bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building a bioeconomy in the heartland
Authors: Dunham Lee , Ahn Mark , York Anne S. 
Published: March 2012

PurposeThe purpose of this paper is to investigate the gap between the resources required to build a strong biotechnology ecosystem in Nebraska and the perception of resources currently available within the state for doing so.Design/methodology/approachUsing resource‐based theory along with data from a Battelle survey commissioned by BioNebraska, the authors first identify the human and financial capital needed to support a viable biotechnology industry sector, benchmarking with other regions currently undertaking such development. The authors then compare identified resource requirements with data from a survey of BioNebraska members regarding their perceptions of the importance of these resources to, and their availability within, Nebraska.FindingsThis process revealed gaps in several key resource areas that could impede the state's ability to achieve its sector development goals.Practical implicationsIn the authors' view, understanding the gap between resources required and resources available for building a high technology industry sector, as well as benchmarking against the competition, are key first steps in developing successful economic policy.Originality/valueThe paper discusses the implications of gaps in several key resource areas for future success and makes recommendations for possible ways in which Nebraska decision makers might develop necessary resources. Also addressed is the importance of considering the perceptions of key stakeholders and decision makers regarding the resources required for developing knowledge industries such as biotechnology.
A comparative study on the level of efficiency between Islamic and conventional banking systems in Malaysia
Authors: Hisham Yahya Mohamed , Muhammad Junaina , Razak Abdul Hadi Abdul 
Published: March 2012

PurposeThe purpose of this paper is to study the difference (or lack of difference) in the efficiency level of Islamic and conventional banking in Malaysia. Are the Islamic banks performing as good as the conventional banks, even though they are constrained by Islamic tenets?Design/methodology/approachData envelopment analysis is used to measure the efficiency levels of banks in both sectors.FindingsIt is found that there is no significant difference in the level of efficiency between Islamic banks and conventional banks.Research limitations/implicationsThe period of study is only three years, with only two banks which have been operating for more than three years, while the other Islamic banks in this study are just beginning their operation in Islamic banking. The inclusion of foreign banks operating in Malaysia in this analysis might distort the findings, as foreign banks have different capital structures and objectives compared to local ones.Practical implicationsThe paper shows that even though Islamic banks are limited by Islamic tenets in their operations, they are able to maintain a performance that is equivalent to the conventional banks.Originality/valueThe paper makes comparisons of the efficiency levels between two different banking systems.
Prediction of breed composition in an admixed cattle population
Authors: Frkonja A. , Gredler B. , Schnyder U. , Curik I. , Sölkner J. 
Published: March 2012

SummarySwiss Fleckvieh was established in 1970 as a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Breed composition is currently reported based on pedigree information. Information on a large number of molecular markers potentially provides more accurate information. For the analysis, we used Illumina BovineSNP50 Genotyping Beadchip data for 90 pure SI, 100 pure RHF and 305 admixed bulls. The scope of the study was to compare the performance of hidden Markov models, as implemented in structure software, with methods conventionally used in genomic selection [BayesB, partial least squares regression (PLSR), least absolute shrinkage and selection operator (LASSO) variable selection)] for predicting breed composition. We checked the performance of algorithms for a set of 40 492 single nucleotide polymorphisms (SNPs), subsets of evenly distributed SNPs and subsets with different allele frequencies in the pure populations, using FST as an indicator. Key results are correlations of admixture levels estimated with the various algorithms with admixture based on pedigree information. For the full set, PLSR, BayesB and structure performed in a very similar manner (correlations of 0.97), whereas the correlation of LASSO and pedigree admixture was lower (0.93). With decreasing number of SNPs, correlations decreased substantially only for 5% or 1% of all SNPs. With SNPs chosen according to FST, results were similar to results obtained with the full set. Only when using 96 and 48 SNPs with the highest FST, correlations dropped to 0.92 and 0.90 respectively. Reducing the number of pure animals in training sets to 50, 20 and 10 each did not cause a drop in the correlation with pedigree admixture.
Clinical significance of the ratio between FOXP3 positive regulatory T cell and interleukin‐17 secreting cell in renal allograft biopsies with acute T‐cell‐mediated rejection
Authors: Chung Byung H. , Oh Hye J. , Piao Shang G. , Hwang Hyeon S. , Sun In O. , Choi Sun R. , Park Hoon S. , Choi Bum S. , Choi Yeong J. , Park Cheol W. , Kim Yong‐Soo , Cho Mi‐La , Yang Chul W. 
Published: March 2012

