bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Sea Surface Temperature on Humidity and Temperature in the Outflow of Tropical Deep Convection
Authors: Luo Zhengzhao Johnny , Kley Dieter , Johnson Richard H. , Liu G. Y. , Nawrath Susanne , Smit Herman G. J. 
Published: August 2011

Abstract
Multiple years of measurements of tropical upper-tropospheric temperature and humidity by the Measurement of Ozone and Water Vapor by Airbus In-Service Aircraft (MOZAIC) project are analyzed in the vicinity of deep convective outflow to study the variations of temperature and humidity and to investigate the influence of the sea surface temperature (SST) on the outflow air properties. The principal findings are the following. 1) The distribution of relative humidity with respect to ice (RHi) depends on where a convective system is sampled by the MOZAIC aircraft: deep inside the system, RHi is unimodal with the mode at ~114%; near the outskirts of the system, bimodal distribution of RHi starts to emerge with a dry mode at around 40% and a moist mode at 100%. The results are compared with previous studies using in situ measurements and model simulations. It is suggested that the difference in the RHi distribution can be explained by the variation of vertical motions associated with a convective system. 2) Analysis of MOZAIC data shows that a fractional increase of specific humidity with SST, q−1 dq/dSTT, near the convective outflow is about 0.16–0.18 K−1. These values agree well with previous studies using satellite data. Because MOZAIC measurements of temperature and humidity are independent, the authors further analyze the SST dependence of RHi and temperature individually. Temperature increases with SST for both prevalent flight levels (238 and 262 hPa); RHi stays close to constant with respect to SST for 238 hPa but shows an increasing trend for the 262-hPa level. Analysis conducted in this study represents a unique observational basis against which model simulations of upper-tropospheric humidity and its connection to deep convection and SST can be evaluated.
Large Decadal Decline of the Arctic Multiyear Ice Cover
Authors: Comiso Josefino C. 
Published: August 2011

Abstract
The perennial ice area was drastically reduced to 38% of its climatological average in 2007 but recovered slightly in 2008, 2009, and 2010 with the areas being 10%, 24%, and 11% higher than in 2007, respectively. However, trends in extent and area remained strongly negative at −12.2% and −13.5% decade−1, respectively. The thick component of the perennial ice, called multiyear ice, as detected by satellite data during the winters of 1979–2011 was studied, and results reveal that the multiyear ice extent and area are declining at an even more rapid rate of −15.1% and −17.2% decade−1, respectively, with a record low value in 2008 followed by higher values in 2009, 2010, and 2011. Such a high rate in the decline of the thick component of the Arctic ice cover means a reduction in the average ice thickness and an even more vulnerable perennial ice cover. The decline of the multiyear ice area from 2007 to 2008 was not as strong as that of the perennial ice area from 2006 to 2007, suggesting a strong role of second-year ice melt in the latter. The sea ice cover is shown to be strongly correlated with surface temperature, which is increasing at about 3 times the global average in the Arctic but appears weakly correlated with the Arctic Oscillation (AO), which controls the atmospheric circulation in the region. An 8–9-yr cycle is apparent in the multiyear ice record, which could explain, in part, the slight recovery in the last 3 yr.
Therapy and Prognosis of Intracranial Invasive Olfactory Neuroblastoma
Authors: Jiang Guang‐Yi , Li Fang‐Cheng , Chen Wen‐Kuan , Liu An‐Min , Cai Wang‐Qing 
Published: August 2011

