bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of aquifer parameters from residual drawdowns
Authors: Kambhammettu B. V. N. P. , King J. P.
Published: June 2010

Reliable and accurate estimation of aquifer parameters is a key process in efficiently managing the groundwater resources of a region. Today, a number of stochastic optimisation tools are available to solve the non-linear aquifer parameters using gradient-based techniques. However, these tools use conventional stabilisation techniques in estimating the non-linear parameters. In the present study, an attempt was made to accelerate and stabilise the conventional Levenberg–Marquardt algorithm. A generalised Matlab code was developed to estimate the transmissivity and storage coefficient of the confined aquifer by considering the residual drawdowns measured in a single observation well. The applicability of the present method was illustrated by considering two datasets from different sources and the results were compared with previous research. Statistical analysis on the estimated parameters demonstrated that the present method can estimate the confined aquifer parameters accurately with a more rapid convergence in comparison with the conventional algorithms.
A numerical study of saline contamination of a coastal aquifer
Authors: Perera E. D. P. , Jinno K. , Tsutsumi A. , Hiroshiro Y.
Published: June 2010

A three-dimensional mathematical model of variable density groundwater flow and miscible solute transport is developed to investigate the saltwater contamination of a coastal aquifer in west Japan. The selected area is an agricultural region located on a coastal aquifer where the groundwater is being consumed continuously as the main water source for drinking, greenhouses and industries. The salinity of the pumped water has been analysed periodically and it has been found that the threat of saltwater intrusion is emerging due to the continuous exploitation of groundwater. Owing to the distributed nature of pumping-well locations and non-uniform geological conditions, a three-dimensional model is needed to understand the saline contamination of the coastal aquifer. A numerical model was built by using the finite difference framework, taking into account the development of a transition zone and the variation of fluid density within it. The model simulates the saturated and unsaturated zone groundwater flow under the influence of a variable density situation in the coastal aquifer. Moreover, it can be used as a numerical tool to simulate the salinity contamination of the freshwater in this coastal aquifer.
Consequences of SCHIP Expansions for Household Well-Being
Authors: Leininger Lindsey , Levy Helen , Schanzenbach Diane
Published: June 2010

About 7.4 million children were covered by the State Childrens Health Insurance Program (SCHIP) at some point during fiscal year 2008. Many of these children would probably have had private coverage in the absence of SCHIP; recent estimates of the extent of crowd-out associated with SCHIP are about 60 percent (Gruber and Simon 2008). The high rate of crowd-out means that the program is not as effective as it could be at reducing the number of uninsured children and has been a political liability for the program. Both political concerns and policy research focusing on crowd-out in SCHIP build on more than a decade of similar attention to the crowd-out associated with the Medicaid expansions of the late 1980s and early 1990s. While there is little doubt that expanding eligibility for public insurance to children who are not poor will lead some to substitute public for private coverage, this substitution should increase total resources available to these households in two ways. First, those who drop private coverage in order to enroll their children in SCHIP can take whatever they had been spending on health insurance and spend it on something else. Second, public insurance requires less cost-sharing than a typical private insurance policy, providing first-dollar coverage with minimal co-payments. This means that switching from private to public coverage reduces a familys out-of-pocket medical spending, freeing up even more of the familys resources for other uses. From the perspective of a low-income family, then, crowd-out is a windfall. In this paper we ask: what do these families do with the additional resources? We address this question with an empirical analysis of consumption data from the Consumer Expenditure Survey. We find that eligibility for SCHIP is associated with an increase in overall expenditure, and most of this increase is allocated to consumption of transportation or saving for retirement. These results suggest that the SCHIP expansions substantially improved the material well-being of the low-income families it is intended to assist  including those who had previously been paying for their own coverage. This evidence should allow a better accounting of the benefits and not just the costs of recent expansions in public health insurance programs.
The Effect of Differing Audience Response System Question Types on Student Attention in the Veterinary Medical Classroom
Authors: Rush Bonnie R. , Hafen McArthur , Biller David S. , Davis Elizabeth G. , Klimek Judy A. , Kukanich Butch , Larson Robert L. , Roush James K. , Schermerhorn Thomas , Wilkerson Melinda J. , White Brad J.
Published: June 2010

The purpose of this study was to evaluate the ability of specific types of multiple-choice questions delivered using an Audience Response System (ARS) to maintain student attention in a professional educational setting. Veterinary students (N=324) enrolled in the first three years of the professional curriculum were presented with four different ARS question types (knowledge base, discussion, polling, and psychological investment) and no ARS questions (control) during five lectures presented by 10 instructors in 10 core courses. Toward the end of the lecture, students were polled to determine the relative effectiveness of specific question types. Student participation was high (76.1%±2.0), and most students indicated that the system enhanced the lecture (64.4%). Knowledge base and discussion questions resulted in the highest student-reported attention to lecture content. Questions polling students about their experiences resulted in attention rates similar to those without use of ARS technology. Psychological investment questions, based on upcoming lecture content, detracted from student attention. Faculty preparation time for three ARS questions was shorter for knowledge base questions (22.3 min) compared with discussion and psychological investment questions (38.6 min and 34.7 min, respectively). Polling questions required less time to prepare (22.2 min) than discussion questions but were not different from other types. Faculty stated that the investment in preparation time was justified on the basis of the impact on classroom atmosphere. These findings indicate that audience response systems enhance attention and interest during lectures when used to pose questions that require application of an existing knowledge base and allow for peer interaction.
Multifront Assault on Antigen Presentation by Japanese Encephalitis Virus Subverts CD8+ T Cell Responses
Authors: Aleyas Abi G. , Han Young Woo , George Junu A. , Kim Bumseok , Kim Koanhoi , Lee Chong-Kil , Eo Seong Kug
Published: June 2010