SummaryThe aim of this study is to investigate the clinical significance of the ratio between interleukin‐17 (IL‐17) secreting cell and FOXP3‐positive regulatory T cell (FOXP3+ Treg) infiltration in renal allograft tissues with acute T‐cell‐mediated rejection (ATCMR). Fifty‐six patients with biopsy‐proven ATCMR were included. Infiltration of FOXP3+ Treg and IL‐17‐secreting cells was evaluated with immunostaining for FOXP3 or IL‐17 on the biopsy specimens, and the patients were divided into the FOXP3 high group (Log FOXP3/IL‐17 > 0·45) or the IL‐17 high group (Log FOXP3/IL‐17 < 0·45). We compared the allograft function, severity of tissue injury, and clinical outcome between the two groups. In the IL‐17 high group, allograft function was significantly decreased compared with the FOXP3 high group (P < 0·05). The severity of interstitial and tubular injury in the IL‐17 high group was higher than the FOXP3 high group (P < 0·05). The proportions of steroid‐resistant rejection, incomplete recovery and recurrent ATCMR were higher in the IL‐17 high group than in the FOXP3 high group (all indicators, P < 0·05). The IL‐17 high group showed lower 1‐year (54% versus 90%, P < 0·05) and 5‐year (38% versus 85%, P < 0·05) allograft survival rates compared with the FOXP3 high group. Multivariate analysis revealed that the FOXP3/IL‐17 ratio was a significant predictor for allograft outcome. The FOXP3/IL‐17 ratio is a useful indicator for representing the severity of tissue injury, allograft dysfunction and for predicting the clinical outcome of ATCMR.
Microsatellite genotyping reveals end‐Pleistocene decline in mammoth autosomal genetic variation
Authors: NYSTRÖM VERONICA , HUMPHREY JOANNE , SKOGLUND PONTUS , McKEOWN NIALL J. , VARTANYAN SERGEY , SHAW PAUL W. , LIDÉN KERSTIN , JAKOBSSON MATTIAS , BARNES IAN , ANGERBJÖRN ANDERS , LISTER ADRIAN , DALÉN LOVE 
Published: March 2012

AbstractThe last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon‐dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population‐level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north‐eastern Siberia from before 60 000 years ago up until the species’ final disappearance c. 4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9 ka. Simulation‐based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.
Hyper‐Immunoglobulin M Syndrome Type 3 with Normal CD40 Cell Surface Expression
Authors: Karaca N. E. , Forveille M. , Aksu G. , Durandy A. , Kutukculer N. 
Published: March 2012

AbstractMutations of theCD40gene have been found in patients with autosomal recessive hyper‐immunoglobulin M (HIGM) syndrome type 3. Five patients from four unrelated families withCD40mutation have been reported so far. Clinical manifestations include recurrent sinopulmonary infections,Pneumocystis cariniipneumonia andCryptosporidium parvuminfection. Affected patients typically have very low levels of IgG and IgA and normal or high levels of IgM. Flow cytometry analysis of these five patients demonstrated that peripheral blood B lymphocytes lacked expression of surface CD40. Herein, we present two siblings from second‐degree consanguineous Turkish parents with homozygousCD40deletion of four nucleotides including the stop codon resulting presumably to a longer protein. Clinical and immunological profile of these patients is similar to the already reported HIGM3 patients except normal CD40 expression on B lymphocytes. This observation emphasizes the requirement ofCD40mutation analysis for definite diagnosis of HIGM3 despite normal flow cytometric expression of CD40, particularly if the immunological and clinical profile is suggestive for HIGM3.
Inter‐field variability in the microbial communities of hydrothermal vent deposits from a back‐arc basin
Authors: FLORES G. E. , SHAKYA M. , MENEGHIN J. , YANG Z. K. , SEEWALD J. S. , GEOFF WHEAT C. , PODAR M. , REYSENBACH A.‐L. 
Published: March 2012

