bluuebunny/crossref_metadata_2025_split huggingface dataset:
El rol de las variables de nivel individual en la formación de capital social organizativo. El caso de una microempresa de base tecnológica
Authors: Roman Castillo Ruth Esperanza , Smida Ali 
Published: June 2013

La noción de “capital social organizativo” (CSO) exalta los beneficios del desarrollo y mantenimiento de relaciones sociales internas y externas de calidad por una empresa. Este artículo presenta el caso de « Kirvit Ltda », una microempresa de base tecnológica colombiana. El objetivo es analizar los momentos de formación de CSO que acompañan la innovación de uno de sus productos, focalizados sobre la acción de tres variables llamadas “de nivel individual”. El tipo de empresa analizado se utiliza igualmente para reflexionar sobre las particularidades de la formación de CSO con respecto al tamaño y naturaleza de la empresa.
Using the iPlant Collaborative Discovery Environment
Authors: Oliver Shannon L. , Lenards Andrew J. , Barthelson Roger A. , Merchant Nirav , McKay Sheldon J. 
Published: June 2013

AbstractThe iPlant Collaborative is an academic consortium whose mission is to develop an informatics and social infrastructure to address the “grand challenges” in plant biology. Its cyberinfrastructure supports the computational needs of the research community and facilitates solving major challenges in plant science. The Discovery Environment provides a powerful and rich graphical interface to the iPlant Collaborative cyberinfrastructure by creating an accessible virtual workbench that enables all levels of expertise, ranging from students to traditional biology researchers and computational experts, to explore, analyze, and share their data. By providing access to iPlant's robust data‐management system and high‐performance computing resources, the Discovery Environment also creates a unified space in which researchers can access scalable tools. Researchers can use available Applications (Apps) to execute analyses on their data, as well as customize or integrate their own tools to better meet the specific needs of their research. These Apps can also be used in workflows that automate more complicated analyses. This module describes how to use the main features of the Discovery Environment, using bioinformatics workflows for high‐throughput sequence data as examples. Curr. Protoc. Bioinform. 42:1.22.1‐1.22.26. © 2013 by John Wiley & Sons, Inc.
Phylogenetic Analysis with the iPlant Discovery Environment
Authors: Matasci Naim , McKay Sheldon 
Published: June 2013

AbstractThe iPlant Collaborative's Discovery Environment is a unified Web portal to many bioinformatics applications and analytical workflows, including various methods of phylogenetic analysis. This unit describes example protocols for phylogenetic analyses, starting at sequence retrieval from the GenBank sequence database, through to multiple sequence alignment inference and visualization of phylogenetic trees. Methods for extracting smaller sub‐trees from very large phylogenies, and the comparative method of continuous ancestral character state reconstruction based on observed morphology of extant species related to their phylogenetic relationships, are also presented. Curr. Protoc. Bioinform. 42:6.13.1‐6.13.13. © 2013 by John Wiley & Sons, Inc.
Creating Databases for Biological Information: An Introduction
Authors: Stein Lincoln 
Published: June 2013

AbstractThe essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, relational databases, and NoSQL databases. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system. Curr. Protoc. Bioinform. 42:9.1.1‐9.1.10. © 2013 by John Wiley & Sons, Inc.
Cell‐Based Proteome Profiling Using an Affinity‐Based Probe (AfBP) Derived from 3‐Deazaneplanocin A (DzNep)
Authors: Tam Eric K. W. , Li Zhengqiu , Goh Yi Ling , Cheng Xiamin , Wong Sze Yue , Santhanakrishnan Sridhar , Chai Christina L. L. , Yao Shao Q. 
Published: June 2013

