bluuebunny/crossref_metadata_2025 huggingface dataset:
How and why do college students use Wikipedia?
Authors: Lim Sook
Published: July 2009

The purposes of this study were to explore college students' perceptions, uses of, and motivations for using Wikipedia, and to understand their information behavior concerning Wikipedia based on social cognitive theory (SCT). A Web survey was used to collect data in the spring of 2008. The study sample consisted of students from an introductory undergraduate course at a large public university in the midwestern United States. A total of 134 students participated in the study, resulting in a 32.8% response rate. The major findings of the study include the following: Approximately one‐third of the students reported using Wikipedia for academic purposes. The students tended to use Wikipedia for quickly checking facts and finding background information. They had positive past experiences with Wikipedia; however, interestingly, their perceptions of its information quality were not correspondingly high. The level of their confidence in evaluating Wikipedia's information quality was, at most, moderate. Respondents' past experience with Wikipedia, their positive emotional state, their disposition to believe information in Wikipedia, and information utility were positively related to their outcome expectations of Wikipedia. However, among the factors affecting outcome expectations, only information utility and respondents' positive emotions toward Wikipedia were related to their use of it. Further, when all of the independent variables, including the mediator, outcome expectations, were considered, only the variable information utility was related to Wikipedia use, which may imply a limited applicability of SCT to understanding Wikipedia use. However, more empirical evidence is needed to determine the applicability of this theory to Wikipedia use. Finally, this study supports the knowledge value of Wikipedia (Fallis, 2008), despite students' cautious attitudes toward Wikipedia. The study suggests that educators and librarians need to provide better guidelines for using Wikipedia, rather than prohibiting Wikipedia use altogether.
An extensive study on automated Dewey Decimal Classification
Authors: Wang Jun
Published: July 2009

In this paper, we present a theoretical analysis and extensive experiments on the automated assignment of Dewey Decimal Classification (DDC) classes to bibliographic data with a supervised machine‐learning approach. Library classification systems, such as the DDC, impose great obstacles on state‐of‐art text categorization (TC) technologies, including deep hierarchy, data sparseness, and skewed distribution. We first analyze statistically the document and category distributions over the DDC, and discuss the obstacles imposed by bibliographic corpora and library classification schemes on TC technology. To overcome these obstacles, we propose an innovative algorithm to reshape the DDC structure into a balanced virtual tree by balancing the category distribution and flattening the hierarchy. To improve the classification effectiveness to a level acceptable to real‐world applications, we propose an interactive classification model that is able to predict a class of any depth within a limited number of user interactions. The experiments are conducted on a large bibliographic collection created by the Library of Congress within the science and technology domains over 10 years. With no more than three interactions, a classification accuracy of nearly 90% is achieved, thus providing a practical solution to the automatic bibliographic classification problem.
Visual overviews for discovering key papers and influences across research fronts
Authors: Aris Aleks , Shneiderman Ben , Qazvinian Vahed , Radev Dragomir
Published: July 2009

Gaining a rapid overview of an emerging scientific topic, sometimes called research fronts, is an increasingly common task due to the growing amount of interdisciplinary collaboration. Visual overviews that show temporal patterns of paper publication and citation links among papers can help researchers and analysts to see the rate of growth of topics, identify key papers, and understand influences across subdisciplines. This article applies a novel network‐visualization tool based on meaningful layouts of nodes to present research fronts and show citation links that indicate influences across research fronts. To demonstrate the value of two‐dimensional layouts with multiple regions and user control of link visibility, we conducted a design‐oriented, preliminary case study with 6 domain experts over a 4‐month period. The main benefits were being able (a) to easily identify key papers and see the increasing number of papers within a research front, and (b) to quickly see the strength and direction of influence across related research fronts.
Loads of special authorship functions: Linear growth in the percentage of “equal first authors” and corresponding authors
Authors: Hu Xiaojun
Published: July 2009

We show that between 1999 and 2008 the percentage of articles with more than one corresponding author or with several authors that contributed equally, leading to so‐called “equal first authors,” has steadily been on the rise. Increasing numbers of corresponding authors and equally contributing authors may lead to increased stress on teamwork if not properly acknowledged in research evaluation exercises.
Specific DNA G‐quadruplexes bind to ethanolamines
Authors: Cheng Xiaohong , Liu Xiangjun , Bing Tao , Zhao Rui , Xiong Shaoxiang , Shangguan Dihua
Published: July 2009

A significant number of G‐quadruplex‐forming sequences have been revealed in human genome by bioinformatic searches, implying that G‐quadruplexes may be involved in important biological processes and may be new chemotherapeutic targets. Therefore, it is important to discover the potential interactions of G‐quadruplexes with other molecules or groups. Here we describe a class of G‐quadruplexes, which can bind to ethanolamine groups that widely exist in biomolecules and drug molecules. The specific interaction of these G‐quadruplexes with ethanolamine groups was identified by high performance affinity chromatography (HPAC) using immobilized ethanolamine and diethanolamine as stationary phase reagents. The circular dichroism (CD) spectra and native polyacrylamide gel electrophoresis (PAGE) show that these ethanolamine binding quadruplexes adopt an intramolecularly parallel structure. The relationship of ethanolamine binding and G‐quadruplexe structure provides new clues for the G‐quadruplex‐related studies as well as for the molecular designs of therapeutic reagents. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 874–883, 2009.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Simple and accurate modeling of the output transition time in nanometer CMOS gates
Authors: Alioto Massimo , Palumbo Gaetano , Poli Massimo
Published: July 2009

In this paper, a model of the output transition time on nanometer CMOS gates is proposed. The development of this model follows the general approach used by Auvergne in (IEE Electron. Lett.2002;38(4):175–177,IEEE Trans. Circuits Systems—part I2000;47(9):1362–1369,IEEE Proc. ISCAS2001;5:363–366,IEEE Trans. Computer‐Aided Design Integr. Circuits Systems2002;21(11):1352–1363), which separately models the output transition time under fast and slow inputs. The proposed model is based on a combined transient and DC circuit analysis, and requires a few simulations. This approach allows for strongly reducing the number of required parameters and simulations compared with other models proposed in the literature.

