bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of blood on liver metabolite profiling – a combined metabolomic and proteomic approach
Authors: Ly‐Verdú Saray , Schaefer Alexander , Kahle Melanie , Groeger Thomas , Neschen Susanne , Arteaga‐Salas Jose M. , Ueffing Marius , de Angelis Martin Hrabe , Zimmermann Ralf
Published: August 2013

Metabolomics has entered the well‐established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.e. with blood removed) and unperfused mice liver tissue (i.e. containing blood) were compared by two‐dimensional gas chromatography time of flight mass spectrometry (GC × GC‐TOFMS) for the metabolomic part, and by liquid chromatography tandem mass spectrometry (LC‐MS/MS) for the proteomic part. Our data showed significant differences between the unperfused and perfused liver tissue samples. Furthermore, we also observed an overlap of blood and tissue metabolite profiles in our data, suggesting that the perfusion of liver tissue prior to analysis is beneficial for an accurate metabolic profile of this organ. Copyright © 2013 John Wiley & Sons, Ltd.
Partnerships between institutional repositories, domain repositories and publishers
Authors: Steinhart Gail
Published: August 2013

Editor's Summary

At ASIS&T's RDAP13 Summit, one panel explored the shared interests and challenges faced by researchers, institutions, various repositories, publishers and the public. Common hurdles include engaging researchers in the process at the outset, organizing and documenting research data, contending with diverse media types and file formats, spanning disciplines and rewarding participation. Amy Nurnberger of Columbia University Library noted the importance of understanding authors' needs and recognizing comparable issues faced by libraries and publishers. Jared Lyle of the Inter‐university Consortium for Political and Social Research stressed the value of working with researchers early in their process and establishing a personal, supportive and consultative connection. John Kunze described tools available through the California Digital Library to facilitate data curation at several stages of the research process, ultimately depositing data to a repository and enabling its publication and sharing. The collective experiences highlighted common themes, including the value of local collections and partnerships as well as the need to simplify the process with easy‐to‐use tools.
The relevance of research data sharing and reuse studies
Authors: Weber Nicholas M.
Published: August 2013

Editor's Summary

As big data takes the limelight, it is critical that the value of research data is appreciated and the field of information science garners respect for its contributions. Despite being a logical leader in data management and curation, information science competes with other disciplines in handling research data and often fails to demonstrate its own expertise. Two developments presented through the annual Research Data Access & Preservation (RDAP) Summits hold promise for promoting the field and demonstrating its relevance to data management topics. First, the use of formal and systematic planning for data management is expanding, driven by requirements of many funding agencies. Second, research is offering insights into how researchers appraise, share and reuse data, with identification of data quality indicators related to satisfaction. As the effective use of research data becomes more pressing, the field of information science should lead in demonstrating the value derived from professional data curation, and the RDAP community must define and articulate its own research agenda.
RDAP13 poster session summary
Authors: Doty Jennifer
Published: August 2013

Editor's Summary

Posters presented at the 2013 Research Data Access & Preservation Summit (RDAP) spanned an array of topics of current interest for research data managers. Helping doctoral candidates archive their research data was the focus of one, stressing the need to provide support early in the researchers' process. Another described a multi‐format data literacy program geared to graduate level researchers. The presentation on one university's “DataDay” described a training workshop designed to help librarians understand the research data lifecycle and pass on essential points to researchers. Another team of presenters offered a methodical approach to establishing the provenance of research datasets that later appear in other contexts. Several posters addressed data management policies and practices at the institutional level, with one offering model policy language and guidelines and another analyzing current and likely future trends and needs to support archiving research data. The full collection of posters reveals the breadth of issues, progress to date and advances to come for the area.
Reflections on our future
Authors: Engelbart Douglas C.
Published: August 2013

Editor's Summary

In an article first published in the Bulletin in 1996, Douglas Engelbart looks back to the late 1950s and recalls the seeds of the future information age, its digital context and computer‐mediated collaboration. He realized early work on hypermedia interactions threatened the paradigm; people were unable to expand their vision beyond the present. Yet traditional methods were insufficient to deal with complex and urgent problems, and the massively growing scale of information challenges would necessitate human adaptation. Though developments in digital information were promising, progress in the commercial sector was necessary for broad acceptance. Engelbart applied the concept of bootstrapping, with teams collaborating to carry out a process and to simultaneously improve capability. The Association for Information Science and Technology (nee American Society for Information Science) can serve as a bootstrapping facilitator in a network of associations to apply and augment information management advances to make its own and its collective work more effective.
Natural Friedelanes
Authors: Shan Wei‐Guang , Zhang Li‐Wen , Xiang Jia‐Gui , Zhan Zha‐Jun
Published: August 2013

This review covers the occurrence and biological activities of all natural friedelane triterpenoids found between 1977 and March 2011. The biogeneses of dimeric friedelanes and several rearranged friedelanes are discussed. The pharmacological properties of representative compounds, including celastrol and correolide, have also been compiled, on the basis of 344 references.
11α‐Ethoxy‐β‐boswellic Acid and Nizwanone, a New Boswellic Acid Derivative and a New Triterpene, Respectively, from Boswellia sacra
Authors: Al‐Harrasi Ahmed , Ali Liaqat , Ur Rehman Najeeb , Hussain Javid , Hussain Hidayat , Al‐Rawahi Ahmed , Shamim Rizvi Tania
Published: August 2013