ObjectiveThere is currently no consensus on a standardized treatment strategy for olfactory neuroblastoma (ONB), especially for intracranial invasion. This purpose of this study is to explore the appropriate treatment modality and prognostic factors of intracranial invasive ONB.Study DesignCase series with chart review.SettingThe study was conducted at the Sun Yat‐sen Memorial Hospital and the Cancer Center of Sun Yat‐sen University, China.Subjects and MethodsTwenty‐five cases of intracranial invasive ONB were collected and investigated using a retrospective review analysis from patients diagnosed between 1980 and 2005.ResultsThe 1‐, 3‐, and 5‐year overall survival rates for the group were 55%, 46%, and 31%, respectively. The subgroups who did not receive surgical treatment had worse survival rates than those who did receive treatment. In particular, patients who did not receive any therapy did not live past 1 year. In contrast, the group of patients treated by intranasal resection in combination with radiotherapy and/or chemotherapy showed a slightly better survival rate. It is important to note that the group of patients treated by craniofacial surgery combined with radiotherapy and/or chemotherapy had a markedly favorable prognosis, with 1‐, 3‐, and 5‐year overall survival rates of up to 100%, 88%, and 66%, respectively.ConclusionsCraniofacial surgery in combination with radiotherapy and/or chemotherapy was an effective treatment for intracranial invasive ONB. In addition, it was found that age may not be an important prognostic factor for intracranial invasive ONB; however, the rate of intracalvarial invasion was found to be a potent marker for predicting the prognosis of patients.
Linear Models with Outliers: Choosing between Conditional-Mean and Conditional-Median Methods
Authors: Harden Jeffrey J. , Desmarais Bruce A. 
Published: August 2011

AbstractState politics researchers commonly employ ordinary least squares (OLS) regression or one of its variants to test linear hypotheses. However, OLS is easily influenced by outliers and thus can produce misleading results when the error term distribution has heavy tails. Here we demonstrate that median regression (MR), an alternative to OLS that conditions the median of the dependent variable (rather than the mean) on the independent variables, can be a solution to this problem. Then we propose and validate a hypothesis test that applied researchers can use to select between OLS and MR in a given sample of data. Finally, we present two examples from state politics research in which (1) the test selects MR over OLS and (2) differences in results between the two methods could lead to different substantive inferences. We conclude that MR and the test we propose can improve linear models in state politics research.
Extracellular matrix structure and nano-mechanics determine megakaryocyte function
Authors: Malara Alessandro , Gruppi Cristian , Pallotta Isabella , Spedden Elise , Tenni Ruggero , Raspanti Mario , Kaplan David , Tira Maria Enrica , Staii Cristian , Balduini Alessandra 
Published: August 2011

Abstract
Cell interactions with matrices via specific receptors control many functions, with chemistry, physics, and membrane elasticity as fundamental elements of the processes involved. Little is known about how biochemical and biophysical processes integrate to generate force and, ultimately, to regulate hemopoiesis into the bone marrow-matrix environment. To address this hypothesis, in this work we focus on the regulation of MK development by type I collagen. By atomic force microscopy analysis, we demonstrate that the tensile strength of fibrils in type I collagen structure is a fundamental requirement to regulate cytoskeleton contractility of human MKs through the activation of integrin-α2β1–dependent Rho-ROCK pathway and MLC-2 phosphorylation. Most importantly, this mechanism seemed to mediate MK migration, fibronectin assembly, and platelet formation. On the contrary, a decrease in mechanical tension caused by N-acetylation of lysine side chains in type I collagen completely reverted these processes by preventing fibrillogenesis.
A randomized trial comparing standard versus high-dose daunorubicin induction in patients with acute myeloid leukemia
Authors: Lee Je-Hwan , Joo Young-Don , Kim Hawk , Bae Sung Hwa , Kim Min Kyoung , Zang Dae Young , Lee Jung-Lim , Lee Gyeong Won , Lee Jung-Hee , Park Jae-Hoo , Kim Dae-Young , Lee Won-Sik , Ryoo Hun Mo , Hyun Myung Soo , Kim Hyo Jung , Min Young Joo , Jang Yae-Eun , Lee Kyoo-Hyung ,   for the Cooperative Study Group A for Hematology
Published: August 2011

