bluuebunny/crossref_metadata_2025_split huggingface dataset:
The economic performance of jatropha, cassava and Eucalyptus production systems for energy in an East African smallholder setting
Authors: van Eijck Janske , Smeets Edward , Faaij André 
Published: May 2012

AbstractThis study evaluates the potential economic feasibility of three smallholder energy crop production systems (jatropha, cassava and eucalyptus) under typical semi‐arid conditions in Eastern Africa. This feasibility is determined by assessing net present values (NPV), internal rates of return (IRR), benefit‐cost ratios (BCR) and payback periods (PBP). In addition, the production costs are compared to the costs of reference energy systems, petrol, diesel and pellets. Low and intermediate input systems are considered and specific attention is paid to the opportunity cost of labour, by considering both family labour (no labour costs) and hired labour. The results show that all family labour settings have positive NPVs and high IRR and BCR values. Moreover, cassava has the highest family labour NPV (2900–5800US$ ha−1) and the shortest PBP, but the required investment costs are high in comparision with the other crops. If hired labour is used, the NPV of eucalyptus is highest (380–1400$/ha−1), and it is also the least sensitive to changes in wages and yields. Jatropha performs best only for the indicator IRR and only with family labour or low labour opportunity costs. The analysis and comparison of bioenergy production costs shows that eucalyptus pellets (2.6–3.1$ GJ−1) are competitive compared with reference pellets at current market prices (5$ GJ−1). Jatropha SVO (19$ GJ−1) and cassava ethanol (19–36$ GJ−1) are only competitive with fossil diesel (21$ GJ−1) and petrol (25$ GJ−1) in a family labour setting. At current values jatropha biodiesel (24–37$ GJ−1) is not competitive. The economic performance is sensitive to variations in crop yields and yield data are highly uncertain. However, this study demonstrates that there is considerable potential for increasing the economic performance by further improvements in yield, harvesting efficiency and conversion efficiency as well as reductions in transport and packaging costs.
Simultaneous chromatic and luminance human electroretinogram responses
Authors: Parry Neil R. A. , Murray Ian J. , Panorgias Athanasios , McKeefry Declan J. , Lee Barry B. , Kremers Jan 
Published: May 2012

Key points
It has recently been shown that, with careful control over stimulation, the electroretinogram (ERG) can reflect the properties of the post‐receptoral parvocellular (P) and magnocellular (M) pathways, which are thought of as the respective substrates for red–green colour and luminance vision.
Using a novel compound stimulus, which contains red–green colour information at the fundamental frequency and luminance information at the second harmonic, we were able to simultaneously record colour and luminance ERGs.
In trichromats, the temporal tuning curves of these components reflected the known properties of the P and M systems, whereas the dichromats showed negligible chromatic response but a normal achromatic response.
Parallel retinal processing that is relevant for vision can be reflected in the ERG.
Abstract  The parallel processing of information forms an important organisational principle of the primate visual system. Here we describe experiments which use a novel chromatic–achromatic temporal compound stimulus to simultaneously identify colour and luminance specific signals in the human electroretinogram (ERG). Luminance and chromatic components are separated in the stimulus; the luminance modulation has twice the temporal frequency of the chromatic modulation. ERGs were recorded from four trichromatic and two dichromatic subjects (1 deuteranope and 1 protanope). At isoluminance, the fundamental (first harmonic) response was elicited by the chromatic component in the stimulus. The trichromatic ERGs possessed low‐pass temporal tuning characteristics, reflecting the activity of parvocellular post‐receptoral mechanisms. There was very little first harmonic response in the dichromats’ ERGs. The second harmonic response was elicited by the luminance modulation in the compound stimulus and showed, in all subjects, band‐pass temporal tuning characteristic of magnocellular activity. Thus it is possible to concurrently elicit ERG responses from the human retina which reflect processing in both chromatic and luminance pathways. As well as providing a clear demonstration of the parallel nature of chromatic and luminance processing in the human retina, the differences that exist between ERGs from trichromatic and dichromatic subjects point to the existence of interactions between afferent post‐receptoral pathways that are in operation from the earliest stages of visual processing.
Levofloxacin Inhibits Rhinovirus Infection in Primary Cultures of Human Tracheal Epithelial Cells
Authors: Yamaya Mutsuo , Nishimura Hidekazu , Hatachi Yukimasa , Yasuda Hiroyasu , Deng Xue , Sasaki Takahiko , Mizuta Katsumi , Kubo Hiroshi , Nagatomi Ryoichi 
Published: May 2012