A new boswellic acid derivative, 11α‐ethoxy‐β‐boswellic acid (EBA; 1) and a new ursane‐type triterpene, named nizwanone (2), were isolated from Omani frankincense Boswellia sacra Flueck. together with two known compounds papyriogenin B and rigidenol. The structures of 1 and 2 were elucidated by detailed spectroscopic analysis using 1H‐ and 13C‐NMR, 1H,1H‐COSY, HMQC, HMBC, and HR‐EI‐MS techniques. The relative configurations of 1 and 2 were assigned by comparative analysis of the NMR spectral data with those of known analogs together with NOESY experiments. Structures of known compounds were identified by comparison with the reported data.
Photodynamic Activity of Plant Extracts from Sarawak, Borneo
Authors: Jong Wan Wui , Tan Pei Jean , Kamarulzaman Fadzly Adzhar , Mejin Michele , Lim Diana , Ang Ida , Naming Margarita , Yeo Tiong Chia , Ho Anthony Siong Hock , Teo Soo Hwang , Lee Hong Boon
Published: August 2013

Photodynamic therapy (PDT) is a medical treatment that involves the irradiation of an administered photosensitizing drug with light of a particular wavelength to activate the photosensitizer to kill abnormal cells. To date, only a small number of photosensitizers have been clinically approved for PDT, and researchers continue to look for new molecules that have more desirable properties for clinical applications. Natural products have long been important sources of pharmaceuticals, and there is a great potential for discovery of novel chemotypes from under‐explored biodiversities in the world. The objective of this study is to mine the terrestrial plants in Sarawak, Borneo Island, for new photosensitizers for PDT. In a screening program from 2004 to 2008, we prepared and studied 2,400 extracts from 888 plants for their photosensitizing activities. This report details the bioprospecting process, preparation and testing of extracts, analysis of the active samples, fractionation of four samples, and isolation and characterization of photosensitizers.
Developmental Changes in the Sterol Composition and the Glycerol Content of Cuticular and Internal Lipids of Three Species of Flies
Authors: Gołębiowski Marek , Cerkowniak Magdalena , Boguś Mieczysława I. , Włóka Emilia , Przybysz Elżbieta , Stepnowski Piotr
Published: August 2013

The glycerol concentration and the composition of cuticular and internal sterols in three medically and forensically important fly species, viz., Musca domestica, Sarcophaga carnaria, and Calliphora vicina, were analyzed. The cuticular and internal lipid extracts were separated by HPLC‐LLSD, after which the sterol fraction was characterized by GC/MS in total ion current (TIC) mode. The cuticular lipids of M. domestica larvae contained seven sterols, while in pupae and females, six sterols were identified. Five sterols were found in the cuticular lipids of M. domestica males. The internal lipids of M. domestica larvae and pupae contained six and seven sterols, respectively, while those of male and female flies contained only five sterols. Sitosterol, cholesterol, and campesterol were the dominant sterols in M. domestica, while campestanol, stigmasterol, sitostanol, and fucosterol were identified in low concentrations or in traces. In contrast, cuticular and internal lipids of S. carnaria and C. vicina contained only cholesterol. Glycerol was identified in all stages of M. domestica, S. carnaria, and C. vicina. For all the three examined fly species, the present study clearly showed species‐specific developmental changes in the composition of cuticular and internal sterols as well as in the glycerol concentration.
Fluorinated Pseudopeptide Analogues of the Neuropeptide 26RFa: Synthesis, Biological, and Structural Studies
Authors: Pierry Camille , Couve‐Bonnaire Samuel , Guilhaudis Laure , Neveu Cindy , Marotte Amélie , Lefranc Benjamin , Cahard Dominique , Ségalas‐Milazzo Isabelle , Leprince Jérôme , Pannecoucke Xavier
Published: August 2013

A series of four fluorinated dipeptide analogues each containing a fluoro‐olefin moiety as peptide bond surrogate has been designed and synthesized. These motifs have been successfully introduced into the bioactive C‐terminal heptapeptide of the neuropeptide 26RFa by conventional SPPS. We then evaluated the ability of the generated pseudopeptides to increase [Ca2+]i in GPR103‐transfected cells. For these fluorinated analogues, greater stability in human serum was observed. Their conformations were also investigated, leading to the valuable identification of differences depending on the position of the fluoro‐olefin moiety in the sequence.
Targeted Engineering of Cyclooctat‐9‐en‐7‐ol Synthase: A Stereospecific Access to Two New Non‐natural Fusicoccane‐Type Diterpenes
Authors: Görner Christian , Häuslein Ina , Schrepfer Patrick , Eisenreich Wolfgang , Brück Thomas
Published: August 2013

The structural diversity of bioactive diterpenes is due to variations in their macrocyclic carbon skeletons. The chemical synthesis of these macrocycles is challenging. However, the bacterial diterpene synthase cyclooctat‐9‐en‐7‐ol synthase (CotB2) generates a complex macrocycle in a single step with geranylgeranyl diphosphate as an aliphatic substrate. This study investigates the catalytic mechanisms of the native and mutant CotB2, with a focus on identifying new carbon macrocycles. The combination of in silico modelling, targeted diterpene cyclase engineering and structural elucidation by using GC–MS, HRMS and NMR analysis resulted in the identification of new terpene olefins. CotB2 mutants produced two new non‐natural fusicoccane‐type macrocycles with potential bioactivities and the monocyclic compound cembrene. The observed product pattern allowed insights into the mechanistic features of CotB2. Applied strategies enable new consolidated synthesis of natural and non‐natural terpenoid bioactives.
TUD‐1‐Encapsulated HY Zeolite: A New Hierarchical Microporous/Mesoporous Composite with Extraordinary Performance in Benzylation Reactions
Authors: Hamdy Mohamed S. , Mul Guido
Published: August 2013

