bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of attosecond‐resolved imaging of the plasmon electric field in metallic nanoparticles
Authors: Prell James S. , Borja Lauren J. , Neumark Daniel M. , Leone Stephen R. 
Published: December 2012

Sub‐cycle photoelectron streaking from silver plasmonic nanospheres is simulated using few‐cycle laser pulses tuned both on and off the plasmon resonance (376 nm vs 800 nm, respectively) to initiate the plasmon. Phase‐locked, isolated attosecond XUV pulses induce photoemission from the nanospheres, and two different types of streaking of the photoelectrons occur simultaneously due to the laser and plasmon electric fields. Streaking is simulated over a wide range of excitation pulse intensities, and final velocity distributions for the photoelectrons emitted at different times are calculated. The resulting velocity distributions exhibit several characteristics attributable to the plasmon electric field. The dipole moment amplitude can be reconstructed using velocity map imaging or time‐of‐flight photoelectron velocity measurements without separate measurement of the laser electric field or deconvolution using an assumed streaking trace shape. These results indicate that photoelectron experiments in table‐top set‐ups can provide unprecedented spatio‐temporal information about sub‐cycle plasmon dynamics in metallic nanostructures.
Development of a new bioprocess scheme using frozen seed train intermediates to initiate CHO cell culture manufacturing campaigns
Authors: Seth Gargi , Hamilton Robert W. , Stapp Thomas R. , Zheng Lisa , Meier Angela , Petty Krista , Leung Stephenie , Chary Srikanth 
Published: December 2012

AbstractAgility to schedule and execute cell culture manufacturing campaigns quickly in a multi‐product facility will play a key role in meeting the growing demand for therapeutic proteins. In an effort to shorten campaign timelines, maximize plant flexibility and resource utilization, we investigated the initiation of cell culture manufacturing campaigns using CHO cells cryopreserved in large volume bags in place of the seed train process flows that are conventionally used in cell culture manufacturing. This approach, termed FASTEC (Frozen Accelerated Seed Train for Execution of a Campaign), involves cultivating cells to high density in a perfusion bioreactor, and cryopreserving cells in multiple disposable bags. Each run for a manufacturing campaign would then come from a thaw of one or more of these cryopreserved bags. This article reviews the development and optimization of individual steps of the FASTEC bioprocess scheme: scaling up cells to greater than 70 × 106 cells/mL and freezing in bags with an optimized controlled rate freezing protocol and using a customized rack configuration. Flow cytometry analysis was also employed to understand the recovery of CHO cells following cryopreservation. Extensive development data were gathered to ensure that the quantity and quality of the drug manufactured using the FASTEC bioprocess scheme was acceptable compared to the conventional seed train process flow. The result of offering comparable manufacturing options offers flexibility to the cell culture manufacturing network. Biotechnol. Bioeng. 2013; 110: 1376–1385. © 2012 Wiley Periodicals, Inc.
Programmable mechanical stimulation influences tendon homeostasis in a bioreactor system
Authors: Wang Tao , Lin Zhen , Day Robert E. , Gardiner Bruce , Landao‐Bassonga Euphemie , Rubenson Jonas , Kirk Thomas B. , Smith David W. , Lloyd David G. , Hardisty Gerard , Wang Allan , Zheng Qiujian , Zheng Ming H. 
Published: December 2012

AbstractIdentification of functional programmable mechanical stimulation (PMS) on tendon not only provides the insight of the tendon homeostasis under physical/pathological condition, but also guides a better engineering strategy for tendon regeneration. The aims of the study are to design a bioreactor system with PMS to mimic the in vivo loading conditions, and to define the impact of different cyclic tensile strain on tendon. Rabbit Achilles tendons were loaded in the bioreactor with/without cyclic tensile loading (0.25 Hz for 8 h/day, 0–9% for 6 days). Tendons without loading lost its structure integrity as evidenced by disorientated collagen fiber, increased type III collagen expression, and increased cell apoptosis. Tendons with 3% of cyclic tensile loading had moderate matrix deterioration and elevated expression levels of MMP‐1, 3, and 12, whilst exceeded loading regime of 9% caused massive rupture of collagen bundle. However, 6% of cyclic tensile strain was able to maintain the structural integrity and cellular function. Our data indicated that an optimal PMS is required to maintain the tendon homeostasis and there is only a narrow range of tensile strain that can induce the anabolic action. The clinical impact of this study is that optimized eccentric training program is needed to achieve maximum beneficial effects on chronic tendinopathy management. Biotechnol. Bioeng. 2013; 110: 1495–1507. © 2012 Wiley Periodicals, Inc.
President's page
Authors: Dillon Andrew 
Published: December 2012

