bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovery Learning and Teaching with Electronic Corpora in an Advanced German Grammar Course
Authors: Vyatkina Nina
Published: May 2013

This study describes the design and implementation of a usage‐based and corpus‐based advanced German grammar course. Teaching materials for the course included DWDS, or Digitales Wörterbuch der deutschen Sprache: a large, representative, free and publicly available corpus of contemporary German texts. The article outlines specific theoretically informed principles for course design and presents a logical progression of corpus‐based grammar‐teaching activities as used in this course. It also reports participants’ post‐course reactions which were very positive. The article contains practical recommendations for educators interested in trying out corpus‐based activities for teaching German grammar at different proficiency levels as well as to different participant groups. Furthermore, it promotes a more holistic perspective toward grammar as a meaning‐making resource compatible with innovative approaches to grammar pedagogy.
Meningococcal carriage in the African meningitis belt
Authors:   The MenAfriCar consortium
Published: May 2013

A meningococcal serogroup A polysaccharide/tetanus toxoid conjugate vaccine (PsA‐TT) (MenAfriVac™) is being deployed in countries of the African meningitis belt. Experience with other polysaccharide/protein conjugate vaccines has shown that an important part of their success has been their ability to prevent the acquisition of pharyngeal carriage and hence to stop transmission and induce herd immunity. If PsA‐TT is to achieve the goal of preventing epidemics, it must be able to prevent the acquisition of pharyngeal carriage as well as invasive meningococcal disease and whether PsA‐TT can prevent pharyngeal carriage needs to be determined. To address this issue, a consortium (the African Meningococcal Carriage (MenAfriCar) consortium) was established in 2009 to investigate the pattern of meningococcal carriage in countries of the African meningitis belt prior to and after the introduction of PsA‐TT. This article describes how the consortium was established, its objectives and the standardised field and laboratory methods that were used to achieve these objectives. The experience of the MenAfriCar consortium will help in planning future studies on the epidemiology of meningococcal carriage in countries of the African meningitis belt and elsewhere.
Development and evaluation of a model for predicting Lolium rigidum emergence in winter cereal crops in the Mediterranean area
Authors: Izquierdo J , Bastida F , Lezaún J M , Sánchez del Arco M J , Gonzalez‐Andujar J L
Published: May 2013

Lolium rigidum is an extremely competitive and prevalent grass weed in cereal fields of Mediterranean areas. The proper timing of control measures is a prerequisite to maximising herbicide efficacy, in terms of both improved control and reduced herbicide inputs. The development of models to predict emergence flushes will contribute to this goal. Pooled cumulative emergence data obtained during three seasons from a cereal field were used to develop a Gompertz model. This explained relative seedling emergence from crop sowing onwards as a function of: (i) standard soil thermal time accumulation (TT) with a base temperature of 1.8°C and (ii) soil thermal time accumulation corrected for soil moisture (cTT). For the latter, no thermal time accumulation was computed for days in which the soil water balance within the upper 10‐cm soil layer indicated no water available for plants, because evapotranspiration was greater than rainfall plus the stored water remaining from the previous day. The model was validated with six datasets from four different sites and seasons. Compared with TT, the model based on cTT showed better performance in predicting L. rigidum emergence, particularly in predicting the end of emergence. Complemented with in‐field observations to minimise deviations, the model may be used as a predictive tool to better control this weed in dryland cereal fields of Mediterranean climate areas.
Phylogeny and systematics of Old World serotine bats (genus Eptesicus, Vespertilionidae, Chiroptera): an integrative approach
Authors: Juste Javier , Benda Petr , Garcia‐Mudarra Juan Luis , Ibáñez Carlos
Published: May 2013

Integrative taxonomy aims to document biodiversity by incorporating all useful characters to increase confidence in hypotheses about phylogenetic relationships. In this study, we combine data obtained independently from morphology, two maternally inherited mtDNA genes and two biparentally inherited nuDNA genes to make phylogenetic and taxonomic hypotheses about the Palaearctic members of the bat genus Eptesicus (Vespertilionidae). This genus is distributed worldwide (except for Antarctica) and is highly diversified, presenting one of the most entangled taxonomic puzzles among all mammals. Our results support restoring the genus Rhyneptesicus and separating E. isabellinus and E. pachyomus from E. serotinus and E. ognevi and E. anatolicus from E. bottae. Differences in the phylogenetic hypotheses from mtDNA and nuDNA data suggest the occurrence within E. serotinus of evolutionary processes such as mtDNA capture and secondary contacts between partially differentiated ecomorphs. These two evolutionary processes deserve more in‐depth studies within the group.
Damage to spruce stands in the Kysuce and Orava region determined from the National Forest Inventory
Authors: Šebeň Vladimír , Bošeľa Michal , Konôpka Bohdan
Published: May 2013

