bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in Land–Atmosphere Interactions from CMIP5 Simulations
Authors: Dirmeyer Paul A. , Jin Yan , Singh Bohar , Yan Xiaoqin 
Published: January 2013

AbstractData from 15 models of phase 5 of the Coupled Model Intercomparison Project (CMIP5) for preindustrial, historical, and future climate change experiments are examined for consensus changes in land surface variables, fluxes, and metrics relevant to land–atmosphere interactions. Consensus changes in soil moisture and latent heat fluxes for past-to-present and present-to-future periods are consistent with CMIP3 simulations, showing a general drying trend over land (less soil moisture, less evaporation) over most of the globe, with the notable exception of high northern latitudes during winter. Sensible heat flux and net radiation declined from preindustrial times to current conditions according to the multimodel consensus, mainly due to increasing aerosols, but that trend reverses abruptly in the future projection. No broad trends are found in soil moisture memory except for reductions during boreal winter associated with high-latitude warming and diminution of frozen soils. Land–atmosphere coupling is projected to increase in the future across most of the globe, meaning a greater control by soil moisture variations on surface fluxes and the lower troposphere. There is also a strong consensus for a deepening atmospheric boundary layer and diminished gradients across the entrainment zone at the top of the boundary layer, indicating that the land surface feedback on the atmosphere should become stronger both in absolute terms and relative to the influence of the conditions of the free atmosphere. Coupled with the trend toward greater hydrologic extremes such as severe droughts, the land surface seems likely to play a greater role in amplifying both extremes and trends in climate on subseasonal and longer time scales.
A Physically Based Runoff Routing Model for Land Surface and Earth System Models
Authors: Li Hongyi , Wigmosta Mark S. , Wu Huan , Huang Maoyi , Ke Yinghai , Coleman André M. , Leung L. Ruby 
Published: January 2013

AbstractA new physically based runoff routing model, called the Model for Scale Adaptive River Transport (MOSART), has been developed to be applicable across local, regional, and global scales. Within each spatial unit, surface runoff is first routed across hillslopes and then discharged along with subsurface runoff into a “tributary subnetwork” before entering the main channel. The spatial units are thus linked via routing through the main channel network, which is constructed in a scale-consistent way across different spatial resolutions. All model parameters are physically based, and only a small subset requires calibration. MOSART has been applied to the Columbia River basin at ⅙°, ⅛°, ¼°, and ½° spatial resolutions and was evaluated using naturalized or observed streamflow at a number of gauge stations. MOSART is compared to two other routing models widely used with land surface models, the River Transport Model (RTM) in the Community Land Model (CLM) and the Lohmann routing model, included as a postprocessor in the Variable Infiltration Capacity (VIC) model package, yielding consistent performance at multiple resolutions. MOSART is further evaluated using the channel velocities derived from field measurements or a hydraulic model at various locations and is shown to be capable of producing the seasonal variation and magnitude of channel velocities reasonably well at different resolutions. Moreover, the impacts of spatial resolution on model simulations are systematically examined at local and regional scales. Finally, the limitations of MOSART and future directions for improvements are discussed.
Relation between Tropical Easterly Waves, Convection, and Tropical Cyclogenesis: A Lagrangian Perspective
Authors: Leppert Kenneth D. , Cecil Daniel J. , Petersen Walter A. 
Published: January 2013

Abstract
In this study, a wave-following Lagrangian framework was used to examine the evolution of tropical easterly wave structure, circulation, and convection in the days leading up to and including tropical cyclogenesis in the Atlantic and east Pacific basins. After easterly waves were separated into northerly, southerly, trough, and ridge phases using the National Centers for Environmental Prediction–National Center for Atmospheric Research reanalysis 700-hPa meridional wind, waves that developed a tropical cyclone [developing waves (DWs)] and waves that never developed a cyclone [nondeveloping waves (NDWs)] were identified. Day zero (D0) was defined as the day on which a tropical depression was identified for DWs or the day the waves achieved maximum 850-hPa vorticity for NDWs. Both waves types were then traced from five days prior to D0 (D − 5) through one day after D0. Results suggest that as genesis is approached for DWs, the coverage by convection and cold cloudiness (e.g., fractional coverage by infrared brightness temperatures ≤240 K) increases, while convective intensity (e.g., lightning flash rate) decreases. Therefore, the coverage by convection appears to be more important than the intensity of convection for tropical cyclogenesis. In contrast, convective coverage and intensity both increase from D − 5 to D0 for NDWs. Compared to NDWs, DWs are associated with significantly greater coverage by cold cloudiness, large-scale moisture throughout a deep layer, and large-scale, upper-level (~200 hPa) divergence, especially within the trough and southerly phases, suggesting that these parameters are most important for cyclogenesis and for distinguishing DWs from NDWs.
IL-17A is essential to the development of elastase-induced pulmonary inflammation and emphysema in mice
Authors: Kurimoto Etsuko , Miyahara Nobuaki , Kanehiro Arihiko , Waseda Koichi , Taniguchi Akihiko , Ikeda Genyo , Koga Hikari , Nishimori Hisakazu , Tanimoto Yasushi , Kataoka Mikio , Iwakura Yoichiro , Gelfand Erwin W , Tanimoto Mitsune 
Published: January 2013

