bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse
Authors: Shin Chang Jin , Davis Melissa J. , Ragan Mark A. 
Published: October 2009

AbstractProtein–protein interactions (PPIs) underpin key biological processes in cells. Describing and interpreting this network of interactions is a key focus of computational systems biology. While mouse is commonly used as a model system for mammalian biology, the description of mouse PPIs available in public interaction databases is remarkably poor. Collectively, public resources such as BIND, IntACT and MINT contain only a few thousand mouse PPIs, far behind the many tens or hundreds of thousands likely to exist. To supplement this lack and to take advantage of other high‐throughput omic data sets in mouse, here we identify that portion of the human interactome with orthologs in mouse, and from that infer a mouse interolog network. By inferring interactions in mouse based on only the most closely related species with abundant PPI data (human), we create a view of mouse interactions enriched for shared mammalian biological processes. We also demonstrate that available methods for determining orthologs between even closely related species produce distinctly different results, and we propose an integrated view of mouse–human orthology from which to infer a broader interolog network.
Experimental and computational tools useful for (re)construction of dynamic kinase–substrate networks
Authors: Tan Chris Soon Heng , Linding Rune 
Published: October 2009

AbstractThe explosion of site‐ and context‐specific in vivo phosphorylation events presents a potentially rich source of biological knowledge and calls for novel data analysis and modeling paradigms. Perhaps the most immediate challenge is delineating detected phosphorylation sites to their effector kinases. This is important for (re)constructing transient kinase–substrate interaction networks that are essential for mechanistic understanding of cellular behaviors and therapeutic intervention, but has largely eluded high‐throughput protein‐interaction studies due to their transient nature and strong dependencies on cellular context. Here, we surveyed some of the computational approaches developed to dissect phosphorylation data detected in systematic proteomic experiments and reviewed some experimental and computational approaches used to map phosphorylation sites to their effector kinases in efforts aimed at reconstructing biological signaling networks.
Benchmarking yeast two‐hybrid systems using the interactions of bacterial motility proteins
Authors: Rajagopala Seesandra Venkatappa , Hughes Kelly T. , Uetz Peter 
Published: October 2009

AbstractYeast two‐hybrid screens often produce vastly non‐overlapping interaction data when the screens are conducted in different laboratories, or use different vectors, strains, or reporter genes. Here we investigate the underlying reasons for such inconsistencies and compare the effect of seven different vectors and their yeast two‐hybrid interactions. Genome‐wide array screens with 49 motility‐related baits from Treponema pallidum yielded 77 and 165 interactions with bait vectors pLP‐GBKT7 and pAS1‐LP, respectively, including 21 overlapping interactions. In addition, 90 motility‐related proteins from Escherichia coli were tested in all pairwise combinations and yielded 140 interactions when tested with pGBKT7g/pGADT7g vectors but only 47 when tested with pDEST32/pDEST22. We discuss the factors that determine these effects, including copy number, the nature of the fusion protein, and species‐specific differences that explain non‐conserved interactions among species. The pDEST22/pDEST32 vectors produce a higher fraction of interactions that are conserved and that are biologically relevant when compared with the pGBKT7/pGADT7‐related vectors, but the latter appear to be more sensitive and thus detect more interactions overall.
Gram‐positive bacteria produce membrane vesicles: Proteomics‐based characterization of Staphylococcus aureus‐derived membrane vesicles
Authors: Lee Eun‐Young , Choi Do‐Young , Kim Dae‐Kyum , Kim Jung‐Wook , Park Jung Ok , Kim Sungjee , Kim Sang‐Hyun , Desiderio Dominic M. , Kim Yoon‐Keun , Kim Kwang‐Pyo , Gho Yong Song 
Published: October 2009