Abstract
We conducted a phase 3 randomized trial comparing 2 different doses of daunorubicin as induction chemotherapy in young adults (60 years of age or younger) with acute myeloid leukemia (AML). Of 383 patients who were analyzed, 189 received standard-dose daunorubicin (SD-DN, 45 mg/m2 per day times 3 days) and 194 received high-dose daunorubicin (HD-DN, 90 mg/m2 per day times 3 days) in addition to cytarabine (200 mg/m2 per day times 7 days) to induce complete remission (CR). The CR rates were 72.0% in the SD-DN arm and 82.5% in the HD-DN arm (P = .014). At a median follow-up of 52.6 months, overall (OS) and event-free (EFS) survival were higher in the HD-DN arm than in the SD-DN arm (OS, 46.8% vs 34.6%, P = .030; EFS, 40.8% vs 28.4%, P = .030). Differences in CR rate and both OS and EFS remained significant after adjusting for other variables (CR, hazard ratio [HR], 1.802, P = .024; OS, HR, 0.739, P = .032; EFS, HR, 0.774, P = .048). The survival benefits of HD-DN therapy were evident principally in patients with intermediate-risk cytogenetic features. The toxicity profiles were similar in the 2 arms. In conclusion, HD-DN improved both the CR rate and survival duration compared with SD-DN in young adults with AML. This study is registered at www.clinicaltrials.gov as #NCT00474006.
The emphysematous lung is abnormally sensitive to TRAIL-mediated apoptosis
Authors: Morissette Mathieu C , Parent Julie , Milot Julie 
Published: August 2011

Abstract

Background
Alveolar apoptosis is increased in the emphysematous lung. However, mechanisms involved are not fully understood. Recently, we demonstrated that levels of TRAIL receptor 1 and 2, levels of p53, and Bax/Bcl-xL ratio were elevated in the lung of subjects with emphysema, despite smoking cessation. Thus, we postulate that due to chronic pulmonary oxidative stress, the emphysematous lung would be abnormally sensitive to TRAIL-mediated apoptosis.

Methodology
A549 cells were exposed to rTRAIL, cigarette smoke extract, and/or H2O2 prior to caspase-3 activity measurement and annexin V staining assessment. In addition, freshly resected lung samples were obtained from non-emphysematous and emphysematous subjects and exposed ex vivo to rTRAIL for up to 18 hours. Lung samples were harvested and levels of active caspase-3 and caspase-8 were measured from tissue lysates.

Results
Both cigarette smoke extract and H2O2 were able to sensitize A549 cells to TRAIL-mediated apoptosis. Moreover, following exposure to rTRAIL, caspase-3 and -8 were activated in lung explants from emphysematous subjects while being decreased in lung explants from non-emphysematous subjects.

Significance of the study
Alveolar sensitivity to TRAIL-mediated apoptosis is strongly increased in the emphysematous lung due to the presence of oxidative stress. This might be a new mechanism leading to increased alveolar apoptosis and persistent alveolar destruction following smoking cessation.
In vitro activation and enzyme kinetic analysis of recombinant midgut serine proteases from the Dengue vector mosquito Aedes aegypti
Authors: Rascón Alberto A , Gearin Johnathon , Isoe Jun , Miesfeld Roger L 
Published: August 2011

Abstract

Background
The major Dengue virus vector Aedes aegypti requires nutrients obtained from blood meal proteins to complete the gonotrophic cycle. Although bioinformatic analyses of Ae. aegypti midgut serine proteases have provided evolutionary insights, very little is known about the biochemical activity of these digestive enzymes.

Results
We used peptide specific antibodies to show that midgut serine proteases are expressed as zymogen precursors, which are cleaved to the mature form after blood feeding. Since midgut protein levels are insufficient to purify active proteases directly from blood fed mosquitoes, we engineered recombinant proteins encoding a heterologous enterokinase cleavage site to permit generation of the bona fide mature form of four midgut serine proteases (AaET, AaLT, AaSPVI, AaSPVII) for enzyme kinetic analysis. Cleavage of the chromogenic trypsin substrate BApNA showed that AaET has a catalytic efficiency (kcat/KM) that is ~30 times higher than bovine trypsin, and ~2-3 times higher than AaSPVI and AaSPVII, however, AaLT does not cleave BApNA. To measure the enzyme activities of the mosquito midgut proteases using natural substrates, we developed a quantitative cleavage assay based on cleavage of albumin and hemoglobin proteins. These studies revealed that the recombinant AaLT enzyme was indeed catalytically active, and cleaved albumin and hemoglobin with equivalent efficiency to that of AaET, AaSPVI, and AaSPVII. Structural modeling of the AaLT and AaSPVI mature forms indicated that AaLT is most similar to serine collagenases, whereas AaSPVI appears to be a classic trypsin.