The analytical model proposed is very simple and has a clear physical meaning, thereby allowing an efficient implementation in CAD tools performing timing analysis, as well as an easy scalability through different processes and technology generations. Spectre simulations on a 65 nm CMOS technology and the 45, 32, 22 nm Berkeley Predictive Technology Models (BPTM) [Berkeley Predictive Technology Model (BPTM). ONLINE@11/25/2008:http://www.eas.asu.edu/∼ptm/] show that the model accuracy is the same as the state‐of‐the‐art models, with an average error of only 4%. Comparison with currently used table‐based models showed also a significant reduction in the CPU time needed to simulate and characterize CMOS logic gates. Copyright © 2009 John Wiley & Sons, Ltd.
Scalable analysis of flow cytometry data using R/Bioconductor
Authors: Klinke David J. , Brundage Kathleen M.
Published: July 2009

Flow cytometry is one of the fundamental research tools available to the life scientist. The ability to observe multidimensional changes in protein expression and activity at single‐cell resolution for a large number of cells provides a unique perspective on the behavior of cell populations. However, the analysis of complex multidimensional data is one of the obstacles for wider use of polychromatic flow cytometry. Recent enhancements to an open‐source platform—R/Bioconductor—enable the graphical and data analysis of flow cytometry data. Prior examples have focused on high‐throughput applications. To facilitate wider use of this platform for flow cytometry, the analysis of a dataset, obtained following isolation of CD4+CD62L+T cells from Balb/c splenocytes using magnetic microbeads, is presented as a form of tutorial. A common workflow for analyzing flow cytometry data was presented using R/Bioconductor. In addition, density function estimation and principal component analysis are provided as examples of more complex analyses. The compendium presented here is intended to help illuminate a path for inquisitive readers to explore their own data using R/Bioconductor (available as Supporting Information). © 2009 International Society for Advancement of Cytometry
Clonal B‐cell population in a reactive lymph node in acquired immunodeficiency syndrome
Authors: Cozzolino Immacolata , Nappa Salvatore , Picardi Marco , De Renzo Amalia , Troncone Giancarlo , Palombini Lucio , Zeppa Pio
Published: July 2009

A 40‐year‐old female, HIV positive, stage C, since 4 years, complained of a right cervical lymph node swelling. Two years before, the patient had been diagnosed with follicular B‐cell non‐Hodgkin lymphoma (FL); she had been treated with four cycles of multiagent chemotherapy plus rituximab, the last cycle being administered 10 months before coming to our attention. An ultrasound (US) guided fine‐needle cytology (FNC) showed an atypical lymphoid cell proliferation. The phenotype evidenced by flow cytometry (FC) analysis was D5: 10%, CD19: 49%, CD23: 10%, FMC7: 0%, CD10: 40%, CD10/19: 40%, lambda light chain 40%, kappa light chain 0%. FDG‐positron emission tomography (PET/CT) scan showed positivity in the corresponding cervical area. Since low LDH values and a reduced lymph node size were observed, the lymph node was therefore excised; the histology revealed a reactive hyperplastic lymph node with florid follicular pattern. A subsequent PCR analysis, performed on DNA extracted from a whole histological section, did not evidence IgH rearrangement. The patient is currently undergoing strict clinical and instrumental follow‐up, including PET every 3 months; after 13 months, she is alive without recurrence of lymphoma. Clonal B‐cell populations in non‐lymphomatous processes have been described in mucosa‐associated lymphoid cell populations and reactive lymph nodes, and are considered non‐malignant, antigen driven, proliferations of B‐lymphocytes determined by an abnormal response to bacterial or viral antigen stimulation. The present case occurred in an HIV patient and was clinically complex because of the patient's history of FL. This experience suggests much attention in the evaluation of radiological, cytological, and FC data and in clinical correlation in patients suffering from autoimmune or immunodeficiency syndromes. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Metastatic hepatocellular carcinoma presenting as a pancreatic mass by computed tomography scan and mimicking a primary neuroendocrine tumor: A potential pitfall in aspiration cytology
Authors: Fitzhugh Valerie A. , Kim Stacey A. , Borcich Anthony , Zhu Hongfa , Wu Maoxin , Szporn Arnold H. , Chen Hua
Published: July 2009

Hepatocellular carcinoma (HCC) is a highly malignant neoplasm, often presenting at late stage and portending a poor prognosis for the patient. The peripancreatic fat is a rare site of extrahepatic metastasis, and metastatic HCC can mimic primary pancreatic neoplasms, even in this location. It is crucial to be aware of this pitfall in the evaluation of aspiration cytology of pancreatic neoplasms and to develop a strategy to reach the correct diagnosis. We present an endoscopic ultrasound fine‐needle aspiration diagnosis of metastatic HCC presenting as a pancreatic mass radiologically that had neuroendocrine features on various cytological and histological preparations. The metastatic lesions were located surgically in the peripancreatic adipose tissue with involvement of one peripancreatic lymph node. This case illustrates the utility of FNA for diagnosing uncommon presentations of HCC and the importance of clinical history, cell block, and an immunocytochemical panel in determining the origin of the tumor. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Cytology of head and neck squamous cell carcinoma variants
Authors: Chute Deborah J. , Stelow Edward B.
Published: July 2009

