bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Energy Flux Partitioning in Urban Environments: Links with Surface Seasonal Properties
Authors: Loridan Thomas , Grimmond C. S. B. 
Published: September 2011

AbstractA better understanding of links between the properties of the urban environment and the exchange to the atmosphere is central to a wide range of applications. The numerous measurements of surface energy balance data in urban areas enable intercomparison of observed fluxes from distinct environments. This study analyzes a large database in two new ways. First, instead of normalizing fluxes using net all-wave radiation only the incoming radiative fluxes are used, to remove the surface attributes from the denominator. Second, because data are now available year-round, indices are developed to characterize the fraction of the surface (built; vegetation) actively engaged in energy exchanges. These account for shading patterns within city streets and seasonal changes in vegetation phenology; their impact on the partitioning of the incoming radiation is analyzed. Data from 19 sites in North America, Europe, Africa, and Asia (including 6-yr-long observation campaigns) are used to derive generalized surface–flux relations. The midday-period outgoing radiative fraction decreases with an increasing total active surface index, the stored energy fraction increases with an active built index, and the latent heat fraction increases with an active vegetated index. Parameterizations of these energy exchange ratios as a function of the surface indices [i.e., the Flux Ratio–Active Index Surface Exchange (FRAISE) scheme] are developed. These are used to define four urban zones that characterize energy partitioning on the basis of their active surface indices. An independent evaluation of FRAISE, using three additional sites from the Basel Urban Boundary Layer Experiment (BUBBLE), yields accurate predictions of the midday flux partitioning at each location.
Impact of a Vertical Vorticity Constraint in Variational Dual-Doppler Wind Analysis: Tests with Real and Simulated Supercell Data
Authors: Potvin Corey K. , Shapiro Alan , Xue Ming 
Published: September 2011

Abstract
One of the greatest challenges to dual-Doppler retrieval of the vertical wind is the lack of low-level divergence information available to the mass conservation constraint. This study examines the impact of a vertical vorticity equation constraint on vertical velocity retrievals when radar observations are lacking near the ground. The analysis proceeds in a three-dimensional variational data assimilation (3DVAR) framework with the anelastic form of the vertical vorticity equation imposed along with traditional data, mass conservation, and smoothness constraints. The technique is tested using emulated radial wind observations of a supercell storm simulated by the Advanced Regional Prediction System (ARPS), as well as real dual-Doppler observations of a supercell storm that occurred in Oklahoma on 8 May 2003. Special attention is given to procedures to evaluate the vorticity tendency term, including spatially variable advection correction and estimation of the intrinsic evolution. Volume scan times ranging from 5 min, typical of operational radar networks, down to 30 s, achievable by rapid-scan mobile radars, are considered. The vorticity constraint substantially improves the vertical velocity retrievals in our experiments, particularly for volume scan times smaller than 2 min.
Quality‐of‐Life Outcomes in Transoral Robotic Surgery
Authors: Hurtuk Agnes M. , Marcinow Anna , Agrawal Amit , Old Matthew , Teknos Theodoros N. , Ozer Enver 
Published: September 2011

ObjectiveTo report long‐term, health‐related quality‐of‐life (HRQOL) outcomes in patients treated with transoral robotic surgery (TORS).Study DesignProspective, longitudinal, clinical study on functional and HRQOL outcomes in TORS.SettingUniversity tertiary care facility.Subjects and MethodsPatients who underwent TORS were asked to complete a Head and Neck Cancer Inventory before treatment and at 3 weeks and 3, 6, and 12 months postoperatively. Demographic, clinicopathological, and follow‐up data were collected.ResultsSixty‐four patients who underwent TORS were enrolled. A total of 113 TORS procedures were performed. The mean follow‐up time was 16.3 ± 7.49 months. The HRQOL was assessed at 3 weeks and at 3, 6, and 12 months, with a response rate of 78%, 44%, 41%, and 28%, respectively. TORS was performed most frequently for squamous cell carcinoma (88%). There was a decrease from baseline in the speech, eating, aesthetic, social, and overall QOL domains immediately after treatment. At the 1‐year follow‐up, the HRQOL scores in the aesthetic, social, and overall QOL domains were in the high domain. Patients with malignant lesions had significantly lower postoperative HRQOL scores in the speech, eating, social, and overall QOL domains (P <. 05). Patients who underwent adjuvant radiation therapy or chemotherapy and radiation therapy had lower postoperative scores in the eating, social, and overall QOL domains (P <. 05).ConclusionThe preliminary data show that patients who undergo TORS for malignancies and receive adjuvant therapy tend to have lower HRQOL outcomes. TORS is a promising, minimally invasive, endoscopic alternative surgical treatment of laryngopharyngeal tumors.
Shoulder Sport-Specific Impairments After Arthroscopic Bankart Repair
Authors: Stein Thomas , Linke Ralf Dieter , Buckup Johannes , Efe Turgay , von Eisenhart-Rothe Rudiger , Hoffmann Reinhard , Jäger Alwin , Welsch Frederic 
Published: September 2011

