bluuebunny/crossref_metadata_2025 huggingface dataset:
A whole-genome assembly of the domestic cow, Bos taurus
Authors: Zimin Aleksey V , Delcher Arthur L , Florea Liliana , Kelley David R , Schatz Michael C , Puiu Daniela , Hanrahan Finnian , Pertea Geo , Van Tassell Curtis P , Sonstegard Tad S , Marçais Guillaume , Roberts Michael , Subramanian Poorani , Yorke James A , Salzberg Steven L
Published: April 2009

Background

The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods.

Results

We have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions.

Conclusions

By using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome.
Neutrophils rescue gingival epithelial cells from bacterial-induced apoptosis
Authors: Galicia Johnah C , Benakanakere Manjunatha R , Stathopoulou Panagiota G , Kinane Denis F
Published: April 2009

During mucosal infection, neutrophils prevent epithelial cell apoptosis by phagocytosing bacteria prior to undergoing apoptosis themselves.

In the pathogenesis of chronic inflammatory periodontal disease, neutrophils are recognized as a major cellular component from the histopathology of the periodontal lesion around teeth and from clinical cases where absence or dysfunction of neutrophils results in major periodontal destruction. Neutrophils are recruited in vast numbers into the gingival crevice during periodontal inflammation, attracted by microbial plaque chemoattractants and chemokines released following microbial perturbation of gingival epithelial cells. Porphyromonas gingivalis, a major periodontopathogen, triggers a vast array of cellular responses in gingival epithelial cells but also induces apoptosis. We demonstrate here that neutrophils, when combined in a P. gingivalis challenge assay of epithelial cells, prevent epithelial cell apoptosis by phagocytosing P. gingivalis and later undergoing apoptosis themselves. By removing P. gingivalis by phagocytosis, neutrophils also protect the host from the harmful effects of its microbial proteases, which degrade inflammatory cytokines and other host molecules.
Cellular expression and antimicrobial function of a phylogenetically conserved novel histone 1x-like protein on mouse cells: a potential new class of pattern recognition receptor
Authors: Evans Donald L , Connor Meghan A , Moss Lauren D , Lackay Sarah , Leary John H , Krunkosky Thomas , Jaso-Friedmann Liliana
Published: April 2009

A novel bifunctional histone 1X-like protein is a soluble antimicrobial and a membrane pattern recognition receptor.

A H1x-like protein (i.e., NCAMP-1) is expressed on the membrane and in GEs from fish NK-like cells. In the present study, we identify the imprinting control region mouse NCAMP-1 ortholog using NCAMP-1 polyclonal antibodies and mAb. Polychromatic flow cytometry revealed NCAMP-1 expression on PBLs (Gr-1+ PMNs were 21.1% NCAMP-1+; DX-5+  NK cells were 12.2% NCAMP-1+), mesenteric LN cells (CD11c+ DCs were 23.2% NCAMP-1+; Gr-1+ PMNs were 24.8% NCAMP-1+; CD21+ B cells were 17.8% NCAMP-1+), and splenocytes (CD11c+ were 39.6% NCAMP-1+; Gr-1+ PMNs were 40.9% NCAMP-1+; DX-5+ NK cells were 24.3% NCAMP-1+; CD21+ B cells were 28.5% NCAMP-1+). Western blot analysis using pNCAMP-1 and GEs from RAW 264.7 cells produced a 32-kDa signal. GEs from RAW 264.7 cells produced a significant reduction in Escherichia coli CFU. This antimicrobial killing activity was inhibited by pretreatment of the extract with (polyclonal) anti-NCAMP-1. Treatment with preimmune serum did not reduce bacterial cell killing. Confocal microscopy using NCAMP-1 and LAMP-1 mAb demonstrated that NCAMP-1 was located on the membrane and in cytosolic vesicles of RAW 264.7 cells and did not appear to colocalize with LAMP-1. NCAMP-1 may participate as a bifunctional protein on cells. It is expressed on the membranes of phagocytic cells, NK cells, and APCs in mice as well as in the granules of macrophages. In phagocytic cells, NCAMP-1 may participate in a nonregulated exocytosis pathway of cellular secretion.
In Vivo and ex Vivo Regulation of Visfatin Production by Leptin in Human and Murine Adipose Tissue: Role of Mitogen-Activated Protein Kinase and Phosphatidylinositol 3-Kinase Signaling Pathways
Authors: Tan Bee K. , Chen Jing , Brown James , Adya Raghu , Ramanjaneya Manjunath , Menon Vinod , Bailey Clifford J. , Lehnert Hendrik , Randeva Harpal S.
Published: April 2009