Japanese encephalitis virus (JEV) is a frequent cause of acute and epidemic viral encephalitis. However, there is little information describing the mechanisms by which JEV subverts immune responses that may predispose the host to secondary infections. In this study, we found that JEV induced the subversion of CD8+ T cell responses in a transient manner that was closely correlated with viral multiplication. Subsequently, analysis using a TCR-transgenic system revealed that CD8+ T cells purified from JEV-infected mice showed impaired responses, and that naive CD8+ T cells adoptively transferred into JEV-infected recipients showed less expanded responses. Furthermore, JEV altered the splenic dendritic cell (DC) subpopulation via preferential depletion of CD8α+CD11c+ DCs without changing the plasmacytoid DCs and induced a significant reduction in the surface expression of MHC class II and CD40, but not MHC class I, CD80, and CD86 molecules. Finally, JEV was shown to inhibit the presentation of MHC class I-restricted Ag in DCs, and this immune suppression was ameliorated via the activation of DCs by TLR agonists. Collectively, our data indicate that JEV precludes the functions of Ag-presenting machinery, such as depletion of CD8α+CD11c+ DCs and downregulation of MHC class I-restricted Ag presentation, thereby leading to immune subversion of CD8+ T cells.
Dyslipidemia Induces Opposing Effects on Intrapulmonary and Extrapulmonary Host Defense through Divergent TLR Response Phenotypes
Authors: Madenspacher Jennifer H. , Draper David W. , Smoak Kathleen A. , Li Haitao , Griffiths Gary L. , Suratt Benjamin T. , Wilson Martha D. , Rudel Lawrence L. , Fessler Michael B.
Published: June 2010

Dyslipidemia influences innate immune responses in the bloodstream, but whether and how pulmonary innate immunity is sensitive to circulating lipoproteins is largely unknown. To define whether dyslipidemia impacts responses to bacteria in the airspace and, if so, whether differently from its effects in other tissues, airspace, bloodstream, and i.p. responses to LPS and Klebsiella pneumoniae were investigated using murine models of dyslipidemia. Dyslipidemia reduced neutrophil (PMN) recruitment to the airspace in response to LPS and K. pneumoniae by impairing both chemokine induction in the airspace and PMN chemotaxis, thereby compromising pulmonary bacterial clearance. Paradoxically, bacteria were cleared more effectively from the bloodstream during dyslipidemia. This enhanced systemic response was due, at least in part, to basal circulating neutrophilia and basal TLR4/MyD88-dependent serum cytokine induction and enhanced serum cytokine responses to systemically administered TLR ligands. Dyslipidemia did not globally impair PMN transvascular trafficking to, and host defense within all loci, because neutrophilia, cytokine induction, and bacterial clearance were enhanced within the infected peritoneum. Peritoneal macrophages from dyslipidemic animals were primed for more robust TLR responses, reflecting increased lipid rafts and increased TLR4 expression, whereas macrophages from the airspace, in which cholesterol was maintained constant during dyslipidemia, had normal responses and rafts. Dyslipidemia thus imparts opposing effects upon intra- and extrapulmonary host defense by inducing tissue-divergent TLR response phenotypes and dysregulating airspace/blood compartmental levels of PMNs and cytokines. We propose that the airspace is a “privileged” site, thereby uniquely sensitive to dyslipidemia.
Dendritic Cell-Mediated In Vivo Bone Resorption
Authors: Maitra Radhashree , Follenzi Antonia , Yaghoobian Arash , Montagna Cristina , Merlin Simone , Cannizzo Elvira S. , Hardin John A. , Cobelli Neil , Stanley E. Richard , Santambrogio Laura
Published: June 2010

Osteoclasts are resident cells of the bone that are primarily involved in the physiological and pathological remodeling of this tissue. Mature osteoclasts are multinucleated giant cells that are generated from the fusion of circulating precursors originating from the monocyte/macrophage lineage. During inflammatory bone conditions in vivo, de novo osteoclastogenesis is observed but it is currently unknown whether, besides increased osteoclast differentiation from undifferentiated precursors, other cell types can generate a multinucleated giant cell phenotype with bone resorbing activity. In this study, an animal model of calvaria-induced aseptic osteolysis was used to analyze possible bone resorption capabilities of dendritic cells (DCs). We determined by FACS analysis and confocal microscopy that injected GFP-labeled immature DCs were readily recruited to the site of osteolysis. Upon recruitment, the cathepsin K-positive DCs were observed in bone-resorbing pits. Additionally, chromosomal painting identified nuclei from female DCs, previously injected into a male recipient, among the nuclei of giant cells at sites of osteolysis. Finally, osteolysis was also observed upon recruitment of CD11c-GFP conventional DCs in Csf1r−/− mice, which exhibit a severe depletion of resident osteoclasts and tissue macrophages. Altogether, our analysis indicates that DCs may have an important role in bone resorption associated with various inflammatory diseases.
Tumor-Activated Monocytes Promote Expansion of IL-17–Producing CD8+ T Cells in Hepatocellular Carcinoma Patients
Authors: Kuang Dong-Ming , Peng Chen , Zhao Qiyi , Wu Yan , Zhu Ling-Yan , Wang Jianen , Yin Xiao-Yu , Li Lian , Zheng Limin
Published: June 2010

