bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Ensemble-Based Four-Dimensional Variational Data Assimilation Scheme. Part II: Observing System Simulation Experiments with Advanced Research WRF (ARW)
Authors: Liu Chengsi , Xiao Qingnong , Wang Bin 
Published: November 2008

Abstract
An ensemble-based four-dimensional variational data assimilation (En4DVAR) algorithm and its performance in a low-dimension space with a one-dimensional shallow-water model have been presented in Part I. This algorithm adopts the standard incremental approach and preconditioning in the variational algorithm but avoids the need for a tangent linear model and its adjoint so that it can be easily incorporated into variational assimilation systems. The current study explores techniques for En4DVAR application in real-dimension data assimilation. The EOF decomposed correlation function operator and analysis time tuning are formulated to reduce the impact of sampling errors in En4DVAR upon its analysis. With the Advanced Research Weather Research and Forecasting (ARW-WRF) model, Observing System Simulation Experiments (OSSEs) are designed and their performance in real-dimension data assimilation is examined. It is found that the designed En4DVAR localization techniques can effectively alleviate the impacts of sampling errors upon analysis. Most forecast errors and biases in ARW are reduced by En4DVAR compared to those in a control experiment. En3DVAR cycling experiments are used to compare the ensemble-based sequential algorithm with the ensemble-based retrospective algorithm. These experiments indicate that the ensemble-based retrospective assimilation, En4DVAR, produces an overall better analysis than the ensemble-based sequential algorithm, En3DVAR, cycling approach.
The crystal chemistry of the gedrite-group amphiboles. II. Stereochemistry and chemical relations
Authors: Hawthorne F. C. , Schindler M. , Abdu Y. , Sokolova E. , Evans B. W. , Ishida K. 
Published: November 2008

AbstractThe general formula of the amphiboles of this series may be written as NaxMg2(Mg(5-y)Aly,)(Si(8-z)Alz)O22(OH)2, where Mg = Mg + Fe2+ + Mn2+ and Al = Al + Fe3+ + Ti. The individual <T–O> distances are linear functions of their [4]Al content, and the [4]Al content is strongly ordered in the following way: T1B > T1A » T2B » T2A. The <M1-O>, <M2-O> and <M3–O> distances are linear functions of the mean ionic radius of their constituent cations. End-member compositions may be written as follows: A☐Mg2Mg5Si8O22(OH)2O22(OH)2; A☐Mg2(Mg3Al2)(Si6Al2)O22(OH)2; ANaMg2Mg5(Si7Al) These compositions define a plane in xyz space across which the data of Schindler et al. (2008), measured on amphiboles from amphibolites, follow a tightly constrained trajectory. Anthophyllite–gedrite amphiboles equilibrated under significantly different P-T conditions (e.g. igneous rocks, contact-metamorphic rocks) follow trends that diverge from this trajectory, with greater Na and [4]Al contents and relatively smaller [6]Al contents. Detailed examination of the local bond topology involving the A and M2 sites indicates that the maximum degree of bond-valence compensation will occur for incorporation of ANa and M2Al in the ratio 4:10, and hence 2.5 ANa = M2Al in these amphiboles. This relation closely fits the data of Schindler et al. (2008), suggesting that the variation in chemical composition in anthophyllite–gedrite amphiboles is strongly constrained by the anion bond-valence requirements of the Pnma amphibole structure. We further suggest that different compositional trends for ortho-amphiboles equilibrated under different P-T conditions are the result of the valence-sum rule operating with (different) bond-lengths characteristic of these P-T conditions.
Initial therapy of acute graft-versus-host disease with low-dose prednisone does not compromise patient outcomes
Authors: Mielcarek Marco , Storer Barry E. , Boeckh Michael , Carpenter Paul A. , McDonald George B. , Deeg H. Joachim , Nash Richard A. , Flowers Mary E. D. , Doney Kristine , Lee Stephanie , Marr Kieren A. , Furlong Terry , Storb Rainer , Appelbaum Frederick R. , Martin Paul J. 
Published: November 2008