AbstractAlthough archaea, Gram‐negative bacteria, and mammalian cells constitutively secrete membrane vesicles (MVs) as a mechanism for cell‐free intercellular communication, this cellular process has been overlooked in Gram‐positive bacteria. Here, we found for the first time that Gram‐positive bacteria naturally produce MVs into the extracellular milieu. Further characterizations showed that the density and size of Staphylococcus aureus‐derived MVs are both similar to those of Gram‐negative bacteria. With a proteomics approach, we identified with high confidence a total of 90 protein components of S. aureus‐derived MVs. In the group of identified proteins, the highly enriched extracellular proteins suggested that a specific sorting mechanism for vesicular proteins exists. We also identified proteins that facilitate the transfer of proteins to other bacteria, as well to eliminate competing organisms, antibiotic resistance, pathological functions in systemic infections, and MV biogenesis. Taken together, these observations suggest that the secretion of MVs is an evolutionally conserved, universal process that occurs from simple organisms to complex multicellular organisms. This information will help us not only to elucidate the biogenesis and functions of MVs, but also to develop therapeutic tools for vaccines, diagnosis, and antibiotics effective against pathogenic strains of Gram‐positive bacteria.
Other than IPG‐DALT: 2‐DE variants
Authors: Miller Ingrid , Eberini Ivano , Gianazza Elisabetta 
Published: October 2009

AbstractSpecial problems require special solutions. That is why, despite the trend towards standardization of the procedures in proteomic investigations, a number of alternative protocols, based on 2‐DE, have been devised with time and are applied to the resolution of proteins on which the performance of IPG‐DALT is poor. The difficult‐to‐handle samples include high pI, high molecular size and high hydrophobicity proteins. The protocol variants entail changes in the gel media and/or the use of unusual additives (often surfactants or solvents). But also:Specific questions require specific answers. When the aim is not the resolution of individual polypeptide chains in a fully unfolded state but the analysis of higher‐order structures (proteins assembled from subunits, complexes assembled from interacting proteins) the standard conditions under which IPG‐DALT is performed turn inadequate. Electrophoresis is then performed either in first dimension or in both first dimension and second dimension under non‐denaturing (native) and/or non‐reducing conditions.
Technologies for plasma membrane proteomics
Authors: Cordwell Stuart J. , Thingholm Tine E. 
Published: October 2009

AbstractCell–cell and intracellular signaling are critical mechanisms by which an organism can respond quickly and appropriately to internal or environmental stimuli. Transmission of the stimulus to effector proteins must be coordinated, rapid and transient such that the response is not exaggerated and the overall balance of the cell or tissue is retained. Proteomics technology has traditionally been adept at analyzing effector proteins (such as cytoskeletal and heat shock proteins, and those involved in metabolic processes) in studies examining the effects of altered environmental or nutritional conditions, drugs, or genetic manipulation, since these proteins are often highly abundant, soluble and therefore amenable to analysis. Conversely, the proteins mediating the transmission of the signal have been generally under‐represented, typically because of their low abundance. One mechanism that has overcome this to some extent is the advent of very high‐resolution phosphoproteomics techniques, which have enabled temporal profiling of intracellular signal pathways via quantitative assessment of peptide phosphorylation sites. One group of proteins, however, that still remains under‐represented in proteomics studies are those found in the plasma membrane (PM). Such proteins are crucial in sensing changes in the external environment and in stimulating the transmission of the signal intracellularly. This review examines PM proteins and appraises the proteomics approaches currently available for providing a comprehensive analysis of these crucial mediators of signal pathways. We discuss different strategies for enrichment and solubilization of these proteins and include discussion on cross‐linking of PM complexes and glycoproteomics as the basis for purification prior to proteomic analyses.
Intrathoracic nontuberculous mycobacterial infections in otherwise healthy children
Authors: Freeman Alexandra F. , Olivier Kenneth N. , Rubio Thomas T. , Bartlett Glen , Ochi James W , Claypool Reginald J. , Ding Li , Kuhns Douglas B. , Holland Steven M. 
Published: October 2009