Abstract3‐Deazaneplanocin A (DzNep), a global histone methylation inhibitor, has attracted significant interest in epigenetic research in recent years. The molecular mechanism of action and the cellular off‐targets of DzNep, however, are still not well‐understood. Our aim was to develop novel DzNep‐derived small‐molecule probes suitable to be used in live mammalian cells for identification of potential cellular targets of DzNep under physiologically relevant settings. In the current study, we have successfully designed, synthesized, and tested one such probe, called Dz-1. Dz-1 is a ‘clickable’ affinity‐based probe (AfBP) derived from DzNep with minimal structural modifications. The probe was found to be highly cell‐permeable, and possessed similar anti‐apoptotic activities as DzNep in MCF‐7 mammalian cells. Two additional control probes were made as negative labeling/pull‐down probes in order to minimize false identification of background proteins due to unavoidable, intrinsic nonspecific photo‐crosslinking reactions. All three probes were subsequently used for in‐situ proteome profiling in live mammalian cells, followed by large‐scale pull‐down/LC‐MS/MS analysis for identification of potential cellular protein targets that might interact with DzNep in native cellular environments. Our LC‐MS/MS results revealed some highly enriched proteins that had not been reported as potential DzNep targets. These proteins might constitute unknown cellular off‐targets of DzNep. Though further validation experiments are needed in order to unequivocally confirm these off‐targets, our findings shed new light on the future use of DzNep as a validated chemical probe for epigenetic research and as a potential drug candidate for cancer therapy.
A Robust Tracking Control for a Class of Uncertain Chaotic Systems
Authors: Chang Yeong‐Chan 
Published: June 2013

AbstractThis paper addresses the problem of designing robust tracking control for a large class of uncertain nonlinear chaotic systems. This class of chaotic systems can be perturbed simultaneously by plant uncertainties, unmodeled time‐varying perturbations, time delays, and external disturbances. Through the backstepping design procedure and suitably choosing the Lyapunov–Krasovskii functionals, a hybrid adaptive robust tracking control scheme is developed such that all of the states and signals of the closed‐loop system are bounded and the tracking error is uniformly ultimately bounded. Consequently, the control scheme developed here can be extended to handle robust tracking control for a broader class of perturbed nonlinear chaotic systems involving a significant degree of uncertainty. Finally, a simulation is made to demonstrate the effectiveness of the proposed control algorithms.
In silico design and construction of metal‐binding hybrid proteins for specific removal of cadmium based on CS3 pili display on the surface of Escherichia coli
Authors: Eskandari Vajiheh , Yakhchali Bagher , Sadeghi Mehdi , Karkhane Ali Asghar 
Published: June 2013

AbstractIn this study, through a combination of bioinformatics and genetic engineering procedures, high‐affinity metal‐binding peptides were designed and expressed on the surface of Escherichia coli for selective Cd2+ adsorption. Putative cadmium‐binding motifs were identified by searches against the Prosite database and permissive sites in the major subunit (CstH) of the enterotoxigenic E. coli pili were predicted based on the data derived from modeling of 3D structures, secondary structure prediction and assignment, inspection of protein hydropathy and exposed regions, and also protein interaction sites. The metal‐binding motifs were inserted into one permissive site of the CstH (amino acid 38) with the aid of the SOEing PCR technique. The capacity and selectivity of the recombinant bacteria displaying hybrid pili to adsorb cadmium were evaluated with the atomic absorption procedure. The levels of Cd2+ accumulation in the recombinant E. coli strains were 13.9‐ and 11.33‐fold higher than those in the control strain. Cd2+ was selectively absorbed from a solution containing equal concentrations of four metals, resulting in more than 90% of the total adsorbed metals being Cd2+, showing a relatively high affinity for Cd2+ over other coexisting metal ions.
Experimental characterization of next‐generation expanded‐bed adsorbents for capture of a recombinant protein expressed in high‐cell‐density yeast fermentation
Authors: Kelly William , Garcia Phillip , McDermott Stefanie , Mullen Peter , Kamguia Guy , Jones Gerard , Ubiera Antonio , Göklen Kent 
Published: June 2013