Abstract
We hypothesized that initial treatment of acute graft-versus-host disease (GVHD) with low-dose glucocorticoids (prednisone-equivalent dose of 1 mg/kg per day) instead of standard-dose glucocorticoids (prednisone-equivalent dose of 2 mg/kg per day) does not compromise major transplantation outcomes. We retrospectively analyzed outcomes among 733 patients who received transplants between 2000 and 2005 according to initial treatment with low-dose (n = 347) versus standard-dose (n = 386) systemic glucocorticoids. The mean cumulative prednisone-equivalent doses at day 100 after starting treatment were 44 and 87 mg/kg for patients given low-dose and standard-dose glucocorticoids, respectively. Adjusted outcomes between the groups given low-dose versus standard-dose glucocorticoids were not statistically significantly different: overall mortality (hazard ratio [HR], 1.10; 95% confidence interval [CI], 0.9-1.4), relapse (HR, 1.22; 95% CI, 0.9-1.7), nonrelapse mortality (HR, 1.06; 95% CI, 0.8-1.5). The small number of patients with grades III/IV acute GVHD at onset precluded definitive conclusions for this subgroup. In multivariate analysis, the risks of invasive fungal infections (HR, 0.59; 95% CI, 0.3-1.0) and the duration of hospitalization (odds ratio, 0.62; 95% CI, 0.4-0.9) were reduced in the low-dose prednisone group. We conclude that initial treatment with low-dose glucocorticoids for patients with grades I-II GVHD did not compromise disease control or mortality and was associated with decreased toxicity.
Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines
Authors: Ge Xiaomeng , Chen Weihua , Song Shuhui , Wang Weiwei , Hu Songnian , Yu Jun 
Published: November 2008

Abstract

Background
The mature embryo of rice (Oryza sativa, L.) is a synchronized and integrated tissue mass laying the foundation at molecular level for its growth, development, and differentiation toward a developing and ultimately a mature plant. We carried out an EST (expressed-sequence-tags)-based transcriptomic study, aiming at gaining molecular insights into embryonic development of a rice hybrid triad–an elite hybrid rice LYP9 and its parental lines (93-11 and PA64s)–and possible relatedness to heterosis.

Results
We generated 27,566 high-quality ESTs from cDNA libraries made from mature rice embryos. We classified these ESTs into 7,557 unigenes (2,511 contigs and 5,046 singletons) and 7,250 (95.9%) of them were annotated. We noticed that the high-abundance genes in mature rice embryos belong to two major functional categories, stress-tolerance and preparation-for-development, and we also identified 191 differentially-expressed genes (General Chi-squared test, P-value <= 0.05) between LYP9 and its parental lines, representing typical expression patterns including over-dominance, high- and low-parent dominance, additivity, and under-dominance. In LYP9, the majority of embryo-associated genes were found not only abundantly and specifically enriched but also significantly up-regulated.

Conclusion
Our results suggested that massively strengthening tissue-(or stage-) characteristic functions may contribute to heterosis rather than a few simple mechanistic explanations at the individual gene level. In addition, the large collection of rice embryonic ESTs provides significant amount of data for future comparative analyses on plant development, especially for the important crops of the grass family.
Cellular and molecular mechanisms of cigarette smoke-induced lung damage and prevention by vitamin C
Authors: Banerjee Shuvojit , Chattopadhyay Ranajoy , Ghosh Arunava , Koley Hemanta , Panda Koustubh , Roy Siddhartha , Chattopadhyay Dhrubajyoti , Chatterjee Indu B 
Published: November 2008

