bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexible structure alignment by chaining aligned fragment pairs
allowing twists
Authors: Ye Yuzhen , Godzik Adam 
Published: October 2003

Abstract
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

Abstract
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

Abstract
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

AbstractStarLink 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

AbstractThin 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

AbstractThis 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

AbstractBackground: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.
Upper bounds on maximum likelihood for phylogenetic trees
Authors: Hendy Michael D. , Holland Barbara R. 
Published: October 2003

Abstract
We introduce a mechanism for analytically deriving upper bounds on the maximum likelihood for genetic sequence data on sets of phylogenies. A simple ‘partition’ bound is introduced for general models. Tighter bounds are developed for the simplest model of evolution, the two state symmetric model of nucleotide substitution under the molecular clock. This follows earlier theoretical work which has been restricted to this model by analytic complexity. A weakness of current numerical computation is that reported ‘maximum likelihood’ results cannot be guaranteed, both for a specified tree (because of the possibility of multiple maxima) or over the full tree space (as the computation is intractable for large sets of trees). The bounds we develop here can be used to conclusively eliminate large proportions of tree space in the search for the maximum likelihood tree. This is vital in the development of a branch and bound search strategy for identifying the maximum likelihood tree. We report the results from a simulation study of approximately 106 data sets generated on clock-like trees of five leaves. In each trial a likelihood value of one specific instance of a parameterised tree is compared to the bound determined for each of the 105 possible rooted binary trees. The proportion of trees that are eliminated from the search for the maximum likelihood tree ranged from 92% to almost 98%, indicating a computational speed–up factor of between 12 and 44.
Contact: m.hendy@massey.ac.nz
*To whom correspondence should be addressed.
Analyzing resistance phenomena in HIV with bioinformatics
methods
Authors: Lengauer Thomas 
Published: October 2003

Abstract
We report on research that is targeted towards understanding the resistance phenomena that HIV undergoes in the presence of selective pressure presented by combination drug therapies. The ultimate goal of this research is to support the physician with helpful models for HIV resistance and to aid his decision as to how to adapt his therapy to the resistance phenomena observed in a patient. The talk will present the medical background of the problem and the following major results:
1. The Arevir database collecting data on HIV resistance. The data are derived from two sources, namely from genotyped patients (wrt to the dominant HIV strain observed in their blood serum) together with their medical history and from in-vitro measurements of the resistance of many HIV strains against single HIV drugs.
2. Statistical learning methods for predicting the resistance of a given HIV strain against single HIV drugs. This software is available via the geno2pheno server on the internet under http://www.genafor.org
3. New bioinformatics contributions that present a model of HIV resistance against combination drug therapies and makes suggestions for therapy adaption that take estimated future mutational path of the virus into account.
These results were achieved within a cooperation funded by DFG and comprising Niko Beerenwinkel (MPI Saarbücken), Martin Däumer (Univ. Cologne), Daniel Hoffmann (caesar Bonn), Rolf Kaiser (Univ. Cologne), Klaus Korn (Univ. Erlangen), Joachim Selbig (MPI Plant Physiology, Golm) Barbara Schmidt (Univ. Erlangen) and Hauke Walter (Univ. Erlangen).
Contact: lengauer@mpi-sb.mpg.de&#x2028; http://www.mpi-sb.mpg.de/~lengauer/
Artificial gene networks for objective comparison of analysis
algorithms
Authors: Mendes Pedro , Sha Wei , Ye Keying 
Published: October 2003

Abstract
Motivation: Large-scale gene expression profiling generates data sets that are rich in observed features but poor in numbers of observations. The analysis of such data sets is a challenge that has been object of vigorous research. The algorithms in use for this purpose have been poorly documented and rarely compared objectively, posing a problem of uncertainty about the outcomes of the analyses. One way to objectively test such analysis algorithms is to apply them on computational gene network models for which the mechanisms are completely know.
Results: We present a system that generates random artificial gene networks according to well-defined topological and kinetic properties. These are used to run in silico experiments simulating real laboratory microarray experiments. Noise with controlled properties is added to the simulation results several times emulating measurement replicates, before expression ratios are calculated.
Availability: The data sets and kinetic models described here are available from http://www.vbi.vt.edu/~mendes/AGN/as biochemical dynamic models in SBML and Gepasi formats.
Contact: mendes@vt.edu
*To whom correspondence should be addressed.
Comparative genomics of malaria parasites and its exploitation
in a rodent malaria model
Authors: Waters Andy 
Published: October 2003

