling methods. Nevetheless, the practice of sampling state paths from HMMs does not seem to have been widely adopted, and important applications have been overlooked. We show how sampling can be used for finding alternative splicings for genes, including alternative splicings that are conserved between genes from related organisms. We also show how sampling from the posterior distribution is a natural way to compute probabilities for predicted exons and gene structures being correct under the assumed model. Finally, we describe a new memory efficient sampling algorithm for certain classes of HMMs which provides a practical sampling alternative to the Hirschberg algorithm for optimal alignment. The ideas presented have applications not only to gene finding and HMMs but more generally to stochastic context free grammars and RNA structure prediction.

Key words: suboptimal parses, sampling, hidden Markov model, conserved alternative splicing

Contact: lpachter@math.berkeley.edu

*To whom correspondence should be addressed.
Divide-and-conquer multiple alignment with segment-based
constraints
Authors: Sammeth Michael , Morgenstern Burkhard , Stoye Jens
Published: October 2003

A large number of methods for multiple sequence alignment are currenty available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global strategies can be outperformed by approaches based on local similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed approaches that include both global and local features have shown promising results. Herein, we introduce a new algorithm for multiple sequence alignment that integrates the global divide-and-conquer approach with the local segment-based approach, thereby combining the strengths of those two strategies.

Contact: micha@sammeth.net

*To whom correspondence should be addressed.
Gene prediction with a hidden Markov model and a new intron
submodel
Authors: Stanke Mario , Waack Stephan
Published: October 2003

Motivation: The problem of finding the genes in eukaryotic DNA sequences by computational methods is still not satisfactorily solved. Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons.

Results: We have developed a new program, AUGUSTUS, for the ab initio prediction of protein coding genes in eukaryotic genomes. The program is based on a Hidden Markov Model and integrates a number of known methods and submodels. It employs a new way of modeling intron lengths. We use a new donor splice site model, a new model for a short region directly upstream of the donor splice site model that takes the reading frame into account and apply a method that allows better GC-content dependent parameter estimation. AUGUSTUS predicts on longer sequences far more human and drosophila genes accurately than the ab initio gene prediction programs we compared it with, while at the same time being more specific.

Availability: A web interface for AUGUSTUS and the executable program are located at http://augustus.gobics.de.

Supplementary Information: The datasets used for testing and training are available at http://augustus.gobics.de/datasets/

Contact: mstanke@gwdg.de

*To whom correspondence should be addressed.
Extracting active pathways from gene expression data
Authors: Vert Jean Philippe , Kanehisa Minoru
Published: October 2003

Motivation: A promising way to make sense out of gene expression profiles is to relate them to the activity of metabolic and signalling pathways. Each pathway usually involves many genes, such as enzymes, which can themselves participate in many pathways. The set of all known pathways can therefore be represented by a complex network of genes. Searching for regularities in the set of gene expression profiles with respect to the topology of this gene network is a way to automatically extract active pathways and their associated patterns of activity.

Method: We present a method to perform this task, which consists in encoding both the gene network and the set of profiles into two kernel functions, and performing a regularized form of canonical correlation analysis between the two kernels.

Results: When applied to publicly available expression data the method is able to extract biologically relevant expression patterns, as well as pathways with related activity.

Contact: Jean-Philippe.Vert@mines.org

*To whom corespondence should be addressed.
Flexible structure alignment by chaining aligned fragment pairs
allowing twists
Authors: Ye Yuzhen , Godzik Adam
Published: October 2003

Motivation: Protein structures are flexible and undergo structural rearrangements as part of their function, and yet most existing protein structure comparison methods treat them as rigid bodies, which may lead to incorrect alignment.

Results: We have developed the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT), a new method for structural alignment of proteins. The FATCAT approach simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference protein. In contrast, currently existing flexible structure alignment programs treat the hinge detection as a post-process of a standard rigid body alignment. We illustrate the advantages of the FATCAT approach by several examples of comparison between proteins known to adopt different conformations, where the FATCAT algorithm achieves more accurate structure alignments than current methods, while at the same time introducing fewer hinges.