AbstractDiverse microbial communities thrive on and in deep‐sea hydrothermal vent mineral deposits. However, our understanding of the inter‐field variability in these communities is poor, as limited sampling and sequencing efforts have hampered most previous studies. To explore the inter‐field variability in these communities, we used barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA gene to characterize the archaeal and bacterial communities of over 30 hydrothermal deposit samples from six vent fields located along the Eastern Lau Spreading Center. Overall, the bacterial and archaeal communities of the Eastern Lau Spreading Center are similar to other active vent deposits, with a high diversity of Epsilonproteobacteria and thermophilic Archaea. However, the archaeal and bacterial communities from the southernmost vent field, Mariner, were significantly different from the other vent fields. At Mariner, the epsilonproteobacterial genus Nautilia and the archaeal family Thermococcaceae were prevalent in most samples, while Lebetimonas and Thermofilaceae were more abundant at the other vent fields. These differences appear to be influenced in part by the unique geochemistry of the Mariner fluids resulting from active degassing of a subsurface magma chamber. These results show that microbial communities associated with hydrothermal vent deposits in back‐arc basins are taxonomically similar to those from mid‐ocean ridge systems, but differences in geologic processes between vent fields in a back‐arc basin can influence microbial community structure.
Slow receptor dissociation is not a key factor in the duration of action of inhaled long‐acting β2‐adrenoceptor agonists
Authors: Sykes David A , Charlton Steven J 
Published: March 2012

BACKGROUND AND PURPOSE β2‐Adrenoceptor agonists are important bronchodilators used for the treatment of chronic obstructive pulmonary disease and asthma. Clinical data on β2‐adrenoceptor agonists show a range of onset and duration of action. We have investigated whether the receptor binding kinetics of β2‐adrenoceptor agonists can explain their observed onset of action and duration of effect in the clinic.EXPERIMENTAL APPROACH [3H]‐DHA was used to label β2‐adrenoceptors expressed in CHO‐cell membranes (Kd of 0.084 nM). Competition kinetic experiments were performed in the presence of unlabelled β2 agonists at 37°C in HBSS containing GTP. To determine the kinetic parameters, three concentrations (10, 3 and 1 ×Ki) of the unlabelled compound were employed against a fixed concentration of [3H]‐DHA (0.6 nM).KEY RESULTS The clinically used β2‐adrenoceptor agonists exhibited a range of association and dissociation rates. The kinetic Kd and the competition Ki values of the eight β2‐adrenoceptor agonists examined were strongly correlated, suggesting that the method had produced accurate koff and kon rates. The kinetic on‐rate was highly correlated with equilibrium binding affinity.CONCLUSIONS AND IMPLICATIONS Although the β2‐adrenoceptor agonists displayed a range of kinetic rate parameters, simulations at relevant drug concentrations suggest that receptor kinetics do not play an important role in determining onset of action in the clinic. In addition, it is unlikely that receptor kinetics exert an important influence on the duration of action of these agonists, as indacaterol (once daily dosing) had a shorter residency time at the receptor than salmeterol (twice daily dosing).
Application of collagen hydrogel/sponge scaffold facilitates periodontal wound healing in class II furcation defects in beagle dogs
Authors: Kosen Y. , Miyaji H. , Kato A. , Sugaya T. , Kawanami M. 
Published: March 2012