The most common diagnosis rendered with head and neck fine needle aspiration (FNA) biopsy is metastatic squamous cell carcinoma (SCC). While most cases of metastatic SCC pose little diagnostic difficulty, the diagnosis of metastatic histologic variants of SCC, often coupled with less common etiologies, can be more problematic. This manuscript reviews the clinicopathologic features of the histologic variants of upper aerodigestive tract SCC (verrucous, papillary, spindle cell, undifferentiated, acantholytic, and basaloid) and uncommon etiologies of head and neck SCC (human papillomavirus, Epstein‐Barr Virus, and NUT midline carcinomas). Particular attention is paid to the cytologic features of these lesions. Differential diagnoses and the use of ancillary testing are discussed. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
Cytopathological diagnosis of adult retinoblastoma in a vitrectomy specimen
Authors: Orellana Maria E. , Brimo Fadi , Auger Manon , Galic John , Deschenes Jean , Burnier Miguel N.
Published: July 2009

Retinoblastoma (RB) is extremely rare in adults. We describe a case of RB diagnosed by cytology in a vitrectomy specimen of a 23‐year‐old patient who presented with diminished visual acuity and retinal detachment in the absence of a clinically‐visible mass. Cytological examination of the vitreous fluid showed clusters of loosely cohesive atypical cells with high nuclear to cytoplasmic ratio and “salt and pepper” chromatin pattern in a background of normal neuronal retinal cells. Nuclear molding was present as well as numerous apoptotic bodies. The cells were focally positive for epithelial markers and showed strong and diffuse positivity for neuroendocrine markers. Ki‐67 stained 90% of the “atypical cells” nuclei, in contrast to nonneoplastic retinal neuronal cells, which were negative for the marker. A diagnosis of RB was rendered, and subsequently was confirmed in the enucleation specimen. The cytological differential diagnosis is discussed as well as the role that cytology and immunohistochemistry can play in differentiating neoplastic cells from normal retinal cellular elements in vitreous fluid specimens. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
Orbital sarcoma in HIV positive patient: A diagnostic dilemma
Authors: Gupta Nalini , Gupta Pankaj , Sharma Upender , Vashishta Rakesh Kumar , Rajwanshi Arvind
Published: July 2009

Diagnosis of a high‐grade sarcoma on fine needle aspiration cytology (FNAC) may not pose any difficulty; however, further sub‐typing is sometimes difficult. The clinical data, investigations, and finer points on cytomorphology may help for proper categorization of the tumor, however, we encountered a case of orbital sarcoma in an Human Immunodeficiency Virus (HIV) positive patient, in which further sub‐typing was difficult even on histopathology and immunohistochemistry was helpful. The diagnostic difficulties on FNA cytology smears as well as histopathology are highlighted. Diagn. Cytopathol. 2010. © 2009 Wiley‐Liss, Inc.
What drives cell morphogenesis: A look inside the vertebrate photoreceptor
Authors: Kennedy Breandán , Malicki Jarema
Published: July 2009

Vision mediating photoreceptor cells are specialized light‐sensitive neurons in the outer layer of the vertebrate retina. The human retina contains approximately 130 million of such photoreceptors, which enable images of the external environment to be captured at high resolution and high sensitivity. Rod and cone photoreceptor subtypes are further specialized for sensing light in low and high illumination, respectively. To enable visual function, these photoreceptors have developed elaborate morphological domains for the detection of light (outer segments), for changing cell shape (inner segments), and for communication with neighboring retinal neurons (synaptic terminals). Furthermore, rod and cone subtypes feature unique morphological variations of these specialized characteristics. Here, we review the major aspects of vertebrate photoreceptor morphology and key genetic mechanisms that drive their formation. These mechanisms are necessary for cell differentiation as well as function. Their defects lead to cell death. Developmental Dynamics 238:2115–2138, 2009. © 2009 Wiley‐Liss, Inc.
Cadherin‐11 controls otolith assembly: Evidence for extracellular cadherin activity
Authors: Clendenon Sherry G. , Shah Bijal , Miller Caroline A. , Schmeisser Glen , Walter Amanda , Gattone Vincent H. , Barald Kate F. , Liu Qin , Marrs James A.
Published: July 2009

Cadherin‐11/Cdh11 is expressed through early development and strongly during inner ear development (otic placode and vesicle). Here we show that antisense knockdown of Cdh11 during early zebrafish development interferes with otolith formation. Immunofluorescence labeling showed that Cdh11 expression was concentrated on and within the otolith. Cdh11 was faintly detected at the lateral surface (sites of cell–cell contact) of otic epithelial cells and in the cytoplasm. Strongly labeled Cdh11 containing puncta were detected within the otolymph (the fluid within the otic vesicle) and associated with the otolith surface. BODIPY‐ceramine‐labeled vesicular structures detected in the otolymph were larger and more numerous in Cdh11 knockdown embryos. We present evidence supporting a working model that vesicular structures containing Cdh11 (perhaps containing biomineralization components) are exported from the otic epithelium into the otolymph, adhere to one another and to the surface of the growing otolith, facilitating otolith growth. Developmental Dynamics, 2009. © 2009 Wiley‐Liss, Inc.
The interaction between DC and Plasmodium berghei/chabaudi‐infected erythrocytes in mice involves direct cell‐to‐cell contact, internalization and TLR
Authors: Seixas Elsa , Moura Nunes José F. , Matos Inês , Coutinho António
Published: July 2009