An analysis of the status of spruce stands in the Kysuce and Orava region was performed and their health condition was compared to the spruce forest constitution in the rest of Slovakia. For this purpose, the inventory plots established within the first circle of National Forest Inventory (NFI) in 2005 and 2006 were used. The Kysuce and Orava regions significantly differ from the rest of Slovak forests by its high proportion of spruce. The health status of the spruce stands in these regions, according to the salvage felling as a result of the damage caused prevailingly by stem rotting and bark beetles appears worse than in the rest of Slovakia. The analysis showed that not only the acute damage of spruce stands (insects) but also the chronic damage of trees (rotting, mechanical damage during logging) is more serious in these regions than in the rest of Slovakia. The browsing caused by deer game (data does not include young stands) in both regions as well as in the rest of Slovakia seems to be low and not so serious compared to the previously mentioned types of damage. Other sorts of damage (stem breakage, standing dead trees, or damage by insect) have also small proportion. More detailed analyses of NFI data with acceptable precision were possible only for most frequent kinds of damages such as stem rotting and damage by logging. The results showed the frequency of rotting tended to be higher with increasing stand age. Influence of altitude on the frequency of the damage was not evident. Since variability of selected types of damage on spruce forest in the target regions was high, all results are presented with the precision at 68 % confidence interval.
Various content of manganese in selected forest tree species and plants in the undergrowth
Authors: Kula E. , Hrdlička P. , Hedbávný J. , Švec P.
Published: May 2013

The content of manganese in foliage and other parts of trees and undergrowth plants were monitored in the site with heavy level of manganese in soil. The difference between the species and also between parts of the same plant was confirmed. Manganese was accumulated from the soil environment, especially by the speciesBetula pendula, Fagus sylvatica, Sorbus aucuparia, Larix decidua, Vaccinium myrtilus, Rubus ideus, Rubus fruticosus and Digitalis purpurea, where the content of manganese in leaves exceeded 5000 mg kg-1.
Earthworms (Lumbricidae) from a surface layer and wireworms (Elateridae) of forest stands in the anthropogenically-disturbed area of the Děčínská vrchovina Upland (Czech Republic)
Authors: Kula E. , Švarc P.
Published: May 2013

In the area negatively affected by air pollution in the past, the earthworm assemblages and the occurrence of wireworms (Elateridae) in forest ecosystems were evaluated in relation to site conditions. From soil samples taken in 38 stands (Fagus, Betula, Alnus, Quercus, Pinus, Larix, Abies) earthworms and wireworms were extracted by means of Tullgren funnels. Eudominant species (Dendrobaena vejdovskyi, D. octaedra, D. illyrica) are typical representatives of forest ecosystems of the Ore Mountains. Relationships were proved to a tree species creating a forest stand and the pH of Ah horizon. The area is characterized by the generally low diversity of earthworms particularly in young stands of beech and Norway spruce. Faunistically rich sites occurred only in a mixed stand (birch, mountain ash, larch) and in a blue spruce monoculture. Reduced abundance of earthworms in the organic matter of mounds was surprising. The type/form of soil preparation, forest weed cover and the age of trees did not affect significantly the earthworm assemblages. The abundance of wireworms was increased in pine and larch stands and reduced in alder and blue spruce stands. The increasing pH value negatively affected the abundance of wireworms.
Time trends of SO42- concentration and deposition of S-SO42- in precipitation, throughfall and soil solutions in a beech forest stand in the Štiavnické vrchy Mts.
Authors: Janík Rastislav , Bublinec E. , Dubová M.
Published: May 2013

The work summarises the data assembled and compared during a 22-year research on deposition and concentrations of sulphate sulphur in soil solutions in a submountain beech forest in the Štiavnické vrchy Mts. We also investigated the sulphur amounts in throughfall and in precipitation water in open area. The average sulphur concentration in atmospheric precipitation on the open plot was 14.92 mg.l-1, in the forest stand 17.13 mg.l-1. The sulphur deposition in soil increased with increasing depth: from the average of 18.9 kg.ha-1.y-1 in the surface humus to 26.7 kg.ha-1.y-1 in a depth of 0.25 m. The average concentration in the surface humus was 19.06 mg.l-1 , at a depth of 0.25 m it was 29.32 mg.l-1. The total amount deposed in the soil over the whole study period was 587.1 kg.ha-1S-SO42-. The annual dynamics exhibited the highest SO42- concentration values in the winter and spring, the lowest values were recorded in the summer and autumn. Regression analysis revealed that the sulphur content in soil solutions was very significantly influenced by sulphur content in atmospheric deposition. There has also been confirmed a major impact of rainfall total on sulphur content in precipitation water as well as in soil solutions. In general, it has been confirmed a decreasing trend for sulphur in atmospheric deposition
Pitfalls for Accurate Steady-State Port Flow Simulations
Authors: Yang Xiaofeng , Chen Zhaohui , Kuo Tang-Wei
Published: May 2013

Steady-state port flow simulations were carried out with a commercial three-dimensional (3D) computational fluid dynamics (CFD) code using Cartesian mesh with cut cells to study the prediction accuracy. The accuracy is assessed by comparing predicted and measured mass-flow rate and swirl and tumble torques at various valve lifts using different boundary condition setup and mesh topology relative to port orientation. The measured data are taken from standard steady-state flow bench tests of a production intake port. The predicted mass-flow rates agree to within 1% with the measured data between the intermediate and high valve lifts. At low valve lifts, slight overprediction in mass-flow rate can be observed. The predicted swirl and tumble torques are within 25% of the flow bench measurements. Several meshing parameters were examined in this study. These include: inlet plenum shape and outlet plenum/extension size, embedded sphere with varying minimum mesh size, finer meshes on port and valve surface, orientation of valve, and port centerline relative to the mesh lines. For all model orientations examined, only the mesh topology with the valve axis aligned closely with the mesh lines can capture the mass-flow rate drop for very high valve lifts due to flow separation. This study further demonstrated that it is possible to perform 3D CFD flow analyses to adequately simulate steady-state flow bench tests.
A generalized 2D pencil beam scaling algorithm for proton dose calculation in heterogeneous slab geometries
Authors: Westerly David C. , Mo Xiaohu , Tomé Wolfgang A. , Mackie Thomas R. , DeLuca Paul M.
Published: May 2013