The proinflammatory IL-17–producing CD8+ T cells (Tc17 cells) have recently been detected in tumors, but the nature and regulation of these cells in human tumors are presently unknown. We have recently found that IL-17+ cells are accumulated in human hepatocellular carcinomas (HCC), where they promote disease progression by fostering angiogenesis. In this study, we showed that Tc17 cells constitute a remarkable portion of IL-17–producing cells in human HCC. Although most circulating Tc17 cells were negative for IFN-γ, >80% of Tc17 cells in HCC tissues were positive for IFN-γ, and they were enriched predominantly in invading tumor edge. Most CD68+ cells located in invading tumor edge exhibited an activated phenotype and, accordingly, the activated monocytes isolated from HCC tissues were significantly superior to those isolated from nontumor tissues in inducing expansion of Tc17 cells in vitro with phenotypic features similar to those isolated from tumors. Compared with IL-17−IFN-γ+CD8+ cells, these IFN-γ+Tc17 cells have significantly higher expression of proinflammatory cytokines (IL-2, IL-22, and TNF-α), but reduced expression of granzyme B and perforin. Moreover, we found that tumor-activated monocytes secreted a set of key cytokines (IL-1β, IL-6, and IL-23) to trigger the proliferation of Tc17 cells. These data reveal an intriguing mechanism in which human Tc17 cells are generated by a fine-tuned collaborative action between different types of immune cells in distinct tumor microenvironments.
Obesity Increases the Production of Proinflammatory Mediators from Adipose Tissue T Cells and Compromises TCR Repertoire Diversity: Implications for Systemic Inflammation and Insulin Resistance
Authors: Yang Hyunwon , Youm Yun-Hee , Vandanmagsar Bolormaa , Ravussin Anthony , Gimble Jeffrey M. , Greenway Frank , Stephens Jacqueline M. , Mynatt Randall L. , Dixit Vishwa Deep
Published: June 2010

Emerging evidence suggests that increases in activated T cell populations in adipose tissue may contribute toward obesity-associated metabolic syndrome. The present study investigates three unanswered questions: 1) Do adipose-resident T cells (ARTs) from lean and obese mice have altered cytokine production in response to TCR ligation?; 2) Do the extralymphoid ARTs possess a unique TCR repertoire compared with lymphoid-resident T cells and whether obesity alters the TCR diversity in specific adipose depots?; and 3) Does short-term elimination of T cells in epididymal fat pad without disturbing the systemic T cell homeostasis regulate inflammation and insulin-action during obesity? We found that obesity reduced the frequency of naive ART cells in s.c. fat and increased the effector-memory populations in visceral fat. The ARTs from diet-induced obese (DIO) mice had a higher frequency of IFN-γ+, granzyme B+ cells, and upon TCR ligation, the ARTs from DIO mice produced increased levels of proinflammatory mediators. Importantly, compared with splenic T cells, ARTs exhibited markedly restricted TCR diversity, which was further compromised by obesity. Acute depletion of T cells from epididymal fat pads improved insulin action in young DIO mice but did not reverse obesity-associated feed forward cascade of chronic systemic inflammation and insulin resistance in middle-aged DIO mice. Collectively, these data establish that ARTs have a restricted TCR-Vβ repertoire, and T cells contribute toward the complex proinflammatory microenvironment of adipose tissue in obesity. Development of future long-term T cell depletion protocols specific to visceral fat may represent an additional strategy to manage obesity-associated comorbidities.
A Genome-Wide Profiling of the Humoral Immune Response to Chlamydia trachomatis Infection Reveals Vaccine Candidate Antigens Expressed in Humans
Authors: Wang Jie , Zhang Yingqian , Lu Chunxue , Lei Lei , Yu Ping , Zhong Guangming
Published: June 2010

A whole genome scale proteome array consisting of 908 open reading frames encoded in Chlamydia trachomatis genome and plasmid was used to profile anti-chlamydial Ab responses. A total of 719 chlamydial proteins was recognized by one or more antisera from 99 women urogenitally infected with C. trachomatis. Revealing such a large C. trachomatis ANTIGENome in humans might partially be attributed to the significantly improved detection sensitivity of the whole genome scale proteome array assay because both linear and conformation-dependent Abs were detected by the array assay. Twenty-seven of the 719 Ags were recognized by ≥50% antisera, thus designated as immunodominant Ags. Comparison of Ag profiles recognized by live chlamydial organism-infected versus dead organism-immunized hosts led to the identification of infection-dependent or in vivo expressed Ags. The infection-dependent Ags induced Abs only in live organism-infected, but not in dead organism-immunized hosts. Many of these Ags were highly expressed during replication, but only minimally packaged into the infectious elementary bodies. Because inactivated whole chlamydial organism-based vaccines failed to induce protection in humans, identification of the infection-dependent or in vivo expressed immunodominant Ags in humans should greatly facilitate the selection of promising chlamydial subunit vaccine candidates for further evaluation. This approach may also be applicable to other pathogens.
Phosphorylation of Leukocyte PECAM and Its Association with Detergent-Resistant Membranes Regulate Transendothelial Migration
Authors: Florey Oliver , Durgan Joanne , Muller William
Published: June 2010