Kosen Y, Miyaji H, Kato A, Sugaya T, Kawanami M. Application of collagen hydrogel/sponge scaffold facilitates periodontal wound healing in class II furcation defects in beagle dogs. J Periodont Res 2012; 47: 626–634. © 2012 John Wiley & Sons A/SBackground and Objective:  A three‐dimensional scaffold may play an important role in periodontal tissue engineering. We prepared bio‐safe collagen hydrogel, which exhibits properties similar to those of native extracellular matrix. The aim of this study was to examine the effect of implantation of collagen hydrogel/sponge scaffold on periodontal wound healing in class II furcation defects in dogs.Material and Methods:  The collagen hydrogel/sponge scaffold was prepared by injecting collagen hydrogel, cross‐linked to the ascorbate‐copper ion system, into a collagen sponge. Class II furcation defects (of 5 mm depth and 3 mm width) were surgically created in beagle dogs. The exposed root surface was planed and demineralized with EDTA. In the experimental group, the defect was filled with collagen hydrogel/sponge scaffold. In the control group, no implantation was performed. Histometric parameters were evaluated 2 and 4 wk after surgery.Results:  At 2 wk, the collagen hydrogel/sponge scaffold displayed high biocompatibility and biodegradability with numerous cells infiltrating the scaffold. In the experimental group, reconstruction of alveolar bone and cementum was frequently observed 4 wk after surgery. Periodontal ligament tissue was also re‐established between alveolar bone and cementum. Volumes of new bone, new cementum and new periodontal ligament were significantly greater in the experimental group than in the control group. In addition, epithelial down‐growth was suppressed by application of collagen hydrogel.Conclusion:  The collagen hydrogel/sponge scaffold possessed high tissue compatibility and degradability. Implantation of the scaffold facilitated periodontal wound healing in class II furcation defects in beagle dogs.
Odontocete bycatch and depredation in longline fisheries: A review of available literature and of potential solutions
Authors: Hamer Derek J. , Childerhouse Simon J. , Gales Nick J. 
Published: March 2012

AbstractOperational interactions between odontocetes (i.e., toothed whales) and longline gear are a global phenomenon that may threaten the conservation of odontocete populations and the economic viability of longline fisheries. This review attempts to define the issue, summarize the trends and geographical extent of its occurrence over the last half century, explore the potential impact on odontocetes and on fisheries, and describe potential acoustic and physical mitigation solutions.Reports of odontocete bycatch rates are highly variable (between 0.002 and 0.231 individuals killed per set) and at least 20 species may be involved. Information about marine mammal population size, migration patterns and life history characteristics are scarce, although at least one population may be in decline due to losses attributable to longline bycatch. Information about the financial impact of depredation on pelagic longline fisheries is also scarce, although estimates of daily fleet‐wide losses range between US$1,034 and US$8,495 (overall fleet income was not reported). Such biological and financial losses may be unsustainable.Recent developments in acoustic and physical mitigation technologies have yielded mixed results. Acoustic mitigation technologies have no moving parts, although require complex electronics. To date, they are insufficiently developed and their efficacy has been difficult to assess. Physical mitigation technologies generally require complex moving parts, although they are relatively simple to develop and assess. Further development and testing remains necessary before widespread implementation would be possible. Development of these approaches should be prioritized and a “toolbox” of various strategies and solutions should be compiled, because a single panacea to the problem is unlikely to emerge.
Effects of Airflow and Changing Humidity on the Aerosolization of Respirable Fungal Fragments and Conidia of Botrytis cinerea
Authors: Madsen Anne Mette 
Published: March 2012

ABSTRACT

The purpose of this study was to investigate the aerosolization of particles (micro- and macroconidia and fragments) from
Botrytis cinerea
cultures in relation to potential human inhalation in indoor environments. The influence of the following factors on the aerosolization of
B. cinerea
particles was studied: exposure to airflow, relative humidity (rh), changing rh, and plant or building materials. The aerodynamic diameter (
d

a

) and the respirable fraction of the aerosolized particles were determined. Conidia and fragments of
B. cinerea
were not aerosolized as a response to a decrease in the rh. In contrast, both micro- and macroconidia and fungal fragments were aerosolized when exposed to an airflow of 1.5 m s
−1
or 0.5 m s
−1
. Significantly more particles of microconidial size and fragment size were aerosolized at a low rh (18 to 40% rh) than at a higher rh (60 to 80% rh) when cultures were exposed to airflow. The size of the respirable fraction of the aerosolized particles was dependent on the rh but not on the growth material. At high rh, about 30% of the aerosolized particles were of respirable size, while at low rh, about 70% were of respirable size. During low rh, more fungal (1→3)-β-
d
-glucan and chitinase were aerosolized than during high rh. In conclusion, exposure to external physical forces such as airflow is necessary for the aerosolization of particles from
B. cinerea
. The amount and size distribution are highly affected by the rh, and more particles of respirable sizes were aerosolized at low rh than at high rh.
Modular Glucuronoxylan-Specific Xylanase with a Family CBM35 Carbohydrate-Binding Module
Authors: Valenzuela Susana Valeria , Diaz Pilar , Pastor F. I. Javier 
Published: March 2012

