bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pertussis toxin–sensitive G proteins regulate lymphoid lineage specification in multipotent hematopoietic progenitors
Authors: Lai Anne Y. , Watanabe Akiko , O'Brien Tommy , Kondo Motonari 
Published: April 2009

AbstractLymphoid and myeloid lineage segregation is a major developmental step during early hematopoiesis from hematopoietic stem cells. It is not clear, however, whether multipotent progenitors (MPPs) adopt a lymphoid or myeloid fate through stochastic mechanisms, or whether this process can be regulated by extracellular stimuli. In this study, we show that lymphoid lineage specification occurs in MPPs before lymphoid lineage priming, during which MPPs migrate from the proximal to the distal region relative to the endosteum of the bone marrow. Lymphoid-specified MPPs have low myeloid differentiation potential in vivo, but potently differentiate into myeloid cells in vitro. When treated with pertussis toxin, an inhibitor of G protein–coupled receptor signaling, lymphoid-specified MPPs regain in vivo myeloid potential, and their localization is dispersed in the bone marrow. These results clearly demonstrate that specific microenvironments that favorably support lymphoid or myeloid lineage development exist at structurally distinct regions in the bone marrow.
Lymphoid tissue–specific homing of bone marrow–derived dendritic cells
Authors: Creusot Rémi J. , Yaghoubi Shahriar S. , Chang Pearl , Chia Justine , Contag Christopher H. , Gambhir Sanjiv S. , Fathman C. Garrison 
Published: April 2009

Abstract
Because of their potent immunoregulatory capacity, dendritic cells (DCs) have been exploited as therapeutic tools to boost immune responses against tumors or pathogens, or dampen autoimmune or allergic responses. Murine bone marrow–derived DCs (BM-DCs) are the closest known equivalent of the blood monocyte-derived DCs that have been used for human therapy. Current imaging methods have proven unable to properly address the migration of injected DCs to small and deep tissues in mice and humans. This study presents the first extensive analysis of BM-DC homing to lymph nodes (and other selected tissues) after intravenous and intraperitoneal inoculation. After intravenous delivery, DCs accumulated in the spleen, and preferentially in the pancreatic and lung-draining lymph nodes. In contrast, DCs injected intraperitoneally were found predominantly in peritoneal lymph nodes (pancreatic in particular), and in omentum-associated lymphoid tissue. This uneven distribution of BM-DCs, independent of the mouse strain and also observed within pancreatic lymph nodes, resulted in the uneven induction of immune response in different lymphoid tissues. These data have important implications for the design of systemic cellular therapy with DCs, and in particular underlie a previously unsuspected potential for specific treatment of diseases such as autoimmune diabetes and pancreatic cancer.
Systemic mastocytosis in 342 consecutive adults: survival studies and prognostic factors
Authors: Lim Ken-Hong , Tefferi Ayalew , Lasho Terra L. , Finke Christy , Patnaik Mrinal , Butterfield Joseph H. , McClure Rebecca F. , Li Chin-Yang , Pardanani Animesh 
Published: April 2009

AbstractClinical phenotype in systemic mastocytosis (SM) is markedly variable, which complicates prognostication and decision making regarding the choice and timing of therapy. In a retrospective study of 342 consecutive adult patients with SM seen at the Mayo Clinic between 1976 and 2007, disease subdesignation according to the World Health Organization (WHO) proposal was indolent (ISM) in 159 (46%), with associated clonal hematologic non–mast cell lineage disease (SM-AHNMD) in 138 (40%), aggressive (ASM) in 41 (12%), and mast cell leukemia in 4 (1%). KITD816V was detected in bone marrow–derived DNA by allele-specific polymerase chain reaction (PCR) in 68% of 165 patients evaluated (ISM, 78%; ASM, 82%; SM-AHNMD, 60%; P = .03); JAK2V617F was detected in 4%, all in SM-AHNMD. Compared with those with nonindolent SM, life expectancy in ISM was superior and not significantly different from that of the age- and sex-matched US population. In addition, multivariable analysis identified advanced age, weight loss, anemia, thrombocytopenia, hypoalbuminemia, and excess bone marrow blasts as independent adverse prognostic factors for survival. The current study validates the prognostic relevance of the WHO subclassification of SM and provides additional information of value in terms of both risk stratification and interpretation of clinical presentation and laboratory results.
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning
Authors: Arakaki Adrian K , Huang Ying , Skolnick Jeffrey 
Published: April 2009