AbstractBackgroundCigarette smoke-induced cellular and molecular mechanisms of lung injury are not clear. Cigarette smoke is a complex mixture containing long-lived radicals, including p-benzosemiquinone that causes oxidative damage. Earlier we had reported that oxidative protein damage is an initial event in smoke-induced lung injury. Considering that p-benzosemiquinone may be a causative factor of lung injury, we have isolated p-benzosemiquinone and compared its pathophysiological effects with cigarette smoke. Since vitamin C is a strong antioxidant, we have also determined the modulatory effect of vitamin C for preventing the pathophysiological events.MethodsVitamin C-restricted guinea pigs were exposed to cigarette smoke (5 cigarettes/day; 2 puffs/cigarette) for 21 days with and without supplementation of 15 mg vitamin C/guinea pig/day. Oxidative damage, apoptosis and lung injury were assessedin vitro,ex vivoin A549 cells as well asin vivoin guinea pigs. Inflammation was measured by neutrophilia in BALF. p-Benzosemiquinone was isolated from freshly prepared aqueous extract of cigarette smoke and characterized by various physico-chemical methods, including mass, NMR and ESR spectroscopy. p-Benzosemiquinone-induced lung damage was examined by intratracheal instillation in guinea pigs. Lung damage was measured by increased air spaces, as evidenced by histology and morphometric analysis. Oxidative protein damage, MMPs, VEGF and VEGFR2 were measured by western blot analysis, and formation of Michael adducts using MALDI-TOF-MS. Apoptosis was evidenced by TUNEL assay, activation of caspase 3, degradation of PARP and increased Bax/Bcl-2 ratio using immunoblot analysis and confocal microscopy.ResultsExposure of guinea pigs to cigarette smoke resulted in progressive protein damage, inflammation, apoptosis and lung injury up to 21 days of the experimental period. Administration of 15 mg of vitamin C/guinea pig/day prevented all these pathophysiological effects. p-Benzosemiquinone mimicked cigarette smoke in causing protein modification and apoptosisin vitroand in A549 cellsex vivoas well as apoptosis and lung damagein vivo. All these pathophysiological events were also prevented by vitamin C.Conclusionp-Benzosemiquinone appears to be a major causative factor of cigarette smoke-induced oxidative protein damage that leads to apoptosis and lung injury. The pathophysiological events are prevented by a moderately large dose of vitamin C.
A rapid, non-invasive procedure for quantitative assessment of drought survival using chlorophyll fluorescence
Authors: Woo Nick S , Badger Murray R , Pogson Barry J 
Published: November 2008

Abstract

Background
Analysis of survival is commonly used as a means of comparing the performance of plant lines under drought. However, the assessment of plant water status during such studies typically involves detachment to estimate water shock, imprecise methods of estimation or invasive measurements such as osmotic adjustment that influence or annul further evaluation of a specimen's response to drought.

Results
This article presents a procedure for rapid, inexpensive and non-invasive assessment of the survival of soil-grown plants during drought treatment. The changes in major photosynthetic parameters during increasing water deficit were monitored via chlorophyll fluorescence imaging and the selection of the maximum efficiency of photosystem II (Fv/Fm) parameter as the most straightforward and practical means of monitoring survival is described. The veracity of this technique is validated through application to a variety of Arabidopsis thaliana ecotypes and mutant lines with altered tolerance to drought or reduced photosynthetic efficiencies.

Conclusion
The method presented here allows the acquisition of quantitative numerical estimates of Arabidopsis drought survival times that are amenable to statistical analysis. Furthermore, the required measurements can be obtained quickly and non-invasively using inexpensive equipment and with minimal expertise in chlorophyll fluorometry. This technique enables the rapid assessment and comparison of the relative viability of germplasm during drought, and may complement detailed physiological and water relations studies.
Characteristics of repair tissue in second-look and third-look biopsies from patients treated with engineered cartilage: relationship to symptomatology and time after implantation
Authors: Brun Paola , Dickinson Sally C , Zavan Barbara , Cortivo Roberta , Hollander Anthony P , Abatangelo Giovanni 
Published: November 2008

Abstract
Introduction
The present study established characteristics of tissue regrowth in patients suffering knee lesions treated with grafts of autologous chondrocytes grown on three-dimensional hyaluronic acid biomaterials.

Methods
This multicentred study involved a second-look arthroscopy/biopsy, 5 to 33 months post implant (n = 63). Seven patients allowed a third-look biopsy, three of which were performed 18 months post implant. Characteristics of tissues were histologically and histochemically evaluated. The remaining bone stubs were evaluated for cartilage/bone integration. For data analysis, biopsies were further divided into those obtained from postoperative symptomatic patients (n = 41) or from asymptomatic patients (n = 22).

Results
The percentage of hyaline regenerated tissues was significantly greater in biopsies obtained after, versus within, 18 months of implantation. Differences were also observed between symptomatic and asymptomatic patients: reparative tissues taken from symptomatic patients 18 months after grafting were mainly fibrocartilage or mixed (hyaline–fibrocartilage) tissue, while tissues taken from asymptomatic patients were hyaline cartilage in 83% of biopsies. In a small group of asymptomatic patients (n = 3), second-look and third-look biopsies taken 18 months after surgery confirmed maturation of the newly formed tissue over time. Cartilage maturation occurred from the inner regions of the graft, in contact with subchondral bone, towards the periphery of the implant.

