bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of organic waste for the production of added-value holocellulases with Cellulomonas flavigena PR-22 and Trichoderma reesei MCG 80
Authors: Escamilla-Alvarado Carlos , Poggi-Varaldo Héctor M , Ponce-Noyola M Teresa
Published: June 2013

We evaluated the production of holocellulases from the cellulolytic microorganisms Cellulomonas flavigena PR-22 and Trichoderma reesei MCG 80 using as substrates the organic fraction of municipal solid waste (OFMSW) and digestates from a hydrogenogenic-methanogenic bioenergy production process. The first set of experiments (E1) used the mutant actinobacteria C. flavigena PR-22 whereas another set (E2) used the mutant filamentous fungi T. reesei MCG 80. In E1 with OFMSW as substrate, xylanolytic activities ranged from 1800 to 3900 international units gholocellulose−1 (IU ghol−1), whereas the cellulolytic activities ranged from 220 to 420 IU ghol−1. The variation of agitation speed did not have a significant effect on enzyme activity, whereas the increase of substrate concentration had a significant negative effect on both xylanolytic and cellulolytic activities on a holocellulose feed basis. Regarding E2, the OFMSW was evaluated at 1, 2 and 3 % volatile solids (VS). At 2 % VS the best filter paper activities were 1200 filter paper units (FPU) l−1; however, in a holocellulase basis the best result was 67 FPU ghol−1, corresponding to 1 % VS. Next, OFMSW was compared with OFMSW supplemented with lactose, digested solids from hydrogenogenic fermentation (D1) and digested solids from a two-stage process (D2). Against expectations, no positive effect was found in OFMSW due to lactose. The best enzymatic titres were in the order D1 > OFMSW ≈ OFMSW + lactose > D2. The use of digestates from hydrogenogenic fermentation for enzyme production holds promise for waste management. It promotes energy and added-value bioproduct generation—a green alternative to common practice of management and disposal of organic wastes.
Bone regeneration potential of the new chitosan-based alloplastic biomaterial
Authors: Bojar Witold , Kucharska Martyna , Ciach Tomasz , Koperski Łukasz , Jastrzębski Zenon , Szałwiński Michał
Published: June 2013

Over the last few years, alloplastic bone substitute materials are raising much interest as an alternative to autologic transplants and xenogenic materials especially in oral surgery. These non-immunogenic and completely resorbable biomaterials are becoming the basis for complete and predictable guided bone regeneration in many cases. The objective of our research was to evaluate the dynamics of bone formation in rats’ skulls after implantation of the new chitosan/tricalcium phosphate/alginate biomaterial in comparison to the commercially available alloplastic bone graft. A total of 45 adult male rats weighing 300–400 g were used for the study. The 85-mm-diameter defects in calvaria bone were prepared with a trephine bur, and then filled with the bone substitute materials: chitosan/tricalcium phosphate/alginate or easy-graft Classic (Degradable Solutions AG) (EA) or left just with the blood clot. Animals were sacrificed at 1 and 3 months for histological, histomorphometrical and micro-tomographic evaluations. Histological evaluation at 1 month showed early new bone formation, observed around the experimental biomaterial (CH/TCP/Alg). There were no features of purulent inflammation and necrosis or granulomatous inflammation. Microscopic examination after 3 months following the surgery revealed trabecular bone formation around chitosan-based bone graft with no significant inflammatory response. Less satisfactory and differing results were observed for the commercially available EA and control blood clot. The tested material (chitosan) showed a high degree of biocompatibility and osteoconductivity in comparison with the control groups. Additionally, it seemed to be a “user-friendly” material for oral surgeons.
Kinetics of a twinning step
Authors: Liu Lifeng , Vainchtein Anna , Wang YangYang
Published: June 2013

We study the kinetics of a step propagating along a twin boundary in a cubic lattice undergoing an antiplane shear deformation. To model twinning, we consider a piecewise quadratic double-well interaction potential with respect to one component of the shear strain and harmonic interaction with respect to another. We construct semi-analytical traveling wave solutions that correspond to a steady step propagation and obtain the kinetic relation between the applied stress and the velocity of the step. We show that this relation strongly depends on the width of the spinodal region where the double-well potential is non-convex and on the material anisotropy parameter. In the limiting case when the spinodal region degenerates to a point, we construct new solutions that extend the kinetic relation obtained in the earlier work of Celli, Flytzanis and Ishioka into the low-velocity regime. Numerical simulations suggest stability of some of the obtained solutions, including low-velocity step motion when the spinodal region is sufficiently wide. When the applied stress is above a certain threshold, nucleation and steady propagation of multiple steps are observed.
Increasing the Value of Evaluation to Philanthropic Foundations
Authors: Greenwald Howard P.
Published: June 2013