Purpose:

Pencil beam algorithms are commonly used for proton therapy dose calculations. Szymanowski and Oelfke [“Two‐dimensional pencil beam scaling: An improved proton dose algorithm for heterogeneous media,” Phys. Med. Biol. 47, – (2002) ] developed a two‐dimensional (2D) scaling algorithm which accurately models the radial pencil beam width as a function of depth in heterogeneous slab geometries using a scaled expression for the radial kernel width in water as a function of depth and kinetic energy. However, an assumption made in the derivation of the technique limits its range of validity to cases where the input expression for the radial kernel width in water is derived from a local scattering power model. The goal of this work is to derive a generalized form of 2D pencil beam scaling that is independent of the scattering power model and appropriate for use with any expression for the radial kernel width in water as a function of depth.

Methods:

Using Fermi‐Eyges transport theory, the authors derive an expression for the radial pencil beam width in heterogeneous slab geometries which is independent of the proton scattering power and related quantities. The authors then perform test calculations in homogeneous and heterogeneous slab phantoms using both the original 2D scaling model and the new model with expressions for the radial kernel width in water computed from both local and nonlocal scattering power models, as well as a nonlocal parameterization of Molière scattering theory. In addition to kernel width calculations, dose calculations are also performed for a narrow Gaussian proton beam.

Results:

Pencil beam width calculations indicate that both 2D scaling formalisms perform well when the radial kernel width in water is derived from a local scattering power model. Computing the radial kernel width from a nonlocal scattering model results in the local 2D scaling formula under‐predicting the pencil beam width by as much as 1.4 mm (21%) at the depth of the Bragg peak for a 220 MeV proton beam in homogeneous water. This translates into a 32% dose discrepancy for a 5 mm Gaussian proton beam. Similar trends were observed for calculations made in heterogeneous slab phantoms where it was also noted that errors tend to increase with greater beam penetration. The generalized 2D scaling model performs well in all situations, with a maximum dose error of 0.3% at the Bragg peak in a heterogeneous phantom containing 3 cm of hard bone.

Conclusions:

The authors have derived a generalized form of 2D pencil beam scaling which is independent of the proton scattering power model and robust to the functional form of the radial kernel width in water used for the calculations. Sample calculations made with this model show excellent agreement with expected values in both homogeneous water and heterogeneous phantoms.
Photon charge experiment
Authors: Hankins A. , Rackson C. , Kim W. J.
Published: May 2013

The deflection of a laser beam traveling through a modulated electric field is measured using phase-sensitive detection to place an upper bound on the photon charge. An upper limit of 10−14e is obtained. Our approach provides a simple experimental scheme for angle measurements and is suitable as a laboratory exercise for both advanced undergraduate and beginning graduate students in physical science.
Modern cosmology: Interactive computer simulations that use recent observational surveys
Authors: Moldenhauer Jacob , Engelhardt Larry , Stone Keenan M. , Shuler Ezekiel
Published: May 2013

We present a collection of new, open-source computational tools for numerically modeling recent large-scale observational data sets using modern cosmology theory. These tools allow both students and researchers to constrain the parameter values in competitive cosmological models, thereby discovering both the accelerated expansion of the universe and its composition (e.g., dark matter and dark energy). These programs have several features to help the non-cosmologist build an understanding of cosmological models and their relation to observational data, including a built-in collection of several real observational data sets. The current list of built-in observations includes several recent supernovae Type-Ia surveys, baryon acoustic oscillations, the cosmic microwave background radiation, gamma-ray bursts, and measurements of the Hubble parameter. In this article, we discuss specific results for testing cosmological models using these observational data.
Skewness and shock formation in laboratory-scale supersonic jet data
Authors: Gee Kent L. , Neilsen Tracianne B. , Atchley Anthony A.
Published: May 2013

Spatial properties of noise statistics near unheated, laboratory-scale supersonic jets yield insights into source characteristics and near-field shock formation. Primary findings are (1) waveforms with positive pressure skewness radiate from the source with a directivity upstream of maximum overall level and (2) skewness of the time derivative of the pressure waveforms increases significantly with range, indicating formation of shocks during propagation. These results corroborate findings of a previous study involving full-scale engine data. Further, a comparison of ideally and over-expanded laboratory data show that while derivative skewness maps are similar, waveform skewness maps are substantially different for the two cases.
Kinetic Enrichment of
34
S during Proteobacterial Thiosulfate Oxidation and the Conserved Role of SoxB in S-S Bond Breaking
Authors: Alam Masrure , Pyne Prosenjit , Mazumdar Aninda , Peketi Aditya , Ghosh Wriddhiman
Published: May 2013

