bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of viral hepatitis‐related hepatocellular carcinoma to post‐transplant outcomes
Authors: Younossi Z. M. , Stepanova M. , Saab S. , Ahmed A. , Lam B. , Srishord M. , Venkatesan C. , Wai H. , Henry L.
Published: August 2015

Hepatocellular carcinoma (HCC) is the most common complication of HCV infection leading to liver transplantation. We evaluated the impact of aetiology of liver disease on patient and graft survival following liver transplantation for HCC. From the Scientific Registry of Transplant Recipients (2002–2011), all adults who underwent liver transplantation for HCC were retrospectively included. Aetiology of liver disease was grouped into HCV, HBV, HCV–HBV co‐infection and nonviral liver disease. Of 8,733 liver transplant recipients with HCC, 5507 had HCV, 631 had HBV, 163 were co‐infected, and 2432 had nonviral causes of liver disease. In follow‐up (48 ± 32 months), 8.2% had graft failure and 29.5% died. The mean rates of graft failure were 9.5%, 4.7%, 6.1% and 6.4% in HCV, HBV, HCV–HBV co‐infection and nonviral liver disease, respectively (P < 0.0001). Post‐transplant mortality rate in patients with HBV was 20.2%, HCV 31.0%, HCV–HBV 28.5% and nonviral 28.5% (P < 0.0001). This difference was significant starting one year post‐transplant and became even more prominent later in follow‐up. Five‐year post‐transplant survival was 64.7% in HCV, 77.7% in HBV, 71.0% in HCV–HBV and 69.1% in nonviral HCC (P < 0.0001). A diagnosis of HCV in patients with HCC was also independently associated with an increased risk of both graft failure (adjusted hazard ratio = 1.84 (1.46–2.33), P < 0.0001) and mortality (1.35 (1.21–1.50), P < 0.0001) in multivariate analysis. Patients with HCV‐related HCC are at higher risk of adverse post‐transplant outcomes. These patients should be considered for preemptive interferon‐free antiviral therapy prior to or immediately following liver transplantation.
Language Variation in the Diaspora: Polish Immigrant Communities in the U.S. and the U.K.
Authors: Newlin‐Łukowicz Luiza
Published: August 2015

Ethnicity has long been known to affect language variation. However, existing studies have overwhelmingly focused on the speech of the largest, non‐White minority groups and have rarely investigated within‐group variation. In this paper, I review sociolinguistic studies of a White minority group in two different settings and argue that the study of sociolinguistic variation across and within minority groups can help disentangle and systematize the effect of ethnicity on language. I focus on reports of linguistic variation for Polish immigrants in the United States (a case of sustained, long‐term immigration) and in the United Kingdom (a case of recent migration with indefinite plans for long‐term residence). Through these two case studies, I illustrate that a strong Polish identity affects speakers’ adoption of regional variation in English.
Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent‐wide lineage admixture
Authors: Havrdová Alena , Douda Jan , Krak Karol , Vít Petr , Hadincová Věroslava , Zákravský Petr , Mandák Bohumil
Published: August 2015

Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent‐wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear‐edge populations in the Mediterranean region more vulnerable to extinction due to climate change.
Frontolimbic neural circuit changes in emotional processing and inhibitory control associated with clinical improvement following transference‐focused psychotherapy in borderline personality disorder
Authors: Perez David L. , Vago David R. , Pan Hong , Root James , Tuescher Oliver , Fuchs Benjamin H. , Leung Lorene , Epstein Jane , Cain Nicole M. , Clarkin John F. , Lenzenweger Mark F. , Kernberg Otto F. , Levy Kenneth N. , Silbersweig David A. , Stern Emily
Published: August 2015

Aims

Borderline personality disorder (BPD) is characterized by self‐regulation deficits, including impulsivity and affective lability. Transference‐focused psychotherapy (TFP) is an evidence‐based treatment proven to reduce symptoms across multiple cognitive–emotional domains in BPD. This pilot study aimed to investigate neural activation associated with, and predictive of, clinical improvement in emotional and behavioral regulation in BPD following TFP.

Methods

BPD subjects (n = 10) were scanned pre‐ and post‐TFP treatment using a within‐subjects design. A disorder‐specific emotional–linguistic go/no‐go functional magnetic resonance imaging paradigm was used to probe the interaction between negative emotional processing and inhibitory control.

Results

Analyses demonstrated significant treatment‐related effects with relative increased dorsal prefrontal (dorsal anterior cingulate, dorsolateral prefrontal, and frontopolar cortices) activation, and relative decreased ventrolateral prefrontal cortex and hippocampal activation following treatment. Clinical improvement in constraint correlated positively with relative increased left dorsal anterior cingulate cortex activation. Clinical improvement in affective lability correlated positively with left posterior‐medial orbitofrontal cortex/ventral striatum activation, and negatively with right amygdala/parahippocampal activation. Post‐treatment improvements in constraint were predicted by pre‐treatment right dorsal anterior cingulate cortex hypoactivation, and pre‐treatment left posterior‐medial orbitofrontal cortex/ventral striatum hypoactivation predicted improvements in affective lability.