AbstractBackgroundNontuberculous mycobacterial (NTM) infection is typically associated with lymphadenitis in immune competent children, and disseminated disease in children with immune deficiencies. Isolated pulmonary NTM disease is seen in cystic fibrosis, and is increasingly recognized in immunocompetent elderly women, where it is associated with an increased incidence of cystic fibrosis transmembrane regulator (CFTR) mutations. Thoracic NTM infection has been reported rarely in otherwise healthy children. We aimed to determine whether otherwise healthy children with pulmonary NTM disease had immunologic abnormalities or CFTR mutations. Clinical presentations of five otherwise healthy children with pulmonary NTM were reviewed. Immunologic studies were performed including a complete blood cell count (CBC), flow cytometric lymphocyte phenotyping and IFN‐gamma receptor expression, in vitro cytokine stimulation, and serum immunoglobulin levels. Mutational analysis was performed for CFTR. The children ranged in age from 12 months to 2.5 years at diagnosis. Four presented with new onset wheezing or stridor failing bronchodilator therapy. One child was asymptomatic. Endobronchial lesions and/or hilar lymph nodes causing bronchial obstruction were identified in all patients. Mycobacterium avium complex was cultured from four patients, and Mycobacterium abscessus from one patient. All patients were successfully treated with anti‐mycobacterial therapy with or without surgery. No definitive immunologic abnormalities were identified. No clinically significant mutations were found in CFTR. Pulmonary NTM infection should be considered in otherwise healthy young children presenting with refractory stridor or wheezing with endobronchial lesions or hilar lymphadenopathy. It does not appear to be associated with recognized underlying immune deficiency or CFTR mutations. Pediatr Pulmonol. 2009; 44:1051–1056. ©2009 Wiley‐Liss, Inc.
Daycare attendance and risk for respiratory morbidity among young very low birth weight children
Authors: Hagen Erika W. , Sadek‐Badawi Mona , Palta Mari 
Published: October 2009

AbstractDaycare attendance and very low birth weight (VLBW, ≤1,500 g) are associated with respiratory morbidity during childhood. The objective of this study was to evaluate whether daycare attendance is associated with even higher risk for respiratory problems among VLBW children. We hypothesized that VLBW children attending daycare, in a private home or daycare center, are at higher risk for respiratory problems than VLBW children not attending daycare. We also investigated whether the effect of daycare is independent or synergistic with respiratory risk resulting from being VLBW, as indicated by having bronchopulmonary dysplasia (BPD) as a neonate. We conducted a prospective study of VLBW children followed from birth to age 2–3 (N = 715). Logistic regression was used to evaluate the relationship between daycare attendance and respiratory problems, adjusting for known neonatal risk factors for poor respiratory outcomes. Attending daycare in either a private home or in a daycare center was significantly associated with higher risk of lower respiratory infections than never attending. Attending a daycare center was also associated with higher risk for wheezy chest, cough without a cold, and respiratory medication use. While having BPD was associated with increased risk for respiratory problems, daycare attendance and BPD were not found to be synergistic risk factors for respiratory problems among VLBW children, but acted independently to increase risk. This implies that the increase in risk for respiratory problems associated with daycare attendance may be similar among VLBW children and those of normal birth weight. Pediatr Pulmonol. 2009; 44:1093–1099. ©2009 Wiley‐Liss, Inc.
Cystic fibrosis HRCT scores correlate strongly with pseudomonas infection
Authors: Robinson Terry E. , Leung Ann N. , Chen Xiaorong , Moss Richard B. , Emond M.J. 
Published: October 2009