This article synthesizes interview data from evaluation directors and top executives of philanthropic foundations on how evaluation might better advance their missions. In key informant interviews, respondents commented on the purposes of evaluation from the foundation’s perspective, challenges to effective evaluation, and the means by which evaluation could be made more valuable to foundations. Informants emphasized promoting accountability, improving programs, advancing organizational learning, and disseminating intervention models as desired uses of evaluation. Application of appropriate research techniques, relevance and timing of evaluation products, and internal thinking and social dynamics within foundations were cited as challenges to evaluation. Emerging concerns include the need to evaluate achievements of foundations as a whole and for evaluation to further develop as a science. In terms of increasing the value of evaluation, the current study indicates the importance of improved relationships and dialogue between evaluators and foundation personnel, stronger leadership consensus within foundations regarding evaluation, and safeguarding of the evaluation process.
Plural provision of primary medical care in England, 2002–2012
Authors: Sheaff Rod
Published: June 2013

Objectives:

Health care reforms often include provider diversification, including privatization, to increase competition and thereby health care quality and efficiency. Donabedian's organizational theory implies that the consequences will vary according to the providers' ownership. The aim was to examine how far that theory applies to changes in English NHS primary medical care (general practice) since 1998, and the consequences for patterns of service provision.

Methods:

Framework analysis whose categories and structure reflected Donabedian's theory and its implications, populated with data from a systematic review, administrative sources and press rapportage.

Results:

Two patterns of provider diversification occurred: 'native' diversification among existing providers and plural provision as providers with different types of ownership were introduced. Native diversification occurred through: extensive recruitment of salaried GPs; extending the range of services provided by general practices; introducing limited liability partnerships; establishing GPs with special clinical interests; and introducing a wider range of services for GPs to refer to. All of these had little apparent effect on competition between general practices. Plural provision involved: increased primary care provision by corporations; introducing GP-owned firms; establishing social enterprises (initially mostly out-of-hours cooperatives); and Primary Care Trusts taking over general practices. Plural provision was on a smaller scale than native diversification and appeared to go into reverse in 2011.

Conclusions:

Although the available data confirm the implications of Donabedian's theory, there are exceptions. Native diversification and plural provision policies differ in their implications for service development.
Projection effects and specification bias in spatial models of European Parliament elections
Authors: Grand Peter , Tiemann Guido
Published: June 2013

Substantial empirical evidence suggests that voters cast their ballot not only by considering the different policy positions of parties or candidates, but also appear to pull candidates/parties they prefer closer to their own ideal position (‘assimilation’) while pushing candidates/parties they dislike, farther away (‘contrast’). These effects are called ‘projection effects’. We illustrate that voters’ perceptions of policy positions of candidates/parties are contaminated by non-spatial considerations. Building on data from the EES series, we empirically demonstrate that projection effects are substantively meaningful and statistically significant in elections to the European Parliament. We moreover distinguish between unsystematic projection bias that only depends on the closeness to a specific candidate or party and systematic projection bias that is also affected by party-, voter-, and context-specific determinants.
Making methods sociable: dialogue, ethics and authorship in qualitative research
Authors: Sinha Shamser , Back Les
Published: June 2013

The article argues for fostering sociable forms of dialogue in qualitative research. Conventional research shares an emphasis on extracting narratives with judicial and invasive state modes of enquiry rather than on learning from a genuine two-way dialogue between participants and researchers. Using a study of young migrants, we show how involving participants as observers and shapers of analytical dialogue can produce circulations of communication oscillating across the researcher’s and participant’s horizons of understanding. This produces new insight, beyond the limits of qualitative investigation, that extracts information from participants, and in so doing, has the potential to affect shifts in perception that animate and enchant experience. It has consequences for rethinking authorship that share, credit and specify responsibility. Developing such an approach opposes the ‘ethical hypochondria’ characterising qualitative research culture, where ‘automatic anonymity’ is limiting the potential of research to travel, connect people and engage the public imagination.
LIN28B-mediated expression of fetal hemoglobin and production of fetal-like erythrocytes from adult human erythroblasts ex vivo
Authors: Lee Y. Terry , de Vasconcellos Jaira F. , Yuan Joan , Byrnes Colleen , Noh Seung-Jae , Meier Emily R. , Kim Ki Soon , Rabel Antoinette , Kaushal Megha , Muljo Stefan A. , Miller Jeffery L.
Published: June 2013

Key Points

LIN28B regulates HbF expression in erythroblasts that are cultured from umbilical cord and adult human blood. LIN28B expression manifested a more fetal-like phenotype among adult human erythroblasts.
Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB
Authors: Bezuidt Oliver KI , Klockgether Jens , Elsen Sylvie , Attree Ina , Davenport Colin F , Tümmler Burkhard
Published: June 2013

Background

Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex.