Conclusions

These preliminary findings demonstrate potential TFP‐associated alterations in frontolimbic circuitry and begin to identify neural mechanisms associated with a psychodynamically oriented psychotherapy.
Enhancement of XeF2-assisted gallium ion beam etching of silicon layer and endpoint detection from backside in circuit editing
Authors: Xia Deying , Notte John , Stern Lewis , Goetze Bernhard
Published: August 2015

Within the semiconductor industry, backside circuit editing is the process of modifying individual nanometer-scale devices after they have been fabricated by conventional mass production techniques. The technique includes the removal of bulk silicon, to reach the devices, followed by the removal of small and precisely defined volumes of silicon and other materials. It also includes the ability to deposit precise patterns of conductors or insulators to modify the devices in question. Essential to the circuit edit processes are the focused ion beam (FIB) instruments, usually providing a gallium ion beam, to sputter away the volumes which need to be removed. When used in conjunction with specific “precursor” gases, the FIB instrument can deposit metals and insulators in arbitrary patterns to achieve the desired circuit repair or modification. Other gases, such as xenon difluoride (XeF2), can work in conjunction with the FIB to improve the effectiveness and the rate of material removal. Our experimental investigation found that the removal rate of backside silicon by a gallium FIB could be enhanced by 100 times when used in conjunction with the XeF2 gas. The XeF2 also reduced the redeposition of the removed silicon material, making the removal more effective. And importantly, the production of secondary electrons was found to offer a viable endpoint signal to indicate the transition to a new material.
An analytic, Fourier domain description of shear wave propagation in a viscoelastic medium using asymmetric Gaussian sources
Authors: Rouze Ned C. , Palmeri Mark L. , Nightingale Kathryn R.
Published: August 2015

Recent measurements of shear wave propagation in viscoelastic materials have been analyzed by constructing the two-dimensional Fourier transform (2D-FT) of the spatial-temporal shear wave signal and using an analysis procedure derived under the assumption the wave is described as a plane wave, or as the asymptotic form of a wave expanding radially from a cylindrically symmetric source. This study presents an exact, analytic expression for the 2D-FT description of shear wave propagation in viscoelastic materials following asymmetric Gaussian excitations and uses this expression to evaluate the bias in 2D-FT measurements obtained using the plane or cylindrical wave assumptions. A wide range of biases are observed depending on specific values of frequency, aspect ratio R of the source asymmetry, and material properties. These biases can be reduced significantly by weighting the shear wave signal in the spatial domain to correct for the geometric spreading of the shear wavefront using a factor of xp. The optimal weighting power p is found to be near the theoretical value of 0.5 for the case of a cylindrical source with R = 1, and decreases for asymmetric sources with R > 1.
Ultrasonic particle sizing in aqueous suspensions of solid particles of unknown density
Authors: Al-Lashi Raied S. , Challis Richard E.
Published: August 2015

Estimates of particle size distributions (PSDs) in solid-in-liquid suspensions can be made on the basis of measurements of ultrasonic wave attenuation combined with a mathematical propagation model, which typically requires seven physical parameters to describe each phase of the mixture. The estimation process is insensitive to all of these except the density of the solid particles, which may not be known or difficult to measure. This paper proposes that an unknown density value is incorporated into the sizing computation as a free variable. It is shown that this leads to an accurate estimate of PSD, as well as the unknown density.
Automatic classification of delphinids based on the representative frequencies of whistles
Authors: Lin Tzu-Hao , Chou Lien-Siang
Published: August 2015

Classification of odontocete species remains a challenging task for passive acoustic monitoring. Classifiers that have been developed use spectral features extracted from echolocation clicks and whistle contours. Most of these contour-based classifiers require complete contours to reduce measurement errors. Therefore, overlapping contours and partially detected contours in an automatic detection algorithm may increase the bias for contour-based classifiers. In this study, classification was conducted on each recording section without extracting individual contours. The local-max detector was used to extract representative frequencies of delphinid whistles and each section was divided into multiple non-overlapping fragments. Three acoustical parameters were measured from the distribution of representative frequencies in each fragment. By using the statistical features of the acoustical parameters and the percentage of overlapping whistles, correct classification rate of 70.3% was reached for the recordings of seven species (Tursiops truncatus, Delphinus delphis, Delphinus capensis, Peponocephala electra, Grampus griseus, Stenella longirostris longirostris, and Stenella attenuata) archived in MobySound.org. In addition, correct classification rate was not dramatically reduced in various simulated noise conditions. This algorithm can be employed in acoustic observatories to classify different delphinid species and facilitate future studies on the community ecology of odontocetes.
Extension of the generic amyloid hypothesis to nonproteinaceous metabolite assemblies
Authors: Shaham-Niv Shira , Adler-Abramovich Lihi , Schnaider Lee , Gazit Ehud
Published: August 2015