During chemolithoautotrophic thiosulfate oxidation, the phylogenetically diverged proteobacteria
Paracoccus pantotrophus
,
Tetrathiobacter kashmirensis
, and
Thiomicrospira crunogena
rendered steady enrichment of
34
S in the end product sulfate, with overall fractionation ranging between −4.6‰ and +5.8‰. The fractionation kinetics of
T. crunogena
was essentially similar to that of
P. pantotrophus
, albeit the former had a slightly higher magnitude and rate of
34
S enrichment. In the case of
T. kashmirensis
, the only significant departure of its fractionation curve from that of
P. pantotrophus
was observed during the first 36 h of thiosulfate-dependent growth, in the course of which tetrathionate intermediate formation is completed and sulfate production starts. The almost-identical
34
S enrichment rates observed during the peak sulfate-producing stage of all three processes indicated the potential involvement of identical S-S bond-breaking enzymes. Concurrent proteomic analyses detected the hydrolase SoxB (which is known to cleave terminal sulfone groups from SoxYZ-bound cysteine
S
-thiosulfonates, as well as cysteine
S
-sulfonates, in
P. pantotrophus
) in the actively sulfate-producing cells of all three species. The inducible expression of
soxB
during tetrathionate oxidation, as well as the second leg of thiosulfate oxidation, by
T. kashmirensis
is significant because the current Sox pathway does not accommodate tetrathionate as one of its substrates. Notably, however, no other Sox protein except SoxB could be detected upon matrix-assisted laser desorption ionization mass spectrometry analysis of all such
T. kashmirensis
proteins as appeared to be thiosulfate inducible in 2-dimensional gel electrophoresis. Instead, several other redox proteins were found to be at least 2-fold overexpressed during thiosulfate- or tetrathionate-dependent growth, thereby indicating that there is more to tetrathionate oxidation than SoxB alone.
Engineering of Ralstonia eutropha H16 for Autotrophic and Heterotrophic Production of Methyl Ketones
Authors: Mï¿½ller Jana , MacEachran Daniel , Burd Helcio , Sathitsuksanoh Noppadon , Bi Changhao , Yeh Yi-Chun , Lee Taek Soon , Hillson Nathan J. , Chhabra Swapnil R. , Singer Steven W. , Beller Harry R.
Published: May 2013

Ralstonia eutropha
is a facultatively chemolithoautotrophic bacterium able to grow with organic substrates or H
2
and CO
2
under aerobic conditions. Under conditions of nutrient imbalance,
R. eutropha
produces copious amounts of poly[(
R
)-3-hydroxybutyrate] (PHB). Its ability to utilize CO
2
as a sole carbon source renders it an interesting new candidate host for the production of renewable liquid transportation fuels. We engineered
R. eutropha
for the production of fatty acid-derived, diesel-range methyl ketones. Modifications engineered in
R. eutropha
included overexpression of a cytoplasmic version of the TesA thioesterase, which led to a substantial (>150-fold) increase in fatty acid titer under certain conditions. In addition, deletion of two putative β-oxidation operons and heterologous expression of three genes (the acyl coenzyme A oxidase gene from
Micrococcus luteus
and
fadB
and
fadM
from
Escherichia coli
) led to the production of 50 to 65 mg/liter of diesel-range methyl ketones under heterotrophic growth conditions and 50 to 180 mg/liter under chemolithoautotrophic growth conditions (with CO
2
and H
2
as the sole carbon source and electron donor, respectively). Induction of the methyl ketone pathway diverted substantial carbon flux away from PHB biosynthesis and appeared to enhance carbon flux through the pathway for biosynthesis of fatty acids, which are the precursors of methyl ketones.
An Engineered Strong Promoter for Streptomycetes
Authors: Wang Weishan , Li Xiao , Wang Juan , Xiang Sihai , Feng Xiaozhou , Yang Keqian
Published: May 2013

Well-characterized promoters are essential tools for metabolic engineering and synthetic biology. In
Streptomyces coelicolor
, the native
kasO
p is a temporally expressed promoter strictly controlled by two regulators, ScbR and ScbR2. In this work, first,
kasO
p was engineered to remove a common binding site of ScbR and ScbR2 upstream of its core region, thus generating a stronger promoter,
kasO
p
3
. Second, another ScbR binding site internal to the
kasO
p
3
core promoter region was abolished by random mutation and screening of the mutant library to obtain the strongest promoter,
kasO
p* (where the asterisk is used to distinguish the engineered promoter from the native promoter). The activities of
kasO
p* were compared with those of two known strong promoters,
ermE
p* and SF14p, in three
Streptomyces
species.
kasO
p* showed the highest activity at the transcription and protein levels in all three hosts. Furthermore, relative to
ermE
p* and SF14p,
kasO
p* was shown to confer the highest actinorhodin production level when used to drive the expression of
actII
-ORF4 in
S. coelicolor
. Therefore,
kasO
p* is a simple and well-defined strong promoter useful for gene overexpression in streptomycetes.
Identification of Critical Genes for Growth in Olive Brine by Transposon Mutagenesis of Lactobacillus pentosus C11
Authors: Perpetuini G. , Scornec H. , Tofalo R. , Serror P. , Schirone M. , Suzzi G. , Corsetti A. , Cavin J. F. , Licandro-Seraut H.
Published: May 2013

