bluuebunny/crossref_metadata_2025_split huggingface dataset:
Campylobacter Monitoring in German Broiler Flocks: An Explorative Time Series Analysis
Authors: Hartnack S. , Doherr M. G. , Alter T. , Toutounian‐Mashad K. , Greiner M. 
Published: September 2008

Summary Campylobacter, a major zoonotic pathogen, displays seasonality in poultry and in humans. In order to identify temporal patterns in the prevalence of thermophilic Campylobacter spp. in a voluntary monitoring programme in broiler flocks in Germany and in the reported human incidence, time series methods were used. The data originated between May 2004 and June 2007. By the use of seasonal decomposition, autocorrelation and cross‐correlation functions, it could be shown that an annual seasonality is present. However, the peak month differs between sample submission, prevalence in broilers and human incidence. Strikingly, the peak in human campylobacterioses preceded the peak in broiler prevalence in Lower Saxony rather than occurring after it. Significant cross‐correlations between monthly temperature and prevalence in broilers as well as between human incidence, monthly temperature, rainfall and wind‐force were identified. The results highlight the necessity to quantify the transmission of Campylobacter from broiler to humans and to include climatic factors in order to gain further insight into the epidemiology of this zoonotic disease.
Cell Wall Chitosaccharides Are Essential Components and Exposed Patterns of the Phytopathogenic OomyceteAphanomyces euteiches
Authors: Badreddine Ilham , Lafitte Claude , Heux Laurent , Skandalis Nicholas , Spanou Zacharoula , Martinez Yves , Esquerré-Tugayé Marie-Thérèse , Bulone Vincent , Dumas Bernard , Bottin Arnaud 
Published: September 2008

ABSTRACTChitin is an essential component of fungal cell walls, where it forms a crystalline scaffold, and chitooligosaccharides derived from it are signaling molecules recognized by the hosts of pathogenic fungi. Oomycetes are cellulosic fungus-like microorganisms which most often lack chitin in their cell walls. Here we present the first study of the cell wall of the oomyceteAphanomyces euteiches, a major parasite of legume plants. Biochemical analyses demonstrated the presence of ca. 10%N-acetyl-d-glucosamine (GlcNAc) in the cell wall. Further characterization of the GlcNAc-containing material revealed that it corresponds to noncrystalline chitosaccharides associated with glucans, rather than to chitin per se. Two putative chitin synthase (CHS) genes were identified by data mining of anA. euteichesexpressed sequence tag collection and Southern blot analysis, and full-length cDNA sequences of both genes were obtained. Phylogeny analysis indicated that oomycete CHS diversification occurred before the divergence of the major oomycete lineages. Remarkably, lectin labeling showed that theAphanomyces euteicheschitosaccharides are exposed at the cell wall surface, and study of the effect of the CHS inhibitor nikkomycin Z demonstrated that they are involved in cell wall function. These data open new perspectives for the development of antioomycete drugs and further studies of the molecular mechanisms involved in the recognition of pathogenic oomycetes by the host plants.
Two Homologous Agr-Like Quorum-Sensing Systems Cooperatively Control Adherence, Cell Morphology, and Cell Viability Properties inLactobacillus plantarumWCFS1
Authors: Fujii Toshio , Ingham Colin , Nakayama Jiro , Beerthuyzen Marke , Kunuki Ryoko , Molenaar Douwe , Sturme Mark , Vaughan Elaine , Kleerebezem Michiel , de Vos Willem 
Published: September 2008

ABSTRACTA two-component regulatory system ofLactobacillus plantarum, encoded by genes designatedlamKandlamR(hpk10andrrp10), was studied. ThelamKandlamRgenes encode proteins which are highly homologous to the quorum-sensing histidine kinase LamC and the response regulator LamA, respectively. Transcription analysis of thelamKRoperon and thelamBDCAoperon and liquid chromatography-mass spectrometry analysis of production of the LamD558 autoinducing peptide were performed for ΔlamA, ΔlamR, ΔlamAΔlamRdeletion mutants and a wild-type strain. The results suggested thatlamAandlamRare cooperating genes. In addition, typical phenotypes of the ΔlamAmutant, such as reduced adherence to glass surfaces and filamentous cell morphology, were enhanced in the ΔlamAΔlamRmutant. Microarray analysis suggested that the same cell wall polysaccharide synthesis genes, stress response-related genes, and cell wall protein-encoding genes were affected in the ΔlamAand ΔlamAΔlamRmutants. However, the regulation ratio was more significant for the ΔlamAΔlamRmutant, indicating the cooperative effect of LamA and LamR.
Performance of self-reported occupational exposure compared to a job-exposure matrix approach in asthma and chronic rhinitis
Authors: Quinlan P J , Earnest G , Eisner M D , Yelin E H , Katz P P , Balmes J R , Blanc P D 
Published: September 2008