AbstractEditor's SummaryTaking on the reins as ASIS&T president for 2013, the author sets his sights on fulfilling and expanding upon previous presidents' initiatives. This year's efforts will focus on building strength through a more international membership, energizing student chapters to stimulate early professional involvement, broadening engagement in ASIS&T events from Annual Meetings to webinars and providing the most relevant and content‐rich material. The role of the organization, its service to members and the sense of identity and community it engenders deserve examination. ASIS&T must reach out to other groups in the information sector but strive to realize its claim as the preeminent information society. Aligning with the growing iSchool movement may well be a step in that direction.
Case Study: Developing the PLOS thesaurus
Authors: Dupuich Jonas , Carr Gabe 
Published: December 2012

AbstractEditor's SummaryA thesaurus should quietly streamline website operations behind the scenes but can become an obstacle if it is inadequate or falls out of date, the situation the Public Library of Science (PLOS) realized in 2011. The organization sought help from Access Innovations, Inc., to bring its thesaurus up to speed, comply with the Z39.19 standard and ensure support of machine categorization of content. An analysis revealed over‐ and under‐used terms and provided recommendations and specific guidance. With this knowledge and various use cases, PLOS determined a new customized thesaurus was needed. Access Innovations expanded and organized the original PLOS vocabulary of 3,132 terms to produce a thesaurus of more than 10,000 terms covering 10 science topics in seven levels. PLOS monitored weekly progress, and subject matter experts reviewed the draft for terminology and organization. Thesaurus terms will be applied to content as subject metadata using Data Harmony's MAIstro, a rule‐based categorization system permitting editorial oversight and incremental improvements. After testing and tuning rules for accuracy, the system will be used to automatically index all PLOS content.
Indexing electronic medical records using a taxonomy
Authors: Kuranz John , Gilles Barbara 
Published: December 2012

AbstractEditor's SummaryWith the move toward patient electronic medical records (EMRs), accessing information for insurance coding and research depends on standardized taxonomies to organize and index the content. Controlled vocabularies are necessary to interpret content consistently. Established quasi‐taxonomies provide codes for medical conditions and treatments, but applying these codes as metadata to index the records is laborious, requiring translation from natural language in the EMR to a code's verbal equivalent to the code. Indexing systems can streamline the categorization process for greater efficiency and accuracy by using Bayesian engines or a rule‐based approach. Analyzing discrepancies between human indexing and the software system results shows where editorial intervention is needed for continual improvement, with a goal of 85% or higher accuracy. Using a categorization system with a hierarchical taxonomy enables deep, precise indexing or quick, automatic filtering to more general concepts. The accuracy of medical indexing systems varies widely, based on the degree of automation and capacity for semantic analysis.
Building a taxonomy for auto‐classification
Authors: Pohs Wendi 
Published: December 2012

AbstractEditor's SummaryTaxonomies have expanded from browsing aids to the foundation for automatic classification. Early auto‐classification methods grouped documents having similar collections of words, but current software can provide far greater accuracy. Text‐mining tools can spot recognizable entities as potential taxonomy terms or top‐level categories. Developing a taxonomy further to coordinate with auto‐classification software requires appreciation of how the software works, whether it uses an approach based on lexical analysis, rules for word co‐occurrence or machine learning with predictive analysis. The taxonomy model is typically hierarchical with term specificity dictated by the end user's need for detail. Synonyms and variants are redirected to the term for classification. The classification tool must be configured to be consistent with the typical document format and style of the collection. Testing the classification scheme, critical to reveal inaccuracies and omissions, is an iterative process expanding from a stable test set to validation on a large corpus before final implementation.
Building controlled vocabularies for metadata harmonization
Authors: Zaharee Marcie 
Published: December 2012