AbstractBackgroundWe previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment.ResultsWe have developed two new EFICAz components, analogs to the two FDR-based components, where the discrimination between homo and heterofunctional members is based on the evaluation, via Support Vector Machine models, of all the aligned positions between the query sequence and the multiple sequence alignments associated to the enzyme families. Benchmark results indicate that: i) the new SVM-based components outperform their FDR-based counterparts, and ii) both SVM-based and FDR-based components generate unique predictions. We developed classification tree models to optimally combine the results from the six EFICAz components into a final EC number prediction. The new implementation of our approach, EFICAz2, exhibits a highly improved prediction precision at MTTSI < 30% compared to the original EFICAz, with only a slight decrease in prediction recall. A comparative analysis of enzyme function annotation of the human proteome by EFICAz2and KEGG shows that: i) when both sources make EC number assignments for the same protein sequence, the assignments tend to be consistent and ii) EFICAz2generates considerably more unique assignments than KEGG.ConclusionPerformance benchmarks and the comparison with KEGG demonstrate that EFICAz2is a powerful and precise tool for enzyme function annotation, with multiple applications in genome analysis and metabolic pathway reconstruction. The EFICAz2web service is available at:http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.html
Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14
Authors: Ding Feng , Tang Petrus , Hsu Mei-Hua , Cui Peng , Hu Songnian , Yu Jun , Chiu Cheng-Hsun 
Published: April 2009

Abstract

Background

Streptococcus pneumoniae serotype 14 is one of the most common pneumococcal serotypes that cause invasive pneumococcal diseases worldwide. Serotype 14 often expresses resistance to a variety of antimicrobial agents, resulting in difficulties in treatment. To gain insight into the evolution of virulence and antimicrobial resistance traits in S. pneumoniae from the genome level, we sequenced the entire genome of a serotype 14 isolate (CGSP14), and carried out comprehensive comparison with other pneumococcal genomes. Multiple serotype 14 clinical isolates were also genotyped by multilocus sequence typing (MLST).

Results
Comparative genomic analysis revealed that the CGSP14 acquired a number of new genes by horizontal gene transfer (HGT), most of which were associated with virulence and antimicrobial resistance and clustered in mobile genetic elements. The most remarkable feature is the acquisition of two conjugative transposons and one resistance island encoding eight resistance genes. Results of MLST suggested that the major driving force for the genome evolution is the environmental drug pressure.

Conclusion
The genome sequence of S. pneumoniae serotype 14 shows a bacterium with rapid adaptations to its lifecycle in human community. These include a versatile genome content, with a wide range of mobile elements, and chromosomal rearrangement; the latter re-balanced the genome after events of HGT.
Immunogenicity and safety of concomitant administration of a measles, mumps and rubella vaccine (M-M-RvaxPro®) and a varicella vaccine (VARIVAX®) by intramuscular or subcutaneous routes at separate injection sites: a randomised clinical trial
Authors: Gillet Yves , Habermehl Pirmin , Thomas Stéphane , Eymin Cécile , Fiquet Anne 
Published: April 2009