ABSTRACT

Xyn30D from the xylanolytic strain
Paenibacillus barcinonensis
has been identified and characterized. The enzyme shows a modular structure comprising a catalytic module family 30 (GH30) and a carbohydrate-binding module family 35 (CBM35). Like GH30 xylanases, recombinant Xyn30D efficiently hydrolyzed glucuronoxylans and methyl-glucuronic acid branched xylooligosaccharides but showed no catalytic activity on arabinose-substituted xylans. Kinetic parameters of Xyn30D were determined on beechwood xylan, showing a

K
m

of 14.72 mg/ml and a
k
cat
value of 1,510 min
−1
. The multidomain structure of Xyn30D clearly distinguishes it from the GH30 xylanases characterized to date, which are single-domain enzymes. The modules of the enzyme were individually expressed in a recombinant host and characterized. The isolated GH30 catalytic module showed specific activity, mode of action on xylan, and kinetic parameters that were similar to those of the full-length enzyme. Computer modeling of the three-dimensional structure of Xyn30D showed that the catalytic module is comprised of a common (β/α)
8
barrel linked to a side-associated β-structure. Several derivatives of the catalytic module with decreasing deletions of this associated structure were constructed. None of them showed catalytic activity, indicating the importance of the side β-structure in the catalysis of Xyn30D. Binding properties of the isolated carbohydrate-binding module were analyzed by affinity gel electrophoresis, which showed that the CBM35 of the enzyme binds to soluble glucuronoxylans and arabinoxylans. Analysis by isothermal titration calorimetry showed that CBM35 binds to glucuronic acid and requires calcium ions for binding. Occurrence of a CBM35 in a glucuronoxylan-specific xylanase is a differential trait of the enzyme characterized.
EscA Is a Crucial Component of the Type III Secretion System of Enteropathogenic Escherichia coli
Authors: Sal-Man Neta , Biemans-Oldehinkel Esther , Sharon David , Croxen Matthew A. , Scholz Roland , Foster Leonard J. , Finlay B. Brett 
Published: March 2012

ABSTRACT

The virulence of many Gram-negative pathogens is associated with type III secretion systems (T3SSs), which deliver virulence effector proteins into the cytoplasm of host cells. Components of enteropathogenic
Escherichia coli
(EPEC) T3SS are encoded within the locus of enterocyte effacement (LEE). While most LEE-encoded T3SS proteins in EPEC have assigned names and functions, a few of them remain poorly characterized. Here, we studied a small LEE-encoded protein, Orf15, that shows no homology to other T3SS/flagellar proteins and is only present in attaching and effacing pathogens, including enterohemorrhagic
E. coli
and
Citrobacter rodentium
. Our findings demonstrated that it is essential for type III secretion (T3S) and that it is localized to the periplasm and associated with the inner membrane. Membrane association was driven by the N-terminal 19 amino acid residues, which were also shown to be essential for T3S. Consistent with its localization, Orf15 was found to interact with the EPEC T3SS outer membrane ring component, EscC, which was previously shown to be embedded within the outer membrane and protruding into the periplasmic space. Interestingly, we found that the predicted coiled-coil structure of Orf15 is critical for the protein's function. Overall, our findings suggest that Orf15 is a structural protein that contributes to the structural integrity of the T3S complex, and therefore we propose to rename it EscA.
Dreams, Genius Loci and Structures
Authors: Samyn Philippe 
Published: March 2012

Structures and services are profoundly characteristic of the designs of Samyn and Partners in a quest for constructions that tally with the client's dreams and wishes and are in harmony with the genius loci (the special atmosphere of a particular place). The development of my theory on volume and displacement indicators permanently fuels our structural design work. Projects that did not come to fruition also foster research and are therefore just as important as those that were actually built. The approach will thus be illustrated by some projects as well as completed constructions.