Visfatin is an adipogenic adipokine with increased levels in obesity, properties common to leptin. Thus, leptin may modulate visfatin production in adipose tissue (AT). Therefore, we investigated the effects of leptin on visfatin levels in 3T3-L1 adipocytes and human/murine AT, with or without a leptin antagonist. The potential signaling pathways and mechanisms regulating visfatin production in AT was also studied. Real-time RT-PCR and Western blotting were used to assess the relative mRNA and protein expression of visfatin. ELISA was performed to measure visfatin levels in conditioned media of AT explants, and small interfering RNA technology was used to reduce leptin receptor expression. Leptin significantly (P < 0.01) increased visfatin levels in human and murine AT with a maximal response at leptin 10−9m, returning to baseline at leptin 10−7m. Importantly, ip leptin administration to C57BL/6 ob/ob mice further supported leptin-induced visfatin protein production in omental AT (P < 0.05). Additionally, soluble leptin receptor levels rose with concentration dependency to a maximal response at leptin 10−7m (P < 0.01). The use of a leptin antagonist negated the induction of visfatin and soluble leptin receptor by leptin. Furthermore, leptin-induced visfatin production was significantly decreased in the presence of MAPK and phosphatidylinositol 3-kinase inhibitors. Also, when the leptin receptor gene was knocked down using small interfering RNA, leptin-induced visfatin expression was significantly decreased. Thus, leptin increases visfatin production in AT in vivo and ex vivo via pathways involving MAPK and phosphatidylinositol 3-kinase signaling. The pleiotropic effects of leptin may be partially mediated by visfatin.
Hypothyroidism Decreases the Biogenesis in Free Mitochondria and Neuronal Oxygen Consumption in the Cerebral Cortex of Developing Rats
Authors: Martinez Bienvenida , Rodrigues Tiago B. , Gine Elena , Kaninda John P. , Perez-Castillo Ana , Santos Angel
Published: April 2009

Thyroid hormone plays a critical role in mitochondrial biogenesis in two areas of the developing brain, the cerebral cortex and the striatum. Here we analyzed, in the cerebral cortex of neonatal rats, the effect of hypothyroidism on the biogenesis in free and synaptosomal mitochondria by analyzing, in isolated mitochondria, the activity of respiratory complex I, oxidative phosphorylation, oxygen consumption, and the expression of mitochondrial genome. In addition, we studied the effect of thyroid hormone in oxygen consumption in vivo by determining metabolic flow through 13C nuclear magnetic resonance spectroscopy. Our results clearly show that in vivo, hypothyroidism markedly reduces oxygen consumption in the neural population of the cerebral cortex. This effect correlates with decreased free mitochondria biogenesis. In contrast, no effect was observed in the biogenesis in synaptosomal mitochondria. The parameters analyzed were markedly improved after T3 administration. These results suggest that a reduced biogenesis and the subsequent reduction of respiratory capacity in free mitochondria could be the underlying cause of decreased oxygen consumption in the neurons of the cerebral cortex of hypothyroid neonates.
Pioglitazone Inhibits Toll-Like Receptor Expression and Activity in Human Monocytes and db/db Mice
Authors: Dasu Mohan R. , Park Samuel , Devaraj Sridevi , Jialal Ishwarlal
Published: April 2009

Toll-like receptors (TLRs) are key innate immune sensors of endogenous damage signals and play an important role in inflammatory diseases like diabetes and atherosclerosis. Pioglitazone (PIO), a peroxisome proliferator-activated receptor (PPAR)-γ agonist, has been reported to be an antiinflammatory agent. Thus, in the present study, we examined the antiinflammatory effects of PIO on TLR2 and TLR4 expression in human monocytes exposed to Pam3CSK4 (Pam; TLR2 ligand) and purified lipopolysaccharide (LPS; TLR4 ligand) using flow cytometry and real-time RT-PCR. Monocytes were isolated from healthy human volunteers and pretreated with PIO (1 μm) followed by Pam (170 ng/ml) and LPS (160 ng/ml) challenge. PIO significantly decreased Pam- and LPS-induced TLR2 (−56%) and TLR4 (−78%) expression (P < 0.05). In addition, PIO decreased TLR ligand-induced nuclear factor-κB activity (−63%), IL-1β (−50%), IL-6 (−52%), monocyte chemoattractant protein-1(−83%), and TNF-α (−87%) compared with control. Next, PIO-treated db/db mice (n = 6/group) showed decreased TLR2 (−60%) and TLR4 (−45%) expression in peritoneal macrophages compared with vehicle control mice (P < 0.001) with associated decrease in MyD88-dependent signaling and nuclear factor-κB activation. Data suggest that Pam- and LPS-induced TLR2 and TLR4 expression are inhibited by PIO in human monocytes and db/db mice. Thus, we define a novel pathway by which PIO could induce antiinflammatory effects.
The Progesterone Receptor Coactivator Hic-5 Is Involved in the Pathophysiology of Endometriosis
Authors: Aghajanova Lusine , Velarde Michael C. , Giudice Linda C.
Published: April 2009