AbstractBackgroundIn order to establish a valid surrogate outcome measure, it must be shown that the outcome measure (chest HRCT scores in cystic fibrosis [CF] patients) demonstrates strong statistical association with established endpoints of disease, such as Pseudomonas aeruginosa (Pa) airway acquisition, acute exacerbations, or mortality.MethodsWe estimated and tested the association between Pa infection status (Pa+ vs. Pa−) and baseline chest HRCT scores in 25 children with mild‐to‐moderate CF lung disease. For comparison, we estimated the association between Pa status and pulmonary function tests (PFTs), chest X‐rays (CXR) scores, and BMI. Pa acquisition was determined from respiratory culture results and systematic review of clinic notes.ResultsAll subjects had respiratory cultures performed prior to or at baseline with a median of 19 months of retrospective culture observation (SD = 15.7 months, range: 0–52.5 months). The difference between age‐adjusted mean total HRCT score for Pa+ versus Pa− was highly significant (P < 0.00001) with a near‐perfect separation between scores in Pa+ versus Pa− patients. Similar results were found for several HRCT sub‐scores. Among PFTs, only residual volume‐to‐total lung capacity (RV/TLC) had a significant difference between group means (P = 0.03), but the overlap between groups in RV/TLC measurements was large.ConclusionsCF HRCT scores correlate highly with Pa acquisition, a clinically meaningful measure of progressing CF lung disease. HRCT scores are highly sensitive at predicting Pa acquisition status, while most PFT measures, chest radiograph (CXR) scores, and body mass index are not. These results provide further evidence that HRCT is appropriate for use in patient care and as an outcome measure in clinical trials. Pediatr Pulmonol. 2009; 44:1107–1117. ©2009 Wiley‐Liss, Inc.
Effect of spray application technique on spray deposition in greenhouse strawberries and tomatoes
Authors: Braekman Pascal , Foque Dieter , Messens Winy , Van Labeke Marie‐Christine , Pieters Jan G , Nuyttens David 
Published: October 2009

AbstractBACKGROUND: Increasingly, Flemish greenhouse growers are using spray booms instead of spray guns to apply plant protection products. Although the advantages of spray booms are well known, growers still have many questions concerning nozzle choice and settings. Spray deposition using a vertical spray boom in tomatoes and strawberries was compared with reference spray equipment. Five different settings of nozzle type, size and pressure were tested with the spray boom.RESULTS: In general, the standard vertical spray boom performed better than the reference spray equipment in strawberries (spray gun) and in tomatoes (air‐assisted sprayer). Nozzle type and settings significantly affected spray deposition and crop penetration. Highest overall deposits in strawberries were achieved using air‐inclusion or extended‐range nozzles. In tomatoes, the extended‐range nozzles and the twin air‐inclusion nozzles performed best. Using smaller‐size extended‐range nozzles above the recommended pressure range resulted in lower deposits, especially inside the crop canopy.CONCLUSIONS: The use of a vertical spray boom is a promising technique for applying plant protection products in a safe and efficient way in tomatoes and strawberries, and nozzle choice and setting should be carefully considered. Copyright © 2009 Society of Chemical Industry
Single‐wall carbon nanotubes: spintronics in the Luttinger liquid phase
Authors: Dóra Balázs , Gulácsi Miklós , Rusznyák Ádám , Koltai János , Zólyomi Viktor , Kürti Jenö , Simon Ferenc 
Published: October 2009

AbstractWe study the electron spin resonance (ESR) intensity in the Luttinger liquid phase of carbon nanotubes. The ESR measurables such as the signal intensity and the line‐width are calculated in the framework of Luttinger liquid theory with broken spin rotational symmetry as a function of magnetic field and temperature. The linewidth is broadened significantly at high temperatures, and the intensity is well describes by Lorentzians. At very low temperatures, however, the ESR lineshape becomes asymmetric around the resonance, and is characterized by threshold behavior. These observables are of special importance for the spintronics applications of carbon nanotubes.
Control of p‐doping on single‐walled carbon nanotubes with nitronium hexafluoroantimonate in liquid phase
Authors: Kim Ki Kang , Bae Jung Jun , Kim Soo Min , Park Hyeon Ki , An Kay Hyeok , Lee Young Hee 
Published: October 2009