Early interactions between blood‐stage Plasmodium parasites and cells of the innate immune system are very important in shaping the adaptive immune response to malaria, and a number of studies have suggested that DC are responsible for this phenomenon. Therefore, we examined the capacity of murine BM‐derived DC to internalize parasites, be activated and produce cytokines upon in vitro interaction with murine erythrocytes infected with two different strains of rodent malaria parasites (Plasmodium berghei and Plasmodium chabaudi chabaudi). We show that the increased expression of MHC class II and co‐stimulatory molecules and increased production of cytokines by DC following Plasmodium infection involves internalization of infected RBC. Such DC activation not only requires direct cell‐to‐cell contact and internalization of infected RBC by DC but also involves TLR4, TLR9, MyD88 and signaling via NF‐κB; however, TLR involvement in survival to Plasmodium infection was found to be negligible.
Immunisation route‐dependent expression of IL‐4/IL‐13 can modulate HIV‐specific CD8+ CTL avidity
Authors: Ranasinghe Charani , Ramshaw Ian A.
Published: July 2009

All HIV‐1 ‘systemic vaccine trials’ in humans have yielded poor outcomes. Thus, it is important to understand whether the route of delivery influences the quality of protective CTL immunity. Using heterologous poxvirus immunisation we have shown that systemically (i.m./i.m.) immunised CD8+ T cells generated higher levels of IL‐4/IL‐13 compared to mucosal delivery and expression also correlated with i.m./i.m. immunised mice eliciting CTL of lower avidity. Studies using IL‐4−/− and IL‐13−/− KO mice have shown that the capacity to express IFN‐γ, IL‐4 and/or IL‐13 by KdGag197–205‐specific CTL differed between these groups and was inversely correlated with CTL avidity (IL‐13−/−>IL‐4−/−>BALB/c), although no significant differences in the magnitude of CTL responses were observed between IL‐13−/− and wild type mice. When IL‐13 was reconstituted in IL‐13−/− splenocytes in vitro, their ability to bind tetramers also decreased significantly. Our data reveal that total absence of IL‐13 can greatly enhance CTL avidity. In contrast, extracellular IL‐4 appears to be important in maintaining long‐term Th1/Th2 balance in CTL, even though expression of IL‐4 by CTL markedly reduced avidity. STAT6−/− mice also showed memory CTL of higher avidity. Furthermore, CCL5 expression in KdGag197–205‐specific CTL was also regulated by IL‐4/IL‐13.
Multiple tissue‐specific isoforms of sulfatide activate CD1d‐restricted type II NKT cells
Authors: Blomqvist Maria , Rhost Sara , Teneberg Susann , Löfbom Linda , Østerbye Thomas , Brigl Manfred , Månsson Jan‐Eric , Cardell Susanna L.
Published: July 2009

The glycosphingolipid sulfatide (SO3‐3Galβ1Cer) is a demonstrated ligand for a subset of CD1d‐restricted NKT cells, which could regulate experimental autoimmune encephalomyelitis, a murine model for multiple sclerosis, as well as tumor immunity and experimental hepatitis. Native sulfatide is a mixture of sulfatide isoforms, i.e. sulfatide molecules with different long‐chain bases and fatty acid chain lengths and saturation. Here, we demonstrate that sulfatide‐specific CD1d‐restricted murine NKT hybridomas recognized several different sulfatide isoforms. These included the physiologically relevant isoforms C24:1 and C24:0, major constituents of the myelin sheet of the nervous system, and C16:0, prominent in the pancreatic islet β‐cells. The most potent sulfatide isoform was lysosulfatide (lacking a fatty acid). Shortened fatty acid chain length (C24:1 versus C18:1), or saturation of the long fatty acid (C24:0), resulted in reduced stimulatory capacity, and fatty acid hydroxylation abolished the response. Moreover, sulfatide was not responsible for the natural autoreactivity toward splenocytes by XV19 T hybridoma cells. Our results reveal a promiscuity in the recognition of sulfatide isoforms by a CD1d‐restricted NKT‐cell clone, and suggest that sulfatide, a major component of the myelin sheet and pancreatic β‐cells, is one of several natural ligands for type II CD1d‐restricted NKT cells.
CREB and AP‐1 activation regulates MKP‐1 induction by LPS or M‐CSF and their kinetics correlate with macrophage activation versus proliferation
Authors: Casals‐Casas Cristina , Álvarez Eva , Serra Maria , de la Torre Carolina , Farrera Consol , Sánchez‐Tilló Ester , Caelles Carme , Lloberas Jorge , Celada Antonio
Published: July 2009

MAPK phosphatase‐1 (MKP‐1) is a protein phosphatase that plays a crucial role in innate immunity. This phosphatase inactivates ERK1/2, which are involved in two opposite functional activities of the macrophage, namely proliferation and activation. Here we found that although macrophage proliferation and activation induce MKP‐1 with different kinetics, gene expression is mediated by the proximal promoter sequences localized between −380 and −180 bp. Mutagenesis experiments of the proximal element determined that CRE/AP‐1 is required for LPS‐ or M‐CSF‐induced activation of the MKP‐1 gene. Moreover, the results from gel shift analysis and chromatin immunoprecipitation indicated that c‐Jun and CREB bind to the CRE/AP‐1 box. The distinct kinetics shown by M‐CSF and LPS correlates with the induction of JNK and c‐jun, as well as the requirement for Raf‐1. The signal transduction pathways that activate the induction of MKP‐1 correlate kinetically with induction by M‐CSF and LPS.
The effect of allogeneic in vitro stimulation and in vivo immunization on memory CD4+ T‐cell APOBEC3G expression and HIV‐1 infectivity
Authors: Jeffrey Pido‐Lopez , Wang Yufei , Seidl Thomas , Babaahmady Kaboutar , Vaughan Robert , Lehner Thomas
Published: July 2009