Endometriosis is an estrogen-dependent disorder primarily associated with pelvic pain and infertility in up to 10% of women of reproductive age. Recent studies suggest that resistance to progesterone action may contribute to the development and pathophysiology of this disorder. In this study we examined the in vivo and in vitro expression and function of one progesterone receptor (PR) coactivator, Hic-5, in human endometrium and endometrial stromal fibroblasts (hESFs) from 29 women with and 30 (control) women without endometriosis. Hic-5 was highly expressed in stromal, but not epithelial, cells in women without endometriosis, in a cycle-dependent manner. In contrast, Hic-5 expression was not regulated during the menstrual cycle in hESFs from women with endometriosis and was significantly reduced in hESFs from women with vs. without disease. Hic-5 mRNA expression throughout the cycle in endometrium from control women, but not those with endometriosis, correlated with expression of PR. Hic-5 mRNA in hESFs was significantly up-regulated in control but not endometriosis hESFs after treatment in vitro with 8-bromoadenosine-cAMP for 96 h but only modestly after 14 d of progesterone treatment. Hic-5 silencing did not influence cAMP-regulated gene expression but affected genes regulated solely by progesterone (e.g. DKK1 and calcitonin). Together the data suggest that the proposed progesterone resistance in endometrium from women with endometriosis derives, in part, from impaired expression of the PR coactivator, Hic-5, in endometrial tissue and cultured endometrial stromal fibroblasts.
MBX-102/JNJ39659100, a Novel Peroxisome Proliferator-Activated Receptor-Ligand with Weak Transactivation Activity Retains Antidiabetic Properties in the Absence of Weight Gain and Edema
Authors: Gregoire Francine M. , Zhang Fang , Clarke Holly J. , Gustafson Thomas A. , Sears Dorothy D. , Favelyukis Svetlana , Lenhard James , Rentzeperis Dennis , Clemens L. Edward , Mu Yi , Lavan Brian E.
Published: April 2009

MBX-102/JNJ39659100 (MBX-102) is in clinical development as an oral glucose-lowering agent for the treatment of type 2 diabetes. MBX-102 is a nonthiazolidinedione (TZD) selective partial agonist of peroxisome proliferator-activated receptor (PPAR)-γ that is differentiated from the TZDs structurally, mechanistically, preclinically and clinically. In diabetic rodent models, MBX-102 has insulin-sensitizing and glucose-lowering properties comparable to TZDs without dose-dependent increases in body weight. In vitro, in contrast with full PPAR-γ agonist treatment, MBX-102 fails to drive human and murine adipocyte differentiation and selectively modulates the expression of a subset of PPAR-γ target genes in mature adipocytes. Moreover, MBX-102 does not inhibit osteoblastogenesis of murine mesenchymal cells. Compared with full PPAR-γ agonists, MBX-102 displays differential interactions with the PPAR-γ ligand binding domain and possesses reduced ability to recruit coactivators. Interestingly, in primary mouse macrophages, MBX-102 displays enhanced antiinflammatory properties compared with other PPAR-γ or α/γ agonists, suggesting that MBX-102 has more potent transrepression activity. In summary, MBX-102 is a selective PPAR-γ modulator with weak transactivation but robust transrepression activity. MBX-102 exhibits full therapeutic activity without the classical PPAR-γ side effects and may represent the next generation insulin sensitizer.
Stem cells, signals and vertebrate body axis extension
Authors: Wilson Valerie , Olivera-Martinez Isabel , Storey Kate G.
Published: April 2009

The progressive generation of chick and mouse axial tissues – the spinal cord, skeleton and musculature of the body – has long been proposed to depend on the activity of multipotent stem cells. Here, we evaluate evidence for the existence and multipotency of axial stem cells. We show that although the data strongly support their existence, there is little definitive information about their multipotency or extent of contribution to the axis. We also review the location and molecular characteristics of these putative stem cells, along with their evolutionary conservation in vertebrates and the signalling mechanisms that regulate and arrest axis extension.
Defining retinal progenitor cell competence inXenopus laevisby clonal analysis
Authors: Wong Lily L. , Rapaport David H.
Published: April 2009

Extrinsic cues and intrinsic competence act in concert for cell fate determination in the developing vertebrate retina. However, what controls competence and how precise is the control are largely unknown. We studied the regulation of competence by examining the order in which individual retinal progenitor cells (RPCs) generate daughters. Experiments were performed in Xenopus laevis, whose full complement of retinal cells is formed in 2 days. We lineage-labeled RPCs at the optic vesicle stage. Subsequently we administered a cell cycle marker, 5-bromodeoxyuridine (BrdU) at early, middle or late periods of retinogenesis. Under these conditions, and in this animal,BrdU is not cleared by the time of analysis, allowing cumulative labeling. All retinal cell types were generated throughout nearly the entire retinogenesis period. When we examined the order that individual RPCs generated daughters,we discovered a regular and consistent sequence according to phenotype: RGC,Ho, CPr, RPr, Am, BP, MG. The precision of the order between the clones supports a model in which RPCs proceed through stepwise changes in competence to make each cell type, and do so unidirectionally. Because every cell type can be generated simultaneously within the same retinal environment, the change in RPC competence is likely to be autonomous.
Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression
Authors: Maier Annette T. , Stehling-Sun Sandra , Wollmann Heike , Demar Monika , Hong Ray L. , Haubeiß Silke , Weigel Detlef , Lohmann Jan U.
Published: April 2009