Contacts: adam@burnham.org

*To whom correspondence should be addressed.
Mass transfer, clearance and plasma concentration of procalcitonin during continuous venovenous hemofiltration in patients with septic shock and acute oliguric renal failure
Authors: Level Claude , Chauveau Philippe , Guisset Olivier , Cazin Marie Cécile , Lasseur Catherine , Gabinsky Claude , Winnock Stéphane , Montaudon Danièle , Bedry Régis , Nouts Caroline , Pillet Odile , Benissan Georges Gbikpi , Favarel-Guarrigues Jean Claude , Castaing Yves
Published: October 2003

Objectives

To measure the mass transfer and clearance of procalcitonin (PCT) in patients with septic shock during continuous venovenous hemofiltration (CVVH), and to assess the mechanisms of elimination of PCT.

Setting

The medical department of intensive care.

Design

A prospective, observational study.

Patients

Thirteen critically ill patients with septic shock and oliguric acute renal failure requiring continuous venovenous postdilution hemofiltration with a high-flux membrane (AN69 or polyamide) and a 'conventional' substitution volume (< 2.5 l/hour).

Measurements and main results

PCT was measured with the Lumitest PCT Brahms® in the prefilter and postfilter plasma, in the ultrafiltrate at the beginning of CVVH (T0) and 15 min (T15'), 60 min (T60') and 6 hours (T6h) after setup of CVVH, and in the prefilter every 24 hours during 4 days. Mass transfer was determined and the clearance and the sieving coefficient were calculated according to the mass conservation principle. Plasma and ultrafiltrate clearances, respectively, at T15', T60' and T6h were 37 ± 8.6 ml/min (not significant) and 1.8 ± 1.7 ml/min (P < 0.01), 34.7 ± 4.1 ml/min (not significant) and 2.3 ± 1.8 ml/min (P < 0.01), and 31.5 ± 7 ml/min (not significant) and 5 ± 2.3 ml/min (P < 0.01). The sieving coefficient significantly increased from 0.07 at T15' to 0.19 at T6h, with no difference according to the nature of the membrane. PCT plasma levels were not significantly modified during the course of CCVH.

Conclusions

We conclude that PCT is removed from the plasma of patients with septic shock during CCVH. Most of the mass is eliminated by convective flow, but adsorption also contributes to elimination during the first hours of CVVH. The effect of PCT removal with a conventional CVVH substitution fluid rate (<2.5 l/hour) on PCT plasma concentration seems to be limited, and PCT remains a useful diagnostic marker in these septic patients. The impact of high-volume hemofiltration on the PCT clearance, the mass transfer and the plasma concentration should be evaluated in further studies.
Life-sustaining treatment decisions in Portuguese intensive care units: a national survey of intensive care physicians
Authors: Cardoso Teresa , Fonseca Teresa , Pereira Sofia , Lencastre Luís
Published: October 2003

Introduction

The objective of the present study was to evaluate the opinion of Portuguese intensive care physicians regarding 'do-not-resuscitate' (DNR) orders and decisions to withhold/withdraw treatment.

Methods

A questionnaire was sent to all physicians working on a full-time basis in all intensive care units (ICUs) registered with the Portuguese Intensive Care Society.

Results

A total of 266 questionnaires were sent and 175 (66%) were returned. Physicians from 79% of the ICUs participated. All participants stated that DNR orders are applied in their units, and 98.3% stated that decisions to withhold treatment and 95.4% stated that decisions to withdraw treatment are also applied. About three quarters indicated that only the medical group makes these decisions. Fewer than 15% of the responders stated that they involve nurses, 9% involve patients and fewer than 11% involve patients' relatives in end-of-life decisions. Physicians with more than 10 years of clinical experience more frequently indicated that they involve nurses in these decisions (P < 0.05), and agnostic/atheist doctors more frequently involve patients' relatives in decisions to withhold/withdraw treatment (P < 0.05). When asked about who they thought should be involved, more than 26% indicated nurses, more than 35% indicated the patient and more than 25% indicated patients' relatives. More experienced doctors more frequently felt that nurses should be involved (P < 0.05), and male doctors more frequently stated that patients' relatives should be involved in DNR orders (P < 0.05). When a decision to withdraw treatment is made, 76.8% of 151 respondents indicated that they would initiate palliative care; no respondent indicated that they would administer drugs to accelerate the expected outcome.