ABSTRACT
Respiratory virus infections, including infections with rhinoviruses (RVs), are related to exacerbations of chronic obstructive pulmonary disease (COPD). A new quinolone antibiotic, levofloxacin (LVFX), has been used to treat bacterial infections that cause COPD exacerbations as well as bacterial infections that are secondary to viral infection in COPD patients. However, the inhibitory effects of LVFX on RV infection and RV infection-induced airway inflammation have not been studied. We examined the effects of LVFX on type 14 rhinovirus (RV14) (a major human RV) infection of human tracheal epithelial cells pretreated with LVFX. LVFX pretreatment reduced the RV14 titer, the level of cytokines in the supernatant, the amount of RV14 RNA in the cells after RV14 infection, and the cells' susceptibility to RV14 infection. LVFX pretreatment decreased the mRNA level of intercellular adhesion molecule 1 (ICAM-1), a receptor for RV14, in the cells and the concentration of the soluble form of ICAM-1 in the supernatant before RV14 infection. LVFX pretreatment also decreased the number and the fluorescence intensity of the acidic endosomes from which RV14 RNA enters the cytoplasm. LVFX pretreatment inhibited the activation of nuclear factor κB proteins, including p50 and p65, in nuclear extracts. LVFX pretreatment did not reduce the titers of RV2 (a minor human RV) but reduced the titers of RV15 (a major human RV). These results suggest that LVFX inhibits major-group rhinovirus infections in part by reducing ICAM-1 expression levels and the number of acidic endosomes. LVFX may also modulate airway inflammation in rhinoviral infections.
2-Alkylaminoethyl-1,1-Bisphosphonic Acids Are Potent Inhibitors of the Enzymatic Activity of Trypanosoma cruzi Squalene Synthase
Authors: Rodrígues-Poveda Carlos A. , González-Pacanowska Dolores , Szajnman Sergio H. , Rodríguez Juan B. 
Published: May 2012

ABSTRACT

As part of our efforts aimed at searching for new antiparasitic agents, the effect of representative 2-alkylaminoethyl-1,1-bisphosphonic acids on
Trypanosoma cruzi
squalene synthase (
Tc
SQS) was investigated. These compounds had proven to be potent inhibitors of
T. cruzi
. This cellular activity had been associated with an inhibition of the enzymatic activity of
T. cruzi
farnesyl diphosphate synthase. 2-Alkylaminoethyl-1,1-bisphosphonic acids appear to have a dual action, since they also inhibit
Tc
SQS at the nanomolar range.
Production of the Antimicrobial Secondary Metabolite Indigoidine Contributes to Competitive Surface Colonization by the Marine Roseobacter Phaeobacter sp. Strain Y4I
Authors: Cude W. Nathan , Mooney Jason , Tavanaei Arash A. , Hadden Mary K. , Frank Ashley M. , Gulvik Christopher A. , May Amanda L. , Buchan Alison 
Published: May 2012

ABSTRACT

Members of the
Roseobacter
lineage of marine bacteria are prolific surface colonizers in marine coastal environments, and antimicrobial secondary metabolite production has been hypothesized to provide a competitive advantage to colonizing roseobacters. Here, we report that the roseobacter
Phaeobacter
sp. strain Y4I produces the blue pigment indigoidine via a nonribosomal peptide synthase (NRPS)-based biosynthetic pathway encoded by a novel series of genetically linked genes:
igiBCDFE
. A Tn
5
-based random mutagenesis library of Y4I showed a perfect correlation between indigoidine production by the
Phaeobacter
strain and inhibition of
Vibrio fischeri
on agar plates, revealing a previously unrecognized bioactivity of this molecule. In addition, igiD null mutants (igiD encoding the indigoidine NRPS) were more resistant to hydrogen peroxide, less motile, and faster to colonize an artificial surface than the wild-type strain. Collectively, these data provide evidence for pleiotropic effects of indigoidine production in this strain. Gene expression assays support phenotypic observations and demonstrate that
igiD
gene expression is upregulated during growth on surfaces. Furthermore, competitive cocultures of
V. fischeri
and Y4I show that the production of indigoidine by Y4I significantly inhibits colonization of
V. fischeri
on surfaces. This study is the first to characterize a secondary metabolite produced by an NRPS in roseobacters.
Microbial Degradation of 2,4-Dichlorophenoxyacetic Acid on the Greenland Ice Sheet
Authors: Stibal Marek , Bælum Jacob , Holben William E. , Sørensen Sebastian R. , Jensen Anders , Jacobsen Carsten S. 
Published: May 2012