Flowers develop from floral meristems, which harbor stem cells that support the growth of floral organs. The MADS domain transcription factor AGAMOUS (AG)plays a central role in floral patterning and is required not only for the specification of the two reproductive organ types, but also for termination of stem cell fate. Using a highly conserved cis-regulatory motif as bait, we identified the bZIP transcription factor PERIANTHIA (PAN) as a direct regulator of AG in Arabidopsis. PAN and AGexpression domains overlap, and mutations in either the PAN-binding site or PAN itself abolish the activity of a reporter devoid of redundant elements. Whereas under long-day conditions pan mutants have merely altered floral organ number, they display in addition typical AGloss-of-function phenotypes when grown under short days. Consistently, we found reduced AG RNA levels in these flowers. Finally, we show that PAN expression persists in ag mutant flowers, suggesting that PAN and AG are engaged in a negative-feedback loop,which might be mediated by the stem-cell-inducing transcription factor WUSCHEL(WUS).
Floral stem cell termination involves the direct regulation ofAGAMOUSby PERIANTHIA
Authors: Das Pradeep , Ito Toshiro , Wellmer Frank , Vernoux Teva , Dedieu Annick , Traas Jan , Meyerowitz Elliot M.
Published: April 2009

In Arabidopsis, the population of stem cells present in young flower buds is lost after the production of a fixed number of floral organs. The precisely timed repression of the stem cell identity gene WUSCHEL(WUS) by the floral homeotic protein AGAMOUS (AG) is a key part of this process. In this study, we report on the identification of a novel input into the process of floral stem cell regulation. We use genetics and chromatin immunoprecipitation assays to demonstrate that the bZIP transcription factor PERIANTHIA (PAN) plays a role in regulating stem cell fate by directly controlling AG expression and suggest that this activity is spatially restricted to the centermost region of the AG expression domain. These results suggest that the termination of floral stem cell fate is a multiply redundant process involving loci with unrelated floral patterning functions.
Beta-Methylamino-L-Alanine Analysis by Liquid Chromatography Tandem Mass Spectrometry with iTRAQ as the Derivative
Authors: Kushnir Mark M. , Bergquist Jonas
Published: April 2009

Amino acid BMMA is produced by cyanobacteria and has been linked to the development of neurodegenerative diseases. We developed a method for quantitative analysis of BMAA in biological samples and plant extracts. The method is utilizing iTRAQ and LC-MS/MS detection using multiple reaction monitoring mode. The method uses 50 μL of sample and has a limit of quantitation of 300 ng mL−1, within-run run imprecision below 1%. Using this method we analyzed human serum samples, human cerebrospinal fluid samples and extract of the cycad seed. No BMAA could be detected in the human samples. Content of BMAA in the seed was 50 mg kg−1.
Quantification of an Oligonucleotide Containing a Sequence Failure Product: Comparison of Isotope Dilution Mass Spectrometry with other Quantification Methods
Authors: Kinumi Tomoya , Narukawa Tomohiro , Fujii Shin-Ichiro , Eyama Sakae , Saeki Mika , Takatsu Akiko
Published: April 2009

There is an increasing demand to develop a method for accurate quantification of DNA. Because current methods such as the ultraviolet (UV) absorption-based method are only capable of relative quantification, the quantification result depends completely on the reference material. To achieve accurate quantification of DNA, we have performed isotope dilution mass spectrometry (ID MS)-based quantification of oligonucleotides. We chose a 20-mer synthetic oligonucleotide as the analyte with a longer sequence failure product. Oligonucleotides sometimes contain sequence failure products, which are difficult to remove. It is important to quantify a target product in such a mixture. After evaluating the content of the sequence failure product, the analyte spiked with stable isotopically labeled deoxynucleotide monophosphates (dNMPs) was digested by enzyme to its constituent dNMPs or deoxynucleosides and quantified by liquid chromatography-mass spectrometry. The obtained mass fractions of the 20-mer oligonucleotide showed a good agreement with the results based on phosphate analysis by inductively-coupled plasma-optical emission spectrometry and ion chromatography. UV absorption, the general method for DNA quantification, resulted in under-estimation. On the other hand, the mass fraction obtained by the gravimetric method was over-estimated. This study shows that the ID MS method can determine the precise mass fraction of the target oligonucleotide with the sequence failure product and possesses potential as the primary method for the certification of DNA as a reference material.
Analysis of Caffeic Acid Derivatives from Osmanthus Yunnanensis Using Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry
Authors: Wu Zhi-Jun , Ma Xiao-Li , Fang Dong-Mei , Qi Hua-Yi , Ren Wei-Jian , Zhang Guo-Lin
Published: April 2009

A series of six caffeic acid derivatives (1–6) in Osmanthus yunnanensis were investigated by electrospray quadrupole time-of-flight tandem mass spectrometry (ESI-QToF-MS/MS) in both negative- and positive-ion modes. High-quality MS/MS spectra of [M + H]+ are generated from high-abundance protonated parent ions obtained by addition of ammonium chloride to the solutions. Fragmentation mechanisms of [M – H]− and [M + H]+ precursor ions were proposed and elemental compositions of most of the product ions were confirmed on the basis of the high-resolution ESI-collision-induced dissociation (CID)-MS/MS spectra. It was found that the fragment ions at m/z 179, m/z 161, m/z 135 and m/z 134 in negative-ion mode and at m/z 163, m/z 145 and m/z 135 in positive mode should be the characteristic ions of caffeic acid. In addition, the radical fragment ions with high abundance were observed for many caffeic acid derivatives especially for 4. The structural elements of unknown compounds 7 and 8 were tentatively identified on based on tandem mass spectra of known ones.
Decomposition of Charge-State Distributions for a Better Understanding of Electrospray Mass Spectra of Bioorganic Compounds. Part 1: Basic Formalism
Authors: Raznikov Valeriy V. , Raznikova Marina O.
Published: April 2009