Results

The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains.

Conclusions

The higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage DNA.
Correlation between metabolic syndrome and knee osteoarthritis: data from the Korean National Health and Nutrition Examination Survey (KNHANES)
Authors: Han Chang Dong , Yang Ik Hwan , Lee Woo Suk , Park Yoo Jung , Park Kwan Kyu
Published: June 2013

Background

This study was designed to investigate the correlations of knee osteoarthritis (OA) with metabolic syndrome (MetS) and MetS parameters in Korean subjects.

Methods

This study included data from 270 subjects with knee OA and 1964 control subjects with a mean age of 54.56 (SD 11.53) years taken from the Korean National Health and Nutritional Examination Survey (KNHANES) 2008. Multivariate logistic regression analysis was conducted to examine possible associations for knee OA with MetS and MetS parameters.

Results

MetS was shown to be associated with an increased risk of knee OA in female subjects in unadjusted analysis (OR 1.798, 95% CI 1.392, 2.322), but this significance disappeared when adjusted for confounding factors (OR 1.117, 95% CI 0.805, 1.550). No significant association between MetS and knee OA was found in male subjects. Among parameters of MetS, only high waist circumference (WC) in female subjects was significantly associated with an increased prevalence of knee OA, even after adjusting for confounding factors, while no other significant associations were found in both male and female subjects.

Conclusion

We found that WC was associated with knee OA in female subjects, but neither MetS nor any parameters thereof were shown to be associated with knee OA in the Korean subjects of this study. Although we found no relationship between a pre-inflammatory state of MetS and knee OA, we believe further investigation of this relationship in various aspects is warranted, as MetS may also be a risk factor for complications in knee OA related procedures.
Reactivation of immune responses against Mycobacterium tuberculosis by boosting with the CpG oligomer in aged mice primarily vaccinated with Mycobacterium bovis BCG
Authors: Taniguchi Keiichi , Takii Takemasa , Yamamoto Saburo , Maeyama Jun-ichi , Iho Sumiko , Maruyama Mitsuo , Iizuka Narushi , Ozeki Yuriko , Matsumoto Sohkichi , Hasegawa Tomohiro , Miyatake Yuuji , Itoh Saotomo , Onozaki Kikuo
Published: June 2013

Background

Mycobacterium bovis bacillus Calmette Guérin (BCG) vaccine, which has been inoculated to more than one billion people world-wide, has significant effect in preventing tuberculous meningitis and miliary tuberculosis (TB) in neonate and early childhood. However, BCG fails to adequately protect against pulmonary TB and reactivation of latent infections in adults. To overcome this problem, adequate booster is urgently desired in adult who received prior BCG vaccination, and appropriate animal models that substitute human cases would be highly valuable for further experimentation.

Findings

The booster effect of the synthesized CpG oligomer (Oligo-B) on aged mice which had been primarily vaccinated with BCG at the age of 4-week old. The specific Th1 type reaction, production of interferon-γ, in response to TB antigens, purified protein derivatives (PPD) and protection against challenge with Mycobacterium tuberculosis (MTB) H37Rv decreased with increasing age and were not observed in 89-week old mice. In order to rejuvenate the Th1 type response against PPD and protection activity against MTB infection, Oligo-B, which is known to augment Th1 responses, was administered as a booster to 81-90-week old mice (late 50’s in human equivalent) vaccinated with BCG at 4-week old. The boosting with Oligo-B increased the number of CD4+ CD44high CD62Lhigh, central memory type T cell. Furthermore, the Oligo-B boosting rejuvenated the ability of mice to protect against infection with MTB H37Rv.