The formation of amyloid fibrils by nonprotein metabolites presents a new paradigm in self-assembly and metabolic disorders.
Structural basis of Lewis
b
antigen binding by the
Helicobacter pylori
adhesin BabA
Authors: Hage Naim , Howard Tina , Phillips Chris , Brassington Claire , Overman Ross , Debreczeni Judit , Gellert Paul , Stolnik Snow , Winkler G. Sebastiaan , Falcone Franco H.
Published: August 2015

X-ray structure of BabA bound to Lewis
b
reveals molecular interactions used by
H. pylori
to colonize the gastric mucosa.
Total structure determination of surface doping [Ag
46
Au
24
(SR)
32
](BPh
4
)
2
nanocluster and its structure-related catalytic property
Authors: Wang Shuxin , Jin Shan , Yang Sha , Chen Shuang , Song Yongbo , Zhang Jun , Zhu Manzhou
Published: August 2015

X-ray crystallography of the first and the largest AgAu nanoparticles with a doping shell and its structure-related property.
Locomotor play drives motor skill acquisition at the expense of growth: A life history trade-off
Authors: Berghänel Andreas , Schülke Oliver , Ostner Julia
Published: August 2015

Investment in play can take ontogenetic priority over unconstrained physical development with consequences for life history.
CRISPR-Cas9 delivery to hard-to-transfect cells via membrane deformation
Authors: Han Xin , Liu Zongbin , Jo Myeong chan , Zhang Kai , Li Ying , Zeng Zihua , Li Nan , Zu Youli , Qin Lidong
Published: August 2015

Virus-free gene editing possible at chromosomes through stretching cells in a micropost array, even for hard-to-transfect cells.
A general consumer-resource population model
Authors: Lafferty Kevin D. , DeLeo Giulio , Briggs Cheryl J. , Dobson Andrew P. , Gross Thilo , Kuris Armand M.
Published: August 2015

A model for who eats and who is eaten

There are many types of interactions between those that eat and those that are eaten. A multitude of theoretical equations describe these dynamics, from predator and prey to parasite and host. Lafferty
et al.
show that all forms of these relationships come down to fundamental consumer-resource interactions. Derived from the myriad complex interactions, a simple model can accommodate any such interaction, simplifying past models into a general theory of eat and be eaten.

Science
, this issue p.
854
Boreal forest health and global change
Authors: Gauthier S. , Bernier P. , Kuuluvainen T. , Shvidenko A. Z. , Schepaschenko D. G.
Published: August 2015

The boreal forest, one of the largest biomes on Earth, provides ecosystem services that benefit society at levels ranging from local to global. Currently, about two-thirds of the area covered by this biome is under some form of management, mostly for wood production. Services such as climate regulation are also provided by both the unmanaged and managed boreal forests. Although most of the boreal forests have retained the resilience to cope with current disturbances, projected environmental changes of unprecedented speed and amplitude pose a substantial threat to their health. Management options to reduce these threats are available and could be implemented, but economic incentives and a greater focus on the boreal biome in international fora are needed to support further adaptation and mitigation actions.
Response to Comment on “Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet”
Authors: Wang Ping , Scherler Dirk , Liu-Zeng Jing , Mey Jürgen , Avouac Jean-Philippe , Zhang Yunda , Shi Dingguo
Published: August 2015

In their Comment, Zeitler
et al
. do not challenge our results or interpretation. Our study does not disprove coupling between tectonic uplift and erosion but suggests that this coupling cannot be the sole explanation of rapid uplift in the Himalayan syntaxes.
Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities
Authors: Steven Blaire , Kuske Cheryl R. , Gallegos-Graves La Verne , Reed Sasha C. , Belnap Jayne
Published: August 2015

Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased
Cyanobacteria
abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.
Distribution, Activities, and Interactions of Methanogens and Sulfate-Reducing Prokaryotes in the Florida Everglades
Authors: Bae Hee-Sung , Holmes M. Elizabeth , Chanton Jeffrey P. , Reddy K. Ramesh , Ogram Andrew
Published: August 2015