Allogeneic immunity is one of the most potent natural immune responses. APOBEC3G (A3G) is an intracellular anti‐viral factor that deaminates cytidine to uridine. Allogeneic stimulation of human CD4+ T cells in vitro upregulated A3G mRNA and a significant correlation was found between the mixed leukocyte reaction and A3G mRNA. The mechanism of upregulation of A3G mRNA involves interaction between HLA on DC and TCR of CD4+ T cells, which is ZAP70 and downstream ERK phosphokinase signalling dependent and induces CD40L and A3G mRNA expression in CD4+ T cells. Alloimmune‐induced A3G was found to be significantly increased in CD45RA−, CCR5+ and CD45RA−CCR7− subsets of effector memory T cells. In vivo studies of women alloimmunized with their partners' PBMC also showed a significant increase in A3G protein in CD4+ T cells, CD45RO+ memory and CCR7− effector memory T cells. The functional effect of allostimulation upregulating A3G mRNA was demonstrated by a significant decrease in in vitro infectivity, using GFP‐labelled pseudovirus and confirmed by a decrease in HIV‐1 (BaL) infection of primary CD4+ T cells. The results suggest that alloimmunization offers an alternative or complementary strategy in inducing an innate anti‐viral factor that inhibits HIV‐1 infection.
Novel HIV‐1 clade B candidate vaccines designed for HLA‐B*5101+ patients protected mice against chimaeric ecotropic HIV‐1 challenge
Authors: Roshorm Yaowaluck , Hong Jessie P. , Kobayashi Naoki , McMichael Andrew J. , Volsky David J. , Potash Mary Jane , Takiguchi Masafumi , Hanke Tomáš
Published: July 2009

Novel candidate HIV‐1 vaccines have been constructed, which are tailor‐designed for HLA‐B*5101+ patients infected with HIV‐1 clade B. These vaccines employ novel immunogen HIVB‐B*5101 derived from consensus HIV‐1 clade B Gag p17 and p24 regions coupled to two Pol‐derived B*5101‐restricted epitopes, which are together with a third B*5101 epitope in Gag dominant in HIV‐1‐infected long‐term non‐progressing patients. Both plasmid DNA and modified vaccinia virus Ankara (MVA) vectors supported high expression levels of the HIVB‐B*5101 immunogen in cultured cells. Heterologous DNA prime‐recombinant MVA boost regimen induced efficiently HIV‐1‐specific CD8+ T‐cell responses in BALB/c mice. These vaccine‐elicited T cells were multifunctional, killed efficiently target cells in vivo, and protected mice against challenge with ecotropic HIV‐1/NL4‐3 and ecotropic HIV‐1/NDK chimaeric viruses with HIV‐1 clade B or D backbones, respectively, and ecotropic murine leukemia virus gp80 envelope, and therefore did so in the absence of anti‐HIV‐1 gp120 antibodies. These results support further development of HIVB‐B*5101 vaccines in combined heterologous‐modality regimens. The use of allele‐specific vaccines in humans is discussed in the context of other developments in the HIV‐1 field.
Invariant NKT cells and CD1d+ cells amass in human omentum and are depleted in patients with cancer and obesity
Authors: Lynch Lydia , O'Shea Donal , Winter Desmond C. , Geoghegan Justin , Doherty Derek G. , O'Farrelly Cliona
Published: July 2009

Invariant NKT (iNKT) cells recognize lipid antigens presented by CD1d and respond rapidly by killing tumor cells and release cytokines that activate and regulate adaptive immune responses. They are essential for tumor rejection in various mouse models, but clinical trials in humans involving iNKT cells have been less successful, partly due to their rarity in humans compared with mice. Here we describe an accumulation of functional iNKT cells in human omentum, a migratory organ with healing properties. Analysis of 39 omental samples revealed that T cells are the predominant lymphoid cell type and of these, 10% expressed the invariant Vα24Jα18 TCR chain, found on iNKT cells, higher than in any other human organ tested to date. About 15% of omental hematopoietic cells expressed CD1d, compared with 1% in blood (p<0.001). Enriched omental iNKT cells killed CD1d+ targets and released IFN‐γ and IL‐4 upon activation. Omental iNKT‐cell frequencies were lower in patients with severe obesity (p=0.005), and with colorectal carcinoma (p=0.004) compared with lean healthy subjects. These data suggest a novel role for the omentum in immune regulation and tumor immunity and identify it as a potential source of iNKT cells for therapeutic use.
The C‐type lectin DC‐SIGN internalizes soluble antigens and HIV‐1 virions via a clathrin‐dependent mechanism
Authors: Cambi Alessandra , Beeren Inge , Joosten Ben , Fransen Jack A. , Figdor Carl G.
Published: July 2009

Dendritic cells (DC), professional Ag‐presenting cells located in mucosae and lymphoid organs, operate at the interface of innate and adaptive immunity and are likely the first cells to encounter invading HIV‐1. Although the C‐type lectin DC‐Specific ICAM‐3‐grabbing non‐integrin (DC‐SIGN) binds to several viruses, including HIV‐1, its direct involvement in viral entry remains controversial. Despite its central role in DC function, little is known about the underlying molecular mechanism(s) of DC‐SIGN‐mediated Ag uptake. Here, we analyzed the early stages of DC‐SIGN‐mediated endocytosis and demonstrate that both membrane cholesterol and dynamin are required. Confocal microscopy and clathrin RNAi showed that DC‐SIGN‐mediated internalization occurs via clathrin‐coated pits. Electron microscopy of ultrathin sections showed the involvement of DC‐SIGN in clathrin‐dependent HIV‐1 internalization by DC. Currently, DC‐specific C‐type lectins are considered potential target in anti‐tumor clinical trials. Detailed information about how different Ag are internalized via these receptors will facilitate the rational design of targeted therapeutic strategies.
CTL quality and the control of human retroviral infections
Authors: Bangham Charles R. M.
Published: July 2009