Leukocyte migration across the endothelial lining is a critical step in the body’s response to infection and inflammation. The homophilic interaction between endothelial PECAM and leukocyte PECAM is essential for this process. The molecular events that are triggered in the endothelial cell by PECAM engagement have been well characterized; however, the function of leukocyte PECAM remains to be elucidated. To study this, we first blocked leukocyte transmigration using anti-PECAM Ab and then specifically activated leukocyte PECAM. This was sufficient to overcome the block and promote transmigration, suggesting an active signaling role for leukocyte PECAM. Consistent with this, we found that ligation of leukocyte PECAM induces phosphorylation of two tyrosine residues on its cytoplasmic tail. By performing RNA interference-rescue experiments, we demonstrate that these phosphorylation events are indispensable for transendothelial migration. Finally, we show that leukocyte PECAM translocates to a detergent-resistant membrane (DRM) during transmigration. PECAM localized in DRMs displays reduced phosphorylation and does not support transmigration. Together, these data support a model whereby engagement of leukocyte PECAM induces its transient tyrosine phosphorylation and induction of downstream signals that drive transmigration. These signals are then downregulated following PECAM translocation to DRMs.
Water column nutrients control growth and C:N ratios of symbiont‐bearing benthic foraminifera on the Great Barrier Reef, Australia
Authors: Uthicke Sven , Altenrath Christine
Published: June 2010

In situ growth of two abundant diatom‐bearing benthic foraminiferal species (Amphistegina radiata, Heterostegina depressa) was investigated to elucidate whether differences in abundance between inshore and offshore reefs are influenced by water quality. Five experiments were conducted over 2 yr, comparing growth rates of foraminifera at inshore coral reefs, which are exposed to terrestrial runoff, with those at reefs further offshore. Concentrations of most dissolved and particulate water quality variables were significantly higher inshore and during periods of high runoff (summer wet season). Foraminiferal growth was generally significantly lower on inshore reefs than offshore reefs, and growth of both species was reduced during the wet season. Depth transplantations confirmed that light was not an important factor in growth regulation. In contrast, multiple regression analyses of the effects of water quality variables on foraminiferal growth explained 69% of the variance in growth for A. radiata and 78% for H. depressa. Increased concentrations of dissolved nitrogen were associated with reduced growth. Intracellular carbon‐to‐nitrogen ratios in the foraminifera also reflected patterns in water quality, with generally lower values in foraminifera from inshore or during periods of high runoff, driven by higher intracellular N contents during these periods. It is suggested that increased nutrient availability releases foraminiferal symbionts from nutrient limitation. This may lead to reduced translocation of organic carbon to the host and resulting reduced host growth.
Factors influencing zooplankton size structure at contrasting temperatures in coastal shallow lakes: Implications for effects of climate change
Authors: Brucet Sandra , Boix Dani , Quintana Xavier D. , Jensen Elisabeth , Nathansen Louise W. , Trochine Carolina , Meerhoff Mariana , Gascón Stáphanie , Jeppesena Erik
Published: June 2010

We assessed the importance of temperature, salinity, and predation for the size structure of zooplankton and provided insight into the future ecological structure and function of shallow lakes in a warmer climate. Artificial plants were introduced in eight comparable coastal shallow brackish lakes located at two contrasting temperatures: cold‐temperate and Mediterranean climate region. Zooplankton, fish, and macroinvertebrates were sampled within the plants and at open‐water habitats. The fish communities of these brackish lakes were characterized by small‐sized individuals, highly associated with submerged plants. Overall, higher densities of small planktivorous fish were recorded in the Mediterranean compared to the cold‐temperate region, likely reflecting temperature‐related differences as have been observed in freshwater lakes. Our results suggest that fish predation is the major control of zooplankton size structure in brackish lakes, since fish density was related to a decrease in mean body size and density of zooplankton and this was reflected in a unimodal shaped biomass‐size spectrum with dominance of small sizes and low size diversity. Salinity might play a more indirect role by shaping zooplankton communities toward more salt‐tolerant species. In a global‐warming perspective, these results suggest that changes in the trophic structure of shallow lakes in temperate regions might be expected as a result of the warmer temperatures and the potentially associated increases in salinity. The decrease in the density of large‐bodied zooplankton might reduce the grazing on phytoplankton and thus the chances of maintaining the clear water state in these ecosystems.
Electroencephalography (EEG) and Event‐Related Potentials (ERPs) with Human Participants
Authors: Light Gregory A. , Williams Lisa E. , Minow Falk , Sprock Joyce , Rissling Anthony , Sharp Richard , Swerdlow Neal R. , Braff David L.
Published: June 2010