To gain insight into the mechanisms controlling methanogenic pathways in the Florida Everglades, the distribution and functional activities of methanogens and sulfate-reducing prokaryotes (SRPs) were investigated in soils (0 to 2 or 0 to 4 cm depth) across the well-documented nutrient gradient in the water conservation areas (WCAs) caused by runoff from the adjacent Everglades Agricultural Area. The methyl coenzyme M reductase gene (
mcrA
) sequences that were retrieved from WCA-2A, an area with relatively high concentrations of SO
4
2−
(≥39 μM), indicated that methanogens inhabiting this area were broadly distributed within the orders
Methanomicrobiales
,
Methanosarcinales
,
Methanocellales
,
Methanobacteriales
, and
Methanomassiliicoccales
. In more than 3 years of monitoring, quantitative PCR (qPCR) using newly designed group-specific primers revealed that the hydrogenotrophic
Methanomicrobiales
were more numerous than the
Methanosaetaceae
obligatory acetotrophs in SO
4
2−
-rich areas of WCA-2A, while the
Methanosaetaceae
were dominant over the
Methanomicrobiales
in WCA-3A (with relatively low SO
4
2−
concentrations; ≤4 μM). qPCR of
dsrB
sequences also indicated that SRPs are present at greater numbers than methanogens in the WCAs. In an incubation study with WCA-2A soils, addition of MoO
4
2−
(a specific inhibitor of SRP activity) resulted in increased methane production rates, lower apparent fractionation factors [α
app
; defined as (amount of δ
13
CO
2
+ 1,000)/(amount of δ
13
CH
4
+ 1,000)], and higher
Methanosaetaceae
mcrA
transcript levels compared to those for the controls without MoO
4
2−
. These results indicate that SRPs play crucial roles in controlling methanogenic pathways and in shaping the structures of methanogen assemblages as a function of position along the nutrient gradient.
Spatial Patterns of Carbonate Biomineralization in Biofilms
Authors: Li Xiaobao , Chopp David L. , Russin William A. , Brannon Paul T. , Parsek Matthew R. , Packman Aaron I.
Published: August 2015

Microbially catalyzed precipitation of carbonate minerals is an important process in diverse biological, geological, and engineered systems. However, the processes that regulate carbonate biomineralization and their impacts on biofilms are largely unexplored, mainly because of the inability of current methods to directly observe biomineralization within biofilms. Here, we present a method for
in situ
, real-time imaging of biomineralization in biofilms and use it to show that
Pseudomonas aeruginosa
biofilms produce morphologically distinct carbonate deposits that substantially modify biofilm structures. The patterns of carbonate biomineralization produced
in situ
were substantially different from those caused by accumulation of particles produced by abiotic precipitation. Contrary to the common expectation that mineral precipitation should occur at the biofilm surface, we found that biomineralization started at the base of the biofilm. The carbonate deposits grew over time, detaching biofilm-resident cells and deforming the biofilm morphology. These findings indicate that biomineralization is a general regulator of biofilm architecture and properties.
A New Class of Tungsten-Containing Oxidoreductase in Caldicellulosiruptor, a Genus of Plant Biomass-Degrading Thermophilic Bacteria
Authors: Scott Israel M. , Rubinstein Gabe M. , Lipscomb Gina L. , Basen Mirko , Schut Gerrit J. , Rhaesa Amanda M. , Lancaster W. Andrew , Poole Farris L. , Kelly Robert M. , Adams Michael W. W.
Published: August 2015

Caldicellulosiruptor bescii
grows optimally at 78°C and is able to decompose high concentrations of lignocellulosic plant biomass without the need for thermochemical pretreatment.
C. bescii
ferments both C
5
and C
6
sugars primarily to hydrogen gas, lactate, acetate, and CO
2
and is of particular interest for metabolic engineering applications given the recent availability of a genetic system. Developing optimal strains for technological use requires a detailed understanding of primary metabolism, particularly when the goal is to divert all available reductant (electrons) toward highly reduced products such as biofuels. During an analysis of the
C. bescii
genome sequence for oxidoreductase-type enzymes, evidence was uncovered to suggest that the primary redox metabolism of
C. bescii
has a completely uncharacterized aspect involving tungsten, a rarely used element in biology. An active tungsten utilization pathway in
C. bescii
was demonstrated by the heterologous production of a tungsten-requiring, aldehyde-oxidizing enzyme (AOR) from the hyperthermophilic archaeon
Pyrococcus furiosus
. Furthermore,
C. bescii
also contains a tungsten-based AOR-type enzyme, here termed XOR, which is phylogenetically unique, representing a completely new member of the AOR tungstoenzyme family. Moreover, in
C. bescii
, XOR represents ca. 2% of the cytoplasmic protein. XOR is proposed to play a key, but as yet undetermined, role in the primary redox metabolism of this cellulolytic microorganism.
Identification of the
mcpA
and
mcpM
Genes, Encoding Methyl-Accepting Proteins Involved in Amino Acid and
l
-Malate Chemotaxis, and Involvement of McpM-Mediated Chemotaxis in Plant Infection by Ralstonia pseudosolanacearum (Formerly Ralstonia solanacearum Phylotypes I and III)
Authors: Hida Akiko , Oku Shota , Kawasaki Takeru , Nakashimada Yutaka , Tajima Takahisa , Kato Junichi
Published: August 2015