A new composite material consisting of amorphous TUD‐1 encapsulating crystalline zeolite Y was synthesized. Samples with different HY zeolite loadings (10, 20, 40, and 60 wt %) were prepared, and the resulting solid products were characterized with elemental analysis, XRD, N2 physisorption, 27Al MAS NMR, IR, pyridine adsorption in combination with FTIR, temperature‐programmed desorption of ammonia, HRSEM, and HRTEM. Characterization data confirm the presence of a thin layer of the mesoporous TUD‐1 phase with a thickness of 30–100 nm surrounding the zeolite crystals. The catalytic performance of the composite was studied in the Friedel–Crafts benzylation of benzene with benzyl alcohol at 353 K. The catalytic activity of the HY/TUD‐1 composite was higher than that of HY zeolite, whereas the composite showed a much slower rate of deactivation. The improved performance of the composite is related to beneficial changes in the acidity of the HY crystal through chemical interactions with TUD‐1.
Near‐infrared spectroscopy and partial least squares‐class modeling (PLS‐CM) for metabolomics fingerprinting discrimination of intervention breakfasts ingested by obese individuals
Authors: Álvarez‐Sánchez Beatriz , Priego‐Capote Feliciano , García‐Olmo Juan , Ortiz‐Fernández María C. , Sarabia‐Peinador Luis A. , Luque de Castro María D.
Published: August 2013

Near‐infrared spectroscopy has been used in nutritional metabolomics fingerprinting for the assessment of the intake of intervention breakfasts prepared with four different vegetable oils that were previously subjected to a deep frying process of 20 cycles for 5 min at 180°C. The target oils were an extra virgin olive oil and three varieties of refined sunflower oil. Of the three latter, one of them was used as such, other was spiked with a synthetic oxidation inhibitor (dimethylsiloxane) and, finally, the last one was enriched with an extract of phenolic compounds from olive pomace, the antioxidant properties of which are well known. Urine sampled from individuals before intake and 2 and 4 h after intake was directly analyzed by NIRS to obtain fingerprint characteristics of the metabolome composition. The resulting urinary patterns were combined for statistical analysis by unsupervised and supervised approaches. Partial least squares‐class modeling enabled to develop class‐models for each intervention breakfast, thus achieving discrimination of urinary fingerprints from individuals after breakfast intake. The models were statistically characterized by estimation of sensitivity and specificity parameters for the training and evaluation (validation) steps. The application of variable importance in projection algorithm enabled to detect the spectral regions with higher significance to explain the variability observed in the partial least squares class‐models. Quantitative differences of variable importance in projection scores discriminated among the different classes under study. Copyright © 2013 John Wiley & Sons, Ltd.
Structural Design of Ionic Conduction Paths in Molecular Crystals for Selective and Enhanced Lithium Ion Conduction
Authors: Moriya Makoto , Kato Daiki , Sakamoto Wataru , Yogo Toshinobu
Published: August 2013

The molecular crystals [Li{N(SO2CF3)2}{C6H4(OCH3)2}2] and [Li{N(SO2CF3)2}{C6F2H2(OCH3)2}2] with solid‐state lithium ion conductivity have been synthesized by the addition of two equivalents of 1,2‐dimethoxybenzene or 1,2‐difluoro‐4,5‐dimethoxybenzene to Li{N(SO2CF3)2}, respectively. Single‐crystal X‐ray diffraction analysis revealed the formation of ionic conduction paths with an ordered arrangement of lithium ions in these crystal structures, afforded by the self‐ assembled stacking of molecular‐based channels consisting of N(SO2CF3)2 anion and 1,2‐dimethoxybenzene frameworks as a result of intermolecular aromatic and hydrogen interactions. These compounds show selective lithium ion conductivity as the anions behave as a component unit of the conduction paths. The relationship between the crystal structure and ionic conductivity of the molecular crystals provides a clue to the development of novel solid electrolytes based on molecular crystals showing fast and selective lithium ion conduction.
Synthesis of Poly(benzothiadiazole‐co‐dithienobenzodithiophenes) and Effect of Thiophene Insertion for High‐Performance Polymer Solar Cells
Authors: Yun Hui‐Jun , Lee Yun‐Ji , Yoo Seung‐Jin , Chung Dae Sung , Kim Yun‐Hi , Kwon Soon‐Ki
Published: August 2013

We describe herein the synthesis of novel donor–acceptor conjugated polymers with dithienobenzodithiophenes (DTBDT) as the electron donor and 2,1,3‐benzothiadiazole as the electron acceptor for high‐performance organic photovoltaics (OPVs). We studied the effects of strategically inserting thiophene into the DTBDT as a substituent on the skeletal structure on the opto‐electronic performances of fabricated devices. From UV/Vis absorption, electrochemical, and field‐effect transistor analyses, we found that the thiophene‐containing DTBDT derivative can substantially increase the orbital overlap area between adjacent conjugated chains and thus dramatically enhance charge‐carrier mobility up to 0.55 cm2 V−1 s−1. The outstanding charge‐transport characteristics of this polymer allowed the realization of high‐performance organic solar cells with a power conversion efficiency (PCE) of 5.1 %. Detailed studies on the morphological factors that enable the maximum PCE of the polymer solar cells are discussed along with a hole/electron mobility analysis based on the space‐charge‐limited current model.
Tunable Emissive Lanthanidomesogen Derived from a Room‐Temperature Liquid‐Crystalline Schiff‐Base Ligand
Authors: Pramanik Harun A. R. , Das Gobinda , Bhattacharjee Chira R. , Paul Pradip C. , Mondal Paritosh , Prasad S. Krishna , Rao D. S. Shankar
Published: August 2013