ABSTRACT

The Greenland ice sheet (GrIS) receives organic carbon (OC) of anthropogenic origin, including pesticides, from the atmosphere and/or local sources, and the fate of these compounds in the ice is currently unknown. The ability of supraglacial heterotrophic microbes to mineralize different types of OC is likely a significant factor determining the fate of anthropogenic OC on the ice sheet. Here we determine the potential of the microbial community from the surface of the GrIS to mineralize the widely used herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). Surface ice cores were collected and incubated for up to 529 days in microcosms simulating
in situ
conditions. Mineralization of side chain- and ring-labeled [
14
C]2,4-D was measured in the samples, and quantitative PCR targeting the
tfdA
genes in total DNA extracted from the ice after the experiment was performed. We show that the supraglacial microbial community on the GrIS contains microbes that are capable of degrading 2,4-D and that they are likely present in very low numbers. They can mineralize 2,4-D at a rate of up to 1 nmol per m
2
per day, equivalent to ∼26 ng C m
−2
day
−1
. Thus, the GrIS should not be considered a mere reservoir of all atmospheric contaminants, as it is likely that some deposited compounds will be removed from the system via biodegradation processes before their potential release due to the accelerated melting of the ice sheet.
Accessing the Inaccessible: Molecular Tools for Bifidobacteria
Authors: Sun Zhongke , Baur Annika , Zhurina Daria , Yuan Jing , Riedel Christian U. 
Published: May 2012

ABSTRACTBifidobacteria are an important group of the human intestinal microbiota that have been shown to exert a number of beneficial probiotic effects on the health status of their host. Due to these effects, bifidobacteria have attracted strong interest in health care and food industries for probiotic applications and several species are listed as so-called “generally recognized as safe” (GRAS) microorganisms. Moreover, recent studies have pointed out their potential as an alternative or supplementary strategy in tumor therapy or as live vaccines. In order to study the mechanisms by which these organisms exert their beneficial effects and to generate recombinant strains that can be used as drug delivery vectors or live vaccines, appropriate molecular tools are indispensable. This review provides an overview of the currently available methods and tools to generate recombinant strains of bifidobacteria. The currently used protocols for transformation of bifidobacteria, as well as replicons, selection markers, and determinants of expression, will be summarized. We will further discuss promoters, terminators, and localization signals that have been used for successful generation of expression vectors.
Cold Atmospheric Air Plasma Sterilization against Spores and Other Microorganisms of Clinical Interest
Authors: Klämpfl Tobias G. , Isbary Georg , Shimizu Tetsuji , Li Yang-Fang , Zimmermann Julia L. , Stolz Wilhelm , Schlegel Jürgen , Morfill Gregor E. , Schmidt Hans-Ulrich 
Published: May 2012

ABSTRACT

Physical cold atmospheric surface microdischarge (SMD) plasma operating in ambient air has promising properties for the sterilization of sensitive medical devices where conventional methods are not applicable. Furthermore, SMD plasma could revolutionize the field of disinfection at health care facilities. The antimicrobial effects on Gram-negative and Gram-positive bacteria of clinical relevance, as well as the fungus
Candida albicans
, were tested. Thirty seconds of plasma treatment led to a 4 to 6 log
10
CFU reduction on agar plates.
C. albicans
was the hardest to inactivate. The sterilizing effect on standard bioindicators (bacterial endospores) was evaluated on dry test specimens that were wrapped in Tyvek coupons. The experimental
D
23
°
C
values for
Bacillus subtilis
,
Bacillus pumilus
,
Bacillus atrophaeus
, and
Geobacillus stearothermophilus
were determined as 0.3 min, 0.5 min, 0.6 min, and 0.9 min, respectively. These decimal reduction times (
D
values) are distinctly lower than
D
values obtained with other reference methods. Importantly, the high inactivation rate was independent of the material of the test specimen. Possible inactivation mechanisms for relevant microorganisms are briefly discussed, emphasizing the important role of neutral reactive plasma species and pointing to recent diagnostic methods that will contribute to a better understanding of the strong biocidal effect of SMD air plasma.
Galacturonic Acid Inhibits the Growth of Saccharomyces cerevisiae on Galactose, Xylose, and Arabinose
Authors: Huisjes Eline H. , de Hulster Erik , van Dam Jan C. , Pronk Jack T. , van Maris Antonius J. A. 
Published: May 2012

