bluuebunny/crossref_metadata_2025_split huggingface dataset:
SUITABILITY INDEX FOR COASTAL ENVIRONMENT RESTORATION IN ENCLOSED BAY
Authors: Horie Takehito , Okada Tomonari , Watanuki Akira 
Published: December 2012

HSI (Habitat Suitability Index) models are a numerical index that describes the habitat quality for individual species of aquatic organism. This models are composed of SI (suitability index) models, which show the cause-and-effect relationships between biomass of target species and the variation of individual water environmental factors. Fish are often used as the environmental indicator species of HSI models, because fish are strongly related to marine algae, sea grass, water quality, and so forth, and fish are predator high in the food chain for the aquatic system.
In order to restore the marine environment of Tokyo Bay, in Japan(Fig.1), some SI models have been proposed. However, we have few precision SI models on target fish. Therefore, the objective of this study is to reveal the relationship between seasonal or daily variations of water environment components in Tokyo bay or in offshore sea area of the Pacific coast of Tokyo metro (Fig.1) and the total mass of fish living in Tokyo bay in order to create precision SI models of fish.
MODELLING OF A NEARSHORE PLACED SAND MOUND
Authors: Smith Ernest R. , D'Alessandro Felice , Tomasicchio Giuseppe Roberto , Gailani Joseph Z. 
Published: December 2012

Nearshore placement of sand is becoming a more popular option in two related types of coastal engineering projects: beach nourishment and inlet dredging. Placing the sand in the nearshore instead of directly on the beach can reduce the costs of a beach nourishment project (Douglass 1995); furthermore, the environmental impact to the beach and dune ecosystem may be perceived to be less for open-water disposal with subsequent migration than for direct placement on the beach. Nearshore placement of sand is also an option in navigation dredging projects for similar reasons. Several design and planning questions relate to the fate of dredged sand placed in the nearshore. Can we economically use profile nourishment, and what is the certainty that a constructed submerged feature will move onshore or remain in place? And if it will move, what is the rate of its movement? Another question concerns how deep material should be placed. In order to answer these questions, together with physical model experiments, several empirical/numerical models have been developed in the past in the United States as a part of the Corps of Engineers 'Dredging Research Program' (DRP) (Hands 1991, Larson and Kraus 1992).
Hydrodynamic modelling of the nearshore environment has reached a verifiable level of maturity in the last decades as a result of well-defined equations, established numerical solutions and quality laboratory and field data. On the contrary, modelling of sediment transport and beach profile evolution has not yet approached a similar level of accuracy. Most commonly applied models to predict beach profile modifications and to estimate the migration rate of nearshore constructed sand mounds rely on empirical relationships (Douglass 1995). More recently, the numerical model C-SHORE (Kobayashi et al. 2007; Figlus et al. 2011) was developed resulting in simple, practical and accurate code that predicts beach-dune profile evolution over the near-shore region in response to waves, currents and water levels. In the present work, a calibration and verification procedure is considered for the numerical model C-SHORE (Kobayashi et al. 2007) and the empirical model (Douglass 1995).
PROJECT PERFORMANCE AND MONITORING OF A REVETMENT, COCOS BAY, EAST TRINIDAD
Authors: O'Brien-Delpesh Charmaine , Gray-Bernard Candice , Tang-Kai Marisha 
Published: December 2012

