bluuebunny/crossref_metadata_2025_split huggingface dataset:
A region‐appearance‐based adaptive variational model for 3D liver segmentation
Authors: Peng Jialin , Dong Fangfang , Chen Yunmei , Kong Dexing 
Published: March 2014

Purpose:Liver segmentation from computed tomography images is a challenging task owing to pixel intensity overlapping, ambiguous edges, and complex backgrounds. The authors address this problem with a novel active surface scheme, which minimizes an energy functional combining both edge‐ and region‐based information.Methods:In this semiautomatic method, the evolving surface is principally attracted to strong edges but is facilitated by the region‐based information where edge information is missing. As avoiding oversegmentation is the primary challenge, the authors take into account multiple features and appearance context information. Discriminative cues, such as multilayer consecutiveness and local organ deformation are also implicitly incorporated. Case‐specific intensity and appearance constraints are included to cope with the typically large appearance variations over multiple images. Spatially adaptive balancing weights are employed to handle the nonuniformity of image features.Results:Comparisons and validations on difficult cases showed that the authors’ model can effectively discriminate the liver from adhering background tissues. Boundaries weak in gradient or with no local evidence (e.g., small edge gaps or parts with similar intensity to the background) were delineated without additional user constraint. With an average surface distance of 0.9 mm and an average volume overlap of 93.9% on the MICCAI data set, the authors’ model outperformed most state‐of‐the‐art methods. Validations on eight volumes with different initial conditions had segmentation score variances mostly less than unity.Conclusions:The proposed model can efficiently delineate ambiguous liver edges from complex tissue backgrounds with reproducibility. Quantitative validations and comparative results demonstrate the accuracy and efficacy of the model.
Automatic registration of CT images to patient during the initial phase of bronchoscopy: A clinical pilot study
Authors: Hofstad Erlend Fagertun , Sorger Hanne , Leira Håkon Olav , Amundsen Tore , Langø Thomas 
Published: March 2014

Purpose:Electromagnetic based navigated bronchoscopy using preoperative CT images has reached the clinic during the last decade. One of the challenges is the “CT to patient anatomy alignment” of the CT images acquired days or even weeks ahead of bronchoscopy. An automatic registration method, without manual registration of anatomical landmarks, was developed, implemented, and evaluated in the current study.Methods:The registration method aligns automatically the preoperative CT images to the patientˈs anatomy during the initial part of the bronchoscopy. The algorithm is a modified version of an iterative closest point algorithm, which in addition to the positions also utilizes the orientation of the bronchoscope and the running direction of the CT centerline. The method was evaluated both by model‐based simulated bronchoscopies and by clinical data from six real bronchoscopies. In the clinical evaluation, an electromagnetic position sensor was placed temporarily in the working channel close to the tip of a conventional bronchoscope. Position data, which were acquired while the bronchoscope was moving inside the airways, were registered to the centerline extracted from the airways in the CT image.Results:A mean registration accuracy of 3.0 ± 1.4 mm was found when simulating bronchoscopies. In the clinical part of the study, the registration method was successfully applied to the data from all six patients. The positions of the bronchoscope tip aligned to the CT centerline with a mean distance range 4.7–6.5 mm.Conclusions:The authors have developed and evaluated an automatic registration algorithm for electromagnetic navigated bronchoscopy. It functioned to its purpose and did not affect the workflow for the bronchoscopic investigation of the six patients included in the study.
Inhibition by Cellular Vacuolar ATPase Impairs Human Papillomavirus Uncoating and Infection
Authors: Müller Konstantin H. , Spoden Gilles A. , Scheffer Konstanze D. , Brunnhöfer Regina , De Brabander Jef K. , Maier Martin E. , Florin Luise , Muller Claude P. 
Published: March 2014