Sequence analysis has revealed the presence of 22 putative methyl-accepting chemotaxis protein (
mcp
) genes in the
Ralstonia pseudosolanacearum
GMI1000 genome. PCR analysis and DNA sequencing showed that the highly motile
R. pseudosolanacearum
strain Ps29 possesses homologs of all 22
R. pseudosolanacearum
GMI1000
mcp
genes. We constructed a complete collection of single
mcp
gene deletion mutants of
R. pseudosolanacearum
Ps29 by unmarked gene deletion. Screening of the mutant collection revealed that
R. pseudosolanacearum
Ps29 mutants of RSp0507 and RSc0606 homologs were defective in chemotaxis to
l
-malate and amino acids, respectively. RSp0507 and RSc0606 homologs were designated
mcpM
and
mcpA
. While wild-type
R. pseudosolanacearum
strain Ps29 displayed attraction to 16 amino acids, the
mcpA
mutant showed no response to 12 of these amino acids and decreased responses to 4 amino acids. We constructed
mcpA
and
mcpM
deletion mutants of highly virulent
R. pseudosolanacearum
strain MAFF106611 to investigate the contribution of chemotaxis to
l
-malate and amino acids to tomato plant infection. Neither single mutant exhibited altered virulence for tomato plants when tested by root dip inoculation assays. In contrast, the
mcpM
mutant (but not the
mcpA
mutant) was significantly less infectious than the wild type when tested by a sand soak inoculation assay, which requires bacteria to locate and invade host roots from sand. Thus, McpM-mediated chemotaxis, possibly reflecting chemotaxis to
l
-malate, facilitates
R. pseudosolanacearum
motility to tomato roots in sand.
Fluorescence Assay for Evaluating Microbicidal Activity of Hand Antiseptics
Authors: Lopez-Gigosos Rosa M. , Mariscal Alberto , Mariscal-Lopez Eloisa , Gutierrez-Bedmar Mario , Fernandez Joaquin
Published: August 2015

We developed a fluorescent β-
d
-glucuronidase activity (BGA)-based assay for detecting and quantifying
Escherichia coli
in samples to assess the biocide efficacy of hand antiseptics. The fluorescence level is proportional to the number of viable
E. coli
organisms present. We compared our assay results to those of the
E. coli
plate count method specified by the European standard for testing hygienic hand rub disinfectant products (EN1500). The plate count method requires excessive handling and materials and is not valid if the number of organisms per plate is too low or high for counting in many of the samples. We optimized the fluorescent assay based on the cleavage of 4-methylumbelliferyl-β-
d
-glucuronide by adding 4-nitrophenyl-β-
d
-glucuronide, a nonfluorogenic BGA substrate, to induce glucuronidase activity and reduce assay time. Furthermore, our method can be automated and eliminates the need for multiple dilutions. Fluorescence was temporally monitored, and the time required to reach a specific value of fluorescence was correlated with the initial number of viable
E. coli
organisms on the samples. There was a positive correlation (
P
< 0.05) with a high correlation coefficient (
R
2
= 0.82) between the
E. coli
counts by plate count and fluorescence methods. Reported effects in fluorescent BGA were compared to the EN1500 plate count method with five hand disinfectants. We found our method more advantageous, because it was as sensitive as the EN1500 method, requires less time to complete, and is less expensive and less laborious than conventional plating techniques.
The Gastrointestinal Tract as a Potential Infection Reservoir of Digital Dermatitis-Associated Treponemes in Beef Cattle and Sheep
Authors: Sullivan L. E. , Carter S. D. , Duncan J. S. , Grove-White D. H. , Angell J. W. , Evans N. J.
Published: August 2015

Digital dermatitis (DD) is an important cause of lameness in dairy cattle worldwide. It has now been reported in beef cattle and also sheep (contagious ovine digital dermatitis [CODD]). Three
Treponema
phylogroups are consistently isolated from lesions,
Treponema medium-
like,
Treponema phagedenis
-like, and
Treponema pedis
. The gastrointestinal (GI) tract and feces are suggested sites of treponemal infection in dairy cattle; however, isolation of DD-associated treponemes from these areas has previously failed. This study surveyed gingival tissues, rectal tissues, and feces of beef cattle and sheep for the molecular presence (PCR) and isolation of the three cultivable DD-treponeme phylogroups. Of the sheep gingival (
n
= 40) and rectal (
n
= 40) tissues, 1/40 gingival tissues was positive for DD-associated treponemes (
T. pedis
), as were 3/40 rectal tissues (one containing
T. medium-
like and two containing
T. pedis
). No DD-associated treponeme DNA was amplified from beef cattle rectal tissues (
n
= 40); however, 4/40 beef gingival tissues were positive for DD-associated treponemes (all containing
T. phagedenis
-like). A
T. phagedenis
-like DD-associated treponeme was isolated from the rectal tissue of a CODD symptomatic sheep. Beef cattle (
n
= 41) and sheep (
n
= 79) feces failed to amplify DD-associated
Treponema
DNA. Twenty-two treponemes were isolated from sheep feces; however, upon phylogenetic analysis, these clustered with the considered nonpathogenic treponemes. This study detected DD-associated treponemes in the GI tract tissues of sheep and beef cattle and successfully isolated a DD-associated treponeme from ruminant rectal tissue. This gives evidence that the GI tract is an important infection reservoir of DD-associated treponemes in multiple DD-infected species.
Hypothetical Protein Avin_16040 as the S-Layer Protein of Azotobacter vinelandii and Its Involvement in Plant Root Surface Attachment
Authors: Liew Pauline Woan Ying , Jong Bor Chyan , Najimudin Nazalan
Published: August 2015