The eastern shoreline of Trinidad has been suffering extensively from erosion over the years. This coast is exposed to the Atlantic Ocean and is subjected to large swells especially during the North Atlantic winter period, storms and hurricanes. The coastal area of Cocos Bay located on the east coast of Trinidad between the Nariva and Ortoire Rivers has been undergoing severe erosion at a rate of approximately 0.5 m to 1.7 m per year. In 2005, the Ministry of Works and Transport, Drainage Division started the construction of a 2.3 km long rubble revetment (rip rap) which was completed in 2008. The function of the revetment was to control erosion and flooding thereby protecting the Manzanilla-Mayaro Road which is a major artery linking the oil and gas sector as well as several coastal villages. This revetment formed the emergency intervention phase of a three phase solution recommended along the South Cocos Bay. Conforming to the Certificate of Environmental Clearance (CEC), the Ministry of Works and Transport, Drainage Division has been monitoring the possible impacts of the structure on the beach environment from post construction to present and its structural integrity. During the last five years, the monitoring study has revealed that in the vicinity of the revetment, erosion and flooding have been mitigated; however there has been narrowing of the beach even though the gradient has remained the same.
Flanking has also been observed immediately north and south of the revetment. In regards to the structural integrity of the revetment, the armour layer which was constructed using local rock (blue limestone), 200 - 300 kg is showing signs of weathering and shearing. This has resulted in voids in the armour layer which has exposed the filter and underlayers. It is recommended that in order to maintain the functionality and structural integrity over a design life of 25 years, the armour layer be repaired with a suitable material which has historically been sourced externally. The post documents the prevailing wave climate, previous coastal evolution modelling, and the pre and post construction profile records. The shoreline response to the revetment is predicted using GENESIS and compared to the actual response based on an analysis of the beach profile monitoring records are also presented.
Single‐Crystalline p‐Type Zn3As2 Nanowires for Field‐Effect Transistors and Visible‐Light Photodetectors on Rigid and Flexible Substrates
Authors: Chen Gui , Liu Zhe , Liang Bo , Yu Gang , Xie Zhong , Huang Hongtao , Liu Bin , Wang Xianfu , Chen Di , Zhu Ming‐Qiang , Shen Guozhen 
Published: December 2012

AbstractZn3As2 is an important p‐type semiconductor with the merit of high effective mobility. The synthesis of single‐crystalline Zn3As2 nanowires (NWs) via a simple chemical vapor deposition method is reported. High‐performance single Zn3As2 NW field‐effect transistors (FETs) on rigid SiO2/Si substrates and visible‐light photodetectors on rigid and flexible substrates are fabricated and studied. As‐fabricated single‐NW FETs exhibit typical p‐type transistor characteristics with the features of high mobility (305.5 cm2 V−1 s−1) and a high Ion/Ioff ratio (105). Single‐NW photodetectors on SiO2/Si substrate show good sensitivity to visible light. Using the contact printing process, large‐scale ordered Zn3As2 NW arrays are successfully assembled on SiO2/Si substrate to prepare NW thin‐film transistors and photodetectors. The NW‐array photodetectors on rigid SiO2/Si substrate and flexible PET substrate exhibit enhanced optoelectronic performance compared with the single‐NW devices. The results reveal that the p‐type Zn3As2 NWs have important applications in future electronic and optoelectronic devices.
Photocrosslinkable Kappa‐Carrageenan Hydrogels for Tissue Engineering Applications
Authors: Mihaila Silvia M. , Gaharwar Akhilesh K. , Reis Rui L. , Marques Alexandra P. , Gomes Manuela E. , Khademhosseini Ali 
Published: December 2012

AbstractKappa carrageenan (κ‐CA) is a natural‐origin polymer that closely mimics the glycosaminoglycan structure, one of the most important constituents of native tissues extracellular matrix. Previously, it has been shown that κ‐CA can crosslink via ionic interactions rendering strong, but brittle hydrogels. In this study, we introduce photocrosslinkable methacrylate moieties on the κ‐CA backbone to create physically and chemically crosslinked hydrogels highlighting their use in the context of tissue engineering. By varying the degree of methacrylation, the effect on hydrogel crosslinking was investigated in terms of hydration degree, dissolution profiles, morphological, mechanical, and rheological properties. Furthermore, the viability of fibroblast cells cultured inside the photocrosslinked hydrogels was investigated. The combination of chemical and physical crosslinking procedures enables the formation of hydrogels with highly versatile physical and chemical properties, while maintaining the viability of encapsulated cells. To our best knowledge, this is the first study reporting the synthesis of photocrosslinkable κ‐CA with controllable compressive moduli, swelling ratios and pore size distributions. Moreover, by micromolding approaches, spatially controlled geometries and cell distribution patterns could be obtained, thus enabling the development of cell‐material platforms that can be applied and tailored to a broad range of tissue engineering strategies.
Population transcriptomics with single‐cell resolution: A new field made possible by microfluidics
Authors: Plessy Charles , Desbois Linda , Fujii Teruo , Carninci Piero 
Published: December 2012

AbstractTissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells.
A simple and sensitive spectrofluorimetric method for the determination of furosemide using zinc(II)–1,4‐bis(imidazol‐1‐ylmethyl)benzene complexes
Authors: Liu Yali , Wang Huijuan , Wang Jian , Li Yuanfang 
Published: December 2012

ABSTRACTA novel spectrofluorometric method for the determination of furosemide (FUR) is described. The method is based on enhancement of fluorescence emission of FUR in the presence of zinc (II) complexes of 1,4‐bis(imidazol‐1‐ylmethyl)benzene. Under optimum conditions, the enhanced fluorescence intensity is linearly related to the concentration of FUR. The proposed method has been successfully applied to the determination of FUR in pharmaceutical preparations. The possible mechanism of this reaction is discussed briefly based on data from fluorescence spectroscopy, UV–vis absorption and infrared spectroscopy. Copyright © 2012 John Wiley & Sons, Ltd.
Extreme thermophilic ethanol production from rapeseed straw: Using the newly isolated Thermoanaerobacter pentosaceus and combining it with Saccharomyces cerevisiae in a two‐step process
Authors: Tomás Ana Faria , Karagöz Pınar , Karakashev Dimitar , Angelidaki Irini 
Published: December 2012

AbstractThe newly isolated extreme thermophile Thermoanaerobacter pentosaceus was used for ethanol production from alkaline‐peroxide pretreated rapeseed straw (PRS). Both the liquid and solid fractions of PRS were used. T. pentosaceus was able to metabolize the typical process inhibitors present in lignocellulosic hydrolysate, namely 5‐hydroxymethyl furfural (HMF) and furfural, up to concentrations of 1 and 0.5 g L−1, respectively. Above these levels, xylose consumption was inhibited up to 70% (at 3.4 g‐furfural L−1) and 75% (at 3.4 g‐HMF L−1). T. pentosaceus was able to grow and produce ethanol directly from the liquid fraction of PRS, without any dilution or need for additives. However, when the hydrolysate was used undiluted the ethanol yield was only 37% compared to yield of the control, in which pure sugars in synthetic medium were used. The decrease of ethanol yield was attributed to the high amounts of salts resulting from the alkaline‐peroxide pretreatment. Finally, a two‐stage ethanol production process from PRS using Saccharomyces cerevisiae (utilization of hexoses in the first step) and T. pentosaceus (utilization of pentoses in the second step) was developed. Results showed that the two strains together could achieve up to 85% of the theoretical ethanol yield based on the sugar composition of the rapeseed straw, which was 14% and 50% higher compared to the yield with the yeast or the bacteria alone, respectively. Biotechnol. Bioeng. 2013; 110: 1574–1582. © 2012 Wiley Periodicals, Inc.
A screening model to predict microalgae biomass growth in photobioreactors and raceway ponds
Authors: Huesemann M. H. , Van Wagenen J. , Miller T. , Chavis A. , Hobbs S. , Crowe B. 
Published: December 2012