ABSTRACT
Several viruses, including human papillomaviruses, depend on endosomal acidification for successful infection. Hence, the multisubunit enzyme vacuolar ATPase (V-ATPase), which is mainly responsible for endosome acidification in the cell, represents an attractive target for antiviral strategies. In the present study, we show that V-ATPase is required for human papillomavirus (HPV) infection and that uncoating/disassembly but not endocytosis is affected by V-ATPase inhibition. The infection inhibitory potencies of saliphenylhalamide, a proven V-ATPase inhibitor, and its derivatives, as well as those of other V-ATPase inhibitors, were analyzed on different HPV types in relevant cell lines. Variation in the selectivity indices among V-ATPase inhibitors was high, while variation for the same inhibitor against different HPV subtypes was low, indicating that broad-spectrum anti-HPV activity can be provided.
Tannin Degradation by a Novel Tannase Enzyme Present in Some Lactobacillus plantarum Strains
Authors: Jiménez Natalia , Esteban-Torres María , Mancheño José Miguel , de las Rivas Blanca , Muñoz Rosario 
Published: March 2014

ABSTRACT

Lactobacillus plantarum
is frequently isolated from the fermentation of plant material where tannins are abundant.
L. plantarum
strains possess tannase activity to degrade plant tannins. An
L. plantarum
tannase (TanB
Lp
, formerly called TanLp1) was previously identified and biochemically characterized. In this study, we report the identification and characterization of a novel tannase (TanA
Lp
). While all 29
L. plantarum
strains analyzed in the study possess the

tanB
Lp

gene, the gene

tanA
Lp

was present in only four strains. Upon methyl gallate exposure, the expression of

tanB
Lp

was induced, whereas

tanA
Lp

expression was not affected. TanA
Lp
showed only 27% sequence identity to TanB
Lp
, but the residues involved in tannase activity are conserved. Optimum activity for TanA
Lp
was observed at 30°C and pH 6 in the presence of Ca
2+
ions. TanA
Lp
was able to hydrolyze gallate and protocatechuate esters with a short aliphatic alcohol substituent. Moreover, TanA
Lp
was able to fully hydrolyze complex gallotannins, such as tannic acid. The presence of the extracellular TanA
Lp
tannase in some
L. plantarum
strains provides them an advantage for the initial degradation of complex tannins present in plant environments.
Development of a Markerless Knockout Method for Actinobacillus succinogenes
Authors: Joshi Rajasi V. , Schindler Bryan D. , McPherson Nikolas R. , Tiwari Kanupriya , Vieille Claire 
Published: March 2014

ABSTRACT

Actinobacillus succinogenes
is one of the best natural succinate-producing organisms, but it still needs engineering to further increase succinate yield and productivity. In this study, we developed a markerless knockout method for
A. succinogenes
using natural transformation or electroporation. The
Escherichia coli
isocitrate dehydrogenase gene with flanking flippase recognition target sites was used as the positive selection marker, making use of
A. succinogenes
's auxotrophy for glutamate to select for growth on isocitrate. The
Saccharomyces cerevisiae
flippase recombinase (Flp) was used to remove the selection marker, allowing its reuse. Finally, the plasmid expressing
flp
was cured using acridine orange. We demonstrate that at least two consecutive deletions can be introduced into the same strain using this approach, that no more than a total of 1 kb of DNA is needed on each side of the selection cassette to protect from exonuclease activity during transformation, and that no more than 200 bp of homologous DNA is needed on each side for efficient recombination. We also demonstrate that electroporation can be used as an alternative transformation method to obtain knockout mutants and that an enriched defined medium can be used for direct selection of knockout mutants on agar plates with high efficiency. Single-knockout mutants of the fumarate reductase and of the pyruvate formate lyase-encoding genes were obtained using this knockout strategy. Double-knockout mutants were also obtained by deleting the citrate lyase-, β-galactosidase-, and aconitase-encoding genes in the pyruvate formate lyase knockout mutant strain.
Fluorescent Fingerprints of Endolithic Phototrophic Cyanobacteria Living within Halite Rocks in the Atacama Desert
Authors: Roldán M. , Ascaso C. , Wierzchos J. 
Published: March 2014

