bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization ofVP7andVP4genes of rotavirus strains: 1990–1994 and 2000–2002
Authors: ZADE J. K. , CHHABRA P. , CHITAMBAR S. D. 
Published: December 2008

SUMMARYA total of 90 rotavirus-positive faecal specimens collected from patients hospitalized with diarrhoea in 1990–1994 (n=77) and 2000–2002 (n=13) were investigated for VP7 and VP4 genotypes. The specimens included 21 typable and 69 non-reactive or multireactive rotavirus strains as monitored by monoclonal antibody-based serotyping ELISA. Genotyping was carried out by multiplex PCR/sequencing using primers specific for bothVP7andVP4genes. The contribution of common genotypes (G1P[8], G2P[4], G3P[8], G4P[8]) in causing rotavirus diarrhoea was 79·2% and 92·3% in the years 1990–1994 and 2000–2002, respectively, while G9P[8] infections were detected at lower levels (1·3% and 7·7%) at both time-points. There was a predominance of G1P[8] in 1990–1994 and of G2P[4] in 2000–2002. The detection of unusual rotavirus strains (G1P[6], G1P[4], G1P[19], G2P[8], G3P[4], G4P[6]) in 19·5% of the patients indicated a significant contribution of reassortants in causing diarrhoea in western India.
Cancer and immune-mediated disease in people who have had meningococcal disease: record-linkage studies
Authors: GOLDACRE M. J. , WOTTON C. J. , YEATES D. G. R. 
Published: December 2008

SUMMARYThe mechanisms that cause susceptibility to invasive meningococcal disease are largely unknown, but are likely to have important genetic and immunological components. We postulated that susceptibility to meningococcal disease might be associated with altered risks of development of other clinical disease. We studied cancer and immune-mediated disease in people who have been hospitalized with meningococcal disease. In cohorts of people who had invasive meningococcal disease, compared with reference cohorts, the rate ratio for cancer in an Oxford dataset studied from 1963 to 1998 was 0·88 [95% confidence interval (CI) 0·42–1·61] and in an all-England dataset studied from 1999 to 2005 it was 1·02 (95% CI 0·80–1·27). The respective rate ratios for immune-mediated disease were 1·49 (95% CI 0·81–2·50) and 0·69 (95% CI 0·53–0·89). Susceptibility to meningococcal disease was not associated with an altered risk of cancer. Occurrence of immune-mediated disease was, if anything, low in the large all-England cohort of people who had meningococcal disease.
Compilation of a new bathymetric dataset of South Georgia
Authors: Fretwell P.T. , Tate A.J. , Deen T.J. , Belchier M. 
Published: December 2008

AbstractWe introduce a new bathymetric compilation of the area around South Georgia in the Southern Ocean. Using a variety of data sources including multi and single-beam swath bathymetry we have constructed a gridded bathymetric dataset of the shelf and near-shelf sea-floor areas. The grid has been constructed using a layered hierarchy dependent upon accuracy of each dataset. The spikes and errors have been checked both manually and with a novel semi-automated process. We discuss the resulting bathymetry and the potential uses of the new dataset.
Morphology, evolution and stratigraphic distribution in the Middle Ordovician conodont genus Microzarkodina
Authors: Löfgren Anita , Tolmacheva Tatiana 
Published: December 2008

ABSTRACTMicrozarkodina is a genus of mainly Middle Ordovician conodonts that has its centre of distribution in Baltoscandia, and much less commonly occurs in southern China, Australia, Argentina and Laurentia. In Baltica a series of species, Microzarkodina russica n. sp., M. flabellum, M. parva, M. bella, M. hagetiana and M. ozarkodella, established themselves successfully. The succession of species ranges from just below the base of the Middle Ordovician (M. russica) to the upper part of the Middle Ordovician (M. ozarkodella). The species are frequently used for biostratigraphical purposes. The largely contemporaneous species Microzarkodina bella and M. hagetiana probably both evolved from M. parva and mostly occurred in separate areas. Microzarkodina ozarkodella probably evolved from M. hagetiana. This present investigation is based on a total of 94,208 elements, collected from 20 sections and one drill-core site in Sweden, one drill-core site and one outcrop in Estonia and two sections in the St Petersburg area in Russia. The Microzarkodina apparatus probably consisted of 15 or 17 elements: four P, two or four M and nine S elements. The S elements include different Sa, Sb1, Sb2, and Sc element types.
Isoform-specific differences in the nitrite reductase activity of nitric oxide synthases under hypoxia
Authors: Mikula Ivan , Durocher Suzanne , Martasek Pavel , Mutus Bulent , Slama-Schwok Anny 
Published: December 2008