AbstractExpanded‐bed adsorption (EBA) can be particularly useful in protein recovery from high‐cell‐density fermentation broth where conventional methods for harvest and clarification, such as continuous centrifugation and depth filtration, demand long processing times and are associated with high costs. In this work, the use of next‐generation high‐particle‐density EBA adsorbents, including two mixed‐mode resins, for the direct capture of a recombinant protein expressed in yeast at high cell densities is evaluated. Using classical experimental approaches and under different conditions (pH, salt, etc.), Langmuir isotherm parameters for these resins are obtained along with pore diffusivity values. Additional batch adsorption studies with Fastline® MabDirect, the resin that demonstrated the highest static binding capacity for the recombinant protein of interest under the conditions evaluated in this study, indicate competitive binding of nontarget proteins and approximately a 30% reduction in equilibrium binding capacity to 50 mg/mL settled bed in the presence of a 5%–10% cell concentration. Packed‐bed (PB) dynamic binding capacities for the MabDirect resin (25–40 mg/mL PB) were significantly higher than for the Fastline® HSA resin and for the MabDirect MM resin in expanded‐bed mode (5–10 mg/mL settled bed). Bed expansion behavior for the mMabDirect MM resin along with process yield and eluate purity are identified as a function of linear velocity and cell density, demonstrating process feasibility for pilot scale use.
Dorsal and ventral stimuli in sandwich‐like microenvironments. Effect on cell differentiation
Authors: Ballester‐Beltrán José , Lebourg Myriam , Salmerón‐Sánchez Manuel 
Published: June 2013

ABSTRACTWhile most of the in vivo extracellular matrices are 3D, most of the in vitro cultures are 2D—where only ventral adhesion is permitted—thus modifying cell behavior as a way to self‐adaptation to this unnatural environment. We hypothesize that the excitation of dorsal receptors in cells already attached on a 2D surface (sandwich culture) could cover the gap between 2D and 3D cell–material interactions and result in a more physiological cell behavior. In this study we investigate the role of dorsal stimulation on myoblast differentiation within different poly(L‐lactic acid) (PLLA) sandwich‐like microenvironments, including plain material and aligned fibers. Enhanced cell differentiation levels were found for cells cultured with dorsal fibronectin‐coated films. Seeking to understand the underlying mechanisms, experiments were carried out with (i) different types of dorsal stimuli (FN, albumin, FN after blocking the RGD integrin‐binding site and activating dorsal cell integrin receptors), (ii) in the presence of an inhibitor of cell contractility, and (iii) increasing the frequency of culture medium changes to assess the effect of paracrine factors. Furthermore, FAK and integrin expressions, determined by Western blotting, revealed differences between cell sandwiches and 2D controls. Results show a stimuli‐dependent response to dorsal excitation, proving that integrin outside‐in signaling is involved in the enhanced cell differentiation. Due to their easiness and versatility, these sandwich‐like systems are excellent candidates to get deeper insights into the study of 3D cell behavior and to direct cell fate within multilayer constructs. Biotechnol. Bioeng. 2013;110: 3048–3058. © 2013 Wiley Periodicals, Inc.
Proton‐Conducting Supramolecular Metallogels from the Lowest Molecular Weight Assembler Ligand: A Quote for Simplicity
Authors: Saha Subhadeep , Schön Eva‐Maria , Cativiela Carlos , Díaz Díaz David , Banerjee Rahul 
Published: June 2013

AbstractOxalic acid has been proven to be the lowest molecular weight organic ligand able to form robust supramolecular metallogel networks in the presence of metal salts. In particular, two novel multifunctional metallogels were readily prepared at room temperature by simple mixing of stock solutions of CuII acetate monohydrate or CuII perchlorate hexahydrate and oxalic acid dihydrate. Formation of different polymorphs and unprecedented proton conduction under anhydrous conditions were also demonstrated with some of these materials.
Short‐term Effect of Verapamil on Coronary No‐Reflow Associated With Percutaneous Coronary Intervention in Patients With Acute Coronary Syndrome: A Systematic Review and Meta‐analysis of Randomized Controlled Trials
Authors: Su Qiang , Li Lang , Liu Yangchun 
Published: June 2013