Olive brine represents a stressful environment due to the high NaCl concentration, presence of phenolic compounds known as antimicrobials, and low availability of nutrients. Thus, only a few strains of lactic acid bacteria (LAB) are adapted to grow in and ferment table olives. To identify the mechanisms by which these few strains are able to grow in olive brine,
Lactobacillus pentosus
C11, a particularly resistant strain isolated from naturally fermented table olives, was mutagenized by random transposition using the P
junc
-TpaseIS
1223
system (H. Licandro-Seraut, S. Brinster, M. van de Guchte, H. Scornec, E. Maguin, P. Sansonetti, J. F. Cavin, and P. Serror, Appl. Environ. Microbiol. 78:5417–5423, 2012). A library of 6,000 mutants was generated and screened for adaptation and subsequent growth in a medium, named BSM (brine screening medium), which presents the stressful conditions encountered in olive brine. Five transposition mutants impaired in growth on BSM were identified. Transposition occurred in two open reading frames and in three transcription terminators affecting stability of transcripts. Thus, several essential genes for adaptation and growth of
L. pentosus
C11 in olive brine were identified.
Neurospora crassa NKIN2, a Kinesin-3 Motor, Transports Early Endosomes and Is Required for Polarized Growth
Authors: Seidel Constanze , Moreno-Velásquez Sergio David , Riquelme Meritxell , Fischer Reinhard
Published: May 2013

Biological motors are molecular nanomachines, which convert chemical energy into mechanical forces. The combination of mechanoenzymes with structural components, such as the cytoskeleton, enables eukaryotic cells to overcome entropy, generate molecular gradients, and establish polarity. Hyphae of filamentous fungi are among the most polarized cells, and polarity defects are most obvious. Here, we studied the role of the kinesin-3 motor, NKIN2, in
Neurospora crassa
. We found that NKIN2 localizes as fast-moving spots in the cytoplasm of mature hyphae. To test whether the spots represented early endosomes, the Rab5 GTPase YPT52 was used as an endosomal marker. NKIN2 colocalized with YPT52. Deletion of
nkin2
caused strongly reduced endosomal movement. Combined, these results confirm the involvement of NKIN2 in early endosome transport. Introduction of a rigor mutation into NKIN2 labeled with green fluorescent protein (GFP) resulted in decoration of microtubules. Interestingly, NKIN2
rigor
was associated with a subpopulation of microtubules, as had been shown earlier for the
Aspergillus nidulans
orthologue UncA. Other kinesins did not show this specificity.
A SAS-6-Like Protein Suggests that the Toxoplasma Conoid Complex Evolved from Flagellar Components
Authors: de Leon Jessica Cruz , Scheumann Nicole , Beatty Wandy , Beck Josh R. , Tran Johnson Q. , Yau Candace , Bradley Peter J. , Gull Keith , Wickstead Bill , Morrissette Naomi S.
Published: May 2013

SAS-6 is required for centriole biogenesis in diverse eukaryotes. Here, we describe a novel family of SAS-6-like (SAS6L) proteins that share an N-terminal domain with SAS-6 but lack coiled-coil tails. SAS6L proteins are found in a subset of eukaryotes that contain SAS-6, including diverse protozoa and green algae. In the apicomplexan parasiteToxoplasma gondii, SAS-6 localizes to the centriole but SAS6L is found above the conoid, an enigmatic tubulin-containing structure found at the apex of a subset of alveolate organisms. Loss of SAS6L causes reduced fitness inToxoplasma. TheTrypanosoma bruceihomolog of SAS6L localizes to the basal-plate region, the site in the axoneme where the central-pair microtubules are nucleated. When endogenous SAS6L is overexpressed inToxoplasmatachyzoites orTrypanosomatrypomastigotes, it forms prominent filaments that extend through the cell cytoplasm, indicating that it retains a capacity to form higher-order structures despite lacking a coiled-coil domain. We conclude that although SAS6L proteins share a conserved domain with SAS-6, they are a functionally distinct family that predates the last common ancestor of eukaryotes. Moreover, the distinct localization of the SAS6L protein inTrypanosomaandToxoplasmaadds weight to the hypothesis that the conoid complex evolved from flagellar components.
Gene Expression and Physiological Role of Pseudomonas aeruginosa Methionine Sulfoxide Reductases during Oxidative Stress
Authors: Romsang Adisak , Atichartpongkul Sopapan , Trinachartvanit Wachareeporn , Vattanaviboon Paiboon , Mongkolsuk Skorn
Published: May 2013

Pseudomonas aeruginosa
PAO1 has two differentially expressed methionine sulfoxide reductase genes:
msrA
(PA5018) and
msrB
(PA2827). The
msrA
gene is expressed constitutively at a high level throughout all growth phases, whereas
msrB
expression is highly induced by oxidative stress, such as sodium hypochlorite (NaOCl) treatment. Inactivation of either
msrA
or
msrB
or both genes (
msrA msrB
mutant) rendered the mutants less resistant than the parental PAO1 strain to oxidants such as NaOCl and H
2
O
2
. Unexpectedly,
msr
mutants have disparate resistance patterns when exposed to paraquat, a superoxide generator. The
msrA
mutant had a higher paraquat resistance level than the
msrB
mutant, which had a lower paraquat resistance level than the PAO1 strain. The expression levels of
msrA
showed an inverse correlation with the paraquat resistance level, and this atypical paraquat resistance pattern was not observed with
msrB
. Virulence testing using a
Drosophila melanogaster
model revealed that the
msrA
,
msrB
, and, to a greater extent,
msrA msrB
double mutants had an attenuated virulence phenotype. The data indicate that
msrA
and
msrB
are essential genes for oxidative stress protection and bacterial virulence. The pattern of expression and mutant phenotypes of
P. aeruginosa
msrA
and
msrB
differ from previously characterized
msr
genes from other bacteria. Thus, as highly conserved genes, the
msrA
and
msrB
have diverse expression patterns and physiological roles that depend on the environmental niche where the bacteria thrive.
BB0172, a Borrelia burgdorferi Outer Membrane Protein That Binds Integrin α
3
β
1
Authors: Wood Elaine , Tamborero Silvia , Mingarro Ismael , Esteve-Gassent Maria D.
Published: May 2013