Nitrite (NO2−) recycling to nitric oxide (NO) is catalysed by a number of enzymes and induces a protective vasodilation effect under hypoxia/ischaemia. In the present work, we tested the in vitro ability of the three NOS (nitric oxide synthase) isoforms to release NO from nitrite under anoxia using electrochemical detection, chemiluminescence and absorption spectroscopy. The release of free NO from anoxic nitrite solutions at 15 μM was specific to the endothelial NOS isoform (eNOS) and did not occur with the neuronal (nNOS) or inducible (iNOS) isoforms. Unlike xanthine oxidase, the eNOS reductase domain did not recycle nitrite to NO, and wild-type eNOS did not reduce nitrate. Our data suggest that structural and, by inference, dynamic differences between nNOS and eNOS in the distal haem side account for eNOS being the only isoform capable of converting nitrite into NO at pH 7.6. In human dermal microvascular endothelial cells under careful control of oxygen tension, the rates of NO formation determined by chemiluminescence were enhanced ∼3.6- and ∼8.3-fold under hypoxia (2 p.p.m. O2) and anoxia (argon) respectively compared with normoxia (∼22 p.p.m. O2) using 10 μM extracellular nitrite. NOS inhibitors inhibited this hypoxic NO release. Our data show that eNOS is unique in that it releases NO under all oxygen levels from normoxia to complete anoxia at physiological micromolar nitrite concentrations. The magnitude of the hypoxic NO release by the endothelial cells suggest that the endothelium could provide an appropriate response to acute episodic ischaemia and may explain the observed eNOS-expression-specific protective effect as a short-term response in animal models of acute hypoxia.
Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn341, Tyr60 and Phe351 in tetrahydrofolate binding
Authors: Pai Vinitha R. , Rajaram V. , Bisht Shveta , Bhavani B. S. , Rao N. Appaji , Murthy M. R. N. , Savithri H. S. 
Published: December 2008

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5′-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THF. SHMT also catalyses several THF-independent side reactions such as cleavage of β-hydroxy amino acids, transamination, racemization and decarboxylation. In the present study, the residues Asn341, Tyr60 and Phe351, which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe351 to glycine did not have any effect on either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn341 and Tyr60 are pivotal for the binding of THF/FTHF, whereas Phe351 is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.
Kinetics and thermodynamics of metal-loaded transferrins: transferrin receptor 1 interactions
Authors: Ha-Duong Nguyêt-Thanh , Hémadi Miryana , Chikh Zohra , Chahine Jean-Michel El Hage 
Published: December 2008