AbstractWe report that nitronium hexafluoroantimonate (NHFA) can be used as a strong p‐type dopant on single‐walled carbon nanotubes (SWCNTs). The diameter range of SWCNTs in this work ranged from 1.2 to 1.8 nm. The NHFA was dissolved in a mixed solution of tetramethylsilane/1,2‐dichloroethane (1:1 by weight) with SWCNTs. The treated samples in liquid phase were characterized by UV–VIS–NIR absorption and Raman spectroscopies. We found that with increasing the NHFA concentration, the van Hove singularity‐related transitions (${\rm E}_{11}^{\rm S}$, ${\rm E}_{22}^{\rm S}$, and ${\rm E}_{11}^{\rm M}$) in the optical absorption spectra disappeared gradually and a new transition peak was clearly observed near 1.33 eV. G‐band in the Raman spectra was upshifted to 1618 cm−1 from 1587 cm−1 of the pristine peak due to the phonon stiffening, an evidence of p‐type doping. The sheet resistance of the SWCNT film was reduced up to 90%. After thermal annealing, the Raman spectra were recovered, similar to those of the pristine sample without any damage.
Online three‐dimensional SLAM by registration of large planar surface segments and closed‐form pose‐graph relaxation
Authors: Pathak Kaustubh , Birk Andreas , Vaskevicius Narunas , Pfingsthorn Max , Schwertfeger Sören , Poppinga Jann 
Published: October 2009

AbstractA fast pose‐graph relaxation technique is presented for enhancing the consistency of three‐dimensional (3D) maps created by registering large planar surface patches. The surface patches are extracted from point clouds sampled from a 3D range sensor. The plane‐based registration method offers an alternative to the state‐of‐the‐art algorithms and provides advantages in terms of robustness, speed, and storage. One of its features is that it results in an accurate determination of rotation, although a lack of predominant surfaces in certain directions may result in translational uncertainty in those directions. Hence, a loop‐closing and relaxation problem is formulated that gains significant speed by relaxing only the translational errors and utilizes the full‐translation covariance determined during pairwise registration. This leads to a fast 3D simultaneous localization and mapping suited for online operations. The approach is tested in two disaster scenarios that were mapped at the NIST 2008 Response Robot Evaluation Exercise in Disaster City, Texas. The two data sets from a collapsed car park and a flooding disaster consist of 26 and 70 3D scans, respectively. The results of these experiments show that our approach can generate 3D maps without motion estimates by odometry and that it outperforms iterative closest point–based mapping with respect to speed and robustness. © 2009 Wiley Periodicals, Inc.
Mining maximal quasi‐bicliques: Novel algorithm and applications in the stock market and protein networks
Authors: Sim Kelvin , Li Jinyan , Gopalkrishnan Vivekanand , Liu Guimei 
Published: October 2009

AbstractSeveral real‐world applications require mining of bicliques, as they represent correlated pairs of data clusters. However, the mining quality is adversely affected by missing and noisy data. Moreover, some applications only requirestronginteractions between data members of the pairs, but bicliques are pairs that displaycompleteinteractions. We address these two limitations by proposingmaximal quasi‐bicliques. Maximal quasi‐bicliques tolerate erroneous and missing data, and also relax the interactions between the data members of their pairs. Besides, maximal quasi‐bicliques do not suffer from skewed distribution of missing edges that prior quasi‐bicliques have. We develop an algorithmMQBminer, which mines the complete set of maximal quasi‐bicliques from either bipartite or non‐bipartite graphs. We demonstrate the versatility and effectiveness of maximal quasi‐bicliques to discover highly correlated pairs of data in two diverse real‐world datasets. First, we propose to solve a novel financial stocks analysis problem using maximal quasi‐bicliques to co‐cluster stocks and financial ratios. Results show that the stocks in our co‐clusters usually have significant correlations in their price performance. Second, we use maximal quasi‐bicliques on a mining protein network problem and we show that pairs of protein groups mined by maximal quasi‐bicliques are more significant than those mined by maximal bicliques. Copyright © 2009 Wiley Periodicals, Inc., A Wiley Company
Does self‐efficacy affect entrepreneurial investment?
Authors: Cassar Gavin , Friedman Henry 
Published: October 2009

AbstractWe empirically examine the effect of self‐efficacy on entrepreneurial investment choices. We identify various attributes of entrepreneurial investment and argue that higher self‐efficacy is associated with more aggressive entrepreneurial investment decisions. We show that self‐efficacy increases the likelihood of being a nascent entrepreneur and creating an operating business. Self‐efficacy also increases the proportion of personal wealth invested in the venture and the amount of hours per week the entrepreneur devotes to the venture. These results are significant even when controlling for other known characteristics associated with entrepreneurial investment. Copyright © 2009 Strategic Management Society.