Abstract

Background
Pulmonary emphysema is characterized by alveolar destruction and persistent inflammation of the airways. Although IL-17A contributes to many chronic inflammatory diseases, it’s role in the inflammatory response of elastase-induced emphysema remains unclear.

Methods
In a model of elastase-induced pulmonary emphysema we examined the response of IL-17A-deficient mice, monitoring airway inflammation, static compliance, lung histology and levels of neutrophil-related chemokine and pro-inflammatory cytokines in bronchoalveolar lavage (BAL) fluid.

Results
Wild-type mice developed emphysematous changes in the lung tissue on day 21 after elastase treatment, whereas emphysematous changes were decreased in IL-17A-deficient mice compared to wild-type mice. Neutrophilia in BAL fluid, seen in elastase-treated wild-type mice, was reduced in elastase-treated IL-17A-deficient mice on day 4, associated with decreased levels of KC, MIP-2 and IL-1 beta. Elastase-treated wild-type mice showed increased IL-17A levels as well as increased numbers of IL-17A+ CD4 T cells in the lung in the initial period following elastase treatment.

Conclusions
These data identify the important contribution of IL-17A in the development of elastase-induced pulmonary inflammation and emphysema. Targeting IL-17A in emphysema may be a potential therapeutic strategy for delaying disease progression.
Predicting PDZ domain mediated protein interactions from structure
Authors: Hui Shirley , Xing Xiang , Bader Gary D 
Published: January 2013

AbstractBackgroundPDZ domains are structural protein domains that recognize simple linear amino acid motifs, often at protein C-termini, and mediate protein-protein interactions (PPIs) in important biological processes, such as ion channel regulation, cell polarity and neural development. PDZ domain-peptide interaction predictors have been developed based on domain and peptide sequence information. Since domain structure is known to influence binding specificity, we hypothesized that structural information could be used to predict new interactions compared to sequence-based predictors.ResultsWe developed a novel computational predictor of PDZ domain and C-terminal peptide interactions using a support vector machine trained with PDZ domain structure and peptide sequence information. Performance was estimated using extensive cross validation testing. We used the structure-based predictor to scan the human proteome for ligands of 218 PDZ domains and show that the predictions correspond to known PDZ domain-peptide interactions and PPIs in curated databases. The structure-based predictor is complementary to the sequence-based predictor, finding unique known and novel PPIs, and is less dependent on training-testing domain sequence similarity. We used a functional enrichment analysis of our hits to create a predicted map of PDZ domain biology. This map highlights PDZ domain involvement in diverse biological processes, some only found by the structure-based predictor. Based on this analysis, we predict novel PDZ domain involvement in xenobiotic metabolism and suggest new interactions for other processes including wound healing and Wnt signalling.ConclusionsWe built a structure-based predictor of PDZ domain-peptide interactions, which can be used to scan C-terminal proteomes for PDZ interactions. We also show that the structure-based predictor finds many known PDZ mediated PPIs in human that were not found by our previous sequence-based predictor and is less dependent on training-testing domain sequence similarity. Using both predictors, we defined a functional map of human PDZ domain biology and predict novel PDZ domain function. Users may access our structure-based and previous sequence-based predictors athttp://webservice.baderlab.org/domains/POW.
Inferring homologous protein-protein interactions through pair position specific scoring matrix
Authors: Lin Chun-Yu , Chen Yung-Chiang , Lo Yu-Shu , Yang Jinn-Moon 
Published: January 2013

Abstract

Background
The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions. In the post-genomic era, to rapidly identify homologous PPIs for analyzing the contact residue pairs of their interfaces within DDIs on a genomic scale is essential to determine PPI networks and the PPI interface evolution across multiple species.