Conclusions
These data show that in vitro activation of recombinant serine proteases containing a heterologous enterokinase cleavage site can be used to investigate enzyme kinetics and substrate cleavage properties of biologically important mosquito proteases.
Classifying short genomic fragments from novel lineages using composition and homology
Authors: Parks Donovan H , MacDonald Norman J , Beiko Robert G 
Published: August 2011

Abstract

Background
The assignment of taxonomic attributions to DNA fragments recovered directly from the environment is a vital step in metagenomic data analysis. Assignments can be made using rank-specific classifiers, which assign reads to taxonomic labels from a predetermined level such as named species or strain, or rank-flexible classifiers, which choose an appropriate taxonomic rank for each sequence in a data set. The choice of rank typically depends on the optimal model for a given sequence and on the breadth of taxonomic groups seen in a set of close-to-optimal models. Homology-based (e.g., LCA) and composition-based (e.g., PhyloPythia, TACOA) rank-flexible classifiers have been proposed, but there is at present no hybrid approach that utilizes both homology and composition.

Results
We first develop a hybrid, rank-specific classifier based on BLAST and Naïve Bayes (NB) that has comparable accuracy and a faster running time than the current best approach, PhymmBL. By substituting LCA for BLAST or allowing the inclusion of suboptimal NB models, we obtain a rank-flexible classifier. This hybrid classifier outperforms established rank-flexible approaches on simulated metagenomic fragments of length 200 bp to 1000 bp and is able to assign taxonomic attributions to a subset of sequences with few misclassifications. We then demonstrate the performance of different classifiers on an enhanced biological phosphorous removal metagenome, illustrating the advantages of rank-flexible classifiers when representative genomes are absent from the set of reference genomes. Application to a glacier ice metagenome demonstrates that similar taxonomic profiles are obtained across a set of classifiers which are increasingly conservative in their classification.

Conclusions
Our NB-based classification scheme is faster than the current best composition-based algorithm, Phymm, while providing equally accurate predictions. The rank-flexible variant of NB, which we term ε-NB, is complementary to LCA and can be combined with it to yield conservative prediction sets of very high confidence. The simple parameterization of LCA and ε-NB allows for tuning of the balance between more predictions and increased precision, allowing the user to account for the sensitivity of downstream analyses to misclassified or unclassified sequences.
Development of a classification scheme for disease-related enzyme information
Authors: Söhngen Carola , Chang Antje , Schomburg Dietmar 
Published: August 2011

Abstract

Background
BRENDA (BR aunschweig EN zyme DA tabase, http://www.brenda-enzymes.org) is a major resource for enzyme related information. First and foremost, it provides data which are manually curated from the primary literature. DRENDA (D isease RE lated EN zyme information DA tabase) complements BRENDA with a focus on the automatic search and categorization of enzyme and disease related information from title and abstracts of primary publications. In a two-step procedure DRENDA makes use of text mining and machine learning methods.

Results
Currently enzyme and disease related references are biannually updated as part of the standard BRENDA update. 910,897 relations of EC-numbers and diseases were extracted from titles or abstracts and are included in the second release in 2010. The enzyme and disease entity recognition has been successfully enhanced by a further relation classification via machine learning. The classification step has been evaluated by a 5-fold cross validation and achieves an F1 score between 0.802 ± 0.032 and 0.738 ± 0.033 depending on the categories and pre-processing procedures. In the eventual DRENDA content every category reaches a classification specificity of at least 96.7% and a precision that ranges from 86-98% in the highest confidence level, and 64-83% for the smallest confidence level associated with higher recall.