Conclusions
The study indicates that, in asymptomatic patients after chondrocyte implantation, regenerated tissue undergoes a process of maturation that in the majority of cases takes longer than 18 months for completion and leads to hyaline tissue and not fibrous cartilage. Persistence of symptoms might reflect the presence of a nonhyaline cartilage repair tissue.
A systematic review on quality indicators for tight glycaemic control in critically ill patients: need for an unambiguous indicator reference subset
Authors: Eslami Saeid , de Keizer Nicolette F , de Jonge Evert , Schultz Marcus J , Abu-Hanna Ameen 
Published: November 2008

Abstract
Introduction
The objectives of this study were to systematically identify and summarize quality indicators of tight glycaemic control in critically ill patients, and to inspect the applicability of their definitions.

Methods
We searched in MEDLINE® for all studies evaluating a tight glycaemic control protocol and/or quality of glucose control that reported original data from a clinical trial or observational study on critically ill adult patients.

Results
Forty-nine studies met the inclusion criteria; 30 different indicators were extracted and categorized into four nonorthogonal categories: blood glucose zones (for example, 'hypoglycaemia'); blood glucose levels (for example, 'mean blood glucose level'); time intervals (for example, 'time to occurrence of an event'); and protocol characteristics (for example, 'blood glucose sampling frequency'). Hypoglycaemia-related indicators were used in 43 out of 49 studies, acting as a proxy for safety, but they employed many different definitions. Blood glucose level summaries were used in 41 out of 49 studies, reported as means and/or medians during the study period or at a certain time point (for example, the morning blood glucose level or blood glucose level upon starting insulin therapy). Time spent in the predefined blood glucose level range, time needed to reach the defined blood glucose level target, hyperglycaemia-related indicators and protocol-related indicators were other frequently used indicators. Most indicators differ in their definitions even when they are meant to measure the same underlying concept. More importantly, many definitions are not precise, prohibiting their applicability and hence the reproducibility and comparability of research results.

Conclusions
An unambiguous indicator reference subset is necessary. The result of this systematic review can be used as a starting point from which to develop a standard list of well defined indicators that are associated with clinical outcomes or that concur with clinicians' subjective views on the quality of the regulatory process.
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
Authors: Podar Mircea , Anderson Iain , Makarova Kira S , Elkins James G , Ivanova Natalia , Wall Mark A , Lykidis Athanasios , Mavromatis Kostantinos , Sun Hui , Hudson Matthew E , Chen Wenqiong , Deciu Cosmin , Hutchison Don , Eads Jonathan R , Anderson Abraham , Fernandes Fillipe , Szeto Ernest , Lapidus Alla , Kyrpides Nikos C , Saier Milton H , Richardson Paul M , Rachel Reinhard , Huber Harald , Eisen Jonathan A , Koonin Eugene V , Keller Martin , Stetter Karl O 
Published: November 2008

Abstract
Background
The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship.

Results
We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources.

Conclusions
A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.
Phase II Study of Carboplatin and Pemetrexed for the Treatment of Platinum-Sensitive Recurrent Ovarian Cancer
Authors: Matulonis Ursula A. , Horowitz Neil S. , Campos Susana M. , Lee Hang , Lee Julie , Krasner Carolyn N. , Berlin Suzanne , Roche Maria R. , Duska Linda R. , Pereira Lauren , Kendall Deborah , Penson Richard T. 
Published: November 2008