A novel photoluminescent room‐temperature liquid‐crystalline salicylaldimine Schiff base with a short alkoxy substituent and a series of lanthanide(III) complexes of the type [Ln(LH)3(NO3)3] (Ln=La, Pr, Sm, Gd, Tb, Dy; LH=(E)‐5‐(hexyloxy)‐2‐ [{2‐(2‐hydroxyethylamino)ethylimino]methyl}phenol) have been synthesized and characterized by FTIR, 1H and 13C NMR, UV/Vis, and FAB‐MS analyses. The ligand coordinates to the metal ions in its zwitterionic form. The thermal behavior of the compounds was investigated by polarizing optical microscopy (POM) and differential scanning calorimetry (DSC). The ligand exhibits an enantiotropic hexagonal columnar (Colh) mesophase at room temperature and the complexes show an enantiotropic lamellar columnar (ColL) phase at around 120 °C with high thermal stability. Based on XRD results, different space‐filling models have been proposed for the ligand and complexes to account for the columnar mesomorphism. The ligand exhibits intense blue emission both in solution and in the condensed state. The most intense emissions were observed for the samarium and terbium complexes, with the samarium complex glowing with a bright‐orange light (ca. 560–644 nm) and the terbium complex emitting green light (ca. 490–622 nm) upon UV irradiation. DFT calculations performed by using the DMol3 program at the BLYP/DNP level of theory revealed a nine‐coordinate structure for the lanthanide complexes.
Total Synthesis of Enantiopure Pyrrhoxanthin: Alternative Methods for the Stereoselective Preparation of 4‐Alkylidenebutenolides
Authors: Vaz Belén , Otero Leticia , Álvarez Rosana , de Lera Ángel R.
Published: August 2013

A new stereocontrolled total synthesis of the configurationally labile C37‐norcarotenoid pyrrhoxanthin in enantiopure form has been completed. A highly stereoselective Horner–Wadsworth–Emmons (HWE) condensation of a C17‐allylphosphonate and a C20‐aldehyde was used as the last conjunctive step. Both a Sonogashira reaction to form the C17‐phosphonate and the final HWE condensation proved to be compatible with the sensitive C7–C10 enyne E configuration. Regioselective (5‐exo‐dig) silver‐promoted lactonization reactions of three alternative pent‐2‐en‐4‐ynoic acid precursors with increased complexity, including a fully functionalized C20‐fragment, were explored for the preparation of the γ‐alkylidenebutenolide fragment. This survey extends the existing methodologies for the preparation of oxygen‐containing carotenoids (xanthophylls) and streamlines the synthesis of additional members of the C37‐norcarotenoid butenolide family of natural products.
Unusual Inherent Electrochemistry of Graphene Oxides Prepared Using Permanganate Oxidants
Authors: Eng Alex Yong Sheng , Ambrosi Adriano , Chua Chun Kiang , Šaněk Filip , Sofer Zdeněk , Pumera Martin
Published: August 2013

Graphene and graphene oxides are materials of significant interest in electrochemical devices such as supercapacitors, batteries, fuel cells, and sensors. Graphene oxides and reduced graphenes are typically prepared by oxidizing graphite in strong mineral acid mixtures with chlorate (Staudenmaier, Hofmann) or permanganate (Hummers, Tour) oxidants. Herein, we reveal that graphene oxides pose inherent electrochemistry, that is, they can be oxidized or reduced at relatively mild potentials (within the range ±1 V) that are lower than typical battery potentials. This inherent electrochemistry of graphene differs dramatically from that of the used oxidants. Graphene oxides prepared using chlorate exhibit chemically irreversible reductions, whereas graphene oxides prepared through permanganate‐based methods exhibit very unusual inherent chemically reversible electrochemistry of oxygen‐containing groups. Insight into the electrochemical behaviour was obtained through cyclic voltammetry, chronoamperometry, and X‐ray photoelectron spectroscopy experiments. Our findings are of extreme importance for the electrochemistry community as they reveal that electrode materials undergo cyclic changes in charge/discharge cycles, which has strong implications for energy‐storage and sensing devices.
Forest Leaf Area Index (LAI) Estimation Using Airborne Discrete‐Return Lidar Data
Authors: She‐Zhou LUO , Cheng WANG , Gui‐Bin ZHANG , Xiao‐Huan XI , Gui‐Cai LI
Published: August 2013