Understanding the basic neural processes that underlie complex higher‐order cognitive operations and functional domains is a fundamental goal of cognitive neuroscience. Electroencephalography (EEG) is a non‐invasive and relatively inexpensive method for assessing neurophysiological function that can be used to achieve this goal. EEG measures the electrical activity of large, synchronously firing populations of neurons in the brain with electrodes placed on the scalp. This unit outlines the basics of setting up an EEG experiment with human participants, including equipment, and a step‐by‐step guide to applying and preparing an electrode cap. Also included are support protocols for two event‐related potential (ERP) paradigms, P50 suppression, and mismatch negativity (MMN), which are measures of early sensory processing. These paradigms can be used to assess the integrity of early sensory processing in normal individuals and clinical populations, such as individuals with schizophrenia. Curr. Protoc. Neurosci. 52:6.25.1‐6.25.24. © 2010 by John Wiley & Sons, Inc.
Analyzing Binding Data
Authors: Motulsky Harvey J. , Neubig Richard R.
Published: June 2010

Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.Curr. Protoc. Neurosci. 52:7.5.1‐7.5.65. © 2010 by John Wiley & Sons, Inc.
Isolation of Mitochondria from the CNS
Authors: Kristian Tibor
Published: June 2010

This unit contains a protocol describing the isolation of brain mitochondria by using discontinuous Percoll gradient centrifugation. The Percoll density gradient centrifugation separates synaptosomes, myelin, and free nonsynaptic mitochondria released from cells during tissue homogenization into individual fractions. Mitochondria entrapped in synaptosomes (synaptic mitochondria) can be liberated using nitrogen cavitation and then further purified by Percoll gradient centrifugation. These methods yield mitochondria that exhibit good respiratory coupling and high respiratory rates. Curr. Protoc. Neurosci. 52:7.22.1‐7.22.12. © 2010 by John Wiley & Sons, Inc.
Approaches to Spectral Imaging Hardware
Authors: Lerner Jeremy M. , Gat Nahum , Wachman Elliot
Published: June 2010

Instruments used for spectral, multispectral, and hyperspectral imaging in the biosciences have evolved significantly over the last 15 years. However, very few are calibrated and have had their performance validated. Now that spectral imaging systems are appearing in clinics and pathology laboratories, there is a growing need for calibration and validation according to universal standards. In addition, some systems produce spectral artifacts that, at the very least, challenge data integrity if left unrecognized. This unit includes a comparison of the band‐pass and light‐transmission characteristics of electronic tunable filters, interferometers, and wavelength‐dispersive spectral imaging instruments, as well as a description of how they work. Methods are described to test wavelength accuracy and perform radiometric calibration. A real‐life example of spectral artifacts is dissected in detail in order to show how to detect, diagnose, verify, and work around their presence when they cannot be eliminated. Curr. Protoc. Cytom. 53:12.20.1‐12.20.40. © 2009 by John Wiley & Sons, Inc.
Electrically Addressable Hybrid Architectures of Zinc Oxide Nanowires Grown on Aligned Carbon Nanotubes
Authors: Ok Jong G. , Tawfick Sameh H. , Juggernauth K. Anne , Sun Kai , Zhang Yongyi , Hart A. John
Published: June 2010

The fabrication and characterization of hybrid architectures of ZnO nanowires (ZNWs) grown on organized carbon nanotubes (CNTs), by a two‐step chemical vapor deposition (CVD) process involving CNT growth from a hydrocarbon source followed by ZNW growth using a Zn metal source, is reported. The ZNWs grow uniformly and radially from individual CNTs and CNT bundles, and the aligned morphology of the CNTs is not disturbed by the ZNW growth process. The nucleation and growth of ZnO crystals on CNTs are analyzed in relation to the classical vapor–solid mechanism. Importantly, the CNTs make uniform and distributed electrical contact to the ZNWs, with up to a 1000‐fold yield advantage over conventional ZNW growth on a flat substrate. Hybrid ZNW/CNT sheets are fabricated by scalable CVD, rolling, and printing methods; and their electrical properties, which are governed by transport through the anisotropic CNT network, are characterized. Functional interaction between the ZNWs and CNTs is demonstrated by photoconductive behavior and photocurrent generation of the hybrid material under UV illumination. There is significant future opportunity to extend these processing methods to fabricate other functional oxides on CNTs, and to build devices that harness the attractive properties of ZNWs and CNTs with high volumetric efficiency over large areas.
Large‐Area Nanoscale Patterning of Functional Materials by Nanomolding in Capillaries
Authors: Duan Xuexin , Zhao Yiping , Berenschot Erwin , Tas Niels R. , Reinhoudt David N. , Huskens Jurriaan
Published: June 2010

Within the past years there has been much effort in developing and improving new techniques for the nanoscale patterning of functional materials used in promising applications like nano(opto)electronics. Here a high‐resolution soft lithography technique—nanomolding in capillaries (NAMIC)—is demonstrated. Composite PDMS stamps with sub‐100 nm features are fabricated by nanoimprint lithography to yield nanomolds for NAMIC. NAMIC is used to pattern different functional materials such as fluorescent dyes, proteins, nanoparticles, thermoplastic polymers, and conductive polymers at the nanometer scale over large areas. These results show that NAMIC is a simple, versatile, low‐cost, and high‐throughput nanopatterning tool.
Product and process innovation in the Italian food industry
Authors: Capitanio Fabian , Coppola Adele , Pascucci Stefano
Published: June 2010