AbstractEditor's SummaryOrganizations using controlled vocabularies are highly diverse, but they all rely on using a terminology list that is internally standardized, commonly understood and widely applied for metatagging. The basic steps for creating a controlled vocabulary, taxonomy or thesaurus are the same for each case, starting with determining the scope to be covered and identifying representative content sources. This step is followed by gathering and organizing terms, enhancing them with synonyms and relationships and often by subject‐matter‐expert review. Using a dedicated taxonomy management tool is recommended to facilitate management, visualization and export in machine‐readable format such as OWL or SKOS. Posting the controlled vocabulary to a registry or data warehouse enables sharing and may stimulate broad acceptance. The MITRE Corporation has followed this process in developing taxonomies consistent with the Department of Defense's Net‐Centric Data Strategy, which bases shared understanding within and among DoD programs on the use of controlled vocabularies and crosswalking equivalent data elements.
CLIR/DLF digital curation postdoctoral fellowship – The hybrid role of data curator
Authors: Kouper Inna 
Published: December 2012

AbstractEditor's SummaryData with high potential information value must be carefully selected, appraised, organized, stored and disseminated. Recognizing this critical management need, the Council on Library and Information Resources' Digital Library Federation (CLIR/DLF), the Alfred P. Sloan Foundation and six universities have partnered to sponsor the Data Curation Fellowship Program. This two‐year postdoctoral fellowship brings together information professionals interested in acquiring the diverse skills needed to become a professional data curator, serving as researcher, librarian, technology adopter and policy maker. Acknowledging differences in their own views and experiences, early fellows recognized the need to promote a culture of data sharing to connect stakeholders across technology, disciplinary and institutional boundaries and to develop an infrastructure to support data curation. It is hoped that serious work in data curation will lead to professional recognition of the specialty.
Effect of percutaneous atrial septal defect and patent foramen ovale device closure on degree of aortic regurgitation
Authors: Loar Robert W. , Johnson Jonathan N. , Cabalka Allison K. , Cetta Frank , Hagler Donald J. , Eidem Benjamin W. , Taggart Nathaniel W. 
Published: December 2012

BackgroundIn recent years, percutaneous device closure has become commonplace for treatment of atrial septal defect (ASD) and patent foramen ovale (PFO). However, the effect of device closure on aortic valve regurgitation (AR) has been questioned.ObjectiveThe purpose of this study was to define changes in AR using echocardiography, before and after device closure of ASD or PFO.MethodsWe retrospectively reviewed all patients who had percutaneous device closure of ASD or PFO at our institution between 2005 and 2009. We compared the preprocedure echocardiogram to the most recent follow‐up study. All investigators were blinded to referral diagnosis, patient demographics, and size and type of the device placed. Aortic regurgitation was graded as none/trivial, mild, moderate, or severe.ResultsOverall, 322 patients qualified for inclusion; 204 with PFO and 118 with ASD. Mean age at time of closure was 48 ± 20 years (range 3–85 years). Mean duration of follow‐up was 1.2 years (range 2 months to 5 years). Only two patients (0.6%) demonstrated any appreciable increase in AR severity. However, both of these patients manifested a clinically insignificant change from a trivial to mild grade of aortic regurgitation.ConclusionsPercutaneous device closure of PFO or ASD does not increase the incidence or severity of AR over medium‐term follow‐up. © 2012 Wiley Periodicals, Inc.
Degradation of 2,4‐DCP by the Immobilized Laccase on the Carrier of Fe3O4@SiO2‐NH2
Authors: Huan Weiwei , Yang Yuxiang , Wu Bin , Yuan Hongming , Zhang Yani , Liu Xiangnong 
Published: December 2012