Background: Reports of return to shoulder-dependent sport after surgical stabilization previously underestimated impairments, which were not reflected in the score systems used. Hypothesis: Return to shoulder-dependent sport depends on the type of sport performed. Study Design: Case series; Level of evidence, 4. Methods: Forty-seven athletes (26.9 years of age at surgery) who underwent isolated arthroscopic Bankart repair were longitudinally monitored by shoulder-dependent sport-specific activity (Shoulder Sport Activity Score [SSAS]) and ability (Athletic Shoulder Outcome Scoring System [ASOSS]) scores and visual analog scales for reachieved proficiency level, sport-specific shoulder pain, and functional deficits. Data were assessed at 4 points of treatment: preoperatively, and postoperatively after 6, 16, and 32 months (P0-P3). Athletes were analyzed separately according to shoulder sport: noncollision/nonoverhead (G1), collision (G2), overhead (G3), and martial arts (G4). Results: The G1 and G2 athletes had reachieved the preinjury sport activity and sport proficiency status and excellent ASOSS scores after 32 months (SSASG1 = 7.2, SSASG2 = 8.1, ASOSSG1 = 94.4, ASOSSG2 = 95.2), whereas G3 and G4 athletes remained at an inferior activity level (SSASG3 = 8.0, SSASG4 = 8.3) and proficiency level. The ASOSS documented a prolonged period of shoulder rehabilitation for G3 and G4 athletes to reach a good shoulder-dependent sport ability outcome after 32 months (ASOSSG3 = 89.0, ASOSSG4 = 93.1). All groups recorded persisting limitations in visual analog scales for sport-specific shoulder function and pain. The established scores (Rowe = 95.9, Walch-Duplay = 93.3, Constant = 94.0) did not reflect these sport-specific impairments. Athletes with 5 or more preoperative dislocations had significantly longer surgery-to-sport resumption intervals with a prolonged proficiency recovery. Conclusion: The athletes’ shoulder stabilization resulted in a prolonged rehabilitation depending on the functional demand of the performed shoulder-dependent sport, as shown by the specific shoulder sport score systems.
Gene mutation patterns and their prognostic impact in a cohort of 1185 patients with acute myeloid leukemia
Authors: Shen Yang , Zhu Yong-Mei , Fan Xing , Shi Jing-Yi , Wang Qin-Rong , Yan Xiao-Jing , Gu Zhao-Hui , Wang Yan-Yan , Chen Bing , Jiang Chun-Lei , Yan Han , Chen Fei-Fei , Chen Hai-Min , Chen Zhu , Jin Jie , Chen Sai-Juan 
Published: September 2011

Abstract
To evaluate the prognostic value of genetic mutations for acute myeloid leukemia (AML) patients, we examined the gene status for both fusion products such as AML1 (CBFα)–ETO, CBFβ-MYH11, PML-RARα, and MLL rearrangement as a result of chromosomal translocations and mutations in genes including FLT3, C-KIT, N-RAS, NPM1, CEBPA, WT1, ASXL1, DNMT3A, MLL, IDH1, IDH2, and TET2 in 1185 AML patients. Clinical analysis was mainly carried out among 605 cases without recognizable karyotype abnormalities except for 11q23. Of these 605 patients, 452 (74.7%) were found to have at least 1 mutation, and the relationship of gene mutations with clinical outcome was investigated. We revealed a correlation pattern among NPM1, DNMT3A, FLT3, IDH1, IDH2, CEBPA, and TET2 mutations. Multivariate analysis identified DNMT3A and MLL mutations as independent factors predicting inferior overall survival (OS) and event-free survival (EFS), whereas biallelic CEBPA mutations or NPM1 mutations without DNMT3A mutations conferred a better OS and EFS in both the whole group and among younger patients < 60 years of age. The use of molecular markers allowed us to subdivide the series of 605 patients into distinct prognostic groups with potential clinical relevance.
Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma
Authors: Rossi Davide , Deaglio Silvia , Dominguez-Sola David , Rasi Silvia , Vaisitti Tiziana , Agostinelli Claudio , Spina Valeria , Bruscaggin Alessio , Monti Sara , Cerri Michaela , Cresta Stefania , Fangazio Marco , Arcaini Luca , Lucioni Marco , Marasca Roberto , Thieblemont Catherine , Capello Daniela , Facchetti Fabio , Kwee Ivo , Pileri Stefano A. , Foà Robin , Bertoni Francesco , Dalla-Favera Riccardo , Pasqualucci Laura , Gaidano Gianluca 
Published: September 2011