PurposeMore efficacious, less toxic combinations are needed to treat platinum-sensitive recurrent epithelial ovarian cancer (EOC). Pemetrexed is a multitargeted antifolate with manageable toxicity and has been combined with carboplatin to treat other cancers.Patients and MethodsThis is a phase II study of carboplatin area under the curve 5 with pemetrexed 500 mg/m2administered intravenously on day 1 every 21 days for six cycles or for up to eight cycles if clinical benefit occurred. Eligible patients had platinum-sensitive recurrent EOC, peritoneal serous cancer, or fallopian tube cancer. The primary objective was to determine response rate defined by Response Evaluation Criteria in Solid Tumors; other end points included toxicities, progression-free survival (PFS), and overall survival (OS).ResultsForty-five patients were accrued; 44 patients received treatment. Overall response rate was 51.1%; there were no complete responses (0%), 23 confirmed partial responses (51.1%), two unconfirmed partial responses (4.4%), 14 patients with stable disease (31.1%), and two patients with progressive disease after two cycles (4.4%). Grade 3 and 4 hematologic toxicities included neutropenia (41%), thrombocytopenia (23%), and anemia (9%); there were no episodes of febrile neutropenia. Grade 3 and 4 nonhematologic toxicities included fatigue (11%), nausea (5%), vomiting (5%), diarrhea (5%), syncope (5%), and pulmonary embolism (5%). Median PFS time was 7.57 months (95% CI, 6.44 to 10.18 months), mean OS time was 20.3 months, and median OS has not yet been reached with a mean follow-up time of 15.3 months.ConclusionCarboplatin/pemetrexed is a well-tolerated regimen with activity in platinum-sensitive recurrent EOC; further testing of this regimen in platinum-sensitive EOC patients is warranted.
Improved Survival in Lymphoma Patients Receiving Sirolimus for Graft-Versus-Host Disease Prophylaxis After Allogeneic Hematopoietic Stem-Cell Transplantation With Reduced-Intensity Conditioning
Authors: Armand Philippe , Gannamaneni Supriya , Kim Haesook T. , Cutler Corey S. , Ho Vincent T. , Koreth John , Alyea Edwin P. , LaCasce Ann S. , Jacobsen Eric D. , Fisher David C. , Brown Jennifer R. , Canellos George P. , Freedman Arnold S. , Soiffer Robert J. , Antin Joseph H. 
Published: November 2008

Purpose Inhibitors of the mammalian target of rapamycin (mTOR) kinase have shown clinical activity in several lymphoma subtypes. Sirolimus, an mTOR inhibitor, also has activity in the treatment and prophylaxis of graft-versus-host disease (GVHD) after allogeneic hematopoietic stem-cell transplantation (HSCT). We hypothesized that the use of sirolimus for GVHD prophylaxis in patients with lymphoma might lead to improved survival after transplantation through a decreased incidence of disease progression. Patients and Methods We retrospectively analyzed 190 patients who underwent transplantation for lymphoma. We compared the outcomes of patients who received sirolimus for GVHD prophylaxis with those of patients who received transplantation with a combination of a calcineurin inhibitor and methotrexate without sirolimus. Results Overall survival (OS) after transplantation was significantly superior in the sirolimus group, which was confirmed in multivariable analysis. The benefit was restricted to patients undergoing reduced-intensity conditioning (RIC) HSCT (3-year OS, 66% for sirolimus group v 38% for no-sirolimus group; P = .007; hazard ratio [HR] for mortality in multivariable analysis = 0.5, P = .042). Patients who received sirolimus had a similar incidence of nonrelapse mortality but a decreased incidence of disease progression compared with patients who did not receive sirolimus (3-year cumulative incidence of progression, 42% v 74%, respectively; P < .001; HR for progression in multivariable analysis = 0.4, P = .01). The effect of sirolimus persisted after adjusting for the occurrence of GVHD. No such survival advantage was apparent in a similar comparison of patients who underwent transplantation for diseases other than lymphoma. Conclusion This study suggests that sirolimus can independently decrease the risk of lymphoma progression after RIC HSCT, paving the way for prospective clinical trials.
Practical stability analysis for transient system dynamics
Authors: Meijaard J P , Popov A A 
Published: November 2008

The stability of multi-body systems in transient conditions, such as vehicles under braking, is considered. Stability in this case is not univocal, because according to the widely used classical definitions of Lyapunov and Malkin, nearly all motions taking place over a finite time are stable. Here, the use of the concept of practical stability is proposed, which is concerned with a limited growth of perturbations expected to be present in a real system. A viable calculation procedure for applying this concept to multi-body systems is proposed, in which the equations of motion and their linearizations are generated and analysed in a symbolic program, AutoSim. Applications are made to the acceleration of a non-linear Jeffcott rotor through its critical speed and the braking of a motorcycle. The rotor remains stable, provided that the acceleration is sufficiently large and the mass eccentricity sufficiently small. For the motorcycle, braking mainly enhances the wobble mode, whereas locking of the rear wheel may lead to a fall.