AbstractIn this paper, the laccase immobilized on Fe3O4@SiO2‐NH2nanoparticles was successfully prepared by the glutaraldehyde cross‐linking method. The degradations of 2,4‐dichlorophenol (2,4‐DCP) catalyzed by laccase and immobilized laccase were carried out. The optimal conditions regarding degradation efficiency were also discussed, which include reaction time, pH value, temperature, concentration of 2,4‐DCP and laccase. When laccase was immobilized on Fe3O4@SiO2‐NH2carrier by crosslinking with glutaraldehyde, the stability and repetition were improved significantly. The removal efficiency of 2,4‐DCP by immobilized laccase still remained over 59% after six cycles of operation. Degradation of 2,4‐DCP is a first‐order reaction and the activation energies of 2,4‐DCP catalyzed by laccase and immobilized laccase are 51.93 kJ·mol−1and 44.12 kJ·mol−1, respectively. The results demonstrate the immobilized laccase had a faster degradation rate than the free laccase; the magnetic carrier Fe3O4@MSS‐NH2can promote the degradation reaction.
Synthesis and Pharmacological Properties of 5‐Alkyl Substituted Nicotine Analogs
Authors: Wang Jing , Li Xi , Yuan Qianjia , Ren Jiangmeng , Huang Jin , Zeng Bubing 
Published: December 2012

AbstractThis paper describes a concise and practical route to enantiomerically enriched 5‐alkyl substituted nicotine analogs. The Vilsmeier reaction was used to construct the nicotinaldehydes ring followed by the introduction of the chiral homoallylic alcohol by organic boron reagent and the cyclization of the pyrrolidine ring through the reduction of a chiral azide. 17 analogs have been synthesized and their corresponding biological activities were tested, in which compounds 10d and 10g exhibit excellent IC50 values against RD and SY‐SY5Y.
Gold‐Catalyzed Direct Indolation of Tetrahydroisoquinolines
Authors: Zhang Yan , Luo Sha , Feng Bainian , Zhu Chengjian 
Published: December 2012

AbstractNitrogen‐containing heterocyclic compounds are important motifs of pharmaceuticals and functional materials, and there has been a growing interest in new synthetic methods for their preparations. In this paper, we report a direct cross‐coupling reaction of indole with N‐aryl tetrahydroisoquinolines in the presence of gold catalyst. The reaction is compatible with a wide range of substituted indoles, to enable the formation of various alkylated heteroarenes under very mild reaction conditions.
Utilizing Natural Liner Materials for Heavy Metal Removal in Simulated Landfill Conditions
Authors: Turan Nurdan Gamze , Gümüşel E. Beril 
Published: December 2012

AbstractInorganic industrial waste landfills have the potential to contaminate subsurface groundwater supplies through migration of leachates down to the water table and into groundwater aquifers, despite the use of compacted low permeability clay or polyethene liners. This paper aims the removal of Cu2+ and Zn2+ in the leachate from an industrial waste landfill using natural materials (natural zeolite, expanded vermiculite, pumice, illite, kaolinite, and bentonite) as a liner material. Cu2+ and Zn2+ concentrations for all treatments decreased during the process. Of all the different natural materials, natural zeolite, expanded vermiculite and pumice, with bentonite, were effective in removing Cu2+ and Zn2+ present in the leachate. However, the use of illite and kaolinite with bentonite as liner materials could be of disadvantage in Cu2+ and Zn2+ removal from leachate. The adsorption kinetic models were also tested for the validity. The second order kinetics with the high correlation coefficients best described adsorption kinetic data.
Generation of Power by Microbial Fuel Cell with Ferricyanide in Biodegradation of Benzene
Authors: Wu Chih‐Hung , Lai Chi‐Yung , Lin Chi‐Wen , Kao Min‐Hsiu 
Published: December 2012

AbstractThe power generation potential of a microbial fuel cell (MFC) during the process of benzene biodegradation with potassium ferricyanide (0–200 mM) as the terminal electron acceptor was evaluated. Experimental results demonstrate that benzene was used as the sole carbon source in generating electricity by a mixed culture. The power density increased from 0.0276 to 2.1 mW m−2 as the concentration of potassium ferricyanide in the cathode chamber was increased from 0 to 200 mM. With a benzene concentration of 10.87 mg L−1 and a potassium ferricyanide concentration of between 0 and 150 mM, complete degradation of benzene was achieved in 22–24.5 h. However, when the concentration of potassium ferricyanide was raised to 200 mM, the time required for complete benzene degradation was prolonged to 35 h. The results of this investigation can be used as a basis for future assessments of the power generation capacity of MFCs that are used to treat benzene‐contaminated wastewater.
Functional and neurochemical development in the normal and degenerating mouse retina
Authors: Gibson Riki , Fletcher Erica L. , Vingrys Algis J. , Zhu Yuan , Vessey Kirstan A. , Kalloniatis Michael 
Published: December 2012