Conclusion

The probability of survival from the acute episode and patients' wishes were the most important criteria influencing end-of-life decisions. These decisions are made only by the medical group in most of the responding ICUs, with little input from nursing staff, patients, or patients' relatives, although many respondents expressed a wish to involve them more in this process. Sex, experience and religious beliefs of the respondents influences the way in which these decisions are made.
StarLink: Impacts on the U.S. corn market and world trade
Authors: Lin William , Price Gregory K. , Allen Edward W.
Published: October 2003

StarLink disrupted the U.S. corn market during the 2000/01 marketing year as a result of inadvertent commingling. The potential, upper‐bound volume of marketed StarLink‐commingled corn from the 2000 crop located near wet and dry millers prior to October 1, 2000, is estimated at 124 million bushels. The percentage of corn shipments that tested positive mostly ranged from 5 to 10%, varying by mode of transportation. Price differentials between StarLink‐commingled and StarLink‐free corn commonly ranged between 7 and 12 cents per bushel during the early stage of the incident. These differentials eroded quickly due largely to Aventis' compensation of additional transportation costs when StarLink‐commingled shipments had to be rerouted to approved uses. While StarLink had a negative impact on U.S. corn exports, most of the reductions in exports to Japan and South Korea during the period from November 2000 through March 2002 were due to increased competition from rival exporters. [EconLit citations: Q130, Q170]. © 2003 Wiley Periodicals, Inc. Agribusiness 19: 473–488, 2003.
Supersonic molecular beam growth of thin films of organic materials: A novel approach to controlling the structure, morphology, and functional properties
Authors: Iannotta Salvatore , Toccoli Tullio
Published: October 2003

Thin films of semiconducting molecular materials can be grown with a seeded supersonic molecular beam epitaxy (SuMBE), which provides unprecedented control over structural, morphological, and, therefore, functional properties. This novel technique of deposition takes full advantage of its ability to regulate the initial state of the molecular precursors in the beams and, in particular, the kinetic energy, to control the morphology, structure, and functional properties of growing films. This article reviews the state of the art of SuMBE, discussing the basic aspects of the technique and the major achievements so far. The major results obtained with respect to growth on dielectrics and metal substrates of films of oligothiophenes and pentacene and with respect to the codeposition of phthalocyanines and fullerenes are discussed and compared with the state of the art of more conventional organic molecular beam deposition. The potential impact of SuMBE in the field of π‐conjugated materials and devices is also examined. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2501–2521, 2003
Abnormal tenocyte morphology is more prevalent than collagen disruption in asymptomatic athletes' patellar tendons
Authors: Cook J. L. , Feller J. A. , Bonar S. F. , Khan K. M.
Published: October 2003

This study investigated the prevalence of each of the four features of patellar tendinosis in asymptomatic athletic subjects undergoing patellar tendon anterior cruciate ligament (ACL) reconstruction.

Fifty subjects (39 males and 11 females) undergoing ACL reconstruction using a patellar tendon graft were screened for previous tendon symptoms, training and playing history and had their patellar tendons examined with ultrasound prior to surgery. During surgery, a small piece of proximal posterocentral tendon was harvested, fixed and examined under light microscopy. Histopathological changes were graded for severity.

Results demonstrate that 18 tendons were abnormal on light microscopy and 32 were normal. There were no differences between subjects with and without pathology in respect of training, recovery after surgery and basic anthropometric measures. Three tendons were abnormal on ultrasound but only one had proximal and central changes.

Tendons showed a consistent series of changes. Tenocyte changes were found in all but one of the abnormal tendons. In all but one of the tendons with increased ground substance there were tenocyte changes, and collagen separation was always associated with both tenocyte changes and increased ground substance. No tendons demonstrated neovascularization.