Objectives:Self-reported exposure to vapours, gas, dust or fumes (VGDF) has been widely used as an occupational exposure metric in epidemiological studies of chronic lung diseases. Our objective was to characterise the performance of VGDF for repeatability, systematic misclassification, and sensitivity and specificity against exposure likelihood by a job-exposure matrix (JEM).Methods:We analysed data from two interviews, 24 months apart, of adults with asthma and chronic rhinitis. Using distinct job as the unit of analysis, we tested a single response item (exposure to VGDF) against assignment using a JEM. We further analysed VGDF and the JEM among a subset of 199 subjects who reported the same job at both interviews, using logistic regression analysis to test factors associated with VGDF inconsistency and discordance with the JEM.Results:VGDF was reported for 193 (44%) of 436 distinct jobs held by the 348 subjects studied; moderate to high exposure likelihood by JEM was assigned to 120 jobs (28%). The sensitivity and specificity of VGDF against JEM were 71% and 66%, respectively. Among 199 subjects with the same job at both interviews, 32% had a discordant VGDF status (κ = 0.35). Those with chronic rhinitis without concomitant asthma compared to asthma alone were more likely to have a VGDF report discordant with the JEM (OR 3.6, 95% CI 1.4 to 9.0; p = 0.01). Rhinitis was also associated with reported VGDF in a job classified by the JEM as low exposure (OR 3.9, 95% CI 1.6 to 9.4; p = 0.003).Conclusion:The VGDF item is moderately sensitive measured against JEM as a benchmark. The measure is a useful assessment method for epidemiological studies of occupational exposure risk.
Socio-economic differences in the association between sickness absence and mortality: the prospective DREAM study of Danish private sector employees
Authors: Lund T , Kivimäki M , Christensen K B , Labriola M 
Published: September 2008

Objectives:To examine duration of sickness absence as a risk marker for future mortality by socio-economic position among all private sector employees in Denmark in 1998–2004.Methods:All residents in Denmark employed in the private sector receiving sickness absence compensation in 1998 were investigated in a prospective cohort study. 236 207 persons (38.2% women, 61.8% men, age range 18–65, mean age 37.8 years) alive on 1 January 2001 were included in the study. Mortality from 1 January 2001 to 31 December 2004 was assessed using national register data. Deaths in 1999 and 2000 were excluded to determine the status of sickness absence duration as an early risk marker. For analyses within occupational grades, data were available for a sub-population of 137 607 study participants.Results:3040 persons died during follow-up. The age-adjusted risk of future mortality increased by duration of sickness absence in a graded fashion among men and non-blue collar workers. Among women and blue collar workers, there was no association of mortality with duration of sickness absences below 6 weeks. However, employees with ⩾6 weeks of absence compared to those with 1-week absence had a substantial excess risk of death in all groups: adjusted hazard ratio 2.2 (95% CI 1.8 to 2.7) for women, 2.1 (95% CI 1.8 to 2.4) for men, 3.7 (95% CI 1.9 to 7.2) in white collar occupations, 3.3 (95% CI 2.2 to 5.0) in intermediate grade occupations and 2.0 (95% CI 1.7 to 2.3) in blue collar occupations.Conclusion:Administratively collected data on sickness absence compensation for periods ⩾6 weeks identified “at risk” groups for future excess mortality in male and female private sector employees across occupational grade levels.
Climate Response of Linear and Quadratic Functionals Using the Fluctuation–Dissipation Theorem
Authors: Gritsun Andrey , Branstator Grant , Majda Andrew 
Published: September 2008