The driving factors of innovation in the Italian food sector could be identified either in internal and in external dynamics. On one hand, the responses to the competition with new actors coming from emerging countries and the reaction to high‐tech products demand evolution. On the other hand, endogenous dynamics appear to become more important for the strategic behaviour of the firms: a higher qualification of the human capital, a more clear orientation for high quality products, organization changes, and relation capacity development. Starting from these considerations, this paper developed an econometric analysis using information from one of the most important national dataset for innovation analysis. The results pointed out that a determinant to successfully develop and introduce product innovation is the capacity to built relationships on the product markets (i.e., with the modern distribution), while the territorial context determines a higher/lower relevance of each of the driving factors of innovation. [EconLit citations: L100; L200; L660]. © 2010 Wiley Periodicals, Inc.
The Growth of Micromycetes in Activated Sludge Media
Authors: Häuslerová J.
Published: June 2010

Today already numerous micromycetes are a recognized part of the biocenosis of growth in receiving waters strongly polluted by organically rich waste waters and of growth on biofilter media surfaces. The principal representatives are some Deuteromycetes, Mucorales and Saccharomycetaceae, whereas the so‐called true aquatic fungi (Oomycetes) with the exception of Leptomitus lacteus are practically absent. The growth of micromycetes in activated sludge remains still an unanswered question. Generally, the filaments in the activated sludge are ascribed to filamentous bacteria and as long as fungi were isolated from activated sludge their presence has been reported only in the form of spores.

The nitrogen deficiency with regard to carbon present in the waste water is considered as one of the factors enhancing the development of fungi in the activated sludge. In a series of 13 tests carried out on laboratory‐scale batch models using synthetic waste water, where the carbon source was glucose and the nitrogen source was (a) sodium nitrate, (b) ammonium sulphate, and (c) peptone, the fungal growth was studied in different models with the BOD:N ratio varying from 20 to 1000. The models were seeded with thickened activated sludge from the municipal sewage works. The sludge did not contain any microscopically detectable forms of fungoid growth. It was found that the fungi in activated‐sludge medium grow well and both in the forms of single cells, occuring independently and in chains, as well as in the form of long branched filaments. In some instances, the micromycetes formed up to 80 to 100 per cent of the biocenosis of the activated‐sludge flocs, but the dependency of their development on the increasing BOD:N ratios in the waste water has not been ascertained.

Fifteen species of micromycetes were isolated and identified, and in addition several representatives of Saccharomycetaceae, which were not identified.
Zur akuten Toxizität von Herbiziden gegenüber ausgewählten Wasserorganismen Teil 2: Triazinherbizide und Amitrol
Authors: Tscheu‐Schlüter M.
Published: June 2010

Eine Weiterentwicklung der wassertoxikologischen Auswertemethodik im Vergleich zu Teil I (TSCHEU‐SCHLÜTER 1974) erfolgte vor allem über die beiden Rechenprogramme ALTEST und PROBIT. Als Testorganismen für sechs Triazine und Amitrol dienten die planktische Grünalge Ankistrodesmus falcatus (CORDA) RALFS und der Guppy (Poecilia reticulata PETERS). Die gelösten Anteile der Triazine wurden mit dem Universal‐Spektrophotometer VSU 1 von Carl Zeiss Jena bestimmt.

Die geprüften Triazine wirken als starke Photosynthesegifte und Amitrol als allgemeines Stoffwechselgift mit Schwellenkonzentrationen (SC) kleiner als 1 mg/1 auf die Testalge hoch giftig. Beziehungen zwischen Algentoxizität und chemischer Struktur werden für die Triazine aufgezeigt. Für Poecilia sind die Triazine mit SC <10 mg/1 stark giftig.

An Hand der Ergebnisse mit Amitrol und dem Handelsprodukt Azaplant werden mögliche große Toxizitätsunterschiede zwischen Wirkstoff und formuliertem Handelsprodukt nachgewiesen (Abb. 4).

Tabelle 7 enthält Empfehlungen höchstzulässiger Konzentrationen für Vorfluter der Güteklasse 2 (β‐mesosaprob) für sechs Triazine, Amitrol und Azaplant.

Abschließend wird ein Vergleich der Toxizität der Testsubstanzen für Wasserorganismen und Warmblüter gezogen.
Characterization of a dual specificity aryl acid adenylation enzyme with dual function in nikkomycin biosynthesis
Authors: Moon Mary , Van Lanen Steven G.
Published: June 2010

Nikkomycin Z is a dipeptide antifungal antibiotic characterized by two nonproteinogenic amino acids, nikkomycin CZ and 4‐(4′‐hydroxy‐2′‐pyridinyl)‐homothreonine (HPHT). The HPHT scaffold is assembled by an aldol reaction between 2‐oxobutyrate and picolinaldehyde, the latter of which is derived from picolinic acid that is activated and loaded to coenzyme A by the aryl‐activating adenylation enzyme, NikE. We now provide evidence that NikE is also involved in the activation and loading of the α‐keto acid precursor, 4‐(2′‐pyridinyl)‐2‐oxo‐4‐hydroxyisovalerate (POHIV), to a phosphopantetheinyl group of an acyl carrier protein domain of NikT. POHIV was synthesized using Escherichia coli 2‐dehydro‐3‐deoxy‐phosphogluconate aldolase, and phenylalanine dehydrogenase from Bacillus sp. NRRL B‐14911 was used to prepare the α‐amino acid, 4‐(2′‐pyridinyl)‐homothreonine (PHT). Using the carboxylic acid‐dependent, ATP‐[32P]PPi exchange assay, NikE is shown to activate both picolinic acid and POHIV but not PHT. Furthermore, NikE loads POHIV to holo‐NikT to generate a new thioester‐linked intermediate, which was not observed using a NikT(S33A) mutant. Thus, NikE activates two distinct carboxylic acids to form two new thioester intermediates, one of which is subsequently reduced to the aldehyde and the other that likely serves as a substrate for the aminotransferase domain of NikT prior to condensation with nikkomycin CZ to yield the dipeptide. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 791–801, 2010.
The serine palmitoyltransferase from Sphingomonas wittichii RW1: An interesting link to an unusual acyl carrier protein
Authors: Raman Marine C. C. , Johnson Kenneth A. , Clarke David J. , Naismith James H. , Campopiano Dominic J.
Published: June 2010

