bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extreme Value Analysis of Tropical Cyclone Trapped-Fetch Waves
Authors: MacAfee Allan W. , Wong Samuel W. K. 
Published: November 2007

Abstract
Many of the extreme ocean wave events generated by tropical cyclones (TCs) can be explained by examining one component of the spectral wave field, the trapped-fetch wave (TFW). Using a Lagrangian TFW model, a parametric model representation of the local TC wind fields, and the National Hurricane Center’s hurricane database archive, a dataset of TFWs was created from all TCs in the Atlantic Ocean, Gulf of Mexico, and Caribbean Sea from 1851 to 2005. The wave height at each hourly position along a TFW trajectory was sorted into 2° × 2° latitude–longitude grid squares. Five grid squares (north of Hispaniola, Gulf of Mexico, Carolina coast, south of Nova Scotia, and south of Newfoundland) were used to determine if extreme value theory could be applied to the extremes in the TFW dataset. The statistical results justify accepting that a generalized Pareto distribution (GPD) model with a threshold of 6 m could be fitted to the data: the datasets were mostly modeled adequately, and much of the output information was useful. Additional tests were performed by sorting the TFW data into the marine areas in Atlantic Canada, which are of particular interest to the Meteorological Service of Canada because of the high ocean traffic, offshore drilling activities, and commercial fishery. GPD models were fitted, and return periods and the 95% confidence intervals (CIs) for 10-, 15-, and 20-m return levels were computed. The results further justified the use of the GPD model; hence, extension to the remaining grid squares was warranted. Of the 607 grid squares successfully modeled, the percentage of grid squares with finite lower (upper) values for the 10-, 15-, and 20-m return level CIs were 100 (80), 94 (53), and 90 (16), respectively. The lower success rate of 20-m TFW CIs was expected, given the rarity of 20-m TFWs: of the 5 713 625 hourly TFW points, only 13 958, or 0.24%, were 20 m or higher. Overall, the distribution of the successfully modeled grid squares in the data domain agreed with TFW theory and TC climatology. As a direct result of this study, the summary datasets and return level plots were integrated into application software for use by risk managers. A description of the applications illustrates their use in addressing various questions on extreme TFWs.
Evaluation and Comparison of Noah and Pleim–Xiu Land Surface Models in MM5 Using GÖTE2001 Data: Spatial and Temporal Variations in Near-Surface Air Temperature
Authors: Miao J-F. , Chen D. , Borne K. 
Published: November 2007

Abstract
In this study, the performance of two advanced land surface models (LSMs; Noah LSM and Pleim–Xiu LSM) coupled with the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5), version 3.7.2, in simulating the near-surface air temperature in the greater Göteborg area in Sweden is evaluated and compared using the GÖTE2001 field campaign data. Further, the effects of different planetary boundary layer schemes [Eta and Medium-Range Forecast (MRF) PBLs] for Noah LSM and soil moisture initialization approaches for Pleim–Xiu LSM are investigated. The investigation focuses on the evaluation and comparison of diurnal cycle intensity and maximum and minimum temperatures, as well as the urban heat island during the daytime and nighttime under the clear-sky and cloudy/rainy weather conditions for different experimental schemes. The results indicate that 1) there is an evident difference between Noah LSM and Pleim–Xiu LSM in simulating the near-surface air temperature, especially in the modeled urban heat island; 2) there is no evident difference in the model performance between the Eta PBL and MRF PBL coupled with the Noah LSM; and 3) soil moisture initialization is of crucial importance for model performance in the Pleim–Xiu LSM. In addition, owing to the recent release of MM5, version 3.7.3, some experiments done with version 3.7.2 were repeated to reveal the effects of the modifications in the Noah LSM and Pleim–Xiu LSM. The modification to longwave radiation parameterizations in Noah LSM significantly improves model performance while the adjustment of emissivity, one of the vegetation properties, affects Pleim–Xiu LSM performance to a larger extent. The study suggests that improvements both in Noah LSM physics and in Pleim–Xiu LSM initialization of soil moisture and parameterization of vegetation properties are important.
Changes in Shoulder and Elbow Passive Range of Motion after Pitching in Professional Baseball Players
Authors: Reinold Michael M. , Wilk Kevin E. , Macrina Leonard C. , Sheheane Chris , Dun Shouchen , Fleisig Glenn S. , Crenshaw Ken , Andrews James R. 
Published: November 2007