The CTL response plays a central part in deciding the outcome of viral infections. Evidence from host and viral genetics, gene expression microarrays and assays of T‐cell phenotype and function indicate that individual differences in the efficiency of the virus‐specific CTL response strongly determine the outcome of infection with the human retroviruses HTLV‐1 and HIV‐1. It is now believed that differences in anti‐viral CTL efficiency or “quality” at the single‐cell level are critical in determining the efficacy of the host response to viruses. However, it is difficult to identify and quantify the reasons for this apparent individual variation in CTL efficiency, because of the chronic course of infection and the dynamical complexity of the equilibrium that is established between the virus and the host immune response. Specifically, it is unclear whether the observed variations among infected hosts,i.e. in the frequency, phenotype and function or quality of T cells, are the causes or effects – or both – of the variation in the efficiency of virus control.
Getting to the crux of the matter: IL‐23 and Th17 cell accumulation in the CNS
Authors: Segal Benjamin M.
Published: July 2009

IL‐23 plays a critical role in EAE induced by the active immunization of C57BL/6 mice with an immunodominant epitope of myelin oligodendrocyte glycoprotein (MOG35–55). It was initially assumed that the pathogenic effects of IL‐23 were directly related to the generation, expansion and/or stabilization of autoreactive CD4+ Th17 cells. However, a number of recent studies have uncovered discrepancies between the requirement for IL‐23, as opposed to Th17 cells or their products (IL‐17A, IL‐17F and IL‐22), in the development of EAE. In this issue of the European Journal of Immunology, it is demonstrated that impairment of IL‐23 signaling does not impede the expansion of myelin‐specific CD4+ T cells in peripheral lymphoid tissues but inhibits their accumulation in the CNS. This paper contributes to a growing body of data that implicates IL‐23 in the acquisition of CNS homing properties by autoreactive effector cells.
Cover Picture: Eur. J. Immunol. 7/09
Authors: Cambi Alessandra , Beeren Inge , Joosten Ben , Fransen Jack A. , Figdor Carl G.
Published: July 2009

The cover image depicts the co‐staining of DC‐SIGN and EEA‐1 in dendritic cells and shows the co‐localization of the endocytosed ligand with markers of the early endosomal compartments. The image was taken from the article by Cambi et al. (pp. 1923–1929), in which the authors analyze the role of the C‐type lectin DC‐SIGN in viral entry. The authors show that DC‐SIGN is involved in clathrin‐dependent HIV‐1 internalization by dendritic cells.
Designer Peptides: Attempt to Control Peptide Structure by Exploiting Ferrocene as a Scaffold
Authors: Lataifeh Anas , Beheshti Samaneh , Kraatz Heinz‐Bernhard
Published: July 2009

The design of peptides that display a β‐sheet‐like secondary structure remains a challenge. Molecular scaffolds, such as ferrocene (Fc) can help to overcome some of these challenges. Monosubstituted Fc derivatives offer no control over the self‐assembly of the conjugates, and the formation of supramolecular structures is entirely serendipitous. 1,n′‐disubstituted Fc derivatives provide a significant level of control over the direction of the peptide, their relative orientation, and the intramolecular hydrogen‐bonding patterns, which increases the rigidity of the molecule and in many cases, generates a new H‐bonding interface for intermolecular assembly. In this Microreview, we explore the use of ferrocene as a scaffold in the design of structurally well‐defined peptide conjugates. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
New Helical Zinc Complexes with Schiff Base Derivatives of β‐Diketonates or β‐Keto Esters and Ethylenediamine
Authors: Kotova Oxana , Semenov Sergey , Eliseeva Svetlana , Troyanov Sergey , Lyssenko Konstantin , Kuzmina Natalia
Published: July 2009

The tetradentate Schiff bases H2L = H2AC [N,N′‐ethylene‐bis(4‐iminopentan‐2‐one)], H2MAL1 [N,N′‐ethylene‐bis(methyl‐3‐iminobutanoate)], and H2MAL2 [N,N′‐ethylene‐bis(tert‐butyl‐3‐iminobutanoate)] were found to possess sufficient flexibility and were tailored to self assemble with zinc ions to form neutral bimetallic helicates with the overall composition Zn2L2. In solution for all ligands, an equilibrium between the tautomeric forms exists, which was confirmed by IR and NMR spectroscopy. X‐ray single‐crystal analysis performed for H2MAL1 (1) and H2MAL2 (2) reveals that they have similar geometrical parameters and crystallize in a trans conformation. In the crystal structures of the zinc complexes [Zn2(AC)2]·C6H6 (3), [Zn2(MAL1)2]·0.5C7H8 (4), and [Zn2(MAL2)2]·C7H8 (5), the Schiff base ligands are helically wrapped around the two four‐coordinate metal ions, which leads to an idealized D2 symmetry. The coordination polyhedron around the Zn ions in 3–5 can be described as a tetrahedral geometry comprising two O‐ and two N‐donor atoms of the Schiff base ligands. The intramolecular separation Zn···Zn varies from 3.465 to 3.628 Å. The total length of the helix is 5.85, 5.84, and 6.01 Å for structures 3, 4, and 5, respectively, while the helical pitch values are in the range 7.8–9.2 Å. Both the ligands H2L and the zinc helicates are thermally stable up to ≈150–160 °C, as shown by thermogravimetric analysis under a nitrogen atmosphere. The formation of the zinc complexes in solution is confirmed by spectrophotometric titrations, along with ESI‐MS, and has almost no effect on the absorption spectra of H2L. The Schiff bases and the Zn2L2 complexes display broad‐band, blue emission in the range 350–600 nm under a 337‐nm excitation at 77 K. Finally, the impact of electronic effects of the Schiff base substituents on the structure of the Zn complexes, especially on bond lengths within the chelate rings, and the absorption and photoluminescence spectra, are discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Gas chromatographic behavior of fatty acid derivatives for mass spectrometry on low‐polarity capillary columns
Authors: Dubois Nolwenn , Barnathan Gilles , Gouygou Jean‐Paul , Bergé Jean‐Pascal
Published: July 2009