Abstract
Splenic marginal zone lymphoma (SMZL) is one of the few B-cell lymphoma types that remain orphan of molecular lesions in cancer-related genes. Detection of active NF-κB signaling in 14 (58%) of 24 SMZLs prompted the investigation of NF-κB molecular alterations in 101 SMZLs. Mutations and copy number abnormalities of NF-κB genes occurred in 36 (36%) of 101 SMZLs and targeted both canonical (TNFAIP3 and IKBKB) and noncanonical (BIRC3, TRAF3, MAP3K14) NF-κB pathways. Most alterations were mutually exclusive, documenting the existence of multiple independent mechanisms affecting NF-κB in SMZL. BIRC3 inactivation in SMZL recurred because of somatic mutations that disrupted the same RING domain that in extranodal marginal zone lymphoma is removed by the t(11;18) translocation, which points to BIRC3 disruption as a common mechanism across marginal zone B-cell lymphomagenesis. Genetic lesions of NF-κB provide a molecular basis for the pathogenesis of more than 30% of SMZLs and offer a suitable target for NF-κB therapeutic approaches in this lymphoma.
Critical role for Syk in responses to vascular injury
Authors: Andre Patrick , Morooka Toshifumi , Sim Derek , Abe Keith , Lowell Clifford , Nanda Nisha , Delaney Suzanne , Siu Gail , Yan Yibing , Hollenbach Stan , Pandey Anjali , Gao Huiyun , Wang Yunmei , Nakajima Kohsuke , Parikh Sahil A. , Shi Can , Phillips David , Owen Whyte , Sinha Uma , Simon Daniel I. 
Published: September 2011

AbstractAlthough current antiplatelet therapies provide potent antithrombotic effects, their efficacy is limited by a heightened risk of bleeding and failure to affect vascular remodeling after injury. New lines of research suggest that thrombosis and hemorrhage may be uncoupled at the interface of pathways controlling thrombosis and inflammation. Here, as one remarkable example, studies using a novel and highly selective pharmacologic inhibitor of the spleen tyrosine kinase Syk [PRT060318; 2-((1R,2S)-2-aminocyclohexylamino)-4-(m-tolylamino)pyrimidine-5-carboxamide] coupled with genetic experiments, demonstrate that Syk inhibition ameliorates both the acute and chronic responses to vascular injury without affecting hemostasis. Specifically, lack of Syk (murine radiation chimeras) attenuated shear-induced thrombus formation ex vivo, and PRT060318 strongly inhibited arterial thrombosis in vivo in multiple animal species while having minimal impact on bleeding. Furthermore, leukocyte-platelet–dependent responses to vascular injury, including inflammatory cell recruitment and neointima formation, were markedly inhibited by PRT060318. Thus, Syk controls acute and long-term responses to arterial vascular injury. The therapeutic potential of Syk may be exemplary of a new class of antiatherothrombotic agents that target the interface between thrombosis and inflammation.
Predictors of greater than 80% 2-year mortality in primary myelofibrosis: a Mayo Clinic study of 884 karyotypically annotated patients
Authors: Tefferi Ayalew , Jimma Thitina , Gangat Naseema , Vaidya Rakhee , Begna Kebede H. , Hanson Curtis A. , Van Dyke Daniel L. , Caramazza Domenica , Pardanani Animesh 
Published: September 2011

Abstract
DIPSS-plus (the Dynamic International Prognostic Scoring System-plus) includes 8 risk factors for survival in primary myelofibrosis. In the present study of 884 karyotypically annotated patients with primary myelofibrosis, we sought to identify 1 or 2 parameters that can reliably predict death in the first 2 years of disease. After a median of 8.2 years from time of referral to the Mayo Clinic, 564 deaths (64% of patients in the study) had been recorded. Risk factors associated with > 80% 2-year mortality included monosomal karyotype, inv(3)/i(17q) abnormalities, or any 2 of the following: circulating blasts > 9%, leukocytes ≥ 40 × 109/L, or other unfavorable karyotype. Patients with any 1 of these risk profiles (n = 52) displayed significantly shorter overall survival than those otherwise belonging to a high-risk category per DIPSS-plus (n = 298); respective median survivals were 9 and 23 months (hazard ratio 2.2, 95% confidence interval 1.6-3.1; P < .01). The present information complements DIPSS-plus in the selection of primary myelofibrosis patients for high-risk treatment approaches.
Beyond corticosteroids: future prospects in the management of inflammation in COPD
Authors: Roche N. , Marthan R. , Berger P. , Chambellan A. , Chanez P. , Aguilaniu B. , Brillet P-Y , Burgel P-R , Chaouat A. , Devillier P. , Escamilla R. , Louis R. , Mal H. , Muir J-F , Pérez T. , Similowski T. , Wallaert B. , Aubier M. 
Published: September 2011