Abstract
A generalization of the fluctuation–dissipation theorem (FDT) that allows generation of linear response operators that estimate the response of functionals of system state variables is tested for a system defined by an atmospheric general circulation model (AGCM). A sketch of the proof of this generalization is provided, followed by comparison of response estimates based on the theory and actual responses of the AGCM for various idealized anomalous equatorial heat sources. Tested response quantities include precipitation, variances of bandpass and low-pass streamfunction, and momentum and heat fluxes. The solutions from the FDT operators are very similar to the AGCM solutions in terms of structure while overestimating response amplitudes by about 20%. As an example of an application of such response operators, the FDT operator that estimates the response of bandpass upper-tropospheric streamfunction variance is used to find the most efficient means of disturbing the Atlantic storm tracks by tropical heating. The results of the study suggest that the generalized FDT is an attractive method for systematically studying response attributes of the climate system that are of interest to climate scientists and society.
An Empirical Parameterization of Heterogeneous Ice Nucleation for Multiple Chemical Species of Aerosol
Authors: Phillips Vaughan T. J. , DeMott Paul J. , Andronache Constantin 
Published: September 2008

Abstract
A novel, flexible framework is proposed for parameterizing the heterogeneous nucleation of ice within clouds. It has empirically derived dependencies on the chemistry and surface area of multiple species of ice nucleus (IN) aerosols. Effects from variability in mean size, spectral width, and mass loading of aerosols are represented via their influences on surface area. The parameterization is intended for application in large-scale atmospheric and cloud models that can predict 1) the supersaturation of water vapor, which requires a representation of vertical velocity on the cloud scale, and 2) concentrations of a variety of insoluble aerosol species.
Observational data constraining the parameterization are principally from coincident field studies of IN activity and insoluble aerosol in the troposphere. The continuous flow diffusion chamber (CFDC) was deployed. Aerosol species are grouped by the parameterization into three basic types: dust and metallic compounds, inorganic black carbon, and insoluble organic aerosols.
Further field observations inform the partitioning of measured IN concentrations among these basic groups of aerosol. The scarcity of heterogeneous nucleation, observed at humidities well below water saturation for warm subzero temperatures, is represented. Conventional and inside-out contact nucleation by IN is treated with a constant shift of their freezing temperatures.
The empirical parameterization is described and compared with available field and laboratory observations and other schemes. Alternative schemes differ by up to five orders of magnitude in their freezing fractions (−30°C). New knowledge from future observational advances may be easily assimilated into the scheme’s framework. The essence of this versatile framework is the use of data concerning atmospheric IN sampled directly from the troposphere.
An APOA1 promoter polymorphism is associated with cognitive performance in patients with multiple sclerosis
Authors: Koutsis G , Panas M , Giogkaraki E , Karadima G , Sfagos C , Vassilopoulos D 
Published: September 2008

Background Elevated ApoA1 levels have been associated with decreased dementia risk. The A-allele of the APOA1 –75G/A promoter polymorphism has been associated with elevated ApoA1 levels. Objective We sought to investigate the effect of the APOA1 –75G/A promoter polymorphism on cognitive performance in patients with multiple sclerosis (MS). Methods A total of 138 patients with MS and 43 controls were studied and underwent neuropsychological assessment with Rao’s Brief Repeatable Battery and the Stroop test. All patients were genotyped for APOA1. Results APOA1 A-allele carriers displayed superior overall cognitive performance compared with non-carriers ( P 0.008) and had a three-fold decrease in the relative risk of overall cognitive impairment (OR 0.29, 95% CI 0.11–0.74). Regarding performance on individual cognitive domains, although APOA1 A-allele carriers performed better than non-carriers on all tests, this was significant only for semantic verbal fluency and the Stroop interference task ( P 0.036 and 0.018, respectively). Conclusions We found an association of the APOA1 –75G/A promoter polymorphism with cognitive performance in MS. This effect was most prominent on semantic verbal fluency and the Stroop interference task.
Interleukin-1–mediated hematopoietic cell regulation in the aorta-gonad-mesonephros region of the mouse embryo
Authors: Orelio Claudia , Haak Esther , Peeters Marian , Dzierzak Elaine 
Published: September 2008