Lyme disease is a multisystemic disorder caused by
Borrelia burgdorferi
infection. Upon infection, some
B. burgdorferi
genes are upregulated, including members of the microbial surface components recognizing adhesive matrix molecule (MSCRAMM) protein family, which facilitate
B. burgdorferi
adherence to extracellular matrix components of the host. Comparative genome analysis has revealed a new family of
B. burgdorferi
proteins containing the von Willebrand factor A (vWFA) domain. In the present study, we characterized the expression and membrane association of the vWFA domain-containing protein BB0172 by using
in vitro
transcription/translation systems in the presence of microsomal membranes and with detergent phase separation assays. Our results showed evidence of BB0172 localization in the outer membrane, the orientation of the vWFA domain to the extracellular environment, and its function as a metal ion-dependent integrin-binding protein. This is the first report of a borrelial adhesin with a metal ion-dependent adhesion site (MIDAS) motif that is similar to those observed in eukaryotic integrins and has a similar function.
Role of Polyphosphate in Thermophilic Synechococcus sp. from Microbial Mats
Authors: Gomez-Garcia Maria R. , Fazeli Fariba , Grote Alexandra , Grossman Arthur R. , Bhaya Devaki
Published: May 2013

Synechococcus
OS-B′, a thermophilic unicellular cyanobacterium, recently isolated from the microbial mats in Octopus Spring (Yellowstone National Park), induces a suite of genes, including phosphatases and transporters, in response to phosphorus (P) starvation. Here we describe two different approaches to examine the ability of
Synechococcus
OS-B′ to synthesize and break down polyphosphate (poly P), a key storage compound in many prokaryotes. First, we developed a transformation protocol to create mutants in the polyphosphate kinase (
ppk
), the major enzyme responsible for the synthesis of poly P. The
ppk
mutant exhibited a pleiotropic phenotype with defects in poly P accumulation, aberrant levels of Pho regulon transcripts, growth defects, and changes in cell size and exopolysaccharide levels, among others. Second, we measured transcripts of
ppk
and
ppx
(encoding the polyphosphatase) directly from mat samples and found that the levels varied dramatically over a diel cycle. We also used Western blot analysis to quantify levels of PPK and PPX and found that these enzymes differentially accumulated during the diel cycle. Levels of polyphosphate kinase peaked at night, while polyphosphatase levels were highest during the early morning hours. We hypothesize that the opposing activities of these two enzymes allow cells to store and utilize poly P to optimize growth over a diel cycle.
A Differential Fluorescence-Based Genetic Screen Identifies Listeria monocytogenes Determinants Required for Intracellular Replication
Authors: Perry Kyle J. , Higgins Darren E.
Published: May 2013

Listeria monocytogenes
is a Gram-positive, facultative intracellular pathogen capable of causing severe invasive disease with high mortality rates in humans. While previous studies have largely elucidated the bacterial and host cell mechanisms necessary for invasion, vacuolar escape, and subsequent cell-to-cell spread, the
L. monocytogenes
factors required for rapid replication within the restrictive environment of the host cell cytosol are poorly understood. In this report, we describe a differential fluorescence-based genetic screen utilizing fluorescence-activated cell sorting (FACS) and high-throughput microscopy to identify
L. monocytogenes
mutants defective in optimal intracellular replication. Bacteria harboring deletions within the identified gene
menD
or
pepP
were defective for growth in primary murine macrophages and plaque formation in monolayers of L2 fibroblasts, thus validating the ability of the screening method to identify intracellular replication-defective mutants. Genetic complementation of the
menD
and
pepP
deletion strains rescued the
in vitro
intracellular infection defects. Furthermore, the
menD
deletion strain displayed a general extracellular replication defect that could be complemented by growth under anaerobic conditions, while the intracellular growth defect of this strain could be complemented by the addition of exogenous menaquinone. As prior studies have indicated the importance of aerobic metabolism for
L. monocytogenes
infection, these findings provide further evidence for the importance of menaquinone and aerobic metabolism for
L. monocytogenes
pathogenesis. Lastly, both the
menD
and
pepP
deletion strains were attenuated during
in vivo
infection of mice. These findings demonstrate that the differential fluorescence-based screening approach provides a powerful tool for the identification of intracellular replication determinants in multiple bacterial systems.
Mutational Analysis of the Multiple-Antibiotic Resistance Regulator MarR Reveals a Ligand Binding Pocket at the Interface between the Dimerization and DNA Binding Domains
Authors: Duval Valérie , McMurry Laura M. , Foster Kimberly , Head James F. , Levy Stuart B.
Published: May 2013