Transferrin receptor 1 (R) and human serum transferrin (T) are the two main actors in iron acquisition by the cell. R binds TFe2 (iron-loaded transferrin), which allows its internalization in the cytoplasm by endocytosis. T also forms complexes with metals other than iron. In order to follow the iron-acquisition pathway, these metals should obey at least two essential rules: (i) formation of a strong complex with T; and (ii) interaction of this complex with R. In the present paper, we propose a general mechanism for the interaction of five metal-loaded Ts [Fe(III), Al(III), Bi(III), Ga(III) and Co(III)] with R and we discuss their potential incorporation by the iron-acquisition pathway. With iron- and cobalt-loaded Ts, the interaction of R takes place in two steps: the first is detected by the T-jump technique and occurs in the 100 μs range, whereas the second is slow and occurs in the hour range. Bi(III)- and Ga(III)-loaded Ts interact with R in a single fast kinetic step, which occurs in the 100–500 μs range. No interaction is detected between R and aluminium-saturated T. The fast steps are ascribed to the interaction of the C-lobe of metal-loaded T with the helical domain of R: dissociation constant, K′1, of 0.50±0.07, 0.82±0.25, 4±0.4 and 1.10±0.12 μM for Fe(III), Co(III), Bi(III) and Ga(III) respectively. The second slow steps are ascribed to changes in the conformation of the protein–protein adducts which increase the stability to achieve, at thermodynamic equilibrium, an overall dissociation constant, K1, of 2.3 and 25 nM for Fe(III) and Co(III) respectively. This last step occurs over several hours, whereas endocytosis takes place in several minutes. This implies that metal-loaded Ts are internalized with only the C-lobe interacting with R. This suggests that, despite a lower affinity for R when compared with TFe2, some metal-loaded Ts can compete kinetically with TFe2 for the interaction with R and thus follow the iron-acquisition pathway.
Residual dipolar couplings as a tool to study molecular recognition of ubiquitin
Authors: Lakomek Nils-Alexander , Lange Oliver F. , Walter Korvin F.A. , Farès Christophe , Egger Dalia , Lunkenheimer Peter , Meiler Jens , Grubmüller Helmut , Becker Stefan , de Groot Bert L. , Griesinger Christian 
Published: December 2008

RDCs (residual dipolar couplings) in NMR spectroscopy provide information about protein dynamics complementary to NMR relaxation methods, especially in the previously inaccessible time window between the protein correlation time τc and 50 μs. For ubiquitin, new modes of motion of the protein backbone could be detected using RDC-based techniques. An ensemble of ubiquitin based on these RDC values is found to comprise all different conformations that ubiquitin adopts upon binding to different recognition proteins. These conformations in protein–protein complexes had been derived from 46 X-ray structures. Thus, for ubiquitin recognition by other proteins, conformational selection rather than induced fit seems to be the dominant mechanism.
Lectin–glycoconjugate interactions in health and disease
Authors: Kilpatrick David C. 
Published: December 2008

It is increasingly being acknowledged that complex carbohydrates mediate a huge variety of cellular interactions, permitting and regulating recognition and signalling events. This is achieved by the enormous range and complexity of branched structures in glycoconjugates and the ability of carbohydrate-binding proteins (lectins) to decipher this ‘glycocode’. Approx. 120 participants attended the 23rd International Lectin Meeting (Interlec-23) held at the Universities of Edinburgh (2 days) and Stirling (4 days) between 11 and 16 July 2008. These ‘Interlecs’ are truly international multi-disciplinary symposia, providing opportunities for scientists from different backgrounds, but with a common interest in some aspect of protein–carbohydrate interactions, to present their work in an informal and stimulating atmosphere. A major aim is always to induce cross-fertilization of ideas and concepts, and Interlec-23 was intended to have some bias towards lectins (galectins, collectins, selectins, siglecs etc.) and their ligands in human health and disease. Delegates from over 30 countries attended this meeting which was divided into seven oral sessions opened by a keynote speaker. This issue of Biochemical Society Transactions contains papers based on the keynote lectures and is therefore representative of the main themes of Interlec-23.
Gastrointestinal Tract Colonization With Fluoroquinolone-Resistant Escherichia coli in Hospitalized Patients: Changes Over Time in Risk Factors for Resistance
Authors: Lautenbach Ebbing , Metlay Joshua P. , Weiner Mark G. , Bilker Warren B. , Tolomeo Pam , Mao Xiangqun , Nachamkin Irving , Fishman Neil O. 
Published: December 2008