The gas chromatographic properties of four derivatives of fatty acids (FA), namely fatty acid methyl esters, picolinyl esters, N‐acyl pyrrolidides and 4,4‐dimethyloxazoline derivatives, which contain various structural features (double bonds, branching, hydroxyl group) in their acyl chains have been compared on a low‐polarity capillary column with a mass spectrometer as detector. Temperature programming rates yielding the highest resolution were optimized for each derivative by means of computer‐assisted column temperature optimization software. Indeed, the Drylab software represents a valuable assistance for estimating the optimum analysis conditions. Time and efforts required for such method development can greatly be reduced. Different parameters (derivatization procedure, total run time, resolution and response factor) are discussed. N‐Acyl pyrrolidides and picolinyl esters appear quite powerful for structure elucidation of polyunsaturated FA by GC‐MS, and both these types of FA derivatives can be very well separated on a low‐polarity phase.
Consecutive reactions in an oleic acid and acetic anhydride reaction medium
Authors: Peydecastaing Jerome , Vaca‐Garcia Carlos , Borredon Elisabeth
Published: July 2009

When mixing acetic anhydride and oleic acid, two consecutive reactions take place. The first one yields acetic‐oleic anhydride (AOA) and acetic acid. In the second one, oleic acid reacts with AOA to form oleic anhydride at 5% in a mixture when the initial molar ratio is 1:1. Therefore, at equilibrium, the global reaction yields a mixture of AOA, acetic anhydride, oleic acid, acetic acid and oleic anhydride. Based on a new HPLC protocol, all the species of the reaction medium could be separated and quantified. This permitted for the first time to study the kinetics and thermodynamics of the reaction. In the 30–70 °C range, reactions were of order 2 with partial orders of 1 for each reactant. Equilibrium constants were determined for both reactions. Enthalpy, entropy and activation energies were calculated for the main reaction. The influence of molar ratio on the composition at equilibrium was also investigated. The synthesis of AOA could thus be understood and new data were obtained for this singular molecule scarcely cited in the CAS database.
Chemical composition of Pinus sibirica nut oils
Authors: Zadernowski Ryszard , Naczk Marian , Czaplicki Sylwester
Published: July 2009

The chemical composition of oil obtained from Pinus sibirica was investigated. The nonpolar lipids were the predominant lipid fraction while the triacylglycerols were the major component of this fraction. α‐ and γ‐tocopherols were the dominant tocopherols in pine oils. Eleven fatty acids (FA) were identified in pine nut oil. The unsaturated FA comprised over 90% of the total FA. Of these, polyunsaturated FA accounted for 66% of the total FA. 18:2 and 18:3 acids were the dominant unsaturated FA, while palmitic and stearic acids were the major saturated FA. Three unusual FA, namely 10,13‐octadecadienoic, gorlic and 11,13‐eicosadienoic acid, were tentatively identified in pine nut oil.
Effect of biodiesel blends on North American heavy‐duty diesel engine emissions
Authors: Yanowitz Janet , McCormick Robert L.
Published: July 2009

We conducted an assessment of North American heavy‐duty engine emission test results for biodiesel from 49 experimental studies, including both engine dynamometer and vehicle test results. Comparison with a commercial database showed that the engines in the emissions database are not representative of the existing North American in‐use fleet as of 2007; more than 50% of the tested engines were of 1995 or earlier vintage. Nevertheless, the results show that the use of a common biodiesel blend (B20) consistently reduces emissions of particulate matter, hydrocarbons, and carbon monoxide by 10–20%. Tests with B20 show varying effects on oxides of nitrogen (NOx). If results for pre‐1992 two‐cycle 6V‐92TA(E) engines (which represent 0.2% of the 2007 in‐use fleet but 28% of the engines tested) are removed, then there is no statistical evidence that the average NOx emissions from B0 and B20 are different (p value of 0.50 for an estimated average increase of 1%). Several researchers have used changes in engine calibration to eliminate any NOx penalty associated with B20 (in engines that show an increase in NOx with B20), while still maintaining the advantages of B20 in reducing other pollutants. The emissions effect of B20 on heavy‐duty diesel truck emissions did not show any correlation with model year or type of fuel injection equipment.
Extraction, transesterification and process control in biodiesel production from Jatropha curcas
Authors: Nazir Novizar , Ramli Nazaruddin , Mangunwidjaja Djumali , Hambali Erliza , Setyaningsih Dwi , Yuliani Sri , Yarmo Mohd. Ambar , Salimon Jumat
Published: July 2009

Biodiesel has gained worldwide popularity as an alternative energy source due to its renewable, non‐toxic, biodegradable and non‐flammable properties. It also has low emission profiles and is environmentally beneficial. Biodiesel can be used either in pure form or blended with conventional petrodiesel in automobiles without any major engine modifications. Various non‐edible and edible oils can be used for the preparation of biodiesel. With no competition with food uses, the use of non‐edible oils as alternative source for engine fuel will be important. Among the non‐edible oils, such as Pongamia, Argemone and Castor, Jatropha curcas has tremendous potential for biodiesel production. J. curcas, growing mainly in tropical and sub‐tropical climates across the developing world, is a multipurpose species with many attributes and considerable potentials. In this article, we review the oil extraction and characterization, the role of different catalysts on transesterification, the current state‐of‐the‐art in biodiesel production, the process control and future potential improvement of biodiesel production from J. curcas.
Extraction, purification and characterization of wax from flax (Linum usitatissimum) straw
Authors: Athukorala Yasantha , Mazza Giuseppe , Oomah B. Dave
Published: July 2009