It appears that cellular changes must be present if there is an increase in ground substance, or collagen and vascular changes. Further research is required to confirm these findings. © 2003 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Torasemide vs. furosemide in primary care patients with chronic heart failure NYHA II to IV—efficacy and quality of life
Authors: Müller Karin , Gamba Giancesare , Jaquet Françoise , Hess Bernhard
Published: October 2003

Background:

The hypothesis was that torasemide, due to more predictable pharmacokinetics/pharmacodynamics, induces greater improvements in functional and social limitation than furosemide and reduces the frequency of hospitalisations in primary care patients with chronic heart failure (CHF).

Patients and Methods:

Prospective, randomized, unblinded study in primary care, 237 patients with CHF (NYHA II–IV), all on ACE inhibitors. Randomisation: torasemide (n=122) or furosemide (n=115), treated for 9 months. Endpoints: Clinical efficacy, quality of life, safety, tolerability, hospitalisations.

Results:

Clinical improvement was observed in both groups, but the trend to improve by at least one NYHA class was significant only in torasemide‐ (P=0.014), but not in furosemide‐treated patients. There were no differences with regard to adverse events and hospitalisation due to CHF. Overall, tolerability (P=0.0001) and improvement in daily restrictions (P=0.0002) were significantly higher, number of mictions at 3, 6 and 12 h after diuretic intake (P<0.001 at all time points) and urgency to urinate (P<0.0001) significantly lower in torasemide‐ vs. furosemide‐treated patients.

Conclusion:

CHF patients treated with torasemide gain a higher benefit in quality of life than furosemide treated patients, due to torasemide's dual effect on both clinical status and social function.
Diversity of platinum-group element mineralization styles in the North Atlantic Igneous Province: new evidence from Rum, UK
Authors: POWER M. R. , PIRRIE D. , ANDERSEN J. C. Ø.
Published: October 2003

Two generations of sulphide-hosted platinum-group element mineralization occur in the West Sgaorishal ultramafic plug, Rum. Disseminated Cu and Ni sulphides around the margin of the plug host a restricted platinum-group mineral assemblage that is dominated by Pd bismutho-tellurides and sperrylite (PtAs2) with subordinate electrum (AuAg), froodite (PdBi2) and unidentified Pt–Bi–Te phases. Later sulphide-rich dykes cross-cut the plug and host an assemblage dominated by Pd bismutho-tellurides, sperrylite and locally very abundant paolovite (Pd2Sn). Whole rock combined platinum-group element+Au concentrations are proportional to the sulphide abundance with slightly elevated values in disseminated sulphide lithologies (>400 ppb) and very high values (>2000 ppb) in the sulphide-rich dykes. Both generations have relatively flat chondrite-normalized plots indicating a primitive magmatic source. Negative δ34S values (−9.2 to −18.3 ‰) indicate that the disseminated mineralization is due to contamination probably derived from Jurassic sedimentary rocks leading to sulphur saturation and collection of platinum-group elements. The sulphide-rich dykes must have entrained a platinum-group element-rich sulphide liquid collected from a much larger volume of magma. The presence of platinum-group elements and sulphide-rich dykes with δ34S values between −10.8 and −15.0 ‰ indicates that parts of the Rum Layered Suite became sulphur saturated through magmatic contamination. It appears likely that platinum-group element mineralization styles within the southern North Atlantic Igneous Province are diverse and may be present in a wider variety of mineralogical associations than previously recognized.
An application of Nd isotope mapping in structural geology: delineating an allochthonous Grenvillian terrane at North Bay, Ontario
Authors: DICKIN A. P. , MCNUTT R. H.
Published: October 2003

Fifty new Nd isotope analyses are presented from the North Bay area of the Grenville Province in Ontario. These data are used to map the extent of an allochthonous Grenvillian terrane which is an outlier of the Allochthonous Polycyclic Belt of the Grenville Province. Amphibolite facies orthogneisses from the allochthonous terrane have depleted mantle Nd model ages (TDM) below 1.8 Ga, whereas the gneisses of the structurally underlying parautochthon almost invariably have model ages above 1.8 Ga. The distribution of model ages is consistent with the distribution of distinct types of metabasic rock, used by other researchers as the criterion for recognizing rocks of the allochthonous and parautochthonous belts of the Grenville Province. The agreement between these different types of evidence demonstrates that Nd isotope mapping is a reliable and powerful tool for mapping terrane boundaries in high-grade metamorphic belts.
Chongqing's Most Wanted: Worker Mobility and Resistance in China's Nationalist Arsenals, 1937–1945
Authors: Howard Joshua H.
Published: October 2003