Conclusions
The DRENDA processing chain analyses PubMed, locates references with disease-related information on enzymes and categorises their focus according to the categories
causal interaction
,
therapeutic application
,
diagnostic usage
and
ongoing research
. The categorisation gives an impression on the focus of the located references. Thus, the relation categorisation can facilitate orientation within the rapidly growing number of references with impact on diseases and enzymes. The DRENDA information is available as additional information in BRENDA.
Deploying mutation impact text-mining software with the SADI Semantic Web Services framework
Authors: Riazanov Alexandre , Laurila Jonas Bergman , Baker Christopher JO 
Published: August 2011

Abstract

Background
Mutation impact extraction is an important task designed to harvest relevant annotations from scientific documents for reuse in multiple contexts. Our previous work on text mining for mutation impacts resulted in (i) the development of a GATE-based pipeline that mines texts for information about impacts of mutations on proteins, (ii) the population of this information into our OWL DL mutation impact ontology, and (iii) establishing an experimental semantic database for storing the results of text mining.

Results
This article explores the possibility of using the SADI framework as a medium for publishing our mutation impact software and data. SADI is a set of conventions for creating web services with semantic descriptions that facilitate automatic discovery and orchestration. We describe a case study exploring and demonstrating the utility of the SADI approach in our context. We describe several SADI services we created based on our text mining API and data, and demonstrate how they can be used in a number of biologically meaningful scenarios through a SPARQL interface (SHARE) to SADI services. In all cases we pay special attention to the integration of mutation impact services with external SADI services providing information about related biological entities, such as proteins, pathways, and drugs.

Conclusion
We have identified that SADI provides an effective way of exposing our mutation impact data such that it can be leveraged by a variety of stakeholders in multiple use cases. The solutions we provide for our use cases can serve as examples to potential SADI adopters trying to solve similar integration problems.
Transcription analysis on response of swine lung to H1N1 swine influenza virus
Authors: Li Yongtao , Zhou Hongbo , Wen Zhibin , Wu Shujuan , Huang Canhui , Jia Guangmin , Chen Huanchun , Jin Meilin 
Published: August 2011

Abstract

Background
As a mild, highly contagious, respiratory disease, swine influenza always damages the innate immune systems, and increases susceptibility to secondary infections which results in considerable morbidity and mortality in pigs. Nevertheless, the systematical host response of pigs to swine influenza virus infection remains largely unknown. To explore it, a time-course gene expression profiling was performed for comprehensive analysis of the global host response induced by H1N1 swine influenza virus in pigs.

Results
At the early stage of H1N1 swine virus infection, pigs were suffering mild respiratory symptoms and pathological changes. A total of 268 porcine genes showing differential expression (DE) after inoculation were identified to compare with the controls on day 3 post infection (PID) (Fold change ≥ 2, p < 0.05). The DE genes were involved in many vital functional classes, mainly including signal transduction, immune response, inflammatory response, cell adhesion and cell-cell signalling. Noticeably, the genes associated with immune and inflammatory response showed highly overexpressed. Through the pathway analysis, the significant pathways mainly concerned with Cell adhesion molecules, Cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway and MAPK signaling pathway, suggesting that the host took different strategies to activate these pathways so as to prevent virus infections at the early stage. However, on PID 7, the predominant function classes of DE genes included signal transduction, metabolism, transcription, development and transport. Furthermore, the most significant pathways switched to PPAR signaling pathway and complement and coagulation cascades, showing that the host might start to repair excessive tissue damage by anti-inflammatory functions. These results on PID 7 demonstrated beneficial turnover for host to prevent excessive inflammatory damage and recover the normal state by activating these clusters of genes.

Conclusions
This study shows how the target organ responds to H1N1 swine influenza virus infection in pigs. The observed gene expression profile could help to screen the potential host agents for reducing the prevalence of swine influenza virus and further understand the molecular pathogenesis associated with H1N1 infection in pigs.