Conclusions

Th1-adjuvant CpG oligo DNA, such as Oligo-B, may be a promising booster when coupled with BCG priming.
First Report on Circulation of Echinococcus ortleppi in the one Humped Camel (Camelus dromedaries), Sudan
Authors: Ahmed Mohamed E , Eltom Kamal H , Musa Nasreen O , Ali Ibtisam A , Elamin Fatima M , Grobusch Martin P , Aradaib Imadeldin E
Published: June 2013

Background

Echinococcus granulosus (EG) complex, the cause of cystic echinococcosis (CE), infects humans and several other animal species worldwide and hence the disease is of public health importance. Ten genetic variants, or genotypes designated as (G1-G10), are distributed worldwide based on genetic diversity. The objective of this study was to provide some sequence data and phylogeny of EG isolates recovered from the Sudanese one-humped camel (Camelus dromedaries). Fifty samples of hydatid cysts were collected from the one- humped camels (Camelus dromedaries) at Taboul slaughter house, central Sudan. DNAs were extracted from protoscolices and/or associated germinal layers of hydatid cysts using a commercial kit. The mitochondrial NADH dehydrogenase subunit 1 (NADH1) gene and the cytochrome C oxidase subunit 1 (cox1) gene were used as targets for polymerase chain reaction (PCR) amplification. The PCR products were purified and partial sequences were generated. Sequences were further examined by sequence analysis and subsequent phylogeny to compare these sequences to those from known strains of EG circulating globally.

Results

The identity of the PCR products were confirmed as NADH1 and cox1 nucleotide sequences using the Basic Local Alignment Search Tool (BLAST) of NCBI (National Center for Biotechnology Information, Bethesda, MD). The phylogenetic analysis showed that 98% (n = 49) of the isolates clustered with Echinococcus canadensis genotype 6 (G6), whereas only one isolate (2%) clustered with Echinococcus ortleppi (G5).

Conclusions

This investigation expands on the existing sequence data generated from EG isolates recovered from camel in the Sudan. The circulation of the cattle genotype (G5) in the one-humped camel is reported here for the first time.
Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle
Authors: Jupe Julietta , Stam Remco , Howden Andrew JM , Morris Jenny A , Zhang Runxuan , Hedley Pete E , Huitema Edgar
Published: June 2013

Background

Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome sequences of both hosts and microbes, little is known about the signal interplay between them during infection. In particular, accurate descriptions of coordinate relationships between host and microbe transcriptional programs are lacking.

Results

Here, we explore the molecular interaction between the hemi-biotrophic broad host range pathogen Phytophthora capsici and tomato. Infection assays and use of a composite microarray allowed us to unveil distinct changes in both P. capsici and tomato transcriptomes, associated with biotrophy and the subsequent switch to necrotrophy. These included two distinct transcriptional changes associated with early infection and the biotrophy to necrotrophy transition that may contribute to infection and completion of the P. capsici lifecycle

Conclusions

Our results suggest dynamic but highly regulated transcriptional programming in both host and pathogen that underpin P. capsici disease and hemi-biotrophy. Dynamic expression changes of both effector-coding genes and host factors involved in immunity, suggests modulation of host immune signaling by both host and pathogen. With new unprecedented detail on transcriptional reprogramming, we can now explore the coordinate relationships that drive host-microbe interactions and the basic processes that underpin pathogen lifestyles. Deliberate alteration of lifestyle-associated transcriptional changes may allow prevention or perhaps disruption of hemi-biotrophic disease cycles and limit damage caused by epidemics.
A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Authors: Philippe Romain , Paux Etienne , Bertin Isabelle , Sourdille Pierre , Choulet Fréderic , Laugier Christel , Šimková Hana , Šafář Jan , Bellec Arnaud , Vautrin Sonia , Frenkel Zeev , Cattonaro Federica , Magni Federica , Scalabrin Simone , Martis Mihaela M , Mayer Klaus FX , Korol Abraham , Bergès Hélène , Doležel Jaroslav , Feuillet Catherine
Published: June 2013

Background

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

Results

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

Conclusions

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
Separating homeologs by phasing in the tetraploid wheat transcriptome
Authors: Krasileva Ksenia V , Buffalo Vince , Bailey Paul , Pearce Stephen , Ayling Sarah , Tabbita Facundo , Soria Marcelo , Wang Shichen ,   IWGS Consortium, Akhunov Eduard , Uauy Cristobal , Dubcovsky Jorge
Published: June 2013

Background

The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs.

Results

A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing.

Conclusions

Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.
Conditionally immortalized stem cell lines from human spinal cord retain regional identity and generate functional V2a interneurons and motorneurons
Authors: Cocks Graham , Romanyuk Nataliya , Amemori Takashi , Jendelova Pavla , Forostyak Oksana , Jeffries Aaron R , Perfect Leo , Thuret Sandrine , Dayanithi Govindan , Sykova Eva , Price Jack
Published: June 2013

Introduction

The use of immortalized neural stem cells either as models of neural development in vitro or as cellular therapies in central nervous system (CNS) disorders has been controversial. This controversy has centered on the capacity of immortalized cells to retain characteristic features of the progenitor cells resident in the tissue of origin from which they were derived, and the potential for tumorogenicity as a result of immortalization. Here, we report the generation of conditionally immortalized neural stem cell lines from human fetal spinal cord tissue, which addresses these issues.