ABSTRACT

The efficient fermentation of mixed substrates is essential for the microbial conversion of second-generation feedstocks, including pectin-rich waste streams such as citrus peel and sugar beet pulp. Galacturonic acid is a major constituent of hydrolysates of these pectin-rich materials. The yeast
Saccharomyces cerevisiae
, the main producer of bioethanol, cannot use this sugar acid. The impact of galacturonic acid on alcoholic fermentation by
S. cerevisiae
was investigated with anaerobic batch cultures grown on mixtures of glucose and galactose at various galacturonic acid concentrations and on a mixture of glucose, xylose, and arabinose. In cultures grown at pH 5.0, which is well above the pK
a
value of galacturonic acid (3.51), the addition of 10 g · liter
−1
galacturonic acid did not affect galactose fermentation kinetics and growth. In cultures grown at pH 3.5, the addition of 10 g · liter
−1
galacturonic acid did not significantly affect glucose consumption. However, at this lower pH, galacturonic acid completely inhibited growth on galactose and reduced galactose consumption rates by 87%. Additionally, it was shown that galacturonic acid strongly inhibits the fermentation of xylose and arabinose by the engineered pentose-fermenting
S. cerevisiae
strain IMS0010. The data indicate that inhibition occurs when nondissociated galacturonic acid is present extracellularly and corroborate the hypothesis that a combination of a decreased substrate uptake rate due to competitive inhibition on Gal2p, an increased energy requirement to maintain cellular homeostasis, and/or an accumulation of galacturonic acid 1-phosphate contributes to the inhibition. The role of galacturonic acid as an inhibitor of sugar fermentation should be considered in the design of yeast fermentation processes based on pectin-rich feedstocks.
Identification and Functional Characterization of Rca1, a Transcription Factor Involved in both Antifungal Susceptibility and Host Response in Candida albicans
Authors: Vandeputte Patrick , Pradervand Sylvain , Ischer Françoise , Coste Alix T. , Ferrari Sélène , Harshman Keith , Sanglard Dominique 
Published: May 2012

ABSTRACT

The identification of novel transcription factors associated with antifungal response may allow the discovery of fungus-specific targets for new therapeutic strategies. A collection of 241
Candida albicans
transcriptional regulator mutants was screened for altered susceptibility to fluconazole, caspofungin, amphotericin B, and 5-fluorocytosine. Thirteen of these mutants not yet identified in terms of their role in antifungal response were further investigated, and the function of one of them, a mutant of orf19.6102 (
RCA1
), was characterized by transcriptome analysis. Strand-specific RNA sequencing and phenotypic tests assigned Rca1 as the regulator of hyphal formation through the cyclic AMP/protein kinase A (cAMP/PKA) signaling pathway and the transcription factor Efg1, but also probably through its interaction with a transcriptional repressor, most likely Tup1. The mechanisms responsible for the high level of resistance to caspofungin and fluconazole observed resulting from
RCA1
deletion were investigated. From our observations, we propose that caspofungin resistance was the consequence of the deregulation of cell wall gene expression and that fluconazole resistance was linked to the modulation of the cAMP/PKA signaling pathway activity. In conclusion, our large-scale screening of a
C. albicans
transcription factor mutant collection allowed the identification of new effectors of the response to antifungals. The functional characterization of Rca1 assigned this transcription factor and its downstream targets as promising candidates for the development of new therapeutic strategies, as Rca1 influences host sensing, hyphal development, and antifungal response.
Expansion of Variant Diversity Associated with a High Prevalence of Pathogen Strain Superinfection under Conditions of Natural Transmission
Authors: Ueti Massaro W. , Tan Yunbing , Broschat Shira L. , Castañeda Ortiz Elizabeth J. , Camacho-Nuez Minerva , Mosqueda Juan J. , Scoles Glen A. , Grimes Matthew , Brayton Kelly A. , Palmer Guy H. 
Published: May 2012