AbstractBackgroundTo evaluate the clinical efficacy and safety of intracoronary verapamil injection in the prevention and treatment of coronary no‐reflow after percutaneous coronary intervention (PCI).HypothesisIntracoronary verapamil injection may be beneficial in preventing no‐reflow/slow‐flow after PCI.MethodsWe searched PubMed, Embase, and the Cochrane Central Register of Controlled Trials database. Randomized trials comparing the efficacy and safety of intracoronary verapamil infusion vs control in patients with acute coronary syndrome (ACS) were included. Meta‐analysis was performed by RevMan 5.0 software (Cochrane Collaboration, Copenhagen, Denmark) .ResultsSeven trials involving 539 patients were included in the analysis. Verapamil treatment was significantly more effective in decreasing the incidence of no‐reflow (risk ratio [RR]: 0.33; 95% confidence interval [CI]: 0.23 to 0.50) as well as reducing the corrected thrombolysis in myocardial infarction (TIMI) frame count (CTFC) (weighted mean difference: −11.62; 95% CI: −16.04 to −7.21) and improving the TIMI myocardial perfusion grade (TMPG) (RR: 0.43; 95% CI: 0.29 to 0.64). Verapamil also reduced the 30‐day wall motion index (WMI) compared to the control. Moreover, the procedure reduced the incidence of major adverse cardiac events (MACEs) in ACS patients during hospitalization (RR: 0.37; 95% CI: 0.17 to 0.80) and 2 months after PCI (RR: 0.56; 95% CI: 0.33 to 0.95). However, administration of verapamil did not provide an additional improvement of left ventricular ejection fraction regardless of the time that had passed post‐PCI.ConclusionsIntracoronary verapamil injection is beneficial in preventing no‐reflow/slow‐flow, reducing CTFC, improving TMPG, and lowering WMI. It is also likely to reduce the 2‐month MACEs in ACS patients post‐PCI.
Reconstructing shifts in vital rates driven by long‐term environmental change: a new demographic method based on readily available data
Authors: González Edgar J. , Martorell Carlos 
Published: June 2013

AbstractFrequently, vital rates are driven by directional, long‐term environmental changes. Many of these are of great importance, such as land degradation, climate change, and succession. Traditional demographic methods assume a constant or stationary environment, and thus are inappropriate to analyze populations subject to these changes. They also require repeat surveys of the individuals as change unfolds. Methods for reconstructing such lengthy processes are needed. We present a model that, based on a time series of population size structures and densities, reconstructs the impact of directional environmental changes on vital rates. The model uses integral projection models and maximum likelihood to identify the rates that best reconstructs the time series. The procedure was validated with artificial and real data. The former involved simulated species with widely different demographic behaviors. The latter used a chronosequence of populations of an endangered cactus subject to increasing anthropogenic disturbance. In our simulations, the vital rates and their change were always reconstructed accurately. Nevertheless, the model frequently produced alternative results. The use of coarse knowledge of the species' biology (whether vital rates increase or decrease with size or their plausible values) allowed the correct rates to be identified with a 90% success rate. With real data, the model correctly reconstructed the effects of disturbance on vital rates. These effects were previously known from two populations for which demographic data were available. Our procedure seems robust, as the data violated several of the model's assumptions. Thus, time series of size structures and densities contain the necessary information to reconstruct changing vital rates. However, additional biological knowledge may be required to provide reliable results. Because time series of size structures and densities are available for many species or can be rapidly generated, our model can contribute to understand populations that face highly pressing environmental problems.
Kinetic and Thermodynamic Investigations of CO2 Insertion Reactions into Ru–Me and Ru–H Bonds – An Experimental and Computational Study
Authors: Darensbourg Donald J. , Kyran Samuel J. , Yeung Andrew D. , Bengali Ashfaq A. 
Published: June 2013

AbstractThe rates of CO2 insertion into trans‐Ru(dmpe)2(Me)H [1, dmpe = 1,2‐bis(dimethylphosphino)ethane] and trans‐Ru(dmpe)2(Me)2 (2) derivatives were monitored by in situ infrared and 1H NMR spectroscopy. The reactions are first order in both CO2 and metal complex concentrations, and CO2 insertion into the Ru–H bond of 1 occurs instantaneously at 0 °C. The reverse process, decarboxylation, was observed to occur readily at ambient temperature as revealed by 13CO2 exchange with subsequent CO2 insertion into the Ru–Me bond at higher temperatures. No further CO2 insertion into the Ru–H bond of the resulting acetate complex was observed. The activation barrier for CO2 insertion into the first Ru–Me bond of 2 was determined to have ΔH‡ and ΔS‡ values of 12.7 ± 0.6 kcal mol–1 and –31.9 ± 2.0 e.u., respectively, which are indicative of a highly ordered transition state. The rate of CO2 insertion into the second Ru–Me bond was two orders of magnitude slower at ambient temperature and resulted in the formation of trans‐Ru(dmpe)2(O2CMe)2. In general, the insertion of CO2 into the Ru–H or Ru–Me bonds of trans‐Ru(dmpe)2(X)R (R = H or Me) was disvavored in the presence of poorly electron‐donating X ligands. For example, the insertion of CO2 into the Ru–H bond of trans‐Ru(dmpe)2(Cl)H was not observed even under forcing conditions. Computational results were in excellent agreement with these observations and predict a significant enhancement in CO2 activity and resultant complex stability if dmpe is replaced with tetramethylethylenediamine (tmeda).
A Highly Regio‐ and Diastereoselective Phosphane‐Catalyzed [3+2] Annulation of Morita–Baylis–Hillman Carbonates with Cyclic N‐Acyl Ketimines
Authors: Yang Li‐Jun , Cai Hua , Nie Jing , Ma Jun‐An 
Published: June 2013