AbstractA microalgae biomass growth model was developed for screening novel strains for their potential to exhibit high biomass productivities under nutrient‐replete conditions in photobioreactors or outdoor ponds. Growth is modeled by first estimating the light attenuation by biomass according to Beer‐Lambert's Law, and then calculating the specific growth rate in discretized culture volume slices that receive declining light intensities due to attenuation. The model uses only two physical and two species‐specific biological input parameters, all of which are relatively easy to determine: incident light intensity, culture depth, as well as the biomass light absorption coefficient and the specific growth rate as a function of light intensity. Roux bottle culture experiments were performed with Nannochloropsis salina at constant temperature (23°C) at six different incident light intensities (10, 25, 50, 100, 250, and 850 µmol/m2 s) to determine both the specific growth rate under non‐shading conditions and the biomass light absorption coefficient as a function of light intensity. The model was successful in predicting the biomass growth rate in these Roux bottle batch cultures during the light‐limited linear phase at different incident light intensities. Model predictions were moderately sensitive to minor variations in the values of input parameters. The model was also successful in predicting the growth performance of Chlorella sp. cultured in LED‐lighted 800 L raceway ponds operated in batch mode at constant temperature (30°C) and constant light intensity (1,650 µmol/m2 s). Measurements of oxygen concentrations as a function of time demonstrated that following exposure to darkness, it takes at least 5 s for cells to initiate dark respiration. As a result, biomass loss due to dark respiration in the aphotic zone of a culture is unlikely to occur in highly mixed small‐scale photobioreactors where cells move rapidly in and out of the light. By contrast, as supported also by the growth model, biomass loss due to dark respiration occurs in the dark zones of the relatively less well‐mixed pond cultures. In addition to screening novel microalgae strains for high biomass productivities, the model can also be used for optimizing the pond design and operation. Additional research is needed to validate the biomass growth model for other microalgae species and for the more realistic case of fluctuating temperatures and light intensities observed in outdoor pond cultures. Biotechnol. Bioeng. 2013; 110: 1583–1594. © 2012 Wiley Periodicals, Inc.
Non‐invasive online detection of microbial lysine formation in stirred tank bioreactors by using calorespirometry
Authors: Regestein Lars , Maskow Thomas , Tack Andreas , Knabben Ingo , Wunderlich Martin , Lerchner Johannes , Büchs Jochen 
Published: December 2012

AbstractNon‐invasive methods for online monitoring of biotechnological processes without compromising the integrity of the reactor system are very important to generate continuous data. Even though calorimetry has been used in conventional biochemical analysis for decades, it has not yet been specifically applied for online detection of product formation at technical scale. Thus, this article demonstrates a calorespirometric method for online detection of microbial lysine formation in stirred tank bioreactors. The respective heat generation of two bacterial strains, Corynebacterium glutamicum ATCC 13032 (wild‐type) and C. glutamicum DM1730 (lysine producer), was compared with the O2‐consumption in order to determine whether lysine was formed. As validation of the proposed calorespirometric method, the online results agreed well with the offline measured data. This study has proven that calorespirometry is a viable non‐invasive technique to detect product formation at any time point. Biotechnol. Bioeng. 2013; 110: 1386–1395. © 2012 Wiley Periodicals, Inc.
Global gene expression of Dehalococcoides within a robust dynamic TCE‐dechlorinating community under conditions of periodic substrate supply
Authors: West Kimberlee A. , Lee Patrick K.H. , Johnson David R. , Zinder Stephen H. , Alvarez‐Cohen Lisa 
Published: December 2012