AbstractHematopoiesis during development is a dynamic process, with many factors involved in the emergence and regulation of hematopoietic stem cells (HSCs) and progenitor cells. Whereas previous studies have focused on developmental signaling and transcription factors in embryonic hematopoiesis, the role of well-known adult hematopoietic cytokines in the embryonic hematopoietic system has been largely unexplored. The cytokine interleukin-1 (IL-1), best known for its proinflammatory properties, has radioprotective effects on adult bone marrow HSCs, induces HSC mobilization, and increases HSC proliferation and/or differentiation. Here we examine IL-1 and its possible role in regulating hematopoiesis in the midgestation mouse embryo. We show that IL-1, IL-1 receptors (IL-1Rs), and signaling mediators are expressed in the aorta-gonad-mesonephros (AGM) region during the time when HSCs emerge in this site. IL-1 signaling is functional in the AGM, and the IL-1RI is expressed ventrally in the aortic subregion by some hematopoietic, endothelial, and mesenchymal cells. In vivo analyses of IL-1RI–deficient embryos show an increased myeloid differentiation, concomitant with a slight decrease in AGM HSC activity. Our results suggest that IL-1 is an important homeostatic regulator at the earliest time of HSC development, acting to limit the differentiation of some HSCs along the myeloid lineage.
BCR-ABL fusion transcript types and levels and their interaction with secondary genetic changes in determining the phenotype of Philadelphia chromosome–positive leukemias
Authors: Jones Dan , Luthra Rajyalakshmi , Cortes Jorge , Thomas Deborah , O'Brien Susan , Bueso-Ramos Carlos , Hai Seema , Ravandi Farhad , de Lima Marcos , Kantarjian Hagop , Jorgensen Jeffrey L. 
Published: September 2008

Abstract
It remains unresolved how different BCR-ABL transcripts differentially drive lymphoid and myeloid proliferation in Philadelphia chromosome–positive (Ph+) leukemias. We compared BCR-ABL transcript type and level with kinase domain (KD) mutation status, genotype, and phenotype in 1855 Ph+ leukemias. Compared with e1a2/p190 BCR-ABL cases, de novo e13-e14a2/p210 Ph+ lymphoid leukemia more frequently showed CML-type background, had higher blast-normalized BCR-ABL transcript levels, and more frequent persistent BCR-ABL transcript in the absence of detectable lymphoblasts. Secondary lymphoid blast transformation of CML was exclusively due to e13/e14a2/p210 BCR-ABL but was associated, at a much higher level than p210 myeloid transformation, with acquisition of new KD mutations and/or Ph genomic amplification. In contrast, myeloid blast transformation was more frequently accompanied by new acquisition of acute myeloid leukemia-type chromosomal aberrations, particularly involving the EVI1 and RUNX1 loci. Therefore, higher kinase activity by mutation, transcriptional up-regulation or gene amplification appears required for lymphoid transformation by p210 BCR-ABL.
Pharmacokinetics, pharmacodynamics, efficacy, and safety of a new recombinant asparaginase preparation in children with previously untreated acute lymphoblastic leukemia: a randomized phase 2 clinical trial
Authors: Pieters Rob , Appel Inge , Kuehnel Hans-Juergen , Tetzlaff-Fohr Iris , Pichlmeier Uwe , van der Vaart Inekee , Visser Eline , Stigter Rolinda 
Published: September 2008

Abstract
The pharmacokinetics, pharmacodynamics, efficacy, and safety of a new recom-binant Escherichia coli–asparaginase preparation was compared with Asparaginase medac. Thirty-two children with acute lymphoblastic leukemia were randomized to receive one of both agents at a dose of 5000 U/m2 every 3 days, for a total of 8 doses during induction treatment. The serum activity-time profile after the first dose of recombinant asparaginase was similar to that of Asparaginase medac. The trough serum activities were greater than the desired threshold of 100 U/L in both treatment groups. Asparagine was completely depleted in serum and in cerebrospinal fluid, whereas glutamine levels were only moderately influenced. No significant difference between the 2 treatments regarding the degree of asparagine depletion, duration of depletion, complete remission rate, and minimal residual disease status at the end of induction, overall frequency or intensity of adverse events was seen. Observed adverse reactions are known as possible and labeled side effects of asparaginase treatment and chemotherapy. We conclude that the new recombinant asparaginase and other native Asparaginase medac are bioequivalent and have the same pharmacodynamic effects and the same direct toxicity profile in children with acute lymphoblastic leukemia. This trial was registered at http://www.controlled-trials.com as no. ISRCTN 75734403.
The hazards of blood transfusion in historical perspective
Authors: Alter Harvey J. , Klein Harvey G. 
Published: September 2008