AbstractBackgroundWhen this trial was initiated, the combined measles, mumps and rubella (MMR) vaccine was licensed for subcutaneous administration in all European countries and for intramuscular administration in some countries, whereas varicella vaccine was licensed only for subcutaneous administration. This study evaluated the intramuscular administration of an MMR vaccine (M-M-RvaxPro®) and a varicella vaccine (VARIVAX®) compared with the subcutaneous route.MethodsAn open-label randomised trial was performed in France and Germany. Healthy children, aged 12 to18 months, received single injections of M-M-RvaxPro and VARIVAX concomitantly at separate injection sites. Both vaccines were administered either intramuscularly (IM group,n= 374) or subcutaneously (SC group,n= 378). Immunogenicity was assessed before vaccination and 42 days after vaccination. Injection-site erythema, swelling and pain were recorded from days 0 to 4 after vaccination. Body temperature was monitored daily between 0 and 42 days after vaccination. Other adverse events were recorded up to 42 days after vaccination and serious adverse events until the second study visit.ResultsAntibody response rates at day 42 in the per-protocol set of children initially seronegative to measles, mumps, rubella or varicella were similar between the IM and SC groups for all four antigens. Response rates were 94 to 96% for measles, 98% for both mumps and rubella and 86 to 88% for varicella. For children initially seronegative to varicella, 99% achieved the seroconversion threshold (antibody concentrations of ≥ 1.25 gpELISA units/ml). Erythema and swelling were the most frequently reported injection-site reactions for both vaccines. Most injection-site reactions were of mild intensity or small size (≤ 2.5 cm). There was a trend for lower rates of injection-site erythema and swelling in the IM group. The incidence and nature of systemic adverse events were comparable for the two routes of administration, except varicella-like rashes, which were less frequent in the IM group.ConclusionThe immunogenicities of M-M-RvaxPro and VARIVAX administered by the intramuscular route were comparable with those following subcutaneous administration, and the tolerability of the two vaccines was comparable regardless of administration route. Integration of both administration routes in the current European indications for the two vaccines will now allow physicians in Europe to choose their preferred administration route in routine clinical practice.Trial registrationClinicalTrials.gov NCT00432523
A pilot study of a new test to predict extubation failure
Authors: Solsona José F , Díaz Yolanda , Vázquez Antonia , Pilar Gracia Maria , Zapatero Ana , Marrugat Jaume 
Published: April 2009

Abstract
Introduction
To determine whether subjecting patients to 100 ml of additional dead space after a 120-minute weaning trial could predict readiness for extubation.

Methods
This was a prospective, non-randomised pilot study in an intensive care unit at a university hospital with 14 beds. It included all non-tracheostomised patients with improvement of the underlying cause of acute respiratory failure, and those with no need for vasoactive or sedative drugs were eligible. Patients fulfilling the Consensus Conference on Weaning extubation criteria after 120 minutes spontaneous breathing (n = 152) were included. To the endotracheal tube, 100 cc dead space was added for 30 minutes. Patients tolerating the test were extubated; those not tolerating it received six hours of supplementary ventilation before extubation. The measurements taken and main results were: arterial pressure, heart rate, respiratory rate, oxygen saturation, end-tidal carbon dioxide and signs of respiratory insufficiency were recorded every five minutes; and arterial blood gases were measured at the beginning and end of the test. Extubation failure was defined as the need for mechanical and non-invasive ventilation within 48 hours of extubation.

Results
Twenty-two patients (14.5%) experienced extubation failure. Only intercostal retraction was independently associated with extubation failure. The sensitivity (40.9%) and specificity (97.7%) yield a probability of extubation failure of 75.1% for patients not tolerating the test versus 9.3% for those tolerating it.

Conclusions
Observing intercostal retraction after adding dead space may help detect susceptibility to extubation failure. The ideal amount of dead space remains to be determined.