The
Escherichia coli
regulator MarR represses the multiple-antibiotic resistance operon
marRAB
and responds to phenolic compounds, including sodium salicylate, which inhibit its activity. Crystals obtained in the presence of a high concentration of salicylate indicated two possible salicylate sites, SAL-A and SAL-B. However, it was unclear whether these sites were physiologically significant or were simply a result of the crystallization conditions. A study carried out on MarR homologue MTH313 suggested the presence of a salicylate binding site buried at the interface between the dimerization and the DNA-binding domains. Interestingly, the authors of the study indicated a similar pocket conserved in the MarR structure. Since no mutagenesis analysis had been performed to test which amino acids were essential in salicylate binding, we examined the role of residues that could potentially interact with salicylate. We demonstrated that mutations in residues shown as interacting with salicylate at SAL-A and SAL-B in the MarR-salicylate structure had no effect on salicylate binding, indicating that these sites were not the physiological regulatory sites. However, some of these residues (P57, R86, M74, and R77) were important for DNA binding. Furthermore, mutations in residues R16, D26, and K44 significantly reduced binding to both salicylate and 2,4-dinitrophenol, while a mutation in residue H19 impaired the binding to 2,4-dinitrophenol only. These findings indicate, as for MTH313, the presence of a ligand binding pocket located between the dimerization and DNA binding domains.
Extrapulmonary disseminated tuberculosis with tuberculous adrenalitis: a stitch in time saves nine
Authors: Rajasekharan Chandrasekharan , Ajithkumar Sivasankarannair , Anto Varghese , Parvathy Rajasekharan
Published: May 2013

A 40-year-old manual labourer presented with easy fatiguability, recurrent vomiting and loss of weight of 3 months, duration. Upon examination, there was significant axillary and cervical lymphadenopathy. No pallor, icterus or clubbing was evident. There was generalised hyperpigmentation and multiple oral ulcers. The blood pressure 90/60 mm Hg in the right upper limb in the supine position. Investigations showed a low serum cortisol. Mantoux test was strongly positive (20 mm).A fine needle aspiration biopsy of the cervical lymph node revealed reactive changes. Bone marrow aspiration and biopsy were normal. Cervical lymph node biopsy showed caseating granulomas suggestive of tuberculous lymphadenitis. A CT scan of the abdomen showed bilaterally enlarged adrenal glands with hypodense areas suggestive of necrosis. He was diagnosed with extrapulmonary disseminated tuberculosis with tuberculous adrenalitis. He was started on directly observed therapy (DOTS) for disseminated tuberculosis and 40 mg of prednisolone. He is improving with treatment.
Parathyroidectomy in the presence of central venous stenosis
Authors: Megson Matthew
Published: May 2013

Hyperparathyroidism is common in the end-stage renal failure and may require surgical intervention. In addition, following multiple vascular access attempts central venous stenosis may occur. The results in high-volume venous blood flow through neck collaterals. Here, we describe a case of severe secondary hyperparathyroidism, high flow arteriovenous fistula and central venous occlusion unresponsive to radiological intervention. A four-gland exploration was undertaken and global parathyroidectomy was performed. Despite meticulous attention to haemostasis, blood loss was considerable from the skin edges although thyroid veins were easily controlled with a drop of 2.1 g/dl in haemoglobin. Postoperative hypocalcaemia requiring intravenous calcium occurred as expected from the severity of his bone disease (preoperative parathyroid hormone (PTH) 26 times the upper normal range). The patient recovered well, despite a small subcutaneous haematoma and remains asymptomatic.
Advanced adenocarcinoma in a colonic interposition segment
Authors: Aryal Madan Raj , Mainali Naba Raj , Jalota Leena , Altomare John F
Published: May 2013

Although rarely reported in the literature, adenomatous polyp and adenocarcinoma can occur as a late complication in an interposed colonic segment. We describe a case of a late stage adenocarcinoma in a colonic interposition performed for benign oesophageal stricture.
Anastomotic leakage as an outcome measure for quality of colorectal cancer surgery
Authors: Snijders H S , Henneman D , van Leersum N L , ten Berge M , Fiocco M , Karsten T M , Havenga K , Wiggers T , Dekker J W , Tollenaar R A E M , Wouters M W J M
Published: May 2013

Introduction

When comparing mortality rates between hospitals to explore hospital performance, there is an important role for adjustment for differences in case-mix. Identifying outcome measures that are less influenced by differences in case-mix may be valuable. The main goal of this study was to explore whether hospital differences in anastomotic leakage (AL) and postoperative mortality are due to differences in case-mix or to differences in treatment factors.

Methods

Data of the Dutch Surgical Colorectal Audit were used. Case-mix factors and treatment-related factors were identified from the literature and their association with AL and mortality were analysed with logistic regression. Hospital differences in observed AL and mortality rates, and adjusted rates based on the logistic regression models were shown. The reduction in hospital variance after adjustment was analysed with Levene's test for equality of variances.

Results

17 of 22 case-mix factors and 4 of 11 treatment factors related to AL derived from the literature were available in the database. Variation in observed AL rates between hospitals was large with a maximum rate of 17%. This variation could not be attributed to differences in case-mix but more to differences in treatment factors. Hospital variation in observed mortality rates was significantly reduced after adjustment for differences in case-mix.