Inflammation plays a central role in the pathophysiology of chronic obstructive pulmonary disease (COPD). Exposure to cigarette smoke induces the recruitment of inflammatory cells in the airways and stimulates innate and adaptive immune mechanisms. Airway inflammation is involved in increased bronchial wall thickness, increased bronchial smooth muscle tone, mucus hypersecretion and loss of parenchymal elastic structures. Oxidative stress impairs tissue integrity, accelerates lung ageing and reduces the efficacy of corticosteroids by decreasing levels of histone deacetylase-2. Protease–antiprotease imbalance impairs tissues and is involved in inflammatory processes. Inflammation is also present in the pulmonary artery wall and at the systemic level in COPD patients, and may be involved in COPD-associated comorbidities.Proximal airways inflammation contributes to symptoms of chronic bronchitis while distal and parenchymal inflammation relates to airflow obstruction, emphysema and hyperinflation. Basal levels of airways and systemic inflammation are increased in frequent exacerbators.Inhaled corticosteroids are much less effective in COPD than in asthma, which relates to the intrinsically poor reversibility of COPD-related airflow obstruction and to molecular mechanisms of resistance relating to oxidative stress. Ongoing research aims at developing new drugs targeting more intimately COPD-specific mechanisms of inflammation, hypersecretion and tissue destruction and repair. Among new anti-inflammatory agents, phosphodiesterase-4 inhibitors have been the first to emerge.
Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails
Authors: Bock Ina , Kudithipudi Srikanth , Tamas Raluca , Kungulovski Goran , Dhayalan Arunkumar , Jeltsch Albert 
Published: September 2011

Abstract

Background
Epigenetic reading domains are involved in the regulation of gene expression and chromatin state by interacting with histones in a post-translational modification specific manner. A detailed knowledge of the target modifications of reading domains, including enhancing and inhibiting secondary modifications, will lead to a better understanding of the biological signaling processes mediated by reading domains.

Results
We describe the application of Celluspots peptide arrays which contain 384 histone peptides carrying 59 post translational modifications in different combinations as an inexpensive, reliable and fast method for initial screening for specific interactions of reading domains with modified histone peptides. To validate the method, we tested the binding specificities of seven known epigenetic reading domains on Celluspots peptide arrays, viz. the HP1ß and MPP8 Chromo domains, JMJD2A and 53BP1 Tudor domains, Dnmt3a PWWP domain, Rag2 PHD domain and BRD2 Bromo domain. In general, the binding results agreed with literature data with respect to the primary specificity of the reading domains, but in almost all cases we obtained additional new information concerning the influence of secondary modifications surrounding the target modification.

Conclusions
We conclude that Celluspots peptide arrays are powerful screening tools for studying the specificity of putative reading domains binding to modified histone peptides.
Clustering with position-specific constraints on variance: Applying redescending M-estimators to label-free LC-MS data analysis
Authors: Frühwirth Rudolf , Mani D R , Pyne Saumyadipta 
Published: September 2011

AbstractBackgroundClustering is a widely applicable pattern recognition method for discovering groups of similar observations in data. While there are a large variety of clustering algorithms, very few of these can enforce constraints on the variation of attributes for data points included in a given cluster. In particular, a clustering algorithm that can limit variation within a cluster according to that cluster's position (centroid location) can produce effective and optimal results in many important applications ranging from clustering of silicon pixels or calorimeter cells in high-energy physics to label-free liquid chromatography based mass spectrometry (LC-MS) data analysis in proteomics and metabolomics.ResultsWe present MEDEA (M-Estimator with DEterministic Annealing), an M-estimator based, new unsupervised algorithm that is designed to enforce position-specific constraints on variance during the clustering process. The utility of MEDEA is demonstrated by applying it to the problem of "peak matching"--identifying the common LC-MS peaks across multiple samples--in proteomic biomarker discovery. Using real-life datasets, we show that MEDEA not only outperforms current state-of-the-art model-based clustering methods, but also results in an implementation that is significantly more efficient, and hence applicable to much larger LC-MS data sets.ConclusionsMEDEA is an effective and efficient solution to the problem of peak matching in label-free LC-MS data. The program implementing the MEDEA algorithm, including datasets, clustering results, and supplementary information is available from the author website athttp://www.hephy.at/user/fru/medea/.
A eukaryotic-type signalling system of Pseudomonas aeruginosa contributes to oxidative stress resistance, intracellular survival and virulence
Authors: Goldová Jana , Ulrych Aleš , Hercík Kamil , Branny Pavel 
Published: September 2011