A proteomic analysis of a soil-dwelling, plant growth-promoting
Azotobacter vinelandii
strain showed the presence of a protein encoded by the hypothetical
Avin_16040
gene when the bacterial cells were attached to the
Oryza sativa
root surface. An
Avin_16040
deletion mutant demonstrated reduced cellular adherence to the root surface, surface hydrophobicity, and biofilm formation compared to those of the wild type. By atomic force microscopy (AFM) analysis of the cell surface topography, the deletion mutant displayed a cell surface architectural pattern that was different from that of the wild type.
Escherichia coli
transformed with the wild-type
Avin_16040
gene displayed on its cell surface organized motifs which looked like the S-layer monomers of
A. vinelandii
. The recombinant
E. coli
also demonstrated enhanced adhesion to the root surface.
pH Tolerance in Freshwater Bacterioplankton: Trait Variation of the Community as Measured by Leucine Incorporation
Authors: Bååth Erland , Kritzberg Emma
Published: August 2015

pH is an important factor determining bacterial community composition in soil and water. We have directly determined the community tolerance (trait variation) to pH in communities from 22 lakes and streams ranging in pH from 4 to 9 using a growth-based method not relying on distinguishing between individual populations. The pH in the water samples was altered to up to 16 pH values, covering
in situ
pH ± 2.5 U, and the tolerance was assessed by measuring bacterial growth (Leu incorporation) instantaneously after pH adjustment. The resulting unimodal response curves, reflecting community tolerance to pH, were well modeled with a double logistic equation (mean
R
2
= 0.97). The optimal pH for growth (pH
opt
) among the bacterial communities was closely correlated with
in situ
pH, with a slope (0.89 ± 0.099) close to unity. The pH interval, in which growth was ≥90% of that at pH
opt
, was 1.1 to 3 pH units wide (mean 2.0 pH units). Tolerance response curves of communities originating from circum-neutral pH were symmetrical, whereas in high-pH (8.9) and especially in low-pH (<5.5) waters, asymmetric tolerance curves were found. In low-pH waters, decreasing pH was more detrimental for bacterial growth than increasing pH, with a tendency for the opposite for high-pH waters. A pH tolerance index, using the ratio of growth at only two pH values (pH 4 and 8), was closely related to pH
opt
(
R
2
= 0.83), allowing for easy determination of pH tolerance during rapid changes in pH.
Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen
Authors: Kittelmann Sandra , Kirk Michelle R. , Jonker Arjan , McCulloch Alan , Janssen Peter H.
Published: August 2015

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (
R
= 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (
R
= 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants.
Anaerobic Growth of Corynebacterium glutamicum via Mixed-Acid Fermentation
Authors: Michel Andrea , Koch-Koerfges Abigail , Krumbach Karin , Brocker Melanie , Bott Michael
Published: August 2015

Corynebacterium glutamicum
, a model organism in microbial biotechnology, is known to metabolize glucose under oxygen-deprived conditions to
l
-lactate, succinate, and acetate without significant growth. This property is exploited for efficient production of lactate and succinate. Our detailed analysis revealed that marginal growth takes place under anaerobic conditions with glucose, fructose, sucrose, or ribose as a carbon and energy source but not with gluconate, pyruvate, lactate, propionate, or acetate. Supplementation of glucose minimal medium with tryptone strongly enhanced growth up to a final optical density at 600 nm (OD
600
) of 12, whereas tryptone alone did not allow growth. Amino acids with a high ATP demand for biosynthesis and amino acids of the glutamate family were particularly important for growth stimulation, indicating ATP limitation and a restricted carbon flux into the oxidative tricarboxylic acid cycle toward 2-oxoglutarate. Anaerobic cultivation in a bioreactor with constant nitrogen flushing disclosed that CO
2
is required to achieve maximal growth and that the pH tolerance is reduced compared to that under aerobic conditions, reflecting a decreased capability for pH homeostasis. Continued growth under anaerobic conditions indicated the absence of an oxygen-requiring reaction that is essential for biomass formation. The results provide an improved understanding of the physiology of
C. glutamicum
under anaerobic conditions.
Differences in Host Innate Responses among Coccidioides Isolates in a Murine Model of Pulmonary Coccidioidomycosis
Authors: Lewis Eric R. G. , David Victoria R. , Doyle Adina L. , Rajabi Khadijeh , Kiefer Jeffrey A. , Pirrotte Patrick , Barker Bridget M.
Published: August 2015