Conclusions

Hospital variation in AL is relatively independent of differences in case-mix. In contrast to ‘postoperative mortality’ the observed AL rates of hospitals evaluated in our study were only slightly affected after adjustment for case-mix factors. Therefore, AL rates may be suitable as an outcome indicator for measurement of surgical quality of care.
Hurdles to the global antipolio campaign in Pakistan: an outline of the current status and future prospects to achieve a polio free world
Authors: Khan Tariq , Qazi Javaria
Published: May 2013

The Global Polio Eradication Initiative to eradicate polio completely by the year 2000 has been successful, except for three endemic and some non-endemic countries. Pakistan, one of the three endemic polio reservoirs, is posing a serious threat to the success of the initiative. Currently, the expanded programme on immunisation has been geared to win the race over polio virus in Pakistan. After the remarkable decrease in polio cases from 198 in 2011 to only 58 in 2012, Pakistan seemed to be at the verge of success. However, hurdles continue to retard the campaign. The war against terrorism, misconceptions about polio vaccine, religious misinterpretations, frustration among vaccinators, lack of awareness, social considerations, natural calamities, inaccessibility, and inefficient vaccines and so on are continually rupturing the foundations of the worldwide initiative in the country. Weak health management is found at the hub of majority of the challenges. Stricter policies, well managed and supervised plans and strategic actions, risk analysis and enhanced communication may help giving the final punch to polio virus in the country. Analysis suggested that there is some literature available on the challenges to polio elimination, yet there is not a single publication up to date that considers all the possible hurdles in a single manuscript. This paper sorts out the breaches that hamper the goal of eliminating polio from Pakistan. We have evaluated all the possible barriers and explained them with a perspective that will help develop area specific strategies against polio virus and thus eradicate polio virus from the world.
Understanding risk factors for perioperative ischemic events with carotid stenting: is patient age over 80 years or is unfavorable arch anatomy to blame?
Authors: Dumont Travis M , Mokin Maxim , Wach Michael M , Drummond Patrick S , Siddiqui Adnan H , Levy Elad I , Hopkins L Nelson
Published: May 2013

Objective

Several studies have reported increased perioperative risk after carotid artery stenting (CAS) for patients ≥80 years of age; however, most have not considered unfavorable anatomic features noted more frequently in this population as a confounding variable. The purpose of this study was to show a correlation between poor aortic arch anatomy and perioperative ischemic complications after CAS.

Methods

Our prospectively maintained database was queried for all CAS procedures performed on symptomatic patients between 2009 and 2011. Retrospective analysis of consecutive CAS procedures was performed. The primary endpoint was perioperative (within 30 days) ischemic events (stroke, transient ischemic attack (TIA)). Event incidence was compared between groups dichotomized by age and anatomical features. Incidence of unfavorable arch (acute angle between aortic arch and treated common carotid artery) was compared between age groups.

Results

Perioperative ischemic events included four ischemic strokes and three TIAs (all events ipsilateral to the treated vessel). Event incidence was more frequent in patients with unfavorable arch anatomy (7.9%) than in those with favorable aortic arch features (0.7%) (p=0.0073). Event incidence in patients ≥80 years of age (4.5%) was not statistically different than that in patients <80 years (2.3%) (p=0.428). Unfavorable aortic arch anatomy was increased in frequency in patients aged 80 years and over (<80 years, 29%; ≥80 years, 52%; p<0.001).

Conclusions

In the present series, the incidence of perioperative complications was increased in patients with unfavorable aortic arch anatomy but not in patients ≥80 years. CAS represents a revascularization option for patients of all ages; however, patients with unfavorable aortic arch anatomy may represent a group at relatively high risk for periprocedural ischemic events.
MINIMUM UNCERTAINTY AND ENTANGLEMENT
Authors: HARI DASS N. D. , QURESHI TABISH , SHEEL ADITI
Published: May 2013

We address the question, does a system A being entangled with another system B, put any constraints on the Heisenberg uncertainty relation (or the Schrödinger–Robertson inequality)? We find that the equality of the uncertainty relation cannot be reached for any two noncommuting observables, for finite dimensional Hilbert spaces if the Schmidt rank of the entangled state is maximal. One consequence is that the lower bound of the uncertainty relation can never be attained for any two observables for qubits, if the state is entangled. For infinite-dimensional Hilbert space too, we show that there is a class of physically interesting entangled states for which no two noncommuting observables can attain the minimum uncertainty equality.
NEGATIVITY AND GEOMETRIC QUANTUM DISCORD AS INDICATORS OF QUANTUM PHASE TRANSITION IN THE XY MODEL WITH DZYALOSHINSKII–MORIYA INTERACTION
Authors: XU SHUAI , SONG XUE KE , YE LIU
Published: May 2013

In this paper, we use the negativity and geometric quantum discord (GQD) to investigate the quantum phase transition (QPT) in the anisotropic spin-1/2 XY model with staggered Dzyaloshinskii–Moriya (DM) interaction using the quantum renormalization-group method, and the results show that the negativity and GQD can both obtain the quantum critical points associated with QPTs after several iterations of the renormalization. In addition to this, we discuss how the strength of the DM interaction and anisotropic parameter make the effect on the negativity and GQD for different RG steps. At last, we give out the relationship between negativity and GQD, and verify that with anisotropy parameter and the strength of DM interaction increased, the squared negativity and the normalization of GQD tend to equal in this model.