ABSTRACT

Superinfection occurs when a second, genetically distinct pathogen strain infects a host that has already mounted an immune response to a primary strain. For antigenically variant pathogens, the primary strain itself expresses a broad diversity of variants over time. Thus, successful superinfection would require that the secondary strain express a unique set of variants. We tested this hypothesis under conditions of natural transmission in both temperate and tropical regions where, respectively, single-strain infections and strain superinfections of the tick-borne pathogen
Anaplasma marginale
predominate. Our conclusion that strain superinfection is associated with a significant increase in variant diversity is supported by progressive analysis of variant composition: (i) animals with naturally acquired superinfection had a statistically significantly greater number of unique variant sequences than animals either experimentally infected with single strains or infected with a single strain naturally, (ii) the greater number of unique sequences reflected a statistically significant increase in primary structural diversity in the superinfected animals, and (iii) the increase in primary structural diversity reflected increased combinations of the newly identified hypervariable microdomains. The role of population immunity in establishing temporal and spatial patterns of infection and disease has been well established. The results of the present study, which examined strain structure under conditions of natural transmission and population immunity, support that high levels of endemicity also drive pathogen divergence toward greater strain diversity.
DivIVA-Mediated Polar Localization of ComN, a Posttranscriptional Regulator of Bacillus subtilis
Authors: dos Santos Valquiria Tiago , Bisson-Filho Alexandre W. , Gueiros-Filho Frederico J. 
Published: May 2012

ABSTRACT

ComN (YrzD) is a small, 98-amino-acid protein recently shown to be involved in the posttranscriptional control of the late competence
comE
operon in
Bacillus subtilis
. We show here that ComN localizes to the division site and cell poles in a DivIVA-dependent fashion. Yeast two-hybrid and glutathione
S
-transferase pulldown experiments showed that ComN interacts directly with DivIVA. ComN is not essential for the polar assembly of the core competence DNA uptake machinery. Nevertheless, polar localization of ComN should play some role in competence acquisition because delocalization of ComN leads to a small reduction in competence efficiency. We found that ComN promotes the accumulation of its target
comE
mRNA to septal and polar sites. Thus, we speculate that localized translation of ComE proteins may be required for efficient competence development. Our results underscore the versatility of DivIVA as a promoter of the differentiation of bacterial poles and demonstrate that the repertoire of polarly localized molecules in
B. subtilis
is broad, including a regulator of gene expression and its target mRNA. Moreover, our findings suggest that mRNA localization may play a role in the subcellular organization of bacteria.
The relationship between walking speed and changes in cardiovascular risk factors during a 12-day walking tour to Santiago de Compostela: a cohort study
Authors: Bemelmans Remy H H , Blommaert Paulus P , Wassink Annemarie M J , Coll Blai , Spiering Wilko , van der Graaf Yolanda , Visseren Frank L J 
Published: May 2012

ObjectivesPhysical exercise has beneficial effects on cardiovascular risk factors. Knowledge about the effect of exercise intensity, specifically walking speed, on cardiovascular risk factors is limited. We report the relationship between walking speed and changes in cardiovascular risk factors in participants of a 12-day walking tour to Santiago de Compostela.DesignProspective cohort study.SettingSingle-centre study with healthy middle-aged volunteers.ParticipantsHealthy middle-aged men (n=15) and women (n=14). Subjects using lipid-lowering medication were excluded.InterventionParticipants walked 281±10 km of the classical route to Santiago de Compostela in 12 days in 2009.Primary and secondary outcome measuresWalking speed was recorded and blood pressure, weight, waist circumference, lipids and glucose were measured every other day. Changes in risk factors were compared between gender-pooled groups with faster and slower walking speed. Second, the relationship between walking speed and changes in risk factors was quantified using a linear mixed effects model.ResultsIn the faster walking speed (4.6±0.2 km/h) group, high-density lipoprotein cholesterol (HDL-c) increased more than in the slower walking speed (4.1±0.2 km/h) group (difference in change between groups: 0.20; 95% CI −0.02 to 0.42 mmol/l), while low-density lipoprotein cholesterol (LDL-c) and total cholesterol decreased more in the slower walking speed group (differences in changes between groups: LDL-c: −0.50; 95% CI −0.88 to −0.12 mmol/l and total cholesterol: −0.75; 95% CI −1.19 to −0.31 mmol/l). A 1 km/h higher walking speed was related to an increase in HDL-c (0.24; 95% CI 0.12 to 0.30 mmol/l), LDL-c (0.18; 95% CI −0.16 to 0.42 mmol/l) and total cholesterol (0.36; 95% CI 0.12 to 0.60 mmol/l), adjusted for age, gender, smoking, body mass index and heart rate, during the whole walking tour.ConclusionsWalking the same distance faster improves HDL-c more, while LDL-c and total cholesterol decrease more with lower walking speed independent of changes in body weight in healthy middle-aged subjects.