Serine palmitoyltransferase (SPT) catalyses the first step in the de novo biosynthesis of sphingolipids (SLs). It uses a decarboxylative Claisen‐like condensation reaction to couple L‐serine with palmitoyl‐CoA to generate a long‐chain base product, 3‐ketodihydrosphingosine. SLs are produced by mammals, plants, yeast, and some bacteria, and we have exploited the complete genome sequence of Sphingomonas wittichii to begin a complete analysis of bacterial sphingolipid biosynthesis. Here, we describe the enzymatic characterization of the SPT from this organism and present its high‐resolution x‐ray structure. Moreover, we identified an open reading frame with high sequence homology to acyl carrier proteins (ACPs) that are common to fatty acid biosynthetic pathways. This small protein was co‐expressed with the SPT and we isolated and characterised the apo‐ and holo‐forms of the ACP. Our studies suggest a link between fatty acid and sphingolipid metabolism. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 811–822, 2010.
Recent advancements in the biosynthetic mechanisms for polyketide‐derived mycotoxins
Authors: Huffman Justin , Gerber Ryan , Du Liangcheng
Published: June 2010

Polyketides (PKs) are a large group of natural products produced by microorganisms and plants. They are biopolymers of acetate and other short carboxylates and are biosynthesized by multifunctional enzymes called polyketide synthases (PKSs). This review discusses the biosynthesis of four toxic PK, aflatoxins, fumonisins, ochratoxins (OTs), and zearalenone. These metabolites are structurally diverse and differ in their mechanisms of toxicity. However, they are all of concern in food safety and agriculture because of their toxic properties and their frequent accumulation in crops used for food and feed. The focus is on the recent advancements in the understanding of the molecular mechanisms for the biosynthesis of these mycotoxins. Several of the mycotoxin PKSs have been genetically and biochemically studied while other PKSs remain to be investigated. Multiple post‐PKS modifications are often required for the maturation of the mycotoxins. Many of these modification steps for aflatoxins and fumonisins are well established while the post‐PKS modifications for zearalenone and OTs remain to be biochemically characterized. More efforts are needed to completely illustrate the biosynthetic mechanisms for this important group of PKs. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 764–776, 2010.
Heterologous expression of the biosynthetic gene clusters of coumermycin A1, clorobiocin and caprazamycins in genetically modified Streptomyces coelicolor strains
Authors: Flinspach Katrin , Westrich Lucia , Kaysser Leonard , Siebenberg Stefanie , Gomez‐Escribano Juan Pablo , Bibb Mervyn , Gust Bertolt , Heide Lutz
Published: June 2010

The biosynthetic gene clusters of the aminocoumarin antibiotics clorobiocin and coumermycin A1 and of the liponucleoside antibiotic caprazamycin were stably integrated into the genomes of different host strains derived from Streptomyces coelicolor A3(2). For the heterologous expression of clorobiocin derivatives in a chemically defined medium, inclusion of 0.6% of the siloxylated ethylene oxide/propylene oxide copolymer Q2‐5247 into the growth medium proved to result in a 4.8‐fold increase of productivity. Presumably, this copolymer acts as an oxygen carrier. The additional inclusion of cobalt chloride (0.2–2 mg l−1) dramatically increased the percentage of the desired compound clorobiocin within the total produced clorobiocin derivatives. This is very likely due to a stimulation of a cobalamin‐dependent methylation reaction catalyzed by the enzyme CloN6 of clorobiocin biosynthesis. All three investigated host strains (S. coelicolor M512, M1146 and M1154) gave similar production rates of total clorobiocin derivatives (on average, 158 mg l−1 in the presence of 0.6% Q2‐5247 and 0.2 mg l−1 CoCl2). In contrast, heterologous production of caprazamycin derivatives was optimal in strain M1154 (amounts of 152 mg l−1 on average). © 2010 Wiley Periodicals, Inc. Biopolymers 93: 823–832, 2010.
Probing the active site of MIO‐dependent aminomutases, key catalysts in the biosynthesis of β‐amino acids incorporated in secondary metabolites
Authors: Cooke Heather A. , Bruner Steven D.
Published: June 2010