The Leaf Area Index (LAI) is one of the most important parameters, which controls biological and physical processes associated with vegetation on the Earth's surface, such as photosynthesis, respiration, transpiration, carbon and nutrient cycles, and rainfall interception. Therefore, rapid, reliable and objective estimations of LAI are essential. In this study, we used a simplified approach to compute laser penetration index (LPI) from airborne discrete‐return LiDAR data, and LPI was computed based on corrected echo intensity for the first time. Using the variable of LPI, we built an LAI estimation model based on Beer‐Lambert law. This approach was applied to a forest area in Dayakou, Gansu Province of China. The accuracy of the corrected intensity‐derived LAI estimation model was compared with that of uncorrected intensity‐derived and echo counts‐derived model. The results show that the corrected echoes intensity can improve the accuracy of LAI estimation. To assess validity and generalization of the model, we validated the optimum model using the Leave‐One‐Out Cross‐Validation (LOOCV) procedure, and show that the model has no overfitting and is more general. Finally, we examined the accuracy of predicted LAIs with 16 field‐measured LAIs which were not involved in the modeling process and indicated that LAI can be estimated with a high accuracy in mountains area by corrected echo intensity. The comparison indicates the LiDAR‐derived LAI (R2=0.825, RMSE=0.165) is much higher than that of the LAI from Landsat TM images (R2=0.605, RMSE=0.257). It means that airborne LiDAR data can be used to obtain high‐accuracy LAI estimation and provide reliable data for ecological environment research.
Characteristics of Deep Crust Structure Beneath Western Yunnan
Authors: En‐Hui ZHANG , Hai LOU , Shi‐Xu JIA , Yong‐Hua LI
Published: August 2013

One two‐dimensional P wave velocity model of the crust and uppermost mantle was established based on the integrative interpretation of travel‐time data and amplitude information from the deep seismic sounding on the Pu'er‐Luxi profile, western Yunnan. Our results show strong lateral variations in crustal thickness along the profile, which is about 35 km in the southwest and 43 km in the northeast Yunnan. Average crustal P velocities are low with respect to the global average, varying from 5.9 to 6.13 km/s. Combined with previous joint inversion results of receiver functions and surface waves, the average crustal Poisson's ratio (σ) is calculated, 0.23 in the southwest part of the profile and 0.25 in the northeast part of the profile beneath the western Yunnan. The low P wave velocity and σ values for the upper crust layer beneath the southwest part of the profile is indicative of felsic rocks rich in quartz in the α state, while the relative high P wave velocity and σ for the upper crust layer under the northeast part of the profile is indicative of rocks of granitic and granodioritic composition. The P wave velocity and σ for the lower crust layer is 6.25∼6.75 km/s and 0.24∼0.26 km/s beneath the profile, which can be explained by felsic gneisses in the upper part of the lower crust transitioning to amphibolite in the lower part. Our crustal velocity model shows remarkable contrasts across the Red River fault and the velocity difference becomes gentler with increasing depth. The crustal thickness across the Red River fault is also significantly different. The variation of the velocity and crustal thickness across the Xiaojiang fault is not so remarkable.
Evaluation of a new 1H/31P dual‐tuned birdcage coil for 31P spectroscopy
Authors: Potter W.M. , Wang L. , McCully K.K. , Zhao Q.
Published: August 2013

We introduce a new dual‐tuned hydrogen/phosphorus (1H/31P) birdcage coil, referred to as split birdcage coil, and evaluate its performance using both simulations and magnetic resonance (MR) experiments on a 3 T MR scanner. The proposed coil simplifies the practical matters of tuning and matching, which makes the coil easily reproducible. Simulations were run with the finite difference in time domain method to evaluate the sensitivity and homogeneity of the magnetic field generated by the proposed 1H coils. Following simulations, MR experiments were conducted using both a phantom and human thigh to compare the proposed design with a currently available commercial dual‐tuned flexible surface coil, referred to as flex surface coil, for signal to noise ratio (SNR) as well as homogeneity for the 31P coil. At regions deep within the human thigh, the split birdcage coil was able to acquire spectroscopic signal with a higher average SNR than the flex surface coil. For all regions except those close to the flex surface coil, the split birdcage coil matched or exceeded the performance of the flex surface coil. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 43B: 90‐99, 2013
Design and implementation of an FPGA‐based timing pulse programmer for pulsed‐electron paramagnetic resonance applications
Authors: Sun Li , Savory Joshua J. , Warncke Kurt
Published: August 2013

The design, construction, and implementation of a field‐programmable gate array (FPGA)‐based pulse programmer for pulsed‐electron paramagnetic resonance experiments is described. The FPGA pulse programmer offers advantages in design flexibility and cost over previous pulse programmers, which are based on commercial digital delay generators, logic pattern generators, and application‐specific integrated circuit designs. The FPGA pulse progammer features a novel transition‐based algorithm and command protocol, which is optimized for the timing structure required for most pulsed magnetic resonance experiments. The algorithm was implemented by using a Spartan‐6 FPGA (Xilinx), which provides an easily accessible and cost effective solution for FPGA interfacing. An auxiliary board was designed for the FPGA‐instrument interface, which buffers the FPGA outputs for increased power consumption and capacitive load requirements. Device specifications include: Nanosecond pulse formation (transition edge rise/fall times, ≤3 ns), low jitter (≤150 ps), large number of channels (16 implemented; 48 available), and long pulse duration (no limit). The hardware and software for the device were designed for facile reconfiguration to match user experimental requirements and constraints. Operation of the device is demonstrated and benchmarked by applications to one‐dimensional electron spin echo envelope modulation and two‐dimensional hyperfine sublevel correlation (HYSCORE) experiments. The FPGA approach is transferrable to applications in nuclear magnetic resonance (magnetic resonance imaging), and to pulse perturbation and detection bandwidths in spectroscopies up through the optical range. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 43B: 100‐109, 2013
Fine‐needle aspirations of pancreatic serous cystadenomas: Improving diagnostic yield with cell blocks and α‐inhibin immunohistochemistry
Authors: Salomao Marcela , Remotti Helen , Allendorf John D. , Poneros John M. , Sethi Amrita , Gonda Tamas A. , Saqi Anjali
Published: August 2013

BACKGROUND

The diagnosis of serous cystadenoma (SCA), a rare benign pancreatic neoplasm, can alter the management of patients with pancreatic masses. Although characteristic imaging findings and fluid chemical analysis have been described, SCAs are not always recognized preoperatively. Furthermore, scant cellular yield on fine‐needle aspiration (FNA) often leads to a nondiagnostic or nonspecific benign diagnosis. α‐Inhibin (AI), a sensitive marker for SCA, is infrequently required for diagnosis in surgical specimens due to their characteristic histologic appearance. The objective of the current study was to determine whether AI staining can improve SCA diagnosis on FNA specimens.