Historians of the Sino-Japanese War (1937–45) have concentrated on rural China to explain how the Communists mobilized the peasantry as a revolutionary force. Although clarifying the CCP's ascension to power in 1949, this focus has impeded our understanding of social change and conflict in the Nationalist controlled territories, especially the wartime capital of Chongqing. Thus, it is difficult to understand how the Nationalists exacerbated the alienation of urban social groups during the 1940s or how the CCP began to find consensus in the cities after 1946. Even standard explanations for the Nationalist collapse—government factionalism, hyperinflation, military blunders, and malfeasance—with their focus on government elites and institutions have rendered invisible the role of social classes as agents of historical change. The few studies of wartime labor have instead emphasized the patriotic contributions of workers and their relative passivity under the four-class bloc envisioned by the united front.
From Orientals to Imagined Britons: Baghdadi Jews in Shanghai
Authors: Betta Chiara
Published: October 2003

Studies and reminiscences, which dissect the communities of the Baghdadi trade diaspora, have so far tended to over-emphasize the smooth Anglicization process experienced by Baghdadi Jews in British India, Singapore and China in the late nineteenth and early twentieth century. The myth of the Sassoons as the ‘Rothschilds of the East’ has, in particular, distorted and enhanced the representation of Baghdadi Jews as wealthy, Anglicized and thoroughly integrated in British social circles. In reality, if we want to unravel the multi-layered history of Baghdadi Jews from India to Japan we must not only analyse in depth the complexities of the westernization process of the Baghdadi upper classes but also reconstruct carefully class divisions within Baghdadi communities. With this aim in mind, this essay will investigate the various strands of identity developed by Baghdadis during their stay in Shanghai and will especially focus on the local allegiances forged between Baghdadi and British settlers, the so-called Shanghailanders. The following pages will, at the same time, delineate the social structure of the Baghdadi community in Shanghai and will indicate that westernized affluent Baghdadis were forced to confront painfully their own ‘other’: destitute vagrant co-religionists who hailed from the Middle East and India and roamed between the various nodes of the Baghdadi diaspora. The period considered in this essay stretches from 1845, the year the first Baghdadi trader set foot in the city, to the middle of the 1930s when large numbers of Jewish refugees from Europe started to flock to Shanghai in search of a safe haven.
A NEW SECTION OF BEGONIA (BEGONIACEAE) FROM WEST CENTRAL AFRICA
Authors: DE WILDE J. J. F. E. , PLANA V.
Published: October 2003

Previous analyses of macromorphological and molecular data on the continental African species Begonia iucunda (Begoniaceae) suggest that it occupies an isolated phylogenetic position within a clade consisting otherwise of species in sections Cristasemen, Filicibegonia, Loasibegonia and Scutobegonia. Accordingly, the new monotypic section Chasmophila is here described. Its taxonomic position and relationship to other African sections are discussed and data on its distribution and ecology are presented.
Observations at low latitudes of magnetic merging signatures within a flux transfer event during a northward interplanetary magnetic field
Authors: Chandler M. O. , Avanov L. A.
Published: October 2003

Flux transfer events (FTE) have been postulated to result from transient magnetic merging. If so, the ion distributions within an event should exhibit features known to result from merging. Observations of an FTE by instruments on the Polar spacecraft revealed classical merging signatures that included: (1) D‐shaped, accelerated, magnetosheath ion distributions, (2) a well‐defined de Hoffman‐Teller frame, (3) local stress balance, and (4) a P‐N magnetic field signature. This FTE was observed near the magnetic equator at ∼13 magnetic local time under conditions of a strongly northward interplanetary magnetic field (IMF) (clock angle of <10°). The nature of the ion distributions and the consistency of the measured cutoff speed with that calculated from the measured local magnetic field and the derived de Hoffman‐Teller speed show the ion injection to be local. Coupled with the northward IMF, these results lead to the conclusion that component merging in the low‐latitude region was responsible for the FTE.