Methods

Clonal neural stem cell lines were derived from 10-week-old human fetal spinal cord and conditionally immortalized with an inducible form of cMyc. The derived lines were karyotyped, transcriptionally profiled by microarray, and assessed against a panel of spinal cord progenitor markers with immunocytochemistry. In addition, the lines were differentiated and assessed for the presence of neuronal fate markers and functional calcium channels. Finally, a clonal line expressing eGFP was grafted into lesioned rat spinal cord and assessed for survival, differentiation characteristics, and tumorogenicity.

Results

We demonstrate that these clonal lines (a) retain a clear transcriptional signature of ventral spinal cord progenitors and a normal karyotype after extensive propagation in vitro, (b) differentiate into relevant ventral neuronal subtypes with functional T-, L-, N-, and P/Q-type Ca2+ channels and spontaneous calcium oscillations, and (c) stably engraft into lesioned rat spinal cord without tumorogenicity.

Conclusions

We propose that these cells represent a useful tool both for the in vitro study of differentiation into ventral spinal cord neuronal subtypes, and for examining the potential of conditionally immortalized neural stem cells to facilitate functional recovery after spinal cord injury or disease.
THE DEVELOPMENT OF Children’s USE OF DISCOURSELIKEIN PEER INTERACTION
Authors: Odato Christopher V.
Published: June 2013

This article examines the use of like as a discourse marker and discourse particle in the spontaneous speech of children age 3-10. Data come from recorded interactions between same-sex peers. Discourse like appeared in the speech of children as young as age 4. Young children used like primarily as a discourse particle preceding determiner phrases. Like was observed in a greater number of syntactic positions as speakers’ ages increased and began to appear in different syntactic positions in approximately the order in which they developed in the language historically. Boys age 6 and younger were less likely than girls to use like and used it less frequently and in fewer syntactic positions than girls. the results suggest that boys and girls follow similar developmental trajectories but that girls become more sophisticated users of like at an earlier age than boys.
Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme
Authors: Curtis Edward A. , Bartel David P.
Published: June 2013

The relationship between genotype and phenotype is often described as an adaptive fitness landscape. In this study, we used a combination of recombination, in vitro selection, and comparative sequence analysis to characterize the fitness landscape of a previously isolated kinase ribozyme. Point mutations present in improved variants of this ribozyme were recombined in vitro in more than 1014different arrangements using synthetic shuffling, and active variants were isolated by in vitro selection. Mutual information analysis of 65 recombinant ribozymes isolated in the selection revealed a rugged fitness landscape in which approximately one-third of the 91 pairs of positions analyzed showed evidence of correlation. Pairs of correlated positions overlapped to form densely connected networks, and groups of maximally connected nucleotides occurred significantly more often in these networks than they did in randomized control networks with the same number of links. The activity of the most efficient recombinant ribozyme isolated from the synthetically shuffled pool was 30-fold greater than that of any of the ribozymes used to build it, which indicates that synthetic shuffling can be a rich source of ribozyme variants with improved properties.
Performance characteristics of consensus approaches for small and minor paroxysmal nocturnal hemoglobinuria clone determination by flow cytometry
Authors: Marinov Iuri , Kohoutová Martina , Tkáčová Vlasta , Pešek Adam , Čermák Jaroslav , Cetkovský Petr
Published: June 2013

Background:Evaluation of paroxysmal nocturnal hemoglobinuria (PNH) clones by flow cytometry (FCM) is not standardized and is associated with consistent inter-laboratory variability.

Methods:In order to rule out the influence of particular approach in generating final results, we analyzed the performance characteristics of individual consensus strategies for small to intermediate (1%–20%) and minor (<1%) PNH clones within the white blood cell (WBC) and red blood cell (RBC) compartments with sensitivity up to 0.1%.

Results:Coefficient of variation (CV) for precision/reproducibility analysis ranged from 0.67%/1.49% to 2.56%/3.09% for granulocytes, from 0.93%/3.09% to 7.76%/12.06% for monocytes and from 0.41%/4.73% to 6.53%/5.1% for RBCs. Coefficient of determination (r2) for linear regression analysis ranged from 0.95 to 0.99, Wilcoxon ranks test showed no statistically significant differences (p>0.05), Bland-Altman analysis demonstrated performance agreement with mean bias ranging from −0.18 to 1.24.