Further development in our approach for the interpretation of a mass spectral peak series resulting from unique modifications at a number of molecular sites is described and its application for the analysis of electrospray mass spectra of multiply-charged ions of biopolymers is specified. This method was based initially on the assumption that the modifications are mutually independent. The output is a set of modification probabilities for the considered molecular sites, which explains the observed peak intensity distribution with the best accuracy. It is shown here that the method is also applicable, in some cases, to the strong interaction between modified sites. This is important for the formation of multiply-charged ions, at least in the gas phase, since it should be significantly influenced by the internal electric fields. The capabilities and limitations of this approach are discussed. One limitation is that only unimodal distributions (those having only one maximum) are possible in the considered model. Another is that relatively large biomolecules may not be suitable for this type of analysis. Some experimental results of the application of this method are described in Part 2 of this work.
Testing the APT with the Maximum Sharpe Ratio of Extracted Factors
Authors: Zhang Chu
Published: April 2009

This paper develops a test of the asymptotic arbitrage pricing theory (APT) via the maximum squared Sharpe ratio of the factors extracted from individual stocks using the Connor-Korajczyk method. The test treats the beta pricing relation as approximate without predetermining the systematic factors, unlike the existing tests that take the relationship as exact and systematic factors as given. This paper also examines the magnitude of pricing errors bounded partly by the maximum squared Sharpe ratio. For most 60-month subperiods of the sample, the hypothesis that the maximum squared Sharpe ratio for monthly returns is greater than 0.25 can be rejected. Simulation indicates that the average pricing error in monthly returns is less than 0.001. These results support the asymptotic APT.
Investor Competence, Trading Frequency, and Home Bias
Authors: Graham John R. , Harvey Campbell R. , Huang Hai
Published: April 2009

People are more willing to bet on their own judgments when they feel skillful or knowledgeable. We investigate whether this “competence effect” influences trading frequency and home bias. We find that investors who feel competent trade more often and have more internationally diversified portfolios. We also find that male investors, and investors with larger portfolios or more education, are more likely to perceive themselves as competent than are female investors, and investors with smaller portfolios or less education. Our paper also contributes to understanding the theoretical link between overconfidence and trading frequency. Existing theories on trading frequency have focused on one aspect of overconfidence, i.e., miscalibration. Our paper offers a potential mechanism for the “better-than-average” aspect of overconfidence to influence trading frequency. In the context of our paper, overconfident investors tend to perceive themselves to be more competent, and thus are more willing to act on their beliefs, leading to higher trading frequency.
What makes a group of good citizens? The role of perceived group‐level fit and critical psychological states in organizational teams
Authors: Shin Yuhyung , Choi Jin Nam
Published: April 2009

Recent studies have expanded the construct of organizational citizenship behaviour (OCB) to the group level and demonstrated its significance in predicting group performance. In this study, we have further expanded this growing stream of research regarding group‐level OCB (GOCB), by identifying distinct group characteristics that predict GOCB. Specifically, we have isolated perceived group–organization (G–O) fit and group–task (G–T) fit as meaningful antecedents of GOCB. We further propose that the perceived G–O and G–T fit influence GOCB by shaping two intermediate psychological states of group members: cohesion and group efficacy. Our findings, which were based on multi‐source data collected from 43 organizational teams, demonstrated that cohesion completely mediated the effect of perceived G–O fit on GOCB. Group efficacy, however, proved not to be a significant mediator of the relationship between perceived G–T fit and GOCB. Instead, G–T fit had a significant direct effect on GOCB. This study highlights the significance of group‐level conceptualization of group–environment interaction as a potential driver of various group processes and outcomes.
3-Alkylpyridinium salts from Haplosclerida marine sponges: Isolation, structure elucidations, and biosynthetic considerations
Authors: Laville Rémi , Amade Philippe , Thomas Olivier P.
Published: April 2009

A very little studied marine sponge Callyspongia sp. collected off the coast of Martinique was chemically investigated. The study led to the isolation and structure characterization of two new 3-alkylpyridinium salts which belonged to the recently isolated pachychaline family. Structures were elucidated by 1D, 2D NMR and detailed high-resolution electron spray ionization mass spectra (HRESIMS)-MS studies. The use of HRESIMS-MS studies proved to be highly efficient to identify two other close derivatives in a mixture. Finally, these studies allowed us to propose a general biosynthetic pathway leading to important 3-alkylpyridinium salts.
A widely tunable wavelength converter based on nonlinear polarization rotation in a carbon-nanotube-deposited D-shaped fiber
Authors: Chow K. K. , Yamashita S. , Song Y. W.
Published: April 2009