Coccidioides immitisandCoccidioides posadasiiare soil-dwelling fungi and the causative agents of coccidioidomycosis, a mycosis endemic to certain semiarid regions in the Americas. The most common route of infection is by inhalation of airborneCoccidioidesarthroconidia. Once a susceptible host inhales the conidia, a transition to mature endosporulated spherules can occur within the first 5 days of infection. For this study, we examined the host response in a murine model of coccidioidomycosis during a time period of infection that has not been well characterized. We collected lung tissue and bronchoalveolar lavage fluid (BALF) from BALB/c mice that were infected with aC. immitispure strain, aC. immitishybrid strain, or aC. posadasiistrain as well as uninfected mice. We compared the host responses to theCoccidioidesstrains used in this study by assessing the level of transcription of selected cytokine genes in lung tissues and characterized host and fungal proteins present in BALF. Host response varied depending on theCoccidioidesstrain that was used and did not appear to be overly robust. This study provides a foundation to begin to dissect the host immune response early in infection, to detect abundantCoccidioidesproteins, and to develop diagnostics that target these early time points of infection.
Steroid-sensitive nephrotic syndrome: an evidence-based update of immunosuppressive treatment in children
Authors: Larkins Nicholas , Kim Siah , Craig Jonathan , Hodson Elisabeth
Published: August 2015

Nephrotic syndrome is one of the most common paediatric glomerular diseases, with an incidence of around two per 100 000 children per year. Corticosteroids are the mainstay of treatment, with 85%–90% of children going into remission with an 8-week course of treatment. Unfortunately, nephrotic syndrome follows a relapsing and remitting course in the majority, with 90% relapsing at least once. About half will progress to frequently relapsing nephrotic syndrome (FRNS) or steroid-dependent nephrotic syndrome (SDNS). Different initial steroid regimens have been evaluated since the first trials in Europe and America in the 1960s. Most trials have been designed to evaluate the optimal duration of the initial therapy, rather than different cumulative doses of corticosteroid, or the management of relapses. Until recently, these data suggested that an initial treatment duration of up to 6 months reduced the number of children developing a relapse, without evidence of increased steroid toxicity. Recently, three large, well-designed randomised control trials were published, which demonstrated no significant reduction in risk of relapse or of developing FRNS by extended treatment compared with 2 or 3 months. While there are few trial data to guide the treatment of individual relapses in steroid-sensitive nephrotic syndrome (SSNS), there is some evidence that a short course of corticosteroid therapy during upper respiratory tract infection may prevent relapse. In patients with FRNS or SDNS who continue to relapse despite low-dose alternate-day steroids a number of non-corticosteroid, steroid-sparing immunosuppressive agents (cyclophosphamide, ciclosporin, tacrolimus, mycophenolate mofetil, levamisole, rituximab) have been shown to reduce the risk of relapse and of FRNS. However, there are limited head-to-head data to inform which agent should be preferred. In this article, we review recent data from randomised trials to update paediatricians on the current evidence supporting interventions in SSNS.
Spinal epidural abscess and meningitis following short-term epidural catheterisation for postoperative analgaesia
Authors: van Rappard Juliaan R M , Tolenaar Jip L , Smits Anke B , Go Peter M N Y H
Published: August 2015

We present a case of a patient with a spinal epidural abscess (SEA) and meningitis following short-term epidural catheterisation for postoperative pain relief after a laparoscopic sigmoid resection. On the fifth postoperative day, 2 days after removal of the epidural catheter, the patient developed high fever, leucocytosis and elevated C reactive protein. Blood cultures showed a methicillin-sensitiveStaphylococcus aureusinfection. A photon emission tomography scan revealed increased activity of the spinal canal, suggestingS. aureusmeningitis. A gadolinium-enhanced MRI showed a SEA that was localised at the epidural catheter insertion site. Conservative management with intravenous flucloxacillin was initiated, as no neurological deficits were seen. At last follow-up, 8 weeks postoperatively, the patient showed complete recovery.
Measurement of physical activity in older adult interventions: a systematic review
Authors: Falck Ryan S , McDonald Samantha M , Beets Michael W , Brazendale Keith , Liu-Ambrose Teresa
Published: August 2015

Background

Interventions to promote physical activity (PA) among older adults can positively impact PA behaviour and other health outcomes. Measurement of PA must be valid and reliable; however, the degree to which studies employ valid and reliable measures of PA is unclear. The purpose of this systematic review was to evaluate the measurement tools used in interventions to increase PA among older adults (65+ years), including both self-report measures and objective measures. In addition, the implications of these different measurement tools on study results were evaluated and discussed.