ABSTRACT

Halite deposits from the hyperarid zone of the Atacama Desert reveal the presence of endolithic microbial colonization dominated by cyanobacteria associated with heterotrophic bacteria and archaea. Using the λ-scan confocal laser scanning microscopy (CLSM) option, this study examines the autofluorescence emission spectra produced by single cyanobacterial cells found inside halite rocks and by their photosynthetic pigments. Photosynthetic pigments could be identified according to the shapes of the emission spectra and wavelengths of fluorescence peaks. According to their fluorescence fingerprints, three groups of cyanobacterial cells were identified within this natural extreme microhabitat: (i) cells producing a single fluorescence peak corresponding to the emission range of phycobiliproteins and chlorophyll
a
, (ii) cells producing two fluorescence peaks within the red and green signal ranges, and (iii) cells emitting only low-intensity fluorescence within the nonspecific green fluorescence signal range. Photosynthetic pigment fingerprints emerged as indicators of the preservation state or viability of the cells. These observations were supported by a cell plasma membrane integrity test based on Sytox Green DNA staining and by transmission electron microscopy ultrastructural observations of cyanobacterial cells.
Vibriophages and Their Interactions with the Fish Pathogen Vibrio anguillarum
Authors: Tan Demeng , Gram Lone , Middelboe Mathias 
Published: March 2014

ABSTRACTVibrio anguillarumis an important pathogen in aquaculture, responsible for the disease vibriosis in many fish and invertebrate species. Disease control by antibiotics is a concern due to potential development and spread of antibiotic resistance. The use of bacteriophages to control the pathogen may offer a non-antibiotic-based approach to reduce vibriosis. A detailed understanding of the phage-host interaction is needed to evaluate the potential of phages to control the pathogen. In this study, we examined the diversity and interactions of 11 vibriophages, 24V. anguillarumstrains, and 13Vibriospecies strains. Together, the host ranges of the 11 phages covered all of the tested 37Vibriosp. host strains, which represented considerable temporal (20 years) and geographical (9 countries) differences in their origins of isolation. Thus, despite the occurrence of unique susceptibility patterns of the individual host isolates, key phenotypic properties related to phage susceptibility are distributed worldwide and maintained in the globalVibriocommunity for decades. The phage susceptibility pattern of the isolates did not show any relation to the physiological relationships obtained from Biolog GN2 profiles, demonstrating that similar phage susceptibility patterns occur across broad phylogenetic and physiological differences inVibriostrains. Subsequent culture experiments with two phages and twoV. anguillarumhosts demonstrated an initial strong lytic potential of the phages. However, rapid regrowth of both phage-resistant and phage-sensitive cells following the initial lysis suggested that several mechanisms of protection against phage infection had developed in the host populations.
Elevated CO
2
and Phosphate Limitation Favor Micromonas pusilla through Stimulated Growth and Reduced Viral Impact
Authors: Maat Douwe S. , Crawfurd Katherine J. , Timmermans Klaas R. , Brussaard Corina P. D. 
Published: March 2014

ABSTRACT

Growth and viral infection of the marine picoeukaryote
Micromonas pusilla
was studied under a future-ocean scenario of elevated partial CO
2
(pCO
2
; 750 μatm versus the present-day 370 μatm) and simultaneous limitation of phosphorus (P). Independent of the pCO
2
level, the ratios of
M. pusilla
cellular carbon (C) to nitrogen (N), C:P and N:P, increased with increasing P stress. Furthermore, in the P-limited chemostats at growth rates of 0.32 and 0.97 of the maximum growth rate (μ
max
), the supply of elevated pCO
2
led to an additional rise in cellular C:N and C:P ratios, as well as a 1.4-fold increase in
M. pusilla
abundance. Viral lysis was not affected by pCO
2
, but P limitation led to a 150% prolongation of the latent period (6 to 12 h) and an 80% reduction in viral burst sizes (63 viruses per cell) compared to P-replete conditions (4 to 8 h latent period and burst size of 320). Growth at 0.32 μ
max
further prolonged the latent period by another 150% (12 to 18 h). Thus, enhanced P stress due to climate change-induced strengthened vertical stratification can be expected to lead to reduced and delayed virus production in picoeukaryotes. This effect is tempered, but likely not counteracted, by the increase in cell abundance under elevated pCO
2
. Although the influence of potential P-limitation-relieving factors, such as the uptake of organic P and P utilization during infection, is unclear, our current results suggest that when P limitation prevails in future oceans, picoeukaryotes and grazing will be favored over larger-sized phytoplankton and viral lysis, with increased matter and nutrient flow to higher trophic levels.
Efficient Synthesis of Eriodictyol from
l
-Tyrosine in Escherichia coli
Authors: Zhu Saijie , Wu Junjun , Du Guocheng , Zhou Jingwen , Chen Jian 
Published: March 2014