Conclusions:Our results confirmed very good performance characteristics for precision and reproducibility analysis, excellent correlation and favorable agreement between strategies, suggesting that reported inter-laboratory variability is related mainly to incorrect performance and/or insufficient experience with PNH testing by flow cytometry, rather than to relevant limitations of any particular approach.
Implementation of Homotopy Perturbation Method to Solve a Population Balance Model in Fluidized Bed
Authors: Dutta Abhishek , Constales Denis , Van Keer Roger , Heynderickx Geraldine J.
Published: June 2013

Abstract: A particle population balance formulation for a circulating fluidized bed, involving aggregation and breakage of particles, is solved using the homotopy perturbation method (HPM). The homotopy method deforms a difficult problem into a simple problem, which then can be easily solved. The HPM solution is compared with the solution obtained using a standard finite difference method. Using homotopy, a good approximation of the finite difference solution is obtained within a few iteration steps. The results reveal that the homotopy method is an effective and simple tool to solve nonlinear partial integro-differential equations and has a wide scope and applicability to solve complex engineering problems. The reliability of the algorithm is tested using three different feed inlet particle size (diameter) distributions to indicate the robustness of this method.
Two-Dimensional Modeling of an Externally Irradiated Slurry Photoreactor
Authors: Palmisano Giovanni , Loddo Vittorio , Augugliaro Vincenzo
Published: June 2013

A batch cylindrical photocatalytic reactor, externally irradiated by 1–6 UV fluorescent lamps and containing a stirred slurry of polycrystalline TiO2, was modeled by coupling a modified Langmuir–Hinshelwood kinetics together with a two-dimensional light intensity field. The radiation field has been determined on the main assumptions of diffuse radiation, isotropic scattering and negligible backward reflected photon flow. The model has been applied to the photocatalytic oxidation of organic substrates which do not undergo homogeneous photochemical degradation. The model is characterized by the following four parameters: the kinetic constants of substrate adsorption, desorption and degradation and the exponent of the power law expressing the kinetics dependence on the light intensity. The model constants may be determined by applying a simple least-squares best fitting procedure.
Effects of Feed Powder Quantity and Compression Pressure on the Tensile Strength of Eurycoma longifolia Jack Tablets Using Different Binders
Authors: Abdul Hamid Aziana Azlin , Yusof Yus Aniza , Chin Nyuk L. , Mohamed Suhaila , Salleh Faiqa
Published: June 2013

This study investigated the direct compression properties of Eurycoma longifolia Jack tablets using binary mixtures such as microcrystalline cellulose (mcc) and κ-carrageenan (carr). The mixtures were compacted to various compression pressures ranging from 7.5 to 74 MPa at a constant compression speed of 5 mm/min. The tensile strengths of the tablets were determined by a diametral compression test. A linear relationship between the tensile strength and the compression pressure was observed under the conditions of the test; hence, the slopes of the data were obtained by fitting linear trend lines. This paper shows that binary mixtures of 30% mcc and 70% Eurycoma longifolia Jack give the highest values for constant (a slope) compared with the other binary mixtures of both binders. Thus, this approach can be used to develop formulations for Eurycoma longifolia Jack tablets.
Interactive Learning Research: Application of Cognitive Load Theory to Nursing Education
Authors: Hessler Karen L. , Henderson Ann M.
Published: June 2013

The purpose of this research was to investigate the effectiveness of interactive self-paced computerized case study compared to traditional hand-written paper case study on the outcomes of student knowledge, attitude, and retention of the content delivered. Cognitive load theory (CLT) provided the theoretical framework for the study. A quasi-experimental pre-test post-test design with random group assignment was used to measure by self-report survey student cognitive load and interactivity level of the intervention. Student scores on quizzes in semester 1 and post-test follow-up quizzes in semester 3 were assessed for the intervention’s effects on knowledge retention. While no significant statistical differences were found between groups, the students in the interactive case study group rated their case study as more fun and interactive. These students also scored consistently higher on the post-test quiz items in their third semester, showing the viability of using CLT to improve student retention of nursing curricula information.
The Relevance of Indigenous Knowledge for Nursing Curriculum
Authors: Stansfield Della , Browne Annette J.
Published: June 2013