Background The overhead throwing athlete has unique range of motion characteristics of the shoulder and elbow. Numerous theories exist to explain these characteristics; however, the precise cause is not known. Although it is accepted that range of Motion is altered, the acute effect of baseball pitching on shoulder and elbow range of motion has not been established. Hypothesis There will be a reduction in passive range of motion immediately after baseball pitching. Study Design Controlled laboratory study. Methods Sixty-seven asymptomatic male professional baseball pitchers participated in the study. Passive range of motion Measurements were recorded using a customized bubble goniometer for shoulder external rotation, shoulder internal rotation, total shoulder rotational motion, elbow flexion, and elbow extension on the dominant and nondominant arms. Testing was performed on the first day of spring training. Measurements were taken before, immediately after, and 24 hours after pitching. Results A significant decrease in shoulder internal rotation (−9.5°), total motion (−10.7°), and elbow extension (−3.2°) occurred immediately after baseball pitching in the dominant shoulder ( P < .001). These changes continued to exist 24 hours after pitching. No differences were noted on the nondominant side. Conclusion Passive range of motion is significantly decreased immediately after baseball pitching. This decrease in range of motion continues to be present 24 hours after throwing. High levels of eccentric muscle activity have previously been observed in the shoulder external rotators and elbow flexors during pitching. These eccentric muscle contractions may contribute to acute musculotendinous adaptations and altered range of motion. The results of this study may suggest a newly defined mechanism to range of motion adaptations in the overhead throwing athlete resulting from acute musculoskeletal adaptations, in addition to Potential osseous and capsular adaptations.
On the dynamics of acute EBV infection and the pathogenesis of infectious mononucleosis
Authors: Hadinoto Vey , Shapiro Michael , Greenough Thomas C. , Sullivan John L. , Luzuriaga Katherine , Thorley-Lawson David A. 
Published: November 2007

AbstractMemory B cells latently infected with Epstein-Barr virus (mBLats) in the blood disappear rapidly on presentation with acute symptomatic primary infection (acute infectious mononucleosis [AIM]). They undergo a simple exponential decay (average half-life: 7.5 ± 3.7 days) similar to that of normal memory B cells. The cytotoxic T lymphocyte (CTL) response to immediate early (IE) lytic antigens (CTLIEs) also decays over this time period, but no such correlation was observed for the CTL response to lytic or latent antigens or to the levels of virions shed into saliva. We have estimated the average half-life of CTLIEs to be 73 (± 23) days. We propose that cycles of infection and reactivation occur in the initial stages of infection that produce high levels of mBLats in the circulation. Eventually the immune response arises and minimizes these cycles leaving the high levels of mBLats in the blood to decay through simple memory B-cell homeostasis mechanisms. This triggers the cells to reactivate the virus whereupon most are killed by CTLIEs before they can release virus and infect new cells. The release of antigens caused by this large-scale destruction of infected cells may trigger the symptoms of AIM and be a cofactor in other AIM-associated diseases.
A common pathway mediated through Toll-like receptors leads to T- and natural killer–cell immunosuppression
Authors: Vaknin Ilan , Blinder Liora , Wang Lynn , Gazit Roi , Shapira Elena , Genina Olga , Pines Mark , Pikarsky Eli , Baniyash Michal 
Published: November 2007