Results
In this study, we proposed "pair P osition S pecific S coring M atrix (pair PSSM)" to identify homologous PPIs. The pair PSSM can successfully distinguish the true protein complexes from unreasonable protein pairs with about 90% accuracy. For the test set including 1,122 representative heterodimers and 2,708,746 non-interacting protein pairs, the mean average precision and mean false positive rate of pair PSSM were 0.42 and 0.31, respectively. Moreover, we applied pair PSSM to identify ~450,000 homologous PPIs with their interacting domains and residues in seven common organisms (e.g. Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Escherichia coli).

Conclusions
Our pair PSSM is able to provide statistical significance of residue pairs using evolutionary profiles and a scoring system for inferring homologous PPIs. According to our best knowledge, the pair PSSM is the first method for searching homologous PPIs across multiple species using pair position specific scoring matrix and a 3D dimer as the template to map interacting domain pairs of these PPIs. We believe that pair PSSM is able to provide valuable insights for the PPI evolution and networks across multiple species.
A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees
Authors: Sand Andreas , Brodal Gerth Stølting , Fagerberg Rolf , Pedersen Christian NS , Mailund Thomas 
Published: January 2013

Abstract
The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equal or different. We present an algorithm that computes the triplet distance between two rooted binary trees in time O (n log2
n). The algorithm is related to an algorithm for computing the quartet distance between two unrooted binary trees in time O (n log n). While the quartet distance algorithm has a very severe overhead in the asymptotic time complexity that makes it impractical compared to O (n
2) time algorithms, we show through experiments that the triplet distance algorithm can be implemented to give a competitive wall-time running time.
Building Markov state models with solvent dynamics
Authors: Gu Chen , Chang Huang-Wei , Maibaum Lutz , Pande Vijay S , Carlsson Gunnar E , Guibas Leonidas J 
Published: January 2013

Abstract

Background
Markov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dynamics. However, the solvent information in molecular simulations are often ignored in current methods, because of the large number of solvent molecules in a system and the indistinguishability of solvent molecules upon their exchange.

Methods
We present a solvent signature that compactly summarizes the solvent distribution in the high-dimensional data, and then define a distance metric between different configurations using this signature. We next incorporate the solvent information into the construction of Markov state models and present a fast geometric clustering algorithm which combines both the solute-based and solvent-based distances.

Results
We have tested our method on several different molecular dynamical systems, including alanine dipeptide, carbon nanotube, and benzene rings. With the new solvent-based signatures, we are able to identify different solvent distributions near the solute. Furthermore, when the solute has a concave shape, we can also capture the water number inside the solute structure. Finally we have compared the performances of different Markov state models. The experiment results show that our approach improves the existing methods both in the computational running time and the metastability.

Conclusions
In this paper we have initiated an study to build Markov state models for molecular dynamical systems with solvent degrees of freedom. The methods we described should also be broadly applicable to a wide range of biomolecular simulation analyses.
Expanding the boundaries of local similarity analysis
Authors: Durno W Evan , Hanson Niels W , Konwar Kishori M , Hallam Steven J 
Published: January 2013

Abstract

Background
Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets.

Results
To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm
2
n) to O(m
2
n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FAST LSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software.

Conclusions
The FAST LSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FAST LSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.
Disease resistance is related to inherent swimming performance in Atlantic salmon
Authors: Castro Vicente , Grisdale-Helland Barbara , Jørgensen Sven M , Helgerud Jan , Claireaux Guy , Farrell Anthony P , Krasnov Aleksei , Helland Ståle J , Takle Harald 
Published: January 2013

Abstract

Background
Like humans, fish can be classified according to their athletic performance. Sustained exercise training of fish can improve growth and physical capacity, and recent results have documented improved disease resistance in exercised Atlantic salmon. In this study we investigated the effects of inherent swimming performance and exercise training on disease resistance in Atlantic salmon.
Atlantic salmon were first classified as either poor or good according to their swimming performance in a screening test and then exercise trained for 10 weeks using one of two constant-velocity or two interval-velocity training regimes for comparison against control trained fish (low speed continuously). Disease resistance was assessed by a viral disease challenge test (infectious pancreatic necrosis) and gene expression analyses of the host response in selected organs.