Trial registration
Current Controlled Trials ISRCTN76206152.
Multicenter Phase II Trial of Neoadjuvant Pemetrexed Plus Cisplatin Followed by Extrapleural Pneumonectomy and Radiation for Malignant Pleural Mesothelioma
Authors: Krug Lee M. , Pass Harvey I. , Rusch Valerie W. , Kindler Hedy L. , Sugarbaker David J. , Rosenzweig Kenneth E. , Flores Raja , Friedberg Joseph S. , Pisters Katherine , Monberg Matthew , Obasaju Coleman K. , Vogelzang Nicholas J. 
Published: April 2009

Purpose Neoadjuvant pemetrexed plus cisplatin was administered, followed by extrapleural pneumonectomy (EPP) and hemithoracic radiation (RT), to assess the feasibility and efficacy of trimodality therapy in stage I to III malignant pleural mesothelioma. Patients and Methods Requirements included stage T1-3 N0-2 disease, no prior surgical resection, adequate organ function (including predicted postoperative forced expiratory volume in 1 second ≥ 35%), and performance status 0 to 1. Patients received pemetrexed 500 mg/m2 plus cisplatin 75 mg/m2 for four cycles. Patients without disease progression underwent EPP followed by RT (54 Gy). The primary end point was pathologic complete response (pCR) rate. Results Seventy-seven patients received chemotherapy. All four cycles were administered to 83% of patients. The radiologic response rate was 32.5% (95% CI, 22.2 to 44.1). Fifty-seven patients proceeded to EPP, which was completed in 54 patients. Three pCRs were observed (5% of EPP). Forty of 44 patients completed irradiation. Median survival in the overall population was 16.8 months (95% CI, 13.6 to 23.2 months; censorship, 33.8%). Patients completing all therapy had a median survival of 29.1 months and a 2-year survival rate of 61.2%. Radiologic response of complete or partial response was associated with a median survival of 26.0 months compared with 13.9 months for patients with stable disease or progressive disease (P = .05). Conclusion This multicenter trial showed that trimodality therapy with neoadjuvant pemetrexed plus cisplatin is feasible with a reasonable long-term survival rate, particularly for patients who completed all therapy. Radiologic response to chemotherapy, but not sex, histology, disease stage, or nodal status, was associated with improved survival.
Intrinsic mechanical properties of the perfused armoured catfish heart with special reference to the effects of hypercapnic acidosis on maximum cardiac performance
Authors: Hanson Linda M. , Baker Daniel W. , Kuchel Louise J. , Farrell Anthony P. , Val Adalberto L. , Brauner Colin J. 
Published: April 2009

SUMMARYThe armoured catfish, Pterygoplichthys pardalis, is known to be extremely tolerant of environmental hypercarbia (elevated water CO2tensions), which occurs in their natural environment. In addition, previous studies have demonstrated that during exposure to hypercarbia, P. pardalis does not exhibit extracellular pH compensation and thus the heart and other organs must continue to function despite a severe extracellular acidosis. We used an in situ perfused heart preparation to determine the effects of an extracellular hypercapnic (elevated CO2 in the animal) acidosis (1–7.5% CO2) on heart function, specifically cardiac output, power output, heart rate and stroke volume. The present study is the first to comprehensively examine cardiac function in an acidosis-tolerant teleost. When compared with control conditions, maximum cardiac performance was unaffected at levels of CO2 as high as 5%, far exceeding the hypercapnic tolerance of other teleosts. Moreover, P. pardalis exhibited only a moderate decrease(∼35%) in cardiac performance when exposed to 7.5% CO2, and full cardiac performance was restored in six out of seven hearts upon return to control conditions. Myocardial intracellular pH (pHi) was protected in situ, as has been found in vivo, and this protection extended to the highest level of CO2 (7.5%)investigated. Thus, maintained heart function during a hypercapnic acidosis in P. pardalis is probably associated with preferential pHiregulation of the heart, but ultimately is not sufficient to prevent loss of cardiac function. Our findings suggest the need for further study to elucidate the mechanisms behind this remarkable cardiac hypercapnic tolerance.
Mixed-mode homogeneous charge compression ignition—direct injection combustion on common rail diesel engines: An experimental characterization
Authors: Chiara F , Canova M 
Published: April 2009