The chemical composition and selected physical parameters of wax extracted from flax straw with supercritical CO2 (SC‐CO2) and hexane have been determined. From the GC/MS results, clear variations in composition and component distributions were observed between SC‐CO2‐ and hexane‐extracted samples. The major components of the SC‐CO2 and hexane extracts from three flax cultivars were: fatty acids (36–49%), fatty alcohols (20–26%), aldehydes (10–14%), wax esters (5–12%), sterols (7–9%) and alkanes (4–5%). Purification of SC‐CO2‐extracted wax with silica gel chromatography yielded 0.4–0.5% (dry matter) and was composed primarily of wax esters (C44, C46 and C48) and alkanes (C27, C29 and C31). UV‐Vis scans of the purified wax samples exhibited two main peaks indicating the presence of conjugated dienes and carotenoids or related compounds. Fourier transform infrared results showed prominent peaks at 2918 (‐C‐H), 2849 (‐C‐H), 1745 (‐C=O), 1462 (‐C‐H), 1169 (‐C‐O) and 719 cm–1 (‐(CH2)n‐), with NorLin wax showing a slightly deviating pattern compared to the other samples. Thermal analysis by differential scanning calorimetry revealed a mean melting point of 55–56 °C and oxidation temperatures of 146–153 °C for purified wax from flax straw processed using different procedures.
Oxidation products of free polyunsaturated fatty acids in wheat varieties
Authors: Levandi Tuuli , Püssa Tõnu , Vaher Merike , Toomik Peeter , Kaljurand Mihkel
Published: July 2009

Oxygenated fatty acids (oxylipins) are secondary metabolites of polyunsaturated fatty acids (PUFA). Here, we present a novel high‐performance liquid chromatograpic separation on a reversed‐phase column (RP‐HPLC) coupled with electrospray ionization‐tandem mass spectrometry (ESI‐MS/MS) for the determination of various (per)oxidation products of linoleic (cis,cis‐9,12‐octadecadienoic) acid in eight different varieties (four spring and four winter varieties) of wheat (Triticum aestivum). The procedure includes extraction of oxylipins, chromatograpic separation using a linear gradient of aqueous formic acid and acetonitrile, with subsequent identification of compounds by MS/MS. Among the identified oxylipins, leukotoxin (LTX)‐diol and its isomer (iso‐LTX‐diol) are known as potentially toxic substances. The obtained data was used further for comparison of different wheat varieties by principal component analysis (PCA). From the results of PCA, differences can be observed in the patterns of wheat varieties.
Preparation of diacylglycerol‐enriched palm olein by phospholipase A1‐catalyzed partial hydrolysis
Authors: Wang Yong , Zhao Mouming , Ou Shiyi , Song Keke , Han Xue
Published: July 2009

Partial hydrolysis of palm olein catalyzed by phospholipase A1 (Lecitase Ultra) in a solvent‐free system was carried out to produce diacylglycerol (DAG)‐enriched palm olein (DEPO). Four reaction parameters, namely, reaction time (2–10 h), water content (20–60 wt‐% of the oil mass), enzyme load (10–50 U/g of the oil mass), and reaction temperature (30–60 °C), were investigated. The optimal conditions for partial hydrolysis of palm olein catalyzed by Lecitase Ultra were obtained by an orthogonal experiment as follows: 45 °C reaction temperature, 44 wt‐% water content, 8 h reaction time, and an enzyme load of 34 U/g. The upper oil layer of the reaction mixture with an acid value of 54.26 ± 0.86 mg KOH/g was first molecularly distilled at 150 °C to yield a DEPO with 35.51 wt‐% of DAG. The DEPO was distilled again at 250 °C to obtain a DAG oil with 74.52 wt‐% of DAG. The composition of the acylglycerols of palm olein and the DEPO were analyzed and identified by high‐performance liquid chromatography (HPLC) and HPLC/electrospray ionization/mass spectrometry. The released fatty acids from the partial hydrolysis of palm olein catalyzed by phospholipase A1 showed a higher saturated fatty acid content than that of the raw material.
Molecular Tailored Histidine‐Based Complexing Surfactants: From Micelles to Hydrogels
Authors: Gizzi Patrick , Pasc Andreea , Dupuy Nicolas , Parant Stéphane , Henry Bernard , Gérardin Christine
Published: July 2009

Novel histidine‐based complexing surfactants, designed as AA‐His‐EOm‐Cn, containing trifunctional moduli (peptidic/hydrophilic/hydrophobic) were synthesized by a modular step‐by‐step procedure, which allowed easy structural changes, and consequently correlations between their molecular structures and their self‐assembling properties could be established. Thus, micelles or hydrogels could be obtained by simply modifying the hydrophobic tail lengths or the junction between the different moduli of the designed compounds. At low pH values, all compounds were surface active in aqueous solutions. At higher pH values, in the range 8–10, micellization took place for decyl compounds (n = 10), whereas hydrogelation occurred for longer chain lengths (n = 12, 14), and this, at very‐low concentrations of surfactant (<0.3 wt.‐%), could thus act as low molecular weight gelator (LMWG). The driving forces for gel formation were noncovalent intermolecular interactions such as π‐stacking and hydrophobic and hydrogen‐bonding interactions.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)