AbstractT- and natural killer (NK)–cell immunosuppression associated with ζ-chain down-regulation has been described in cancer, autoimmune, and infectious diseases. However, the precise stimuli leading to this bystander phenomenon in such different pathogen-dependent and sterile pathologies remained unresolved. Here, we demonstrate that Toll-like receptors (TLRs) play a major role in the induction of innate and adaptive immune system suppression; repetitive administration of single TLR 2, 3, 4, or 9 agonists, which do not exhibit any virulent or immune invasive properties, was sufficient to induce a bystander NK- and T-cell immunosuppression associated with ζ-chain down-regulation mediated by myeloid suppressor cells, as observed in the course of active pathologies. We identified a 35-amino acid (aa) region within the ζ-chain as being responsible for its degradation under TLR-mediated chronic inflammation. Furthermore, we provide evidence that ζ-chain levels could serve as a biomarker for chronic inflammation-dependent immunosuppression. Thus, although acute TLR-mediated activation could be beneficial in clearing pathogens or may serve as an immune adjuvant, such activation could be detrimental under sustained conditions.
The attitudes of brain cancer patients and their caregivers towards death and dying: a qualitative study
Authors: Lipsman Nir , Skanda Abby , Kimmelman Jonathan , Bernstein Mark 
Published: November 2007

Abstract

Background
Much money and energy has been spent on the study of the molecular biology of malignant brain tumours. However, little attention has been paid to the wishes of patients afflicted with these incurable tumours, and how this might influence treatment considerations.

Methods
We interviewed 29 individuals – 7 patients dying of a malignant brain tumor and 22 loved ones. One-on-one interviews were conducted according to a pre-designed interview guide. A combination of open-ended questions, as well as clinical scenarios was presented to participants in order to understand what is meaningful and valuable to them when determining treatment options and management approaches. The results were analyzed, coded, and interpreted using qualitative analytic techniques in order to arrive at several common overarching themes.

Results
Seven major themes were identified. In general, respondents were united in viewing brain cancer as unique amongst malignancies, due in large part to the premium placed on mental competence and cognitive functioning. Importantly, participants found their experiences, however difficult, led to the discovery of inner strength and resilience. Responses were usually framed within an interpersonal context, and participants were generally grateful for the opportunity to speak about their experiences. Attitudes towards religion, spirituality, and euthanasia were also probed.

Conclusion
Several important themes underlie the experiences of brain cancer patients and their caregivers. It is important to consider these when managing these patients and to respect not only their autonomy but also the complex interpersonal toll that a malignant diagnosis can have.
Estimation of progression of multi-state chronic disease using the Markov model and prevalence pool concept
Authors: Shih Hui-Chuan , Chou Pesus , Liu Chi-Ming , Tung Tao-Hsin 
Published: November 2007

AbstractBackgroundWe propose a simple new method for estimating progression of a chronic disease with multi-state properties by unifying the prevalence pool concept with the Markov process model.MethodsEstimation of progression rates in the multi-state model is performed using the E-M algorithm. This approach is applied to data on Type 2 diabetes screening.ResultsGood convergence of estimations is demonstrated. In contrast to previous Markov models, the major advantage of our proposed method is that integrating the prevalence pool equation (that the numbers entering the prevalence pool is equal to the number leaving it) into the likelihood function not only simplifies the likelihood function but makes estimation of parameters stable.ConclusionThis approach may be useful in quantifying the progression of a variety of chronic diseases.
The herpes simplex virus UL20 protein functions in glycoprotein K (gK) intracellular transport and virus-induced cell fusion are independent of UL20 functions in cytoplasmic virion envelopment
Authors: Melancon Jeffrey M , Fulmer Preston A , Kousoulas Konstantin G 
Published: November 2007