In recent years, increasing attention has been given to the study of homogeneous charge compression ignition (HCCI) for automotive diesel engines, due to its potential to lower NO x and particulate matter (PM) emissions. However, controlling the combustion process and engineering a mixture preparation method that does not require significant modifications to the engine hardware are still significant barriers to a vehicle implementation. In this scenario, external mixture formation, performed through a diesel fuel atomizer, is a simple and reliable method to obtain a truly homogeneous charge, resulting in ultra-low NO x and negligible PM formation. This technology does not require any modification to the engine compression ratio or to the fuel direct injection (DI) system. The possibility of combining two separate fuelling systems allows for mixed-mode HCCI—DI combustion, where a diesel-type combustion is induced during HCCI operations, increasing the IMEP and the output engine torque. This would allow for a seamless transition from HCCI to conventional DI mode at high load, while retaining the HCCI combustion benefits on emissions at part-load engine operating conditions. Building on preliminary experimental results proving the feasibility and benefits of the HCCI combustion with external mixture preparation on a high-speed common rail diesel engine, the proposed work aims at extending the HCCI combustion characterization, in order to define an engine operating region for its application. Then, mixed-mode HCCI—DI operations were investigated as a strategy to overcome the IMEP limitations of pure HCCI combustion. The analysis of HCCI—DI combustion aims at studying the effect of important control parameters, such as EGR ratio and direct injection timing, on combustion and emissions, showing the effects of partial HCCI combustion at higher engine loads.
Book Reviews
Authors: Lev Benjamin 
Published: April 2009

In Book Reviews, we review an extensive and diverse range of books. They cover theory and applications in operations research, statistics, management science, econometrics, mathematics, computers, and information systems. In addition, we include books in other fields that emphasize technical applications. However, we do not review software. To submit a book for review, please send it to me at the above address. Although we cannot review all books because of space limitations, we do list all books that we receive. We commission all book reviews and do not accept unsolicited reviews. To become a reviewer, please send me your name, address, and specific areas of expertise. We encourage readers to suggest books for review or to ask publishers to send copies of such books. The authors or editors of books we review in this issue are Xi-Ren Cao, Joanna Józefowska, Konstantin Kogan, Charles S. Tapiero, and Jonathan Koomey.
Rejoinder—Robust Prediction and Unrealistic Assumptions
Authors: Tsang Eric W. K. 
Published: April 2009

In the response to my commentary on his 2007 editorial entitled “It's the Findings, Stupid, Not the Assumptions,” Steven Shugan raises a number of thought-provoking ideas. In this rejoinder, I focus on three issues that Shugan and I hold the most divergent views. First, while Shugan uses the terms “realistic” and “realism” in several different meanings, I define the realism of an assumption as the extent to which it corresponds with the real world. Second, Shugan makes a strong claim that predictions can be objectively evaluated whereas assumptions cannot. I refute his claim by arguing that testing predictions and testing assumptions follow the same research process of checking whether the proposition concerned corresponds with reality. Third, Shugan maintains that given predictive accuracy, assumptions need not be realistic. I hold an opposite view for the obvious reason that the same prediction may be generated by completely different mechanisms, which in turn are based on different assumptions. Last but not least, the example of socialist economic planning shows that unrealistic assumptions can generate dangerous theories.
Measuring the Impact of Experimental Parameters upon the Estimated Thermal Conductivity of Closed-Cell Foam Insulation Subjected to an Accelerated Aging Protocol: Two-Year Results
Authors: Stovall Therese 
Published: April 2009

Abstract
The thermal conductivity of many closed-cell foam insulation products changes over time as production gases diffuse out of the cell matrix and atmospheric gases diffuse into the cells. Thin slicing has been shown to be an effective means of accelerating this process in such a way as to produce meaningful results. Efforts to produce a more prescriptive version of the ASTM C1303, “Standard Test Method for Predicting Long-Term Thermal Resistance of Closed-Cell Foam Insulation,” have led to a broad ruggedness test. This test includes the aging of full-size insulation specimens for time periods up to 5 years for later comparison to the predicted results. Experimental parameters under investigation include: slice thickness, slice origin (at the surface or from the core of the slab), thin-slice stack composition, product facings, original product thickness, product density, and product type. This paper will compare the results after two years of full-thickness aging.