We demonstrate widely tunable wavelength conversion based on cross-phase modulation induced nonlinear polarization rotation in a carbon nanotubes (CNTs) deposited D-shaped fiber. A 5-centimeter-long CNT-deposited D-shaped fiber is used as the nonlinear medium for wavelength conversion of a 10 Gb/s non-return-to-zero signal. Wavelength tunable converted signal over 40 nm is obtained with around 2.5-dB power penalty in the bit-error-rate measurements.
Comparison of LDL Cholesterol Concentrations by Friedewald Calculation and Direct Measurement in Relation to Cardiovascular Events in 27 331 Women
Authors: Mora Samia , Rifai Nader , Buring Julie E , Ridker Paul M
Published: April 2009

Background: National Cholesterol Education Program (NCEP) guidelines recommend development of direct assays for LDL cholesterol (LDL-C) measurement, but it is unclear how these assays compare with Friedewald calculation in predicting cardiovascular disease (CVD).

Methods: In a study of 27 331 healthy women with triglycerides ≤4.52 mmol/L (≤400 mg/dL), baseline fasting Friedewald LDL-C was compared with fasting and nonfasting direct homogenous measurement for incident CVD during an 11-year period.

Results: Fasting LDL-C measurements obtained by the 2 methods were highly correlated (r = 0.976, P < 0.001). Compared with fasting Friedewald LDL-C, mean fasting direct LDL-C was 0.15 mmol/L (5.6 mg/dL) lower and nonfasting direct LDL-C 0.30 mmol/L (11.5 mg/dL) lower, both P < 0.0001. The adjusted hazard ratio per 1-SD increment was 1.23 [95% CI 1.15–1.32; 1-SD 0.88 mmol/L (34.1 mg/dL)] for fasting direct LDL-C and 1.22 [95% CI 1.14–1.30; 1-SD 0.90 mmol/L (34.9 mg/dL)] for fasting Friedewald. Nonfasting LDL-C was not associated with CVD by either method. Fasting LDL-C measurements fell into the same NCEP risk category with either method for 79.3% of participants, whereas they differed by 1 NCEP category for 20.7% of participants, with most classified into a lower-risk category by direct LDL-C.

Conclusions: The association of LDL-C with CVD by the 2 methods was nearly identical in fasting samples. However, the lower direct LDL-C concentrations may misclassify many individuals into a lower NCEP category. Moreover, the lack of association of nonfasting direct LDL-C with CVD raises questions regarding the clinical utility of a direct assay for LDL-C in nonfasting blood samples.
A Review of Virtual Week for Prospective Memory Assessment: Clinical Implications
Authors: Rendell Peter G. , Henry Julie D.
Published: April 2009

It is now recognised that prospective memory (PM) failures are commonly observed in clinical groups, and have important implications for functional independence. However, well-validated measures of PM have traditionally been lacking, making this construct difficult to assess in clinical practice. Rendell and Craik's (2000) Virtual Week measure was developed as an indicator of PM, and has been shown to have good psychometric properties and be sensitive to the effects of normal and abnormal adult ageing, as well as various forms of pathology. In this article, an overview of Virtual Week's characteristics is presented, and the literature relating to use of this measure in various populations reviewed. The potential implications of the development of a new computerised version of Virtual Week for clinical practice are discussed.
Memory for Intentions Screening Test: Psychometric Properties and Clinical Evidence
Authors: Raskin Sarah A.
Published: April 2009

As the field of prospective memory (ProM) research has expanded, recognition of the need to make a clinical diagnosis of ProM difficulties has also increased. In addition, there is increasing interest in understanding in more detail the ways in which ProM deficits differ in populations with different underlying neurological dysfunctions. While questionnaires, naturalistic studies and laboratory studies have all been invaluable in furthering our understanding of ProM, until recently there has not been a standardised clinical measure. The Memory for Intentions Screening Test (MIST) was designed to be a relatively brief clinical measure of ProM in clinical populations. The MIST allows for comparisons of performance with event-based and time-based cues. The MIST also has some items with a short (2-minute) and some with a long (15-minute) delay period. Finally, the MIST contains items that require a verbal response as well as items that require an action response. The MIST has now been used in studies of normal ageing as well as a range of clinical populations, including individuals with traumatic brain injury, individuals with HIV infection and individuals with schizophrenia. The psychometric properties of the MIST have been found to be acceptable. Data from each of the clinical populations that have been administered the MIST demonstrate good specificity and sensitivity of the measure as well as the ability to begin to make comparisons about different patterns of performance between disease types.
Time-Based Prospective Memory in Children With Autism Spectrum Disorder
Authors: Altgassen Mareike , Williams Tim I. , Bölte Sven , Kliegel Matthias
Published: April 2009

In this study, for the first time, prospective memory was investigated in 11 school-aged children with autism spectrum disorders and 11 matched neurotypical controls. A computerised time-based prospective memory task was embedded in a visuospatial working memory test and required participants to remember to respond to certain target times. Controls had significantly more correct prospective memory responses than the autism spectrum group. Moreover, controls checked the time more often and increased time-monitoring more steeply as the target times approached. These differences in time-checking may suggest that prospective memory in autism spectrum disorders is affected by reduced self-initiated processing as indicated by reduced task monitoring.
Between Dissonance and Dissidence: Socialist Modernism in the German Democratic Republic
Authors: Silverberg Laura
Published: April 2009