ABSTRACT

The health benefits of flavonoids for humans are increasingly attracting attention. Because the extraction of high-purity flavonoids from plants presents a major obstacle, interest has emerged in biosynthesizing them using microbial hosts. Eriodictyol is a flavonoid with anti-inflammatory and antioxidant activities. Its efficient synthesis has been hampered by two factors: the poor expression of cytochrome P450 and the low intracellular malonyl coenzyme A (malonyl-CoA) concentration in
Escherichia coli
. To address these issues, a truncated plant P450 flavonoid, flavonoid 3′-hydroxylase (tF3′H), was functionally expressed as a fusion protein with a truncated P450 reductase (tCPR) in
E. coli
. This allowed the engineered
E. coli
to produce eriodictyol from
l
-tyrosine by simultaneously coexpressing the fusion protein with tyrosine ammonia lyase (TAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), and chalcone isomerase (CHI). In addition, metabolic engineering was employed to enhance the availability of malonyl-CoA so as to achieve a new metabolic balance and rebalance the relative expression of genes to enhance eriodictyol accumulation. This approach made the production of eriodictyol 203% higher than that in the control strain. By using these strategies, the production of eriodictyol from
l
-tyrosine reached 107 mg/liter. The present work offers an approach to the efficient synthesis of other hydroxylated flavonoids from
l
-tyrosine or even glucose in
E. coli
.
Nitrogen Fertilization Has a Stronger Effect on Soil Nitrogen-Fixing Bacterial Communities than Elevated Atmospheric CO
2
Authors: Berthrong Sean T. , Yeager Chris M. , Gallegos-Graves Laverne , Steven Blaire , Eichorst Stephanie A. , Jackson Robert B. , Kuske Cheryl R. 
Published: March 2014

ABSTRACT

Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO
2
and N deposition. Using the
nifH
gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO
2
conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO
2
to affect these communities in the temperate pine forest. Based on data from Sanger sequencing and quantitative PCR, the soil
nifH
composition in the three forest systems was dominated by species in the
Geobacteraceae
and, to a lesser extent,
Alphaproteobacteria
. The N-fixing-bacterial-community structure was subtly altered after 10 or more years of elevated atmospheric CO
2
, and the observed shifts differed in each biome. In the pine forest, N fertilization had a stronger effect on
nifH
community structure than elevated CO
2
and suppressed the diversity and abundance of N-fixing bacteria under elevated atmospheric CO
2
conditions. These results indicate that N-fixing bacteria have complex, interacting responses that will be important for understanding ecosystem productivity in a changing climate.
Distinct Roles of Candida albicans-Specific Genes in Host-Pathogen Interactions
Authors: Wilson Duncan , Mayer François L. , Miramón Pedro , Citiulo Francesco , Slesiona Silvia , Jacobsen Ilse D. , Hube Bernhard 
Published: March 2014

ABSTRACT

Human fungal pathogens are distributed throughout their kingdom, suggesting that pathogenic potential evolved independently.
Candida albicans
is the most virulent member of the CUG clade of yeasts and a common cause of both superficial and invasive infections. We therefore hypothesized that
C. albicans
possesses distinct pathogenicity mechanisms.
In silico
genome subtraction and comparative transcriptional analysis identified a total of 65

C.
a
lbicans

-
s
pecific
g
enes (ASGs) expressed during infection. Phenotypic characterization of six ASG-null mutants demonstrated that these genes are dispensable for
in vitro
growth but play defined roles in host-pathogen interactions. Based on these analyses, we investigated two ASGs in greater detail. An orf19.6688Δ mutant was found to be fully virulent in a mouse model of disseminated candidiasis and to induce higher levels of the proinflammatory cytokine interleukin-1β (IL-1β) following incubation with murine macrophages. A
pga16
Δ mutant, on the other hand, exhibited attenuated virulence. Moreover, we provide evidence that secondary filamentation events (multiple hyphae emerging from a mother cell and hyphal branching) contribute to pathogenicity:
PGA16
deletion did not influence primary hypha formation or extension following contact with epithelial cells; however, multiple hyphae and hyphal branching were strongly reduced. Significantly, these hyphae failed to damage host cells as effectively as the multiple hypha structures formed by wild-type
C. albicans
cells. Together, our data show that species-specific genes of a eukaryotic pathogen can play important roles in pathogenicity.
A Novel ESX-1 Locus Reveals that Surface-Associated ESX-1 Substrates Mediate Virulence in Mycobacterium marinum
Authors: Kennedy George M. , Hooley Gwendolyn C. , Champion Matthew M. , Mba Medie Felix , Champion Patricia A. DiGiuseppe 
Published: March 2014