Results
An inherently good swimming performance was associated with improved disease resistance, as good swimmers showed significantly better survival compared to poor swimmers in the viral challenge test. Differences in mortalities between poor and good swimmers were correlated with cardiac mRNA expression of virus responsive genes reflecting the infection status. Although not significant, fish trained at constant-velocity showed a trend towards higher survival than fish trained at either short or long intervals. Finally, only constant training at high intensity had a significant positive effect on fish growth compared to control trained fish.

Conclusions
This is the first evidence suggesting that inherent swimming performance is associated with disease resistance in fish.
Mobile technology supporting trainee doctors’ workplace learning and patient care: an evaluation
Authors: Hardyman Wendy , Bullock Alison , Brown Alice , Carter-Ingram Sophie , Stacey Mark 
Published: January 2013

Abstract

Background
The amount of information needed by doctors has exploded. The nature of knowledge (explicit and tacit) and processes of knowledge acquisition and participation are complex. Aiming to assist workplace learning, Wales Deanery funded “iDoc”, a project offering trainee doctors a Smartphone library of medical textbooks.

Methods
Data on trainee doctors’ (Foundation Year 2) workplace information seeking practice was collected by questionnaire in 2011 (n = 260). iDoc baseline questionnaires (n = 193) collected data on Smartphone usage alongside other workplace information sources. Case reports (n = 117) detail specific instances of Smartphone use.

Results
Most frequently (daily) used information sources in the workplace: senior medical staff (80% F2 survey; 79% iDoc baseline); peers (70%; 58%); and other medical/nursing team staff (53% both datasets). Smartphones were used more frequently by males (p < 0.01). Foundation Year 1 (newly qualified) was judged the most useful time to have a Smartphone library because of increased responsibility and lack of knowledge/experience.
Preferred information source varied by question type: hard copy texts for information-based questions; varied resources for skills queries; and seniors for more complex problems. Case reports showed mobile technology used for simple (information-based), complex (problem-based) clinical questions and clinical procedures (skills-based scenarios). From thematic analysis, the Smartphone library assisted: teaching and learning from observation; transition from medical student to new doctor; trainee doctors’ discussions with seniors; independent practice; patient care; and this ‘just-in-time’ access to reliable information supported confident and efficient decision-making.

Conclusion
A variety of information sources are used regularly in the workplace. Colleagues are used daily but seniors are not always available. During transitions, constant access to the electronic library was valued. It helped prepare trainee doctors for discussions with their seniors, assisting the interchange between explicit and tacit knowledge.
By supporting accurate prescribing and treatment planning, the electronic library contributed to enhanced patient care. Trainees were more rapidly able to medicate patients to reduce pain and more quickly call for specific assessments. However, clinical decision-making often requires dialogue: what Smartphone technology can do is augment, not replace, discussion with their colleagues in the community of practice.
Microstructure and optical properties of Pr3+-doped hafnium silicate films
Authors: An YongTao , Labbé Christophe , Khomenkova Larysa , Morales Magali , Portier Xavier , Gourbilleau Fabrice 
Published: January 2013

Abstract
In this study, we report on the evolution of the microstructure and photoluminescence properties of Pr3+-doped hafnium silicate thin films as a function of annealing temperature (T
A). The composition and microstructure of the films were characterized by means of Rutherford backscattering spectrometry, spectroscopic ellipsometry, Fourier transform infrared absorption, and X-ray diffraction, while the emission properties have been studied by means of photoluminescence (PL) and PL excitation (PLE) spectroscopies. It was observed that a post-annealing treatment favors the phase separation in hafnium silicate matrix being more evident at 950°C. The HfO2 phase demonstrates a pronounced crystallization in tetragonal phase upon 950°C annealing. Pr3+ emission appeared at T
A = 950°C, and the highest efficiency of Pr3+ ion emission was detected upon a thermal treatment at 1,000°C. Analysis of the PLE spectra reveals an efficient energy transfer from matrix defects towards Pr3+ ions. It is considered that oxygen vacancies act as effective Pr3+ sensitizer. Finally, a PL study of undoped HfO2 and HfSiO
x
matrices is performed to evidence the energy transfer.
On the transcendence of some power series
Authors: Karadeniz Gözeri Gül , Pekin Ayten , Kılıçman Adem 
Published: January 2013

AbstractIn this study, we consider some power series with rational coefficients and investigate transcendence of the values of these series for Liouville number arguments. It is proved that these values are either a Liouville number or a rational number under certain conditions.AMS Subject Classification:11J81, 11J17.