Abstract
The HSV-1 UL20 protein (UL20p) and glycoprotein K (gK) are both important determinants of cytoplasmic virion morphogenesis and virus-induced cell fusion. In this manuscript, we examined the effect of UL20 mutations on the coordinate transport and Trans Golgi Network (TGN) localization of UL20p and gK, virus-induced cell fusion and infectious virus production. Deletion of 18 amino acids from the UL20p carboxyl terminus (UL20 mutant 204t) inhibited intracellular transport and cell-surface expression of both gK and UL20, resulting in accumulation of UL20p and gK in the endoplasmic reticulum (ER) in agreement with the inability of 204t to complement UL20-null virus replication and virus-induced cell fusion. In contrast, less severe carboxyl terminal deletions of either 11 or six amino acids (UL20 mutants 211t and 216t, respectively) allowed efficient UL20p and gK intracellular transport, cell-surface expression and TGN colocalization. However, while both 211t and 216t failed to complement for infectious virus production, 216t complemented for virus-induced cell fusion, but 211t did not. These results indicated that the carboxyl terminal six amino acids of UL20p were crucial for infectious virus production, but not involved in intracellular localization of UL20p/gK and concomitant virus-induced cell fusion. In the amino terminus of UL20, UL20p mutants were produced changing one or both of the Y38 and Y49 residues found within putative phosphorylation sites. UL20p tyrosine-modified mutants with both tyrosine residues changed enabled efficient intracellular transport and TGN localization of UL20p and gK, but failed to complement for either infectious virus production, or virus-induced cell fusion. These results show that UL20p functions in cytoplasmic envelopment are separable from UL20 functions in UL20p intracellular transport, cell surface expression and virus-induced cell fusion.
Platelet-derived exosomes from septic shock patients induce myocardial dysfunction
Authors: Azevedo Luciano Cesar Pontes , Janiszewski Mariano , Pontieri Vera , Pedro Marcelo de Almeida , Bassi Estevão , Tucci Paulo José Ferreira , Laurindo Francisco Rafael Martins 
Published: November 2007

Abstract
Introduction
Mechanisms underlying inotropic failure in septic shock are incompletely understood. We previously identified the presence of exosomes in the plasma of septic shock patients. These exosomes are released mainly by platelets, produce superoxide, and induce apoptosis in vascular cells by a redox-dependent pathway. We hypothesized that circulating platelet-derived exosomes could contribute to inotropic dysfunction of sepsis.

Methods
We collected blood samples from 55 patients with septic shock and 12 healthy volunteers for exosome separation. Exosomes from septic patients and healthy individuals were investigated concerning their myocardial depressant effect in isolated heart and papillary muscle preparations.

Results
Exosomes from the plasma of septic patients significantly decreased positive and negative derivatives of left ventricular pressure in isolated rabbit hearts or developed tension and its first positive derivative in papillary muscles. Exosomes from healthy individuals decreased these variables non-significantly. In hearts from rabbits previously exposed to endotoxin, septic exosomes decreased positive and negative derivatives of ventricular pressure. This negative inotropic effect was fully reversible upon withdrawal of exosomes. Nitric oxide (NO) production from exosomes derived from septic shock patients was demonstrated by fluorescence. Also, there was an increase in myocardial nitrate content after exposure to septic exosomes.

Conclusion
Circulating platelet-derived exosomes from septic patients induced myocardial dysfunction in isolated heart and papillary muscle preparations, a phenomenon enhanced by previous in vivo exposure to lipopolysaccharide. The generation of NO by septic exosomes and the increased myocardial nitrate content after incubation with exosomes from septic patients suggest an NO-dependent mechanism that may contribute to myocardial dysfunction of sepsis.
The global landscape of sequence diversity
Authors: Peregrín-Álvarez José Manuel , Parkinson John 
Published: November 2007

Abstract
Background
Systematic comparisons between genomic sequence datasets have revealed a wide spectrum of sequence specificity from sequences that are highly conserved to those that are specific to individual species. Due to the limited number of fully sequenced eukaryotic genomes, analyses of this spectrum have largely focused on prokaryotes. Combining existing genomic datasets with the partial genomes of 193 eukaryotes derived from collections of expressed sequence tags, we performed a quantitative analysis of the sequence specificity spectrum to provide a global view of the origins and extent of sequence diversity across the three domains of life.

Results
Comparisons with prokaryotic datasets reveal a greater genetic diversity within eukaryotes that may be related to differences in modes of genetic inheritance. Mapping this diversity within a phylogenetic framework revealed that the majority of sequences are either highly conserved or specific to the species or taxon from which they derive. Between these two extremes, several evolutionary landmarks consisting of large numbers of sequences conserved within specific taxonomic groups were identified. For example, 8% of sequences derived from metazoan species are specific and conserved within the metazoan lineage. Many of these sequences likely mediate metazoan specific functions, such as cell-cell communication and differentiation.