Indigenous knowledge (IK) has the potential to complement the dominant epistemologies central to nursing curricula. Acknowledging IK as a thriving set of worldviews, we discuss how nursing educators might access and integrate IK in ways that are respectful and sustainable. IK is highlighted as an entry point for understanding concepts such as cultural safety, ethical space, and relational practice and as a strength-based approach to learning about Aboriginal people’s health. As with any use of knowledge, consideration must be given to issues of ownership, misappropriation, institutional responsibility, Indigenous protocol, and the creation of partnerships. Recommendations are provided for educators wishing to explore how to incorporate IK into nursing curriculum. With appropriate partnerships, protocols, and processes in place, the incorporation of IK may provide educators and students an opportunity to explore divergent epistemologies, philosophies, and worldviews, thereby encouraging broader perspectives about the world, ways of being, various types of knowledge, and nursing care.
Texture Inpainting Using Covariance in Wavelet Domain
Authors: Biradar Rajkumar L. , Kohir Vinayadatt V.
Published: June 2013

In this article, the covariance of wavelet transform coefficients is used to obtain a texture inpainted image. The covariance is obtained by the maximum likelihood estimate. The integration of wavelet decomposition and maximum likelihood estimate of a group of pixels (texture) captures the best-fitting texture used to fill in the inpainting area. The image is decomposed into four wavelet coefficient images by using wavelet transform. These wavelet coefficient images are divided into small square patches. The damaged region in each coefficient image is filled by searching a similar square patch around the damaged region in that particular wavelet coefficient image by using covariance.
Knowledge-Based Features for Place Classification of Unvoiced Stops
Authors: Karjigi Veena , Rao Preeti
Published: June 2013

The classification of unvoiced stops in consonant–vowel (CV) syllables, segmented from continuous speech, is investigated by features related to speech production. As burst and vocalic transitions contribute to identification of stops in the CV context, features are computed from both regions. Although formants are the truly discriminating articulatory features, their estimation from the speech signal is a challenge especially in unvoiced regions like the release burst of stops. This may be compensated partially by sub-band energy-based features. In this work, formant features from the vocalic region are combined with features from the burst region comprising sub-band energies, as well as features from a formant tracking method developed for unvoiced regions. The overall combination of features at the classifier level obtains an accuracy of 84.4%, which is significantly better than that obtained with solely sub-band features on unvoiced stops in CV syllables of TIMIT.
Building an Academic Community: Minority Serving Institutions and How They Influence Students Pursuing Undergraduate Degrees in STEM
Authors: Flower III Alonzo M.
Published: June 2013

Scientific and technological innovation, according to a report by the National Academy of Sciences (2007), can only be secured with individuals’ success in science, technology, engineering, and mathematics (STEM). Because STEM remains White and male-dominated, programs that focus on increasing the participation of female and minority students has been of great interest to organizations, universities, and national agencies (e.g., National Science Foundation [NSF]) alike. Ways to increase students’ interest, participation, matriculation, and completion of STEM undergraduate degrees have been discussed throughout the scholarly community – from primary to secondary to postsecondary school officials and researchers.
Effect of Reducing Agent on the Dispersion of Pt Nanoparticles on Electrospun Nb0.1Ti0.9O2 Nanofibers
Authors: Alvar Esmaeil Navaei , Zhou Biao , Eichhorn S. Holger
Published: June 2013

Degradation of the catalyst and catalyst support is an essential limitation of polymer electrolyte membrane (PEM) fuel cells containing commercial platinum on carbon catalysts. Catalysts based on platinum nanoparticles coated onto nanostructured TiO2 materials are presently investigated as a more stable and equally cost effective alternative. Reported here is the synthesis of two different Pt/Nb0.1Ti0.9O2 catalysts that were prepared by chemical reduction of H2PtCl6 with either sodium borohydride in ethanolic surfactant solution or ethylene glycol. X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and high-resolution transmission electron microscopy confirmed the deposition of Pt nanoparticles on the surface of the nanofibers and revealed average sizes of 5.4 nm and 7.6 nm for reduction with ethylene glycol and sodium borohydride, respectively. The formation of smaller sized Pt nanoparticles in ethylene glycol is reasoned with the passivation of the nanoparticle surface by glycolic anions. Cyclic voltammetry measurements confirmed a higher electrochemical specific surface area (ESCA) of about 5.45 m2/gPt for the catalyst with smaller nanoparticles while the other catalyst reached only 4.96m2/gPt. Both catalysts retain about 60% of their electrochemically active surface area after 1000 voltammetric cycles in the range of 0.03 to 1.4 V vs. RHE. This relatively high value of activity retention is explained with a strong interaction between Pt nanoparticles and Nb0.1Ti0.9O2 support.
Design of an optical transmission WDM link using plastic optical fibers
Authors: Louro P. , Soares P. , Ferraz H. , Pinho P. , Vieira M.
Published: June 2013