Abstract
There is an abundance of malaria parasite genome sequence from both human-infectious and model parasites. It is very clear that the similarity of the biology of different Plasmodium species is reflected in the largely conserved organisation of their genomes. The differences between the parasite genomes are most obviously confined to the sub-telomeric regions where the multigene families that are involved in antigenic variation are located. Comparitive genomics may help improve the annotation of the conserved more centromeric regions of the prototype Plasmodium genome and pinpoint genes under stringent selection or experiencing rapid drift. Detailed comparison of Plasmodium genomes can catalogue genome recombination, gene grouping and perhaps indicate higher order levels of genome structure. The significant conservation of gene content including genes that encode surface proteins involved in cell-cell interactions means that the more extensive repertoire of experimental possibilities afforded by model parasites can be exploited to provide biological insights that remain relevant to drug and vaccine research. This will be illustrated by data drawn from the research activities in which the LUMC group participates.
Contact: Waters@lumc.nl&#x2028; http://www.lumc.nl/1040/research/malaria/contact-andy.html
Food Type Effects on the Population Growth Patterns of Littoral Rotifers and Cladocerans
Authors: García C. Enríquez , Nandini S. , Sarma S. S. S. 
Published: October 2003

AbstractLittoral rotifers and cladocerans feed on bacteria, phytoplankton, and detritus. In comparison to planktonic organisms their species diversity is high, yet little is known about their biology. In this study we present data on the functional response of the cladocerans Macrothrix triserialis and Alona rectangula, and the rotifer Brachionus macracanthus to different levels of the alga Chlorella vulgaris. Based on the incipient limiting level, we chose the food concentration and tested the population growth on four types of diets for three cladoceran species — Macrothrix triserialis, Alona rectangula, and Chydorus sphaericus — and three rotifer species — Brachionus macracanthus, Lecane quadridentata, and Platyias quadricornis. We studied growth rates of each of these species on diets of live Chlorella vulgaris, heat‐killed Chlorella vulgaris, baker's yeast (Saccharomyces cerevisiae), and field collected detritus. The incipient limiting level was around 0.9 · 106 cells mL−1 of Chlorella for the tested zooplankton species. The population growth patterns showed that, in general, the cladocerans took 25…50 d to reach their peak population densities, which ranged from 10…75 ind. mL−11. Among the rotifers L. quadridentata and B. macracanthus had equally high growth rates on live and heat‐killed forms of C. vulgaris while P. quadricornis grew best on detritus. The growth rates ranged from 0.03…0.21 d−1. The similarities and differences between littoral and planktonic organisms in relation to food type and availability have been discussed.
Biodegradation of Nonylphenol Ethoxylate Surfactants in Biofilm Reactors
Authors: Goel Anubha , Müller Margit B. , Sharma Mukesh , Frimmel Fritz H. 
Published: October 2003

AbstractThe primary degradation of a technical nonylphenol ethoxylate surfactant with an average chain length of 10 ethoxylate units (NPEO‐10) was studied in a flow‐through system by means of miniaturized biofilm reactors (mBFR) with bacteria from an activated sludge plant. 5 mg/L of the test compound (total EO concentration) were spiked in synthetic wastewater (SWW) and fed to the reactors continuously for 64 days. Compound removal and the formation of degradation products (DP) were monitored under both oxic and anoxic conditions. Solid‐phase extraction and RP‐HPLC with fluorescence detection were employed for sample preparation and analysis. Better removal of the parent compound was seen with the oxic reactors (50 to 70%) than with the anoxic reactors (30 to 50%). Compared to SWW organic matter, the test compound proved to be of refractory nature. The appearance of degradation products in the effluent was earlier with anoxic reactors despite their lower elimination efficiency. After extraction of biomass only minor amounts of NPEO‐10 and metabolites were found, indicating that small amounts were present in adsorbed or intracellular form. Ultimate biodegradation of NPEO‐10 and of octylphenol ethoxylates (OPEO‐9.5; average chain length of 9.5 EO units) was tested by means of manometric respirometry at a theoretical oxygen demand (ThOD) of 100 mg/L. Whereas NPEO‐10 was biodegraded by only 26%, at best, in 28 days, OPEO‐9.5 degradation amounted to (40 ± 5)%.
Sulfur and Selenium: The Role of Oxidation State in Protein Structure and Function
Authors: Jacob Claus , Giles Gregory I. , Giles Niroshini M. , Sies Helmut 
Published: October 2003

AbstractSulfur and selenium occur in proteins as constituents of the amino acids cysteine, methionine, selenocysteine, and selenomethionine. Recent research underscores that these amino acids are truly exceptional. Their redox activity under physiological conditions allows an amazing variety of posttranslational protein modifications, metal free redox pathways, and unusual chalcogen redox states that increasingly attract the attention of biological chemists. Unlike any other amino acid, the “redox chameleon” cysteine can participate in several distinct redox pathways, including exchange and radical reactions, as well as atom‐, electron‐, and hydride‐transfer reactions. It occurs in various oxidation states in the human body, each of which exhibits distinctive chemical properties (e.g. redox activity, metal binding) and biological activity. The position of selenium in the periodic table between the metals and the nonmetals makes selenoproteins ideal catalysts for many biological redox transformations. It is therefore apparent that the chalcogen amino acids cysteine, methionine, selenocysteine, and selenomethionine exhibit a unique biological chemistry that is the source of exciting research opportunities.