Methods

Four electronic research databases (MEDLINE, PsychINFO, Web of Science and EBSCO) were used to identify published intervention studies measuring the PA behaviour of adults over 65 years of age. Studies were eligible if: (1) PA was an outcome; (2) there was a comparison group and (3) the manuscript was published in English. Data describing measurement methods and properties were extracted and reviewed.

Results

Of the 44 studies included in this systematic review, 32 used self-report measures, 9 used objective measures and 3 used both measures. 29% of studies used a PA measure that had neither established validity nor reliability, and only 63% of measures in the interventions had established both validity and reliability. Only 57% of measures had population-specific reliability and 66% had population-specific validity.

Conclusions

A majority of intervention studies to help increase older adult PA used self-report measures, even though many have little evidence of validity and reliability. We recommend that future researchers utilise valid and reliable measures of PA with well-established evidence of psychometric properties such as hip-accelerometers and the Community Health Activities Model Program for Seniors (CHAMPS) Physical Activity Questionnaire for Older Adults.
Utility of current obesity thresholds in signaling diabetes risk in the James Bay Cree ofEeyou Istchee
Authors: Manjoo Priya , Dannenbaum David , Joseph Lawrence , Torrie Jill , Dasgupta Kaberi
Published: August 2015

Objective

The anthropometric thresholds signaling type 2 diabetes risk have not been well defined for Aboriginal communities. This study examined current thresholds in terms of ability to capture diabetes risk in the Cree ofEeyou Istcheein northern Quebec, Canada.

Research design and methods

The study cohort for this analysis included adult participants from the Nituuchischaayihtitaau Aschii Multi-Community Environment and Health Study with complete data on anthropometric measures, fasting glucose, and insulin. Diabetes risk was defined as Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) value >2. Positive and negative likelihood ratios (PLR, NLR) of existing obesity thresholds were evaluated (WHO; International Diabetes Federation, IDF; Adult Treatment Panel III, ATP III). Receiver operating curves were examined to estimate optimal thresholds. In a sensitivity analysis, diabetes risk was defined as HOMA-IR >2.7.

Results

The WHO 30 kg/m2body mass index (BMI) threshold performed well in women (PLR 5.56, 95% CI 1.95 to 15.9; NLR 0.24, 95% CI 0.19 to 0.31) and men (PLR 7.51, 95% CI 2.94 to 19.2; NLR 0.33, 95% CI 0.27 to 0.41). It was close to the estimated optimal threshold (28.5 kg/m2). The ATP III waist circumference threshold (102 cm) performed well in men (PLR 4.64, 95% CI 2.47 to 8.71; NLR 0.21, 95% CI 0.16 to 0.28) and was close to the estimated optimal threshold (101 cm). With diabetes risk defined at HOMA-IR >2.7, PLR values were slightly lower with narrower 95% CIs and optimal thresholds were slightly higher; PLR values remained above 3. For other current thresholds, estimated optimal values were higher and none had a PLR above 2.

Conclusions

A BMI of 30 kg/m2in women and men, and a 102 cm waist circumference in men, are meaningful obesity thresholds in this Aboriginal population. Other thresholds require a further evaluation.
Traffic pollution at the home address and pregnancy outcomes in Stockholm, Sweden
Authors: Olsson David , Mogren Ingrid , Eneroth Kristina , Forsberg Bertil
Published: August 2015

Background

For the past two decades, several studies have reported associations between elevated levels of ambient air pollution and adverse pregnancy outcomes, although with varying conclusions.

Objectives

To examine possible associations between the traffic pollution situation at the home address, for women who did not change address during pregnancy, and three types of pregnancy outcomes: spontaneous preterm delivery, children born small for gestational age (SGA) and pregnancy-induced hypertensive disorders.

Methods

We used data for the Greater Stockholm Area from the Swedish Medical Birth Register to construct a cohort based on all pregnancies conceived between July 1997 and March 2006, n=100 190. The pregnancy average nitrogen oxide, NOx, levels and annual mean daily vehicles at the home address were used as exposure variables. Mixed-model logistic regression was performed to assess any associations between exposure and outcome.

Results

There was an association between elevated traffic pollution exposure during pregnancy and pregnancy-induced hypertensive disorders. A 10 µg/m3increase in the pregnancy average NOx level at the home address resulted in an OR of 1.17 (95% CI 1.10 to 1.26). The 2nd to 4th quartiles of NOx were all associated with an increased risk of SGA, but there was no difference in the risk estimate among the higher quartiles. There was a tendency of a higher risk of spontaneous preterm delivery in relation to higher levels of NOx. There was no evidence of an association between vehicle flow, the cruder indicator of traffic pollution, and the studied outcomes in this study.

Conclusions

In this large cohort, there was a fairly strong association between vehicle exhaust levels at the home address and pregnancy-induced hypertensive disorders, after adjustment for important risk factors.