Both communist party officials and western observers have typically interpreted the composition of modernist music in the Eastern Bloc as an act of dissidence. Yet in the German Democratic Republic (GDR), the most consequential arguments in favor of modernism came from socialists and party members. Their advocacy of modernism challenged official socialist realist doctrine, but they shared with party bureaucrats the conviction that music ought to contribute to the development of socialist society. Such efforts to reform musical life from a Marxist-Leninist standpoint were typical of the first generation of East Germany's intelligentsia, who saw socialist rule as the only guarantee against the reemergence of German fascism. Two of East Germany's most prominent composers, Hanns Eisler and Paul Dessau, routinely used the twelve-tone method in works carrying an explicitly socialist text. During preparations for the 1964 Music Congress, aesthetician Günter Mayer drew from Eisler's Lenin Requiem and Dessau's Appell der Arbeiterklasse to argue that modernist techniques were highly appropriate for giving expression to contemporary social conditions. The efforts of these socialists to reconcile modernist techniques with their understanding of socialism undermine basic divisions between communism and capitalism, complicity and dissent, and socialist realism and western modernism.
The 1945 Stravinsky Debates: Nigg, Messiaen, and the Early Cold War in France
Authors: Sprout Leslie A.
Published: April 2009

In spring 1945, a small group of students, among them Serge Nigg and Pierre Boulez, protested during the first performances in liberated Paris of the neoclassical works Stravinsky had composed in America. Whereas Boulez's biographers have interpreted the student protests as a sign of René Leibowitz's successful promotion of serialism in France, scholars of the Cold War have seen the 1945 concerts as a precursor to Stravinsky's participation in the 1952 L'Œuvre du XXe siècle, a festival in Paris indirectly funded by the CIA. These interpretations subsume the immediate postwar period in France within a synchronic view of the early Cold War era. But the 1945 protests against Stravinsky were not about the decisive embrace of a single musical style; rather, they were about the desire of young French composers to play an active role in shaping the postwar future of music in France.

In 1945, Nigg—and not Boulez—represented the aesthetic opinions of a generation of French composers who had grown up during the German occupation of Paris and the political aspirations of those who, like Nigg, flocked to the French Communist Party at war's end. Nigg's participation in the 1945 Stravinsky debates gives us occasion to examine his earliest musical compositions and the political opinions he would express with increasing ideological fervor in the 1950s. Although in verbal pronouncements he supported socialist realism, Nigg's rare and complex use of a French folk tune in his 1954 Piano Concerto betrays his ambivalence about the Soviet demand for communist composers to reject "falsely cosmopolitan tendencies" in favor of their national cultural heritage. Having rejected in 1945 both Stravinsky's neoclassicism and French nationalism (the latter tainted by associations with Vichy during the occupation), Nigg had to choose in the early Cold War between his aesthetic and political loyalties.
Latest information on Sterkfontein's Australopithecus skeleton and a new look at Australopithecus
Authors: Clarke R.J.
Published: April 2009

After a decade of careful excavation, it is now possible to explain how the skeleton came to be in that isolated position in the cavern. Furthermore, it is apparent that the fossil does not belong to either Australopithecus africanus or to A. afarensis, but to an individual belonging to, or closely affiliated to, the second Australopithecus species that is represented in Sterkfontein Member 4 and Makapansgat.
What can we learn about the meaning of race from the classification of population groups during apartheid?
Authors: Erasmus Yvonne , Ellison George T.H.
Published: April 2009

This paper examines what might be learnt about the meaning of race from the formalization of racial classification and reclassification under apartheid, generated by the 1950 Population Registration Act. It draws on 69 (re)classification appeals heard by the South African Supreme Court between 1950 and 1991, and in-depth interviews with a civil servant, expert witness and scientist involved in the (re)classification process. The Supreme Court data indicate that the three classificatory criteria set out in the act (appearance, descent, and acceptance) were ambiguous and subject to substantial debate and reinterpretation by the courts, which principally relied on acceptance. This is supported by the interviewees, who lamented the 'unscientific' classifications they were obliged to perform, yet accepted these as the inevitable consequence of the role social practices play in determining and accepting the classification applied. These findings suggest that there was not a single concrete definition of race during apartheid. Instead, race was whatever people understood or wanted it to be, and racial classification could be attained through 'performing' an identity with sufficient proficiency to 'get away with it'. This provides a crucial insight into the meaning of race elsewhere—as simply a flexible, yet pragmatic and 'acceptable' social classification of group identity.
Surface polarity determination of wood fibres after different pre- treatments and bisulphite pulping
Authors: Meincken M. , Matyumza N.C.
Published: April 2009