AbstractThe rd1 mouse is a well‐established animal model for human retinitis pigmentosa (RP). We used electroretinography (ERG) to evaluate retinal function and postembedding immunocytochemistry to determine the changes in cellular amino acid expression in the normal (C57Bl6) and degenerating mouse retina (rd1), as a function of age during development and the onset of degeneration. In the normal mouse retina, photoreceptoral and post‐photoreceptoral ERG responses improved simultaneously from eye‐opening until adult levels were achieved at approximately postnatal day (P) 30. Maturation of amino acid neurochemistry preceded the development of retinal function in the normal retina. Amino acid levels increased immediately from birth and reached stable levels by eye‐opening. In contrast, in the rd1 mouse, both rod and cone pathway function rapidly reduced from eye‐opening and by P21 became undetectable. Interestingly, at P18 cone responses were still comparable between the normal and degenerating retina. Before eye opening, the pattern of amino acid immunoreactivity in the rd1 retina was similar to the normal retina. Alterations in neurochemistry were observed after the onset of rod photoreceptor cell death. The most obvious change was the reduction in neurotransmitter immunoreactivity within the synaptic layers and some cell classes of the rd1 retina. Reduction of glutamine and glutamate was observed in Müller cells before established gliosis markers. Overall, these results suggest the rapid maturation of neurochemistry by eye opening followed by functional maturation by P30 in the normal retina. The dystrophic retina displays similar neurochemistry to control retina before eye opening but a subsequent decline. J. Comp. Neurol. 521:1251–1267, 2013. © 2012 Wiley Periodicals, Inc.
NMDA‐like receptors in the nervous system of the crab Neohelice granulata: A neuroanatomical description
Authors: Hepp Yanil , Tano Martín Carbó , Pedreira María Eugenia , Freudenthal Ramiro A.M. 
Published: December 2012

AbstractN‐Methyl‐D‐aspartate receptors (NMDARs) are involved in learning and memory processes in vertebrates and invertebrates. In Neohelice granulata, NMDARs are involved in the storage of associative memories (see references in text). The aim of this work was to characterize this type of glutamate receptor in Neohelice and to describe its distribution in the central nervous system (CNS). As a first step, a detailed study of the CNS of N. granulata was performed at the neuropil level, with special focus on one of the main structures involved in this type of memory, the supraesophageal ganglion, called central brain. The characterization of the NMDAR was achieved by identifying the essential subunit of these receptors, the NR1‐like subunit. The NR1‐like signals were found via western blot and immunohistochemistry techniques in each of the major ganglia: the eyestalk ganglia, the central brain, and the thoracic ganglion. Western blots yielded two bands for the crab NR1‐like subunit, at ∼88 and ∼84 kDa. This subunit is present in all the major ganglia, and shows a strong localization in synaptosomal membranes. NMDARs are distributed throughout the majority of each ganglion but show prominent signal intensity in some distinguishable neuropils and neurons. This is the first general description of the N. granulata nervous system as a whole and the first study of NMDARs in the CNS of decapods. The preferential localization of the receptor in some neuropils and neurons indicates the presence of possible new targets for memory processing and storage. J. Comp. Neurol. 521:2279–2297, 2013. © 2012 Wiley Periodicals, Inc.
Lehrman's dictum: Information and explanation in developmental biology
Authors: Griffiths Paul E. 
Published: December 2012

AbstractThe integration of concepts from evolutionary developmental biology, such as the homology concept, into developmental psychobiology has great potential. However, evolutionary developmental biology is an attempt to integrate evolutionary and developmental explanation and developmental psychobiology has traditionally been concerned to avoid conflating these two kinds of explanation. This article examines a recent attempt to explain development in terms of “inherited information.” The resulting explanation is an evolutionary explanation of development of a kind typical of evolutionary developmental biology. But its proponent mistakes it for an actual developmental explanation. Any integration of evolutionary developmental biology and developmental psychobiology should pay close attention to longstanding concerns about conflating evolutionary and developmental explanations. © 2012 Wiley Periodicals, Inc. Dev Psychobiol 55: 22–32, 2013.