Objective.The prevalence of fluoroquinolone (FQ) resistance in Escherichia coli has increased markedly in recent years. Despite the important role of gastrointestinal tract colonization with FQ-resistant E. coli (FQREC), the prevalence of and risk factors for FQREC colonization among the general hospitalized patient population have not been described, to our knowledge. The objective of this study was to identify the prevalence of and risk factors for FQREC colonization among hospitalized patients.Design.Three-year case-control study. Case patients (ie, all subjects with FQREC colonization) were compared with control patients (ie, all subjects without FQREC colonization).Setting.Two large medical centers within an academic health system.Participants.All patients hospitalized at the 2 study hospitals.Main Outcome Measure.Three annual fecal surveillance surveys were conducted. All patients colonized with FQREC (levofloxacin minimum inhibitory concentration, ≥ 8 μg/mL) were identified.Results.Of the 774 subjects, 89 (11.5%) were colonized with FQREC. Although there was a significant association between prior FQ use and FQREC colonization on bivariable analysis (odds ratio [OR], 2.02 [95% confidence interval {CI}, 1.14–3.46]; P = .01), there was statistically significant effect modification by year of study (P = .005). In multivariable analyses, after controlling for the hospital and for the duration of hospitalization prior to sampling, the association between FQ use and FQREC colonization was as follows: adjusted OR (aOR), 0.97 (95% CI, 0.29–3.23) in 2002; aOR, 1.41 (95% CI, 0.57–3.50) in 2003; and aOR, 9.87 (95% CI, 3.67–26.55) in 2004.Conclusions.The association between prior FQ use and FQREC colonization varied significantly by study year, suggesting that the clinical epidemiology of resistant organisms may change over time. Furthermore, in the context of recent work showing significant changes in FQREC prevalence as well as changes in FQ resistance mechanisms (specifically, efflux overexpression) over the same time period, these results suggest a previously unrecognized complexity in the relationship between the clinical and molecular epidemiology of FQ resistance.
Incidence Rate and Variable Cost of Nosocomial Infections in Different Types of Intensive Care Units
Authors: Chen Yin-Yin , Wang Fu-Der , Liu Cheng-Yi , Chou Pesus 
Published: December 2008

Objective.Nosocomial infection (NI) is one of the most serious healthcare issues currently influencing healthcare costs. This study estimates the impact of NI on costs in intensive care units (ICUs).Design.Prospective surveillance by a retrospective cohort study.Setting.A medical ICU, a surgical ICU, and a mixed medical and surgical ICU in a large tertiary referral medical center.Methods.Surveillance for NIs was conducted for all patients admitted to adult ICUs from 2003 through 2005. Retrospective chart review was conducted for each patient. The generalized linear modeling approach was used to assess the relationship of NIs to the increase in variable costs in individual ICUs and in all ICUs.Results.A total of 401 NIs occurred in 320 of 2,757 screened patients. The incidence rate was 12.1% in the medical ICU, 14.7% in the surgical ICU, and 16.7% in the mixed medical and surgical ICU (P> .05). All of the mean variable costs were significantly higher for patients with NI than they were for patients without NI, after controlling for covariates. The medical ICU had the greatest increase in mean cost ($13,456, which was 3.52 times [95% confidence interval {CI}, 2.94–4.22 times] the mean cost for patients without NI), followed by the mixed medical and surgical ICU ($6,748, which was 2.74 times [95% CI, 2.33–3.22 times] the mean cost for patients without NI) and the surgical ICU ($5,433, which was 2.46 times [95% CI, 1.99–3.05 times] the mean cost for patients without NI). Mean cost increases according to the site of NI were $6,056 for bloodstream infection (2.36 times [95% CI, 1.97–2.84 times] the mean cost for patients without NI), $4,287 for respiratory tract infection (1.91 times [95% CI, 1.57–2.32 times] the mean cost for patients without NI), $1,955 for urinary tract infection (1.42 times [95% CI, 1.18–1.72 times] the mean cost for patients without NI), and $1,051 for surgical site infection (1.23 times [95% CI, 0.90–1.68 times] the mean cost for patients without NI).Conclusions.The medical ICU had the lowest rate of NI and the largest excess costs, the surgical ICU had the lowest excess costs, and the mixed medical and surgical ICU had the highest rate of NI. The cost is largely attributable to bloodstream infection and respiratory tract infection.
Study of Blood Contact in Simulated Surgical Needlestick Injuries With Single or Double Latex Gloving
Authors: Wittmann Andreas , Kralj Nenad , Köver Jan , Gasthaus Klaus , Hofmann Friedrich 
Published: December 2008