The surgace polarity of pulp fibres originating from four different wood species commonly used for pulping in South Africa has been determined after various pre-treatments, and after magnesium bisulphite pulping. The presence as well as the distribution of polar groups on the fibre surface strongly affects inter-fibre bonding in paper. Bonding consists mostly of hydrogen bonds between free hydroxyl groups on the fibre surface. Surface polarity was examined by atomic force microscopy in pulsed-force mode. This technique allows the imaging of the polarity of a surface with a nanometre-scale molecular resolution. It is thus sensitive to individual functional groups, mostly hydrophilic hydroxyl groups. Polarity differences between the various wood species have been observed. We compare these observations with the varying pulp quality that arises from the pulp composition. Improvement in pulp quality may be possible if fibre surface properties are used as guidance criteria for the choice of a specific pre-treatment method.
Perspectives on botanical research publications in South Africa: an assessment of five local journals from 1988 to 2002, a period of transition and transformation
Authors: Bredenkamp C.L. , Smith G.F.
Published: April 2009

South Africa has every right to take pride in its rich and unique botanical diversity. As part of investigating the discipline of botany in the country, we have assessed the contents of five botany-related South African journals in the period 1988–2002, analysing the sub-disciplines, affiliations of the contributors, and the age, gender and race of the first authors. The results show various trends, such as a decline in the number of articles during the 1990s and then an increase in 2001 and 2002. A specific niche for each of the five journals has been identified. These journals have adopted strategies and introduced improvements to survive change in the evolving scientific environment. Most articles are from authors in the age group 31–40; men accounted for 68 percent of botanical papers and women 32 percent. Whites authored 94%, and other racial groups 6%. The botanical sciences are among the leaders in South African research publications in terms of output and citations.
Co-authorship networks in South African chemistry and mathematics
Authors: Durbach Ian N. , Naidoo Deevashan , Mouton Johann
Published: April 2009

Co-authorship networks are graphs in which the nodes of the graph represent authors and two authors are connected by an edge if they have written one or more papers together. When applied to the authorship of scholarly papers, analysing the structure of a co-authorship network can provide useful insights into the way in which research is carried out in a particular field. We examine two co-authorship networks in our article, constructed from papers written on the subjects of chemistry and mathematics during the period 1990 to 2005, in which at least one of the authors was South African. Local results are compared with other studies conducted in much larger discipline-wide networks. We find that many of the same patterns exist locally, with the main difference being a far more fragmented South African mathematics network. We discuss some tentative implications of these results.
Radiometric dating of hillslope calcrete in the Negev Desert, Israel
Authors: Vogel J.C. , Geyh M.A.
Published: April 2009

The radiometric dating of calcrete is often problematical because impurities and open system conditions affect the apparent ages obtained. By applying both radiocarbon and uranium-series dating to calcrete in colluvium, it is shown that such conditions can be identified. In correlation with the stratigraphy, it is found that partial recrystallization severely decreases the radiocarbon ages of the upslope and shallower samples further down, whereas incorporation of limestone fragments from bedrock significantly increases the apparent ages of some of the uranium-series samples. It is concluded that the hillslope calcrete at the study site near Sede Beker in the Negev Desert, Israel, mainly developed shortly after 40 kyr ago, at a time when the Jordan Valley was being inundated to form the fossil Lake Lisan. Since their formation would have required higher rainfall than today, the results provide further evidence that the whole region was experiencing an increase in precipitation.
When to stay, when to go: trade-offs for southern African arid-zone birds in times of drought
Authors: Dean W.R.J. , Barnard P. , Anderson M.D.
Published: April 2009

Arid environments remind one of the punctuated equilibrium theory of evolution: they experience long periods of stasis and low productivity, interrupted with episodic rainfall which spurs reproduction and movement. Birds, as highly dispersive organisms, are among the most dramatic indicators of these fluctuations. Here we review birds' two main strategies, residency and nomadism, and the trade-offs faced by individuals in uncertain times. In general, wet years stimulate higher densities of nests (i.e. smaller territories), larger clutch sizes, unseasonal breeding, and at some times of year, higher breeding success. Rainfall above a certain threshold triggers breeding in resident species and an influx of nomadic species which breed and then move on. The environmental cues which trigger nomadism are sometimes poorly understood, but include distant thunderstorms for aquatic species, and perhaps for insectivores. Environmental cues that draw nomadic granivores to areas that have had recent rain are not known.
Agriculture production's sensitivity to changes in climate in South Africa
Authors: Blignaut James , Ueckermann Liza , Aronson James
Published: April 2009

South Africa in general has been approximately 2% hotter and at least 6% drier over the ten years between 1997 and 2006 compared to the 1970s. The use of water has also increased greatly over this same period. By 2000, 98.6% of that year's surface water yield and 41% of the annual utilisable potential of groundwater was allocated to use. Irrigation agriculture, comprising 60% of total consumption, is by far the largest single consumer of water. Given these climatic and water use changes as a backdrop, we employed a panel data econometric model to estimate how sensitive the nation's agriculture may be to changes in rainfall. Net agricultural income in the provinces, contributing 10% or more to total production of both field crops and horticulture, is likely to be negatively affected by a decline in rainfall, especially rain-fed agriculture. For the country as a whole, each 1% decline in rainfall is likely to lead to a 1.1% decline in the production of maize (a summer grain) and a 0.5% decline in winter wheat. These results are discussed with respect to both established and emerging farmers, and the type of agriculture that should be favoured or phased out in different parts of the country, in view of current and projected trends in climate, increasing water use, and declining water availability.