Abstract

Background
The genome of Pseudomonas aeruginosa contains at least three genes encoding eukaryotic-type Ser/Thr protein kinases, one of which, ppkA, has been implicated in P. aeruginosa virulence. Together with the adjacent pppA phosphatase gene, they belong to the type VI secretion system (H1-T6SS) locus, which is important for bacterial pathogenesis. To determine the biological function of this protein pair, we prepared a pppA-ppkA double mutant and characterised its phenotype and transcriptomic profiles.

Results
Phenotypic studies revealed that the mutant grew slower than the wild-type strain in minimal media and exhibited reduced secretion of pyoverdine. In addition, the mutant had altered sensitivity to oxidative and hyperosmotic stress conditions. Consequently, mutant cells had an impaired ability to survive in murine macrophages and an attenuated virulence in the plant model of infection. Whole-genome transcriptome analysis revealed that pppA-ppkA deletion affects the expression of oxidative stress-responsive genes, stationary phase σ-factor RpoS-regulated genes, and quorum-sensing regulons. The transcriptome of the pppA-ppkA mutant was also analysed under conditions of oxidative stress and showed an impaired response to the stress, manifested by a weaker induction of stress adaptation genes as well as the genes of the SOS regulon. In addition, expression of either RpoS-regulated genes or quorum-sensing-dependent genes was also affected. Complementation analysis confirmed that the transcription levels of the differentially expressed genes were specifically restored when the pppA and ppkA genes were expressed ectopically.

Conclusions
Our results suggest that in addition to its crucial role in controlling the activity of P. aeruginosa H1-T6SS at the post-translational level, the PppA-PpkA pair also affects the transcription of stress-responsive genes. Based on these data, it is likely that the reduced virulence of the mutant strain results from an impaired ability to survive in the host due to the limited response to stress conditions.
The C242T polymorphism of the p22-phox gene (CYBA) is associated with higher left ventricular mass in Brazilian hypertensive patients
Authors: Schreiber Roberto , Ferreira-Sae Maria C , Ronchi Juliana A , Pio-Magalhães José A , Cipolli José A , Matos-Souza José R , Mill José G , Vercesi Aníbal E , Krieger José E , Franchini Kleber G , Pereira Alexandre C , Nadruz Junior Wilson 
Published: September 2011

Abstract

Background
Reactive oxygen species have been implicated in the physiopathogenesis of hypertensive end-organ damage. This study investigated the impact of the C242T polymorphism of the p22-phox gene (CYBA) on left ventricular structure in Brazilian hypertensive subjects.

Methods
We cross-sectionally evaluated 561 patients from 2 independent centers [Campinas (n = 441) and Vitória (n = 120)] by clinical history, physical examination, anthropometry, analysis of metabolic and echocardiography parameters as well as p22-phox C242T polymorphism genotyping. In addition, NADPH-oxidase activity was quantified in peripheral mononuclear cells from a subgroup of Campinas sample.

Results
Genotype frequencies in both samples were consistent with the Hardy- Weinberg equilibrium. Subjects with the T allele presented higher left ventricular mass/height2.7 than those carrying the CC genotype in Campinas (76.8 ± 1.6 vs 70.9 ± 1.4 g/m2.7; p = 0.009), and in Vitória (45.6 ± 1.9 vs 39.9 ± 1.4 g/m2.7; p = 0.023) samples. These results were confirmed by stepwise regression analyses adjusted for age, gender, blood pressure, metabolic variables and use of anti-hypertensive medications. In addition, increased NADPH-oxidase activity was detected in peripheral mononuclear cells from T allele carriers compared with CC genotype carriers (p = 0.03).

Conclusions
The T allele of the p22-phox C242T polymorphism is associated with higher left ventricular mass/height2.7 and increased NADPH-oxidase activity in Brazilian hypertensive patients. These data suggest that genetic variation within NADPH-oxidase components may modulate left ventricular remodeling in subjects with systemic hypertension.