METHODS

Fifteen confirmed cases of SCA with prior FNA specimens were selected for this study. FNAs were evaluated for cellularity, cellular arrangement, and cytomorphology. Resection specimens were reviewed.

RESULTS

Of the 15 FNA cases, approximately 75% demonstrated scant cellularity (11 of 15 cases). On smears, the cells were arranged as flat sheets, corresponding to strips of cells on cell block sections. The cells were small and round to cuboidal, with clear cytoplasm; occasional plasmacytoid cells and oncocytic cells were identified. Flattened cells, corresponding to attenuated epithelial cells lining macrocysts on the resections, were also noted. Stromal fragments were present in 5 FNAs and correlated with the hyalinized stroma in the resection specimens. AI immunostaining was positive in 88% of cases (7 of 8 of cases), thereby supporting the diagnosis of SCA.

CONCLUSIONS

The results of the current study indicate that low cellularity and bland cytology are inherent to SCAs. Performing cell blocks and AI staining on FNA specimens is useful for establishing the diagnosis of SCA. An immunohistochemical panel including AI, chromogranin, and synaptophysin may enhance the diagnostic accuracy of pancreatic FNA specimens. Cancer (Cancer Cytopathol) 2014;122:33–39. © 2013 American Cancer Society.
Patterns of cortical input to the primary motor area in the marmoset monkey
Authors: Burman Kathleen J. , Bakola Sophia , Richardson Karyn E. , Reser David H. , Rosa Marcello G.P.
Published: August 2013

In primates the primary motor cortex (M1) forms a topographic map of the body, whereby neurons in the medial part of this area control movements involving trunk and hindlimb muscles, those in the intermediate part control movements involving forelimb muscles, and those in the lateral part control movements of facial and other head muscles. This topography is accompanied by changes in cytoarchitectural characteristics, raising the question of whether the anatomical connections also vary between different parts of M1. To address this issue, we compared the patterns of cortical afferents revealed by retrograde tracer injections in different locations within M1 of marmoset monkeys. We found that the entire extent of this area is unified by projections from the dorsocaudal and medial subdivisions of premotor cortex (areas 6DC and 6M), from somatosensory areas 3a, 3b, 1/2, and S2, and from posterior parietal area PE. While cingulate areas projected to all subdivisions, they preferentially targeted the medial part of M1. Conversely, the ventral premotor areas were preferentially connected with the lateral part of M1. Smaller but consistent inputs originated in frontal area 6DR, ventral posterior parietal cortex, the retroinsular cortex, and area TPt. Connections with intraparietal, prefrontal, and temporal areas were very sparse, and variable. Our results demonstrate that M1 is unified by a consistent pattern of major connections, but also shows regional variations in terms of minor inputs. These differences likely reflect requirements for control of voluntary movement involving different body parts. J. Comp. Neurol. 522:811–843, 2014. © 2013 Wiley Periodicals, Inc.
Rax regulates hypothalamic tanycyte differentiation and barrier function in mice
Authors: Miranda‐Angulo Ana L. , Byerly Mardi S. , Mesa Janny , Wang Hong , Blackshaw Seth
Published: August 2013

The wall of the ventral third ventricle is composed of two distinct cell populations: tanycytes and ependymal cells. Tanycytes regulate many aspects of hypothalamic physiology, but little is known about the transcriptional network that regulates their development and function. We observed that the retina and anterior neural fold homeobox transcription factor (Rax) is selectively expressed in hypothalamic tanycytes, and showed a complementary pattern of expression to markers of hypothalamic ependymal cells, such as Rarres2 (retinoic acid receptor responder [tazarotene induced] 2). To determine whether Rax controls tanycyte differentiation and function, we generated Rax haploinsufficient mice and examined their cellular and molecular phenotype in adulthood. These mice appeared grossly normal, but careful examination revealed a thinning of the third ventricular wall and reduction of both tanycyte and ependymal markers. These experiments show that Rax is required for hypothalamic tanycyte and ependymal cell differentiation. Rax haploinsufficiency also resulted in the ectopic presence of ependymal cells in the α2 tanycytic zone, where few ependymal cells are normally found, suggesting that Rax is selectively required for α2 tanycyte differentiation. These changes in the ventricular wall were associated with reduced diffusion of Evans Blue tracer from the ventricle to the hypothalamic parenchyma, with no apparent repercussion on the gross anatomical or behavioral phenotype of these mice. In conclusion, we have provided evidence that Rax is required for the normal differentiation and patterning of hypothalamic tanycytes and ependymal cells, as well as for maintenance of the cerebrospinal fluid–hypothalamus barrier. J. Comp. Neurol. 522:876–899, 2014. © 2013 The Authors. The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.
Torsional Dynamics of Thioflavin T in Room‐Temperature Ionic Liquids: An Effect of Heterogeneity of the Medium
Authors: Chatterjee Aninda , Maity Banibrata , Seth Debabrata
Published: August 2013