ABSTRACT

EsxA (ESAT-6) and EsxB (CFP-10) are virulence factors exported by the ESX-1 system in mycobacterial pathogens. In
Mycobacterium marinum
, an established model for ESX-1 secretion in
Mycobacterium tuberculosis
, genes required for ESX-1 export reside at the extended region of difference 1 (RD1) locus. In this study, a novel locus required for ESX-1 export in
M. marinum
was identified outside the RD1 locus. An
M. marinum
strain bearing a transposon-insertion between the
MMAR
_
1663
and
MMAR
_
1664
genes exhibited smooth-colony morphology, was deficient for ESX-1 export, was nonhemolytic, and was attenuated for virulence. Genetic complementation revealed a restoration of colony morphology and a partial restoration of virulence in cell culture models. Yet hemolysis and the export of ESX-1 substrates into the bacteriological medium
in vitro
as measured by both immunoblotting and quantitative proteomics were not restored. We show that genetic complementation of the transposon insertion strain partially restored the translocation of EsxA and EsxB to the mycobacterial cell surface. Our findings indicate that the export of EsxA and EsxB to the cell surface, rather than secretion into the bacteriological medium, correlates with virulence in
M. marinum
. Together, these findings not only expand the known genetic loci required for ESX-1 secretion in
M. marinum
but also provide an explanation for the observed disparity between
in vitro
ESX-1 export and virulence.
All in the Family: Kin Contact Leads to Outer Membrane Exchange
Authors: Hartzell Trish 
Published: March 2014

ABSTRACT

The ability to recognize related cells in a population can confer evolutionary benefits. For example, some bacteria use contact-dependent inhibition proteins to distinguish kin from nonkin. Kinship recognition is taken to a new level in
Myxococcus
, which uses the dual-purpose TraA protein for kin recognition and outer membrane and lipoprotein exchange. In this issue of the
Journal of Bacteriology
, Wei et al. (
X. Wei, C. N. Vassallo, D. T. Pathak, D. Wall, J. Bacteriol. 196:1807–1814, 2014
) show that Tra-dependent exchange can be uncoupled from outer membrane vesicle/tube formation, reported elsewhere to mediate outer membrane exchange.
Spectral Analysis of Heart Rate Variability during Trigger Point Acupuncture
Authors: Kitagawa Yoji , Kimura Kenichi , Yoshida Sohei 
Published: March 2014

Objectives To clarify changes in the cardiovascular autonomic nervous system function due to trigger point acupuncture, we evaluated differences in responses between acupuncture at trigger points and those at other sites using spectral analysis of heart rate variability. Methods Subjects were 35 healthy men. Before measurements began the subjects were assigned to a trigger point acupuncture or control group based on the presence/absence of referred pain on applying pressure to a taut band within the right tibialis anterior muscle. The measurements were conducted in a room with a temperature of 25°C, with subjects in a long sitting position after 10 min rest. Acupuncture needles were retained for 10 min at two sites on the right tibialis anterior muscle. ECG was performed simultaneously with measurements of blood pressure and the respiratory cycle. Based on the R–R interval on the ECG, frequency analysis was performed, low-frequency (LF) and high-frequency (HF) components were extracted and the ratio of LF to HF components (LF/HF) was evaluated. Results The trigger point acupuncture group showed a transient decrease in heart rate and an increase in the HF component but no significant changes in LF/HF. In the control group, no significant changes were observed in heart rate, the HF component or LF/HF. There were no consistent changes in systolic or diastolic blood pressure in either group. Conclusions These data suggest that acupuncture stimulation of trigger points of the tibialis anterior muscle transiently increases parasympathetic nerve activity.