AbstractA highly regio‐ and diastereoselective phosphane‐catalyzed [3+2] annulation of Morita–Baylis–Hillman (MBH) carbonates with cyclic N‐acyl‐substituted ketimines was developed. In the presence of the catalyst PBu3 (10 mol‐%), a series of N‐fused tricyclic products were obtained in excellent yields and diastereoselectivities under mild conditions. An example of a catalytic enantioselective annulation is also presented.
Flow network derivation from a high resolution DEM in a low relief, agrarian landscape
Authors: Schwanghart Wolfgang , Groom Geoff , Kuhn Nikolaus J. , Heckrath Goswin 
Published: June 2013

ABSTRACTDigital flow networks derived from digital elevation models (DEMs) sensitively react to errors due to measurement, data processing and data representation. Since high‐resolution DEMs are increasingly used in geomorphological and hydrological research, automated and semi‐automated procedures to reduce the impact of such errors on flow networks are required. One such technique is stream‐carving, a hydrological conditioning technique to ensure drainage connectivity in DEMs towards the DEM edges. Here we test and modify a state‐of‐the‐art carving algorithm for flow network derivation in a low‐relief, agricultural landscape characterized by a large number of spurious, topographic depressions. Our results show that the investigated algorithm reconstructs a benchmark network insufficiently in terms of carving energy, distance and a topological network measure. The modification to the algorithm that performed best, combines the least‐cost auxiliary topography (LCAT) carving with a constrained breaching algorithm that explicitly takes automatically identified channel locations into account. We applied our methods to a low relief landscape, but the results can be transferred to flow network derivation of DEMs in moderate to mountainous relief in situations where the valley bottom is broad and flat and precise derivations of the flow networks are needed. Copyright © 2013 John Wiley & Sons, Ltd.
Direction‐of‐Change Financial Time Series Forecasting using a Similarity‐Based Classification Model
Authors: Skabar Andrew 
Published: June 2013

ABSTRACTA similarity‐based classification model is proposed whereby densities of positive and negative returns in a delay‐embedded input space are estimated from a graphical representation of the data using an eigenvector centrality measure, and subsequently combined under Bayes' theorem to predict the probability of upward/downward movements. Application to directional forecasting of the daily close price of the Dow Jones Industrial Average over a 20‐year out‐of‐sample period yields performance superior to random walk and logistic regression models, and on a par with that of multilayer perceptrons. A feature of the classifier is that it is parameter free, parameters entering the model only via the measure used to determine pairwise similarity between data points. This allows intuitions about the nature of time series to be elegantly integrated into the model. The recursive nature of eigenvector centrality makes it better able to deal with sparsely populated input spaces than conventional approaches based on density estimation. Copyright © 2013 John Wiley & Sons, Ltd.
Heterogeneous Asymmetric Dynamic Conditional Correlation Model with Stock Return and Range
Authors: Asai Manabu 
Published: June 2013

ABSTRACTThe paper considers the return and range model with dynamic conditional correlations (DCC). The paper suggests the new specifications for the asymmetric effects on log‐volatilities and dynamic correlations, combined with long‐run dependences. The new DCC model can be estimated by the quasi‐maximum likelihood method. Empirical analysis on Nikkei 225, Hang Seng and Straits Times indices shows the daily, weekly and monthly pattern of asymmetric effects. For the period including the global financial crisis, the new DCC model provides plausible one‐step‐ahead forecasts of the VaR thresholds, and yields positive economic values of switching from other DCC models. Copyright © 2013 John Wiley & Sons, Ltd.