The ultrafast excited‐state dynamics of a fibril binding dye, thioflavin T (ThT), has been studied in two room‐temperature ionic liquids (RTILs): 1‐Butyl‐1‐methylpyrrolidinium bis(trifluoromethylsulfonyl)imide and methyltrioctylammonium bis(trifluoromethylsulfonyl)imide. Previously, in most studies, it was observed that the excited‐state dynamics of the ThT dye were dependent on the viscosity of the medium. In our study, by using RTILs, we have demonstrated that the excited‐state dynamics of ThT are not only viscosity dependent, but also dependent on the heterogeneous nature of the medium. The effect of structural heterogeneity present in neat RTILs on the excited‐state dynamics of ThT was observed. For both RTILs, excitation wavelength dependency on the emission properties of ThT was observed.
Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides
Authors: Lanza Giuseppe , Chiacchio Maria A.
Published: August 2013

Secondary structures for AcAlanNH2 (n=2–4) peptides have been analyzed by means of ab initio MP2, CCSD(T), and DFT‐B3PW91 methods using large basis sets and including implicit hydration effects and thermal corrections. In addition to the classical “pure” right‐handed 310‐ and α‐helices, left‐handed polyproline II, inverse γ‐turn, and fully extended conformations, a large number of “mixed” structures obtained by combining characteristic φ/ψ angles of each residue in every way have been found. All mixed structures are energetically accessible and can be present at significant levels in aqueous solution. Furthermore, they represent the way through which hierarchical unfolding of 310‐ and α‐helices or nonhierarchical polyproline II to fully extended transitions occur. Computational results are in qualitative agreement with the large amount of experimental data for simpler polyalanines and provide significant insight into their thermodynamic properties and how these can be modulated by interactions with solvent.
On the Addition of Aryl Radicals to Graphene: The Importance of Nonbonded Interactions
Authors: Denis Pablo A.
Published: August 2013

Dispersion‐corrected density functional theory is utilized to study the addition of aryl radicals to perfect and defective graphene. Although the perfect sheet shows a low reactivity against aryl diazonium salts, the agglomeration of these groups and the addition onto defect sites improves the feasibility of the reaction by increasing binding energies per aryl group up to 27 kcal mol−1. It is found that if a single phenyl radical interacts with graphene, the covalent and noncovalent additions have similar binding energies, but in the particular case of the nitrophenyl group, the adsorption is stronger than the chemisorption. The single vacancy shows the largest reactivity, increasing the binding energy per aryl group by about 80 kcal mol−1. The zigzag edge ranks second, enhancing the reactivity 5.4 times with respect to the perfect sheet. The less reactive defect site is the Stone–Wales type, but even in this case the addition of an isolated aryl radical is exergonic. The arylation process is favored if the groups are attached nearby and on different sublattices. This is particularly true for the ortho and para positions. However, the enhancement of the binding energies decreases quickly if the distance between the two aryl radicals is increased, thereby making the addition on the perfect sheet difficult. A bandgap of 1–2 eV can be opened on functionalization of the graphene sheets with aryl radicals, but for certain configurations the sheet can maintain its semimetallic character even if there is one aryl radical per eight carbon atoms. At the highest level of functionalization achieved, that is, one aryl group per five carbon atoms, the bandgap is 1.9 eV. Regarding the effect of using aryl groups with different substituents, it is found that they all induce the same bandgap and thus the presence of NO2, H, or Br is not relevant for the alteration of the electronic properties. Finally, it is observed that the presence of tetrafluoroborate can induce metallic character in graphene.
Synthesis of 9‐Oxononanoic Acid, a Precursor for Biopolymers
Authors: Otte Konrad B. , Kirtz Marko , Nestl Bettina M. , Hauer Bernhard
Published: August 2013

Polymers based on renewable resources have become increasingly important. The natural functionalization of fats and oils enables an easy access to interesting monomeric building blocks, which in turn transform the derivative biopolymers into high‐performance materials. Unfortunately, interesting building blocks of medium‐chain length are difficult to obtain by traditional chemical means. Herein, a biotechnological pathway is established that could provide an environmentally suitable and sustainable alternative. A multiple enzyme two‐step one‐pot process efficiently catalyzed by a coupled 9S‐lipoxygenase (St‐LOX1, Solanum tuberosum) and 9/13‐hydroperoxide lyase (Cm‐9/13HPL, Cucumis melo) cascade reaction is proposed as a potential route for the conversion of linoleic acid into 9‐oxononanoic acid, which is a precursor for biopolymers. Lipoxygenase catalyzes the insertion of oxygen into linoleic acid through a radical mechanism to give 9S‐hydroperoxy‐octadecadienoic acid (9S‐HPODE) as a cascade intermediate, which is subsequently cleaved by the action of Cm‐9/13HPL. This one‐pot process afforded a yield of 73 % combined with high selectivity. The best reaction performance was achieved when lipoxygenase and hydroperoxide lyase were applied in a successive rather than a simultaneous manner. Green leaf volatiles, which are desired flavor and fragrance products, are formed as by‐products in this reaction cascade. Furthermore, we have investigated the enantioselectivity of 9/13‐HPLs, which exhibited a strong preference for 9S‐HPODE over 9R‐HPODE.
A new look at cytoskeletal NOS‐1 and β‐dystroglycan changes in developing muscle and brain in control and mdx dystrophic mice
Authors: Janke Alyssa , Upadhaya Ritika , Snow Wanda M. , Anderson Judy E.
Published: August 2013