The tyrosine aminomutase SgTAM produces (S)‐ß‐tyrosine from L‐tyrosine in the biosynthesis of the enediyne antitumor antibiotic C‐1027. This conversion is promoted by the methylideneimidazole‐5‐one (MIO) prosthetic group. MIO was first identified in the homologous family of ammonia lyases, which deaminate aromatic amino acids to form α,ß‐unsaturated carboxylates. Studies of substrate specificity have been described for lyases but there have been limited reports in altering the substrate specificity of aminomutases. Furthermore, it remains unclear as to what structural properties are responsible for catalyzing the presumed readdition of the amino group into the α,ß‐unsaturated intermediates to form ß‐amino acids. Attempts to elucidate specificity and mechanistic determinants of SgTAM have also proved to be difficult as it is recalcitrant to perturbations to the active site via mutagenesis. An X‐ray cocrystal structure of the SgTAM mutant of the catalytic base with L‐tyrosine verified important substrate binding residues as well as the enzymatic base. Further mutagenesis revealed that removal of these crucial interactions renders the enzyme inactive. Proposed structural determinants for mutase activity probed via mutagenesis, time‐point assays and X‐ray crystallography revealed a complicated role for these residues in maintaining key quaternary structure properties that aid in catalysis. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 802–810, 2010.
Heparin or enoxaparin anticoagulation for primary percutaneous coronary intervention
Authors: Brieger David , Collet Jean‐Philippe , Silvain Johanne , Landivier Antoine , Barthélémy Olivier , Beygui Farzin , Bellemain‐Appaix Anne , Mercadier Anne , Choussat Remi , Vignolles Nicolas , Costagliola Dominique , Montalescot Gilles
Published: June 2010

Objectives: The aim of this study was to compare efficacy and safety outcomes among patients receiving enoxaparin or unfractionated heparin (UFH) while undergoing percutaneous coronary intervention (PCI) for ST‐segment elevation myocardial infarction (STEMI). Background: Primary PCI (pPCI) for ST elevation has traditionally been supported by UFH. The low molecular weight heparin enoxaparin may provide better outcomes when used for pPCI. Methods: Consecutive eligible patients (580) undergoing pPCI enrolled in the prospective electronic Pitié‐Salpêtrière registry of ischemic coronary syndromes (e‐PARIS) registry were grouped according to whether they received UFH or enoxaparin as the sole anticoagulant. Logistic regression modeling, propensity‐weighted adjustment, and sensitivity analyses were used to evaluate efficacy and safety endpoints for enoxaparin vs. UFH. Results: Enoxaparin was administered to 346 patients and UFH to 234 without ACT or anti‐Xa guided dose adjustment. PCI was performed through the radial artery in 90%, with frequent (75%) use of GPIIb/IIIa antagonists. Patients receiving enoxaparin were more likely to be therapeutically anticoagulated during the procedure (68% vs. 50%, P < 0.0001) and were less likely to experience death or recurrent myocardial infarction (MI) in hospital (adjusted OR 0.28 95% CI (0.12–0.68) or by 30 days (adjusted OR 0.35 95% CI 0.16–0.81). All cause mortality was also reduced in hospital (adjusted OR 0.32, 95% CI (0.12–0.85) and to 30 days (adjusted OR 0.40 95% CI 0.17–0.99). Other ischemic endpoints were similarly reduced with enoxaparin. Thrombolysis in myocardial infarction (TIMI) major bleeding events were numerically fewer among patients receiving enoxaparin (1.2% vs. 2.6%, P = 0.2). Conclusions: In patients with STEMI presenting for PCI, enoxaparin was associated with a reduction in all ischemic complications, more frequent therapeutic anticoagulation, and no increase in major bleeding when compared against unfractionated heparin. © 2010 Wiley‐Liss, Inc.
Retrograde transcatheter closure of ventricular septal defects in children using the Amplatzer Duct Occluder II
Authors: Koneti Nageswara Rao , Penumatsa Raghava Raju , Kanchi Vasudevan , Arramraj Srinivas Kumar , S. Jaishankar , Bhupathiraju Somaraju
Published: June 2010

Objectives: To describe the technique and results of transcatheter closure of ventricular septal defects (VSDs) by a modified retrograde transarterial approach using the new Amplatzer Duct Occluder II (ADO II). Background: Transcatheter device closure of ventricular septal defects (VSDs) by antegrade method is well established, but a challenging procedure. We describe a retrograde technique that obviates the need for arteriovenous looping. Material and Methods: This is a prospective study from a single center. Between April 2009 and February 2010 13 children were identified for closure of various types of perimembranous and muscular VSDs using the ADO II device. All had met the criteria for surgical closure. Following left ventricular angiogram two were excluded as technically nonfeasible. The median age was 48 months (range 15–78). The median weight was 14 kg (range 7.5–20). The device was successfully deployed in the 11 selected children by the method described. The follow‐up evaluation included chest roentgenogram, ECG, and echocardiogram on day 1, at 6 weeks, at 3, 6, and 12 months. Results: The immediate and follow up complete closure rates were 73 and 82%, respectively. The median fluoroscopic time was 14 min (range 8.2–45). There were no procedure related complications. All patients were doing well at median follow up of 10 months; none showing any conduction abnormality. Conclusion: Transcatheter retrograde device closure of selected cases of Ventricular Septal Defects using the Amplatzer Duct Occluder II is simple and appears safe in the short term and can be completed within a short fluoroscopic time.© 2010 Wiley‐Liss, Inc.