In this paper we present the design of an optical transmission system, using plastic optical fiber (POF), which operates in the visible range of the electromagnetic spectrum. The optical signals are generated by modulated visible LEDs, transmitted through POF and at the reception end a pin-pin photodetector is implemented. A computer simulation tool dedicated to the analysis of optical circuits was used for preliminary analysis of the optical system. The performance of the optical link was analyzed by BER prediction variation on the transmission rate. The tested optical system was assembled using high efficiency LEDs of the same wavelengths, a commercial POF and a pin-pin photodetector based on a-SiC:H/a-SI:H. This detector behaves as an optical filter with controlled wavelength sensitivity. Different optical signals, obtained by adequate modulation of LED optical sources, were coupled into the POF and the combined optical signal at the fiber termination was directed onto the photodetector active area. The output photocurrent was measured with and without optical bias. Results compare the use of a pin-pin transducer device in free space and in a POF transmission link.
A methodology for probabilistic real-time forecasting – an urban case study
Authors: René Jeanne-Rose , Madsen Henrik , Mark Ole
Published: June 2013

The phenomenon of urban flooding due to rainfall exceeding the design capacity of drainage systems is a global problem and can have significant economic and social consequences. The complex nature of quantitative precipitation forecasts (QPFs) from numerical weather prediction (NWP) models has facilitated a need to model and manage uncertainty. This paper presents a probabilistic approach for modelling uncertainty from single-valued QPFs at different forecast lead times. The uncertainty models in the form of probability distributions of rainfall forecasts combined with a sewer model is an important advancement in real-time forecasting at the urban scale. The methodological approach utilized in this paper involves a retrospective comparison between historical forecasted rainfall from a NWP model and observed rainfall from rain gauges from which conditional probability distributions of rainfall forecasts are derived. Two different sampling methods, respectively, a direct rainfall quantile approach and the Latin hypercube sampling-based method were used to determine the uncertainty in forecasted variables (water level, volume) for a test urban area, the city of Aarhus. The results show the potential for applying probabilistic rainfall forecasts and their subsequent use in urban drainage forecasting for estimation of prediction uncertainty.
Identification of dominant sources of sea level pressure for precipitation forecasting over Wales
Authors: Ahmadi Azadeh , Han Dawei
Published: June 2013

Downscaling methods are utilized to assess the effects of large scale atmospheric circulation on local hydrological variables such as precipitation and runoff. In this paper, a methodology of statistical downscaling using a support vector machine (SVM) approach is presented to simulate and predict the precipitation using general circulation model (GCM) data. Due to the complexity and issues related to finding a relationship between the large scale climatic parameters and local precipitation, the climate variables (predictors) affecting monthly precipitation variations over Wales are identified using a combination of the methods including the principal component analysis (PCA), fuzzy clustering, backward selection, forward selection, and Gamma test (GT). The effectiveness of those tools is illustrated through their implementations in the case study. It has been found that although the GT itself fails to identify the best input variable combination, it provides useful and narrowed-down options for further exploration. The best input variable combination is achieved by the GT and forward selection method. This approach can be a useful way for assessing the impacts of climate variables on precipitation forecasting.
Water renewal timescales in an ecological reconstructed lagoon in China
Authors: Gao Xueping , Chen Yuanyuan , Zhang Chen
Published: June 2013

To improve water quality and construct a landscape lagoon in China, an ecological reconstruction plan for the Qilihai Lagoon (Changli County, Hebei) is proposed. A three-dimensional numerical model (EFDC) was used to study the water renewal capacity in the reconstructed lagoon by using residence time, exposure time and connectivity as timescales. The influences of wind and the depth of the tidal inlet of the lagoon on water renewal capacity were also investigated. The results show that the transport and diffusion processes in the lagoon were strongly influenced by wind and the modification of the tidal inlet. The lagoon under a no wind condition exhibited a low water renewal capacity, especially at the end areas (exposure time, 700–1,000 days). The wind action notably enhanced the water renewal capacity in the lagoon, and the exposure times were all lower than 400 days in the whole region. The optimal inlet depth for the water renewal in the lagoon was predicted to be 4.0 m. The connectivity matrices identified which areas of the domain would be most affected by a pollution source under different conditions. This study examines transport and diffusion processes in a reconstructed lagoon, which could be informative for ecological reconstruction planning.