AbstractA microarray targeting four sequenced strains in the Dehalococcoides (Dhc) genus was used to analyze gene expression in a robust long‐term trichloroethene (TCE)‐degrading microbial community (designated ANAS) during feeding cycles that involve conditions of periodic substrate supply. The Dhc transcriptome was examined at three time‐points throughout a batch feeding cycle: T1 (27 h) when TCE, dichloroethene (DCE), and vinyl chloride (VC) were present; T2 (54 h) when only VC remained; and T3 (13 days) when Dhc had been starved of substrate for 9 days. Ninety percent of the Dhc open reading frames (ORFs) that were detected in the ANAS DNA were found to be expressed as RNA sometime during the time course, demonstrating extraordinary utilization of the streamlined genome. Ninety‐seven percent of these transcripts were differentially expressed during the time course indicating efficiency of transcription through regulation in Dhc. Most Dhc genes were significantly down‐regulated at T3, responding to a lack of substrate as would be expected. The tceA and vcrA genes, which code for proteins with known chlorinated ethene reduction functions, were highly expressed at both T1 and T2, whereas two other putative reductive dehalogenase genes (DET0173 and DET1545) were most highly expressed at T2, likely in response to the presence of VC. Hydrogenases were most highly expressed at T1, reflecting their important role in accumulating electrons used to initiate reductive dechlorination and other biosynthesis pathways. Cobalamin transport genes were preferentially expressed at T2, reflecting an increase in corrinoid transport as chloroethenes were degraded and a decrease in activity of the transport system after dehalogenation was complete. This is the first application of a microarray targeting a known genus, including both core genomes and identified strain‐specific genes, to improve our understanding of transcriptional dynamics within an undefined microbial community. Biotechnol. Bioeng. 2013; 110: 1333–1341. © 2012 Wiley Periodicals, Inc.
A redox trap to augment the intein toolbox
Authors: Callahan Brian P. , Stanger Matthew , Belfort Marlene 
Published: December 2012

AbstractThe unregulated activity of inteins during expression and consequent side reactions during work‐up limits their widespread use in biotechnology and chemical biology. Therefore, we exploited a mechanism‐based approach to regulate intein autocatalysis for biotechnological application. The system, inspired by our previous structural studies, is based on reversible trapping of the intein's catalytic cysteine residue through a disulfide bond. Using standard mutagenesis, the disulfide trap can be implemented to impart redox control over different inteins and for a variety of applications both in vitro and in Escherichia coli. Thereby, we first enhanced the output for bioconjugation in intein‐mediated protein ligation, also referred to as expressed protein ligation, where precursor recovery and product yield were augmented fourfold to sixfold. Second, in bioseparation experiments, the redox trap boosted precursor recovery and product yield twofold. Finally, the disulfide‐trap intein technology stimulated development of a novel bacterial redox sensor. This sensor reliably identified hyperoxic E. coli harboring mutations that disrupt the reductive pathways for thioredoxin and glutathione, against a background of wild‐type cells. Biotechnol. Bioeng. 2013; 110: 1565–1573. © 2012 Wiley Periodicals, Inc.
A thin‐walled polydimethylsiloxane bioreactor for high‐density hepatocyte sandwich culture
Authors: Tan Guo‐Dong Sean , Toh Guoyang William , Birgersson Erik , Robens Jeffrey , van Noort Danny , Leo Hwa Liang 
Published: December 2012

AbstractIn vitro drug testing requires long‐term maintenance of hepatocyte liver specific functions. Hepatocytes cultured at a higher seeding density in a sandwich configuration exhibit an increased level of liver specific functions when compared to low density cultures due to the better cell to cell contacts that promote long term maintenance of polarity and liver specific functions. However, culturing hepatocytes at high seeding densities in a standard 24‐well plate poses problems in terms of the mass transport of nutrients and oxygen to the cells. In view of this drawback, we have developed a polydimethylsiloxane (PDMS) bioreactor that was able to maintain the long‐term liver specific functions of a hepatocyte sandwich culture at a high seeding density. The bioreactor was fabricated with PDMS, an oxygen permeable material, which allowed direct oxygenation and perfusion to take place simultaneously. The mass transport of oxygen and the level of shear stress acting on the cells were analyzed by computational fluid dynamics (CFD). The combination of both direct oxygenation and perfusion has a synergistic effect on the liver specific function of a high density hepatocyte sandwich culture over a period of 9 days. Biotechnol. Bioeng. 2013; 110: 1663–1673. © 2012 Wiley Periodicals, Inc.