Objective.Needlestick injuries are the most common injuries that occur among operation room personnel in the health care service. The risk of infection after a needlestick injury during surgery greatly depends on the quantity of pathogenic germs transferred at the point of injury. The aim of this study was to measure the quantity of blood transferred at the point of a percutaneous injury by using radioactively labeled blood.Design.This study was conducted to evaluate the risk of infection through blood contact by simulating surgical needlestick injuries ex vivo. The tests were conducted by puncturing single and double latex gloves with diverse sharp devices and objects that were contaminated with Technetium solution–labeled blood.Results.A mean volume of 0.064 μL of blood was transferred in punctures with the an automatic lancet at a depth of 2.4 mm through 1 layer of latex. When the double-gloving indicator technique was used, a mean volume of only 0.011 μL of blood was transferred (median, 0.007 μL); thus, by wearing 2 pairs of gloves, the transferred volume of blood was reduced by a factor of 5.8.Conclusions.The results revealed that double gloving leads to a significant reduction in the quantity of blood transferred during needlestick injury.
Evaluating the effect of predation mortality on forage species population dynamics in the Northeast US continental shelf ecosystem using multispecies virtual population analysis
Authors: Tyrrell Megan C. , Link Jason S. , Moustahfid Hassan , Overholtz William J. 
Published: December 2008

AbstractTyrrell, M. C., Link, J. S., Moustahfid, H., and Overholtz, W. J. 2008. Evaluating the effect of predation mortality on forage species population dynamics in the Northeast US continental shelf ecosystem using multispecies virtual population analysis. – ICES Journal of Marine Science, 65: 1689–1700. An expanded version of multispecies virtual population analysis (MSVPA) is used to analyse the effects of predation by 14 key predators on Atlantic herring and Atlantic mackerel in the Northwest Atlantic ecosystem for the period 1982–2002. For herring, MSVPA produced greater abundance estimates than single-species assessments, especially for the youngest age classes. The average rate of predation mortality for herring aged 0 and 1 was also higher than the standard total natural mortality rate (0.2) for the 21-year time frame (0.84–3.2). The same was true for mackerel in this MSVPA (0.37–1.6). Consumptive removals of herring and mackerel generally increased over time. From 1999 to 2001, the biomass removed by predators exceeded each species' commercial landings. The sum of consumption and landings notably exceeded the multispecies maximum sustainable yield for herring for the years 1995–2002 and for mackerel for the period 1999–2002. We highlight the importance of accounting for predation on forage species in the context of changes to the fish community that have taken place in the Northwest Atlantic over the past few decades.
Modelling the target strength of Trachurus symmetricus murphyi based on high-resolution swimbladder morphometry using an MRI scanner
Authors: Peña Héctor , Foote Kenneth G. 
Published: December 2008

Abstract
Peña, H., and Foote, K. G. 2008. Modelling the target strength of Trachurus symmetricus murphyi based on high-resolution swimbladder morphometry using an MRI scanner. – ICES Journal of Marine Science, 65: 1751–1761. The acoustic target strength (TS) of Chilean jack mackerel (Trachurus symmetricus murphyi) was computed from three-dimensional reconstructions of the swimbladder form. The primary morphometric data were derived from high-resolution images made with a clinical whole-body 3-tesla magnetic resonance imaging (MRI) scanner. The fish were obtained from a commercial purse-seiner operating off Chile during 2003. Transverse MRI sequences of 18 fish were performed with a volumetric pixel 0.5 × 0.5 mm in cross section and 0.7 mm in the axial direction. From each transverse section, the swimbladder contour was traced manually using a digital pen tablet and smoothed using an automatic interpolation routine. The digital contours were used to build a triangular mesh spanning the swimbladder surface. The high-resolution swimbladder models revealed details such as undulations in the dorsal surface of the swimbladder caused by the backbone, and holes where the haemal spines penetrate the posterior end of the swimbladder. The Kirchhoff approximation was used to compute TS as a function of fish orientation at 38 kHz. The mean dorsal-aspect TS was computed for several orientation patterns and regressed on the logarithm of total fish length to derive operationally simple formulae.