Conclusion
Through the use of partial genome datasets, this study provides a unique perspective of sequence conservation across the three domains of life. The provision of taxon restricted sequences should prove valuable for future computational and biochemical analyses aimed at understanding evolutionary and functional relationships.
Eosinophils induce DC maturation, regulating immunity
Authors: Lotfi Ramin , Lotze Michael Thomas 
Published: November 2007

AbstractThere are increased eosinophils in tumors, and they are generally associated with a good prognosis, whereas their presence in rejecting allografts is largely seen as a harbinger of poor outcome. The biologic role of eosinophils in their pathogenesis is more poorly understood than in allergy and asthma. Myeloid conventional dendritic cells (DCs) and conversely, plasmacytoid DCs are similarly associated with a good prognosis in cancer patients. We hypothesize that eosinophils, similar to NK cells, could mature DCs, and that could be responsible for regulating immunity in the setting of necrosis-associated chronic inflammation as occurs in cancer and transplant rejection. We have demonstrated that CpG DNA promotes eosinophil-induced DC maturation. As such, a greater linkage than had previously been considered between innate immune cells such as eosinophils and the adaptive immune response can be considered. Granulocytes were isolated from normal human whole blood by density gradient centrifugation followed by ammonium chloride-potassium lysis of the remaining red cells. Eosinophils were negatively separated using magnetic beads. Immature DCs were generated from CD-14 positively separated monocytes, which were cultured for 6 days with GM-CSF and IL-4. CpG ODN 2395 (CpG-C) as a pathogen-associated molecular pattern surrogate was used to induce eosinophil-based DC maturation. Transwells were used to assess cell–cell interaction between eosinophils and DCs. Eosinophil survival was assessed by flow cytometry; cells, which did not stain with Sytox-Orange, were considered viable. In the presence of CpG-C, eosinophils induced DC maturation. Similar results were obtained when eosinophils were pretreated with CpG for 4 h, washed, and cocultured afterwards with DCs. Eosinophil-induced maturation of DCs directly correlated with the eosinophil:DC ratio. Transwell studies showed that the direct cell–cell interaction between eosinophils and DCs enhances maturation. CpGs did not adversely affect eosinophil survival; thus, we could exclude the possibility that DC maturation was caused by sensing eosinophil cell death. While eosinophil-derived neurotoxin did not contribute to the described effect, DCs took up and internalized major basic protein (MBP), which was released from CpG-stimulated eosinophils, revealed by confocal imaging and flow cytometry. Thus, the DC maturational-inducing effect of eosinophils may be a result of released MBP from eosinophils. CpG-activated eosinophils mature conventional DCs. The role of viral or bacterial products or potentially, host-derived DNA as eosinophil activators with consequent DC maturation should be considered in more detail in the inflammatory settings in which eosinophils have been observed.
Commercial peptidoglycan preparations are contaminated with superantigen-like activity that stimulates IL-17 production
Authors: Li Hanfen , Nooh Mohammed M , Kotb Malak , Re Fabio 
Published: November 2007

AbstractThe immunomodulatory properties of peptidoglycan (PGN), a constituent of the bacterial cell wall, have been studied extensively but with contrasting results. Recent studies have demonstrated that the TLR2-mediated inflammatory responses elicited by Gram-positive PGN preparations are in fact a result of contaminating lipoproteins and lipoteichoic acid that can be removed only through sophisticated extraction procedures. Here, we report that commercial preparations of Staphylococcus aureus or Streptococcus pyogenes PGN are contaminated with bacterial superantigens (SAg). The T cell-derived cytokines IL-17A and IL-17F were induced by PGN preparations but not by TLR agonists or nucleotide-binding and oligomerization domain-like receptor agonists in human PBMC. IL-17 induction by PGN preparations was sensitive to protease digestion and required TCR signaling. Bacterial SAg could be detected by immunoblot in the PGN preparations, and purified recombinant SAg were powerful inducers of IL-17. Finally, the PGN preparations stimulated proliferation and expansion of T cells bearing specific TCR Vβ elements. Our results suggest that a large body of literature that relied on commercial PGN preparations to study inflammatory diseases, such as arthritis, where IL-17 also plays an important role, should be interpreted with caution and possibly revisited. Future studies aimed at characterizing the activities of PGN should use PGN preparations of proven purity.