AbstractThe beginning of the modern era of blood transfusion coincided with World War II and the resultant need for massive blood replacement. Soon thereafter, the hazards of transfusion, particularly hepatitis and hemolytic transfusion reactions, became increasingly evident. The past half century has seen the near eradication of transfusion-associated hepatitis as well as the emergence of multiple new pathogens, most notably HIV. Specific donor screening assays and other interventions have minimized, but not eliminated, infectious disease transmission. Other transfusion hazards persist, including human error resulting in the inadvertent transfusion of incompatible blood, acute and delayed transfusion reactions, transfusion-related acute lung injury (TRALI), transfusion-associated graft-versus-host disease (TA-GVHD), and transfusion-induced immunomodulation. These infectious and noninfectious hazards are reviewed briefly in the context of their historical evolution.
How I treat rare venous thromboses
Authors: Martinelli Ida , Franchini Massimo , Mannucci Pier Mannuccio 
Published: September 2008

Abstract
Venous thromboembolism may involve venous sites other than the lower limbs, such as cerebral, splanchnic, and upper limb veins. Although uncommon, these thromboses may be clinically severe and challenging for caregivers. In this review, the main pathogenic, clinical, and therapeutic features of thromboses in rare venous sites are discussed. Even though there was a lot of recent progress in understanding the mechanistic role of inherited and acquired thrombophilia and of the interactions between different risk factors, the optimal management of these patients is still unsettled, being currently based on the consensus of experts due to the lack of randomized trials. The implementation of large interdisciplinary registries is a necessary weapon to optimize the treatment of rare venous diseases.
Homozygous deletion of HFE produces a phenotype similar to the HFE p.C282Y/p.C282Y genotype
Authors: Le Gac Gérald , Gourlaouen Isabelle , Ronsin Christophe , Géromel Vanna , Bourgarit Anne , Parquet Nathalie , Quemener Sylvia , Le Maréchal Cédric , Chen Jian-Min , Férec Claude 
Published: September 2008

Abstract
Hemochromatosis is predominantly associated with the HFE p.C282Y homozygous genotype, which is carried by approximately 1 person in 200 in Northern European populations. However, p.C282Y homozygosity is often characterized by incomplete penetrance. Here, we describe the case of a woman who had a major structural alteration in the HFE gene. Molecular characterization revealed an Alu-mediated recombination leading to the loss of the entire HFE gene sequence. Although homozygous for the HFE deleted allele, the woman had a phenotype similar to that seen in most women homozygous for the common p.C282Y mutation. Contrasting with previously reported results in Hfe knockout and Hfe knockin mice, our report gives further evidence that progression of the disease depends on modifying factors.
"TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis
Authors: Nikamanon Pornpat , Pun Elroy , Chou Wayne , Koter Marek D , Gershon Paul D 
Published: September 2008

Abstract

Background
Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to automate data processing and analysis from sample fractionating (LC-MALDI) mass-spectrometry-based HDX workflows are not publicly available.

Results
An integrated data pipeline (Solvent Explorer/TOF2H) has been developed for the processing of LC-MALDI-derived HDX data. Based on an experiment-wide template, and taking an ab initio approach to chromatographic and spectral peak finding, initial data processing is based on accurate mass-matching to fully deisotoped peaklists accommodating, in MS/MS-confirmed peptide library searches, ambiguous mass-hits to non-target proteins. Isotope-shift re-interrogation of library search results allows quick assessment of the extent of deuteration from peaklist data alone. During raw spectrum editing, each spectral segment is validated in real time, consistent with the manageable spectral numbers resulting from LC-MALDI experiments. A semi-automated spectral-segment editor includes a semi-automated or automated assessment of the quality of all spectral segments as they are pooled across an XIC peak for summing, centroid mass determination, building of rates plots on-the-fly, and automated back exchange correction. The resulting deuterium uptake rates plots from various experiments can be averaged, subtracted, re-scaled, error-barred, and/or scatter-plotted from individual spectral segment centroids, compared to solvent exposure and hydrogen bonding predictions and receive a color suggestion for 3D visualization. This software lends itself to a "divorced" HDX approach in which MS/MS-confirmed peptide libraries are built via nano or standard ESI without source modification, and HDX is performed via LC-MALDI using a standard MALDI-TOF. The complete TOF2H package includes additional (eg LC analysis) modules.

Conclusion
"TOF2H" provides a comprehensive HDX data analysis package that has accelerated the processing of LC-MALDI-based HDX data in the authors' lab from weeks to hours. It runs in a standard MS Windows (XP or Vista) environment, and can be downloaded http://tof2h.bio.uci.edu or obtained from the authors at no cost.