Background: Loss of dystrophin profoundly affects muscle function and cognition. Changes in the dystrophin‐glycoprotein complex (DGC) including disruption of nitric oxide synthase (NOS‐1) may result from loss of dystrophin or secondarily after muscle damage. Disruptions in NOS‐1 and beta‐dystroglycan (bDG) were examined in developing diaphragm, quadriceps, and two brain regions between control and mdx mice at embryonic day E18 and postnatal days P1, P10, and P28. Age‐dependent differential muscle loading allowed us to test the hypothesis that DGC changes are dependent on muscle use. Results: Muscle development, including loss of central nucleation and the localization of NOS‐1 and bDG, was earlier in diaphragm than quadriceps; these features were differentially disrupted in dystrophic muscles. The NOS‐1/bDG ratio, an index of DGC stability, was higher in dystrophic diaphragm (P10–P28) and quadriceps (P28) than controls. There were also distinct regional differences in NOS‐1 and bDG in brain tissues with age and strain. NOS‐1 increased with age in control forebrain and cerebellum, and in mdx cerebellum; NOS‐1 and bDG were higher in control than mdx mouse forebrain. Conclusions: Important developmental changes in structure and muscle DGC preceded the hallmarks of dystrophy, and are consistent with the impact of muscle‐specific differential loading during maturation. Developmental Dynamics 242:1369–1381, 2013. © 2013 Wiley Periodicals, Inc.
Apoptotic cells enhance sphingosine‐1‐phosphate receptor 1 dependent macrophage migration
Authors: Weichand Benjamin , Weis Nicole , Weigert Andreas , Grossmann Nina , Levkau Bodo , Brüne Bernhard
Published: August 2013

The lipid sphingosine‐1‐phosphate (S1P) is a chemokine for a variety of immune cells including lymphocytes and monocytes. Migration toward S1P is determined by the S1P receptor expression profile, with S1PR1/3 (where S1PR is S1P receptor) stimulating and S1PR2 attenuating migration. However, the impact and physiological significance of S1P‐induced migration of macrophages is largely unclear. We observed that alternative activation of human macrophages, by IL‐4 or apoptotic cells (ACs), enhanced S1PR1 expression. Moreover, ACs provoked macrophage migration toward S1P in an S1PR1‐dependent manner as confirmed by pharmacological receptor inhibition and S1PR1‐deficient murine macrophages. In a mouse model of resolving peritoneal inflammation, F4/80‐driven deletion of S1PR1 reduced postinflammatory macrophage emigration from inflammatory sites. S1PR1 expression on macrophages might, therefore, be relevant for restoring tissue homeostasis during the resolution of inflammation.
Endocytosis‐free DNA sensing by cell surface TLR9 in neutrophils: Rapid defense with autoimmune risks
Authors: Miyake Kensuke , Onji Masahiro
Published: August 2013

TLR9 senses microbial DNA, but may also respond to self‐DNA. To prevent the initiation of innate immune responses to self‐DNA, TLR9 is thought to sense microbial DNA in endolysosomes, and not at the cell surface. A report by Lindau et al. in this issue of the European Journal of Immunology [Eur. J. Immunol. 2013. 43: 2101–2113] shows that TLR9 is expressed on the surface of human and mouse neutrophils and, furthermore, shows that cell surface TLR9, instead of endosomal TLR9, senses DNA in neutrophils. These findings demonstrate that DNA sensing by TLR9 in neutrophils is quite distinct from that in DCs or macrophages. The unique DNA sensing by cell surface TLR9 in neutrophils may reflect their role in inducing rapid inflammation by degranulation with a minimal role in engulfing microbial products for antigen presentation.
On the Reactivity of Zinc Hydroxide Acetate Dihydrate in Ethanol
Authors: Moezzi Amir , Cortie Michael B. , Shimmon Ronald , McDonagh Andrew M.
Published: August 2013

Zinc hydroxide acetate dihydrate, Zn5(OH)8(CH3CO2)2·2H2O, reacts in ethanol at room temperature to yield a mixture of zinc oxide and anhydrous zinc acetate. The process is driven by dehydration of the starting salt. Dehydration of Zn5(OH)8(CH3CO2)2·2H2O also occurs when it is heated in air, but the product obtained in that case depends on the heating rate, environment and temperature. For example, when it is kept in a sealed silica capillary at 100 °C, Zn5(OH)8(CH3CO2)2·1.5H2O is formed after 15 min, whereas treatment in the range 90–100 °C in an open environment results in the formation of anhydrous zinc hydroxide acetate. Heating of any of these products further causes their decomposition to Zn(CH3CO2)2 and ZnO. The coordination bonding mode of the acetate groups in the anhydrous layered zinc hydroxide acetate prepared by reaction with ethanol was studied by using solid‐state NMR spectroscopy. The presence of chelating, unidentate and bidentate bridging modes for the carbonyl carbon atom was revealed, but there was no evidence for the inclusion of ethanol in the resultant structure. Therefore, the reaction in ethanol offers a convenient strategy to prepare anhydrous zinc hydroxide acetate and/or zinc oxide, because it avoids the sensitivity of the thermally induced dehydroxlation process to time, temperature and environment.